Index

_

__contains__() (schrodinger.application.bioluminate.anarci.loop_ranges.LoopRange method) (schrodinger.application.matsci.msutils.EnumMetaWithContains method) (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) (schrodinger.application.phase.packages.phase_utils.RestrictedRange method) (schrodinger.infra.mmlist.mmlist method) (schrodinger.project.project.Project method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.utils.cgxutils.FragmentLibrary method) (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.scollections.IdItemsView method) (schrodinger.utils.scollections.IdSet method) (schrodinger.utils.sea.sea.List method) (schrodinger.utils.sea.sea.Map method) __init__() (schrodinger.active_learning.al_driver.ActiveLearningJob method) (schrodinger.active_learning.al_driver.Option method) (schrodinger.active_learning.al_node.ActiveLearningNode method) (schrodinger.active_learning.al_node.ActiveLearningNodeSupplier method) (schrodinger.active_learning.al_node.KnownScoreProviderNode method) (schrodinger.active_learning.al_node.LigandMLEvalNode method) (schrodinger.active_learning.al_node.LigandMLTrainNode method) (schrodinger.active_learning.al_node.PrepareSmilesNode method) (schrodinger.active_learning.al_node.ScoreProviderNode method) (schrodinger.active_learning.al_report.ALPilotReportMaker method) (schrodinger.active_learning.al_report.ALReportMaker method) (schrodinger.active_learning.al_report.ALScreenReportMaker method) (schrodinger.active_learning.fake_nodes.DummyCalculateScoreNode method) (schrodinger.active_learning.fake_nodes.DummyPilotScoreNode method) (schrodinger.active_learning.fake_nodes.DummyRescoreNode method) (schrodinger.active_learning.mq_backend.Backend method) (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) (schrodinger.active_learning.mq_driver.Worker method) (schrodinger.active_learning.mq_worker.LigandMLBackend method) (schrodinger.active_learning.mq_worker.Worker method) (schrodinger.analysis.enrichment.calculator.Calculator method) (schrodinger.analysis.enrichment.enrichment_input.FingerprintComponent method) (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method) (schrodinger.analysis.enrichment.plotter.Plotter method) (schrodinger.analysis.substructure.ConnectedMoleculeChain method) (schrodinger.analysis.transformations.TransformsRepository method) (schrodinger.analysis.visanalysis.vdexception.VDException method) (schrodinger.analysis.visanalysis.volumedata.VolumeData method) (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) (schrodinger.application.bindingsite.atomtyping.AtomTyper method) (schrodinger.application.bindingsite.cavutils.Cavity method) (schrodinger.application.bindingsite.cavutils.Grid method) (schrodinger.application.bindingsite.intfield.Field method) (schrodinger.application.bioluminate.actions.factory.Factory method) (schrodinger.application.bioluminate.actions.factory.SAction method) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult method) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciDomainResult method) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults method) (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment method) (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainHitsTable method) (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainNumbering method) (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment method) (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering method) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit method) (schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo method) (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult method) (schrodinger.application.bioluminate.anarci.loop_ranges.LoopRange method) (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueZone method) (schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl method) (schrodinger.application.bioluminate.antibody.assembly.AtomPair method) (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction method) (schrodinger.application.bioluminate.antibody.grafting.GraftingInput method) (schrodinger.application.bioluminate.antibody.grafting.GraftingOutput method) (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput method) (schrodinger.application.bioluminate.antibody.io.csv_reader.BaseInvalidAntibodyCSVError method) (schrodinger.application.bioluminate.antibody.io.csv_reader.InvalidCSVFormattingError method) (schrodinger.application.bioluminate.antibody.io.csv_reader.InvalidRowError method) (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog method) (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable method) (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch method) (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput method) (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchOutput method) (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.bioluminate.antibody.search_results_table.FullTable method) (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel method) (schrodinger.application.bioluminate.antibody.search_results_table.SplitTable method) (schrodinger.application.bioluminate.antibody.search_results_table.TableView method) (schrodinger.application.bioluminate.antibody.sequence_indexer.InvalidQueryLengthError method) (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) (schrodinger.application.bioluminate.bwidgets.ImportWidget method) (schrodinger.application.bioluminate.bwidgets.NumericLineEdit method) (schrodinger.application.bioluminate.bwidgets.QuickHelpButton method) (schrodinger.application.bioluminate.bwidgets.RowActionItem method) (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog method) (schrodinger.application.bioluminate.classify.NumberedResidue method) (schrodinger.application.bioluminate.classify.NumberedSequence method) (schrodinger.application.bioluminate.classify.ProteinClass method) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) (schrodinger.application.bioluminate.escomp.PotGrid method) (schrodinger.application.bioluminate.escomp.ResidualPotential method) (schrodinger.application.bioluminate.interaction_calculator.InteractingResidue method) (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) (schrodinger.application.bioluminate.interaction_calculator.InteractionParams method) (schrodinger.application.bioluminate.interaction_calculator.Interactions method) (schrodinger.application.bioluminate.interaction_calculator.PiStackFinder method) (schrodinger.application.bioluminate.methionine_oxidation.HmcAnalyzer method) (schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer method) (schrodinger.application.bioluminate.mutation.MacromoleculeMutator method) (schrodinger.application.bioluminate.mutation.Mutation method) (schrodinger.application.bioluminate.mutation.MutationStructureMap method) (schrodinger.application.bioluminate.patch_utils.patch_finder.Patch method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchAnalysis method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) (schrodinger.application.bioluminate.patch_utils.patch_finder.ProteinProperties method) (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo method) (schrodinger.application.bioluminate.patch_utils.patch_finder.ResPatchData method) (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) (schrodinger.application.bioluminate.patch_utils.settings.PatchTypeSettings method) (schrodinger.application.bioluminate.pml_menus.ActionMenu method) (schrodinger.application.bioluminate.pml_menus.AntibodyPreset method) (schrodinger.application.bioluminate.pml_menus.AntibodyPresetAHo method) (schrodinger.application.bioluminate.pml_menus.AntibodyPresetChothia method) (schrodinger.application.bioluminate.pml_menus.AntibodyPresetEnhancedChothia method) (schrodinger.application.bioluminate.pml_menus.AntibodyPresetIMGT method) (schrodinger.application.bioluminate.pml_menus.AntibodyPresetKabat method) (schrodinger.application.bioluminate.pml_menus.AntibodyPresetSubMenu method) (schrodinger.application.bioluminate.pml_menus.AroundExpandSubMenu method) (schrodinger.application.bioluminate.pml_menus.AsMenu method) (schrodinger.application.bioluminate.pml_menus.AutoColorSubMenu method) (schrodinger.application.bioluminate.pml_menus.ColorByElementSubMenu method) (schrodinger.application.bioluminate.pml_menus.ColorBySubstructure method) (schrodinger.application.bioluminate.pml_menus.ColorChainbows method) (schrodinger.application.bioluminate.pml_menus.ColorChainSubMenu method) (schrodinger.application.bioluminate.pml_menus.ColorChooserPanel method) (schrodinger.application.bioluminate.pml_menus.ColorLabel method) (schrodinger.application.bioluminate.pml_menus.ColorMenu method) (schrodinger.application.bioluminate.pml_menus.ColorSpectrumSubMenu method) (schrodinger.application.bioluminate.pml_menus.ColorSubstructureSubMenu method) (schrodinger.application.bioluminate.pml_menus.CompleteSubMenu method) (schrodinger.application.bioluminate.pml_menus.ComputeSubMenu method) (schrodinger.application.bioluminate.pml_menus.ComputeSurfaceArea method) (schrodinger.application.bioluminate.pml_menus.CustomColor method) (schrodinger.application.bioluminate.pml_menus.CustomRecentColor method) (schrodinger.application.bioluminate.pml_menus.EntrySubMenu method) (schrodinger.application.bioluminate.pml_menus.ExcludeSubMenu method) (schrodinger.application.bioluminate.pml_menus.Expand method) (schrodinger.application.bioluminate.pml_menus.Extend method) (schrodinger.application.bioluminate.pml_menus.ExtendSubMenu method) (schrodinger.application.bioluminate.pml_menus.FindPCSubMenu method) (schrodinger.application.bioluminate.pml_menus.GeneralContextSubMenu method) (schrodinger.application.bioluminate.pml_menus.GenerateSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateSubMenu method) (schrodinger.application.bioluminate.pml_menus.GenerateSymmetryMates method) (schrodinger.application.bioluminate.pml_menus.GenSelectionSubMenu method) (schrodinger.application.bioluminate.pml_menus.GenSymMatesSubMenu method) (schrodinger.application.bioluminate.pml_menus.HideHydrogenSubMenu method) (schrodinger.application.bioluminate.pml_menus.HideMenu method) (schrodinger.application.bioluminate.pml_menus.HydrogenSubMenu method) (schrodinger.application.bioluminate.pml_menus.IncludeSubMenu method) (schrodinger.application.bioluminate.pml_menus.InvertCompleteSelection method) (schrodinger.application.bioluminate.pml_menus.InvertSubMenu method) (schrodinger.application.bioluminate.pml_menus.LabelAtom method) (schrodinger.application.bioluminate.pml_menus.LabelAtomIdentSubMenu method) (schrodinger.application.bioluminate.pml_menus.LabelMenu method) (schrodinger.application.bioluminate.pml_menus.LabelOtherSubMenu method) (schrodinger.application.bioluminate.pml_menus.LigandPreset method) (schrodinger.application.bioluminate.pml_menus.LigandSitesSubMenu method) (schrodinger.application.bioluminate.pml_menus.MAction method) (schrodinger.application.bioluminate.pml_menus.MakeProjectEntry method) (schrodinger.application.bioluminate.pml_menus.ModifySubMenu method) (schrodinger.application.bioluminate.pml_menus.MWidgetAction method) (schrodinger.application.bioluminate.pml_menus.ObjectFreeContextSubMenu method) (schrodinger.application.bioluminate.pml_menus.PMLMenu method) (schrodinger.application.bioluminate.pml_menus.PolarContactsSubMenu method) (schrodinger.application.bioluminate.pml_menus.PresetSubMenu method) (schrodinger.application.bioluminate.pml_menus.PrettyPubPreset method) (schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu method) (schrodinger.application.bioluminate.pml_menus.RegionInfo method) (schrodinger.application.bioluminate.pml_menus.RestrictSelection method) (schrodinger.application.bioluminate.pml_menus.RestrictSubMenu method) (schrodinger.application.bioluminate.pml_menus.ResultsWindow method) (schrodinger.application.bioluminate.pml_menus.RockData method) (schrodinger.application.bioluminate.pml_menus.SelectedAtomContextActionSubMenu method) (schrodinger.application.bioluminate.pml_menus.SelectionSubMenu method) (schrodinger.application.bioluminate.pml_menus.ShowMenu method) (schrodinger.application.bioluminate.pml_menus.ShowOrganicMenu method) (schrodinger.application.bioluminate.pml_menus.ShowSubstructureMenu method) (schrodinger.application.bioluminate.pml_menus.SimplePreset method) (schrodinger.application.bioluminate.pml_menus.SubstructureContextSubMenu method) (schrodinger.application.bioluminate.pml_menus.SurfaceAreaSubMenu method) (schrodinger.application.bioluminate.pml_menus.ToggleState method) (schrodinger.application.bioluminate.pml_menus.ToggleStateSubMenu method) (schrodinger.application.bioluminate.pose_filtering.hdx_io.InvalidPropertyError method) (schrodinger.application.bioluminate.pose_filtering.hdx_io.InvalidProteinStateError method) (schrodinger.application.bioluminate.pose_filtering.hdx_io.InvalidSubstructureTypeError method) (schrodinger.application.bioluminate.pose_filtering.hdx_io.InvalidTimeSliceError method) (schrodinger.application.bioluminate.pose_filtering.hdx_io.MissingColumnsError method) (schrodinger.application.bioluminate.pose_filtering.residue_filter.FilterCriteria method) (schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter method) (schrodinger.application.bioluminate.pose_filtering.residue_filter.ResidueFilter method) (schrodinger.application.bioluminate.pose_filtering.residue_filter.SasaResidueFilter method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.bioluminate.propfilter.PropertySelectorWithRanges method) (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.bioluminate.propfilter.StringDatabaseCriterion method) (schrodinger.application.bioluminate.propfilter.ValueSelectionDialog method) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) (schrodinger.application.bioluminate.protein.protein.Consensus method) (schrodinger.application.bioluminate.protein.protein.OrderedResidueDict method) (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) (schrodinger.application.bioluminate.protein.protein.PrimeStructure method) (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) (schrodinger.application.bioluminate.protein.protein.Refiner method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart method) (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) (schrodinger.application.bioluminate.reactive_residues.ResidueData method) (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) (schrodinger.application.bioluminate.sliderchart.SliderPlot method) (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) (schrodinger.application.bioluminate.ssv.toolbars.FindToolBar method) (schrodinger.application.bioluminate.ssv.toolbars.ImportToolBar method) (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) (schrodinger.application.bioluminate.tcr.docking_angles.DescriptiveAngles method) (schrodinger.application.bioluminate.tcr.docking_angles.TcrChainIds method) (schrodinger.application.bioluminate.update_germline_db.translate_db.GermlineEntry method) (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method) (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) (schrodinger.application.canvas.r_group.Data method) (schrodinger.application.canvas.r_group.RGroupFinder method) (schrodinger.application.canvas.r_group.TempAtom method) (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method) (schrodinger.application.canvas.similarity.CanvasSimilarityNotImplemented method) (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method) (schrodinger.application.canvas.utils.ChmCSVTools method) (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.combiglide.corehop.AttachmentPoint method) (schrodinger.application.combiglide.corehop.SubstCoreDatabase method) (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.DiversityFingerprinter method) (schrodinger.application.combinatorial_diversity.diversity_selector.DiversitySelector method) (schrodinger.application.combinatorial_diversity.diversity_selector.PropertyFilter method) (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method) (schrodinger.application.combinatorial_explorer.route_screener.RouteScreener method) (schrodinger.application.combinatorial_screen.combinatorial_screener.CombinatorialScreener method) (schrodinger.application.dendrogram.core_class.Deepest0 method) (schrodinger.application.dendrogram.core_class.Deepest1 method) (schrodinger.application.dendrogram.core_class.Deepest2 method) (schrodinger.application.dendrogram.core_class.Deepest3a method) (schrodinger.application.dendrogram.core_class.Deepest3b method) (schrodinger.application.dendrogram.core_class.Deepest4 method) (schrodinger.application.dendrogram.core_class.Deepest5 method) (schrodinger.application.dendrogram.core_class.Deepest6 method) (schrodinger.application.dendrogram.core_class.GetPartitions method) (schrodinger.application.dendrogram.gradientSelector.ColorSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) (schrodinger.application.dendrogram.gradientSelector.PropertyWidget method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.dfa.DFA method) (schrodinger.application.desmond.antlr3.exceptions.EarlyExitException method) (schrodinger.application.desmond.antlr3.exceptions.FailedPredicateException method) (schrodinger.application.desmond.antlr3.exceptions.MismatchedRangeException method) (schrodinger.application.desmond.antlr3.exceptions.MismatchedSetException method) (schrodinger.application.desmond.antlr3.exceptions.MismatchedTokenException method) (schrodinger.application.desmond.antlr3.exceptions.MismatchedTreeNodeException method) (schrodinger.application.desmond.antlr3.exceptions.MissingTokenException method) (schrodinger.application.desmond.antlr3.exceptions.NoViableAltException method) (schrodinger.application.desmond.antlr3.exceptions.RecognitionException method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method) (schrodinger.application.desmond.antlr3.recognizers.RecognizerSharedState method) (schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.DeleteOp method) (schrodinger.application.desmond.antlr3.streams.ReplaceOp method) (schrodinger.application.desmond.antlr3.streams.RewriteOperation method) (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteCardinalityException method) (schrodinger.application.desmond.antlr3.tree.RewriteEarlyExitException method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) (schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method) (schrodinger.application.desmond.antlr3.tree.TreeVisitor method) (schrodinger.application.desmond.antlr3.treewizard.TreePattern method) (schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer method) (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method) (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.application.desmond.arkdb.ArkDb method) (schrodinger.application.desmond.arkdb.Datum method) (schrodinger.application.desmond.bennett.CalcBAR method) (schrodinger.application.desmond.cmj.AslValidator method) (schrodinger.application.desmond.cmj.Engine method) (schrodinger.application.desmond.cmj.Job method) (schrodinger.application.desmond.cmj.Job.Time method) (schrodinger.application.desmond.cmj.JobManager method) (schrodinger.application.desmond.cmj.JobOutput method) (schrodinger.application.desmond.cmj.JobStatus method) (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.cmj.StructureStageBase method) (schrodinger.application.desmond.cms.AtomGroup method) (schrodinger.application.desmond.cms.Cms method) (schrodinger.application.desmond.cms.Constraint method) (schrodinger.application.desmond.cms.FBHWPosRestrainArray method) (schrodinger.application.desmond.cms.PosRestrainArray method) (schrodinger.application.desmond.cms.Pseudo method) (schrodinger.application.desmond.cms.Restrain method) (schrodinger.application.desmond.cms.RestrainGroupContainer method) (schrodinger.application.desmond.cms.Site method) (schrodinger.application.desmond.cms.Vdw method) (schrodinger.application.desmond.cns_io.CNSData method) (schrodinger.application.desmond.constants.MaePropertyName method) (schrodinger.application.desmond.correlation_tau.ConfidenceInterval method) (schrodinger.application.desmond.cwidget.AdvLabel method) (schrodinger.application.desmond.cwidget.EntryField method) (schrodinger.application.desmond.cwidget.FileEntry method) (schrodinger.application.desmond.driver_utils.MPISettings method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.ArraySyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.BinaryThreadSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.MetaSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.RMSDSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.SimpleSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.ThreadSyntax method) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.atom_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.bind_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.block_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.comp_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_meta_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_output_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expComp_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expr_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.exprOrBind_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.factor_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.fcnCall_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.header_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.if__return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.iter_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.meta_term_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.output_term_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.prog_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.series_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.signedExpComp_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.static_return method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.varWithType_return method) (schrodinger.application.desmond.enhsamp.ASLObject method) (schrodinger.application.desmond.enhsamp.Bind method) (schrodinger.application.desmond.enhsamp.binding method) (schrodinger.application.desmond.enhsamp.Env method) (schrodinger.application.desmond.enhsamp.FcnCall method) (schrodinger.application.desmond.enhsamp.If method) (schrodinger.application.desmond.enhsamp.Iter method) (schrodinger.application.desmond.enhsamp.Let method) (schrodinger.application.desmond.enhsamp.Lit method) (schrodinger.application.desmond.enhsamp.Meta method) (schrodinger.application.desmond.enhsamp.Node method) (schrodinger.application.desmond.enhsamp.Series method) (schrodinger.application.desmond.enhsamp.String method) (schrodinger.application.desmond.enhsamp.Var method) (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.FEPTorsions method) (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer method) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData method) (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase method) (schrodinger.application.desmond.fep_edge_report_maker.PRMEdgeReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker method) (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.desmond.fep_schedule.FepSchedule method) (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) (schrodinger.application.desmond.fep_scholar_util.FEPStructureObject method) (schrodinger.application.desmond.fep_scholar_util.MappingAnnotator method) (schrodinger.application.desmond.fep_scholar_util.MetaAtom method) (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) (schrodinger.application.desmond.fepana.DeltaEnergy method) (schrodinger.application.desmond.fepana.FreeEnergyContrib method) (schrodinger.application.desmond.fepana.Restraint method) (schrodinger.application.desmond.feputils.LabelSpinner method) (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) (schrodinger.application.desmond.ffiostructure.FFIOStructure method) (schrodinger.application.desmond.gaussian_filter.GaussianFilter method) (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.AtomGroupRow method) (schrodinger.application.desmond.gui.DesmondBasicConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.application.desmond.gui.DesmondRestGuiConfigDialog method) (schrodinger.application.desmond.gui.EnsembleClassFrame method) (schrodinger.application.desmond.gui.EnsembleTab method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.HorizontalBar method) (schrodinger.application.desmond.gui.InputGroup method) (schrodinger.application.desmond.gui.IntegrationTab method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.MdcAdvancedDialog method) (schrodinger.application.desmond.gui.MdcMiscTab method) (schrodinger.application.desmond.gui.MdGroup method) (schrodinger.application.desmond.gui.MinAdvancedDialog method) (schrodinger.application.desmond.gui.MinMiscTab method) (schrodinger.application.desmond.gui.OutputTab method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.PosResRow method) (schrodinger.application.desmond.gui.RandVelFrame method) (schrodinger.application.desmond.gui.RelaxFrame method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.gui.SimOptionsFrame method) (schrodinger.application.desmond.gui.SingleGpuDesmondGuiConfigDialog method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.desmond.gui.TempItemDelegate method) (schrodinger.application.desmond.image_generator.ImageGenerator method) (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) (schrodinger.application.desmond.kinetics.cleanup.CleanUp method) (schrodinger.application.desmond.kinetics.mtd_cleanup.CleanUp method) (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.desmond.maestro.Workspace method) (schrodinger.application.desmond.measurement.Measurement method) (schrodinger.application.desmond.memory.MemoryGauger method) (schrodinger.application.desmond.meta.CmsModel method) (schrodinger.application.desmond.meta.CV method) (schrodinger.application.desmond.meta.CVAngle method) (schrodinger.application.desmond.meta.CVDihedral method) (schrodinger.application.desmond.meta.CVDist method) (schrodinger.application.desmond.meta.CVrgyr method) (schrodinger.application.desmond.meta.CVrgyr_mass method) (schrodinger.application.desmond.meta.CVrmsd method) (schrodinger.application.desmond.meta.CVrmsd_symm method) (schrodinger.application.desmond.meta.CVwhim method) (schrodinger.application.desmond.meta.CVzdist method) (schrodinger.application.desmond.meta.CVzdist0 method) (schrodinger.application.desmond.meta.Meta method) (schrodinger.application.desmond.meta.MetaDynamicsAnalysis method) (schrodinger.application.desmond.msj_defaults.TagSpec method) (schrodinger.application.desmond.msj_generator.common.BaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.constant_ph.ConstantpHMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.covalent_ligand.CovalentMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.metalloprotein.MetalMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.protein.CombinedProteinMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator method) (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator method) (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams method) (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsWorkflowParams method) (schrodinger.application.desmond.msj_generator.mxmd.MixedSolventMsjGenerator method) (schrodinger.application.desmond.msj_generator.subjob_msj.BaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams method) (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingWorkflowParams method) (schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams method) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams method) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHWorkflowParams method) (schrodinger.application.desmond.msj_generator.workflow_params.MapperParams method) (schrodinger.application.desmond.msj_generator.workflow_params.MapperWorkflowParams method) (schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinMapperParams method) (schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinWorkflowParams method) (schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams method) (schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventWorkflowParams method) (schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams method) (schrodinger.application.desmond.msj_generator.workflow_params.ProteinWorkflowParams method) (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams method) (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams method) (schrodinger.application.desmond.msj_generator.workflow_params.SolubilityWorkflowParams method) (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams method) (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsWorkflowParams method) (schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams method) (schrodinger.application.desmond.multisim.parser.Msj method) (schrodinger.application.desmond.multisimstartup.Help method) (schrodinger.application.desmond.multisimstartup.Startup method) (schrodinger.application.desmond.multisimstartup.Startup.Help method) (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot method) (schrodinger.application.desmond.mxmd.mxmd_cleanup.Spot method) (schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent method) (schrodinger.application.desmond.mxmd.mxmd_system_builder.CosolventBoxGenerator method) (schrodinger.application.desmond.new_fep_edge_data.FepData method) (schrodinger.application.desmond.new_fep_edge_data.TorsionPotential method) (schrodinger.application.desmond.physical_leg_infra.LegProcess method) (schrodinger.application.desmond.picklejar.PicklableMetaClass method) (schrodinger.application.desmond.process_fep_traj.GenRepStructureForAbsoluteFep method) (schrodinger.application.desmond.process_fep_traj.GenRepStructureForFep method) (schrodinger.application.desmond.process_fep_traj.GenRepStructureForSublimationFep method) (schrodinger.application.desmond.queue.JobAdapter method) (schrodinger.application.desmond.queue.Queue method) (schrodinger.application.desmond.replica_dE.replica_container method) (schrodinger.application.desmond.replica_dE.replica_energy method) (schrodinger.application.desmond.replica_dE.replicas_monitor method) (schrodinger.application.desmond.replica_sid_generator.AlchemAsl method) (schrodinger.application.desmond.replica_sid_generator.FEPReport method) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) (schrodinger.application.desmond.rest_inp.RestInput method) (schrodinger.application.desmond.rl_helper.NumberedCanvas method) (schrodinger.application.desmond.simulation_block_data.Array_Prop method) (schrodinger.application.desmond.simulation_block_test.Block method) (schrodinger.application.desmond.simulation_block_test.BoxSize method) (schrodinger.application.desmond.simulation_block_test.E_f method) (schrodinger.application.desmond.simulation_block_test.E_k method) (schrodinger.application.desmond.simulation_block_test.E_x method) (schrodinger.application.desmond.simulation_block_test.Energy method) (schrodinger.application.desmond.simulation_block_test.Job_Details method) (schrodinger.application.desmond.simulation_block_test.PotentialEnergy method) (schrodinger.application.desmond.simulation_block_test.Pressure method) (schrodinger.application.desmond.simulation_block_test.T_0 method) (schrodinger.application.desmond.simulation_block_test.Temperature method) (schrodinger.application.desmond.simulation_block_test.Test method) (schrodinger.application.desmond.simulation_block_test.V method) (schrodinger.application.desmond.stage.analysis.Analysis method) (schrodinger.application.desmond.stage.analysis.AnalysisJob method) (schrodinger.application.desmond.stage.analysis.FepanaJob method) (schrodinger.application.desmond.stage.analysis.MetadynamicsAnalysisJob method) (schrodinger.application.desmond.stage.analysis.PLAnalysis method) (schrodinger.application.desmond.stage.analysis.Reporter method) (schrodinger.application.desmond.stage.analysis.SeaJob method) (schrodinger.application.desmond.stage.analysis.TimeSeriesAnalysisJob method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult method) (schrodinger.application.desmond.stage.app.constant_ph.SiteAndProtonationIds method) (schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob method) (schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis method) (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) (schrodinger.application.desmond.stage.app.watermap.WaterMapCluster method) (schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis method) (schrodinger.application.desmond.stage.fep_mapper.CombinedProteinFepMapper method) (schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper method) (schrodinger.application.desmond.stage.fep_mapper.FepMapper method) (schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup method) (schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper method) (schrodinger.application.desmond.stage.jobs.DesmondBackendJob method) (schrodinger.application.desmond.stage.jobs.DesmondJob method) (schrodinger.application.desmond.stage.jobs.FepJob method) (schrodinger.application.desmond.stage.jobs.SnapcoreCoordinates method) (schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield method) (schrodinger.application.desmond.stage.prepare.structure.BuildGeometry method) (schrodinger.application.desmond.stage.simulate.Concatenate method) (schrodinger.application.desmond.stage.simulate.DesmondExtend method) (schrodinger.application.desmond.stage.simulate.FepVrun method) (schrodinger.application.desmond.stage.simulate.GCMCCapable method) (schrodinger.application.desmond.stage.simulate.LambdaHopping method) (schrodinger.application.desmond.stage.simulate.ReplicaExchange method) (schrodinger.application.desmond.stage.simulate.SimulateBase method) (schrodinger.application.desmond.stage.simulate.Vrun method) (schrodinger.application.desmond.stage.utils.SystemBuilder method) (schrodinger.application.desmond.stage.workflow.Concluder method) (schrodinger.application.desmond.stage.workflow.Extern method) (schrodinger.application.desmond.stage.workflow.Primer method) (schrodinger.application.desmond.stage.workflow.Stop method) (schrodinger.application.desmond.stage.workflow.Task method) (schrodinger.application.desmond.stage.workflow.Trim method) (schrodinger.application.desmond.starter.generator.fep_residue_scanning.JobPreparedFiles method) (schrodinger.application.desmond.starter.starter.Starter method) (schrodinger.application.desmond.starter.ui.cmdline.BaseArgs method) (schrodinger.application.desmond.starter.ui.cmdline.SingleOptionAction method) (schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs method) (schrodinger.application.desmond.starter.ui.mxmd.MxmdArgs method) (schrodinger.application.desmond.starter.ui.unbinding_kinetics.UnbindingKineticsArgs method) (schrodinger.application.desmond.struc.CompStruc method) (schrodinger.application.desmond.struc.FormHashes method) (schrodinger.application.desmond.struc.FormMols method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) (schrodinger.application.desmond.systype.SysType method) (schrodinger.application.desmond.task.ParchTrajectoryForAbsoluteFep method) (schrodinger.application.desmond.task.ParchTrajectoryForFep method) (schrodinger.application.desmond.task.ParchTrajectoryForFepLambda method) (schrodinger.application.desmond.task.ParchTrajectoryForSolubilityFep method) (schrodinger.application.desmond.task.Premise method) (schrodinger.application.desmond.task.Task method) (schrodinger.application.desmond.task.TrajectoryForSolubilityFep method) (schrodinger.application.desmond.test_utils.FileRegistration method) (schrodinger.application.desmond.test_utils.FileRegistry method) (schrodinger.application.desmond.test_utils.UnregisteredFile method) (schrodinger.application.desmond.torsion_related.BondRotator method) (schrodinger.application.desmond.torsion_related.TorsionPotential method) (schrodinger.application.desmond.util.Counter method) (schrodinger.application.desmond.util.TestSuite method) (schrodinger.application.fpsim.FPsimSearcher method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.StageInfo method) (schrodinger.application.glide.client_module.GlideClientModule method) (schrodinger.application.glide.client_module.GlideClientModuleAdapter method) (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) (schrodinger.application.glide.glide.Constraint method) (schrodinger.application.glide.glide.ConstraintGroup method) (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.Feature method) (schrodinger.application.glide.glide.FeaturePattern method) (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.glide.glide.Grid method) (schrodinger.application.glide.glide.Gridgen method) (schrodinger.application.glide.glide.HydrophobicConstraint method) (schrodinger.application.glide.glide.MetalConstraint method) (schrodinger.application.glide.glide.MetCoordConstraint method) (schrodinger.application.glide.glide.NOEConstraint method) (schrodinger.application.glide.glide.PositionalConstraint method) (schrodinger.application.glide.glideanalysis.PoseLibrary method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.glide.http_client.AbstractGlideServerManager method) (schrodinger.application.glide.http_client.GlideResult method) (schrodinger.application.glide.http_client.GlideResultIterator method) (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.glide.http_client.HTTPClient method) (schrodinger.application.glide.http_client.NonBlockingBackendChecker method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) (schrodinger.application.glide.http_client.NonBlockingHTTPClient method) (schrodinger.application.glide.http_client.SubprocessJobAdapter method) (schrodinger.application.glide.http_client.ZmqClient method) (schrodinger.application.glide.ligand_designer.GridgenRunningException method) (schrodinger.application.glide.poseviewconvert.Complex method) (schrodinger.application.glide.sort_parser_common.ObsoleteAction method) (schrodinger.application.glide.sort_utils.BestPoseFilter method) (schrodinger.application.glide.sort_utils.CustomScoringFunction method) (schrodinger.application.glide.sort_utils.GlideSortUtility method) (schrodinger.application.glide.sort_utils.ReceptorTable method) (schrodinger.application.glide.sort_utils.SortCriterion method) (schrodinger.application.glide.sort_utils.SortValidator method) (schrodinger.application.glide.sort_utils.TempFileNameIterator method) (schrodinger.application.glide.utils.DictAction method) (schrodinger.application.glide.utils.EnvAction method) (schrodinger.application.glide.utils.EpvReader method) (schrodinger.application.glide.utils.LigandNumberIterator method) (schrodinger.application.glide.utils.PoseWriter method) (schrodinger.application.glide.utils.Progress method) (schrodinger.application.glide.xpdes.XpPVParser method) (schrodinger.application.inputconfig.InputConfig method) (schrodinger.application.jaguar.autots_bonding.AutoTSStructureReader method) (schrodinger.application.jaguar.autots_bonding.Coordinate method) (schrodinger.application.jaguar.autots_exceptions.MMTypingFailure method) (schrodinger.application.jaguar.autots_exceptions.TSFrequencyError method) (schrodinger.application.jaguar.autots_input.AutoTSInput method) (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper method) (schrodinger.application.jaguar.basis.BasisSet method) (schrodinger.application.jaguar.discretized_1d_function.DiscretelySampledFunction method) (schrodinger.application.jaguar.esol_input.EsolInput method) (schrodinger.application.jaguar.file_logger.FileLogger method) (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog method) (schrodinger.application.jaguar.gui.base_panel.PropertiesMixin method) (schrodinger.application.jaguar.gui.base_panel.StandardStatusMixin method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelector method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.jaguar.gui.basis_selector.BasisSetListWidgetItem method) (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.jaguar.gui.filedialog.FileDialogWithExtraCombo method) (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.application.jaguar.gui.input_tab_widgets.MethodDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog method) 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(schrodinger.application.transforms.filters.StructurePropertyFilter method) (schrodinger.application.transforms.filters.TanimotoFilter method) (schrodinger.application.transforms.ligprep.LigandPrep method) (schrodinger.application.transforms.template.workflow.CarbonCountingWorkflow method) (schrodinger.application.vss.config.Config method) (schrodinger.application.vss.control.DiseControl method) (schrodinger.application.vss.control.GlideALControl method) (schrodinger.application.vss.control.GlideControl method) (schrodinger.application.vss.control.LigandMLControl method) (schrodinger.application.vss.control.RunnerControl method) (schrodinger.application.vss.control.ShapeControl method) (schrodinger.application.vss.csvsmiles.CsvSmilesFile method) (schrodinger.application.vss.database.Database method) (schrodinger.application.watermap.shapes.ShapeFactory method) (schrodinger.application.watermap.watermap_inp.WaterMapInput method) (schrodinger.application.xtb.input.XTBInput method) (schrodinger.application.xtb.keywords.XTBKeyword method) (schrodinger.application.xtb.output.XTBOutput method) (schrodinger.application.xtb.textparser.TextParser method) (schrodinger.comparison.atom_mapper.BaseAtomMapper method) (schrodinger.comparison.atom_mapper.ConnectivityAtomMapper method) (schrodinger.comparison.atom_mapper.CSPAtomMapper method) (schrodinger.comparison.atom_mapper.LewisAtomMapper method) (schrodinger.comparison.results.ResultSet method) (schrodinger.forcefield.common.AtomTypingFailure method) (schrodinger.forcefield.minimizer.Constraint method) (schrodinger.forcefield.minimizer.Restraint method) (schrodinger.graphics3d.arrow.MaestroArrow method) (schrodinger.graphics3d.box.MaestroBox method) (schrodinger.graphics3d.box.MaestroParallelepiped method) (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.ellipsoid.MaestroEllipsoid method) (schrodinger.graphics3d.gridbox.GridBox method) 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(schrodinger.job.queue.RunningJobs method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.job.remote_command.CommandError method) (schrodinger.job.resource.ComputeRequirement method) (schrodinger.livedesign.biologics.fasta.PolymerAssembler method) (schrodinger.livedesign.biologics.registration.BioPolymer method) (schrodinger.livedesign.biologics.sequence.AlignedSequence method) (schrodinger.livedesign.check_reaction.RxnCheckResult method) (schrodinger.livedesign.rgfile_parse.ForwardRGMolSupplier method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBar method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBarSketcherDialog method) (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) (schrodinger.maestro_utils.maestro_sync.PLPTarget method) (schrodinger.maestro_utils.maestro_sync.ProjectEntryMaestroSync method) (schrodinger.maestro_utils.maestro_sync.TitleTarget method) (schrodinger.math.mathutils.Interpolate1D 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(schrodinger.protein.annotation.ProteinSequenceAnnotations method) (schrodinger.protein.annotation.SeqTypeMixin method) (schrodinger.protein.assignment.Interactors method) (schrodinger.protein.assignment.NetworkSolver method) (schrodinger.protein.assignment.PropKaException method) (schrodinger.protein.assignment.ProtAssign method) (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) (schrodinger.protein.assignment.WaterStateEnumerator 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(schrodinger.protein.sequence.GapRegion method) (schrodinger.protein.sequence.ProteinSequence method) (schrodinger.protein.tasks.clustal.AbstractAlignmentJob method) (schrodinger.protein.tasks.clustal.ClustalJob method) (schrodinger.protein.tasks.muscle.MuscleJob method) (schrodinger.rdkit.filtering.ComparableMol method) (schrodinger.rdkit.filtering.JSONFilterAdapter method) (schrodinger.rdkit.molio.BaseCsvMolReader method) (schrodinger.rdkit.molio.BasePfxMolReader method) (schrodinger.rdkit.molio.CsvMergeHandler method) (schrodinger.rdkit.molio.CsvMolReader method) (schrodinger.rdkit.molio.CsvMolWriter method) (schrodinger.rdkit.molio.GzippedSDMolSupplier method) (schrodinger.rdkit.molio.MolWriter method) (schrodinger.rdkit.molio.NoneSkipper method) (schrodinger.rdkit.molio.PfxMolWriter method) (schrodinger.rdkit.molio.RdkitMergeHandler method) (schrodinger.rdkit.molio.RdkitMolWriter method) (schrodinger.rdkit.molio.StructureMergeHandler method) 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(schrodinger.ui.qt.swidgets.FileBaseNameValidator method) (schrodinger.ui.qt.swidgets.HelpButton method) (schrodinger.ui.qt.swidgets.ImageLabel method) (schrodinger.ui.qt.swidgets.InfoButton method) (schrodinger.ui.qt.swidgets.InstantToolTipTableView method) (schrodinger.ui.qt.swidgets.LargeSpinner method) (schrodinger.ui.qt.swidgets.LigandDetectionLink method) (schrodinger.ui.qt.swidgets.LineEditWithDisabledText method) (schrodinger.ui.qt.swidgets.MinMaxSpinBoxTether method) (schrodinger.ui.qt.swidgets.NewNameDialog method) (schrodinger.ui.qt.swidgets.PersistentMenu method) (schrodinger.ui.qt.swidgets.PlaceholderComboMixin method) (schrodinger.ui.qt.swidgets.ProjectTableButton method) (schrodinger.ui.qt.swidgets.ResetButton method) (schrodinger.ui.qt.swidgets.SaveButton method) (schrodinger.ui.qt.swidgets.SavedItemsManager method) (schrodinger.ui.qt.swidgets.SavedMenuItem method) (schrodinger.ui.qt.swidgets.SCheckBox method) (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) (schrodinger.ui.qt.swidgets.SCheckBoxToggle method) (schrodinger.ui.qt.swidgets.SCheckBoxWithSubWidget method) (schrodinger.ui.qt.swidgets.SComboBox method) (schrodinger.ui.qt.swidgets.SDialog method) (schrodinger.ui.qt.swidgets.SDoubleSpinBox method) (schrodinger.ui.qt.swidgets.SelectorWithPopUp method) (schrodinger.ui.qt.swidgets.SFilteredListWidget method) (schrodinger.ui.qt.swidgets.SFrame method) (schrodinger.ui.qt.swidgets.SGridLayout method) (schrodinger.ui.qt.swidgets.SGroupBox method) (schrodinger.ui.qt.swidgets.SHBoxLayout method) (schrodinger.ui.qt.swidgets.SHLine method) (schrodinger.ui.qt.swidgets.SLabel method) (schrodinger.ui.qt.swidgets.SLabeledComboBox method) (schrodinger.ui.qt.swidgets.SLabeledDoubleSpinBox method) (schrodinger.ui.qt.swidgets.SLabeledEdit method) (schrodinger.ui.qt.swidgets.SLabeledRadioButtonGroup method) (schrodinger.ui.qt.swidgets.SLabeledSlider method) (schrodinger.ui.qt.swidgets.SLabeledSpinBox method) (schrodinger.ui.qt.swidgets.SLineEdit method) (schrodinger.ui.qt.swidgets.SListWidget method) (schrodinger.ui.qt.swidgets.SmallCloseButton method) (schrodinger.ui.qt.swidgets.SMARTSEdit method) (schrodinger.ui.qt.swidgets.SNonEmptyStringValidator method) (schrodinger.ui.qt.swidgets.SNonNegativeIntValidator method) (schrodinger.ui.qt.swidgets.SNonNegativeRealValidator method) (schrodinger.ui.qt.swidgets.SNumberListValidator method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) (schrodinger.ui.qt.swidgets.Spinner method) (schrodinger.ui.qt.swidgets.SpinnerIcon method) (schrodinger.ui.qt.swidgets.SPosIntListValidator method) (schrodinger.ui.qt.swidgets.SPushButton method) (schrodinger.ui.qt.swidgets.SRadioButton method) (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) (schrodinger.ui.qt.swidgets.SRadioButtonWithSubWidget method) (schrodinger.ui.qt.swidgets.SRealValidator method) (schrodinger.ui.qt.swidgets.SRegularExpressionValidator method) (schrodinger.ui.qt.swidgets.SRetainableMenu method) (schrodinger.ui.qt.swidgets.SSpinBox method) (schrodinger.ui.qt.swidgets.SSplitter method) (schrodinger.ui.qt.swidgets.STableView method) (schrodinger.ui.qt.swidgets.STableWidget method) (schrodinger.ui.qt.swidgets.STableWidgetItem method) (schrodinger.ui.qt.swidgets.STabWidget method) (schrodinger.ui.qt.swidgets.StdMenuItem method) (schrodinger.ui.qt.swidgets.SToolButton method) (schrodinger.ui.qt.swidgets.STwoButtonBox method) (schrodinger.ui.qt.swidgets.SValidIndicator method) (schrodinger.ui.qt.swidgets.SVBoxLayout method) (schrodinger.ui.qt.swidgets.TextSearchBar method) (schrodinger.ui.qt.swidgets.TrashButton method) (schrodinger.ui.qt.swidgets.VerticalLabel method) (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.GenericViewerDelegate method) (schrodinger.ui.qt.table.PerColumnSortableHeaderView method) (schrodinger.ui.qt.table.PerColumnSortableTableView method) (schrodinger.ui.qt.table.SEasySDTable method) (schrodinger.ui.qt.table.SHeaderView method) (schrodinger.ui.qt.table.StructureDataViewerDelegate method) (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ToolTipFilter method) (schrodinger.ui.qt.table.ViewerModel method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) (schrodinger.ui.qt.table_helper.CheckableHeaderView method) (schrodinger.ui.qt.table_helper.Column method) (schrodinger.ui.qt.table_helper.DataMethodDecoratorMixin method) (schrodinger.ui.qt.table_helper.PtRowBasedTableModel method) (schrodinger.ui.qt.table_helper.PythonSortProxyModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) (schrodinger.ui.qt.table_helper.SampleDataTableViewMixin method) (schrodinger.ui.qt.table_speed_up.AbstractFlagCacheProxyMixin method) (schrodinger.ui.qt.table_speed_up.DataCache method) (schrodinger.ui.qt.table_speed_up.MultipleSpeedUpDelegatesViewMixin method) (schrodinger.ui.qt.table_speed_up.SpeedUpDelegate method) (schrodinger.ui.qt.table_speed_up.SpeedUpDelegateViewMixin method) (schrodinger.ui.qt.tablewidget.Cell method) (schrodinger.ui.qt.tablewidget.CellIterator method) (schrodinger.ui.qt.tablewidget.Column method) (schrodinger.ui.qt.tablewidget.ColumnIterator method) (schrodinger.ui.qt.tablewidget.HorizontalHeader method) (schrodinger.ui.qt.tablewidget.MyWindow method) (schrodinger.ui.qt.tablewidget.Row method) (schrodinger.ui.qt.tablewidget.RowIterator method) (schrodinger.ui.qt.tablewidget.SelfContainedTable method) (schrodinger.ui.qt.tablewidget.TableWidget method) (schrodinger.ui.qt.tablewidget.VerticalHeader method) (schrodinger.ui.qt.tasks.taskbarwidgets.NameLineEdit method) (schrodinger.ui.qt.tasks.taskbarwidgets.TaskWidgetMixin method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressBar method) (schrodinger.ui.qt.tasks.taskwidgets.SettingsButton method) (schrodinger.ui.qt.tasks.taskwidgets.SpinnerLabel method) (schrodinger.ui.qt.tasks.taskwidgets.SpinnerStartButton method) (schrodinger.ui.qt.tasks.taskwidgets.StartButton method) (schrodinger.ui.qt.tooltips.TooltipMixin method) (schrodinger.ui.qt.utils.BorderlessPopUpFrame method) (schrodinger.ui.qt.utils.ButtonAcceptsFocusMixin method) (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator method) (schrodinger.ui.qt.utils.JobLaunchWaitCursorContext method) (schrodinger.ui.qt.utils.LineEditWithSampleText method) (schrodinger.ui.qt.utils.MaestroPythonBannerManager method) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) (schrodinger.ui.qt.xsignals.XSignal method) (schrodinger.ui.residueselector.CustomResidueMixin method) (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorFrame method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) (schrodinger.ui.residueselector.MutationSelectorMixin method) (schrodinger.ui.residueselector.ResidueGroups method) (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) (schrodinger.ui.two_d_viewer.AtomPropertyDialog method) (schrodinger.ui.two_d_viewer.Cell method) (schrodinger.ui.two_d_viewer.CellContextualMenu method) (schrodinger.ui.two_d_viewer.CtPropsDialog method) (schrodinger.ui.two_d_viewer.TwoDTableDelegate method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) (schrodinger.ui.two_d_viewer.TwoDTableView method) (schrodinger.ui.two_d_viewer.TwoDViewer method) (schrodinger.ui.two_d_viewer.ZoomWidget method) (schrodinger.utils.cgxutils.FragmentLibrary method) (schrodinger.utils.env.EnvironmentContext method) (schrodinger.utils.env.MultiEnvironmentContext method) (schrodinger.utils.fileutils.chdir method) (schrodinger.utils.fileutils.MultiFileReader method) (schrodinger.utils.funcchains.FuncChainMixin method) (schrodinger.utils.funcgroups.FuncData method) (schrodinger.utils.funcgroups.FuncGroupMarker method) (schrodinger.utils.funcgroups.FuncGroupMixin method) (schrodinger.utils.installation_check.TestJob method) (schrodinger.utils.installation_check.TestJobDJ method) (schrodinger.utils.license.License method) (schrodinger.utils.license.LicenseStatus method) (schrodinger.utils.ligfilter.AslCriterion method) (schrodinger.utils.ligfilter.Criterion method) (schrodinger.utils.ligfilter.CriterionParser method) (schrodinger.utils.ligfilter.Definition method) (schrodinger.utils.ligfilter.DefinitionParser method) (schrodinger.utils.ligfilter.PredefinedCriterion method) (schrodinger.utils.ligfilter.PropertyCriterion method) (schrodinger.utils.ligfilter.SmartsCriterion method) (schrodinger.utils.moduleproxy.ModuleProxy method) (schrodinger.utils.multifpfile.MultiFPFile method) (schrodinger.utils.multifpfile.MultiFPFileWriter method) (schrodinger.utils.preferences.Preferences method) (schrodinger.utils.profiling.Profiler method) (schrodinger.utils.profiling.SystemResourceTimer method) (schrodinger.utils.profiling.SystemResourceTimes method) (schrodinger.utils.profiling.Timer method) (schrodinger.utils.pymol.PymolInstance method) (schrodinger.utils.pymol.RowProxy method) (schrodinger.utils.pymol.VisRecord method) (schrodinger.utils.pymol.WorkspaceIdMapper method) (schrodinger.utils.qapplication.CantCreateQApplicationError method) (schrodinger.utils.qt_utils.ABCMetaQObject method) (schrodinger.utils.qt_utils.EventLoop method) (schrodinger.utils.qt_utils.SignalAndSlot method) (schrodinger.utils.qt_utils.suppress_signals method) (schrodinger.utils.scollections.DefaultFactoryDictMixin method) (schrodinger.utils.scollections.DefaultIdDict method) (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.scollections.IdItemsView method) (schrodinger.utils.scollections.IdSet method) (schrodinger.utils.sea.evalor.Evalor method) (schrodinger.utils.sea.sea.Atom method) (schrodinger.utils.sea.sea.Hydrogen method) (schrodinger.utils.sea.sea.Key method) (schrodinger.utils.sea.sea.List method) (schrodinger.utils.sea.sea.Map method) (schrodinger.utils.sea.sea.Sea method) (schrodinger.utils.singledashoptionparser.SingleDashOption method) (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method) (schrodinger.utils.thread_utils.ThreadTool method)

__len__() (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult method) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.cmj.JobOutput method) (schrodinger.application.desmond.cms.PosRestrainArray method) (schrodinger.application.desmond.struc.CompStruc method) (schrodinger.application.glide.http_client.GlideResult method) (schrodinger.application.glide.sort_utils.ReceptorTable method) (schrodinger.application.jaguar.results.RoutineTimes method) (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) (schrodinger.application.matsci.elasticity.strain.DeformedStructureSet method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) (schrodinger.application.matsci.species.SpeciesCollection method) (schrodinger.application.qsite.input.QMRegion method) (schrodinger.graphics3d.common.Group method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.mmim.MMIMDict method) (schrodinger.infra.mmkv.MMKVArgList method) (schrodinger.infra.mmlist.mmlist method) (schrodinger.infra.table.Table method) (schrodinger.job.queue.LinkedList method) (schrodinger.job.queue.PriorityQueue method) (schrodinger.project.project.EmptyIterator method) (schrodinger.project.project.Project method) (schrodinger.project.surface.SurfaceDict method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.rdkit.molio.CsvMolReader method) (schrodinger.rdkit.molio.NoneSkipper method) (schrodinger.rdkit.molio.PfxMolReader method) (schrodinger.stepper.stepper.UnbatchedChain method) (schrodinger.structure._AtomBondContainer method) (schrodinger.structure._AtomCollection method) (schrodinger.structure._StructureAtomContainer method) (schrodinger.structure._StructureAtomProperty method) (schrodinger.structure._StructureBondContainer method) (schrodinger.structure._StructureBondProperty method) (schrodinger.structure._StructureProperty method) (schrodinger.structutils.color.ColorScheme method) (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) (schrodinger.tasks.queue.QueueResults method) (schrodinger.tasks.taskmanager.TaskManager method) (schrodinger.trajectory.prody.ensemble.Ensemble method) (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.ui.qt.tablewidget.CellIterator method) (schrodinger.ui.qt.tablewidget.ColumnIterator method) (schrodinger.ui.qt.tablewidget.RowIterator method) (schrodinger.utils.cgxutils.FragmentLibrary method) (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.scollections.IdItemsView method) (schrodinger.utils.scollections.IdSet method) _AtomBondContainer (class in schrodinger.structure) _AtomCollection (class in schrodinger.structure) _BaseWriter (class in schrodinger.structure) _Chain (class in schrodinger.structure) _Molecule (class in schrodinger.structure) _NotSortable (class in schrodinger.structure) _ReaderWriterContextManager (class in schrodinger.structure) _Ring (class in schrodinger.structure) _StructureAtomContainer (class in schrodinger.structure) _StructureAtomProperty (class in schrodinger.structure) _StructureBondContainer (class in schrodinger.structure) _StructureBondProperty (class in schrodinger.structure) _StructureProperty (class in schrodinger.structure)

A

A (schrodinger.protein.annotation.TCRRegionLabel attribute) (schrodinger.ui.qt.mapperwidgets.param_editor.MyEnum attribute) A2cell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) A2Gmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice) A2invcell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) A4 (schrodinger.application.phase.shape_screen_reporter.option_utils.PageSize attribute) A_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) A_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) AABranchingConnectorItem (class in schrodinger.protein.helm.helm_renderer) Aacg_SiteMap_Multijob (class in schrodinger.application.desmond.stage.app.matsci) AALinearConnectorItem (class in schrodinger.protein.helm.helm_renderer) AB (schrodinger.livedesign.biologics.fasta.PolymerType attribute) AB_HC (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) AB_HC1 (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) AB_HC2 (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) AB_LC (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) AB_LC1 (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) AB_LC2 (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) ABAB (schrodinger.application.matsci.nano.constants.Constants attribute) ABBE_NFREQ (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) ABBE_NUMBER_PROP (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) AbbeNumber (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) abbreviation (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) ABCD (schrodinger.application.matsci.nano.constants.Constants attribute) ABCMetaQObject (class in schrodinger.utils.qt_utils) abeles() (in module schrodinger.application.matsci.gsas.GSASIIpwd) AbFEPEdgeData (class in schrodinger.application.desmond.fep_edge_data) ABFEPReportMaker (class in schrodinger.application.desmond.fep_edge_report_maker) abo_options (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) abo_optionsChanged (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) abo_optionsReplaced (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) ABORT (schrodinger.ui.qt.forcefield.forcefield.OPLSDirResult attribute) AbortException aboutToQuitMaestro() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) aboutToShowAdvancedSettings (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) aboutToStartTask (schrodinger.ui.qt.tasks.taskwidgets.StartButton attribute) aboutToUpdatePositions (schrodinger.ui.dendrogram.DendrogramGraphicTree attribute) abs_schrodinger_path() (in module schrodinger.utils.subprocess) absolute (schrodinger.application.matsci.reaction_workflow_utils.MmodEnergyKeys attribute) ABSOLUTE_BINDING (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) AbsoluteBindingMsjGenerator (class in schrodinger.application.desmond.msj_generator.fep.absolute_binding) AbsoluteBindingResult (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) AbsoluteBindingSimLegParams (class in schrodinger.application.desmond.msj_generator.workflow_params) AbsoluteBindingWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) Absorb() (in module schrodinger.application.matsci.gsas.GSASIIpwd) AbsorbDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd) ABSTRACT (schrodinger.models.parameters.ParamType attribute) abstract_only() (in module schrodinger.models.parameters) AbstractAdapter (class in schrodinger.models.adapters.abstractadapter) AbstractAligner (class in schrodinger.protein.align) AbstractAlignmentJob (class in schrodinger.protein.tasks.clustal) AbstractCmdTask (class in schrodinger.tasks.tasks) AbstractComboTask (class in schrodinger.tasks.tasks) AbstractCustomDelegate (class in schrodinger.ui.qt.delegates) AbstractDebugViewer (class in schrodinger.ui.qt.appframework2.debugcore) AbstractDelegateWithEditIcon (class in schrodinger.ui.qt.delegates) AbstractExportPanel (class in schrodinger.application.livedesign.ld_export) AbstractFlagCacheProxyMixin (class in schrodinger.ui.qt.table_speed_up) AbstractFlagCacheProxyMixinMetaclass (class in schrodinger.ui.qt.table_speed_up) AbstractGlideServerManager (class in schrodinger.application.glide.http_client) AbstractHTTPClient (class in schrodinger.application.glide.http_client) AbstractJsonSerializer (class in schrodinger.models.jsonable) AbstractMaestroCallbackMixin (class in schrodinger.ui.qt.appframework2.maestro_callback) AbstractNetworkView (class in schrodinger.ui.qt.network_visualizer) AbstractNWPairwiseAligner (class in schrodinger.protein.align) AbstractPairwiseAligner (class in schrodinger.protein.align) AbstractPlot (class in schrodinger.stepper.viz) AbstractPredictor (class in schrodinger.protein.predictors) AbstractPredictor.Input (class in schrodinger.protein.predictors) AbstractProteinSequenceAnnotationsMixin (class in schrodinger.protein.annotation) AbstractProteinSequenceMixin (class in schrodinger.protein.sequence) AbstractRDMolImageLabel (class in schrodinger.ui.qt.rdmol_views) AbstractRegionFinder (class in schrodinger.protein.annotation) AbstractSelectionLineEdit (class in schrodinger.application.livedesign.panel_components) AbstractSelectionPopUp (class in schrodinger.application.livedesign.panel_components) AbstractSelectionPopUpDelegate (class in schrodinger.application.livedesign.panel_components) AbstractSequence (class in schrodinger.protein.sequence) AbstractSequence.ORIGIN (class in schrodinger.protein.sequence) AbstractSequenceAnnotations (class in schrodinger.protein.annotation) AbstractSequenceElement (class in schrodinger.protein.residue) AbstractSingleChainSequence (class in schrodinger.protein.sequence) AbstractStructureAligner (class in schrodinger.protein.align) AbstractStructureAligner.Result (class in schrodinger.protein.align) AbstractTask (class in schrodinger.tasks.tasks) AbstractTaskBar (class in schrodinger.ui.qt.tasks.taskwidgets) AbstractTorsionAnalyzer (class in schrodinger.trajectory.trajectory_gui_dir.custom_analyzers) AbstractUnusableModuleFinder (class in schrodinger.infra.unusable_module_importer) ACC_LEVEL (class in schrodinger.application.jaguar.csrch_input_constants) acc_prediction (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) acc_predictionChanged (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) acc_predictionReplaced (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) ACCEPT (in module schrodinger.ui.qt.pop_up_widgets) accept() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog method) (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.bioluminate.propfilter.ValueSelectionDialog method) (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.matsci.chargegui.ChargeDialog method) (schrodinger.application.matsci.deswidgets.AdvancedMDOptions method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.NewPresetDialog method) (schrodinger.application.matsci.jagwidgets.SolventDialog method) (schrodinger.application.matsci.jobdirdlg.NewJobDirDialog method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.reordergui.ReorderAtomsDialog method) (schrodinger.application.matsci.reportutils.ReportOutputsDialog method) (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog method) (schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog method) (schrodinger.application.matsci.wfmanagement.WorkflowNamerDialog method) (schrodinger.ui.chooseligand.ChooseLigandDialog method) (schrodinger.ui.picking.MaestrolessPickLigandDialog method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.formlayout.FormDialog method) (schrodinger.ui.qt.propertyselector.PropertySelectorDialog method) (schrodinger.ui.qt.rename_favorite_dialog.RenameFavoriteDialog method) (schrodinger.ui.qt.schart.AxesDialog method) (schrodinger.ui.qt.schart.BinsDialog method) (schrodinger.ui.qt.schart.SeriesDialog method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) (schrodinger.ui.qt.swidgets.NewNameDialog method) (schrodinger.ui.two_d_viewer.AtomPropertyDialog method) (schrodinger.ui.two_d_viewer.CtPropsDialog method) ACCEPT_MULTI (in module schrodinger.ui.qt.pop_up_widgets) accept_reject_parse() (in module schrodinger.application.desmond.replica_exchange_review) accept_test() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) accepted (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin property) ACCEPTED_FRAMEWORK_COLOR (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) ACCEPTOR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) AcceptorConstraint (class in schrodinger.application.glide.glide) acceptors (schrodinger.protein.assignment.Interactors attribute) AcceptsFocusPushButton (class in schrodinger.ui.qt.utils) AccproPredictor (class in schrodinger.protein.predictors) accumulate() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) ACCURACY_LEVELS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) ACCURATE (schrodinger.application.matsci.qualityslider.QualitySlider attribute) ACENTRIC_DIPOLE (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) AcentricDipoleDirector (class in schrodinger.application.matsci.order_parameter_mod) Acidic (schrodinger.protein.helm.helm_renderer.HexColor attribute) AcidicHydrophilic (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) ack() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) acosd() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIImath) (in module schrodinger.application.matsci.gsas.GSASIIpwd) acquireLicenseForSmartDistribution() (schrodinger.job.queue.JobControlJob method) acs_summary_string() (schrodinger.application.jaguar.simple_spec.Peak method) action (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) action_factory (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) action_names (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) actionChanged (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) ActionComboBox (class in schrodinger.ui.qt.swidgets) ActionMenu (class in schrodinger.application.bioluminate.pml_menus) ActionPushButton (class in schrodinger.ui.qt.swidgets) actionReplaced (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) Actions (in module schrodinger.ui.qt.appframework2.wizards) actionTriggered() (schrodinger.ui.qt.swidgets.ActionComboBox method) activate() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.matsci.mswidgets.ProcessBusyDialog method) (schrodinger.ui.qt.appframework.WriteDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) activate_modules() (in module schrodinger.tasks.remote_modules) ACTIVATION_LOOP (schrodinger.protein.annotation.KinaseFeatureLabel attribute) ACTIVE (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.job.queue.JobState attribute) (schrodinger.ui.qt.standard.design_tokens.BorderColors attribute) (schrodinger.ui.qt.standard.design_tokens.StateColors attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) active_atom_pairs() (in module schrodinger.application.jaguar.autots_bonding) active_cdr_names() (schrodinger.application.bioluminate.antibody.grafting.GraftingInput method) active_db_paths (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) active_db_pathsChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) active_db_pathsReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) active_jobs (schrodinger.job.queue.JobDJ property) active_jobs_only (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) active_jobs_onlyChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) active_jobs_onlyReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) active_reactant_atom_pairs() (in module schrodinger.application.jaguar.autots_bonding) active_total (schrodinger.application.desmond.cms.Cms property) active_total_from_nactive_gids() (schrodinger.application.desmond.cms.Cms method) ActiveBondSearchFailure activeConstraintsToggled (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab attribute) ActiveCoord (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) ActiveDatabaseDialog (class in schrodinger.application.bioluminate.antibody.management) ActiveDatabaseTable (class in schrodinger.application.bioluminate.antibody.management) ActiveLearning (class in schrodinger.seam.examples.active_learning_weigher) ActiveLearningJob (class in schrodinger.active_learning.al_driver) ActiveLearningNode (class in schrodinger.active_learning.al_node) ActiveLearningNodeSupplier (class in schrodinger.active_learning.al_node) ActiveLearningShapeScreenJob (class in schrodinger.application.phase.packages.shape_screen_al_driver) ActiveOptimizationTab (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) activeSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) activeSubTabName() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) activeTask() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) ActiveTransitionStateTab (class in schrodinger.application.jaguar.gui.tabs.transition_state_tab) adapt_interval (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) adapt_iterations (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) adaptAngles() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) adapter() (in module schrodinger.models.json) adapter47007() (schrodinger.protein.sequence.ProteinSequence class method) adapter48002() (schrodinger.protein.alignment.ProteinAlignment class method) (schrodinger.protein.sequence.ProteinSequence class method) adapter52065() (schrodinger.protein.sequence.ProteinSequence class method) adapter55040() (schrodinger.tasks.jobtasks.HostSettings class method) adapter_50002() (schrodinger.protein.properties.SequenceProperty class method) adaptFF() (schrodinger.application.matsci.cgforcefield.ForceField method) adaptive_ligand_restraint (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) adaptor (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser property) adaptRestraints() (schrodinger.application.matsci.cgforcefield.RestraintAdaptationMixin method) add (schrodinger.ui.qt.appframework2.maestro_callback.CallbackInfo attribute) add() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.cmj.JobOutput method) (schrodinger.application.desmond.cms.DictRestrainGroup method) (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.comparison.results.ResultSet method) (schrodinger.graphics3d.common.Group method) (schrodinger.job.queue.LinkedList method) (schrodinger.job.queue.RunningJobs method) (schrodinger.project.surface.SurfaceDict method) (schrodinger.rdkit.sorted_molwriter.SortedMolWriter method) (schrodinger.structutils.color.ColorScheme method) (schrodinger.ui.qt.appframework2.validation.ValidationResults method) (schrodinger.utils.scollections.IdSet method) add_alignment_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) ADD_ALL (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute) add_amide_constraints() (in module schrodinger.structutils.rgroup_enumerate) add_analysis_argument() (in module schrodinger.application.matsci.equilibrium_md) add_and_parse_SMILES() (in module schrodinger.application.desmond.rl_helper) add_annotator() (schrodinger.ui.qt.structure2d.structure_item method) add_annotator_function_return() (schrodinger.ui.qt.structure2d.structure_item method) add_any_arg() (in module schrodinger.application.phase.packages.phase_database_job_utils) add_arguments() (in module schrodinger.application.phase.packages.shape_creation_logic) add_arrowhead() (schrodinger.protein.helm.helm_renderer.ArrowheadConnectorMixin method) add_atom_highlight() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) add_atom_properties() (in module schrodinger.application.matsci.packmol) add_attachment_points() (schrodinger.application.canvas.r_group.Data method) add_axis_margins() (in module schrodinger.ui.qt.smatplotlib) add_barrier_to_msj() (in module schrodinger.application.matsci.desconfig) add_blimit_arg() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_boltzmann_energy_argument() (in module schrodinger.application.matsci.parserutils) add_bond_arrow() (schrodinger.ui.qt.structure2d.ColoredArrowAnnotator method) add_bonds_in_rings() (schrodinger.application.canvas.r_group.Data method) add_build_args() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) add_cg_forcefield_parser_arguments() (in module schrodinger.application.matsci.parserutils) add_charge_flag() (in module schrodinger.application.matsci.kmc) add_chiral_hs() (in module schrodinger.livedesign.preprocessor) add_chunk_row() (in module schrodinger.application.bb_database.bb_task_utils) add_cluster_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) add_code() (schrodinger.infra.mmcheck.ReturnCode method) add_column() (in module schrodinger.application.matsci.kmc) add_com_to_pairs_table() (in module schrodinger.application.matsci.kmc) add_common_context_items() (in module schrodinger.application.bioluminate.pml_menus) add_compress_subjobs_parser_argument() (in module schrodinger.application.matsci.parserutils) add_conf_treatment_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) add_confgen_options() (in module schrodinger.application.phase.packages.conformer_reader) add_conformational_search_to_parser() (in module schrodinger.application.matsci.parserutils) add_convert_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) add_core() (schrodinger.application.canvas.r_group.Data method) add_core_bonds() (schrodinger.application.canvas.r_group.Data method) add_core_ct() (schrodinger.application.canvas.r_group.Data method) add_cpu_gpu_host_arguments() (in module schrodinger.application.matsci.parserutils) add_create_args() (in module schrodinger.application.phase.packages.oned_option_utils) (in module schrodinger.application.phase.shape_screen_reporter.option_utils) add_crest_csearch() (in module schrodinger.application.matsci.reaction_workflow_utils) add_ct_data() (in module schrodinger.application.canvas.r_group) add_ct_offset() (schrodinger.application.canvas.r_group.Data method) add_cubic_chorus_box_props() (in module schrodinger.application.matsci.desmondutils) add_cuda_stubs_for_tensorflow() (in module schrodinger.utils.env) add_current_to_states() (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) add_custom_eq_rows() (in module schrodinger.application.matsci.reaction_workflow_utils) add_custom_rate_rows() (in module schrodinger.application.matsci.reaction_workflow_utils) add_database_options() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) (in module schrodinger.application.phase.packages.phase_screen_utils) add_database_screening_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) add_dedup_geom_eps_parser_argument() (in module schrodinger.application.matsci.parserutils) add_delete_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) add_describe_args() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) (in module schrodinger.application.phase.packages.oned_option_utils) add_descriptors() (in module schrodinger.rdkit.filtering) (in module schrodinger.structutils.rgroup_enumerate) add_descriptors_gen() (in module schrodinger.rdkit.filtering) add_desmond_license_to_job_builder() (in module schrodinger.application.matsci.jobutils) add_desmond_license_to_job_spec() (in module schrodinger.application.matsci.jobutils) add_desmond_ms_logo() (in module schrodinger.application.matsci.gutils) add_desmond_parser_arguments() (in module schrodinger.application.matsci.parserutils) add_disulfide_bond() (in module schrodinger.protein.residue) add_energy_atom_groups() (in module schrodinger.application.matsci.desmondutils) add_enums_as_attributes() (in module schrodinger.utils.qt_utils) add_error() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.licensing.licadmin.ServerInfo method) add_explicit_hydrogens() (in module schrodinger.livedesign.preprocessor) add_export_args() (in module schrodinger.application.phase.packages.oned_option_utils) (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) (in module schrodinger.application.phase.shape_screen_reporter.option_utils) add_extract_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) add_feature_matching_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) add_fep_lic() (in module schrodinger.application.desmond.license) add_file_options() (in module schrodinger.application.phase.packages.conformer_reader) add_file_options_group() (in module schrodinger.application.glide.sort_parser_common) add_file_screening_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) add_file_to_aljob_restart_dict() (in module schrodinger.active_learning.al_utils) add_filter_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) add_filter_parser_group() (in module schrodinger.application.glide.sort_parser_common) add_filtering_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) add_filters() (in module schrodinger.rdkit.filtering) add_functional_rings() (schrodinger.application.canvas.r_group.Data method) add_generate_arguments() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) add_geom_argument() (in module schrodinger.application.matsci.parserutils) add_halogen_interaction() (in module schrodinger.application.desmond.sid_plots.pl_lid) add_hidden_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_hidden_options() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) add_histo() (in module schrodinger.application.desmond.event_analysis.pl_image_tools) add_host_lists() (in module schrodinger.pipeline.pipeline) add_hs_to_aromatic_nitrogen() (in module schrodinger.livedesign.convert) add_hydrogens (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) add_hydrogens() (in module schrodinger.structutils.build) (schrodinger.application.desmond.fep_struc.SchrodStruc method) add_hydrogensChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) add_hydrogensReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) ADD_HYPO_PT (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) ADD_HYPO_WS (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) add_import_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_import_only_args() (in module schrodinger.application.phase.packages.phase_database_job_utils) add_import_or_splice_args() (in module schrodinger.application.phase.packages.phase_database_job_utils) add_inactive_solvent() (in module schrodinger.application.desmond.gcmc_utils) add_inactive_solvent_file() (in module schrodinger.application.desmond.gcmc_utils) add_index_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) add_input_file() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.glide.utils) add_isub_option() (in module schrodinger.application.hitexpander) add_items_to_glayout() (in module schrodinger.ui.qt.utils) add_jaguar_dict_keywords_flag() (in module schrodinger.application.matsci.parserutils) add_jaguar_files_to_jc_backend() (in module schrodinger.application.matsci.jaguarworkflows) add_jaguar_lic() (in module schrodinger.application.matsci.jobutils) add_job() (schrodinger.application.desmond.cmj.StageBase method) add_jobcontrol_args() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.shape_screen_arg_utils) add_jobcontrol_arguments() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) add_jobcontrol_options() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) (in module schrodinger.utils.cmdline) add_jobs() (schrodinger.application.desmond.cmj.JobManager method) (schrodinger.application.desmond.cmj.StageBase method) add_key_file_args() (in module schrodinger.application.bb_database.bb_arg_utils) add_keyword_parser_argument() (in module schrodinger.application.matsci.parserutils) add_kmc_flags() (in module schrodinger.application.matsci.kmc) add_labeled_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) add_ligand_sts() (in module schrodinger.protein.assignment) add_ligprep_arguments() (in module schrodinger.application.phase.packages.shape_ligprep) add_local_type_force_field_to_job_builder() (in module schrodinger.application.matsci.cgforcefield) add_local_type_force_field_to_job_builder_w_check() (in module schrodinger.application.matsci.cgforcefield) add_logfile() (in module schrodinger.application.glide.utils) add_logger_file_handler() (in module schrodinger.protein.process_enamine_db) add_macromodel_csearch() (in module schrodinger.application.matsci.reaction_workflow_utils) add_maestro_banner() (in module schrodinger.application.matsci.gutils) add_matching_options() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) add_max_retries_argument() (in module schrodinger.application.matsci.parserutils) add_md_basic_argument() (in module schrodinger.application.matsci.equilibrium_md) add_md_lic() (in module schrodinger.application.desmond.license) add_md_output_argument() (in module schrodinger.application.matsci.equilibrium_md) add_menu_with_dummy_actions() (in module schrodinger.ui.qt.standard_widgets.buttons) add_merge_args() (in module schrodinger.application.phase.packages.oned_option_utils) add_merge_arguments() (in module schrodinger.application.phase.packages.shape_screen_gpu_update) add_metal_center_element_argument() (in module schrodinger.application.matsci.parserutils) add_methyl_ring() (in module schrodinger.application.canvas.r_group) add_methyl_standard() (in module schrodinger.application.canvas.r_group) add_miller_plane() (in module schrodinger.application.matsci.maestrocmds) add_modes_group() (in module schrodinger.application.glide.sort_parser_common) add_mopac_parser_argument() (in module schrodinger.application.matsci.parserutils) add_multi_job_finalizer() (in module schrodinger.job.queue) add_neighbor_charges_to_jaginput() (in module schrodinger.application.matsci.clusterstruct) add_new (schrodinger.application.livedesign.live_report_widget.LRSelectionMode attribute) ADD_NEW (schrodinger.application.matsci.permittivity.MultiStageMd attribute) add_new_database_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_new_flag() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_obsolete_args() (in module schrodinger.application.glide.sort_parser_common) add_optional_args_group() (in module schrodinger.application.bb_database.bb_arg_utils) add_or_update_bond_order() (in module schrodinger.application.matsci.msutils) add_or_update_bond_type() (in module schrodinger.application.matsci.msutils) add_out_rep_parser_argument() (in module schrodinger.application.matsci.parserutils) add_outfile_to_backend() (in module schrodinger.application.matsci.jobutils) add_output() (schrodinger.application.desmond.enhsamp.Env method) (schrodinger.application.licensing.licerror.LicenseError method) add_output_file() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.glide.utils) add_output_options_group() (in module schrodinger.application.glide.sort_parser_common) add_overlapEnergyTable() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) add_oxt_cap() (in module schrodinger.protein.nonstandard_residues) add_package_dir_to_path() (in module schrodinger.application.utils) add_pairs_to_database() (in module schrodinger.application.matsci.kmc) add_para_job_options() (in module schrodinger.application.macromodel.paraUtils) add_parser_opts() (in module schrodinger.application.matsci.equilibrium_md) add_physical_arguments() (in module schrodinger.application.matsci.parserutils) add_physicochemical_properties() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) add_physicochemical_properties_to_hits() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) add_plugin() (in module schrodinger.application.desmond.config_utils) add_point() (schrodinger.protein.analysis.Report.data_set method) (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method) add_position() (schrodinger.application.canvas.r_group.Data method) add_prefer_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) add_prepared_props() (in module schrodinger.application.prepwizard) add_print_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) add_project_creation_options() (in module schrodinger.application.phase.packages.hypo_refine.option_utils) add_property_biasing_options() (in module schrodinger.application.combinatorial_diversity.driver_utils) add_property_value() (schrodinger.application.canvas.r_group.Data method) add_protonation_state() (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) add_qe_parallel_parser_arguments() (in module schrodinger.application.matsci.espresso.utils) add_qrun_args() (in module schrodinger.application.bb_database.bb_arg_utils) add_qsplit_args() (in module schrodinger.application.bb_database.bb_arg_utils) add_query_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) add_r_group() (schrodinger.application.canvas.r_group.Data method) add_r_groups_to_atom() (schrodinger.application.canvas.r_group.Data method) add_random_seed_parser_argument() (in module schrodinger.application.matsci.parserutils) add_reactants_to_database() (in module schrodinger.application.combinatorial_explorer.driver_utils) add_refinement_options() (in module schrodinger.application.phase.packages.hypo_refine.option_utils) add_remove_props() (in module schrodinger.application.matsci.reaction_workflow_utils) add_replicas_dF_table() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) add_reporting_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) add_reporting_options() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) (in module schrodinger.application.phase.packages.phase_screen_utils) add_required_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) ADD_RESET_THIS_TASK_OPTION (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin attribute) add_rest_region() (in module schrodinger.application.desmond.rest_inp) add_restart_parser_arguments() (in module schrodinger.application.matsci.parserutils) add_restraint_atom_marker() (in module schrodinger.application.desmond.stage.prepare.forcefield) add_restraint_reference() (in module schrodinger.application.desmond.stage.prepare.forcefield) add_result_raw() (schrodinger.comparison.results.ResultSet method) add_results_raw() (schrodinger.comparison.results.ResultSet method) add_revise_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) add_rg_ct() (schrodinger.application.canvas.r_group.Data method) add_ring_spear_dummies() (in module schrodinger.application.matsci.packmol) add_rings() (schrodinger.application.canvas.r_group.Data method) add_rl_pair_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) add_rl_pairs (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) add_robust_jaguar_argument() (in module schrodinger.application.matsci.parserutils) add_run_args() (in module schrodinger.application.phase.packages.oned_option_utils) add_save_desmond_files_parser_argument() (in module schrodinger.application.matsci.parserutils) add_schrodinger_column() (in module schrodinger.application.matsci.kmc) add_scoring_group() (in module schrodinger.application.glide.sort_parser_common) add_scoring_options() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) add_screen_args() (in module schrodinger.application.combinatorial_explorer.driver_utils) add_shape_generation_options() (in module schrodinger.application.phase.packages.shape_generator) add_shape_treatment_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) add_signature() (schrodinger.application.licensing.flexlm.Feature method) add_signatures() (schrodinger.application.licensing.flexlm.License method) add_sim_algorithm_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) add_smarts_method_argument() (in module schrodinger.application.matsci.parserutils) add_smiles() (in module schrodinger.structutils.smilesfilter) add_spacer() (in module schrodinger.application.desmond.rl_helper) add_splice_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_split_args() (in module schrodinger.application.phase.packages.oned_option_utils) add_split_arguments() (in module schrodinger.application.phase.packages.shape_screen_gpu_update) add_spot() (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot method) add_standard_confgen_options() (in module schrodinger.application.phase.packages.conformer_reader) add_standard_options() (in module schrodinger.utils.cmdline) add_static() (schrodinger.application.desmond.enhsamp.Env method) add_subjob_files_to_backend() (in module schrodinger.application.matsci.jobutils) add_subset_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) add_table() (in module schrodinger.application.desmond.rl_helper) add_tag() (schrodinger.utils.sea.sea.Sea method) add_task_help_flag() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_task_options() (in module schrodinger.tasks.cmdline) add_temp_hydrogen() (in module schrodinger.application.matsci.rxn_path) add_terminal_oxygens (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) add_terminal_oxygens() (in module schrodinger.protein.captermini) add_terminal_oxygensChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) add_terminal_oxygensReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) ADD_TIP (schrodinger.application.matsci.mswidgets.Stepper attribute) add_to_backend() (in module schrodinger.application.matsci.jobutils) add_to_data() (in module schrodinger.application.canvas.r_group) add_tpp_parser_argument() (in module schrodinger.application.matsci.parserutils) add_traj_analysis_parser_arguments() (in module schrodinger.application.matsci.parserutils) add_transformations() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) add_undocumented_args() (in module schrodinger.application.glide.sort_parser_common) add_validator() (in module schrodinger.ui.qt.appframework2.validation) add_var() (schrodinger.application.desmond.enhsamp.binding method) add_verbose_flag() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_votca_logo() (in module schrodinger.application.matsci.kmcgui) add_vtable() (in module schrodinger.application.desmond.rl_helper) add_wam_to_cms() (in module schrodinger.application.matsci.jobutils) add_watermap_lic() (in module schrodinger.application.desmond.license) add_widget_to_menu() (in module schrodinger.ui.qt.utils) add_xtb_parser_argument() (in module schrodinger.application.matsci.parserutils) add_zmatrix_lines() (in module schrodinger.application.matsci.zmutils) addAction() (schrodinger.ui.qt.swidgets.ActionComboBox method) (schrodinger.ui.qt.swidgets.ActionPushButton method) (schrodinger.ui.qt.swidgets.SComboBox method) addActionItem() (schrodinger.application.bioluminate.bwidgets.RowActionItem method) addActions() (schrodinger.application.bioluminate.actions.factory.Factory method) addAdvancedWidgets() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) addAlignmentAxesToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addAlignToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addAllAndNone() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) addAllCallbacks() (schrodinger.ui.qt.input_selector.InputSelector method) addAndAttachSeries() (schrodinger.ui.qt.schart.SChart method) addAndSelectItem() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) addAndSelectLocationItem() (schrodinger.ui.qt.forcefield.pathselectorwidget.PathSelectorWidget method) addAngleRestraint() (schrodinger.structutils.minimize.Minimizer method) addAnnotation() (schrodinger.application.matsci.density_analysis_widget.MeasurementLine method) addAnnotationAction() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) addAntibodyNumberingToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addAtom() (schrodinger.structure.Structure method) (schrodinger.ui.qt.structure2d.CircleAnnotator method) addAtomGroup() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) (schrodinger.application.matsci.species.SpeciesData method) addAtomGroupRow() (schrodinger.application.desmond.gui.AtomGroupFrame method) addAtomProps() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) addAtoms() (schrodinger.structure.Structure method) addBarrier() (schrodinger.application.matsci.desconfig.BarrierHeader method) addBidentateLigand() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) addBinderDummy() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) addBond() (schrodinger.structure.Structure method) (schrodinger.structure.StructureAtom method) addBondEnergy() (schrodinger.application.matsci.fragments.UniqueTracker method) addBonds() (schrodinger.structure.Structure method) addBranchingAtoms() (schrodinger.application.matsci.amorphous.PolymerFragments method) addButton() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) addButtonToBottomLayout() (schrodinger.ui.qt.appframework.AppFramework method) AddButtonWithIndicatorAndPopUp (class in schrodinger.ui.qt.pop_up_widgets) addc() (schrodinger.application.macromodel.utils.ComUtil method) addCallback() (schrodinger.ui.qt.input_selector.InputSelector method) addCappingLigands() (schrodinger.application.matsci.sculptcomplex.Sculptor method) addCentralWidget() (schrodinger.ui.qt.appframework.AppFramework method) addChain() (schrodinger.protein.getpdb_utility.Code method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) addCharges() (schrodinger.application.matsci.clusterstruct.SpeciesData method) addChart() (schrodinger.stepper.viz.VizWebpage method) addChild() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.ui.dendrogram.DendrogramNode method) (schrodinger.ui.qt.dendrogram.NewickNode method) addChildren() (schrodinger.application.desmond.antlr3.tree.BaseTree method) addCIonBodies() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) addColor() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) addColorStop() (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) addColumn() (schrodinger.application.desmond.gui.TableModel method) (schrodinger.ui.qt.swidgets.STableWidget method) addCOMAtoms() (schrodinger.application.matsci.clusterstruct.COMTracker method) addCommandLineOptions() (schrodinger.job.app.App method) addComment() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) addConcentrationProperty() (schrodinger.structutils.rgroup_enumerate.Concentration method) addConnection() (schrodinger.livedesign.biologics.registration.BioPolymer method) addConsButtonPressed() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) addConsensusToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addConstantProperties() (schrodinger.application.matsci.cgforcefield.FFIOParam method) addConstraint() (schrodinger.application.glide.glide.ConstraintGroup method) addConstraintGroup() (schrodinger.application.glide.glide.Dock method) addContext() (schrodinger.application.bioluminate.actions.factory.Factory method) addCoord() (schrodinger.application.matsci.zmutils.ZAtom method) addCoordinate() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) addCostProperties() (schrodinger.application.ligprep.ionizer.Ionizer method) addCriterion() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) addCriterionRow() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.CriteriaLayout method) addCustomSites() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addCV() (schrodinger.application.desmond.meta.Meta method) addData() (schrodinger.application.livedesign.panel_components.AbstractSelectionLineEdit method) (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit method) addDatabase() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog method) addDataSeries() (schrodinger.ui.qt.schart.SChart method) addDataSet() (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin method) addDataToExportTask() (schrodinger.application.livedesign.export_models.Base3DExportSpec method) (schrodinger.application.livedesign.export_models.DataExportSpec method) (schrodinger.application.livedesign.export_models.FFCExportSpec method) (schrodinger.application.livedesign.export_models.PropertyExportSpec method) addDefinition() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) AddDefinitionDialog (class in schrodinger.ui.ligfilter) addDefinitionsFromFile() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) addDesignator() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) addDesmondPBC() (schrodinger.application.matsci.amorphous.Scaffold method) addDistanceRestraint() (schrodinger.structutils.minimize.Minimizer method) addDisulfideBond() (schrodinger.protein.alignment.ProteinAlignment method) addDummyAtoms() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) added (schrodinger.models.diffy.DictDiff attribute) (schrodinger.models.diffy.ListDiff attribute) (schrodinger.models.diffy.SetDiff attribute) ADDED_NOTHING (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) ADDED_PARENT (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) ADDED_PARENT_NAME (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) ADDED_RING_SYS (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) addEdge() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) addEdges() (schrodinger.application.matsci.permittivity.WorkflowParser method) (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) addEigenpair() (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.trajectory.prody.pca.PCA method) addElements() (schrodinger.protein.alignment.BaseAlignment method) addEnefileToAdditionalInfiles() (schrodinger.application.matsci.permittivity.MdPostAnalysis method) addEntry() (schrodinger.ui.qt.appframework2.debugwidgets.LogTable method) (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) addEnv() (schrodinger.job.launcher.Launcher method) addEtaDummy() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) addExcludedVolumes() (schrodinger.application.phase.phase_markers.PhaseXvolMarkers method) addExistingButton() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) addExpectedInput() (schrodinger.pipeline.stage.Stage method) addExpectedOutput() (schrodinger.pipeline.stage.Stage method) addext() (in module schrodinger.trajectory.prody.writenmd) addFeatureDefinitionPresets() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) addFeaturesForWorkspaceLigands() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addFeatureTypeEquivalencies() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) addFigure() (schrodinger.application.matsci.reportutils.PDFBuilder method) addFile() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) addFilesToBackend() (schrodinger.application.matsci.desmondutils.SystemBuilder method) addFileWidgets() (schrodinger.ui.qt.input_selector.InputSelector method) addFinalizer() (schrodinger.job.queue.BaseJob method) addFinalPoint() (schrodinger.application.matsci.density_analysis_widget.MeasurementLine method) addFindToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addFloatSpinBox() (schrodinger.ui.qt.dendrogram.GuiPanel method) addFlowables() (schrodinger.application.matsci.reportutils.PDFBuilder method) addFooters() (schrodinger.application.matsci.reportutils.PDFBuilder method) addForceInputFile() (schrodinger.job.launcher.Launcher method) addFromFile() (schrodinger.project.surface.SurfaceDict method) addFuncToGroup() (schrodinger.utils.funcgroups.FuncGroupMixin method) addGapsBeforeIndices() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) addGapsByIndices() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) addGapsToChainStartsAndEnds() (schrodinger.protein.sequence.CombinedChainProteinSequence method) addGetSignalsAndSlotsCallback() (schrodinger.models.mappers.TargetParamMapper method) addGroupingProps() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) addGroupPrereq() (schrodinger.job.queue.BaseJob method) addHarmonicRestraints() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) addHelpButton() (schrodinger.ui.qt.appframework2.af2.StatusBar method) addHistogram() (schrodinger.ui.qt.schart.SChart method) addHostSelector() (schrodinger.ui.qt.tasks.configwidgets.HostLayoutWidget method) addHoverCallback() (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) addHydrogenCap() (schrodinger.application.qsite.input.QSiteInput method) AddHydrogens (class in schrodinger.application.bioluminate.pml_menus) AddHydrogens() (in module schrodinger.application.matsci.gsas.GSASIImath) addHydrogens() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) addHypoFromPT() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addHypoFromWorkspace() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addHypothesisFromEntry() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addIdealAnchors() (schrodinger.application.matsci.sculptcomplex.Sculptor method) addImportToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addIndicesToGroup() (schrodinger.application.matsci.atom_group.MSAtomGroupsBase method) addInputFile() (schrodinger.job.app.App method) (schrodinger.job.launcher.Launcher method) addInputFiles() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) addIonProperties() (schrodinger.application.ligprep.ionizer.Ionizer method) addIons() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) addItem() (schrodinger.ui.qt.swidgets.ActionComboBox method) (schrodinger.ui.qt.swidgets.ActionPushButton method) (schrodinger.ui.qt.swidgets.SComboBox method) addItems() (schrodinger.application.matsci.density_analysis_widget.ASLSelectorCheckableComboBox method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.swidgets.SComboBox method) addItemsFromDict() (schrodinger.ui.qt.swidgets.SComboBox method) additional_command_arguments() (in module schrodinger.application.desmond.launch_utils) ADDITIONAL_SEARCH_ALONGS (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) addJaguarMarker (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute) addJaguarMarker() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) addJaguarMarkerForRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel method) addJob() (schrodinger.job.queue.JobDJ method) addJobsToJobDj() (schrodinger.application.matsci.permittivity.WorkflowParser method) addKey() (schrodinger.utils.ligfilter.Definition method) addKwargs() (schrodinger.application.matsci.genetic_optimization.Property static method) addLabel() (schrodinger.ui.qt.rdmol_views.RDMolTooltipWithLabel method) (schrodinger.ui.qt.structure2d.LabeledStructureToolTip method) addLaunchEnv() (schrodinger.job.queue.JobControlJob method) addLayer() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) addLeafProperty() (schrodinger.ui.qt.dendrogram.Dendrogram method) addLicense() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) (schrodinger.job.launcher.Launcher method) addLicenseReservation() (schrodinger.stepper.stepper.StepTaskMixin method) (schrodinger.tasks.tasks.AbstractTask method) addLigandDesignator() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) addLine() (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ExtraSectionData method) addLoadStructButton() (schrodinger.application.matsci.appbase.ViewerGuiMixin method) addLoadTrajButton() (schrodinger.application.matsci.deswidgets.TrajAnalysisGuiMixin method) addLogFile() (schrodinger.job.app.App method) (schrodinger.job.launcher.Launcher method) addMapping() (schrodinger.models.mappers.TargetParamMapper method) (schrodinger.ui.qt.datamapper.TrackingDataWidgetMapper method) addMarker() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) addMarkerFromAsl() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) addMatchToAtoms() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) addMeasurement() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) addMember() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) addMethod() (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListPopUp method) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListToolButton method) addMonodentateLigand() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) addNamedProperties() (schrodinger.application.matsci.cgforcefield.FFIOParam method) (schrodinger.application.matsci.cgforcefield.FFIOSite method) addNavigationNode() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) addNew() (schrodinger.application.livedesign.panel_components.AbstractSelectionLineEdit method) (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit method) addNewConstraint() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) AddNewLineEdit (class in schrodinger.application.livedesign.panel_components) addNewLiveReport() (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) addNode() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) addNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) addNodeToGroup() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) addNormalsToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addNumericLineEdit() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) addOneItem() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) addOneRow() (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) addOptionalRestartFiles() (schrodinger.active_learning.al_node.ActiveLearningNode method) addOptionalRestartFilesDict() (schrodinger.active_learning.al_driver.ActiveLearningJob method) addOptions() (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog method) (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method) addOutputFile() (schrodinger.job.launcher.Launcher method) (schrodinger.pipeline.stage.Stage method) addOutputFileBE() (schrodinger.job.app.App method) addOutputFileFE() (schrodinger.job.app.App method) addPABJaguarMarker() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) addPage() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) addPair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) addPanel() (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) addParams() (schrodinger.application.matsci.cgforcefield.FFIOParam method) addParent() (schrodinger.application.dendrogram.core_class.RingSysStorage class method) addParentalInformationProperties() (schrodinger.application.matsci.jwsteps.BaseStep method) addParserOptions() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions class method) addPath() (schrodinger.application.livedesign.panel_components.PathTreeDict method) addPattern() (schrodinger.ui.ligfilter.LigfilterFrame method) addPatternCriterion() (schrodinger.ui.ligfilter.LigfilterFrame method) addPBCProperties() (schrodinger.application.matsci.amorphous.Scaffold method) addPersistentAction() (schrodinger.ui.qt.swidgets.PersistentMenu method) addPkaMarkers() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) addPointsToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addPosFrozen() (schrodinger.structutils.minimize.Minimizer method) addPosResRow() (schrodinger.application.desmond.gui.RestraintsTab method) addPosRestraint() (schrodinger.structutils.minimize.Minimizer method) addPostprocessor() (schrodinger.tasks.tasks.AbstractTask method) addPredefinedCriterion() (schrodinger.ui.ligfilter.LigfilterFrame method) addPreprocessor() (schrodinger.tasks.tasks.AbstractTask method) addPrereq() (schrodinger.job.queue.BaseJob method) addPreviousFreezerFile() (schrodinger.application.matsci.genetic_optimization.StructureGenome method) addProcessors() (schrodinger.job.queue.ResourceHost method) addProduct() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) addProjectCloseCallback() (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) addProjectJobNote() (schrodinger.ui.qt.appframework2.af2.JobApp method) addProjects() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) addProjectUpdateCallback() (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) addPropCriterion() (schrodinger.ui.ligfilter.LigfilterFrame method) addProperties() (schrodinger.application.matsci.cgforcefield.ForceField method) addPropertyClicked() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) addpropop1Modified() (schrodinger.ui.ligfilter.LigfilterFrame method) addPropsToStructure() (schrodinger.application.matsci.amorphous.Monomer static method) addProxy() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) addQMCut() (schrodinger.application.qsite.input.QSiteInput method) addQMMolecule() (schrodinger.application.qsite.input.QSiteInput method) addRandomChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) addRandomChannelsFromAll() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) addRandomChannelsOnTheFly() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) addRangeWidgets() (schrodinger.ui.qt.input_selector.InputSelector method) addReactant() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) addReactionInstance() (schrodinger.application.pathfinder.route.RetroSynthesisNode method) addRecoveryResults() (schrodinger.active_learning.al_report.ALPilotReportMaker method) (schrodinger.active_learning.al_report.ALScreenReportMaker method) addRefCtMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addReplicaNode() (schrodinger.application.matsci.permittivity.WorkflowParser method) addRequiredOutputFile() (schrodinger.job.launcher.Launcher method) addResidue() (schrodinger.application.bioluminate.pml_menus.RegionInfo method) addResidues() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) addResidueToTable() (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) addResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method) address (schrodinger.job.cert.CertInfo attribute) AddressError addRestraints() (schrodinger.application.matsci.cgforcefield.RestraintAdaptationMixin method) addRingSys() (schrodinger.application.dendrogram.core_class.RingSysStorage class method) addRotationAtoms() (schrodinger.application.matsci.etarotamers.HapticLigand method) addRow() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.matsci.kmc.AtomsTable method) (schrodinger.application.matsci.kmc.FragmentsTable method) (schrodinger.application.matsci.kmc.FramesTable method) (schrodinger.application.matsci.kmc.MatSciSitesTable method) (schrodinger.application.matsci.kmc.MoleculesTable method) (schrodinger.application.matsci.kmc.PairsMixin method) (schrodinger.application.matsci.kmc.SchrodingerTable method) (schrodinger.application.matsci.kmc.SegmentsTable method) (schrodinger.application.matsci.kmc.SegmentTypesTable method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.swidgets.STableWidget method) ADDROW_COMMAND (schrodinger.application.matsci.kmc.Table attribute) addRows() (schrodinger.ui.qt.swidgets.STableWidget method) addRunDetail() (schrodinger.active_learning.al_report.ALPilotReportMaker method) (schrodinger.active_learning.al_report.ALScreenReportMaker method) addSalt() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) addScriptArgs() (schrodinger.job.launcher.Launcher method) addSegmentPlaneIntersectionsToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addSeparator() (schrodinger.ui.qt.swidgets.ActionComboBox method) (schrodinger.ui.qt.swidgets.ActionPushButton method) addSeq() (schrodinger.protein.alignment.BaseAlignment method) addSeqs() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.alignment.CombinedChainProteinAlignment method) addSeqsToAlnSet() (schrodinger.protein.alignment.BaseAlignment method) addSeries() (schrodinger.ui.qt.schart.SChart method) addSite() (schrodinger.application.matsci.sculptcomplex.CoordinationInfo method) addSites() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addSolventBodies() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) addSource() (schrodinger.application.fpsim.FPsimSearcher method) addSpaceGroupPBC() (schrodinger.application.matsci.amorphous.Scaffold method) addSpacer() (schrodinger.application.matsci.reportutils.PDFBuilder method) addSpeciesAsProps() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) addSphere() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) addSpinBoxLayout() (schrodinger.application.matsci.mswidgets.MultiSlider method) addStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) (schrodinger.pipeline.input.LinearWriter method) (schrodinger.pipeline.input.Writer method) addStep() (schrodinger.stepper.stepper.UnbatchedChain method) addStretch() (schrodinger.ui.qt.swidgets.SFrame method) addStructureBodies() (schrodinger.application.matsci.packmol.BilayerInputFile method) (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) (schrodinger.application.matsci.packmol.PackmolInputFile method) addStructureBody() (schrodinger.application.matsci.packmol.PackmolInputFile method) addStructureFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addStructures() (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) addSubclass() (schrodinger.application.matsci.permittivity.WorkflowParser method) addSubjobs() (schrodinger.application.matsci.permittivity.WorkflowParser method) addSubMenu() (schrodinger.application.bioluminate.actions.factory.Factory method) addSubParam() (schrodinger.models.parameters.CompoundParam class method) addSubprocessStackedWidget() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) addSubTabMarker() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) addSubTabs() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) addSubview() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) addSuggestion() (schrodinger.ui.qt.recent_completer.StringListModelInterface method) addSurfaceToProject() (schrodinger.project.surface.ProjectSurface class method) addSurfactantBodies() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) addTask() (schrodinger.application.livedesign.ld_import_utils.LDImportTaskManager method) (schrodinger.tasks.queue.TaskDJ method) (schrodinger.tasks.queue.TaskQueue method) addTasks() (schrodinger.tasks.queue.QueueResults method) addTempHydrogens() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) addTempInputFile() (schrodinger.job.launcher.Launcher method) addThumb() (schrodinger.application.matsci.mswidgets.MultiSlider method) addTimerButton() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) addToAuxListbox() (schrodinger.ui.qt.propertyselector.PropertySelector method) addToChain() (schrodinger.application.matsci.amorphous.BaseMoiety method) ADDTOENTRY (schrodinger.job.launchparams.ProjectDisposition attribute) addToFFST() (schrodinger.application.matsci.cgforcefield.FFIOParam method) addToJaguarInput() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ExtraSectionData method) addTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addToolBars() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addToPlot() (schrodinger.application.matsci.reaction_workflow_utils.SiblingNode method) addToQueue() (schrodinger.application.matsci.fragments.NonUniqueTracker method) (schrodinger.application.matsci.fragments.UniqueTracker method) addTorsionRestraint() (schrodinger.structutils.minimize.Minimizer method) addToWorkspace() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant method) addTPPIfNeeded() (schrodinger.application.matsci.jwsteps.BaseStep method) addTree() (schrodinger.ui.qt.dendrogram.DendrogramSyncer method) addTrendLine() (schrodinger.ui.qt.schart.SChart method) addUndoRedoToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addVacuum() (schrodinger.application.matsci.nano.slab.Surface method) addValue() (schrodinger.application.phase.packages.oned_task_utils.BasicStatsAccumulator method) addVar() (schrodinger.pipeline.input.LinearWriter method) (schrodinger.pipeline.input.Writer method) addVelocityIfNeeded() (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) addWeightPropsToTemplateStructures() (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget method) addWidget() (schrodinger.ui.qt.swidgets.SFrame method) addWidgetsToLayout() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) addWorkspaceChangeCallback() (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) addXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) Adenine (schrodinger.protein.helm.helm_renderer.HexColor attribute) adf() (schrodinger.application.macromodel.utils.ComUtil method) adjHKLmax() (in module schrodinger.application.matsci.gsas.GSASIImath) adjust() (schrodinger.application.jaguar.autots_bonding.Coordinate method) (schrodinger.structure.Structure method) adjust_min_max_values() (in module schrodinger.ui.qt.filter_dialog_dir.filter_widgets) adjust_min_pop() (in module schrodinger.application.combinatorial_diversity.driver_utils) adjust_phi() (schrodinger.ui.qt.rama.Rama method) adjust_psi() (schrodinger.ui.qt.rama.Rama method) adjust_resnums() (in module schrodinger.application.bioluminate.antibody.assembly) adjust_symbol_size() (schrodinger.ui.qt.rama.Rama method) adjustACellClashVDWScale() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) adjustACellDensity() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) adjustAtomIds() (schrodinger.application.matsci.amorphous.PolymerFragment method) adjustChainStarts() (schrodinger.protein.alignment.CombinedChainProteinAlignment method) adjustCombos() (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) adjustCommandForQueue() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) adjustDihedral() (schrodinger.protein.captermini.CapTermini method) adjustExclusions() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) adjustImproperDihedral() (in module schrodinger.structutils.build) adjustLabels() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) adjustName() (schrodinger.application.dendrogram.core_class.Utilities static method) adjustWindowClosing() (schrodinger.ui.qt.navtoolbar.NavToolbar method) ADOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) ADVANCED (schrodinger.trajectory.trajectory_gui_dir.playback_settings.Tab attribute) advanced_pymol_settings (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) advanced_pymol_settingsChanged (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) advanced_pymol_settingsReplaced (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) AdvancedMDOptions (class in schrodinger.application.matsci.deswidgets) AdvancedSettings (class in schrodinger.trajectory.trajectory_gui_dir.advanced_settings) advancedSettingsChanged (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings attribute) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) advancedSettingsDismissed (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings attribute) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) AdvancedSettingsModel (class in schrodinger.application.pymol.gui_models) AdvancedSettingsPopUp (class in schrodinger.application.pymol.export_to_pymol_gui) advanceSelection() (schrodinger.application.matsci.reordergui.ReferenceFrame method) advice (schrodinger.application.licensing.licerror.LicenseError property) AdvLabel (class in schrodinger.application.desmond.cwidget) AdvOptionsFrame (class in schrodinger.application.desmond.gui) af2SettingsGetValue() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) (schrodinger.ui.picking.MaestrolessPickResidueDialog method) (schrodinger.ui.qt.appframework2.settings.AttributeSettingWrapper method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) af2SettingsSetValue() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) (schrodinger.ui.picking.MaestrolessPickResidueDialog method) (schrodinger.ui.qt.appframework2.settings.AttributeSettingWrapper method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) AFR (schrodinger.protein.annotation.TCRRegionLabel attribute) AFTERSUPERPOSITION (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) AGGREGATE_CALCULATIONS (schrodinger.application.bioluminate.protein.protein.PropertyCalculator attribute) AHEAD (schrodinger.application.matsci.nano.xtal.PBCBond attribute) AIDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) aids (schrodinger.application.desmond.new_fep_edge_data.TorsionPotential property) (schrodinger.application.matsci.atom_group.HelixData attribute) (schrodinger.application.matsci.species.SUB_STRUCT_INFO attribute) AIDX_TYPE (schrodinger.application.desmond.cms.PosRestrainArray attribute) al_get_parser() (in module schrodinger.active_learning.fake_nodes) al_parse_args() (in module schrodinger.active_learning.fake_nodes) al_parse_input_file() (in module schrodinger.active_learning.fake_nodes) al_validate_args() (in module schrodinger.active_learning.fake_nodes) ALABFEPStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) AlchemAsl (class in schrodinger.application.desmond.replica_sid_generator) ALCHEMICAL (schrodinger.application.desmond.constants.SystemType attribute) alchemical_solvent (schrodinger.application.desmond.new_fep_edge_data.FepData property) alchemical_water (schrodinger.application.desmond.struc.CompStruc attribute) ALCHEMICAL_WATER (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) Alchemist (class in schrodinger.application.matsci.enumeration) ALDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) Alessandro (schrodinger.protein.predictors.DiproPredictor.DiproFormat attribute) ALGlideStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) algorithm (schrodinger.application.licensing.licserver.client.LocalEntitlementValidation attribute) ALGORITHM_TYPE (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData attribute) alie_analysis() (in module schrodinger.application.jaguar.textparser) alie_analysis_precision (schrodinger.application.jaguar.results.JaguarResults attribute) alie_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) align (schrodinger.structutils.structalign2.Alignment attribute) align() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method) (schrodinger.structutils.structalign.StructAlign method) align_after_download (schrodinger.protein.tasks.blast.BlastSettings attribute) align_after_downloadChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) align_after_downloadReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) align_alignment() (in module schrodinger.protein.sequence) align_all_molecules() (in module schrodinger.application.jaguar.autots_rmsd) align_all_to_reference() (in module schrodinger.livedesign.biologics.sequence) align_and_update_graph() (in module schrodinger.application.desmond.membrane_utils) align_asl (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction attribute) ALIGN_AUTO (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin attribute) ALIGN_BOTTOM (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin attribute) align_cap() (in module schrodinger.application.desmond.struc) align_chmmol() (in module schrodinger.application.desmond.depictor) align_core_only (schrodinger.application.desmond.msj_generator.workflow_params.MapperParams attribute) align_from_chains() (in module schrodinger.protein.sequence) align_frozen_atoms() (in module schrodinger.application.jaguar.autots_bonding) align_helm_polymer_sequences() (in module schrodinger.livedesign.biologics.sequence) align_horizontally() (in module schrodinger.rdkit.alignment) ALIGN_LEFT (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin attribute) align_many() (in module schrodinger.structutils.structalign2) align_pair() (in module schrodinger.structutils.structalign2) align_pairs (schrodinger.application.phase.packages.mmp3d_driver_utils.SubjobType attribute) align_pairs() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) align_path_strs() (in module schrodinger.application.jaguar.autots_rmsd) align_pos() (in module schrodinger.comparison.struc) ALIGN_RIGHT (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin attribute) align_sel_res_only (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) align_sel_res_onlyChanged (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) align_sel_res_onlyReplaced (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) align_sequences() (in module schrodinger.livedesign.biologics.sequence) align_st_by_mol() (in module schrodinger.comparison.struc) align_structures() (in module schrodinger.application.bioluminate.antibody.assembly) ALIGN_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) ALIGN_TOP (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin attribute) alignAllToReference() (schrodinger.ui.two_d_viewer.TwoDViewer method) alignCellsToReference() (schrodinger.ui.two_d_viewer.TwoDTableModel method) alignCenterCollect() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) alignChainStarts() (schrodinger.protein.alignment.CombinedChainProteinAlignment method) AlignCore (class in schrodinger.application.desmond.stage.deprecate) aligned_weights (schrodinger.application.desmond.kinetics.utils.RmsdSelection attribute) AlignedMolStructureGenerator (class in schrodinger.application.pathfinder.aligner) AlignedSequence (class in schrodinger.livedesign.biologics.sequence) alignLigands() (schrodinger.application.matsci.sculptcomplex.Sculptor method) AlignLigandsTask (class in schrodinger.application.livedesign.tasks) AlignLigandsTask.Input (class in schrodinger.application.livedesign.tasks) AlignLigandsTask.Output (class in schrodinger.application.livedesign.tasks) Alignment (class in schrodinger.structutils.structalign2) alignment (schrodinger.application.bioluminate.antibody.grafting.GraftingInput attribute) (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) (schrodinger.protein.gpcr.tasks.GPCRTask.Output attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask.Output attribute) alignment() (schrodinger.ui.qt.delegates.PictureDelegate method) alignment_args (schrodinger.application.livedesign.tasks.AlignLigandsTask.Input attribute) alignment_argsChanged (schrodinger.application.livedesign.tasks.AlignLigandsTask.Input attribute) alignment_argsReplaced (schrodinger.application.livedesign.tasks.AlignLigandsTask.Input attribute) alignment_details (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciDomainResult attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults attribute) alignment_set (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) alignmentAboutToBeCleared (schrodinger.protein.alignment.AlignmentSignals attribute) AlignmentAsl (class in schrodinger.application.bioluminate.antibody.assembly) alignmentChanged (schrodinger.protein.gpcr.tasks.GPCRTask.Output attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask.Output attribute) alignmentCleared (schrodinger.protein.alignment.AlignmentSignals attribute) alignmentNumColumnsAboutToChange (schrodinger.protein.alignment.AlignmentSignals attribute) alignmentNumColumnsChanged (schrodinger.protein.alignment.AlignmentSignals attribute) alignmentReplaced (schrodinger.protein.gpcr.tasks.GPCRTask.Output attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask.Output attribute) ALIGNMENTS (schrodinger.ui.qt.schart.SChart attribute) AlignmentSet (class in schrodinger.protein.alignment) AlignmentSignals (class in schrodinger.protein.alignment) AlignMethod (class in schrodinger.application.phase.packages.ligand_aligner) alignOnXAxis() (schrodinger.application.matsci.amorphous.Monomer method) alignPolyhedron() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) aligns_with (schrodinger.protein.nonstandard_residues.AminoAcid property) alignSites() (schrodinger.structutils.sitealign.BindingSiteAligner method) alignStructure() (schrodinger.structutils.structalign.StructAlign method) alignStructWithPlane() (schrodinger.application.matsci.espresso.qeinput.StructureType method) alignToVector() (schrodinger.application.matsci.amorphous.BaseMoiety method)

Aliphatic (schrodinger.protein.helm.helm_renderer.HexColor attribute) ALL (schrodinger.application.desmond.constants.REST_REGION_RULE attribute) (schrodinger.application.desmond.constants.SidedError attribute) (schrodinger.application.livedesign.tasks.CoreAtomsOptions attribute) (schrodinger.application.matsci.fragments.FragmentReactor attribute) (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) (schrodinger.application.pymol.gui_models.ProjectTableExportMode attribute) (schrodinger.project.pandasutils.WhichColumns attribute) (schrodinger.project.pandasutils.WhichRows attribute) (schrodinger.tasks.queue.AutoFileMode attribute) (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) all() (schrodinger.infra.mmbitset.Bitset method) ALL_ANCHORS (schrodinger.protein.alignment.AnchoredResidueError attribute) all_atoms() (in module schrodinger.application.desmond.struc) all_basisnames() (in module schrodinger.application.jaguar.jaguar_keyword_utils) ALL_CONSTRAINTS_BUTTON (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) all_dftnames() (in module schrodinger.application.jaguar.jaguar_keyword_utils) ALL_HEAVY (schrodinger.application.livedesign.tasks.CoreAtomsOptions attribute) ALL_IN_LIMITED_RANGE (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute) ALL_IN_RANGE (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute) all_jobs (schrodinger.job.queue.JobDJ property) ALL_KEYS (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) all_keywords() (in module schrodinger.application.jaguar.jaguar_keyword_utils) all_meaningful_keywords() (in module schrodinger.application.jaguar.jaguar_keyword_utils) all_multicomb() (in module schrodinger.application.desmond.autopartition) all_properties() (in module schrodinger.application.matsci.genetic_optimization) ALL_RANDOM_CHANNELS (schrodinger.application.matsci.rxn_channel.Constants attribute) ALL_RESIDUES (schrodinger.application.bioluminate.protein.protein.PrimeConfig attribute) (schrodinger.ui.picking.MaestrolessPickResidueDialog attribute) (schrodinger.ui.residueselector.ResidueGroups attribute) all_rows (schrodinger.project.project.EntryGroup property) (schrodinger.project.project.Project property) ALL_SMARTS (schrodinger.application.matsci.automated_cg_mapping.StructData attribute) (schrodinger.application.matsci.rxn_channel.Constants attribute) ALL_SOLVENT_KEYWORDS (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) all_stage_family() (in module schrodinger.application.desmond.stage.workflow) ALL_STRUCS (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) all_structures (schrodinger.protein.alignment.BaseAlignment property) all_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property) ALL_TYPES (schrodinger.application.matsci.rxn_channel.Constants attribute) all_were_assigned() (in module schrodinger.application.jaguar.nmr_utils) allaid_gids (schrodinger.application.desmond.cms.Cms property) allCheckedText() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) allConstraintsActive() (schrodinger.application.jaguar.input.JaguarInput method) allCoordinatesDeleted (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) allDescriptorFullLabels() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method) allFacesIntersected() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) allGroupsAreCapping() (schrodinger.application.matsci.sculptcomplex.CoordinationInfo method) ALLINDICIES (schrodinger.application.matsci.nano.sheet.Grow attribute) allInRange() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) allInteractingResidues() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) allItems() (schrodinger.ui.qt.swidgets.SListWidget method) allItemsIter() (schrodinger.ui.qt.swidgets.SListWidget method) AllOps() (in module schrodinger.application.matsci.gsas.GSASIIspc) ALLOW_ADD_LIVE_REPORTS (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel attribute) allow_add_live_reports (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) ALLOW_ADSORPTION_ONTO (schrodinger.application.matsci.rxn_channel.Constants attribute) ALLOW_ADSORPTION_ONTO_METAVAR (schrodinger.application.matsci.rxn_channel.Constants attribute) allow_custom_weights (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) allow_custom_weightsChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) allow_custom_weightsReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) allow_multiple_chains (schrodinger.protein.tasks.blast.BlastSettings attribute) allow_multiple_chainsChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) allow_multiple_chainsReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) ALLOW_RESIDUE_OVERLAP (schrodinger.application.matsci.automated_cg_mapping.DpdMapper attribute) ALLOW_SCAN_CONSTRAINT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom attribute) allow_structure_input() (in module schrodinger.ui.sketcher_image) allow_structure_list_input() (in module schrodinger.ui.sketcher_image) allowAtomSelection() (schrodinger.application.matsci.chargegui.ChargeDialog method) ALLOWED (schrodinger.ui.qt.rama.RamaClassification attribute) ALLOWED_COLOR (schrodinger.ui.qt.rama.RamaContourMixin attribute) ALLOWED_FP_TYPES (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) allowed_gap_extend (schrodinger.protein.tasks.blast.BlastSettings attribute) allowed_gap_extendChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) allowed_gap_extendReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) allowed_host_types (schrodinger.tasks.jobtasks.HostSettings attribute) allowed_host_typesChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) (schrodinger.tasks.jobtasks.HostSettings attribute) allowed_host_typesReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) (schrodinger.tasks.jobtasks.HostSettings attribute) ALLOWED_INPUT (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) ALLOWED_KEYS (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) ALLOWED_OUTPUT (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) ALLOWED_TO_MATCH (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) AllowedHostTypes (class in schrodinger.tasks.jobtasks) allowEditing() (schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets.PlotTitleLineEdit method) allPrimitives() (schrodinger.graphics3d.common.Group method) allSettingsChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) allSignals() (schrodinger.protein.alignment.AlignmentSignals method) allSignalsAndNames() (schrodinger.protein.alignment.AlignmentSignals method) allText() (schrodinger.ui.qt.swidgets.SListWidget method) allTransmutationsCompleted() (schrodinger.application.matsci.enumeration.Alchemist method) (schrodinger.application.matsci.enumeration.ElementAlchemist method) (schrodinger.application.matsci.enumeration.VacancyAlchemist method) aln (schrodinger.protein.alignment.AlignmentSignals property) (schrodinger.protein.predictors.AbstractPredictor.Input attribute) (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) alnChanged (schrodinger.protein.predictors.AbstractPredictor.Input attribute) (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) alnReplaced (schrodinger.protein.predictors.AbstractPredictor.Input attribute) (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) alnSetChanged (schrodinger.protein.alignment.AlignmentSignals attribute) alnSetForSeq() (schrodinger.protein.alignment.BaseAlignment method) alnSetNames() (schrodinger.protein.alignment.BaseAlignment method) alnSets() (schrodinger.protein.alignment.BaseAlignment method) AlogDFilter (class in schrodinger.application.transforms.filters) AlogP() (in module schrodinger.rdkit.filtering) alpa_homo_lumo_energy() (in module schrodinger.application.mopac.results_main) alpha (schrodinger.application.bioluminate.tcr.docking_angles.TcrChainIds attribute) ALPHA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) (schrodinger.application.jaguar.hess_guess.LindhConstants attribute) alpha_beta_mix (schrodinger.application.jaguar.input.MixedPairs attribute) ALPHA_C (schrodinger.protein.annotation.KinaseFeatureLabel attribute) alpha_fdpolar() (in module schrodinger.application.jaguar.textparser) ALPHA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) alpha_mix (schrodinger.application.jaguar.input.MixedPairs attribute) ALPHA_ORBITALS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) ALPHA_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) alpha_polar() (in module schrodinger.application.jaguar.textparser) alpha_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute) alpha_somo_lumo_energy() (in module schrodinger.application.mopac.results_main) ALPHA_THRESH (schrodinger.application.matsci.mecp_mod.MECPStep attribute) ALPHABET (schrodinger.protein.sequence.AbstractProteinSequenceMixin property) (schrodinger.protein.sequence.AbstractSequence attribute) (schrodinger.protein.sequence.DNASequence attribute) (schrodinger.protein.sequence.NASequence attribute) (schrodinger.protein.sequence.NucleicAcidSequence attribute) (schrodinger.protein.sequence.NucleicSequenceMeta attribute) (schrodinger.protein.sequence.ProteinSequenceMeta property) (schrodinger.protein.sequence.RNASequence attribute) alphabetizeNames() (schrodinger.ui.qt.propertyselector.PropertySelector method) AlphaHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) AlphaLimitedColorPickerButton (class in schrodinger.ui.qt.color_picker) ALPilotReportMaker (class in schrodinger.active_learning.al_report) alreadyParsedRule() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) AlreadyRegisteredServerException ALReportMaker (class in schrodinger.active_learning.al_report) ALScreenReportMaker (class in schrodinger.active_learning.al_report) ALSO_REG_BOND_KEY (schrodinger.application.matsci.nano.xtal.PBCBond attribute) ALT_CHARGED_RESIDUES (schrodinger.ui.residueselector.MutationSelectorMixin attribute) alt_ligand_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) alt_ligands (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) alt_matches() (schrodinger.application.licensing.flexlm.Feature method) alt_xyz (schrodinger.structure.StructureAtom property) alter_mmlewis_settings() (in module schrodinger.application.jaguar.autots_bonding) alternates (schrodinger.application.prepwizard2.diagnostics.Problems attribute) alternatesChanged (schrodinger.application.prepwizard2.diagnostics.Problems attribute) alternatesReplaced (schrodinger.application.prepwizard2.diagnostics.Problems attribute) altSettingOrtho (in module schrodinger.application.matsci.gsas.GSASIIspc) ALWAYS_REDOWNLOAD (schrodinger.application.matsci.jobdirdlg.DownloadingMonitorMixin attribute) alwaysLocal() (schrodinger.job.app.App method) amax (schrodinger.application.matsci.reaction_workflow_gui_utils.SequenceData attribute) Ambivalent (schrodinger.protein.residue.BETA_STRAND_PROPENSITY attribute) (schrodinger.protein.residue.HELIX_PROPENSITY attribute) (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) (schrodinger.protein.residue.STERIC_GROUP attribute) (schrodinger.protein.residue.TURN_PROPENSITY attribute) amin (schrodinger.application.matsci.reaction_workflow_gui_utils.SequenceData attribute) amino_acids (schrodinger.protein.nonstandard_residues.ResidueDatabase property) AminoAcid (class in schrodinger.protein.nonstandard_residues) AminoAcidMonomerBase (class in schrodinger.protein.helm.helm_renderer) AmorphousCellBuilder (class in schrodinger.application.matsci.amorphous) Analysis (class in schrodinger.application.desmond.stage.analysis) ANALYSIS (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) ANALYSIS_FRAME_PERCENT (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep attribute) ANALYSIS_TYPE (schrodinger.application.matsci.desconfig.MSJStringer attribute) AnalysisColumns (class in schrodinger.application.bioluminate.pose_filtering.hdx_calc) AnalysisDriverMixin (class in schrodinger.application.matsci.desmondutils) AnalysisJob (class in schrodinger.application.desmond.stage.analysis) AnalysisMSJStringer (class in schrodinger.application.matsci.desconfig) analyze() (in module schrodinger.seam.examples.rescount) (schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer method) (schrodinger.protein.analysis.Report.backbone_dihedral_data_set method) (schrodinger.protein.analysis.Report.Bfactor_data_set method) (schrodinger.protein.analysis.Report.bond_angle_data_set method) (schrodinger.protein.analysis.Report.bond_length_data_set method) (schrodinger.protein.analysis.Report.chirality_data_set method) (schrodinger.protein.analysis.Report.data_set method) (schrodinger.protein.analysis.Report.gamma_Bfactor_data_set method) (schrodinger.protein.analysis.Report.Gfactor_summary_data_set method) (schrodinger.protein.analysis.Report.improper_torsion_data_set method) (schrodinger.protein.analysis.Report.missing_atoms_data_set method) (schrodinger.protein.analysis.Report.peptide_planarity_data_set method) (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method) (schrodinger.protein.analysis.Report.sidechain_dihedral_data_set method) (schrodinger.protein.analysis.Report.sidechain_planarity_data_set method) (schrodinger.protein.analysis.Report.steric_clash_data_set method) analyze_data() (schrodinger.application.desmond.bennett.CalcBAR method) analyze_frame_structure() (schrodinger.application.bioluminate.methionine_oxidation.HmcAnalyzer static method) analyze_frozen_atoms() (in module schrodinger.application.pathfinder.multiroute) analyze_pair() (schrodinger.protein.analysis.Report.steric_clash_data_set method) ANALYZE_SIMULATION (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) analyzed_frames_count (schrodinger.application.bioluminate.methionine_oxidation.MdStats attribute) AnalyzeEnergyOptions (class in schrodinger.application.prime.gui.analyze_energy) AnalyzeEnergyWidget (class in schrodinger.application.prime.gui.analyze_energy) AnalyzeMxmdProbeMixture (class in schrodinger.application.desmond.stage.app.mxmd) analyzeRoutes() (schrodinger.application.pathfinder.analysis.ForwardAnalyzer method) AnalyzeSimulation (class in schrodinger.application.matsci.permittivity) AnalyzeStageData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) anarci_type (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult attribute) AnarciChainResult (class in schrodinger.application.bioluminate.anarci.anarci_adapter) AnarciDomainResult (class in schrodinger.application.bioluminate.anarci.anarci_adapter) AnarciResults (class in schrodinger.application.bioluminate.anarci.anarci_adapter) AnarciType (class in schrodinger.application.bioluminate.anarci.anarci_adapter) AnchoredResidueError anchoredResiduesChanged (schrodinger.protein.alignment.AlignmentSignals attribute) anchorResidues() (schrodinger.protein.alignment.BaseAlignment method) Angle (class in schrodinger.application.jaguar.hess_guess) ANGLE (schrodinger.application.matsci.rxn_path.Coord attribute) angle (schrodinger.structutils.interactions.pi.CationPiInteraction property) (schrodinger.structutils.interactions.pi.PiPiInteraction property) ANGLE (schrodinger.trajectory.trajectory_gui_dir.banners.MeasurementMode attribute) ANGLE_A (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) ANGLE_B (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) angle_bend_energy() (in module schrodinger.application.qsite.output) ANGLE_DEP_TRANSPARENCY (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) ANGLE_ENERGY (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) ANGLE_FBHW (schrodinger.application.desmond.constants.RestrainTypes attribute) angle_iterator() (in module schrodinger.structutils.analyze) ANGLE_TOL (schrodinger.application.matsci.mecp_mod.BFGS attribute) AngleAdaptationMixin (class in schrodinger.application.matsci.cgforcefield) AngleDistortion (class in schrodinger.structutils.check) ANGLELARGE (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) ANGLEMEDIUM (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) (schrodinger.application.matsci.nano.tube.NanoSheet attribute) angles (schrodinger.application.jaguar.hess_guess.CoordinateManager property) ANGLESMALL (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) ANGLEWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) Angstrom (schrodinger.application.jaguar.constants.Unit attribute) Angstrom4 (schrodinger.application.jaguar.constants.Unit attribute) angular_freq_to_freq() (in module schrodinger.application.matsci.anharmonic) ANH_LNQ (schrodinger.application.matsci.reaction_workflow_utils.DF_RATE_TYPE attribute) AnharmonicException AnharmonicPartitionFunction (class in schrodinger.application.matsci.anharmonic) AnharmonicPotentials (class in schrodinger.application.matsci.anharmonic) AnharmonicThermochemicalProperties (class in schrodinger.application.matsci.anharmonic) ANI_1CCX (schrodinger.energy.ANIModel attribute) ANI_CC (schrodinger.application.jaguar.constants.CalcType attribute) ANIMATION_TIME (schrodinger.application.desmond.feputils.LabelSpinner attribute) animationTimeElapsed (schrodinger.application.desmond.feputils.LabelSpinner attribute) ANIModel (class in schrodinger.energy) AnionCation (schrodinger.structutils.interactions.salt_bridge.OrderBy attribute) anionFrameCoordination() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) ANIPrecision (class in schrodinger.energy) AniServerError ANISO_DIMS (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) ANISOTROPIC (schrodinger.application.desmond.constants.IsotropyPolicy attribute) (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) ANISOTROPIC_1D (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) ANISOTROPIC_2D (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) ANN (schrodinger.forcefield.constants.GeometryOptMethod attribute) anneal() (in module schrodinger.application.matsci.gsas.GSASIImath) annealtests() (in module schrodinger.application.matsci.gsas.GSASIImath) annotate() (schrodinger.application.desmond.fep_scholar_util.MappingAnnotator method) (schrodinger.ui.qt.structure2d.AtomLabelAnnotator method) (schrodinger.ui.qt.structure2d.AtomNumberAnnotator method) (schrodinger.ui.qt.structure2d.BaseSquareAnnotator method) (schrodinger.ui.qt.structure2d.CircleAnnotator method) (schrodinger.ui.qt.structure2d.ColoredArrowAnnotator method) annotate_ab_regions() (in module schrodinger.application.bioluminate.antibody.annotate) annotate_atom_indices() (in module schrodinger.protein.assignment) annotate_entry_title() (in module schrodinger.application.prepwizard2.tasks) annotate_ligand_atoms() (in module schrodinger.protein.assignment) annotate_ligand_rotatable_hydrogens() (in module schrodinger.protein.assignment) annotate_plot() (schrodinger.application.jaguar.simple_spec.Peak method) annotate_stereochemistry() (in module schrodinger.protein.process_enamine_db) annotate_structure() (schrodinger.protein.assignment.ProtAssign method) annotate_structure_interactors() (in module schrodinger.protein.assignment) annotate_tcr_regions() (in module schrodinger.application.bioluminate.tcr.annotate) annotation (schrodinger.protein.tasks.kinase.KinaseFeatureTask.Output attribute) ANNOTATION_PROP (in module schrodinger.rdkit.rdkit_adapter) annotation_strings (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult property) annotation_strings_with_gaps (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult property) annotationChanged (schrodinger.protein.tasks.kinase.KinaseFeatureTask.Output attribute) AnnotationClass (schrodinger.protein.sequence.AbstractSequence attribute) (schrodinger.protein.sequence.CombinedChainProteinSequence attribute) (schrodinger.protein.sequence.NucleicAcidSequence attribute) (schrodinger.protein.sequence.ProteinSequence attribute) annotationInvalidated (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) annotationReplaced (schrodinger.protein.tasks.kinase.KinaseFeatureTask.Output attribute) AnnotationResult (class in schrodinger.application.bioluminate.anarci.annotate) annotations (schrodinger.protein.alignment.BaseAlignment property) (schrodinger.protein.sequence.AbstractSequence property) annotationTitleChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractSequence attribute) ANTIBODY (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) ANTIBODY_ARM_FAB_PRIME (schrodinger.livedesign.entity_type.EntityClass attribute) ANTIBODY_ARM_FULL (schrodinger.livedesign.entity_type.EntityClass attribute) antibody_cdr (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) antibody_cdr_scheme (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) antibody_cdr_schemeChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) antibody_cdr_schemeReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) ANTIBODY_H (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType attribute) antibody_heavy_domains (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment property) ANTIBODY_HEAVY_FAB (schrodinger.livedesign.entity_type.EntityClass attribute) ANTIBODY_HEAVY_FAB_PRIME (schrodinger.livedesign.entity_type.EntityClass attribute) ANTIBODY_HEAVY_FULL (schrodinger.livedesign.entity_type.EntityClass attribute) ANTIBODY_HEAVY_FV (schrodinger.livedesign.entity_type.EntityClass attribute) ANTIBODY_K (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType attribute) ANTIBODY_L (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType attribute) antibody_light_domains (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment property) ANTIBODY_LIGHT_FAB (schrodinger.livedesign.entity_type.EntityClass attribute) ANTIBODY_LIGHT_FV (schrodinger.livedesign.entity_type.EntityClass attribute) ANTIBODY_MODEL (schrodinger.infra.structure.WorkflowType attribute) ANTIBODY_NUM_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) antibody_region (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) antibody_regions (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) AntibodyAssembler (class in schrodinger.livedesign.biologics.fasta) AntibodyCDR (class in schrodinger.protein.annotation) (schrodinger.application.prepwizard2.tasks.ProteinFeature attribute) AntibodyCDRLabel (class in schrodinger.protein.annotation) AntibodyNumberingToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) AntibodyPreset (class in schrodinger.application.bioluminate.pml_menus) AntibodyPresetAHo (class in schrodinger.application.bioluminate.pml_menus) AntibodyPresetChothia (class in schrodinger.application.bioluminate.pml_menus) AntibodyPresetEnhancedChothia (class in schrodinger.application.bioluminate.pml_menus) AntibodyPresetIMGT (class in schrodinger.application.bioluminate.pml_menus) AntibodyPresetKabat (class in schrodinger.application.bioluminate.pml_menus) AntibodyPresetSubMenu (class in schrodinger.application.bioluminate.pml_menus) AntibodyRegionLabel (class in schrodinger.protein.annotation) AntibodyRegionsFinder (class in schrodinger.protein.annotation) ANTIGEN (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) antigen_chains (schrodinger.application.bioluminate.antibody.grafting.GraftingInput attribute) ANTIGEN_TYPE (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) AntiparallelPleatedSheet (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) antlr_version (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) antlr_version_str (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) ANTLRFileStream (class in schrodinger.application.desmond.antlr3.streams) ANTLRInputStream (class in schrodinger.application.desmond.antlr3.streams) ANTLRStringStream (class in schrodinger.application.desmond.antlr3.streams) any_atom_in_distance_cell() (in module schrodinger.structutils.measure) ANY_CONTACT (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) any_phase_hypothesis_label_property_checked() (in module schrodinger.application.phase.phase_markers) any_polygons_outside_cell() (in module schrodinger.application.matsci.maestrocmds) any_structured_residues() (in module schrodinger.protein.residue) ANY_VALUE (schrodinger.application.desmond.arkdb.DSC attribute) anyAtomsTooClose() (schrodinger.application.matsci.desconfig.BarrierInfo method) anyConstraintsActive() (schrodinger.application.jaguar.input.JaguarInput method) ao_index() (in module schrodinger.application.mopac.results_main) ao_zeta() (in module schrodinger.application.mopac.results_main) AOM (schrodinger.energy.MonoMetalComplexType attribute) aos_on_grid() (in module schrodinger.application.mopac.mopac_surfaces) APIVersion (schrodinger.job.server.ServerInfo attribute) apodization() (in module schrodinger.application.jaguar.spin_simulator_v2) aposteri_e() (in module schrodinger.application.jaguar.textparser) App (class in schrodinger.job.app) (class in schrodinger.ui.qt.appframework2.af2) app_name (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.BqQueryStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreStage attribute) app_type_override (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) AppDockWidget (class in schrodinger.ui.qt.appframework) APPEND (schrodinger.infra.structure.WriteMode attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.tasks.jobtasks.IncorporationMode attribute) append() (schrodinger.application.desmond.ffiostructure.FFIOStructure method) (schrodinger.application.phase.packages.shape_binary_utils.ShapeFileWriter method) (schrodinger.application.qsite.input.QMRegion method) (schrodinger.infra.mmkv.MMKVArgList method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.rdkit.molio.CsvMolWriter method) (schrodinger.rdkit.molio.MolWriter method) (schrodinger.rdkit.molio.PfxMolWriter method) (schrodinger.rdkit.molio.RdkitMolWriter method) (schrodinger.structure.MaestroWriter method) (schrodinger.structure.MMCIFWriter method) (schrodinger.structure.MultiFileStructureWriter method) (schrodinger.structure.PDBWriter method) (schrodinger.structure.SmilesCsvWriter method) (schrodinger.structure.SmilesStructure method) (schrodinger.structure.SmilesWriter method) (schrodinger.structure.Structure method) (schrodinger.structure.StructureWriter method) (schrodinger.structure.TextualStructure method) (schrodinger.structutils.filter.Filter method) (schrodinger.utils.multifpfile.MultiFPFileWriter method) (schrodinger.utils.sea.sea.List method) (schrodinger.utils.typing.Appendable method) append_comment() (in module schrodinger.application.desmond.util) APPEND_FIT (schrodinger.job.launchparams.ProjectDisposition attribute) append_logfile() (in module schrodinger.application.glide.utils) append_outfiles_to_recover_file() (in module schrodinger.application.jaguar.utils) append_path() (in module schrodinger.utils.env) append_property() (in module schrodinger.application.matsci.smartsutils) append_row_to_data() (in module schrodinger.structutils.block_data) append_stage() (in module schrodinger.application.desmond.cmj) append_unique_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) Appendable (class in schrodinger.utils.typing) appendChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) appendFile() (schrodinger.ui.qt.structtable.StructureReaderDelegate method) appendFileContent() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) appendFromModel() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) APPENDINPLACE (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.tasks.jobtasks.IncorporationMode attribute) APPENDINPLACE_FIT (schrodinger.job.launchparams.ProjectDisposition attribute) appendLigand() (schrodinger.application.glide.poseviewconvert.Complex method) appendMissedFrags() (schrodinger.application.matsci.amorphous.PolymerFragments method) appendReceptor() (schrodinger.application.glide.poseviewconvert.Complex method) appendRow() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) appendRowObject() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) appendRowObjects() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) appendSource() (schrodinger.structutils.rgroup_enumerate.Concentration method) appendStruct() (schrodinger.ui.qt.table.ViewerModel method) appendToSplitGroup() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) appendTrjInOutst2ToCmd() (schrodinger.application.matsci.permittivity.AnalyzeSimulation method) APPENDUNGROUPED (schrodinger.job.launchparams.ProjectDisposition attribute) AppFramework (class in schrodinger.ui.qt.appframework) APPLICATION_NAME (schrodinger.application.desmond.multisimstartup.Startup attribute) ApplicationMode (in module schrodinger.utils.qapplication) apply() (schrodinger.application.desmond.gaussian_filter.GaussianFilter method) (schrodinger.application.pathfinder.analysis.Transformer method) (schrodinger.application.pathfinder.reaction.Reaction method) (schrodinger.structutils.color.ColorScheme method) (schrodinger.ui.qt.formlayout.FormDialog method) (schrodinger.ui.qt.formlayout.PushLayout method) (schrodinger.ui.qt.schart.AxisParams method) (schrodinger.ui.qt.schart.SeriesParams method) (schrodinger.utils.sea.sea.List method) (schrodinger.utils.sea.sea.Map method) (schrodinger.utils.sea.sea.Sea method) apply_biounit() (in module schrodinger.protein.biounit) apply_color_scheme() (in module schrodinger.structutils.color) apply_config_settings_to_step() (in module schrodinger.application.steps.utils) apply_dihedral() (schrodinger.ui.qt.rama.Rama method) apply_exclusion() (in module schrodinger.application.desmond.r_group_asl) apply_het_states() (in module schrodinger.application.prepwizard) apply_jaguar_atom_naming() (in module schrodinger.application.jaguar.input) apply_legacy_spacing_style() (in module schrodinger.ui.qt.style) APPLY_LEGACY_STYLESHEET (schrodinger.application.livedesign.login_gui2.LDLoginPanel attribute) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel attribute) (schrodinger.ui.qt.widgetmixins.basicmixins.SchrodingerStyleMixin attribute) apply_lewis() (in module schrodinger.application.jaguar.utils) apply_natural_analog_properties() (in module schrodinger.protein.process_enamine_db) apply_natural_analog_props() (in module schrodinger.protein.natural_analog) apply_panelx_button_settings() (in module schrodinger.ui.qt.style) apply_panelx_combo_settings() (in module schrodinger.ui.qt.style) apply_panelx_style() (in module schrodinger.ui.qt.style) APPLY_PANELX_STYLESHEET (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel attribute) (schrodinger.ui.qt.widgetmixins.basicmixins.SchrodingerStyleMixin attribute) apply_pkas() (schrodinger.protein.assignment.ProtAssign method) apply_pointgroup_symmetry_op() (in module schrodinger.comparison.struc) apply_random_color() (in module schrodinger.application.livedesign.io_utils) apply_round_trip_hash() (in module schrodinger.application.livedesign.ld_utils) apply_settings() (in module schrodinger.ui.qt.appframework2.settings) apply_similarity_filters() (in module schrodinger.application.pathfinder.multiroute) apply_state() (in module schrodinger.application.prepwizard) apply_state_and_calc_score() (in module schrodinger.application.prepwizard) apply_style_sheet() (in module schrodinger.ui.qt.style) apply_style_sheet_to_button() (in module schrodinger.ui.qt.standard_widgets.buttons) apply_styles() (in module schrodinger.ui.qt.style) apply_substructure_coordinates() (in module schrodinger.rdkit.substructure) apply_substructure_coordinates_from_mapping() (in module schrodinger.rdkit.substructure) apply_to_structure() (schrodinger.application.matsci.elasticity.strain.Deformation method) apply_transform() (in module schrodinger.analysis.transformations) apply_transformations() (in module schrodinger.livedesign.preprocessor) apply_transforms() (in module schrodinger.analysis.transformations) apply_uniform_operator_weights() (in module schrodinger.application.matsci.genetic_optimization) applyAliasedSettings() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) applyBasisSetFilterSettings() (schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog method) ApplyBNSlatt() (in module schrodinger.application.matsci.gsas.GSASIIspc) applyContextDependentDefaults() (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.GlideJob method) applyCount() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyCPKStyle() (schrodinger.structure.Structure method) applyCreate() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyCustomWeight() (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings method) applyDefaultWeight() (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings method) applyDistinct() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyEnergyFilter() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) applyEntryData() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) applyFF() (schrodinger.application.matsci.cgforcefield.ForceField method) applyFilter() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) (schrodinger.ui.qt.filter_list.FilterCheckBox method) applyFilters() (schrodinger.ui.qt.filter_list.FilterListPopUp method) (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) applyFlatMap() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyFlatten() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyGBK() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyGoldsteinSingles() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) applyGroupSelections() (schrodinger.ui.residueselector.MutationSelectorMixin method) applyHetStates() (schrodinger.application.prepwizard2.tasks.GenerateStatesTask method) applyMap() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyMapping() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) applyMethodFilterSettings() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.application.jaguar.gui.input_tab_widgets.MethodDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog method) ApplyModulation() (in module schrodinger.application.matsci.gsas.GSASIImath) applyPreset() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) applyReshuffle() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applySample() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) ApplySeqData() (in module schrodinger.application.matsci.gsas.GSASIImath) applySettings() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterListToolButton method) (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit method) (schrodinger.application.jaguar.gui.theory_selector.FilterTheorySelectorReadOnlyLineEdit method) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListToolButton method) (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp method) applyShowHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) applySideInput() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyState() (schrodinger.application.prepwizard.HetState method) ApplyStringOps() (in module schrodinger.application.matsci.gsas.GSASIIspc) ApplyStringOpsMom() (in module schrodinger.application.matsci.gsas.GSASIIspc) applyStyle() (schrodinger.structure._Chain method) (schrodinger.structure._Molecule method) (schrodinger.structure._Ring method) (schrodinger.structure.Residue method) (schrodinger.structure.Structure method) applySum() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyToDimers() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) applyToJaguarInput() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.OverrideKeywords method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords method) applyTop() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) applyTubeStyle() (schrodinger.structure.Structure method) applyVisibilityAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) applyWireStyle() (schrodinger.structure.Structure method) APPROX (schrodinger.application.matsci.espresso.qeinput.TurboEelsType attribute) approx_eq() (in module schrodinger.application.bioluminate.interaction_calculator) approx_equal() (in module schrodinger.application.desmond.measurement) approx_fhess_p() (in module schrodinger.application.jaguar.qrnn.temp_opt) approx_fprime() (in module schrodinger.application.jaguar.qrnn.temp_opt) approximateVolume() (schrodinger.application.matsci.amorphous.Scaffold static method) AppTemplate (class in schrodinger.ui.qt.appframework2.af2_template) AQUEOUS_DISSOLUTION (schrodinger.application.desmond.constants.PhysicalLegTypes attribute) archive_folder() (in module schrodinger.application.matsci.freevolume) archive_job_data() (in module schrodinger.application.matsci.jobutils) archive_license_file() (in module schrodinger.application.licensing.licserver.install) archive_path (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) archive_wm() (in module schrodinger.application.watermap.utils) ARCHIVED_INPUT (schrodinger.application.matsci.jaguarworkflows.Step attribute) ARCHIVED_KEEPERS (schrodinger.application.matsci.jaguarworkflows.Step attribute) ArchivedProjectException archiveFiles() (schrodinger.application.matsci.jaguarworkflows.Step method) archiveSubDir() (schrodinger.application.matsci.jwsteps.BaseStep method) ArchPopUp (class in schrodinger.application.jaguar.gui.timing) are_bonded() (schrodinger.application.jaguar.hess_guess.CoordinateManager method) are_c_and_z_parallel() (in module schrodinger.application.matsci.nano.xtal) are_conformers() (in module schrodinger.comparison.comparison) (schrodinger.comparison.atom_mapper.BaseAtomMapper method) are_consistently_numbered_conformers() (in module schrodinger.comparison.comparison) are_consistently_ordered_conformers() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) are_diastereomers() (in module schrodinger.comparison.comparison) are_duplicates() (in module schrodinger.application.matsci.buildcomplex) are_enantiomers() (in module schrodinger.comparison.comparison) (schrodinger.comparison.atom_mapper.BaseAtomMapper method) are_heavy_atom_conformers() (in module schrodinger.comparison.comparison) are_isomers() (in module schrodinger.comparison.comparison) are_monomers() (in module schrodinger.application.matsci.rxn_channel) are_same_file() (in module schrodinger.job.launchapi) are_same_geometry() (in module schrodinger.comparison.comparison) are_stereoisomers() (in module schrodinger.comparison.comparison) are_sts_the_same() (in module schrodinger.structutils.createfragments) are_tautomers() (in module schrodinger.comparison.comparison) are_times_invalid() (in module schrodinger.application.desmond.fepana) are_torsion_safe_bonded() (schrodinger.application.jaguar.hess_guess.CoordinateManager method) area (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) areAtomsOrtho() (schrodinger.structutils.assignbondorders.AssignBondOrders method) areBound() (schrodinger.structure.Structure method) areContiguous() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) areCOsPara() (schrodinger.structutils.assignbondorders.AssignBondOrders method) areSameLength() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) areSubjobsAndStageOnSameHost() (schrodinger.pipeline.stage.Stage method) arg_aid_offset() (in module schrodinger.application.desmond.new_fep_edge_data) arg_option() (in module schrodinger.application.desmond.new_fep_edge_data) arg_premise() (in module schrodinger.application.desmond.new_fep_edge_data) arg_string (schrodinger.application.steps.docking.SmilesDockerSettings attribute) (schrodinger.application.steps.ligprep.LigPrepStep.Settings attribute) arg_stringChanged (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) (schrodinger.application.steps.ligprep.LigPrepStep.Settings attribute) arg_stringReplaced (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) (schrodinger.application.steps.ligprep.LigPrepStep.Settings attribute) arginine_interactions() (schrodinger.protein.assignment.HistidinepKaPredictor method) argparser_set_defaults() (in module schrodinger.application.matsci.parserutils) Args (class in schrodinger.application.desmond.starter.ui.constant_ph) (class in schrodinger.application.desmond.starter.ui.fep_absolute_binding) (class in schrodinger.application.desmond.starter.ui.fep_residue_scanning) ArgumentParserError ArgumentParserNoExit (class in schrodinger.application.matsci.espresso.utils) ark_str() (schrodinger.application.desmond.replica_sid_generator.FEPReport method) ArkDb (class in schrodinger.application.desmond.arkdb) ArkDbDelError ArkDbGetError ArkDbPutError ARMCHAIR (schrodinger.application.matsci.nano.constants.Constants attribute) ARMCHAIR_BY_ONE_BASE (schrodinger.application.matsci.nano.sheet.Grow attribute) AROMATIC (schrodinger.livedesign.draw.AromaticBondDisplay attribute) Aromatic (schrodinger.protein.helm.helm_renderer.HexColor attribute) (schrodinger.protein.residue.STERIC_GROUP attribute) aromatic_bond_display (schrodinger.livedesign.draw.ImageGenOptions attribute) AROMATIC_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) AROMATIC_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) AROMATIC_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) AromaticBondDisplay (class in schrodinger.livedesign.draw) Around (class in schrodinger.application.bioluminate.pml_menus) AroundExpandSubMenu (class in schrodinger.application.bioluminate.pml_menus) array_abs_diff() (in module schrodinger.application.jaguar.macro_pka_utils) Array_Prop (class in schrodinger.application.desmond.simulation_block_data) ArrayCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) ArraySyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) arrow (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) ARROW_RADII (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) arrow_tooltip_display() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) ArrowheadConnectorMixin (class in schrodinger.protein.helm.helm_renderer) ArrowLink (class in schrodinger.ui.qt.standard_widgets.hyperlink) as_dict() (schrodinger.application.matsci.wfmanagement.WorkflowMetadata method) as_double() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) AS_INPUT (schrodinger.adapter.Hydrogens attribute) AS_IS (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute) ASCENDING (schrodinger.application.glide.sort_utils.SortOrder attribute) asDict() (schrodinger.application.pathfinder.reaction.Reaction method) (schrodinger.application.pathfinder.reaction.ReagentClass method) asDock() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) aset() (schrodinger.application.macromodel.utils.ComUtil method) asFrame() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) asGlideResult() (schrodinger.application.glide.http_client.GlideResultIterator method) asGrid() (schrodinger.application.bioluminate.bwidgets.ImportWidget method) asind() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIImath) asJSON() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) ask_disconnect_active_connection() (in module schrodinger.application.livedesign.ld_maestro_actions) askOverwrite() (schrodinger.ui.qt.appframework.AppFramework method) askOverwriteIfNecessary() (schrodinger.ui.qt.appframework.AppFramework method) asl (schrodinger.maestro_utils.find_tool_bar.constants.SEARCH_OPTION_DETAILS attribute) (schrodinger.protein.assignment.ProtAssign.amide_changeable attribute) (schrodinger.protein.assignment.ProtAssign.amine_changeable attribute) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable attribute) (schrodinger.protein.assignment.ProtAssign.changeable attribute) (schrodinger.protein.assignment.ProtAssign.histidine_changeable attribute) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable attribute) (schrodinger.protein.assignment.ProtAssign.water_changeable attribute) asl() (schrodinger.application.desmond.maestro.NewEntry method) ASL_COL (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame attribute) ASL_IONS (schrodinger.application.bioluminate.protein.protein.Consensus attribute) (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) ASL_ITEMS (schrodinger.application.matsci.mswidgets.MSAtomSelector attribute) (schrodinger.ui.qt.atomselector.AtomSelector attribute) ASL_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) ASL_LIGAND (schrodinger.application.bioluminate.protein.protein.Consensus attribute) (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) asl_ligand (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) ASL_NOT_ALLOWED (schrodinger.application.matsci.mswidgets.MSAtomSelector attribute) asl_receptor (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) ASL_WATER (schrodinger.application.bioluminate.protein.protein.Consensus attribute) (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) ASL_WATER_NOZOB (schrodinger.application.bioluminate.protein.protein.Consensus attribute) AslCriterion (class in schrodinger.utils.ligfilter) AslException ASLItem (class in schrodinger.ui.qt.atomselector) aslItemClicked() (schrodinger.application.matsci.mswidgets.MSAtomSelector method) (schrodinger.ui.qt.atomselector.AtomSelector method) AslLigandSearcher (class in schrodinger.structutils.analyze) aslModified (schrodinger.ui.qt.atomselector.AtomSelector attribute) ASLObject (class in schrodinger.application.desmond.enhsamp) ASLPopupMenu (class in schrodinger.ui.qt.atomselector) ASLResult (class in schrodinger.protein.align) aslselect_atom() (in module schrodinger.application.desmond.cms) ASLSelectorCheckableComboBox (class in schrodinger.application.matsci.density_analysis_widget) aslTextModified (schrodinger.ui.qt.atomselector.AtomSelector attribute) AslValidator (class in schrodinger.application.desmond.cmj) AsMenu (class in schrodinger.application.bioluminate.pml_menus) asNamedTuple() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) ASP_PH_MAX (schrodinger.application.jaguar.pk50_report.Pk50Factory attribute) ASP_PH_MIN (schrodinger.application.jaguar.pk50_report.Pk50Factory attribute) ASP_PH_STEP (schrodinger.application.jaguar.pk50_report.Pk50Factory attribute) AsparticAcidpKaPredictor (class in schrodinger.protein.assignment) aspectScale() (in module schrodinger.application.desmond.rl_helper) Assay (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) assaySelected (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) AssaySelectionLineEdit (class in schrodinger.application.livedesign.panel_components) AssaySelectionPopUp (class in schrodinger.application.livedesign.panel_components) AssaySelectionPopUpDelegate (class in schrodinger.application.livedesign.panel_components) assemble() (schrodinger.livedesign.biologics.fasta.AntibodyAssembler method) (schrodinger.livedesign.biologics.fasta.NucleicAcidAssembler method) (schrodinger.livedesign.biologics.fasta.PolymerAssembler method) assemble_domains() (in module schrodinger.application.bioluminate.antibody.assembly) assert_approx() (in module schrodinger.application.phase.packages.mmp_compare_utils) assert_not_blinded() (in module schrodinger.livedesign.preprocessor) assert_not_query() (in module schrodinger.livedesign.preprocessor) assert_pcoll_size() (in module schrodinger.seam.testing.util) assert_same_struct() (in module schrodinger.application.matsci.mstest) assert_valid_scaffold() (in module schrodinger.livedesign.rgroup_decomposition) assert_valid_sru_groups() (in module schrodinger.rdkit.substructure) assertAlmostEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertCallAlmostEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertCalledTimes() (schrodinger.application.matsci.mstest.MSTestCase method) assertCallEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertCallIn() (schrodinger.application.matsci.mstest.MSTestCase method) assertCallNotEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertCallNotIn() (schrodinger.application.matsci.mstest.MSTestCase method) assertCanMutateResidues() (schrodinger.protein.sequence.CombinedChainProteinSequence method) assertFlag() (schrodinger.application.matsci.mstest.MSTestCase method) assertInKeywords() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) assertJobFinished() (schrodinger.application.phase.packages.shape_screen_al_node.ShapeScreenJob method) assertStageEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertStructAlmostEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertStructEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertTableContentsEqual() (schrodinger.application.matsci.mstest.MSTestCase method) ASSIGN (schrodinger.application.desmond.constants.CUSTOM_CHARGE_MODE attribute) assign() (schrodinger.structutils.assignbondorders.AssignBondOrders method) (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method) assign_best_combinations() (schrodinger.protein.assignment.ProtAssign method) assign_bond_orders (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) assign_bond_orders() (in module schrodinger.application.matsci.nano.xtal) assign_bond_orders_w_mmlewis() (in module schrodinger.application.matsci.nano.xtal) assign_bond_ordersChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) assign_bond_ordersReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) assign_cluster_combination() (schrodinger.protein.assignment.ProtAssign method) assign_combination() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) assign_ff() (in module schrodinger.application.bioluminate.escomp) assign_force_field() (in module schrodinger.forcefield.common) assign_highlight_options() (in module schrodinger.livedesign.draw) assign_lipid_ff() (in module schrodinger.application.matsci.desmondutils) assign_markers() (in module schrodinger.application.matsci.amorphous) ASSIGN_NEW (schrodinger.application.livedesign.export_models.InvalidGEIdHandlingPolicy attribute) assign_option() (in module schrodinger.forcefield.minimizer) assign_pdb_names() (in module schrodinger.protein.pdbname) assign_residue_numbers() (in module schrodinger.protein.sequence) assign_space_group() (in module schrodinger.application.matsci.nano.xtal) assign_st() (in module schrodinger.structutils.assignbondorders) assign_state() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) assign_state_gap() (schrodinger.protein.assignment.ProtAssign.changeable method) assign_state_of_changeable() (schrodinger.protein.assignment.ProtAssign method) assign_structure_for_minimization() (in module schrodinger.forcefield.minimizer) assign_zero_coords_chirality() (in module schrodinger.livedesign.preprocessor) assignAromaticBonders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignAromaticRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignAromaticRingGroup() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignAromaticRingOrders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) AssignBondOrders (class in schrodinger.structutils.assignbondorders) assignChainOrders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignColorsWithThreshold() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) AssignCustomCharge (class in schrodinger.application.desmond.stage.prepare.forcefield) AssignForcefield (class in schrodinger.application.desmond.stage.prepare.forcefield) assignGroupDoubleBonds() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignGroupTripleBonds() (schrodinger.structutils.assignbondorders.AssignBondOrders method) AssignLambdaSchedule (class in schrodinger.application.desmond.stage.prepare.forcefield) AssignLambdaScheduleError assignLeaves() (in module schrodinger.ui.qt.dendrogram) assignRingAtomIds() (schrodinger.application.matsci.amorphous.PolymerFragments method) assignTemplatedSubstructures() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignTripleBonds() (schrodinger.structutils.assignbondorders.AssignBondOrders method) associated_legs (schrodinger.application.desmond.physical_leg_infra.LegProcess property) ASSOCIATION_TYPE (schrodinger.application.matsci.rxn_channel.Constants attribute) ASSUME_ISOLATED_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) asu_iter() (in module schrodinger.comparison.struc) ASU_LABEL_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) ASU_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) AsyncJobHandler (class in schrodinger.job.jobhandler) at_index_str (schrodinger.application.jaguar.autots_constants.IndexString attribute) at_surface (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) at_values (schrodinger.application.jaguar.scan.Scan property) atan2d() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIImath) (in module schrodinger.application.matsci.gsas.GSASIIpwd) atand() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIImath) (in module schrodinger.application.matsci.gsas.GSASIIpwd) atid2atomsel() (schrodinger.application.desmond.meta.CmsModel method) Atom (class in schrodinger.ui.qt.mapperwidgets.param_editor) (class in schrodinger.utils.sea.sea) ATOM (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame attribute) atom (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) (schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo attribute) (schrodinger.structure._AtomCollection property) (schrodinger.structure.Structure attribute) (schrodinger.structure.StructureBond property) (schrodinger.structure.TextualStructure property) (schrodinger.structutils.markush_enumerate.PlaceHolder attribute) atom() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) (schrodinger.application.glide.glide.MetalConstraint method) atom_b_factor() (in module schrodinger.application.bioluminate.pml_menus) atom_charges() (in module schrodinger.application.mopac.results_main) atom_clicked (schrodinger.application.matsci.reordergui.StructureListWidget attribute) (schrodinger.ui.qt.structure2d.structure_view attribute) atom_color (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) ATOM_DEFINITION (class in schrodinger.application.matsci.cg_mapping) atom_el() (in module schrodinger.application.mopac.results_main) atom_highlighted (schrodinger.application.matsci.reordergui.StructureView attribute) atom_idcs (schrodinger.application.desmond.kinetics.utils.RmsdSelection attribute) atom_idx (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.NODE_GROUP_TYPE attribute) (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) atom_index (schrodinger.structutils.rgroup_enumerate.RGroup attribute) atom_indexes (schrodinger.structutils.analyze.Ligand property) atom_indices (schrodinger.application.bioluminate.protein.protein.Consensus property) atom_indices_are_contiguous() (in module schrodinger.comparison.struc) atom_is_nonpolar() (in module schrodinger.application.bioluminate.protein.protein) ATOM_LABELS (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) atom_map (schrodinger.application.jaguar.autots_rmsd.MapScore attribute) (schrodinger.comparison.atom_mapper.MapScore attribute) atom_mapping (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) (schrodinger.application.desmond.msj_generator.workflow_params.MapperParams attribute) (schrodinger.application.desmond.new_fep_edge_data.FepData property) atom_name (schrodinger.structure.StructureAtom property) atom_name_regex (in module schrodinger.application.jaguar.gui.utils) atom_name_sort_key() (in module schrodinger.application.jaguar.gui.utils) ATOM_NUM (schrodinger.application.matsci.mswidgets.SystemInformationFrame attribute) atom_number (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) atom_numberChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) atom_numberReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) atom_nums (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.NODE_GROUP_TYPE attribute) atom_objects (schrodinger.structutils.analyze.Ligand property) atom_pos (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsPageModel attribute) atom_posChanged (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsPageModel attribute) atom_posReplaced (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsPageModel attribute) atom_pqn() (in module schrodinger.application.mopac.results_main) atom_style (schrodinger.structure.StructureAtom property) atom_symtype() (in module schrodinger.application.mopac.results_main) ATOM_TOTAL (schrodinger.application.desmond.constants.IdConversion attribute) atom_total (schrodinger.application.jaguar.results.JaguarResults property) (schrodinger.structure.Structure property) (schrodinger.structure.TextualStructure property) atom_type (schrodinger.application.desmond.fep_scholar_util.MetaAtom property) (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) ATOM_TYPE (schrodinger.comparison.atom_mapper.BaseAtomMapper attribute) atom_type (schrodinger.structure.StructureAtom property) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) atom_type_name (schrodinger.structure.StructureAtom property) atom_typeMM (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) ATOM_TYPING_SCHEMES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) atom_weights (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) ATOM_WEIGHTS (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget attribute) atom_weightsChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) atom_weightsReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) atom_x_angstroms() (in module schrodinger.application.mopac.results_main) atom_x_opt() (in module schrodinger.application.mopac.results_main) AtomBasis (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) AtomBasisSetDelegate (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) AtomCollectionFrame (class in schrodinger.application.matsci.reaction_workflow_gui_utils) AtomGroup (class in schrodinger.application.desmond.cms) ATOMGROUP_PREFIX (schrodinger.application.desmond.cms.Cms attribute) AtomGroupData (class in schrodinger.application.matsci.clusterstruct) AtomGroupDelegate (class in schrodinger.application.desmond.gui) AtomGroupFrame (class in schrodinger.application.desmond.gui) AtomGroupModel (class in schrodinger.application.desmond.gui) AtomGroupRow (class in schrodinger.application.desmond.gui) atomic_copyfile() (in module schrodinger.utils.fileutils) atomic_number (schrodinger.structure.StructureAtom property) ATOMIC_SYMBOL (schrodinger.application.matsci.nano.constants.Constants attribute) ATOMIC_SYMBOLS (in module schrodinger.application.matsci.atomicsymbols) atomic_weight (schrodinger.application.matsci.atom_group.MSAtom property) (schrodinger.structure.StructureAtom property) ATOMICAVG (schrodinger.application.jaguar.constants.CalcType attribute) AtomicMassUnit (schrodinger.application.jaguar.constants.Unit attribute) atomicsec() (in module schrodinger.application.jaguar.textparser) AtomInfoToolbar (class in schrodinger.ui.qt.navtoolbar) AtomLabelAnnotator (class in schrodinger.ui.qt.structure2d) AtomListEnumerable (class in schrodinger.application.scaffold_enumeration.atomlist) AtomListInfo (class in schrodinger.application.scaffold_enumeration.atomlist) AtomNameLabelValidator (class in schrodinger.application.matsci.atomicsymbolsgui) AtomNameWidgetItem (class in schrodinger.application.matsci.mswidgets) AtomNumberAnnotator (class in schrodinger.ui.qt.structure2d) AtomPair (class in schrodinger.application.bioluminate.antibody.assembly) atomPicked() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) atomPropChanged() (schrodinger.ui.two_d_viewer.TwoDViewer method) atomPropDialog() (schrodinger.ui.two_d_viewer.TwoDViewer method) atomPropertyChanged (schrodinger.ui.two_d_viewer.AtomPropertyDialog attribute) AtomPropertyDialog (class in schrodinger.ui.two_d_viewer) atoms properties atoms (schrodinger.application.bioluminate.protein.protein.Consensus property) ATOMS (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) atoms (schrodinger.application.jaguar.utils.ScanCoord attribute) ATOMS (schrodinger.application.matsci.packmol.PackmolKw attribute) atoms (schrodinger.application.scaffold_enumeration.cxsmiles.MCG attribute) (schrodinger.application.scaffold_enumeration.cxsmiles.SRU attribute) (schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup attribute) (schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup attribute) atoms() (schrodinger.application.glide.glide.MetalConstraint method) atoms_in_ring() (in module schrodinger.application.jaguar.autots_bonding) atomsasl() (in module schrodinger.application.prepwizard) atomsColorChanged (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel attribute) atomsel() (schrodinger.application.desmond.enhsamp.ASLObject method) AtomSelectionDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) atomSelectionDialogAboutToBeShown (schrodinger.ui.qt.atomselector.AtomSelector attribute) atomSelectionDialogDismissed (schrodinger.ui.qt.atomselector.AtomSelector attribute) AtomSelector (class in schrodinger.ui.qt.atomselector) AtomsInRingError (class in schrodinger.structure) AtomsTable (class in schrodinger.application.matsci.kmc) AtomTLS2UIJ() (in module schrodinger.application.matsci.gsas.GSASIImath) atomToLigNumMapping() (schrodinger.ui.qt.ligand_list.LigandListModel method) AtomType (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) AtomTyper (class in schrodinger.application.bindingsite.atomtyping) AtomTypes (class in schrodinger.application.phase.packages.shape_generator) atomTypingCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) AtomTypingFailure AtomWeight (class in schrodinger.ui.qt.atom_weights_table_widget) AtomWeightsSettings (class in schrodinger.ui.qt.atom_weights_table_widget) AtomWeightsSpec (class in schrodinger.ui.qt.atom_weights_table_widget) AtomWeightsTableWidget (class in schrodinger.ui.qt.atom_weights_table_widget) AtomWeightsWidget (class in schrodinger.ui.qt.atom_weights_table_widget) ats (schrodinger.application.desmond.msj_generator.workflow_params.MapperParams attribute) attach_atom_dict_to_structures() (schrodinger.application.jaguar.output.JaguarOutput method) attach_fragment() (in module schrodinger.structutils.build) attach_structure() (in module schrodinger.structutils.build) attachCap() (schrodinger.protein.captermini.CapTermini method) attachment_data_map (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) attachment_items (schrodinger.application.livedesign.export_models.AttachmentData attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) attachment_itemsChanged (schrodinger.application.livedesign.export_models.AttachmentData attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) attachment_itemsReplaced (schrodinger.application.livedesign.export_models.AttachmentData attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) AttachmentAtoms (class in schrodinger.application.matsci.amorphous) AttachmentData (class in schrodinger.application.livedesign.export_models) AttachmentExportTask (class in schrodinger.application.livedesign.export_tasks) AttachmentItem (class in schrodinger.application.livedesign.export_models) AttachmentPoint (class in schrodinger.application.combiglide.corehop) AttachmentTaskInput (class in schrodinger.application.livedesign.export_models) AttachmentTaskOutput (class in schrodinger.application.livedesign.export_models) attachSidechains() (schrodinger.structutils.rgroup_enumerate.RGroupEnumerator method) attempt_ccd_assignment() (in module schrodinger.structutils.ccd) attempt_tripeptide_mutation() (in module schrodinger.protein.process_enamine_db) ATTRACTION (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) AttributableType (class in schrodinger.models.json) AttributeSettingWrapper (class in schrodinger.ui.qt.appframework2.settings) AttrTargetSpec (class in schrodinger.models.mappers) ATYPE_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) AU_TO_KG (schrodinger.application.desmond.constants.Conversion attribute) audit_changes() (in module schrodinger.livedesign.preprocessor) authentication_mode (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) authentication_modeChanged (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) authentication_modeReplaced (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) AuthenticationException AuthenticationMode (class in schrodinger.application.livedesign.login_gui2) authSocketPath (schrodinger.job.server.ServerInfo attribute) AUTO (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PickingModes attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) (schrodinger.ui.qt.schart.SChart attribute) AUTO_DETECT (schrodinger.rdkit_extensions.Format attribute) auto_int() (in module schrodinger.application.desmond.starter.ui.cmdline) auto_partition() (in module schrodinger.application.desmond.autopartition) auto_register_files() (in module schrodinger.tasks.queue) auto_size (schrodinger.ui.qt.table.DataViewerTable attribute) AUTO_TASKDIR (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.TaskDirSetting attribute) AUTO_TOOLTIP (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) auto_update_model (schrodinger.models.mappers.TargetMixin attribute) (schrodinger.models.mappers.TargetParamMapper property) (schrodinger.models.mappers.TargetSpec property) auto_update_target (schrodinger.models.mappers.TargetMixin attribute) (schrodinger.models.mappers.TargetParamMapper property) (schrodinger.models.mappers.TargetSpec property) AutoColorCarbons (class in schrodinger.application.bioluminate.pml_menus) AutoColorObjects (class in schrodinger.application.bioluminate.pml_menus) AutoColorSubMenu (class in schrodinger.application.bioluminate.pml_menus) AUTOCORRELATION (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) autocorrelation() (schrodinger.application.matsci.permittivity.MdPostAnalysis static method) AUTOCORRELATION_FILE_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) AUTOCORRELATION_LABELS (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) autocorrelationWithSum() (schrodinger.application.matsci.permittivity.MdPostAnalysis static method) AutoCycleCarbonColor (class in schrodinger.application.bioluminate.pml_menus) AutoCycleColor (class in schrodinger.application.bioluminate.pml_menus) AutoFileMode (class in schrodinger.tasks.queue) autoMap() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) AutomatedCGMapping (class in schrodinger.application.matsci.automated_cg_mapping) Automatic (schrodinger.application.jaguar.gui.utils.SpinTreatment attribute) AUTOMATIC_BAND (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) AutomaticJobnameMixin (class in schrodinger.application.jaguar.gui.base_panel) autoname_tasks() (in module schrodinger.tasks.queue) autoPlace() (schrodinger.protein.membrane.Membrane_Model method) autoPlaceByMolecule() (schrodinger.protein.membrane.Membrane_Model method) autoprojectsync_call() (in module schrodinger.application.desmond.maestro) AutoQSAR (class in schrodinger.application.matsci.genetic_optimization) autoResize() (schrodinger.ui.qt.structtable.ViewerTable method) autoset_axis_range() (in module schrodinger.ui.qt.smatplotlib) autoSetGpuList() (schrodinger.tasks.hosts.Host method) AUTOTS_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) AutoTSAtomClassConflict AutoTSAtomMapper (class in schrodinger.application.jaguar.autots_rmsd) AutoTSInput (class in schrodinger.application.jaguar.autots_input) AutoTSInvalidConstraintError AutoTSStructureReader (class in schrodinger.application.jaguar.autots_bonding) AutoTSTemplateAtomMapper (class in schrodinger.application.jaguar.autots_rmsd) AV2Q() (in module schrodinger.application.matsci.gsas.GSASIImath) AV_ERROR_MSG (schrodinger.ui.qt.swidgets.SLineEdit attribute) available_color_schemes() (in module schrodinger.structutils.color) available_tokens() (schrodinger.application.licensing.licadmin.LicenseResource method) AVdeg2Q() (in module schrodinger.application.matsci.gsas.GSASIImath) AVE_CELL (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.permittivity.AveCellAnalysis attribute) AveCellAnalysis (class in schrodinger.application.matsci.permittivity) AveCellMSJStringer (class in schrodinger.application.matsci.desconfig) AVECTOR (schrodinger.application.matsci.kmc.SchrodingerTable attribute) AVERAGE (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) average_cavity() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) average_cavity_cns() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) AVERAGE_CELL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) average_energy() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) average_hbond() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) AVERAGE_JEFF (schrodinger.application.matsci.kmc.SchrodingerTable attribute) averageable (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) averageAndSort() (schrodinger.application.matsci.coarsegrain.Internals method) AverageCell (class in schrodinger.application.desmond.stage.app.matsci) averageGangedColumnWidth() (schrodinger.ui.qt.table.DataViewerTable method) averageGangedRowHeight() (schrodinger.ui.qt.table.DataViewerTable method) avg_n_hydrox (schrodinger.application.bioluminate.methionine_oxidation.MdStats attribute) avg_n_waters (schrodinger.application.bioluminate.methionine_oxidation.MdStats attribute) avg_property_key (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) avg_sasa (schrodinger.application.bioluminate.methionine_oxidation.HmcStats attribute) (schrodinger.application.bioluminate.methionine_oxidation.MdStats attribute) avgAnionAnionShortDistance() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgAtomicVol() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgElementAnionShortDistance() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgElementNeighborCount() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgInternals() (schrodinger.application.matsci.coarsegrain.Internals method) avgNeighborCount() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgNeighborIon() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgShortDistance() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgSublatticeEneg() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgSublatticeNeighborCount() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) avgSublatticeNeighborIon() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) AVPAslOption (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data) AXES (schrodinger.application.matsci.amorphous.Box attribute) (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.ui.qt.schart.SChart attribute) AxesDialog (class in schrodinger.ui.qt.schart) AXIS (class in schrodinger.application.matsci.nano.xtal) AXIS_COL (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame attribute) axis_units (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) axisChanged() (schrodinger.application.matsci.density_analysis_widget.DensityTab method) AxisData (class in schrodinger.application.matsci.kmc) AxisParams (class in schrodinger.ui.qt.schart)

B

B (schrodinger.protein.annotation.TCRRegionLabel attribute) b (schrodinger.seam.examples.active_learning_weigher.LinearRegressionModel attribute) B (schrodinger.ui.qt.mapperwidgets.param_editor.MyEnum attribute) B3LYP (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) B_FACTOR (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) b_factor (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) B_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) B_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) back() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) back_substitution_int() (in module schrodinger.application.matsci.cctbx.rot_mx) back_transparency (schrodinger.surface.Surface property) BACKBONE (schrodinger.application.desmond.constants.ConfRestraintType attribute) backbone_dihedrals (in module schrodinger.protein.analysis_params) BACKBONE_INTERACTION (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) BACKBONE_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) BACKBONE_SUFFIX (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner attribute) backboneAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) BackboneDihedral (class in schrodinger.ui.qt.rama) BackButton (class in schrodinger.application.job_monitor.buttons) backClicked() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) Backend (class in schrodinger.active_learning.mq_backend) backend() (schrodinger.job.app.App method) BACKEND_ERROR (schrodinger.application.desmond.cmj.JobStatus attribute) backend_name (schrodinger.protein.tasks.pfam.PfamTask attribute) BACKEND_SINGLE_LETTER_CODE_TO_KINASE_FEATURE (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) background_color (schrodinger.livedesign.draw.ImageGenOptions attribute) BackgroundColors (class in schrodinger.ui.qt.standard.design_tokens) backtrack() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) BacktrackingFailed backup_file() (in module schrodinger.job.queue) backup_files() (in module schrodinger.application.desmond.multisimstartup) backup_trajectories() (in module schrodinger.application.desmond.stage.simulate) backupFile() (in module schrodinger.trajectory.prody.writenmd) BACKWARD (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Direction attribute) BackwardsReader (class in schrodinger.pipeline.pipeutils) BAD (schrodinger.application.desmond.fep_edge_data_classifier.Rating attribute) BAD_INTERNALS (schrodinger.application.jaguar.constants.FatalErrors attribute) BadLDAPInputException BadLicenseInput balance_alie_precision (schrodinger.application.jaguar.results.JaguarResults attribute) balance_charge() (in module schrodinger.application.matsci.desmondutils) balance_esp_precision (schrodinger.application.jaguar.results.JaguarResults attribute) Bale (class in schrodinger.seam.examples.haystack) ball_atom() (in module schrodinger.application.desmond.maestro) (schrodinger.application.desmond.maestro.Workspace method) BandshapeSpectrumFile (class in schrodinger.application.matsci.bandshape_utils) BAndSPreset (class in schrodinger.application.bioluminate.pml_menus) BandStructure (class in schrodinger.application.matsci.espresso.qeoutput) BandsType (class in schrodinger.application.matsci.espresso.qeinput) bannerClosed (schrodinger.ui.qt.utils.MaestroPythonBannerManager attribute) BAR (schrodinger.ui.qt.schart.SeriesParams attribute) BAR_PADDING (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListPopUp attribute) baroMethodChanged() (schrodinger.application.desmond.gui.EnsembleTab method) BarrierCalculationError BarrierHeader (class in schrodinger.application.matsci.desconfig) BarrierInfo (class in schrodinger.application.matsci.desconfig) BarSeriesParams (class in schrodinger.ui.qt.schart) BarSeriesSizeSpinBox (class in schrodinger.ui.qt.schart) barsHovered() (schrodinger.ui.qt.schart.SChart method) Base3DExportSpec (class in schrodinger.application.livedesign.export_models) base64_decode_fd() (in module schrodinger.application.phase.packages.oned_task_utils) base64_encode_fd() (in module schrodinger.application.phase.packages.oned_task_utils) BASE_10 (schrodinger.ui.qt.schart.SChart attribute) BASE_ATOM_GROUP (schrodinger.application.matsci.atom_group.HelixGroups attribute) (schrodinger.application.matsci.atom_group.MSAtomGroupsBase attribute) BASE_ATOM_TYPE (schrodinger.application.matsci.atom_group.HelixArcAtomGroup attribute) (schrodinger.application.matsci.atom_group.MSAtomGroup attribute) base_evaluator() (in module schrodinger.application.matsci.genetic_optimization) base_file_dialog() (in module schrodinger.ui.qt.filedialog) base_functional() (in module schrodinger.application.jaguar.utils) base_per_turn (schrodinger.application.matsci.atom_group.HelixData attribute) base_schedule (class in schrodinger.application.matsci.gsas.GSASIImath) BaseAlignment (class in schrodinger.protein.alignment) BaseAnalysisGui (class in schrodinger.application.matsci.appbase) BaseArgs (class in schrodinger.application.desmond.starter.ui.cmdline) BaseAtomMapper (class in schrodinger.comparison.atom_mapper) BaseBottomBar (class in schrodinger.ui.qt.appframework2.af2) BaseCacheData (class in schrodinger.application.matsci.cache) BaseCriterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) BaseCsvMolReader (class in schrodinger.rdkit.molio) BaseDatabaseManager (class in schrodinger.application.matsci.kmc) BaseDatabaseManager.Cursor (class in schrodinger.application.matsci.kmc) BaseDecorator (class in schrodinger.application.steps.enumerators) BaseDecorator.Settings (class in schrodinger.application.steps.enumerators) BaseDesmondStep (class in schrodinger.application.matsci.jwsteps) BaseDialog (class in schrodinger.ui.qt.basewidgets) BaseDipoleAnalysis (class in schrodinger.application.matsci.permittivity) BaseDipoleAnalysis.SysDipole (class in schrodinger.application.matsci.permittivity) basedir() (schrodinger.utils.installation_check.TestJobDJ method) BaseDriverTask (class in schrodinger.tasks.drivers) BaseEntryData (class in schrodinger.application.livedesign.entry_types) BaseFeaturizer (class in schrodinger.application.matsci.mlearn.base) BaseFepMsjGenerator (in module schrodinger.application.desmond.msj_generator.common) BaseHitAlignTask (class in schrodinger.protein.tasks.hit_align) BaseHitAlignTask.Input (class in schrodinger.protein.tasks.hit_align) BaseHitAlignTask.Output (class in schrodinger.protein.tasks.hit_align) BaseInvalidAntibodyCSVError BaseJaguarPanel (class in schrodinger.application.jaguar.gui.base_panel) BaseJob (class in schrodinger.job.queue) BaseLDTreeItemWrapper (class in schrodinger.application.livedesign.panel_components) BaseLiveReportSelectionPopup (class in schrodinger.application.livedesign.panel_components) BaseMaestroSync (class in schrodinger.maestro_utils.maestro_sync) BaseMapper (class in schrodinger.application.matsci.automated_cg_mapping) BaseMapperParams (class in schrodinger.application.desmond.msj_generator.workflow_params) BaseMergeHandler (class in schrodinger.rdkit.molio) BaseMetaJaguarWorkflowStep (class in schrodinger.application.matsci.jwsteps) BaseMixinCollection (class in schrodinger.ui.qt.widgetmixins.basicmixins) BaseMoiety (class in schrodinger.application.matsci.amorphous) BaseMsjGenerator (class in schrodinger.application.desmond.msj_generator.common) (class in schrodinger.application.desmond.msj_generator.subjob_msj) BaseMutableParam (class in schrodinger.models.parameters) basename_no_ext() (in module schrodinger.application.prime.wrapper) BaseNoJobStep (class in schrodinger.application.matsci.jwsteps) BaseOptionsDialog (class in schrodinger.ui.qt.basewidgets) BaseOptionsPanel (class in schrodinger.ui.qt.appframework2.settings) BasePanel (class in schrodinger.ui.qt.appframework2.baseapp) basepath (schrodinger.application.matsci.espresso.utils.PPSpecies attribute) BasePfxMolReader (class in schrodinger.rdkit.molio) BasePlotFrame (class in schrodinger.application.matsci.density_analysis_widget) BasePrimeAlignment (class in schrodinger.application.prime.wrapper) BaseReceptorLigandData (class in schrodinger.application.livedesign.entry_types) BaseRecognizer (class in schrodinger.application.desmond.antlr3.recognizers) BaseRelaxationStep (class in schrodinger.application.matsci.jwsteps) BaseResidueFilter (class in schrodinger.application.bioluminate.pose_filtering.residue_filter) BaseSearchTreeWidgetHelper (class in schrodinger.application.livedesign.panel_components) BaseSelectionPopUp (class in schrodinger.application.livedesign.panel_components) BaseSignature (class in schrodinger.application.matsci.species) BaseSpinnerWidget (class in schrodinger.application.desmond.feputils) BaseSquareAnnotator (class in schrodinger.ui.qt.structure2d) BaseStep (class in schrodinger.application.matsci.jwsteps) BaseStructureExportTask (class in schrodinger.application.livedesign.export_tasks) BaseStructureExportTask.Output (class in schrodinger.application.livedesign.export_tasks) BaseStructureExportTask86 (class in schrodinger.application.livedesign.export_tasks) BaseSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab) (class in schrodinger.application.jaguar.gui.tabs.properties_tab) BaseTab (class in schrodinger.application.jaguar.gui.tabs.base_tab) BaseTable (class in schrodinger.ui.qt.appframework2.debugwidgets) BaseTemplateListWidgetItem (class in schrodinger.application.matsci.builderwidgets) BaseTextValidator (class in schrodinger.ui.qt.appframework2.validators) BaseTree (class in schrodinger.application.desmond.antlr3.tree) BaseTreeAdaptor (class in schrodinger.application.desmond.antlr3.tree) BaseWidget (class in schrodinger.ui.qt.basewidgets) BaseWizardPanel (class in schrodinger.ui.qt.appframework2.wizards) BaseWorkflow (class in schrodinger.application.matsci.jwsteps) BaseWorkflowFinderDialog (class in schrodinger.application.matsci.wfmanagement) Basic (schrodinger.protein.helm.helm_renderer.HexColor attribute) BASIC (schrodinger.trajectory.trajectory_gui_dir.playback_settings.Tab attribute) basic_windows_path() (in module schrodinger.application.jaguar.utils) BasicHydrophilic (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) BasicStatsAccumulator (class in schrodinger.application.phase.packages.oned_task_utils) Basis (class in schrodinger.application.jaguar.gui.input_tab_widgets) (class in schrodinger.application.jaguar.nmr_basis) BASIS (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) basis (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) BASIS (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) basis_changed (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin attribute) basis_is_supported_for_functional() (in module schrodinger.application.jaguar.jaguar_keyword_utils) basis_of_invariant() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method) basis_of_mirror_plane_with_normal() (in module schrodinger.application.matsci.cctbx.rot_mx) basis_set() (in module schrodinger.application.jaguar.textparser) basis_set_is_valid() (in module schrodinger.application.jaguar.workflow_validation) basisChanged (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) basisFiltersChanged (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView attribute) basisModel() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) basisname_in_list() (in module schrodinger.application.jaguar.jaguar_keyword_utils) BasisSelector (class in schrodinger.application.jaguar.gui.basis_selector) BasisSelectorFilterList (class in schrodinger.application.jaguar.gui.input_tab_widgets) BasisSelectorFilterListToolButton (class in schrodinger.application.jaguar.gui.basis_selector) BasisSelectorFilterPopUp (class in schrodinger.application.jaguar.gui.basis_selector) BasisSelectorLineEdit (class in schrodinger.application.jaguar.gui.basis_selector) BasisSet (class in schrodinger.application.jaguar.basis) BasisSetColumns (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) BasisSetListWidgetItem (class in schrodinger.application.jaguar.gui.basis_selector) BasisSetModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetProxyModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetSelector (class in schrodinger.application.matsci.jagwidgets) BasisSetSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set) BasisSetTableView (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSizeException BasisType (class in schrodinger.application.matsci.espresso.qeinput) batchFinished (schrodinger.application.glide.http_client.NonBlockingGlideServerManager attribute) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) BatchId (schrodinger.job.jobcontrol.Job property) BatchSettings (class in schrodinger.stepper.stepper) BB (schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE attribute) BB_TASK (in module schrodinger.application.bb_database.bb_arg_utils) BBModifiedPhosphateMonomerItem (class in schrodinger.protein.helm.helm_renderer) BBModifiedSugarMonomerItem (class in schrodinger.protein.helm.helm_renderer) BBPhosphateMonomerBase (class in schrodinger.protein.helm.helm_renderer) BBStandardPhosphateMonomerItem (class in schrodinger.protein.helm.helm_renderer) BBStandardSugarMonomerItem (class in schrodinger.protein.helm.helm_renderer) BBSugarMonomerBase (class in schrodinger.protein.helm.helm_renderer) BBValidationError BC_EFIELD_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) BC_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) bc_type (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) BC_W_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) bcc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) bctet1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) bctet2() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) BDEStep (class in schrodinger.application.matsci.jwsteps) bead_graph (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.BEAD_TYPE attribute) bead_names (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.NODE_GROUP_TYPE attribute) bead_nums (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.NODE_GROUP_TYPE attribute) beads (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.BEAD_TYPE attribute) becomeRoot() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) BedrocScreener (class in schrodinger.application.phase.packages.bedroc_screener) BEFORESUPERPOSITION (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) beginBacktrack() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) beginGroup() (schrodinger.utils.preferences.Preferences method) beginResync() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) BEHIND (schrodinger.application.matsci.nano.xtal.PBCBond attribute) BehindMonomer (schrodinger.protein.helm.helm_renderer.ZOrder attribute) Benchmark (class in schrodinger.seam.testing.benchmarks) BenchmarkResult (class in schrodinger.seam.testing.benchmarks) bend_conj_amines (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) BEND_TOLERANCE (schrodinger.application.matsci.atom_group.HelixArcAtomGroup attribute) bennett() (schrodinger.application.desmond.bennett.CalcBAR method) BessIn() (in module schrodinger.application.matsci.gsas.GSASIImath) BessJn() (in module schrodinger.application.matsci.gsas.GSASIImath) best_scoring_element() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) BestPoseFilter (class in schrodinger.application.glide.sort_utils) beta (schrodinger.application.bioluminate.tcr.docking_angles.TcrChainIds attribute) BETA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) beta_au() (in module schrodinger.application.jaguar.utils) beta_fdpolar() (in module schrodinger.application.jaguar.textparser) beta_homo_lumo_energy() (in module schrodinger.application.mopac.results_main) beta_kcalmol() (in module schrodinger.application.jaguar.utils) BETA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) beta_mix (schrodinger.application.jaguar.input.MixedPairs attribute) BETA_ORBITALS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) BETA_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) beta_polar() (in module schrodinger.application.jaguar.textparser) beta_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute) beta_somo_lumo_energy() (in module schrodinger.application.mopac.results_main) BETA_STRAND_PROPENSITY (class in schrodinger.protein.residue) beta_strand_propensity (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) betaij2Uij() (in module schrodinger.application.matsci.gsas.GSASIIlattice) BetaproPredictor (class in schrodinger.protein.predictors) BetaproPredictor.Input (class in schrodinger.protein.predictors) BETTER_LABELS (schrodinger.ui.qt.navtoolbar.SchrodingerSubplotTool attribute) BETWEEN (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericOperator attribute) beyondBindingSiteChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) BFactorPreset (class in schrodinger.application.bioluminate.pml_menus) BFGS (class in schrodinger.application.matsci.mecp_mod) BFR (schrodinger.protein.annotation.TCRRegionLabel attribute) BG_CMD (schrodinger.application.desmond.stage.prepare.structure.BuildGeometry attribute) bias (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) BIAS_FACTOR (schrodinger.application.desmond.kinetics.enhanced_sampling.MtdOption attribute) BIDENTATE (in module schrodinger.application.matsci.buildcomplex) BilayerInputFile (class in schrodinger.application.matsci.packmol) BILAYERSEP (schrodinger.application.matsci.nano.constants.Constants attribute) BILAYERSHIFT (schrodinger.application.matsci.nano.constants.Constants attribute) BilinearHistogramData (class in schrodinger.application.matsci.uq_utils) bin_b_factors() (in module schrodinger.application.bioluminate.pml_menus) bin_by_geometry() (in module schrodinger.application.matsci.reaction_workflow_utils) bin_structures_by_property() (in module schrodinger.application.matsci.reaction_workflow_utils) BinaryThreadSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) Bind (class in schrodinger.application.desmond.enhsamp) bind() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) BIND_PROP (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae attribute) binding (class in schrodinger.application.desmond.enhsamp) BINDING (schrodinger.application.desmond.constants.PhysicalLegTypes attribute) (schrodinger.application.desmond.constants.SystemType attribute) BINDING_SITE (class in schrodinger.protein.annotation) binding_site_cutoff (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) binding_site_cutoffChanged (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) binding_site_cutoffReplaced (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) binding_site_residues (schrodinger.protein.annotation.ProteinSequenceAnnotations property) binding_sites (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) BindingSiteAligner (class in schrodinger.structutils.sitealign) BindingSiteAlignmentTask (class in schrodinger.protein.tasks.binding_site_align) BindingSiteAlignmentTask.Input (class in schrodinger.protein.tasks.binding_site_align) BindingSiteAlignmentTask.Output (class in schrodinger.protein.tasks.binding_site_align) BINS (schrodinger.ui.qt.schart.BinsDialog attribute) (schrodinger.ui.qt.schart.SChart attribute) binsChanged (schrodinger.ui.qt.schart.SHistogramBarSeries attribute) BinsDialog (class in schrodinger.ui.qt.schart) bio_class (schrodinger.livedesign.biologics.registration.BioPolymer property) BioPolymer (class in schrodinger.livedesign.biologics.registration) BiopythonPairwiseAligner (class in schrodinger.protein.align) BiounitOverrunError biounits_from_structure() (in module schrodinger.protein.biounit) BISPECIFIC (schrodinger.application.bioluminate.antibody.io.csv_reader.ModelingMode attribute) BISPECIFIC_ANTIBODY (schrodinger.livedesign.entity_type.EntityClass attribute) BIT_EXT (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute)

bitCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) bitscore (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) Bitset (class in schrodinger.infra.mmbitset) bitset_to_list() (in module schrodinger.utils.multifpfile) bitSetOff() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) bitSetOn() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) Black (schrodinger.protein.helm.helm_renderer.HexColor attribute) BLACK (schrodinger.ui.qt.standard.colors.NativeColors attribute) (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) BlameSidError BLANK_PATTERN (schrodinger.application.matsci.rxn_channel.ChannelDefinitions attribute) BlankableSpinBox (class in schrodinger.application.jaguar.gui.input_tab_widgets) BlankableSpinBoxDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) BlankDebugEventListener (class in schrodinger.application.desmond.antlr3.debug) BLAST (schrodinger.protein.tasks.blast.BlastAlgorithm attribute) BlastAlgorithm (class in schrodinger.protein.tasks.blast) BlastDatabase (class in schrodinger.protein.tasks.blast) BlastSettings (class in schrodinger.protein.tasks.blast) BlastTask (class in schrodinger.protein.tasks.blast) BlastTask.Input (class in schrodinger.protein.tasks.blast) bld_align_file (schrodinger.application.bioluminate.antibody.grafting.GraftingInput property) bld_scaffold_file (schrodinger.application.bioluminate.antibody.grafting.GraftingInput property) BlenResCW() (in module schrodinger.application.matsci.gsas.GSASIIElem) BlenResTOF() (in module schrodinger.application.matsci.gsas.GSASIIElem) BlindedCompoundError BLKSIZE (schrodinger.pipeline.pipeutils.BackwardsReader attribute) blobs() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) Block (class in schrodinger.application.desmond.simulation_block_test) block() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) BLOCK_NAME (schrodinger.application.prime.residue_interaction.InteractionReader attribute) block_signal_propagation() (schrodinger.models.parameters.CompoundParam method) BlockingFunctionTask (class in schrodinger.tasks.tasks) BlockingMixin (class in schrodinger.tasks.tasks) BLOSUM45 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) BLOSUM62 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) BLOSUM80 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) BODY (schrodinger.application.desmond.kinetics.enhanced_sampling.MExpressionSection attribute) bodyToNode() (in module schrodinger.application.desmond.enhsamp) Bohr (schrodinger.application.jaguar.constants.Unit attribute) BOLD (schrodinger.application.phase.phase_markers.FontStyles attribute) (schrodinger.ui.qt.standard.design_tokens.FontWeights attribute) BOLD_ITALIC (schrodinger.application.phase.phase_markers.FontStyles attribute) BOLTZMANN (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor attribute) boltzmann_probability() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) BOLTZMANN_TIP (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor attribute) Bond (class in schrodinger.application.jaguar.hess_guess) BOND (schrodinger.application.matsci.rxn_path.Coord attribute) bond (schrodinger.structure.Structure attribute) (schrodinger.structure.StructureAtom property) BOND_A (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) BOND_B (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) bond_clicked (schrodinger.ui.qt.structure2d.structure_view attribute) bond_crossover() (in module schrodinger.application.matsci.genetic_optimization) BOND_ENERGY (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) bond_in_ring() (in module schrodinger.application.canvas.r_group) bond_iter() (schrodinger.structure._StructureBondContainer static method) bond_iterator() (in module schrodinger.structutils.analyze) bond_length_cache (schrodinger.application.matsci.amorphous.BaseMoiety attribute) bond_order (schrodinger.structutils.rgroup_enumerate.RGroup attribute) BOND_ORDERS_CHOICES (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BOND_ORDERS_DEFAULT (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BOND_SMARTS (schrodinger.application.steps.enumerators.FastFragmenter attribute) bond_stretch_energy() (in module schrodinger.application.qsite.output) bond_total (schrodinger.structure.StructureAtom property) BondCharge (class in schrodinger.application.jaguar.results) bondchg_repulsion_energy() (in module schrodinger.application.qsite.output) BondDistortion (class in schrodinger.structutils.check) bonded_atoms (schrodinger.structure.StructureAtom property) bonded_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) bonded_div (schrodinger.application.desmond.fep_schedule.FepSchedule attribute) (schrodinger.application.desmond.fep_schedule.FepSchemeMixIn attribute) (schrodinger.application.desmond.fep_schedule.FepSchemeSuperquickchargeMixIn attribute) bondedA (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property) (schrodinger.application.desmond.fep_schedule.FepScheduleBinding property) bondedAtomIdInSameRes() (schrodinger.application.matsci.amorphous.PolymerFragments method) bondedB (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property) (schrodinger.application.desmond.fep_schedule.FepScheduleBinding property) BondEnergies (class in schrodinger.application.matsci.fragments) BondError BONDI_PCM_RADII (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) BONDING_CHOICES (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BONDING_DEFAULT (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BONDLENGTH (schrodinger.application.matsci.nano.constants.Constants attribute) bondLigandsToMetal() (schrodinger.application.matsci.sculptcomplex.Sculptor method) bondMatchingEdges() (schrodinger.application.matsci.nano.tube.NanoTube method) BondOrderMismatch bondPair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) BONDPENALTYTHRESH (schrodinger.application.matsci.rxn_path.ReactionPath attribute) bondRemainingNodes() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) bondRingPlaneIntersection() (schrodinger.structutils.ringspear.SpearRing method) BondRotator (class in schrodinger.application.desmond.torsion_related) bonds properties bonds (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction attribute) (schrodinger.application.jaguar.hess_guess.CoordinateManager property) (schrodinger.application.jaguar.utils.LewisStructure attribute) (schrodinger.structutils.markush_enumerate.PlaceHolder attribute) bondToH() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) BondType (class in schrodinger.structure) BONDWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) BoolCriterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) boolean() (in module schrodinger.utils.sea.common) BooleanDatabaseCriterion (class in schrodinger.application.bioluminate.propfilter) BoolOperator (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) BoolParam (class in schrodinger.models.parameters) boot() (schrodinger.application.desmond.cmj.Engine method) boot_setup() (schrodinger.application.desmond.cmj.Engine method) bootstrap() (in module schrodinger.application.desmond.bennett) BootstrapNoiseHistogramData (class in schrodinger.application.matsci.uq_utils) bootstrapped_solvation_free_energy() (in module schrodinger.application.desmond.solubility_utils) BorderColors (class in schrodinger.ui.qt.standard.design_tokens) BorderlessPopUpFrame (class in schrodinger.ui.qt.utils) BorderSizes (class in schrodinger.ui.qt.standard.design_tokens) BORESCH_RESTRAINT (schrodinger.application.desmond.constants.CorrectionTerm attribute) both_bond_types_exist() (in module schrodinger.application.matsci.nano.xtal) BOTTOM (schrodinger.application.desmond.constants.SidedError attribute) (schrodinger.ui.qt.schart.SChart attribute) (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) bottom_axis (schrodinger.ui.qt.schart.SChart property) BOTTOM_DATOR (schrodinger.application.matsci.deswidgets.DesmondMDWEdit attribute) BottomBar (class in schrodinger.ui.qt.appframework2.af2) BottomButtonMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) BottomButtonMixin.BtnPos (class in schrodinger.ui.qt.widgetmixins.basicmixins) BottomButtonMixin.StdBtn (class in schrodinger.ui.qt.widgetmixins.basicmixins) BOUND (schrodinger.application.desmond.kinetics.utils.MtdStatus attribute) bound_hydrogen() (in module schrodinger.application.jaguar.autots_bonding) BoundaryType (class in schrodinger.application.matsci.espresso.qeinput) boundingBoxCallback() (schrodinger.graphics3d.common.Group method) BoundingInformation() (in module schrodinger.analysis.visanalysis.volumedatastructureutils) BoundingInformationL() (in module schrodinger.analysis.visanalysis.volumedatastructureutils) boundingRect() (schrodinger.application.dendrogram.gradientSelector.ColorSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) (schrodinger.ui.qt.schart.Callout method) (schrodinger.ui.qt.structure2d.structure_item method) Box (class in schrodinger.application.matsci.amorphous) BOX (schrodinger.application.matsci.packmol.PackmolKw attribute) box() (schrodinger.application.watermap.shapes.ShapeFactory method) BOX11 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX12 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX13 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX21 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX22 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX23 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX31 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX32 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX33 (schrodinger.application.matsci.kmc.FramesTable attribute) box_letter() (in module schrodinger.protein.residue) box_strucs (schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent property) BoxSize (class in schrodinger.application.desmond.simulation_block_test) BoxWithInnerHull (class in schrodinger.application.matsci.amorphous) BqQueryStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) bracket() (in module schrodinger.application.jaguar.qrnn.temp_opt) bracket_zeros() (in module schrodinger.application.jaguar.discretized_1d_function) break_infinite_segment() (in module schrodinger.application.matsci.graph) BREAK_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) BreakingBond (class in schrodinger.application.matsci.fragments) breakIntoFragments() (schrodinger.application.matsci.amorphous.PolymerFragments method) breakIntoMols() (schrodinger.application.matsci.amorphous.PolymerFragments method) breakSeqIntoLoops() (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportWriter method) breakTemplatePolymer() (schrodinger.application.matsci.amorphous.Monomer method) Brent (class in schrodinger.application.jaguar.qrnn.temp_opt) brent() (in module schrodinger.application.jaguar.qrnn.temp_opt) brokenBonds() (schrodinger.application.pathfinder.route.RouteNode method) BROWNIAN_DYNAMICS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) BROWNIE (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) BROWNIE_MINIMIZE (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) brownie_minimize (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) BrownieMSJStringer (class in schrodinger.application.matsci.desconfig) BROWSE (schrodinger.ui.qt.recent_completer.BrowseAndCreateStringModel attribute) (schrodinger.ui.qt.recent_completer.BrowseStringModel attribute) browse() (schrodinger.application.desmond.cwidget.FileEntry method) (schrodinger.application.pymol.pymol4maestro.panel method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) BrowseAndCreateCombo (class in schrodinger.ui.qt.recent_completer) BrowseAndCreateStringModel (class in schrodinger.ui.qt.recent_completer) browseDirectory() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) browseFiles() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) (schrodinger.ui.qt.input_selector.InputSelector method) BrowsePlaceholderRecentCombo (class in schrodinger.ui.qt.recent_completer) browseSelected (schrodinger.ui.qt.recent_completer.BrowseAndCreateCombo attribute) (schrodinger.ui.qt.recent_completer.BrowsePlaceholderRecentCombo attribute) BrowseStringModel (class in schrodinger.ui.qt.recent_completer) browseSystemFile() (schrodinger.application.desmond.gui.InputGroup method) brute() (in module schrodinger.application.jaguar.qrnn.temp_opt) BS (schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE attribute) BubbleTextItem (class in schrodinger.ui.qt.protein_health_viewer) buffer_width (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) build() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) (schrodinger.application.matsci.reportutils.PDFBuilder method) build_ab() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) build_ab_log_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) build_antibody_models() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) build_cell() (in module schrodinger.application.matsci.nano.sheet) build_chain_settings() (in module schrodinger.application.bioluminate.antibody.grafting) build_coupling_tensors() (schrodinger.application.jaguar.nmr_interactions.Interactions method) build_crystal() (in module schrodinger.application.matsci.maestrocmds) build_database() (in module schrodinger.application.bb_database.bb_task_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) BUILD_GEOMETRY (class in schrodinger.application.desmond.constants) build_irreps() (schrodinger.application.jaguar.nmr_basis.Basis method) build_kwargs() (in module schrodinger.application.matsci.nano.particle) build_natural_analog_dict() (in module schrodinger.protein.natural_analog) build_peptide() (in module schrodinger.protein.buildpeptide) build_polymer_graph() (in module schrodinger.livedesign.biologics.registration) build_ref_charges_and_bonds_cache() (in module schrodinger.structutils.ccd) build_spectrum() (in module schrodinger.application.jaguar.simple_spec) build_stagelinks() (in module schrodinger.application.desmond.cmj) build_stages() (in module schrodinger.application.desmond.cmj) buildBestRotamer() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF method) buildBilayer() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) buildCallbackDicts() (schrodinger.ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin method) buildCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) buildCellDriver() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) buildCGFromParticles() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) buildChain() (schrodinger.application.steps.basesteps.OptionalStepsMixin method) (schrodinger.application.steps.basesteps.Workflow method) (schrodinger.application.steps.enumerators.Synthesizer method) (schrodinger.application.steps.filters.InMemoryUniqueRandomSampleFilter method) (schrodinger.application.steps.filters.ScoreFilter method) (schrodinger.application.steps.filters.ScoreFilterChain method) (schrodinger.stepper.stepper.UnbatchedChain method) buildChannelStrDef() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) buildComboBox() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) buildComplexBuild() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) buildCovariance() (schrodinger.trajectory.prody.pca.PCA method) buildCrystalSuperCell() (schrodinger.application.matsci.nano.xtal.Crystal method) buildCrystalUnitCell() (schrodinger.application.matsci.nano.xtal.Crystal method) buildCustomBar() (schrodinger.ui.qt.appframework2.af2.BaseBottomBar method) buildDerivedAttrs() (schrodinger.application.jaguar.results.DerivedAttrs method) buildDockedLigandsMap() (schrodinger.pipeline.stages.glide.DockingStage method) builder_opts (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) BuilderGrowInCellMixin (class in schrodinger.application.matsci.amorphous) BuilderWithClashDetection (class in schrodinger.application.matsci.amorphous) BuildGeometry (class in schrodinger.application.desmond.stage.prepare.structure) buildingBlocksHaveRings() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) buildLabel() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) buildLattice() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) buildLayer() (schrodinger.application.matsci.nano.interface_mod.Interface method) buildLayers() (schrodinger.application.matsci.nano.interface_mod.Interface method) buildLineEdit() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) buildMultiWallTube() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) buildNanoTubeSheet() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) buildReorderList() (schrodinger.application.matsci.rxn_channel.Products method) buildResidueTypeCombo() (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBar method) BuildServerTask (class in schrodinger.application.glide.ligand_designer) BuildServerTask.Input (class in schrodinger.application.glide.ligand_designer) BuildServerTask.Output (class in schrodinger.application.glide.ligand_designer) buildSlab() (schrodinger.application.matsci.nano.slab.Surface method) buildStandardBar() (schrodinger.ui.qt.appframework2.af2.BottomBar method) (schrodinger.ui.qt.appframework2.af2.JobBottomBar method) (schrodinger.ui.qt.appframework2.af2.MiniJobBottomBar method) (schrodinger.ui.qt.appframework2.af2.OKAndCancelBottomBar method) buildTemplateList() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) buildTree() (in module schrodinger.ui.qt.dendrogram) (schrodinger.ui.dendrogram.DendrogramTreeBuilder method) (schrodinger.ui.qt.dendrogram.Dendrogram method) buildTube() (schrodinger.application.matsci.nano.tube.NanoTube method) buildUnitCell() (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) built_in (schrodinger.protein.nonstandard_residues.AminoAcid property) builtin_dir (schrodinger.application.matsci.builderwidgets.TemplateFamily property) BUILTIN_WF_FILE (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.FreeVolumeStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) BULK (schrodinger.application.matsci.msconst.DIMENSIONALITY attribute) BULK_TYPE_NUM (schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis attribute) bumpIndexes() (schrodinger.application.matsci.zmutils.ZAtom method) (schrodinger.application.matsci.zmutils.ZMatrix method) BURIED (schrodinger.protein.predictors.SolventAccessibility attribute) Buried (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) BURIED_VOLUME_VDW_SCALE (schrodinger.application.matsci.mlearn.features.Complex attribute) BUTTON_OFFSET (schrodinger.ui.qt.swidgets.EllipsisPopUpButton attribute) BUTTON_TEXT (schrodinger.application.job_monitor.job_monitor_widgets.JobBar attribute) (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar attribute) (schrodinger.application.job_monitor.job_monitor_widgets.TopLevelJobBar attribute) (schrodinger.application.matsci.mswidgets.StructureLoader attribute) (schrodinger.application.matsci.rdpattern_gui.SMARTSFrame attribute) BUTTON_TYPE (schrodinger.ui.qt.standard.design_tokens.PropertyNames attribute) ButtonAcceptsFocusMixin (class in schrodinger.ui.qt.utils) buttonChanged() (schrodinger.application.matsci.qualityslider.QualitySlider method) buttonChecked() (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) buttons() (schrodinger.ui.qt.datamapper.MappableButtonGroup method) ButtonTypes (class in schrodinger.ui.qt.standard.design_tokens) ButtonWithArrowMixin (class in schrodinger.ui.qt.standard_widgets.hyperlink) ButtonWithColorPicker (class in schrodinger.ui.qt.color_picker) bval (schrodinger.utils.sea.sea.Atom property) (schrodinger.utils.sea.sea.List property) (schrodinger.utils.sea.sea.Map property) BVECTOR (schrodinger.application.matsci.kmc.SchrodingerTable attribute) BytesSerializer (class in schrodinger.models.jsonable)

C

C (schrodinger.application.bioluminate.update_germline_db.translate_db.Gene attribute) (schrodinger.ui.qt.mapperwidgets.param_editor.MyEnum attribute) C1 (schrodinger.ui.qt.rama.BackboneDihedral attribute) C2 (schrodinger.ui.qt.rama.BackboneDihedral attribute) c6() (schrodinger.application.desmond.cms.Vdw method) C_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) C_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) c_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) c_v() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) C_VACUUM (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) CA (schrodinger.ui.qt.rama.BackboneDihedral attribute) cache_entity_IDs() (in module schrodinger.application.livedesign.import_utils) cache_hostname_plink() (in module schrodinger.utils.sshconfig) cached_topo_descriptor() (in module schrodinger.application.canvas.topo_descriptors) CacheInfo (class in schrodinger.application.matsci.cache) (class in schrodinger.application.matsci.rxn_channel) CAL_CM_TO_MPA (schrodinger.application.desmond.constants.Conversion attribute) calAbbeNum() (schrodinger.application.matsci.permittivity.RefractiveIndex class method) CALC (schrodinger.application.matsci.espresso.qeinput.TurboEelsType attribute) calc_ActivesInN() (in module schrodinger.analysis.enrichment.metrics) calc_ActivesInNStar() (in module schrodinger.analysis.enrichment.metrics) calc_AUAC() (in module schrodinger.analysis.enrichment.metrics) calc_AveNumberOutrankingDecoys() (in module schrodinger.analysis.enrichment.metrics) calc_average_vdw_coeff() (in module schrodinger.application.desmond.cms) calc_BEDROC() (in module schrodinger.analysis.enrichment.metrics) calc_block_average() (in module schrodinger.application.desmond.simulation_block_data) calc_buried_sasa_by_residue() (in module schrodinger.structutils.analyze) calc_cdr_shifts() (in module schrodinger.application.bioluminate.antibody.utils) calc_code (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) calc_code_version (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) calc_complementarity() (in module schrodinger.application.bioluminate.escomp) calc_complementarity_by_atom() (in module schrodinger.application.bioluminate.escomp) (in module schrodinger.application.bioluminate.surfcomp) calc_contrib() (in module schrodinger.application.desmond.fepana) calc_ddg_dataframe() (in module schrodinger.application.desmond.stage.app.lambda_dynamics_analysis) calc_DEF() (in module schrodinger.analysis.enrichment.metrics) calc_DEFP() (in module schrodinger.analysis.enrichment.metrics) calc_DEFStar() (in module schrodinger.analysis.enrichment.metrics) calc_delta_residue_uptake() (in module schrodinger.application.bioluminate.pose_filtering.hdx_calc) calc_delta_sasa_by_res_id() (in module schrodinger.application.bioluminate.pose_filtering.hdx_analysis) calc_EF() (in module schrodinger.analysis.enrichment.metrics) calc_EFF() (in module schrodinger.analysis.enrichment.metrics) calc_EFP() (in module schrodinger.analysis.enrichment.metrics) calc_EFStar() (in module schrodinger.analysis.enrichment.metrics) calc_FOD() (in module schrodinger.analysis.enrichment.metrics) calc_forward_reversed_work_overlap() (in module schrodinger.application.desmond.fepana) calc_free_energy() (in module schrodinger.application.desmond.fepana) calc_free_energy_correction_due_to_restraint() (in module schrodinger.application.desmond.fepana) calc_free_energy_for_abfe_cross_link() (in module schrodinger.application.desmond.fepana) calc_free_energy_for_abfe_cross_link_xu() (in module schrodinger.application.desmond.fepana) calc_free_energy_rtime_function() (in module schrodinger.application.desmond.fepana) calc_free_energy_stime_function() (in module schrodinger.application.desmond.fepana) calc_free_energy_time_function() (in module schrodinger.application.desmond.fepana) calc_freeenergy_rtime_function() (in module schrodinger.application.desmond.fepana) calc_freeenergy_stime_function() (in module schrodinger.application.desmond.fepana) calc_freeenergy_time_function() (in module schrodinger.application.desmond.fepana) calc_hbond_energy() (in module schrodinger.application.prepwizard) calc_HR() (in module schrodinger.analysis.enrichment.metrics) calc_lambda_sim_matrix() (in module schrodinger.application.desmond.fepana) calc_lambda_window_overlap() (in module schrodinger.application.desmond.fepana) calc_ligand_size() (in module schrodinger.application.glide.glide) calc_long_range_dispersion_energy() (in module schrodinger.application.desmond.fepana) calc_mean_tau_and_pval() (in module schrodinger.application.desmond.kinetics.utils) calc_name (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) calc_prob_profile() (in module schrodinger.application.desmond.ana) calc_property() (in module schrodinger.application.matsci.uq_utils) calc_rDsq() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsq2() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqT() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqTSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqZ() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqZSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_residue_uptake() (in module schrodinger.application.bioluminate.pose_filtering.hdx_calc) calc_RIE() (in module schrodinger.analysis.enrichment.metrics) calc_ROC() (in module schrodinger.analysis.enrichment.metrics) calc_rV() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rVsq() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_sasa_by_res_id() (in module schrodinger.application.bioluminate.pose_filtering.hdx_analysis) calc_sensitivity_with_rank() (in module schrodinger.analysis.enrichment.plotter) calc_specificity_with_rank() (in module schrodinger.analysis.enrichment.plotter) calc_state_score() (in module schrodinger.application.prepwizard) calc_substructure_score() (in module schrodinger.application.bioluminate.pose_filtering.hdx_analysis) calc_substructure_scores() (in module schrodinger.application.bioluminate.pose_filtering.hdx_analysis) calc_tension() (in module schrodinger.application.desmond.kinetics.utils) calc_time_curve() (in module schrodinger.application.desmond.fepana) calc_time_series() (in module schrodinger.application.desmond.ana) calc_total_complementarity() (in module schrodinger.application.bioluminate.escomp) (in module schrodinger.application.bioluminate.surfcomp) calc_type() (in module schrodinger.application.jaguar.textparser) calc_V() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_volume() (in module schrodinger.application.desmond.fep_net_charge) calc_work_prob_distr() (in module schrodinger.application.desmond.fepana) calcActivesInN() (schrodinger.analysis.enrichment.calculator.Calculator method) calcActivesInNStar() (schrodinger.analysis.enrichment.calculator.Calculator method) CalcAngle() (in module schrodinger.application.matsci.gsas.GSASIImath) calcAngle() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) CalcAngleDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) calcAntibodyTopography() (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) calcAUAC() (schrodinger.analysis.enrichment.calculator.Calculator method) calcAveNumberOutrankingDecoys() (schrodinger.analysis.enrichment.calculator.Calculator method) CalcBAR (class in schrodinger.application.desmond.bennett) calcBEDROC() (schrodinger.analysis.enrichment.calculator.Calculator method) (schrodinger.application.phase.packages.bedroc_screener.BedrocScreener method) calcBond() (in module schrodinger.application.matsci.gsas.GSASIImath) calcBondScore() (schrodinger.structutils.assignbondorders.AssignBondOrders method) calcConsensusScore() (schrodinger.pipeline.stages.combine.DataFusionMergeStage method) calcCovariance() (in module schrodinger.trajectory.prody.crosscorrelation) calcCrossCorr() (in module schrodinger.trajectory.prody.crosscorrelation) CalcDdg (class in schrodinger.application.desmond.stage.fep_mapper) calcDEF() (schrodinger.analysis.enrichment.calculator.Calculator method) calcDEFP() (schrodinger.analysis.enrichment.calculator.Calculator method) calcDEFStar() (schrodinger.analysis.enrichment.calculator.Calculator method) calcDihedral() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) CalcDist() (in module schrodinger.application.matsci.gsas.GSASIImath) calcDistance() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) CalcDistDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) calcEF() (schrodinger.analysis.enrichment.calculator.Calculator method) calcEFF() (schrodinger.analysis.enrichment.calculator.Calculator method) calcEFP() (schrodinger.analysis.enrichment.calculator.Calculator method) calcEFStar() (schrodinger.analysis.enrichment.calculator.Calculator method) calcFitZoomFactor() (schrodinger.ui.qt.network_views.NetworkViewer method) calcFOD() (schrodinger.analysis.enrichment.calculator.Calculator method) calcHR() (schrodinger.analysis.enrichment.calculator.Calculator method) calcIncident() (in module schrodinger.application.matsci.gsas.GSASIIpwd) calcItemZoomFactor() (schrodinger.ui.qt.network_views.NetworkViewer method) calcModes() (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.trajectory.prody.pca.PCA method) CalcPDF() (in module schrodinger.application.matsci.gsas.GSASIIpwd) calcPlanarAngle() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) calcRamaEnergy() (in module schrodinger.application.matsci.gsas.GSASIImath) calcRIE() (schrodinger.analysis.enrichment.calculator.Calculator method) calcROC() (schrodinger.analysis.enrichment.calculator.Calculator method) calcsDone() (schrodinger.application.matsci.jaguarworkflows.Step method) CalcStackingPWDR() (in module schrodinger.application.matsci.gsas.GSASIIpwd) CalcStackingSADP() (in module schrodinger.application.matsci.gsas.GSASIIpwd) calcTorsionEnergy() (in module schrodinger.application.matsci.gsas.GSASIImath) CalcType (class in schrodinger.application.jaguar.constants) calculate() (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) (schrodinger.application.canvas.r_group.RGroupFinder method) (schrodinger.structutils.rmsd.ConformerRmsd method) calculate1DDensity() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) calculate2DDensity() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) calculate_angle_term() (schrodinger.protein.assignment.ProtAssign.hbond_cluster static method) calculate_average_angle() (in module schrodinger.structutils.assignbondorders) calculate_binding_modes() (in module schrodinger.application.phase.hypothesis_binding_modes) calculate_ciexy() (in module schrodinger.application.matsci.colorutils) calculate_clash_term() (schrodinger.protein.assignment.ProtAssign.hbond_cluster static method) calculate_cri() (in module schrodinger.application.matsci.colorutils) calculate_dihedral() (in module schrodinger.structutils.assignbondorders) calculate_distance_term() (schrodinger.protein.assignment.ProtAssign.hbond_cluster static method) calculate_enhanced_stereo() (in module schrodinger.livedesign.preprocessor) calculate_in_place_rmsd() (in module schrodinger.structutils.rmsd) calculate_interaction_matrix() (in module schrodinger.protein.assignment) calculate_interactions() (in module schrodinger.application.bioluminate.protein_interaction.calculate) calculate_kstest_results() (in module schrodinger.active_learning.al_report) calculate_nits() (in module schrodinger.application.matsci.colorutils) calculate_njobs() (in module schrodinger.application.phase.packages.phase_utils) (in module schrodinger.job.jobcontrol) calculate_num_protons() (in module schrodinger.application.jaguar.gui.utils) calculate_path_msd() (in module schrodinger.application.desmond.kinetics.utils) calculate_planarity() (in module schrodinger.structutils.assignbondorders) calculate_principal_moments() (in module schrodinger.structutils.analyze) calculate_recovery_ratio() (in module schrodinger.active_learning.al_report) calculate_report_rmse() (in module schrodinger.application.desmond.solubility_utils) calculate_restraint_correction_term() (in module schrodinger.application.desmond.stage.prepare.forcefield) calculate_RIP() (in module schrodinger.application.desmond.fep_net_charge) calculate_sasa() (in module schrodinger.structutils.analyze) calculate_sasa_by_atom() (in module schrodinger.structutils.analyze) calculate_sasa_by_residue() (in module schrodinger.structutils.analyze) calculate_solubility_free_energy() (in module schrodinger.application.desmond.solubility_utils) calculate_statistics() (in module schrodinger.application.bioluminate.peptide_sar.statistics) calculate_stats() (schrodinger.application.glide.glideanalysis.PoseLibrary method) calculate_stress() (schrodinger.application.matsci.elasticity.elastic.NthOrderElasticTensor method) calculate_total_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) calculate_unbinding_statistics() (schrodinger.application.desmond.kinetics.mtd_cleanup.CleanUp method) calculate_which_wps_bound() (schrodinger.application.desmond.kinetics.cleanup.CleanUp method) calculateArrow() (in module schrodinger.ui.qt.network_views) calculateAverageDipole() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) CalculateContainingVolume() (in module schrodinger.analysis.visanalysis.volumedatautils) calculateCoords() (schrodinger.graphics3d.arrow.MaestroArrow method) calculateEnergy() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) calculateEnergyDifference() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) calculateHelices() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) calculateHelixProp() (schrodinger.application.matsci.atom_group.HelixArc method) calculateMatrix() (schrodinger.structutils.sitealign.BindingSiteAligner method) calculateMembraneBox() (schrodinger.protein.membrane.Membrane_Model method) CalculateMolWt (class in schrodinger.seam.examples.active_learning_weigher) calculateMutationsList() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator method) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) calculateOverResidues() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) calculatePropertiesCoordinates() (schrodinger.ui.two_d_viewer.TwoDViewer method) calculatePropertyPrecisions() (schrodinger.ui.two_d_viewer.TwoDViewer method) CalculateScoreNode (class in schrodinger.application.phase.packages.shape_screen_al_node) calculateSimilarity() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) calculateSpecificity() (schrodinger.analysis.enrichment.calculator.Calculator method) calculateTopologicalDescriptors() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method) calculateVolume() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) calculateWaterMapDensity() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) calculateXYZBox() (schrodinger.graphics3d.tube.MaestroTube method) CALCULATION (schrodinger.application.matsci.crest.CrestTOML attribute) CALCULATION_MODE (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget attribute) CALCULATIONS (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) Calculator (class in schrodinger.analysis.enrichment.calculator) calcZScores() (schrodinger.pipeline.stages.combine.DataFusionMergeStage method) calDensity() (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) call() (in module schrodinger.utils.subprocess) (schrodinger.ui.qt.formlayout.PushLayout method) call_func_and_wait_for_signal() (in module schrodinger.utils.qt_utils) callback (schrodinger.application.jaguar.textparser.TextParser attribute) (schrodinger.application.qsite.output.QSiteTextParser attribute) (schrodinger.application.xtb.textparser.TextParser attribute) callback() (in module schrodinger.application.jaguar.textparser) (in module schrodinger.application.mopac.results_main) (in module schrodinger.application.qsite.output) (in module schrodinger.application.xtb.textparser) callback_minimal (schrodinger.application.mopac.results_main.MopacMainTextParser attribute) callback_minimal() (in module schrodinger.application.mopac.results_main) CallbackInfo (class in schrodinger.ui.qt.appframework2.maestro_callback) CallbackMonitor (class in schrodinger.ui.qt.appframework2.maestro_callback) callbacks (schrodinger.application.mopac.results_main.MopacMainTextParser attribute) calling_context (schrodinger.tasks.tasks.AbstractTask attribute) calling_contextChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) calling_contextReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) CallingContext (class in schrodinger.tasks.tasks) Callout (class in schrodinger.ui.qt.schart) CALPHA_RUNG (schrodinger.application.desmond.constants.ConfRestraintType attribute) calWriteMeanAndStd() (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) can_atom_hydrogen_bond() (in module schrodinger.structutils.analyze) CAN_CREATE_TRAJECTORY (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.CustomTrajectoryStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.MDCustomMSJStep attribute) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) can_show_online_docs() (in module schrodinger.utils.documentation) can_skip_line() (in module schrodinger.utils.compare) can_write_file() (in module schrodinger.application.licensing.licadmin) canBroaden() (schrodinger.application.matsci.espresso.qeoutput.DOS method) CANCEL (schrodinger.application.job_monitor.job_monitor_models.RequestedStatus attribute) (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.MessageButton attribute) (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) Cancel (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.StdBtn attribute) cancel() (schrodinger.application.glide.http_client.ZmqClient method) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) (schrodinger.application.matsci.qubec_utils.Job method) (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.protein.tasks.clustal.AbstractAlignmentJob method) (schrodinger.ui.qt.pdb_dialog.PDBDialog method) cancelBatch() (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) cancelClicked() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) CANCELED (schrodinger.job.jobcontrol.DisplayStatus attribute) cancelPressed() (schrodinger.application.desmond.gui.AdvOptionsFrame method) cancelRequested (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget attribute) cancelSelected() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) cancelSubmitted() (schrodinger.job.queue.JobControlJob method) CancelSubmittedStatus (class in schrodinger.job.queue) canDriverUseUmbrella() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) cannotDeleteAction() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable method) canonical (schrodinger.application.desmond.struc.FormHashes attribute) (schrodinger.application.desmond.struc.FormMols attribute) canonical_filename() (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.licensing.licadmin.LicenseResource method) CANONICAL_STRUCTURAL (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes attribute) CANONICAL_STRUCTURAL_RES (schrodinger.application.bioluminate.antibody.annotate.Properties attribute) Canonicalize (class in schrodinger.adapter) canonicalize() (in module schrodinger.application.desmond.config_utils) (schrodinger.structutils.smiles.SmilesGenerator method) canonicalize_atom_names() (in module schrodinger.application.jaguar.autots_bonding) canonicalize_ligand() (in module schrodinger.application.desmond.automatic_analysis_generator) canonicalize_R_labels() (in module schrodinger.application.scaffold_enumeration.markush) canorb() (in module schrodinger.application.jaguar.textparser) CANRIGID (schrodinger.application.matsci.kmc.FramesTable attribute) (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) canStart() (schrodinger.application.matsci.jaguarworkflows.Step method) CantAccessModelError CantAlignException CantCreateQApplicationError canvas (schrodinger.application.matsci.msconst.SMARTS_METHOD attribute) Canvas2DSimilarityStage (class in schrodinger.pipeline.stages.canvas) CanvasFingerprintCluster (class in schrodinger.application.canvas.cluster) CanvasFingerprintClusterCLI (class in schrodinger.application.canvas.cluster) CanvasFingerprintClusterGUI (class in schrodinger.application.canvas.clustergui) CanvasFingerprintGenerator (class in schrodinger.application.canvas.fingerprint) CanvasFingerprintGeneratorCLI (class in schrodinger.application.canvas.fingerprint) CanvasFingerprintGeneratorGUI (class in schrodinger.application.canvas.fingerprintgui) CanvasFingerprintSimilarity (class in schrodinger.application.canvas.similarity) CanvasFingerprintSimilarityCLI (class in schrodinger.application.canvas.similarity) CanvasFingerprintSimilarityGUI (class in schrodinger.application.canvas.similaritygui) canvasfp_fpreader() (in module schrodinger.application.hitexpander) CanvasKPLS (class in schrodinger.application.matsci.genetic_optimization) CanvasPattern (class in schrodinger.application.matsci.rdpattern) CanvasSearchTask (class in schrodinger.application.livedesign.tasks) CanvasSearchTask.Input (class in schrodinger.application.livedesign.tasks) CanvasSearchTask.JobConfig (class in schrodinger.application.livedesign.tasks) CanvasSearchTask.Output (class in schrodinger.application.livedesign.tasks) CanvasSimilarityNotImplemented CanvasWithHeaderAndFooter (class in schrodinger.application.matsci.reportutils) cap_termini (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_termini() (in module schrodinger.protein.captermini) cap_termini_min_atoms (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_termini_min_atomsChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_termini_min_atomsReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_terminiChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_terminiReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) capped_smi (schrodinger.application.dendrogram.core_class.RingSysInfo attribute) capped_st (schrodinger.application.dendrogram.core_class.RingSysInfo attribute) cappedResidues() (schrodinger.protein.captermini.CapTermini method) cappedSites() (schrodinger.application.matsci.sculptcomplex.CoordinationInfo method) CAPPING_BOND_LENGTH (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) CAPPINGELEMENT (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) capResidues() (schrodinger.protein.captermini.CapTermini method) capSequences() (schrodinger.protein.captermini.CapTermini method) CapTermini (class in schrodinger.protein.captermini) CAPTION (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) capToStar() (schrodinger.application.dendrogram.core_class.Utilities static method) Capture (class in schrodinger.infra.mmerr) capture() (schrodinger.application.desmond.stage.simulate.SimulateBase method) CARBON_PDBNAME (schrodinger.protein.assignment.AsparticAcidpKaPredictor attribute) (schrodinger.protein.assignment.GlutamicAcidpKaPredictor attribute) CARBON_PDBNAMES (schrodinger.protein.assignment.HistidinepKaPredictor attribute) (schrodinger.protein.assignment.ProtAssign.amide_changeable attribute) CarbonCount (class in schrodinger.application.transforms.template.starter) CarbonCountingWorkflow (class in schrodinger.application.transforms.template.workflow) carboxyl_interactions() (schrodinger.protein.assignment.HistidinepKaPredictor method) CARBOXYLIC_ACID_PKA_SHIFT (schrodinger.protein.assignment.HistidinepKaPredictor attribute) CARRIERTYPE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) CARTESIAN (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) cartesian_hessian() (in module schrodinger.application.jaguar.hess_guess) CARTESIANWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) Cascader (class in schrodinger.application.matsci.amorphous) CascadingCheckboxItem (class in schrodinger.application.livedesign.panel_components) case_insensitive_file_exists() (in module schrodinger.application.matsci.wfmanagement) CaseInsensitiveString (class in schrodinger.application.jaguar.jaguar_diff) cast_type (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) cast_validation_result() (in module schrodinger.ui.qt.appframework2.validation) cat() (in module schrodinger.utils.fileutils) cat_csv_files() (in module schrodinger.rdkit.molio) cat_flat_files() (in module schrodinger.utils.fileutils) CATALYTIC_LOOP (schrodinger.protein.annotation.KinaseFeatureLabel attribute) catch_error_for_dialog() (in module schrodinger.ui.qt.utils) catch_jag_errors() (in module schrodinger.application.jaguar.gui.utils) catch_last_added() (in module schrodinger.application.bioluminate.ssv.viewer) catch_subprocess_errors() (in module schrodinger.utils.sysinfo) categories (schrodinger.application.matsci.builderwidgets.BaseTemplateListWidgetItem property) (schrodinger.application.matsci.builderwidgets.CustomListWidgetItem property) (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) categorize_entries_by_locus() (in module schrodinger.application.bioluminate.update_germline_db.translate_db) categorizeBonds() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) categorizeServers() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) categorizeSymmetryMappings() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) CATEGORY (schrodinger.ui.qt.schart.SChart attribute) category_keys (schrodinger.application.matsci.builderwidgets.TemplateFamily attribute) (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) CategoryOrderError CatHypoConverter (class in schrodinger.application.phase.packages.cat_hypo_converter) cation_centroid (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) cation_pi_interactions() (schrodinger.protein.assignment.HistidinepKaPredictor method) cation_structure (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) CationPiInteraction (class in schrodinger.structutils.interactions.pi) catOpText() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) cauchy_gen (class in schrodinger.application.matsci.gsas.GSASIIpwd) Cavity (class in schrodinger.application.bindingsite.cavutils) cavity_depth (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) CB_TEXT (schrodinger.ui.qt.forcefield.forcefield.ValidateOplsDirMessageBox attribute) CC_SLIDER (schrodinger.application.matsci.mswidgets.MultiSlider attribute) ccd_assign_by_names_and_bonds() (in module schrodinger.structutils.ccd) CCDAtomMapper (class in schrodinger.structutils.ccd) CCDStructureMismatchError cd() (in module schrodinger.utils.installation_check) cdock (schrodinger.application.livedesign.tasks.CovDockTask attribute) cdock_file (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cdock_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cdock_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cdr_name (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput property) cealign() (in module schrodinger.structutils.rmsd) (in module schrodinger.structutils.structalign2) Cell (class in schrodinger.ui.qt.tablewidget) (class in schrodinger.ui.two_d_viewer) cell (schrodinger.application.matsci.clusterstruct.ComInfo attribute) (schrodinger.ui.qt.tablewidget.Column property) (schrodinger.ui.qt.tablewidget.Row property) cell2A() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cell2AB() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cell2Gmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cell2GS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) CELL_DOFREE_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_DOFREE_XML (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_DYNAMICS_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_FACTOR_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_PADDING (schrodinger.application.report2d.PicturePrinter attribute) CellAbsorption() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cellAspectRatio() (schrodinger.ui.qt.structtable.ViewerTable method) CellBlock() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cellClearData() (schrodinger.infra.table.Table method) cellClicked() (schrodinger.ui.two_d_viewer.TwoDViewer method) CellContextualMenu (class in schrodinger.ui.two_d_viewer) CellControlType (class in schrodinger.application.matsci.espresso.qeinput) cellDijFill() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cellDoubleClicked() (schrodinger.ui.two_d_viewer.TwoDViewer method) cellHasData() (schrodinger.infra.table.Table method) CellIterator (class in schrodinger.ui.qt.tablewidget) CellRunInfo (class in schrodinger.application.matsci.jobutils) cellWidget() (schrodinger.ui.qt.swidgets.STableWidget method) CentCheck() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Center (class in schrodinger.application.bioluminate.pml_menus) CENTER (schrodinger.application.desmond.constants.SidedError attribute) (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) center (schrodinger.application.scaffold_enumeration.cxsmiles.MCG attribute) (schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup attribute) (schrodinger.math.multi_parameter_optimization.Transition attribute) Center (schrodinger.ui.qt.pop_up_widgets.PopUpAlignment attribute) center_com() (in module schrodinger.comparison.struc) center_of_mass() (in module schrodinger.application.matsci.cg_mapping) (in module schrodinger.structutils.analyze) center_rotation (schrodinger.application.pymol.mae_sync.MaestroSettingsModel attribute) center_widget_in_table_cell() (in module schrodinger.ui.qt.swidgets) CenteredIconDelegate (class in schrodinger.ui.qt.delegates) CENTERING (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute) CENTERING_OPERATIONS_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) CENTERING_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) centering_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) centering_opers_strs (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) CenteringWidget (class in schrodinger.ui.qt.swidgets) centerPos() (schrodinger.ui.qt.network_views.NetworkNode method) centerStruct() (schrodinger.application.matsci.desmondutils.SystemBuilder method) centrality (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule.RING_INFO attribute) Centroid (class in schrodinger.structutils.interactions.pi) centroid (schrodinger.structutils.analyze.Ligand property) (schrodinger.structutils.ringspear.SpearRing attribute) CentroidBanner (class in schrodinger.trajectory.trajectory_gui_dir.banners) centroidsPicked (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner attribute) cert (schrodinger.application.licensing.licserver.client.LocalEntitlementValidation attribute) (schrodinger.job.cert.CertInfo attribute) CertInfo (class in schrodinger.job.cert) CFG_FILE (schrodinger.application.matsci.permittivity.MultiStageMd attribute) cfg_file() (schrodinger.application.desmond.cmj.JobInput method) CFG_SIM_NAME (schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD attribute) (schrodinger.application.desmond.stage.simulate.ReplicaExchange attribute) (schrodinger.application.desmond.stage.simulate.SimulateBase attribute) cflt_file (schrodinger.application.steps.filters.ProductFilterMixin.Settings attribute) cflt_fileChanged (schrodinger.application.steps.filters.ProductFilterMixin.Settings attribute) cflt_fileReplaced (schrodinger.application.steps.filters.ProductFilterMixin.Settings attribute) CG_AA_ELEMENT_SYMBOL (schrodinger.application.matsci.nano.constants.Constants attribute) CG_CAPPING_ELEMENT (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) CG_ELEMENT1 (schrodinger.application.matsci.nano.constants.Constants attribute) CG_ELEMENT2 (schrodinger.application.matsci.nano.constants.Constants attribute) cg_substructure_matches() (in module schrodinger.rdkit.substructure) CgCoreAnnotator (class in schrodinger.ui.qt.structure2d) cgen() (schrodinger.application.macromodel.utils.ComUtil method) CGFFIOStructure (class in schrodinger.application.matsci.cgforcefield) CGForceFieldSelector (class in schrodinger.application.matsci.cgforcefieldgui) CGGraphHelper (class in schrodinger.application.matsci.automated_cg_mapping) CGMapper (class in schrodinger.application.matsci.cg_mapping) CGMapperMixin (class in schrodinger.application.matsci.cg_mapping) CH (schrodinger.protein.annotation.AntibodyRegionLabel attribute) Chain (class in schrodinger.protein.getpdb_utility) (class in schrodinger.stepper.stepper) chain (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch attribute) CHAIN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain (schrodinger.application.bioluminate.mutation.Mutation attribute) CHAIN (schrodinger.application.bioluminate.pose_filtering.hdx_io.StandardColumns attribute) chain (schrodinger.application.bioluminate.protein_interaction.utils.Residue attribute) (schrodinger.application.licensing.licserver.client.LocalEntitlementValidation attribute) (schrodinger.application.qsite.input.Cut property) (schrodinger.protein.residue.Residue property) (schrodinger.protein.residue.ResidueKey attribute) (schrodinger.protein.sequence.AbstractSingleChainSequence property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.structure.Residue property) (schrodinger.structure.Structure attribute) (schrodinger.structure.StructureAtom property) (schrodinger.structure.TextualStructure property) Chain (schrodinger.ui.picking.PickResidueColumns attribute) chain (schrodinger.ui.qt.rama.BackboneDihedral attribute) CHAIN_FR_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) CHAIN_FR_SIM (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain_id (schrodinger.application.bioluminate.classify.NumberedResidue attribute) CHAIN_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain_name (schrodinger.application.matsci.packmol.PDBdata attribute) (schrodinger.structure.StructureAtom property) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) chain_offsets (schrodinger.protein.sequence.CombinedChainProteinSequence property) CHAIN_SIM (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain_type (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) chainAdded() (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) ChainAlignment (class in schrodinger.application.bioluminate.anarci.anarci_adapter) ChainHitsTable (class in schrodinger.application.bioluminate.anarci.anarci_adapter) chainKey() (schrodinger.protein.residue.ResidueKey method) ChainNumbering (class in schrodinger.application.bioluminate.anarci.anarci_adapter) chainRemoved() (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) chains (schrodinger.protein.sequence.CombinedChainProteinSequence property) ChainTypes (class in schrodinger.application.bioluminate.antibody.grafting) change_bool_flags_to_accept_int() (in module schrodinger.tasks.ldtasks) change_current_pick() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.Rama method) change_directory() (in module schrodinger.application.bioluminate.methionine_oxidation) change_empirical_pka() (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) change_pka() (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) change_plot_colors() (in module schrodinger.application.desmond.report_helper) change_to_rgroup() (in module schrodinger.rdkit.rgroup) change_working_directory() (in module schrodinger.utils.fileutils) changeAxisFontSize() (schrodinger.ui.qt.schart.SChart static method) changeBasis() (schrodinger.application.matsci.nano.tube.NanoSheet method) changeBFactorPlot() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) changeButtonState() (schrodinger.application.matsci.sliceplot.SlicePlot method) changeCoord() (schrodinger.application.matsci.zmutils.ZAtom method) Changed (schrodinger.models.parameters.SignalType attribute) changeEvent() (schrodinger.ui.qt.swidgets.LineEditWithDisabledText method) (schrodinger.ui.qt.swidgets.SCheckBox method) changeGroup() (schrodinger.utils.preferences.Preferences method) changeIcon() (schrodinger.ui.qt.color_picker.ButtonWithColorPicker method) changeLayer() (schrodinger.application.matsci.sliceplot.SlicePlot method) changeLimitsEnd() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) changeLimitsStart() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) changeMarkerAtomsToTempElement() (schrodinger.application.matsci.builderwidgets.SketcherStructureMixin method) changeModel() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) changeMoleculeForParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) changePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) changePreset() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) changeProtein() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) changeProtFile() (schrodinger.application.desmond.gui.RelaxFrame method) changeScaling() (schrodinger.ui.qt.dendrogram.GuiPanel method) changesSaved() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) changeTemplateDirectory() (schrodinger.application.matsci.builderwidgets.TemplateManager method) changeThickness() (schrodinger.ui.qt.dendrogram.GuiPanel method) changeToolTip() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) CHANNEL_FILE (schrodinger.application.matsci.rxn_channel.Constants attribute) ChannelDefinition (class in schrodinger.application.matsci.rxn_channel) ChannelDefinitions (class in schrodinger.application.matsci.rxn_channel) Channels (class in schrodinger.application.matsci.rxn_channel) CHAR_TO_ACC_MAP (schrodinger.protein.predictors.AccproPredictor attribute) CHARGE (schrodinger.application.desmond.constants.Schedule attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) charge (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) CHARGE (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) charge (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) CHARGE (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) charge (schrodinger.application.jaguar.utils.ChgAt attribute) (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.MAPPED_BEAD_INFO attribute) (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) (schrodinger.application.matsci.cgforcefield.VDWData attribute) CHARGE (schrodinger.application.matsci.crest.CrestTOML attribute) (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute) charge (schrodinger.protein.residue.Residue property) charge_arginine_sidechains() (in module schrodinger.protein.assignment) CHARGE_CORR (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) charge_div (schrodinger.application.desmond.fep_schedule.FepSchedule attribute) (schrodinger.application.desmond.fep_schedule.FepSchemeChargeMixIn attribute) (schrodinger.application.desmond.fep_schedule.FepSchemeMixIn attribute) (schrodinger.application.desmond.fep_schedule.FepSchemeQuickchargeMixIn attribute) (schrodinger.application.desmond.fep_schedule.FepSchemeSuperquickchargeMixIn attribute) charge_is_conserved() (in module schrodinger.application.jaguar.autots_validation) charge_is_consistent() (in module schrodinger.application.jaguar.workflow_validation) charge_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) CHARGE_SPIN_INCONSISTANT_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) CHARGE_TRANSFER (schrodinger.energy.MetalForceFieldComponent attribute) chargeA (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property) (schrodinger.application.desmond.fep_schedule.FepScheduleBinding property) chargeB (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property) (schrodinger.application.desmond.fep_schedule.FepScheduleBinding property) ChargeConstraint (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) ChargeConstraintRow (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsColumns (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints) ChargeConstraintsTableView (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) CHARGED (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) charged (schrodinger.application.matsci.kmcgui.PlotInfo attribute) charged_lambda_windows (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) CHARGED_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) CHARGED_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) CHARGED_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) ChargeDialog (class in schrodinger.application.matsci.chargegui) chargedStrucsPresent() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) ChargeFilterStage (class in schrodinger.pipeline.stages.filtering) ChargeFlip() (in module schrodinger.application.matsci.gsas.GSASIImath) ChargePropertySelector (class in schrodinger.application.matsci.chargegui) charges (schrodinger.application.jaguar.utils.LewisStructure attribute) charges_from_ct (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) (schrodinger.structutils.minimize.Minimizer property) ChargeSelectorDelegate (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeSelectorLineEdit (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector) ChargeVectorizer (in module schrodinger.application.bioluminate.peptide_sar.encode) charPositionInLine (schrodinger.application.desmond.antlr3.tree.CommonTree property) CharStream (class in schrodinger.application.desmond.antlr3.streams) CHCL3 (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute) chdir (class in schrodinger.application.matsci.permittivity) (class in schrodinger.utils.fileutils) chdir() (in module schrodinger.application.desmond.util) check() (schrodinger.application.desmond.cmj.JobOutput method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.ArraySyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.Syntax method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.packmol.BilayerInputFile method) (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) check1_subst_code() (in module schrodinger.application.desmond.fep_util) check_attachment_point() (in module schrodinger.structutils.rgroup_enumerate) check_attachment_points_changed() (in module schrodinger.livedesign.preprocessor) check_bond_length() (in module schrodinger.application.bioluminate.antibody.assembly) check_bond_vec_proj() (in module schrodinger.application.matsci.nano.xtal) check_box_size() (in module schrodinger.application.desmond.stage.utils) check_call() (in module schrodinger.utils.subprocess) check_canvas_license() (in module schrodinger.application.canvas.topo_descriptors) check_centroid_rep() (in module schrodinger.application.matsci.reaction_workflow_utils) check_cg_license() (in module schrodinger.application.matsci.jobutils) check_charge_and_multiplicity() (in module schrodinger.application.matsci.jaguarworkflows) check_cms_file() (in module schrodinger.application.desmond.stage.utils) check_cms_trj_properties_are_found() (in module schrodinger.application.matsci.deswidgets) check_command() (in module schrodinger.application.desmond.util) check_config() (in module schrodinger.livedesign.cmdline) check_conflicts() (in module schrodinger.application.jaguar.autots_validation) (in module schrodinger.application.jaguar.hydrokinetic_validation) (in module schrodinger.application.jaguar.macro_pka_validation) (in module schrodinger.application.jaguar.qrnn.validation) (in module schrodinger.application.jaguar.rotation_barriers_validation) (in module schrodinger.application.jaguar.solvation_validation) check_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) check_connection() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) check_coordinates_changed() (in module schrodinger.application.matsci.freevolume) check_cpu_features() (in module schrodinger.utils.sysinfo) CHECK_CRYSTAL_WATER_OVERLAP (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput attribute) check_cstate_changed() (in module schrodinger.livedesign.preprocessor) check_directrunner_license_checkouts() (in module schrodinger.seam.testing.fixtures) check_directrunner_license_checkouts_impl() (in module schrodinger.seam.testing.fixtures) check_discontinued_args() (in module schrodinger.application.desmond.starter.ui.cmdline) check_driver_disk_space() (in module schrodinger.active_learning.al_utils) check_duplicate_titles() (schrodinger.application.desmond.starter.ui.cmdline.FepArgs method) check_enamine_subclass() (in module schrodinger.protein.process_enamine_db) check_feature_string() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) check_ff_assignment() (in module schrodinger.application.matsci.reaction_workflow_utils) check_file_formats() (in module schrodinger.application.glide.sort_parser_common) check_finite_molecules() (in module schrodinger.application.matsci.equilibrium_md) check_for_spears() (in module schrodinger.structutils.ringspear) check_fp_availability() (in module schrodinger.application.hitexpander) check_grad() (in module schrodinger.application.jaguar.qrnn.temp_opt) check_hbond() (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method) (schrodinger.protein.analysis.Report.steric_clash_data_set method) check_if_backbone_atom() (in module schrodinger.application.bioluminate.protein_interaction.calculate) check_if_comparable() (in module schrodinger.protein.residue) check_if_lattice_properties_exist() (in module schrodinger.application.matsci.nano.particle) check_imaginary_frequencies() (in module schrodinger.application.matsci.anharmonic) check_jobname() (in module schrodinger.application.desmond.starter.ui.cmdline) check_kekulization() (in module schrodinger.livedesign.preprocessor) check_key_pair() (in module schrodinger.utils.sshconfig) check_license() (in module schrodinger.application.matsci.jobutils) (in module schrodinger.application.phase.packages.shape_screen_al_driver) check_licenses() (in module schrodinger.application.matsci.jobutils) check_ligand_overlap() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) check_ligand_stability_and_center() (in module schrodinger.application.desmond.kinetics.utils) check_map() (in module schrodinger.utils.sea.evalor) check_memory_use() (in module schrodinger.application.mopac.results_main) check_models() (in module schrodinger.active_learning.al_utils) check_modes() (in module schrodinger.application.glide.sort_parser_common) check_module() (in module schrodinger.application.bioluminate.validate_imported_modules) check_moved_variables() (in module schrodinger.application.matsci.codeutils) CHECK_MSG (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.genetic_optimization.ChemInformatics attribute) check_options() (in module schrodinger.application.matsci.equilibrium_md) check_output() (in module schrodinger.utils.subprocess) check_param() (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher method) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup method) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher method) (schrodinger.application.desmond.stage.simulate.Concatenate method) (schrodinger.application.desmond.stage.simulate.GCMCCapable method) check_parser_args() (in module schrodinger.application.phase.packages.phase_convert_MOE) check_permitted_features_string() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) check_ppj() (schrodinger.application.desmond.starter.ui.cmdline.FepArgs method) check_property_sign() (in module schrodinger.application.matsci.uq_utils) check_reaction() (in module schrodinger.livedesign.bbchem_endpoints) check_reaction_wf_structures() (in module schrodinger.application.matsci.reaction_workflow_utils) check_required_gridfiles() (in module schrodinger.application.glide.utils) check_required_modules() (in module schrodinger.active_learning.al_utils) check_residue_flip_state() (in module schrodinger.protein.assignment) check_restart_host() (in module schrodinger.active_learning.al_utils) check_restrain_diffs() (in module schrodinger.application.desmond.cmj) check_ring_spears() (in module schrodinger.application.matsci.packmol) check_rule() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) check_running_as_root() (in module schrodinger.utils.installation_check) check_rxn() (in module schrodinger.livedesign.check_reaction) check_rxn_atom_mappings_are_valid() (in module schrodinger.livedesign.check_reaction) check_sanity() (in module schrodinger.application.desmond.cms) check_seamrunner_license_checkouts() (in module schrodinger.seam.testing.fixtures) check_seamrunner_license_checkouts_impl() (in module schrodinger.seam.testing.fixtures) CHECK_SOLVENT_OVERLAP (schrodinger.application.desmond.constants.SYSTEM_BUILDER_INP attribute) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput attribute) check_stage_attributes() (in module schrodinger.application.desmond.stage.run_method_parallel) check_subjob_output() (schrodinger.pipeline.stages.glide.DockingStage method) check_subset_existence() (in module schrodinger.pipeline.stages.phase) check_subst_code() (in module schrodinger.application.desmond.fep_util) check_system() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.SysType method) (schrodinger.application.desmond.systype.WatermapTyper static method) check_tau_options() (in module schrodinger.application.matsci.equilibrium_md) check_TS_vetting() (in module schrodinger.application.matsci.reaction_workflow_utils) check_user_query() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) check_valid_key() (in module schrodinger.job.launchapi) CHECKABLE_COLS (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) CHECKABLE_ITEM (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) CheckableHeaderView (class in schrodinger.ui.qt.table_helper) checkAlignment() (schrodinger.application.matsci.nano.particle.CheckInput method) checkAll() (schrodinger.application.matsci.nano.sheet.CheckInput method) (schrodinger.application.matsci.nano.tube.CheckInput method) checkAndmarkPolymerProp() (schrodinger.application.matsci.amorphous.PolymerFragments method) checkAndProcessAllowAdsorptionOnto() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkArgs() (schrodinger.structutils.createfragments.FragmentCreator method) checkASL() (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) (schrodinger.application.matsci.mswidgets.MSAtomSelector method) checkASU() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkAtomUniqueness() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) checkAtomZeroIndex() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) checkBasisSets() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetProxyModel method) checkBilayerSep() (schrodinger.application.matsci.nano.check.CheckInput method) checkBilayerShift() (schrodinger.application.matsci.nano.check.CheckInput method) checkBilayerStackType() (schrodinger.application.matsci.nano.check.CheckInput method) checkBondingAndTranslate() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkBondlength() (schrodinger.application.matsci.nano.check.CheckInput method) CheckboxDelegate (class in schrodinger.ui.qt.delegates) CheckboxIcons (class in schrodinger.ui.qt.standard.design_tokens) checkBoxText() (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) checkCellDims() (schrodinger.application.matsci.nano.check.CheckInput method) checkChannelDefs() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkChannelDefsVsReactants() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkChannelUniqueness() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkChargesMultiplicitiesStates() (schrodinger.application.matsci.mecp_mod.CheckInput static method) checkConflicts() (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.GlideJob method) checkConformationalSearch() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkConnectivity() (schrodinger.application.matsci.rxn_path.CheckInput method) checkConstantVol() (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) checkConstraintCoords() (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) checkCorrectionParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) checkCustomKeysForTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) checkDeadlines() (schrodinger.active_learning.mq_worker.Worker method) checkDefinition() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) checkDefStrFormat() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) checkDict() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) checkDielectric() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) checkDissociationBondLength() (schrodinger.application.matsci.rxn_channel.CheckInput method) CHECKED_DEFAULT (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) CHECKED_DISABLED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) CHECKED_HOVER (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) CHECKED_PRESSED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) checkedFeatures() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) checkEdgetypes() (schrodinger.application.matsci.nano.check.CheckInput method) checkedText() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) CheckElement() (in module schrodinger.application.matsci.gsas.GSASIIElem) checkElements() (schrodinger.application.matsci.nano.check.CheckInput method) checkElitism() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkEntryDatabase() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) checkExcitedStatesType() (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController method) checkExistingFile() (schrodinger.application.matsci.nano.check.CheckInput method) checkFile() (schrodinger.pipeline.stage.Stage method) checkFileExists() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkFiles() (schrodinger.pipeline.stage.Stage method) checkFinalPointRange() (schrodinger.application.matsci.density_analysis_widget.MeasurementLine method) checkForceFieldLicense() (schrodinger.application.glide.glide.GlideJob method) checkForClashes() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) checkForCompletion() (schrodinger.pipeline.stages.qikprop.QikPropStage method) checkForInterStructureClashes() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) checkForIntraStructureClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) checkForMatch() (schrodinger.application.bioluminate.propfilter.BooleanDatabaseCriterion method) (schrodinger.application.bioluminate.propfilter.NumericalDatabaseCriterion method) (schrodinger.application.bioluminate.propfilter.StringDatabaseCriterion method) checkForRings() (schrodinger.application.matsci.montecarlo.ClashChecker method) checkFractionalRedundancies() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkFragmentLibs() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkFreezers() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkGenerations() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkGridfile() (schrodinger.application.glide.ligand_designer.GridgenTask method) checkGuess() (schrodinger.application.matsci.rxn_path.CheckInput method) checkHKLextc() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkHost() (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) checkIfNotAdsorbable() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkIfNotSimpleBond() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkin() (schrodinger.utils.license.License method) checkIndicies() (schrodinger.application.matsci.nano.check.CheckInput method) checkInitialPopulation() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkInoculate() (schrodinger.application.matsci.genetic_optimization.CheckInput method) CheckInput (class in schrodinger.application.matsci.genetic_optimization) (class in schrodinger.application.matsci.mecp_mod) (class in schrodinger.application.matsci.nano.check) (class in schrodinger.application.matsci.nano.particle) (class in schrodinger.application.matsci.nano.sheet) (class in schrodinger.application.matsci.nano.tube) (class in schrodinger.application.matsci.nano.xtal) (class in schrodinger.application.matsci.rxn_channel) (class in schrodinger.application.matsci.rxn_path) checkInput() (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) checkInputFile() (schrodinger.application.matsci.nano.xtal.CheckInput method) (schrodinger.application.matsci.rxn_channel.CheckInput method) checkInputFiles() (schrodinger.application.matsci.rxn_path.CheckInput method) checkInputfileTasktypeDriverpaths() (schrodinger.application.matsci.permittivity.ConfigWriter method) checkInputParams() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) (schrodinger.application.matsci.nano.xtal.Crystal method) (schrodinger.application.matsci.rxn_channel.Channels method) checkInputs() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.glide.DockingStage method) checkInterpolation() (schrodinger.application.matsci.rxn_path.CheckInput method) checkIntersectingBond() (schrodinger.application.matsci.nano.particle.Nanoparticle method) checkJMSWFOutputs() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) checkJob() (schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelection method) checkJobName() (schrodinger.application.matsci.rxn_path.CheckInput method) checkKeywordsLE() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) checkLatticeAngleValues() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkLatticeMaxVolume() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkLatticeParameters() (schrodinger.application.matsci.nano.xtal.CheckInput method) CheckLayout (class in schrodinger.ui.qt.formlayout) checkLigands() (schrodinger.application.livedesign.entry_types.Complexes method) checkLocalDatabase() (schrodinger.protein.tasks.blast.BlastTask method) checkMaeExt() (schrodinger.application.matsci.nano.check.CheckInput method) checkMaeFile() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkMagextc() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkMemoryLimit() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) checkMillerIndices() (schrodinger.application.matsci.nano.plane.CrystalPlane method) checkMixPrevious() (schrodinger.application.matsci.rxn_path.CheckInput method) checkModelFiles() (schrodinger.application.matsci.genetic_optimization.ChemInformatics class method) checkModule() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) checkMoleculeRings() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) checkMultipleMappings() (in module schrodinger.application.canvas.r_group) checkMultiplicity() (schrodinger.application.jaguar.gui.base_panel.ExcitedStateValidatorMixin method) checkMultiplicityProperty() (schrodinger.application.jaguar.gui.base_panel.PropertiesValidatorMixin method) checkNewCoordinate() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) checkNoRxnComplex() (schrodinger.application.matsci.rxn_path.CheckInput method) checkNumBilayers() (schrodinger.application.matsci.nano.check.CheckInput method) checkNumCells() (schrodinger.application.matsci.nano.check.CheckInput method) checkNumEntries() (schrodinger.application.livedesign.entry_types.BaseEntryData method) (schrodinger.application.livedesign.entry_types.Complexes method) checkNumRandomChannels() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkNumUnitCellParams() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkNumWalls() (schrodinger.application.matsci.nano.check.CheckInput method) checkOK() (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.Code method) (schrodinger.protein.getpdb_utility.WholePDB method) checkOperators() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkOrigin() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkOSFileLimit() (schrodinger.active_learning.al_driver.ActiveLearningJob method) checkout() (schrodinger.application.licensing.licadmin.LicenseResource method) checkout_model2_compounds() (in module schrodinger.application.desmond.license) checkout_phase_dbsearch_tokens() (in module schrodinger.application.phase.license) checkout_shape_screen_tokens() (in module schrodinger.application.phase.license) checkOutcome() (schrodinger.active_learning.al_node.LigandMLEvalNode method) (schrodinger.active_learning.al_node.LigandMLTrainNode method) (schrodinger.active_learning.al_node.PrepareSmilesNode method) (schrodinger.active_learning.al_node.ScoreProviderNode method) (schrodinger.application.phase.packages.shape_screen_al_node.PilotScoreNode method) (schrodinger.application.phase.packages.shape_screen_al_node.RescoreNode method) checkOutputFile() (schrodinger.application.matsci.rxn_channel.Channels method) checkParameters() (schrodinger.pipeline.stage.Stage method) checkPkaAtom() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) checkPkaAtoms() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) CHECKPOINT (schrodinger.application.matsci.desconfig.MSJStringer attribute) checkpoint() (schrodinger.utils.profiling.Timer method) CHECKPOINT_REQUESTED (schrodinger.application.desmond.cmj.JobStatus attribute) CHECKPOINT_WITH_RESTART_REQUESTED (schrodinger.application.desmond.cmj.JobStatus attribute) checkPopulationParam() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkPresumedTs() (schrodinger.application.matsci.rxn_path.CheckInput method) checkProducts() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) checkProperties() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkProperty() (schrodinger.application.matsci.genetic_optimization.Property method) checkPropertyType() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) checkPropTableForTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) checkRandomChannelsInput() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkRandomSeed() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkRandomTypes() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkRates() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkReactants() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkReactions() (schrodinger.application.pathfinder.route.RouteNode method) checkReflig() (schrodinger.application.glide.ligand_designer.GridgenTask method) checkReorder() (schrodinger.application.matsci.rxn_path.CheckInput method) checkRequiredProperties() (schrodinger.application.matsci.amorphous.BaseMoiety method) checkResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method) checkReverseInterpolation() (schrodinger.application.matsci.rxn_path.CheckInput method) checkRunning() (schrodinger.application.licensing.licadmin.LocalServerProcess method) checkRxnWFStructures() (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) checkSample() (schrodinger.application.matsci.rxn_path.CheckInput method) checkScaling() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkScanCoords() (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) checkSelection() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkSetTimeInterval() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) checkShapeParams() (schrodinger.application.matsci.nano.particle.CheckInput method) checkSizingPolicies() (schrodinger.ui.qt.table.DataViewerTable method) checkSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) checkSpaceGroup() (schrodinger.application.matsci.nano.xtal.CheckInput method) CheckSpin() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkSSextc() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkSSLaue() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkState() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) (schrodinger.ui.qt.tablewidget.Cell method) checkStructure() (schrodinger.structutils.filter.Filter method) (schrodinger.structutils.filter.SingleFilter method) (schrodinger.structutils.filter.SinglePropFilter method) (schrodinger.structutils.filter.SingleSmartsFilter method) checkStructurePairs() (schrodinger.application.matsci.rxn_path.CheckInput method) checkStructurePrep() (in module schrodinger.ui.qt.utils) checkStructures() (schrodinger.application.matsci.rxn_path.CheckInput method) checkTargets() (schrodinger.application.livedesign.entry_types.Complexes method) checkTau() (schrodinger.application.matsci.equilibrium_md.TrjBase method) checkTermFrag() (schrodinger.application.matsci.nano.check.CheckInput method) checkTerminationParams() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkTournamentSize() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkUpToIndex() (schrodinger.application.matsci.nano.check.CheckInput method) checkUserNames() (schrodinger.application.bioluminate.propfilter.PropertySelectorWithRanges method) (schrodinger.ui.qt.propertyselector.PropertySelector method) checkUserOutputs() (schrodinger.pipeline.pipeline.Pipeline method) checkValidateSettings() (in module schrodinger.application.steps.test) checkValidity() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.EnsembleClassFrame method) (schrodinger.application.desmond.gui.EnsembleTab method) (schrodinger.application.desmond.gui.IntegrationTab method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.OutputTab method) (schrodinger.application.desmond.gui.RandVelFrame method) (schrodinger.application.desmond.gui.RelaxFrame method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.gui.SimOptionsFrame method) checkValidOneLetterCodes() (schrodinger.application.matsci.amorphous.Moieties method) checkValidWeights() (schrodinger.application.matsci.amorphous.Moieties method) checkVel() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) (schrodinger.application.matsci.equilibrium_md.TrjBase method) checkVsdbFile() (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask method) checkWallSep() (schrodinger.application.matsci.nano.check.CheckInput method) checkWeights() (in module schrodinger.trajectory.prody.ensemble) (schrodinger.application.matsci.rxn_path.CheckInput method) Chem (schrodinger.protein.helm.helm_renderer.HexColor attribute) ChemConnectorItem (class in schrodinger.protein.helm.helm_renderer) ChemInformatics (class in schrodinger.application.matsci.genetic_optimization) ChemMonomerItem (class in schrodinger.protein.helm.helm_renderer) ChgAt (class in schrodinger.application.jaguar.utils) child_data (schrodinger.livedesign.registration.RegistrationData attribute) CHILD_NODE_INDEXES (schrodinger.application.matsci.permittivity.WorkflowParser attribute) children (schrodinger.application.jaguar.simple_spec.Peak attribute) chiral_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) CHIRAL_FLAG_0_MEANING (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) chiral_mol (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) chiral_res (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) ChiralCenterCountFilter (class in schrodinger.application.steps.filters) ChiralCenterCountFilter.Settings (class in schrodinger.application.steps.filters) ChiralFlag0Meaning (class in schrodinger.livedesign.preprocessor) chirality (schrodinger.structure.StructureAtom property) ChiralityMismatchError chm_bluebird (class in schrodinger.application.canvas.utils) chm_excel (class in schrodinger.application.canvas.utils) chm_sparse_bitset_from_string() (in module schrodinger.structutils.interactionfp) ChmCSVTools (class in schrodinger.application.canvas.utils) CHOICE_OFF (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) CHOICE_ON (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) choiceChanged (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector attribute) Choices (class in schrodinger.application.jaguar.workflow_keywords) CHOOSE_ATOMS (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) CHOOSE_CANONICAL_TAUTOMER (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) choose_color() (schrodinger.ui.qt.formlayout.ColorButton method) choose_ligand() (in module schrodinger.ui.chooseligand) choose_template_map() (schrodinger.application.jaguar.autots_rmsd.AutoTSTemplateAtomMapper method) chooseFromList() (schrodinger.ui.qt.propertyselector.PropertySelectorDialog method) chooseFromPT() (schrodinger.ui.qt.propertyselector.PropertySelectorDialog method) ChooseLigandDialog (class in schrodinger.ui.chooseligand) ChooseLigandModel (class in schrodinger.ui.chooseligand) chooseSolvent() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) chop() (in module schrodinger.utils.cgxutils) CHORUS_BOX_A_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_B_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BASE_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_C_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_KEY_VECTORS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) chorus_to_lower_triangle() (in module schrodinger.application.matsci.nano.xtal) (in module schrodinger.comparison.struc) CHOTHIA (schrodinger.application.bioluminate.antibody.scaffold_search.NumberingScheme attribute) ciexy_to_cie1960uv() (in module schrodinger.application.matsci.colorutils) ciexy_to_upvp() (in module schrodinger.application.matsci.colorutils) CIF (schrodinger.application.livedesign.export_tasks.FileFormat attribute) (schrodinger.infra.structure.FileFormat attribute) CIFWriter (class in schrodinger.structure) cion_name (schrodinger.application.matsci.packmol.SurfactantInfo attribute) cion_st (schrodinger.application.matsci.packmol.SurfactantInfo attribute) CircleAnnotator (class in schrodinger.ui.qt.structure2d) CIS (in module schrodinger.application.matsci.buildcomplex) cis_excitation_energies() (in module schrodinger.application.jaguar.textparser) CISPRO (schrodinger.ui.qt.rama.RamaResidueType attribute) CL (schrodinger.protein.annotation.AntibodyRegionLabel attribute) CLASH (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) clash_iterator() (in module schrodinger.structutils.interactions.steric_clash) clash_volume() (in module schrodinger.structutils.interactions.steric_clash) ClashChecker (class in schrodinger.application.matsci.montecarlo) clashers (schrodinger.protein.assignment.Interactors attribute) clashes (schrodinger.structutils.clash_resolution.ClashResolutionResult attribute) ClashResolutionResult (class in schrodinger.structutils.clash_resolution) class_evaluator (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) class_kwargs (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) CLASS_NUM (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) classandinstancemethod() (in module schrodinger.models.parameters) ClassEvaluator (class in schrodinger.application.matsci.genetic_optimization) ClassicToken (class in schrodinger.application.desmond.antlr3.tokens) classify_ab_assembly() (in module schrodinger.livedesign.biologics.registration) classify_antibody() (in module schrodinger.livedesign.biologics.registration) classify_nucleotide_polymer() (in module schrodinger.livedesign.biologics.registration) classify_overall_molecule() (in module schrodinger.livedesign.biologics.registration) classify_polymer() (in module schrodinger.livedesign.biologics.registration) classify_protein() (in module schrodinger.livedesign.biologics.registration) classifyMartiniFragments() (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule method) classifyNodeClusters() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) classifyRingNodeTypes() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) Clean (class in schrodinger.application.bioluminate.pml_menus) clean() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) (schrodinger.application.bioluminate.protein.protein.Refiner method) (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) clean_basisname() (in module schrodinger.application.jaguar.jaguar_keyword_utils) clean_beam_traceback() (in module schrodinger.seam.testing.fixtures) clean_beam_traceback_impl() (in module schrodinger.seam.testing.fixtures) clean_ct_properties() (schrodinger.application.desmond.cms.Cms static method) clean_hypo() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils) clean_st() (in module schrodinger.application.jaguar.autots_bonding) clean_string() (in module schrodinger.application.matsci.jobutils) clean_up() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) clean_up_polymer_brackets() (in module schrodinger.livedesign.preprocessor) clean_xtb_input() (in module schrodinger.application.xtb.runner) cleanAndUniquify() (schrodinger.application.matsci.jobutils.StringCleaner method) cleanArrowAndPlanes() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) cleanAtomProperties() (schrodinger.application.matsci.desmondutils.SystemBuilder method) cleanBoolCheck() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) cleanFiles() (schrodinger.application.matsci.jobutils.FileDownloader method) CleanOptionsCheckbox (class in schrodinger.application.matsci.builderwidgets) CleanStateMixin (class in schrodinger.ui.qt.widgetmixins.panelmixins) cleanStructProperties() (schrodinger.application.matsci.desmondutils.SystemBuilder method) CleanUp (class in schrodinger.application.desmond.kinetics.cleanup) (class in schrodinger.application.desmond.kinetics.mtd_cleanup) (class in schrodinger.application.desmond.mxmd.mxmd_cleanup) cleanup (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) cleanup() (in module schrodinger.application.desmond.fep_net_charge) cleanUp() (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) (schrodinger.active_learning.mq_worker.Worker method) cleanup() (schrodinger.application.desmond.cmj.Engine method) (schrodinger.application.glide.glide.ConstraintGroup method) (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.glide.glide.Gridgen method) (schrodinger.application.licensing.flexlm.License method) cleanUp() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) (schrodinger.application.steps.enumerators.RouteEnumerator method) (schrodinger.application.steps.ligprep.LigPrepStep method) cleanup() (schrodinger.protein.assignment.ProtAssign method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) cleanup_external() (in module schrodinger.application.mopac.utils) cleanup_martini_protein() (in module schrodinger.application.matsci.cgforcefield) cleanup_resources() (schrodinger.structutils.minimize.Minimizer method) cleanup_time() (in module schrodinger.application.desmond.fepana) cleanupChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) cleanUpCompletePipelinesDir() (schrodinger.seam.viz.watcherd.Watcher method) CleanupInput (class in schrodinger.application.prepwizard2.tasks) cleanupIntermediateFiles() (schrodinger.pipeline.pipeline.Pipeline method) cleanUpPBCBonds() (schrodinger.application.matsci.nano.xtal.PBCBonds method) cleanupReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) CleanupTask (class in schrodinger.application.prepwizard2.tasks) cleanupTempFiles() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.matsci.reportutils.PDFBuilder method) CLEAR (schrodinger.application.desmond.constants.CUSTOM_CHARGE_MODE attribute) clear() (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.desmond.cmj.JobManager method) (schrodinger.application.desmond.fep_scholar_util.FEPStructureObject method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.desmond.task.Task method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.matsci.cache.BaseCacheData method) (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.phase.featureselector.FeatureSelector method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.graphics3d.common.Group method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.membrane.Membrane_Model method) (schrodinger.structure._StructureAtomProperty method) (schrodinger.structure._StructureProperty method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) (schrodinger.ui.qt.propertyselector.PropertySelectorMenu method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) (schrodinger.ui.qt.structure2d.structure_item method) (schrodinger.ui.qt.swidgets.SFilteredListWidget method) (schrodinger.ui.qt.swidgets.SMARTSEdit method) (schrodinger.ui.qt.table_speed_up.DataCache method) (schrodinger.ui.residueselector.MutationSelectorMixin method) (schrodinger.utils.preferences.Preferences method) (schrodinger.utils.scollections.IdDict method) clear_all_tag() (schrodinger.utils.sea.sea.Sea method) clear_annotations() (in module schrodinger.livedesign.biologics.registration) clear_annotators() (schrodinger.ui.qt.structure2d.structure_item method) clear_asu_and_fractional_properties() (in module schrodinger.application.matsci.nano.xtal) clear_atom_props() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) clear_autots_atom_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_bond_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_st_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_bond_arrows() (schrodinger.ui.qt.structure2d.ColoredArrowAnnotator method) clear_edge_skip_fep() (in module schrodinger.application.desmond.skip_fep_utils) CLEAR_INVALID_WEDGE_BONDS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) clear_layout() (in module schrodinger.ui.qt.utils) clear_ld_library_path() (in module schrodinger.application.livedesign.pse_helpers) clear_marker_properties() (in module schrodinger.application.matsci.buildcomplex) clear_restrain() (schrodinger.application.desmond.cms.Cms method) clear_restraints() (in module schrodinger.application.desmond.stage.prepare.forcefield) clear_selection() (schrodinger.ui.qt.rama.Rama method) clear_structure_skip_fep() (in module schrodinger.application.desmond.skip_fep_utils) clear_user_restraints() (in module schrodinger.application.desmond.stage.prepare.structure) clear_wedge_bonds_from_achiral_centers() (in module schrodinger.livedesign.preprocessor) clearActions() (schrodinger.application.bioluminate.actions.factory.Factory method) clearAlignment() (schrodinger.ui.two_d_viewer.Cell method) clearAllCaching() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinAlignmentAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.protein.sequence.ProteinSequence method) clearAllConstraints() (schrodinger.application.jaguar.input.JaguarInput method) clearAnchors() (schrodinger.protein.alignment.BaseAlignment method) clearAslText() (schrodinger.application.matsci.mswidgets.MSAtomSelector method) clearAtom() (schrodinger.ui.qt.structure2d.RedSquareAnnotator method) clearAtomicBases() (schrodinger.application.jaguar.input.JaguarInput method) clearAtoms() (schrodinger.ui.qt.structure2d.CircleAnnotator method) clearAutQsarModel() (schrodinger.ui.two_d_viewer.TwoDViewer method) clearBrowserText() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) clearCache() (schrodinger.application.matsci.rdpattern.Pattern method) (schrodinger.ui.qt.structtable.StructureViewerDelegate method) (schrodinger.ui.qt.table.StructureDataViewerDelegate method) clearChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) clearConstraintsIfMultiStrucTab() (schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin method) clearConstraintsIfProject() (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin method) clearConstraintsIfWorkspace() (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) clearData() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method) clearDataForEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) clearDataFrame() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) clearDefaultPreset() (schrodinger.models.presets.PresetManager method) clearDescriptors() (schrodinger.protein.sequence.AbstractSequence method) clearDisulfideBondsCache() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) clearFilters() (schrodinger.ui.qt.filter_list.FilterListPopUp method) (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp method) (schrodinger.ui.qt.swidgets.SelectorWithPopUp method) clearFirstLevelParentChildJobs() (schrodinger.application.matsci.permittivity.WorkflowParser method) clearGraph() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) (schrodinger.ui.qt.rama.Rama method) clearHoverLabel() (schrodinger.ui.qt.schart.SChartView method) clearImageCache() (schrodinger.ui.qt.delegates.PictureDelegate method) ClearInitialSuggestionLineEdit (class in schrodinger.application.livedesign.panel_components) clearJobs() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) clearLabelPixmap() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) clearLabels() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) clearLigands() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) clearMessage() (schrodinger.ui.qt.appframework2.af2.StatusBar method) clearModifications() (schrodinger.ui.qt.rdmol_views.AbstractRDMolImageLabel method) clearPfam() (schrodinger.protein.sequence.AbstractSequence method) clearPicked() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) clearProject() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) clearProps() (in module schrodinger.application.matsci.equilibrium_md) clearReferenceHighlighting() (schrodinger.ui.two_d_viewer.TwoDTableModel method) clearResources() (schrodinger.application.licensing.licadmin.LocalServerProcess method) ClearResults() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) clearRowIfEmpty() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate method) clearRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) clearSelected() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) clearSelection() (schrodinger.application.livedesign.export_map_manager.MappingsComboBox method) (schrodinger.application.phase.featureselector.FeatureModel method) (schrodinger.application.phase.phase_markers.PhaseMarkers method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) clearSketcher() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) clearSpheres() (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager method) clearStatusMessage() (schrodinger.ui.qt.widgetmixins.basicmixins.StatusBarMixin method) clearStructs() (schrodinger.ui.qt.table.ViewerModel method) clearTable() (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.two_d_viewer.TwoDViewer method) clearTransformations() (schrodinger.ui.two_d_viewer.Cell method) clearUndoHistory() (schrodinger.ui.qt.network_visualizer.Graph method) click() (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) click_to_run (schrodinger.application.livedesign.upload_utils.CommandType attribute) ClickableLabel (class in schrodinger.ui.qt.label) clicked (schrodinger.application.job_monitor.job_monitor_table.JobDetailsArrowDelegate attribute) (schrodinger.ui.qt.delegates.PushButtonDelegate attribute) (schrodinger.ui.qt.label.ClickableLabel attribute) (schrodinger.ui.qt.tasks.taskwidgets.SpinnerLabel attribute) client (schrodinger.application.glide.http_client.AbstractGlideServerManager property) (schrodinger.application.glide.http_client.GlideServerManager property) (schrodinger.application.glide.http_client.NonBlockingGlideServerManager property) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq property) client_module (schrodinger.application.glide.http_client.GlideServerManager attribute) climb (schrodinger.application.matsci.espresso.qeinput.CustomNEBType attribute) clone() (schrodinger.application.matsci.genetic_optimization.StructureGenome method) (schrodinger.application.qsite.input.Cut method) (schrodinger.application.qsite.input.HydrogenCap method) (schrodinger.utils.sea.sea.Map method) clone_workspace_selection() (in module schrodinger.trajectory.utils) CLOSABLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) close() (in module schrodinger.ui.qt.appframework2.appmethods) (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.desmond.stage.analysis.Reporter method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.phase.packages.conformer_reader.ConformerReader method) (schrodinger.application.phase.packages.shape_ligprep.LigPrep method) (schrodinger.project.project.Project method) (schrodinger.rdkit.molio.BaseCsvMolReader method) (schrodinger.rdkit.molio.BasePfxMolReader method) (schrodinger.rdkit.molio.CsvMolWriter method) (schrodinger.rdkit.molio.PfxMolWriter method) (schrodinger.rdkit.molio.RdkitMolWriter method) (schrodinger.structure.MaestroReader method) (schrodinger.structure.MaestroTextReader method) (schrodinger.structure.MaestroWriter method) (schrodinger.structure.MultiFileStructureWriter method) (schrodinger.structure.PDBReader method) (schrodinger.structure.PDBWriter method) (schrodinger.structure.SmilesCsvReader method) (schrodinger.structure.SmilesCsvWriter method) (schrodinger.structure.SmilesWriter method) (schrodinger.structure.StructureReader method) (schrodinger.structure.StructureWriter method) (schrodinger.utils.cgxutils.FragmentLibrary method) (schrodinger.utils.fileutils.MultiFileReader method) (schrodinger.utils.multifpfile.MultiFPFile method) (schrodinger.utils.multifpfile.MultiFPFileWriter method) (schrodinger.utils.pymol.PymolInstance method) (schrodinger.utils.pymol.PymolScriptInstance method) close_logger_file_handlers() (in module schrodinger.application.matsci.textlogger) close_output() (schrodinger.application.desmond.bennett.CalcBAR method) closeBanner (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner attribute) (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner attribute) closeBanner() (schrodinger.ui.qt.utils.MaestroPythonBannerManager method) closeBlockIfNecessary() (schrodinger.structure.Structure method) (schrodinger.structure.TextualStructure method) CloseButton (class in schrodinger.ui.qt.swidgets) CloseContact (schrodinger.protein.annotation.BINDING_SITE attribute) closed (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector attribute) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel attribute) closeDialog() (schrodinger.application.desmond.gui.AdvOptionsFrame method) closeEvent() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) (schrodinger.application.matsci.chargegui.ChargeDialog method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) (schrodinger.application.matsci.sliceplot.SlicePlot method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) (schrodinger.ui.qt.appframework.AppDockWidget method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.baseapp.DockWidget method) (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) (schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackMixin method) (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) closeFeatureEditDialog (schrodinger.application.phase.phase_markers.PhaseMarkers attribute) closeFile() (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.WholePDB method) closeFiles() (schrodinger.protein.getpdb_utility.Code method) closeKnimePanel() (schrodinger.ui.qt.appframework2.knime_af2.KnimeNodeMixin method) closePanel() (schrodinger.application.bioluminate.pml_menus.ResultsWindow method) (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) closeWindow() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) clustal (schrodinger.utils.fileutils.SeqFormat attribute) ClustalAligner (class in schrodinger.protein.align) ClustalJob (class in schrodinger.protein.tasks.clustal) cluster() (schrodinger.protein.assignment.ProtAssign method) cluster_hits() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) cluster_hits_by_features() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) cluster_hits_by_scaffold() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) cluster_paths() (schrodinger.application.desmond.kinetics.cleanup.CleanUp method) cluster_unbinding_paths() (in module schrodinger.application.desmond.kinetics.utils) ClusterAnalysisStep (class in schrodinger.application.matsci.jwsteps) ClusterBy (class in schrodinger.application.phase.shape_screen_reporter.option_utils) clusterDM() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) clusterFP() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) clustering (schrodinger.application.livedesign.upload_utils.CommandType attribute) ClusterStatisticsPlotDialog (class in schrodinger.application.canvas.clustergui) CluUtil (class in schrodinger.application.macromodel.utils) CM_TO_ANGSTROM (schrodinger.application.matsci.nano.xtal.Crystal attribute) CMD (schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis attribute) (schrodinger.application.desmond.stage.fep_mapper.CalcDdg attribute) cmd (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.application.matsci.multiapp.CMD_DRIVER_DATA attribute) (schrodinger.tasks.tasks.SubprocessMixin attribute) CMD_DRIVER_DATA (class in schrodinger.application.matsci.multiapp) CmdJobMixin (class in schrodinger.application.matsci.multiapp) CmdJobTask (class in schrodinger.tasks.jobtasks) CMDLINE (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.CallingContext attribute) CMDLINE_GEOMETRIES (in module schrodinger.application.matsci.buildcomplex) CMDLINE_TO_GEOMETRY (in module schrodinger.application.matsci.buildcomplex) cmdlist_to_cmd() (in module schrodinger.job.jobwriter) CmlFileReader (class in schrodinger.application.scaffold_enumeration.rdcml) cmp() (schrodinger.application.jaguar.results.BondCharge method) (schrodinger.application.jaguar.results.Dipole method) (schrodinger.application.jaguar.results.Orbital method) (schrodinger.application.jaguar.results.ThermoProp method) Cms (class in schrodinger.application.desmond.cms) CMS (schrodinger.application.livedesign.export_tasks.FileFormat attribute) cms (schrodinger.application.matsci.desmondutils.DesmondModel attribute) CMS (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) cms2pdb() (in module schrodinger.application.desmond.cms_utils) CMS_ENDING (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) cms_file (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) (schrodinger.project.project.ProjectRow property) cms_fileChanged (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) cms_fileReplaced (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) cms_model (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame attribute) CMS_OUT_FNAME (schrodinger.application.desmond.stage.launcher.FepMembraneLauncher attribute) CMS_PARSER (schrodinger.application.matsci.permittivity.CMSParser attribute) cms_structure_reader (schrodinger.project.project.ProjectRow property) cms_trj_optional_job_spec() (in module schrodinger.application.matsci.jobutils) cms_writer() (in module schrodinger.application.matsci.desmondutils) CmsModel (class in schrodinger.application.desmond.meta) (class in schrodinger.application.matsci.equilibrium_md) cmsModels() (schrodinger.ui.qt.input_selector.InputSelector method) CMSParser (class in schrodinger.application.matsci.permittivity) CMSReader (class in schrodinger.application.desmond.ffiostructure) CN_PRESET (schrodinger.application.matsci.mlearn.features.CrystalNNFeatures attribute) CNSData (class in schrodinger.application.desmond.cns_io) COARSE (schrodinger.application.matsci.qualityslider.QualitySlider attribute) CoarseGrainBond (class in schrodinger.application.matsci.cg_mapping) CoarseGrainNameEdit (class in schrodinger.application.matsci.atomicsymbolsgui) Code (class in schrodinger.protein.getpdb_utility) code (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.protein.nonstandard_residues.AminoAcid property) COL_NAMES (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame attribute) COL_NUM_POS (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame attribute) CollagenHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) collapseAll() (schrodinger.application.matsci.mswidgets.MultiStageArea method) collapsed (schrodinger.project.project.EntryGroup property) collect_bbkeys() (in module schrodinger.application.bb_database.bb_task_utils) collect_dg_values() (in module schrodinger.application.desmond.stage.app.fragment_linking.utils) collect_diagnostics() (in module schrodinger.application.licensing.licserver.client) collect_inputfile() (in module schrodinger.application.desmond.cmj) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher method) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper method) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher method) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup method) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis method) (schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher method) (schrodinger.application.desmond.stage.launcher.FepLauncher method) (schrodinger.application.desmond.stage.launcher.Multisim method) (schrodinger.application.desmond.stage.simulate.ReInit method) collect_logs() (in module schrodinger.application.desmond.task) collect_unique_structures() (in module schrodinger.application.matsci.coarsegrain) collectAnharmonicFrequencies() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) collectData() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) collectDiagnosticsRequested (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget attribute) collectEnergies() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) collectFits() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) collectInternals() (schrodinger.application.matsci.rxn_path.ReactionCoords method) collection() (in module schrodinger.application.scaffold_enumeration.layered) collectIonCandidates() (schrodinger.application.ligprep.ionizer.Ionizer method) collectionChanged() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) CollectJobDiagnosticsDialog (class in schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) CollectJobDiagnosticsModel (class in schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) CollectJobDiagnosticsTask (class in schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) CollectJobDiagnosticsTask.output (class in schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) Color (class in schrodinger.structutils.color) color (schrodinger.structure.StructureAtom property) (schrodinger.surface.Surface property) (schrodinger.ui.qt.color_picker.ButtonWithColorPicker property) (schrodinger.ui.qt.formlayout.ColorButton attribute) color() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) color_arg_to_rgb() (in module schrodinger.graphics3d.common) color_atom_groups() (in module schrodinger.application.matsci.maestrocmds) color_atoms() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.matsci.maestrocmds) color_atoms_rgb() (in module schrodinger.application.bioluminate.pml_menus) color_by_element() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.matsci.maestrocmds) color_chainbow_groups() (in module schrodinger.application.bioluminate.pml_menus) color_changed (schrodinger.ui.qt.swidgets.ColorWidget attribute) COLOR_DEFAULT (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager attribute) color_dict (in module schrodinger.application.bioluminate.pml_menus) color_distance() (in module schrodinger.application.matsci.colorutils) COLOR_GRADIENT (schrodinger.seam.viz.render.ColorByTransformCPUTimeStyler attribute) color_potential_surface() (in module schrodinger.application.bioluminate.escomp) color_scheme (schrodinger.surface.Surface property) COLOR_SELECTED (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager attribute) color_source (schrodinger.surface.Surface property) color_temperature() (in module schrodinger.application.matsci.colorutils) color_text() (in module schrodinger.application.matsci.gutils) colorAt() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) colorAtoms() (schrodinger.application.bioluminate.pml_menus.AutoColorObjects method) (schrodinger.application.bioluminate.pml_menus.AutoCycleColor method) (schrodinger.application.bioluminate.pml_menus.RegionInfo method) ColorAtomsByBFactor (class in schrodinger.application.bioluminate.pml_menus) ColorAtomsBySpectrum (class in schrodinger.application.bioluminate.pml_menus) ColorButton (class in schrodinger.ui.qt.formlayout) ColorBy (class in schrodinger.surface) ColorByElementSubMenu (class in schrodinger.application.bioluminate.pml_menus) ColorByLicenseStyler (class in schrodinger.seam.viz.render) colorByMolecule() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) colorByRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) ColorByStageStatusStyler (class in schrodinger.seam.viz.render) ColorByStatusStyler (class in schrodinger.seam.viz.render) ColorBySubstructure (class in schrodinger.application.bioluminate.pml_menus) colorByThreshold() (schrodinger.ui.qt.dendrogram.GuiPanel method) ColorByTransformCPUTimeStyler (class in schrodinger.seam.viz.render) ColorCalphasByBFactor (class in schrodinger.application.bioluminate.pml_menus) ColorCalphasBySpectrum (class in schrodinger.application.bioluminate.pml_menus) ColorCarbons (class in schrodinger.application.bioluminate.pml_menus) ColorCarbonsBySpectrum (class in schrodinger.application.bioluminate.pml_menus) ColorChainbows (class in schrodinger.application.bioluminate.pml_menus) ColorChains (class in schrodinger.application.bioluminate.pml_menus) colorChains() (schrodinger.application.bioluminate.pml_menus.ColorChains method) ColorChainsByCalpha (class in schrodinger.application.bioluminate.pml_menus) ColorChainsByCarbon (class in schrodinger.application.bioluminate.pml_menus) ColorChainSubMenu (class in schrodinger.application.bioluminate.pml_menus) colorChanged (schrodinger.ui.qt.formlayout.ColorButton attribute) ColorChooserPanel (class in schrodinger.application.bioluminate.pml_menus) ColoredArrowAnnotator (class in schrodinger.ui.qt.structure2d) ColorFrom (class in schrodinger.surface) ColorGradients (class in schrodinger.ui.qt.standard.design_tokens) ColorHNOS (class in schrodinger.application.bioluminate.pml_menus) ColorHydrogens (class in schrodinger.application.bioluminate.pml_menus) coloring() (schrodinger.surface.Surface method) ColorLabel (class in schrodinger.application.bioluminate.pml_menus) ColorLayout (class in schrodinger.ui.qt.formlayout) ColorMenu (class in schrodinger.application.bioluminate.pml_menus) ColorObject (class in schrodinger.application.bioluminate.pml_menus) ColorPairFrame (class in schrodinger.application.matsci.reaction_workflow_gui_utils) ColorParam (class in schrodinger.ui.qt.color_picker) ColorRamp (class in schrodinger.structutils.color) ColorRecentCarbons (class in schrodinger.application.bioluminate.pml_menus) ColorRecentHydrogens (class in schrodinger.application.bioluminate.pml_menus) ColorRecentObjects (class in schrodinger.application.bioluminate.pml_menus) ColorRibbonMixin (class in schrodinger.application.bioluminate.pml_menus) COLORS (schrodinger.structutils.color.RainbowColorRamp attribute) (schrodinger.ui.qt.schart.SChart attribute) ColorScheme (class in schrodinger.structutils.color) ColorSelector (class in schrodinger.application.dendrogram.gradientSelector) ColorSpectrumSubMenu (class in schrodinger.application.bioluminate.pml_menus) ColorSubstructureSubMenu (class in schrodinger.application.bioluminate.pml_menus) colorSurfByPatches() (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) ColorWidget (class in schrodinger.ui.qt.swidgets) Column (class in schrodinger.ui.qt.table_helper) (class in schrodinger.ui.qt.tablewidget) COLUMN (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullTable attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitTable attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesModelHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.RelaxedScanCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetTableView attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute)

Column (schrodinger.application.livedesign.panel_components.ExportTableModel attribute) (schrodinger.application.livedesign.panel_components.ExportTableView property) (schrodinger.application.phase.featureselector.FeatureModel attribute) (schrodinger.application.phase.phase_widgets.HypothesisModel attribute) (schrodinger.ui.picking.PickResidueModel attribute) COLUMN (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) Column (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) column (schrodinger.ui.qt.tablewidget.Cell property) column() (schrodinger.application.livedesign.panel_components.ColumnCheckboxItem method) column_count() (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) column_ids (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) column_idsChanged (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) column_idsReplaced (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) column_name (schrodinger.application.bioluminate.pose_filtering.csv_filter.FilterParameters attribute) COLUMN_TYPE (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUpDelegate attribute) columnActionSelected() (schrodinger.ui.two_d_viewer.TwoDViewer method) columnChanged() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) ColumnCheckboxItem (class in schrodinger.application.livedesign.panel_components) columnCount() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.table.ViewerModel method) (schrodinger.ui.qt.table_helper.RowBasedListModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) columnCountChanged() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) ColumnData (class in schrodinger.application.matsci.kmc) ColumnDataType (schrodinger.tasks.ldtasks.FileColumn attribute) (schrodinger.tasks.ldtasks.IntColumn attribute) (schrodinger.tasks.ldtasks.LDColumn attribute) (schrodinger.tasks.ldtasks.PoseColumn attribute) (schrodinger.tasks.ldtasks.RealColumn attribute) (schrodinger.tasks.ldtasks.StringColumn attribute) (schrodinger.tasks.ldtasks.StructureColumn attribute) columnGetDataName() (schrodinger.infra.table.Table method) columnGetDataType() (schrodinger.infra.table.Table method) columnGetName() (schrodinger.infra.table.Table method) columnGetPersistent() (schrodinger.infra.table.Table method) columnGetProperty() (schrodinger.infra.table.Table method) columnGetVisible() (schrodinger.infra.table.Table method) columnGetWidth() (schrodinger.infra.table.Table method) columnHasAllSameResidues() (schrodinger.protein.alignment.BaseAlignment method) ColumnIterator (class in schrodinger.ui.qt.tablewidget) columnResized() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) COLUMNS (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.kmc.AtomsTable attribute) (schrodinger.application.matsci.kmc.FragmentsTable attribute) (schrodinger.application.matsci.kmc.FramesTable attribute) (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) (schrodinger.application.matsci.kmc.MoleculesTable attribute) (schrodinger.application.matsci.kmc.PairsTable attribute) (schrodinger.application.matsci.kmc.SchrodingerTable attribute) (schrodinger.application.matsci.kmc.SegmentsTable attribute) (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) (schrodinger.application.matsci.kmc.SuperExchangeTable attribute) (schrodinger.application.matsci.kmc.Table attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.SpectrumFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) columns (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec attribute) columns() (schrodinger.protein.alignment.BaseAlignment method) columnsChanged (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) (schrodinger.application.livedesign.summary.SummaryTableSpec attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec attribute) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec attribute) ColumnSelectionModel (class in schrodinger.application.livedesign.panel_components) ColumnSelectionProxyModel (class in schrodinger.application.livedesign.panel_components) ColumnSeries (class in schrodinger.ui.qt.mapperwidgets.plptable) columnSetName() (schrodinger.infra.table.Table method) columnSetPersistent() (schrodinger.infra.table.Table method) columnSetProperty() (schrodinger.infra.table.Table method) columnSetVisible() (schrodinger.infra.table.Table method) columnSetWidth() (schrodinger.infra.table.Table method) columnsInserted() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) columnsMoved() (schrodinger.ui.qt.table.DataViewerTable method) columnsRemoved() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) columnsReplaced (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) (schrodinger.application.livedesign.summary.SummaryTableSpec attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec attribute) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec attribute) columnStateChanged (schrodinger.ui.qt.table_helper.CheckableHeaderView attribute) columnWidth() (schrodinger.ui.two_d_viewer.TwoDTableView method) COM_DRX (schrodinger.application.matsci.kmc.PairsMixin attribute) COM_DRY (schrodinger.application.matsci.kmc.PairsMixin attribute) COM_DRZ (schrodinger.application.matsci.kmc.PairsMixin attribute) COMBIGLD_REPLACEMENTS (schrodinger.application.matsci.rxn_path.CheckInput attribute) combinations() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (schrodinger.structutils.rgroup_enumerate.RGroupEnumerator method) CombinatorialScreener (class in schrodinger.application.combinatorial_screen.combinatorial_screener) combine_alignments() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) combine_diverse_structures() (in module schrodinger.application.combinatorial_diversity.driver_utils) combine_fingerprints() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) combine_helm() (in module schrodinger.livedesign.biologics.registration) combine_hit_files() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) (in module schrodinger.application.phase.packages.phase_screen_utils) combine_log_files() (in module schrodinger.active_learning.mq_worker) (in module schrodinger.application.combinatorial_screen.driver_utils) (in module schrodinger.application.phase.packages.phase_utils) combine_oned_hits() (in module schrodinger.application.phase.packages.oned_task_utils) combine_output_files() (in module schrodinger.rdkit.molio) combine_rings() (in module schrodinger.application.desmond.r_group_asl) combine_sentences() (in module schrodinger.application.jaguar.gui.basis_selector) combine_trajectories() (in module schrodinger.application.matsci.desmondutils) combine_two_structures() (in module schrodinger.application.matsci.genetic_optimization) combine_vdw() (in module schrodinger.application.desmond.cms) combineAndReorder() (schrodinger.application.matsci.rxn_channel.Products method) CombinedChainDisulfideBond (class in schrodinger.protein.residue) CombinedChainProteinAlignment (class in schrodinger.protein.alignment) CombinedChainProteinSequence (class in schrodinger.protein.sequence) CombinedChainProteinSequenceAnnotations (class in schrodinger.protein.annotation) CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES (class in schrodinger.protein.annotation) CombinedChainResidueWrapper (class in schrodinger.protein.residue) CombinedChainSequenceAnnotationMeta (class in schrodinger.protein.annotation) CombinedChainSequenceMeta (class in schrodinger.protein.sequence) CombinedProteinFepMapper (class in schrodinger.application.desmond.stage.fep_mapper) CombinedProteinMsjGenerator (class in schrodinger.application.desmond.msj_generator.fep.protein) combinedResForSplitRes() (schrodinger.protein.alignment.CombinedChainProteinAlignment method) combinedSeqForSplitSeq() (schrodinger.protein.alignment.CombinedChainProteinAlignment method) CombinedUi (class in schrodinger.application.jaguar.gui.tabs.base_tab) combineFollows() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) combineMapWith() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) combineOnsagerCsv() (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) COMBINER (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.CombinerStep attribute) CombinerStep (class in schrodinger.application.matsci.jwsteps) CombineStage (class in schrodinger.pipeline.stages.combine) combineTrace() (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) combo (schrodinger.application.matsci.kmcgui.PlotInfo attribute) combo_find_data() (in module schrodinger.ui.qt.utils) COMBO_TEXT (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) ComboBlockingFunctionTask (class in schrodinger.tasks.tasks) COMBOBOX_ROLE (schrodinger.ui.qt.delegates.ComboBoxDelegate attribute) ComboBoxDelegate (class in schrodinger.ui.qt.delegates) ComboBoxWithPopUp (class in schrodinger.ui.qt.pop_up_widgets) ComboJobMixin (class in schrodinger.tasks.jobtasks) ComboJobTask (class in schrodinger.tasks.jobtasks) ComboRadioSelector (class in schrodinger.application.jaguar.gui.tabs.theory_tab) ComboSubprocessTask (class in schrodinger.tasks.tasks) ComInfo (class in schrodinger.application.matsci.clusterstruct) command() (schrodinger.application.bioluminate.pml_menus.AddHydrogens method) (schrodinger.application.bioluminate.pml_menus.AntibodyPreset method) (schrodinger.application.bioluminate.pml_menus.Around method) (schrodinger.application.bioluminate.pml_menus.AutoColorCarbons method) (schrodinger.application.bioluminate.pml_menus.AutoColorObjects method) (schrodinger.application.bioluminate.pml_menus.AutoCycleCarbonColor method) (schrodinger.application.bioluminate.pml_menus.AutoCycleColor method) (schrodinger.application.bioluminate.pml_menus.BAndSPreset method) (schrodinger.application.bioluminate.pml_menus.BFactorPreset method) (schrodinger.application.bioluminate.pml_menus.Center method) (schrodinger.application.bioluminate.pml_menus.Clean method) (schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor method) (schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum method) (schrodinger.application.bioluminate.pml_menus.ColorBySubstructure method) (schrodinger.application.bioluminate.pml_menus.ColorCalphasByBFactor method) (schrodinger.application.bioluminate.pml_menus.ColorCalphasBySpectrum method) (schrodinger.application.bioluminate.pml_menus.ColorCarbons method) (schrodinger.application.bioluminate.pml_menus.ColorCarbonsBySpectrum method) (schrodinger.application.bioluminate.pml_menus.ColorChainbows method) (schrodinger.application.bioluminate.pml_menus.ColorChains method) (schrodinger.application.bioluminate.pml_menus.ColorChainsByCalpha method) (schrodinger.application.bioluminate.pml_menus.ColorChainsByCarbon method) (schrodinger.application.bioluminate.pml_menus.ColorHNOS method) (schrodinger.application.bioluminate.pml_menus.ColorHydrogens method) (schrodinger.application.bioluminate.pml_menus.ColorObject method) (schrodinger.application.bioluminate.pml_menus.ColorRecentCarbons method) (schrodinger.application.bioluminate.pml_menus.ColorRecentHydrogens method) (schrodinger.application.bioluminate.pml_menus.ColorRecentObjects method) (schrodinger.application.bioluminate.pml_menus.ComputeSurfaceArea method) (schrodinger.application.bioluminate.pml_menus.CountAtoms method) (schrodinger.application.bioluminate.pml_menus.CreateEntry method) (schrodinger.application.bioluminate.pml_menus.DefaultPreset method) (schrodinger.application.bioluminate.pml_menus.DeleteAll method) (schrodinger.application.bioluminate.pml_menus.DeleteAtoms method) (schrodinger.application.bioluminate.pml_menus.DeleteProject method) (schrodinger.application.bioluminate.pml_menus.DeleteSelections method) (schrodinger.application.bioluminate.pml_menus.DeleteWS method) (schrodinger.application.bioluminate.pml_menus.Disable method) (schrodinger.application.bioluminate.pml_menus.Duplicate method) (schrodinger.application.bioluminate.pml_menus.ExcludeFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludeInorganicFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludeOrganicFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludePolymerFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludeSolventFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludeVisibleFromSelection method) (schrodinger.application.bioluminate.pml_menus.Expand method) (schrodinger.application.bioluminate.pml_menus.Extend method) (schrodinger.application.bioluminate.pml_menus.GenerateInterfaceSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateLigandSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateSurfResSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateSymmetryMates method) (schrodinger.application.bioluminate.pml_menus.HideAllOthers method) (schrodinger.application.bioluminate.pml_menus.HideAtoms method) (schrodinger.application.bioluminate.pml_menus.HideEverything method) (schrodinger.application.bioluminate.pml_menus.HideHydrogens method) (schrodinger.application.bioluminate.pml_menus.HideLabel method) (schrodinger.application.bioluminate.pml_menus.HideMainChain method) (schrodinger.application.bioluminate.pml_menus.HideNonBonded method) (schrodinger.application.bioluminate.pml_menus.HidePolarHydrogens method) (schrodinger.application.bioluminate.pml_menus.HideRibbons method) (schrodinger.application.bioluminate.pml_menus.HideSideChain method) (schrodinger.application.bioluminate.pml_menus.HideSurface method) (schrodinger.application.bioluminate.pml_menus.HideSymmetryMates method) (schrodinger.application.bioluminate.pml_menus.HideWaters method) (schrodinger.application.bioluminate.pml_menus.IncludeInSelection method) (schrodinger.application.bioluminate.pml_menus.IncludeVisibleInSelection method) (schrodinger.application.bioluminate.pml_menus.InterfacePreset method) (schrodinger.application.bioluminate.pml_menus.LabelAtom method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByProp method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByStereo method) (schrodinger.application.bioluminate.pml_menus.LabelChains method) (schrodinger.application.bioluminate.pml_menus.LabelResidues method) (schrodinger.application.bioluminate.pml_menus.LigandPreset method) (schrodinger.application.bioluminate.pml_menus.MAction method) (schrodinger.application.bioluminate.pml_menus.MakeProjectEntry method) (schrodinger.application.bioluminate.pml_menus.MWidgetAction method) (schrodinger.application.bioluminate.pml_menus.Orient method) (schrodinger.application.bioluminate.pml_menus.Origin method) (schrodinger.application.bioluminate.pml_menus.PolarContactsObject method) (schrodinger.application.bioluminate.pml_menus.PolarContactsOnlyMainchain method) (schrodinger.application.bioluminate.pml_menus.PolarContactsOnlySidechain method) (schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyAtoms method) (schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyNonSolvent method) (schrodinger.application.bioluminate.pml_menus.PolarContactsToEntry method) (schrodinger.application.bioluminate.pml_menus.PolarContactsToEntryWithoutSolvent method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutIntraMainchain method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutMainchain method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutSolvent method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithSidechains method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithSolvent method) (schrodinger.application.bioluminate.pml_menus.PrettyPubPreset method) (schrodinger.application.bioluminate.pml_menus.Quit method) (schrodinger.application.bioluminate.pml_menus.Ray method) (schrodinger.application.bioluminate.pml_menus.Reinitialize method) (schrodinger.application.bioluminate.pml_menus.RemoveHydrogens method) (schrodinger.application.bioluminate.pml_menus.RemovePC method) (schrodinger.application.bioluminate.pml_menus.RemoveWaters method) (schrodinger.application.bioluminate.pml_menus.Rename method) (schrodinger.application.bioluminate.pml_menus.RestrictSelection method) (schrodinger.application.bioluminate.pml_menus.RestrictToInorganic method) (schrodinger.application.bioluminate.pml_menus.RestrictToOrganic method) (schrodinger.application.bioluminate.pml_menus.RestrictToPolymer method) (schrodinger.application.bioluminate.pml_menus.RestrictToSolvent method) (schrodinger.application.bioluminate.pml_menus.RestrictToVisible method) (schrodinger.application.bioluminate.pml_menus.Select method) (schrodinger.application.bioluminate.pml_menus.SelectWithinAny method) (schrodinger.application.bioluminate.pml_menus.SelectWithinCalpha method) (schrodinger.application.bioluminate.pml_menus.SelectWithinChain method) (schrodinger.application.bioluminate.pml_menus.SelectWithinEntry method) (schrodinger.application.bioluminate.pml_menus.SelectWithinMolecule method) (schrodinger.application.bioluminate.pml_menus.SelectWithinResidue method) (schrodinger.application.bioluminate.pml_menus.ShowBAndS method) (schrodinger.application.bioluminate.pml_menus.ShowCartoonOrRibbon method) (schrodinger.application.bioluminate.pml_menus.ShowLabel method) (schrodinger.application.bioluminate.pml_menus.ShowLigandLines method) (schrodinger.application.bioluminate.pml_menus.ShowLigandSpheres method) (schrodinger.application.bioluminate.pml_menus.ShowLigandTubes method) (schrodinger.application.bioluminate.pml_menus.ShowLines method) (schrodinger.application.bioluminate.pml_menus.ShowMesh method) (schrodinger.application.bioluminate.pml_menus.ShowNonBonded method) (schrodinger.application.bioluminate.pml_menus.ShowNonBondedSpheres method) (schrodinger.application.bioluminate.pml_menus.ShowSpheres method) (schrodinger.application.bioluminate.pml_menus.ShowSurface method) (schrodinger.application.bioluminate.pml_menus.ShowTubes method) (schrodinger.application.bioluminate.pml_menus.SimplePreset method) (schrodinger.application.bioluminate.pml_menus.SumFormalCharge method) (schrodinger.application.bioluminate.pml_menus.SumPartialCharge method) (schrodinger.application.bioluminate.pml_menus.TechnicalPreset method) (schrodinger.application.bioluminate.pml_menus.ToggleState method) (schrodinger.application.bioluminate.pml_menus.Zoom method) (schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro method) (schrodinger.ui.chooseligand.TestApp method) command_option (schrodinger.maestro_utils.find_tool_bar.constants.SEARCH_OPTION_DETAILS attribute) commandCallback() (schrodinger.ui.two_d_viewer.TwoDViewer method) CommandError commandify() (in module schrodinger.application.desmond.util) CommandLine (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) Commandline (schrodinger.job.jobcontrol.Job property) commandLine() (schrodinger.job.app.App method) commandLineArgs() (schrodinger.ui.qt.config_dialog.StartDialogParams method) commandLineOptions() (schrodinger.application.jaguar.utils.GenOptions method) (schrodinger.ui.qt.config_dialog.StartDialogParams method) CommandType (class in schrodinger.application.livedesign.upload_utils) commence() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) COMMENT (schrodinger.application.matsci.packmol.PackmolKw attribute) commit() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.desmond.maestro.Workspace method) commitDataToSelected (schrodinger.application.jaguar.gui.input_tab_widgets.CommitMultipleDelegate attribute) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate attribute) commitDataToSelected() (schrodinger.application.jaguar.gui.utils.ProjTableLikeView method) CommitMultipleDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) COMMON_COLUMNS (schrodinger.application.matsci.kmc.SitesMixin attribute) common_fr_data (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) common_fr_dataChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) common_fr_dataReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) common_get_job_spec_from_args() (in module schrodinger.active_learning.al_driver) common_parse_args() (in module schrodinger.active_learning.al_driver) common_validate_args() (in module schrodinger.active_learning.al_driver) CommonErrorNode (class in schrodinger.application.desmond.antlr3.tree) CommonToken (class in schrodinger.application.desmond.antlr3.tokens) CommonTokenStream (class in schrodinger.application.desmond.antlr3.streams) CommonTree (class in schrodinger.application.desmond.antlr3.tree) CommonTreeAdaptor (class in schrodinger.application.desmond.antlr3.tree) CommonTreeNodeStream (class in schrodinger.application.desmond.antlr3.tree) comp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) comp_atom_total (schrodinger.application.desmond.cms.Cms property) COMP_SCORE (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) COMPACT (schrodinger.application.phase.packages.conformer_storage.Format attribute) CompactSolventSelector (class in schrodinger.application.matsci.jagwidgets) ComparableMol (class in schrodinger.rdkit.filtering) comparator() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) compare_a_none() (in module schrodinger.application.jaguar.jaguar_diff) compare_angle() (in module schrodinger.application.jaguar.jaguar_diff) compare_base_features() (in module schrodinger.application.phase.compare_utils) compare_diff_chunks() (in module schrodinger.utils.compare) compare_diff_lines() (in module schrodinger.utils.compare) compare_float() (in module schrodinger.application.jaguar.jaguar_diff) compare_hypo_add_cts() (in module schrodinger.application.phase.compare_utils) compare_hypo_cnst() (in module schrodinger.application.phase.compare_utils) compare_hypo_masks() (in module schrodinger.application.phase.compare_utils) compare_hypo_qsar() (in module schrodinger.application.phase.compare_utils) compare_hypo_rad() (in module schrodinger.application.phase.compare_utils) compare_hypo_ref() (in module schrodinger.application.phase.compare_utils) compare_hypo_rules() (in module schrodinger.application.phase.compare_utils) compare_hypo_sites() (in module schrodinger.application.phase.compare_utils) compare_hypo_tol() (in module schrodinger.application.phase.compare_utils) compare_hypo_vol() (in module schrodinger.application.phase.compare_utils) compare_hypos() (in module schrodinger.application.phase.compare_utils) compare_mean_stdev_samples() (in module schrodinger.application.desmond.new_fep_edge_data) compare_mean_stdev_samples_2() (in module schrodinger.application.desmond.new_fep_edge_data) compare_mean_stdev_samples_4() (in module schrodinger.application.desmond.new_fep_edge_data) compare_mmp_transformations() (in module schrodinger.application.phase.packages.mmp_compare_utils) compare_molecular_formulas() (in module schrodinger.application.matsci.reorder) compare_screen_results() (in module schrodinger.application.phase.compare_utils) compare_sites() (in module schrodinger.application.phase.compare_utils) compare_sphere_lists() (in module schrodinger.application.phase.compare_utils) compare_spheres() (in module schrodinger.application.phase.compare_utils) compare_structure_coordinates() (in module schrodinger.application.phase.compare_utils) compare_structure_coordinates_subset() (in module schrodinger.application.phase.compare_utils) compare_transformations() (in module schrodinger.application.phase.compare_utils) ComparisonFrame (class in schrodinger.application.matsci.reordergui) ComparisonListWidget (class in schrodinger.application.matsci.reordergui) compatibleChildNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) compAtomFromRefAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) compile_xy() (in module schrodinger.application.desmond.gchart) compileDict() (schrodinger.application.glide.glide.GlideJob method) compileOneToManyResults() (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) compileOneToOneResults() (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) COMPLEMENT_FN (schrodinger.protein.sequence.NucleicAcidSequence attribute) COMPLEMENT_FN() (schrodinger.protein.sequence.DNASequence static method) (schrodinger.protein.sequence.RNASequence static method) COMPLETED (schrodinger.job.jobcontrol.DisplayStatus attribute) (schrodinger.seam.viz.inspect.PipelineStatus attribute) (schrodinger.seam.viz.inspect.TransformStatus attribute) completedJobids() (schrodinger.utils.installation_check.TestJobDJ method) completePolymer() (schrodinger.application.matsci.amorphous.Initiator method) CompleteSubMenu (class in schrodinger.application.bioluminate.pml_menus) Complex (class in schrodinger.application.glide.poseviewconvert) (class in schrodinger.application.matsci.mlearn.features) COMPLEX (schrodinger.application.desmond.constants.FepLegTypes attribute) (schrodinger.application.desmond.constants.REST_COMPONENT attribute) complex (schrodinger.application.desmond.new_fep_edge_data.FepLegs attribute) COMPLEX (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsStructure attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) complex_dg (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult attribute) complex_dg_correction (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult attribute) COMPLEX_EQUILIBRATION (schrodinger.application.desmond.constants.DefaultFEPSimulationTimes attribute) COMPLEX_EQUILIBRATION_MUVT (schrodinger.application.desmond.constants.DefaultFEPSimulationTimes attribute) COMPLEX_HOTREGION (schrodinger.application.desmond.constants.REST_PROPERTIES attribute) complex_model (schrodinger.application.desmond.new_fep_edge_data.FepData property) COMPLEX_PERMITTIVITY (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) COMPLEX_PERMITTIVITY_DATA_HEADER (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) COMPLEX_PERMITTIVITY_FILE_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) COMPLEX_SIZE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) complex_st (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult attribute) ComplexBuilder (class in schrodinger.application.matsci.buildcomplex) ComplexConformerRmsd (class in schrodinger.application.matsci.buildcomplex) Complexes (class in schrodinger.application.livedesign.entry_types) ComplexFeatures (class in schrodinger.application.matsci.mlearn.features) ComplexLigandRxMixin (class in schrodinger.application.matsci.builderwidgets) ComplexPermittivity (class in schrodinger.application.matsci.permittivity) ComplexSdfToMae (class in schrodinger.application.matsci.buildcomplex2d) ComplexSdfToMaeException ComplexSdfToRxnWF (class in schrodinger.application.matsci.buildcomplex2d) ComplexSplitter (class in schrodinger.application.matsci.buildcomplex) ComplexTemplateSketcher (class in schrodinger.application.matsci.builderwidgets) compliance_tensor (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) ComplianceTensor (class in schrodinger.application.matsci.elasticity.elastic) component_structures() (in module schrodinger.application.desmond.struc) COMPONENT_TO_COMBINED (schrodinger.application.desmond.constants.IdConversion attribute) components (schrodinger.application.matsci.mlearn.features.MomentData attribute) CompositeKeySyntaxError composition (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) COMPOUND (schrodinger.application.livedesign.live_report_widget.LiveReportType attribute) compound_batches (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) CompoundParam (class in schrodinger.models.parameters) CompoundParamMeta (class in schrodinger.models.parameters) CompoundParamMixin (class in schrodinger.models.parameters) CompoundSource (class in schrodinger.application.livedesign.constants) COMPRESS (schrodinger.application.matsci.desconfig.MSJStringer attribute) compress() (in module schrodinger.pipeline.stages.glide) (in module schrodinger.pipeline.stages.ligprep) COMPRESSED (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) CompressionType (class in schrodinger.rdkit_extensions) COMPRESSIVE (schrodinger.application.matsci.permittivity.MultiStageMd attribute) COMPRESSIVE_PROTOCOL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) COMPRESSIVE_RELAX (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) CompressiveRelaxationStep (class in schrodinger.application.matsci.jwsteps) CompStruc (class in schrodinger.application.desmond.struc) ComptonFac() (in module schrodinger.application.matsci.gsas.GSASIIElem) compute() (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.DiversityFingerprinter method) compute_alogp() (in module schrodinger.application.medchem.property) compute_and_populate_charges() (in module schrodinger.application.matsci.clusterstruct) compute_energy() (in module schrodinger.structutils.minimize) compute_esp_charges() (in module schrodinger.application.matsci.clusterstruct) compute_factor_scores() (in module schrodinger.application.combinatorial_diversity.splitter_utils) compute_filter_score() (in module schrodinger.application.combinatorial_diversity.diversity_selector) compute_max_internal_distance() (in module schrodinger.application.matsci.coarsegrain) compute_medchem_properties() (in module schrodinger.application.medchem.property) compute_mw() (in module schrodinger.application.medchem.property) compute_net_charge_correction() (in module schrodinger.application.desmond.fep_net_charge) compute_net_charge_corrections() (in module schrodinger.application.desmond.fep_net_charge) compute_num_hbond_acceptors() (in module schrodinger.application.medchem.property) compute_num_hbond_donors() (in module schrodinger.application.medchem.property) compute_num_rot_bonds() (in module schrodinger.application.medchem.property) compute_polar_surf_area() (in module schrodinger.application.medchem.property) compute_real_moment_components() (in module schrodinger.application.matsci.jaguarworkflows) compute_rip_correction() (in module schrodinger.application.desmond.fep_net_charge) compute_rmse() (in module schrodinger.application.desmond.correlation_tau) compute_score() (in module schrodinger.application.phase.packages.hypo_refine.screen_utils) compute_sim_to_probes() (in module schrodinger.application.combinatorial_diversity.splitter_utils) compute_similarity() (in module schrodinger.rdkit.filtering) compute_smiles() (in module schrodinger.application.medchem.property) compute_std_conc_gibbs_energy() (in module schrodinger.application.jaguar.utils) compute_tick_interval() (in module schrodinger.ui.qt.schart) compute_title() (in module schrodinger.application.medchem.property) compute_tol_search_direct() (in module schrodinger.application.phase.packages.hypo_refine.screen_utils) computeContextSensitiveRuleFOLLOW() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) computeCostFunction() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) computed_data (schrodinger.livedesign.registration.RegistrationData attribute) computeDensity() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) computeErrorRecoverySet() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) computeFES() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis method) computeOnsagerCoefficients() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) computeOnsagerLambda() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) computePlaneFromAtoms() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) computePlaneFromEntry() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) ComputeRequirement (class in schrodinger.job.resource) computeStats() (schrodinger.application.matsci.kmcgui.NeighborsTab method) ComputeSubMenu (class in schrodinger.application.bioluminate.pml_menus) ComputeSurfaceArea (class in schrodinger.application.bioluminate.pml_menus) computeTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) computeTokenTypes() (in module schrodinger.application.desmond.antlr3.treewizard) ComputeType (class in schrodinger.job.resource) COMTracker (class in schrodinger.application.matsci.clusterstruct) ComUtil (class in schrodinger.application.macromodel.utils) ComUtil_2010 (class in schrodinger.application.macromodel.utils) ComUtilAppSci (class in schrodinger.application.macromodel.utils) CONCAT (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) concat (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) Concatenate (class in schrodinger.application.desmond.stage.simulate) concatenate (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) CONCATENATE (schrodinger.application.matsci.desconfig.MSJStringer attribute) concatenate_and_backup() (in module schrodinger.application.desmond.stage.simulate) concatenate_cfgs() (in module schrodinger.application.desmond.gconfig) concatenate_logs() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.glide.utils) concatenate_relaxation_stages() (in module schrodinger.application.desmond.cmj) concatenate_trajectories() (in module schrodinger.application.desmond.stage.simulate) ConcatMSJStringer (class in schrodinger.application.matsci.desconfig) ConcatParam (class in schrodinger.application.desmond.stage.simulate) Concentration (class in schrodinger.structutils.rgroup_enumerate) CONCENTRATIONS_FILE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) Concluder (class in schrodinger.application.desmond.stage.workflow) CONCRETE (schrodinger.models.parameters.ParamType attribute) concrete_only() (in module schrodinger.models.parameters) cond_1d_dist_mat() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) CONFGEN (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute) ConfidenceInterval (class in schrodinger.application.desmond.correlation_tau) Config (class in schrodinger.application.matsci.permittivity) (class in schrodinger.application.vss.config) config (schrodinger.active_learning.mq_driver.LigandMLZMQDriver property) (schrodinger.application.glide.http_client.AbstractGlideServerManager property) (schrodinger.ui.qt.tasks.configwidgets.ConfigWidgetMixin property) config_ext (schrodinger.application.glide.http_client.AbstractGlideServerManager attribute) (schrodinger.application.glide.http_client.GlideServerManager attribute) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) ConfigDialog (class in schrodinger.ui.qt.config_dialog) (class in schrodinger.ui.qt.tasks.configwidgets) configDialogSettings() (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.knime_af2.KnimeNodeMixin method) ConfigDialogWithPlatformValidation (class in schrodinger.application.matsci.configdlgs) configure() (schrodinger.active_learning.al_driver.ActiveLearningJob method) configure_local_ssh_setup() (in module schrodinger.utils.sshconfig) configure_mq_run() (in module schrodinger.active_learning.al_utils) configure_no_input_splitting() (in module schrodinger.active_learning.al_utils) configure_subplots() (schrodinger.ui.qt.navtoolbar.NavToolbar method) configure_taskdirs() (in module schrodinger.tasks.queue) configureBonds() (schrodinger.application.matsci.nano.particle.Nanoparticle method) configured_servers() (in module schrodinger.job.cert) configureParam() (schrodinger.application.livedesign.ld_export.ExportModel class method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel class method) (schrodinger.application.prepwizard2.tasks.PreprocessInput class method) (schrodinger.models.parameters.CompoundParam class method) ConfigWidgetMixin (class in schrodinger.ui.qt.tasks.configwidgets) ConfigWriter (class in schrodinger.application.matsci.permittivity) ConformationalSearch (class in schrodinger.application.matsci.reaction_workflow_gui_utils) ConformationalSearchException ConformationalSearchMixin (class in schrodinger.application.matsci.reaction_workflow_utils) conformer (schrodinger.structutils.clash_resolution.ClashResolutionResult attribute) CONFORMER_GENERATION (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) conformer_groups (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) ConformerError ConformerReader (class in schrodinger.application.phase.packages.conformer_reader) ConformerReaderOptions (class in schrodinger.application.phase.packages.conformer_reader) ConformerRmsd (class in schrodinger.structutils.rmsd) ConformerRmsdX (class in schrodinger.structutils.rmsd) CONFORMERS_XYZ_OUT (schrodinger.application.matsci.crest.CrestCSearchJob attribute) ConformerSelection (class in schrodinger.application.matsci.reaction_workflow_gui_utils) ConfRestraintType (class in schrodinger.application.desmond.constants) ConfSearch (class in schrodinger.application.macromodel.input) ConfSearchStage (class in schrodinger.pipeline.stages.macromodel) conglomerate_rings() (in module schrodinger.application.canvas.r_group) connect (schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup attribute) connect() (in module schrodinger.structutils.build) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) (schrodinger.application.livedesign.login.LoginManager class method) (schrodinger.utils.qt_utils.SignalAndSlot method) connect_atoms() (in module schrodinger.application.matsci.nano.xtal) connect_job_manager_signals() (in module schrodinger.job.jobhandler) connect_signals() (in module schrodinger.ui.qt.table_helper) connect_to_livedesign() (in module schrodinger.application.livedesign.maestro_ld_connection) connect_to_workspacehub() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) connect_variable_attachment_points() (in module schrodinger.livedesign.preprocessor) connectAction() (schrodinger.application.bioluminate.actions.factory.Factory method) connectConfigDialogToTimer() (schrodinger.application.jaguar.gui.timing.TimerMixin method) CONNECTED (schrodinger.application.livedesign.ldclient_proxy.LDConnectionStatus attribute) connected_atoms (schrodinger.application.desmond.fep_scholar_util.MetaAtom property) ConnectedMoleculeChain (class in schrodinger.analysis.substructure) connecting_atom_ids (schrodinger.application.matsci.amorphous.ConnectionInfo attribute) connectionChanged (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy attribute) ConnectionError connectionFailed (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy attribute) ConnectionInfo (class in schrodinger.application.matsci.amorphous) connections (schrodinger.livedesign.biologics.registration.BioPolymer attribute) ConnectionStorage (class in schrodinger.application.combiglide.connection_storage) ConnectionValidator (class in schrodinger.ui.qt.network_visualizer) ConnectivityAtomMapper (class in schrodinger.comparison.atom_mapper) CONNECTIVITYCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) connectNVEInitialVelocity() (schrodinger.application.matsci.permittivity.MdStageModifier method) connector_item_factory() (in module schrodinger.protein.helm.helm_renderer) connectReplicaNode() (schrodinger.application.matsci.permittivity.WorkflowParser method) connectSignal() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) connectSignalAndSlot() (schrodinger.models.mappers.TargetParamMapper method) connectSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) connectSlot() (schrodinger.application.bioluminate.actions.factory.SAction method) connectToBasicTabForUpdates() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) connectToCells() (schrodinger.application.matsci.nano.xtal.PBCBonds method) connectToJobHub() (schrodinger.application.matsci.jobdirdlg.JobManager method) connectToLD() (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) connectToLiveDesignRequested (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy attribute) connectToViewPositionTabForUpdates() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) cons_file (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cons_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cons_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) Consensus (class in schrodinger.application.bioluminate.protein.protein) (class in schrodinger.protein.annotation) consensus_freq (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) consensus_seq (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) consensus_symbols (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) CONSENSUS_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) ConsensusConfig (class in schrodinger.application.prime.wrapper) consensusCounterions() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) consensusLigands() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) ConsensusToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) consensusWaters() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) consider() (schrodinger.math.sampling.ReservoirSampler method) CONST (class in schrodinger.application.desmond.envir) const_type (schrodinger.application.jaguar.utils.ScanCoord attribute) CONSTANT_AXIS_A (schrodinger.application.desmond.constants.IsotropyPolicy attribute) CONSTANT_AXIS_B (schrodinger.application.desmond.constants.IsotropyPolicy attribute) CONSTANT_AXIS_C (schrodinger.application.desmond.constants.IsotropyPolicy attribute) constant_fold() (schrodinger.application.desmond.enhsamp.FcnCall method) (schrodinger.application.desmond.enhsamp.Node method) CONSTANT_PH (schrodinger.application.desmond.constants.PRODUCT attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) CONSTANT_PROPERTIES (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) (schrodinger.application.matsci.cgforcefield.FFIOSite attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) ConstantpHAnalysis (class in schrodinger.application.desmond.stage.app.constant_ph) ConstantpHMsjGenerator (class in schrodinger.application.desmond.msj_generator.constant_ph) ConstantpHSimLegParams (class in schrodinger.application.desmond.msj_generator.workflow_params) ConstantpHWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) Constants (class in schrodinger.application.desmond.constants) (class in schrodinger.application.matsci.nano.constants) (class in schrodinger.application.matsci.rxn_channel) CONSTRAIN (schrodinger.application.jaguar.rotation_barriers_keywords.TSMethod attribute) constrainAll() (schrodinger.application.matsci.zmutils.ZAtom method) (schrodinger.application.matsci.zmutils.ZMatrix method) constrainAtomXYZ() (schrodinger.application.jaguar.input.JaguarInput method) constrainCoord() (schrodinger.application.matsci.zmutils.ZAtom method) constrainInternal() (schrodinger.application.jaguar.input.JaguarInput method) Constraint (class in schrodinger.application.desmond.cms) (class in schrodinger.application.glide.glide) (class in schrodinger.forcefield.minimizer) CONSTRAINT_SCORE (schrodinger.protein.align.AbstractNWPairwiseAligner attribute) CONSTRAINT_TYPE (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile attribute) (schrodinger.application.matsci.packmol.MicelleInputFile attribute) (schrodinger.application.matsci.packmol.MonolayerInputFile attribute) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile attribute) ConstraintCoordinateColumns (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinateData (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesDelegate (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesModel (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesProxyModel (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) constraintCount() (schrodinger.application.jaguar.input.JaguarInput method) ConstraintError ConstraintFormatError ConstraintGroup (class in schrodinger.application.glide.glide) CONSTRAINTS (schrodinger.application.matsci.crest.CrestTOML attribute) constraints (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) (schrodinger.protein.tasks.sta.STATask.Input attribute) constraints() (schrodinger.application.jaguar.input.JaguarInput method) CONSTRAINTS_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab attribute) constraintsChanged (schrodinger.protein.tasks.sta.STATask.Input attribute) constraintsReplaced (schrodinger.protein.tasks.sta.STATask.Input attribute) constructHostArg() (schrodinger.job.launchparams.LaunchParameters method) consume() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer method) consumeCommandLine() (schrodinger.job.launchparams.LaunchParameters method) consumeHiddenToken() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) consumeInitialHiddenTokens() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) consumeNode() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) consumeToken() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) consumeUntil() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) CONTACT_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) Contained (schrodinger.ui.qt.pop_up_widgets.PopUpMode attribute) CONTAINS (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.TextOperator attribute) contains() (schrodinger.utils.preferences.Preferences method) contains_aqueous_dissolution_legs() (in module schrodinger.application.desmond.solubility_utils) contains_built_in_aa() (in module schrodinger.protein.process_enamine_db) containsMultipleCores() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) Context (class in schrodinger.tasks.taskszmq) contextMenuEvent() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) contextMenuIndicatorClicked (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator attribute) continueResBackbone() (schrodinger.application.matsci.amorphous.PolymerFragments method) CONTOURS_DIR (schrodinger.application.matsci.mlearn.features.Complex attribute) contract_by_molecule() (in module schrodinger.application.matsci.clusterstruct) contract_by_molecule2() (in module schrodinger.application.matsci.clusterstruct) contract_slab_z() (in module schrodinger.application.matsci.clusterstruct) contract_structure() (in module schrodinger.application.matsci.clusterstruct) contract_structure2() (in module schrodinger.application.matsci.clusterstruct) contract_structure_pfx() (in module schrodinger.application.matsci.clusterstruct) ControlType (class in schrodinger.application.matsci.espresso.qeinput) ConvCriteria (class in schrodinger.application.jaguar.results) ConvenientSelectorWithPopUp (class in schrodinger.application.matsci.mswidgets) converge_search() (in module schrodinger.application.macromodel.apps) convergence_category() (in module schrodinger.application.jaguar.textparser) CONVERGENCE_CRITERIA (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) CONVERGENCE_SCHEME_OPTS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) convergenceTypeChanged() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) Conversion (class in schrodinger.application.desmond.constants) CONVERSION (schrodinger.application.matsci.reaction_workflow_utils.JMSWFConformerSelection attribute) (schrodinger.application.matsci.reaction_workflow_utils.MopacConformerSelection attribute) convert() (in module schrodinger.livedesign.convert) (schrodinger.application.matsci.etatoggle.DummyMaker method) (schrodinger.application.matsci.etatoggle.PerAtomMaker method) (schrodinger.models.adapters.abstractadapter.AbstractAdapter class method) convert2DTo3DAndMinimize() (schrodinger.application.matsci.builderwidgets.MinimizeMixin method) convert_attachment_point() (in module schrodinger.structutils.rgroup_enumerate) convert_csv_to_smi() (in module schrodinger.active_learning.al_utils) convert_diff_token_to_float() (in module schrodinger.utils.compare) convert_ffioff_to_dummy() (in module schrodinger.application.desmond.ffiostructure) convert_file() (in module schrodinger.infra.epydoc_to_sphinx) convert_flags_to_underscore() (in module schrodinger.application.glide.utils) convert_fragment_from_v3000() (in module schrodinger.structutils.markush_enumerate) convert_gaps_to_dots() (in module schrodinger.application.prime.wrapper) convert_gaps_to_tildes() (in module schrodinger.application.prime.wrapper) convert_gibbs_energy_to_std_conc() (in module schrodinger.application.jaguar.utils) convert_heavy_hydrogens() (in module schrodinger.livedesign.preprocessor) convert_log_to_exception() (in module schrodinger.rdkit.rdkit_adapter) convert_MOE_hypothesis_to_ct() (in module schrodinger.application.phase.packages.phase_convert_MOE) convert_muts_file() (in module schrodinger.application.bioluminate.mutation) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_n_features() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) convert_nm_and_wavenumber() (in module schrodinger.application.matsci.spectra) convert_old_marker_props_to_new() (in module schrodinger.application.matsci.buildcomplex) convert_project_hypotheses() (in module schrodinger.application.phase.pt_hypothesis) convert_qzip_to_tar_gz_model() (in module schrodinger.active_learning.al_utils) convert_res_file() (in module schrodinger.application.bioluminate.mutation) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_res_list() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_res_to_muts() (in module schrodinger.application.bioluminate.mutation) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_residue_list() (in module schrodinger.application.bioluminate.mutation) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_scaffold_from_v3000() (in module schrodinger.structutils.markush_enumerate) convert_sdf_to_rxnwf() (in module schrodinger.application.matsci.buildcomplex2d) convert_selenomethionines() (in module schrodinger.application.prepwizard) convert_smiles_to_3d() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) convert_sparse_dict_to_list() (in module schrodinger.application.mopac.utils) convert_strain_to_deformation() (in module schrodinger.application.matsci.elasticity.strain) convert_string() (in module schrodinger.infra.mmim) convert_structure_sequence_for_pattern_search() (in module schrodinger.protein.sequence) convert_tar_gz_to_qzip_model() (in module schrodinger.active_learning.al_utils) convert_to_acs_label() (in module schrodinger.application.jaguar.nmr_utils) convert_to_gids() (schrodinger.application.desmond.cms.Cms method) convert_to_ieee() (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) convert_to_local_timezone() (in module schrodinger.application.job_monitor.util) convert_to_molblock() (in module schrodinger.livedesign.preprocessor) convert_to_sd() (in module schrodinger.application.phase.packages.phase_utils) convert_vv2mol() (in module schrodinger.application.desmond.mxmd.mxmd_system_builder) ConvertBondsToDative (class in schrodinger.application.matsci.buildcomplex) convertCOMToAtomCluster() (schrodinger.application.matsci.clusterstruct.COMTracker method) convertDataToPlot() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis static method) convertMultiToOne() (schrodinger.application.matsci.equilibrium_md.MultiDriver method) convertMutsFile() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertPlotToData() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis static method) convertQimageToImage() (in module schrodinger.application.desmond.report_helper) convertResFile() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertResidueList() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertResList() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertResToMuts() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertSmiToMae() (schrodinger.application.phase.packages.shape_screen_al_node.ShapeScreenJob method) convertSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) convertToCartesian() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) convertToClassToken() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) convertToEnv() (schrodinger.job.launchparams.LaunchParameters method) convertToJLaunchOptions() (schrodinger.job.launchparams.LaunchParameters method) convertToMMSortFieldsList() (in module schrodinger.project.project) convertToZMatrix() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) ConvertZOBToSingle (class in schrodinger.application.matsci.buildcomplex) ConvexPolyhedron (class in schrodinger.application.matsci.shapes) Coord (class in schrodinger.application.matsci.rxn_path) (class in schrodinger.ui.qt.mapperwidgets.param_editor) coord (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) coord2mae() (in module schrodinger.application.xtb.utilities) coord_in_ring() (in module schrodinger.application.jaguar.autots_bonding) COORD_LETTERS (schrodinger.application.matsci.zmutils.ZAtom attribute) COORD_NAME (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) COORD_TYPE (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) coord_type (schrodinger.application.jaguar.utils.ScanCoord attribute) coordChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) COORDFILE (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) Coordinate (class in schrodinger.application.jaguar.autots_bonding) COORDINATE_ANGLE_INCREMENT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_ANGLE_OFFSET (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_DISTANCE_INCREMENT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_DISTANCE_OFFSET (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_FUNCS (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_OPTS (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) coordinateAdded (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinateData (class in schrodinger.application.jaguar.gui.tabs.coordinates) coordinateDeleted (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) coordinateDeselected (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinateDialog (class in schrodinger.application.jaguar.gui.base_panel) CoordinateFrame (schrodinger.analysis.visanalysis.volumedata.VolumeData property) CoordinateManager (class in schrodinger.application.jaguar.hess_guess) CoordinateMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) CoordinatePicker (class in schrodinger.application.jaguar.gui.tabs.coordinates) Coordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) coordinateSelected (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinatesModel (class in schrodinger.application.jaguar.gui.tabs.coordinates) CoordinateTab (class in schrodinger.application.jaguar.gui.tabs.coordinates) coordinateTypeChanged() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker method) coordinatingAtoms() (schrodinger.application.matsci.sculptcomplex.Sculptor method) coordination (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) CoordinationInfo (class in schrodinger.application.matsci.sculptcomplex) CoordinationSite (class in schrodinger.application.matsci.siteselector.siteselector) coordReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) coords (schrodinger.application.matsci.espresso.qeoutput.KptLegend attribute) coords_all_zero() (in module schrodinger.livedesign.preprocessor) coords_frozen1() (in module schrodinger.application.jaguar.textparser) coords_frozen2() (in module schrodinger.application.jaguar.textparser) coords_harmonic() (in module schrodinger.application.jaguar.textparser) coords_ind() (in module schrodinger.application.jaguar.textparser) coords_nred() (in module schrodinger.application.jaguar.textparser) coords_opt() (in module schrodinger.application.jaguar.textparser) coords_outside_1st_cell() (in module schrodinger.application.matsci.nano.xtal) Copy (schrodinger.adapter.Properties attribute) (schrodinger.adapter.StereoChemistry attribute) COPY (schrodinger.ui.qt.schart.SChart attribute) copy() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) (schrodinger.application.desmond.ffiostructure.FFIOStructure method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.PerAtomBasisRow method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow method) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) (schrodinger.application.matsci.genetic_optimization.StructureGenome method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.util.OneIndexedList method) (schrodinger.models.jsonable.JsonableSet method) (schrodinger.structure.Structure method) (schrodinger.structutils.color.ColorScheme method) (schrodinger.surface.Surface method) (schrodinger.ui.qt.swidgets.STableWidgetItem method) (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.scollections.IdSet method) copy_and_compress_files() (in module schrodinger.application.desmond.util) copy_atom_constr() (in module schrodinger.application.matsci.espresso.utils) copy_atom_properties() (in module schrodinger.application.matsci.desmondutils) copy_autots_atom_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_bond_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_st_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_bonding() (in module schrodinger.application.jaguar.autots_bonding) copy_chorus_box_props() (in module schrodinger.application.matsci.nano.xtal) copy_cms_and_trj() (in module schrodinger.application.matsci.deswidgets) copy_csv_file() (in module schrodinger.rdkit.molio) copy_custom_config_file() (in module schrodinger.utils.postinstall) copy_customized_files() (in module schrodinger.utils.postinstall) copy_file() (in module schrodinger.application.jaguar.file_logger) copy_from() (schrodinger.utils.sea.evalor.Evalor method) copy_lewis_structure_and_hydrogens() (in module schrodinger.livedesign.preprocessor) copy_msj_and_cfg() (in module schrodinger.application.matsci.desconfig) copy_parser_attributes() (schrodinger.application.desmond.starter.ui.cmdline.BaseArgs method) (schrodinger.application.desmond.starter.ui.cmdline.FepArgs method) (schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args method) (schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs method) (schrodinger.application.desmond.starter.ui.fep_solubility.FepSolubilityArgs method) copy_rates_csv_to_db() (in module schrodinger.application.matsci.kmc) COPY_RESOLUTION (schrodinger.ui.qt.schart.SChart attribute) copy_sql_data() (in module schrodinger.application.matsci.kmc) copy_st_props() (in module schrodinger.application.matsci.msutils) copy_structure_bonding() (in module schrodinger.application.jaguar.utils) copy_to_autorxnwf_file() (in module schrodinger.application.matsci.reaction_workflow_utils) copyalgn() (schrodinger.application.macromodel.utils.ComUtil method) copyAllStructsIntoCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) copyCfgFiles() (schrodinger.application.matsci.permittivity.MultiStageMd method) copyChargeMultBasisFromModel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) copyFiles() (schrodinger.application.matsci.permittivity.StepBase method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) copyImageToClipboard() (schrodinger.ui.qt.navtoolbar.NavToolbar method) (schrodinger.ui.qt.table.DataViewerTable method) copyMaskTargetIfNeeded() (schrodinger.application.matsci.jwsteps.BaseStep method) copyModelFiles() (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) copyReagentFile() (schrodinger.application.pathfinder.reaction.ReagentClass method) copyRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel method) copySelectionFrom() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) copyStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) copyToClipboard() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) (schrodinger.ui.qt.schart.SChart method) (schrodinger.ui.two_d_viewer.CellContextualMenu method) (schrodinger.ui.two_d_viewer.TwoDViewer method) copyTransformations() (schrodinger.ui.two_d_viewer.Cell method) core_atoms (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_atomsChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_atomsReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_complexity (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) core_complexityChanged (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) core_complexityReplaced (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) core_constraint_smarts (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_constraint_smartsChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_constraint_smartsReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_hopping_lambda_windows (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) CORE_LOCALIZATION_METHODS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) core_rmsd (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_rmsdChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_rmsdReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_smarts (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.SmartsFilter.Settings attribute) core_smartsChanged (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.SmartsFilter.Settings attribute) core_smartsReplaced (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.SmartsFilter.Settings attribute) CoreAtomsOptions (class in schrodinger.application.livedesign.tasks) COREHOPPING (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) CorelessSubstitute (class in schrodinger.application.transforms.enumerators) corp_id (schrodinger.application.livedesign.export_models.GEExportItem attribute) (schrodinger.application.livedesign.export_models.MatchCompoundsBy attribute) (schrodinger.tasks.ldtasks.LDInputRow attribute) (schrodinger.tasks.ldtasks.LDOutputRow attribute) corp_id_match_prop (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) corp_id_match_propChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) corp_id_match_propReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) corp_idChanged (schrodinger.application.livedesign.export_models.GEExportItem attribute) (schrodinger.tasks.ldtasks.LDOutputRow attribute) corp_idReplaced (schrodinger.application.livedesign.export_models.GEExportItem attribute) (schrodinger.tasks.ldtasks.LDOutputRow attribute) corp_ids (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) corp_idsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) corp_idsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) CORR_ENERGY (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute) correct_restr() (in module schrodinger.application.desmond.fepana) correct_sgroup_coordinates() (in module schrodinger.livedesign.preprocessor) CorrectionTerm (class in schrodinger.application.desmond.constants) correlation_type() (in module schrodinger.application.jaguar.textparser) CosAngle() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cosd() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIImath) (in module schrodinger.application.matsci.gsas.GSASIIpwd) COSMO_PCM_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) Cosolvent (class in schrodinger.application.desmond.mxmd.mxmd_system_builder) cosolvent (schrodinger.application.desmond.struc.CompStruc attribute) COSOLVENT (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) CosolventBoxGenerator (class in schrodinger.application.desmond.mxmd.mxmd_system_builder) CosSinAngle() (in module schrodinger.application.matsci.gsas.GSASIIlattice) coulomb (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property) (schrodinger.application.desmond.fep_schedule.FepScheduleBinding property) count (schrodinger.application.desmond.cmj.StageBase attribute) (schrodinger.application.jaguar.simple_spec.Peak attribute) (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.application.matsci.species.SpeciesData property) count() (in module schrodinger.application.macromodel.tools) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.ui.qt.swidgets.ActionComboBox method) count_atom_hbonds() (in module schrodinger.protein.captermini) count_atoms_in_smarts() (in module schrodinger.structutils.analyze) count_finished_compounds() (in module schrodinger.application.desmond.stage.fep_mapper) count_heavy_atoms() (in module schrodinger.application.desmond.r_group_asl) count_ligands() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.hitexpander) count_lines() (in module schrodinger.utils.fileutils) count_num_strucs() (in module schrodinger.application.jaguar.gui.utils) count_phosphates_and_sulfurs() (in module schrodinger.application.prepwizard) count_protons() (in module schrodinger.application.jaguar.nmr_utils) count_residues_in_model() (in module schrodinger.livedesign.biologics.registration) count_species_in_cms() (in module schrodinger.application.matsci.clusterstructgui) count_structures() (in module schrodinger.structure) (schrodinger.application.vss.database.Database method) count_traj_frames() (in module schrodinger.application.desmond.gui) count_waters() (in module schrodinger.application.matsci.msutils) CountAtoms (class in schrodinger.application.bioluminate.pml_menus) countChanged (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) countClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection static method) Counter (class in schrodinger.application.desmond.util) countHeavyAtoms() (in module schrodinger.application.desmond.r_group_asl) CountLayout (class in schrodinger.ui.qt.formlayout) countRoots() (in module schrodinger.pipeline.pipeutils) counts_file (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) counts_fileChanged (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) counts_fileReplaced (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) countStructures() (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.structure_selector.StructureSelector method) coupler (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) COUPLER_AT_ORIGIN (schrodinger.application.matsci.amorphous.BaseMoiety attribute) coupler_marker (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) COUPLING_COLUMNS (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) (schrodinger.application.matsci.kmc.PairsTable attribute) couplings (schrodinger.application.jaguar.nmr_utils.NMRData attribute) CouplingStrength (class in schrodinger.application.jaguar.nmr_interactions) COV_FACTOR (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) COV_MIN (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) COV_OFFSET (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) COVALENT_LIGAND (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) CovalentDockingComplexes (class in schrodinger.application.livedesign.entry_types) CovalentFEPEdgeData (class in schrodinger.application.desmond.fep_edge_data) CovalentFepMapper (class in schrodinger.application.desmond.stage.fep_mapper) CovalentMsjGenerator (class in schrodinger.application.desmond.msj_generator.fep.covalent_ligand) covdock_inp_file (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) covdock_inp_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) covdock_inp_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) covdock_opts (schrodinger.application.livedesign.tasks.CovDockTask attribute) CovDockTask (class in schrodinger.application.livedesign.tasks) CovDockTask.Input (class in schrodinger.application.livedesign.tasks) CovDockTask.JobConfig (class in schrodinger.application.livedesign.tasks) CovDockTask.Output (class in schrodinger.application.livedesign.tasks) CPCM_PCM_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) CPU (schrodinger.job.resource.ComputeType attribute) CPU_AND_GPU (schrodinger.tasks.jobtasks.AllowedHostTypes attribute) CPU_AND_GPU_PLACEHOLDER_ARG (schrodinger.tasks.jobtasks.HostSettings attribute) CPU_ONLY (schrodinger.tasks.jobtasks.AllowedHostTypes attribute) CPU_PLACEHOLDER_ARG (schrodinger.tasks.jobtasks.HostSettings attribute) cpu_time (schrodinger.seam.viz.inspect.PipelineDisplayInfo attribute) cpu_time() (in module schrodinger.application.jaguar.textparser) CPU_UNIT_LABEL (schrodinger.application.matsci.configdlgs.PerStrucConfigDialog attribute) (schrodinger.application.matsci.configdlgs.PerStrucSingleGpuConfigDialog attribute) (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) cpus (schrodinger.application.jaguar.gui.timing.TimingResults.PER_ENTRY_DATA attribute) cpus3Edited() (schrodinger.ui.qt.config_dialog.ConfigDialog method) cputime_seconds (schrodinger.seam.metric.ExecutionMetrics attribute) CPUTYPE (schrodinger.tasks.hosts.Host attribute) cpx_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_forward (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_forward_dg (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_end_time_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_ensemble (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_ff (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_rest_exchanges (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_result (schrodinger.application.desmond.fep_edge_data.FEPTorsions property) cpx_salt_info (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_salt_molecules (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_sid_lp_results (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) cpx_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_sid_pl_results (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_sid_protein_residues (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_sid_snapshot_times_ps (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_sim_time (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_start_time_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_temperature (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_timestep_interval (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_timestep_list (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_total_atoms (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_total_replicas (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_total_waters (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cpx_user_restraint (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) cradius (schrodinger.application.matsci.elementalprops.ElementalProperties property) CREATE (schrodinger.application.livedesign.mapping_widgets.MappingMode attribute) create() (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.application.matsci.desconfig.BarrierInfo class method) (schrodinger.application.matsci.kmc.Table method) create_2d_img() (in module schrodinger.application.livedesign.two_d_render) create_action_menu() (in module schrodinger.application.bioluminate.pml_menus) create_alignment_from_chains() (in module schrodinger.protein.sequence) create_archive_file() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.licserver.client) create_archive_from_oplsdir() (in module schrodinger.forcefield.custom_params) create_argparse_namespace() (in module schrodinger.application.phase.packages.phase_option_utils) create_argument_parser() (in module schrodinger.utils.cmdline) create_atom_tag() (in module schrodinger.application.desmond.maestro) (schrodinger.application.desmond.maestro.Workspace method) create_autots_template_file() (in module schrodinger.application.jaguar.hydrokinetic_input) create_biounits() (in module schrodinger.ui.qt.pdb_dialog) create_blast_db() (in module schrodinger.protein.gpcr.update_gpcr_db) create_bonds() (in module schrodinger.application.bioluminate.antibody.assembly) create_center_of_mass_info() (in module schrodinger.application.matsci.clusterstruct) create_cg_molecule_name() (in module schrodinger.application.matsci.coarsegrain) create_cg_system() (in module schrodinger.application.matsci.cgforcefield) create_child_group() (in module schrodinger.project.utils) create_chmmol_from_structure() (in module schrodinger.structutils.analyze) create_clib_archive() (in module schrodinger.application.combinatorial_screen.driver_utils) create_cluster_hypo() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) create_cms_from_mae() (in module schrodinger.application.desmond.repair_cms) create_colorbyele_menu() (in module schrodinger.application.bioluminate.pml_menus) create_combined_ab_data() (in module schrodinger.livedesign.biologics.registration) create_config_dir() (in module schrodinger.utils.postinstall) create_conn() (in module schrodinger.protein.gpcr.sql) create_contour_plot_on_figure() (in module schrodinger.application.desmond.mplchart) create_cpu_and_gpu_hosts() (in module schrodinger.job.queue) create_cpu_gpu_queue() (in module schrodinger.application.matsci.jobutils) create_csv() (in module schrodinger.application.livedesign.io_utils) create_database() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) create_debug_logger() (in module schrodinger.application.matsci.textlogger) create_dimer_structures() (in module schrodinger.application.matsci.clusterstruct) create_distance_cell() (in module schrodinger.application.matsci.clusterstruct) (in module schrodinger.structutils.measure) (in module schrodinger.structutils.ringspear) create_disulfide_bonds() (in module schrodinger.application.prepwizard) create_entry_database() (in module schrodinger.protein.gpcr.update_gpcr_db) create_fep_launcher_jobs() (in module schrodinger.application.desmond.stage.launcher) create_ffio_block() (in module schrodinger.application.matsci.cgforcefield) create_fragment_structure() (in module schrodinger.structutils.rgroup_enumerate) create_full_system_from_comp() (in module schrodinger.application.desmond.repair_cms) create_glycosylation_bonds() (in module schrodinger.application.prepwizard) create_guesses() (in module schrodinger.application.jaguar.input) create_hard_link() (in module schrodinger.utils.fileutils) create_hide_menu() (in module schrodinger.application.bioluminate.pml_menus) create_hybrid() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) create_hypo (schrodinger.application.phase.input.InputSpecs attribute) create_interaction_distance() (in module schrodinger.utils.pymol) create_interactions_group() (in module schrodinger.utils.pymol) create_isosurface_from_grid_data() (in module schrodinger.surface) create_job() (in module schrodinger.application.matsci.jaguarworkflows) create_job_spec_function() (in module schrodinger.application.matsci.jobutils) create_label_menu() (in module schrodinger.application.bioluminate.pml_menus) create_lid() (in module schrodinger.application.livedesign.ld_glide_utils) create_live_report() (in module schrodinger.application.livedesign.export_tasks) create_logger() (in module schrodinger.application.matsci.textlogger) create_minimizer_if_needed() (in module schrodinger.application.matsci.msminimize) CREATE_MODE_PAGE (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp attribute) create_modify_menu() (in module schrodinger.application.bioluminate.pml_menus) create_module() (schrodinger.infra.unusable_module_importer.UnusableModuleLoader class method) create_mol_env_fig() (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker method) create_mol_series_fig() (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker method) create_movie (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) create_movieChanged (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) create_movieReplaced (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) create_mpl_plot_on_figure() (in module schrodinger.application.desmond.mplchart) create_msj() (in module schrodinger.application.matsci.desconfig) create_nearest_neighbor_cluster() (in module schrodinger.application.matsci.clusterstruct) CREATE_NEW (schrodinger.ui.qt.recent_completer.BrowseAndCreateStringModel attribute) create_new_box() (in module schrodinger.application.matsci.nano.xtal) create_new_database() (in module schrodinger.application.bb_database.bb_task_utils) create_new_structure() (in module schrodinger.structure) create_non_pbc_cluster() (in module schrodinger.application.matsci.clusterstruct) create_nonbonded_extents() (in module schrodinger.application.matsci.nano.xtal) create_normal() (in module schrodinger.graphics3d.common) create_nx_graph() (in module schrodinger.structutils.analyze) create_okay_file() (in module schrodinger.application.phase.packages.phase_database_job_utils) create_oligomer() (in module schrodinger.application.matsci.mlearn.descriptor) create_oned_data_file() (in module schrodinger.application.phase.packages.oned_task_utils) create_palmitoylation_bonds() (in module schrodinger.application.prepwizard) create_pbc() (in module schrodinger.application.matsci.clusterstruct) (in module schrodinger.structutils.ringspear) create_phase_project() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) create_pi_cation_interaction_distance() (in module schrodinger.utils.pymol) create_pi_pi_interaction_distance() (in module schrodinger.utils.pymol) create_polymer_name() (in module schrodinger.application.matsci.polymer) create_postmortem() (in module schrodinger.application.livedesign.io_utils) create_postmortem_args() (in module schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) create_project() (in module schrodinger.application.phase.packages.hypo_refine.project_utils) create_projects() (in module schrodinger.application.phase.packages.hypo_refine.project_utils) create_queue() (in module schrodinger.application.matsci.jobutils) CREATE_RADIOBUTTON_NAMES (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) create_reactant_files() (in module schrodinger.application.combinatorial_screen.driver_utils) create_reactant_fp_file() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) create_reagent_library() (in module schrodinger.application.pathfinder.synthesis) create_registration_data() (in module schrodinger.livedesign.biologics.registration) create_restart_jobcmd() (in module schrodinger.application.matsci.jobutils) create_restart_launcher() (in module schrodinger.application.matsci.jobutils) create_results_directory() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) create_rotated_complexes() (in module schrodinger.application.matsci.etarotamers) create_run_dir() (in module schrodinger.application.matsci.jobutils) create_selection() (in module schrodinger.utils.pymol) create_show_menu() (in module schrodinger.application.bioluminate.pml_menus) create_show_organic_menu() (in module schrodinger.application.bioluminate.pml_menus) create_show_substructure_menu() (in module schrodinger.application.bioluminate.pml_menus) create_sim_cormat() (in module schrodinger.application.combinatorial_diversity.splitter_utils) create_sketcher() (in module schrodinger.application.desmond.fep_edge_report_maker) create_smap() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) create_structure_from_hypothesis() (in module schrodinger.application.phase.packages.oned_task_utils) create_stub_license() (in module schrodinger.application.licensing.licadmin) create_subgroup() (in module schrodinger.project.utils) create_subjob() (in module schrodinger.application.matsci.jobutils) create_surface() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.bioluminate.surfcomp) create_surface_from_void() (in module schrodinger.application.matsci.freevolume) create_surface_on_figure() (in module schrodinger.application.desmond.mplchart) create_task() (schrodinger.application.livedesign.tasks.AlignLigandsTask class method) (schrodinger.application.livedesign.tasks.CanvasSearchTask class method) (schrodinger.application.livedesign.tasks.CovDockTask class method) (schrodinger.application.livedesign.tasks.EpikClassicTask class method) (schrodinger.application.livedesign.tasks.EpikTask class method) (schrodinger.application.livedesign.tasks.FlexAlignTask class method) (schrodinger.application.livedesign.tasks.GlideTask class method) (schrodinger.application.livedesign.tasks.LigandStrainTask class method) (schrodinger.application.livedesign.tasks.LigFilterTask class method) (schrodinger.application.livedesign.tasks.LigPrepTask class method) (schrodinger.application.livedesign.tasks.MemPermTask class method) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask class method) (schrodinger.application.livedesign.tasks.QikPropTask class method) (schrodinger.application.livedesign.tasks.RBSSTask class method) (schrodinger.application.livedesign.tasks.StrainRescoreTask class method) (schrodinger.application.livedesign.tasks.TugAlignTask class method) create_torsions_plot() (schrodinger.application.desmond.fep_edge_report_maker.ABFEPReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker method) create_user_hypo() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) create_workflows() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) create_xvol (schrodinger.application.phase.input.InputSpecs attribute) createActions() (schrodinger.application.bioluminate.actions.factory.Factory method) createAlignFile() (schrodinger.application.bioluminate.protein.protein.PrimeStructure method) createAllGrowthSpaces() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) createAllReactions() (schrodinger.application.matsci.fragments.FragmentReactor method) createArrow() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) createAttachmentItems() (schrodinger.application.livedesign.export_models.FFCExportSpec method) createAxis() (schrodinger.ui.qt.schart.SChart method) createBasicStructure() (schrodinger.application.matsci.sculptcomplex.Sculptor method) createBottomBar() (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) createCell() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) createChargeProperties() (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) createCmd() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) createCommand() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) createComplex() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) createConformers() (schrodinger.application.matsci.reaction_workflow_utils.ConformationalSearchMixin method) createControlButtons() (schrodinger.application.matsci.mswidgets.StageFrame method) createCriterionForProp() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) createDummies() (schrodinger.application.matsci.etatoggle.DummyMaker method) createEdge() (schrodinger.ui.qt.network_views.NetworkViewer method) createEditableFrame() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) createEditor() (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.TempItemDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBoxDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate method) (schrodinger.ui.qt.delegates.CheckboxDelegate method) (schrodinger.ui.qt.delegates.ComboBoxDelegate method) (schrodinger.ui.qt.delegates.MatplotlibDelegate method) (schrodinger.ui.qt.delegates.MouseTrackingDelegateMixin method) (schrodinger.ui.qt.delegates.ProgressBarDelegate method) (schrodinger.ui.qt.delegates.SpinBoxDelegate method) (schrodinger.ui.qt.delegates.WorkspaceInclusionDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate method) createEndSubFragment() (schrodinger.application.matsci.amorphous.PolymerFragments method) CreateEntry (class in schrodinger.application.bioluminate.pml_menus) createExcludedVolumeClash() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createExcludedVolumeReceptor() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createExcludedVolumeShell() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createFamilies() (schrodinger.ui.qt.propertyselector.PropertySelector method) createFragForInitiator() (schrodinger.application.matsci.amorphous.PolymerFragments method) createFromToken() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) createFromType() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) createGroupMapping() (schrodinger.application.matsci.automated_cg_mapping.StructData method) createImportWidget() (schrodinger.application.bioluminate.bwidgets.ImportWidget method) CreateInpFile() (schrodinger.application.livedesign.tasks.CovDockTask method) createInputSelector() (schrodinger.ui.qt.appframework2.af2.App method) createInputSt2() (schrodinger.application.matsci.permittivity.AnalyzeSimulation method) createInterfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) createIter() (schrodinger.application.bioluminate.interaction_calculator.PiStackFinder class method) createJob() (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) createJobDir() (schrodinger.ui.qt.appframework2.af2.JobApp method) createLabel() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) createLabels() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.SmallMoleculeTorsions method) createLigandStructures() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) CreateLike() (in module schrodinger.analysis.visanalysis.volumedatautils) createMap() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) createMatMinerDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createMenus() (schrodinger.ui.qt.appframework.AppFramework method) createMimic() (schrodinger.application.matsci.clusterstruct.COMTracker method) createModifiedGuess() (schrodinger.application.jaguar.input.JaguarInput method) createMols() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createMorganDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createMSJ() (schrodinger.application.matsci.permittivity.MultiStageMd method) createNewGroup() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) (schrodinger.project.project.Project method) createNewSelected (schrodinger.ui.qt.recent_completer.BrowseAndCreateCombo attribute) createNode() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) createObject() (schrodinger.graphics3d.tube.MaestroTube method) CreateOrEditMappingsDialog (class in schrodinger.application.livedesign.mapping_widgets) CreateOrEditMappingsModel (class in schrodinger.application.livedesign.mapping_widgets) createPhaseHypothesis() (schrodinger.application.phase.packages.phase_convert_MOE.PhpMOEConverter method) createPixmaps() (schrodinger.ui.qt.swidgets.SValidIndicator method) createPlane() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) createPolymerDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createProductGroups() (schrodinger.application.matsci.fragments.FragmentReactor method) createQJobFromCommand() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) createRdkitDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createReactantTracker() (schrodinger.application.matsci.fragments.FragmentReactor method) createReorderedEntry() (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) createResourceHost() (schrodinger.job.queue.JobDJ static method) createRotatedStructures() (schrodinger.application.matsci.etarotamers.HapticLigand method) CreateScreeningDBTask (class in schrodinger.application.phase.shape_screen_reporter.tasks) CreateScreeningDBTask.Input (class in schrodinger.application.phase.shape_screen_reporter.tasks) createSection() (schrodinger.application.jaguar.input.JaguarInput method) createSequence() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) createSketcher() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) createSlab() (schrodinger.application.matsci.sliceplot.SlicePlot method) createSmilesStructure() (schrodinger.structure.SmilesReader method) createSourceLayout() (schrodinger.ui.qt.structure_selector.StructureSelector method) createStage() (schrodinger.pipeline.pipeline.Pipeline method) createStateReactions() (schrodinger.application.matsci.fragments.FragmentReactor method) createString() (schrodinger.application.matsci.desconfig.MSJStringer method) createSubsetForCompsWithoutSites() (schrodinger.pipeline.stages.phase.DBConfSitesStage method) createSubWidgets() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) createSurfaces() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) createTemplateFile() (schrodinger.application.bioluminate.protein.protein.PrimeStructure method) createTextSequence() (schrodinger.application.bioluminate.pml_menus.AntibodyPreset method) createTip4pFfio() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) createToken() (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) createTopFrame() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) createTrainingCsvFile() (schrodinger.active_learning.al_node.LigandMLTrainNode method) createTrendLine() (schrodinger.ui.qt.schart.SeriesData method) createUniqueElement() (schrodinger.application.matsci.espresso.utils.MagSpecies method) createViewFrame() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) CreateWhenNeeded (class in schrodinger.infra.util) createWidget() (schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog method) (schrodinger.application.matsci.wfmanagement.WorkflowFinderDialog method) (schrodinger.application.matsci.wfmanagement.WorkflowManagerDialog method) createWidgets() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.StringCriterion method) createWithPayload() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method) CREATION_COMMAND (schrodinger.application.matsci.kmc.Table attribute) CREATOR (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) CREDENTIALS (schrodinger.application.livedesign.login_gui2.AuthenticationMode attribute) credentials_host (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) credentials_hostChanged (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) credentials_hostReplaced (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) Crest (class in schrodinger.application.matsci.crest) CrestCSearch (class in schrodinger.application.matsci.crest) CrestCSearchJob (class in schrodinger.application.matsci.crest) CrestException CrestJob (class in schrodinger.application.matsci.crest) CrestTOML (class in schrodinger.application.matsci.crest) criteriaChanged (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget attribute) CriteriaLayout (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) CriteriaListModel (class in schrodinger.application.bioluminate.propfilter) (class in schrodinger.ui.ligfilter) Criterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_core) (class in schrodinger.utils.ligfilter) criterion_changed (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector attribute) CRITERION_CHOICES (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion attribute) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolCriterion attribute) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion attribute) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.StringCriterion attribute) criterionChanged (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion attribute) criterionChanged() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) CriterionParser (class in schrodinger.utils.ligfilter) criterionTypeChanged() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion method) critical_points() (schrodinger.application.jaguar.discretized_1d_function.DiscretelySampledFunction method) criticalEllipse() (in module schrodinger.application.matsci.gsas.GSASIIlattice) CriticalPointsFailure crop_image() (in module schrodinger.application.desmond.report_helper) cross_angle (schrodinger.application.bioluminate.tcr.docking_angles.DescriptiveAngles attribute) CROSS_ENERGY_ONLY (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute) CROSS_LINK (schrodinger.application.desmond.stage.utils.SystemBuilder attribute) CROSSHAIR_COLOR (schrodinger.ui.qt.rama.RamaContourMixin attribute) CROSSHAIR_LINEWIDTH (schrodinger.ui.qt.rama.RamaContourMixin attribute) crossover (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) crossprod() (in module schrodinger.application.desmond.cms) CrsAng() (in module schrodinger.application.matsci.gsas.GSASIIlattice) crunch() (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.cmj.StructureStageBase method) (schrodinger.application.desmond.stage.analysis.Analysis method) (schrodinger.application.desmond.stage.analysis.FepAnalysis method) (schrodinger.application.desmond.stage.analysis.PLAnalysis method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher method) (schrodinger.application.desmond.stage.app.constant_ph.ConstantpHAnalysis method) (schrodinger.application.desmond.stage.app.kinetics.PathUnbinding method) (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingAnalysis method) (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup method) (schrodinger.application.desmond.stage.app.kinetics.RamdCleanup method) (schrodinger.application.desmond.stage.app.kinetics.RamdGenerateUnbindingPath method) (schrodinger.application.desmond.stage.app.kinetics.RamdSetup method) (schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD method) (schrodinger.application.desmond.stage.app.kinetics.ValidateStability method) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher method) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsSplitReceptor method) (schrodinger.application.desmond.stage.app.lambda_dynamics_analysis.LambdaDynamicsAnalysis method) (schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob method) (schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem method) (schrodinger.application.desmond.stage.app.matsci.FrozenPhononCorrection method) (schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis method) (schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture method) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis method) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup method) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup method) (schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures method) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis method) (schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher method) (schrodinger.application.desmond.stage.app.watermap.WaterMapCluster method) (schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis method) (schrodinger.application.desmond.stage.deprecate.MustSkip method) (schrodinger.application.desmond.stage.fep_mapper.CalcDdg method) (schrodinger.application.desmond.stage.fep_mapper.CombinedProteinFepMapper method) (schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper method) (schrodinger.application.desmond.stage.fep_mapper.FepMapper method) (schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup method) (schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper method) (schrodinger.application.desmond.stage.launcher.FepMembraneLauncher method) (schrodinger.application.desmond.stage.launcher.Multisim method) (schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield method) (schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule method) (schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher method) (schrodinger.application.desmond.stage.prepare.forcefield.LambdaDynamicsAssignForcefield method) (schrodinger.application.desmond.stage.prepare.structure.BuildGeometry method) (schrodinger.application.desmond.stage.prepare.structure.LambdaDynamicsBuildGeometry method) (schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator method) (schrodinger.application.desmond.stage.simulate.DesmondExtend method) (schrodinger.application.desmond.stage.simulate.FepVrun method) (schrodinger.application.desmond.stage.simulate.LambdaHopping method) (schrodinger.application.desmond.stage.simulate.ReInit method) (schrodinger.application.desmond.stage.simulate.SimulateBase method) (schrodinger.application.desmond.stage.simulate.Vrun method) (schrodinger.application.desmond.stage.utils.SystemBuilder method) (schrodinger.application.desmond.stage.workflow.Extern method) (schrodinger.application.desmond.stage.workflow.Stop method) (schrodinger.application.desmond.stage.workflow.Task method) (schrodinger.application.desmond.stage.workflow.Trim method) Crystal (class in schrodinger.application.matsci.nano.xtal) CRYSTAL_ENVIRON (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) crystal_structure (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) CRYSTAL_SYSTEM (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) crystal_system (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) CRYSTAL_SYSTEM_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) CRYSTAL_SYSTEMS (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute) CRYSTAL_VECTOR (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) crystal_water (schrodinger.application.desmond.struc.CompStruc attribute) CRYSTAL_WATER (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) CrystalNNFeatures (class in schrodinger.application.matsci.mlearn.features) CrystalPlane (class in schrodinger.application.matsci.nano.plane) CrystalSystems (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Cubic (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Hexagonal (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Monoclinic (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Orthorhombic (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Tetragonal (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Triclinic (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Trigonal (class in schrodinger.application.matsci.nano.space_groups) crystalVectorPicked() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) CS_METHOD (class in schrodinger.application.jaguar.csrch_input_constants) csearchEngineChanged() (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch method) CSP (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) CSPAtomMapper (class in schrodinger.comparison.atom_mapper) CSTART (schrodinger.application.matsci.cgforcefield.FFIODihedral attribute) (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) csv (schrodinger.utils.fileutils.SeqFormat attribute) csv_file (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) csv_fileChanged (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) csv_fileReplaced (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) CSV_HEADER_3D (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) CSV_HEADER_AXIS (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) CSV_HEADER_PLANE (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) csv_index (schrodinger.active_learning.mq_driver.Worker attribute) csv_mol_reader_class (schrodinger.rdkit.molio.PfxMolIterator attribute) (schrodinger.rdkit.molio.PfxMolReader attribute) CSV_OUT_EXT (schrodinger.application.matsci.permittivity.JaguarMerge attribute) CsvMergeHandler (class in schrodinger.rdkit.molio) CsvMolIterator (class in schrodinger.rdkit.molio) CsvMolReader (class in schrodinger.rdkit.molio) CsvMolWriter (class in schrodinger.rdkit.molio) CsvSmilesFile (class in schrodinger.application.vss.csvsmiles) CT (schrodinger.application.desmond.cmj.AslValidator attribute) ct (schrodinger.application.desmond.maestro.Workspace property) ct2chmmol() (in module schrodinger.application.desmond.depictor) ct_to_multipart() (schrodinger.application.glide.http_client.AbstractHTTPClient method) CTerm (schrodinger.protein.annotation.GPCRSegmentLabel attribute) ctPropertiesChanged (schrodinger.ui.two_d_viewer.CtPropsDialog attribute) CtPropsDialog (class in schrodinger.ui.two_d_viewer) CTSTR (schrodinger.application.desmond.cmj.AslValidator attribute) Cube (class in schrodinger.application.matsci.shapes) Cubeoctahedron (class in schrodinger.application.matsci.shapes) cubic() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) CUBIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) CURRENT (schrodinger.trajectory.trajectory_gui_dir.display_settings_data.DisplayOnly attribute) current_file (schrodinger.ui.qt.input_selector.InputSelector attribute) current_filename (schrodinger.structure.MultiFileStructureReader attribute) CURRENT_FRAME_WITH_COMPONENT_CTS (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute) current_job (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_jobChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_jobReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) CURRENT_MAGNITUDE_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_MAGNITUDE_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) current_progress (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) current_progress_display() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) current_progressChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) current_progressReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) current_project_jobs_only (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_jobs_onlyChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_jobs_onlyReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_name (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_nameChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_nameReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_source (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) current_sourceChanged (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) current_sourceReplaced (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) current_top_level_job (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_top_level_jobChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_top_level_jobReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) CURRENT_VAL (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) CURRENT_X_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_X_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_Y_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_Y_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_Z_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_Z_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) currentCategory() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) currentChoice() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) currentCriterion() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) currentData() (schrodinger.ui.qt.swidgets.SComboBox method) currentDBInfo() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) currentDir (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) currentFrameOnly() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) currentFrameWithComponentStructures() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) currentHost() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) currentIndex() (schrodinger.ui.qt.formlayout.CountLayout method) (schrodinger.ui.qt.formlayout.RadioLayout method) currentIndexChanged (schrodinger.ui.qt.swidgets.SComboBox attribute) currentLabel() (schrodinger.ui.qt.swidgets.STabWidget method) currentPanel() (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) currentProjectID() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) currentProjectName() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) currentScheme() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) currentSelection (schrodinger.ui.qt.datamapper.MappableButtonGroup attribute) currentSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.clusterstructgui.SpeciesCombo method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) currentText() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) currsize (schrodinger.application.matsci.cache.CacheInfo attribute) curvatures() (schrodinger.surface.Surface method) CUSTOM (schrodinger.application.livedesign.tasks.CoreAtomsOptions attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) Custom (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) (schrodinger.protein.nonstandard_residues.StructureSource attribute) CUSTOM (schrodinger.protein.tasks.blast.BlastDatabase attribute) Custom (schrodinger.ui.qt.appframework2.jobnames.JobnameType attribute) custom() (in module schrodinger.ui.qt.appframework2.appmethods) custom_aln (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) custom_alnChanged (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) custom_alnReplaced (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) custom_annotation (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) CUSTOM_CHARGE_MODE (class in schrodinger.application.desmond.constants) custom_charge_mode (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) CUSTOM_CLASS_FILE_OPTION (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) custom_color_dicts (in module schrodinger.application.bioluminate.pml_menus) custom_config_file_exists() (in module schrodinger.utils.postinstall) custom_database_path (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastSettings attribute) custom_database_pathChanged (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastSettings attribute) custom_database_pathReplaced (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastSettings attribute) custom_fasta_file (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) custom_fasta_fileChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) custom_fasta_fileReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) custom_functional() (in module schrodinger.application.jaguar.textparser) CUSTOM_HYPO_TEXT (schrodinger.application.phase.featureselector.FeatureModel attribute) custom_is_list() (in module schrodinger.application.inputconfig) custom_is_string_list() (in module schrodinger.application.inputconfig) custom_menu_item() (in module schrodinger.ui.qt.appframework2.appmethods) CUSTOM_MSJ (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) custom_probe_dir (schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams attribute) CUSTOM_RESOLUTION_INDEX (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) CUSTOM_SELECTION (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute) custom_text (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_text_final (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_text_finalChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_text_finalReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_textChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_textReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_weight (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) custom_weightChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) custom_weightReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) CUSTOM_WIDGET_INDEX (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) CustomAngles (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) CustomASLStructureAligner (class in schrodinger.protein.align) CustomClassEvaluator (class in schrodinger.application.matsci.genetic_optimization) CustomCmsStep (class in schrodinger.application.matsci.jwsteps) CustomCmsToMaeStep (class in schrodinger.application.matsci.jwsteps) CustomColor (class in schrodinger.application.bioluminate.pml_menus) CustomConfigFiles (class in schrodinger.utils.postinstall) customDirChanged (schrodinger.application.matsci.builderwidgets.TemplateManager attribute) CustomDisplaySettings (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings) CustomFamilyTask (class in schrodinger.protein.tasks.hit_align) CustomFamilyTask.Input (class in schrodinger.protein.tasks.hit_align) CustomFileDialog (class in schrodinger.ui.qt.filedialog) CustomGPUComboBox (class in schrodinger.application.desmond.fep_dialog) customizeFuncResult() (schrodinger.utils.funcchains.FuncChainMarker method) customizeInputAndCommand() (schrodinger.application.matsci.permittivity.JaguarCalculation method) CustomListWidgetItem (class in schrodinger.application.matsci.builderwidgets) CustomMaeStep (class in schrodinger.application.matsci.jwsteps) CustomMDType (class in schrodinger.application.matsci.espresso.qeinput) CustomNEBType (class in schrodinger.application.matsci.espresso.qeinput) customOPLSDir() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) customOPLSDirForModel() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) customOPLSPathChanged (schrodinger.ui.qt.forcefield.ffglobalpreferencewidget.FFGlobalPreferenceWidget attribute) CustomProgressBar (class in schrodinger.ui.qt.appframework) CustomRecentColor (class in schrodinger.application.bioluminate.pml_menus) CustomResidueCheckBox (class in schrodinger.ui.residueselector) CustomResidueMixin (class in schrodinger.ui.residueselector) CustomResidueRadioButton (class in schrodinger.ui.residueselector) CustomResMutationSelectorFrame (class in schrodinger.ui.residueselector) CustomResMutationSelectorMixin (class in schrodinger.ui.residueselector) CustomResMutationSelectorPopUp (class in schrodinger.ui.residueselector) CustomScoringFunction (class in schrodinger.application.glide.sort_utils) CustomScriptLine (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) CustomSideBarMixin (class in schrodinger.ui.qt.filedialog) CustomToolbar (class in schrodinger.application.matsci.density_analysis_widget) CustomTrajectoryStep (class in schrodinger.application.matsci.jwsteps) CustomUnpickler (class in schrodinger.application.desmond.picklejar) Cut (class in schrodinger.application.qsite.input) CUT20 (schrodinger.application.jaguar.results.InputDeviation attribute) cut20 (schrodinger.application.jaguar.results.NofailResult attribute) cutAwayExcess() (schrodinger.application.matsci.nano.particle.Nanoparticle method) cutoff (schrodinger.application.matsci.espresso.qeinput.FreePositionsType.PWallType attribute) CUTOFF_COMBO_ITEMS (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) cutoffChanged (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider attribute) cutoffChanged() (schrodinger.application.matsci.kmcgui.NeighborsTab method) cutoffLength (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute) cutOutNanoSheet() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) CV (class in schrodinger.application.desmond.meta) cv (schrodinger.application.matsci.espresso.qeoutput.PhDOS.Thermo attribute) CVAngle (class in schrodinger.application.desmond.meta) cvangle_floor_template (schrodinger.application.desmond.meta.CVAngle attribute) cvangle_grp_template (schrodinger.application.desmond.meta.CVAngle attribute) cvangle_template (schrodinger.application.desmond.meta.CVAngle attribute) cvangle_wall_template (schrodinger.application.desmond.meta.CVAngle attribute) CVDihedral (class in schrodinger.application.desmond.meta) cvdihedral_grp_template (schrodinger.application.desmond.meta.CVDihedral attribute) cvdihedral_template (schrodinger.application.desmond.meta.CVDihedral attribute) CVDist (class in schrodinger.application.desmond.meta) cvdist_floor_template (schrodinger.application.desmond.meta.CVDist attribute) (schrodinger.application.desmond.meta.CVzdist attribute) cvdist_grp_template (schrodinger.application.desmond.meta.CVDist attribute) cvdist_template (schrodinger.application.desmond.meta.CVDist attribute) cvdist_wall_template (schrodinger.application.desmond.meta.CVDist attribute) (schrodinger.application.desmond.meta.CVzdist attribute) cvdw_coeff (schrodinger.application.glide.sort_utils.CustomScoringFunction attribute) CVECTOR (schrodinger.application.matsci.kmc.SchrodingerTable attribute) CVrgyr (class in schrodinger.application.desmond.meta) CVrgyr_mass (class in schrodinger.application.desmond.meta) cvrgyr_mass_template (schrodinger.application.desmond.meta.CVrgyr_mass attribute) cvrgyr_template (schrodinger.application.desmond.meta.CVrgyr attribute) CVrmsd (class in schrodinger.application.desmond.meta) cvrmsd_conf_template (schrodinger.application.desmond.meta.CVrmsd_symm attribute) cvrmsd_setup_template (schrodinger.application.desmond.meta.CVrmsd_symm attribute) CVrmsd_symm (class in schrodinger.application.desmond.meta) cvrmsd_template (schrodinger.application.desmond.meta.CVrmsd attribute) (schrodinger.application.desmond.meta.CVrmsd_symm attribute) cvrmsd_wall_template (schrodinger.application.desmond.meta.CVrmsd attribute) (schrodinger.application.desmond.meta.CVrmsd_symm attribute) cvrmsd_weights_template (schrodinger.application.desmond.meta.CVrmsd attribute) CVSEQ_INTERVAL (schrodinger.application.desmond.kinetics.enhanced_sampling.MtdOption attribute) CVwhim (class in schrodinger.application.desmond.meta) cvwhim_template (schrodinger.application.desmond.meta.CVwhim attribute) CVzdist (class in schrodinger.application.desmond.meta) CVzdist0 (class in schrodinger.application.desmond.meta) cvzdist0_template (schrodinger.application.desmond.meta.CVzdist0 attribute) cvzdist_template (schrodinger.application.desmond.meta.CVzdist attribute) cycle() (schrodinger.ui.qt.swidgets.SpinnerIcon method) cycle_feature_flag() (in module schrodinger.application.matsci.mstest) Cylinder (class in schrodinger.application.matsci.shapes) Cytosine (schrodinger.protein.helm.helm_renderer.HexColor attribute)

D

D (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) (schrodinger.application.bioluminate.update_germline_db.translate_db.Gene attribute) D1d (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) DAminoAcidMonomerItem (class in schrodinger.protein.helm.helm_renderer) DARK_GRAY (schrodinger.ui.qt.standard.colors.NativeColors attribute) darken_colors_by_cavity_depth (schrodinger.surface.Surface property) DarkModeColors (class in schrodinger.ui.qt.standard.colors) DarkRed (schrodinger.protein.helm.helm_renderer.HexColor attribute) Data (class in schrodinger.application.canvas.r_group) (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) data (schrodinger.application.matsci.coarsegrain.InternalInfo attribute) (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) (schrodinger.comparison.results.ResultSet property) DATA (schrodinger.job.util.DirectoryType attribute) data (schrodinger.ui.qt.radial_plot.Sector attribute) data() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.livedesign.panel_components.EndpointSelectionModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) (schrodinger.ui.qt.network_visualizer.Edge method) (schrodinger.ui.qt.recent_completer.SeparatorStringModel method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) (schrodinger.ui.qt.table_helper.DataMethodDecoratorMixin method) (schrodinger.ui.qt.table_helper.DataMethodDecoratorProxyMixin method) (schrodinger.ui.qt.table_helper.PtRowBasedTableModel method) (schrodinger.ui.qt.table_speed_up.MultipleRolesRoleModelMixin method) (schrodinger.ui.qt.table_speed_up.MultipleRolesRoleProxyMixin method) (schrodinger.ui.qt.table_speed_up.MultipleRolesRoleProxyPassthroughMixin method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) DATA_CACHE_SIZE (schrodinger.ui.qt.table_speed_up.MultipleSpeedUpDelegatesViewMixin attribute) data_changed (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase attribute) DATA_CLASSES (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData attribute) data_column (schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart attribute) data_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) data_field_names (schrodinger.livedesign.registration.RegistrationOptions attribute) DATA_MAX (schrodinger.ui.qt.rama.RamaContourMixin attribute) data_method() (in module schrodinger.ui.qt.table_helper) DATA_MIN (schrodinger.ui.qt.rama.RamaContourMixin attribute) data_name (schrodinger.application.livedesign.data_classes.LDData property) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) data_nameChanged (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) data_nameReplaced (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) data_violations (schrodinger.application.bioluminate.antibody.io.csv_reader.InvalidRowError property) Database (class in schrodinger.application.vss.database) DATABASE (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase attribute) database (schrodinger.application.phase.packages.phase_screen_driver_utils.SourceFormat attribute) database_changed (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase attribute) database_name (schrodinger.protein.tasks.blast.BlastSettings attribute) database_nameChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) database_nameReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) database_parameter_key (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) databaseComboChanged() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) DatabaseInfo (class in schrodinger.application.matsci.kmcgui) databases (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput attribute) DATABASES (schrodinger.infra.licensing.SimilarityEndpoint attribute) databaseType (schrodinger.job.server.ServerInfo attribute) DataCache (class in schrodinger.ui.qt.table_speed_up) dataChanged (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates attribute) (schrodinger.ui.qt.pop_up_widgets.PopUp attribute) (schrodinger.ui.residueselector.MutationSelectorMixin attribute) (schrodinger.ui.residueselector.MutationSelectorPopUp attribute) dataChanged() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView method) DataClass (schrodinger.models.parameters.BaseMutableParam attribute) (schrodinger.models.parameters.BoolParam attribute) (schrodinger.models.parameters.CompoundParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.FloatParam attribute) (schrodinger.models.parameters.IntParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.Param attribute) (schrodinger.models.parameters.ParamListParam attribute) (schrodinger.models.parameters.SetParam attribute) (schrodinger.models.parameters.StringParam attribute) (schrodinger.models.parameters.StructureParam attribute) (schrodinger.models.parameters.TupleParam attribute) (schrodinger.tasks.jobtasks.HostParam attribute) (schrodinger.ui.qt.color_picker.ColorParam attribute) DataExportSpec (class in schrodinger.application.livedesign.export_models) DataFile (class in schrodinger.application.transforms.dofn_utils) DataFusionMergeStage (class in schrodinger.pipeline.stages.combine) DataMethodDecoratorMixin (class in schrodinger.ui.qt.table_helper) DataMethodDecoratorProxyMixin (class in schrodinger.ui.qt.table_helper) DataModel (class in schrodinger.application.bioluminate.protein_report_widget) DataModelWithChart (class in schrodinger.application.bioluminate.protein_structure_quality) dataName() (schrodinger.structure.PropertyName method) dataName2ViewName() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion class method) dataNameIterator() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) DataPointLocator (class in schrodinger.analysis.visanalysis.volumedatautils) dataRequested() (schrodinger.application.matsci.reportutils.ReportInfo method) DataType (class in schrodinger.application.matsci.espresso.qeinput) (schrodinger.application.steps.dataclasses.MolToSmilesSerializer attribute) (schrodinger.application.steps.dataclasses.ScoredMolSerializer attribute) (schrodinger.application.steps.enumerators.RouteSerializer attribute) (schrodinger.stepper.stepper.Serializer attribute) DataViewerTable (class in schrodinger.ui.qt.table) DataViolation (class in schrodinger.application.bioluminate.antibody.io.csv_reader) DateTimeSerializer (class in schrodinger.models.jsonable) Dative (schrodinger.structure.BondType attribute) Datum (class in schrodinger.application.desmond.arkdb) daylight_locus() (in module schrodinger.application.matsci.colorutils) daylight_radiator() (in module schrodinger.application.matsci.colorutils) DBConfSitesStage (class in schrodinger.pipeline.stages.phase) DBExportStage (class in schrodinger.pipeline.stages.phase) dbg (schrodinger.application.desmond.antlr3.debug.DebugParser property) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream property) DBManageStage (class in schrodinger.pipeline.stages.phase) dbscan_cluster() (in module schrodinger.math.mathutils) ddg (schrodinger.application.desmond.new_fep_edge_data.FepData property) ddg_corrections_map (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ddg_corrections_sum (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) deactivate() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) deactivateTabs() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) debug (schrodinger.application.glide.glideanalysis.PoseLibrary attribute) (schrodinger.application.jaguar.nmr_utils.NMRData attribute) DEBUG (schrodinger.utils.cmdline.Options attribute) debug() (in module schrodinger.structutils.assignbondorders) (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) debug_func() (in module schrodinger.ui.qt.appframework2.debugcore) debug_func_args() (in module schrodinger.ui.qt.appframework2.debugcore) debug_mode (schrodinger.stepper.stepper.StepTaskInput attribute) debug_modeChanged (schrodinger.stepper.stepper.StepTaskInput attribute) debug_modeReplaced (schrodinger.stepper.stepper.StepTaskInput attribute) debug_mols() (in module schrodinger.application.pathfinder.reaction) debug_outfile (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) debug_print() (in module schrodinger.utils.sea.common) debugbond() (in module schrodinger.structutils.assignbondorders) debugbonders() (in module schrodinger.structutils.assignbondorders) debugEnabled() (schrodinger.job.launchapi.JobSpecification method) DebugEventListener (class in schrodinger.application.desmond.antlr3.debug) DebugEventSocketProxy (class in schrodinger.application.desmond.antlr3.debug) DebugFlag (class in schrodinger.seam.debug) debugger (schrodinger.application.desmond.driver_utils.MPISettings attribute) DEBUGGER (schrodinger.utils.cmdline.Options attribute) debuggroup() (in module schrodinger.structutils.assignbondorders) DebugParser (class in schrodinger.application.desmond.antlr3.debug) debugPrint() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) debugReactants() (schrodinger.application.pathfinder.reaction.Reaction method) DebugStderr (class in schrodinger.ui.qt.appframework2.debugcore) DebugStdout (class in schrodinger.ui.qt.appframework2.debugcore) DebugTokenStream (class in schrodinger.application.desmond.antlr3.debug) DebugTreeAdaptor (class in schrodinger.application.desmond.antlr3.debug) DebugViewer (class in schrodinger.ui.qt.appframework2.debug_gui) Debye (schrodinger.application.jaguar.constants.Unit attribute) Decimal (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) decimals (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) decl() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) decl_meta() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) decl_output() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) declare_template (schrodinger.application.desmond.meta.Meta attribute) decode() (in module schrodinger.models.json) (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer class method) (schrodinger.seam.coders.MolCoder method) (schrodinger.seam.coders.MolToSmilesCoder method) (schrodinger.seam.coders.RouteNodeCoder method) (schrodinger.seam.coders.StructureCoder method) decode_base64_cmd() (in module schrodinger.application.matsci.textlogger) decode_position_vector() (in module schrodinger.application.bioluminate.peptide_sar.encode) decode_restraints() (in module schrodinger.application.desmond.stage.prepare.forcefield) decode_str() (in module schrodinger.application.desmond.cms) decode_string_from_structure_property() (in module schrodinger.application.desmond.struc) decode_to_server_info() (in module schrodinger.job.server) decode_transformations() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) decode_value() (in module schrodinger.application.bioluminate.peptide_sar.encode) (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer class method) decomp_rawfep_structure() (in module schrodinger.application.desmond.cms) decompose_to_comp_ct() (in module schrodinger.application.desmond.repair_cms) deconverge() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) Decorate (class in schrodinger.application.transforms.enumerators) decorate_watermap() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) decorateAxes() (schrodinger.application.matsci.sliceplot.SlicePlot method) Decorator (class in schrodinger.application.steps.enumerators) decreaseSpeed() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) DECREMENT() (in module schrodinger.application.desmond.fep_scholar_util) decrement_state_of_changeable() (schrodinger.protein.assignment.ProtAssign method) decrementNestingLevel() (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) decrypt_cms() (in module schrodinger.application.matsci.enc) DedupeAndRandomSampleFilter (class in schrodinger.stepper.core_steps) DedupeAndRandomSampleFilter.Settings (class in schrodinger.stepper.core_steps) deduplicate_routes (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) deduplicate_routesChanged (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) deduplicate_routesReplaced (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) deduplicate_sequences() (in module schrodinger.livedesign.biologics.modeling) deduplicate_strain_rescore_input() (in module schrodinger.application.livedesign.ld_strain_rescore_utils) deduplicate_xy_data() (in module schrodinger.math.mathutils) DeduplicateRoutes (class in schrodinger.application.transforms.enumerators) deduplication_hash (schrodinger.livedesign.biologics.registration.BioPolymer property) (schrodinger.livedesign.registration.RegistrationData attribute) DeduplicationStep (class in schrodinger.stepper.core_steps) DEE_Backtracking (class in schrodinger.application.canvas.r_group_dee) DEE_EnergyMatrix (class in schrodinger.application.canvas.r_group_dee) deep_find_signals() (in module schrodinger.ui.qt.appframework2.debugwidgets) deep_update_dict() (in module schrodinger.application.matsci.msutils) DeepChem (class in schrodinger.application.matsci.genetic_optimization) deepCopy() (schrodinger.application.matsci.amorphous.PolymerFragment method) Deepest0 (class in schrodinger.application.dendrogram.core_class) Deepest1 (class in schrodinger.application.dendrogram.core_class) Deepest2 (class in schrodinger.application.dendrogram.core_class) Deepest3a (class in schrodinger.application.dendrogram.core_class) Deepest3b (class in schrodinger.application.dendrogram.core_class) Deepest4 (class in schrodinger.application.dendrogram.core_class) Deepest5 (class in schrodinger.application.dendrogram.core_class) Deepest6 (class in schrodinger.application.dendrogram.core_class) deepFindSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) DEF2_SVPD (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) DEFAULT (schrodinger.application.desmond.constants.REST_REGION_RULE attribute) (schrodinger.application.desmond.constants.Schedule attribute) (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute) default (schrodinger.application.desmond.starter.ui.cmdline.Option attribute) DEFAULT (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) default (schrodinger.application.glide.sort_utils.SortCriterion attribute) (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute) (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute) (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute) DEFAULT (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) default (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword property) (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) (schrodinger.application.matsci.kmc.ColumnData attribute) DEFAULT (schrodinger.application.matsci.reaction_workflow_utils.DF_RATE_TYPE attribute) default (schrodinger.application.matsci.reaction_workflow_utils.JaguarKeyStructPropData attribute) DEFAULT (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Slab attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) (schrodinger.forcefield.constants.GeometryOptMethod attribute) (schrodinger.ui.qt.forcefield.forcefield.OPLSDirResult attribute) (schrodinger.ui.qt.standard.design_tokens.BorderColors attribute) (schrodinger.ui.qt.standard.design_tokens.BorderSizes attribute) (schrodinger.ui.qt.standard.design_tokens.FontSizes attribute) (schrodinger.ui.qt.standard.design_tokens.FontWeights attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) default() (schrodinger.application.desmond.cmj.JobErrorHandler static method) default_accounter() (in module schrodinger.application.desmond.starter.starter) DEFAULT_ALCHEMICAL_EXCLUDE_DIST (schrodinger.application.desmond.stage.prepare.structure.BuildGeometry attribute) DEFAULT_ALLOWED_MODES (schrodinger.tasks.jobtasks.IncorporationParam attribute) DEFAULT_ALPHA_CEILING (schrodinger.ui.qt.color_picker.AlphaLimitedColorPickerButton attribute) default_args() (in module schrodinger.active_learning.al_utils) DEFAULT_ATOM_TYPING_SCHEMES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) DEFAULT_AXIS_BUFFER_PCT (schrodinger.ui.qt.schart.SChart attribute) DEFAULT_AXIS_FONT_SIZE (schrodinger.ui.qt.schart.SChart attribute) default_basis (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel property) DEFAULT_BASIS_SET (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) DEFAULT_BIN_WIDTH (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) DEFAULT_BULK_TYPE (schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis attribute) DEFAULT_CATEGORY_LABEL_ANGLE (schrodinger.ui.qt.schart.SChart attribute) DEFAULT_COULOMB (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) default_custom_fraglib() (in module schrodinger.utils.cgxutils) DEFAULT_DATA (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) DEFAULT_DEBUGGER_PORT (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy attribute) DEFAULT_DENSITY (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) DEFAULT_ENVIRON (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) DEFAULT_FILTERS (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) (schrodinger.application.glide.sort_utils.GlideSortUtility attribute) default_frac_unbound_thresholds_str (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup attribute) DEFAULT_GROUP_NAME (schrodinger.application.matsci.appbase.ProcessPtStructuresApp attribute) DEFAULT_HEADERS (schrodinger.application.matsci.mswidgets.SystemInformationFrame attribute) DEFAULT_HORIZONTAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) DEFAULT_ICON_HEIGHT (schrodinger.application.desmond.feputils.LabelSpinner attribute) DEFAULT_ICON_PREFIX (schrodinger.ui.qt.navtoolbar.MaestroNavToolbar attribute) DEFAULT_IPOLAR (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) default_jaguar_basis() (in module schrodinger.application.jaguar.basis) DEFAULT_JAGUAR_OPTIONS (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) (schrodinger.application.matsci.permittivity.JaguarFinerCalculation attribute) DEFAULT_JOB_NAME (schrodinger.application.matsci.reaction_workflow_utils.DescriptorsMixin attribute) DEFAULT_JOBNAME (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) (schrodinger.application.matsci.permittivity.AveCellAnalysis attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) (schrodinger.application.matsci.permittivity.CMSParser attribute) (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) (schrodinger.application.matsci.permittivity.JaguarMerge attribute) (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) DEFAULT_KWARGS (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) default_label() (schrodinger.seam.transforms.samplers.RandomSample method) default_logging_config() (in module schrodinger.utils.log) DEFAULT_MAE_EXT (schrodinger.application.matsci.nano.constants.Constants attribute) DEFAULT_MARKER_SIZE (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama attribute) (schrodinger.ui.qt.rama.RamaScatterMixin attribute) default_method (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain property) DEFAULT_MOSS_ATNUM (schrodinger.application.jaguar.gui.tabs.properties_tab.MossbauerSubTab attribute) DEFAULT_MOSS_NUC_QUADRUPOLE_MOMENT (schrodinger.application.jaguar.gui.tabs.properties_tab.MossbauerSubTab attribute) DEFAULT_MSJ_HEADER (schrodinger.application.matsci.permittivity.MultiStageMd attribute) DEFAULT_NONCATEGORY_LABEL_ANGLE (schrodinger.ui.qt.schart.SChart attribute) DEFAULT_NUMBER_OF_MOLECULES (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) DEFAULT_NUMBER_OF_POLYMERS (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) DEFAULT_ORBITAL (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) default_p_value_thresholds_str (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup attribute) DEFAULT_POP_UP_MODE (schrodinger.ui.qt.pop_up_widgets.ComboBoxWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.LineEditWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.LinkButtonWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.PushButtonWithIndicatorAndPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.PushButtonWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.ToolButtonWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin attribute) DEFAULT_PROB_PROFILE_SETTING (schrodinger.application.desmond.stage.analysis.Analysis attribute) DEFAULT_PROGRAM_NAME (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream attribute) DEFAULT_RANDOM_TYPES (schrodinger.application.matsci.rxn_channel.Constants attribute) DEFAULT_RANGE (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka attribute) DEFAULT_REF (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) DEFAULT_SETTING (class in schrodinger.application.desmond.msj_defaults) default_size_factor (schrodinger.ui.qt.network_views.NetworkNode attribute) DEFAULT_SORT_COLUMN (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel attribute) DEFAULT_SORT_CRITERIA (schrodinger.application.glide.sort_utils.GlideSortUtility attribute) DEFAULT_SORT_ORDER (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) DEFAULT_START_FRAME (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) DEFAULT_STEP_SIZE (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel attribute) DEFAULT_SUB_TAB_VISIBILITY (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) DEFAULT_TASKDIR_SETTING (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.stepper.stepper.StepTaskMixin attribute) (schrodinger.tasks.tasks.AbstractTask attribute) default_text (schrodinger.application.livedesign.panel_components.AddNewLineEdit attribute) default_theory (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel property) DEFAULT_THEORY (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) DEFAULT_TOKEN_CHANNEL (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) DEFAULT_TOOLBARS (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) DEFAULT_TOOLS (schrodinger.ui.qt.schart.SChart attribute) DEFAULT_TOOLTIP (schrodinger.ui.qt.atomselector.AtomSelector attribute) DEFAULT_TRANSPARENCY (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings attribute) DEFAULT_VERTICAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) DEFAULT_WEIGHT (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow attribute) default_weight (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) default_weightChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) default_weightReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) DEFAULT_X_RADIUS (schrodinger.protein.helm.helm_renderer.DAminoAcidMonomerItem attribute) (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin attribute) DEFAULT_Y_RADIUS (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin attribute) DefaultFactoryDict (class in schrodinger.utils.scollections) DefaultFactoryDictMixin (class in schrodinger.utils.scollections) DefaultFEPSimulationTimes (class in schrodinger.application.desmond.constants) DefaultIdDict (class in schrodinger.utils.scollections) DefaultMessageDelegate (class in schrodinger.ui.qt.delegates) DefaultMonomerItem (schrodinger.protein.helm.helm_renderer.ZOrder attribute) DEFAULTMSG (schrodinger.application.matsci.nano.check.CheckInput attribute) DefaultPreset (class in schrodinger.application.bioluminate.pml_menus) DEFAULTS (schrodinger.application.matsci.deswidgets.DesmondMDWidgets attribute) (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) (schrodinger.application.matsci.espresso.qeinput.BasisType attribute) (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) (schrodinger.application.matsci.espresso.qeinput.ControlType attribute) (schrodinger.application.matsci.espresso.qeinput.CustomMDType attribute) (schrodinger.application.matsci.espresso.qeinput.DftType attribute) (schrodinger.application.matsci.espresso.qeinput.DftUType attribute) (schrodinger.application.matsci.espresso.qeinput.ElasticControlType attribute) (schrodinger.application.matsci.espresso.qeinput.ElasticType attribute) (schrodinger.application.matsci.espresso.qeinput.ElectronControlType attribute) (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) (schrodinger.application.matsci.espresso.qeinput.FreePositionsType attribute) (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) (schrodinger.application.matsci.espresso.qeinput.HPType attribute) (schrodinger.application.matsci.espresso.qeinput.HybridType attribute) (schrodinger.application.matsci.espresso.qeinput.IonControlType attribute) (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) (schrodinger.application.matsci.espresso.qeinput.MdType attribute) (schrodinger.application.matsci.espresso.qeinput.NEBPathType attribute) (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) (schrodinger.application.matsci.espresso.qeinput.PHDynmatType attribute) (schrodinger.application.matsci.espresso.qeinput.PPlotType attribute) (schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType attribute) (schrodinger.application.matsci.espresso.qeinput.SpinType attribute) (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboEelsType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboLanczosType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) (schrodinger.application.matsci.espresso.qeinput.VdwType attribute) (schrodinger.protein.tasks.blast.BlastSettings attribute) defaultValue() (schrodinger.models.parameters.CompoundParam class method) (schrodinger.models.parameters.Param class method) define_options() (in module schrodinger.application.desmond.starter.ui.cmdline) DefineASLDialog (class in schrodinger.application.matsci.mswidgets) defineAtom() (schrodinger.application.matsci.cg_mapping.Particle method) defineBins() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) defineBox() (schrodinger.application.matsci.amorphous.Scaffold method) defineBoxFromNonPBCStruct() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineBoxFromPBC() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineBoxFromScaffold() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineCustomSettings() (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) defineDimensions() (schrodinger.application.matsci.nano.tube.NanoSheet method) definedShadowBonds() (schrodinger.application.matsci.cgforcefield.ForceField static method) defineIgnoredParams() (schrodinger.models.presets.PresetManager method) (schrodinger.models.presets.TaskPanelPresetManager method) defineInputParams() (schrodinger.models.presets.PresetManager method) defineInternals() (schrodinger.application.matsci.cgforcefield.ForceField method) defineMappings() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage method) (schrodinger.application.jaguar.jaguar_config_dialog.JaguarHostSelector method) (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.job_monitor.job_monitor_progress_bar.ProgressBar method) (schrodinger.application.job_monitor.job_monitor_widgets.JobBar method) (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.ServerRegistrationMixin method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export.LDExportPanelMixin method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel method) (schrodinger.application.livedesign.widgets.InvalidGEIdWarningDialog method) (schrodinger.application.pymol.export_to_pymol_gui.AdvancedSettingsPopUp method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget method) (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager method) (schrodinger.ui.qt.fp_selector_widget.FingerprintsSelectorWidget method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.tasks.configwidgets.IncorporationSelector method) (schrodinger.ui.qt.tasks.configwidgets.JobnameWidget method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressBar method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.StartButton method) (schrodinger.ui.qt.tasks.taskwidgets.StatusLabel method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) DefineMappingsException defineNewNormal() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) definePanelSettings() (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.ui.qt.appframework2.settings.SettingsPanelMixin method) defines_integer_atom_props() (in module schrodinger.application.matsci.smartsutils) defineTaskPostprocessors() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) defineTaskPreprocessors() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) defineTorsionIndexes() (schrodinger.application.matsci.etarotamers.HapticLigand method) defineVectors() (schrodinger.application.matsci.nano.tube.NanoSheet method) defineVoids() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) Definition (class in schrodinger.utils.ligfilter) DEFINITION_ID (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) definition_id (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) DefinitionParser (class in schrodinger.utils.ligfilter) DefinitionViewerDialog (class in schrodinger.ui.ligfilter) deform_cms_model() (in module schrodinger.application.matsci.desmondutils) Deformation (class in schrodinger.application.matsci.elasticity.strain) deformation_matrix (schrodinger.application.matsci.elasticity.strain.Strain property) DeformCell (class in schrodinger.application.desmond.stage.app.matsci) DeformedStructureSet (class in schrodinger.application.matsci.elasticity.strain) Degree (schrodinger.application.jaguar.constants.Unit attribute) degree (schrodinger.ui.qt.network_visualizer.Node property) degree() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) degree_seconds_mapping_dict (schrodinger.application.pymol.pymol4maestro.panel attribute) degreeOfPolymerization() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) degreesCurrentIndexChanged() (schrodinger.application.pymol.pymol4maestro.panel method) dehydrated_step (schrodinger.stepper.stepper.StepTaskInput attribute) dehydrated_stepChanged (schrodinger.stepper.stepper.StepTaskInput attribute) dehydrated_stepReplaced (schrodinger.stepper.stepper.StepTaskInput attribute) del_from() (schrodinger.application.desmond.arkdb.Datum method) del_from_carat() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) del_key() (schrodinger.utils.sea.sea.Map method) DelayedInputValidation() (schrodinger.active_learning.al_driver.ActiveLearningJob method) delChiralMatchAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) delConnectivity() (schrodinger.application.matsci.amorphous.PolymerFragments method) delDanglingTermAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) delegate() (schrodinger.ui.qt.structtable.ViewerTable method) DELEGATE_CLASS (schrodinger.ui.qt.table_speed_up.SpeedUpDelegateViewMixin attribute) DelegatingIndentedHelpFormatter (class in schrodinger.utils.singledashoptionparser) deletable (schrodinger.project.project.ProjectRow property) delete() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) (schrodinger.application.desmond.arkdb.ArkDb method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.desmond.multisim.parser.Msj method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.project.project.ProjectRow method) (schrodinger.project.surface.ProjectSurface method) (schrodinger.structure.StructureBond method) (schrodinger.surface.Surface method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) delete_all_atom_group() (schrodinger.application.desmond.cms.Cms method) delete_all_pbc_bonds() (in module schrodinger.application.matsci.nano.xtal) delete_all_rows() (in module schrodinger.application.matsci.kmc) delete_atom() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) delete_atom_group() (schrodinger.application.desmond.cms.Cms method) delete_atom_properties() (in module schrodinger.application.desmond.struc) delete_atom_tag() (schrodinger.application.desmond.maestro.Workspace method) delete_atoms() (schrodinger.protein.assignment.ProtAssign method) delete_bonds() (in module schrodinger.structutils.build) delete_bonds_to_atoms() (in module schrodinger.structutils.build) DELETE_BOTH (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) DELETE_CONSTRAINT (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) delete_duplicate_atoms() (in module schrodinger.application.matsci.nano.xtal) delete_far_waters (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_far_waters() (in module schrodinger.application.prepwizard) delete_far_watersChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_far_watersReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_fepio() (in module schrodinger.application.desmond.cms) delete_ffio_ff() (in module schrodinger.application.desmond.struc) delete_ghosts() (in module schrodinger.application.jaguar.utils) delete_group() (in module schrodinger.application.matsci.maestrocmds) delete_group_properties() (in module schrodinger.application.matsci.smartsutils) delete_hydrogens() (in module schrodinger.structutils.build) DELETE_MAPPING_PREFKEY (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog attribute) delete_molecules_from_aa_model() (in module schrodinger.application.matsci.desmondutils) delete_molecules_from_cg_model() (in module schrodinger.application.matsci.desmondutils) delete_molecules_from_comps() (in module schrodinger.application.matsci.desmondutils) delete_molecules_from_model() (in module schrodinger.application.matsci.desmondutils) delete_non_bridging_waters() (in module schrodinger.application.prepwizard) delete_nonbridging_waters (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_nonbridging_watersChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_nonbridging_watersReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_pbc_bonds() (in module schrodinger.application.matsci.nano.xtal) DELETE_PROPERTY (schrodinger.application.matsci.enumeration.VacancyAlchemist attribute) DELETE_SCAN (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) delete_structure_properties() (in module schrodinger.application.desmond.struc) delete_substitution_site_bonds() (schrodinger.application.matsci.reaction_workflow_utils.Sites static method) delete_temp_project_directory() (in module schrodinger.project.project) DELETE_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) delete_workflow_metadata() (in module schrodinger.application.matsci.wfmanagement) delete_zobs() (in module schrodinger.structutils.build) DeleteAll (class in schrodinger.application.bioluminate.pml_menus) deleteAll() (schrodinger.ui.ligfilter.AddDefinitionDialog method) deleteAllPredictions() (schrodinger.protein.sequence.AbstractSingleChainSequence method) deleteAllRestraints() (schrodinger.structutils.minimize.Minimizer method) deleteAllRows() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.infra.table.Table method) (schrodinger.ui.qt.swidgets.STableWidget method) deleteAnchors() (schrodinger.application.matsci.sculptcomplex.Sculptor method) deleteAngles() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) deleteAtomGroupRow() (schrodinger.application.desmond.gui.AtomGroupFrame method) DeleteAtoms (class in schrodinger.application.bioluminate.pml_menus) deleteAtoms() (schrodinger.application.matsci.enumeration.VacancyAlchemist method) (schrodinger.structure.Structure method) deleteAtomsByAsl() (schrodinger.application.desmond.maestro.NewEntry method) deleteBond() (schrodinger.structure.Structure method) (schrodinger.structure.StructureAtom method) DeleteButton (class in schrodinger.ui.qt.swidgets) deleteByEntry() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) deleteBySequences() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) deleteChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) deleteClicked (schrodinger.application.matsci.mswidgets.SavedASLItem attribute) (schrodinger.ui.qt.swidgets.SavedMenuItem attribute) deleteColumn() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.swidgets.STableWidget method) deleteCurrentRow() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) deleteEntry() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) deleteExtraAngles() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) deleteGroup() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) deleteItems() (schrodinger.ui.qt.network_visualizer.Graph method) deleteJobRecordRequested (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget attribute) deleteJobs() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) deleteKey() (schrodinger.application.jaguar.input.JaguarInput method) deleteKeys() (schrodinger.application.jaguar.input.JaguarInput method) deleteMapping() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) deleteNode() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) DeleteOp (class in schrodinger.application.desmond.antlr3.streams) deleteOtherBranches() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) deletePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) deleteParticipant (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) deletePosResRow() (schrodinger.application.desmond.gui.RestraintsTab method) deletePrediction() (schrodinger.protein.sequence.AbstractSingleChainSequence method) deletePreset() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) (schrodinger.models.presets.PresetManager method) deleteProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) DeleteProject (class in schrodinger.application.bioluminate.pml_menus) deletePropertyFromAllAtoms() (schrodinger.structure.Structure method) deleteRow() (schrodinger.infra.table.Table method) (schrodinger.project.project.Project method) deleteRowAction() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable method) deleteSavedItem() (schrodinger.ui.qt.swidgets.ItemsManagerMixin method) deleteSection() (schrodinger.application.jaguar.input.JaguarInput method) deleteSelectedItems() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.Graph method) deleteSelectedRows() (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) (schrodinger.ui.qt.swidgets.STableWidget method) DeleteSelections (class in schrodinger.application.bioluminate.pml_menus) deleteSolventFromSt() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) deleteStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) deleteStructure() (schrodinger.application.jaguar.input.JaguarInput method) deleteTemplate() (schrodinger.application.matsci.builderwidgets.TemplateManager method) deleteTmpHydrogens() (schrodinger.application.matsci.rxn_channel.Products method) DeleteWatersTask (class in schrodinger.application.prepwizard2.tasks) deleteWorkflow() (schrodinger.application.matsci.wfmanagement.WorkflowManagerMixin method) DeleteWS (class in schrodinger.application.bioluminate.pml_menus) deletion_penalty (schrodinger.structutils.structalign.StructAlign property) delFromAuxListbox() (schrodinger.ui.qt.propertyselector.PropertySelector method) DELIM (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) delimiter (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) delKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) delta (schrodinger.application.bindingsite.cavutils.Grid property) DELTA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) (schrodinger.application.jaguar.qrnn.keywords.Models attribute) DELTA_2022_1 (schrodinger.energy.QRNNModel attribute) delta_delta_g (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) DELTA_TRANSFER (schrodinger.application.jaguar.qrnn.keywords.Models attribute) DELTA_TRANSFER_2022_1 (schrodinger.energy.QRNNModel attribute) DELTAE_12E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DELTAE_12H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DELTAE_21E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DELTAE_21H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DELTAE_COLUMNS (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DeltaEnergy (class in schrodinger.application.desmond.fepana) deltaGIsChecked() (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab method) delTempHydrogens() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) delwater_hbond_cutoff (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delwater_hbond_cutoffChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delwater_hbond_cutoffReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delZigZagMatchAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) den() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) Den2Vol() (in module schrodinger.application.matsci.gsas.GSASIImath) Dendrogram (class in schrodinger.ui.qt.dendrogram) DendrogramGraphicNode (class in schrodinger.ui.dendrogram) DendrogramGraphicNodeLabel (class in schrodinger.ui.dendrogram) DendrogramGraphicTree (class in schrodinger.ui.dendrogram) DendrogramGraphicTreeCoordinatesPreferences (class in schrodinger.ui.dendrogram) DendrogramNode (class in schrodinger.ui.dendrogram) DendrogramNodeBFIterator (class in schrodinger.ui.dendrogram) DendrogramPlotDialog (class in schrodinger.application.canvas.clustergui) DendrogramScene (class in schrodinger.ui.dendrogram) DendrogramSyncer (class in schrodinger.ui.qt.dendrogram) DendrogramTreeBuilder (class in schrodinger.ui.dendrogram) DendrogramView (class in schrodinger.ui.dendrogram) DENSE_MATRIX (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) DENSEAROUND (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) density (schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent property) (schrodinger.application.jaguar.gui.utils.Solvent attribute) DENSITY (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_EXT (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_REPLICA_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_REPLICA_PROP_REX (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_STD_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_STD_REPLICA_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DensityAnalysis (class in schrodinger.application.matsci.permittivity) DensityAnalysisMixin (class in schrodinger.application.matsci.density_analysis) DensityTab (class in schrodinger.application.matsci.density_analysis_widget) DEOXY_SUBTYPES (schrodinger.livedesign.biologics.fasta.NucleicAcidAssembler attribute) DeoxyribonucleotideType (class in schrodinger.protein.residue) Depictor() (in module schrodinger.application.desmond.depictor) depletion_at_t12() (in module schrodinger.application.jaguar.kinetics) deploymentCheck() (schrodinger.stepper.app.StepperApplication class method) deprecate_module() (in module schrodinger.utils.deprecation) DEPRECATED (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) deprecated() (in module schrodinger.utils.deprecation) DeprecationError depreference_call() (in module schrodinger.application.desmond.maestro) deprot_ids (schrodinger.application.desmond.stage.app.constant_ph.SiteAndProtonationIds attribute) depth (schrodinger.application.matsci.cgforcefield.ShadowData attribute) (schrodinger.application.pathfinder.analysis.RetrosynthesisState attribute) (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) depth() (schrodinger.application.pathfinder.route.RouteNode method) depthChanged (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) depthReplaced (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) deregisterSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) derivative() (schrodinger.application.jaguar.qrnn.temp_opt.MemoizeJac method) derive_beginning_res() (in module schrodinger.application.bioluminate.antibody.antibody_homology_report_writer) derive_ending_res() (in module schrodinger.application.bioluminate.antibody.antibody_homology_report_writer) derive_project_name() (in module schrodinger.application.phase.packages.hypo_refine.project_utils) derive_token_name() (in module schrodinger.ui.qt.standard.design_tokens) DerivedAttrs (class in schrodinger.application.jaguar.results) deriveReferenceResidueInfo() (schrodinger.application.bioluminate.antibody.sequence_indexer.DVDSequenceIndexer method) (schrodinger.application.bioluminate.antibody.sequence_indexer.SCFVSequenceIndexer method) (schrodinger.application.bioluminate.antibody.sequence_indexer.SingleDomainAbSequenceIndexer method) Desalt (class in schrodinger.application.transforms.chem) desalt_mol() (in module schrodinger.application.pathfinder.synthesis) desalt_structure() (in module schrodinger.structutils.build) DESCENDING (schrodinger.application.glide.sort_utils.SortOrder attribute) describe() (schrodinger.application.desmond.cmj.Job method) (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.analysis.FepanaJob method) (schrodinger.application.desmond.stage.jobs.DesmondJob method) (schrodinger.application.desmond.stage.jobs.FepJob method) (schrodinger.application.desmond.stage.workflow.Concluder method) (schrodinger.application.desmond.stage.workflow.Primer method) describe_database() (in module schrodinger.application.bb_database.bb_task_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) describe_oned_data_file() (in module schrodinger.application.phase.packages.oned_task_utils) description (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) (schrodinger.application.desmond.test_utils.FileRegistration attribute) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword property) (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.application.livedesign.entry_types.BaseEntryData attribute) (schrodinger.application.livedesign.entry_types.Complexes attribute) (schrodinger.application.livedesign.entry_types.CovalentDockingComplexes attribute) (schrodinger.application.livedesign.entry_types.DockedPoses attribute) (schrodinger.application.livedesign.entry_types.Ligands attribute) (schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute) (schrodinger.application.livedesign.export_models.AttachmentData attribute) DESCRIPTION (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Slab attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) description (schrodinger.protein.nonstandard_residues.AminoAcid property) (schrodinger.protein.properties.SequenceProperty attribute) descriptionChanged (schrodinger.application.livedesign.export_models.AttachmentData attribute) (schrodinger.protein.properties.SequenceProperty attribute) descriptionReplaced (schrodinger.application.livedesign.export_models.AttachmentData attribute) (schrodinger.protein.properties.SequenceProperty attribute) DescriptiveAngles (class in schrodinger.application.bioluminate.tcr.docking_angles) Descriptor (class in schrodinger.application.canvas.topo_descriptors) (class in schrodinger.application.matsci.order_parameter_mod) (class in schrodinger.application.matsci.reaction_workflow_gui_utils) DESCRIPTOR (schrodinger.models.parameters.ParamType attribute) Descriptor (schrodinger.protein.properties.PropertyType attribute) (schrodinger.protein.properties.SequenceProperty attribute) DESCRIPTOR_DICT (schrodinger.application.matsci.rxn_channel.ChannelDefinitions attribute) descriptor_only() (in module schrodinger.models.parameters) DESCRIPTORS (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor attribute) descriptors (schrodinger.protein.residue.Residue property) (schrodinger.protein.sequence.AbstractSequence property) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) descriptorsChanged (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) descriptorsCleared (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractSequence attribute) DescriptorsMixin (class in schrodinger.application.matsci.reaction_workflow_utils) descriptorsReplaced (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) DescriptorUtility (in module schrodinger.application.matsci.mlearn.features) deselect() (schrodinger.ui.qt.tablewidget.Cell method) (schrodinger.ui.qt.tablewidget.Row method) deselectAll() (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.residueselector.MutationSelectorMixin method) deselected (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite attribute) deselectEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) deselectOtherEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) deselectSelectedSites() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) deserialize() (schrodinger.application.desmond.cmj.Engine static method) (schrodinger.application.desmond.picklejar.PickleJar static method) (schrodinger.application.steps.dataclasses.MolToSmilesSerializer method) (schrodinger.stepper.stepper.Serializer method) deserialize_bernoulli_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_compact() (in module schrodinger.application.phase.packages.conformer_storage) deserialize_complement_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_conformations() (in module schrodinger.utils.cgxutils) deserialize_csr_matrix() (in module schrodinger.application.matsci.mlearn.sklearn_json.csr) deserialize_decision_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_decision_tree_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_gaussian_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_gradient_boosting() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_gradient_boosting_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_het_states() (in module schrodinger.application.prepwizard) deserialize_label_binarizer() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_lasso_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_lda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_linear_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_logistic_regression() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_lossless() (in module schrodinger.application.phase.packages.conformer_storage) deserialize_mlp() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_mlp_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_model() (in module schrodinger.application.matsci.mlearn.sklearn_json) deserialize_multinomial_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_params_random_state() (in module schrodinger.application.matsci.mlearn.sklearn_json.common) deserialize_pca() (in module schrodinger.application.matsci.mlearn.sklearn_json.decomposition) deserialize_perceptron() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_qda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_random_forest() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_random_forest_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_ridge_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_svm() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_svr() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) Desmond DESMOND (schrodinger.energy.ANIModel attribute) desmond_build_version() (in module schrodinger.application.desmond.bld_ver) DESMOND_CMD (schrodinger.application.desmond.stage.simulate.SimulateBase attribute) DESMOND_DATA_DIR (schrodinger.application.desmond.envir.CONST attribute) DESMOND_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute) DESMOND_LIB_DIR (schrodinger.application.desmond.envir.CONST attribute)

DESMOND_UNIT_CONVERTERS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) DESMOND_VERSION (schrodinger.application.desmond.envir.CONST attribute) DesmondBackendJob (class in schrodinger.application.desmond.stage.jobs) DesmondBasicConfigDialog (class in schrodinger.application.desmond.gui) DesmondBoxSize (class in schrodinger.application.desmond.system_builder_util) DesmondExtend (class in schrodinger.application.desmond.stage.simulate) DesmondGuiConfigDialog (class in schrodinger.application.desmond.gui) DesmondJob (class in schrodinger.application.desmond.stage.jobs) DesmondMDWEdit (class in schrodinger.application.matsci.deswidgets) DesmondMDWidgets (class in schrodinger.application.matsci.deswidgets) DesmondMDWidgets.NUM_FRMS_TYPE (class in schrodinger.application.matsci.deswidgets) DesmondModel (class in schrodinger.application.matsci.desmondutils) DesmondRestGuiConfigDialog (class in schrodinger.application.desmond.gui) DesmondSubhostConfigDialog (class in schrodinger.application.matsci.configdlgs) DesmondTyper (class in schrodinger.application.desmond.systype) dest (schrodinger.application.desmond.starter.ui.cmdline.Option attribute) det (schrodinger.application.matsci.elasticity.tensors.SquareTensor property) Detached (schrodinger.ui.qt.pop_up_widgets.PopUpMode attribute) detailed_atom_smarts() (in module schrodinger.application.matsci.rdpattern) detailsData() (schrodinger.application.bioluminate.patch_utils.patch_finder.Patch method) detect() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) detect_custom_mmffld_data() (in module schrodinger.application.matsci.amorphous) detect_license_file_type() (in module schrodinger.application.licensing.licserver.install) detect_property_types() (in module schrodinger.application.combinatorial_diversity.driver_utils) detect_queue() (in module schrodinger.application.desmond.driver_utils) detect_tetrahedral() (in module schrodinger.application.matsci.rxn_channel) DETECTED_LIGAND (schrodinger.application.prepwizard.HetType attribute) DetectionError determinant() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) determine() (schrodinger.application.desmond.cmj.StageBase method) determine_active_bonds_info() (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper method) determine_attachment_bonds() (in module schrodinger.application.canvas.r_group) determine_attachments() (in module schrodinger.application.canvas.r_group) determine_box_size() (in module schrodinger.application.matsci.desmondutils) determine_ccd_pdbres() (in module schrodinger.structutils.ccd) determine_gap() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) determine_his_ccd_pdbres() (in module schrodinger.structutils.ccd) determine_jobtype() (in module schrodinger.application.inputconfig) (in module schrodinger.ui.qt.appframework2.jobnames) determine_na_type() (in module schrodinger.livedesign.biologics.registration) determine_rgroup_indexes() (in module schrodinger.application.canvas.r_group) determine_rings_in_attachments() (in module schrodinger.application.canvas.r_group) determine_source_path() (in module schrodinger.application.matsci.jobutils) determineAromaticAtomType() (schrodinger.structutils.assignbondorders.AssignBondOrders method) determineAromaticAtomTypes() (schrodinger.structutils.assignbondorders.AssignBondOrders method) determineBasisVectors() (schrodinger.application.matsci.nano.xtal.Crystal method) determineCouplerLocation() (schrodinger.application.matsci.amorphous.BaseMoiety method) determineLatticeNumbering() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) determineQueueResource() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) dev_keywords() (in module schrodinger.application.glide.utils) dev_principal_invariants (schrodinger.application.matsci.elasticity.stress.Stress property) deviator_stress (schrodinger.application.matsci.elasticity.stress.Stress property) DEVICE (schrodinger.application.livedesign.live_report_widget.LiveReportType attribute) df_per_window (schrodinger.application.desmond.new_fep_edge_data.FepData property) DF_RATE_TYPE (class in schrodinger.application.matsci.reaction_workflow_utils) DFA (class in schrodinger.application.desmond.antlr3.dfa) DFA12_accept (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_eof (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_eot (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_max (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_min (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_special (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_transition (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA15_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DfCustomEqColumns (class in schrodinger.application.matsci.reaction_workflow_utils) DfCustomRateColumns (class in schrodinger.application.matsci.reaction_workflow_utils) DFG (schrodinger.protein.annotation.KinaseFeatureLabel attribute) DFT (schrodinger.application.jaguar.constants.CalcType attribute) (schrodinger.forcefield.constants.GeometryOptMethod attribute) DFT_BASE_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab attribute) dft_functional (schrodinger.application.matsci.espresso.utils.PseudoData attribute) DFT_GRID_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFT_ONLY (schrodinger.application.jaguar.gui.theory_selector.DftTheorySelectorFilterListPopUp attribute) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListPopUp attribute) DFT_ONLY_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFT_OR_HF_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFTComboRadioSelector (class in schrodinger.application.jaguar.gui.tabs.theory_tab) DFTNAME (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) dftnames_markup() (in module schrodinger.application.jaguar.jaguar_keyword_utils) DftTheorySelectorFilterListPopUp (class in schrodinger.application.jaguar.gui.theory_selector) DftTheorySelectorFilterListToolButton (class in schrodinger.application.jaguar.gui.theory_selector) DftType (class in schrodinger.application.matsci.espresso.qeinput) dftu (schrodinger.application.matsci.espresso.qeinput.DftType property) DftUType (class in schrodinger.application.matsci.espresso.qeinput) dg (schrodinger.application.desmond.new_fep_edge_data.FepData property) dg_forward_time_function (schrodinger.application.desmond.new_fep_edge_data.FepData property) dg_reverse_time_function (schrodinger.application.desmond.new_fep_edge_data.FepData property) dg_sliding_time_function (schrodinger.application.desmond.new_fep_edge_data.FepData property) DIAG (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) DIAG_TYPE (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) DiagnosticsCollectionError diagonalize_symmat() (in module schrodinger.application.combinatorial_diversity.splitter_utils) Dial (class in schrodinger.ui.qt.dialbox) dial_changed_delta (schrodinger.ui.qt.dialbox.Dial attribute) (schrodinger.ui.qt.dialbox.XYZDialBox attribute) DIAL_NAMES (schrodinger.ui.qt.dialbox.XYZDialBox attribute) dialChangedDelta() (schrodinger.ui.qt.dialbox.XYZDialBox method) dialog() (schrodinger.ui.qt.appframework.ReadDialog method) DIALOG_ID (schrodinger.application.matsci.mswidgets.StructureLoader attribute) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame attribute) DIALOG_SIZE (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog attribute) DialogParameters (class in schrodinger.ui.qt.config_dialog) diameter (schrodinger.application.matsci.atom_group.HelixData attribute) Dict2Values() (in module schrodinger.application.matsci.gsas.GSASIIpwd) dict_delete_and_decrement_keys() (in module schrodinger.application.matsci.rxn_channel) dict_to_str() (in module schrodinger.application.matsci.nano.particle) DictAction (class in schrodinger.application.glide.utils) DictDiff (class in schrodinger.models.diffy) dictKeys() (schrodinger.application.canvas.utils.ChmCSVTools method) DictParam (class in schrodinger.models.parameters) DictRestrainGroup (class in schrodinger.application.desmond.cms) dictValues() (schrodinger.application.canvas.utils.ChmCSVTools method) died() (schrodinger.pipeline.pipeline.StageJob method) dielectric (schrodinger.application.jaguar.gui.utils.Solvent attribute) DIELECTRIC (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) dielectric_constant (schrodinger.structutils.minimize.Minimizer property) diff() (in module schrodinger.utils.sea.sea) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.jaguar.results.DerivedAttrs method) (schrodinger.application.jaguar.results.JaguarAtomicResults method) (schrodinger.application.jaguar.results.JaguarResults method) (schrodinger.application.jaguar.results.RoutineTimes method) DiffCompareArgumentParser (class in schrodinger.utils.compare) difference() (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.utils.scollections.IdSet method) difference_update() (schrodinger.utils.scollections.IdSet method) different() (in module schrodinger.application.jaguar.gui.tabs.solvation_tab) DIFFHIGHVAL (schrodinger.application.matsci.rxn_path.ReactionPath attribute) DIFFLOWTHRESH (schrodinger.application.matsci.rxn_path.ReactionPath attribute) DIFFUSION_COL_MAP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSION_FILE_EXT (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) DIFFUSION_FILE_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSION_PROPS_MAP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DiffusionGKStep (class in schrodinger.application.matsci.jwsteps) DiffusionMSDStep (class in schrodinger.application.matsci.jwsteps) diffusivity (schrodinger.application.matsci.equilibrium_md.MsdTrajBase.DIFFUSIVITY attribute) DIFFUSIVITY_1D_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_1D_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_1D_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_2D_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_2D_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_2D_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_3D_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_3D_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_3D_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_VECTOR_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_X_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_X_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_X_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Y_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Y_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Y_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Z_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Z_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Z_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DiffusivityMsdAnalysis (class in schrodinger.application.matsci.equilibrium_md) dih (schrodinger.application.desmond.torsion_related.TorsionPotential attribute) DIHED_ENERGY (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) Dihedral (class in schrodinger.application.jaguar.hess_guess) DIHEDRAL (schrodinger.application.matsci.rxn_path.Coord attribute) dihedral_type (schrodinger.ui.qt.rama.BackboneDihedral attribute) dihedrals (schrodinger.application.jaguar.hess_guess.CoordinateManager property) DihedralSpinBox (class in schrodinger.ui.qt.rama) DIHEDRALWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) DIMENSION_MAP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIMENSIONALITY (class in schrodinger.application.matsci.msconst) Dimer (class in schrodinger.application.matsci.clusterstruct) DimerNEBType (class in schrodinger.application.matsci.espresso.qeinput) DimerSpeciesSelector (class in schrodinger.application.matsci.clusterstructgui) Dipole (class in schrodinger.application.jaguar.results) DIPOLE (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) dipole() (in module schrodinger.application.mopac.results_main) DIPOLE_CAP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) dipole_esp() (in module schrodinger.application.mopac.results_main) DIPOLE_INTERVAL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) DIPOLE_SQ (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SQ_INDEX (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SQ_MEAN (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SQ_MEAN_INDEX (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) dipole_strength_precision (schrodinger.application.jaguar.results.NormalMode attribute) DIPOLE_SUSCEPTIBILITY_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SUSCEPTIBILITY_STD_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SUSCEPTIBILITY_STORE_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) dipole_xyz() (in module schrodinger.application.mopac.results_main) DipoleAnalysis (class in schrodinger.application.matsci.permittivity) DipoleDirector (class in schrodinger.application.matsci.order_parameter_mod) DipoleStrength (schrodinger.application.jaguar.constants.Unit attribute) DiproPredictor (class in schrodinger.protein.predictors) DiproPredictor.DiproFormat (class in schrodinger.protein.predictors) dir (schrodinger.application.combinatorial_explorer.driver_utils.RouteSourceType attribute) DIR (schrodinger.application.matsci.desconfig.MSJStringer attribute) Dir (schrodinger.job.jobcontrol.Job property) DIR_SELECTOR_ID (schrodinger.application.matsci.reportutils.ReportOutputsDialog attribute) DIRECT (schrodinger.application.jaguar.qrnn.keywords.Models attribute) DIRECT_2022_1 (schrodinger.energy.QRNNModel attribute) DIRECT_TRANSFER (schrodinger.application.jaguar.qrnn.keywords.Models attribute) DIRECT_TRANSFER_2022_3 (schrodinger.energy.QRNNModel attribute) Direction (class in schrodinger.models.presets) (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data) DIRECTION (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) directionChanged() (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) DIRECTIONS (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) Director (class in schrodinger.application.matsci.order_parameter_mod) directories (schrodinger.application.licensing.licserver.exceptions.NoWritableDirectoryError attribute) directory (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) directoryChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.ui.qt.directory_selector.DirectorySelector attribute) directoryReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) DirectorySelector (class in schrodinger.ui.qt.directory_selector) DirectoryType (class in schrodinger.job.util) dis_solvent_correction() (in module schrodinger.application.desmond.fep_net_charge) Disable (class in schrodinger.application.bioluminate.pml_menus) (schrodinger.adapter.Canonicalize attribute) (schrodinger.adapter.Generate2DCoordinates attribute) (schrodinger.adapter.LabelAtoms attribute) (schrodinger.adapter.Sanitize attribute) (schrodinger.adapter.UniqueFilter attribute) disable() (schrodinger.project.project.Project method) disable_core() (in module schrodinger.utils.sysinfo) disable_dummy_maestro_imports() (in module schrodinger.infra.unusable_module_importer) disable_dummy_missing_product_imports() (in module schrodinger.infra.unusable_module_importer) disable_dummy_non_post_test_imports() (in module schrodinger.infra.unusable_module_importer) disable_lr_columns (schrodinger.application.livedesign.panel_components.ExportTableModel property) disable_mmerr (class in schrodinger.infra.mmerr) disable_table_sort() (in module schrodinger.application.matsci.gutils) DISABLE_TYPE_KEY (schrodinger.application.matsci.espresso.qeinput.HPType attribute) DISABLED (schrodinger.ui.qt.standard.design_tokens.BorderColors attribute) (schrodinger.ui.qt.standard.design_tokens.StateColors attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) DISABLED_BUTTON (schrodinger.ui.qt.standard.design_tokens.BackgroundColors attribute) DISABLED_BUTTON_BACKGROUND (schrodinger.ui.qt.standard.colors.LightModeColors attribute) DISABLED_BUTTON_BORDER (schrodinger.ui.qt.standard.colors.LightModeColors attribute) DISABLED_BUTTON_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) DISABLED_FORM_FIELD (schrodinger.ui.qt.standard.design_tokens.BackgroundColors attribute) DISABLED_STYLE (schrodinger.ui.qt.delegates.LinkDelegate attribute) DISABLED_TEXTS (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget attribute) DisabledSymmetryWarning disableResidue() (schrodinger.ui.residueselector.MutationSelectorMixin method) disableResidues() (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) (schrodinger.ui.residueselector.MutationSelectorMixin method) disableSidechainPacking() (schrodinger.protein.reliability.ProteinCheckParameters method) disableSmartDistribution() (schrodinger.job.queue.JobDJ method) disableUnselectedItems() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) disallow_grpc_workers() (in module schrodinger.seam.testing.fixtures) disallowedMutations() (schrodinger.ui.residueselector.ResidueGroups method) discard() (schrodinger.utils.scollections.IdSet method) discard_lewis_data() (in module schrodinger.comparison.atom_mapper) discardChanges() (schrodinger.ui.qt.widgetmixins.panelmixins.CleanStateMixin method) discardTokenType() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) disconnect() (schrodinger.application.glide.http_client.ZmqClient method) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.utils.qt_utils.SignalAndSlot method) disconnect_from_workspacehub() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) disconnect_signals() (in module schrodinger.ui.qt.table_helper) DISCONNECTED (schrodinger.application.livedesign.ldclient_proxy.LDConnectionStatus attribute) disconnected (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) disconnectOrigNode() (schrodinger.application.matsci.permittivity.WorkflowParser method) disconnectSignal() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) disconnectSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) disconnectSlots() (schrodinger.application.bioluminate.actions.factory.SAction method) DiscretelySampledFunction (class in schrodinger.application.jaguar.discretized_1d_function) DiseControl (class in schrodinger.application.vss.control) DISORDER_SYSTEM (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) Disordered (class in schrodinger.protein.predictors) DisorderedSystemBuilder (class in schrodinger.application.desmond.stage.prepare.structure) DisorderedSystemBuilderStep (class in schrodinger.application.matsci.jwsteps) DisorderSystemBuilder (class in schrodinger.application.matsci.permittivity) DISP_CORR (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) dispersity() (in module schrodinger.application.matsci.amorphous) displaced_weights (schrodinger.application.desmond.kinetics.utils.RmsdSelection attribute) displacement_prec (schrodinger.application.jaguar.results.ConvCriteria attribute) display() (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.qt.filter_dialog.FilterDialog method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) display_asl() (schrodinger.application.desmond.maestro.Workspace method) display_atoms() (in module schrodinger.application.bioluminate.pml_menus) display_atoms_as() (in module schrodinger.application.bioluminate.pml_menus) DISPLAY_DATA_CLASS (schrodinger.ui.qt.delegates.PictureDelegate attribute) (schrodinger.ui.qt.delegates.RdMolDelegate attribute) (schrodinger.ui.qt.delegates.StructureDelegate attribute) display_image() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.livedesign.cmdline) display_name (schrodinger.application.matsci.builderwidgets.BaseTemplateListWidgetItem property) (schrodinger.application.matsci.builderwidgets.CustomListWidgetItem property) (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) (schrodinger.protein.properties.SequenceProperty attribute) display_nameChanged (schrodinger.protein.properties.SequenceProperty attribute) display_nameReplaced (schrodinger.protein.properties.SequenceProperty attribute) display_only_asl() (schrodinger.application.desmond.maestro.Workspace method) display_residue() (schrodinger.ui.qt.rama.Rama method) display_ribbons() (in module schrodinger.application.bioluminate.pml_menus) display_string (schrodinger.livedesign.registration.RegistrationData attribute) display_structure() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.Rama method) displayDefault() (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec method) displayedEntryIds() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) displayLabels() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) displayLocalAtoms() (schrodinger.application.matsci.sliceplot.SlicePlot method) DisplayOnly (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_data) displayProperties() (schrodinger.ui.qt.propertyselector.PropertySelector method) displayPropsDialog() (schrodinger.ui.two_d_viewer.TwoDViewer method) displayRecognitionError() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) DisplaySettingsData (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_data) DisplaySettingsManager (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_manager) DisplayStatus (class in schrodinger.job.jobcontrol) (schrodinger.job.jobcontrol.Job property) displayTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) DisproPredictor (class in schrodinger.protein.predictors) Dissimilar (schrodinger.protein.alignment.ResidueSimilarity attribute) dissociate() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) DISSOCIATION_BOND_LENGTH (schrodinger.application.matsci.rxn_channel.Constants attribute) DISSOCIATION_TYPE (schrodinger.application.matsci.rxn_channel.Constants attribute) dist3() (in module schrodinger.application.bindingsite.cavutils) dist_cell_iterator() (in module schrodinger.structutils.measure) distance (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) DISTANCE (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) distance (schrodinger.application.qsite.input.HydrogenCap property) (schrodinger.structutils.interactions.pi.CationPiInteraction property) (schrodinger.structutils.interactions.pi.PiPiInteraction property) DISTANCE (schrodinger.trajectory.trajectory_gui_dir.banners.MeasurementMode attribute) distance_cutoff (schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter attribute) distance_from_planckian() (in module schrodinger.application.matsci.colorutils) DISTANCE_THRESH (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) distance_vectors() (in module schrodinger.application.jaguar.hess_guess) DistanceCellIterator (class in schrodinger.structutils.measure) distanceChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) DistanceMatrixPlotDialog (class in schrodinger.application.canvas.clustergui) distanceReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) DistinctStructures (class in schrodinger.application.transforms.filters) Distortion (class in schrodinger.structutils.check) distribute_hypos() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) distributeCpus() (schrodinger.pipeline.pipeline.Pipeline method) DISULFIDE (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) disulfide_bond (schrodinger.protein.residue.CombinedChainResidueWrapper property) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) disulfide_bonds (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.sequence.AbstractProteinSequenceMixin property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.protein.sequence.ProteinSequence property) DisulfideBond (class in schrodinger.protein.residue) disulfideBondsCacheCleared (schrodinger.protein.sequence.AbstractProteinSequenceMixin attribute) DisulfideConnectorMixin (class in schrodinger.protein.helm.helm_renderer) DisulfideCyclicConnectorItem (class in schrodinger.protein.helm.helm_renderer) DisulfideLinearConnectorItem (class in schrodinger.protein.helm.helm_renderer) DISULFIDES (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) disulfides (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) disulfidesChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) disulfidesReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) DiversityFingerprinter (class in schrodinger.application.combinatorial_diversity.diversity_fingerprinter) diversitySelect() (schrodinger.active_learning.al_node.PrepareSmilesNode method) DiversitySelector (class in schrodinger.application.combinatorial_diversity.diversity_selector) DiversitySplitter (class in schrodinger.application.combinatorial_diversity.diversity_splitter) divide() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) Divider (class in schrodinger.application.matsci.mswidgets) DLG_TITLE (schrodinger.application.matsci.jobdirdlg.InteractiveFileDownloader attribute) dlst() (schrodinger.application.macromodel.utils.ComUtil method) DMPC (schrodinger.application.desmond.constants.LIPID_BILAYERS attribute) DNA (schrodinger.application.bioluminate.mutation.PolymerType attribute) DNA_ANTISENSE (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) DNA_SENSE (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) DNASequence (class in schrodinger.protein.sequence) do() (schrodinger.utils.pymol.PymolInstance method) do_any_residues_have_missing_side_chains() (in module schrodinger.application.prepwizard) do_cleanup (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_cleanupChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_cleanupReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_GET() (schrodinger.application.glide.http_server.GlideHTTPHandler method) do_hbond (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_hbondChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_hbondReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) DO_NOT_CHECK_PATH (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) do_nothing() (schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro method) do_POST() (schrodinger.application.glide.http_server.GlideHTTPHandler method) do_preprocess (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_preprocessChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_preprocessReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_rings_share_atoms() (in module schrodinger.structutils.assignbondorders) doApplyClustering() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) doBonding() (schrodinger.application.matsci.nano.xtal.Crystal method) doBondOrders() (schrodinger.application.matsci.nano.tube.NanoTube method) (schrodinger.application.matsci.nano.xtal.Crystal method) doc (schrodinger.project.project.ProjectRow attribute) DoCalibInst() (in module schrodinger.application.matsci.gsas.GSASIIpwd) Dock (class in schrodinger.application.glide.glide) (class in schrodinger.application.transforms.dock) dock() (schrodinger.application.glide.http_client.AbstractHTTPClient method) (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.glide.http_client.HTTPClient method) (schrodinger.application.glide.http_client.NonBlockingHTTPClient method) (schrodinger.application.glide.http_client.ZmqClient method) dock_widget (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) Dockable() (schrodinger.application.transforms.dock.Dock static method) DOCKABLE_TAG (schrodinger.application.transforms.dock.Dock attribute) DockableMixinCollection (class in schrodinger.ui.qt.widgetmixins.basicmixins) dockBatch() (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) DockedPoses (class in schrodinger.application.livedesign.entry_types) docking_config_setup() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage method) docking_keywords (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) docking_keywordsChanged (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) docking_keywordsReplaced (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) DockingStage (class in schrodinger.pipeline.stages.glide) dockSmiles() (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.glide.http_client.HTTPClient method) (schrodinger.application.glide.http_client.NonBlockingHTTPClient method) DockWidget (class in schrodinger.ui.qt.appframework2.baseapp) doCluster() (schrodinger.application.macromodel.utils.CluUtil method) doCommand() (schrodinger.application.matsci.jobutils.LoggingSubprocessJob method) (schrodinger.application.matsci.packmol.StdInJob method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.utils.installation_check.TestJob method) doctype() (schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method) Dodecahedron (class in schrodinger.application.matsci.shapes) dodecahedron() (schrodinger.application.watermap.shapes.ShapeFactory method) doEnumeration() (schrodinger.application.matsci.reaction_workflow_utils.EnumerateReactionWorkflow method) does_res_have_missing_side_chains() (in module schrodinger.application.prepwizard) doGroup() (schrodinger.utils.pymol.RowProxy method) domain (schrodinger.application.bioluminate.antibody.sequence_indexer.DVDSequenceIndexer property) (schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo attribute) (schrodinger.application.bioluminate.antibody.sequence_indexer.SingleDomainAbSequenceIndexer property) Domain (schrodinger.protein.annotation.Domains attribute) domain_structure (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction attribute) DomainAlignment (class in schrodinger.application.bioluminate.anarci.anarci_adapter) DomainArrangement (class in schrodinger.protein.predictors) DomainAssemblyInstruction (class in schrodinger.application.bioluminate.antibody.assembly) DomainForming (schrodinger.protein.predictors.DomainArrangement attribute) DomainNumbering (class in schrodinger.application.bioluminate.anarci.anarci_adapter) Domains (class in schrodinger.protein.annotation) domains (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) domainsChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin attribute) DomproPredictor (class in schrodinger.protein.predictors) donateNodes() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) done (schrodinger.application.pathfinder.analysis.RetrosynthesisState attribute) DONE (schrodinger.job.queue.JobState attribute) (schrodinger.tasks.ldtasks.Status attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.Status attribute) done_jobs (schrodinger.job.queue.JobDJ property) done_tasks (schrodinger.tasks.queue.QueueResults attribute) done_tasksChanged (schrodinger.tasks.queue.QueueResults attribute) done_tasksReplaced (schrodinger.tasks.queue.QueueResults attribute) doneEditingSMARTS() (schrodinger.ui.qt.swidgets.SMARTSEdit method) doneReordering() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) doNonLinearFit() (schrodinger.application.matsci.rxn_path.ReactionPath method) DONOR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) DonorConstraint (class in schrodinger.application.glide.glide) donors (schrodinger.protein.assignment.Interactors attribute) DoNothing (schrodinger.ui.qt.config_dialog.RequestedAction attribute) dont_ignore_stereo() (in module schrodinger.application.glide.utils) DoPeakFit() (in module schrodinger.application.matsci.gsas.GSASIIpwd) doPropertyEvaluation() (schrodinger.application.matsci.nano.xtal.Crystal method) doPropsMatch() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method) DOS (class in schrodinger.application.matsci.espresso.qeoutput) DOS_FREQ_DEGAUSS (schrodinger.application.matsci.espresso.qeoutput.PhDOS attribute) DOS_FREQ_GRID_SPACING (schrodinger.application.matsci.espresso.qeoutput.PhDOS attribute) doStateOptimizations() (schrodinger.application.matsci.mecp_mod.MECP method) DOT (schrodinger.application.matsci.desconfig.MSJStringer attribute) dot (schrodinger.surface.Style attribute) (schrodinger.surface.Surface.Style attribute) dot() (schrodinger.pipeline.pipeutils.DotPrinter method) dot_endpoint() (schrodinger.seam.viz.watcher.WatcherWebServer method) dotdot (schrodinger.application.desmond.antlr3.tree.TreeParser attribute) dotdotPattern (schrodinger.application.desmond.antlr3.tree.TreeParser attribute) doTermination() (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.slab.Surface method) (schrodinger.application.matsci.nano.tube.NanoTube method) DotPrinter (class in schrodinger.pipeline.pipeutils) dotprod() (in module schrodinger.application.desmond.cms) doTranslation() (schrodinger.application.matsci.nano.xtal.Crystal method) DOUBLE (schrodinger.energy.ANIPrecision attribute) Double (schrodinger.structure.BondType attribute) DOUBLE_DISPLACEMENT_TYPE (schrodinger.application.matsci.rxn_channel.Constants attribute) DOUBLE_PRECISION (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) DOUBLE_SIDED_HBOND_PKA_SHIFT (schrodinger.protein.assignment.HistidinepKaPredictor attribute) DoubleClickButtonMixin (class in schrodinger.ui.qt.standard_widgets.buttons) doubleClicked (schrodinger.ui.qt.standard_widgets.buttons.DoubleClickButtonMixin attribute) DoubleClickSplitStyledButton (class in schrodinger.ui.qt.standard_widgets.buttons) doubleEtc (schrodinger.application.desmond.antlr3.tree.TreeParser attribute) doubleEtcPattern (schrodinger.application.desmond.antlr3.tree.TreeParser attribute) doublequote (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) doubleRingAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) DoubleSigmoid (class in schrodinger.math.multi_parameter_optimization) doubted_geom() (in module schrodinger.application.jaguar.textparser) DOWN (schrodinger.models.presets.Direction attribute) DOWN_ARROW (schrodinger.ui.qt.standard.design_tokens.ScrollbarIcons attribute) download() (schrodinger.job.jobcontrol.Job method) download_all_entry_data() (in module schrodinger.protein.gpcr.gpcrdb) download_and_decompress() (in module schrodinger.application.pathfinder.multiroute) download_and_login_ld_client() (in module schrodinger.tasks.ldtasks) download_blob() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) download_cif() (in module schrodinger.protein.getpdb) download_em_map() (in module schrodinger.protein.getpdb) download_ent() (in module schrodinger.protein.getpdb) download_exported_csv_from_bucket() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) download_fasta() (in module schrodinger.protein.getpdb) download_file() (in module schrodinger.protein.getpdb) DOWNLOAD_FILE_ENDINGS (schrodinger.application.matsci.jobdirdlg.DownloadingMonitorMixin attribute) download_format() (in module schrodinger.protein.getpdb_utility) download_icon_tooltip() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) download_job() (in module schrodinger.job.download) download_ld_client() (in module schrodinger.application.livedesign.login) download_linux_packages_requirement() (in module schrodinger.utils.installation_check) download_nodelocked_license() (in module schrodinger.application.licensing.licadmin) download_pdb() (in module schrodinger.protein.getpdb) DOWNLOAD_PENDING (schrodinger.application.job_monitor.job_monitor_models.DownloadStatus attribute) download_reflection_data() (in module schrodinger.protein.getpdb) download_server_license() (in module schrodinger.application.licensing.licadmin) download_sf() (in module schrodinger.protein.getpdb) download_status (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) download_statusChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) download_statusReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) download_structures (schrodinger.protein.tasks.blast.BlastSettings attribute) download_structuresChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) download_structuresReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) DOWNLOADED (schrodinger.application.job_monitor.job_monitor_models.DownloadStatus attribute) downloadFile() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) downloadFilesToDir() (schrodinger.application.matsci.jobdirdlg.InteractiveFileDownloader method) DownloadingMonitorMixin (class in schrodinger.application.matsci.jobdirdlg) downloadJobFiles() (schrodinger.application.matsci.jobdirdlg.DownloadingMonitorMixin method) downloadJobFilesIfNecessary() (schrodinger.application.matsci.jobdirdlg.DownloadingMonitorMixin method) downloadJobFileToTemp() (schrodinger.application.matsci.jobdirdlg.InteractiveFileDownloader method) (schrodinger.application.matsci.jobutils.FileDownloader method) DownloadStatus (class in schrodinger.application.job_monitor.job_monitor_models) doXCluster() (schrodinger.application.macromodel.utils.CluUtil method) DpdMapper (class in schrodinger.application.matsci.automated_cg_mapping) DpdMolecule (class in schrodinger.application.matsci.automated_cg_mapping) dpi (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) DPPC (schrodinger.application.desmond.constants.LIPID_BILAYERS attribute) drag() (schrodinger.ui.qt.rama.Rama method) dragEnterEvent() (schrodinger.ui.two_d_viewer.TwoDTableView method) draw() (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.application.matsci.permittivity.WorkflowParser method) draw2DPicture() (schrodinger.ui.qt.structure2d.LabeledStructureToolTip method) draw_axes() (schrodinger.ui.qt.rama.RamaContourMixin method) draw_image() (in module schrodinger.livedesign.draw) draw_picture_into_rect() (in module schrodinger.ui.qt.structtable) (in module schrodinger.ui.qt.swidgets) draw_regions() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.RamaContourMixin method) DRAW_STYLE (schrodinger.ui.qt.delegates.CheckboxDelegate attribute) (schrodinger.ui.qt.delegates.ProgressBarDelegate attribute) (schrodinger.ui.qt.delegates.RadioButtonDelegate attribute) DRAW_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) drawAndUpdate() (schrodinger.ui.qt.smatplotlib.SmatplotlibCanvas method) drawChmmol() (schrodinger.ui.qt.structure2d.StructurePicture method) drawDataIntoRect() (schrodinger.ui.qt.table.StructureDataViewerDelegate method) drawFixedContents() (schrodinger.application.desmond.rl_helper.NumberedCanvas method) (schrodinger.application.matsci.reportutils.CanvasWithHeaderAndFooter method) drawPlot() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) drawRDMol() (schrodinger.ui.qt.structure2d.StructurePicture method) drawStructure() (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.ui.qt.structure2d.StructurePicture method) drawTicks() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) drawTree() (schrodinger.ui.dendrogram.DendrogramScene method) DRIFT_VEL (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) driv() (schrodinger.application.macromodel.utils.ComUtil method) DRIVER (schrodinger.application.matsci.jwsteps.BaseNoJobStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.FreeVolumeStep attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) (schrodinger.application.matsci.jwsteps.VoidStep attribute) driver (schrodinger.application.matsci.multiapp.CMD_DRIVER_DATA attribute) DRIVER_HOST (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog attribute) driver_host_settings (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) driver_host_settingsChanged (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) driver_host_settingsReplaced (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) driver_logging() (in module schrodinger.application.matsci.textlogger) driver_main() (in module schrodinger.application.matsci.jobutils) DRIVER_PATH (schrodinger.application.matsci.jwsteps.BaseNoJobStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.CombinerStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.FreeVolumeStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) (schrodinger.application.matsci.jwsteps.VoidStep attribute) (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) (schrodinger.application.matsci.permittivity.AveCellAnalysis attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) (schrodinger.application.matsci.permittivity.CMSParser attribute) (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) (schrodinger.application.matsci.permittivity.JaguarMerge attribute) (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) (schrodinger.application.matsci.permittivity.StepBase attribute) DRIVERHOST (schrodinger.utils.cmdline.Options attribute) DriverParser (class in schrodinger.application.matsci.parserutils) driverReservesCores() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) DROPDOWN_BUTTON (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) DROPDOWN_LINK (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) dropEvent() (schrodinger.ui.two_d_viewer.TwoDTableView method) dropped_file (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) dropped_fileChanged (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) dropped_fileReplaced (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) DRUDE_INVERSE_FORCE_CONSTANT_SCALING (class in schrodinger.application.desmond.constants) DRUG_DISCOVERY (schrodinger.application.livedesign.ldclient_proxy.LDMode attribute) DrugLikeSplitStage (class in schrodinger.pipeline.stages.filtering) DRX (schrodinger.application.matsci.kmc.PairsMixin attribute) DRY (schrodinger.application.matsci.kmc.PairsMixin attribute) DRZ (schrodinger.application.matsci.kmc.PairsMixin attribute) DS_DNA (schrodinger.livedesign.entity_type.EntityClass attribute) DS_RNA (schrodinger.livedesign.entity_type.EntityClass attribute) DSB_DRIVER (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) DSC (class in schrodinger.application.desmond.arkdb) Dsp2pos() (in module schrodinger.application.matsci.gsas.GSASIIlattice) dsq (schrodinger.application.matsci.clusterstruct.Neighbor attribute) DTDTreeBuilder (class in schrodinger.application.jaguar.keywordDB) dtor() (schrodinger.application.desmond.maestro.NewEntryGroup method) DTYPE (schrodinger.application.desmond.cms.FBHWPosRestrainArray attribute) (schrodinger.application.desmond.cms.PosRestrainArray attribute) DU_BUTTON_ID (schrodinger.ui.qt.periodictable.PeriodicTableDialog attribute) DU_ELEMENT (schrodinger.ui.qt.periodictable.PeriodicTableDialog attribute) DU_SYMBOL (schrodinger.ui.qt.periodictable.PeriodicTableDialog attribute) DummiesToHydrogens (class in schrodinger.application.matsci.buildcomplex2d) DUMMY (schrodinger.energy.MonoMetalComplexType attribute) dummy() (in module schrodinger.application.desmond.starter.starter) DUMMY_ATOMIC_NUMBER (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae attribute) DUMMY_ELEMENT (schrodinger.application.matsci.cg_mapping.CoarseGrainBond attribute) DUMMY_FIELDS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) DummyCalculateScoreNode (class in schrodinger.active_learning.fake_nodes) DummyGpuHost (class in schrodinger.ui.qt.config_dialog) DummyMaestroModule (class in schrodinger.infra.unusable_module_importer) DummyMaker (class in schrodinger.application.matsci.etatoggle) DummyModule (class in schrodinger.infra.unusable_module_importer) DummyPilotScoreNode (class in schrodinger.active_learning.fake_nodes) DummyRescoreNode (class in schrodinger.active_learning.fake_nodes) dump() (in module schrodinger.models.json) (schrodinger.job.queue.JobDJ method) (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.stage.Stage method) (schrodinger.utils.sea.sea.Sea method) dump_output_csv_file() (in module schrodinger.application.jaguar.macro_pka_utils) dump_yaml_file() (in module schrodinger.application.matsci.yamlutils) dumpBE() (schrodinger.job.app.App method) dumpFE() (schrodinger.job.app.App method) dumps() (in module schrodinger.models.json) dumpSavedItems() (schrodinger.ui.qt.swidgets.ItemsManagerMixin method) dup() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method) Duplicate (class in schrodinger.application.bioluminate.pml_menus) DUPLICATE (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) duplicate() (schrodinger.application.desmond.maestro.NewEntryGroup method) duplicate_entry() (in module schrodinger.application.desmond.maestro) DuplicateColumnError duplicateRelaxStage() (schrodinger.application.matsci.permittivity.MdStageModifier method) duplicateRings() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) dupNode() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) dupTree() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) duration (schrodinger.application.jaguar.output.JaguarOutput property) (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) (schrodinger.seam.runners.events.PipelineFinished attribute) (schrodinger.seam.viz.inspect.PipelineDisplayInfo attribute) durationChanged (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) (schrodinger.seam.runners.events.PipelineFinished attribute) durationEdited() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) durationOptionChanged() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) durationReplaced (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) (schrodinger.seam.runners.events.PipelineFinished attribute) DurationType (class in schrodinger.trajectory.trajectory_gui_dir.export_movie) dval (schrodinger.utils.sea.sea.Atom property) (schrodinger.utils.sea.sea.List property) (schrodinger.utils.sea.sea.Map property) DVDSequenceIndexer (class in schrodinger.application.bioluminate.antibody.sequence_indexer) DYNAMIC_SORT_FILTER (schrodinger.ui.qt.table_helper.PythonSortProxyModel attribute) dynamics (schrodinger.application.matsci.espresso.qeinput.IonControlType property) DynamicTypeDelegate (class in schrodinger.ui.qt.mapperwidgets.param_editor) DynamXColumns (class in schrodinger.application.bioluminate.pose_filtering.hdx_io)

E

e (schrodinger.comparison.results.Result attribute) E_ANNIHILIATIONS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) E_f (class in schrodinger.application.desmond.simulation_block_test) E_INJECTIONS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) E_k (class in schrodinger.application.desmond.simulation_block_test) E_x (class in schrodinger.application.desmond.simulation_block_test) EA_LABEL() (in module schrodinger.application.matsci.cgforcefieldgui) EANION (schrodinger.application.matsci.kmc.SegmentsTable attribute) early_stop() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) EarlyExitException ECATION (schrodinger.application.matsci.kmc.SegmentsTable attribute) ECD_Spectrum (class in schrodinger.application.matsci.spectra) ECDSAWithSHA256 (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) ECDSAWithSHA384 (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) ECDSAWithSHA512 (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) echo_log_files() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) ECL (schrodinger.protein.annotation.GPCRSegmentLabel attribute) ecutrho (schrodinger.application.matsci.espresso.utils.PPSpecies attribute) (schrodinger.application.matsci.espresso.utils.PseudoData attribute) ecutwfc (schrodinger.application.matsci.espresso.utils.PPSpecies attribute) (schrodinger.application.matsci.espresso.utils.PseudoData attribute) EDA (class in schrodinger.trajectory.prody.pca) Edge (class in schrodinger.application.matsci.shapes) (class in schrodinger.ui.qt.network_visualizer) edge (schrodinger.structure._Ring property) edge_id (schrodinger.application.desmond.new_fep_edge_data.FepData property) edgeCount() (schrodinger.ui.qt.network_visualizer.Graph method) edgeHovered() (schrodinger.ui.qt.network_views.NetworkViewer method) edgeMenu() (schrodinger.ui.qt.network_views.NetworkViewer method) EDGES (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) (schrodinger.ui.qt.schart.BinsDialog attribute) edges() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) EDGES_ADDED (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) EDGES_DELETED (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) edgesChanged (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) EDGETYPE1 (schrodinger.application.matsci.nano.constants.Constants attribute) EDGETYPE2 (schrodinger.application.matsci.nano.constants.Constants attribute) EDGETYPES (schrodinger.application.matsci.nano.constants.Constants attribute) edgeUnhovered() (schrodinger.ui.qt.network_views.NetworkViewer method) EDIT (schrodinger.application.livedesign.mapping_widgets.MappingMode attribute) EDIT_DLG_CLASS (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) EDIT_ICON (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUpDelegate attribute) (schrodinger.ui.qt.delegates.AbstractDelegateWithEditIcon attribute) (schrodinger.ui.qt.delegates.ComboBoxDelegate attribute) edit_parameters() (schrodinger.ui.qt.navtoolbar.NavToolbar method) EDITABLE_COLS (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) EDITABLE_ITEM (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) EditButton (class in schrodinger.ui.qt.swidgets) EditDialog (class in schrodinger.application.jaguar.gui.edit_dialog) editFigureOptions() (schrodinger.ui.qt.navtoolbar.NavToolbar method) editingFinished (schrodinger.application.phase.phase_markers.PhaseMarkers attribute) editInput() (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) editorEvent() (schrodinger.application.job_monitor.job_monitor_table.JobDetailsArrowDelegate method) (schrodinger.ui.qt.delegates.CheckboxDelegate method) (schrodinger.ui.qt.delegates.PushButtonDelegate method) (schrodinger.ui.qt.delegates.ToolTipIconDelegate method) (schrodinger.ui.qt.delegates.WorkspaceInclusionDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) EditWithFocusOutEvent (class in schrodinger.ui.qt.swidgets) EDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) EELS (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) ef_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) EFERMI_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) eff_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) effectiveRadius() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) efield (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) efp_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) efs_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) eigenvalues() (in module schrodinger.application.mopac.results_main) eigenvectors() (in module schrodinger.application.mopac.results_main) einsum_sequence() (schrodinger.application.matsci.elasticity.tensors.Tensor method) El2EstVol() (in module schrodinger.application.matsci.gsas.GSASIImath) El2Mass() (in module schrodinger.application.matsci.gsas.GSASIImath) elapsed (schrodinger.utils.profiling.Timer property) elapsed_timer() (in module schrodinger.application.matsci.permittivity) ElapsedFormatter (class in schrodinger.stepper.stepper) ElasticConstantsStep (class in schrodinger.application.matsci.jwsteps) ElasticConstantsStressStep (class in schrodinger.application.matsci.jwsteps) ElasticControlType (class in schrodinger.application.matsci.espresso.qeinput) ElasticTensor (class in schrodinger.application.matsci.elasticity.elastic) ElasticType (class in schrodinger.application.matsci.espresso.qeinput) ele_smoothing() (in module schrodinger.application.bioluminate.patch_utils.msurfext) ELECTRIC_POLARIZABILITY (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_FREQ_PROP (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_INTERCEPT (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_INTERCEPT_FREQ (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_PROP (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_SLOPE (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_SLOPE_FREQ (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ElectricPolarizability (class in schrodinger.application.matsci.permittivity) electron_transfer() (in module schrodinger.application.jaguar.textparser) ElectronControlType (class in schrodinger.application.matsci.espresso.qeinput) electronic_e() (in module schrodinger.application.jaguar.textparser) electrostatic14_energy() (in module schrodinger.application.qsite.output) electrostatic_energy() (in module schrodinger.application.qsite.output) element (schrodinger.application.matsci.espresso.utils.PseudoData attribute) ELEMENT (schrodinger.application.matsci.kmc.AtomsTable attribute) element (schrodinger.application.matsci.sculptcomplex.SiteAtom attribute) (schrodinger.application.phase.packages.shape_generator.AtomTypes attribute) (schrodinger.structure.StructureAtom property) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) ELEMENT1 (schrodinger.application.matsci.nano.constants.Constants attribute) ELEMENT2 (schrodinger.application.matsci.nano.constants.Constants attribute) elemental_generator() (in module schrodinger.application.matsci.mlearn.features) elemental_mutator() (in module schrodinger.application.matsci.genetic_optimization) ElementAlchemist (class in schrodinger.application.matsci.enumeration) ElementalProperties (class in schrodinger.application.matsci.elementalprops) ElementButton (class in schrodinger.ui.qt.periodictable) elementChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) ElementClass (schrodinger.protein.sequence.AbstractSequence attribute) (schrodinger.protein.sequence.CombinedChainProteinSequence attribute) (schrodinger.protein.sequence.NucleicAcidSequence attribute) (schrodinger.protein.sequence.ProteinSequence attribute) ElementEdit (class in schrodinger.application.matsci.atomicsymbolsgui) ElementListEdit (class in schrodinger.application.matsci.atomicsymbolsgui) ElementListValidator (class in schrodinger.application.matsci.atomicsymbolsgui) elementReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) elements (schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo attribute) ELEMENTS (schrodinger.ui.qt.periodictable.PeriodicTableDialog attribute) elementSelected (schrodinger.ui.qt.periodictable.PeriodicTableDialogSingleClick attribute) elementsToContiguousColumns() (schrodinger.protein.alignment.BaseAlignment method) ElementType (class in schrodinger.protein.residue) ElementValidator (class in schrodinger.application.matsci.atomicsymbolsgui) ElemPosition() (in module schrodinger.application.matsci.gsas.GSASIIspc) elide_rich_text() (in module schrodinger.ui.qt.swidgets) ElidedLabel (class in schrodinger.ui.qt.swidgets) ElidedTextHTMLParser (class in schrodinger.ui.qt.swidgets) ElidedTextHTMLParser.HTMLType (class in schrodinger.ui.qt.swidgets) elideRichText() (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) eliminatePairs() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) eliminateSingles() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) ellipseSize() (in module schrodinger.application.matsci.gsas.GSASIIpwd) ellipseSizeDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd) EllipsisPopUpButton (class in schrodinger.ui.qt.swidgets) elmnt_mult_dict() (in module schrodinger.application.jaguar.utils) ElongatedMicelleInputFile (class in schrodinger.application.matsci.packmol) elst() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.ComUtilAppSci method) EmbeddedSolventWidget (class in schrodinger.application.matsci.jagwidgets) embl (schrodinger.utils.fileutils.SeqFormat attribute) EmbraceConfSearch (class in schrodinger.application.macromodel.input) EmbraceMinimization (class in schrodinger.application.macromodel.input) emit() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.utils.qt_utils.SignalAndSlot method) emitAddMarker() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) emitAnnTitleChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitCountChanged() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) emitElementSelected() (schrodinger.ui.qt.periodictable.PeriodicTableDialogSingleClick method) emitErrorMessage() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) emitRemoveMarker() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) emitSeqNameChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitSeqResChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitSetMarkerHighlighting() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) EmittingScrollBar (class in schrodinger.ui.qt.table) emitTutorialSignal() (schrodinger.ui.qt.swidgets.HelpButton method) emitValueChanged() (schrodinger.application.matsci.mswidgets.MultiSlider method) emodel_coeff (schrodinger.application.glide.sort_utils.CustomScoringFunction attribute) EMPHASIZED_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) empirical_pka_predictor() (schrodinger.protein.assignment.ProtAssign method) empty() (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.matsci.wfmanagement.WorkflowMetadata method) EMPTY_PATH_TUPLE (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) EmptyInputError EmptyIterator (class in schrodinger.project.project) emptyMethod() (schrodinger.ui.qt.appframework2.appmethods.MethodsDict method) EN_ANALYSIS (schrodinger.application.matsci.desconfig.MSJStringer attribute) Enable (schrodinger.adapter.Canonicalize attribute) (schrodinger.adapter.Generate2DCoordinates attribute) (schrodinger.adapter.LabelAtoms attribute) (schrodinger.adapter.Sanitize attribute) (schrodinger.adapter.UniqueFilter attribute) enable() (schrodinger.project.project.Project method) enable_deprecated() (in module schrodinger.utils.deprecation) enable_dummy_maestro_imports() (in module schrodinger.infra.unusable_module_importer) enable_dummy_missing_product_imports() (in module schrodinger.infra.unusable_module_importer) enable_dummy_non_post_test_imports() (in module schrodinger.infra.unusable_module_importer) ENABLE_ITEM (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) enable_lasso (schrodinger.ui.picking.PickMixedToggle property) enable_maestro_features (schrodinger.ui.two_d_viewer.TwoDViewer attribute) enable_one_graph_stage (schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams attribute) ENABLE_WHEN_NO_STRUC (schrodinger.application.jaguar.gui.basis_selector.BasisSelector attribute) enableActiveChkIfConstraintsAdded() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) enableAllFeatures() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) enableAllItems() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) (schrodinger.ui.qt.swidgets.SComboBox method) enableButtonViaCheckBox() (schrodinger.ui.qt.swidgets.ColorWidget method) enableCustomSeed() (schrodinger.application.desmond.gui.RandVelFrame method) enabled (schrodinger.rdkit.rdkit_adapter.RdkitLoggerstate attribute) ENABLED_STYLE (schrodinger.ui.qt.delegates.LinkDelegate attribute) enableExcitedState() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) enableExcitedStatesType() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) enableItems() (schrodinger.ui.qt.swidgets.SComboBox method) enableMaestroSync() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) enableOK() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) enablePlatformValidation() (schrodinger.application.desmond.gui.DesmondBasicConfigDialog method) enableRows() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) enableSaveButton() (schrodinger.ui.qt.rename_favorite_dialog.RenameFavoriteDialog method) enableSelectedCoordinates() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) enableSidechainPacking() (schrodinger.protein.reliability.ProteinCheckParameters method) enableSimulationGroupBox() (schrodinger.application.desmond.gui.GuiApp method) enableStructureCombos() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) enableWithCBox() (schrodinger.application.matsci.chargegui.FFInfo method) encode() (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer class method) (schrodinger.seam.coders.MolCoder method) (schrodinger.seam.coders.MolToSmilesCoder method) (schrodinger.seam.coders.RouteNodeCoder method) (schrodinger.seam.coders.StructureCoder method) encode_acc() (in module schrodinger.protein.predictors) encode_char() (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer class method) encode_extended() (in module schrodinger.application.desmond.gchart) encode_restraints() (in module schrodinger.application.desmond.stage.prepare.forcefield) encode_seqs() (in module schrodinger.application.bioluminate.peptide_sar.encode) encode_simple() (in module schrodinger.application.desmond.gchart) encode_ssa() (in module schrodinger.protein.predictors) encode_str() (in module schrodinger.application.desmond.cms) encode_string_into_structure_property() (in module schrodinger.application.desmond.struc) encodeForPatternSearch() (schrodinger.protein.sequence.NucleicAcidSequence method) (schrodinger.protein.sequence.ProteinSequence method) ENCODING_KEY (schrodinger.models.jsonable.JsonableSet attribute) (schrodinger.models.jsonable.JsonableTuple attribute) encrypt_cms() (in module schrodinger.application.matsci.enc) END (schrodinger.application.bioluminate.pose_filtering.hdx_io.DynamXColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.HDExaminerColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.StandardColumns attribute) (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) (schrodinger.application.matsci.packmol.PackmolKw attribute) end (schrodinger.protein.annotation.AntibodyCDR attribute) (schrodinger.protein.annotation.Region attribute) (schrodinger.protein.helm.helm_renderer.HelmConnector attribute) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) end_geometry() (in module schrodinger.application.jaguar.textparser) end_index (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering attribute) END_OF_DEF_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) end_progress() (in module schrodinger.application.bioluminate.pml_menus) end_residue (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) end_scan() (in module schrodinger.application.jaguar.textparser) END_TAG (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser.HTMLType attribute) end_time (schrodinger.seam.viz.inspect.PipelineDisplayInfo attribute) end_time() (in module schrodinger.application.jaguar.textparser) endBacktrack() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) endChanged() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) endDate (schrodinger.application.licensing.licserver.client.LocalEntitlement attribute) endFilter() (schrodinger.ui.qt.swidgets.SFilteredListWidget method) endGeopt() (schrodinger.application.jaguar.textparser.TextParser method) endGroup() (schrodinger.utils.preferences.Preferences method) endIRC() (schrodinger.application.jaguar.textparser.TextParser method) Endpoint (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) endpoint() (in module schrodinger.seam.viz.watcher) EndpointInfo (class in schrodinger.seam.viz.watcher) EndpointSelectionLineEdit (class in schrodinger.application.livedesign.panel_components) EndpointSelectionModel (class in schrodinger.application.livedesign.panel_components) EndpointSelectionPopUp (class in schrodinger.application.livedesign.panel_components) EndpointSelectionPopUpDelegate (class in schrodinger.application.livedesign.panel_components) endRangeModified() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) endResync() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) endScan() (schrodinger.application.jaguar.textparser.TextParser method) ENE (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) ENE_INTERVAL (schrodinger.application.matsci.desconfig.MSJStringer attribute) eneg (schrodinger.application.matsci.elementalprops.ElementalProperties property) enegrp (schrodinger.application.matsci.deswidgets.DesmondMDWidgets.NUM_FRMS_TYPE attribute) ENEGRP_NFRM_LABEL (schrodinger.application.matsci.deswidgets.DesmondMDWidgets attribute) ENEGRP_VALUE (class in schrodinger.application.desmond.ene_utils) EneGrpProp (class in schrodinger.application.desmond.ene_utils) EnergeticSpan (class in schrodinger.application.matsci.reaction_workflow_utils) EnergeticSpanException Energy (class in schrodinger.application.desmond.simulation_block_test) energy (schrodinger.application.jaguar.input.GuessOrbital attribute) (schrodinger.application.jaguar.results.JaguarResults property) (schrodinger.application.jaguar.results.NofailResult attribute) energy() (in module schrodinger.application.xtb.textparser) Energy_Barrier_kcal_per_mol (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) energy_convergence (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) ENERGY_CORR (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) energy_criterion (schrodinger.structutils.minimize.Minimizer property) ENERGY_GROUPS (class in schrodinger.application.desmond.constants) ENERGY_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) energy_key (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) ENERGY_KEY (schrodinger.application.matsci.reaction_workflow_utils.JMSWFConformerSelection attribute) (schrodinger.application.matsci.reaction_workflow_utils.MopacConformerSelection attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) energy_lj_repulsive_only (schrodinger.structutils.minimize.Minimizer property) energy_no_electrostatics (schrodinger.structutils.minimize.Minimizer property) energy_prec (schrodinger.application.jaguar.results.ConvCriteria attribute) energy_precision (schrodinger.application.jaguar.results.JaguarResults attribute) (schrodinger.application.qsite.output.QSiteResults attribute) energy_precision_hartree (schrodinger.application.jaguar.results.DerivedAttrs attribute) energy_profile (schrodinger.application.desmond.new_fep_edge_data.TorsionPotential property) Energy_Property (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) ENERGY_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) ENERGY_UNIT_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) EnergyAnalysisProperty (class in schrodinger.application.matsci.reaction_workflow_utils) EnergyAndGradients (class in schrodinger.application.matsci.mecp_mod) EnergyDiagramPlotter (class in schrodinger.application.matsci.reaction_workflow_utils) EnergyListing (class in schrodinger.application.macromodel.input) EnergySurface (class in schrodinger.application.matsci.amorphous) eneseq (schrodinger.application.matsci.deswidgets.DesmondMDWidgets.NUM_FRMS_TYPE attribute) ENESEQ_NFRM_LABEL (schrodinger.application.matsci.deswidgets.DesmondMDWidgets attribute) ENEUTRAL (schrodinger.application.matsci.kmc.SegmentsTable attribute) enforce_rdkit_smarts() (in module schrodinger.structutils.analyze) enforceBasis() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) enforceOneChecked() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) enforceScrollBarPolicies() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) EnforcingValidatorMixin (class in schrodinger.ui.qt.swidgets) Engine (class in schrodinger.application.desmond.cmj) engine (schrodinger.application.matsci.espresso.qeinput.DataType attribute) EnhancedComboBox (class in schrodinger.application.jaguar.gui.utils) ensClassChanged() (schrodinger.application.desmond.gui.EnsembleClassFrame method) Ensemble (class in schrodinger.trajectory.prody.ensemble) ensemble (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) ENSEMBLE (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) ensemble (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) ENSEMBLE_CLASS (schrodinger.application.matsci.desconfig.MSJStringer attribute) ENSEMBLE_METHOD (schrodinger.application.matsci.desconfig.MSJStringer attribute) Ensemble_Priority_Queue (class in schrodinger.application.glide.ensemble_selection) EnsembleClassFrame (class in schrodinger.application.desmond.gui) Ensembles (class in schrodinger.application.desmond.constants) ensembles (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue property) EnsembleTab (class in schrodinger.application.desmond.gui) ensure_decoys() (in module schrodinger.application.vss.tasks) ensure_file_exists() (in module schrodinger.application.desmond.util) ensure_localhost_server_running() (in module schrodinger.job.server) ensure_logfile() (in module schrodinger.utils.installation_check) ensure_logger() (in module schrodinger.application.bindingsite.common) ensure_project_entry() (in module schrodinger.application.matsci.maestrocmds) ensure_proper_extension() (in module schrodinger.application.bioluminate.pml_menus) ensure_user_is_logged_in() (in module schrodinger.application.livedesign.ld_maestro_actions) ensure_value_in_range() (in module schrodinger.application.bioluminate.protein_interaction.tasks) ensureValidity() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) enter_scope() (schrodinger.application.desmond.enhsamp.binding method) enterAlt() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) enterDecision() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) enterDisplaySnapshotMode() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) enterEvent() (schrodinger.application.bioluminate.pml_menus.ColorLabel method) (schrodinger.ui.qt.swidgets.HelpButton method) enterRule() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) enterSubRule() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) enterZoomView() (schrodinger.ui.two_d_viewer.TwoDViewer method) entity_class (schrodinger.livedesign.registration.RegistrationData attribute) entity_image_path() (in module schrodinger.livedesign.entity_type) entity_registration() (in module schrodinger.livedesign.cmdline) entity_registration_status (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entity_registration_statusChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entity_registration_statusReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) EntityClass (class in schrodinger.livedesign.entity_type) EntityFile (class in schrodinger.tasks.ldtasks) EntityRegistrationStatus (class in schrodinger.application.livedesign.export_models) entries_excluded() (in module schrodinger.ui.qt.appframework2.maestro_callback) entries_included() (in module schrodinger.ui.qt.appframework2.maestro_callback) entriesInfoChanged (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync attribute) entropy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) ENTRY (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) entry (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) entry_data (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entry_dataChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entry_dataReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entry_excluded() (in module schrodinger.project.utils) entry_id (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTupleMacroPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) (schrodinger.application.matsci.sculptcomplex.SiteAtom attribute) (schrodinger.project.project.ProjectRow property) (schrodinger.protein.residue.ResidueKey attribute) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.structure.StructureAtom property) entry_idChanged (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) entry_idReplaced (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) entry_index (schrodinger.application.matsci.sculptcomplex.SiteAtom attribute) entry_is_included() (in module schrodinger.project.utils) entry_is_locked() (in module schrodinger.project.utils) entry_is_marked() (in module schrodinger.project.utils) entry_is_pinned() (in module schrodinger.project.utils) entry_is_selected() (in module schrodinger.project.utils) entry_name (schrodinger.protein.sequence.CombinedChainProteinSequence property) ENTRY_NAME_KEY (schrodinger.application.matsci.nano.xtal.CheckInput attribute) (schrodinger.application.matsci.rxn_channel.CheckInput attribute) entry_singular (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData attribute) entry_type (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_description (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_descriptionChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_descriptionReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_name (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_nameChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_nameReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ENTRY_TYPE_NAMES (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) entry_typeChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_typeReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) entryByName() (schrodinger.utils.installation_check.TestJobDJ method) EntryField (class in schrodinger.application.desmond.cwidget) EntryGroup (class in schrodinger.project.project) EntryGroupManager (class in schrodinger.project.manager) entryIds() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) ENTRYKEY (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) EntryMode (class in schrodinger.application.pymol.pymol4maestro) ENTRYNAMEKEY (schrodinger.application.matsci.rxn_path.CheckInput attribute) ENTRYPOINT (schrodinger.tasks.tasks.AbstractComboTask attribute) entrySelectionChanged (schrodinger.application.livedesign.maestro_sync.EntrySelectionMaestroSync attribute) EntrySelectionMaestroSync (class in schrodinger.application.livedesign.maestro_sync) EntrySubMenu (class in schrodinger.application.bioluminate.pml_menus) EntrySurface (class in schrodinger.project.project) EntryTimingTable (class in schrodinger.application.jaguar.gui.timing) entryTitles() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) enum_speedup() (in module schrodinger.infra.util) EnumerableMixin (class in schrodinger.application.scaffold_enumeration.common) enumerate_acceptor_acceptor_states() (schrodinger.protein.assignment.WaterStateEnumerator method) enumerate_acceptor_states() (schrodinger.protein.assignment.WaterStateEnumerator method) enumerate_changeable_states() (schrodinger.protein.assignment.ProtAssign method) enumerate_donor_donor_states() (schrodinger.protein.assignment.WaterStateEnumerator method) enumerate_donor_states() (schrodinger.protein.assignment.WaterStateEnumerator method) enumerate_rgroups() (in module schrodinger.application.scaffold_enumeration.layered) enumerate_states() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) enumerate_stereoisomers() (in module schrodinger.livedesign.bbchem_endpoints) enumerate_swap() (in module schrodinger.application.matsci.reaction_workflow_utils) enumerateChannels() (schrodinger.application.matsci.rxn_channel.Channels method) EnumerateReactionWorkflow (class in schrodinger.application.matsci.reaction_workflow_utils) EnumerateRoutes (class in schrodinger.application.transforms.enumerators) EnumerateSwap (class in schrodinger.application.matsci.reaction_workflow_utils) EnumerateSwapMixin (class in schrodinger.application.matsci.reaction_workflow_utils) EnumMetaWithContains (class in schrodinger.application.matsci.msutils) EnumParam (class in schrodinger.models.parameters) Env (class in schrodinger.application.desmond.enhsamp) env (schrodinger.application.desmond.driver_utils.MPISettings attribute) ENV (schrodinger.application.licensing.licserver.client.ServerIdentifierSourceType attribute) env_dict (schrodinger.application.desmond.driver_utils.MPISettings attribute) env_update_and_run() (in module schrodinger.utils.installation_check) env_var_feature_flag_is_set() (in module schrodinger.utils.featureflags.featureflags) EnvAction (class in schrodinger.application.glide.utils) ENVIRONMENT (schrodinger.application.desmond.constants.REST_COMPONENT attribute) environment (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) environment variable PATH, [1] PYTHONPATH, [1], [2], [3], [4], [5], [6] SCHRODINGER SCHRODINGER_PYTHONPATH, [1] SCHRODINGER_SCRIPTS, [1], [2] EnvironmentContext (class in schrodinger.utils.env) Envs (schrodinger.job.jobcontrol.Job property) EnvVar (class in schrodinger.utils.openmpi) EOF (schrodinger.application.desmond.antlr3.streams.CharStream attribute) EP (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings attribute) epik_args (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) epik_argsChanged (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) epik_argsReplaced (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) epik_classic_args (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_argsChanged (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_argsReplaced (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_infile (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_infileChanged (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_infileReplaced (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_lic() (in module schrodinger.application.desmond.license) epik_pH (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHt (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHtChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHtReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) EpikClassicTask (class in schrodinger.application.livedesign.tasks) EpikClassicTask.Input (class in schrodinger.application.livedesign.tasks) EpikClassicTask.JobConfig (class in schrodinger.application.livedesign.tasks) EpikClassicTask.Output (class in schrodinger.application.livedesign.tasks) EpikTask (class in schrodinger.application.livedesign.tasks) EpikTask.Input (class in schrodinger.application.livedesign.tasks) EpikTask.JobConfig (class in schrodinger.application.livedesign.tasks) EpikTask.Output (class in schrodinger.application.livedesign.tasks) epn() (in module schrodinger.application.jaguar.textparser) epn_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) EPS_METAL_ERR (schrodinger.application.matsci.espresso.qeoutput.Output attribute) EpsilonType (class in schrodinger.application.matsci.espresso.qeinput) EPV_RECEP (schrodinger.application.glide.sort_utils.StructureType attribute) EpvReader (class in schrodinger.application.glide.utils) eq_re (schrodinger.application.jaguar.utils.GenOptions attribute) equal_rotations() (in module schrodinger.application.matsci.nano.space_groups) equalize_number_waters() (in module schrodinger.application.desmond.gcmc_utils) EQUALS (schrodinger.application.matsci.genetic_optimization.Property attribute) equals() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.application.matsci.wfmanagement.WorkflowMetadata method) equilibrate_time (schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams attribute) EQUILIBRATION (schrodinger.application.desmond.constants.DefaultFEPSimulationTimes attribute) equilibration_time (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) equilibrium() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) equilibrium_constant() (in module schrodinger.application.jaguar.kinetics) EquilibriumMdBase (class in schrodinger.application.matsci.equilibrium_md) erf_then_divide() (in module schrodinger.application.bioluminate.patch_utils.msurfext) err (schrodinger.application.licensing.licserver.client.LocalEntitlement attribute) (schrodinger.application.licensing.licserver.client.ServerIdentifier attribute) (schrodinger.utils.sea.evalor.Evalor property)

err_handler() (schrodinger.application.desmond.stage.jobs.DesmondJob static method) Error (class in schrodinger.job.host_check) error (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) ERROR (schrodinger.application.jaguar.utils.GenOptions attribute) (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.MessageType attribute) error() (in module schrodinger.application.matsci.gutils) (schrodinger.application.desmond.antlr3.dfa.DFA method) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) (schrodinger.application.matsci.espresso.utils.ArgumentParserNoExit method) (schrodinger.application.matsci.parserutils.DriverParser method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.swidgets.SDialog method) (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) (schrodinger.utils.ligfilter.CriterionParser method) (schrodinger.utils.ligfilter.DefinitionParser method) ERROR_BACKGROUND_BRUSH (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) error_code (schrodinger.utils.license.LicenseStatus property) error_dialog() (in module schrodinger.application.desmond.gui) error_message (schrodinger.application.desmond.test_utils.UnregisteredFile attribute) (schrodinger.seam.runners.events.StageFailed attribute) error_message() (in module schrodinger.application.xtb.textparser) error_messageChanged (schrodinger.seam.runners.events.StageFailed attribute) error_messageReplaced (schrodinger.seam.runners.events.StageFailed attribute) error_msg (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) error_msgChanged (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) error_msgReplaced (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) error_pattern (schrodinger.infra.mmcheck.ReturnCode attribute) ERROR_POST (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) ERROR_PRE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) ERROR_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) error_threshold (schrodinger.stepper.stepper.BatchSettings attribute) error_thresholdChanged (schrodinger.stepper.stepper.BatchSettings attribute) error_thresholdReplaced (schrodinger.stepper.stepper.BatchSettings attribute) ErrorForDialog errorNode() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) errorOccurred (schrodinger.application.glide.http_client.NonBlockingGlideServerManager attribute) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) (schrodinger.application.glide.http_client.NonBlockingHTTPClient attribute) Errors (schrodinger.job.jobcontrol.Job property) errors() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) ES_EXCLUDE_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) escape_string() (in module schrodinger.application.desmond.cmj) escapeNewlines() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) esm (schrodinger.application.matsci.espresso.qeinput.BoundaryType property) ESM_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) EsmType (class in schrodinger.application.matsci.espresso.qeinput) (class in schrodinger.application.matsci.espresso.qeoutput) EsolInput (class in schrodinger.application.jaguar.esol_input) esp_analysis() (in module schrodinger.application.jaguar.textparser) esp_analysis_precision (schrodinger.application.jaguar.results.JaguarResults attribute) ESP_ATOMS (schrodinger.application.jaguar.results.JaguarOptions attribute) ESP_ATOMS_AND_BOND_MIDPOINTS (schrodinger.application.jaguar.results.JaguarOptions attribute) esp_charge() (in module schrodinger.application.mopac.results_main) esp_charges() (in module schrodinger.application.jaguar.textparser) esp_fit_atoms() (in module schrodinger.application.jaguar.textparser) esp_fit_atoms_and_bonds() (in module schrodinger.application.jaguar.textparser) ESP_FOR_MD (schrodinger.application.matsci.jaguar_multistage_workflow_utils.QMMoleculeKeywords attribute) ESP_NONE (schrodinger.application.jaguar.results.JaguarOptions attribute) esp_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) ESPSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) estate_is_physical() (in module schrodinger.application.jaguar.workflow_validation) estimate_memory() (in module schrodinger.application.desmond.memory) estimate_shape_data_size() (in module schrodinger.application.phase.packages.shape_creation_logic) estimate_size() (schrodinger.seam.coders.MolCoder method) estimate_time_cost() (in module schrodinger.active_learning.al_node) (in module schrodinger.application.phase.packages.shape_screen_al_node) estimateMaxHeight() (schrodinger.ui.qt.pop_up_widgets.PopUp method) estimateMaxWidth() (schrodinger.ui.qt.pop_up_widgets.PopUp method) estimateRadius() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) estimateResolution() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) EtaFFAssignmentError EtaFindingMixin (class in schrodinger.application.matsci.buildcomplex) EtaRotamersException eth0_is_missing() (in module schrodinger.application.licensing.licadmin) etot() (in module schrodinger.application.jaguar.textparser) ev() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method) ev_to_hartree() (in module schrodinger.application.matsci.mecp_mod) evalColMetadataDicts() (in module schrodinger.application.matsci.gsas.GSASIIfiles) evalDJ() (schrodinger.active_learning.al_node.LigandMLEvalNode method) evalMQ() (schrodinger.active_learning.al_node.LigandMLEvalNode method) Evalor (class in schrodinger.utils.sea.evalor) evaluate() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis method) (schrodinger.application.jaguar.discretized_1d_function.DiscretelySampledFunction method) (schrodinger.application.matsci.genetic_optimization.StructureGenome method) evaluate_asl() (in module schrodinger.structutils.analyze) evaluate_f() (in module schrodinger.application.matsci.anharmonic) (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) evaluate_matched_list() (in module schrodinger.application.desmond.smarts) evaluate_multiple_smarts() (in module schrodinger.structutils.analyze) evaluate_net_smarts() (in module schrodinger.application.desmond.smarts) evaluate_smarts() (in module schrodinger.adapter) (in module schrodinger.application.matsci.rdpattern) (in module schrodinger.structutils.analyze) evaluate_smarts_by_molecule() (in module schrodinger.application.matsci.rdpattern) (in module schrodinger.structutils.analyze) evaluate_smarts_canvas() (in module schrodinger.structutils.analyze) evaluate_smarts_ex() (in module schrodinger.application.canvas.r_group) evaluate_substructure() (in module schrodinger.structutils.analyze) evaluateAsl() (schrodinger.structutils.rmsd.ConformerRmsd method) evaluateASLs() (schrodinger.protein.align.CustomASLStructureAligner method) evaluateLiveReportText() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) evaluateMultipleSmarts() (schrodinger.application.matsci.rdpattern.EvaluateSMARTS method) EvaluateRoutes (class in schrodinger.application.transforms.enumerators) EvaluateSMARTS (class in schrodinger.application.matsci.rdpattern) evaluateSmarts() (schrodinger.application.matsci.rdpattern.CanvasPattern method) (schrodinger.application.matsci.rdpattern.Pattern method) (schrodinger.application.matsci.rdpattern_gui.GuiPattern method) evaluateSmiles() (schrodinger.application.matsci.rdpattern.Pattern method) evaluateSpeciesCriterion() (schrodinger.application.matsci.clusterstruct.Dimer method) evaluator (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) evalue (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) evalue_threshold (schrodinger.protein.tasks.blast.BlastSettings attribute) evalue_thresholdChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) evalue_thresholdReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) EvaporationStep (class in schrodinger.application.matsci.jwsteps) event (class in schrodinger.application.licensing.lmgrd_log_parser) event() (schrodinger.application.matsci.builderwidgets.StructureLabel method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin method) (schrodinger.ui.residueselector.CustomResidueMixin method) eventFilter() (schrodinger.application.jaguar.gui.input_tab_widgets.CommitMultipleDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.livedesign.live_report_widget.SwallowEnterFilter method) (schrodinger.application.matsci.gutils.WheelEventFilterer method) (schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackWidgetMixin method) (schrodinger.ui.qt.delegates.LinkDelegate method) (schrodinger.ui.qt.delegates.MouseTrackingDelegateMixin method) (schrodinger.ui.qt.delegates.PushButtonDelegate method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate method) (schrodinger.ui.qt.smatplotlib.SmatplotlibCanvas method) (schrodinger.ui.qt.swidgets.PersistentMenu method) (schrodinger.ui.qt.swidgets.SLineEdit method) (schrodinger.ui.qt.swidgets.SRetainableMenu method) (schrodinger.ui.qt.table.ToolTipFilter method) (schrodinger.ui.two_d_viewer.TwoDViewer method) EventLoop (class in schrodinger.utils.qt_utils) evolution() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) examine_constraints() (in module schrodinger.application.jaguar.autots_bonding) example_name (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_nameChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_nameReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_prop_string (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_prop_stringChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_prop_stringReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) ExampleStage (class in schrodinger.pipeline.stages.example) exc_energy_precision_ev (schrodinger.application.jaguar.results.DerivedAttrs attribute) exc_energy_precision_nm (schrodinger.application.jaguar.results.DerivedAttrs attribute) exc_precision (schrodinger.application.jaguar.results.JaguarResults attribute) EXCEPTION (schrodinger.application.steps.licensing.LicenseMixin attribute) exception_class_name (schrodinger.tasks.tasks.FailureInfo attribute) exception_class_nameChanged (schrodinger.tasks.tasks.FailureInfo attribute) exception_class_nameReplaced (schrodinger.tasks.tasks.FailureInfo attribute) ExceptionDialog (class in schrodinger.infra.exception_handler_dir.exception_dialog) ExceptionRecorder (class in schrodinger.infra.exception_handler) exchange_acceptance_ratio() (schrodinger.application.desmond.bennett.CalcBAR method) excited_state (schrodinger.application.jaguar.gui.tabs.theory_tab.ExcitedStateInfo attribute) EXCITED_STATE_CB_TEXT (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabOptimization attribute) excited_state_changed (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget attribute) EXCITED_STATE_KEYWORDS (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) excited_state_mode (schrodinger.application.jaguar.gui.tabs.theory_tab.ExcitedStateInfo attribute) EXCITED_STATE_TEXT (schrodinger.application.jaguar.gui.theory_tab_widgets.HFExcitedStateWidget attribute) EXCITED_STATE_TYPES (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabOptimization attribute) ExcitedStateInfo (class in schrodinger.application.jaguar.gui.tabs.theory_tab) ExcitedStateValidatorMixin (class in schrodinger.application.jaguar.gui.base_panel) ExcitedStateWidget (class in schrodinger.application.jaguar.gui.theory_tab_widgets) exclude() (schrodinger.ui.ligfilter.AddDefinitionDialog method) exclude_amino_acids (schrodinger.structutils.analyze.AslLigandSearcher property) exclude_ions (schrodinger.structutils.analyze.AslLigandSearcher property) excludeCommandParser() (schrodinger.application.ligprep.ionizer.Ionizer method) excluded_residues (schrodinger.structutils.analyze.AslLigandSearcher property) ExcludedVolumeGenerator (class in schrodinger.application.phase.create_xvol) excludeEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) ExcludeFromSelection (class in schrodinger.application.bioluminate.pml_menus) ExcludeInorganicFromSelection (class in schrodinger.application.bioluminate.pml_menus) ExcludeOrganicFromSelection (class in schrodinger.application.bioluminate.pml_menus) excludeOtherEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) ExcludePolymerFromSelection (class in schrodinger.application.bioluminate.pml_menus) excludes() (schrodinger.utils.ligfilter.Definition method) ExcludeSolventFromSelection (class in schrodinger.application.bioluminate.pml_menus) ExcludeSubMenu (class in schrodinger.application.bioluminate.pml_menus) ExcludeVisibleFromSelection (class in schrodinger.application.bioluminate.pml_menus) EXCLUSION_BIG_RING_SIZE (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner attribute) ExclVols (schrodinger.application.phase.phase_widgets.HypothesisColumns attribute) EXE (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) EXEC (schrodinger.job.util.DirectoryType attribute) exec() (schrodinger.application.jaguar.update_pka_settings.UpdatePKASettingsDlg method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.filedialog.FileDialog method) (schrodinger.ui.qt.forcefield.ffprojectsettingsdlg.FFProjectSettingsDlg method) (schrodinger.ui.qt.messagebox.MessageBox method) (schrodinger.ui.qt.pdb_dialog.PDBDialog method) (schrodinger.utils.qt_utils.EventLoop method) exec_dir (schrodinger.application.desmond.kinetics.mtd_cleanup.CleanUp property) exec_module() (schrodinger.infra.unusable_module_importer.UnusableModuleLoader static method) execRemoteQueryDialog() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) ExecStagesWithSlowCoder (class in schrodinger.seam.testing.benchmarks) execText() (schrodinger.ui.qt.appframework2.debugwidgets.ExecWidget method) execute() (in module schrodinger.application.desmond.task) (in module schrodinger.application.phase.packages.shape_creation_logic) (schrodinger.application.desmond.antlr3.streams.InsertBeforeOp method) (schrodinger.application.desmond.antlr3.streams.ReplaceOp method) (schrodinger.application.desmond.antlr3.streams.RewriteOperation method) (schrodinger.application.desmond.task.Task method) execute_cmd() (in module schrodinger.application.matsci.maestrocmds) execute_lictest() (in module schrodinger.application.licensing.licadmin) execute_lictool() (in module schrodinger.application.licensing.licserver.client) execute_lmutil() (in module schrodinger.application.licensing.licadmin) execution_cputime_seconds (schrodinger.seam.metric.ExecutionMetrics attribute) EXECUTION_MODE (schrodinger.tasks.ldtasks.LDTask attribute) ExecutionMetrics (class in schrodinger.seam.metric) ExecutionMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) ExecutionMode (class in schrodinger.tasks.ldtasks) ExecWidget (class in schrodinger.ui.qt.appframework2.debugwidgets) EXISTING_RESTRAINT (class in schrodinger.application.desmond.constants) existingDatabaseJobFilename() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) exit() (schrodinger.pipeline.stage.Stage method) (schrodinger.utils.compare.DiffCompareArgumentParser method) exit_code (schrodinger.tasks.tasks.SubprocessMixin attribute) exit_code_is_defined() (in module schrodinger.application.desmond.cmj) exit_event_loop_on_exception() (in module schrodinger.utils.qt_utils) exit_if_incompatible_with_desmond() (in module schrodinger.application.matsci.desmondutils) ExitCode (schrodinger.job.jobcontrol.Job property) exitDecision() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) exitDisplaySnapshotMode() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) exitRule() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) ExitStatus (schrodinger.job.jobcontrol.Job property) exitSubRule() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) exitZoomView() (schrodinger.ui.two_d_viewer.TwoDViewer method) Expand (class in schrodinger.application.bioluminate.pml_menus) expand() (schrodinger.application.transforms.chem.Desalt method) (schrodinger.application.transforms.chem.Standardize method) (schrodinger.application.transforms.chem.Uncharge method) (schrodinger.application.transforms.dock.Dock method) (schrodinger.application.transforms.enumerators.CorelessSubstitute method) (schrodinger.application.transforms.enumerators.Decorate method) (schrodinger.application.transforms.enumerators.DeduplicateRoutes method) (schrodinger.application.transforms.enumerators.EnumerateRoutes method) (schrodinger.application.transforms.enumerators.EvaluateRoutes method) (schrodinger.application.transforms.enumerators.Fragment method) (schrodinger.application.transforms.enumerators.Substitute method) (schrodinger.application.transforms.enumerators.SubstructureSubstitute method) (schrodinger.application.transforms.enumerators.Synthesize method) (schrodinger.application.transforms.enumerators.SystematicSynthesize method) (schrodinger.application.transforms.filters.AlogDFilter method) (schrodinger.application.transforms.filters.DistinctStructures method) (schrodinger.application.transforms.filters.FepAmenable method) (schrodinger.application.transforms.filters.ProductFilter method) (schrodinger.application.transforms.filters.StructurePropertyFilter method) (schrodinger.application.transforms.filters.TanimotoFilter method) (schrodinger.application.transforms.ligprep.LigandPrep method) (schrodinger.application.transforms.template.starter.CarbonCount method) (schrodinger.application.transforms.template.workflow.CarbonCountingWorkflow method) (schrodinger.seam.debug.IPythonInspect method) (schrodinger.seam.examples.active_learning_weigher.ActiveLearning method) (schrodinger.seam.examples.active_learning_weigher.CalculateMolWt method) (schrodinger.seam.examples.active_learning_weigher.Iteration method) (schrodinger.seam.examples.active_learning_weigher.PickRandomly method) (schrodinger.seam.examples.active_learning_weigher.PickTopScoring method) (schrodinger.seam.transforms.partitioners.FixedSample method) (schrodinger.seam.transforms.partitioners.Top method) (schrodinger.seam.transforms.samplers.RandomSample method) (schrodinger.stepper.shims.ShimMapStep method) (schrodinger.stepper.shims.ShimReduceStep method) (schrodinger.utils.ligfilter.Definition method) (schrodinger.utils.ligfilter.SmartsCriterion method) expand_concatenated_stages() (in module schrodinger.application.matsci.desconfig) expand_macro() (in module schrodinger.application.desmond.util) (in module schrodinger.utils.sea.sea) expand_query() (in module schrodinger.rdkit.substructure) expand_settings_from_group() (in module schrodinger.ui.qt.appframework2.af2) expand_solutions() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) expandAll() (schrodinger.application.matsci.mswidgets.MultiStageArea method) ExpandCell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) expandFamily() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) expandNodeClusters() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) expandResidualMapping() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) expandToNodes() (schrodinger.ui.qt.network_views.NetworkViewer method) expComp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) expect_single_datum() (in module schrodinger.application.desmond.arkdb) expected_text_width() (in module schrodinger.application.matsci.gutils) expecter() (schrodinger.application.desmond.enhanced_sampling.FcnTypes.BinaryThreadSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.MetaSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.RMSDSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.SimpleSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.ThreadSyntax method) ExperimentalPersistentWorkerOptions (class in schrodinger.seam.options.pipeline_options) expiration_str() (schrodinger.application.licensing.flexlm.Feature method) EXPLICIT (schrodinger.adapter.Hydrogens attribute) EXPLICIT_HYDROGENS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) ExplicitHydrogens (class in schrodinger.livedesign.preprocessor) explore_solutions() (schrodinger.protein.assignment.NetworkSolver method) exploreEdge() (schrodinger.ui.qt.network_views.NetworkViewer method) export() (schrodinger.application.desmond.replica_dE.replica_container method) (schrodinger.application.desmond.replica_dE.replicas_monitor method) (schrodinger.application.desmond.replica_sid_generator.FEPReport method) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) (schrodinger.application.pymol.export_handler.ExportToPyMolMediator method) Export2DTask (class in schrodinger.application.livedesign.export_tasks) Export3DTask (class in schrodinger.application.livedesign.export_tasks) export_3d (schrodinger.application.livedesign.export_models.TaskInput attribute) export_3dChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) export_3dReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) export_asl (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) export_dE_data() (schrodinger.application.desmond.replica_dE.replica_container method) export_file_path (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) export_frame_option (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) export_generic_entities (schrodinger.application.livedesign.export_models.TaskInput attribute) export_generic_entitiesChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) export_generic_entitiesReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) export_hits_or_hypo() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) export_mode (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) export_modeChanged (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) export_modeReplaced (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) export_oned_data_file() (in module schrodinger.application.phase.packages.oned_task_utils) export_plp_to_csv() (in module schrodinger.ui.qt.mapperwidgets.plptable) EXPORT_ROW_CLASS (schrodinger.application.livedesign.export_map_manager.ExportMap attribute) export_specs (schrodinger.application.livedesign.export_models.SummaryModel attribute) export_specsChanged (schrodinger.application.livedesign.export_models.SummaryModel attribute) export_specsReplaced (schrodinger.application.livedesign.export_models.SummaryModel attribute) export_table_model (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) export_table_modelChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) export_table_modelReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) export_task (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_taskChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_taskReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) EXPORT_TEXT (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) export_text (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_textChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_textReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_to_bucket() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) export_to_csv() (in module schrodinger.ui.qt.table) export_to_csv_with_dialog() (in module schrodinger.ui.qt.table) export_to_ld() (in module schrodinger.application.livedesign.export_tasks) export_to_option (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) EXPORT_TRJ_FILE_PREF (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter attribute) ExportableProxyModel (class in schrodinger.ui.qt.table) exportAllTables() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) exportBuriedVolumeContour() (schrodinger.application.matsci.mlearn.features.Complex method) exportButtonClicked (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures attribute) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures attribute) exportClicked() (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) exportCurrentTable() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) exportData() (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame method) exportDatabase() (schrodinger.protein.nonstandard_residues.ResidueDatabase static method) exportEnergyDiagrams() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) exportFailed (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) ExportFrameOption (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums) exportImage() (schrodinger.ui.qt.schart.SChart method) exportImages() (schrodinger.ui.two_d_viewer.TwoDViewer method) ExportMainPanel (class in schrodinger.application.livedesign.ld_export_gui) ExportMap (class in schrodinger.application.livedesign.export_map_manager) ExportMapManager (class in schrodinger.application.livedesign.export_map_manager) ExportMode (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums) ExportModel (class in schrodinger.application.livedesign.ld_export) ExportMovieDialog (class in schrodinger.trajectory.trajectory_gui_dir.export_movie) ExportPanelWizard (class in schrodinger.application.livedesign.ld_export_gui) exportPresets() (schrodinger.models.presets.PresetManager method) ExportRow (class in schrodinger.application.livedesign.panel_components) exportSelectedEntries() (schrodinger.project.project.Project method) ExportSetupPanel (class in schrodinger.application.livedesign.ld_export_gui) ExportStructures (class in schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures) (class in schrodinger.trajectory.trajectory_gui_dir.export_structures) exportStructures() (schrodinger.ui.two_d_viewer.TwoDViewer method) exportStructuresForDebugging() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) ExportTableColumns (class in schrodinger.application.livedesign.panel_components) ExportTableDataColumnDelegate (class in schrodinger.application.livedesign.panel_components) ExportTableModel (class in schrodinger.application.livedesign.panel_components) exportTables() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) ExportTableView (class in schrodinger.application.livedesign.panel_components) ExportTask87 (class in schrodinger.application.livedesign.export_tasks) exportTo2dSdFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) exportTo3dSdWithSmilesFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) exportToCsv() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.table.ExportableProxyModel method) exportToHtml() (schrodinger.ui.two_d_viewer.TwoDViewer method) ExportToOption (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums) exportToPdfFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) exportToPngFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) ExportToPyMolMediator (class in schrodinger.application.pymol.export_handler) ExportToPyMolPanel (class in schrodinger.application.pymol.export_to_pymol_gui) ExportToPymolSettings (class in schrodinger.application.pymol.gui_models) exportTrace() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) exportTrajectory() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) ExportType (class in schrodinger.application.livedesign.export_tasks) EXPOSED (schrodinger.protein.predictors.SolventAccessibility attribute) Exposure (schrodinger.application.glide.xpdes.TermKeywords attribute) exposure_tendency (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) expr() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) expression_error() (schrodinger.utils.ligfilter.CriterionParser method) exprOrBind() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) expval (schrodinger.application.matsci.espresso.qeinput.FreePositionsType.PWallType attribute) ext (schrodinger.application.glide.utils.OutfileNameAttributes attribute) EXT (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.genetic_optimization.DeepChem attribute) ext_gcd() (in module schrodinger.application.matsci.nano.plane) EXT_OPEN_VALUES (schrodinger.protein.tasks.blast.BlastSettings attribute) Extend (class in schrodinger.application.bioluminate.pml_menus) EXTEND (schrodinger.application.desmond.constants.UiMode attribute) extend() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.structure.Structure method) (schrodinger.structure.StructureWriter method) (schrodinger.utils.sea.sea.List method) (schrodinger.utils.typing.Extendable method) extend_comp() (in module schrodinger.application.matsci.desmondutils) extend_connection_colors() (in module schrodinger.application.combiglide.connection_storage) extend_hotregion() (in module schrodinger.application.desmond.r_group_asl) extend_path() (in module schrodinger.application.desmond.kinetics.utils) extend_phosphate_states() (in module schrodinger.application.prepwizard) extend_sulfate_states() (in module schrodinger.application.prepwizard) extend_targeted_to_hyds() (schrodinger.protein.assignment.ProtAssign method) Extendable (class in schrodinger.utils.typing) extendBrokenAnnotations() (schrodinger.protein.gpcr.tasks.GPCRTask method) EXTENDED (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants attribute) Extended (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) extended (schrodinger.surface.MolSurfType attribute) EXTENDED_ENERGY (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) EXTENDED_SMILES (schrodinger.rdkit_extensions.Format attribute) EXTENDED_TIP (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants attribute) extended_windows_path() (in module schrodinger.utils.fileutils) ExtendSubMenu (class in schrodinger.application.bioluminate.pml_menus) extendWithSpectator() (schrodinger.application.matsci.rxn_channel.Products method) Extern (class in schrodinger.application.desmond.stage.workflow) EXTERNAL_FILE (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportToOption attribute) external_program_energy() (in module schrodinger.application.jaguar.textparser) external_program_nn_energy_stddev() (in module schrodinger.application.jaguar.textparser) ExternalMethod (class in schrodinger.application.jaguar.rotation_barriers_keywords) EXTRA_COLS (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) EXTRA_INPUT_FILES_DICT (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) extra_keywords (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain property) extra_keywords_args() (in module schrodinger.application.glide.utils) EXTRA_NROOT (schrodinger.application.matsci.mecp_mod.JaguarJobs attribute) extract() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) (schrodinger.structure.Structure method) extract_active_titles_from_csv() (in module schrodinger.analysis.enrichment.enrichment_input) extract_active_titles_from_list() (in module schrodinger.analysis.enrichment.enrichment_input) extract_active_titles_from_mae() (in module schrodinger.analysis.enrichment.enrichment_input) extract_active_titles_from_txt() (in module schrodinger.analysis.enrichment.enrichment_input) extract_and_contract() (in module schrodinger.application.matsci.cg_mapping) extract_archive() (in module schrodinger.application.combinatorial_screen.driver_utils) extract_binding_sites() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) extract_biopolymer_graph() (in module schrodinger.livedesign.biologics.registration) extract_cfg() (in module schrodinger.application.desmond.gconfig) extract_chain() (in module schrodinger.ui.qt.pdb_dialog) extract_chiral_center_data() (in module schrodinger.protein.process_enamine_db) extract_chorus_lattice_vector() (in module schrodinger.application.matsci.nano.xtal) extract_compressed_files() (in module schrodinger.active_learning.al_utils) extract_dict() (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) extract_epik_states() (in module schrodinger.protein.assignment) extract_file_from_grid() (in module schrodinger.application.glide.utils) extract_grid_and_radius() (in module schrodinger.application.matsci.freevolume) extract_het_from_complex() (in module schrodinger.application.prepwizard) extract_hets_from_complex() (in module schrodinger.application.prepwizard) extract_hypotheses() (in module schrodinger.application.phase.hypothesis) extract_job_data() (in module schrodinger.application.matsci.jobutils) extract_most_exposed_solute_molecules() (in module schrodinger.application.desmond.solubility_utils) extract_path_from_cms() (in module schrodinger.application.desmond.kinetics.utils) extract_Phob_pack_ligand_indices() (in module schrodinger.application.glide.xpdes) extract_properties() (in module schrodinger.pipeline.stages.phase) extract_ranks_from_csv() (in module schrodinger.analysis.enrichment.enrichment_input) extract_ranks_from_list() (in module schrodinger.analysis.enrichment.enrichment_input) extract_ranks_from_mae() (in module schrodinger.analysis.enrichment.enrichment_input) extract_ranks_from_structures() (in module schrodinger.analysis.enrichment.enrichment_input) extract_reactive_path() (in module schrodinger.application.desmond.kinetics.utils) extract_receptor_without_hets() (in module schrodinger.application.prepwizard) extract_registration_data() (in module schrodinger.livedesign.biologics.registration) extract_route_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) extract_smiles_and_cids() (in module schrodinger.application.vss.pilot) extract_solute_ct() (in module schrodinger.application.desmond.solubility_utils) extract_state_charges_and_orders() (in module schrodinger.application.prepwizard) extract_structure() (in module schrodinger.structutils.build) extract_structures() (in module schrodinger.application.phase.hypothesis) (in module schrodinger.rdkit.molio) extract_subjob_chunks() (in module schrodinger.application.combinatorial_diversity.driver_utils) extract_supercell() (in module schrodinger.comparison.struc) extract_titration_states() (schrodinger.application.desmond.cms.Cms method) extract_with_asl() (schrodinger.application.desmond.cms.Cms method) extract_with_comp_selection() (schrodinger.application.desmond.cms.Cms method) extractBarriers() (schrodinger.application.matsci.desconfig.BarrierHeader static method) ExtractClustersStep (class in schrodinger.application.matsci.jwsteps) extractData() (schrodinger.application.matsci.cgforcefield.FFIOAngle method) (schrodinger.application.matsci.cgforcefield.FFIOBond method) (schrodinger.application.matsci.cgforcefield.FFIODihedral method) (schrodinger.application.matsci.cgforcefield.FFIOImproper method) (schrodinger.application.matsci.cgforcefield.FFIOParam method) (schrodinger.application.matsci.cgforcefield.FFIOSite method) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) extractInformationFromTreeNodeStream() (schrodinger.application.desmond.antlr3.exceptions.RecognitionException method) extractMoieties() (schrodinger.application.matsci.amorphous.PolymerFragments method) ExtractSoluteStructure (class in schrodinger.application.desmond.stage.prepare.structure) extractSolventFromSt() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) extractStateChargesAndOrders() (schrodinger.application.prepwizard.HetState method) extractStructure() (schrodinger.structure._AtomCollection method) ExtractStructures (class in schrodinger.application.desmond.stage.prepare.structure) ExtractSubSystem (class in schrodinger.application.desmond.stage.app.matsci) extractWithMap() (schrodinger.application.matsci.amorphous.PolymerFragments method) ExtraSectionData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils)

F

f3d_Exception FAB (schrodinger.livedesign.entity_type.EntityClass attribute) FAB2 (schrodinger.livedesign.entity_type.EntityClass attribute) fab_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) Face (class in schrodinger.application.matsci.shapes) FACIAL (in module schrodinger.application.matsci.buildcomplex) factor() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) factorize() (in module schrodinger.application.matsci.gsas.GSASIIpwd) Factory (class in schrodinger.application.bioluminate.actions.factory) failed (schrodinger.application.desmond.cmj.Job property) FAILED (schrodinger.job.jobcontrol.DisplayStatus attribute) (schrodinger.job.queue.CancelSubmittedStatus attribute) (schrodinger.job.queue.JobState attribute) (schrodinger.seam.viz.inspect.PipelineStatus attribute) (schrodinger.seam.viz.inspect.TransformStatus attribute) (schrodinger.tasks.ldtasks.Status attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.Status attribute) failed() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) FAILED_ALL (schrodinger.tasks.queue.AutoFileMode attribute) failed_files (schrodinger.structure.MultiFileStructureReader attribute) failed_jobs (schrodinger.job.queue.JobDJ property) FAILED_LOG (schrodinger.tasks.queue.AutoFileMode attribute) FAILED_MESSAGE (schrodinger.application.glide.ligand_designer.GridgenTask attribute) FAILED_RETRYABLE (schrodinger.job.queue.JobState attribute) failed_tasks (schrodinger.tasks.queue.QueueResults attribute) failed_tasksChanged (schrodinger.tasks.queue.QueueResults attribute) failed_tasksReplaced (schrodinger.tasks.queue.QueueResults attribute) FAILED_TO_ACQUIRE_LICENSE (schrodinger.job.queue.CancelSubmittedStatus attribute) FAILED_TO_LAUNCH (schrodinger.job.queue.PrintableStatus attribute) FailedPredicateException failure_info (schrodinger.tasks.tasks.AbstractTask attribute) failure_infoChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) failure_infoReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) failure_infos (schrodinger.tasks.queue.QueueReport attribute) failure_infosChanged (schrodinger.tasks.queue.QueueReport attribute) failure_infosReplaced (schrodinger.tasks.queue.QueueReport attribute) FailureInfo (class in schrodinger.tasks.tasks) FAIR (schrodinger.application.desmond.fep_edge_data_classifier.Rating attribute) FakeMaestro (class in schrodinger.application.bioluminate.protein_structure_quality) FALLBACK_BASE_NAME (schrodinger.application.matsci.jaguarworkflows.WorkFlow attribute) FALSE (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolOperator attribute) family (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) family_name (schrodinger.application.livedesign.data_classes.LDData property) FamilyPairwiseAligner (class in schrodinger.protein.align) FAR_EXCLUSION (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) FAR_TERMS (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) FarContact (schrodinger.protein.annotation.BINDING_SITE attribute) fast (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer attribute) (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute) fast_sa (class in schrodinger.application.matsci.gsas.GSASIImath) FASTA (schrodinger.infra.structure.FileFormat attribute) (schrodinger.rdkit_extensions.Format attribute) fasta (schrodinger.utils.fileutils.SeqFormat attribute) FASTA_DNA (schrodinger.rdkit_extensions.Format attribute) FASTA_PEPTIDE (schrodinger.rdkit_extensions.Format attribute) FASTA_RNA (schrodinger.rdkit_extensions.Format attribute) fasta_single_entity_mapping (schrodinger.livedesign.registration.RegistrationOptions attribute) FastaHeader (class in schrodinger.livedesign.biologics.fasta) fastas_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) FastDecorator (class in schrodinger.application.steps.enumerators) FastFragmenter (class in schrodinger.application.steps.enumerators) FastFragmenter.Settings (class in schrodinger.application.steps.enumerators) FASTSIM (schrodinger.infra.licensing.SimilarityEndpoint attribute) fatal() (in module schrodinger.application.desmond.util) fatal_error() (in module schrodinger.application.jaguar.textparser) FatalCoordinateError FatalErrors (class in schrodinger.application.jaguar.constants) faux_epi_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) favicon_endpoints() (schrodinger.seam.viz.watcher.WatcherWebServer method) FAVORABLE_COLOR (schrodinger.ui.qt.rama.RamaContourMixin attribute) FAVORED (schrodinger.ui.qt.rama.RamaClassification attribute) FBHWPosRestrainArray (class in schrodinger.application.desmond.cms) FC_LABEL() (in module schrodinger.application.matsci.cgforcefieldgui) fcc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) fcjde_gen (class in schrodinger.application.matsci.gsas.GSASIIpwd) FcnCall (class in schrodinger.application.desmond.enhsamp) fcnCall() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) FDPOL_FREQ1 (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) FDPOLAR_ALPHA1 (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) FDPOLAR_FREQ1 (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) Feature (class in schrodinger.application.glide.glide) (class in schrodinger.application.licensing.flexlm) feature (schrodinger.application.licensing.lmgrd_log_parser.event attribute) feature_coordinates (schrodinger.application.phase.phase_markers.PhaseFeatureMarker property) feature_counter (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) FEATURE_DEFINITION_PRESETS (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo attribute) FEATURE_EQUIV_PRESETS (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo attribute) feature_expiring() (in module schrodinger.application.licensing.licadmin) FEATURE_FLAGS (schrodinger.utils.postinstall.CustomConfigFiles attribute) feature_name (schrodinger.application.phase.phase_markers.PhaseFeatureMarker property) FEATURE_QCOLORS() (in module schrodinger.application.phase.constants) FEATURE_TYPE (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) feature_type (schrodinger.application.phase.phase_markers.PhaseFeatureMarker property) FeatureColumns (class in schrodinger.application.phase.featureselector) featureExists() (schrodinger.application.phase.phase_markers.PhaseMarkers method) FeatureMatchCombo (class in schrodinger.application.phase.phase_widgets) FeatureModel (class in schrodinger.application.phase.featureselector) FeatureName (schrodinger.application.phase.featureselector.FeatureColumns attribute) FeatureOptionsCombo (class in schrodinger.application.phase.phase_widgets) FeaturePattern (class in schrodinger.application.glide.glide) FeatureRow (class in schrodinger.application.phase.featureselector) FEATURES (schrodinger.application.matsci.mlearn.features.LatticeFeatures attribute) features (schrodinger.application.phase.shape_screen_reporter.option_utils.ClusterBy attribute) FeatureSelector (class in schrodinger.application.phase.featureselector) featureToggled (schrodinger.application.phase.featureselector.FeatureModel attribute) Featurize (class in schrodinger.application.matsci.mlearn.descriptor) featurize() (schrodinger.application.matsci.mlearn.features.CrystalNNFeatures method) FeaturizeError fedit() (in module schrodinger.ui.qt.formlayout) FeedbackSubplotToolQt (class in schrodinger.ui.qt.navtoolbar) FEP (schrodinger.application.desmond.constants.PRODUCT attribute) fep() (schrodinger.application.macromodel.utils.ComUtil method) FEP_GROUPS (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) fep_lic() (in module schrodinger.application.desmond.license) fep_mut (schrodinger.application.desmond.struc.CompStruc attribute) FEP_PLUS (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) (schrodinger.infra.structure.WorkflowType attribute) fep_ref (schrodinger.application.desmond.struc.CompStruc attribute) fep_references_file (schrodinger.application.steps.filters.FepFilter.Settings attribute) fep_references_fileChanged (schrodinger.application.steps.filters.FepFilter.Settings attribute) fep_references_fileReplaced (schrodinger.application.steps.filters.FepFilter.Settings attribute) fep_simulation_details (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) FEP_STATE_KEYS (class in schrodinger.application.desmond.constants) fep_type (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator property) (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator property) (schrodinger.application.desmond.msj_generator.fep.covalent_ligand.CovalentMsjGenerator property) (schrodinger.application.desmond.msj_generator.fep.metalloprotein.MetalMsjGenerator property) (schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator property) (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator property) (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator property) (schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams attribute) (schrodinger.application.desmond.new_fep_edge_data.FepData property) FEP_TYPES (class in schrodinger.application.desmond.constants) FepAbsoluteBindingAnalysis (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAbsoluteBindingFepLauncher (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAbsoluteBindingFepPrimer (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAbsoluteBindingLauncher (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAbsoluteBindingLauncherBase (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAbsoluteBindingMdLauncher (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAbsoluteBindingMdPrimer (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAbsoluteBindingPrimer (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAbsoluteBindingStructurePrimer (class in schrodinger.application.desmond.stage.app.absolute_binding.stage) FepAmenable (class in schrodinger.application.transforms.filters) FepanaJob (class in schrodinger.application.desmond.stage.analysis) FepAnalysis (class in schrodinger.application.desmond.stage.analysis) FepArgs (class in schrodinger.application.desmond.starter.ui.cmdline) FepBaseMsjGenerator (class in schrodinger.application.desmond.msj_generator.common) FEPConfigDialog (class in schrodinger.application.desmond.fep_dialog) FepData (class in schrodinger.application.desmond.new_fep_edge_data) FEPEdgeData (class in schrodinger.application.desmond.fep_edge_data) FEPEdgeReportMaker (class in schrodinger.application.desmond.fep_edge_report_maker) FEPEdgeReportMakerBase (class in schrodinger.application.desmond.fep_edge_report_maker) FepFilter (class in schrodinger.application.steps.filters) FepFilter.Settings (class in schrodinger.application.steps.filters) fepio (schrodinger.application.desmond.ffiostructure.FFIOStructure attribute) FepJob (class in schrodinger.application.desmond.stage.jobs) FepLambdas (class in schrodinger.application.desmond.new_fep_edge_data) FepLauncher (class in schrodinger.application.desmond.stage.launcher) FepLegs (class in schrodinger.application.desmond.new_fep_edge_data) FepLegTypes (class in schrodinger.application.desmond.constants) FepMapper (class in schrodinger.application.desmond.stage.fep_mapper) FepMapperCleanup (class in schrodinger.application.desmond.stage.fep_mapper) FepMapperReport (class in schrodinger.application.desmond.stage.deprecate) FepMembraneLauncher (class in schrodinger.application.desmond.stage.launcher) FepPlusArgs (class in schrodinger.application.desmond.starter.ui.fep_plus) FEPReport (class in schrodinger.application.desmond.replica_sid_generator) FEPReportMaker (class in schrodinger.application.desmond.fep_reporter) FepSchedule (class in schrodinger.application.desmond.fep_schedule) FepScheduleAlchemical (class in schrodinger.application.desmond.fep_schedule) FepScheduleAlchemicalCharge (class in schrodinger.application.desmond.fep_schedule) FepScheduleAlchemicalDefault (class in schrodinger.application.desmond.fep_schedule) FepScheduleBinding (class in schrodinger.application.desmond.fep_schedule) FepScheduleBindingDefault (class in schrodinger.application.desmond.fep_schedule) FepSchemeChargeMixIn (class in schrodinger.application.desmond.fep_schedule) FepSchemeMixIn (class in schrodinger.application.desmond.fep_schedule) FepSchemeQuickchargeMixIn (class in schrodinger.application.desmond.fep_schedule) FepSchemeSuperquickchargeMixIn (class in schrodinger.application.desmond.fep_schedule) FEPScholarMapper (class in schrodinger.application.desmond.fep_scholar_util) FEPScholarMsjGenerator (class in schrodinger.application.desmond.fep_scholar_msj_generator) FEPSimulationReport (class in schrodinger.application.desmond.replica_sid_generator) FepSolubilityArgs (class in schrodinger.application.desmond.starter.ui.fep_solubility) FEPStructureObject (class in schrodinger.application.desmond.fep_scholar_util) FEPTorsions (class in schrodinger.application.desmond.fep_edge_data) FEPTorsionsContainer (class in schrodinger.application.desmond.fep_edge_data) FepVrun (class in schrodinger.application.desmond.stage.simulate) fetchPPDB() (schrodinger.application.matsci.espresso.qeinput.StructureType method) ff_host (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) ff_structure_file (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) ffbuilder (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) ffc_export_specs (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ffc_export_specsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ffc_export_specsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) FFCExportSpec (class in schrodinger.application.livedesign.export_models) ffComboBox (class in schrodinger.ui.qt.forcefield.ffselector) FFCustomOPLSSettingMixin (class in schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget) FFCustomOPLSSettingWidget (class in schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget) FFGlobalPreferenceWidget (class in schrodinger.ui.qt.forcefield.ffglobalpreferencewidget) FFInfo (class in schrodinger.application.matsci.chargegui) ffio (schrodinger.application.desmond.ffiostructure.FFIOStructure attribute) FFIO_ATOM_VEL() (in module schrodinger.application.matsci.msprops) ffio_delete_atoms() (in module schrodinger.application.desmond.gcmc_utils) ffio_extend_ct() (in module schrodinger.application.desmond.gcmc_utils) ffio_refresh() (schrodinger.application.desmond.cms.Cms method) FFIOAngle (class in schrodinger.application.matsci.cgforcefield) FFIOBond (class in schrodinger.application.matsci.cgforcefield) FFIODihedral (class in schrodinger.application.matsci.cgforcefield) FFIOExclusion (class in schrodinger.application.matsci.cgforcefield) FFIOImproper (class in schrodinger.application.matsci.cgforcefield) FFIOParam (class in schrodinger.application.matsci.cgforcefield) FFIOSite (class in schrodinger.application.matsci.cgforcefield) FFIOStructure (class in schrodinger.application.desmond.ffiostructure) FFIOVdwType (class in schrodinger.application.matsci.cgforcefield) FFIOVdwTypesCombined (class in schrodinger.application.matsci.cgforcefield) ffld() (in module schrodinger.application.qsite.output) ffld_project_incompatible() (in module schrodinger.forcefield.test.fixtures) ffld_project_ring() (in module schrodinger.forcefield.test.fixtures) ffld_project_skipped() (in module schrodinger.forcefield.test.fixtures) ffld_use_db_v2() (in module schrodinger.forcefield.test.fixtures) FFLD_WATER (schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield attribute) FFProjectSettingsDlg (class in schrodinger.ui.qt.forcefield.ffprojectsettingsdlg) FFSettingsButton (class in schrodinger.ui.qt.forcefield.ffsettingsbutton) fh_mut_coord (schrodinger.application.desmond.stage.jobs.SnapcoreCoordinates attribute) fh_ref_coord (schrodinger.application.desmond.stage.jobs.SnapcoreCoordinates attribute) Field (class in schrodinger.application.bindingsite.intfield) field (schrodinger.application.jaguar.nmr_utils.NMRData attribute) FieldColumn (class in schrodinger.ui.qt.mapperwidgets.plptable) FIELDX (schrodinger.application.matsci.kmc.SchrodingerTable attribute) FIELDY (schrodinger.application.matsci.kmc.SchrodingerTable attribute) FIELDZ (schrodinger.application.matsci.kmc.SchrodingerTable attribute) FIFOCacheData (class in schrodinger.application.matsci.cache) figure_edit() (in module schrodinger.ui.qt.figureoptions) FILE (schrodinger.application.matsci.genetic_optimization.GlassTransitionTemperature attribute) (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) (schrodinger.application.matsci.mswidgets.StructureLoader attribute) file (schrodinger.application.phase.packages.phase_screen_driver_utils.SourceFormat attribute) FILE (schrodinger.ui.qt.input_selector.InputSelector attribute) File (schrodinger.ui.qt.structure_selector.InputSource attribute) file_arguments_for_launch_command() (in module schrodinger.job.jobcontrol) file_batches (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) file_batchesChanged (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) file_batchesReplaced (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) file_config() (in module schrodinger.utils.log) FILE_CORRUPT (schrodinger.application.desmond.cmj.JobStatus attribute) file_dirname() (in module schrodinger.application.licensing.licadmin) FILE_EXT (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) file_format (schrodinger.application.livedesign.export_models.GETaskInput attribute) file_formatChanged (schrodinger.application.livedesign.export_models.GETaskInput attribute) file_formatReplaced (schrodinger.application.livedesign.export_models.GETaskInput attribute) FILE_IMPORT_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) file_name (schrodinger.application.prime.wrapper.PrimeTemplate property) FILE_NAME_COL (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame attribute) FILE_NOT_FOUND (schrodinger.application.desmond.cmj.JobStatus attribute) file_path (schrodinger.application.livedesign.export_models.AttachmentItem attribute) (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_pathChanged (schrodinger.application.livedesign.export_models.AttachmentItem attribute) (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_pathReplaced (schrodinger.application.livedesign.export_models.AttachmentItem attribute) (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_paths (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_pathsChanged (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_pathsReplaced (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) FILE_PICK_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) FILE_SELECTOR_CLASS (schrodinger.ui.qt.structure_selector.SlimStructureSelector attribute) (schrodinger.ui.qt.structure_selector.StructureSelector attribute) file_to_tmp_fn() (in module schrodinger.application.matsci.msutils) file_type (schrodinger.application.livedesign.export_models.AttachmentItem attribute) FILE_TYPE (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) file_typeChanged (schrodinger.application.livedesign.export_models.AttachmentItem attribute) FILE_TYPEChanged (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) file_typeReplaced (schrodinger.application.livedesign.export_models.AttachmentItem attribute) FILE_TYPEReplaced (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) FileBaseNameValidator (class in schrodinger.ui.qt.swidgets) FileBatch (class in schrodinger.application.livedesign.export_models) FileColumn (class in schrodinger.tasks.ldtasks) FileDebugViewer (class in schrodinger.ui.qt.appframework2.debugcore) FileDialog (class in schrodinger.ui.qt.filedialog) FileDialogWithExtraCombo (class in schrodinger.application.jaguar.gui.filedialog) FileDownloader (class in schrodinger.application.matsci.jobutils) FileDownloadError FileEntry (class in schrodinger.application.desmond.cwidget) FileExists (class in schrodinger.ui.qt.appframework2.validators) fileExplorerError (schrodinger.application.job_monitor.buttons.FileExplorerMenuButton attribute) FileExplorerMenuButton (class in schrodinger.application.job_monitor.buttons) FileFormat (class in schrodinger.application.livedesign.export_tasks) (class in schrodinger.infra.structure) FileInMixin (class in schrodinger.application.steps.dataclasses) FileLayout (class in schrodinger.ui.qt.formlayout) FileLogger (class in schrodinger.application.jaguar.file_logger) FileLoggerError FileMolWorkflow (class in schrodinger.application.steps.basesteps) filename (schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent property) (schrodinger.application.desmond.test_utils.UnregisteredFile attribute) (schrodinger.application.jaguar.input.JaguarInput property) (schrodinger.application.jaguar.nmr_utils.NMRData attribute) (schrodinger.application.steps.converters.MaeFileWriter.Settings attribute) filenameChanged (schrodinger.application.steps.converters.MaeFileWriter.Settings attribute) filenameReplaced (schrodinger.application.steps.converters.MaeFileWriter.Settings attribute) filepath (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filepathChanged (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filepathReplaced (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) FileRegistration (class in schrodinger.application.desmond.test_utils) FileRegistrationTag (class in schrodinger.application.desmond.test_utils) FileRegistry (class in schrodinger.application.desmond.test_utils) FILES (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) files (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.structure.MultiFileStructureReader attribute) filesChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame attribute) fileSelectionChanged (schrodinger.ui.qt.file_selector.FileSelector attribute) FileSelector (class in schrodinger.ui.qt.file_selector) FileSize (schrodinger.infra.structure.FileSplitStrategy attribute) FileSplitStrategy (class in schrodinger.infra.structure) filesReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) FileStream (in module schrodinger.application.desmond.antlr3.streams) FILETYPE (schrodinger.application.matsci.packmol.PackmolKw attribute) fill() (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.infra.mmbitset.Bitset method) fill_table_with_data_frame() (in module schrodinger.application.matsci.gutils) fillAdsCache() (schrodinger.application.matsci.rxn_channel.CacheInfo method) FillAtomLookUp() (in module schrodinger.application.matsci.gsas.GSASIImath) fillAtoms() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillBranchPoints() (schrodinger.application.matsci.amorphous.Initiator method) fillBuffer() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) fillFolderTree() (schrodinger.application.livedesign.ld_folder_tree.LDFolderTree method) fillFragments() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillFrames() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillgmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice) fillloops (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillloopsChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillloopsReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillMolecules() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillPairs() (schrodinger.application.matsci.kmc.BaseDatabaseManager method) fillSchrodinger() (schrodinger.application.matsci.kmc.BaseDatabaseManager method) fillSegments() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillSegmentTypes() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillsidechains (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillsidechainsChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillsidechainsReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillSites() (schrodinger.application.matsci.kmc.MatSciDatabaseManager method) fillStatusLabel() (schrodinger.application.matsci.builderwidgets.ItemRow method) FillUnitCell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) fillWithResults() (schrodinger.application.jaguar.gui.timing.TimerInfoDialog method) Filter (class in schrodinger.structutils.filter) (class in schrodinger.ui.qt.filter_dialog_dir.filter_core) filter() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.math.sampling.SystematicSampler class method) (schrodinger.rdkit.filtering.JSONFilterAdapter method) (schrodinger.structutils.filter.Filter method) filter_csv() (in module schrodinger.application.bioluminate.pose_filtering.csv_filter) filter_data() (schrodinger.application.desmond.bennett.CalcBAR method) filter_degen_res_atoms() (in module schrodinger.application.desmond.sid_plots.pl_interactions) filter_fep_structures() (in module schrodinger.application.desmond.stage.app.absolute_binding.struc) filter_file (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.steps.filters.PropertyFilter.Settings attribute) filter_fileChanged (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.steps.filters.PropertyFilter.Settings attribute) filter_fileReplaced (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.steps.filters.PropertyFilter.Settings attribute) filter_glide_results() (in module schrodinger.application.livedesign.ld_glide_utils) filter_hits() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) filter_hydrogen_from_list() (in module schrodinger.application.jaguar.gui.input_tab_widgets_pka) filter_jobs() (schrodinger.application.desmond.cmj.JobManager method) (schrodinger.application.desmond.cmj.StageBase method) filter_missing_entry() (in module schrodinger.application.livedesign.panel_components) filter_monatomic_mols() (in module schrodinger.application.desmond.struc) filter_nonshared_rotatables() (in module schrodinger.protein.assignment) filter_qt_msg() (in module schrodinger.infra.qt_message_handler) filter_query (schrodinger.protein.tasks.blast.BlastSettings attribute) filter_queryChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) filter_queryReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) filter_reactions() (in module schrodinger.application.pathfinder.analysis) filter_res_ids() (schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter method) (schrodinger.application.bioluminate.pose_filtering.residue_filter.ResidueFilter method) (schrodinger.application.bioluminate.pose_filtering.residue_filter.SasaResidueFilter method) filter_residues_mutating_to_custom() (in module schrodinger.protein.nonstandard_residues) filter_routes() (in module schrodinger.application.combinatorial_explorer.driver_utils) filter_string_from_extensions() (in module schrodinger.ui.qt.filedialog) filter_string_from_formats() (in module schrodinger.ui.qt.filedialog) filter_string_from_supported() (in module schrodinger.ui.qt.appframework) filter_structure_chains() (in module schrodinger.application.bioluminate.tcr.annotate) filter_structures() (in module schrodinger.application.bioluminate.pose_filtering.csv_filter) filter_terms (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filter_termsChanged (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filter_termsReplaced (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filter_undesired_states() (in module schrodinger.application.prepwizard) filterAcceptsColumn() (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesProxyModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel method) filterAcceptsIndex() (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterAcceptsParent() (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterAcceptsRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) (schrodinger.application.livedesign.panel_components.ColumnSelectionProxyModel method) (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterAll() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) FilterBasisSelectorReadOnlyLineEdit (class in schrodinger.application.jaguar.gui.basis_selector) FilterCheckBox (class in schrodinger.ui.qt.filter_list) FilterCriteria (class in schrodinger.application.bioluminate.pose_filtering.residue_filter) FilterDBTask (class in schrodinger.application.phase.shape_screen_reporter.tasks) FilterDBTask.Input (class in schrodinger.application.phase.shape_screen_reporter.tasks) FilterDBTask.Output (class in schrodinger.application.phase.shape_screen_reporter.tasks) FilterDialog (class in schrodinger.ui.qt.filter_dialog) filtered_combinations() (in module schrodinger.structutils.rgroup_enumerate) filtered_combinations_for_selection() (in module schrodinger.structutils.rgroup_enumerate) filtered_row_nums (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Output attribute) filtered_row_numsChanged (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Output attribute) filtered_row_numsReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Output attribute) FilteredComplexTemplateSketcher (class in schrodinger.application.matsci.builderwidgets) FilteredSketcherBox (class in schrodinger.application.matsci.builderwidgets) FilteredTemplateSelector (class in schrodinger.application.matsci.builderwidgets) filterEntities() (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask method) filterFile() (schrodinger.pipeline.stages.filtering.SubSetStage method) filteringChanged() (schrodinger.ui.qt.propertyselector.PropertySelector method) filterList() (schrodinger.application.bioluminate.propfilter.SelectingFilteredListWidget method) (schrodinger.application.matsci.wfmanagement.WorkflowFilterWidget method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) (schrodinger.ui.qt.swidgets.SFilteredListWidget method) FilterListPopUp (class in schrodinger.ui.qt.filter_list) FilterParameters (class in schrodinger.application.bioluminate.pose_filtering.csv_filter) filterProperties() (schrodinger.ui.qt.propertyselector.PropertySelector method) FilterReporter (class in schrodinger.structutils.smilesfilter) filterRowsByExcitedState() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) filters (schrodinger.application.bioluminate.pose_filtering.residue_filter.FilterCriteria attribute) filters_unsanitizable() (in module schrodinger.application.transforms.chem) filtersChanged (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetDelegate attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.MethodDelegate attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog attribute) (schrodinger.application.jaguar.gui.theory_selector.FilterTheorySelectorReadOnlyLineEdit attribute) (schrodinger.ui.qt.filter_list.FilterListPopUp attribute) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp attribute) filterSelectionChanged() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) filtersInvalidated (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) filterSmilesFile() (schrodinger.pipeline.stages.filtering.SubSetStage method) filterTemplates() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) FilterTheorySelectorReadOnlyLineEdit (class in schrodinger.application.jaguar.gui.theory_selector) FilterWidget (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) filterWorkflows() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) final (schrodinger.application.jaguar.scan.Scan property) (schrodinger.application.jaguar.utils.ScanCoord attribute) final_dg (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult property) FINAL_VAL (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) finalize() (schrodinger.application.xtb.textparser.TextParser static method) (schrodinger.job.queue.BaseJob method) finalize_job() (schrodinger.application.desmond.cmj.StageBase method) finalize_smap() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) finalize_stage() (schrodinger.application.desmond.cmj.StageBase method) finalize_subjob() (in module schrodinger.application.matsci.jobutils) finalizeJMSWFOutput() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) finalizeSideGroup() (schrodinger.application.matsci.amorphous.BaseMoiety method) finalizeStep() (schrodinger.application.matsci.permittivity.AnalyzeSimulation static method) (schrodinger.application.matsci.permittivity.AveCellAnalysis static method) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis static method) (schrodinger.application.matsci.permittivity.ComplexPermittivity static method) (schrodinger.application.matsci.permittivity.DensityAnalysis static method) (schrodinger.application.matsci.permittivity.ElectricPolarizability static method) (schrodinger.application.matsci.permittivity.JaguarCalculation static method) (schrodinger.application.matsci.permittivity.JaguarMerge static method) (schrodinger.application.matsci.permittivity.RefractiveIndex static method) (schrodinger.application.matsci.permittivity.StaticPermittivity static method) (schrodinger.application.matsci.permittivity.StepBase static method) (schrodinger.application.matsci.permittivity.SusceptibilityMerge static method) FinalTSFailure find() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.application.desmond.arkdb.ArkDb method) (schrodinger.application.desmond.multisim.parser.Msj method) find_ab_chain() (in module schrodinger.livedesign.biologics.registration) find_abs_by_connectivity() (in module schrodinger.livedesign.biologics.registration) find_all_entries() (in module schrodinger.application.bioluminate.pml_menus) find_all_rings() (in module schrodinger.structutils.rings) find_all_table_entry_objects() (in module schrodinger.application.bioluminate.pml_menus) find_antibodies() (in module schrodinger.livedesign.biologics.registration) find_atom() (in module schrodinger.protein.nonstandard_residues) find_atom_with_pdb_name() (in module schrodinger.ui.residueselector) find_atoms_closest_to_atoms() (in module schrodinger.application.matsci.clusterstruct) find_atoms_near_point() (in module schrodinger.application.matsci.reorder) find_atoms_to_remove() (in module schrodinger.application.matsci.buildcomplex) find_attached_atom_index() (in module schrodinger.application.matsci.amorphous) find_backbone() (in module schrodinger.application.matsci.graph) find_best_core_match() (in module schrodinger.application.canvas.r_group) find_best_match_with_director() (in module schrodinger.application.matsci.rxn_channel) find_block() (schrodinger.application.desmond.simulation_block_test.Block method) find_box() (in module schrodinger.application.desmond.struc) find_buddies_on_other_surf() (in module schrodinger.application.bioluminate.surfcomp) find_center_of_atoms() (in module schrodinger.application.bioluminate.pml_menus) find_checkpoint_file() (in module schrodinger.application.desmond.launch_utils) find_class() (schrodinger.application.desmond.picklejar.CustomUnpickler method) find_closest_point() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.Rama method) find_closest_rotbond() (in module schrodinger.application.desmond.r_group_asl) find_closest_xval() (in module schrodinger.application.matsci.spectra) find_common (schrodinger.application.phase.input.InputSpecs attribute) find_common_properties() (in module schrodinger.structutils.analyze) find_common_substructure() (in module schrodinger.structutils.analyze) find_component_cts() (in module schrodinger.application.desmond.fep_net_charge) find_decorated_methods() (in module schrodinger.infra.util) find_distortions() (in module schrodinger.structutils.check) find_duplicate_titles() (in module schrodinger.application.desmond.struc) find_eq_stress() (in module schrodinger.application.matsci.elasticity.elastic) find_equivalent_atoms() (in module schrodinger.application.glide.gui) (in module schrodinger.structutils.analyze) find_equivalent_st() (in module schrodinger.application.desmond.system_builder_util) find_families() (in module schrodinger.protein.gpcr.gpcrdb) find_fmpdb_file() (in module schrodinger.application.desmond.starter.generator.common) find_forcefield_invalid_structures() (in module schrodinger.application.matsci.desmondutils) find_frag_from_closest_rotbond() (in module schrodinger.application.desmond.r_group_asl) find_full_product_version() (in module schrodinger.application.utils) find_furthest_atom_along_vector() (in module schrodinger.application.matsci.nano.xtal) find_generalized_pattern() (in module schrodinger.protein.sequence) find_good_bond_vector() (in module schrodinger.application.matsci.rxn_channel) find_grd_file() (in module schrodinger.application.glide.utils) find_group_data() (in module schrodinger.application.matsci.smartsutils) find_hbond_hydrogen() (schrodinger.protein.analysis.Report.steric_clash_data_set method) find_head_tail() (in module schrodinger.application.matsci.graph) find_hets() (in module schrodinger.protein.findhets) find_isolated_water_molecules() (in module schrodinger.protein.reliability) find_key_for_value() (in module schrodinger.application.jaguar.gui.utils) find_key_pair() (in module schrodinger.utils.sshconfig) find_knime_java_path() (in module schrodinger.utils.env) find_license_file() (in module schrodinger.application.licensing.flexlm) find_license_files() (in module schrodinger.application.licensing.licserver.client) find_license_resources() (in module schrodinger.application.licensing.licadmin) find_ligand_sites() (in module schrodinger.application.desmond.kinetics.utils) find_ligands() (in module schrodinger.structutils.analyze) FIND_LIGANDS_KWARGS (schrodinger.application.prime.wrapper.PrimeTemplate attribute) find_local_pdb() (in module schrodinger.protein.getpdb) find_local_repository() (in module schrodinger.protein.getpdb) find_lone_hydrogen() (in module schrodinger.application.matsci.buildcomplex) find_metal() (in module schrodinger.application.matsci.etarotamers) find_metals_in_structure() (in module schrodinger.application.prepwizard) find_missing_coupling_data() (in module schrodinger.application.matsci.kmc) find_missing_res_atoms() (in module schrodinger.application.prepwizard2.diagnostics) find_missing_site_energies() (in module schrodinger.application.matsci.kmc) find_mol_species_from_rdmol() (in module schrodinger.application.matsci.clusterstruct) find_molecule_fragments() (in module schrodinger.application.matsci.clusterstruct) find_molecules_closest_to_atoms() (in module schrodinger.application.matsci.clusterstruct) find_most_recent_graph_output() (in module schrodinger.application.desmond.stage.fep_mapper) find_n1_atom() (in module schrodinger.protein.pdbname) find_na_entities() (in module schrodinger.livedesign.biologics.registration) find_new_group_id() (in module schrodinger.application.matsci.automated_cg_mapping) find_next_residue() (in module schrodinger.application.desmond.cms) find_origin_on_structure_exterior() (in module schrodinger.application.matsci.nano.xtal) find_overlapping_atoms() (in module schrodinger.structutils.analyze) find_oxt_atom() (in module schrodinger.protein.pdbname) find_pattern() (in module schrodinger.protein.sequence) find_pi_cation_interactions() (in module schrodinger.structutils.interactions.pi) find_pi_pi_interactions() (in module schrodinger.structutils.interactions.pi) find_polar_contacts() (in module schrodinger.application.bioluminate.pml_menus) find_polygon_vertices() (in module schrodinger.application.matsci.nano.tools) find_polymer_species() (in module schrodinger.application.matsci.polymer) find_ppw_atom() (in module schrodinger.application.prepwizard) find_prev_residue() (in module schrodinger.application.desmond.cms) find_product_package_dir() (in module schrodinger.application.utils) find_protein_sites() (in module schrodinger.application.desmond.kinetics.utils) find_protonation_state_changes() (schrodinger.protein.assignment.ProtAssign method) find_reactions() (in module schrodinger.application.combinatorial_screen.driver_utils) find_recap_bonds() (in module schrodinger.structutils.createfragments) find_res_species() (in module schrodinger.application.matsci.clusterstruct) find_residue_atom() (in module schrodinger.application.bioluminate.protein.utils) find_residues_with_multiple_occupancies() (in module schrodinger.application.prepwizard2.diagnostics) find_rgroup_from_smarts() (in module schrodinger.structutils.rgroup_enumerate) find_ring_atoms() (in module schrodinger.structutils.rings) find_ring_bonds() (in module schrodinger.structutils.rings) find_ring_systems() (in module schrodinger.structutils.rings) find_rings() (in module schrodinger.structutils.rings) (schrodinger.structure.Structure method) find_scaffolds() (in module schrodinger.application.bioluminate.antibody.scaffold_search) find_segments() (in module schrodinger.application.matsci.graph) find_shortest_bond_path() (in module schrodinger.structutils.analyze) find_signals() (in module schrodinger.ui.qt.appframework2.debugwidgets) find_spec() (schrodinger.infra.unusable_module_importer.AbstractUnusableModuleFinder method) (schrodinger.infra.unusable_module_importer.NonPostTestUnusableModuleFinder method) find_species() (in module schrodinger.application.matsci.clusterstruct) find_stage() (in module schrodinger.application.desmond.launch_utils) find_stage_number() (in module schrodinger.application.desmond.launch_utils) find_stages() (schrodinger.application.desmond.multisim.parser.Msj method) find_staying_atom() (in module schrodinger.structutils.rgroup_enumerate) FIND_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) find_user_libstdcpp() (in module schrodinger.utils.installation_check) find_validators() (in module schrodinger.ui.qt.appframework2.validation) FINDALL (schrodinger.application.jaguar.utils.LewisModes attribute) FindAllNeighbors() (in module schrodinger.application.matsci.gsas.GSASIImath) findAntibodyRegions() (schrodinger.application.bioluminate.pml_menus.AntibodyPreset method) findAromaticBonders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) findAromaticRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) FindAtomIndexByIDs() (in module schrodinger.application.matsci.gsas.GSASIImath) findAttachedAtomIndex() (schrodinger.application.matsci.amorphous.BaseMoiety method) findAttachmentMarkers() (schrodinger.application.matsci.builderwidgets.MinimizeMixin method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) findBackbone() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Monomer method) findBackbone2BranchingPoint() (schrodinger.application.matsci.amorphous.BaseMoiety method) findBackboneAngles() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) findBackboneAtomsIds() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) findBindingAtoms() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) findBondGroups() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) findBondsToBreak() (schrodinger.application.matsci.amorphous.Monomer method) findChiAtoms() (schrodinger.protein.rotamers.Rotamers method) findCommonDatanames() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) findCoordinate() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) findData() (schrodinger.ui.qt.swidgets.SComboBox method) findDataPy() (schrodinger.ui.qt.swidgets.SComboBox method) finder (schrodinger.application.matsci.species.SC_TYPE_DATA attribute) findEtaGroups() (schrodinger.application.matsci.buildcomplex.EtaFindingMixin method) findExclusiveAtoms() (schrodinger.application.matsci.automated_cg_mapping.StructData method) findFirstDisorderedMolecule() (schrodinger.application.matsci.montecarlo.Metropolizer method) findFragments() (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule method) findFreeVolume() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) findFuncGroupsFromMolecule() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) findGenerations() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) findGroupsFromMolecule() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) findGroupsInSet() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) findGroupsMapping() (schrodinger.application.matsci.automated_cg_mapping.StructData method) findHead() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Terminator method) findHeadTail() (schrodinger.application.matsci.amorphous.PolymerFragments static method) findHeadTailBranch() (schrodinger.application.matsci.amorphous.Monomer method) findHetAtoms() (schrodinger.application.prepwizard.HetState method) findHydrophobicCenter() (schrodinger.protein.membrane.Membrane_Model method) findInStructure() (schrodinger.ui.picking.ResidueRow method) findInvalidFFStructures() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) findItem() (schrodinger.application.livedesign.panel_components.LDSelectionModel method)

findLargestTranslat() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) findLocally() (schrodinger.protein.getpdb_utility.Code method) findManageOutfiles() (schrodinger.pipeline.stages.phase.DBExportStage method) findMarkHeadTailMarkers() (schrodinger.application.matsci.amorphous.Moieties method) findMinVolume() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) FindMolecule() (in module schrodinger.application.matsci.gsas.GSASIImath) findNeighborFrags() (schrodinger.application.matsci.amorphous.PolymerFragments method) findNeighboringCells() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) FindNeighbors() (in module schrodinger.application.matsci.gsas.GSASIImath) findNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) findNonlinearAngle() (schrodinger.application.matsci.zmutils.ZMatrix method) FindNonstandard() (in module schrodinger.application.matsci.gsas.GSASIIlattice) findNTerminiAtomIds() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) findOffset() (in module schrodinger.application.matsci.gsas.GSASIImath) findOrCreateDBEntry() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) findOxygenToReplace() (schrodinger.protein.captermini.CapTermini method) findPath() (schrodinger.application.livedesign.panel_components.PathTreeDict method) findPattern() (schrodinger.protein.alignment.ProteinAlignment method) FindPCSubMenu (class in schrodinger.application.bioluminate.pml_menus) findPoint() (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin method) findPotentialTripleBondAtoms() (schrodinger.structutils.assignbondorders.AssignBondOrders method) findReagentFile() (schrodinger.application.pathfinder.reaction.ReagentClass method) (schrodinger.application.pathfinder.route.ReagentNode method) findResidue() (schrodinger.structure.Structure method) findResidues() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) findRings() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) (schrodinger.application.matsci.montecarlo.ClashChecker method) (schrodinger.structutils.assignbondorders.AssignBondOrders method) findRingSideGroup() (schrodinger.application.matsci.amorphous.Monomer method) findRingSpears() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) findRotatableBonds() (schrodinger.application.matsci.amorphous.BaseMoiety method) findRowsMatching() (schrodinger.project.project.Project method) findSameGenerationIndices() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) findSideGroup() (schrodinger.application.matsci.amorphous.BaseMoiety method) findSimpleHeadTailMarkers() (schrodinger.application.matsci.amorphous.Moieties method) findSMARTSError() (schrodinger.ui.qt.swidgets.SMARTSEdit method) findSMARTSMatchingIndexes() (schrodinger.application.matsci.automated_cg_mapping.StructData method) findSpears() (schrodinger.structutils.ringspear.SpearRing method) findSpecies() (schrodinger.application.matsci.speciesgui.GroupingMethodSelector method) findSpeciesInStruct() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) findSSOffset() (in module schrodinger.application.matsci.gsas.GSASIImath) findStructAromaticBonds() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) findTextChanged() (schrodinger.application.bioluminate.ssv.toolbars.FindToolBar method) FindToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) (class in schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) FindToolBarSketcherDialog (class in schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) findTotalEnergyProp() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) findXvolSphereIndex() (schrodinger.application.phase.phase_markers.PhaseMarkers method) FINGERPRINT_TYPES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) fingerprintChanged (schrodinger.ui.qt.fp_selector_widget.FingerprintsPopUp attribute) FingerprintComponent (class in schrodinger.analysis.enrichment.enrichment_input) FingerprintsModel (class in schrodinger.ui.qt.fp_selector_widget) FingerprintsPopUp (class in schrodinger.ui.qt.fp_selector_widget) FingerprintsSelectorWidget (class in schrodinger.ui.qt.fp_selector_widget) FingerprintUse (class in schrodinger.livedesign.search) finish() (schrodinger.application.bioluminate.pml_menus.PresetAction method) (schrodinger.application.desmond.cmj.Job method) (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) (schrodinger.application.glide.http_server.GlideHTTPHandler method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.pipeline.pipeline.StageJob method) (schrodinger.ui.qt.structure2d.StructureToolTip method) finish_bundle() (schrodinger.seam.examples.haystack.Bale method) finish_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) FINISHED (schrodinger.application.fragment_virtual_screening.frag_vs_utils.StageStatus attribute) finished (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel attribute) (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard attribute) finishGuess() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) finishPolymerFrags() (schrodinger.application.matsci.amorphous.PolymerFragments method) finishPrevStep() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) finishProcessingJobControlJob() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.SubdirectoryStepMixin method) FIRST (schrodinger.application.matsci.permittivity.MdStageModifier attribute) first() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) FIRST_CELL (schrodinger.application.matsci.nano.xtal.PBCBonds attribute) first_line_re (schrodinger.application.jaguar.textparser.TextParser attribute) first_property() (in module schrodinger.application.matsci.genetic_optimization) FIRST_SEP (schrodinger.application.matsci.rxn_channel.ChannelDefinition attribute) firstNode() (schrodinger.ui.qt.network_visualizer.ConnectionValidator method) fit() (schrodinger.application.matsci.mlearn.base.BaseFeaturizer method) FIT_ESP_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab attribute) fit_plane_to_points() (in module schrodinger.structutils.measure) fit_plane_to_points_as_list() (in module schrodinger.structutils.measure) fit_points_to_circle() (in module schrodinger.application.matsci.geometry) FIT_SELECTED_ATOMS (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) fit_structure_to_ellipsoid() (in module schrodinger.application.matsci.geometry) fit_to_structure() (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) fitCellsToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fitColumnsToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fitColumnToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) FitError fitLine() (schrodinger.ui.qt.schart.SeriesData static method) fitMsd() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase static method) fitness (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) fitRowsToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fitRowToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) FitTexture() (in module schrodinger.application.matsci.gsas.GSASIImath) fitToColumns() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fitToRows() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fix_all_metal_bond_orders() (in module schrodinger.application.matsci.buildcomplex) fix_and_validate_res_structure() (in module schrodinger.protein.nonstandard_residues) fix_cmd() (in module schrodinger.job.jobcontrol) fix_common_structure_mistakes() (in module schrodinger.application.prepwizard) fix_elements() (schrodinger.protein.assignment.ProtAssign method) fix_filenames() (schrodinger.application.desmond.cms.Cms method) fix_for_prime() (in module schrodinger.application.prime.primefix) fix_formal_charge() (in module schrodinger.application.prime.primefix) fix_free_volume_coordinates() (in module schrodinger.application.matsci.freevolume) fix_idx_traj_path() (in module schrodinger.application.desmond.cms) fix_jaguar_file_links() (in module schrodinger.application.matsci.jaguarworkflows) fix_linear_angles() (in module schrodinger.application.matsci.coarsegrain) fix_metal_bond_orders() (in module schrodinger.application.matsci.buildcomplex) fix_metal_bonding() (in module schrodinger.application.matsci.nano.xtal) fix_N4s() (schrodinger.structutils.assignbondorders.AssignBondOrders method) FIX_SITE_KEYWORDS (schrodinger.application.matsci.kmc.SchrodingerTable attribute) fix_splitter() (in module schrodinger.ui.qt.filedialog) fix_sulfur_charges() (in module schrodinger.application.prepwizard) fixAll() (schrodinger.application.prime.primefix.FixForPrime method) fixDiameter() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) fixDisconnectedDonors() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) fixDNACaps() (schrodinger.application.prime.primefix.FixForPrime method) FIXED (schrodinger.application.matsci.packmol.PackmolKw attribute) fixed_bundle_size_999() (in module schrodinger.seam.testing.fixtures) FIXED_VALUE (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) FixedSample (class in schrodinger.seam.transforms.partitioners) FixedSizeRDMolImageLabel (class in schrodinger.ui.qt.rdmol_views) fixFormalCharge() (schrodinger.structutils.assignbondorders.AssignBondOrders method) FixForPrime (class in schrodinger.application.prime.primefix) fixheavy (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) fixheavyChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) fixheavyReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) fixHets() (schrodinger.application.prime.primefix.FixForPrime method) fixHydrogens() (schrodinger.application.matsci.enumeration.ElementAlchemist method) fixKetones() (schrodinger.structutils.assignbondorders.AssignBondOrders method) fixLegend() (schrodinger.ui.qt.schart.SHistogramBarSet method) fixLocations() (schrodinger.application.matsci.sculptcomplex.Sculptor method) fixMetals() (schrodinger.application.prime.primefix.FixForPrime method) fixMono() (in module schrodinger.application.matsci.gsas.GSASIIspc) fixPdbresAndPdbnames() (schrodinger.application.prime.primefix.FixForPrime method) fixRibbons() (schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin method) fixRingSpears() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) fixSize() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fixSolute() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) fixSpecialResidues() (schrodinger.application.prime.primefix.FixForPrime method) fixup() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.FrameIntValidator method) fixup_duplicate_properties() (in module schrodinger.application.desmond.struc) FixValence() (in module schrodinger.application.matsci.gsas.GSASIIElem) FIZZLED (schrodinger.application.desmond.cmj.JobStatus attribute) flag (schrodinger.application.matsci.mlearn.features.MomentData attribute) FLAG_ABBE_NUMBER_WAVELENGTH (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) FLAG_COMPOSITION (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) flag_context_manager() (in module schrodinger.infra.util) FLAG_DATA_LAST_FRAC (schrodinger.application.matsci.permittivity.DipoleAnalysis attribute) FLAG_DENSITY (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) FLAG_ELEC_POLARIZABILITY (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) FLAG_ELECTRIC_POLAR (schrodinger.application.matsci.permittivity.CMSParser attribute) FLAG_JAGUAR_FINER_OPTIONS (schrodinger.application.matsci.permittivity.JaguarFinerCalculation attribute) FLAG_JAGUAR_OPTIONS (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) FLAG_MOLECULES (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) FLAG_MONOMER_CHARGE (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) FLAG_NORMALIZATION (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) FLAG_NUM_CRU (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) FLAG_PARALLEL (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) FLAG_POLYMER_CRU_NUM (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) FLAG_REFRACTIVE_INDEX_WAVELENGTH (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) FLAG_SLICE_INTVL (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) FLAG_TO_KEY (schrodinger.application.matsci.permittivity.MultiStageMd attribute) FlagCacheProxyMixin (class in schrodinger.ui.qt.table_speed_up) FLAGS (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.VoidStep attribute) flags() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.livedesign.panel_components.EndpointSelectionModel method) (schrodinger.application.livedesign.panel_components.ExportTableModel method) (schrodinger.application.livedesign.panel_components.LDSelectionModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.recent_completer.SeparatorStringModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) (schrodinger.ui.qt.table_speed_up.FlagCacheProxyMixin method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) FLAGS_ADD_DOUBLE_DASH (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) FLAGS_ADD_INPUT_NAME (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) FLAGS_ADD_JOB_NAME (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) FLAGS_ADD_TPP (schrodinger.application.matsci.jwsteps.BaseMetaJaguarWorkflowStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) FLAGS_INPUT_NAME_FLAG (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) flat_enumerator() (in module schrodinger.application.scaffold_enumeration.layered) flat_list_enumerator() (in module schrodinger.application.scaffold_enumeration.layered) FlatButton (class in schrodinger.ui.qt.standard_widgets.buttons) flatten() (in module schrodinger.application.matsci.msutils) (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis class method) flatten_list() (in module schrodinger.application.bioluminate.surfcomp) flatten_sibling_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) flattenChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions static method) flattenWithoutDict() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) FlattenWithSlowCoder (class in schrodinger.seam.testing.benchmarks) flex_align_args (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) flex_align_argsChanged (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) flex_align_argsReplaced (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) FlexAlignTask (class in schrodinger.application.livedesign.tasks) FlexAlignTask.Input (class in schrodinger.application.livedesign.tasks) FlexAlignTask.Output (class in schrodinger.application.livedesign.tasks) flexdist (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) flexdistChanged (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) flexdistReplaced (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) FLEXHILLS_INTERVAL (schrodinger.application.desmond.kinetics.enhanced_sampling.MtdOption attribute) FLEXIBLE (schrodinger.application.desmond.constants.IsotropyPolicy attribute) (schrodinger.application.desmond.constants.Schedule attribute) flip_isomer() (in module schrodinger.protein.nonstandard_residues) flip_ring_conformation() (in module schrodinger.application.jaguar.utils) flipDirection() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) flipHorizontal() (schrodinger.ui.two_d_viewer.TwoDViewer method) flipTailFirst() (schrodinger.application.matsci.amorphous.Monomer method) flipVertical() (schrodinger.ui.two_d_viewer.TwoDViewer method) Flnh() (in module schrodinger.application.matsci.gsas.GSASIIlattice) FLOAT (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute) float() (schrodinger.ui.qt.swidgets.SLineEdit method) FLOAT_BASE (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor attribute) FLOAT_FIELDS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) FLOAT_PROP_PREFIX (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) float_valid() (schrodinger.ui.qt.formlayout.FormDialog method) FLOATABLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) floatChange() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) FloatParam (class in schrodinger.models.parameters) floatValue() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) (schrodinger.ui.qt.swidgets.SLabeledSlider method) FlorySchulzDistribution (class in schrodinger.application.matsci.amorphous) fluc_ct (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) flush() (schrodinger.ui.qt.appframework2.debugcore.DebugStderr class method) (schrodinger.ui.qt.appframework2.debugcore.DebugStdout class method) fmin() (in module schrodinger.application.jaguar.qrnn.temp_opt) fmin_bfgs() (in module schrodinger.application.jaguar.qrnn.temp_opt) fmin_cg() (in module schrodinger.application.jaguar.qrnn.temp_opt) fmin_ncg() (in module schrodinger.application.jaguar.qrnn.temp_opt) fmin_powell() (in module schrodinger.application.jaguar.qrnn.temp_opt) fminbound() (in module schrodinger.application.jaguar.qrnn.temp_opt) focusFinder() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) focusInEvent() (schrodinger.application.livedesign.panel_components.AddNewLineEdit method) (schrodinger.ui.qt.pop_up_widgets.LineEditWithPopUp method) focusOutEvent() (schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets.PlotTitleLineEdit method) (schrodinger.ui.qt.swidgets.EditWithFocusOutEvent method) fod_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) Folder (schrodinger.application.livedesign.panel_components.LRSort attribute) FOLDING (schrodinger.application.desmond.constants.PhysicalLegTypes attribute) FOLLOW_45_in_static244 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_46_in_decl_output296 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_47_in_decl_meta349 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_48_in_meta_term592 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_48_in_output_term404 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_49_in_meta_term664 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_49_in_output_term476 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_meta_term681 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_meta_term745 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_meta_term809 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_output_term493 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_output_term557 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_51_in_meta_term724 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_51_in_output_term536 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_52_in_meta_term786 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_53_in_meta_term852 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_54_in_meta_term922 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_55_in_series1392 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_56_in_if_1436 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_57_in_if_1442 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_58_in_if_1448 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_ADDOP_in_signedExpComp1111 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_atom_in_comp1149 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_BCLOSE_in_comp1158 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_bind_in_exprOrBind1017 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_block_in_atom1379 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_block_in_prog160 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_BOPEN_in_comp1152 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_CCLOSE_in_atom1381 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COLON_in_iter1484 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_decl_meta358 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_decl_output305 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_fcnCall1192 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_series1401 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_static251 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_comp_in_expComp1129 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COPEN_in_atom1376 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_decl_in_header191 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_decl_meta_in_decl222 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_decl_output_in_decl226 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EOF_in_prog162 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_bind1029 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_iter1478 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term600 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term671 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term728 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term792 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term855 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term927 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_output_term412 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_output_term483 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_output_term540 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EXP_in_expComp1132 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expComp_in_signedExpComp1121 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_atom1354 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_bind1033 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_comp1156 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_exprOrBind1013 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_fcnCall1189 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_fcnCall1195 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_if_1440 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_if_1446 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_if_1452 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_iter1482 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_iter1488 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_series1413 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_exprOrBind_in_block980 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_exprOrBind_in_block987 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_factor_in_expr1057 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_factor_in_expr1070 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_fcnCall_in_atom1267 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_header_in_prog158 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_atom1304 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_bind1027 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_fcnCall1182 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_iter1476 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_varWithType272 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_if__in_atom1248 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_iter_in_series1398 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_iter_in_series1405 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_atom1332 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_meta_term687 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_meta_term751 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_meta_term815 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_meta_term869 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_output_term499 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_output_term563 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_varWithType276 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_meta_term_in_decl_meta355 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_meta_term_in_decl_meta362 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_output_term_in_decl_output302 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_output_term_in_decl_output309 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_atom1356 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_decl_meta366 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_decl_output313 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_fcnCall1201 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_series1409 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_varWithType278 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_atom1351 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_decl_meta351 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_decl_output298 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_fcnCall1185 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_series1394 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_varWithType274 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SEMI_in_block983 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SEMI_in_block991 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SEMI_in_header193 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_series_in_atom1229 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_set_in_expr1061 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_set_in_factor1086 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_signedExpComp_in_expComp1135 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_signedExpComp_in_factor1081 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_signedExpComp_in_factor1096 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_static_in_decl230 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_STRING_in_atom1286 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_STRING_in_meta_term614 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_STRING_in_meta_term941 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_STRING_in_output_term426 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SUBTROP_in_meta_term675 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SUBTROP_in_output_term487 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SUBTROP_in_signedExpComp1116 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_varWithType_in_static248 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_varWithType_in_static255 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FONT (schrodinger.ui.qt.delegates.DefaultMessageDelegate attribute) font_is_installed() (in module schrodinger.ui.qt.formlayout) font_role() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) FontLayout (class in schrodinger.ui.qt.formlayout) FontSizes (class in schrodinger.ui.qt.standard.design_tokens) FontStyles (class in schrodinger.application.phase.phase_markers) FontWeights (class in schrodinger.ui.qt.standard.design_tokens) Footer (class in schrodinger.application.matsci.reportutils) FOOTER (schrodinger.application.desmond.kinetics.enhanced_sampling.MExpressionSection attribute) FOOTERS (schrodinger.application.matsci.reportutils.CanvasWithHeaderAndFooter attribute) FORBIDDEN_TO_MATCH (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) force_constant_precision (schrodinger.application.jaguar.results.NormalMode attribute) force_copy2() (in module schrodinger.utils.fileutils) force_dummy_missing_product_imports() (in module schrodinger.infra.unusable_module_importer) force_field (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) force_field_name_to_file_name() (in module schrodinger.application.matsci.cgforcefield) force_fieldChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) force_fieldReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) force_list (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) force_listChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) force_listReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) force_remove() (in module schrodinger.utils.fileutils) force_rename() (in module schrodinger.utils.fileutils) force_rmtree() (in module schrodinger.utils.fileutils) force_rmtree_resist_nfs() (in module schrodinger.application.matsci.msutils) FORCED_ACCEPTOR_PKA_SHIFT (schrodinger.protein.assignment.HistidinepKaPredictor attribute) ForceField (class in schrodinger.application.matsci.cgforcefield) Forcefield (class in schrodinger.application.matsci.msutils) forcefield (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) FORCEFIELD (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox attribute) ForcefieldBuilder (class in schrodinger.application.desmond.stage.deprecate) ForcefieldBuilderLauncher (class in schrodinger.application.desmond.stage.prepare.forcefield) forceFieldChanged (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector attribute) forceFieldChanged() (schrodinger.application.matsci.chargegui.FFInfo method) ForceFieldDialog (class in schrodinger.application.matsci.chargegui) forcefieldOptionChanged (schrodinger.ui.qt.forcefield.ffselector.MaestroForceFieldSelector attribute) ForceFieldOptions (class in schrodinger.forcefield.ffld_options) ForceFieldSelector (class in schrodinger.ui.qt.forcefield.ffselector) ForceFieldSelectorUi (class in schrodinger.ui.qt.forcefield.ffselector) forceIndexReassignment() (schrodinger.protein.annotation.AbstractRegionFinder method) forces (schrodinger.application.jaguar.results.JaguarResults property) forces() (in module schrodinger.application.jaguar.textparser) FORCES_KEY (schrodinger.application.matsci.espresso.qeinput.ControlType attribute) forces_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) forceSetChecked() (schrodinger.ui.qt.swidgets.SCheckBox method) forceSetText() (schrodinger.ui.qt.swidgets.LineEditWithDisabledText method) ForEachDo (class in schrodinger.application.desmond.arkdb) forEdgeInRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) FOREGROUND (schrodinger.ui.qt.delegates.DefaultMessageDelegate attribute) foreground_role() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) forgetMessageBoxResponse() (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) forgetResponse() (schrodinger.ui.qt.messagebox.MessageBox method) ForkStep (class in schrodinger.stepper.sideinputs) form_jaguar_cpu_flags() (in module schrodinger.ui.qt.config_dialog) form_set_val_string() (in module schrodinger.application.matsci.kmc) formal_charge (schrodinger.structure.Structure property) (schrodinger.structure.StructureAtom property) FORMALCHARGED (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) formASL() (schrodinger.application.bioluminate.pml_menus.RegionInfo method) Format (class in schrodinger.application.phase.packages.conformer_storage) (class in schrodinger.livedesign.draw) (class in schrodinger.rdkit_extensions) format() (in module schrodinger.application.jaguar.check_headers) (schrodinger.analysis.enrichment.calculator.Calculator static method) (schrodinger.application.hitexpander.LogFormatter method) (schrodinger.application.matsci.textlogger.GetLogger.MyFormatter method) (schrodinger.stepper.stepper.ElapsedFormatter method) format_alignment_ids() (in module schrodinger.application.matsci.nano.particle) format_charge() (in module schrodinger.application.ligprep.ionizer) format_description() (in module schrodinger.application.licensing.licserver.main) FORMAT_END (schrodinger.application.matsci.cg_mapping.CoarseGrainBond attribute) format_host() (in module schrodinger.application.livedesign.login) format_human_time() (in module schrodinger.application.glide.utils) format_info() (in module schrodinger.application.matsci.typography) format_isotope_latex() (in module schrodinger.application.jaguar.simple_spec) format_json() (in module schrodinger.utils.featureflags.write) format_list_to_filter_string() (in module schrodinger.ui.qt.input_selector) format_numbered_message() (in module schrodinger.application.livedesign.entry_types) format_option_strings() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method) format_pressure() (in module schrodinger.application.matsci.jaguarworkflows) format_row() (in module schrodinger.application.glide.utils) format_species_display_name() (in module schrodinger.application.matsci.species) FORMAT_START (schrodinger.application.matsci.cg_mapping.CoarseGrainBond attribute) format_structure_label() (in module schrodinger.application.desmond.feputils) format_temperature() (in module schrodinger.application.matsci.jaguarworkflows) format_time() (in module schrodinger.application.jaguar.utils) format_tooltip() (in module schrodinger.application.matsci.gutils) format_usage_row() (in module schrodinger.application.licensing.lmgrd_log_parser) FormatError formatFloat() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) FormatInpFile() (schrodinger.application.livedesign.tasks.GlideTask method) formatLoopTable() (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportWriter method) formatParticleLabel() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond static method) FORMATS (schrodinger.application.matsci.textlogger.GetLogger.MyFormatter attribute) formatTime() (schrodinger.application.jaguar.gui.timing.TimingResults method) FormComboWidget (class in schrodinger.ui.qt.formlayout) formCommand() (schrodinger.utils.installation_check.TestJob method) FormDialog (class in schrodinger.ui.qt.formlayout) FormHashes (class in schrodinger.application.desmond.struc) formJaguarCPUFlags() (schrodinger.ui.qt.config_dialog.StartDialogParams method) formLine() (schrodinger.application.matsci.desconfig.ConcatMSJStringer method) (schrodinger.application.matsci.desconfig.MSJStringer method) FormMols (class in schrodinger.application.desmond.struc) FormTabWidget (class in schrodinger.ui.qt.formlayout) formula (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) formula_res (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) FormWidget (class in schrodinger.ui.qt.formlayout) fortfloat() (in module schrodinger.application.mopac.results_main) FORWARD (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Direction attribute) ForwardAnalyzer (class in schrodinger.application.pathfinder.analysis) ForwardRGMolSupplier (class in schrodinger.livedesign.rgfile_parse) Fourier4DMap() (in module schrodinger.application.matsci.gsas.GSASIImath) FourierMap() (in module schrodinger.application.matsci.gsas.GSASIImath) FP_CLASSES (schrodinger.application.matsci.cgforcefield.ForceField attribute) FP_EXT (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) FP_TEXT_FILE (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) fp_type (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) fp_typeChanged (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) fp_typeReplaced (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) fp_types() (in module schrodinger.application.hitexpander) FPcalc() (in module schrodinger.application.matsci.gsas.GSASIIElem) FPsimSearcher (class in schrodinger.application.fpsim) FPTypeCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) fracCrenel() (in module schrodinger.application.matsci.gsas.GSASIImath) fracFourier() (in module schrodinger.application.matsci.gsas.GSASIImath) FractionAromatic() (in module schrodinger.rdkit.filtering) FRAG (schrodinger.application.matsci.kmc.AtomsTable attribute) frag_handle (schrodinger.application.combiglide.corehop.SubstCoreDatabase attribute) FRAG_ID (schrodinger.application.bioluminate.pose_filtering.hdx_calc.AnalysisColumns attribute) frag_is_smaller() (in module schrodinger.livedesign.preprocessor) Fragment (class in schrodinger.application.ligprep.ionizer) (class in schrodinger.application.matsci.fragments) (class in schrodinger.application.transforms.enumerators) FRAGMENT (schrodinger.application.desmond.constants.FepLegTypes attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) FRAGMENT_HYDRATION (schrodinger.application.desmond.constants.FepLegTypes attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) FRAGMENT_LINKING (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) fragment_mutator() (in module schrodinger.application.matsci.genetic_optimization) FRAGMENT_NAME (schrodinger.application.matsci.nano.constants.Constants attribute) FRAGMENT_SOLVATION (schrodinger.application.desmond.constants.CorrectionTerm attribute) fragment_to_molecule() (in module schrodinger.application.steps.utils) FragmentCreator (class in schrodinger.structutils.createfragments) fragmentIDs (schrodinger.structutils.markush_enumerate.Scaffold property) FragmentLibrary (class in schrodinger.utils.cgxutils) FragmentLinkingPrimer (class in schrodinger.application.desmond.stage.app.fragment_linking.stage) FragmentReactor (class in schrodinger.application.matsci.fragments) FragmentReader (class in schrodinger.structutils.markush_enumerate) fragments() (schrodinger.application.matsci.amorphous.PolymerFragment method) FragmentsIterator (class in schrodinger.structutils.markush_enumerate) FragmentsTable (class in schrodinger.application.matsci.kmc) fragmentStructure() (schrodinger.structutils.createfragments.FragmentCreator method) fragmentStructureForEA() (schrodinger.structutils.createfragments.FragmentCreator method) FragmentVSStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) FRAME (schrodinger.application.matsci.kmc.Table attribute) frame_count (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) FRAME_DURATION_STEP (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) frame_number (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameListItem property) FRAME_SETTINGS_DICT (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) frameDurationChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) FrameIntValidator (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings) FrameListItem (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_panel) frameOptionChanged() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) FrameRangeValidator (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_panel) frames_list (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) FrameSpinBox (class in schrodinger.application.matsci.deswidgets) FramesTable (class in schrodinger.application.matsci.kmc) FrameStructureExporter (class in schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter) FrameworkModel (class in schrodinger.application.bioluminate.antibody.search_results_table) FrameworkTemplate (class in schrodinger.application.bioluminate.antibody.utils) free_energy() (in module schrodinger.application.xtb.textparser) free_energy_costs() (in module schrodinger.application.ligprep.ionizer) freeAll() (schrodinger.application.matsci.zmutils.ZAtom method) freeAtom() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomAngle() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomBond() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomDihedral() (schrodinger.application.matsci.zmutils.ZMatrix method) freeCachedEntries() (schrodinger.project.project.Project method) freeCoord() (schrodinger.application.matsci.zmutils.ZAtom method) FreeEnergy (class in schrodinger.application.jaguar.utils) FreeEnergyContrib (class in schrodinger.application.desmond.fepana) FreePositionsType (class in schrodinger.application.matsci.espresso.qeinput) FreePositionsType.PWallType (class in schrodinger.application.matsci.espresso.qeinput) FreeVolumeDriver (class in schrodinger.application.matsci.freevolume) FreeVolumeException FreeVolumeStep (class in schrodinger.application.matsci.jwsteps) freeze_atom() (in module schrodinger.application.desmond.remd) freeze_atoms() (in module schrodinger.application.desmond.predict_remd_temp) freeze_existing_hydrogens() (schrodinger.protein.assignment.ProtAssign method) FREQ_KEY (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) FREQ_TITLE (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) freq_to_angular_freq() (in module schrodinger.application.matsci.anharmonic) frequencies() (in module schrodinger.application.jaguar.textparser) frequencies_old() (in module schrodinger.application.jaguar.textparser) frequency (schrodinger.application.matsci.bandshape_utils.NormalMode attribute) frequency_precision (schrodinger.application.jaguar.results.NormalMode attribute) freshenParentAndChildIndexes() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) from_anarci_resinfo() (schrodinger.application.bioluminate.classify.NumberedResidue class method) from_anarci_tuple() (schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo static method) from_atom_indices() (schrodinger.forcefield.minimizer.Restraint class method) from_CA_index() (schrodinger.ui.qt.rama.BackboneDihedral class method) from_deformation() (schrodinger.application.matsci.elasticity.strain.Strain class method) from_dict() (in module schrodinger.application.matsci.mlearn.sklearn_json) (schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams class method) (schrodinger.application.matsci.wfmanagement.WorkflowMetadata class method) (schrodinger.job.server.ServerInfo class method) from_domain_result() (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult class method) from_end (schrodinger.protein.sequence.GapRegion attribute) from_family_data_dict() (schrodinger.application.bioluminate.tcr.docking_angles.TcrChainIds class method) from_idx (schrodinger.application.matsci.reaction_workflow_utils.Site attribute) from_independent_strains() (schrodinger.application.matsci.elasticity.elastic.ElasticTensor class method) from_index_amount() (schrodinger.application.matsci.elasticity.strain.Deformation class method) (schrodinger.application.matsci.elasticity.strain.Strain class method) from_initial_population() (in module schrodinger.application.matsci.genetic_optimization) from_json() (in module schrodinger.application.matsci.mlearn.sklearn_json) from_list() (schrodinger.infra.mmbitset.Bitset class method) from_maestro() (in module schrodinger.protein.getpdb_utility) from_pymatgen_structure() (in module schrodinger.application.matsci.pmgutils) from_rdkit() (in module schrodinger.rdkit.rdkit_adapter) from_res_3l (schrodinger.application.bioluminate.mutation.Mutation attribute) from_residue() (schrodinger.ui.qt.rama.BackboneDihedral class method) (schrodinger.ui.qt.rama.RamaResidueType class method) from_start (schrodinger.protein.sequence.GapRegion attribute) from_string() (schrodinger.application.desmond.measurement.Measurement class method) from_style (schrodinger.structure.StructureBond property) from_values_indices() (schrodinger.application.matsci.elasticity.tensors.Tensor class method) from_voigt() (schrodinger.application.matsci.elasticity.tensors.Tensor class method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection class method) from_yaml() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) fromAnarciChainResultAndSeq() (schrodinger.application.bioluminate.classify.ProteinClass class method) fromAnarciDomainResult() (schrodinger.application.bioluminate.classify.ProteinClass class method) fromArgs() (schrodinger.application.glide.sort_utils.GlideSortUtility class method) fromArgv() (in module schrodinger.infra.ark) fromAtom() (schrodinger.application.matsci.espresso.qeoutput.MagresAtom class method) fromClustalFile() (schrodinger.protein.alignment.ProteinAlignment class method) fromConfig() (schrodinger.livedesign.preprocessor.PreprocessorOptions static method) fromData() (schrodinger.application.matsci.nano.space_groups.SpaceGroup class method) fromDict() (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction class method) (schrodinger.application.phase.packages.shape_generator.SerializableShapeGenerator method) fromDirectory() (schrodinger.seam.viz.watcherd.Watcher class method) fromEtotString() (schrodinger.application.jaguar.results.ScfIteration static method) fromFastaFile() (schrodinger.protein.alignment.ProteinAlignment class method) fromFastaString() (schrodinger.protein.alignment.ProteinAlignment class method) fromFastaStringList() (schrodinger.protein.alignment.ProteinAlignment class method) fromFile() (schrodinger.application.matsci.espresso.qeoutput.Magres class method) (schrodinger.application.matsci.espresso.qeoutput.PhDOSTensors class method) FromFile() (schrodinger.application.transforms.ligprep.LigandPrep class method) fromFile() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter class method) FromFilterFile() (schrodinger.application.transforms.filters.ProductFilter class method) fromIterable() (schrodinger.utils.scollections.DefaultIdDict class method) (schrodinger.utils.scollections.IdDict class method) (schrodinger.utils.scollections.IdSet class method) fromJagin() (schrodinger.application.matsci.zmutils.ZAtom class method) fromJobControlHost() (schrodinger.tasks.hosts.Host class method) fromJobObject() (schrodinger.application.job_monitor.job_monitor_models.JobModel static method) fromJson() (schrodinger.application.glide.http_client.GlideResult class method) fromJSON() (schrodinger.job.launchapi.JobSpecification static method) (schrodinger.job.launchapi.TaskSpecification static method) fromJson() (schrodinger.models.json.JsonableClassMixin class method) fromJSON() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter class method) fromJsonData() (schrodinger.application.matsci.freevolume.JsonObject class method) fromJsonFilename() (schrodinger.tasks.tasks.AbstractTask class method) fromJsonImplementation() (schrodinger.application.bioluminate.pose_filtering.residue_filter.BaseResidueFilter class method) (schrodinger.application.livedesign.data_classes.LDData class method) (schrodinger.application.livedesign.export_models.JsonablePropertyName class method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel class method) (schrodinger.application.livedesign.panel_components.BaseLDTreeItemWrapper class method) (schrodinger.application.livedesign.panel_components.ExportRow class method) (schrodinger.application.livedesign.panel_components.ExportTableModel class method) (schrodinger.application.prepwizard.JsonableHetStates class method) (schrodinger.models.json.JsonableClassMixin class method) (schrodinger.models.jsonable.JsonableBytes class method) (schrodinger.models.jsonable.JsonableEnum class method) (schrodinger.models.jsonable.JsonableIntEnum class method) (schrodinger.models.jsonable.JsonableSet class method) (schrodinger.models.jsonable.JsonableStructure class method) (schrodinger.models.jsonable.JsonableTuple class method) (schrodinger.models.parameters.CompoundParam class method) (schrodinger.protein.alignment.ProteinAlignment class method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES class method) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES class method) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES class method) (schrodinger.protein.residue.Gap class method) (schrodinger.protein.residue.Residue class method) (schrodinger.protein.sequence.ProteinSequence class method) (schrodinger.protein.tasks.blast.BlastSettings class method) (schrodinger.protein.tasks.blast.BlastTask.Input class method) (schrodinger.seam.metric.ExecutionMetrics class method) (schrodinger.seam.runners.events.SeamEvent class method) (schrodinger.tasks.hosts.Gpu class method) (schrodinger.tasks.hosts.Host class method) (schrodinger.tasks.jobtasks.HostSettings class method) fromList() (schrodinger.application.matsci.espresso.qeoutput.MagresAtom class method) fromPHDOS() (schrodinger.application.matsci.espresso.qeoutput.PhDOS class method) fromProteinSequence() (schrodinger.livedesign.biologics.sequence.AlignedSequence static method) fromRdkitStatus() (schrodinger.rdkit.rdkit_adapter.RdkitLoggerstate class method) fromScaffoldMatch() (schrodinger.application.bioluminate.antibody.grafting.GraftingInput class method) fromSeqDict() (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput class method) fromSequence() (schrodinger.application.bioluminate.classify.ProteinClass class method) fromSmartsError() (schrodinger.application.canvas.r_group.RGroupException class method) fromSPM() (schrodinger.application.matsci.espresso.qeoutput.PhDOS class method) fromString() (in module schrodinger.infra.ark) (schrodinger.application.jaguar.utils.GenOptions static method) (schrodinger.application.steps.dataclasses.MolToSmilesSerializer method) (schrodinger.application.steps.dataclasses.ScoredMolSerializer method) (schrodinger.application.steps.enumerators.RouteSerializer method) (schrodinger.stepper.stepper.Serializer method) (schrodinger.structure.StructureReader static method) fromStructure() (schrodinger.application.matsci.espresso.qeoutput.Magres class method) (schrodinger.application.matsci.espresso.utils.MagSpecies method) (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.protein.alignment.ProteinAlignment class method) fromText() (schrodinger.application.jaguar.gui.input_tab_widgets.Basis class method) fromVIB() (schrodinger.application.matsci.espresso.qeoutput.PhDOS class method) front_transparency (schrodinger.surface.Surface property) FROZEN_PHONON_CORR (schrodinger.application.matsci.desconfig.MSJStringer attribute) FrozenPhononCorrection (class in schrodinger.application.desmond.stage.app.matsci) FrozenPhononStringer (class in schrodinger.application.matsci.desconfig) frozenset_cached_property (class in schrodinger.application.matsci.cache) FrozenStep (class in schrodinger.application.matsci.jaguarworkflows) fruchterman_reingold_layout() (in module schrodinger.ui.qt.network_visualizer) FSCALE (schrodinger.application.matsci.packmol.PackmolKw attribute) fst_copy() (in module schrodinger.application.matsci.enc) fukui_indices() (in module schrodinger.application.jaguar.textparser) FukuiIndices (class in schrodinger.application.jaguar.results) FULL (schrodinger.livedesign.preprocessor.GenerateCoordinates attribute) FULL_ALIGNED (schrodinger.livedesign.preprocessor.GenerateCoordinates attribute) FULL_HERMANN_MAUGUIN_SYMBOL (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) FULL_MOVIE (schrodinger.trajectory.trajectory_gui_dir.export_movie.DurationType attribute) FULL_MOVIE_MAX_VALUE (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) FULL_MOVIE_MIN_VALUE (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) FULL_NAME_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) full_summary_string() (schrodinger.application.jaguar.simple_spec.Peak method) FullColumns (class in schrodinger.application.bioluminate.antibody.search_results_table) fullname (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo property) (schrodinger.application.desmond.new_fep_edge_data.ResData property) (schrodinger.project.project.Project property) (schrodinger.protein.sequence.AbstractSingleChainSequence property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) fullName() (schrodinger.application.desmond.fep_edge_data.ResData method) FullProxyModel (class in schrodinger.application.bioluminate.antibody.search_results_table) fullsystem_ct (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property) FullTable (class in schrodinger.application.bioluminate.antibody.search_results_table) FULLY_ANALYTIC_ACCURACY (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) fully_conserved (schrodinger.protein.annotation.Consensus attribute) FULLY_REL (schrodinger.application.matsci.espresso.utils.UPFParser attribute) FULLY_RESTRAINED (schrodinger.application.desmond.constants.DRUDE_INVERSE_FORCE_CONSTANT_SCALING attribute) func (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) func() (in module schrodinger.application.mopac.results_main) funcbottom() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) FuncChainMarker (class in schrodinger.utils.funcchains) FuncChainMixin (class in schrodinger.utils.funcchains) FuncData (class in schrodinger.utils.funcgroups) FuncGroupMarker (class in schrodinger.utils.funcgroups) FuncGroupMixin (class in schrodinger.utils.funcgroups) funchspace() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) funcleft() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) funcright() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) FUNCTION (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwType attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) function (schrodinger.application.matsci.kmcgui.PlotInfo attribute) functional() (in module schrodinger.application.jaguar.textparser) functop() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) funcwspace() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) further_annotate_ligand_atoms() (in module schrodinger.protein.assignment) fused_ring_nonbond_iterator() (in module schrodinger.application.matsci.coarsegrain) FusedRing (class in schrodinger.application.matsci.coarsegrain) fuseIonFragment() (schrodinger.application.ligprep.ionizer.Ionizer method) fuzzy_aromatic_matching (schrodinger.rdkit.substructure.QueryOptions attribute) FV (schrodinger.livedesign.entity_type.EntityClass attribute) FVAL_DICT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVAL_KEYS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVAL_VALUES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVALINCREMENT (schrodinger.application.matsci.rxn_path.ReactionPath attribute)

G

G2Print() (in module schrodinger.application.matsci.gsas.GSASIIfiles) G2printLevel (in module schrodinger.application.matsci.gsas.GSASIIfiles) G2SetPrintLevel() (in module schrodinger.application.matsci.gsas.GSASIIfiles) g_reuss (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) g_voigt (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) g_vrh (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) GAMMA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) GAMMA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) GAMMA_ONLY_KEY (schrodinger.application.matsci.espresso.qeinput.BasisType attribute) GAMMA_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) gamma_polar() (in module schrodinger.application.jaguar.textparser) gamma_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute) Gap (class in schrodinger.protein.residue) gap_char (schrodinger.protein.sequence.AbstractSequence property) gap_extend_cost (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_extend_costChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_extend_costReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_open_cost (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_open_costChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_open_costReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_penalty (schrodinger.structutils.structalign.StructAlign property) gapless_idx_in_seq (schrodinger.protein.residue.AbstractSequenceElement property) GapRegion (class in schrodinger.protein.sequence) gas_phase() (in module schrodinger.application.jaguar.textparser) GATE_KEEPER (schrodinger.protein.annotation.KinaseFeatureLabel attribute) gather_rings() (in module schrodinger.structutils.interactions.pi) gatherAlnSets() (schrodinger.protein.alignment.BaseAlignment method) gaulegf() (in module schrodinger.application.matsci.gsas.GSASIImath) gaussian_delta() (in module schrodinger.application.matsci.espresso.qeoutput) GAUSSIAN_HEIGHT (schrodinger.application.desmond.kinetics.enhanced_sampling.MtdOption attribute) GaussianFilter (class in schrodinger.application.desmond.gaussian_filter) gbk_executor (schrodinger.seam.testing.benchmarks.GroupByKey property) GBL_FORCE (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) gcg (schrodinger.utils.fileutils.SeqFormat attribute) GCMC (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) gcmc (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) GCMC_INFO (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute) gcmc_solvent (schrodinger.application.desmond.struc.CompStruc attribute) GCMCCapable (class in schrodinger.application.desmond.stage.simulate) gdata() (schrodinger.ui.qt.network_visualizer.Node method) ge_export_items (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ge_export_itemsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ge_export_itemsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ge_file_format (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ge_file_formatChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ge_file_formatReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ge_task (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) gedge (schrodinger.ui.qt.network_visualizer.Edge property) GEExportItem (class in schrodinger.application.livedesign.export_models) gen (schrodinger.application.qsite.input.QSiteInput property) gen_alpha_helix_restraint() (in module schrodinger.application.desmond.cms) gen_charges_spins() (in module schrodinger.application.jaguar.textparser) gen_dE_files() (in module schrodinger.application.desmond.deltaE) gen_fastas() (in module schrodinger.application.bioluminate.epitope.psc_workflow) gen_faux_epitopes() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_file_list() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_jobname() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_mifs() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_names() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_normgrid_data() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) gen_protein_rmsf_image() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) gen_random_color() (in module schrodinger.application.combiglide.connection_storage) gen_replica() (in module schrodinger.application.desmond.config_utils) gen_resnums_and_inscodes() (in module schrodinger.protein.sequence) gen_restraint() (schrodinger.application.desmond.stage.utils.SystemBuilder static method) gen_sim_mat() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_temperature_for_solute_tempering() (in module schrodinger.application.desmond.config_utils) gen_test() (in module schrodinger.application.desmond.simulation_block_test) gen_xvals() (in module schrodinger.application.matsci.spectra) genAllJobs() (schrodinger.job.queue.BaseJob method) genAllPrereqs() (schrodinger.job.queue.BaseJob method) GenAtom() (in module schrodinger.application.matsci.gsas.GSASIIspc) Gene (class in schrodinger.application.bioluminate.update_germline_db.translate_db) GENERAL (schrodinger.ui.qt.rama.RamaResidueType attribute) GENERAL_VEC_1 (schrodinger.application.matsci.nano.xtal.Crystal attribute) GENERAL_VEC_2 (schrodinger.application.matsci.nano.xtal.Crystal attribute) GENERAL_VEC_3 (schrodinger.application.matsci.nano.xtal.Crystal attribute) GeneralContextSubMenu (class in schrodinger.application.bioluminate.pml_menus) GeneralIcons (class in schrodinger.ui.qt.standard.design_tokens) GeneralInfo (class in schrodinger.application.licensing.licserver.client) generate() (in module schrodinger.application.desmond.starter.generator.constant_ph) (in module schrodinger.application.desmond.starter.generator.fep_absolute_binding) (in module schrodinger.application.desmond.starter.generator.fep_plus) (in module schrodinger.application.desmond.starter.generator.fep_residue_scanning) (in module schrodinger.application.desmond.starter.generator.fep_solubility) (in module schrodinger.application.desmond.starter.generator.mxmd) (in module schrodinger.application.desmond.starter.generator.unbinding_kinetics) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.desmond.image_generator.ImageGenerator method) (schrodinger.application.desmond.mxmd.mxmd_system_builder.CosolventBoxGenerator method) Generate2DCoordinates (class in schrodinger.adapter) generate2dCoords() (schrodinger.ui.two_d_viewer.TwoDViewer method) generate3dConformation() (schrodinger.structure.Structure method) generate_3d_structure() (in module schrodinger.protein.process_enamine_db) generate_aligned_2d_ligand_pair() (in module schrodinger.application.desmond.report_helper) generate_all_keywords() (in module schrodinger.application.jaguar.autots_keywords) (in module schrodinger.application.jaguar.esol_keywords) (in module schrodinger.application.jaguar.hydrokinetic_keywords) (in module schrodinger.application.jaguar.macro_pka_keywords) (in module schrodinger.application.jaguar.qrnn.keywords) (in module schrodinger.application.jaguar.rotation_barriers_keywords) (in module schrodinger.application.jaguar.solvation_keywords) (in module schrodinger.application.xtb.keywords) generate_annotated_ct() (in module schrodinger.protein.assignment) generate_annotation() (in module schrodinger.application.prepwizard2.tasks) generate_asl() (in module schrodinger.structutils.analyze) generate_asl_for_atom_by_mode() (in module schrodinger.ui.qt.atomselector) generate_attributes() (schrodinger.application.jaguar.results.RoutineTimes method) generate_canonical_tautomer() (in module schrodinger.livedesign.preprocessor) generate_cms_file_from_entry() (in module schrodinger.trajectory.utils) generate_complex_msj() (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) generate_coordinates (schrodinger.application.steps.converters.MolToStructureConverter.Settings attribute) GENERATE_COORDINATES (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) generate_coordinates() (in module schrodinger.livedesign.preprocessor) generate_coordinatesChanged (schrodinger.application.steps.converters.MolToStructureConverter.Settings attribute) generate_coordinatesReplaced (schrodinger.application.steps.converters.MolToStructureConverter.Settings attribute) generate_core_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_criterion() (in module schrodinger.utils.ligfilter) generate_crystal_mates() (in module schrodinger.structutils.analyze) generate_curve() (in module schrodinger.application.matsci.spectra) generate_custom_res_names() (in module schrodinger.protein.nonstandard_residues) generate_default_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_dendrogram() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) generate_description() (in module schrodinger.application.jaguar.gui.basis_selector) generate_ffbuilder_options() (in module schrodinger.application.desmond.feputils) generate_fingerprints() (in module schrodinger.application.combinatorial_diversity.driver_utils) generate_fingerprints_from_csv() (in module schrodinger.application.combinatorial_diversity.driver_utils) generate_fingerprints_from_smi() (in module schrodinger.application.combinatorial_diversity.driver_utils) generate_hierarchial_key() (in module schrodinger.application.matsci.hdfutils) generate_hot_atoms_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_image() (in module schrodinger.livedesign.bbchem_endpoints) generate_job_name() (in module schrodinger.application.jaguar.gui.utils) generate_jobname() (schrodinger.application.desmond.starter.ui.cmdline.BaseArgs method) generate_keywords() (schrodinger.application.jaguar.autots_input.AutoTSInput static method) (schrodinger.application.jaguar.esol_input.EsolInput static method) (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput static method) (schrodinger.application.jaguar.macro_pka_input.MacroKaInput static method) (schrodinger.application.jaguar.qrnn.input.QRNNInput static method) (schrodinger.application.jaguar.rotation_barriers_input.RotationBarriersInput static method) (schrodinger.application.jaguar.solvation_input.SolvationInput static method) (schrodinger.application.jaguar.workflow_input.WorkflowInput static method) (schrodinger.application.xtb.input.XTBInput static method) generate_lid() (in module schrodinger.application.livedesign.lid) generate_ligand_2d_image() (in module schrodinger.application.desmond.report_helper) generate_ligand_2d_placeholder() (in module schrodinger.application.desmond.report_helper) generate_loop_ranges() (in module schrodinger.application.bioluminate.anarci.loop_ranges) generate_mae_file_with_unique_title() (in module schrodinger.active_learning.al_utils) generate_main_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator method) (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator method) (schrodinger.application.desmond.msj_generator.mxmd.MixedSolventMsjGenerator method) (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) generate_mapping_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_mates() (schrodinger.protein.assignment.ProtAssign method) generate_md_msj() (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator method) (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator method) (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) generate_membrane_msj() (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) generate_meta_cfg() (in module schrodinger.application.desmond.meta) generate_metal_and_ion_states() (in module schrodinger.application.prepwizard) generate_method() (in module schrodinger.models.parameters) generate_molecular_formula() (in module schrodinger.structutils.analyze) generate_mols() (in module schrodinger.application.pathfinder.multiroute) (schrodinger.application.pathfinder.multiroute.MultiRouteEnumerator method) generate_msj() (schrodinger.application.desmond.msj_generator.constant_ph.ConstantpHMsjGenerator method) generate_mutant_combinations() (in module schrodinger.application.bioluminate.mutation) generate_mutation_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_partial_charges() (in module schrodinger.forcefield.common) generate_phosphate_and_sulfur_states() (in module schrodinger.application.prepwizard) generate_pic_with_text() (in module schrodinger.ui.two_d_viewer) generate_picture() (schrodinger.ui.qt.structure2d.structure_item method) generate_postmortem() (in module schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) generate_preference_key() (in module schrodinger.ui.qt.appframework2.settings) generate_qimage_from_chmmol() (in module schrodinger.ui.qt.structure2d) generate_qimage_from_structure() (in module schrodinger.ui.qt.structure2d) generate_ramd_msj() (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) generate_records() (in module schrodinger.active_learning.mq_driver) (in module schrodinger.application.bioluminate.update_germline_db.translate_db) generate_residue_asl() (in module schrodinger.structutils.analyze) generate_residue_number_asl() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) generate_return_code_dict() (in module schrodinger.infra.mmcheck) generate_sar_analysis_image() (in module schrodinger.livedesign.bbchem_endpoints) generate_scripts() (in module schrodinger.application.desmond.fep_scholar_util) (in module schrodinger.application.desmond.feputils) generate_shape_gpu_fingerprints() (in module schrodinger.application.phase.packages.shape_diversity) generate_smarts() (in module schrodinger.structutils.analyze) generate_smarts_canvas() (in module schrodinger.structutils.analyze) generate_smiles() (in module schrodinger.application.matsci.msutils) (in module schrodinger.structutils.analyze) generate_solvation_msj() (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator method) generate_solvent_msj() (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator method) generate_states_settings (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) generate_states_settingsChanged (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) generate_states_settingsReplaced (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) generate_subjob_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator method) (schrodinger.application.desmond.msj_generator.mxmd.MixedSolventMsjGenerator method) generate_tautomer_code() (in module schrodinger.structutils.analyze) generate_tautomer_hash() (in module schrodinger.structutils.analyze) generate_unbind_msj() (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) generate_unique_group_name() (in module schrodinger.project.utils) generate_vacuum_msj() (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator method) generate_votca_database() (in module schrodinger.application.matsci.kmc) generate_watermap_pse() (in module schrodinger.application.livedesign.pse_helpers) generateAlignedStructure() (schrodinger.application.pathfinder.aligner.AlignedMolStructureGenerator method) generateAlignmentFile() (schrodinger.protein.predictors.AbstractPredictor method) generateBaseName() (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) generateBoundingRect() (schrodinger.ui.qt.schart.Callout method) generateCellForEntry() (schrodinger.ui.two_d_viewer.TwoDViewer method) generateCfg() (schrodinger.application.desmond.meta.Meta method) GenerateCoordinates (class in schrodinger.livedesign.preprocessor) generateCsvFile() (schrodinger.pipeline.stages.glide.DockingStage method) generateCSVTable() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) generateDM() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) generateExportFiles() (schrodinger.application.livedesign.export_tasks.Export2DTask method) (schrodinger.application.livedesign.export_tasks.Export3DTask method) (schrodinger.application.livedesign.export_tasks.ExportTask87 method) generateExtraInput() (schrodinger.application.matsci.genetic_optimization.AutoQSAR method) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) generateFingerprint() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) generateHtml() (schrodinger.application.report2d.Report2D method) (schrodinger.ui.two_d_viewer.TwoDViewer method) generateIdentitySubMatrix() (schrodinger.protein.align.BiopythonPairwiseAligner method) generateInputFile() (schrodinger.protein.predictors.AbstractPredictor method) (schrodinger.protein.predictors.AccproPredictor method) (schrodinger.protein.predictors.BetaproPredictor method) (schrodinger.protein.predictors.DiproPredictor method) (schrodinger.protein.predictors.DisproPredictor method) (schrodinger.protein.predictors.DomproPredictor method) (schrodinger.protein.predictors.SsproPredictor method) GenerateInterfaceSelection (class in schrodinger.application.bioluminate.pml_menus) generateJaguarInputForTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) generateJaguarStatus() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.StandardStatusMixin method) (schrodinger.application.jaguar.gui.base_panel.TaskStatusMixin method) GenerateLigandSelection (class in schrodinger.application.bioluminate.pml_menus) generateModelFile() (schrodinger.protein.predictors.AbstractPredictor method) GenerateMxmdBox (class in schrodinger.application.desmond.stage.app.mxmd) generateNeutralizedStates() (schrodinger.ui.two_d_viewer.TwoDViewer method) generateNeutralStateIfNeeded() (schrodinger.ui.two_d_viewer.Cell method) generatePdf() (schrodinger.application.report2d.Report2D method) (schrodinger.ui.two_d_viewer.TwoDViewer method) generatePicFromCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) generatePicture() (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.ui.qt.structtable.StructureReaderDelegate method) (schrodinger.ui.qt.structtable.StructureViewerDelegate method) (schrodinger.ui.qt.table.StructureDataViewerDelegate method) generatePictureHighlight() (schrodinger.application.desmond.fep_scholar_util.ScholarStructureItem method) generatePlotData() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) GeneratePropsStage (class in schrodinger.pipeline.stages.filtering) generateResidueMap() (schrodinger.protein.sequence.AbstractSingleChainSequence method) GenerateSelection (class in schrodinger.application.bioluminate.pml_menus) generateSeqProjectRows() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) generateSeqStructures() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) GenerateSolubilityFepStructures (class in schrodinger.application.desmond.stage.app.solubility) generateSpecs() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) generateStateCT() (schrodinger.application.ligprep.ionizer.Ionizer method) GenerateStatesInput (class in schrodinger.application.prepwizard2.tasks) GenerateStatesSettings (class in schrodinger.application.prepwizard2.tasks) GenerateStatesTask (class in schrodinger.application.prepwizard2.tasks) generateStatus() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.ui.qt.appframework2.af2.JobApp method) generateSubMatrix() (schrodinger.protein.align.BiopythonPairwiseAligner method) (schrodinger.protein.align.FamilyPairwiseAligner method) GenerateSubMenu (class in schrodinger.application.bioluminate.pml_menus) GenerateSurfResSelection (class in schrodinger.application.bioluminate.pml_menus) generateSymmetryEquiv() (schrodinger.application.matsci.nano.sheet.SymmetryEquiv method) GenerateSymmetryMates (class in schrodinger.application.bioluminate.pml_menus) generateXls() (schrodinger.application.report2d.Report2D method) GenericAngle (class in schrodinger.application.jaguar.hess_guess) GenericEntities (class in schrodinger.application.livedesign.entry_types) GenericEntityExportTask (class in schrodinger.application.livedesign.export_tasks) GenericType (class in schrodinger.application.matsci.espresso.qeinput) GenericViewerDelegate (class in schrodinger.ui.qt.table) genEtaRotamers() (schrodinger.application.matsci.reaction_workflow_utils.ConformationalSearchMixin static method) GeneticOptimization (class in schrodinger.application.matsci.genetic_optimization) genFileName() (schrodinger.pipeline.stage.Stage method) GenHBravais() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GenHKL() (in module schrodinger.application.matsci.gsas.GSASIIspc) GenHKLf() (in module schrodinger.application.matsci.gsas.GSASIIspc) GenHLaue() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GenMagOps() (in module schrodinger.application.matsci.gsas.GSASIIspc) genomes (schrodinger.protein.tasks.blast.BlastTask.Input attribute) genomesChanged (schrodinger.protein.tasks.blast.BlastTask.Input attribute) genomesReplaced (schrodinger.protein.tasks.blast.BlastTask.Input attribute) GenOptions (class in schrodinger.application.jaguar.utils) genOutputFileName() (schrodinger.pipeline.stage.Stage method) GenPfHKLs() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GenRepStructureForAbsoluteFep (class in schrodinger.application.desmond.process_fep_traj) GenRepStructureForFep (class in schrodinger.application.desmond.process_fep_traj) GenRepStructureForSublimationFep (class in schrodinger.application.desmond.process_fep_traj) gensec() (in module schrodinger.application.jaguar.textparser) GenSelectionSubMenu (class in schrodinger.application.bioluminate.pml_menus) GenSHCoeff() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GenSSHLaue() (in module schrodinger.application.matsci.gsas.GSASIIlattice) gensym() (schrodinger.application.desmond.enhsamp.Env method) GenSymMatesSubMenu (class in schrodinger.application.bioluminate.pml_menus) GEO_MAX_ITERS (schrodinger.application.jaguar.constants.FatalErrors attribute) geom() (schrodinger.application.macromodel.utils.ComUtil method) GEOM_AND_SETTINGS (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) GEOM_ONLY (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) GeomConstraint (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) geometry_read() (in module schrodinger.application.jaguar.textparser) geometry_scan_step() (in module schrodinger.application.jaguar.textparser) GEOMETRY_TO_CMDLINE (in module schrodinger.application.matsci.buildcomplex) GeometryOptMethod (class in schrodinger.forcefield.constants) GEOPT_CONV_CRITERIA (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) geopt_convcrit() (in module schrodinger.application.jaguar.textparser) geopt_geometry() (in module schrodinger.application.jaguar.textparser) geopt_nops_on() (in module schrodinger.application.jaguar.textparser) geopt_step_number() (in module schrodinger.application.jaguar.textparser) geopt_stuck1() (in module schrodinger.application.jaguar.textparser) geopt_stuck2() (in module schrodinger.application.jaguar.textparser) GermlineEntry (class in schrodinger.application.bioluminate.update_germline_db.translate_db) get() (in module schrodinger.application.desmond.envir) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.TokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) (schrodinger.application.desmond.arkdb.ArkDb method) (schrodinger.application.desmond.cmj.JobOutput method) (schrodinger.application.desmond.multisim.parser.Msj method) (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.job.jobcontrol.Job method) (schrodinger.structure._StructureAtomProperty method) (schrodinger.ui.qt.formlayout.FormComboWidget method) (schrodinger.ui.qt.formlayout.FormDialog method) (schrodinger.ui.qt.formlayout.FormTabWidget method) (schrodinger.ui.qt.formlayout.FormWidget method) (schrodinger.utils.preferences.Preferences method) get14EleEnergy() (schrodinger.structutils.minimize.Minimizer method) get14LJEnergy() (schrodinger.structutils.minimize.Minimizer method) get2dStructure() (schrodinger.structure.SmilesStructure method) get3DExportItems() (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask method) get3DExportSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) get3DIsomers() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) get3dStructure() (schrodinger.structure.SmilesStructure method) (schrodinger.structure.Structure method) get_2d_ligand_image() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase method) get_2d_tors_annotated_lig_pair() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase method) get_2Dimage() (in module schrodinger.application.jaguar.macro_pka_utils) get_2var_plot() (in module schrodinger.application.desmond.mplchart) get_3_letter_mutation() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator static method) get_3_letter_mutation_list() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) get_3d_isomers() (in module schrodinger.application.matsci.buildcomplex2d) get_3point_normal() (in module schrodinger.application.jaguar.utils) get_ab_annotations() (in module schrodinger.livedesign.biologics.sequence) get_abfep_args_instance() (in module schrodinger.application.desmond.starter.ui.fep_absolute_binding) get_abfep_cross_link() (in module schrodinger.application.desmond.fepana) get_abfep_options() (in module schrodinger.application.desmond.starter.ui.fep_absolute_binding) get_absolute_binding_num_lambda_windows() (in module schrodinger.application.desmond.fep_schedule) get_absolute_enthalpy_entropy_ratio() (in module schrodinger.application.watermap.shapes) get_absolute_free_ratio() (in module schrodinger.application.watermap.shapes) get_acs_name() (schrodinger.application.jaguar.simple_spec.Peak method) get_action_obj_name() (in module schrodinger.application.bioluminate.actions.factory) get_activated_module_names() (in module schrodinger.tasks.remote_modules) get_active_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_active_sample_size() (in module schrodinger.analysis.enrichment.metrics) get_active_sample_size_star() (in module schrodinger.analysis.enrichment.metrics) get_activity_cliffs() (in module schrodinger.application.phase.packages.mmp2d) get_added() (in module schrodinger.models.diffy) get_added_dict() (in module schrodinger.models.diffy) get_added_list() (in module schrodinger.models.diffy) get_added_set() (in module schrodinger.models.diffy) get_adjustable_atoms() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_adjusted_opacity() (in module schrodinger.application.desmond.sid_plots.pl_lid) get_alchem_solv() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_align_ct() (in module schrodinger.application.bioluminate.antibody.utils) get_align_data() (in module schrodinger.application.bioluminate.antibody.utils) get_align_seq_data() (in module schrodinger.application.bioluminate.antibody.utils) get_aligned_chmmol_from_ct() (in module schrodinger.application.desmond.depictor) get_aligned_coordinates() (in module schrodinger.application.desmond.frag_snap) get_aligned_coordinates_from_fragments() (in module schrodinger.application.desmond.frag_snap) get_aligned_fragment_coords() (in module schrodinger.application.desmond.frag_snap) get_aligned_mols() (in module schrodinger.application.jaguar.macro_pka_utils) get_aligned_pictures() (in module schrodinger.ui.qt.structure2d) get_aligned_residues() (in module schrodinger.protein.sequence) get_aligned_structure_residues() (in module schrodinger.protein.sequence) get_aligner_options() (in module schrodinger.application.phase.packages.align_ligands_driver_options) get_alignment_matrix() (in module schrodinger.structutils.transform) get_all_atomic_subparams() (in module schrodinger.models.parameters) get_all_atoms_marked_as_neighbors() (in module schrodinger.application.matsci.clusterstruct) get_all_compound_subparams() (in module schrodinger.models.parameters) get_all_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_all_force_field_paths() (in module schrodinger.application.matsci.cgforcefield) get_all_loggerstates() (in module schrodinger.rdkit.rdkit_adapter) get_all_orthant_strings() (in module schrodinger.application.combinatorial_diversity.splitter_utils) get_all_replaced_signals() (in module schrodinger.models.parameters) get_all_residues() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_all_steps_and_chains() (in module schrodinger.stepper.stepper) get_all_subjobs() (in module schrodinger.application.matsci.jobutils) get_allowed_ncpu() (in module schrodinger.active_learning.al_utils) get_analysis() (schrodinger.application.desmond.replica_sid_generator.FEPReport method) get_analyzer() (in module schrodinger.application.bioluminate.methionine_oxidation) get_anarci_alignment_best_match() (in module schrodinger.application.bioluminate.tcr.annotate) get_anarci_chain_result() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_anarci_results() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_anarci_results_from_fasta() (in module schrodinger.application.bioluminate.anarci.annotate) get_angle() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_angle_between_vectors() (in module schrodinger.structutils.transform) get_angle_in_degrees() (in module schrodinger.application.matsci.mecp_mod) get_angle_potential_type() (in module schrodinger.application.matsci.coarsegrain) get_angles() (schrodinger.application.desmond.torsion_related.TorsionPotential method) get_anion() (in module schrodinger.application.matsci.mlearn.features) get_annotated_atom() (in module schrodinger.protein.assignment) get_annotated_atom_property() (in module schrodinger.protein.assignment) get_annotated_user_labels() (in module schrodinger.seam.viz.inspect) get_annotation_position() (in module schrodinger.ui.qt.smatplotlib) get_annotation_strings() (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult method) get_annotation_strings_with_gaps() (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult method) get_annotations() (in module schrodinger.application.bioluminate.anarci.annotate) get_annotations_for_helm_model() (in module schrodinger.livedesign.biologics.sequence) get_annotations_from_results() (in module schrodinger.application.bioluminate.anarci.annotate) get_antibody_heavy_domains() (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment method) get_antibody_light_domains() (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment method) get_antibody_scheme() (in module schrodinger.application.bioluminate.antibody.utils) get_antibody_type_char() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_APBS_potential_grid() (in module schrodinger.application.bioluminate.escomp) get_api() (in module schrodinger.application.phase.packages.conformer_storage) get_appdata_dir() (in module schrodinger.utils.fileutils) get_application() (in module schrodinger.utils.qapplication) get_approximate_atomic_sasa() (in module schrodinger.structutils.analyze) get_approximate_sasa() (in module schrodinger.structutils.analyze) get_arg_parser() (in module schrodinger.utils.compare) get_ark_results() (schrodinger.application.desmond.replica_sid_generator.FEPReport method) get_arm_indices() (in module schrodinger.livedesign.biologics.sequence) get_arms() (in module schrodinger.livedesign.biologics.registration) get_arms_by_annotation() (in module schrodinger.livedesign.biologics.registration) get_arms_by_connectivity() (in module schrodinger.livedesign.biologics.registration) get_aromatic_hydrogen_bonds() (in module schrodinger.structutils.interactions.hbond) get_ase_atoms() (in module schrodinger.application.matsci.aseutils) get_asl_chain_name() (in module schrodinger.application.bioluminate.pml_menus) get_asl_for_ppw_atoms() (in module schrodinger.application.prepwizard) get_asl_for_search_option() (in module schrodinger.maestro_utils.find_tool_bar.constants) get_asl_from_meta_asl() (in module schrodinger.application.desmond.cms) get_asl_from_selection_picking_dialog() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_ASP_curve() (schrodinger.application.jaguar.pk50_report.Pk50Factory method) get_assembled_structure() (in module schrodinger.application.matsci.swap_fragments_utils) get_assembler_type() (in module schrodinger.livedesign.biologics.fasta) get_assignments() (schrodinger.application.jaguar.pk50_report.Pk50Factory method) get_ASU_RMSD() (in module schrodinger.comparison.struc) get_asu_volume() (in module schrodinger.comparison.struc) get_atom() (in module schrodinger.application.bioluminate.antibody.assembly) (schrodinger.application.desmond.maestro.Workspace method) get_atom_chirality() (in module schrodinger.application.canvas.r_group) get_atom_elements() (in module schrodinger.application.scaffold_enumeration.atomlist) get_atom_ffio_velocity() (in module schrodinger.application.matsci.desmondutils) get_atom_group() (schrodinger.application.desmond.cms.Cms method) get_atom_id() (in module schrodinger.application.scaffold_enumeration.common) get_atom_id_map() (in module schrodinger.application.scaffold_enumeration.common) get_atom_indices() (schrodinger.protein.analysis.Report.local_residue method) get_atom_info() (in module schrodinger.application.jaguar.gui.utils) get_atom_key() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_atom_label_font() (in module schrodinger.application.phase.phase_markers) get_atom_layers() (in module schrodinger.application.matsci.freevolume) get_atom_name_formula() (in module schrodinger.application.matsci.coarsegrain) get_atom_numbering_chirality() (in module schrodinger.comparison.chirality) get_atom_positions() (in module schrodinger.application.bindingsite.cavutils) get_atom_radii_lines() (in module schrodinger.application.matsci.packmol) get_atom_reference_coordinates() (in module schrodinger.application.desmond.struc) get_atom_string() (in module schrodinger.protein.assignment) get_atom_type() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) get_atom_type_dict() (in module schrodinger.application.matsci.rxn_channel) get_atomic_element() (in module schrodinger.application.matsci.msutils) get_atomic_element_symbols() (in module schrodinger.application.matsci.nano.util) get_atoms_asl() (in module schrodinger.application.matsci.maestrocmds) get_atoms_by_orig_anum() (in module schrodinger.application.prepwizard) get_atoms_close_to_point() (in module schrodinger.structutils.measure) get_atoms_close_to_structure() (in module schrodinger.structutils.measure) get_atoms_close_to_subset() (in module schrodinger.structutils.measure) get_atoms_from_asl() (in module schrodinger.structutils.analyze) get_atoms_from_uid() (in module schrodinger.application.desmond.maestro) get_atoms_mapping() (in module schrodinger.livedesign.preprocessor) get_atoms_to_minimize() (in module schrodinger.application.bioluminate.antibody.assembly) get_atoms_with_improper_atom_types() (in module schrodinger.application.prepwizard2.diagnostics) get_attach() (schrodinger.application.canvas.r_group.TempAtom method) get_attachment() (in module schrodinger.application.glide.http_server) get_attachment_bonds() (in module schrodinger.application.desmond.r_group_asl) get_attachment_point() (in module schrodinger.structutils.rgroup_enumerate) get_attachment_points() (in module schrodinger.structutils.markush_enumerate) (schrodinger.application.canvas.r_group.Data method) get_available_properties() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_average_box_volume() (in module schrodinger.application.desmond.fepana) get_average_structure() (in module schrodinger.structutils.analyze) get_averaged_properties() (in module schrodinger.application.matsci.boltzmann_avg_props) get_avg() (in module schrodinger.application.matsci.desmondutils) get_axis_of_rotation() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_b64decoded_str() (in module schrodinger.application.desmond.cmdline) get_b64encoded_str() (in module schrodinger.application.desmond.cmdline) get_backbone_atoms() (in module schrodinger.application.matsci.geometry) get_backbone_indices() (schrodinger.protein.analysis.Report.local_residue method) get_backend() (in module schrodinger.job.jobcontrol) get_backend_args() (in module schrodinger.active_learning.mq_worker) get_backend_argv() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) get_backend_first_host() (in module schrodinger.application.matsci.jobutils) get_backend_host_list() (in module schrodinger.job.jobcontrol) get_backend_hosts_str() (in module schrodinger.application.matsci.jobutils) get_base64_str_from_structure() (in module schrodinger.application.matsci.coarsegrain) get_base_entry_group() (in module schrodinger.project.utils) get_base_esp_jobname() (in module schrodinger.application.matsci.clusterstruct) get_base_names() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_basename() (in module schrodinger.utils.fileutils) get_basename_if_relative_path() (in module schrodinger.application.desmond.util) get_bases() (in module schrodinger.application.jaguar.basis) get_basis() (in module schrodinger.application.mopac.mopac_surfaces) get_basis_display_name() (in module schrodinger.application.jaguar.gui.basis_selector) get_basis_set_list_items() (in module schrodinger.application.jaguar.gui.basis_selector) get_bead_count() (in module schrodinger.application.matsci.coarsegrain) get_benchmarks() (in module schrodinger.seam.testing.benchmarks) get_best_domain_result() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_best_image_scale() (in module schrodinger.ui.sketcher_image) get_bfnorm() (in module schrodinger.application.mopac.mopac_surfaces) get_big_fused_rings() (in module schrodinger.application.desmond.r_group_asl) get_bilinear_fit_property() (in module schrodinger.application.matsci.uq_utils) get_bilinear_prop() (in module schrodinger.application.matsci.uq_utils) get_bilinear_prop_from_points() (in module schrodinger.application.matsci.uq_utils) get_bilinear_regions() (in module schrodinger.application.matsci.uq_utils) get_bilinear_regression() (in module schrodinger.application.matsci.uq_utils) get_bio_database() (in module schrodinger.application.bioluminate.antibody.utils) get_bispecific_model_job() (in module schrodinger.livedesign.biologics.modeling) get_block_summary() (in module schrodinger.application.desmond.simulation_block_data) get_blocks() (in module schrodinger.structutils.block_data) get_bond_id() (in module schrodinger.application.scaffold_enumeration.common) get_bond_labels() (in module schrodinger.application.pathfinder.synthesis) get_bond_type_dict() (in module schrodinger.application.matsci.rxn_channel) get_bonded_hydrogens() (in module schrodinger.application.ligprep.ionizer) get_bonds() (in module schrodinger.application.jaguar.utils) get_bonds_in_molecule() (in module schrodinger.application.matsci.rxn_channel) get_bonds_in_rings() (schrodinger.application.canvas.r_group.Data method) get_bonds_mapping() (in module schrodinger.livedesign.preprocessor) get_bound_cache() (in module schrodinger.application.matsci.cache) get_box() (in module schrodinger.application.desmond.cms) get_boxsize() (in module schrodinger.application.desmond.cms) get_boxvolume() (in module schrodinger.application.desmond.cms) get_bracket_info() (schrodinger.application.jaguar.qrnn.temp_opt.Brent method) get_bridging_waters() (in module schrodinger.application.prepwizard) get_bs_base_name() (in module schrodinger.application.matsci.bandshape_utils) get_bs_ext() (in module schrodinger.application.matsci.bandshape_utils) get_bs_spectrum_file_temps_keys() (in module schrodinger.application.matsci.bandshape_utils) get_buildtime_file() (in module schrodinger.utils.machid) get_built_in_aa_names() (in module schrodinger.protein.process_enamine_db) get_built_in_residues() (schrodinger.protein.nonstandard_residues.ResidueDatabase class method) get_builtin_directory() (in module schrodinger.application.matsci.builderwidgets) get_builtin_template_items() (in module schrodinger.application.matsci.builderwidgets) get_bulk_solvent_accessible_atoms() (in module schrodinger.protein.assignment) get_bumped_release_version() (in module schrodinger) get_bundled_libstdcpp() (in module schrodinger.utils.installation_check) get_CA_atom_props() (in module schrodinger.protein.properties) get_ca_positions() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_canvas_program() (in module schrodinger.protein.natural_analog) get_carat_map() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_carb_atom_identifier_map() (in module schrodinger.application.matsci.polymer) get_carboxyl_atoms() (in module schrodinger.protein.assignment) get_carts_from_anchor_string() (in module schrodinger.application.matsci.nano.xtal) get_carts_from_center_string() (in module schrodinger.application.matsci.nano.xtal) get_cell() (in module schrodinger.application.matsci.nano.xtal) get_cell_fast() (in module schrodinger.application.matsci.nano.xtal) (in module schrodinger.comparison.struc) get_cell_pairs() (in module schrodinger.application.matsci.nano.xtal) get_cells() (in module schrodinger.application.matsci.packmol) get_center() (in module schrodinger.application.matsci.geometry) (in module schrodinger.math.multi_parameter_optimization) get_center_gridlen() (in module schrodinger.application.bioluminate.escomp) get_center_of_mass_weight() (in module schrodinger.application.matsci.cg_mapping) get_centroid() (in module schrodinger.application.matsci.shapes) (in module schrodinger.structutils.transform) get_centroid_from_residues() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_centroid_radial_distance_vector() (in module schrodinger.comparison.struc) get_centroid_RMSDn() (in module schrodinger.comparison.struc) get_cert() (in module schrodinger.job.cert) get_cert_with_ldap() (in module schrodinger.job.cert) get_cert_with_socket_auth() (in module schrodinger.job.cert) get_cfg_names_from_msj_data() (in module schrodinger.application.matsci.desconfig) get_cfg_names_from_msj_file() (in module schrodinger.application.matsci.desconfig) get_cg_cutoff_data() (in module schrodinger.application.matsci.coarsegrain) get_cg_molecule_hash() (in module schrodinger.application.matsci.coarsegrain) get_cg_particle_indices() (in module schrodinger.application.matsci.cg_mapping) get_cg_radii_lines() (in module schrodinger.application.matsci.packmol) get_cg_structure() (in module schrodinger.ui.sketcher_extensions) get_cgparticle_to_element_mapper() (in module schrodinger.rdkit.coarsegrain) get_chain_fasta_sequence() (in module schrodinger.protein.sequence) get_chain_sequence() (in module schrodinger.application.bioluminate.antibody.annotate) get_chain_sequences() (in module schrodinger.application.prepwizard) get_charge() (in module schrodinger.application.bioluminate.propka_parse) (schrodinger.application.desmond.cms.Cms method) get_charged_prop_value() (in module schrodinger.application.matsci.kmcgui) get_charges() (in module schrodinger.application.jaguar.utils) get_check_also_reg_bond() (in module schrodinger.application.matsci.nano.xtal) get_check_min_jaguar_keywords() (in module schrodinger.application.matsci.reaction_workflow_utils) get_checkpoint_dir() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_checkpoint_file_and_restart_number() (in module schrodinger.application.desmond.launch_utils) get_checkpoint_file_path() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_checksum() (in module schrodinger.application.matsci.espresso.ppdb) get_child_like_parent() (in module schrodinger.application.matsci.genetic_optimization) get_chiral_atoms() (in module schrodinger.structutils.analyze) get_chiral_centers() (in module schrodinger.comparison.chirality) get_chiral_hash() (in module schrodinger.application.matsci.cg_mapping) get_chiral_pair() (in module schrodinger.application.matsci.cg_mapping) get_chiralities() (in module schrodinger.structutils.analyze) get_chirality() (in module schrodinger.comparison.chirality) get_chmmol_bonds_from_atoms() (in module schrodinger.application.desmond.fep_scholar_util) (in module schrodinger.ui.qt.structure2d) get_chorus_from_params() (in module schrodinger.application.matsci.nano.xtal) get_chorus_properties() (in module schrodinger.application.matsci.nano.xtal) get_chunk_file_name() (in module schrodinger.application.bb_database.bb_task_utils) get_chunk_info() (in module schrodinger.application.bb_database.bb_task_utils) get_chunk_row() (in module schrodinger.application.bb_database.bb_task_utils) get_chunk_rows() (in module schrodinger.application.bb_database.bb_task_utils) get_circular_delta() (in module schrodinger.ui.qt.dialbox) get_class_map() (in module schrodinger.application.matsci.packmol) get_cli_geom_str() (in module schrodinger.application.matsci.buildcomplex) get_clib_dir() (in module schrodinger.application.combinatorial_screen.driver_utils) get_close_atoms() (in module schrodinger.structutils.measure) get_close_coordinates() (in module schrodinger.structutils.measure) get_close_interactors() (schrodinger.protein.assignment.ProtAssign.changeable method) get_close_residues_asl() (in module schrodinger.structutils.interactions.protein_protein_interactions) get_closest_atom() (in module schrodinger.application.matsci.swap_fragments_utils) get_clustal_path() (in module schrodinger.protein.tasks.clustal) get_cluster_atom_ids() (in module schrodinger.application.matsci.clusterstruct) get_cms() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_cms_and_trj_path() (in module schrodinger.application.matsci.deswidgets) get_cms_and_trj_path_from_st() (in module schrodinger.application.matsci.desmondutils) get_cms_file_path() (in module schrodinger.trajectory.utils) get_cms_path_from_proj_table() (in module schrodinger.application.matsci.deswidgets) get_coarse_grain_msj_family_header() (in module schrodinger.application.matsci.coarsegrain) get_coarse_grain_msj_header() (in module schrodinger.application.matsci.coarsegrain) get_coarsegrain_smiles() (in module schrodinger.rdkit.coarsegrain) get_code() (schrodinger.infra.unusable_module_importer.UnusableModuleLoader class method) get_collapsed_index() (in module schrodinger.application.matsci.nano.xtal) get_color() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.matsci.amorphous) (schrodinger.application.desmond.torsion_related.TorsionPotential method) (schrodinger.ui.qt.formlayout.ColorButton method) get_color_by_entry() (in module schrodinger.application.watermap.shapes) get_color_list() (in module schrodinger.application.combiglide.connection_storage) get_color_scheme() (in module schrodinger.structutils.color) get_colors() (in module schrodinger.application.matsci.maestrocmds) get_com_and_axes() (in module schrodinger.application.bindingsite.cavutils) get_combinatorial_synthesis_command() (in module schrodinger.application.combinatorial_screen.driver_utils) get_combined_exclusion_str() (in module schrodinger.application.matsci.coarsegrain) get_command() (in module schrodinger.job.queue) get_command_line_host_list() (in module schrodinger.job.jobcontrol) get_command_option_for_search_option() (in module schrodinger.maestro_utils.find_tool_bar.constants) get_common_args() (in module schrodinger.application.phase.packages.hypo_refine.job_utils) (in module schrodinger.application.phase.packages.phase_screen_driver_utils) get_common_atom_property_names() (in module schrodinger.application.matsci.msutils) get_common_fep_options() (in module schrodinger.application.desmond.starter.ui.cmdline) get_common_float_atom_property_names() (in module schrodinger.application.matsci.msutils) get_common_float_property_names() (in module schrodinger.application.matsci.msutils) get_common_options() (in module schrodinger.application.desmond.starter.ui.cmdline) get_complete_spectrum() (in module schrodinger.application.matsci.colorutils) get_compound_id_pairs() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) get_compound_smiles() (in module schrodinger.application.phase.packages.mmp2d) get_compressive_relaxation_stringers() (in module schrodinger.application.matsci.desconfig) get_concat_stages() (in module schrodinger.application.desmond.cmj) get_conclusion_string() (in module schrodinger.active_learning.al_report) get_confgen_options() (in module schrodinger.application.phase.packages.conformer_reader) get_confidence_interval_error() (in module schrodinger.application.matsci.mlearn.descriptor) get_config() (in module schrodinger.application.matsci.permittivity) get_config_as_json() (in module schrodinger.application.glide.http_server) get_config_filename() (in module schrodinger.application.jaguar.user_config) get_config_from_options() (in module schrodinger.application.matsci.permittivity) get_conformer_dict() (in module schrodinger.application.matsci.boltzmann_avg_props) get_conformer_radial_distance_vector() (in module schrodinger.comparison.struc) get_conformer_reader() (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) get_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) get_connected_components() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) get_connected_ring_bonds() (in module schrodinger.application.canvas.r_group) get_connection_color() (in module schrodinger.application.combiglide.connection_storage) get_connection_status() (in module schrodinger.application.livedesign.maestro_ld_connection) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_const_ref_filename() (in module schrodinger.application.bioluminate.anarci.annotate) get_constant_domain_bounds() (in module schrodinger.application.bioluminate.anarci.annotate) get_constraint() (schrodinger.application.desmond.cms.Cms method) get_contiguous_groups() (in module schrodinger.protein.alignment) get_contrast() (in module schrodinger.ui.qt.standard.colors) get_contrasting_color() (in module schrodinger.ui.qt.standard.colors) get_control_from_dict() (in module schrodinger.application.vss.control) get_control_from_file() (in module schrodinger.application.vss.control) get_conv_from_vecs() (in module schrodinger.application.matsci.nano.xtal) get_coords_array_from_list() (in module schrodinger.structutils.transform) get_coords_dict() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_core() (schrodinger.application.canvas.r_group.Data method) get_core_bonds() (schrodinger.application.canvas.r_group.Data method) get_core_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_core_map() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_core_num() (in module schrodinger.application.matsci.equilibrium_md) get_cores() (schrodinger.application.canvas.r_group.Data method) get_corporate_id() (in module schrodinger.tasks.ldtasks) get_corresponding_header() (schrodinger.livedesign.biologics.fasta.PolymerAssembler class method) get_cov_lig_info() (in module schrodinger.application.desmond.replica_sid_generator) get_cov_parameter() (in module schrodinger.application.matsci.nano.xtal) get_cov_radii() (in module schrodinger.application.matsci.nano.xtal) get_cov_radius() (in module schrodinger.application.matsci.nano.xtal) get_cpu() (in module schrodinger.utils.sysinfo) get_cpu_and_gpu_hosts() (in module schrodinger.application.matsci.parserutils) get_cpu_gpu_info() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_cross() (in module schrodinger.graphics3d.common) get_csv() (in module schrodinger.application.desmond.stage.app.absolute_binding.stage) get_csv_file_column_count() (in module schrodinger.utils.fileutils) get_csv_header() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.desmond.stage.app.absolute_binding.stage) (in module schrodinger.application.glide.utils) (schrodinger.active_learning.mq_backend.Backend method) get_csv_name() (in module schrodinger.application.bioluminate.methionine_oxidation) get_CSV_path() (in module schrodinger.application.matsci.stress_strain) get_csv_props() (in module schrodinger.application.glide.utils) get_csv_row() (in module schrodinger.application.desmond.stage.app.absolute_binding.stage) get_ct() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) get_ct_atoms_count() (in module schrodinger.application.matsci.msutils) get_ct_offsets() (schrodinger.application.canvas.r_group.Data method) get_ct_property() (in module schrodinger.application.glide.sort_utils) get_cts() (schrodinger.application.desmond.cms.Cms method) get_cuboid_vol() (in module schrodinger.application.matsci.packmol) get_current_project_name() (in module schrodinger.ui.qt.forcefield.ffprojectsettingsdlg) get_current_time() (in module schrodinger.job.queue) get_current_utc_timestamp() (in module schrodinger.application.job_monitor.util) get_custom_keq_rates() (in module schrodinger.application.matsci.reaction_workflow_utils) get_custom_opls_dir() (in module schrodinger.ui.qt.forcefield.forcefield) get_custom_rate() (in module schrodinger.application.matsci.reaction_workflow_utils) get_custom_reagent_classes() (in module schrodinger.application.pathfinder.reaction) get_cut_bonds() (in module schrodinger.application.matsci.swap_fragments_utils) get_cutoff() (in module schrodinger.application.desmond.ene_utils) (in module schrodinger.application.matsci.desmondutils) (schrodinger.comparison.results.ResultSet method) get_cutoff_from_reduced_density() (in module schrodinger.application.matsci.cgforcefield) get_data_file() (in module schrodinger.application.glide.utils) get_data_frame_from_project() (in module schrodinger.project.pandasutils) get_database_manager_class() (in module schrodinger.application.matsci.kmc) get_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_db_amino_acids() (in module schrodinger.protein.nonstandard_residues) get_db_filename() (in module schrodinger.protein.gpcr.sql) get_db_residues() (in module schrodinger.protein.nonstandard_residues) get_db_structure_path() (in module schrodinger.application.matsci.kmc) get_db_table_length() (in module schrodinger.application.matsci.kmc) get_debug_level() (in module schrodinger.stepper.stepper) get_decoy_sample_size() (in module schrodinger.analysis.enrichment.metrics) get_deduped_monomers() (in module schrodinger.application.matsci.rxn_channel) get_deduplication_hash() (in module schrodinger.livedesign.biologics.registration) get_default_box_size() (in module schrodinger.application.glide.glide) get_default_criterion_parser() (in module schrodinger.utils.ligfilter) get_default_docking_keyword_value() (in module schrodinger.application.glide.glide) get_default_far_timestep() (in module schrodinger.application.matsci.desmondutils) get_default_feature_definitions() (in module schrodinger.application.phase.packages.phase_utils) get_default_forcefield() (in module schrodinger.application.matsci.msutils) get_default_host() (in module schrodinger.tasks.jobtasks) get_default_launch_timeout() (in module schrodinger.job.queue) get_default_minimal_caps_filename() (in module schrodinger.application.pathfinder.reaction) get_default_near_timestep() (in module schrodinger.application.matsci.desmondutils) get_default_opls_version() (in module schrodinger.ui.qt.forcefield.forcefield) get_default_params() (in module schrodinger.structutils.interactions.hbond) get_default_physical_leg_type() (in module schrodinger.application.desmond.physical_leg_infra) get_default_pymol_location() (in module schrodinger.application.pymol.utils) get_default_reactions_filename() (in module schrodinger.application.pathfinder.reaction) get_default_reagent_classes_filename() (in module schrodinger.application.pathfinder.reaction) get_default_serializer() (in module schrodinger.models.jsonable) get_default_setting() (in module schrodinger.application.desmond.config_utils) get_default_user_dbfile() (in module schrodinger.protein.nonstandard_residues) get_degrees_of_freedom() (in module schrodinger.application.desmond.remd) (schrodinger.application.desmond.cms.Cms method) get_delta_energy() (in module schrodinger.application.matsci.jaguarworkflows) get_delta_property_values() (in module schrodinger.application.bioluminate.residue_scanning.properties) get_delta_time() (in module schrodinger.application.desmond.fepana) get_denovo_parameters() (in module schrodinger.application.phase.utils) get_density() (in module schrodinger.application.matsci.amorphous) get_density_from_ene() (in module schrodinger.application.desmond.ene_utils) get_density_from_scale_factor() (in module schrodinger.application.matsci.cgforcefield) get_depth() (schrodinger.application.jaguar.simple_spec.Peak method) get_depth_limits() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_descriptive_angles() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_descriptors_from_file() (in module schrodinger.application.matsci.order_parameter_mod) get_desktop_dir() (in module schrodinger.utils.fileutils) get_desmond_frames_from_options() (in module schrodinger.application.matsci.desmondutils) get_desmond_frames_in_range() (in module schrodinger.application.matsci.desmondutils) get_desmond_trj_frames() (in module schrodinger.application.matsci.desmondutils) get_detailed() (in module schrodinger.application.bioluminate.propka_parse) get_dialog() (schrodinger.ui.qt.formlayout.FormWidget method) get_dict_reader() (schrodinger.application.vss.csvsmiles.CsvSmilesFile method) get_dict_writer() (schrodinger.application.vss.csvsmiles.CsvSmilesFile method) get_diff() (in module schrodinger.models.diffy) get_diff_chunks() (in module schrodinger.utils.compare) get_diff_dict() (in module schrodinger.models.diffy) get_diff_list() (in module schrodinger.models.diffy) get_diff_output_with_numerical_tolerance() (in module schrodinger.utils.compare) get_diff_set() (in module schrodinger.models.diffy) get_diff_tokens_in_line() (in module schrodinger.utils.compare) get_dihedral_atoms() (in module schrodinger.protein.assignment) get_dimensionality_from_st() (in module schrodinger.application.matsci.pbcutils) get_dimer_com_sep() (in module schrodinger.application.matsci.kmc) get_dimers_in_structure() (in module schrodinger.application.matsci.clusterstruct) get_dimers_with_molecule() (in module schrodinger.application.matsci.clusterstruct) get_directory() (in module schrodinger.utils.fileutils) get_directory_path() (in module schrodinger.utils.fileutils) get_directory_size() (in module schrodinger.utils.fileutils) get_disabled_lib_dir() (in module schrodinger.utils.postinstall) get_dise() (in module schrodinger.application.vss.dise) get_disorder_groups() (in module schrodinger.application.matsci.pbcutils) get_display_string() (in module schrodinger.livedesign.biologics.registration) get_dissolution_dg_from_legs() (in module schrodinger.application.desmond.solubility_utils) get_dist() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_distance() (in module schrodinger.application.desmond.meta) (in module schrodinger.application.matsci.colorutils) get_distance_cell() (in module schrodinger.application.matsci.mlearn.features) get_distributed_fp_commands() (in module schrodinger.application.combinatorial_screen.driver_utils) get_distributed_fp_generation_commands() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_distributed_screen_commands() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_distributed_selection_commands() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_distributed_shape_screen_commands() (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) get_distro_package() (in module schrodinger.utils.installation_check) get_disulfide_bonds() (in module schrodinger.structutils.interactions.ssbond) get_disulfide_center_point() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_docs_dir() (in module schrodinger.utils.documentation) (in module schrodinger.utils.fileutils) get_domain_type_shorthand() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_dominant_path_idx() (in module schrodinger.application.desmond.kinetics.utils) get_donor_acceptor_bonds() (in module schrodinger.structutils.interactions.hbond) get_double_sigmoid() (in module schrodinger.math.multi_parameter_optimization) get_dpd_scale_factor_from_FF() (in module schrodinger.application.matsci.cgforcefield) get_dummy_atoms() (in module schrodinger.application.matsci.etatoggle) (in module schrodinger.application.matsci.msutils) get_dummy_filter() (in module schrodinger.structutils.rgroup_enumerate) get_duplicate_atoms() (in module schrodinger.application.matsci.nano.xtal) get_e_pair_rates_from_database() (in module schrodinger.application.matsci.kmc) get_edge_from_struct_file() (in module schrodinger.application.desmond.stage.launcher) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase method) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher method) (schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher method) (schrodinger.application.desmond.stage.launcher.FepLauncher method) get_edge_normals() (in module schrodinger.structutils.assignbondorders) get_eigenvectors() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_element() (in module schrodinger.application.matsci.espresso.utils) get_element_counts() (in module schrodinger.application.matsci.atomicsymbols) get_element_histogram() (in module schrodinger.application.matsci.genetic_optimization) get_element_mutator_dict() (in module schrodinger.application.matsci.genetic_optimization) get_element_priority() (in module schrodinger.application.matsci.nano.xtal) get_enabled_flags() (in module schrodinger.seam.debug) get_enamine_dbfile() (in module schrodinger.protein.nonstandard_residues) get_enc_module() (in module schrodinger.application.matsci.codeutils) get_encryption_key() (in module schrodinger.application.matsci.enc) get_endpoint_cmsfiles() (schrodinger.application.desmond.stage.analysis.FepanaJob method) get_energy() (in module schrodinger.application.macromodel.apps) get_energy_db_term() (in module schrodinger.application.matsci.reaction_workflow_utils) get_energy_group_output_filename() (in module schrodinger.application.desmond.config_utils) get_energy_table() (in module schrodinger.application.desmond.fepana) get_enrichment_calculator() (in module schrodinger.application.glide.glideanalysis) get_ensemble() (in module schrodinger.application.desmond.config_utils) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_ensemble_class_method() (in module schrodinger.application.desmond.config_utils) get_ensemble_from_cfg() (in module schrodinger.application.desmond.simulation_block_data) get_ent() (in module schrodinger.protein.getpdb) get_enthalpy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_entity_class() (in module schrodinger.livedesign.biologics.registration) get_entries() (in module schrodinger.application.matsci.reaction_workflow_gui_utils) (in module schrodinger.ui.qt.entryselector) get_entropy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_entry() (in module schrodinger.ui.qt.entryselector) get_entry_group() (in module schrodinger.project.utils) get_entry_id() (in module schrodinger.application.desmond.maestro) get_entry_title() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_entryname_prefix() (in module schrodinger.application.desmond.maestro) get_enum_member() (in module schrodinger.application.matsci.msutils) get_env_var_warning() (in module schrodinger.utils.featureflags.featureflags) get_environ_log_level() (in module schrodinger.utils.log) get_environ_with_mpi() (in module schrodinger.application.desmond.driver_utils) get_eprop_data() (in module schrodinger.application.matsci.reaction_workflow_utils) get_error_file() (in module schrodinger.application.desmond.driver_utils) get_error_icon() (in module schrodinger.ui.qt.tasks.taskwidgets) get_eta_marker_indexes() (in module schrodinger.application.matsci.buildcomplex) get_example_mol_tag() (in module schrodinger.application.matsci.clusterstruct) get_exception_handler() (in module schrodinger.infra.exception_handler) get_exec() (in module schrodinger.application.desmond.config_utils) get_exec_name() (in module schrodinger.application.desmond.config_utils) get_existing_directory() (in module schrodinger.ui.qt.filedialog) get_existing_filepath() (in module schrodinger.utils.fileutils) get_existing_files() (in module schrodinger.application.bioluminate.drivers.io) (in module schrodinger.application.matsci.jaguar_restart) get_existing_fp_file() (in module schrodinger.application.combinatorial_screen.driver_utils) get_existing_fp_files() (in module schrodinger.application.combinatorial_screen.driver_utils) get_existing_phase_database() (in module schrodinger.ui.qt.filedialog) get_existing_project_name() (in module schrodinger.ui.qt.filedialog) get_extracted_and_maps() (in module schrodinger.application.matsci.swap_fragments_utils) get_extracted_atom_index() (in module schrodinger.application.matsci.clusterstruct) get_families() (in module schrodinger.protein.gpcr.annotate) get_family_region_bounds() (in module schrodinger.application.bioluminate.anarci.annotate) get_family_region_bounds_from_chain_result() (in module schrodinger.application.bioluminate.anarci.annotate) get_family_region_bounds_from_domain_result() (in module schrodinger.application.bioluminate.anarci.annotate) get_fasta_helm_models() (in module schrodinger.livedesign.biologics.fasta) get_fasta_monomers() (in module schrodinger.livedesign.biologics.sequence) get_fasta_sequences() (in module schrodinger.protein.sequence) get_feature_overlap_mappings() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) get_feature_text() (in module schrodinger.application.phase.constants) get_features() (in module schrodinger.utils.featureflags.featureflags) get_fep_cts() (in module schrodinger.application.desmond.r_group_asl) (schrodinger.application.desmond.cms.Cms method) get_fep_lambda_schedule() (in module schrodinger.application.desmond.config_utils) get_fep_lambdas() (in module schrodinger.application.desmond.config_utils) get_fep_leg_types() (in module schrodinger.application.desmond.physical_leg_infra) get_fep_mapping() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_fep_output_filename() (in module schrodinger.application.desmond.config_utils) get_fep_plus_options() (in module schrodinger.application.desmond.starter.ui.fep_plus) get_fep_schedule() (in module schrodinger.application.desmond.fep_schedule) get_fep_schedule_class() (in module schrodinger.application.desmond.fep_schedule) get_fep_simulation_details() (in module schrodinger.application.desmond.fep_edge_data) get_fep_structures() (in module schrodinger.application.desmond.struc) get_fep_supported_ff_names() (in module schrodinger.application.desmond.starter.ui.cmdline) get_fepio_sub_block_std_prop_getter() (in module schrodinger.application.desmond.ffiostructure) get_fepio_sub_block_std_prop_setter() (in module schrodinger.application.desmond.ffiostructure) get_fepio_sub_block_std_prop_short_name() (in module schrodinger.application.desmond.ffiostructure) get_ff() (schrodinger.application.desmond.cms.Cms method) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_ffio_sub_block_std_prop_getter() (in module schrodinger.application.desmond.ffiostructure) get_ffio_sub_block_std_prop_setter() (in module schrodinger.application.desmond.ffiostructure) get_ffio_sub_block_std_prop_short_name() (in module schrodinger.application.desmond.ffiostructure) get_fflags_env_to_export() (in module schrodinger.utils.featureflags.featureflags) get_field_from_log() (in module schrodinger.application.desmond.fepana) get_field_strength_string() (in module schrodinger.application.matsci.kmcgui) get_fieldnames() (in module schrodinger.rdkit.molio) get_file() (in module schrodinger.job.files) (schrodinger.application.matsci.permittivity.Config static method) get_file_data() (in module schrodinger.application.matsci.freevolume) (in module schrodinger.application.matsci.spectra) get_file_ext() (in module schrodinger.active_learning.al_utils) get_file_extension() (in module schrodinger.utils.fileutils) get_file_format() (in module schrodinger.utils.fileutils) get_file_from_options() (schrodinger.application.matsci.permittivity.Config class method) get_file_names_from_list_file() (in module schrodinger.application.phase.packages.phase_utils) get_file_names_of_duplicates() (in module schrodinger.application.matsci.reaction_workflow_utils) get_file_path() (in module schrodinger.application.matsci.jobutils) (schrodinger.application.desmond.test_utils.FileRegistry method) get_file_path_errors() (in module schrodinger.application.desmond.util) get_file_registration() (schrodinger.application.desmond.test_utils.FileRegistry method) get_file_url() (in module schrodinger.job.launchapi) get_filename() (in module schrodinger.application.matsci.hdfutils) get_files() (in module schrodinger.application.matsci.equilibrium_md) get_files_from_folder() (in module schrodinger.utils.fileutils) get_filter() (in module schrodinger.rdkit.filtering) get_filter_columns() (in module schrodinger.application.combinatorial_diversity.diversity_selector) get_filter_path() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) get_filter_properties() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_final_state() (in module schrodinger.application.matsci.mecp_mod) get_find_toolbar() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_fingerprint() (in module schrodinger.rdkit.filtering) get_fingerprint_components() (in module schrodinger.analysis.enrichment.enrichment_input) get_fingerprint_types() (in module schrodinger.utils.multifpfile) get_fingerprints() (schrodinger.utils.multifpfile.MultiFPFile method) get_first_hostid() (in module schrodinger.application.licensing.licadmin) get_first_hostname() (in module schrodinger.ui.qt.appframework2.jobs) get_flat_color_list() (in module schrodinger.application.combiglide.connection_storage) get_flexhills_mexpr() (in module schrodinger.application.desmond.kinetics.enhanced_sampling) get_flexlm_search_path() (in module schrodinger.application.licensing.licadmin) get_font() (schrodinger.ui.qt.formlayout.FontLayout method) get_font_id() (in module schrodinger.utils.pymol) get_force_field_file_path() (in module schrodinger.application.matsci.cgforcefield) get_force_field_name() (in module schrodinger.application.matsci.cgforcefield) get_forcefield_typer() (in module schrodinger.application.matsci.parserutils) get_forcefield_typer_and_number_getter() (in module schrodinger.application.matsci.parserutils) get_form_hashes() (in module schrodinger.application.desmond.struc) get_form_mols() (in module schrodinger.application.desmond.struc) get_format_arguments() (in module schrodinger.livedesign.biologics.modeling) get_format_handler() (in module schrodinger.rdkit.molio) get_formatted_residue() (in module schrodinger.protein.residue) get_formatted_residue_range() (in module schrodinger.protein.residue) get_formulas_basename() (in module schrodinger.application.matsci.nano.interface_mod) get_fp_basename() (in module schrodinger.application.pathfinder.multiroute) get_fp_domain() (in module schrodinger.application.combinatorial_diversity.diversity_selector) get_fp_file() (in module schrodinger.application.pathfinder.multiroute) get_fp_files() (in module schrodinger.application.combinatorial_screen.driver_utils) get_fp_matrix() (in module schrodinger.protein.natural_analog) get_frag_structure() (in module schrodinger.structutils.build) get_fragment() (in module schrodinger.application.desmond.r_group_asl) get_fragment_smiles() (in module schrodinger.application.matsci.rxn_channel) get_fragment_structure() (in module schrodinger.protein.buildpeptide) get_fragments_from_att_points() (in module schrodinger.application.desmond.r_group_asl) get_fragname() (schrodinger.application.desmond.cms.Cms method) get_free_energy() (in module schrodinger.application.bioluminate.propka_parse) get_free_energy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_free_volume_structure() (in module schrodinger.application.matsci.freevolume) get_freezer_structure() (in module schrodinger.application.matsci.genetic_optimization) get_from() (schrodinger.application.desmond.arkdb.Datum method) get_frozen_atoms() (in module schrodinger.application.pathfinder.analysis) get_fullsys_ct_atom_index_range() (schrodinger.application.desmond.cms.Cms method) get_fullsystem_ct() (in module schrodinger.application.desmond.mxmd.mxmd_system_builder) get_functional_rings() (schrodinger.application.canvas.r_group.Data method) get_fused_cycles() (in module schrodinger.application.matsci.graph) get_gamut_area() (in module schrodinger.application.matsci.colorutils) get_gas_phase_zpe_key() (in module schrodinger.application.matsci.jaguarworkflows) get_gcd_list_ints() (in module schrodinger.application.matsci.nano.xtal) get_generated_fingerprint_filename() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_generation_log_file_name() (in module schrodinger.application.matsci.genetic_optimization) get_generic_end_structure() (in module schrodinger.application.matsci.amorphous) get_git_hashes() (in module schrodinger.application.glide.utils) get_glibc_version() (in module schrodinger.utils.sysinfo) get_glide_job() (in module schrodinger.application.glide.glide) get_glide_sort_path() (in module schrodinger.application.phase.packages.phase_utils) get_global_logger() (in module schrodinger.application.matsci.textlogger) get_global_quantity() (in module schrodinger.application.desmond.fepana) get_gluepoints() (in module schrodinger.application.desmond.cms) get_gpcrdb_url() (in module schrodinger.protein.gpcr.annotate) get_gpgpu_params() (in module schrodinger.job.jobcontrol) get_GPGPUs() (in module schrodinger.tasks.hosts) get_gpu_qarg() (in module schrodinger.application.matsci.espresso.utils) get_graph_file_path_base() (in module schrodinger.application.desmond.file_utils) get_grid_data() (schrodinger.application.desmond.cns_io.CNSData method) get_grid_parameters() (in module schrodinger.application.bindingsite.cavutils) get_grid_radius_property_values() (in module schrodinger.application.matsci.freevolume) get_group_atom_indices() (in module schrodinger.application.matsci.smartsutils) get_group_names() (in module schrodinger.application.matsci.smartsutils) get_group_numbers() (in module schrodinger.application.matsci.smartsutils) get_grow_idxs() (in module schrodinger.application.matsci.rxn_channel) get_guess() (in module schrodinger.application.matsci.mecp_mod) get_guide_atoms() (in module schrodinger.structutils.structalign2) get_h_pair_rates_from_database() (in module schrodinger.application.matsci.kmc) get_halogen_bond_statistics() (in module schrodinger.application.desmond.sid_plots.pl_interactions) get_halogen_bonds() (in module schrodinger.structutils.interactions.hbond) get_handle_for_block() (in module schrodinger.structutils.block_data) get_handlers_for_key() (in module schrodinger.infra.mmkv) get_hbond_direction() (in module schrodinger.application.bindingsite.intfield) get_hbond_params() (in module schrodinger.structutils.interactions.hbond) get_hdf_io() (in module schrodinger.application.matsci.hdfutils) get_hdf_keys() (in module schrodinger.application.matsci.hdfutils) get_hdx_adapter() (in module schrodinger.application.bioluminate.pose_filtering.hdx_io) get_hdx_ms_properties() (in module schrodinger.application.bioluminate.pose_filtering.hdx_io) get_hdx_test_file() (in module schrodinger.application.bioluminate.pose_filtering.test) get_header() (in module schrodinger.application.desmond.solubility_utils) get_header_solvation() (in module schrodinger.application.desmond.solubility_utils) get_heavies() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_heavy_atoms() (in module schrodinger.application.desmond.r_group_asl) get_heavy_neighbors() (in module schrodinger.protein.assignment) get_height() (in module schrodinger.rdkit.alignment) get_het_atom_numbers() (in module schrodinger.application.prepwizard) get_het_from_state() (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) get_het_name() (in module schrodinger.application.prepwizard) get_hidden_cms_file_path() (in module schrodinger.trajectory.utils) get_histogram() (schrodinger.application.desmond.replica_dE.replicas_monitor method) get_hits_file_names() (in module schrodinger.application.phase.packages.oned_task_utils) get_hkl() (in module schrodinger.application.matsci.nano.slab) get_hkl_indices() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_hmmerpath() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_home_dir() (in module schrodinger.utils.fileutils) get_homebox() (in module schrodinger.application.desmond.config_utils) get_host() (in module schrodinger.application.desmond.license) (in module schrodinger.job.jobcontrol) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_host_args() (in module schrodinger.application.phase.packages.phase_utils) get_host_by_name() (in module schrodinger.tasks.hosts) get_host_entries() (in module schrodinger.utils.installation_check) get_host_from_hostname() (in module schrodinger.ui.qt.config_dialog) get_host_list() (in module schrodinger.job.jobcontrol) get_host_ncpu() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.glide.utils) (in module schrodinger.application.phase.packages.shape_screen_al_utils) get_hostfile() (in module schrodinger.job.jobcontrol) get_hostid() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.utils.sysinfo) get_hostname() (in module schrodinger.utils.sysinfo) get_hostnames() (in module schrodinger.utils.net) get_hosts() (in module schrodinger.job.jobcontrol) (in module schrodinger.tasks.hosts) (in module schrodinger.tasks.jobtasks) (in module schrodinger.ui.qt.config_dialog) get_hostsChanged_signal() (in module schrodinger.tasks.hosts) get_hot_atoms() (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_huang_rhys_fs() (in module schrodinger.application.matsci.bandshape_utils) get_hydrogen_bond_type() (in module schrodinger.application.bioluminate.protein_interaction.calculate) get_hydrogen_bonds() (in module schrodinger.structutils.interactions.hbond) get_hyperbola_fit_property() (in module schrodinger.application.matsci.uq_utils) get_hyperbola_prop_from_points() (in module schrodinger.application.matsci.uq_utils) get_hyperbola_regression() (in module schrodinger.application.matsci.uq_utils) get_hypo_monitor() (in module schrodinger.application.phase.pt_hypothesis) get_hypos() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) get_hypothesis_entry_ids() (in module schrodinger.application.phase.pt_hypothesis) get_hypothesis_from_project() (in module schrodinger.application.phase.pt_hypothesis) get_icon() (in module schrodinger.ui.qt.figureoptions) (in module schrodinger.ui.qt.icons) (in module schrodinger.ui.two_d_viewer) get_icon_metadata_from_csv() (in module schrodinger.ui.qt.standard.icons.icons) get_icon_path_for_status() (in module schrodinger.application.job_monitor.job_monitor_table) get_ids_from_pairs() (in module schrodinger.application.phase.packages.mmp2d) get_idx() (in module schrodinger.application.desmond.automatic_analysis_generator) get_idx_groups() (in module schrodinger.application.matsci.reaction_workflow_utils) (in module schrodinger.application.matsci.swap_fragments_utils) get_idx_groups_str() (in module schrodinger.application.matsci.swap_fragments_utils) get_idxs() (in module schrodinger.application.matsci.packmol) (in module schrodinger.application.matsci.swap_fragments_utils) get_idxs_marked_atoms() (in module schrodinger.application.matsci.swap_fragments_utils) get_idxs_str() (in module schrodinger.application.matsci.swap_fragments_utils) get_image() (in module schrodinger.active_learning.al_report) (in module schrodinger.application.desmond.rl_helper) get_image_bytes() (in module schrodinger.protein.helm.image_generation) (in module schrodinger.ui.sketcher_image) get_imports() (in module schrodinger.application.matsci.codeutils) get_in_cms_from_cpt() (in module schrodinger.application.desmond.gui) get_included_entry_ids() (in module schrodinger.project.utils) get_included_force_field_paths() (in module schrodinger.application.matsci.cgforcefield) get_included_hypotheses_ids() (in module schrodinger.application.phase.phase_markers) get_included_structures() (in module schrodinger.project.utils) get_index() (schrodinger.application.canvas.r_group.TempAtom method) get_index_from_default_name() (in module schrodinger.application.matsci.msutils) get_indices_from_unbinding_subjob() (in module schrodinger.application.desmond.kinetics.utils) get_inferred_statuses() (in module schrodinger.seam.viz.inspect) get_infile_type() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_input_files() (in module schrodinger.application.desmond.multisimstartup) (in module schrodinger.application.phase.packages.hypo_refine.job_utils) (in module schrodinger.application.phase.packages.shape_creation_logic) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) get_input_files_possibly_list() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_input_screen_files() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_input_smarts_files() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_input_subset_files() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_inscribe_extents() (in module schrodinger.comparison.struc) get_installation_check_commands() (in module schrodinger.utils.installation_check) get_installed_hostfiles() (in module schrodinger.job.jobcontrol) get_int_tuples_from_str_property() (in module schrodinger.application.matsci.reaction_workflow_utils) get_interaction_data() (in module schrodinger.utils.pymol) get_interaction_label() (in module schrodinger.protein.assignment) get_interaction_sites() (in module schrodinger.application.bindingsite.intfield) get_interface_atoms() (in module schrodinger.structutils.interactions.protein_protein_interactions) get_interface_kwargs() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_interface_normal() (in module schrodinger.application.matsci.msutils) get_internal_coordinates() (schrodinger.application.jaguar.hess_guess.CoordinateManager method) get_internal_energy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_internal_info() (in module schrodinger.application.matsci.coarsegrain) get_internal_zip_path() (in module schrodinger.application.phase.packages.phase_utils) get_intersection() (in module schrodinger.math.multi_parameter_optimization) get_inverse_reactions_by_reagent() (in module schrodinger.application.pathfinder.reaction) get_inversion_index() (in module schrodinger.application.matsci.nano.util) get_isoelectronic_mutator_indicies() (in module schrodinger.application.matsci.genetic_optimization) get_iterator() (in module schrodinger.application.matsci.msutils) get_j_label() (schrodinger.application.jaguar.simple_spec.Peak method) get_j_summary() (schrodinger.application.jaguar.simple_spec.Peak method) get_jaguar_keywords_list() (in module schrodinger.application.matsci.reaction_workflow_utils) get_jaguar_max_atoms() (in module schrodinger.application.matsci.jaguarworkflows) get_jaguar_out_mae() (in module schrodinger.application.matsci.jaguarworkflows) get_jaguar_output() (in module schrodinger.application.matsci.jaguarworkflows) get_job_command_in_startup() (in module schrodinger.application.desmond.cmdline) get_job_details() (in module schrodinger.application.desmond.simulation_block_test) get_job_from_hub() (in module schrodinger.application.matsci.jobutils) get_job_output_filenames() (in module schrodinger.application.glide.utils) get_job_spec_builder_from_args() (schrodinger.stepper.app.StepperApplication class method) get_job_spec_from_args() (in module schrodinger.active_learning.mq_driver) (in module schrodinger.active_learning.mq_worker) (in module schrodinger.application.bioluminate.methionine_oxidation) (in module schrodinger.application.bioluminate.patch_utils.pre_analyze) (in module schrodinger.application.desmond.gpgpu.test_gpgpu) (in module schrodinger.application.matsci.packmol) (in module schrodinger.application.phase.packages.shape_screen_al_driver) (schrodinger.stepper.app.StepperApplication class method) get_job_type() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_jobdj() (in module schrodinger.active_learning.al_node) (in module schrodinger.application.phase.packages.shape_screen_al_utils) get_jobhost() (in module schrodinger.application.matsci.jobutils) get_jobhost_name() (in module schrodinger.application.matsci.jobutils) get_jobhosts() (in module schrodinger.application.matsci.jobutils) get_jobname() (in module schrodinger.application.bb_database.bb_job_utils) (in module schrodinger.application.bioluminate.methionine_oxidation) (in module schrodinger.application.combinatorial_diversity.driver_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) (in module schrodinger.application.combinatorial_screen.driver_utils) (in module schrodinger.application.glide.utils) (in module schrodinger.application.jaguar.utils) (in module schrodinger.application.matsci.jobutils) (in module schrodinger.application.matsci.parserutils) (in module schrodinger.application.phase.packages.oned_task_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) (in module schrodinger.application.phase.packages.phase_utils) (in module schrodinger.application.phase.packages.shape_screen_job_utils) (in module schrodinger.application.phase.shape_screen_reporter.task_utils) (in module schrodinger.application.vss.tasks) (in module schrodinger.job.jobcontrol) (in module schrodinger.utils.fileutils) get_jobname_and_outfile() (in module schrodinger.application.phase.packages.shape_creation_logic) get_jobtype_name() (in module schrodinger.application.licensing.licadmin) get_json_formatted_structure_hierarchy() (in module schrodinger.livedesign.bbchem_endpoints) get_json_from_map_file() (in module schrodinger.utils.documentation) get_json_version_from_file() (in module schrodinger.models.json) get_json_version_from_string() (in module schrodinger.models.json) get_keep_idxs() (in module schrodinger.application.matsci.swap_fragments_utils) get_keep_struc_tags() (in module schrodinger.application.desmond.keep_struc_tags) (in module schrodinger.application.desmond.msj_generator.keep_struc_tags) get_kekule_smiles() (in module schrodinger.application.pathfinder.route) get_keq() (in module schrodinger.application.matsci.reaction_workflow_utils) get_kernel_version() (in module schrodinger.utils.sysinfo) get_key_files() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.bb_database.bb_job_utils) get_key_limits() (in module schrodinger.application.bb_database.bb_task_utils) get_key_name() (in module schrodinger.application.licensing.licadmin) get_keyword() (in module schrodinger.application.glide.glide) get_keywords_dicts() (in module schrodinger.application.glide.glide) get_keywords_set() (in module schrodinger.application.glide.glide) get_label() (in module schrodinger.application.bioluminate.peptide_sar.label) get_labeled_scores() (in module schrodinger.application.bioluminate.peptide_sar.sar) get_ladder_polymer_relaxation_stringers() (in module schrodinger.application.matsci.desconfig) get_lambda() (schrodinger.application.desmond.fep_schedule.FepSchedule method) get_lambda_atom_indices() (schrodinger.application.desmond.cms.Cms method) get_largest_moment_normalized_vector() (in module schrodinger.structutils.analyze) get_last_20_lines() (in module schrodinger.pipeline.pipeutils) get_last_exception() (in module schrodinger.utils.qt_utils) get_last_forced_EZ_property_index() (in module schrodinger.structutils.rgroup_enumerate) get_last_selected_directory() (in module schrodinger.ui.qt.filedialog) get_lattice_param_from_enegrp() (in module schrodinger.application.desmond.ene_utils) get_lattice_param_properties() (in module schrodinger.application.matsci.nano.xtal) get_lattice_properties() (in module schrodinger.application.matsci.nano.particle) get_lattice_vectors() (in module schrodinger.application.matsci.nano.sheet) (in module schrodinger.application.matsci.nano.xtal) get_launch_command_from_args() (in module schrodinger.job.jobcontrol) get_launch_command_without_toplevel() (in module schrodinger.job.jobcontrol) get_launcher() (schrodinger.application.desmond.multisimstartup.Startup method) get_ld_client() (in module schrodinger.application.livedesign.login) get_ld_library_path_for_system_ssh() (in module schrodinger.utils.env) get_LD_mode() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_LD_similarity_score() (in module schrodinger.livedesign.cmdline) get_LD_version() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_ldclient_download_dir() (in module schrodinger.application.livedesign.login) get_ldclient_enums() (in module schrodinger.application.livedesign.login) get_ldclient_models() (in module schrodinger.application.livedesign.login) get_ldclient_requests() (in module schrodinger.application.livedesign.login) get_ldclient_responses() (in module schrodinger.application.livedesign.login) get_lead_confs() (in module schrodinger.application.macromodel.apps) get_leg_name_from_jobname() (in module schrodinger.application.desmond.util) get_leg_type_from_jobname() (in module schrodinger.application.desmond.util) get_legal_name() (schrodinger.utils.pymol.PymolInstance method) get_lib_dir() (in module schrodinger.utils.postinstall) get_libpath() (in module schrodinger.application.pathfinder.reaction) get_libstdcpp_version() (in module schrodinger.utils.installation_check) get_license() (in module schrodinger.application.canvas.utils) get_license_request_info() (in module schrodinger.application.licensing.netsuiteapi) get_license_sources() (in module schrodinger.application.licensing.licserver.client) get_licenses() (in module schrodinger.application.desmond.multisimstartup) get_ligand() (in module schrodinger.ui.qt.structure2d) get_ligand1_atom_dict() (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) get_ligand2_atom_dict() (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) get_ligand_asl() (in module schrodinger.structutils.sitealign) get_ligand_atom_indices() (in module schrodinger.protein.assignment) get_ligand_id_pairs() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) get_ligand_interactors() (in module schrodinger.protein.assignment) get_ligand_ml_metric() (in module schrodinger.active_learning.al_report) get_ligand_name() (in module schrodinger.application.matsci.buildcomplex) get_ligand_rmsd() (in module schrodinger.application.desmond.util) get_ligand_titles() (in module schrodinger.application.phase.packages.hypo_refine.project_utils) get_ligands() (in module schrodinger.application.desmond.feputils) (in module schrodinger.application.livedesign.entry_types) get_ligands_info() (in module schrodinger.application.matsci.buildcomplex) get_ligprep_command() (in module schrodinger.application.vss.tasks) get_ligprep_files() (in module schrodinger.application.glide.utils) get_ligprep_parser() (in module schrodinger.application.glide.utils) get_limit_for_export_mode() (in module schrodinger.application.pymol.export_handler) get_limited_sanitized_mol() (in module schrodinger.livedesign.preprocessor) get_linked_path() (in module schrodinger.application.licensing.flexlm) get_listof_props_ene() (in module schrodinger.application.desmond.simulation_block_data) get_lnq_key() (in module schrodinger.application.matsci.jaguarworkflows) (in module schrodinger.application.matsci.reaction_workflow_utils) get_local_appdata_dir() (in module schrodinger.utils.fileutils) get_local_gpgpus() (in module schrodinger.infra.gpgpu_utils) get_local_server() (in module schrodinger.application.licensing.licadmin) get_local_symmetry() (in module schrodinger.application.desmond.meta) get_lock() (in module schrodinger.application.pathfinder.multiroute) get_log_props() (in module schrodinger.application.desmond.simulation_block_data) get_loggable_float() (in module schrodinger.application.matsci.genetic_optimization) get_logger() (in module schrodinger.utils.log) get_loggerstates() (in module schrodinger.rdkit.rdkit_adapter) get_logging_tag() (in module schrodinger.application.matsci.jobutils) get_long_family_name() (in module schrodinger.application.livedesign.data_classes) get_loop_instructions() (schrodinger.application.bioluminate.antibody.grafting.GraftingInput method) get_loop_ranges() (in module schrodinger.application.bioluminate.anarci.loop_ranges) get_low_energy_conformers() (in module schrodinger.application.matsci.genetic_optimization) get_low_energy_reps() (in module schrodinger.structutils.analyze) get_luma() (in module schrodinger.ui.qt.standard.colors) get_machid_output() (in module schrodinger.application.licensing.licadmin) get_macro() (in module schrodinger.application.jaguar.user_config) (schrodinger.application.jaguar.keywordDB.Keyword method) (schrodinger.application.jaguar.keywordDB.Setting method) get_macro_dict() (in module schrodinger.utils.sea.sea) get_maestro() (in module schrodinger) get_maestro_find_toolbar_layout() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_maestro_forcefield_selector() (in module schrodinger.ui.qt.forcefield.ffselector) get_maestro_params() (in module schrodinger.structutils.interactions.hbond) get_maestro_scripts_path() (in module schrodinger.utils.maestro_scripts_path) get_maestro_view_settings() (in module schrodinger.application.pymol.mae_sync) get_mag_hubbu() (in module schrodinger.application.matsci.espresso.utils) get_map_model_to_template() (in module schrodinger.application.bioluminate.antibody.assembly) get_map_rdk_to_sdgr() (in module schrodinger.rdkit.rdkit_adapter) get_map_sdgr_to_rdk() (in module schrodinger.rdkit.rdkit_adapter) get_mappings() (in module schrodinger.comparison.struc) get_marked_func_order() (in module schrodinger.utils.funcgroups) get_marker_atom_indexes_from_structure() (in module schrodinger.application.matsci.buildcomplex) get_marker_color() (schrodinger.ui.qt.rama.RamaScatterMixin method) get_martini_antifreeze_type_from_type() (in module schrodinger.application.matsci.coarsegrain) get_martini_bond_force_constant() (in module schrodinger.application.matsci.coarsegrain) get_martini_epsilon() (in module schrodinger.application.matsci.coarsegrain) get_martini_eq_length() (in module schrodinger.application.matsci.coarsegrain) get_martini_ring_type_from_type() (in module schrodinger.application.matsci.coarsegrain) get_martini_sigma() (in module schrodinger.application.matsci.coarsegrain) get_martini_subtypes() (in module schrodinger.application.matsci.coarsegrain) get_martini_tiny_type_from_type() (in module schrodinger.application.matsci.coarsegrain) get_martini_type_from_super_type() (in module schrodinger.application.matsci.coarsegrain) get_mask_name() (in module schrodinger.application.phase.phase_markers) get_mass() (in module schrodinger.application.matsci.coarsegrain) (schrodinger.application.desmond.cms.Cms method) get_master_oned_properties() (in module schrodinger.application.phase.packages.oned_task_utils) get_match_options() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils) get_matching_ws_atoms() (in module schrodinger.application.bioluminate.pml_menus) get_matching_ws_entries() (in module schrodinger.application.bioluminate.pml_menus) get_materials_relaxation_stringers() (in module schrodinger.application.matsci.desconfig) get_matplotlib_toolbar_message() (in module schrodinger.application.matsci.gutils) get_matrix_value() (in module schrodinger.protein.residue) get_matsci_module_graph() (in module schrodinger.application.matsci.codeutils) get_matsci_module_paths() (in module schrodinger.application.matsci.codeutils) get_matsci_user_data_dir() (in module schrodinger.application.matsci.msutils) get_max_and_rms_and_len() (in module schrodinger.application.matsci.mecp_mod) get_max_batch_size() (in module schrodinger.application.glide.sort_utils) get_max_chem_valencies() (in module schrodinger.application.matsci.elementalprops) get_max_chem_valencies_with_exceptions() (in module schrodinger.application.matsci.elementalprops) get_max_cov_radius() (in module schrodinger.application.matsci.nano.xtal) get_max_distance_btw_groups() (in module schrodinger.application.matsci.packmol) get_max_height() (schrodinger.application.jaguar.simple_spec.Peak method) get_max_hits() (in module schrodinger.application.phase.packages.phase_screen_utils) get_max_ppm() (schrodinger.application.jaguar.simple_spec.Peak method) get_max_torsion_deviation() (in module schrodinger.comparison.struc) get_max_valencies() (in module schrodinger.application.matsci.elementalprops) get_maximum_vdw_radius() (in module schrodinger.application.matsci.amorphous) get_mcs_atoms() (in module schrodinger.ui.two_d_viewer) get_md_jobs() (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher method) (schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher method) get_md_results() (in module schrodinger.application.matsci.equilibrium_md) get_mean() (in module schrodinger.application.desmond.fepana) get_measurement_items() (in module schrodinger.utils.pymol) get_MEL_class() (in module schrodinger.application.pathfinder.reaction) get_membrane_cts() (schrodinger.application.desmond.cms.Cms method) get_membrane_launcher_input() (in module schrodinger.application.desmond.membrane_utils) get_meta_cfg_filename() (in module schrodinger.application.desmond.meta) get_metals_and_neighbors() (in module schrodinger.structutils.rgroup_enumerate) get_methionines() (in module schrodinger.application.bioluminate.methionine_oxidation) get_mhc_vectors() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_min_max_avg() (in module schrodinger.application.matsci.uq_utils) get_min_pop() (in module schrodinger.application.phase.packages.shape_diversity) get_min_ppm() (schrodinger.application.jaguar.simple_spec.Peak method) get_min_sites() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) get_missed_atom_id_groups() (in module schrodinger.application.matsci.amorphous) get_missing_columns() (in module schrodinger.application.bioluminate.pose_filtering.hdx_io) get_mmct_max_valencies() (in module schrodinger.application.matsci.elementalprops) get_mmlewis_bonding() (in module schrodinger.application.jaguar.autots_bonding) get_mmod_energy_key() (in module schrodinger.application.matsci.reaction_workflow_utils) get_mmod_energy_keys() (in module schrodinger.application.matsci.reaction_workflow_utils) get_mmod_rel_energy_key() (in module schrodinger.application.matsci.reaction_workflow_utils) get_mmshare_common_dir() (in module schrodinger.utils.fileutils) get_mmshare_data_dir() (in module schrodinger.utils.fileutils) get_mmshare_dir() (in module schrodinger.utils.fileutils) get_mmshare_listing() (in module schrodinger.application.licensing.licadmin) get_mmshare_reagent_data_dir() (in module schrodinger.application.pathfinder.reaction) get_mmshare_scripts_dir() (in module schrodinger.utils.fileutils) get_mmshare_version() (in module schrodinger) get_mode_for_search_option() (in module schrodinger.maestro_utils.find_tool_bar.constants) get_model() (in module schrodinger.application.matsci.equilibrium_md) get_model_by_name() (in module schrodinger.application.livedesign.upload_utils) get_model_ff_name() (in module schrodinger.application.matsci.desmondutils) get_model_from_pt_row() (in module schrodinger.application.desmond.gui) get_model_system_type() (in module schrodinger.application.desmond.cms) get_module_docstring() (in module schrodinger.utils.install_scripts) get_module_from_path() (in module schrodinger.utils.imputils) get_mol() (in module schrodinger.rdkit.molio) get_mol_formula() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_mol_ids() (schrodinger.utils.multifpfile.MultiFPFile method) get_mol_layers() (in module schrodinger.rdkit_extensions) get_mol_reader() (in module schrodinger.rdkit.molio) get_mol_series_plot() (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker method) get_mol_writer() (in module schrodinger.rdkit.molio) get_molecular_formula() (in module schrodinger.application.matsci.species) get_molecular_weight() (in module schrodinger.application.matsci.msutils) (in module schrodinger.application.matsci.reaction_workflow_utils) get_molecule_exposures() (in module schrodinger.application.desmond.solubility_utils) get_molecules_pseudos() (in module schrodinger.application.matsci.desmondutils) get_monomer_data() (in module schrodinger.livedesign.biologics.sequence) get_mopfile_text() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) get_moved() (in module schrodinger.models.diffy) get_moved_list() (in module schrodinger.models.diffy) get_mpi_related_envvars() (in module schrodinger.application.desmond.driver_utils) get_mpircores() (in module schrodinger.application.matsci.espresso.utils) get_mpirun_cmd() (in module schrodinger.application.desmond.driver_utils) get_mpl_backend_name() (in module schrodinger) get_msg() (in module schrodinger.application.matsci.reaction_workflow_utils) get_msj_backend() (in module schrodinger.application.desmond.config_utils) get_msj_filename() (in module schrodinger.application.desmond.util) get_msj_template_path() (in module schrodinger.application.desmond.gui) get_mtd_footer_mexpr() (in module schrodinger.application.desmond.kinetics.enhanced_sampling) get_mtd_header_mexpr() (in module schrodinger.application.desmond.kinetics.enhanced_sampling) get_mtd_info() (in module schrodinger.application.desmond.kinetics.utils) get_mtd_results() (in module schrodinger.application.desmond.kinetics.utils) get_multisim_command() (in module schrodinger.application.matsci.desmondutils) get_multisim_stage_numbers() (in module schrodinger.application.desmond.launch_utils) get_multisim_subjob_names() (in module schrodinger.application.desmond.launch_utils) get_muscle_path() (in module schrodinger.protein.tasks.muscle) get_mutate_to_filename() (in module schrodinger.protein.nonstandard_residues) get_mutation_atoms_and_bonds() (in module schrodinger.application.desmond.fep_scholar_util) get_mutation_encoding() (in module schrodinger.application.bioluminate.peptide_sar.encode) get_mwc_to_nm_transform() (in module schrodinger.application.matsci.bandshape_utils) get_mydocuments_dir() (in module schrodinger.utils.fileutils) get_mynetworkplaces_dir() (in module schrodinger.utils.fileutils) get_n_vdw_and_charge_div() (schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule static method) get_name() (schrodinger.infra.mmcheck.ReturnCode method) get_name_element_mapper_cg() (in module schrodinger.application.matsci.rdpattern) get_name_file() (in module schrodinger.application.jaguar.input) get_name_filter() (in module schrodinger.utils.fileutils) get_name_w_mol_n() (in module schrodinger.application.matsci.order_parameter_mod) get_name_wo_mol_n() (in module schrodinger.application.matsci.order_parameter_mod) get_names() (in module schrodinger.application.matsci.coarsegrain) get_natom_btw_two_cells() (in module schrodinger.application.matsci.nano.xtal) get_natoms() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_natural_analog() (in module schrodinger.protein.helm.helm_renderer) get_natural_analog_map() (in module schrodinger.protein.process_enamine_db) get_nearest_image() (in module schrodinger.application.matsci.pbcutils) get_neighboring_atom_distances() (in module schrodinger.application.bioluminate.protein_interaction.calculate) get_neighbors() (in module schrodinger.structutils.assignbondorders) get_netsuite_license() (in module schrodinger.application.licensing.licadmin) get_network_info() (in module schrodinger.application.licensing.licadmin) get_neutralization_patterns() (in module schrodinger.application.pathfinder.synthesis) get_new_filename() (in module schrodinger.application.vss.tasks) get_new_index() (schrodinger.protein.assignment.ProtAssign.changeable method) get_next_filename() (in module schrodinger.utils.fileutils) get_next_filename_prefix() (in module schrodinger.utils.fileutils) get_next_jobname() (in module schrodinger.ui.qt.appframework) (in module schrodinger.ui.qt.appframework2.jobnames) get_next_name() (in module schrodinger.application.matsci.msutils) get_next_partition() (in module schrodinger.application.desmond.autopartition) get_next_partition_array() (in module schrodinger.application.dendrogram.core_class) get_niggli_params() (in module schrodinger.comparison.struc) get_nmr() (in module schrodinger.application.jaguar.textparser) get_nmr_shifts() (in module schrodinger.application.jaguar.textparser) get_nodefilename() (in module schrodinger.application.desmond.driver_utils) get_nonbond_potential_type() (in module schrodinger.application.matsci.coarsegrain) get_nondefault_features() (in module schrodinger.utils.featureflags.featureflags) get_nonduplicated_atom() (in module schrodinger.application.desmond.remd) get_nonzero_data() (in module schrodinger.application.matsci.uq_utils) get_normal_modes() (in module schrodinger.application.matsci.anharmonic) get_normal_surf() (in module schrodinger.application.matsci.nano.xtal) get_normal_surf_from_HKL() (in module schrodinger.application.matsci.nano.xtal) get_normalized() (in module schrodinger.graphics3d.common) get_normalized_spanning_vectors() (in module schrodinger.application.matsci.nano.xtal) get_normalized_vector() (in module schrodinger.structutils.transform) get_npseudos_per_molecule() (in module schrodinger.application.matsci.desmondutils) get_nrep() (schrodinger.application.desmond.replica_dE.replica_container method) (schrodinger.application.desmond.replica_dE.replicas_monitor method) get_nucleotide_dihedrals() (in module schrodinger.trajectory.trajectory_gui_dir.custom_analyzers) get_null_job() (in module schrodinger.application.job_monitor.job_monitor_models) get_null_mag_element() (in module schrodinger.application.matsci.espresso.utils) get_num_clashes_with_metals() (in module schrodinger.application.prepwizard) get_num_constraint() (in module schrodinger.application.desmond.remd) (schrodinger.application.desmond.cms.Cms method) get_num_license_tokens() (in module schrodinger.application.combinatorial_screen.driver_utils) get_num_missing_data() (in module schrodinger.application.matsci.kmc) get_num_nonwateratom() (in module schrodinger.application.desmond.remd) get_num_nprocs() (in module schrodinger.ui.qt.config_dialog) get_num_probes() (in module schrodinger.application.phase.packages.shape_diversity) get_num_rotatable_bonds() (in module schrodinger.structutils.analyze) get_num_simple_bonds() (in module schrodinger.application.matsci.genetic_optimization) get_num_subjobs() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) (in module schrodinger.application.phase.packages.phase_screen_driver_utils) get_num_wateratom() (in module schrodinger.application.desmond.remd) get_number_atoms() (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) get_number_density_from_cms() (in module schrodinger.application.desmond.fepana) get_number_electrons() (in module schrodinger.application.jaguar.utils) get_numbers_by_region_name() (in module schrodinger.application.bioluminate.anarci.annotate) get_numeric_operator() (in module schrodinger.application.bioluminate.pose_filtering.operators) get_numeric_operators_by_name() (in module schrodinger.application.bioluminate.pose_filtering.operators) get_numeric_property_range() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) get_nwaters() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_obj_value() (in module schrodinger.ui.qt.appframework2.settings) get_old2new() (in module schrodinger.application.desmond.torsion_related) get_one_step_route() (in module schrodinger.application.pathfinder.synthesis) get_oned_data_file_attributes() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_data_file_distribution() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_data_file_names() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_data_file_properties() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_data_file_row_count() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_data_file_rows() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_data_file_splits() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_query() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_query_row() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_query_rows() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_query_structures() (in module schrodinger.application.phase.packages.oned_task_utils) get_oned_screen_command() (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) get_op_trans_idx() (in module schrodinger.comparison.struc) get_opacity() (in module schrodinger.application.desmond.fep_edge_report_maker) get_open_file_name() (in module schrodinger.ui.qt.filedialog) (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog static method) get_open_file_names() (in module schrodinger.ui.qt.filedialog) (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog static method) get_open_wm_file_name() (in module schrodinger.ui.qt.filedialog) get_openmpi_env() (in module schrodinger.utils.openmpi) get_openmpi_prefix() (in module schrodinger.utils.openmpi) get_opls_dir() (in module schrodinger.utils.cmdline) get_opls_dir_cmd() (in module schrodinger.application.desmond.feputils) get_opls_version_display_name() (in module schrodinger.ui.qt.forcefield.forcefield) get_optimal_atom_mapping() (in module schrodinger.structutils.rmsd) get_option() (in module schrodinger.application.matsci.jobutils) (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method) get_ordered_backbone_atoms() (in module schrodinger.application.matsci.geometry) get_ordered_polymer_backbone() (in module schrodinger.application.matsci.geometry) get_orig_atom_idx() (in module schrodinger.application.matsci.amorphous) get_orig_seq_name() (in module schrodinger.protein.tasks.structure_alignment) get_orig_title() (in module schrodinger.application.matsci.reaction_workflow_utils) get_orthant_strings() (in module schrodinger.application.combinatorial_diversity.splitter_utils) get_osname() (in module schrodinger.utils.sysinfo) get_other_item() (in module schrodinger.application.matsci.amorphous) get_other_reactive_indexes() (in module schrodinger.application.matsci.msprops) get_out_file_paths() (in module schrodinger.application.matsci.bandshape_utils) get_out_filename() (in module schrodinger.application.bioluminate.anarci.annotate) get_out_mae_path() (in module schrodinger.application.matsci.jaguarworkflows) get_out_rep() (in module schrodinger.application.matsci.reaction_workflow_utils) get_outermost_group() (in module schrodinger.application.desmond.kinetics.utils) get_outfile_name() (in module schrodinger.livedesign.biologics.modeling) get_output_file_name() (in module schrodinger.application.glide.utils) (in module schrodinger.application.matsci.genetic_optimization) get_output_hypo() (in module schrodinger.application.phase.packages.hypo_refine.job_utils) get_output_jobs() (schrodinger.application.desmond.cmj.StageBase method) get_output_logger() (in module schrodinger.utils.log) get_output_logger_handler() (in module schrodinger.utils.log) get_output_projects() (in module schrodinger.application.phase.packages.hypo_refine.job_utils) get_output_writer() (in module schrodinger.application.pathfinder.multiroute) get_overlap_dim() (in module schrodinger.application.jaguar.output) get_overlapping_atoms() (in module schrodinger.application.prepwizard2.diagnostics) get_pair_info() (in module schrodinger.application.matsci.kmc) get_pair_rates_from_database() (in module schrodinger.application.matsci.kmc) get_pair_rule_env_ids() (in module schrodinger.application.phase.packages.mmp2d) get_pairs_from_database() (in module schrodinger.application.matsci.kmc) get_pairs_table() (in module schrodinger.application.matsci.kmc) get_pairwise_sequence_similarity() (in module schrodinger.protein.sequence) get_parallelepiped_vertices() (in module schrodinger.application.matsci.shapes) get_param_string() (in module schrodinger.application.matsci.textlogger) get_params_from_chorus() (in module schrodinger.application.matsci.nano.xtal) get_params_from_vectors() (in module schrodinger.application.matsci.nano.xtal) get_parent_jobname() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_pargph() (in module schrodinger.application.desmond.rl_helper) get_parser() (in module schrodinger.active_learning.mq_driver) (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.combinatorial_diversity.driver_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) (in module schrodinger.application.combinatorial_screen.driver_utils) (in module schrodinger.application.desmond.starter.ui.cmdline) (in module schrodinger.application.licensing.licserver.main) (in module schrodinger.application.matsci.packmol) (in module schrodinger.application.phase.packages.align_ligands_driver_options) (in module schrodinger.application.phase.packages.hypo_refine.option_utils) (in module schrodinger.application.phase.packages.mmp3d_driver_utils) (in module schrodinger.application.phase.packages.oned_option_utils) (in module schrodinger.application.phase.packages.phase_convert_MOE) (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_screen_driver_utils) (in module schrodinger.application.phase.packages.shape_screen_al_driver) (in module schrodinger.application.phase.packages.shape_screen_arg_utils) (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) (in module schrodinger.application.phase.shape_screen_reporter.option_utils) (in module schrodinger.seam.viz.watcher) (in module schrodinger.seam.viz.watcherd) get_password() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_path_from_module() (in module schrodinger.utils.imputils) get_pathway() (in module schrodinger.application.desmond.fepana) get_pattern() (in module schrodinger.application.matsci.rdpattern) (schrodinger.application.matsci.xrd.XRDCalculator method) get_pbc() (in module schrodinger.structutils.pbc_tools) get_pbc_bonded_atom_pairs() (in module schrodinger.application.matsci.nano.xtal) get_pbc_bonds_dict() (in module schrodinger.application.matsci.nano.xtal) get_pbc_origin() (in module schrodinger.application.matsci.nano.xtal) get_pdb() (in module schrodinger.protein.getpdb) get_pdb_data() (in module schrodinger.application.matsci.packmol) get_pdb_id() (in module schrodinger.application.prepwizard) get_penalty() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_pending_splice_data() (in module schrodinger.application.phase.packages.phase_database_job_utils) get_pending_subjobs() (in module schrodinger.application.phase.packages.phase_database_job_utils) get_percent_screen_curve_points() (in module schrodinger.analysis.enrichment.plotter) get_persistent_value() (in module schrodinger.ui.qt.appframework2.settings) get_perspective() (in module schrodinger.application.pymol.mae_sync) get_perturbed_indices() (schrodinger.application.matsci.elasticity.strain.Deformation method) get_pfx_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_pfx_size() (in module schrodinger.rdkit.molio) get_pH_population_factors() (schrodinger.application.jaguar.macro_pka_utils.PhPopulations method) get_phase_markers() (in module schrodinger.application.phase.phase_markers) get_phs_from_replica_info() (in module schrodinger.application.desmond.starter.generator.fep_residue_scanning) get_physical_properties() (in module schrodinger.application.matsci.nano.xtal) get_picked() (schrodinger.ui.qt.rama.Rama method) get_picture_as_text() (in module schrodinger.ui.qt.swidgets) get_pipeline_info() (in module schrodinger.seam.viz.inspect) get_pipeline_start_time() (in module schrodinger.seam.viz.inspect) get_pka() (in module schrodinger.protein.assignment) get_pkeywords() (in module schrodinger.application.matsci.espresso.utils) get_placeholders() (in module schrodinger.structutils.markush_enumerate) get_plane_alignment_angle() (in module schrodinger.application.jaguar.utils) get_plane_trans_cart_to_frac() (in module schrodinger.application.matsci.desconfig) get_platform_incompatibility_message() (in module schrodinger.utils.platform) get_player_toolbar() (in module schrodinger.trajectory.trajectoryviewer) get_PLDB_SMARTS() (in module schrodinger.livedesign.bbchem_endpoints) get_plot_data() (in module schrodinger.analysis.enrichment.plotter) get_plottable_table_data() (in module schrodinger.application.matsci.kmcgui) get_pointgroup_symmetry_ops() (in module schrodinger.comparison.struc) get_points_in_region() (in module schrodinger.application.matsci.uq_utils) get_polygon_area() (in module schrodinger.application.matsci.shapes) get_polymer_annotations() (in module schrodinger.livedesign.biologics.sequence) get_populations_at_pH() (schrodinger.application.jaguar.macro_pka_utils.PhPopulations method) get_portnum() (in module schrodinger.tasks.taskszmq) get_pos_vel() (schrodinger.application.desmond.cms.Cms method) get_postmortem_command() (in module schrodinger.utils.installation_check) get_potential() (schrodinger.application.desmond.torsion_related.TorsionPotential method) get_potential_alignment() (in module schrodinger.comparison.struc) get_powder_diffraction_pattern() (in module schrodinger.application.matsci.spectra) get_ppdb() (in module schrodinger.application.matsci.espresso.ppdb) get_preference() (in module schrodinger.utils.preferences) get_preference_handler() (in module schrodinger.ui.qt.appframework2.settings) get_prejobs() (schrodinger.application.desmond.cmj.StageBase method) get_present_props() (in module schrodinger.application.matsci.reaction_workflow_utils) get_present_props_from_sts() (in module schrodinger.application.matsci.reaction_workflow_utils) get_pressure() (in module schrodinger.application.matsci.jaguarworkflows) get_pressures_temps() (in module schrodinger.application.matsci.reaction_workflow_utils) get_pretty_geom_str() (in module schrodinger.application.matsci.buildcomplex) get_prevent_chirality_flip_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_prime_factors() (in module schrodinger.application.desmond.autopartition) get_primitive_cell() (in module schrodinger.application.matsci.nano.xtal) get_print_simbox_data() (in module schrodinger.application.desmond.simulation_block_data) get_prob_from_temp_ladder() (in module schrodinger.application.desmond.remd) get_probe_paths() (in module schrodinger.application.desmond.mxmd.mxmd_system_builder) get_probes_structure() (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot method) get_problems() (in module schrodinger.application.prepwizard2.diagnostics) get_proc_time() (schrodinger.application.desmond.cmj.Job method) get_procs() (in module schrodinger.application.matsci.jobutils) get_product() (in module schrodinger.application.licensing.licadmin) get_product_description() (in module schrodinger.utils.machid) get_product_git_hashes() (in module schrodinger.utils.machid) get_product_info() (in module schrodinger.application.desmond.util) get_product_name() (in module schrodinger.application.glide.utils) get_profile_name_key() (in module schrodinger.utils.documentation) get_project_file_names() (in module schrodinger.application.phase.packages.hypo_refine.project_utils) get_project_group_hierarchy() (in module schrodinger.application.matsci.msutils) get_project_preference_custom_opls_path() (in module schrodinger.ui.qt.forcefield.forcefield) get_prop() (in module schrodinger.application.glide.utils) (in module schrodinger.application.glide.xpdes) get_prop_from_ene() (in module schrodinger.application.desmond.ene_utils) get_prop_idx() (in module schrodinger.application.glide.xpdes) get_prop_list() (schrodinger.application.canvas.r_group.Data method) get_prop_name_to_display_name_map() (in module schrodinger.protein.properties) get_prop_value() (schrodinger.application.desmond.simulation_block_data.Array_Prop method) get_prop_values() (schrodinger.application.canvas.r_group.Data method) get_proper_path() (in module schrodinger.application.phase.packages.phase_utils) get_properties() (in module schrodinger.application.livedesign.ld_utils) get_properties_datanames_from_entry_data() (in module schrodinger.application.livedesign.ld_utils) get_properties_from_inputfiles() (in module schrodinger.application.matsci.permittivity) get_property_info() (in module schrodinger.application.matsci.genetic_optimization) get_property_keys_from_keywords() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) get_property_name() (in module schrodinger.structutils.smiles) get_property_names() (in module schrodinger.application.phase.packages.mmp2d) get_property_positions() (in module schrodinger.application.phase.packages.oned_task_utils) get_property_type() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_property_value() (in module schrodinger.application.livedesign.ld_utils) get_property_values() (in module schrodinger.application.phase.packages.mmp2d) get_props() (in module schrodinger.application.glide.utils) get_protein() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) get_protein_alphabet() (in module schrodinger.protein.residue) get_protein_families() (in module schrodinger.protein.gpcr.gpcrdb) get_protein_family() (in module schrodinger.application.bioluminate.classify) get_protein_family_data() (in module schrodinger.application.bioluminate.classify) get_protein_label_string() (in module schrodinger.application.desmond.feputils) get_protein_residues_sequence_tags() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData method) get_protein_rmsf() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) get_proteins() (in module schrodinger.application.desmond.feputils) get_proxy_periodic_table() (in module schrodinger.rdkit.coarsegrain) get_pseudochirality() (in module schrodinger.comparison.chirality) get_PT() (in module schrodinger.project.utils) get_ptensor_from_enegrp() (in module schrodinger.application.desmond.ene_utils) get_ptensor_from_plugin() (in module schrodinger.application.matsci.desmondutils) get_ptensor_from_trj() (in module schrodinger.application.matsci.desmondutils) get_public_class_tokens_by_name() (in module schrodinger.ui.qt.standard.design_tokens) get_public_databases() (in module schrodinger.application.fpsim) get_public_ids() (in module schrodinger.application.phase.packages.mmp2d) get_pv_file_merged_structures() (in module schrodinger.application.glide.poseviewconvert) get_pyatom_from_cppatom() (in module schrodinger.structure) get_pymatgen_mol() (in module schrodinger.comparison.struc) get_pymatgen_structure() (in module schrodinger.application.matsci.pmgutils) get_pymol_cmd() (in module schrodinger.utils.fileutils) get_pymol_location_preference() (in module schrodinger.application.pymol.utils) get_pymol_scripts_dir() (in module schrodinger.application.pymol.utils) get_python_versions() (in module schrodinger.application.matsci.gsas.GSASIIfiles) get_qcolor() (in module schrodinger.application.desmond.report_helper) get_qimage() (in module schrodinger.ui.sketcher_image) get_qpicture() (in module schrodinger.ui.sketcher_image) get_qpicture_highlight() (in module schrodinger.ui.qt.structure2d) get_qpicture_protected() (in module schrodinger.ui.qt.structure2d) get_query_job_config() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) get_query_subjobs() (in module schrodinger.application.phase.packages.phase_database_job_utils) get_r_group_for_atom() (schrodinger.application.canvas.r_group.Data method) get_r_groups() (schrodinger.application.canvas.r_group.Data method) get_r_groups_per_atom() (schrodinger.application.canvas.r_group.Data method) get_random_csearch_seed() (in module schrodinger.application.matsci.genetic_optimization) get_random_nonzero_to_one() (in module schrodinger.application.matsci.amorphous) get_random_structure() (in module schrodinger.application.matsci.genetic_optimization) get_ranged_float_typer() (in module schrodinger.application.matsci.parserutils) get_ranged_int_typer() (in module schrodinger.application.matsci.parserutils) get_rate() (in module schrodinger.math.multi_parameter_optimization) get_raw_file_name() (in module schrodinger.application.glide.utils) get_raw_user_labels() (in module schrodinger.seam.viz.inspect) get_rb_potential() (in module schrodinger.application.desmond.torsion_related) get_rb_torsions_potential() (in module schrodinger.application.desmond.torsion_related) get_rdkit_atoms() (in module schrodinger.application.matsci.smartsutils) get_reactant_classes_from_routes() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_reactant_combo_sim() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) get_reactant_files() (in module schrodinger.application.combinatorial_screen.driver_utils) get_reactions() (in module schrodinger.application.pathfinder.reaction) get_reactions_data() (in module schrodinger.application.matsci.reaction_workflow_utils) get_readable_cmd_list() (in module schrodinger.ui.qt.appframework2.af2) get_reader() (in module schrodinger.application.bioluminate.antibody.io.csv_reader) (in module schrodinger.pipeline.pipeutils) get_reagent_sources() (in module schrodinger.application.pathfinder.synthesis) get_recep_structure_from_grid() (in module schrodinger.application.glide.utils) get_reciprocal_lattice_vectors() (in module schrodinger.application.matsci.nano.xtal) get_reduced_density_from_cutoff() (in module schrodinger.application.matsci.cgforcefield) get_reduced_smiles() (in module schrodinger.application.desmond.struc) get_ref_nov_close_pairs() (in module schrodinger.application.matsci.swap_fragments_utils) get_ref_receptor() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) get_reference_ct() (in module schrodinger.application.desmond.struc) get_reference_data() (in module schrodinger.application.matsci.shapes) get_reflection_matrix() (in module schrodinger.structutils.transform) get_reflig() (in module schrodinger.application.glide.http_server) (schrodinger.application.glide.client_module.GlideClientModule method) get_regex_patterns_of_lines_to_skip() (in module schrodinger.utils.compare) get_region_bounds() (in module schrodinger.application.bioluminate.anarci.annotate) get_region_lengths() (in module schrodinger.application.bioluminate.anarci.annotate) get_region_to_replace() (in module schrodinger.application.bioluminate.antibody.assembly) get_registration_data() (in module schrodinger.livedesign.biologics.registration) (in module schrodinger.livedesign.registration) get_release_name() (in module schrodinger) get_remote_gpgpus() (in module schrodinger.infra.gpgpu_utils) get_remote_path() (in module schrodinger.job.remote_command) get_removed() (in module schrodinger.models.diffy) get_removed_dict() (in module schrodinger.models.diffy) get_removed_list() (in module schrodinger.models.diffy) get_removed_set() (in module schrodinger.models.diffy) get_rep_confs() (in module schrodinger.application.macromodel.apps) get_rep_stage_idx() (in module schrodinger.application.matsci.reaction_workflow_utils) get_replica_exchange_stage_number() (in module schrodinger.application.desmond.util) get_replica_setting() (in module schrodinger.application.desmond.config_utils) get_report() (in module schrodinger.application.desmond.solubility_utils) get_report_maker() (in module schrodinger.active_learning.al_report) get_representatives() (in module schrodinger.application.matsci.boltzmann_avg_props) get_required_licenses() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_res_ct_and_atom_idx() (in module schrodinger.application.desmond.struc) get_res_type() (in module schrodinger.livedesign.biologics.sequence) get_res_zones_by_res_type() (in module schrodinger.application.bioluminate.antibody.annotate) get_reserved_aa_names() (in module schrodinger.protein.process_enamine_db) get_reserves_cores_state() (in module schrodinger.application.matsci.equilibrium_md) get_residue_annotations() (in module schrodinger.protein.gpcr.annotate) get_residue_asl() (in module schrodinger.application.bioluminate.protein.protein) (in module schrodinger.structutils.sitealign) get_residue_database() (in module schrodinger.protein.nonstandard_residues) get_residue_flip_state() (in module schrodinger.protein.assignment) get_residue_from_changeable() (in module schrodinger.protein.assignment) get_residue_key() (in module schrodinger.protein.residue) get_residue_label() (in module schrodinger.application.desmond.fep_edge_report_maker) (schrodinger.ui.qt.rama.Rama method) get_residue_name() (in module schrodinger.application.desmond.fep_edge_data) (in module schrodinger.protein.helix) (schrodinger.protein.analysis.Report method) get_residue_neighborhoods() (in module schrodinger.protein.assignment) get_residue_representation() (in module schrodinger.application.bioluminate.protein_interaction.utils) get_residue_site_output() (in module schrodinger.application.desmond.lambda_dynamics_utils) get_residue_sitename() (in module schrodinger.application.desmond.struc) get_residue_sites_output() (in module schrodinger.application.desmond.lambda_dynamics_utils) get_residue_sorting_key() (in module schrodinger.application.bioluminate.protein_interaction.utils) get_residue_string() (in module schrodinger.protein.assignment) get_residues() (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) get_residues_asl() (in module schrodinger.application.bioluminate.protein.protein) get_residues_between() (in module schrodinger.structutils.residue) get_residues_by_connectivity() (in module schrodinger.structure) get_residues_containing_atoms() (in module schrodinger.structutils.residue) get_residues_for_asl() (in module schrodinger.application.bioluminate.protein_protein_docking_shared) get_residues_unsorted() (in module schrodinger.structure) get_residues_within() (in module schrodinger.application.bioluminate.protein.protein) get_residues_within_bounds() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_resname() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_rest_density_img() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase method) get_rest_density_plot() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase method) get_rest_density_text (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker property) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase property) get_rest_input() (in module schrodinger.application.desmond.rest_inp) get_rest_params() (in module schrodinger.application.desmond.remd) get_rest_region() (in module schrodinger.application.desmond.rest_inp) get_rest_replica() (in module schrodinger.application.desmond.config_utils) get_restart_id_filename() (in module schrodinger.application.matsci.jobutils) get_restart_opls_dir() (in module schrodinger.application.desmond.feputils) get_restart_options() (in module schrodinger.application.matsci.jobutils) get_restart_stage_from_engine() (in module schrodinger.application.desmond.launch_utils) get_restart_zip_files() (in module schrodinger.application.matsci.jaguar_restart) get_restartable_subjob_args() (in module schrodinger.application.phase.packages.phase_database_job_utils) get_restrain() (in module schrodinger.application.desmond.cmj) (schrodinger.application.desmond.cms.Cms method) get_restrain_angle_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_restrain_atom_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_restrain_dihedral_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_restrain_distance_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_restraints() (in module schrodinger.application.desmond.cmj) get_restraints_file_options() (in module schrodinger.application.desmond.feputils) get_restraints_xor_convert_restrain() (in module schrodinger.application.desmond.cmj) get_result() (schrodinger.application.jaguar.qrnn.temp_opt.Brent method) get_results_by_ligand() (in module schrodinger.application.desmond.stage.app.absolute_binding.stage) get_return_type_enum() (in module schrodinger.tasks.ldtasks) get_rev_dict() (in module schrodinger.application.matsci.cgforcefield) get_rg_ct() (schrodinger.application.canvas.r_group.Data method) get_RGB_enthalpy_entropy() (in module schrodinger.application.watermap.shapes) get_RGB_free() (in module schrodinger.application.watermap.shapes) get_rgb_from_color_index() (in module schrodinger.structutils.color) get_RGE_sources() (in module schrodinger.application.matsci.reaction_workflow_utils) get_rgroup_decomp() (in module schrodinger.livedesign.rgroup_decomposition) get_rgroup_DEE() (in module schrodinger.application.canvas.r_group) get_rgroup_labels() (in module schrodinger.livedesign.bbchem_endpoints) get_rgroup_MCS() (in module schrodinger.application.canvas.r_group) get_rgroup_SMARTS() (in module schrodinger.application.canvas.r_group) get_ring_atom_coords() (in module schrodinger.structutils.assignbondorders) get_rings() (schrodinger.application.canvas.r_group.Data method) get_rings_in_group() (in module schrodinger.structutils.assignbondorders) get_rlabels_map() (in module schrodinger.application.scaffold_enumeration.markush) get_rlabels_set() (in module schrodinger.application.scaffold_enumeration.markush) get_roc_curve_points() (in module schrodinger.analysis.enrichment.plotter) get_rotable_bonds() (in module schrodinger.application.desmond.r_group_asl) get_rotamers() (in module schrodinger.application.matsci.etarotamers) get_rotatable_bonds() (in module schrodinger.application.desmond.automatic_analysis_generator) get_rotatable_haptic_ligands() (in module schrodinger.application.matsci.etarotamers) get_rotatable_id_to_atom() (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) get_rotated_vector() (in module schrodinger.application.matsci.nano.util) get_rotation_matrix() (in module schrodinger.structutils.transform) get_rotation_matrix_from_eulers() (in module schrodinger.structutils.transform) get_round_trip_hash() (in module schrodinger.application.livedesign.ld_utils) get_route_files_from_zip() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_route_input_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_route_source_type() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_row() (in module schrodinger.project.utils) get_row_data() (in module schrodinger.ui.qt.table) get_row_from_proj_table() (in module schrodinger.application.matsci.deswidgets) get_row_from_pt() (in module schrodinger.application.matsci.gutils) get_rows() (in module schrodinger.project.utils) get_rows_to_export() (in module schrodinger.application.phase.packages.oned_task_utils) get_rsh_exec() (in module schrodinger.job.remote_command) get_rule_env_rule_id() (in module schrodinger.application.phase.packages.mmp2d) get_rule_env_stats() (in module schrodinger.application.phase.packages.mmp2d) get_rule_id_rule_smiles() (in module schrodinger.application.phase.packages.mmp2d) get_runtime_path() (in module schrodinger.application.glide.utils) (in module schrodinger.application.phase.packages.shape_screen_al_utils) (in module schrodinger.job.jobcontrol) get_runtime_relpath() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) get_rxnwf_graph() (in module schrodinger.application.matsci.reaction_workflow_utils) get_rxnwf_structures() (in module schrodinger.application.matsci.boltzmann_avg_props) get_s_inv12() (in module schrodinger.application.mopac.mopac_surfaces) get_safe_package() (in module schrodinger.application.matsci.codeutils) get_safe_yaml_with_tuples() (in module schrodinger.application.matsci.yamlutils) get_salt_bridge_params() (in module schrodinger.structutils.interactions.salt_bridge) get_salt_bridges() (in module schrodinger.structutils.interactions.salt_bridge) get_sample_property_value() (in module schrodinger.application.livedesign.ld_utils) get_save_file_name() (in module schrodinger.ui.qt.filedialog) get_saved_db_file() (in module schrodinger.protein.nonstandard_residues) get_sbt_tests() (in module schrodinger.application.desmond.simulation_block_test) get_sca_by_res() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) get_scaff_without_non_graph_hydrogen_rgroups() (in module schrodinger.livedesign.rgroup_decomposition) get_scale_factor_from_density() (in module schrodinger.application.matsci.cgforcefield) get_scaled() (schrodinger.application.matsci.elasticity.tensors.SquareTensor method) get_scaled_volume() (in module schrodinger.application.matsci.cgforcefield) get_scheme_region_prop() (in module schrodinger.application.bioluminate.tcr.annotate) get_schrodinger_db_value() (in module schrodinger.application.matsci.kmc) get_schrodinger_package_dirs() (in module schrodinger.infra.unusable_module_importer) get_schrodinger_run() (in module schrodinger.tasks.tasks) get_schrodinger_temp_dir() (in module schrodinger.utils.fileutils) get_score_pred_as_array() (in module schrodinger.active_learning.al_report) get_scored_seqs() (in module schrodinger.application.bioluminate.peptide_sar.io) get_scored_wt() (in module schrodinger.application.bioluminate.peptide_sar.io) get_scores() (in module schrodinger.application.jaguar.utils) get_screen_dict() (in module schrodinger.application.phase.packages.hypo_refine.project_utils) get_script_property_info_dict() (in module schrodinger.application.matsci.genetic_optimization) get_sd_property() (in module schrodinger.application.glide.sort_utils) get_sd_reader() (in module schrodinger.livedesign.convert) get_sdgr_atom_index() (in module schrodinger.application.matsci.rdpattern) get_section() (in module schrodinger.application.jaguar.output) get_selected_entry_ids() (in module schrodinger.project.utils) get_selected_structures() (in module schrodinger.project.utils) get_semicrystalline_relaxation1_stringers() (in module schrodinger.application.matsci.desconfig) get_semicrystalline_relaxation2_stringers() (in module schrodinger.application.matsci.desconfig) get_sentinel_sites() (in module schrodinger.application.matsci.buildcomplex) get_seq_data() (in module schrodinger.application.matsci.anharmonic) get_seq_labels() (in module schrodinger.application.bioluminate.peptide_sar.label) get_seqres() (in module schrodinger.protein.seqres) get_sequence() (in module schrodinger.protein.gpcr.annotate) get_sequence_file_format() (in module schrodinger.utils.fileutils) get_sequence_filter_chain_name() (in module schrodinger.livedesign.biologics.sequence) get_sequence_indexer() (in module schrodinger.application.bioluminate.antibody.sequence_indexer) get_sequence_numbering() (in module schrodinger.application.bioluminate.classify) get_sequence_viewer_data() (in module schrodinger.livedesign.biologics.sequence) get_server_info() (in module schrodinger.job.server) get_server_processes() (in module schrodinger.application.licensing.licadmin) get_server_tls_names() (in module schrodinger.application.licensing.licserver.server) get_set() (schrodinger.protein.analysis.Report method) get_settings() (in module schrodinger.application.bb_database.bb_task_utils) (in module schrodinger.ui.qt.appframework2.settings) get_sgroups() (in module schrodinger.application.scaffold_enumeration.common) get_sha1() (in module schrodinger.application.livedesign.ld_utils) (in module schrodinger.application.pathfinder.multiroute) get_shape_data() (schrodinger.application.vss.config.Config method) (schrodinger.application.vss.database.Database method) get_shape_generator() (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) get_shape_gpu_hits_positions() (in module schrodinger.application.phase.packages.shape_diversity) get_shape_object_by_name() (in module schrodinger.application.matsci.shapes) get_shape_queries() (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) get_shape_query() (in module schrodinger.application.vss.tasks) get_shapes_file_metadata() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) get_shared_file_listing() (in module schrodinger.application.licensing.licadmin) get_shell_runner() (in module schrodinger.application.matsci.espresso.utils) get_shifts() (schrodinger.application.jaguar.simple_spec.Peak method) get_shortest_distance() (in module schrodinger.structutils.measure) get_sibling_ownership_information() (in module schrodinger.application.matsci.reaction_workflow_utils) get_sidechain_att_atom() (in module schrodinger.application.desmond.struc) get_sidechain_indices() (schrodinger.protein.analysis.Report.local_residue method) get_sigmoid() (in module schrodinger.math.multi_parameter_optimization) get_signal() (schrodinger.application.jaguar.simple_spec.Peak method) get_signal_name() (in module schrodinger.application.desmond.driver_utils) get_signals() (in module schrodinger.utils.qt_utils) get_signed_angles_for_ring_flip_torsions() (in module schrodinger.application.jaguar.utils) get_significant_figures() (in module schrodinger.math.mathutils) get_sim_time_message() (in module schrodinger.application.desmond.starter.ui.cmdline) get_sim_time_ns() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_simbox_output_filename() (in module schrodinger.application.desmond.config_utils) get_simple_model_job() (in module schrodinger.livedesign.biologics.modeling) get_simple_supercell() (in module schrodinger.application.matsci.nano.xtal) get_simple_supercell_matrix() (in module schrodinger.application.matsci.nano.xtal) get_single_bond_length() (in module schrodinger.structutils.assignbondorders) get_single_chain_peptide_helm_model() (in module schrodinger.livedesign.biologics.fasta) get_single_letter_code() (in module schrodinger.protein.sequence) get_site_mask_summary() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils) get_site_masks() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils) get_site_nondefaults() (in module schrodinger.utils.featureflags.featureflags) get_site_tol() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils) get_site_tol_probes() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils) get_site_tol_summary() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils) get_sites() (in module schrodinger.application.matsci.reaction_workflow_utils) get_sites_table() (in module schrodinger.application.matsci.kmc) get_size_of() (in module schrodinger.application.matsci.jobutils) get_ska_transformation_matrix() (in module schrodinger.application.ska) get_skipped_file_name() (in module schrodinger.application.glide.utils) get_slice_limits() (in module schrodinger.application.bb_database.bb_arg_utils) get_smallest_metal_penalty() (in module schrodinger.application.prepwizard) get_smart_distribution_from_environ() (in module schrodinger.application.matsci.jobutils) get_smarts_from_sketcher() (in module schrodinger.ui.sketcher_smarts_dialog) get_smarts_from_ws() (in module schrodinger.application.matsci.smartsutilsgui) get_smarts_from_ws_selection() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_smi_header() (in module schrodinger.active_learning.al_utils) get_smiles() (in module schrodinger.application.matsci.reaction_workflow_utils) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method) (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_smiles_and_map() (in module schrodinger.application.matsci.rdpattern) get_smiles_column() (in module schrodinger.application.combinatorial_diversity.diversity_selector) get_smiles_csv() (schrodinger.application.vss.config.Config method) (schrodinger.application.vss.database.Database method) get_smiles_from_al_csv_or_smi_line() (in module schrodinger.active_learning.al_utils) get_smiles_wrapped_process() (in module schrodinger.application.transforms.test) get_snapshot_panel() (in module schrodinger.trajectory.trajectoryviewer) get_solvation_dg() (in module schrodinger.application.desmond.solubility_utils) get_solvent_cts() (schrodinger.application.desmond.cms.Cms method) get_solvent_infos() (in module schrodinger.application.matsci.packmol) get_sort_filters_from_config() (in module schrodinger.application.glide.utils) get_sorted_atomic_smarts() (in module schrodinger.application.matsci.rxn_channel) get_sorted_shortest_path() (in module schrodinger.application.matsci.graph) get_source_file_path() (in module schrodinger.application.livedesign.ld_utils) get_source_files() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) get_source_format() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) get_source_path() (in module schrodinger.application.matsci.jobutils) get_sources_from_r_labels() (in module schrodinger.structutils.rgroup_enumerate) get_spacegroups() (in module schrodinger.application.matsci.nano.space_groups) get_spec_dict() (in module schrodinger.application.combiglide.utils) get_species_display_names() (in module schrodinger.application.matsci.clusterstruct) get_species_display_names_from_cms() (in module schrodinger.application.matsci.clusterstructgui) get_species_from_mol() (in module schrodinger.application.matsci.clusterstruct) get_species_masses() (in module schrodinger.application.matsci.clusterstruct) get_spectral_params() (in module schrodinger.application.jaguar.spin_simulator_v2) get_spectrum() (in module schrodinger.application.jaguar.simple_spec) get_spectrum_type() (in module schrodinger.application.matsci.bandshape_utils) get_spglib_symmops() (in module schrodinger.application.matsci.elasticity.tensors) get_spherical_cluster_RMSDn() (in module schrodinger.comparison.struc) get_spin_icons() (in module schrodinger.ui.qt.tasks.taskwidgets) get_split_file_names() (in module schrodinger.application.phase.packages.oned_task_utils) get_splitting_pattern() (in module schrodinger.application.jaguar.simple_spec) get_splittings() (schrodinger.application.jaguar.simple_spec.Peak method) get_sql_output_name() (in module schrodinger.application.matsci.kmc) get_st_entity_id_map() (in module schrodinger.application.livedesign.import_utils) get_st_jaguar_output() (in module schrodinger.application.matsci.anharmonic) get_stage_idx() (in module schrodinger.application.matsci.reaction_workflow_utils) get_standard_cell() (in module schrodinger.comparison.struc) get_standard_icon_pixmap() (in module schrodinger.ui.qt.icons) get_standardized_aa_structure() (in module schrodinger.protein.process_enamine_db) get_start_index_for_entries() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_starting_sasas() (in module schrodinger.application.bioluminate.methionine_oxidation) get_state_penalties() (in module schrodinger.application.prepwizard) get_state_sites() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_state_string() (in module schrodinger.utils.featureflags.featureflags) get_static_constraints() (in module schrodinger.application.jaguar.autots_bonding) get_std_cell_from_spglib_dataset() (in module schrodinger.application.matsci.nano.xtal) get_steric_clashes() (in module schrodinger.structutils.interactions.steric_clash) get_stoich_charge() (in module schrodinger.application.jaguar.autots_validation) get_stoichiometry_string() (in module schrodinger.application.jaguar.utils) get_strain_state_dict() (in module schrodinger.application.matsci.elasticity.elastic) get_strained_cell() (in module schrodinger.application.matsci.nano.xtal) get_stream_handler() (in module schrodinger.utils.log) get_string_from_flag() (in module schrodinger.application.matsci.jobutils) get_stripped_defaults() (in module schrodinger.application.matsci.parserutils) get_struct_from_CIF() (in module schrodinger.application.matsci.nano.xtal) get_structure() (in module schrodinger.application.matsci.aseutils) (in module schrodinger.project.utils) (in module schrodinger.ui.sketcher_extensions) get_structure_digest() (in module schrodinger.application.glide.ligand_designer) get_structure_file_format() (in module schrodinger.application.phase.packages.shape_ligprep) (in module schrodinger.utils.fileutils) get_structure_file_reader() (in module schrodinger.application.phase.packages.oned_task_utils) get_structure_from_base64_str() (in module schrodinger.application.matsci.coarsegrain) get_structure_ids() (in module schrodinger.application.livedesign.io_utils) get_structure_index() (in module schrodinger.application.bioluminate.protein_interaction.tasks) get_structure_info_via_structure_group_search() (in module schrodinger.application.livedesign.ld_import_utils) get_structure_item() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase method) get_structure_record_class() (in module schrodinger.application.glide.sort_utils) get_structure_residue() (in module schrodinger.application.bioluminate.protein_interaction.utils) get_structure_residue_chain_key() (in module schrodinger.protein.residue) get_structure_residue_key() (in module schrodinger.protein.residue) get_structure_score() (in module schrodinger.application.matsci.genetic_optimization) get_structure_sequences() (in module schrodinger.protein.sequence) get_structure_with_contiguous_molecules() (in module schrodinger.application.matsci.rxn_channel) get_structures() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) get_structures_for_entry_ids() (in module schrodinger.project.utils) get_structures_from_bytes() (in module schrodinger.structure) get_structures_subset() (in module schrodinger.driver.structsubset) get_style_sheet_text() (in module schrodinger.ui.qt.style) get_sub_graphs() (in module schrodinger.application.matsci.graph) get_sub_host_str() (in module schrodinger.application.matsci.reaction_workflow_utils) get_subgraphs() (in module schrodinger.thirdparty.networkx_algos) get_subjob_commands() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_subjob_commands_classic() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_subjob_commands_fast() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_subjob_counts_fast() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_subjob_msj_template() (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) get_subjob_names() (in module schrodinger.application.phase.packages.phase_utils) (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) get_subjob_names_classic() (in module schrodinger.application.phase.packages.shape_screen_job_utils) get_subparam_type_hints() (in module schrodinger.models.paramtools) get_subset_file() (in module schrodinger.application.phase.packages.phase_screen_utils) get_subset_name() (in module schrodinger.application.phase.packages.phase_utils) get_subst_from_mapping() (in module schrodinger.application.desmond.fep_mapping) get_subst_score() (schrodinger.application.combiglide.corehop.SubstCoreDatabase method) get_subtrees() (in module schrodinger.thirdparty.networkx_algos) get_summary() (in module schrodinger.application.bioluminate.propka_parse) get_super_transformation_matrix() (in module schrodinger.structutils.rmsd) get_superposition_idxs() (in module schrodinger.application.matsci.swap_fragments_utils) get_supported_ff_names() (schrodinger.application.desmond.starter.ui.cmdline.BaseArgs class method) get_surface_kwargs() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_surfaces() (in module schrodinger.application.bioluminate.pml_menus) get_surfactant_infos() (in module schrodinger.application.matsci.packmol) get_surfnet_gaps() (in module schrodinger.application.bindingsite.cavutils) get_symmetric() (in module schrodinger.application.matsci.elasticity.tensors) get_symmops_from_spglib() (in module schrodinger.application.matsci.nano.space_groups) get_tcr_bounds() (in module schrodinger.application.bioluminate.tcr.annotate) get_tcr_centroid() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_tcr_disulfide_axis() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_tcr_interdomain_axis() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_tcr_type_name() (in module schrodinger.application.bioluminate.tcr.annotate) get_tcr_variable_domain_details() (in module schrodinger.application.bioluminate.tcr.annotate) get_temp_from_bs_spectrum_file_key() (in module schrodinger.application.matsci.bandshape_utils) get_temp_press_key_ext() (in module schrodinger.application.matsci.jaguarworkflows) get_tempearture() (in module schrodinger.application.desmond.config_utils) get_temperature() (in module schrodinger.application.matsci.jaguarworkflows) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_template_vars() (in module schrodinger.application.livedesign.upload_utils) get_testable_value() (in module schrodinger.application.phase.packages.phase_database_job_utils) get_tg_props() (in module schrodinger.application.matsci.msprops) get_thread_id() (in module schrodinger.utils.thread_utils) get_thread_name() (in module schrodinger.utils.thread_utils) get_ticks() (in module schrodinger.application.desmond.fep_edge_data) get_time() (in module schrodinger.pipeline.stage) (schrodinger.application.desmond.cmj.Job static method) get_time_cost() (in module schrodinger.active_learning.al_report) get_time_for_leg() (schrodinger.application.desmond.starter.ui.cmdline.FepArgs method) (schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args method) (schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs method) (schrodinger.application.desmond.starter.ui.fep_solubility.FepSolubilityArgs method) get_title() (in module schrodinger.application.pathfinder.reaction) get_titles_by_failure() (in module schrodinger.protein.process_enamine_db) get_titles_of_duplicates() (in module schrodinger.application.matsci.reaction_workflow_utils) get_titration_ct() (schrodinger.application.desmond.cms.Cms method) get_titration_sites() (in module schrodinger.application.desmond.cms) get_titration_states() (in module schrodinger.application.desmond.cms) get_tkd_value() (in module schrodinger.application.matsci.elasticity.tensors) get_token() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_tokens_by_name() (in module schrodinger.ui.qt.standard.design_tokens) get_tooltip_for_search_option() (in module schrodinger.maestro_utils.find_tool_bar.constants) get_top_entry() (in module schrodinger.project.utils) get_top_level_props() (in module schrodinger.application.desmond.simulation_block_data) get_top_ligands_from_csv_list() (in module schrodinger.active_learning.al_node) get_top_ligands_from_csv_list_as_smi() (in module schrodinger.application.phase.packages.shape_screen_al_utils) get_top_poses_from_sorted_ligands() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) get_topic_dict() (in module schrodinger.utils.documentation) get_topic_fragment() (in module schrodinger.utils.documentation) get_torsion_atoms() (in module schrodinger.comparison.struc) get_torsions() (in module schrodinger.comparison.struc) get_torsions_plot() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase method) (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker method) get_total_charge() (in module schrodinger.application.jaguar.utils) get_total_proc() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) get_trait() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.SysType method) (schrodinger.application.desmond.systype.TyperBase static method) get_traj_filename() (in module schrodinger.application.desmond.util) get_trajectory_path() (in module schrodinger.application.livedesign.ld_utils) (in module schrodinger.project.utils) (in module schrodinger.trajectory.utils) get_transfer_free_energy() (in module schrodinger.application.desmond.solubility_utils) get_transformation_matrix() (in module schrodinger.application.matsci.nano.xtal) get_transformations() (in module schrodinger.application.phase.packages.mmp2d) get_transformed_vectors() (in module schrodinger.application.matsci.nano.xtal) get_transformer_reactions() (in module schrodinger.application.steps.enumerators) get_transition_type() (in module schrodinger.application.matsci.bandshape_utils) get_transitions() (in module schrodinger.application.matsci.bandshape_utils) get_translated_xyz_vec() (in module schrodinger.application.matsci.bandshape_utils) get_translation_matrix() (in module schrodinger.structutils.transform) get_translation_vector() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) get_trj_dir_name() (in module schrodinger.application.matsci.parserutils) get_trj_from_cms_file() (in module schrodinger.application.matsci.order_parameter_mod) get_tube_dimensions() (in module schrodinger.application.matsci.nano.tube) get_tube_unit_cell() (in module schrodinger.application.matsci.nano.tube) get_tube_vectors() (in module schrodinger.application.matsci.nano.tube) get_type() (schrodinger.application.canvas.r_group.TempAtom method) (schrodinger.application.desmond.enhsamp.Bind method) (schrodinger.application.desmond.enhsamp.FcnCall method) (schrodinger.application.desmond.enhsamp.If method) (schrodinger.application.desmond.enhsamp.Iter method) (schrodinger.application.desmond.enhsamp.Let method) (schrodinger.application.desmond.enhsamp.Lit method) (schrodinger.application.desmond.enhsamp.Node method) (schrodinger.application.desmond.enhsamp.Series method) (schrodinger.application.desmond.enhsamp.String method) (schrodinger.application.desmond.enhsamp.Var method) get_type_dict_from_ff_file() (in module schrodinger.application.matsci.cgforcefield) get_type_dict_from_st() (in module schrodinger.application.matsci.coarsegrain) get_type_name() (in module schrodinger.application.matsci.cgforcefield) get_typenames() (schrodinger.utils.multifpfile.MultiFPFile method) get_umbrella_mode_command_line() (in module schrodinger.application.desmond.fep_util) get_uname() (in module schrodinger.utils.sysinfo) get_unbinding_pathway() (in module schrodinger.application.desmond.kinetics.utils) get_unencrypted_text() (in module schrodinger.application.matsci.enc) get_unique_aa_names() (in module schrodinger.protein.process_enamine_db) get_unique_bonds() (in module schrodinger.application.matsci.coarsegrain) get_unique_cms_file_name() (in module schrodinger.trajectory.utils) get_unique_geom_title() (in module schrodinger.application.matsci.reaction_workflow_utils) get_unique_molecule_nums() (in module schrodinger.application.matsci.species) get_unique_molecule_struct() (in module schrodinger.application.matsci.species) get_unique_name() (in module schrodinger.application.matsci.msutils) get_unique_ordered_list() (in module schrodinger.application.matsci.msutils) get_unique_res_name() (in module schrodinger.protein.nonstandard_residues) get_unique_seq_names() (in module schrodinger.protein.tasks.structure_alignment) get_unique_titles() (in module schrodinger.application.matsci.mlearn.features) get_unit_cell_formula() (in module schrodinger.application.matsci.nano.xtal) get_unit_lattice_vector_info() (in module schrodinger.application.matsci.nano.xtal) get_unit_vector() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_unmodified_trajectory_entry_ct() (in module schrodinger.trajectory.trajectoryviewer) get_unsatisfied_donors() (in module schrodinger.protein.assignment) get_unsupported_atoms() (in module schrodinger.application.jaguar.basis) get_unsupported_graphics_card() (in module schrodinger.infra.gpgpu_utils) get_unused_name() (schrodinger.utils.pymol.PymolInstance method) get_update_delay() (in module schrodinger.job.queue) get_updated() (in module schrodinger.models.diffy) get_updated_dict() (in module schrodinger.models.diffy) get_updated_msj_block() (in module schrodinger.application.desmond.config_utils) get_updated_time_display() (in module schrodinger.application.job_monitor.job_monitor_table) get_updated_time_tooltip() (in module schrodinger.application.job_monitor.job_monitor_table) get_uploaded_model_url() (in module schrodinger.application.livedesign.upload_utils) get_url() (in module schrodinger.protein.gpcr.gpcrdb) get_user_feature_env() (in module schrodinger.utils.featureflags.featureflags) get_user_label_to_stage_mapping() (in module schrodinger.seam.viz.inspect) get_user_name() (in module schrodinger.application.matsci.msprops) get_user_props() (in module schrodinger.application.phase.packages.oned_app_utils) get_userdata_dir() (in module schrodinger.utils.fileutils) get_username() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_uvec() (in module schrodinger.application.matsci.elasticity.tensors) get_val() (in module schrodinger.utils.sea.sea) get_val_from_cmdline() (in module schrodinger.application.matsci.msutils) get_valid_header_groups_string() (in module schrodinger.application.bioluminate.antibody.io.csv_reader) get_validation_pixmaps() (in module schrodinger.ui.qt.icons) get_value() (schrodinger.utils.sea.sea.Map method) get_values_to_match() (in module schrodinger.application.phase.packages.oned_task_utils) get_variable_region_names() (in module schrodinger.application.bioluminate.anarci.annotate) get_vartype_enum() (in module schrodinger.tasks.ldtasks) get_vdw() (schrodinger.application.desmond.cms.Cms method) get_vdw_radius() (schrodinger.protein.analysis.Report method) get_vdw_type_name() (in module schrodinger.application.matsci.cgforcefield) get_vector_atoms_from_internal_coords() (schrodinger.protein.membrane.Membrane_Model method) get_vector_magnitude() (in module schrodinger.structutils.transform) get_vectors_from_chorus() (in module schrodinger.application.matsci.nano.xtal) get_vectors_from_residues() (in module schrodinger.application.bioluminate.tcr.docking_angles) get_version() (schrodinger.models.json.JsonableClassMixin method) get_vetted_vec_index() (in module schrodinger.application.jaguar.textparser) get_view_atoms() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_view_item_options() (in module schrodinger.ui.qt.utils) get_visible_ws_asl() (in module schrodinger.application.bioluminate.pml_menus) get_visible_ws_atoms() (in module schrodinger.application.bioluminate.pml_menus) get_voids_data() (in module schrodinger.application.matsci.freevolume) get_voigt_dict() (schrodinger.application.matsci.elasticity.tensors.Tensor static method) get_volume_and_density() (in module schrodinger.comparison.struc) get_volume_data() (in module schrodinger.application.matsci.freevolume) get_volume_from_params() (in module schrodinger.application.matsci.nano.xtal) get_volume_from_vecs() (in module schrodinger.application.matsci.nano.xtal) get_water_atom_indices() (schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield static method) get_weighted_score() (in module schrodinger.math.multi_parameter_optimization) get_widgets() (in module schrodinger.ui.qt.layout) (schrodinger.ui.qt.formlayout.FormComboWidget method) (schrodinger.ui.qt.formlayout.FormTabWidget method) (schrodinger.ui.qt.formlayout.FormWidget method) get_widgets_in_layout() (in module schrodinger.ui.qt.utils) get_wildcard_energy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_windows_drive_sidebar_links() (in module schrodinger.ui.qt.filedialog) get_workflow_node_names() (in module schrodinger.active_learning.al_driver) get_working_resources() (in module schrodinger.application.licensing.licadmin) get_workspace_structure() (in module schrodinger.ui.qt.input_selector) get_workspacehub_connection_requests() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_writer() (in module schrodinger.application.matsci.packmol) get_ws_grid_wmap_files() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage method) get_ws_sip_docking_config() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage method) get_x() (schrodinger.application.canvas.r_group.TempAtom method) get_xlink_type_atoms() (in module schrodinger.application.matsci.freevolume) get_xy_plot() (in module schrodinger.application.desmond.mplchart) get_xy_plot_widget() (in module schrodinger.application.desmond.mplchart) get_xy_url() (in module schrodinger.application.desmond.gchart) get_xyz_matches() (in module schrodinger.comparison.struc) get_xyz_RMSDn() (in module schrodinger.comparison.struc) get_y() (schrodinger.application.canvas.r_group.TempAtom method) get_z() (schrodinger.application.canvas.r_group.TempAtom method) get_zip_contents() (in module schrodinger.active_learning.al_utils) getAbbeNum() (schrodinger.application.matsci.permittivity.RefractiveIndex class method) getAbbeWavelengths() (schrodinger.application.matsci.permittivity.ElectricPolarizability static method) getAbstractColumns() (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) getAbstractParam() (schrodinger.models.parameters.CompoundParam method) getAccuracyAndInitialGuessKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getAction() (schrodinger.application.bioluminate.actions.factory.Factory method) getActiveCoordItem() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab method) getActiveHost() (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel method) getActiveProcCounts() (schrodinger.job.queue.JobDJ method) getActiveProcsOnHost() (schrodinger.job.queue.JobDJ method) getActiveRankCsvRows() (schrodinger.analysis.enrichment.calculator.Calculator method) getAcuteAngle() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getAddedFuncs() (schrodinger.utils.funcgroups.FuncGroupMixin method) getAdditionalDataDir() (schrodinger.project.project.Project method) getAdjustedDisplacement() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) getAdjustedNJobs() (schrodinger.pipeline.stage.Stage method) getAdjustedYValues() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) getAdvancedSettingString() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getAliasedSettings() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) getAliasedValue() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) getAlignedMobileStructures() (schrodinger.structutils.sitealign.BindingSiteAligner method) getAlignmentMinimizedWithSpaces() (schrodinger.protein.alignment.BaseAlignment method) getAlignmentScore() (schrodinger.protein.align.BiopythonPairwiseAligner method) (schrodinger.protein.align.SchrodingerPairwiseAligner method) getAlignmentVector() (schrodinger.application.matsci.nano.particle.Nanoparticle method) getAllAngles() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllArrayCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAllAtomicBases() (schrodinger.application.jaguar.input.JaguarInput method) getAllAtomIds() (schrodinger.application.matsci.clusterstruct.SpeciesData method) (schrodinger.application.matsci.species.SpeciesData method) getAllAtomPairs() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllCells() (schrodinger.ui.two_d_viewer.TwoDViewer method) getAllChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getAllComponents() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getAllData() (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) getAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getAllHypoIDs() (schrodinger.application.phase.phase_widgets.HypothesisModel method) getAllHypotheses() (schrodinger.application.phase.phase_widgets.HypothesisModel method) getAllJaguarMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) getAllJobs() (schrodinger.application.matsci.jobdirdlg.JobManager method) getAllMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) getAllModelFiles() (schrodinger.application.matsci.genetic_optimization.ChemInformatics static method) getAllMoietyNames() (schrodinger.application.matsci.amorphous.Moieties method) getAllowedProcessors() (schrodinger.job.queue.ResourceHost method) getAllowedRange() (schrodinger.application.glide.glide.GlideJob method) getAllowedRows() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) getAllParentIndices() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond method) getAllPotentialAtomChargeProperties() (schrodinger.application.matsci.chargegui.ChargePropertySelector static method) getAllPreferences() (schrodinger.utils.preferences.Preferences method) getAllProperties() (schrodinger.ui.qt.propertyselector.PropertySelectorList method) getAllResidueStrings() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput method) getAllSegmentTypes() (schrodinger.application.matsci.kmc.Table static method) getAllSpaceGroups() (schrodinger.application.matsci.nano.space_groups.SpaceGroups method) getAllStages() (schrodinger.application.matsci.permittivity.MultiStageMd class method) getAllStandardItems() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) getAllTableModels() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) getAllTopLevelJobs() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) getAllTorsions() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllUniqueTrackers() (schrodinger.application.matsci.fragments.FragmentReactor method) getAllUsedTheoryLevels() (schrodinger.application.jaguar.gui.tabs.base_tab.LoadsTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getAllVibData() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getAllVisibleLeaves() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) getAllWorldCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAlnFilename() (schrodinger.application.prime.wrapper.BasePrimeAlignment method) getAlnSet() (schrodinger.protein.alignment.BaseAlignment method) getAlpha() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getAlphaCarbon() (schrodinger.structure.Residue method) getAlphaParameter() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getAminoAcid() (schrodinger.protein.nonstandard_residues.ResidueDatabase method) getAnalysis() (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) getAncestor() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) getAncestors() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) getAnchoredResidues() (schrodinger.protein.alignment.BaseAlignment method) getAnchoredResiduesWithRef() (schrodinger.protein.alignment.BaseAlignment method) getAngleDerv() (in module schrodinger.application.matsci.gsas.GSASIImath) GetAngleSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getAngleType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getAngSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getAnharmonicVibPartitionFunctions() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getAnnotation() (schrodinger.protein.sequence.AbstractSequence method) getAnnotationValueForComparison() (schrodinger.protein.sequence.AbstractSequence method) getAntibodyCDR() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAntibodyCDRs() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAntibodyRegion() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAntibodyRegions() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.AntibodyRegionsFinder method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getApp() (schrodinger.ui.qt.appframework.AppFramework method) getApplicationHeaderFields() (schrodinger.job.jobcontrol.Job method) getApplicationHeaderString() (schrodinger.job.jobcontrol.Job method) getApplyGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getArcCenter() (schrodinger.application.matsci.atom_group.HelixArc method) getArginineType() (schrodinger.ui.residueselector.ResidueGroups method) getArgList() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) getAromaticRingAtoms() (schrodinger.application.dendrogram.core_class.Utilities static method) getArray() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getArrayNx3() (schrodinger.trajectory.prody.mode.VectorBase method) getArrowheadPos() (schrodinger.protein.helm.helm_renderer.ArrowheadConnectorMixin method) GetAsfMean() (in module schrodinger.application.matsci.gsas.GSASIIpwd) GETaskInput (class in schrodinger.application.livedesign.export_models) GETaskOutput (class in schrodinger.application.livedesign.export_models) getAsl() (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo method) (schrodinger.application.bioluminate.patch_utils.patch_finder.ResPatchData method) getASL() (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) getAsl() (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.structure.Residue method) (schrodinger.ui.qt.atomselector.AtomSelector method) getASLExcludingLigand() (in module schrodinger.application.desmond.automatic_analysis_generator) getASLName() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) getAspartateType() (schrodinger.ui.residueselector.ResidueGroups method) getAssayFolderPath() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) getAssignedAndUnassigned() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getAssociationChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getAsymmetricUnit() (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) getAtArrayCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtArrayCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtom() (schrodinger.ui.qt.structure2d.RedSquareAnnotator method) getAtomBondTypingSchemeDescription() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getAtomByPdbName() (schrodinger.structure.Residue method) getAtomColorList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getAtomConeAngle() (schrodinger.application.matsci.mlearn.features.Ligand method) GetAtomCoordsByID() (in module schrodinger.application.matsci.gsas.GSASIImath) getAtomCount() (schrodinger.application.jaguar.input.JaguarInput method) getAtomDefinitions() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getAtomEntry() (schrodinger.application.desmond.maestro.NewEntryGroup method) GetAtomFracByID() (in module schrodinger.application.matsci.gsas.GSASIImath) getAtomGroupKeyName() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) getAtomGroups() (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.matsci.species.SpeciesData method) getAtomHighlights() (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) getAtomicBasis() (schrodinger.application.jaguar.input.JaguarInput method) getAtomicCharge() (schrodinger.application.jaguar.input.JaguarInput method) getAtomicChargeAttr() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getAtomicMultiplicity() (schrodinger.application.jaguar.input.JaguarInput method) getAtomicNonPolarSASAGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getAtomicNumAttr() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getAtomicPolarSASAGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getAtomicSpecies() (schrodinger.application.matsci.espresso.qeinput.StructureType method) getAtomicStructure() (schrodinger.application.matsci.espresso.qeinput.StructureType method) getAtomIndices() (schrodinger.application.matsci.coarsegrain.FusedRing method) (schrodinger.structure._AtomCollection method) (schrodinger.structure.Structure method) GetAtomInfo() (in module schrodinger.application.matsci.gsas.GSASIIElem) GetAtomItemsById() (in module schrodinger.application.matsci.gsas.GSASIImath) getAtomList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.structure._AtomCollection method) getAtomName() (schrodinger.application.matsci.zmutils.ZAtom method) getAtomNums() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) getAtomNumsForEntry() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateBasisSetSubTab method) getAtomPolymerNames() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getAtomPropertyNames() (schrodinger.structure.Structure method) getAtomResidueNames() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getAtoms() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) getAtomsAndWeight() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) GetAtomsById() (in module schrodinger.application.matsci.gsas.GSASIImath) getAtomsRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getAtomsToTerminate() (schrodinger.application.matsci.nano.sheet.Grow method) getAtomText() (schrodinger.application.matsci.reordergui.ComparisonListWidget method) (schrodinger.application.matsci.reordergui.ReferenceListWidget method) getAtomTotal() (schrodinger.application.jaguar.results.JaguarResults method) getAtomXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath) getAttachmentData() (schrodinger.application.livedesign.export_models.FFCExportSpec method) getAtWorldCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtWorldCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAugmentedStructGraph() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getAutoCallerString() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) getAutoIndent() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) getAuxListboxSelection() (schrodinger.ui.qt.propertyselector.PropertySelector method) getAvailableGeometries() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) getAvailableMappings() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) getAvailableMappingsByRecency() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) getAvailablePresets() (schrodinger.models.presets.PresetManager method) getAverageDistanceFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getAvgVibData() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getAVPAsl() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getAxisDataRange() (schrodinger.ui.qt.schart.SChart static method) getAxisExtreme() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) getAxisNum() (schrodinger.application.matsci.sliceplot.SlicePlot method) getBackboneIdxs() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getBackboneNitrogen() (schrodinger.structure.Residue method) getBackboneOxygen() (schrodinger.structure.Residue method) getBackground() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getBackgroundDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getBacktrackingLevel() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getBandGap() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) getBaroMethod() (schrodinger.application.desmond.gui.EnsembleTab method) getBarrierTermMSJ() (schrodinger.application.matsci.desconfig.BarrierHeader method) getBasename() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getBaseName() (schrodinger.application.matsci.genetic_optimization.ClassEvaluator method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getBasis() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterListToolButton method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) getBasisForEid() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) getBasisSetSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getBeadSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getBeadsType() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getBending() (schrodinger.structutils.minimize.Minimizer method) getBendingEnergy() (schrodinger.structutils.minimize.Minimizer method) getBestAlignment() (schrodinger.protein.gpcr.tasks.GPCRTask method) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask method) getBestDoubleBond() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getBestMatch() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) getBestNumberOfClusters() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getBestResults() (schrodinger.active_learning.al_node.LigandMLEvalNode method) getBestSpanningVector() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getBeta() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction static method) getBetaCarbon() (schrodinger.structure.Residue method) getBFGSObject() (schrodinger.application.matsci.mecp_mod.MECP method) getBinarySimilarity() (schrodinger.protein.residue.Residue method) getBindingSiteTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) getBinIndices() (schrodinger.ui.qt.schart.SHistogramBarSeries method) getBinnedSites() (schrodinger.application.matsci.reaction_workflow_utils.Sites static method) getBiteAngle() (schrodinger.application.matsci.mlearn.features.Ligand method) getBlastAlignment() (schrodinger.protein.tasks.blast.BlastTask method) getBlastSettings() (schrodinger.protein.tasks.blast.BlastSettings method) getBlock() (schrodinger.application.phase.packages.shape_binary_utils.ShapeFileReader method) GetBLtable() (in module schrodinger.application.matsci.gsas.GSASIIElem) getBLvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem) getBond() (schrodinger.structure.Structure method) getBondAngle() (schrodinger.application.matsci.mlearn.features.Complex method) getBondAtLocation() (schrodinger.ui.qt.structure2d.structure_item method) getBondColorList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondedEnergies() (schrodinger.structutils.minimize.Minimizer method) getBondedEnergyComponents() (schrodinger.structutils.minimize.Minimizer method) getBondedSideChainAtom() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) getBondedSideChainAtoms() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getBondingInfo() (schrodinger.application.matsci.nano.sheet.Grow method) getBondLength() (schrodinger.application.matsci.amorphous.BaseMoiety method) (schrodinger.application.matsci.mlearn.features.Ligand method) getBondList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondListWithIgnored() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondsOrderAttr() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getBoxSliceVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getBoxVectors() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) getBranchColor() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) getBranchConvergentNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getBranchDivergentNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) GetBraviasNum() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getBreakableNonRingBonds() (schrodinger.application.steps.enumerators.FastFragmenter method) getBreakableRingBonds() (schrodinger.application.steps.enumerators.FastFragmenter method) getBuffer() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) getBuildingBlocks() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getBuriedNode() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getBuriedSASALimits() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput method) getBuriedVDWVolumePct() (schrodinger.application.matsci.mlearn.features.Complex method) getBuriedVolumeStructure() (schrodinger.application.matsci.mlearn.features.Complex method) getBuriedXYZ() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getButtonByText() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) getButtonId() (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) getButtons() (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getButtonWithIcon() (schrodinger.application.job_monitor.job_monitor_widgets.JobBar method) getCalculatedData() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) getCalculationDict() (schrodinger.application.matsci.crest.CrestTOML method) getCalculationGUI() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) getCallResult() (schrodinger.application.matsci.mstest.MSTestCase method) getCapperTerminator() (schrodinger.application.matsci.amorphous.PolymerFragments method) getCarbonylCarbon() (schrodinger.structure.Residue method) getCartesianCoords() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getCascadeGenerations() (schrodinger.application.matsci.amorphous.Moieties method) getCategory() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) getCbmVbm() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getCDRResidueList() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getCellFromI() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getCellValue() (schrodinger.ui.qt.table.StructureDataViewerModel method) getCenterIdx() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) getCenterOfMass() (schrodinger.application.matsci.atom_group.MSAtomGroup method) getCenterOrientationOfAtoms() (schrodinger.protein.membrane.Membrane_Model method) getCenterRotation() (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync method) getCentroid() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.atom_group.MSAtomGroup method) (schrodinger.application.matsci.mlearn.features.Ligand method) getCGGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getChain() (schrodinger.structure.StructureAtom method) getChainAtoms() (schrodinger.structure.Structure method)

getChainKey() (schrodinger.protein.residue.Residue method) getChannel() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) getCharErrorDisplay() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) getCharge() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) getChargeConstraintSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getCharIndex() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) getCharPositionInLine() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) getChartImage() (schrodinger.ui.qt.schart.SChart method) getCheckedColumns() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) getCheckedData() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) getCheckedDataCount() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) getCheckedResidues() (schrodinger.ui.residueselector.MutationSelectorMixin method) getCheckedRowNumbers() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) getChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getChildCount() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getChildIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getChildItems() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) getChildren() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.ui.dendrogram.DendrogramGraphicNode method) getChiralAngle() (schrodinger.application.matsci.nano.tube.NanoTube method) getChoiceSpectrum() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing static method) getChorusPBC() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) (schrodinger.application.matsci.nano.tube.NanoTube method) getCircumRadius() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Tetrahedron method) getClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) getClashPenalty() (schrodinger.application.matsci.montecarlo.Metropolizer method) getClassicalParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getCleanupRequested() (schrodinger.pipeline.stage.Stage method) getClosest() (schrodinger.application.bioluminate.protein.protein.Consensus method) getClosestApproach() (schrodinger.application.matsci.montecarlo.Metropolizer method) getClusterContents() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getClusteringMap() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusteringStatistics() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getClusterOrderMap() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterSize() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getClusterStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getClusterTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterVariance() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getCmd() (schrodinger.application.matsci.crest.Crest method) (schrodinger.application.matsci.crest.CrestCSearch method) (schrodinger.application.matsci.genetic_optimization.AutoQSAR method) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) (schrodinger.application.matsci.genetic_optimization.DeepChem method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Jaguar method) (schrodinger.application.matsci.reaction_workflow_gui_utils.QMPreOptimization method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) getCmdFromFlagBlock() (schrodinger.application.matsci.permittivity.TaskProtocol method) getCmdListArgValue() (schrodinger.ui.qt.appframework2.af2.JobApp method) getCMDValue() (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox method) getCode() (schrodinger.structure.Residue method) getColor() (schrodinger.application.dendrogram.gradientSelector.ColorSelector method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) getColoredMapping() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getColorFromWidget() (schrodinger.ui.qt.schart.SeriesParams method) getColorsForPatchVertices() (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) getColumn() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) getColumnIndex() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) (schrodinger.ui.qt.swidgets.STableWidget method) GetColumnMetadata() (in module schrodinger.application.matsci.gsas.GSASIIfiles) getColumnNames() (schrodinger.infra.table.Table method) getColumns() (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) getColumnTotal() (schrodinger.infra.table.Table method) getCommand() (schrodinger.application.desmond.queue.JobAdapter method) (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.queue.BaseJob method) getCommandArgs() (schrodinger.job.launcher.Launcher method) getCommandDir() (schrodinger.job.queue.BaseJob method) getCommandLineArgs() (schrodinger.application.matsci.mswidgets.SaveDesmondFilesWidget method) getCommandLineFlag() (schrodinger.application.matsci.mswidgets.RandomSeedWidget method) getCommandLineFlags() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) getCommandTemplate() (schrodinger.job.launchapi.TaskSpecification method) getCommonBasis() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getCommonBasisForRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) getCommonFunctional() (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) getCommonMethod() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getCommonTheoryForRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) getCommonTheoryLevel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getComName() (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) getCompareKey() (schrodinger.rdkit.molio.BaseMergeHandler method) (schrodinger.rdkit.molio.CsvMergeHandler method) (schrodinger.rdkit.molio.RdkitMergeHandler method) (schrodinger.rdkit.molio.SmiMergeHandler method) (schrodinger.rdkit.molio.StructureMergeHandler method) getComplement() (schrodinger.protein.sequence.NASequence method) (schrodinger.protein.sequence.NucleicAcidSequence method) getCompleteBondList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getComplexDescriptors() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getComUtil() (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) getConeAngle() (schrodinger.application.matsci.mlearn.features.Ligand method) getConfAvgRelEnergies() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) getConfigDialog() (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.timing.TimerMixin method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) getConformers() (schrodinger.application.matsci.crest.CrestCSearch method) (schrodinger.application.phase.packages.conformer_reader.ConformerReader method) getConformerShapes() (schrodinger.application.phase.packages.shape_generator.ShapeGenerator method) getConnectedComponents() (schrodinger.ui.qt.network_visualizer.Graph method) getConnectedTransitionStateTriples() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getConnectionColor() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionFile() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionInfos() (schrodinger.application.matsci.amorphous.PolymerFragments method) getConnectionMaxLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionMinLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionName() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionSize() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectivityChain() (schrodinger.analysis.substructure.ConnectedMoleculeChain method) getConnectorData() (schrodinger.protein.helm.helm_renderer.HelmScene method) getConservation() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) getConstraint() (schrodinger.application.jaguar.input.JaguarInput method) getConstraintIndicesByType() (schrodinger.application.jaguar.input.JaguarInput method) getConstraints() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getConstraintsRefXYZFileName() (schrodinger.application.matsci.crest.Crest method) getConstraintType() (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile method) getContentRect() (schrodinger.ui.qt.delegates.PictureDelegate method) getContractedGraphAndMapping() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getContractedMapping() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getConvergenceCriteriaKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getConvergenceKeywords() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getConvergenceMethodsKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getCoordinates() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) (schrodinger.ui.dendrogram.DendrogramGraphicNode method) getCoordinationVec() (schrodinger.application.matsci.mlearn.features.Ligand method) getCoordName() (schrodinger.application.matsci.zmutils.ZAtom method) getCoords() (schrodinger.application.matsci.espresso.qeoutput.KPoint method) (schrodinger.trajectory.prody.ensemble.Ensemble method) getCoordsStr() (schrodinger.application.matsci.espresso.qeoutput.KPoint method) getCordsIterator() (schrodinger.application.matsci.atom_group.MSAtomGroupsBase method) getCoreBonds() (schrodinger.application.steps.enumerators.FastFragmenter method) getCoreRmsd() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) getCorrectionParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getCount() (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) getCouplerAndGrower() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getCouplerAtom() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getCovariance() (schrodinger.trajectory.prody.nma.NMA method) getCrashLog() (schrodinger.active_learning.mq_worker.LigandMLBackend method) getCriteria() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) getCriterion() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) getCrystalSystem() (schrodinger.application.matsci.nano.space_groups.CrystalSystems method) GetCSpqinel() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetCSuinel() (in module schrodinger.application.matsci.gsas.GSASIIspc) getCsvFilePath() (schrodinger.application.matsci.reportutils.ReportInfo method) getCsvRows() (schrodinger.analysis.enrichment.calculator.Calculator method) GetCSxinel() (in module schrodinger.application.matsci.gsas.GSASIIspc) getCumulativeMatches() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) getCurrentASLData() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getCurrentAtomBondTyping() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getCurrentAxis() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getCurrentButton() (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getCurrentFile() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) getCurrentInfoAndProp() (schrodinger.application.matsci.kmcgui.PropertyCombo method) getCurrentInfoPropAndValues() (schrodinger.application.matsci.kmcgui.PropertyCombo method) getCurrentInputSymbol() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getCurrentJobDir() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) getCurrentLinkage() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getCurrentSelection() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) (schrodinger.ui.qt.datamapper.MappableButtonGroup method) getCurrentSet() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) getCurrentSetting() (schrodinger.application.matsci.qualityslider.QualitySlider method) getCurrentSymbol() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) getCurrentTableModel() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) getCurrentType() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getCurrentValue() (schrodinger.application.matsci.mswidgets.AtomNameWidgetItem method) getCurrServerAddress() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) getCustomChargeInfo() (schrodinger.application.matsci.chargegui.ChargeDialog method) getCustomInfo() (schrodinger.application.matsci.genetic_optimization.Property static method) getCustomOPLSDir() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) getCustomOPLSDIR() (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) getCustomPresetsNames() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) getCWgam() (in module schrodinger.application.matsci.gsas.GSASIImath) getCWgamDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getCWsig() (in module schrodinger.application.matsci.gsas.GSASIImath) getCWsigDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getCylinderSliceVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getData() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) (schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType method) (schrodinger.application.matsci.mswidgets.Stepper method) (schrodinger.application.matsci.spectra.PowderDiffractionFile static method) (schrodinger.application.matsci.spectra.SpectrumFile static method) (schrodinger.ui.qt.network_visualizer.Edge method) (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.network_visualizer.Node method) getDatabaseData() (schrodinger.application.matsci.cgforcefield.ForceField method) getDatabasePath() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) getDataForCorpID() (schrodinger.tasks.ldtasks.LDColumn method) getDataModelClass() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) GetDATSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getDBFile() (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask method) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask method) getDebugLevel() (schrodinger.job.launchparams.LaunchParameters method) getDebugListener() (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) getDebugString() (schrodinger.tasks.tasks.AbstractTask method) getDefault() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getDefaultAtomTypingScheme() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getDefaultCustomTemplateDir() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getDefaultKeywords() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) (schrodinger.application.matsci.jagwidgets.PresetsDialog method) getDefaultPreset() (schrodinger.models.presets.PresetManager method) getDefaultPresetName() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) getDefaultSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getDefaultStderr() (schrodinger.job.launchapi.JobSpecification method) getDefaultStdout() (schrodinger.job.launchapi.JobSpecification method) getDefinition() (schrodinger.ui.ligfilter.AddDefinitionDialog method) getDefinitionDict() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getDelNextResnumByAtomID() (schrodinger.application.matsci.amorphous.PolymerFragments method) getDelNextResnumByResnum() (schrodinger.application.matsci.amorphous.PolymerFragments method) getDeltaE() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getDeltaERxn() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getDendrogramData() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getDensities() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getDensity() (in module schrodinger.application.matsci.gsas.GSASIImath) getDenticity() (schrodinger.application.matsci.mlearn.features.Ligand method) getdEpsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getDescription() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.application.desmond.antlr3.dfa.DFA method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) getDescriptor() (schrodinger.application.matsci.order_parameter_mod.Descriptor method) getDescriptorKeys() (schrodinger.protein.residue.Residue method) getDescriptors() (schrodinger.application.matsci.mlearn.features.Complex method) (schrodinger.application.matsci.mlearn.features.Ligand method) getDescriptorUtilityJob() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getDescriptorValue() (schrodinger.protein.residue.Residue method) getDesiredVolume() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getDesolvationPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getDetailedAtomSmarts() (schrodinger.application.matsci.rdpattern.Pattern method) getDeterminingStates() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getDeterminingStatesTOF() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getDeviations() (schrodinger.trajectory.prody.ensemble.Ensemble method) getdFCJVoigt3() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getDiagonalFinalPoint() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getDict() (schrodinger.application.matsci.msconst.DIMENSIONALITY class method) getDifference() (schrodinger.application.jaguar.autots_bonding.Coordinate method) getDihedralAtoms() (schrodinger.structure.Residue method) getDihedralType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getDiheValues() (schrodinger.application.matsci.amorphous.PolymerFragment method) getDirective() (schrodinger.application.jaguar.input.JaguarInput method) getDirectives() (schrodinger.application.jaguar.input.JaguarInput method) getDirector() (schrodinger.application.matsci.order_parameter_mod.OrderParameter static method) getDirectoryPath() (schrodinger.ui.qt.directory_selector.DirectorySelector method) getDiscontinuousSubalignment() (schrodinger.protein.alignment.BaseAlignment method) getDisplacementFromConstTranslation() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) getDisplayAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getDisplayName() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox static method) getDisplaySmarts() (schrodinger.application.pathfinder.reaction.Reaction method) getDissociationChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getDistance() (schrodinger.ui.dendrogram.DendrogramNode method) getDistanceCellDistance() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) getDistanceConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) getDistanceMatrixFile() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getDistanceToCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getDistDerv() (in module schrodinger.application.matsci.gsas.GSASIImath) GetDistSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getDmatrix() (schrodinger.application.matsci.rxn_path.InternalCoords method) getDOS() (schrodinger.application.matsci.espresso.qeoutput.DOS method) (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) getDot() (schrodinger.seam.viz.watcher.WatcherDirReader method) getDotFromEventsFile() (schrodinger.seam.viz.watcher.WatcherDirReader method) getDoubleAndTripleRingAtoms() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) getDoubleDisplacementChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getDownStreamPolymerJob() (schrodinger.application.matsci.permittivity.StepBase method) getDpdBeadSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getdPsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getDriverPath() (schrodinger.application.matsci.permittivity.TaskProtocol method) getDualGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getDuration() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getEdge() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) getEdgeApproval() (schrodinger.ui.qt.network_visualizer.Graph method) getEdgeLength() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Tetrahedron method) getEdgeList() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getEdges() (schrodinger.application.matsci.shapes.Face method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.schart.SHistogramBarSeries method) getEids() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) getEigv() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) getEigval() (schrodinger.trajectory.prody.mode.Mode method) getEigvals() (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getEigvec() (schrodinger.trajectory.prody.mode.Mode method) getEigvecs() (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getEleEnergy() (schrodinger.structutils.minimize.Minimizer method) getElement() (schrodinger.structutils.assignbondorders.AssignBondOrders method) (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) getElidedTitle() (schrodinger.application.matsci.appbase.StructureLoadButton method) GetElInfo() (in module schrodinger.application.matsci.gsas.GSASIIElem) getEllipsoidSliceVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getElSym() (in module schrodinger.application.matsci.gsas.GSASIIElem) getEndFrameValue() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getEndPos() (schrodinger.protein.helm.helm_renderer.AABranchingConnectorItem method) (schrodinger.protein.helm.helm_renderer.DisulfideConnectorMixin method) (schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin method) getEnergeticSpans() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getEnergies() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) (schrodinger.application.matsci.fragments.BondEnergies method) (schrodinger.application.matsci.fragments.UniqueTracker method) getEnergy() (schrodinger.application.matsci.fragments.BondEnergies method) (schrodinger.application.matsci.montecarlo.Metropolizer method) (schrodinger.application.prime.residue_interaction.InteractionReader method) (schrodinger.structutils.minimize.Minimizer method) getEnergyAndGradients() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) getEnergyAndGradientsObject() (schrodinger.application.matsci.mecp_mod.MECP method) getEnergyConvergencePlot() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getEnergyPropertyValues() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getEnthalpy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getEntries() (schrodinger.analysis.transformations.TransformsRepository method) getEntropy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getEntryIds() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) getEpsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getErrorHandler() (schrodinger.structure.MaestroReader method) (schrodinger.structure.PDBReader method) getErrorHeader() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getErrorMessage() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getEventsFileFromPipelineID() (schrodinger.seam.viz.watcher.WatcherDirReader method) getEwaldRealSpaceFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getExampleAtomGroup() (schrodinger.application.matsci.species.SpeciesData method) getExampleMemberTag() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) getExampleTag() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) (schrodinger.application.matsci.species.ResidueSpeciesFinder method) getExcitedState() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) getExcludedAtomList() (schrodinger.structutils.minimize.Minimizer method) getExcludedVolume() (schrodinger.application.matsci.amorphous.Scaffold method) getExistingDirectory() (schrodinger.ui.qt.filedialog.FileDialog static method) getExistingFragmentTracker() (schrodinger.application.matsci.fragments.FragmentReactor method) getExpandedRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) getExpectedRuntime() (schrodinger.protein.tasks.blast.BlastTask method) getExportSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getExtendedFactors() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getExtendedRingAtomToRings() (schrodinger.application.dendrogram.core_class.Utilities static method) getExtension() (schrodinger.application.matsci.equilibrium_md.Model method) getExtents() (schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method) (schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method) (schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method) getExtentsAndStrainedLength() (schrodinger.application.matsci.nano.interface_mod.Interface method) getExtracyclicAtom() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getExtraInputFiles() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) getExtraMolecularDescriptorsProps() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getFaces() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) getFactors() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials static method) getFCJVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getFCJVoigt3() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getFcnSigs() (in module schrodinger.application.desmond.enhanced_sampling.FcnTypes) getFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeatureCheckbox() (schrodinger.application.phase.featureselector.FeatureSelector method) getFeatureDefinitions() (schrodinger.application.phase.packages.shape_generator.ShapeGenerator method) getFeatureFromId() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeatureNames() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeatures() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getFEPTorsionKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) GetFFC5() (in module schrodinger.application.matsci.gsas.GSASIIElem) getFFCExportSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getFFIOParam() (schrodinger.application.matsci.cgforcefield.ForceField method) GetFFtable() (in module schrodinger.application.matsci.gsas.GSASIIElem) getFFvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem) getFHistogram() (schrodinger.application.desmond.replica_dE.replica_energy method) getFieldNames() (schrodinger.application.matsci.atom_group.HelixData method) getfile() (schrodinger.ui.qt.formlayout.FileLayout method) getFile() (schrodinger.ui.qt.input_selector.InputSelector method) getFileInputInfo() (schrodinger.ui.qt.input_selector.InputSelector method) getFilename() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) getFileName() (schrodinger.application.matsci.order_parameter_mod.Descriptor method) getFilename() (schrodinger.ui.qt.filedialog.OpenDirAsFileDialog method) getFileNameFromDisplayName() (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem static method) getFileNames() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) getFilePath() (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.structure_selector.StructureSelector method) getFilePaths() (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.structure_selector.StructureSelector method) getFiles() (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) (schrodinger.structure.MultiFileStructureWriter method) (schrodinger.ui.qt.input_selector.InputSelector method) getFilesForJobControl() (schrodinger.tasks.ldtasks.FileColumn method) (schrodinger.tasks.ldtasks.LDColumn method) (schrodinger.tasks.ldtasks.PoseColumn method) getFilterName() (schrodinger.ui.qt.filter_dialog.FilterDialog method) getFilterText() (schrodinger.ui.ligfilter.LigfilterFrame method) getFinalForcesHartreePerAngstrom() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFinalPoint() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getFinalStructure() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFinalTotalEnergy() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFingerprint() (schrodinger.ui.qt.fp_selector_widget.FingerprintsPopUp method) getFingerprintDescription() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getFingerprintString() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getFirstCellPositions() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) getFirstChildWithType() (schrodinger.application.desmond.antlr3.tree.BaseTree method) getFirstHost() (schrodinger.job.queue.JobDJ method) getFirstLevelParentNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) getFirstLevelTasknames() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getFirstMatchedfilename() (schrodinger.application.matsci.permittivity.StepBase method) getFirstNode() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) getFirstOutputStructure() (schrodinger.application.matsci.jwsteps.BaseStep method) getFirstSelectedRow() (schrodinger.infra.table.Table method) getFirstTmpResname() (schrodinger.application.matsci.amorphous.Monomer method) getFitRect() (schrodinger.ui.qt.network_views.NetworkViewer method) getFixedColumnsCount() (schrodinger.project.project.Project method) getFlagBlock() (schrodinger.application.matsci.permittivity.TaskProtocol method) getFlags() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) (schrodinger.application.matsci.kmcgui.NeighborsTab method) (schrodinger.application.matsci.kmcgui.Tab method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants method) (schrodinger.application.matsci.speciesgui.GroupingMethodSelector method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) getFMax() (schrodinger.application.desmond.replica_dE.replica_energy method) getFMean() (schrodinger.application.desmond.replica_dE.replica_energy method) getFMin() (schrodinger.application.desmond.replica_dE.replica_energy method) getForceConstant() (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) getForceFieldFlag() (schrodinger.application.matsci.permittivity.DisorderSystemBuilder class method) (schrodinger.application.matsci.permittivity.PolymerBuilder class method) (schrodinger.application.matsci.permittivity.StepBase class method) getForceFieldMenuItem() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) getForceFieldOptions() (schrodinger.ui.qt.forcefield.ffselector.MaestroForceFieldSelector method) getFormattedNames() (schrodinger.application.dendrogram.core_class.GetPartitions method) getFormattedSummaryLine() (schrodinger.application.matsci.mecp_mod.MECPStep method) GetFormFactorCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem) getFpOptions() (schrodinger.application.matsci.genetic_optimization.CanvasKPLS static method) getFragCentroid() (schrodinger.application.matsci.amorphous.PolymerFragments method) getFragments() (schrodinger.application.matsci.fragments.BreakingBond method) getFragmentTags() (schrodinger.application.matsci.fragments.FragmentReactor method) getFragmentTracker() (schrodinger.application.matsci.fragments.FragmentReactor method) getFragRingMapping() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) getFrames() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) getFrameTotal() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getFreePositions() (schrodinger.application.matsci.espresso.qeoutput.Output static method) getFreeVolumeData() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getFreeVolumeVector() (schrodinger.application.matsci.mlearn.features.Complex method) getFreqFromPropkey() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getFreqStageIdxs() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) getFrequencies() (schrodinger.protein.alignment.BaseAlignment method) getFromSelection() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage method) getFromSpacing() (schrodinger.application.matsci.espresso.qeinput.KpointsType method) getFrozenAtoms() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getFuncGroup() (schrodinger.utils.funcgroups.FuncGroupMixin method) getFunctional() (schrodinger.application.jaguar.gui.tabs.base_tab.LoadsTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) getFusedRings() (schrodinger.application.matsci.coarsegrain.FusedRing static method) getFWHM() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getgamFW() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getGap() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getGapCount() (schrodinger.protein.sequence.AbstractSequence method) getGaplessLength() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) getGapOnlyColumns() (schrodinger.protein.alignment.BaseAlignment method) getGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.tasks.sta.STATask method) getGEdge() (schrodinger.ui.qt.network_visualizer.Graph method) GetGenSym() (in module schrodinger.application.matsci.gsas.GSASIIspc) getGibbsFreeEnergy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getGlobalAnnotationData() (schrodinger.protein.alignment.BaseAlignment method) getGlutamateType() (schrodinger.ui.residueselector.ResidueGroups method) getGoodFFTDim() (schrodinger.application.matsci.espresso.utils.MemoryEstimator method) getGPCRAnnotationMap() (schrodinger.protein.gpcr.tasks.GPCRTask method) getGPCRs() (schrodinger.protein.annotation.GPCRSegmentFinder method) getGPCRSegment() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getGPCRSegments() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getGradient() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) getGrammarFileName() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getGravityEnergy() (schrodinger.application.matsci.montecarlo.Metropolizer method) getGrids() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getGridSize() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) getGroup() (schrodinger.utils.preferences.Preferences method) getGroupTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getGroupXYZ() (schrodinger.application.matsci.atom_group.MSAtomGroup method) getGrowParams() (schrodinger.application.matsci.nano.tube.NanoSheet method) getGrowVectors() (schrodinger.application.matsci.nano.sheet.Grow method) getGuessGeometry() (schrodinger.application.matsci.mecp_mod.MECP method) getGUI() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) getHamiltonian() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) getHapticCharacter() (schrodinger.application.matsci.mlearn.features.Ligand method) getHapticity() (schrodinger.application.matsci.mlearn.features.Ligand method) getHarmonicVibPartitionFunctions() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getHeader() (schrodinger.application.canvas.utils.ChmCSVTools method) (schrodinger.application.matsci.atom_group.HelixData method) (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) (schrodinger.rdkit.molio.CsvMergeHandler method) getHeatCapacity() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getHeight() (schrodinger.ui.qt.tablewidget.Row method) getHelixData() (schrodinger.application.matsci.atom_group.HelixGroups method) getHelixDataIterator() (schrodinger.application.matsci.atom_group.HelixGroups method) getHelp() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) getHessian() (schrodinger.application.jaguar.input.JaguarInput method) getHetTypesToProcess() (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings method) getHiddenColCount() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) getHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getHideAtomsBeyondBindingSiteASL() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getHideAtomsNonpolarHydrogensASL() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getHistidineType() (schrodinger.ui.residueselector.ResidueGroups method) getHistogramData() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method) getHits() (schrodinger.protein.gpcr.tasks.GPCRTask method) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask method) (schrodinger.protein.tasks.hit_align.CustomFamilyTask method) getHitsFile() (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask method) getHKLIndices() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getHKLmax() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getHKLMpeak() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getHKLpeak() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getHost() (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.job.jobcontrol.Host method) (schrodinger.job.launchapi.JobSpecification method) getHostCombo() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getHostList() (schrodinger.pipeline.stage.Stage method) getHostname() (schrodinger.job.launchparams.LaunchParameters method) getHostPlaceholderArg() (schrodinger.tasks.jobtasks.HostSettings method) getHostPref() (schrodinger.ui.qt.config_dialog.ConfigDialog method) getHosts() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.config_dialog.GPUConfigDialog method) getHostStr() (schrodinger.application.matsci.genetic_optimization.ClassEvaluator static method) (schrodinger.job.app.App method) (schrodinger.pipeline.stage.Stage method) getHostType() (schrodinger.ui.qt.config_dialog.ConfigDialog method) getHotAtoms() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) getHoveredNode() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) getHSliderMax() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getHSliderMin() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getHtml() (schrodinger.stepper.viz.AbstractPlot method) (schrodinger.stepper.viz.OutputsPlot method) (schrodinger.stepper.viz.TimelinePlot method) (schrodinger.stepper.viz.TopologyChart method) getHydropathyGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getHypoID() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) getHypotheses() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) getHypothesisFeatureRadii() (schrodinger.application.phase.packages.shape_generator.ShapeGenerator method) getHypothesisSitesShape() (schrodinger.application.phase.packages.shape_generator.ShapeGenerator method) getIdentity() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) getIdentityStrict() (schrodinger.protein.residue.Residue method) getIdStr() (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo method) (schrodinger.application.bioluminate.patch_utils.patch_finder.ResPatchData method) getIdx() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) getIFromCell() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getIgnoredSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getImageFromPic() (schrodinger.ui.two_d_viewer.TwoDViewer method) getImagesDirPath() (schrodinger.application.matsci.reportutils.ReportInfo method) getImportantRotatableBonds() (in module schrodinger.application.desmond.r_group_asl) getImpTorsion() (schrodinger.structutils.minimize.Minimizer method) getImpTorsionEnergy() (schrodinger.structutils.minimize.Minimizer method) getIncludedEntry() (schrodinger.application.matsci.appbase.BaseAnalysisGui method) getIncludedState() (schrodinger.ui.two_d_viewer.Cell method) getIncludedStructures() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) getIncludeToggleOffset() (schrodinger.ui.two_d_viewer.TwoDViewer method) getIndex() (schrodinger.trajectory.prody.mode.Mode method) getIndexFromI() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getIndices() (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) (schrodinger.graphics3d.polyhedron.MaestroCube method) (schrodinger.graphics3d.polyhedron.MaestroDodecahedron method) (schrodinger.graphics3d.polyhedron.MaestroIcosahedron method) (schrodinger.graphics3d.polyhedron.MaestroOctahedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) (schrodinger.graphics3d.polyhedron.MaestroTetrahedron method) (schrodinger.trajectory.prody.modeset.ModeSet method) getInfo() (schrodinger.application.matsci.genetic_optimization.ChemInformatics class method) (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) (schrodinger.application.matsci.genetic_optimization.GlassTransitionTemperature static method) (schrodinger.application.matsci.genetic_optimization.RefractiveIndex static method) (schrodinger.application.matsci.genetic_optimization.StructureEvaluator static method) getInfraStructure() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) getIniDiameter() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getInitialGuess() (schrodinger.application.matsci.rxn_path.ReactionPath method) getInitialInputs() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getInitialInvHessian() (schrodinger.application.matsci.mecp_mod.BFGS method) getInitialMapping() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getInitiatorSubBackbone() (schrodinger.application.matsci.amorphous.PolymerFragments method) getInnerRadius() (schrodinger.application.matsci.packmol.LiposomeInputFile method) getInPlaceRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getInput() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.pipeline.stage.Stage method) getInputFile() (schrodinger.ui.qt.appframework.AppFramework method) getInputFiles() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.launchapi.JobSpecification method) getInputKeys() (schrodinger.job.launchapi.TaskSpecification method) getInputMolecule() (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.macro_pka_input.MacroKaInput method) (schrodinger.application.jaguar.solvation_input.SolvationInput method) getInputMolecules() (schrodinger.application.jaguar.esol_input.EsolInput method) (schrodinger.application.jaguar.qrnn.input.QRNNInput method) (schrodinger.application.jaguar.rotation_barriers_input.RotationBarriersInput method) getInputName() (schrodinger.application.matsci.jwsteps.BaseDesmondStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.HOFStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep method) getInputNames() (schrodinger.pipeline.stage.Stage method) getInputPath() (schrodinger.application.matsci.jwsteps.BaseStep method) getInputRows() (schrodinger.tasks.ldtasks.LDTask method) getInputs() (schrodinger.active_learning.mq_worker.Worker method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) getInputsForTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) getInputSource() (schrodinger.ui.qt.appframework.AppFramework method) getInputStream() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) getInputText() (schrodinger.application.jaguar.input.JaguarInput method) getInputTopic() (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) getInstance() (schrodinger.application.livedesign.ld_import_utils.LDImportTaskManager static method) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy class method) (schrodinger.ui.qt.forcefield.ffglobalpreferencewidget.FFGlobalPreferenceWidget static method) getInTemplate() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getInteractionEnergy() (schrodinger.structutils.minimize.Minimizer method) getInteractionEnergyGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getInteractionMatrix() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getInteractionPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getInterChainAnchors() (schrodinger.protein.alignment.CombinedChainProteinAlignment method) getInterface() (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) getInterfaceASL() (schrodinger.application.bioluminate.pml_menus.InterfaceMixin method) getInterfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) getIntermediateNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getInternalEnergy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getInternalEnergyGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getInterpFlagBlock() (schrodinger.application.matsci.permittivity.TaskProtocol method) getInterPlanarSeparation() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getInterpolatedStructure() (schrodinger.application.matsci.rxn_path.ReactionPath method) getIsFarthestFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getIsNearestToCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getIsolates() (schrodinger.ui.qt.network_visualizer.Graph method) getIsomorphicFragments() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getItemByIndex() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getItemFromInt() (schrodinger.application.livedesign.login_gui2.AuthenticationMode class method) getItemTooltip() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) getIter() (schrodinger.application.scaffold_enumeration.common.EnumerableMixin method) getJaguarDescriptors() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getJaguarFlags() (schrodinger.application.matsci.reaction_workflow_utils.DescriptorsMixin method) getJaguarInputFromFile() (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) getJaguarJob() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getJaguarMarker() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) getJaguarNonDefault() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getJaguarRestartFileName() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) getJaguarValue() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getJob() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.job.queue.JobControlJob method) getJobCmd() (schrodinger.application.matsci.multiapp.MultiCmdJobApp method) getJobCount() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) (schrodinger.application.matsci.multiapp.MultiJobApp method) getJobDJ() (schrodinger.job.queue.BaseJob method) (schrodinger.pipeline.stage.Stage method) getJobName() (schrodinger.job.app.App method) getJobname() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchparams.LaunchParameters method) getJobnameSource() (schrodinger.job.launchapi.TaskSpecification method) getJobSpec() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.JobSpecificationBuilder method) (schrodinger.ui.qt.appframework2.af2.JobApp method) getJoiningGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getJsonBlacklist() (schrodinger.application.livedesign.export_models.PoseNameEditModel class method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel class method) (schrodinger.models.parameters.CompoundParam class method) (schrodinger.protein.tasks.blast.BlastTask.Input class method) getJSScript() (schrodinger.stepper.viz.AbstractPlot method) (schrodinger.stepper.viz.OutputsPlot method) (schrodinger.stepper.viz.TimelinePlot method) (schrodinger.stepper.viz.TopologyChart method) getKcalPerMolConversion() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) GetKcl() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GetKclKsl() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getKelleyPenaltyList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getKey() (schrodinger.protein.residue.Residue method) getKeyData() (schrodinger.application.matsci.cgforcefield.ForceField method) getKeyName() (schrodinger.application.matsci.species.BaseSignature method) (schrodinger.application.matsci.species.MolecularFormulaSignature method) (schrodinger.application.matsci.species.PolymerSmilesSignature method) (schrodinger.application.matsci.species.SmilesSignature method) getKeyNamePrefix() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) (schrodinger.application.matsci.species.ResidueSpeciesFinder method) getKeys() (schrodinger.application.matsci.hdfutils.HDFIO method) (schrodinger.application.matsci.hdfutils.HDFProxyPickleIO method) getKeystring() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) getKeyType() (schrodinger.utils.preferences.Preferences method) getKeywordDict() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.KeywordEdit method) (schrodinger.application.matsci.qualityslider.QualitySlider method) getKeywords() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) getKeywordString() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.KeywordEdit method) (schrodinger.application.matsci.qualityslider.QualitySlider method) getKinaseFeatures() (schrodinger.protein.tasks.kinase.KinaseFeatureTask method) getKindOfOps() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) GetKNsym() (in module schrodinger.application.matsci.gsas.GSASIIspc) getKplsData() (schrodinger.ui.two_d_viewer.TwoDViewer method) getKptFromCfg() (schrodinger.application.matsci.espresso.qeoutput.KPoint static method) GetKsl() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getKwargs() (schrodinger.application.matsci.genetic_optimization.Property static method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getLabel() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) (schrodinger.ui.dendrogram.DendrogramNode method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getLabeledMols() (schrodinger.application.pathfinder.route.ReagentNode method) getLabels() (schrodinger.ui.dendrogram.DendrogramTreeBuilder method) getLabelText() (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getLargestSpan() (schrodinger.application.matsci.amorphous.Box method) getLargestVoid() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getLastCustomFeatureNum() (schrodinger.application.phase.featureselector.FeatureModel method) getLastRewriteTokenIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) getLatticeParameters() (schrodinger.application.matsci.nano.xtal.Crystal method) getLatticeProperties() (schrodinger.application.matsci.nano.slab.Surface method) getlattSym() (in module schrodinger.application.matsci.gsas.GSASIIspc) getLaunchCommand() (schrodinger.application.macromodel.utils.ComUtil method) getLaunchDirectory() (schrodinger.job.launchparams.LaunchParameters method) getLaunchSubDir() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) getLayerVolume() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getLDDataTreePopUp() (schrodinger.application.livedesign.panel_components.LDDataTreePopUpButton method) getLeafIndices() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) getLeafTaskNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) getLeftAngles() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getLength() (schrodinger.application.matsci.shapes.Edge method) getLevelDicts() (schrodinger.application.matsci.crest.CrestTOML method) getLicenseFileList() (in module schrodinger.application.licensing.licadmin) getLicenseRequirements() (schrodinger.application.steps.licensing.LicenseMixin method) (schrodinger.application.steps.ligprep.LigPrepStep method) (schrodinger.stepper.stepper.Chain method) getLicenses() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) getLicHost() (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog method) getLigand() (in module schrodinger.application.desmond.automatic_analysis_generator) getLigandCompoundID() (schrodinger.application.livedesign.export_models.ThreeDExportItem method) getLigandCorpID() (schrodinger.application.livedesign.export_models.ThreeDExportItem method) getLigandFragments() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) getLigandID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getLigandImage() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getLigandPropsKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getLigandStructure() (schrodinger.application.matsci.sculptcomplex.Sculptor method) getLigandTitle() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getLimits() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.StringCriterion method) getLinDepPlaneVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getLine() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) getLineData() (schrodinger.application.matsci.espresso.qeoutput.Magres static method) getLinkageDescription() (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method) getLinkageGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getListboxSelection() (schrodinger.ui.qt.propertyselector.PropertySelector method) GetLittleGrpOps() (in module schrodinger.application.matsci.gsas.GSASIIspc) getLiveReportID() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) getLJEnergy() (schrodinger.structutils.minimize.Minimizer method) getLocalArgs() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getLocalInputFiles() (schrodinger.stepper.app.StepperApplication class method) getLocalInputFolders() (schrodinger.stepper.app.StepperApplication class method) getLocationItems() (schrodinger.ui.qt.forcefield.pathselectorwidget.PathSelectorWidget method) getLogAsString() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.tasks.SubprocessMixin method) getLogFilename() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.tasks.SubprocessMixin method) GetLogger (class in schrodinger.application.matsci.textlogger) getLogger() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method) GetLogger.MyFormatter (class in schrodinger.application.matsci.textlogger) getlogin() (in module schrodinger.application.desmond.util) getLogPath() (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask method) getLogs() (schrodinger.seam.viz.watcher.WatcherDirReader method) getLoopMutation() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) getLRDependentColumns() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getLysineType() (schrodinger.ui.residueselector.ResidueGroups method) getMaefilename() (schrodinger.application.jaguar.input.JaguarInput method) getMaestroProjectDisposition() (schrodinger.job.launchparams.LaunchParameters method) getMaestroProjectDispositionString() (schrodinger.job.launchparams.LaunchParameters method) getMaestroProjectName() (schrodinger.job.launchparams.LaunchParameters method) getMaestroPropertiesPopUp() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) getMaestroSettings() (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync method) getMaestroViewname() (schrodinger.job.launchparams.LaunchParameters method) getMaeStructure() (schrodinger.application.matsci.espresso.qeoutput.Output method) (schrodinger.application.matsci.jaguarworkflows.Results method) getMag() (schrodinger.application.matsci.espresso.utils.MagSpecies method) GetMagFormFacCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem) getMajorRadius() (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) getManagedResource() (schrodinger.job.queue.ResourceHost method) getManager() (schrodinger.application.matsci.jobdirdlg.JobManager static method) getMapFilePath() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) getMappableRows() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getMappedBeadInfo() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getMappedParticles() (schrodinger.application.matsci.cg_mapping.CGMapper method) getMappedStruct() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) getMappingFromOrder() (schrodinger.application.matsci.automated_cg_mapping.MartiniMapper method) getMappingModel() (schrodinger.application.livedesign.export_map_manager.ExportMap class method) getMappingOrderPermulations() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) getMarkedAtoms() (schrodinger.application.matsci.reordergui.StructureListWidget method) getMarkerAtoms() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) getMartiniBeadSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getMartiniEdgesInMapping() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) getMaskTarget() (schrodinger.application.matsci.jwsteps.BaseStep method) getMass() (in module schrodinger.application.matsci.gsas.GSASIImath) getMatches() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) (schrodinger.application.ligprep.ionizer.Spec method) getMatchingAtomMap() (schrodinger.structutils.sitealign.SiteMatchLookup method) getMatchingAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getMatrixTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMaxDistanceFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMaxDists() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getMaxRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) getMaxRes() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getMaxRetries() (schrodinger.pipeline.stage.Stage method) getMaxStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) getMaxVibData() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getMaxWorkers() (schrodinger.seam.options.pipeline_options.SeamOptions method) getMCSMatches() (in module schrodinger.application.canvas.r_group) getMDStepStruct() (schrodinger.application.matsci.espresso.qeoutput.Output method) getMeanWave() (in module schrodinger.application.matsci.gsas.GSASIImath) getMenu() (schrodinger.application.bioluminate.actions.factory.Factory method) getMenuAction() (schrodinger.application.matsci.speciesgui.GroupingMethodSelector method) getMenuBar() (schrodinger.application.bioluminate.actions.factory.Factory method) getMenuIndicatorRect() (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator method) getMergeDistanceList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMeshShift() (schrodinger.application.matsci.espresso.qeinput.KpointsType static method) getMessage() (schrodinger.application.desmond.antlr3.tree.RewriteCardinalityException method) getMetadata() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) (schrodinger.application.phase.packages.shape_creation_logic.ShapeCreator method) getMethod() (schrodinger.application.jaguar.gui.tabs.base_tab.LoadsTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListPopUp method) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListToolButton method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) getMethodForEid() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getMetric() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getMetricStyle() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getMExpr() (schrodinger.application.desmond.meta.CV method) (schrodinger.application.desmond.meta.CVAngle method) (schrodinger.application.desmond.meta.CVDihedral method) (schrodinger.application.desmond.meta.CVDist method) (schrodinger.application.desmond.meta.CVrgyr method) (schrodinger.application.desmond.meta.CVrgyr_mass method) (schrodinger.application.desmond.meta.CVrmsd method) (schrodinger.application.desmond.meta.CVrmsd_symm method) (schrodinger.application.desmond.meta.CVwhim method) (schrodinger.application.desmond.meta.CVzdist method) (schrodinger.application.desmond.meta.CVzdist0 method) GetMFtable() (in module schrodinger.application.matsci.gsas.GSASIIElem) getMFvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem) getMinCellLengths() (schrodinger.application.matsci.packmol.BilayerInputFile method) (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile method) getMinDistance() (schrodinger.application.matsci.density_analysis_widget.MeasurementLine method) getMinMax() (schrodinger.application.matsci.amorphous.Box method) getMinRadius() (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.infra.growthspace.GrowthSpaceGenerator method) getMinRes() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getMissingSymbol() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getMissingType() (schrodinger.application.desmond.antlr3.exceptions.MissingTokenException method) getMList() (schrodinger.application.matsci.density_analysis_widget.ImagePlotFrame method) (schrodinger.application.matsci.density_analysis_widget.LinePlotFrame method) getMmJagKeywords() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MossbauerSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MullikenSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MultipoleSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.RamanSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) getMobileStRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getMode() (schrodinger.application.livedesign.login.LoginManager method) getModel() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getModelEdges() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) getModelFile() (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) getModelFiles() (schrodinger.application.matsci.genetic_optimization.ChemInformatics class method) getModelNodes() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) getModels() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelectorButton method) getModelTypeAndTimeStep() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getModule() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) getMoiety() (schrodinger.application.matsci.amorphous.Moieties method) getMoldesFlags() (schrodinger.application.matsci.reaction_workflow_utils.DescriptorsMixin method) getMolecularDescriptorsJob() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getMolecularFormula() (schrodinger.application.matsci.builderwidgets.ItemRow method) getMolecularWeight() (schrodinger.application.matsci.mswidgets.StructureLoader method) getMolecule() (schrodinger.structure.StructureAtom method) getMoleculeAtoms() (schrodinger.structure.Structure method) getMoleculeGraph() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getMoleculeInfo() (schrodinger.application.matsci.kmc.Table method) getMoleculeSmarts() (schrodinger.application.matsci.rdpattern.Pattern method) getMoleculeSmiles() (schrodinger.application.matsci.rdpattern.Pattern method) getMoleculeType() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getMolInfo() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) getMonomer() (schrodinger.application.matsci.amorphous.Moieties method) getMonomerData() (schrodinger.protein.helm.helm_renderer.HelmScene method) getMonomerResizingProposal() (schrodinger.protein.helm.helm_renderer.BBPhosphateMonomerBase method) (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin method) (schrodinger.protein.helm.helm_renderer.NABaseMonomerBase method) getMonomers() (schrodinger.protein.helm.helm_renderer.HelmConnector method) getMonomerTypes() (schrodinger.protein.helm.helm_renderer.HelmConnector method) getMonosaccharideType() (schrodinger.application.matsci.amorphous.Monomer method) getMorganCount() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) getMovieData() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getMovingAtoms() (schrodinger.structure.Structure method) getMsdHeader() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase method) getMSDRelatedFiles() (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) getMSJName() (schrodinger.application.matsci.jwsteps.MDCustomMSJStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) getMSJobKeywords() (schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis method) getMutationFromChanges() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) getMutations() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) getName() (schrodinger.active_learning.al_node.ActiveLearningNode class method) (schrodinger.application.livedesign.export_models.PropertyExportSpec method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.jagwidgets.NewPresetDialog class method) (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.qt.ligand_list.Ligand method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) (schrodinger.ui.qt.swidgets.NewNameDialog method) getNameAndSave() (schrodinger.ui.qt.swidgets.ItemsManagerMixin method) getNameFromFlag() (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) getNanoSheet() (schrodinger.application.matsci.nano.tube.NanoSheet method) getNB14Pairs() (schrodinger.structutils.minimize.Minimizer method) getNBEnergyForTwoAtomLists() (schrodinger.structutils.minimize.Minimizer method) getNbnd() (schrodinger.application.matsci.espresso.qeinput.BandsType method) getNCpus() (schrodinger.pipeline.stage.Stage method) getNeighborCoordVal() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) getNeighboringRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNeighborPBCBond() (schrodinger.application.matsci.nano.xtal.PBCBond method) getNeighbors() (schrodinger.structutils.assignbondorders.AssignBondOrders method) (schrodinger.ui.qt.network_visualizer.Graph method) getNeighborsObj() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNeighborTypes() (schrodinger.application.matsci.nano.sheet.Grow method) getNewAngles() (schrodinger.application.matsci.coarsegrain.Internals method) getNewAssay() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) getNewCell() (schrodinger.application.matsci.amorphous.Scaffold method) getNewCellStructure() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getNewDihedrals() (schrodinger.application.matsci.coarsegrain.Internals method) getNewImpropers() (schrodinger.application.matsci.coarsegrain.Internals method) getNewResidueName() (schrodinger.application.matsci.amorphous.Monomer method) getNewSolution() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) getNextColor() (schrodinger.ui.qt.schart.SChart method) getNextDirname() (schrodinger.application.matsci.permittivity.chdir method) getNextFormattedNameArray() (schrodinger.application.dendrogram.core_class.GetPartitions method) getNextResidue() (schrodinger.protein.sequence.AbstractSequence method) getNextStructure() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getNJobs() (schrodinger.pipeline.stage.Stage method) getNKpts() (schrodinger.application.matsci.espresso.qeinput.KpointsType method) getNode() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) (schrodinger.ui.dendrogram.DendrogramGraphicTree method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) getNodeCentralityType() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getNodeClasses() (schrodinger.active_learning.al_driver.ActiveLearningJob static method) getNodeClusterSets() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getNodeConnectedComponent() (schrodinger.ui.qt.network_visualizer.Graph method) getNodeIndex() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) getNodes() (schrodinger.ui.qt.network_visualizer.Graph method) getNodesToRun() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getNodeToAtomConversion() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getNodeXYZ() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) (schrodinger.application.matsci.freevolume.VoidInfo method) getNonBondedEnergies() (schrodinger.structutils.minimize.Minimizer method) getNonBondType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getNonDefault() (schrodinger.application.jaguar.input.JaguarInput method) getNonDefaultKeys() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.xtb.input.XTBInput method) getNonMembraneRelaxationProtocol() (schrodinger.application.desmond.gui.GuiApp method) getNonPeriodicPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getNonpolarHydrogensTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) getNonRingContToSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getNoRelaxationProtocol() (schrodinger.application.desmond.gui.GuiApp method) getNormal() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getNormalisedValue() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) getNormalOrdering() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getNormalParameters() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData static method) getNormalsAndRadius() (schrodinger.structutils.ringspear.SpearRing method) getNormed() (schrodinger.trajectory.prody.mode.Vector method) getNotes() (schrodinger.application.jaguar.input.JaguarInput method) getNSpin() (schrodinger.application.matsci.espresso.qeinput.SpinType method) getNumAnnValues() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.sequence.AbstractSequence method) getNumber() (schrodinger.application.desmond.replica_dE.replica_energy method) (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getNumberOfClustersList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getNumberOfProcessorsManyNodes() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfProcessorsOneNode() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfQueueSlots() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfSubjobs() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfSyntaxErrors() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getNumberOfType() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) getNumBondOrders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNumBrokenRings() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) getNumCells() (schrodinger.ui.two_d_viewer.TwoDViewer method) getNumClashes() (schrodinger.application.matsci.montecarlo.Metropolizer method) getNumColumns() (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) getNumCpusToValidate() (schrodinger.application.jaguar.gui.base_panel.JaguarConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) GetNumDensity() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getNumGPUS() (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog method) getNumIncludedEntries() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) getNumMarkers() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) getNumNeighbors() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNumNodes() (schrodinger.application.livedesign.entry_types.Complexes method) getNumPlanes() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getNumResidues() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) getNumSelected() (schrodinger.application.prepwizard2.tasks.PreprocessInput method) getNumSelectedEntries() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) getNumSplits() (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.ExtractClustersStep method) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getNumStructures() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.InputTabJobMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.structure.MultiFileStructureWriter method) getNumSubjobsSpinbox() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getNumTargets() (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData method) getNumUnitCells() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getNumUsedCoordSites() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) GetNXUPQsym() (in module schrodinger.application.matsci.gsas.GSASIIspc) getObject() (schrodinger.application.matsci.cgforcefield.FFIOAngle method) (schrodinger.application.matsci.cgforcefield.FFIOBond method) (schrodinger.application.matsci.cgforcefield.FFIODihedral method) (schrodinger.application.matsci.cgforcefield.FFIOExclusion method) (schrodinger.application.matsci.cgforcefield.FFIOParam method) (schrodinger.application.matsci.cgforcefield.FFIOSite method) (schrodinger.application.matsci.cgforcefield.FFIOVdwType method) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getObjValue() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) getOffsetPBCBonds() (schrodinger.application.matsci.nano.xtal.PBCBonds method) getOneLetterCodes() (schrodinger.application.matsci.amorphous.Moieties method) getOneLineRepresentation() (schrodinger.application.pathfinder.route.RouteNode method) getOpcdArgs() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.SbcUtil method) getOpenFileName() (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.filedialog.FileDialog static method) getOpenFileNames() (schrodinger.ui.qt.filedialog.FileDialog static method) getOpenMPSettings() (schrodinger.application.jaguar.gui.base_panel.JaguarConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) GetOpNum() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetOprName() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetOprNames() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetOprPtrName() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetOprPtrNumber() (in module schrodinger.application.matsci.gsas.GSASIIspc) getOptimizationCmd() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) getOptionDesc() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getOptions() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method) (schrodinger.structutils.minimize.Minimizer method) getoptionsGUI() (schrodinger.ui.qt.dendrogram.Dendrogram method) getOptKwargs() (schrodinger.application.matsci.mecp_mod.MECP method) getOrAddColumn() (schrodinger.infra.table.Table method) getOrbitalsKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getOrderedBackbone() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getOrderedIntersections() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getOrderedNodeNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getOrderedTaskSubjobDirs() (schrodinger.application.matsci.permittivity.WorkflowParser method) getOrigin() (schrodinger.application.matsci.nano.interface_mod.Interface method) getOrthantPairs() (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method) getOrthantPopulations() (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method) getOrthantRows() (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method) getOtherNode() (schrodinger.ui.qt.network_views.NetworkEdge method) getOuterChiralIndicies() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getOuterTubeVectors() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getOutfileName() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) getOutput() (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.CombinerStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.pipeline.stage.Stage method) getOutputEnding() (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep method) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep method) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getOutputFile() (schrodinger.job.launchapi.JobSpecification method) getOutputFileNamePattern() (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getOutputFiles() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.launchapi.JobSpecification method) getOutputKeys() (schrodinger.job.launchapi.TaskSpecification method) getOutputName() (schrodinger.application.matsci.jwsteps.BaseDesmondStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep method) (schrodinger.application.matsci.jwsteps.CustomCmsToMaeStep method) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep method) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep method) (schrodinger.application.matsci.jwsteps.EvaporationStep method) (schrodinger.application.matsci.jwsteps.ExtractClustersStep method) (schrodinger.application.matsci.jwsteps.FreeVolumeStep method) (schrodinger.application.matsci.jwsteps.HOFStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep method) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep method) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep method) (schrodinger.application.matsci.jwsteps.PrepForMDStep method) (schrodinger.application.matsci.jwsteps.VoidStep method) (schrodinger.pipeline.stage.Stage method) getOutputNames() (schrodinger.pipeline.stage.Stage method) getOutputPaths() (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) getOutputs() (in module schrodinger.application.steps.test) getOutputsFromSmiles() (in module schrodinger.application.steps.test) getOutputTopic() (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) getOutsideCylinderVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getOutsideEllipsoidVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getOutsideSphereVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getOutsideVol() (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile method) getOverlapEnergyPlot() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getPairFromRow() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getPairInfo() (schrodinger.application.matsci.kmcgui.NeighborsTab method) getPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getPanelInstance() (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin class method) getPanelState() (schrodinger.ui.qt.appframework2.settings.SettingsPanelMixin method) getParallelepipedLineSegments() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getParallelepipedVertices() (schrodinger.application.matsci.shapes.Parallelepiped method) getParamRows() (schrodinger.ui.qt.schart.SeriesParams static method) getParams() (schrodinger.application.matsci.qubec_utils.Qubec method) getParamSignal() (schrodinger.models.parameters.Param class method) getParamSlot() (schrodinger.models.mappers.TargetParamMapper method) getParamValue() (schrodinger.models.parameters.Param class method) getParent() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getParentalInformation() (schrodinger.application.matsci.jwsteps.BaseStep method) getParentBonds() (schrodinger.application.matsci.cg_mapping.Particle static method) getParentCutBonds() (schrodinger.application.matsci.cg_mapping.Particle static method) getParentGroup() (schrodinger.project.project.EntryGroup method) getParentIndices() (schrodinger.application.matsci.cg_mapping.Particle static method) getParentJob() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) getParentTasknameByIndexFromDict() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getParentTasknames() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getParticipants() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) getParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getParticles() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) GetPartitions (class in schrodinger.application.dendrogram.core_class) GetPartitions.NameList (class in schrodinger.application.dendrogram.core_class) getPassword() (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel method) getPatchColorRamp() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) getPath() (schrodinger.application.matsci.kmcgui.DatabaseInfo method) (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) getPathLabelText() (schrodinger.application.matsci.kmcgui.DatabaseInfo method) getPathLength() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getPattern() (schrodinger.application.matsci.rdpattern.Pattern method) getPatternString() (schrodinger.structutils.createfragments.FragmentCreator method) getPBCMinMaxes() (schrodinger.application.matsci.amorphous.Scaffold method) getPBCSide() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getPdbDialog() (in module schrodinger.ui.qt.pdb_dialog) getPDBName() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Initiator method) (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getPDFPath() (schrodinger.application.matsci.reportutils.ReportInfo method) getPDOS() (schrodinger.application.matsci.espresso.qeoutput.PDOS method) getPeakPos() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getPeakProfile() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getPeakProfileDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getPercentOfPosesWithInteractions() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) getPercentScreenCurvePoints() (schrodinger.analysis.enrichment.calculator.Calculator method) getPeriodicPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getPerMolCoeffcient() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) getPerMolFileName() (schrodinger.application.matsci.order_parameter_mod.Descriptor method) getPersistenceKey() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) getPerWindowCoefficients() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) getPhaseHypo() (schrodinger.application.phase.packages.cat_hypo_converter.CatHypoConverter method) getPickingMode() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) getPicture() (schrodinger.ui.qt.delegates.PictureDelegate method) getPictureForCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) getPilotScoreFile() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getPipeFilename() (schrodinger.stepper.sideinputs.ForkStep method) getPiperDict() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method) getPkaAtom() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getPkaAtomObjs() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getPkaAtoms() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getPlaceholderText() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getPlaneBoxIntersections() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getPLISKWList() (in module schrodinger.application.desmond.automatic_analysis_generator) getPLP() (schrodinger.maestro_utils.maestro_sync.PLPTarget method) getPointInBox() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) (schrodinger.application.matsci.amorphous.Scaffold method) getPointsFromCalc() (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method) (schrodinger.analysis.enrichment.plotter.Plotter method) getPolygonVertices() (schrodinger.protein.helm.helm_renderer.NABaseMonomerBase method) getPolymerFragments() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getPoseIds() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) getPosition() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) (schrodinger.application.matsci.desconfig.BarrierInfo static method) getPositions() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getPotentialDoubleBondAtoms() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getPotentialEnergyGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getPotentialReceptorIssues() (schrodinger.application.desmond.feputils.ProteinReliabilityTask method) getPotentialType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getPotentialWallConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) getPPIKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getPrecision() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getPrereqs() (schrodinger.job.queue.BaseJob method) getPreScript() (schrodinger.application.matsci.permittivity.TaskProtocol method) getPressure() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getPreviousResidue() (schrodinger.protein.sequence.AbstractSequence method) getPrimeEnergyByResidues() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getProductAppender() (schrodinger.rdkit.molio.BaseMergeHandler method) (schrodinger.rdkit.molio.CsvMergeHandler method) (schrodinger.rdkit.molio.RdkitMergeHandler method) (schrodinger.rdkit.molio.SmiMergeHandler method) (schrodinger.rdkit.molio.StructureMergeHandler method) getProductComplex() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getProductNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getProductReader() (schrodinger.rdkit.molio.BaseMergeHandler method) (schrodinger.rdkit.molio.CsvMergeHandler method) (schrodinger.rdkit.molio.RdkitMergeHandler method) (schrodinger.rdkit.molio.SmiMergeHandler method) (schrodinger.rdkit.molio.StructureMergeHandler method) getProducts() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) getProgramName() (schrodinger.job.app.App method) (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) getProgressAsPercentage() (schrodinger.job.jobcontrol.Job method) getProgressAsSteps() (schrodinger.job.jobcontrol.Job method) getProgressAsString() (schrodinger.job.jobcontrol.Job method) getProjectID() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) getProjectName() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) getProjectRow() (schrodinger.ui.two_d_viewer.Cell method) getProjectStructure() (schrodinger.application.matsci.reaction_workflow_gui_utils.WorkspaceSuperpositionFrame static method) getprop() (in module schrodinger.livedesign.preprocessor) getPropAndValues() (schrodinger.application.matsci.kmcgui.PropertyCombo method) getProperties() (schrodinger.application.livedesign.entry_types.BaseEntryData method) (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData method) (schrodinger.application.livedesign.entry_types.GenericEntities method) (schrodinger.application.matsci.espresso.qeoutput.Output class method) (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) getPropertiesToShow() (schrodinger.ui.two_d_viewer.TwoDViewer method) getProperty() (schrodinger.application.bioluminate.pml_menus.LabelAtomByEntryIndex method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByMolIndex method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByNumType method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByOccupancy method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByProp method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByVDW method) (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.ui.qt.dendrogram.Dendrogram method) getPropertyEnsemble() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) getPropertyExportSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getPropertyKeys() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) getPropertyLabels() (schrodinger.ui.two_d_viewer.TwoDViewer method) getPropertyMinMax() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) getPropertyNames() (schrodinger.project.project.Project method) (schrodinger.rdkit.filtering.JSONFilterAdapter method) (schrodinger.structure.Structure method) (schrodinger.structutils.filter.PropFilter method) (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getPropertyNamesForSelectedRows() (schrodinger.project.project.Project method) getPropertyPrecision() (schrodinger.project.project.Project method) getPropertyStrings() (schrodinger.application.matsci.genetic_optimization.Property static method) getPropertyValue() (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) getPropName() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getPropsToShowForCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) getProteinTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) getProtFilename() (schrodinger.application.desmond.gui.RelaxFrame method) getProtLigInterKW() (in module schrodinger.application.desmond.automatic_analysis_generator) getPseudo() (schrodinger.application.matsci.espresso.utils.UPFParser method) getPsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getQProp() (schrodinger.application.matsci.chargegui.NeighborTreatment method) getQueryName() (schrodinger.protein.tasks.blast.BlastTask method) (schrodinger.protein.tasks.blast.BlastTask.Input method) getQueue() (schrodinger.application.matsci.genetic_optimization.ClassEvaluator method) (schrodinger.application.matsci.genetic_optimization.RefractiveIndex method) getRadius() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) getRamaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getRandGridXYZ() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getRandomRealization() (schrodinger.application.scaffold_enumeration.common.EnumerableMixin method) getRandXYZ() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getRange() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) getRangeLabel() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) getRangeLimit() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) getRBTransMat() (in module schrodinger.application.matsci.gsas.GSASIImath) getRDMol() (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) getReactantComplex() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getReactantNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getReactants() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getReactantsConformersDict() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowFile method) getReactantTrackers() (schrodinger.application.matsci.fragments.FragmentReactor method) getReactionInternals() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getReactionSet() (schrodinger.application.pathfinder.route.Node method) getReactionSmarts() (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) getReactionSmiles() (schrodinger.application.pathfinder.route.RouteNode method) getReactiveAtoms() (schrodinger.application.matsci.rxn_path.ReactionPath method) getReagentMol() (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) getReagentSmarts() (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) getReagentSource() (schrodinger.application.pathfinder.route.ReagentNode method) getRealization() (schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method) (schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method) (schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method) getRecentTemplatePath() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getRecentTemplatesList() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getReceptorID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getReciprocals() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getReciprocalVal() (schrodinger.application.matsci.desconfig.BarrierHeader static method) getReducedMass() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getReducedMass1() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getReducedMass2() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getRedundantAtoms() (schrodinger.application.matsci.nano.sheet.Grow method) getReferenceEdges() (schrodinger.application.matsci.shapes.Face method) getReferenceEntryId() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) getReferenceFaces() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) getReferenceSeq() (schrodinger.protein.alignment.BaseAlignment method) getReferenceStructure() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) getRefractiveIndex() (schrodinger.application.matsci.permittivity.RefractiveIndex static method) getRelatedFile() (schrodinger.application.matsci.permittivity.MdPostAnalysis static method) getRelatedJobFile() (schrodinger.application.matsci.permittivity.MdPostAnalysis static method) getRelaxationProtocolFile() (schrodinger.application.matsci.permittivity.MultiStageMd class method) getRelaxationStages() (schrodinger.application.matsci.permittivity.MultiStageMd static method) getRelaxationStageStringFromTemplate() (schrodinger.application.desmond.gui.GuiApp method) getRelEnergy() (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection method) getRelicaNodeIndexes() (schrodinger.application.matsci.permittivity.WorkflowParser method) getRelPath() (schrodinger.application.matsci.genetic_optimization.Property static method) getRemoteModulesDir() (schrodinger.tasks.tasks.AbstractComboTask method) getReorderedStructure() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) getReplica() (schrodinger.application.desmond.replica_dE.replica_container method) getReplicaKeywords() (schrodinger.application.matsci.permittivity.TaskProtocol method) getReplicaType() (schrodinger.application.matsci.permittivity.WorkflowParser method) getRepresentativeStructure() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) getResByKey() (schrodinger.protein.sequence.AbstractSingleChainSequence method) getResID() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) getResidualPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidualPotentialByAtom() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidualPotentialByResidue() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidue() (schrodinger.structure.StructureAtom method) getResidueAtomicNonPolarSASA() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueAtomicPolarSASA() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueAtoms() (schrodinger.structure.Structure method) getResidueGroups() (schrodinger.ui.residueselector.MutationSelectorMixin method) getResidueHydropathy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getResidueIndices() (schrodinger.protein.alignment.BaseAlignment method) getResidueInteractionEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueInternalEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResiduepKa() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResiduePotentialEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueRotatableBonds() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidues() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getResidueSASA() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResiduesCenter() (schrodinger.ui.picking.PickResiduesChangedMixin method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) getResiduesData() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getResidueSeqProps() (schrodinger.protein.alignment.BaseAlignment method) getResidueSimilarity() (schrodinger.protein.alignment.BaseAlignment method) getResiduesList() (schrodinger.ui.picking.PickResiduesChangedMixin method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) getResidueSurfComp() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResiduesWithStructure() (schrodinger.protein.alignment.BaseAlignment method) getResidueToggle() (schrodinger.ui.residueselector.MutationSelectorMixin method) getResidueType() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getResistance() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getResolution() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getResources() (schrodinger.stepper.stepper.UnbatchedChain method) getResponse() (schrodinger.ui.qt.forcefield.forcefield.ValidateOplsDirMessageBox method) (schrodinger.ui.qt.messagebox.MessageBox method) (schrodinger.ui.qt.messagebox.QuestionMessageBox method) getRestAngle() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestartNode() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getRestChiral() (in module schrodinger.application.matsci.gsas.GSASIImath) getRESTDensityPlot() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getRestDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestDist() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestPlane() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestPolefig() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestPolefigDerv() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestRama() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestrGroup() (schrodinger.application.desmond.gui.RestraintsTab method) getRestTorsion() (in module schrodinger.application.matsci.gsas.GSASIImath) getResultSeqs() (schrodinger.protein.align.AbstractStructureAligner method) getResultsGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getResultWithThisEnergy() (schrodinger.application.matsci.jaguarworkflows.Results method) getReverse() (schrodinger.protein.sequence.NucleicAcidSequence method) getReverseComplement() (schrodinger.protein.sequence.NASequence method) (schrodinger.protein.sequence.NucleicAcidSequence method) getRGB() (schrodinger.structutils.color.ColorRamp method) getRGroups() (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) getRHistogram() (schrodinger.application.desmond.replica_dE.replica_energy method) getRho() (in module schrodinger.application.matsci.gsas.GSASIImath) getRhos() (in module schrodinger.application.matsci.gsas.GSASIImath) getRingAtomToRings() (schrodinger.application.dendrogram.core_class.Utilities static method) getRingCentroid() (schrodinger.structutils.ringspear.SpearRing method) getRingDataStructures() (schrodinger.application.dendrogram.core_class.Utilities static method) getRingDecorations() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getRingNodeContToSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getRingOrderPermutations() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) getRingSysInfo() (schrodinger.application.dendrogram.core_class.Deepest0 method) (schrodinger.application.dendrogram.core_class.Deepest1 method) (schrodinger.application.dendrogram.core_class.Deepest2 method) (schrodinger.application.dendrogram.core_class.Deepest3a method) (schrodinger.application.dendrogram.core_class.Deepest3b method) (schrodinger.application.dendrogram.core_class.Deepest4 method) (schrodinger.application.dendrogram.core_class.Deepest5 method) (schrodinger.application.dendrogram.core_class.Deepest6 method) getRingSysSt() (schrodinger.application.dendrogram.core_class.Utilities static method) getRLMap() (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData method) getRMax() (schrodinger.application.desmond.replica_dE.replica_energy method) getRMean() (schrodinger.application.desmond.replica_dE.replica_energy method) getRMin() (schrodinger.application.desmond.replica_dE.replica_energy method) getRMSD() (in module schrodinger.trajectory.prody.ensemble) getRmsdDataname() (schrodinger.structutils.rmsd.ConformerRmsd method) getRMSDKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getRMSDLigandKW() (in module schrodinger.application.desmond.automatic_analysis_generator) getRMSFLigandKW() (in module schrodinger.application.desmond.automatic_analysis_generator) getRMSFProtKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getRotamers() (schrodinger.application.matsci.etarotamers.HapticLigand method) getRotatableBondsGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getRotatedComplex() (schrodinger.application.matsci.mlearn.features.Complex method) getRotationToZ() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getRotEnergy() (schrodinger.application.desmond.torsion_related.BondRotator method) getRoutes() (schrodinger.application.pathfinder.route.RetroSynthesisNode method) getRow() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.project.project.Project method) getRowColumnFromI() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getRowCriteria() (schrodinger.ui.ligfilter.CriteriaListModel method) getRowData() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.table.ExportableProxyModel method) getRows() (schrodinger.ui.qt.swidgets.STableWidget method) getRowText() (schrodinger.ui.ligfilter.PatternModel method) getRSquaredList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getRuleInvocationStack() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getRuleMemoization() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getRun() (schrodinger.protein.sequence.AbstractSequence method) getRunningJobIDs() (schrodinger.application.matsci.jobdirdlg.JobManager method) getRuntimePath() (schrodinger.pipeline.stage.Stage method) getRxAtoms() (schrodinger.application.matsci.builderwidgets.SketcherStructureMixin method) getRXNWFInputFiles() (schrodinger.application.matsci.reaction_workflow_utils.EnumerateSwapMixin method) getSampleAtomAndStructTag() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) getSampleAtomId() (schrodinger.application.matsci.species.SpeciesData method) getSampleHistogram() (schrodinger.application.matsci.uq_utils.BilinearHistogramData static method) (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData static method) (schrodinger.application.matsci.uq_utils.HyperbolaHistogramData static method) getSampleIndices() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) getSampleMolNumber() (schrodinger.application.matsci.clusterstruct.SpeciesData method) (schrodinger.application.matsci.clusterstructgui.SpeciesCombo method) getSamplePoints() (schrodinger.application.matsci.rxn_path.ReactionPath method) getSamplePropertyValue() (schrodinger.application.livedesign.entry_types.BaseEntryData method) (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData method) (schrodinger.application.livedesign.entry_types.GenericEntities method) getSampleResidues() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getSampleStructure() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) getSASAGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getSASANonPolarGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getSASAPolarGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getSavedItems() (schrodinger.ui.qt.swidgets.ItemsManagerMixin method) getSaveFileAndDefinition() (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.SaveDefinitionsDialog method) getSaveFileName() (schrodinger.ui.qt.filedialog.FileDialog static method) getScaledEwaldConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getScaleFactor() (schrodinger.protein.helm.helm_renderer.HelmWidget method) getScanCoordinate() (schrodinger.application.jaguar.input.JaguarInput method) getScene() (schrodinger.ui.dendrogram.DendrogramView method) getScenesData() (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync method) getSectionText() (schrodinger.application.jaguar.input.JaguarInput method) getSectorAnnotation() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) getSectorAnnotationLoc() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) getSeed() (schrodinger.application.matsci.mswidgets.RandomSeedWidget method) (schrodinger.application.matsci.permittivity.TaskProtocol method) getSeedFlag() (schrodinger.application.matsci.permittivity.DisorderSystemBuilder class method) (schrodinger.application.matsci.permittivity.StepBase class method) getSegmentPlaneIntersections() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) getSegmentType() (schrodinger.application.matsci.kmc.Table static method) getSelected() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) (schrodinger.ui.qt.propertyselector.PropertySelectorMenu method) getSelectedAslNames() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getSelectedCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) getSelectedDataTitles() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) getSelectedElements() (schrodinger.ui.qt.periodictable.PeriodicTableDialogMultipleClick method) getSelectedEntryIds() (schrodinger.ui.two_d_viewer.TwoDViewer method) getSelectedEntryInfo() (schrodinger.ui.qt.input_selector.InputSelector method) getSelectedExcludedVolumes() (schrodinger.application.phase.featureselector.FeatureModel method) getSelectedFeatureEquivalencies() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) getSelectedFeatures() (schrodinger.application.phase.featureselector.FeatureModel method) (schrodinger.application.phase.featureselector.FeatureSelector method) getSelectedFileName() (schrodinger.application.matsci.builderwidgets.FilteredTemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListToolButton method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateToolButton method) getSelectedIndexes() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) getSelectedItem() (schrodinger.application.matsci.builderwidgets.TemplateSelectorPopUp method) getSelectedItems() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) getSelectedLigand() (schrodinger.ui.chooseligand.ChooseLigandDialog method) getSelectedLocationType() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedMutations() (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) getSelectedName() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedNodes() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) getSelectedPath() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedPatternName() (schrodinger.ui.ligfilter.LigfilterFrame method) getSelectedPreset() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) getSelectedProp() (schrodinger.application.matsci.chargegui.ChargePropertySelector method) getSelectedResult() (schrodinger.application.bioluminate.antibody.search_results_table.FullTable method) (schrodinger.application.bioluminate.antibody.search_results_table.TableView method) getSelectedResults() (schrodinger.application.bioluminate.antibody.search_results_table.SplitTable method) getSelectedRowAtoms() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) getSelectedRowIndexes() (schrodinger.ui.qt.swidgets.STableWidget method) getSelectedRows() (schrodinger.infra.table.Table method) getSelectedRowTotal() (schrodinger.infra.table.Table method) (schrodinger.project.project.Project method) getSelectedStandardItems() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) getSelectedStructure() (schrodinger.application.matsci.builderwidgets.FilteredTemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateToolButton method) getSelectedStructures() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) getSelectedTemplateName() (schrodinger.application.matsci.builderwidgets.FilteredTemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateToolButton method) getSelectedText() (schrodinger.ui.qt.appframework2.debugwidgets.BaseTable method) getSelectedX() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getSelectedXY() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getSelection() (schrodinger.application.matsci.builderwidgets.TemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListToolButton method) (schrodinger.application.matsci.mswidgets.ConvenientSelectorWithPopUp method) (schrodinger.ui.qt.swidgets.SelectorWithPopUp method) getSelectionForceField() (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) getSelectionForceFieldInt() (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) getSelfEnergy() (schrodinger.structutils.minimize.Minimizer method) getSemiPartialRSquaredList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getSeparationRatioList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getSeqAnnotations() (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportWriter method) getSeqsDescriptors() (schrodinger.protein.alignment.BaseAlignment method) getSeqsMatchingRefType() (schrodinger.protein.alignment.BaseAlignment method) getSeqStructure() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) getSequenceViewerImage() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getSeriesXVals() (schrodinger.ui.qt.schart.SChart static method) getSeriesYVals() (schrodinger.ui.qt.schart.SChart static method) getSettings() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp method) getSettingsAffectedBySpinTreatment() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) getSettingsMenuActions() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) GetSGSpin() (in module schrodinger.application.matsci.gsas.GSASIIspc) getShape() (schrodinger.application.phase.packages.shape_generator.ShapeGenerator method) GetSHCoeff() (in module schrodinger.application.matsci.gsas.GSASIImath) getShiftedCoulombFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getShiftedLennardJonesFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getShiftVectorByRecenterMass() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) getSibling() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) getSideAxis() (schrodinger.ui.qt.schart.SChart method) getSignalsAndSlots() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.ServerRegistrationMixin method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.models.mappers.TargetParamMapper method) (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager method) (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.structure_selector.ImportButtonMixin method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskbarwidgets.NameLineEdit method) getSimilarity() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) getSimilarityMetricDescription() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method) getSimilarityScore() (schrodinger.protein.sequence.AbstractSequence method) getSimpleSlabVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSimplified() (schrodinger.application.matsci.bandshape_utils.Transition static method) getSimplifiedTreeData() (schrodinger.application.pathfinder.route.RouteNode method) getSingleDisplacementChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getSiteNumber() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) getSites() (schrodinger.application.matsci.reaction_workflow_utils.Sites static method) (schrodinger.application.phase.phase_markers.PhaseMarkers method) getSiteType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getSize() (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) getSketcherStructure() (schrodinger.application.matsci.builderwidgets.SketcherStructureMixin method) getSkipEtaRotamers() (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch method) getSlabVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSlots() (schrodinger.application.matsci.siteselector.siteselector.Ligand method) (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getSmarts() (schrodinger.analysis.transformations.TransformsRepository method) getSMARTS() (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) getSmartsDictData() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) getSMARTSFromSelection() (schrodinger.ui.ligfilter.AddDefinitionDialog method) getSMARTSPatterns() (schrodinger.ui.qt.swidgets.SMARTSEdit method) getSmiAndShapeScores() (schrodinger.application.phase.packages.shape_screen_al_node.ShapeScreenJob method) getSmiles() (schrodinger.structutils.smiles.SmilesGenerator method) getSmilesAndMap() (schrodinger.structutils.smiles.SmilesGenerator method) getSMILESForFrag() (schrodinger.application.matsci.fragments.Fragment method) getSmilesWrappedOutputs() (in module schrodinger.application.steps.test) getSolubilityKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getSolvent() (schrodinger.application.jaguar.gui.solvent_selector.SolventSelectorFilterListPopUp method) (schrodinger.application.jaguar.gui.solvent_selector.SolventSelectorFilterListToolButton method) getSolventConstraints() (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) getSolventLayers() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getSolventName() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) getSolventsTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) getSOSTOF() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getSourceName() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getSources() (schrodinger.application.fpsim.FPsimSearcher method) getSpanningVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSparseRescodes() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getSpecialProperties() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) getSpecies() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) getSpeciesCount() (schrodinger.application.matsci.species.SpeciesCollection method) getSpeciesFromAtomIndex() (schrodinger.application.matsci.species.SpeciesCollection method) getSpeciesMolNum() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) getSpecificInteractionSummary() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions method) getSpecsString() (schrodinger.application.inputconfig.InputConfig method) getSpectators() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getSpgObjByName() (schrodinger.application.matsci.nano.space_groups.SpaceGroups method) getSpgSymbol() (schrodinger.application.matsci.espresso.qeinput.KpointsType static method) getSphereSliceVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getSpinTreatment() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) getSquareVertices() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSSA() (schrodinger.application.prime.wrapper.BasePrimeAlignment method) getSSBondPartner() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) getSSEProtKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) GetSSfxuinel() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetStackParms() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getStageByJobid() (schrodinger.pipeline.pipeline.Pipeline method) getStageDirectory() (schrodinger.pipeline.stage.Stage method) getStageIndex() (schrodinger.application.matsci.mswidgets.MultiStageArea method) getStageIndicesByMarker() (schrodinger.application.matsci.permittivity.MdStageModifier static method) getStages() (schrodinger.application.matsci.permittivity.MultiStageMd method) getStandardizedSmiles() (schrodinger.structutils.smiles.SmilesGenerator method) getStart() (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method) (schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method) (schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method) getstart_temp() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) getStartFrameValue() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getStartingNodes() (schrodinger.application.pathfinder.route.RouteNode method) getStartPos() (schrodinger.protein.helm.helm_renderer.AABranchingConnectorItem method) (schrodinger.protein.helm.helm_renderer.DisulfideConnectorMixin method) (schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin method) getState() (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.swidgets.SValidIndicator method) getStateChargeAndMultiplicity() (schrodinger.application.matsci.fragments.FragmentReactor method) getStateModifier() (schrodinger.application.matsci.fragments.FragmentReactor method) getStatus() (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) (schrodinger.application.glide.http_client.ZmqClient method) getStatusStrings() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) getStderr() (schrodinger.job.launchapi.JobSpecification method) getStdout() (schrodinger.job.launchapi.JobSpecification method) getStep() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) getStepClass() (schrodinger.stepper.stepper.StepTaskMixin method) getSteps() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSWorkFlow method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.jwsteps.BaseWorkflow method) getStoichiometry() (schrodinger.application.matsci.mlearn.features.Ligand method) getStop() (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method) (schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method) getstr() (in module schrodinger.application.matsci.msutils) getStrainedAdsorptionLayer() (schrodinger.application.matsci.nano.interface_mod.Interface method) getStrainedAngle() (schrodinger.application.matsci.nano.interface_mod.Interface method) getStretch() (schrodinger.structutils.minimize.Minimizer method) getStretchEnergy() (schrodinger.structutils.minimize.Minimizer method) getString() (schrodinger.ui.qt.swidgets.SLineEdit method) getStringers() (schrodinger.application.matsci.jwsteps.BaseRelaxationStep method) (schrodinger.application.matsci.jwsteps.CompressiveRelaxationStep method) (schrodinger.application.matsci.jwsteps.MatSciMDRelaxationStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) (schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation1Step method) (schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation2Step method) (schrodinger.application.matsci.jwsteps.SingleMDStep method) getStrucChargeAndSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getStrucEid() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka method) getStruct() (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem method) (schrodinger.application.matsci.equilibrium_md.CmsModel method) (schrodinger.application.matsci.equilibrium_md.Model method) (schrodinger.ui.qt.table.ViewerModel method) getStructEidMap() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) getStructForChild() (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.CombinerStep method) (schrodinger.application.matsci.jwsteps.ExtractClustersStep method) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getStructFromPtEntry() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) getStructsForWriting() (schrodinger.application.matsci.jwsteps.BaseDesmondStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.BDEStep method) (schrodinger.application.matsci.jwsteps.ExtractClustersStep method) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getStructsOfType() (schrodinger.application.matsci.jwsteps.BDEStep method) getStructToRender() (schrodinger.ui.two_d_viewer.TwoDViewer method) getStructure() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.jaguar.results.JaguarResults method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.builderwidgets.LigandSketcherStructGetter method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Results method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.mswidgets.LipidImporter method) (schrodinger.application.matsci.mswidgets.StructureLoader static method) (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.project.project.ProjectRow method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.structure.TextualStructure method) (schrodinger.structutils.minimize.Minimizer method) getStructureFile() (schrodinger.application.qsite.input.QSiteInput method) getStructureForCoupling() (schrodinger.application.matsci.amorphous.BaseMoiety method) getStructureOutput() (schrodinger.pipeline.pipeline.Pipeline method) getStructureResForRes() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) getStructureResProperties() (schrodinger.protein.residue.Residue method) getStructures() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.livedesign.entry_types.GenericEntities method) (schrodinger.application.matsci.reaction_workflow_utils.EnumerateReactionWorkflow method) (schrodinger.application.matsci.species.SpeciesData method) getStructureSize() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) getStructureTitleForJobname() (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) getStructureWithJagNames() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getStructureWithoutProps() (schrodinger.application.matsci.fragments.UniqueTracker method) getStructureWithProps() (schrodinger.application.matsci.fragments.UniqueTracker method) getStsInfo() (schrodinger.application.livedesign.panel_components.StructSelectionModel method) getSubalignment() (schrodinger.protein.alignment.BaseAlignment method) getSubHostName() (schrodinger.job.launchparams.LaunchParameters method) getSubjobname() (schrodinger.application.matsci.permittivity.WorkflowParser method) getSubjobsLabel() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getSubjobsUnitLabel() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getSubParam() (schrodinger.models.parameters.CompoundParam class method) getSubParams() (schrodinger.models.parameters.CompoundParam class method) getSubplotDialog() (schrodinger.ui.qt.navtoolbar.AtomInfoToolbar method) (schrodinger.ui.qt.navtoolbar.NavToolbar method) getSubsequence() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) getSubStAndAids() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) getSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getSummary() (schrodinger.application.livedesign.entry_types.BaseEntryData method) getSummaryData() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) getSuperimposedRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getSupportedFormats() (schrodinger.application.desmond.image_generator.ImageGenerator method) getSurface() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getSurfaceArea() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.application.matsci.shapes.Cylinder method) (schrodinger.application.matsci.shapes.Sphere method) getSurfaceComplementarityLimits() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput method) getSurfaceNodes() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) (schrodinger.application.matsci.freevolume.Void method) getSurfacePotential() (schrodinger.application.bioluminate.escomp.PotGrid method) getSurfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getSurfactantConstraints() (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) getSurfactantLayers() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getSwappingGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getSwaps() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) (schrodinger.application.matsci.automated_cg_mapping.DpdMapper method) (schrodinger.application.matsci.automated_cg_mapping.MartiniMapper method) getSymbol() (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) getSymbolicLine() (schrodinger.application.matsci.zmutils.ZAtom method) getSymmetrizedCell() (schrodinger.application.matsci.espresso.qeinput.StructureType static method) getSyXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath) getTab() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) getTabByLabel() (schrodinger.ui.qt.swidgets.STabWidget method) getTableLayout() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog method) getTableStyle() (schrodinger.application.matsci.reportutils.PDFBuilder method) getTabParentAndLayout() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) getTargetIndexMap() (schrodinger.application.pathfinder.route.ReagentNode method) getTargetMolecule() (schrodinger.application.matsci.montecarlo.Metropolizer method) getTargetSlot() (schrodinger.models.mappers.TargetParamMapper method) getTask() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) getTaskBar() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) getTaskDir() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.jobtasks.ComboJobTask method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.tasks.tasks.ComboSubprocessTask method) getTaskFilename() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.tasks.AbstractTask method) getTaskManager() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) getTaskName() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getTaskNames() (schrodinger.application.matsci.permittivity.Config method) (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getTaskProtocol() (schrodinger.application.matsci.permittivity.Config method) getTasks() (schrodinger.tasks.queue.TaskQueue method) getTaskSpec() (schrodinger.job.launchapi.TaskSpecificationBuilder method) getTaskSubClass() (schrodinger.application.matsci.permittivity.WorkflowParser class method) getTauT() (in module schrodinger.application.matsci.gsas.GSASIIspc) getTCRRegion() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getTCRRegions() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) (schrodinger.protein.annotation.TCRRegionFinder method) getTemperature() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getTempFilename() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) getTempImageFilename() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.matsci.reportutils.PDFBuilder method) getTemplate() (schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method) getTemplateID() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) getTemplates() (schrodinger.application.matsci.builderwidgets.SketcherBox method) (schrodinger.application.matsci.permittivity.PolymerBuilder static method) getTerminalGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) getTerminatingAtoms() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) getTerminatingIdxs() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getTerminiIdxs() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getText() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.ui.qt.tablewidget.Cell method) getTextStruct() (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem method) getTextSummary() (schrodinger.protein.reliability.Results method) getTheoryAndSpinData() (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) getTheoryLevel() (schrodinger.application.jaguar.gui.tabs.base_tab.LoadsTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) getTheoryLevelForEid() (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getThermoExts() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) getThermoKeys() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AnalyzeStageData method) getThermoMethod() (schrodinger.application.desmond.gui.EnsembleTab method) getThreadId() (schrodinger.utils.thread_utils.ThreadTool method) getThreadName() (schrodinger.utils.thread_utils.ThreadTool method) getThreeLetterResidueCode() (schrodinger.ui.residueselector.ResidueGroups method) getTime() (schrodinger.application.matsci.jobdirdlg.JobManager method) getTimePS() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getTimestepPS() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getTitle() (schrodinger.application.matsci.desconfig.AveCellMSJStringer method) (schrodinger.application.matsci.desconfig.BrownieMSJStringer method) (schrodinger.application.matsci.desconfig.MDMSJStringer method) (schrodinger.application.matsci.desconfig.MSAnalysisMSJStringer method) (schrodinger.application.matsci.desconfig.MSJStringer method) (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getTitles() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getTodoAtoms() (schrodinger.application.matsci.espresso.qeinput.PHControlType static method) getTOFalpha() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFalphaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFbeta() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFbetaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFgamma() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFgammaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFsig() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFsigDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getToken() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel method) getTokenErrorDisplay() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getTokenIndex() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) getTokens() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) getTokenSource() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.TokenStream method) getTokenStartIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getTokenStopIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getTokenStream() (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) getTokenType() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) getToolBar() (schrodinger.application.bioluminate.actions.factory.Factory method) getTopLocationItem() (schrodinger.ui.qt.forcefield.pathselectorwidget.PathSelectorWidget method) getTorsion() (schrodinger.structutils.minimize.Minimizer method) getTorsionConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) getTorsionDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getTorsionEnergy() (schrodinger.structutils.minimize.Minimizer method) getTorsionKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getTorsions() (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.AbstractTorsionAnalyzer method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.NucleotideTorsions method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.ResiduesTorsions method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.SmallMoleculeTorsions method) GetTorsionSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getTorsionValueInRange() (schrodinger.application.matsci.amorphous.TorsionAngler method) getTotal14Pair() (schrodinger.structutils.minimize.Minimizer method) getTotalAggregation() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalAtom() (schrodinger.structutils.minimize.Minimizer method) getTotalBending() (schrodinger.structutils.minimize.Minimizer method) getTotalCharge() (schrodinger.application.matsci.mswidgets.SystemInformationFrame method) getTotalCIonThickness() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getTotalComplementarity() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalEnergy() (schrodinger.structutils.minimize.Minimizer method) getTotalHydrogenBondCount() (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions method) getTotalHydropathy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalImpTorsion() (schrodinger.structutils.minimize.Minimizer method) getTotalInteractionCount() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions method) getTotalInteractionCountLimits() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput method) getTotalMovieFrames() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getTotalNonSurfactantThickness() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getTotalOpenMPCPUs() (schrodinger.ui.qt.config_dialog.ConfigDialog method) getTotalpKa() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalPotentialEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalPrimeEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalProcessors() (schrodinger.job.queue.ResourceHost method) getTotalRotatableBonds() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalSASA() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalSASANonPolar() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalSASAPolar() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalSolubility() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalStretch() (schrodinger.structutils.minimize.Minimizer method) getTotalSurfactantThickness() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getTotalSurfComp() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalTime() (schrodinger.application.jaguar.gui.timing.TimingResults method) getTotalTorsion() (schrodinger.structutils.minimize.Minimizer method) getTotalTypes() (schrodinger.graphics3d.common.Group method) getTPP() (schrodinger.job.launchparams.LaunchParameters method) getTrace() (schrodinger.trajectory.prody.nma.NMA method) getTrajectoryFromCms() (schrodinger.application.matsci.permittivity.MdPostTrajectoryAnalysis static method) getTrajectoryName() (schrodinger.application.matsci.jwsteps.BaseDesmondStep method) (schrodinger.application.matsci.jwsteps.DiffusionGKStep method) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep method) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep method) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep method) getTrajFlags() (schrodinger.application.matsci.deswidgets.TrajAnalysisGuiMixin method) getTransitionStateNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getTranslation() (schrodinger.protein.sequence.NASequence method) (schrodinger.protein.sequence.NucleicAcidSequence method) getTranslationToBox() (schrodinger.application.matsci.amorphous.Box method) getTree() (schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method) (schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method) (schrodinger.application.matsci.espresso.qeoutput.Output method) getTreeAdaptor() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) getTreeData() (schrodinger.application.pathfinder.route.RouteNode method) getTreeNodeStream() (schrodinger.application.desmond.antlr3.tree.TreeParser method) getTreePath() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) getTreeSource() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) getTrialScales() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getTrimmedTable() (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile static method) getTrueValues() (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) getTubeSpacings() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getTutorialsJsonMap() (schrodinger.ui.qt.swidgets.HelpButton class method) getType() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getTypeHint() (schrodinger.models.parameters.DictParam method) (schrodinger.models.parameters.ListParam method) (schrodinger.models.parameters.Param method) (schrodinger.models.parameters.SetParam method) getUnexpectedToken() (schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException method) getUnexpectedType() (schrodinger.application.desmond.antlr3.exceptions.RecognitionException method) GetUnique() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getUniqueDefNames() (schrodinger.application.matsci.cg_mapping.CGMapperMixin static method) getUniqueID() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getUniqueLigands() (schrodinger.application.matsci.buildcomplex.ComplexSplitter static method) getUniqueMolNums() (schrodinger.application.matsci.rdpattern.Pattern method) getUniqueProductTrackers() (schrodinger.application.matsci.fragments.FragmentReactor method) getUniqueSpecies() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) getUnitNormalToDeltaForces() (schrodinger.application.matsci.mecp_mod.MECPStep method) getUnits() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getUnitsData() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) getUnknownKeywords() (schrodinger.application.jaguar.input.JaguarInput method) getUnusedHostList() (schrodinger.pipeline.pipeline.StageJob method) getUpdatedCMSModelCopy() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) getUpdatedCParams() (schrodinger.application.matsci.nano.interface_mod.Interface method) getUpdatedFrameStructure() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) getUseCustomOPLS() (schrodinger.ui.qt.forcefield.ffsettingsbutton.FFSettingsButton method) getUsedHosts() (schrodinger.pipeline.pipeline.Pipeline method) getUserDefinedASLSets() (schrodinger.project.project.Project method) getUsername() (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel method) getUserOutputFiles() (schrodinger.pipeline.pipeline.Pipeline method) getUserOutputs() (schrodinger.pipeline.pipeline.Pipeline method) getUserTemplateList() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getUserText() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) getUserWavelengths() (schrodinger.application.matsci.permittivity.ElectricPolarizability static method) getUtilityDescriptors() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getValidatedOPLSDir() (schrodinger.application.matsci.multiapp.MultiJobApp method) getValidator() (schrodinger.application.matsci.deswidgets.DesmondMDWEdit method) getValue() (schrodinger.application.jaguar.autots_bonding.Coordinate method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.mopac.structure_launchers.StructureLauncher method) (schrodinger.application.xtb.input.XTBInput method) (schrodinger.models.mappers.AttrTargetSpec method) (schrodinger.models.mappers.ParamTargetSpec method) (schrodinger.models.mappers.TargetSpec method) (schrodinger.ui.qt.swidgets.STableWidgetItem method) getvalue() (schrodinger.utils.ligfilter.AslCriterion method) (schrodinger.utils.ligfilter.Criterion method) (schrodinger.utils.ligfilter.PredefinedCriterion method) (schrodinger.utils.ligfilter.PropertyCriterion method) (schrodinger.utils.ligfilter.SmartsCriterion method) getValueFromItem() (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) getValues() (schrodinger.application.matsci.atom_group.HelixData method) (schrodinger.application.matsci.reaction_workflow_gui_utils.UniformSequence method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) getValuesFromFile() (schrodinger.application.matsci.kmcgui.PropertyCombo method) getValuesFromStr() (schrodinger.ui.qt.swidgets.SCheckBoxEdit static method) getVariableLines() (schrodinger.application.matsci.zmutils.ZAtom method) getVariance() (schrodinger.trajectory.prody.mode.Mode method) getVariances() (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getVbmCbm() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) getVCov() (in module schrodinger.application.matsci.gsas.GSASIImath) getVDWSurfaceArea() (schrodinger.application.matsci.mlearn.features.Complex method) getVDWVolume() (schrodinger.application.matsci.mlearn.features.Complex method) getVec() (schrodinger.application.matsci.mlearn.features.Ligand method) getVectorizedDescriptors() (schrodinger.application.matsci.mlearn.features.Complex method) getVerbosity() (schrodinger.pipeline.stage.Stage method) getVertices() (schrodinger.application.matsci.nano.plane.CrystalPlane method) (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.graphics3d.polyhedron.MaestroCube method) (schrodinger.graphics3d.polyhedron.MaestroDodecahedron method) (schrodinger.graphics3d.polyhedron.MaestroIcosahedron method) (schrodinger.graphics3d.polyhedron.MaestroOctahedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) (schrodinger.graphics3d.polyhedron.MaestroTetrahedron method) getVerticesOfAllPlanes() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getVibPartitionFunction() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction static method) getVibrationalTemperature() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getVibStates() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getVibStateWeight() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getVisibleColCount() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) getVisibleColumnIndex() (schrodinger.infra.table.Table method) getVisibleColumnTotal() (schrodinger.infra.table.Table method) getVisiblePropertyNames() (schrodinger.project.project.Project method) getVisibleRowIndex() (schrodinger.infra.table.Table method) getVisibleRowTotal() (schrodinger.infra.table.Table method) getVoidData() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getVoidVolumes() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getVol() (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile method) getVoltage() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getVolume() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Cylinder method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Parallelepiped method) (schrodinger.application.matsci.shapes.Sphere method) (schrodinger.application.matsci.shapes.Tetrahedron method) getVSliderIndexes() (schrodinger.application.matsci.plotwidgets.SliderchartVLPlot method) getVSliderMax() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getVSliderMin() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getWaterModelDict() (schrodinger.application.matsci.mswidgets.WaterTypesComboBox method) getWavAndPolar() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWavAndPolars() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWavAndProp() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWavAndProps() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWave() (in module schrodinger.application.matsci.gsas.GSASIImath) getWavelengths() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWeakestBonds() (schrodinger.application.matsci.fragments.UniqueTracker method) getWeightedRingGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getWeights() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector.ChargeSelectorLineEdit method) (schrodinger.trajectory.prody.ensemble.Ensemble method) getWidth() (schrodinger.ui.qt.tablewidget.Column method) getWidthParameter() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getWidthsCW() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getWidthsTOF() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getWorkerTimeoutInSeconds() (schrodinger.seam.options.pipeline_options.SeamOptions method) getWorkflowPaths() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) getWorkspaceCounts() (schrodinger.protein.alignment.BaseAlignment method) getWorkspaceEntry() (schrodinger.application.desmond.maestro.NewEntryGroup method) getWorkspaceStructure() (schrodinger.ui.qt.appframework2.af2.App method) getX() (schrodinger.application.dendrogram.gradientSelector.ColorSelector method) GetXsectionCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem) getXtalCell() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getXYZ() (schrodinger.application.matsci.atom_group.MSAtom method) (schrodinger.structure.Structure method) GetXYZDist() (in module schrodinger.application.matsci.gsas.GSASIImath) getZmatrix() (schrodinger.application.matsci.rxn_path.InternalCoords method) getZmatText() (schrodinger.application.jaguar.input.JaguarInput method) getZoomCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) gg_task (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) ggraph (schrodinger.ui.qt.network_visualizer.Graph property) GhostAtomIndexError gibbs (schrodinger.application.jaguar.utils.FreeEnergy attribute) gibbs_energy_property_string() (in module schrodinger.application.jaguar.utils) gid (schrodinger.application.desmond.stage.workflow.Task attribute) gid() (schrodinger.application.desmond.cms.Cms method) gid_refresh() (schrodinger.application.desmond.cms.Cms method) GIF_FNAME (schrodinger.ui.qt.swidgets.SpinnerIcon attribute) GIPAWType (class in schrodinger.application.matsci.espresso.qeinput) giveHelp() (schrodinger.ui.qt.swidgets.SDialog method) GlassTransitionTemperature (class in schrodinger.application.matsci.genetic_optimization) glibc() (in module schrodinger.application.jaguar.textparser) Glide glide_data (schrodinger.application.glide.http_server.GlideHTTPHandler attribute) glide_finish() (schrodinger.application.glide.http_server.GlideHTTPHandler method) glide_grid_file (schrodinger.application.steps.docking.GlideSettings attribute) glide_grid_fileChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_grid_fileReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_http_handler (schrodinger.application.glide.http_server.GlideHTTPServer attribute) glide_in_file (schrodinger.application.steps.docking.GlideSettings attribute) glide_in_fileChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_in_fileReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_infile (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) glide_infileChanged (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) glide_infileReplaced (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) glide_input_overrides (schrodinger.application.steps.docking.GlideSettings attribute) glide_input_overridesChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_input_overridesReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_ref_ligand_file (schrodinger.application.steps.docking.GlideSettings attribute) glide_ref_ligand_fileChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_ref_ligand_fileReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_request (schrodinger.application.glide.http_server.GlideHTTPServer attribute) glide_send_response() (schrodinger.application.glide.http_server.GlideHTTPHandler method) glide_server_log_level() (in module schrodinger.application.steps.docking) GLIDE_SERVER_START_TASK_CLASS (schrodinger.application.steps.docking.GlideDocker attribute) (schrodinger.application.steps.docking.MaeGlideDocker attribute) (schrodinger.application.steps.docking.SmilesDocker attribute) glide_shutdown_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) glide_stop (schrodinger.application.glide.http_server.GlideHTTPHandler attribute) glide_timeout (schrodinger.application.glide.http_server.GlideHTTPServer attribute) GlideALControl (class in schrodinger.application.vss.control) GlideClientModule (class in schrodinger.application.glide.client_module) GlideClientModuleAdapter (class in schrodinger.application.glide.client_module) GlideControl (class in schrodinger.application.vss.control) GlideDocker (class in schrodinger.application.steps.docking) GlideDocker.Settings (class in schrodinger.application.steps.docking) GlideError GlideHTTPHandler (class in schrodinger.application.glide.http_server) GlideHTTPServer (class in schrodinger.application.glide.http_server) GlideJob (class in schrodinger.application.glide.glide) GlideResult (class in schrodinger.application.glide.http_client) GlideResultIterator (class in schrodinger.application.glide.http_client) GlideServerManager (class in schrodinger.application.glide.http_client) GlideSettings (class in schrodinger.application.steps.docking) GlideSortStage (class in schrodinger.pipeline.stages.glide) GlideSortUtility (class in schrodinger.application.glide.sort_utils) GlideStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) GlideTask (class in schrodinger.application.livedesign.tasks) GlideTask.Input (class in schrodinger.application.livedesign.tasks) GlideTask.JobConfig (class in schrodinger.application.livedesign.tasks) GlideTask.Output (class in schrodinger.application.livedesign.tasks) GlideWorkspaceMarkers (class in schrodinger.application.glide.gui) Glnh() (in module schrodinger.application.matsci.gsas.GSASIIlattice) global_annotations (schrodinger.protein.alignment.BaseAlignment property) global_st_file (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) global_st_fileChanged (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) global_st_fileReplaced (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) GlobalDoFn() (in module schrodinger.seam.transforms.core) GLOW_COLOR (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) glue() (schrodinger.application.desmond.cms.Cms method) glued_topology (schrodinger.application.desmond.cms.Cms property) GlutamicAcidpKaPredictor (class in schrodinger.protein.assignment) GLY (schrodinger.ui.qt.rama.RamaResidueType attribute) GLYCINE_RICH_LOOP (schrodinger.protein.annotation.KinaseFeatureLabel attribute) Gmat2A() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Gmat2AB() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Gmat2cell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) gnode (schrodinger.ui.qt.network_visualizer.Node property) golden() (in module schrodinger.application.jaguar.qrnn.temp_opt) GOOD (schrodinger.application.desmond.fep_edge_data_classifier.Rating attribute) GOOD_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) gotStatus (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) (schrodinger.application.glide.http_client.ZmqClient attribute) gpcr_anno (schrodinger.protein.gpcr.tasks.GPCRTask.Output attribute) gpcr_generic_number (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) gpcr_segment (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) GPCRSegmentFinder (class in schrodinger.protein.annotation) GPCRSegmentLabel (class in schrodinger.protein.annotation) GPCRTask (class in schrodinger.protein.gpcr.tasks) GPCRTask.Input (class in schrodinger.protein.gpcr.tasks) GPCRTask.Output (class in schrodinger.protein.gpcr.tasks) Gpu (class in schrodinger.tasks.hosts) GPU (schrodinger.job.resource.ComputeType attribute) gpu_hosts_available() (in module schrodinger.ui.qt.config_dialog) GPU_ONLY (schrodinger.tasks.jobtasks.AllowedHostTypes attribute) GPU_PLACEHOLDER_ARG (schrodinger.tasks.jobtasks.HostSettings attribute) GPU_SUBHOST (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog attribute) GPU_UNIT_LABEL (schrodinger.application.matsci.configdlgs.PerStrucConfigDialog attribute) (schrodinger.application.matsci.configdlgs.PerStrucSingleGpuConfigDialog attribute) (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) GPUConfigDialog (class in schrodinger.ui.qt.config_dialog) GpuHostProductMode (class in schrodinger.ui.qt.config_dialog) GPUTYPE (schrodinger.tasks.hosts.Host attribute) grab() (schrodinger.application.desmond.maestro.Workspace method) grabbedColorMoveEvent() (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) grad_prec (schrodinger.application.jaguar.results.ConvCriteria attribute) gradient_convergence (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) gradient_criterion (schrodinger.structutils.minimize.Minimizer property) GradientSelector (class in schrodinger.application.dendrogram.gradientSelector) GradientSelectorView (class in schrodinger.application.dendrogram.gradientSelector) gradientUpdated (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView attribute) graft() (in module schrodinger.application.bioluminate.antibody.grafting) grafted_sts (schrodinger.application.bioluminate.antibody.grafting.GraftingOutput attribute) GraftingInput (class in schrodinger.application.bioluminate.antibody.grafting) GraftingOutput (class in schrodinger.application.bioluminate.antibody.grafting) grammarFileName (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) Graph (class in schrodinger.ui.qt.network_visualizer) graph (schrodinger.application.jaguar.hess_guess.CoordinateManager attribute) (schrodinger.ui.qt.network_visualizer.Edge property) graph_ASP_curves() (in module schrodinger.application.jaguar.pk50_report) graph_file (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) graphChanged (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) GraphData (class in schrodinger.application.jaguar.macro_pka_utils) GraphSignals (class in schrodinger.ui.qt.network_visualizer) GRAY (schrodinger.ui.qt.standard.colors.NativeColors attribute) Gray3 (schrodinger.protein.helm.helm_renderer.HexColor attribute) Gray4 (schrodinger.protein.helm.helm_renderer.HexColor attribute) Gray6 (schrodinger.protein.helm.helm_renderer.HexColor attribute) GRAY_05 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_10 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_20 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_30 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_40 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_90 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GrayColors (class in schrodinger.ui.qt.standard.design_tokens) GREATER (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericOperator attribute) GREATER_THAN (schrodinger.application.matsci.genetic_optimization.Property attribute) greedySelect() (schrodinger.active_learning.al_node.PrepareSmilesNode method) GREEN (schrodinger.ui.qt.standard.colors.NativeColors attribute) green_lagrange_strain (schrodinger.application.matsci.elasticity.strain.Deformation property) greyColorMap() (in module schrodinger.application.matsci.plotwidgets) Grid (class in schrodinger.application.bindingsite.cavutils) (class in schrodinger.application.glide.glide) (class in schrodinger.pipeline.pipeio) grid (schrodinger.application.matsci.freevolume.GridRadius attribute) grid() (in module schrodinger.ui.qt.layout) GRID_DENSITY (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) GRID_DENSITY_REV (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) grid_file (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) grid_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) grid_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) grid_property (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) GridBox (class in schrodinger.graphics3d.gridbox) gridContextMenuRequested() (schrodinger.ui.two_d_viewer.TwoDViewer method) gridfile (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) gridfileChanged (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) gridfileReplaced (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) Gridgen (class in schrodinger.application.glide.glide) GridgenRunningException GridgenStage (class in schrodinger.pipeline.stages.glide) GridgenTask (class in schrodinger.application.glide.ligand_designer) GridgenTask.Input (class in schrodinger.application.glide.ligand_designer) GridgenTask.Output (class in schrodinger.application.glide.ligand_designer) gridJobStarted (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) GridLayoutPopUp (class in schrodinger.ui.residueselector) gridNeighbors() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) GridRadius (class in schrodinger.application.matsci.freevolume) GROOVE_THICKNESS (schrodinger.application.matsci.mswidgets.MultiSlider attribute) ground_multipole_qm() (in module schrodinger.application.jaguar.textparser) Group (class in schrodinger.graphics3d.common) group (schrodinger.application.desmond.starter.ui.cmdline.Option attribute) (schrodinger.project.manager.EntryGroupManager property) (schrodinger.project.project.ProjectRow property) group() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) group_by_connectivity() (in module schrodinger.structutils.analyze) group_id (schrodinger.structutils.markush_enumerate.PlaceHolder attribute) group_infos_by_layer() (in module schrodinger.application.matsci.packmol) GROUP_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) group_ligand_het_states() (in module schrodinger.protein.assignment) group_objects_by_hash() (in module schrodinger.application.matsci.species) group_subtuples_by_key_and_value() (in module schrodinger.application.matsci.nano.particle) group_with_comparison() (in module schrodinger.application.jaguar.utils) groupAromaticRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) groupAtoms() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) (schrodinger.application.matsci.atom_group.MSAtomGroup method) (schrodinger.application.matsci.atom_group.MSRingAtomGroup method) groupby_stoichiometry() (in module schrodinger.application.jaguar.utils) GroupByKey (class in schrodinger.seam.testing.benchmarks) GroupByKeyWithSlowCoder (class in schrodinger.seam.testing.benchmarks) groupHidden() (schrodinger.graphics3d.common.Primitive method) groupIdx() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis class method) GroupingMethodSelector (class in schrodinger.application.matsci.speciesgui) groupName() (schrodinger.maestro_utils.maestro_sync.ProjectEntryMaestroSync method) groups (schrodinger.project.project.Project property) groupShown() (schrodinger.graphics3d.common.Primitive method) groupSymmetricBeads() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) groupTitleChanged (schrodinger.project.manager.EntryGroupManager attribute) GroupWaters (class in schrodinger.application.desmond.stage.prepare.structure) Grow (class in schrodinger.application.matsci.nano.sheet) grow_fragment() (in module schrodinger.protein.buildpeptide) grow_marker (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) grow_mult() (in module schrodinger.structutils.build) grower (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) growFragmentCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) GROWINDICIES (schrodinger.application.matsci.nano.sheet.Grow attribute) growname (schrodinger.structure.StructureAtom property) growNodeCluster() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) GrowthSpaceGenerator (class in schrodinger.infra.growthspace) gscore_coeff (schrodinger.application.glide.sort_utils.CustomScoringFunction attribute) Guanine (schrodinger.protein.helm.helm_renderer.HexColor attribute) guard() (schrodinger.tasks.tasks.AbstractTask method) guard_method() (schrodinger.tasks.tasks.SignalTask static method) guess_seq_type() (in module schrodinger.protein.sequence) guess_value_type() (schrodinger.utils.sea.sea.Atom static method) guessAccepted() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) GUESSCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) guessMode() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) GuessOrbital (class in schrodinger.application.jaguar.input) guessOrder() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) guessRejected() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) GUI (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.CallingContext attribute) gui() (schrodinger.job.app.App method) gui_closed (schrodinger.ui.qt.appframework2.baseapp.BasePanel attribute) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin attribute) gui_validate_local_gpus() (in module schrodinger.ui.qt.config_dialog) GuiApp (class in schrodinger.application.desmond.gui) GuiPanel (class in schrodinger.ui.qt.dendrogram) GuiPattern (class in schrodinger.application.matsci.rdpattern_gui) GVB (schrodinger.application.jaguar.constants.CalcType attribute) GVBLMP2 (schrodinger.application.jaguar.constants.CalcType attribute) gvblmp2() (in module schrodinger.application.jaguar.textparser) GVBRCI (schrodinger.application.jaguar.constants.CalcType attribute) GXG_DATA (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) GXG_DATA_PRIME (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) gz_fname_if_exists() (in module schrodinger.application.desmond.util) GZIP (schrodinger.rdkit_extensions.CompressionType attribute) gzip_file() (in module schrodinger.utils.fileutils) gzip_open() (in module schrodinger.trajectory.prody.writenmd) GzippedSDMolSupplier (class in schrodinger.rdkit.molio)

H

h (schrodinger.application.matsci.espresso.qeoutput.PhDOS.Thermo attribute) H (schrodinger.protein.annotation.AntibodyRegionLabel attribute) H1 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H2 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H2O (schrodinger.energy.Solvent attribute) H3 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H8 (schrodinger.protein.annotation.GPCRSegmentLabel attribute) H_ANNIHILIATIONS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) H_BOND (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) H_bonds (schrodinger.application.glide.xpdes.TermKeywords attribute) H_INJECTIONS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) h_mass (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) h_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) half_life() (in module schrodinger.application.jaguar.kinetics) HALFREVOLUTION (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) HAMILTONIAN (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTabNoSoZora attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabNoSoZora attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabWithSoZora attribute) hamiltonianChanged (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) handle_check_action() (in module schrodinger.application.licensing.licadmin) handle_data() (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) handle_debug_sources() (in module schrodinger.application.licensing.licserver.main) handle_diag_action() (in module schrodinger.application.licensing.licadmin) HANDLE_DISABLED (schrodinger.ui.qt.standard.design_tokens.QSliderIcons attribute) HANDLE_ENABLED (schrodinger.ui.qt.standard.design_tokens.QSliderIcons attribute) handle_endtag() (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) handle_generic_action() (in module schrodinger.application.licensing.licadmin) HANDLE_HOVER (schrodinger.ui.qt.standard.design_tokens.QSliderIcons attribute) handle_info_action() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.licserver.main) handle_install() (in module schrodinger.application.licensing.licserver.main) handle_install_action() (in module schrodinger.application.licensing.licadmin) handle_jobcontrol_message() (schrodinger.application.desmond.cmj.Engine method) handle_list_action() (in module schrodinger.application.licensing.licadmin) handle_live_design_request() (in module schrodinger.application.livedesign.ld_maestro_actions) handle_machineid() (in module schrodinger.application.licensing.licserver.main) HANDLE_PRESSED (schrodinger.ui.qt.standard.design_tokens.QSliderIcons attribute) handle_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) handle_start_action() (in module schrodinger.application.licensing.licadmin) handle_starttag() (schrodinger.application.matsci.espresso.utils.PPHeaderHTMLParser method) (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) handle_stat_action() (in module schrodinger.application.licensing.licadmin) handle_stop_action() (in module schrodinger.application.licensing.licadmin) handle_timeout() (schrodinger.application.glide.http_server.GlideHTTPServer method) handle_ver_action() (in module schrodinger.application.licensing.licadmin) handle_verify_action() (in module schrodinger.application.licensing.licadmin) handleCSV() (schrodinger.active_learning.mq_backend.Backend method) (schrodinger.active_learning.mq_worker.Worker method) HandledError handleDONE() (schrodinger.active_learning.mq_worker.Worker method) handleException() (schrodinger.utils.qt_utils.EventLoop method) handleFileLinkProperties() (schrodinger.application.matsci.jaguarworkflows.Step method) handleFinalGeometry() (schrodinger.application.matsci.mecp_mod.MECPStep method) handleFiniteDifferences() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) handleGET() (schrodinger.active_learning.mq_worker.Worker method) handleInclusonToggled() (schrodinger.ui.two_d_viewer.TwoDTableModel method) handleLDExceptions() (schrodinger.application.livedesign.export_tasks.LDExportTaskMixin method) handleManyToOne() (schrodinger.application.matsci.nano.particle.Nanoparticle method) handleMetalBonding() (schrodinger.application.matsci.rxn_channel.Products method) handleNewDatabaseSource() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) handleObsolete() (schrodinger.protein.getpdb_utility.Code method) handleOneToMany() (schrodinger.application.matsci.nano.particle.Nanoparticle method) handlePING() (schrodinger.active_learning.mq_worker.Worker method) handlePONG() (schrodinger.active_learning.mq_backend.Backend method) (schrodinger.active_learning.mq_worker.Worker method) handleProps() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) (schrodinger.application.matsci.nano.tube.NanoTube method) handleRangeChange() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) handleREADY() (schrodinger.active_learning.mq_worker.Worker method) handleRequest() (schrodinger.active_learning.mq_backend.Backend method) handleRingExclusions() (schrodinger.application.matsci.coarsegrain.Internals method) handleSettings() (schrodinger.application.matsci.nano.xtal.Crystal method) handleShiftClick() (schrodinger.ui.two_d_viewer.TwoDTableModel method) handleSimpleInput() (schrodinger.application.matsci.amorphous.Moieties method) handleStageMessages() (schrodinger.pipeline.pipeline.Pipeline method) handleSTOP() (schrodinger.active_learning.mq_backend.Backend method) (schrodinger.active_learning.mq_worker.Worker method) handleStructure() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) handshake() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) HAPTIC_ATOM_PROP (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae attribute) HapticLigand (class in schrodinger.application.matsci.etarotamers) Hartree (schrodinger.application.jaguar.constants.Unit attribute) hartree_to_kcal_per_mol() (in module schrodinger.application.matsci.mecp_mod) HartreePerBohr (schrodinger.application.jaguar.constants.Unit attribute) has3dCoords() (schrodinger.structure.Structure method) has_antibody_heavy (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult property) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults property) (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment property) has_antibody_light (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult property) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults property) (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment property) has_atom_vel() (in module schrodinger.application.matsci.desmondutils) has_authenticator() (schrodinger.job.server.ServerInfo method) has_block() (in module schrodinger.structutils.block_data) has_branch (schrodinger.protein.helm.helm_renderer.HelmConnector property) has_cert_for_server() (in module schrodinger.job.cert) has_chorus_box_props() (in module schrodinger.application.matsci.desmondutils) has_clash() (in module schrodinger.comparison.struc) has_cloud_services() (in module schrodinger.application.steps.env_keys) has_concatenated_stage() (in module schrodinger.application.matsci.desconfig) has_densities (schrodinger.application.matsci.espresso.qeoutput.PhDOS property) has_desmond_trajectory() (in module schrodinger.project.utils) has_dir() (in module schrodinger.application.desmond.stage.workflow) HAS_E (schrodinger.application.matsci.kmc.PairsTable attribute) (schrodinger.application.matsci.kmc.SitesMixin attribute) has_eigv (schrodinger.application.matsci.espresso.qeoutput.PhDOS property) has_explicit_restraints() (in module schrodinger.application.desmond.cmj) has_fepio() (in module schrodinger.application.desmond.cms) has_ffio() (in module schrodinger.application.desmond.cms) has_file() (in module schrodinger.application.desmond.stage.workflow) has_gipaw (schrodinger.application.matsci.espresso.utils.PseudoData attribute) HAS_H (schrodinger.application.matsci.kmc.PairsTable attribute) (schrodinger.application.matsci.kmc.SitesMixin attribute) has_head_tail_roles_marked() (in module schrodinger.application.matsci.amorphous) has_hubbard() (in module schrodinger.application.matsci.espresso.utils) has_imperfect_packing() (in module schrodinger.application.matsci.packmol) has_interaction_label() (in module schrodinger.protein.assignment) has_keep_and_superpose_atoms() (in module schrodinger.application.matsci.reaction_workflow_utils) has_key() (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.sea.sea.Map method) has_LD_filter_match() (in module schrodinger.livedesign.cmdline) has_LD_substructure_fp_match() (in module schrodinger.livedesign.cmdline) has_LD_substructure_match() (in module schrodinger.livedesign.cmdline) has_license_file_suffix() (in module schrodinger.application.licensing.licadmin) has_materials_trajectory() (in module schrodinger.project.utils) has_model2_file() (in module schrodinger.application.desmond.license) has_option() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method) has_orthorhombic_pbc() (in module schrodinger.application.matsci.desmondutils) has_pair_data() (in module schrodinger.application.matsci.kmc) has_pbc() (in module schrodinger.application.matsci.nano.xtal) has_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) has_player_toolbar() (in module schrodinger.trajectory.trajectoryviewer) has_plink_ssh_host_key() (in module schrodinger.utils.sshconfig) has_plugin() (in module schrodinger.application.desmond.config_utils) has_query_stereo() (in module schrodinger.application.matsci.rdpattern) has_rule() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) has_seqres() (in module schrodinger.protein.seqres) has_snapshot_panel() (in module schrodinger.trajectory.trajectoryviewer) has_space_group_pbc_props() (in module schrodinger.application.matsci.desmondutils) has_stereo_smarts() (in module schrodinger.application.matsci.rdpattern) has_substructure_match() (in module schrodinger.livedesign.bbchem_endpoints) has_tag() (schrodinger.utils.sea.sea.Sea method) has_trajectory() (in module schrodinger.project.utils) has_transition_state() (in module schrodinger.application.matsci.reaction_workflow_utils) has_undefined_stereo() (in module schrodinger.utils.cgxutils) has_valid_custom_OPLS_preference() (in module schrodinger.ui.qt.forcefield.forcefield) has_valid_lewis_structure() (in module schrodinger.structutils.analyze) has_valid_opls_dir (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector property) has_valid_wscore_block() (in module schrodinger.project.utils) has_variable_reactants() (in module schrodinger.application.pathfinder.multiroute) has_velocities (schrodinger.application.desmond.cms.Cms property) has_vertex_colors (schrodinger.surface.Surface property) has_watermap() (in module schrodinger.project.utils) hasAcceptableInput() (schrodinger.application.desmond.cwidget.EntryField method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterListToolButton method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) hasActiveFilters() (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) hasAlnSets() (schrodinger.protein.alignment.BaseAlignment method) hasAncestor() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) hasAtomProperty() (schrodinger.structure.Structure method) hasBrancher() (schrodinger.application.matsci.amorphous.Moieties method) hasCascader() (schrodinger.application.matsci.amorphous.Moieties method) hasChain() (schrodinger.protein.sequence.CombinedChainProteinSequence method) hasChanged() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) hasChirality() (schrodinger.application.matsci.amorphous.Monomer method) hasClashes() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) hasCompleted() (schrodinger.pipeline.stage.Stage method) hasData() (schrodinger.application.prime.residue_interaction.InteractionReader class method) hasDescriptors() (schrodinger.protein.sequence.AbstractSequence method) hasDisabledText() (schrodinger.ui.qt.swidgets.LineEditWithDisabledText method) hasDisorderedRegionsPredictions() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasDisulfideBondPredictions() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasDomainArrangementPredictions() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasEdge() (schrodinger.ui.qt.network_visualizer.Graph method) hasEdges() (schrodinger.ui.qt.schart.SHistogramBarSeries method) hasExited() (schrodinger.job.queue.BaseJob method) hasFepio() (schrodinger.application.desmond.ffiostructure.FFIOStructure method) hasFfio() (schrodinger.application.desmond.ffiostructure.FFIOStructure method) hasFreeEnergy() (schrodinger.application.matsci.fragments.BondEnergies method) hash_for_file() (in module schrodinger.utils.fileutils) hash_idx (schrodinger.application.matsci.reaction_workflow_utils.Site attribute) hash_scheme (schrodinger.livedesign.registration.RegistrationOptions attribute) hash_title() (in module schrodinger.application.desmond.struc) HashableRdMol (class in schrodinger.ui.qt.delegates) HashStructureTitle (class in schrodinger.application.desmond.stage.prepare.structure) hasInteractions() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) hasKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) hasLadder() (schrodinger.application.matsci.amorphous.Moieties method) hasLicenseChecking (schrodinger.job.server.ServerInfo attribute) hasMissingAtoms() (schrodinger.structure.Residue method) hasNext() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) hasPfam() (schrodinger.protein.sequence.AbstractSequence method) hasPositions() (schrodinger.ui.qt.network_visualizer.Graph method) hasRefCtMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hasRings() (schrodinger.application.matsci.amorphous.Moieties method) hasServerAuth (schrodinger.job.server.ServerInfo attribute) hasSetResNum() (schrodinger.protein.residue.Residue method) hasSocketAuth (schrodinger.job.server.ServerInfo attribute) hasSolventAccessibility() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) hasSSAPredictions() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasStarted() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobDJ method) (schrodinger.pipeline.stage.Stage method) hasStructure() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.protein.residue.AbstractSequenceElement method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) hasStructuredResidues() (schrodinger.protein.sequence.AbstractSequence method) hasTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hasTopologicalSymmetry() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) hasUniqueNavigationNodes() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) hasValidBasis() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.PerAtomBasisRow method) hasXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) have_constraints() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) have_frozen_atoms() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) hb_bb (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bbChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bbReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bs (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bsChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bsReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_sb (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_sbChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_sbReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_ss (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_ssChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_ssReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hbond (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) hbond_energy() (in module schrodinger.application.qsite.output) hbond_heavy_max_angle (schrodinger.protein.assignment.ProtAssign.changeable attribute) hbond_heavy_min_angle (schrodinger.protein.assignment.ProtAssign.changeable attribute) hbond_iterator() (in module schrodinger.structutils.analyze) hbond_max_dist (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_max_distChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_max_distReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_acceptor_angle (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_acceptor_angleChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_acceptor_angleReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_angle (schrodinger.protein.assignment.ProtAssign.changeable attribute) hbond_min_donor_angle (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_donor_angleChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_donor_angleReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) HBOND_TYPE (class in schrodinger.application.bioluminate.protein_interaction.calculate) hbondChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) hbondReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) hbox() (in module schrodinger.ui.qt.layout) HC (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) HC1 (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) HC2 (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) HC_SEQ (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) HCENTER (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) HDExaminerColumns (class in schrodinger.application.bioluminate.pose_filtering.hdx_io) HDFIO (class in schrodinger.application.matsci.hdfutils) HDFProxyPickleIO (class in schrodinger.application.matsci.hdfutils) HDFStore() (in module schrodinger.application.matsci.hdfutils) HdxMsProperties (class in schrodinger.application.bioluminate.pose_filtering.hdx_io) HEADER (schrodinger.application.desmond.kinetics.enhanced_sampling.MExpressionSection attribute) header (schrodinger.application.jaguar.results.ScfIteration attribute) (schrodinger.application.matsci.mlearn.features.MomentData attribute) header() (in module schrodinger.application.desmond.rl_helper) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) (schrodinger.application.qsite.input.Cut method) (schrodinger.application.qsite.input.HydrogenCap method) HEADER_BY_SUBTYPE (schrodinger.livedesign.biologics.fasta.AntibodyAssembler attribute) (schrodinger.livedesign.biologics.fasta.NucleicAcidAssembler attribute) (schrodinger.livedesign.biologics.fasta.PolymerAssembler attribute) HEADER_CPUS (schrodinger.application.jaguar.gui.timing.EntryTimingTable attribute) HEADER_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HEADER_TIME (schrodinger.application.jaguar.gui.timing.EntryTimingTable attribute) HEADER_TITLE (schrodinger.application.jaguar.gui.timing.EntryTimingTable attribute) header_titles (schrodinger.ui.qt.appframework2.debugwidgets.LogTable attribute) (schrodinger.ui.qt.appframework2.debugwidgets.LogTagTable attribute) (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable attribute) headerClicked() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) headerData() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.job_monitor.job_monitor_table.TableProxy method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table_helper.RowBasedListModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) headerDataChanged (schrodinger.ui.qt.table.StructureDataViewerModel attribute) HeaderLabel (class in schrodinger.ui.qt.standard_widgets.labels) Headers (class in schrodinger.application.bioluminate.antibody.io.csv_reader) HEADERS (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.SpectrumFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) headerToEnv() (in module schrodinger.application.desmond.enhsamp) HeaderViewWithMenuIndicator (class in schrodinger.ui.qt.utils) health() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) healthier() (in module schrodinger.application.licensing.licadmin) heat_of_formation() (in module schrodinger.application.mopac.results_main) HEAVY (schrodinger.application.bioluminate.antibody.grafting.ChainTypes attribute) (schrodinger.application.bioluminate.antibody.models.VariableDomainType attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) heavy_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) HEAVY_FR_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) HEAVY_FR_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) HEAVY_HYDROGEN_DT (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) HEAVY_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) heavy_sequence (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) heavy_sequenceChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) heavy_sequenceReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) HEAVY_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) heavy_source_name (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) heavy_source_nameChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) heavy_source_nameReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) heavy_template_sequences (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) heavy_template_sequencesChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) heavy_template_sequencesReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) height (schrodinger.application.matsci.reportutils.Footer attribute) (schrodinger.livedesign.draw.ImageGenOptions attribute) heightForWidth() (schrodinger.ui.qt.dialbox.Dial method) HELIX (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) HELIX_COLOR (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) HELIX_PROPENSITY (class in schrodinger.protein.residue) helix_propensity (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) HELIX_TERMINATION_TENDENCY (class in schrodinger.protein.residue) helix_termination_tendency (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) HelixArc (class in schrodinger.application.matsci.atom_group) HelixArcAtomGroup (class in schrodinger.application.matsci.atom_group) HelixBreaking (schrodinger.protein.residue.HELIX_PROPENSITY attribute) HelixData (class in schrodinger.application.matsci.atom_group) HelixEnding (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) HelixGroups (class in schrodinger.application.matsci.atom_group) helixGroupToData() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) HelixStarting (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) HELM (schrodinger.rdkit_extensions.Format attribute) helm_mol_to_binary() (in module schrodinger.livedesign.biologics.registration) HelmConnector (class in schrodinger.protein.helm.helm_renderer) HelmConnectorItemMixin (class in schrodinger.protein.helm.helm_renderer) HelmFallbackImage (class in schrodinger.protein.helm.helm_renderer) helmholtz_free_energy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) HelmMonomer (class in schrodinger.protein.helm.helm_renderer) HelmMonomerItemMixin (class in schrodinger.protein.helm.helm_renderer) HelmMonomerTextLabel (class in schrodinger.protein.helm.helm_renderer) HelmScene (class in schrodinger.protein.helm.helm_renderer) HelmWidget (class in schrodinger.protein.helm.helm_renderer) Help (class in schrodinger.application.desmond.multisimstartup) help (schrodinger.application.desmond.starter.ui.cmdline.Option attribute) HELP (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) Help (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.StdBtn attribute) help() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.matsci.jagwidgets.SolventDialog method) (schrodinger.application.pymol.pymol4maestro.panel method) (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method)

HELP_TOPIC (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) HelpButton (class in schrodinger.ui.qt.swidgets) helpEvent() (schrodinger.ui.qt.delegates.MatplotlibDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) helpPressed() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) hess_array_from_section() (in module schrodinger.application.jaguar.input) hess_section_from_array() (in module schrodinger.application.jaguar.input) HessianLSQ() (in module schrodinger.application.matsci.gsas.GSASIImath) HessianSVD() (in module schrodinger.application.matsci.gsas.GSASIImath) HetState (class in schrodinger.application.prepwizard) HetType (class in schrodinger.application.prepwizard) hex() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) Hex_pairs (schrodinger.application.glide.xpdes.TermKeywords attribute) Hex_sp (schrodinger.application.glide.xpdes.TermKeywords attribute) hex_string (schrodinger.structutils.color.Color property) (schrodinger.surface.Surface.Color property) HEXAGONAL_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) HexColor (class in schrodinger.protein.helm.helm_renderer) HF (schrodinger.application.jaguar.constants.CalcType attribute) HFExcitedStateWidget (class in schrodinger.application.jaguar.gui.theory_tab_widgets) HFR (schrodinger.protein.annotation.AntibodyRegionLabel attribute) HIDDEN (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) hidden (schrodinger.ui.qt.atomselector.ASLPopupMenu attribute) (schrodinger.ui.qt.table.EmittingScrollBar attribute) hide() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.gridbox.GridBox method) (schrodinger.protein.membrane.Membrane_Model method) (schrodinger.surface.Surface method) (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) (schrodinger.ui.qt.tablewidget.Row method) HIDE_ATOM_WIDGETS (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) hide_atoms() (in module schrodinger.application.bioluminate.pml_menus) hide_everything() (in module schrodinger.application.bioluminate.pml_menus) hide_labels() (in module schrodinger.application.bioluminate.pml_menus) hide_layout_elements() (in module schrodinger.ui.qt.utils) hide_non_polar_hydrogens() (in module schrodinger.application.prepwizard2.tasks) hide_phase_hover_markers() (in module schrodinger.application.phase.phase_markers) HIDE_POSE_PAGE (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget attribute) hide_ribbons() (in module schrodinger.application.bioluminate.pml_menus) hide_surface() (in module schrodinger.application.bioluminate.pml_menus) hide_workspace_phase_markers() (in module schrodinger.application.phase.phase_markers) hideAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hideAllFeaturesForEntry() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hideAllJaguarMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) hideAllMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) HideAllOthers (class in schrodinger.application.bioluminate.pml_menus) HideAtoms (class in schrodinger.application.bioluminate.pml_menus) hideDefineButton() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) hideDialog() (schrodinger.application.desmond.gui.AdvOptionsFrame method) hideDoNotShowCheckbox() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) hideEvent() (schrodinger.application.matsci.sliceplot.SlicePlot method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.atomselector.ASLPopupMenu method) (schrodinger.ui.qt.atomselector.AtomSelector method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.swidgets.SEmittingScrollBar method) (schrodinger.ui.qt.table.EmittingScrollBar method) HideEverything (class in schrodinger.application.bioluminate.pml_menus) hideFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) HideHydrogens (class in schrodinger.application.bioluminate.pml_menus) HideHydrogenSubMenu (class in schrodinger.application.bioluminate.pml_menus) HideLabel (class in schrodinger.application.bioluminate.pml_menus) hideLabels() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) hideLayoutElements() (schrodinger.ui.qt.appframework2.af2.App method) HideMainChain (class in schrodinger.application.bioluminate.pml_menus) HideMenu (class in schrodinger.application.bioluminate.pml_menus) HideNonBonded (class in schrodinger.application.bioluminate.pml_menus) HidePolarHydrogens (class in schrodinger.application.bioluminate.pml_menus) hidePopup() (schrodinger.ui.qt.pop_up_widgets.ComboBoxWithPopUp method) hideProgress() (schrodinger.ui.qt.appframework2.af2.StatusBar method) HideRibbons (class in schrodinger.application.bioluminate.pml_menus) hideScheme() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) HideSideChain (class in schrodinger.application.bioluminate.pml_menus) hideSlab() (schrodinger.application.matsci.sliceplot.SlicePlot method) hideSphere() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) hideStructureTooltip() (schrodinger.ui.two_d_viewer.TwoDTableDelegate method) HideSurface (class in schrodinger.application.bioluminate.pml_menus) HideSymmetryMates (class in schrodinger.application.bioluminate.pml_menus) hideTolMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) (schrodinger.application.phase.phase_markers.PhaseTolMarkers method) hideToolbarStyle() (schrodinger.ui.qt.appframework2.af2.BottomBar method) hideToolTip() (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin method) HideWaters (class in schrodinger.application.bioluminate.pml_menus) hideWidgets() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) HIGH (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute) High (schrodinger.protein.annotation.KinaseConservation attribute) HIGH (schrodinger.trajectory.trajectory_gui_dir.export_movie.Quality attribute) HIGH_RMSD (schrodinger.application.desmond.constants.SkipFepReason attribute) high_rmsd (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult attribute) highlight_atom_colors (schrodinger.livedesign.draw.ImageGenOptions attribute) highlight_atoms (schrodinger.livedesign.draw.ImageGenOptions attribute) highlight_bond_colors (schrodinger.livedesign.draw.ImageGenOptions attribute) highlight_bonds (schrodinger.livedesign.draw.ImageGenOptions attribute) HIGHLIGHT_COLOR (schrodinger.application.matsci.mswidgets.MultiSlider attribute) highlightAtom() (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.application.matsci.reordergui.StructurePic method) highlightCompAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) Highlighted (schrodinger.ui.qt.standard_widgets.buttons.StyledButton.Style attribute) HIGHLIGHTED_BUTTON_BACKGROUND (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HIGHLIGHTED_BUTTON_BORDER_DISABLED (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HIGHLIGHTED_BUTTON_BORDER_ENABLED (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HIGHLIGHTED_BUTTON_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HIGHLIGHTED_PRESSED_BUTTON_BACKGROUND_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HighlightedText (schrodinger.ui.qt.standard_widgets.buttons.StyledButton.Style attribute) highlightMapPair() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) highlightMolecule() (schrodinger.application.matsci.kmcgui.MinMaxNeighborWidgets method) highlightRefAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) highlightSuggestedAtom() (schrodinger.application.matsci.reordergui.StructurePic method) HIGHSCORE (schrodinger.protein.predictors.Disordered attribute) HighSymmetryKPath (class in schrodinger.application.matsci.espresso.utils) Hinge (schrodinger.protein.annotation.AntibodyRegionLabel attribute) HINGE (schrodinger.protein.annotation.KinaseFeatureLabel attribute) HistidinepKaPredictor (class in schrodinger.protein.assignment) hit (schrodinger.application.matsci.cache.CacheInfo attribute) hit_tables (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults attribute) hits (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult attribute) hits_file (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) hits_fileChanged (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) hits_fileReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) HKL2SpAng() (in module schrodinger.application.matsci.gsas.GSASIIlattice) HKLS_KEY (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) HKLS_TITLE (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) HMC (schrodinger.application.bioluminate.methionine_oxidation.SamplingMode attribute) HmcAnalyzer (class in schrodinger.application.bioluminate.methionine_oxidation) HmcStats (class in schrodinger.application.bioluminate.methionine_oxidation) HmmerHit (class in schrodinger.application.bioluminate.anarci.anarci_adapter) HOF_PROP (schrodinger.application.matsci.jwsteps.HOFStep attribute) HOFMANN (schrodinger.application.matsci.permittivity.MultiStageMd attribute) HOFMANN_PROTOCOL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) HOFStep (class in schrodinger.application.matsci.jwsteps) HOH_ANGLE (schrodinger.protein.assignment.WaterStateEnumerator attribute) HOME (schrodinger.application.desmond.envir.CONST attribute) home_atom (schrodinger.application.matsci.clusterstruct.Neighbor attribute) homo() (in module schrodinger.application.jaguar.textparser) homo_lumo_energy() (in module schrodinger.application.mopac.results_main) homog_rank_2() (in module schrodinger.application.matsci.cctbx.rot_mx) homogeneous_poisson (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) homogenizeBeadSizes() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) homogenizeRingBeadSizes() (schrodinger.application.matsci.automated_cg_mapping.MartiniMapper method) HomologyRama (class in schrodinger.application.bioluminate.protein_structure_quality) HoneycombBilayers (class in schrodinger.application.matsci.nano.sheet) HoneycombCell (class in schrodinger.application.matsci.nano.sheet) HoneycombLattice (class in schrodinger.application.matsci.nano.sheet) HoneycombUnitCell (class in schrodinger.application.matsci.nano.sheet) honorHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) honorMatchingAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) hook_captured_successful_job() (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.analysis.Analysis method) (schrodinger.application.desmond.stage.analysis.PLAnalysis method) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher method) (schrodinger.application.desmond.stage.app.matsci.FrozenPhononCorrection method) (schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis method) (schrodinger.application.desmond.stage.launcher.FepMembraneLauncher method) (schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield method) (schrodinger.application.desmond.stage.prepare.structure.BuildGeometry method) (schrodinger.application.desmond.stage.simulate.FepVrun method) (schrodinger.application.desmond.stage.simulate.LambdaHopping method) (schrodinger.application.desmond.stage.simulate.ReplicaExchange method) (schrodinger.application.desmond.stage.simulate.SimulateBase method) (schrodinger.application.desmond.stage.utils.SystemBuilder method) hookUpPropTableTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) hookUpTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) HORIZONTAL_ALIGNS (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) HorizontalBar (class in schrodinger.application.desmond.gui) HorizontalHeader (class in schrodinger.application.job_monitor.job_monitor_table) (class in schrodinger.ui.qt.tablewidget) Host (class in schrodinger.job.jobcontrol) (class in schrodinger.tasks.hosts) host (schrodinger.active_learning.mq_driver.Worker attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.licensing.lmgrd_log_parser.event attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) (schrodinger.job.jobcontrol.Host property) Host (schrodinger.job.jobcontrol.Job property) host (schrodinger.tasks.jobtasks.HostSettings attribute) HOST (schrodinger.utils.cmdline.Options attribute) host_check() (in module schrodinger.job.host_check) host_combo (schrodinger.ui.qt.tasks.configwidgets.HostSelector property) HOST_LABEL_TEXT (schrodinger.application.desmond.fep_dialog.FEPConfigDialog attribute) (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) (schrodinger.ui.qt.config_dialog.GPUConfigDialog attribute) host_list_to_str() (in module schrodinger.job.jobcontrol) HOST_PLACEHOLDER_ARGS (schrodinger.tasks.jobtasks.HostSettings attribute) host_settings (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) host_settingsChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) host_settingsReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) HOST_STR (schrodinger.application.matsci.genetic_optimization.ClassEvaluator attribute) host_str_to_list() (in module schrodinger.job.jobcontrol) hostChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) (schrodinger.tasks.jobtasks.HostSettings attribute) HostEntry (schrodinger.job.jobcontrol.Job property) hostfile_is_empty() (in module schrodinger.job.jobcontrol) hostfile_is_valid() (in module schrodinger.job.jobcontrol) hostid_is_local() (in module schrodinger.application.licensing.licadmin) hostid_order() (in module schrodinger.application.licensing.flexlm) HostLayoutWidget (class in schrodinger.ui.qt.tasks.configwidgets) HOSTLIST (schrodinger.utils.cmdline.Options attribute) hostname (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) (schrodinger.job.server.ServerInfo attribute) (schrodinger.stepper.stepper.BatchSettings attribute) hostname() (schrodinger.application.licensing.flexlm.Server method) hostname_and_port() (in module schrodinger.utils.net) hostname_in_registry() (in module schrodinger.utils.sshconfig) hostname_is_local() (in module schrodinger.utils.net) hostnameChanged (schrodinger.stepper.stepper.BatchSettings attribute) hostnameReplaced (schrodinger.stepper.stepper.BatchSettings attribute) HostParam (class in schrodinger.tasks.jobtasks) hostport() (schrodinger.application.licensing.flexlm.Server method) HostProduct (class in schrodinger.ui.qt.config_dialog) hostReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) (schrodinger.tasks.jobtasks.HostSettings attribute) HostSelector (class in schrodinger.ui.qt.tasks.configwidgets) HostSettings (class in schrodinger.tasks.jobtasks) hostType() (schrodinger.tasks.hosts.Host method) HostTypeError HOSTWITHSUBJOBS (schrodinger.utils.cmdline.Options attribute) HOSTWITHTHREADS (schrodinger.utils.cmdline.Options attribute) Hotspot (class in schrodinger.application.desmond.mxmd.mxmd_cleanup) HOVER (schrodinger.ui.qt.standard.design_tokens.BorderColors attribute) (schrodinger.ui.qt.standard.design_tokens.StateColors attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) HOVER_HORIZONTAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) HOVER_LABEL_X_FORMAT (schrodinger.ui.qt.schart.SChartView attribute) HOVER_LABEL_Y_FORMAT (schrodinger.ui.qt.schart.SChartView attribute) HOVER_VERTICAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) hoverEnter (schrodinger.ui.dendrogram.DendrogramGraphicTree attribute) hoverEnterEvent() (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) hoverLeave (schrodinger.ui.dendrogram.DendrogramGraphicTree attribute) hoverLeaveEvent() (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.schart.SChart method) hoverMoveEvent() (schrodinger.application.matsci.reordergui.StructurePic method) (schrodinger.ui.qt.schart.SChart method) HPType (class in schrodinger.application.matsci.espresso.qeinput) hr_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) HRD (schrodinger.protein.annotation.KinaseFeatureLabel attribute) hso_singlet_triplet() (in module schrodinger.application.jaguar.textparser) HsoSingletTripletElement (class in schrodinger.application.jaguar.results) HStrainNames() (in module schrodinger.application.matsci.gsas.GSASIIspc) HStrainVals() (in module schrodinger.application.matsci.gsas.GSASIIspc) HTML (schrodinger.seam.viz.watcher.ResponseType attribute) html_embed_image() (in module schrodinger.application.desmond.util) HTTPClient (class in schrodinger.application.glide.http_client) https_session() (in module schrodinger.utils.installation_check) hubb_j0 (schrodinger.application.matsci.espresso.utils.MagElement attribute) hubb_u (schrodinger.application.matsci.espresso.utils.MagElement attribute) human2opspec() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) hunt() (in module schrodinger.job.hunt_stub) (in module schrodinger.job.util) Hx2Rh() (in module schrodinger.application.matsci.gsas.GSASIIlattice) hybrid (schrodinger.application.matsci.espresso.qeinput.DftType property) HybridMethodsMixin (class in schrodinger.models.parameters) HybridType (class in schrodinger.application.matsci.espresso.qeinput) hyd_charge (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_forward (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_end_time_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_ensemble (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_ff (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_mol_number (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_rest_exchanges (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_sid_molsa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) hyd_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_sid_psa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) hyd_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) hyd_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) hyd_sid_sasa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) hyd_sid_snapshot_times_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_sim_time (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_start_time_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_temperature (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_total_atoms (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_total_replicas (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) hyd_total_waters (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) HYDRATION (schrodinger.application.desmond.constants.FepLegTypes attribute) (schrodinger.application.desmond.constants.PhysicalLegTypes attribute) hydration_fep_sim_time (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) hydration_only (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) Hydrogen (class in schrodinger.utils.sea.sea) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomType attribute) HYDROGEN_BOND_ACCEPTOR (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROGEN_BOND_DONOR (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROGEN_BOND_ORDER (schrodinger.application.matsci.rxn_channel.ReactantMolecule attribute) hydrogen_neighbors() (in module schrodinger.application.prepwizard) HYDROGEN_SYM (schrodinger.application.matsci.rxn_channel.ReactantMolecule attribute) HydrogenCap (class in schrodinger.application.qsite.input) Hydrogens (class in schrodinger.adapter) hydrogens_present() (in module schrodinger.structutils.analyze) HydrogenSubMenu (class in schrodinger.application.bioluminate.pml_menus) HYDROKINETIC_RATING (schrodinger.infra.structure.WorkflowType attribute) HydrokineticInput (class in schrodinger.application.jaguar.hydrokinetic_input) Hydrophilic (schrodinger.protein.helm.helm_renderer.HexColor attribute) hydrophilic_idxs (schrodinger.application.matsci.packmol.SurfactantInfo attribute) hydrophilicity (schrodinger.protein.residue.Residue property) hydrophobic (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute) hydrophobic_idxs (schrodinger.application.matsci.packmol.SurfactantInfo attribute) HYDROPHOBIC_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROPHOBIC_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROPHOBIC_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HydrophobicConstraint (class in schrodinger.application.glide.glide) hydrophobicity (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) hydrophobicity_window_padding (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) HydrophobicVectorizer (in module schrodinger.application.bioluminate.peptide_sar.encode) HYDROXYL (schrodinger.application.bioluminate.methionine_oxidation.NeighborAtom attribute) HyperbolaHistogramData (class in schrodinger.application.matsci.uq_utils) HyperlinkWithArrowWithPopUp (class in schrodinger.ui.residueselector) HypoName (schrodinger.application.phase.featureselector.FeatureColumns attribute) (schrodinger.application.phase.phase_widgets.HypothesisColumns attribute) HypothesesListWidget (class in schrodinger.application.phase.phase_widgets) hypothesisChanged (schrodinger.application.phase.pt_hypothesis.PhaseHypothesisMonitor attribute) HypothesisColumns (class in schrodinger.application.phase.phase_widgets) HypothesisModel (class in schrodinger.application.phase.phase_widgets) HypothesisRow (class in schrodinger.application.phase.phase_widgets) hz_to_ppm() (in module schrodinger.application.jaguar.nmr_utils)

I

IACC_FDPOL (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) IACCG (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) ichoice (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) ichunked() (in module schrodinger.stepper.stepper) ICL (schrodinger.protein.annotation.GPCRSegmentLabel attribute) ICMS (schrodinger.application.matsci.permittivity.CMSParser attribute) icon (schrodinger.ui.qt.swidgets.ActionPushButton attribute) icon() (schrodinger.ui.qt.swidgets.LargeSpinner method) ICON_SIZE (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider attribute) IconMetadata (class in schrodinger.ui.qt.standard.icons.icons) icons (schrodinger.application.matsci.mswidgets.StageFrame property) Icosahedron (class in schrodinger.application.matsci.shapes) icosahedron() (schrodinger.application.watermap.shapes.ShapeFactory method) id (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) (schrodinger.application.desmond.stage.analysis.FepanaJob attribute) (schrodinger.application.desmond.stage.jobs.FepJob attribute) ID (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) id() (schrodinger.application.desmond.fep_struc.Struc method) ID_fab (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) id_or_url (schrodinger.application.livedesign.live_report_widget.LRInputType attribute) ID_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) IdConversion (class in schrodinger.application.desmond.constants) IdDict (class in schrodinger.utils.scollections) idealize_hydrogen_temp_factor() (in module schrodinger.application.prepwizard) idealize_hydrogen_tf (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) idealize_hydrogen_tfChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) idealize_hydrogen_tfReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) ident() (schrodinger.application.licensing.licadmin.LicenseResource method) Identical (schrodinger.protein.alignment.ResidueSimilarity attribute) identifier (schrodinger.protein.nonstandard_residues.AminoAcid property) identify_all_hbonders() (in module schrodinger.protein.assignment) identify_changeables() (schrodinger.protein.assignment.ProtAssign method) identify_forced_amide_states() (schrodinger.protein.assignment.HistidinepKaPredictor method) identify_ligand_changeables() (in module schrodinger.protein.assignment) identify_nonshared_rotatable() (in module schrodinger.protein.assignment) identify_species() (in module schrodinger.protein.assignment) identifyGroups() (schrodinger.structutils.assignbondorders.AssignBondOrders method) identifySolventAtoms() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput static method) identity (schrodinger.livedesign.biologics.sequence.AlignedSequence attribute) IdItemsView (class in schrodinger.utils.scollections) IdSet (class in schrodinger.utils.scollections) idx (schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo attribute) (schrodinger.application.matsci.cg_mapping.ATOM_DEFINITION attribute) idx_in_seq (schrodinger.protein.residue.AbstractSequenceElement property) (schrodinger.protein.residue.CombinedChainResidueWrapper property) If (class in schrodinger.application.desmond.enhsamp) if_() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) IFD_MD (schrodinger.application.desmond.constants.PRODUCT attribute) IFDPOL (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) ig_type_str (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult property) IGEOPT (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) Ignore (schrodinger.adapter.Properties attribute) (schrodinger.adapter.StereoChemistry attribute) IGNORE (schrodinger.application.desmond.constants.EXISTING_RESTRAINT attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.tasks.jobtasks.IncorporationMode attribute) ignore_backbone (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) ignore_backboneChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) ignore_backboneReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) IGNORE_DELAYED_CALLBACKS (schrodinger.ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin attribute) ignore_maestro_callbacks() (in module schrodinger.application.matsci.gutils) IGNORE_POSRE (schrodinger.application.desmond.constants.EXISTING_RESTRAINT attribute) ignore_ssl_warnings() (in module schrodinger.application.matsci.msutils) ignoreCheckboxChanged() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) ignoreMaestroCallbacks() (schrodinger.ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin method) ILEVAL (schrodinger.ui.qt.rama.RamaResidueType attribute) IMAG_TOL (schrodinger.application.matsci.mecp_mod.BFGS attribute) IMAGE_FILE (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) image_to_string() (in module schrodinger.ui.qt.utils) ImageGenerator (class in schrodinger.application.desmond.image_generator) ImageGenOptions (class in schrodinger.livedesign.draw) ImageLabel (class in schrodinger.ui.qt.swidgets) ImagePlotFrame (class in schrodinger.application.matsci.density_analysis_widget) imagesRequested() (schrodinger.application.matsci.reportutils.ReportInfo method) img_format (schrodinger.livedesign.draw.ImageGenOptions attribute) ImgtLoopRange (class in schrodinger.application.bioluminate.anarci.loop_ranges) IminoAcid (schrodinger.protein.helm.helm_renderer.HexColor attribute) (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) IMPLICIT (schrodinger.adapter.Hydrogens attribute) import_canvas() (in module schrodinger.application.canvas.r_group) import_driver() (in module schrodinger.application.matsci.jwsteps) IMPORT_FILE_COL (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame attribute) import_from_file() (in module schrodinger.utils.imputils) import_module_from_file() (in module schrodinger.utils.imputils) import_pt_entries() (in module schrodinger.application.desmond.feputils) import_pv_file() (in module schrodinger.application.desmond.feputils) import_script() (in module schrodinger.utils.imputils) import_structures_from_ld_async() (in module schrodinger.application.livedesign.ld_import_utils) import_structures_to_maestro() (in module schrodinger.application.livedesign.ld_import) import_task (schrodinger.application.livedesign.ld_import_utils.LDImportTask attribute) IMPORT_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) ImportButtonMixin (class in schrodinger.ui.qt.structure_selector) imported_structures (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) imported_structuresChanged (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) imported_structuresReplaced (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) ImportExportBasePanel (class in schrodinger.application.livedesign.ld_base_classes) importFile() (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) importFilterFile() (schrodinger.ui.ligfilter.LigfilterFrame method) importFromFile() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) (schrodinger.application.matsci.mswidgets.StructureLoader method) importFromFilePaths() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromMaestro() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromPDB() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromProjectTable() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromWorkspace() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) (schrodinger.application.matsci.mswidgets.StructureLoader method) importLA() (in module schrodinger.trajectory.prody.ensemble) importLipid() (schrodinger.application.matsci.mswidgets.LipidImporter method) importMapping() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) importName() (in module schrodinger.pipeline.pipeline) importPresets() (schrodinger.models.presets.PresetManager method) importRegion() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) importRequested (schrodinger.ui.qt.structure_selector.ImportButtonMixin attribute) ImportStructure (schrodinger.application.livedesign.ld_maestro_actions_constants.RequestType attribute) importStructure() (schrodinger.project.project.Project method) importStructureFile() (schrodinger.project.project.Project method) ImportTask (class in schrodinger.application.livedesign.ld_tasks) ImportTask.Output (class in schrodinger.application.livedesign.ld_tasks) ImportTaskInput (class in schrodinger.application.livedesign.ld_tasks) ImportToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) ImportWidget (class in schrodinger.application.bioluminate.bwidgets) importWorkspace() (schrodinger.application.matsci.builderwidgets.SketcherBox method) improper_dihedral_iterator() (in module schrodinger.structutils.analyze) IMPROPER_FBHW (schrodinger.application.desmond.constants.RestrainTypes attribute) IN_EXT (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.Jaguar attribute) (schrodinger.application.matsci.packmol.PackmolInputFile attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) in_main_thread() (in module schrodinger.utils.thread_utils) IN_PROCESS (schrodinger.tasks.ldtasks.ExecutionMode attribute) in_temporary_directory() (in module schrodinger.utils.fileutils) in_workspace (schrodinger.project.project.ProjectRow property) in_xy_plane() (in module schrodinger.livedesign.preprocessor) InBounds() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) INC (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) incfg_file() (schrodinger.application.desmond.cmj.JobInput method) INCHI (schrodinger.rdkit_extensions.Format attribute) INCHI_KEY (schrodinger.rdkit_extensions.Format attribute) incident_angle (schrodinger.application.bioluminate.tcr.docking_angles.DescriptiveAngles attribute) incline_angle (schrodinger.application.bioluminate.tcr.docking_angles.DescriptiveAngles attribute) Include (class in schrodinger.ui.qt.table_helper) include() (schrodinger.ui.ligfilter.AddDefinitionDialog method) include_and_show_trajectory() (in module schrodinger.trajectory.trajectoryviewer) include_and_show_trajectory_snapshot() (in module schrodinger.trajectory.trajectoryviewer) include_entries() (in module schrodinger.project.utils) include_epik_states (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) include_epik_statesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) include_epik_statesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) include_only_entry() (in module schrodinger.trajectory.trajectoryviewer) include_property (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) include_propertyChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) include_propertyReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) include_traj (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) include_trajChanged (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) include_trajReplaced (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) INCLUDE_USE_CONSISTENT_ORBITALS_CB (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals attribute) include_x_terms (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) included (schrodinger.application.jaguar.gui.input_tab_widgets.UseFrom attribute) (schrodinger.project.project.EntrySurface property) (schrodinger.ui.qt.ligand_list.LigSource attribute) INCLUDED_ENTRIES (schrodinger.ui.qt.input_selector.InputSelector attribute) INCLUDED_ENTRY (schrodinger.ui.qt.input_selector.InputSelector attribute) included_rows (schrodinger.project.project.EntryGroup property) (schrodinger.project.project.Project property) IncludedEntries (schrodinger.ui.qt.structure_selector.InputSource attribute) IncludedEntry (schrodinger.ui.qt.structure_selector.InputSource attribute) includeEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) IncludeInSelection (class in schrodinger.application.bioluminate.pml_menus) includeOnly() (schrodinger.project.project.ProjectRow method) includeRows() (schrodinger.project.project.Project method) includes() (schrodinger.utils.ligfilter.Definition method) includeSelectedCellsEntries() (schrodinger.ui.two_d_viewer.TwoDViewer method) IncludeSubMenu (class in schrodinger.application.bioluminate.pml_menus) IncludeVisibleInSelection (class in schrodinger.application.bioluminate.pml_menus) INCLUSION (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) inclusion_threshold (schrodinger.protein.tasks.blast.BlastSettings attribute) inclusion_thresholdChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) inclusion_thresholdReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) inclusionAndSelectionAreIdentical() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) inclusionChanged (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync attribute) inclusionStateChanged (schrodinger.ui.qt.appframework2.maestro_callback.InclusionStateMixin attribute) InclusionStateMixin (class in schrodinger.ui.qt.appframework2.maestro_callback) INCOMPATIBLE_PARAMS_MSG (schrodinger.ui.qt.forcefield.forcefield.OPLSValidator attribute) IncompatibleLicenseError IncompleteFragmentError IncompleteOutput InconsistentAttributeError InconsistentDataException InconsistentStructureError, [1] inContext() (schrodinger.application.desmond.antlr3.tree.TreeParser method) incorporation (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) incorporation_file (schrodinger.tasks.jobtasks.JobOutput attribute) incorporation_fileChanged (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) (schrodinger.tasks.jobtasks.JobOutput attribute) incorporation_fileReplaced (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) (schrodinger.tasks.jobtasks.JobOutput attribute) incorporationChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) IncorporationMode (class in schrodinger.tasks.jobtasks) IncorporationParam (class in schrodinger.tasks.jobtasks) incorporationReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) IncorporationSelector (class in schrodinger.ui.qt.tasks.configwidgets) increaseSpeed() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) INCREMENT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) increment_state_of_changeable() (schrodinger.protein.assignment.ProtAssign method) incrementNestingLevel() (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) incrementTorsionValue() (schrodinger.application.matsci.amorphous.TorsionAngler method) IND_DEFAULT (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) IND_DISABLED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) IND_HOVER (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) IND_PRESSED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) INDENT (schrodinger.application.matsci.desconfig.MSJStringer attribute) index (schrodinger.application.desmond.fep_scholar_util.MetaAtom property) (schrodinger.application.jaguar.input.OrbSpec attribute) (schrodinger.application.jaguar.utils.ChgAt attribute) (schrodinger.application.matsci.atom_group.MSAtom property) (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData.RING_NODE_TYPE attribute) (schrodinger.application.matsci.kmc.MoleculeData attribute) (schrodinger.project.project.ProjectRow property) (schrodinger.structure.StructureAtom property) index() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.infra.util.OneIndexedList method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.ui.qt.table_helper.RowBasedListModel method) (schrodinger.utils.sea.sea.List method) index_endpoint() (schrodinger.seam.viz.watcher.WatcherWebServer method) index_in_current_file (schrodinger.structure.MultiFileStructureReader attribute) index_of_flag_in_args() (in module schrodinger.application.mopac.mopac_parser) INDEX_PATTERN (schrodinger.utils.sea.sea.Map attribute) INDEX_PATTERN2 (schrodinger.utils.sea.sea.Map attribute) indexChanged() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) indexChanges() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin static method) indexes (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) indexIsEnabled() (schrodinger.ui.qt.delegates.LinkDelegate method) IndexString (class in schrodinger.application.jaguar.autots_constants) indexToSeqAndIndex() (schrodinger.protein.sequence.CombinedChainProteinSequence method) indexUnbalancedWorkflow() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) indicator (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) indicator_icon() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) INDICES (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) indices (schrodinger.application.jaguar.hess_guess.InternalCoordinate property) (schrodinger.application.matsci.coarsegrain.InternalInfo attribute) INDICES (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) indices (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) indices() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) indicesToPositions() (schrodinger.application.bindingsite.cavutils.Grid method) indicies_from_bonds_deep() (in module schrodinger.application.matsci.rxn_channel) INFERRED (schrodinger.seam.options.pipeline_options.SeamOptions attribute) infile (schrodinger.application.glide.ligand_designer.GridgenTask attribute) infile_setup() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage method) info (schrodinger.application.matsci.cache.BaseCacheData property) info() (in module schrodinger.application.matsci.gutils) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) (schrodinger.application.prepwizard2.tasks.LoggerMixin method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.swidgets.SDialog method) (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) (schrodinger.ui.two_d_viewer.TwoDViewer method) INFO_BTN_STYLESHEET (schrodinger.ui.qt.pop_up_widgets.InfoButtonWithPopUp attribute) INFO_BUTTON_STYLESHEET (schrodinger.ui.qt.swidgets.InfoButton attribute) INFO_H_ICON (schrodinger.ui.qt.swidgets.InfoButton attribute) INFO_ICON (schrodinger.ui.qt.swidgets.InfoButton attribute) info_task (schrodinger.application.livedesign.ld_import_utils.LDImportTask attribute) InfoButton (class in schrodinger.ui.qt.swidgets) InfoButtonWithPopUp (class in schrodinger.ui.qt.pop_up_widgets) INFORMATIONAL_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) InfoTextLabel (class in schrodinger.ui.qt.standard_widgets.labels) InFrontMonomer (schrodinger.protein.helm.helm_renderer.ZOrder attribute) inheritProperties() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) Init (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom.NextGeomFrom attribute) init() (in module schrodinger.protein.remediate) (schrodinger.application.bioluminate.interaction_calculator.Interactions class method) (schrodinger.application.bioluminate.interaction_calculator.ResTuple class method) (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) (schrodinger.application.matsci.gsas.GSASIImath.fast_sa method) (schrodinger.application.matsci.gsas.GSASIImath.log_sa method) init_bennett() (in module schrodinger.application.desmond.fepana) init_count (schrodinger.job.queue.BaseJob attribute) (schrodinger.job.queue.SubprocessJob attribute) init_ff() (schrodinger.application.desmond.torsion_related.TorsionPotential method) init_random_seed() (in module schrodinger.application.matsci.rxn_channel) init_report() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) initAbstract() (schrodinger.models.parameters.Param method) initActionStates() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) initConcrete() (schrodinger.application.glide.ligand_designer.BuildServerTask method) (schrodinger.application.glide.ligand_designer.GridgenTask method) (schrodinger.application.livedesign.ld_export.ExportModel method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.protein.tasks.blast.BlastSettings method) (schrodinger.protein.tasks.blast.BlastTask.Input method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings method) initDlg() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) initFigure() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) initFinalize() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) initFromEpikOutput() (schrodinger.application.prepwizard.HetState class method) initial (schrodinger.application.jaguar.scan.Scan property) (schrodinger.application.jaguar.utils.ScanCoord attribute) INITIAL_GUESS_OPTS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) INITIAL_HESSIAN (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) initial_tokens() (in module schrodinger.application.licensing.lmgrd_log_parser) initializator (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) initialize() (schrodinger.application.jaguar.mmjag.MmJag static method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.permittivity.WorkflowParser method) (schrodinger.infra.mminit.Initializer method) (schrodinger.infra.mmlist.mmlist static method) (schrodinger.infra.table.Table static method) (schrodinger.project.project.Project static method) (schrodinger.seam.examples.active_learning_weigher.LinearRegressionModel class method) initialize_atom_types() (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper method) (schrodinger.application.jaguar.autots_rmsd.AutoTSTemplateAtomMapper method) (schrodinger.comparison.atom_mapper.BaseAtomMapper method) (schrodinger.comparison.atom_mapper.ConnectivityAtomMapper method) (schrodinger.comparison.atom_mapper.CSPAtomMapper method) (schrodinger.comparison.atom_mapper.LewisAtomMapper method) initialize_audit_log() (in module schrodinger.livedesign.preprocessor) initialize_map_data() (in module schrodinger.utils.documentation) initialize_tddft() (in module schrodinger.application.jaguar.textparser) initializeCoordinates() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) initializeDatabase() (schrodinger.application.matsci.kmc.BaseDatabaseManager method) (schrodinger.application.matsci.kmc.MatSciDatabaseManager method) (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) initializeGA() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) initializeGenome() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) initializeLabels() (in module schrodinger.application.dendrogram.proteinDendrogram) initializeLeaves() (schrodinger.ui.qt.dendrogram.Dendrogram method) initializeMmlibs() (schrodinger.application.ligprep.ionizer.Ionizer method) initializeProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) Initializer (class in schrodinger.infra.mminit) initializeTopics() (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) initializeValue() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions method) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask method) (schrodinger.application.livedesign.ld_export.ExportModel method) (schrodinger.application.livedesign.ld_tasks.ImportTask method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel method) (schrodinger.application.pymol.gui_models.AdvancedSettingsModel method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.protein.gpcr.tasks.GPCRTask method) (schrodinger.protein.tasks.blast.BlastSettings method) (schrodinger.stepper.stepper.BatchSettings method) (schrodinger.tasks.jobtasks.HostSettings method) (schrodinger.tasks.tasks.AbstractComboTask method) (schrodinger.tasks.tasks.AbstractTask method) initializeValueMatrix() (schrodinger.ui.qt.table.StructureDataViewerModel method) initializeWithSize() (schrodinger.ui.dendrogram.DendrogramTreeBuilder method) initialSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) InitialSuggestionLineEdit (class in schrodinger.application.livedesign.panel_components) initiateAndAddMdJobs() (schrodinger.application.matsci.equilibrium_md.MultiDriver method) initiateCellSizes() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) initiateMultiMols() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) InitiationError Initiator (class in schrodinger.application.matsci.amorphous) initKnime() (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) initLayOut() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog method) (schrodinger.application.jaguar.jaguar_config_dialog.JaguarHostSelector method) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobBar method) (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) (schrodinger.application.job_monitor.job_monitor_widgets.TopLevelJobBar method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget method) (schrodinger.ui.qt.directory_selector.DirectorySelector method) (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.file_selector.SlimFileSelector method) (schrodinger.ui.qt.mapperwidgets.param_editor.ParamEditor method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.structure_selector.ImportButtonMixin method) (schrodinger.ui.qt.structure_selector.SlimStructureSelector method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.configwidgets.HostLayoutWidget method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.tasks.configwidgets.IncorporationSelector method) (schrodinger.ui.qt.tasks.configwidgets.JobnameWidget method) (schrodinger.ui.qt.tasks.taskwidgets.KillableProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.StatusBarMixin method) initMaestroWriter() (schrodinger.application.matsci.rxn_channel.Channels method) InitMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) initMixinOptions() (schrodinger.application.matsci.appbase.MatSciAppMixin method) initNonPersistent() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) initPositions() (schrodinger.application.matsci.mswidgets.MultiSlider method) initReport() (schrodinger.active_learning.al_report.ALReportMaker method) initServersCombo() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) initSetDefaults() (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) initSetOptions() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel method) (schrodinger.application.livedesign.widgets.InvalidGEIdWarningDialog method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.basewidgets.BaseOptionsDialog method) (schrodinger.ui.qt.presets.save_presets_dialog.SavePresetsDialog method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.SchrodingerStyleMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) (schrodinger.ui.two_d_viewer.AtomPropertyDialog method) (schrodinger.ui.two_d_viewer.CtPropsDialog method) initSetUp() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) (schrodinger.application.jaguar.jaguar_config_dialog.JaguarHostSelector method) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsDialog method) (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.job_monitor.job_monitor_widgets.JobBar method) (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel method) (schrodinger.application.livedesign.widgets.InvalidGEIdWarningDialog method) (schrodinger.application.pymol.export_to_pymol_gui.AdvancedSettingsPopUp method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner method) (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget method) (schrodinger.ui.qt.basewidgets.TaskPanel method) (schrodinger.ui.qt.directory_selector.DirectorySelector method) (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin method) (schrodinger.ui.qt.fp_selector_widget.FingerprintsSelectorWidget method) (schrodinger.ui.qt.mapperwidgets.param_editor.ParamEditor method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.presets.save_presets_dialog.SavePresetsDialog method) (schrodinger.ui.qt.structure_selector.ImportButtonMixin method) (schrodinger.ui.qt.structure_selector.SlimStructureSelector method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.configwidgets.HostLayoutWidget method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.tasks.configwidgets.IncorporationSelector method) (schrodinger.ui.qt.tasks.configwidgets.JobnameWidget method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.JobTaskBar method) (schrodinger.ui.qt.tasks.taskwidgets.KillableProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.StatusBarMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) initSockets() (schrodinger.active_learning.mq_worker.Worker method) initStyleOption() (schrodinger.ui.qt.table_speed_up.SpeedUpDelegate method) initTangledMethod() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) initVariables() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) INJECTS_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) INJECTS_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) InMemoryRandomSampleFilter (class in schrodinger.application.steps.filters) InMemoryRandomSampleFilter.Settings (class in schrodinger.application.steps.filters) InMemoryUniqueRandomSampleFilter (class in schrodinger.application.steps.filters) InMemoryUniqueRandomSampleFilter.Settings (class in schrodinger.application.steps.filters) InMemoryUniqueSmilesFilter (class in schrodinger.application.steps.filters) INPLACE_PROPERTY (schrodinger.structutils.sitealign.SiteMatchLookup attribute) input (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) INPUT (schrodinger.application.matsci.crest.CrestTOML attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) input (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) Input (schrodinger.application.steps.converters.SmilesToMolConverter attribute) (schrodinger.application.steps.dataclasses.FileInMixin attribute) (schrodinger.application.steps.dataclasses.MaeInMixin attribute) (schrodinger.application.steps.dataclasses.MolInMixin attribute) (schrodinger.application.steps.dataclasses.ScoredMolInMixin attribute) (schrodinger.application.steps.dataclasses.ScorerMixin attribute) (schrodinger.application.steps.enumerators.RouteDeduplicator attribute) (schrodinger.application.steps.enumerators.RouteEvaluator attribute) (schrodinger.application.steps.enumerators.TransformApplyer attribute) (schrodinger.application.steps.filters.RangeFilter attribute) input (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) Input (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter attribute) (schrodinger.stepper.core_steps.DeduplicationStep attribute) (schrodinger.stepper.core_steps.RandomSampleFilter attribute) input (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.stepper.stepper.StepTaskMixin attribute) Input (schrodinger.stepper.stepper.UnbatchedChain property) input (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) input_at_index_str (schrodinger.application.jaguar.autots_constants.IndexString attribute) input_changed (schrodinger.ui.qt.input_selector.InputSelector attribute) input_deviation (schrodinger.application.jaguar.results.NofailResult attribute) input_file_arguments() (in module schrodinger.job.jobcontrol) input_file_keys (schrodinger.application.jaguar.autots_input.AutoTSInput attribute) (schrodinger.application.jaguar.esol_input.EsolInput attribute) (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput attribute) (schrodinger.application.jaguar.macro_pka_input.MacroKaInput attribute) (schrodinger.application.jaguar.qrnn.input.QRNNInput attribute) (schrodinger.application.jaguar.rotation_barriers_input.RotationBarriersInput attribute) (schrodinger.application.jaguar.solvation_input.SolvationInput attribute) (schrodinger.application.jaguar.workflow_input.WorkflowInput attribute) (schrodinger.application.xtb.input.XTBInput attribute) input_files (schrodinger.application.vss.control.GlideALControl property) (schrodinger.application.vss.control.GlideControl property) (schrodinger.application.vss.control.LigandMLControl property) (schrodinger.application.vss.control.RunnerControl property) (schrodinger.application.vss.control.ShapeControl property) (schrodinger.application.vss.csvsmiles.CsvSmilesFile property) INPUT_FLAG (schrodinger.application.matsci.crest.Crest attribute) INPUT_FNAME (schrodinger.application.desmond.stage.launcher.FepMembraneLauncher attribute) input_fname (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) input_fnameChanged (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) input_fnameReplaced (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) INPUT_MASK (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CommandLine attribute) input_mol_index_str (schrodinger.application.jaguar.autots_constants.IndexString attribute) input_property_data (schrodinger.livedesign.registration.RegistrationData attribute) INPUT_ST2 (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) input_st_count (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) input_st_countChanged (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) input_st_countReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) input_string (schrodinger.livedesign.registration.RegistrationData attribute) INPUT_SUB_TABS (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) input_summary (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) input_summaryChanged (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) input_summaryReplaced (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) inputChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) (schrodinger.ui.qt.structure_selector.StructureSelector attribute) InputConfig (class in schrodinger.application.inputconfig) inputconfig_subset() (in module schrodinger.application.phase.input) InputDeviation (class in schrodinger.application.jaguar.results) InputEntriesColumns (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesColumnsHB (class in schrodinger.application.jaguar.gui.input_tab_widgets_hb) InputEntriesColumnsMacroPkaByCharge (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesColumnsMacroPkaByPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesColumnsPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesModel (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesModelHB (class in schrodinger.application.jaguar.gui.input_tab_widgets_hb) InputEntriesModelMacroPkaByCharge (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesModelMacroPkaByPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesModelPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesProxyModel (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesView (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesViewPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputError InputFiles (schrodinger.job.jobcontrol.Job property) InputGroup (class in schrodinger.application.desmond.gui) inputLoaded (schrodinger.ui.qt.structure_selector.SlimStructureSelector attribute) InputMultiplicityMixin (class in schrodinger.application.jaguar.gui.base_panel) InputOrder (schrodinger.structutils.interactions.salt_bridge.OrderBy attribute) inputReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute)

InputSelector (class in schrodinger.ui.qt.input_selector) InputSelectorWithDatabase (class in schrodinger.application.matsci.kmcgui) InputSequence (class in schrodinger.application.bioluminate.anarci.anarci_adapter) InputSerializer (schrodinger.application.steps.dataclasses.MolInMixin attribute) (schrodinger.application.steps.dataclasses.ScoredMolInMixin attribute) (schrodinger.application.steps.dataclasses.ScorerMixin attribute) (schrodinger.application.steps.enumerators.RouteDeduplicator attribute) (schrodinger.application.steps.enumerators.RouteEvaluator attribute) (schrodinger.application.steps.filters.RangeFilter attribute) (schrodinger.stepper.stepper.UnbatchedChain property) inputsForStagesDefined() (schrodinger.pipeline.pipeline.Pipeline method) InputSource (class in schrodinger.ui.qt.structure_selector) inputSource() (schrodinger.ui.qt.structure_selector.StructureSelector method) InputSpecs (class in schrodinger.application.phase.input) inputState() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) (schrodinger.ui.qt.input_selector.InputSelector method) InputStream (in module schrodinger.application.desmond.antlr3.streams) InputTab (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabBase (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabCoordinateScan (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabHB (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabJobMixin (class in schrodinger.application.jaguar.gui.base_panel) InputTabMixin (class in schrodinger.application.jaguar.gui.base_panel) InputTabPka (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabWithSubTabs (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputType (class in schrodinger.application.matsci.espresso.qeinput) InputVerificationError ins_code (schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo attribute) inscode (schrodinger.application.bioluminate.mutation.Mutation attribute) (schrodinger.application.bioluminate.protein_interaction.utils.Residue attribute) (schrodinger.application.qsite.input.Cut property) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) (schrodinger.protein.residue.Residue property) (schrodinger.protein.residue.ResidueChainKey attribute) (schrodinger.protein.residue.ResidueKey attribute) (schrodinger.structure.Residue property) (schrodinger.structure.StructureAtom property) (schrodinger.ui.qt.rama.BackboneDihedral attribute) insert() (schrodinger.infra.util.OneIndexedList method) (schrodinger.utils.sea.sea.List method) insert_path_into_cms() (in module schrodinger.application.desmond.kinetics.utils) insertAfter() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) insertBefore() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) InsertBeforeOp (class in schrodinger.application.desmond.antlr3.streams) insertColumn() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.swidgets.STableWidget method) (schrodinger.ui.qt.table.StructureDataViewerModel method) insertColumns() (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) insertElementByChain() (schrodinger.protein.sequence.CombinedChainProteinSequence method) insertElements() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) insertion_code (schrodinger.application.bioluminate.classify.NumberedResidue attribute) InsertionError insertRow() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.table.StructureDataViewerModel method) insertRows() (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) insertSubalignment() (schrodinger.protein.alignment.BaseAlignment method) INSIDE (schrodinger.application.matsci.packmol.PackmolKw attribute) insideFace() (schrodinger.application.matsci.shapes.Face method) insideRectangle() (schrodinger.application.matsci.nano.tube.Rectangle method) INSIDETHRESH (schrodinger.application.matsci.nano.tube.Rectangle attribute) install_handler() (in module schrodinger.infra.qt_message_handler) install_license() (in module schrodinger.application.licensing.licadmin) install_license_text() (in module schrodinger.application.licensing.licadmin) install_local_entitlement() (in module schrodinger.application.licensing.licserver.install) install_local_entitlement_from_key() (in module schrodinger.application.licensing.licserver.install) install_netsuite_license() (in module schrodinger.application.licensing.licadmin) install_remote_pubkey() (in module schrodinger.utils.sshconfig) install_remote_server_license() (in module schrodinger.application.licensing.licadmin) install_schrod_plist() (in module schrodinger.application.licensing.licadmin) install_server_identifier() (in module schrodinger.application.licensing.licserver.install) installed_pathname() (in module schrodinger.application.licensing.licadmin) InstallError installing modules installPopUpEventFilter() (schrodinger.ui.qt.pop_up_widgets.PopUp method) instance (schrodinger.application.livedesign.ld_import_utils.LDImportTaskManager attribute) InstantToolTipTableView (class in schrodinger.ui.qt.swidgets) instruction (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) INT (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute) int() (schrodinger.ui.qt.swidgets.SLineEdit method) INT_KEYWORDS (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) INT_PROP_PREFIX (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) INT_SIZE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) IntColumn (class in schrodinger.tasks.ldtasks) IntegrationTab (class in schrodinger.application.desmond.gui) INTENSITY_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) INTENSITY_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) INTER_CUTOFF (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) InteractingResidue (class in schrodinger.application.bioluminate.interaction_calculator) INTERACTION_NAMES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) InteractionCalculator (class in schrodinger.application.bioluminate.interaction_calculator) InteractionCalculatorError InteractionParams (class in schrodinger.application.bioluminate.interaction_calculator) InteractionReader (class in schrodinger.application.prime.residue_interaction) Interactions (class in schrodinger.application.bioluminate.interaction_calculator) (class in schrodinger.application.jaguar.nmr_interactions) interactions (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) interactionsChanged (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) interactionsReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) interactionSummary() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) InteractionTab (class in schrodinger.application.desmond.gui) interactive prompt InteractiveFileDownloader (class in schrodinger.application.matsci.jobdirdlg) Interactors (class in schrodinger.protein.assignment) INTERBUTTON_SPACING (schrodinger.ui.qt.standard_widgets.buttons.SplitPushButton attribute) Interdomain (schrodinger.protein.predictors.DomainArrangement attribute) Interface (class in schrodinger.application.matsci.nano.interface_mod) INTERFACE (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes attribute) INTERFACE_RES (schrodinger.application.bioluminate.antibody.annotate.Properties attribute) InterfaceMixin (class in schrodinger.application.bioluminate.pml_menus) InterfacePreset (class in schrodinger.application.bioluminate.pml_menus) InterfaceResidueFilter (class in schrodinger.application.bioluminate.pose_filtering.residue_filter) Interfaces (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) interior() (schrodinger.ui.qt.appframework.AppFramework method) internal (schrodinger.application.matsci.msconst.SMARTS_METHOD attribute) INTERNAL (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) internal_coeff (schrodinger.application.glide.sort_utils.CustomScoringFunction attribute) internal_energy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) INTERNAL_PKA (schrodinger.protein.assignment.AsparticAcidpKaPredictor attribute) (schrodinger.protein.assignment.GlutamicAcidpKaPredictor attribute) (schrodinger.protein.assignment.HistidinepKaPredictor attribute) InternalCoordinate (class in schrodinger.application.jaguar.hess_guess) InternalCoords (class in schrodinger.application.matsci.rxn_path) InternalInfo (class in schrodinger.application.matsci.coarsegrain) internalParams (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) Internals (class in schrodinger.application.matsci.coarsegrain) internals_iterator() (in module schrodinger.application.matsci.coarsegrain) INTERPLANAR_SPACING_KEY (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) INTERPLANAR_SPACING_TITLE (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) interpolate() (schrodinger.application.matsci.zmutils.ZMatrix method) Interpolate1D (class in schrodinger.math.mathutils) Interpolate2D (class in schrodinger.math.mathutils) interpolateReactionCoords() (schrodinger.application.matsci.rxn_path.ReactionPath method) INTERPOLATIONCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) interpretFlagBlock() (schrodinger.application.matsci.permittivity.TaskProtocol method) interpretJobServerError() (schrodinger.application.matsci.jobutils.FileDownloader static method) INTERRUPT_ENABLED (schrodinger.tasks.tasks.AbstractTask attribute) INTERSECT_KEYS (schrodinger.application.desmond.cms.FBHWPosRestrainArray attribute) (schrodinger.application.desmond.cms.PosRestrainArray attribute) intersect_line_and_rect() (in module schrodinger.ui.qt.network_views) intersection() (schrodinger.utils.scollections.IdSet method) intersection_update() (schrodinger.utils.scollections.IdSet method) intersectSegmentAndPlane() (schrodinger.application.matsci.shapes.Face method) INTERSMEAR_KEY (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) INTERVAL (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider attribute) IntParam (class in schrodinger.models.parameters) INTRASMEAR_KEY (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) intrinsic_part() (schrodinger.application.matsci.cctbx.rot_mx.translation_part_info method) IntStream (class in schrodinger.application.desmond.antlr3.streams) inv (schrodinger.application.matsci.elasticity.tensors.SquareTensor property) invalid (schrodinger.application.combinatorial_explorer.driver_utils.RouteSourceType attribute) invalid_code() (in module schrodinger.protein.getpdb_utility) invalid_ids (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) invalid_ids_handling_option (schrodinger.application.livedesign.export_models.GETaskInput attribute) invalid_ids_handling_optionChanged (schrodinger.application.livedesign.export_models.GETaskInput attribute) invalid_ids_handling_optionReplaced (schrodinger.application.livedesign.export_models.GETaskInput attribute) INVALID_MAP_NAME_MSG (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog attribute) invalid_smarts_changed (schrodinger.ui.qt.swidgets.SMARTSEdit attribute) INVALID_STATE_BORDER (schrodinger.ui.qt.standard.colors.LightModeColors attribute) invalid_types (schrodinger.application.prepwizard2.diagnostics.Problems attribute) invalid_typesChanged (schrodinger.application.prepwizard2.diagnostics.Problems attribute) invalid_typesReplaced (schrodinger.application.prepwizard2.diagnostics.Problems attribute) InvalidAntibodySequenceError invalidatedDomains (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin attribute) invalidatedLigandContacts (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) invalidatedMaxMinBFactor (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) invalidateMaxMinBFactor() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) invalidateWindowHydrophobicity() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) invalidateWindowIsoelectricPoint() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) InvalidCDFTError InvalidCSVFormattingError InvalidCSVLengthError InvalidFileRegistrationError InvalidFileTypeError InvalidGEIdHandlingPolicy (class in schrodinger.application.livedesign.export_models) InvalidGEIdWarningDialog (class in schrodinger.application.livedesign.widgets) InvalidInput InvalidProjectException InvalidProjectVersion InvalidPropertyError InvalidProteinStateError InvalidQueryLengthError InvalidRequestError InvalidResponseError InvalidRowError InvalidStageFileError InvalidSubstructureTypeError InvalidTagError InvalidTimeSliceError invcell2Gmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice) inverse() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.pathfinder.reaction.Reaction method) inverse_cancel() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) InverseCentimeter (schrodinger.application.jaguar.constants.Unit attribute) invert() (schrodinger.infra.mmbitset.Bitset method) invert_axis (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) invert_chirality() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) invert_reaction_smarts() (in module schrodinger.application.pathfinder.reaction) InvertCompleteSelection (class in schrodinger.application.bioluminate.pml_menus) InvertSubMenu (class in schrodinger.application.bioluminate.pml_menus) invpolfcal() (in module schrodinger.application.matsci.gsas.GSASIIlattice) invQ() (in module schrodinger.application.matsci.gsas.GSASIImath) inWorkspace() (schrodinger.project.project.ProjectRow method) inZoomMode() (schrodinger.ui.two_d_viewer.TwoDViewer method) IO ion (schrodinger.application.desmond.struc.CompStruc attribute) ION (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) ion_action (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar property) ION_DYNAMICS_KEY (schrodinger.application.matsci.espresso.qeinput.IonControlType attribute) IonControlType (class in schrodinger.application.matsci.espresso.qeinput) ionization_potential() (in module schrodinger.application.mopac.results_main) ionizeCommandParser() (schrodinger.application.ligprep.ionizer.Ionizer method) Ionizer (class in schrodinger.application.ligprep.ionizer) ionizeStructure() (schrodinger.application.ligprep.ionizer.Ionizer method) ip_default (schrodinger.application.jaguar.results.JaguarOptions attribute) IPOL (schrodinger.application.matsci.espresso.qeinput.TurboLanczosType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) IPOLAR (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) IPythonInspect (class in schrodinger.seam.debug) ir_intensity_precision (schrodinger.application.jaguar.results.NormalMode attribute) IR_Spectrum (class in schrodinger.application.matsci.spectra) iradius (schrodinger.application.matsci.elementalprops.ElementalProperties property) IRC_IS_NOT_TS (schrodinger.application.jaguar.constants.FatalErrors attribute) irc_point() (in module schrodinger.application.jaguar.textparser) irc_step (schrodinger.application.jaguar.output.JaguarOutput property) irc_summary() (in module schrodinger.application.jaguar.textparser) IRCEndpointError IRCFailure IrcTab (class in schrodinger.application.jaguar.gui.tabs.irc_tab) IRCVettingFailure irr_sph_ten() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) IRREP_DROP (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) is3cTheory() (in module schrodinger.application.jaguar.gui.utils) is3d() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) is_aacg_cms_file() (in module schrodinger.application.aacg.utils) is_aacg_ffio_struct() (in module schrodinger.application.aacg.utils) is_active (schrodinger.application.job_monitor.job_monitor_models.JobModel property) is_alpha (schrodinger.application.jaguar.input.OrbSpec attribute) is_another_best_config() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) is_antibody_heavy_type() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) is_antibody_light_type() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) is_antibody_subunit() (in module schrodinger.livedesign.biologics.registration) is_any_struct_coarse_grain() (in module schrodinger.application.matsci.msutils) is_any_text_label_visible() (in module schrodinger.application.phase.phase_markers) is_atom_list() (in module schrodinger.utils.sea.sea) is_atom_supported() (in module schrodinger.application.jaguar.basis) is_auto_download_active() (in module schrodinger.job.jobhandler) is_aws_service_available() (in module schrodinger.application.steps.env_keys) is_better_match() (in module schrodinger.comparison.struc) is_binary_string() (in module schrodinger.ui.qt.formlayout) is_bond_rotatable() (in module schrodinger.structutils.analyze) is_bs_spectrum_file_key() (in module schrodinger.application.matsci.bandshape_utils) is_builtin_fragment() (in module schrodinger.utils.cgxutils) is_builtin_template (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) is_change() (in module schrodinger.application.bioluminate.peptide_sar.label) is_charged_or_formal_charged() (in module schrodinger.application.desmond.struc) is_chiral() (in module schrodinger.comparison.struc) is_chiral_atom() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) is_cms (schrodinger.application.matsci.freevolume.FreeVolumeDriver property) is_cms_file() (in module schrodinger.utils.fileutils) is_coarse_grain() (in module schrodinger.application.matsci.msutils) is_coarse_grain_input() (in module schrodinger.application.matsci.coarsegrain) is_colinear() (in module schrodinger.structutils.measure) is_color_dark() (in module schrodinger.ui.qt.standard.colors) is_combined_protein_fep() (in module schrodinger.application.desmond.constants) is_complete (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult property) is_concat() (in module schrodinger.application.desmond.config_utils) is_core() (in module schrodinger.application.pathfinder.multiroute) is_core_application() (in module schrodinger.utils.qapplication) is_core_hopping_job() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) is_core_sm() (in module schrodinger.application.pathfinder.multiroute) is_counted() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.License method) is_covalent() (in module schrodinger.application.desmond.starter.generator.fep_plus) is_covalent_ligand() (in module schrodinger.protein.assignment) is_covalently_bound (schrodinger.structutils.analyze.Ligand property) is_csv_file() (in module schrodinger.utils.fileutils) is_csvgz() (in module schrodinger.rdkit.molio) is_curr_project_scratch (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) is_curr_project_scratchChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) is_curr_project_scratchReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) is_cyclic (schrodinger.protein.helm.helm_renderer.HelmConnector attribute) is_d_amino_acid (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_daemon_enabled() (in module schrodinger.seam.viz.watcherd) is_debugging() (in module schrodinger.application.desmond.stage.workflow) is_default (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec attribute) (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) is_defaultChanged (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) is_defaultReplaced (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) is_deoxyribose() (in module schrodinger.livedesign.biologics.registration) is_desmond_product_installed() (in module schrodinger.trajectory.utils) is_deterministic() (schrodinger.seam.coders.MolCoder method) (schrodinger.seam.coders.RouteNodeCoder method) (schrodinger.seam.coders.StructureCoder method) is_dilute() (in module schrodinger.comparison.struc) is_display_present() (in module schrodinger.utils.sysinfo) is_display_snapshot_active (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel property) is_disulfide_bridge (schrodinger.protein.helm.helm_renderer.HelmConnector property) is_dockable() (in module schrodinger.ui.qt.widgetmixins.basicmixins) is_docked() (in module schrodinger.ui.qt.widgetmixins.basicmixins) is_docking_keyword() (in module schrodinger.application.glide.glide) is_downloadable_job_server_job() (in module schrodinger.application.matsci.jobutils) is_downloaded (schrodinger.application.job_monitor.job_monitor_models.JobModel property) is_dpd() (in module schrodinger.application.matsci.cgforcefield) is_dummy_atom() (in module schrodinger.application.matsci.msutils) is_dummy_structure() (in module schrodinger.application.desmond.util) is_editable() (schrodinger.protein.nonstandard_residues.AminoAcid method) is_enabled() (in module schrodinger.seam.debug) is_epv_file() (in module schrodinger.utils.fileutils) is_equal() (in module schrodinger.utils.sea.common) is_equal_formula() (in module schrodinger.application.matsci.msutils) is_equivalent_to_mininplace() (in module schrodinger.application.glide.glide) is_excluded_amino_acid() (in module schrodinger.protein.nonstandard_residues) is_expired() (schrodinger.application.licensing.flexlm.LicenseLine method) is_false() (in module schrodinger.application.glide.glide) is_feature_label_checked() (in module schrodinger.application.phase.phase_markers) is_file_not_found_exception() (in module schrodinger.job.launchapi) is_file_property() (in module schrodinger.application.matsci.permittivity) is_find_toolbar_visible() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) is_finite_scalar() (in module schrodinger.application.jaguar.qrnn.temp_opt) is_fit_to_structure() (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) is_float_valid() (in module schrodinger.ui.qt.formlayout) is_for_gcmc (schrodinger.application.desmond.cms.Cms property) is_for_jc (schrodinger.application.desmond.cmj.Job property) is_force_field_encrypted() (in module schrodinger.application.matsci.cgforcefield) is_from_atom() (schrodinger.application.canvas.r_group.TempAtom method) is_fully_rel (schrodinger.application.matsci.espresso.utils.PseudoData attribute) is_future_license_error() (in module schrodinger.application.licensing.licadmin) is_gap (schrodinger.protein.residue.Gap attribute) (schrodinger.protein.residue.Residue attribute) is_gcmc() (in module schrodinger.application.desmond.config_utils) is_gcp_service_available() (in module schrodinger.application.steps.env_keys) is_good() (schrodinger.application.desmond.cmj.JobStatus method) is_graph_file_path() (in module schrodinger.application.desmond.file_utils) is_grid_good_for_ligand() (in module schrodinger.application.glide.utils) is_gridgen_job() (in module schrodinger.application.glide.glide) is_gridgen_keyword() (in module schrodinger.application.glide.glide) is_gzipped_structure_file() (in module schrodinger.utils.fileutils) is_halogen (schrodinger.structure.StructureAtom property) is_haptic() (in module schrodinger.application.matsci.etatoggle) is_harmonic_angle() (in module schrodinger.application.matsci.coarsegrain) is_hexagonal() (in module schrodinger.application.matsci.pbcutils) is_homo (schrodinger.application.jaguar.input.OrbSpec attribute) is_host_platform_compatible() (in module schrodinger.utils.platform) is_hostname_known() (in module schrodinger.job.jobcontrol) is_hostname_valid() (in module schrodinger.active_learning.al_utils) is_hypothesis_entry() (in module schrodinger.application.phase.pt_hypothesis) is_hypothesis_file() (in module schrodinger.utils.fileutils) is_imgt_ins_code() (in module schrodinger.application.bioluminate.anarci.loop_ranges) is_incomplete (schrodinger.application.desmond.cmj.Job property) is_independent() (schrodinger.application.matsci.elasticity.strain.Deformation method) is_infinite() (in module schrodinger.application.matsci.desmondutils) (in module schrodinger.application.matsci.nano.xtal) is_infinite2() (in module schrodinger.application.matsci.nano.xtal) is_inter_sequence (schrodinger.protein.residue.CombinedChainDisulfideBond property) (schrodinger.protein.residue.DisulfideBond property) is_intra_sequence (schrodinger.protein.residue.CombinedChainDisulfideBond property) (schrodinger.protein.residue.DisulfideBond property) is_ipv4_addr() (in module schrodinger.utils.net) is_iterable() (in module schrodinger.application.matsci.msutils) is_jag_license_needed() (in module schrodinger.application.matsci.jaguarworkflows) is_jaguar_file_property() (in module schrodinger.application.matsci.jaguarworkflows) is_job_server_job() (in module schrodinger.application.matsci.jobutils) is_jobhost_gpu_available() (in module schrodinger.application.matsci.jobutils) is_jobtask() (in module schrodinger.tasks.jobtasks) is_kinase_annotated (schrodinger.protein.sequence.NucleicAcidSequence property) (schrodinger.protein.sequence.ProteinSequence property) is_kinase_cons_annotated (schrodinger.protein.sequence.NucleicAcidSequence property) (schrodinger.protein.sequence.ProteinSequence property) is_lambda_dynamics() (in module schrodinger.application.desmond.config_utils) is_launchable (schrodinger.application.desmond.cmj.Job property) is_lennard_jones() (in module schrodinger.application.matsci.coarsegrain) is_library() (schrodinger.application.licensing.flexlm.License method) is_license_available() (in module schrodinger.utils.license) is_ligand() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) is_like_lennard_jones() (in module schrodinger.application.matsci.cgforcefield) is_list_file() (in module schrodinger.application.phase.packages.shape_screen_job_utils) is_local_server() (schrodinger.application.licensing.licadmin.LicenseResource method) is_local_topic() (in module schrodinger.utils.documentation) is_localhost_platform_compatible() (in module schrodinger.utils.platform) is_mae_or_sd() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) is_maestro_file() (in module schrodinger.utils.fileutils) is_mark_monomer_grow_atom() (in module schrodinger.application.matsci.rxn_channel) is_martini_antifreeze_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_charge_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_ring_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_tiny_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_useries() (in module schrodinger.application.matsci.coarsegrain) is_matsci() (in module schrodinger.utils.license) is_matsci_engine_db() (in module schrodinger.application.matsci.kmc) is_meta() (in module schrodinger.application.desmond.config_utils) is_metal() (in module schrodinger.application.prime.primefix) is_minimize() (in module schrodinger.application.desmond.config_utils) is_missing_module() (in module schrodinger.application.matsci.codeutils) is_mmct_property_name() (in module schrodinger.application.glide.sort_utils) is_model2_server_available() (in module schrodinger.application.desmond.license) is_mopac_file() (in module schrodinger.application.mopac.utils) is_new_result() (schrodinger.comparison.results.ResultSet method) is_no_table_error() (in module schrodinger.application.matsci.kmc) is_nodelocked() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Server method) is_normal_surface() (in module schrodinger.application.matsci.nano.xtal) is_nucleotide_backbone (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_nucleotide_phosphate (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_nucleotide_sugar (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_null() (in module schrodinger.application.pathfinder.synthesis) is_null_job (schrodinger.application.job_monitor.job_monitor_models.JobModel property) is_numeric() (in module schrodinger.application.phase.packages.phase_utils) is_ok() (schrodinger.utils.sea.evalor.Evalor method) is_oned_data_file() (in module schrodinger.application.phase.packages.oned_task_utils) is_open() (schrodinger.application.licensing.flexlm.License method) is_opls2_available() (in module schrodinger.utils.license) is_opls5_not_matsci_allowed() (in module schrodinger.application.matsci.parserutils) is_outlier (schrodinger.ui.qt.rama.BackboneDihedral attribute) is_oxidation_prone() (in module schrodinger.application.bioluminate.methionine_oxidation) is_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) is_pbc_enabled() (in module schrodinger.application.xtb.utilities) is_pdb_file() (in module schrodinger.utils.fileutils) is_permanent() (schrodinger.application.licensing.flexlm.Feature method) is_permanent_counted() (schrodinger.application.licensing.flexlm.License method) is_permanent_library() (schrodinger.application.licensing.flexlm.License method) is_permanent_nodelocked() (schrodinger.application.licensing.flexlm.License method) is_pfx() (in module schrodinger.rdkit.molio) is_phase_database_path() (in module schrodinger.application.phase.packages.phase_utils) is_phase_project_path() (in module schrodinger.application.phase.packages.phase_utils) is_phdb_path() (in module schrodinger.application.hitexpander) is_polymer() (in module schrodinger.livedesign.preprocessor) is_polymer_builder_grow_atom() (in module schrodinger.application.matsci.rxn_channel) is_poseviewer_file() (in module schrodinger.utils.fileutils) is_positive (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) is_positive_int() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) is_positive_numeric() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) is_powerof2() (in module schrodinger.utils.sea.evalor) is_prepped() (in module schrodinger.application.desmond.feputils) is_projected (schrodinger.application.phase.phase_markers.PhaseFeatureMarker property) is_property_label_checked() (in module schrodinger.application.phase.phase_markers) is_pv_file() (in module schrodinger.application.glide.poseviewconvert) is_python_file() (in module schrodinger.application.matsci.codeutils) is_python_pre311() (in module schrodinger.application.matsci.codeutils) is_queryatom_exception() (in module schrodinger.livedesign.preprocessor) is_reagent_file() (in module schrodinger.application.pathfinder.reaction) is_reagent_filename() (in module schrodinger.application.pathfinder.reaction) is_receptor() (in module schrodinger.application.glide.utils) is_rectangular (schrodinger.protein.alignment.BaseAlignment property) is_reinit() (in module schrodinger.application.desmond.config_utils) is_remd() (in module schrodinger.application.desmond.config_utils) is_repulsive_harmonic() (in module schrodinger.application.matsci.coarsegrain) is_required_valid() (in module schrodinger.ui.qt.formlayout) is_res (schrodinger.protein.residue.AbstractSequenceElement property) is_restartable (schrodinger.application.desmond.cmj.Job property) is_restartable_build() (in module schrodinger.application.desmond.cmj) is_restartable_version() (in module schrodinger.application.desmond.cmj) is_retriable (schrodinger.application.desmond.cmj.Job property) is_retriable() (schrodinger.application.desmond.cmj.JobStatus method) is_ring_atom() (in module schrodinger.application.desmond.r_group_asl) is_rotabond() (in module schrodinger.application.desmond.r_group_asl) is_rotation() (schrodinger.application.matsci.elasticity.tensors.SquareTensor method) is_same_day() (in module schrodinger.application.job_monitor.util) is_same_user_connected() (in module schrodinger.application.livedesign.ld_maestro_actions) is_sd_dataname() (in module schrodinger.application.livedesign.ld_utils) is_sd_file() (in module schrodinger.utils.fileutils) is_sd_file_list() (in module schrodinger.application.glide.sort_utils) is_selected (schrodinger.project.project.ProjectRow property) is_server() (in module schrodinger.application.licensing.flexlm) (schrodinger.application.licensing.licadmin.LicenseResource method) is_shifted_lennard_jones() (in module schrodinger.application.matsci.coarsegrain) is_shown() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) is_shown_only() (schrodinger.application.desmond.maestro.NewEntryGroup method) is_signed() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) is_site_grouped() (in module schrodinger.application.phase.phase_markers) is_smarts_bonding_pair() (in module schrodinger.application.matsci.smartsutils) is_smiles_file() (in module schrodinger.utils.fileutils) is_soluble() (in module schrodinger.application.desmond.solubility_utils) is_special_residue() (in module schrodinger.application.bioluminate.antibody.annotate) is_spiro_junction() (in module schrodinger.application.jaguar.utils) is_standard (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_standard_ribose() (in module schrodinger.livedesign.biologics.registration) is_string() (in module schrodinger.ui.qt.formlayout) is_structure_soluble() (in module schrodinger.application.desmond.solubility_utils) is_stub() (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.licensing.licadmin.LicenseResource method) is_subdir() (in module schrodinger.application.desmond.util) is_subpath() (in module schrodinger.utils.fileutils) is_symmetric() (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) is_tcr_type() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) is_text_string() (in module schrodinger.ui.qt.formlayout) is_top_level_job (schrodinger.application.job_monitor.job_monitor_models.JobModel property) is_traj_gcmc() (in module schrodinger.application.matsci.desmondutils) is_transformation() (in module schrodinger.application.pathfinder.analysis) is_triclinic_box() (in module schrodinger.application.desmond.config_utils) is_trigonometric_angle() (in module schrodinger.application.matsci.coarsegrain) is_type_name_encrypted() (in module schrodinger.application.matsci.cgforcefield) is_unit_mx() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method) is_unreachable_hostname() (in module schrodinger.application.licensing.licadmin) is_user_template (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) is_valid() (schrodinger.application.desmond.cmj.AslValidator method) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) is_valid_epv_file() (in module schrodinger.application.glide.utils) is_valid_groupname() (in module schrodinger.application.desmond.gui) is_valid_hostname() (in module schrodinger.job.jobcontrol) is_valid_jobname() (in module schrodinger.utils.fileutils) is_valid_lower_triangle() (in module schrodinger.application.matsci.nano.xtal) is_valid_opls_name() (in module schrodinger.application.desmond.stage.prepare.forcefield) is_valid_property_name() (in module schrodinger.application.matsci.msprops) is_valid_pv_file() (in module schrodinger.application.glide.utils) is_valid_rdkit_property_name() (in module schrodinger.application.transforms.validators) is_valid_str() (in module schrodinger.application.jaguar.jaguar_diff) is_varying_atoms_trajectory_loaded() (in module schrodinger.trajectory.trajectoryviewer) is_voigt_symmetric() (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) is_votca_prop() (in module schrodinger.application.matsci.kmc) is_vrun() (in module schrodinger.application.desmond.config_utils) is_water() (in module schrodinger.application.desmond.remd) is_wildcard() (in module schrodinger.livedesign.preprocessor) is_within_directory() (in module schrodinger.utils.fileutils) is_workspace_non_empty() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) is_xsignal() (in module schrodinger.ui.qt.xsignals) is_zero() (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) is_zipped_graph_file_path() (in module schrodinger.application.desmond.file_utils) isAbstract() (schrodinger.models.parameters.Param class method) isAcceptableEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) isAccepted() (schrodinger.application.matsci.montecarlo.Metropolizer method) isActive() (schrodinger.ui.qt.navtoolbar.AtomInfoToolbar method) isActivelyScrolling() (schrodinger.ui.qt.structtable.ViewerTable method) (schrodinger.ui.qt.table.DataViewerTable method) isAlive() (schrodinger.application.pymol.pymol4maestro.panel method) isAllAtomPolymer() (schrodinger.application.matsci.amorphous.PolymerFragments method) isAlreadyMatched() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) isAntibodyChain() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.NucleicAcidSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) isAntibodyHeavyChain() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) isAntibodyLightChain() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) isAnyTextLabelVisible() (schrodinger.application.phase.phase_markers.PhaseMarkers method) isApplyTimeBasedGradient() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) isAromatic() (schrodinger.structure._Ring method) isAtomAromatic() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomBetweenTwoRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomBoundToAromaticRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomInRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomInSmallRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomMember() (schrodinger.application.matsci.species.SpeciesData method) isBackboneAtom() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin static method) (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) isBackboneSidechain() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) isBackendMode() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.tasks.AbstractComboTask method) isBandshapeTable() (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile static method) isBondRingEdge() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isBrancher() (schrodinger.application.matsci.amorphous.Monomer method) isCanceled() (schrodinger.stepper.stepper.StepJobTask method) isCgPolymer() (schrodinger.application.matsci.amorphous.PolymerFragments method) isChecked() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) isColumnFixed() (schrodinger.project.project.Project method) isColumnGanged() (schrodinger.ui.qt.table.DataViewerTable method) IsCompatible() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) isComplete() (schrodinger.application.glide.http_client.SubprocessJobAdapter method) (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobDJ method) isConformationalSearchesChecked() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) isConnected() (schrodinger.ui.qt.network_visualizer.Graph method) isConnectedToResidue() (schrodinger.structure.Residue method) isCPUHost() (schrodinger.ui.qt.config_dialog.ConfigDialog method) isCurrentMaestroProject() (schrodinger.project.project.Project method) isCustomMaestroAssay() (schrodinger.application.livedesign.panel_components.ExportTableModel method) isDatabaseSource() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) isDebugEnabled() (schrodinger.tasks.tasks.AbstractTask method) isDefault() (schrodinger.application.prepwizard2.tasks.PreprocessInput method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.seam.options.pipeline_options.SeamOptions method) isDefined() (schrodinger.protein.membrane.Membrane_Model method) isDirty() (schrodinger.ui.qt.datamapper.TrackingDataWidgetMapper method) isdisjoint() (schrodinger.utils.scollections.IdSet method) isDisplayOnlyCurrentDisplayedAtoms() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) isDistance() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) isDockableInMaestro() (schrodinger.ui.qt.appframework.AppFramework method) isDownloaded() (schrodinger.job.jobcontrol.Job method) isEditEnabled() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) isEnabled() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) isEnergy() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) isENotationProperty() (schrodinger.project.project.Project method) isEOF() (schrodinger.infra.structure.PyStructureReaderException method) isEquivalent() (schrodinger.application.jaguar.utils.GenOptions method) (schrodinger.structure.Structure method) isEquivalentInput() (schrodinger.application.jaguar.input.JaguarInput method) isFamily() (schrodinger.structure.PropertyName method) isFastMode() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) isFileValid() (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) isFilled() (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) isForward() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) isFullRange() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) isGenericEntity() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel method) isGoodDim() (schrodinger.application.matsci.espresso.utils.MemoryEstimator method) isGPUHost() (schrodinger.ui.qt.config_dialog.ConfigDialog method) isGroupShown() (schrodinger.graphics3d.common.Primitive method) isHeavyChain() (schrodinger.protein.annotation.SeqTypeMixin method) isHeteroaromatic() (schrodinger.structure._Ring method) isHidden() (schrodinger.ui.qt.tablewidget.Column method) (schrodinger.ui.qt.tablewidget.Row method) isIncluded() (schrodinger.ui.two_d_viewer.Cell method) isIndexEnabled() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) isIndexSelected() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) isInDisplayedChain() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) isInfiniteModel() (schrodinger.application.desmond.gui.InputGroup method) isInGuessMode() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) isInside() (schrodinger.application.matsci.nano.particle.Nanoparticle method) IsInteger (class in schrodinger.ui.qt.appframework2.validators) isInterruptionRequested() (schrodinger.tasks.tasks.AbstractTask method) isIntraChainInteractions() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput method) isInvalid() (schrodinger.ui.qt.swidgets.SMARTSEdit method) isItemChecked() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) isItemEnabled() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) isItemHidden() (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListPopUp method) (schrodinger.ui.qt.filter_list.FilterListPopUp method) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp method) isIterable() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis static method) isKeepSideChainAtom() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin static method) isKetoneCarbon() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isKeyConsistentWithPanel() (schrodinger.application.desmond.gui.GuiApp method) isKinaseChain() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.protein.sequence.NucleicAcidSequence method) (schrodinger.protein.sequence.ProteinSequence method) isLadder() (schrodinger.application.matsci.amorphous.Monomer method) isLeaf() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) isLightChain() (schrodinger.protein.annotation.SeqTypeMixin method) isLogAxis() (schrodinger.ui.qt.schart.SChart static method) isLst() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) isMacroPka() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) isMember() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) isMetal() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) isMethod() (schrodinger.application.matsci.msconst.SMARTS_METHOD method) isNewGenericEntity() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel method) isNil() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) isNonDefault() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword method) (schrodinger.application.xtb.input.XTBInput method) iso (schrodinger.application.matsci.espresso.qeoutput.MagresAtom property) isoelectric_point (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) isoelectric_point_window_padding (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) isoelectronic_mutator() (in module schrodinger.application.matsci.genetic_optimization) ISOLATE_PRODUCTS (schrodinger.application.matsci.rxn_channel.Constants attribute) isolateProducts() (schrodinger.application.matsci.rxn_channel.Products method) IsomerError isomeric_atom_sets() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) isOnlySingleBonded() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isotope (schrodinger.application.jaguar.simple_spec.Peak attribute) (schrodinger.structure.StructureAtom property) IsotopeData (class in schrodinger.application.jaguar.nmr_utils) isotopes (schrodinger.application.jaguar.nmr_utils.NMRData attribute) isotopes_are_conserved() (in module schrodinger.application.jaguar.autots_validation) ISOTROPIC (schrodinger.application.desmond.constants.IsotropyPolicy attribute) (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) ISOTROPIC_3D (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) ISOTROPIC_POLARIZABILITY_KEY (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) ISOTROPY (schrodinger.application.matsci.desconfig.MSJStringer attribute) IsotropyPolicy (class in schrodinger.application.desmond.constants) isovalue (schrodinger.surface.Surface property) isOverlapAllowedInMatch() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) isPlaceholderItemSelected() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) isPointInBox() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isPointInHull() (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isPopulated() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) isProteinStructure() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) isQueue() (schrodinger.job.jobcontrol.Host method) isQueued() (schrodinger.job.jobcontrol.Job method) isRangeModifiedByUser() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) isRangePka() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) isRangeToken() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) isReady() (schrodinger.application.glide.http_client.AbstractGlideServerManager method) isReferenceSeq() (schrodinger.protein.alignment.BaseAlignment method) isRingAromatic() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isRingBond() (schrodinger.application.steps.enumerators.FastFragmenter method) isRingEligible() (schrodinger.application.matsci.automated_cg_mapping.DpdMolecule method) (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule method) (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) isRowGanged() (schrodinger.ui.qt.table.DataViewerTable method) isRowSelected() (schrodinger.infra.table.Table method) isRunning() (schrodinger.active_learning.mq_worker.LigandMLBackend method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressBar method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) isScoreImproved() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) isScriptProperty() (schrodinger.application.matsci.genetic_optimization.Property method) isScrolling() (schrodinger.ui.qt.structtable.ViewerTable method) (schrodinger.ui.qt.table.DataViewerTable method) isSelected() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) (schrodinger.ui.dendrogram.DendrogramGraphicTree method) (schrodinger.ui.qt.tablewidget.Cell method) (schrodinger.ui.qt.tablewidget.Row method) isSeparator() (schrodinger.ui.qt.recent_completer.SeparatorStringModel method) isSharedNode() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) isShiftPressed() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) isShown() (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.gridbox.GridBox method) isSideChainAtom() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) isSohnckeGroup() (schrodinger.application.matsci.nano.space_groups.SpaceGroup method) isSolventModelUsed() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) isStandardResidue() (schrodinger.structure.Residue method) isStartable() (schrodinger.tasks.taskmanager.TaskManager method) (schrodinger.tasks.tasks.AbstractTask method) isStartingMaterial() (schrodinger.application.pathfinder.route.RouteNode method) isStoppable() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) isStreamingRunning() (schrodinger.application.job_monitor.job_monitor_file_browser.SubprocessStdOutStreamer method) isStructure() (schrodinger.ui.qt.table.StructureDataViewerDelegate method) issubset() (schrodinger.utils.scollections.IdSet method) issued_str() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) issuperset() (schrodinger.utils.scollections.IdSet method) ist_product_table() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) isTabVisibleByLabel() (schrodinger.ui.qt.swidgets.STabWidget method) isUseConsistentOrbitalsChecked() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals method) isUseCustomizedVersionChecked() (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin method) isValid() (schrodinger.application.glide.glide.Grid method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.rdpattern_gui.SMARTSFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor method) (schrodinger.application.matsci.reaction_workflow_gui_utils.WorkspaceSuperpositionFrame method) (schrodinger.protein.residue.DisulfideBond method) (schrodinger.protein.sequence.AbstractSingleChainSequence class method) (schrodinger.protein.sequence.ProteinSequence class method) (schrodinger.ui.qt.swidgets.SMARTSEdit method) (schrodinger.utils.license.License method) isValidASL() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) isValidAtomIndex() (schrodinger.application.matsci.reordergui.StructureFrame method) isValidEnd() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) isValidFrameRange() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) isValidPoint() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isValidStart() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) isValidStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) isValueAxis() (schrodinger.ui.qt.schart.SChart static method) isVisible() (schrodinger.application.matsci.chargegui.ChargePropertySelector method) (schrodinger.ui.qt.dendrogram.Dendrogram method) isWorkspaceResolution() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) isZwitterionChecked() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) ITALIC (schrodinger.application.phase.phase_markers.FontStyles attribute) ItalicsPlaceholderComboBox (class in schrodinger.ui.qt.standard_widgets.combo_boxes) item() (schrodinger.ui.qt.tablewidget.Cell method) ITEM_KEY (schrodinger.ui.qt.swidgets.SavedSMARTSManager attribute) item_type (schrodinger.application.matsci.builderwidgets.TemplateFamily attribute) ITEM_TYPE_TEXT (schrodinger.application.matsci.mswidgets.MSAtomSelector attribute) (schrodinger.ui.qt.swidgets.ItemsManagerMixin attribute) (schrodinger.ui.qt.swidgets.SavedItemsManager attribute) (schrodinger.ui.qt.swidgets.SavedSMARTSManager attribute) ItemChanged (schrodinger.models.parameters.SignalType attribute) ItemClassMixin (class in schrodinger.models.parameters) itemClicked (schrodinger.application.matsci.mswidgets.SavedASLItem attribute) (schrodinger.ui.qt.atomselector.ASLItem attribute) (schrodinger.ui.qt.swidgets.SavedMenuItem attribute) (schrodinger.ui.qt.swidgets.StdMenuItem attribute) itemClicked() (schrodinger.ui.qt.swidgets.SavedItemsManager method) ItemRow (class in schrodinger.application.matsci.builderwidgets) ItemRowWithTemplates (class in schrodinger.application.matsci.builderwidgets) items() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.swidgets.SComboBox method) (schrodinger.utils.scollections.IdDict method) itemSelected (schrodinger.application.livedesign.panel_components.LDSelectionTreeView attribute) (schrodinger.ui.qt.swidgets.ActionComboBox attribute) itemSelected() (schrodinger.application.matsci.reordergui.StructureListWidget method) ItemsManagerMixin (class in schrodinger.ui.qt.swidgets) Iter (class in schrodinger.application.desmond.enhsamp) iter() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) iter_fingerprints() (schrodinger.utils.multifpfile.MultiFPFile method) ITERABLE_ARG_METHOD_NAMES (schrodinger.models.parameters.BaseMutableParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.SetParam attribute) iterate_minimize_structure() (in module schrodinger.forcefield.minimizer) iterate_to_convergence() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) iterateNeighboringAtoms() (schrodinger.structutils.measure.DistanceCellIterator method) iterateOverSelectedCells() (schrodinger.ui.two_d_viewer.TwoDViewer method) iterateOverSelectedIs() (schrodinger.ui.two_d_viewer.TwoDViewer method) iterateResidues() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) Iteration (class in schrodinger.seam.examples.active_learning_weigher) IterationError iterAtomCollections() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) (schrodinger.application.matsci.species.ResidueSpeciesFinder method) iterInputs() (schrodinger.pipeline.stage.Stage method) iteritems() (schrodinger.utils.cgxutils.FragmentLibrary method) ITERMAX (schrodinger.application.matsci.espresso.qeinput.TurboEelsType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboLanczosType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) ITERMAX0 (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) iterNeighbors() (schrodinger.protein.sequence.AbstractSequence method) iterpose() (schrodinger.trajectory.prody.ensemble.Ensemble method) IUHF (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) iupac_to_smiles() (in module schrodinger.protein.process_enamine_db) ix (schrodinger.comparison.neighbors.MoleculeNeighbor attribute) iy (schrodinger.comparison.neighbors.MoleculeNeighbor attribute) iz (schrodinger.comparison.neighbors.MoleculeNeighbor attribute)

J

J (schrodinger.application.bioluminate.update_germline_db.translate_db.Gene attribute) (schrodinger.application.jaguar.simple_spec.Peak attribute) JAG_GEOPT (schrodinger.infra.structure.WorkflowType attribute) JAG_MACRO_PKA_RESULTS (schrodinger.infra.structure.WorkflowType attribute) JAG_SCAN (schrodinger.infra.structure.WorkflowType attribute) JAG_SPECTRUM_PLOT (schrodinger.infra.structure.WorkflowType attribute) jagInputEdited() (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) (schrodinger.application.jaguar.gui.timing.TimerMixin method) Jaguar (class in schrodinger.application.matsci.genetic_optimization) (class in schrodinger.application.matsci.reaction_workflow_gui_utils) jaguar_atoms() (in module schrodinger.application.qsite.output) jaguar_input_keywords() (in module schrodinger.application.jaguar.jaguar_keyword_utils) jaguar_key (schrodinger.application.matsci.reaction_workflow_utils.JaguarKeyStructPropData attribute) jaguar_keywords_xml_filename() (in module schrodinger.application.jaguar.jaguar_keyword_utils) JAGUAR_MERGE (schrodinger.application.matsci.permittivity.JaguarMerge attribute) JAGUAR_OPTIONS (schrodinger.application.matsci.genetic_optimization.Jaguar attribute) JAGUAR_OUTPUT_ATTR (schrodinger.application.matsci.genetic_optimization.Jaguar attribute) JaguarAtomicResults (class in schrodinger.application.jaguar.results) JaguarCalculation (class in schrodinger.application.matsci.permittivity) JaguarCmdJobTask (class in schrodinger.application.jaguar.jaguar_tasks) JaguarCmdJobTask.JobConfig (class in schrodinger.application.jaguar.jaguar_tasks) JaguarConfigDialog (class in schrodinger.application.jaguar.gui.base_panel) (class in schrodinger.application.jaguar.jaguar_config_dialog) JaguarConfigError JaguarError JaguarFailedException JaguarFinerCalculation (class in schrodinger.application.matsci.permittivity) JaguarGeomNotConverged JaguarHostSelector (class in schrodinger.application.jaguar.jaguar_config_dialog) JaguarHostSettings (class in schrodinger.application.jaguar.jaguar_tasks) JaguarInput (class in schrodinger.application.jaguar.input) JaguarInvalidKeyword JaguarIOError JaguarJob (class in schrodinger.application.matsci.mecp_mod) JaguarJobs (class in schrodinger.application.matsci.mecp_mod) JaguarKeyStructPropData (class in schrodinger.application.matsci.reaction_workflow_utils) JaguarKeywordConflict JaguarKeywordError JaguarKeywordException JaguarKeywordFormatError JaguarKeywordValueError JaguarKeywordValueTypeError JaguarMerge (class in schrodinger.application.matsci.permittivity) JaguarOptions (class in schrodinger.application.jaguar.results) JaguarOptionsDialog (class in schrodinger.application.matsci.jagwidgets) JaguarOutput (class in schrodinger.application.jaguar.output) JaguarOutputNotFound JaguarOutputUnreadable JaguarParseError JaguarResults (class in schrodinger.application.jaguar.results) JaguarRuntimeError JaguarSCFNotConverged JaguarSettingError JaguarSettingWarning JaguarStep (class in schrodinger.application.matsci.jwsteps) JaguarStuckGeometry JaguarUnsupportedBasisSet JaguarUserFacingException jar (schrodinger.application.desmond.picklejar.PickleJar attribute) jbw() (schrodinger.application.macromodel.utils.ComUtil method) jbw_sd() (schrodinger.application.macromodel.utils.ComUtil method) JEFF2_12E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JEFF2_12H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JEFF2_21E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JEFF2_21H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JEFF2E (schrodinger.application.matsci.kmc.PairsTable attribute) JEFF2H (schrodinger.application.matsci.kmc.PairsTable attribute) jin_to_mae() (in module schrodinger.application.jaguar.jagconvert) JMSStep (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) JMSWFConformerSelection (class in schrodinger.application.matsci.reaction_workflow_utils) JMSWFException JMSWFMixin (class in schrodinger.application.matsci.reaction_workflow_utils) JMSWorkFlow (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) jnames (schrodinger.application.jaguar.nmr_utils.NMRData attribute) Job (class in schrodinger.application.desmond.cmj) (class in schrodinger.application.matsci.qubec_utils) (class in schrodinger.job.jobcontrol) job (schrodinger.application.vss.tasks.JobAndOutcomes attribute) Job.Time (class in schrodinger.application.desmond.cmj) JOB_BASE (schrodinger.application.matsci.jwsteps.BaseRelaxationStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.CompressiveRelaxationStep attribute) (schrodinger.application.matsci.jwsteps.CustomCmsStep attribute) (schrodinger.application.matsci.jwsteps.CustomCmsToMaeStep attribute) (schrodinger.application.matsci.jwsteps.CustomMaeStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.FreeVolumeStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.MatSciMDRelaxationStep attribute) (schrodinger.application.matsci.jwsteps.MDCustomMSJStep attribute) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation1Step attribute) (schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation2Step attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.SingleBrownieStep attribute) (schrodinger.application.matsci.jwsteps.SingleMDStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) (schrodinger.application.matsci.jwsteps.VoidStep attribute) job_belongs_to_panel() (in module schrodinger.ui.qt.appframework2.jobs) job_capacity() (in module schrodinger.application.licensing.licadmin) job_capacity_by_product() (in module schrodinger.application.licensing.licadmin) JOB_CLASS (schrodinger.application.matsci.crest.Crest attribute) (schrodinger.application.matsci.crest.CrestCSearch attribute) job_config (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) job_config_factory() (in module schrodinger.tasks.jobtasks) job_configChanged (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) job_configReplaced (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute)

JOB_CONTROL_LOCALHOST (schrodinger.tasks.ldtasks.ExecutionMode attribute) JOB_CONTROL_USER_HOST (schrodinger.tasks.ldtasks.ExecutionMode attribute) Job_Details (class in schrodinger.application.desmond.simulation_block_test) job_id (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_idChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_idReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_ids (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsModel attribute) job_idsChanged (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsModel attribute) job_idsReplaced (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsModel attribute) job_incorporated() (in module schrodinger.job.jobhandler) job_index (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_indexChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_indexReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_name (schrodinger.application.bioluminate.antibody.grafting.GraftingInput attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) JOB_NAME (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) job_nameChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_nameReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_product_names() (in module schrodinger.application.licensing.licadmin) job_started (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_startedChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) job_startedReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) JobAdapter (class in schrodinger.application.desmond.queue) JobAndOutcomes (class in schrodinger.application.vss.tasks) JobApp (class in schrodinger.ui.qt.appframework2.af2) JobAppSuper (in module schrodinger.ui.qt.appframework2.af2) JobBackendCmdMixin (class in schrodinger.tasks.jobtasks) JobBar (class in schrodinger.application.job_monitor.job_monitor_widgets) JOBBE (schrodinger.application.desmond.cmj.Engine attribute) JobBottomBar (class in schrodinger.ui.qt.appframework2.af2) jobCompleted (schrodinger.ui.qt.appframework.AppFramework attribute) (schrodinger.ui.qt.appframework2.af2.JobApp attribute) JobConfig (class in schrodinger.tasks.jobtasks) JobcontrolException JobControlJob (class in schrodinger.job.queue) JobCreationError JobDB (schrodinger.job.jobcontrol.Job property) JobDetailsArrowDelegate (class in schrodinger.application.job_monitor.job_monitor_table) JobDetailsPane (class in schrodinger.application.job_monitor.job_monitor_widgets) JobDir (schrodinger.job.jobcontrol.Job property) jobDir() (schrodinger.ui.qt.appframework2.af2.JobApp method) JobDJ (class in schrodinger.job.queue) JobDJOptions() (schrodinger.pipeline.stage.Stage method) JobErrorHandler (class in schrodinger.application.desmond.cmj) JobFailure JobHandler (class in schrodinger.job.jobhandler) JobHost (schrodinger.job.jobcontrol.Job property) JOBID (schrodinger.application.matsci.kmc.SchrodingerTable attribute) JobId (schrodinger.job.jobcontrol.Job property) jobid() (in module schrodinger.application.jaguar.textparser) JobinfoAndNodeMatched() (schrodinger.application.matsci.permittivity.WorkflowParser method) JobInfoWidget (class in schrodinger.application.job_monitor.job_monitor_widgets) JobInput (class in schrodinger.application.desmond.cmj) jobLaunchFailed (schrodinger.job.jobhandler.AsyncJobHandler attribute) JobLaunchFailure JobLaunchWaitCursorContext (class in schrodinger.ui.qt.utils) JobManager (class in schrodinger.application.desmond.cmj) (class in schrodinger.application.matsci.jobdirdlg) JobModel (class in schrodinger.application.job_monitor.job_monitor_models) JobMonitor (class in schrodinger.application.job_monitor.job_monitor_gui) JobMonitorFileBrowser (class in schrodinger.application.job_monitor.job_monitor_file_browser) JobMonitorPanelModel (class in schrodinger.application.job_monitor.job_monitor_models) JobMonitorType (class in schrodinger.ui.qt.tasks.taskbar2) JobName (class in schrodinger.ui.qt.appframework2.validators) jobname (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) (schrodinger.application.desmond.new_fep_edge_data.FepData property) (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) JOBNAME (schrodinger.application.matsci.desconfig.MSJStringer attribute) jobname (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.qsite.input.QSiteInput property) (schrodinger.tasks.jobtasks.JobConfig attribute) JOBNAME (schrodinger.utils.cmdline.Options attribute) jobname() (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) jobname_display() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) jobname_text_alignment() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) jobname_tooltip_display() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) jobnameArg() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) jobnameChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) jobnameData() (schrodinger.application.jaguar.gui.base_panel.AutomaticJobnameMixin method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.af2_template.SettingsInJobNamesTemplate method) jobnameDataChanged() (schrodinger.ui.qt.appframework2.af2.JobApp method) jobnameReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) JobnameType (class in schrodinger.ui.qt.appframework2.jobnames) JobnameWidget (class in schrodinger.ui.qt.tasks.configwidgets) JobOutput (class in schrodinger.application.desmond.cmj) (class in schrodinger.tasks.jobtasks) JobParameters (class in schrodinger.ui.qt.config_dialog) JobPreparedFiles (class in schrodinger.application.desmond.starter.generator.fep_residue_scanning) JobProgressDelegate (class in schrodinger.application.job_monitor.job_monitor_table) jobs (schrodinger.application.desmond.cmj.JobManager property) (schrodinger.application.desmond.cmj.StageBase property) jobs() (schrodinger.application.licensing.licadmin.LicenseResource method) JOBS_CPUS (schrodinger.application.jaguar.gui.timing.TimerInfoDialog attribute) JobSchrodinger (schrodinger.job.jobcontrol.Job property) jobsCount() (schrodinger.job.queue.RunningJobs method) JobsListPane (class in schrodinger.application.job_monitor.job_monitor_widgets) JobSpecification (class in schrodinger.job.launchapi) JobSpecificationArgsBuilder (class in schrodinger.job.launchapi) JobSpecificationBuilder (class in schrodinger.job.launchapi) JobSpecificationKeyError jobStarted (schrodinger.job.jobhandler.AsyncJobHandler attribute) JobState (class in schrodinger.job.queue) JobStatus (class in schrodinger.application.desmond.cmj) JobStatusButton (class in schrodinger.ui.qt.jobwidgets) JobTableDelegate (class in schrodinger.application.job_monitor.job_monitor_table) JobTableSpec (class in schrodinger.application.job_monitor.job_monitor_table) JobTableWidget (class in schrodinger.application.job_monitor.job_monitor_table) JobTaskBar (class in schrodinger.ui.qt.tasks.taskwidgets) JOBTYPE (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) jobUsesTPP() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) join_asls() (in module schrodinger.application.bioluminate.pml_menus) join_cont_lines() (in module schrodinger.application.licensing.licadmin) join_host_port() (in module schrodinger.utils.net) join_images() (in module schrodinger.ui.qt.utils) join_structure_files() (in module schrodinger.application.jaguar.output) joinBeads() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) joinerChanged() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) JoinFromFileStep (class in schrodinger.stepper.sideinputs) JoinStep (class in schrodinger.stepper.sideinputs) jout_to_jin() (in module schrodinger.application.jaguar.jagconvert) jout_to_mae() (in module schrodinger.application.jaguar.jagconvert) jout_to_multimae() (in module schrodinger.application.jaguar.jagconvert) jsc() (in module schrodinger.job.server) JSFilePathData (class in schrodinger.application.matsci.jobutils) JSON (schrodinger.seam.viz.watcher.ResponseType attribute) json_filename (schrodinger.tasks.tasks.AbstractComboTask property) json_out_filename (schrodinger.tasks.tasks.AbstractComboTask property) json_to_nmrdata() (in module schrodinger.application.jaguar.nmr_utils) JsonableBytes (class in schrodinger.models.jsonable) JsonableClass (schrodinger.models.jsonable.AbstractJsonSerializer attribute) (schrodinger.models.jsonable.BytesSerializer attribute) (schrodinger.models.jsonable.DateTimeSerializer attribute) (schrodinger.models.jsonable.MolSerializer attribute) (schrodinger.models.jsonable.SetSerializer attribute) (schrodinger.models.jsonable.StructureSerializer attribute) (schrodinger.models.jsonable.TupleSerializer attribute) JsonableClassMixin (class in schrodinger.models.json) JsonableEnum (class in schrodinger.models.jsonable) jsonableFromObject() (schrodinger.models.jsonable.AbstractJsonSerializer class method) (schrodinger.models.jsonable.BytesSerializer class method) (schrodinger.models.jsonable.DateTimeSerializer class method) (schrodinger.models.jsonable.MolSerializer class method) (schrodinger.models.jsonable.SetSerializer class method) (schrodinger.models.jsonable.StructureSerializer class method) (schrodinger.models.jsonable.TupleSerializer class method) JsonableHetStates (class in schrodinger.application.prepwizard) JsonableIntEnum (class in schrodinger.models.jsonable) JsonableNamedTuple (class in schrodinger.models.jsonable) JsonablePropertyName (class in schrodinger.application.livedesign.export_models) JsonableSet (class in schrodinger.models.jsonable) JsonableStructure (class in schrodinger.models.jsonable) JsonableTuple (class in schrodinger.models.jsonable) jsonData() (schrodinger.application.matsci.freevolume.JsonObject method) JSONEncodeError JSONFilterAdapter (class in schrodinger.rdkit.filtering) JsonObject (class in schrodinger.application.matsci.freevolume) JUMP_COLUMNS (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JUMPFILE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) JUMPS_12E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JUMPS_12H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JUMPS_21E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JUMPS_21H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) JUMPSUMMARY (schrodinger.application.matsci.kmc.SchrodingerTable attribute) JUSTIFY (schrodinger.ui.qt.swidgets.STableWidgetItem attribute)

K

k_reuss (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) K_STRETCH (schrodinger.application.jaguar.hess_guess.LindhConstants attribute) k_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) k_voigt (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) k_vrh (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) KAPPA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) kcal_prop_to_ev_prop() (in module schrodinger.application.matsci.msprops) KCAL_TO_JOUL (schrodinger.application.desmond.constants.Conversion attribute) KcalPerMol (schrodinger.application.jaguar.constants.Unit attribute) KEEP (schrodinger.application.desmond.constants.CUSTOM_CHARGE_MODE attribute) KEEP_ONLY_LARGEST_STRUCTURE (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) keep_top_n() (in module schrodinger.rdkit.filtering) KEEP_WEDGED (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute) KEKULE (schrodinger.livedesign.draw.AromaticBondDisplay attribute) Keq (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) KERSEQ_INTERVAL (schrodinger.application.desmond.kinetics.enhanced_sampling.MtdOption attribute) Key (class in schrodinger.utils.sea.sea) key (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) (schrodinger.application.desmond.arkdb.Datum property) (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) KEY (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) (schrodinger.application.matsci.genetic_optimization.DeepChem attribute) (schrodinger.application.matsci.genetic_optimization.GlassTransitionTemperature attribute) key (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) KEY (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) key_val_re (schrodinger.application.jaguar.utils.GenOptions attribute) key_value() (schrodinger.utils.sea.sea.Map method) keyChanged (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) KeyPairDict (class in schrodinger.application.matsci.parserutils) keyPressEvent() (schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets.PlotTitleLineEdit method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.debugwidgets.BaseTable method) (schrodinger.ui.qt.appframework2.debugwidgets.ExecWidget method) (schrodinger.ui.qt.filter_list.FilterListPopUp method) (schrodinger.ui.qt.swidgets.SComboBox method) (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.two_d_viewer.TwoDTableView method) (schrodinger.ui.two_d_viewer.TwoDViewer method) keyReplaced (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) KEYS (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.mecp_mod.JaguarJob attribute) keys() (schrodinger.infra.mmim.MMIMDict method) (schrodinger.infra.table.Table method) (schrodinger.structure._StructureAtomProperty method) (schrodinger.structure._StructureBondProperty method) (schrodinger.structure._StructureProperty method) (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.sea.sea.Map method) keyvalue (schrodinger.application.jaguar.gui.utils.Solvent attribute) Keyword (class in schrodinger.application.jaguar.keywordDB) keyword (schrodinger.application.glide.glide.MetalConstraint attribute) (schrodinger.application.glide.glide.MetCoordConstraint attribute) (schrodinger.application.glide.glide.NOEConstraint attribute) (schrodinger.application.glide.glide.PositionalConstraint attribute) keyword() (in module schrodinger.application.jaguar.autots_keywords) (in module schrodinger.application.jaguar.esol_keywords) (in module schrodinger.application.jaguar.hydrokinetic_keywords) (in module schrodinger.application.jaguar.macro_pka_keywords) (in module schrodinger.application.jaguar.qrnn.keywords) (in module schrodinger.application.jaguar.rotation_barriers_keywords) (in module schrodinger.application.jaguar.solvation_keywords) (in module schrodinger.application.xtb.keywords) keyword_coverage() (in module schrodinger.application.jaguar.jaguar_keyword_utils) KEYWORD_DEFAULTS (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) keyword_dict (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) keyword_dict_to_string() (in module schrodinger.application.matsci.msutils) keyword_dictChanged (schrodinger.application.livedesign.tasks.GlideTask.Output attribute)

keyword_dictReplaced (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) keyword_options_string() (schrodinger.application.jaguar.workflow_input.WorkflowInput class method) keyword_spec() (in module schrodinger.application.glide.glide) keyword_string_to_dict() (in module schrodinger.application.matsci.msutils) keyword_value_pair_is_valid() (in module schrodinger.application.jaguar.validation) keyword_value_pairs_are_valid() (in module schrodinger.application.jaguar.validation) KeywordEdit (class in schrodinger.application.matsci.jagwidgets) KeywordEnum (class in schrodinger.application.matsci.msutils) keywords (schrodinger.application.jaguar.workflow_input.WorkflowInput property) keywordsChanged (schrodinger.application.matsci.jagwidgets.SolventDialog attribute) kill() (schrodinger.active_learning.mq_worker.LigandMLBackend method) (schrodinger.application.glide.http_client.SubprocessJobAdapter method) (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.tasks.tasks.SubprocessMixin method) (schrodinger.tasks.tasks.ThreadMixin method) kill_for_smart_distribution() (schrodinger.job.jobcontrol.Job method) KILL_NOW (schrodinger.application.desmond.kinetics.utils.MtdInfo attribute) kill_process() (in module schrodinger.utils.subprocess) KillableProgressDialog (class in schrodinger.ui.qt.tasks.taskwidgets) KILLED (schrodinger.application.desmond.cmj.JobStatus attribute) (schrodinger.application.matsci.mswidgets.ProcessBusyDialog attribute) killJobs() (schrodinger.job.queue.JobDJ method) KilometersPerMol (schrodinger.application.jaguar.constants.Unit attribute) kinase_conservation (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) kinase_features (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) KinaseConservation (class in schrodinger.protein.annotation) kinaseConservationChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractProteinSequenceMixin attribute) KinaseConservationTask (class in schrodinger.protein.tasks.kinase) KinaseConservationTask.Input (class in schrodinger.protein.tasks.kinase) KinaseFeatureAndConservationTask (class in schrodinger.protein.tasks.kinase) KinaseFeatureAndConservationTask.Input (class in schrodinger.protein.tasks.kinase) KinaseFeatureLabel (class in schrodinger.protein.annotation) kinaseFeaturesChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractProteinSequenceMixin attribute) KinaseFeatureTask (class in schrodinger.protein.tasks.kinase) KinaseFeatureTask.Input (class in schrodinger.protein.tasks.kinase) KinaseFeatureTask.Output (class in schrodinger.protein.tasks.kinase) KINETIC_ENERGY (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) KINETIC_TENSOR (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) kinetics_table() (in module schrodinger.application.jaguar.kinetics) KineticsLegTypes (class in schrodinger.application.desmond.constants) KJPerMol (schrodinger.application.jaguar.constants.Unit attribute) KLAMT_PCM_RADII (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) KnimeMixin (class in schrodinger.ui.qt.widgetmixins.panelmixins) KnimeNodeMixin (class in schrodinger.ui.qt.appframework2.knime_af2) known_hostname() (in module schrodinger.utils.sshconfig) KNOWN_LINES (schrodinger.application.matsci.desconfig.MSJStringer attribute) KnownScoreProviderNode (class in schrodinger.active_learning.al_node) kpls_color_from_value() (in module schrodinger.ui.two_d_viewer) KPoint (class in schrodinger.application.matsci.espresso.qeoutput) KpointsType (class in schrodinger.application.matsci.espresso.qeinput) KptLegend (class in schrodinger.application.matsci.espresso.qeoutput) KPTS_MESH_KEY (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) KPTS_TYPES (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) KRYLOV_SWITCHOVER (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) kT (in module schrodinger.protein.analysis) KWW (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) KWW_BETA_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) KWW_INIT_GUESSES (schrodinger.application.matsci.permittivity.ComplexPermittivity attribute) KWW_TAU_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) KYTE_DOOLITTLE_SCALE (schrodinger.application.bioluminate.patch_utils.patch_finder.ProteinProperties attribute)

L

L (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) (schrodinger.protein.annotation.AntibodyRegionLabel attribute) L1 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) L2 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) L3 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) l_qn (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) LA() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) label (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) (schrodinger.application.matsci.espresso.qeoutput.KptLegend attribute) LABEL (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.genetic_optimization.DeepChem attribute) label (schrodinger.protein.annotation.AntibodyCDR attribute) (schrodinger.protein.annotation.Region attribute) (schrodinger.ui.qt.swidgets.SubWidget attribute) label() (schrodinger.tasks.hosts.Host method) label_bond() (in module schrodinger.application.matsci.fragments) label_color (schrodinger.structure.StructureAtom property) label_format (schrodinger.structure.StructureAtom property) LABEL_MAP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) label_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) label_pbc_bonds() (in module schrodinger.application.matsci.nano.xtal) label_pkas (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) label_pkasChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) label_pkasReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) label_prop (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) label_propChanged (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) label_propReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) LABEL_TEXT (schrodinger.application.matsci.sliceplot.SlicePlot attribute) label_user_text (schrodinger.structure.StructureAtom property) labelAsuAtoms() (schrodinger.application.matsci.nano.xtal.Crystal method) LabelAtom (class in schrodinger.application.bioluminate.pml_menus) LabelAtomByEntryIndex (class in schrodinger.application.bioluminate.pml_menus) LabelAtomByMolIndex (class in schrodinger.application.bioluminate.pml_menus) LabelAtomByNumType (class in schrodinger.application.bioluminate.pml_menus) LabelAtomByOccupancy (class in schrodinger.application.bioluminate.pml_menus) LabelAtomByProp (class in schrodinger.application.bioluminate.pml_menus) LabelAtomByStereo (class in schrodinger.application.bioluminate.pml_menus) LabelAtomByVDW (class in schrodinger.application.bioluminate.pml_menus) LabelAtomIdentSubMenu (class in schrodinger.application.bioluminate.pml_menus) LabelAtoms (class in schrodinger.adapter) labelAtoms() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) LabelChains (class in schrodinger.application.bioluminate.pml_menus) labelChains() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) LabelCursor (class in schrodinger.ui.qt.label_cursor) LabelCursorAxes (class in schrodinger.ui.qt.label_cursor) labelDrawn() (schrodinger.ui.qt.label_cursor.LabelCursorAxes method) LabeledStructureToolTip (class in schrodinger.ui.qt.structure2d) LabelMenu (class in schrodinger.application.bioluminate.pml_menus) LabelOtherSubMenu (class in schrodinger.application.bioluminate.pml_menus) LabelResidues (class in schrodinger.application.bioluminate.pml_menus) labelResidues() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) labels (schrodinger.application.jaguar.macro_pka_utils.GraphData attribute) LABELS (schrodinger.application.matsci.qualityslider.QualitySlider attribute) LabelSpinner (class in schrodinger.application.desmond.feputils) labelSymEquivPos() (schrodinger.application.matsci.nano.xtal.Crystal method) LabelTooltip (class in schrodinger.ui.qt.tooltips) lam (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) LAMBDA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) LAMBDA_12E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) LAMBDA_12H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) LAMBDA_21E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) LAMBDA_21H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) LAMBDA_COLUMNS (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) LAMBDA_DYNAMICS (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) lambda_type() (in module schrodinger.application.desmond.config_utils) lambda_windows (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) LambdaDynamicsAnalysis (class in schrodinger.application.desmond.stage.app.lambda_dynamics_analysis) LambdaDynamicsAssignForcefield (class in schrodinger.application.desmond.stage.prepare.forcefield) LambdaDynamicsBuildGeometry (class in schrodinger.application.desmond.stage.prepare.structure) LambdaDynamicsMapper (class in schrodinger.application.desmond.stage.app.lambda_dynamics) LambdaDynamicsMdLauncher (class in schrodinger.application.desmond.stage.app.lambda_dynamics) LambdaDynamicsMsjGenerator (class in schrodinger.application.desmond.msj_generator.lambda_dynamics) LambdaDynamicsSimLegParams (class in schrodinger.application.desmond.msj_generator.lambda_dynamics) LambdaDynamicsSplitReceptor (class in schrodinger.application.desmond.stage.app.lambda_dynamics) LambdaDynamicsStructure (class in schrodinger.application.desmond.stage.app.lambda_dynamics) LambdaDynamicsWorkflowParams (class in schrodinger.application.desmond.msj_generator.lambda_dynamics) LambdaHopping (class in schrodinger.application.desmond.stage.simulate) lambdas (schrodinger.application.desmond.config_utils.LambdaSchedule attribute) (schrodinger.application.desmond.config_utils.ScheduleAngleAttachment attribute) (schrodinger.application.desmond.config_utils.ScheduleAngleCoreDummy attribute) (schrodinger.application.desmond.config_utils.ScheduleAngleCorePhysical attribute) (schrodinger.application.desmond.config_utils.ScheduleBondCoreDummy attribute) (schrodinger.application.desmond.config_utils.ScheduleBondCorePhysical attribute) (schrodinger.application.desmond.config_utils.ScheduleLinear attribute) LambdaSchedule (class in schrodinger.application.desmond.config_utils) LARGE_DENSITY_CHANGE (schrodinger.application.jaguar.constants.FatalErrors attribute) LARGE_DIIS_ERROR (schrodinger.application.jaguar.constants.FatalErrors attribute) LARGE_RHO_K (schrodinger.application.matsci.mecp_mod.BFGS attribute) large_ring_cutoff (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) large_ring_cutoffChanged (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) large_ring_cutoffReplaced (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) LargeSpinner (class in schrodinger.ui.qt.swidgets) LargestRingAtomCount() (in module schrodinger.rdkit.filtering) last_added_entry (schrodinger.project.project.Project property) last_entry_unique_id (schrodinger.application.desmond.maestro.NewEntry attribute) LAST_INDEX (schrodinger.application.desmond.kinetics.utils.MtdInfo attribute) LAST_IRR_KEY (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) last_issued() (schrodinger.application.licensing.flexlm.License method) LAST_RELAX_STAGE_TRJ_INTVL (schrodinger.application.matsci.permittivity.MdStageModifier attribute) last_sequences_imported (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) LAST_STAGE_DICT (schrodinger.application.matsci.permittivity.MultiStageMd attribute) last_updated (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) last_updatedChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) last_updatedReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) lastJobCompleted (schrodinger.ui.qt.appframework2.af2.JobApp attribute) LATEST (schrodinger.utils.openmpi.OpenMPIVersion attribute) Latt2text() (in module schrodinger.application.matsci.gsas.GSASIIspc) lattice (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) lattice_params (schrodinger.comparison.results.Result attribute) LatticeFeatures (class in schrodinger.application.matsci.mlearn.features) LaueUnique() (in module schrodinger.application.matsci.gsas.GSASIIlattice) LaueUnique2() (in module schrodinger.application.matsci.gsas.GSASIIlattice) launch() (in module schrodinger.job.launcher) (schrodinger.application.desmond.multisimstartup.Startup method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.pymol.pymol4maestro.panel method) (schrodinger.job.launcher.Launcher method) LAUNCH_FAILURE (schrodinger.application.desmond.cmj.JobStatus attribute) launch_ffbuilder_gui() (in module schrodinger.ui.qt.forcefield.ffprojectsettingsdlg) launch_file() (in module schrodinger.application.jaguar.input) launch_from_job_spec() (in module schrodinger.job.jobcontrol) launch_job() (in module schrodinger.job.jobcontrol) launch_job_with_callback() (in module schrodinger.job.jobhandler) launch_path() (in module schrodinger.application.jaguar.file_logger) launch_SID() (schrodinger.application.desmond.replica_sid_generator.FEPReport method) launch_subjobs() (in module schrodinger.application.macromodel.paraUtils) launch_time (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) launch_timeChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) launch_timeReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) launchBackend() (schrodinger.job.app.App method) LAUNCHED (schrodinger.job.queue.PrintableStatus attribute) Launcher (class in schrodinger.job.launcher) launcherToCmdList() (schrodinger.ui.qt.appframework2.af2.JobApp method) launchFromJobSpec() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) (schrodinger.application.matsci.multiapp.MultiJobApp method) (schrodinger.ui.qt.appframework2.af2.JobApp method) LAUNCHING (schrodinger.job.queue.JobState attribute) launchJaguarJob() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) launchJobCmd() (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.JobApp method) launchLauncher() (schrodinger.ui.qt.appframework2.af2.JobApp method) LaunchParameters (class in schrodinger.job.launchparams) launchProjectTable() (schrodinger.ui.qt.swidgets.ProjectTableButton method) launchScript() (schrodinger.ui.qt.appframework2.af2.JobApp method) LaunchTime (schrodinger.job.jobcontrol.Job property) LAVENDER (schrodinger.ui.qt.standard.colors.NativeColors attribute) layer (schrodinger.application.matsci.packmol.SolventInfo attribute) (schrodinger.application.matsci.packmol.SurfactantInfo attribute) layOut() (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.jaguar.gui.timing.TimerInfoDialog method) (schrodinger.application.matsci.appbase.ProcessPtStructuresApp method) (schrodinger.application.matsci.chargegui.ChargeDialog method) (schrodinger.application.matsci.chargegui.ForceFieldDialog method) (schrodinger.application.matsci.deswidgets.AdvancedMDOptions method) (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.NewPresetDialog method) (schrodinger.application.matsci.jagwidgets.PresetsDialog method) (schrodinger.application.matsci.jobdirdlg.NewJobDirDialog method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.mswidgets.ProcessBusyDialog method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.mswidgets.SystemInformationFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ColorPairFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.WorkspaceSuperpositionFrame method) (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) (schrodinger.application.matsci.reordergui.ReorderAtomsDialog method) (schrodinger.application.matsci.reportutils.ReportOutputsDialog method) (schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog method) (schrodinger.application.matsci.wfmanagement.WorkflowNamerDialog method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.BaseBottomBar method) (schrodinger.ui.qt.appframework2.af2.BottomBar method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.af2.JobBottomBar method) (schrodinger.ui.qt.appframework2.af2.MiniJobBottomBar method) (schrodinger.ui.qt.appframework2.af2.OKAndCancelBottomBar method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) (schrodinger.ui.qt.schart.AxesDialog method) (schrodinger.ui.qt.schart.BinsDialog method) (schrodinger.ui.qt.schart.SeriesDialog method) (schrodinger.ui.qt.swidgets.NewNameDialog method) (schrodinger.ui.qt.swidgets.SDialog method) layout_type (schrodinger.ui.qt.swidgets.SubWidget attribute) layoutFileSelector() (schrodinger.ui.qt.structure_selector.SlimStructureSelector method) (schrodinger.ui.qt.structure_selector.StructureSelector method) lazy_canvas_import() (in module schrodinger.structutils.analyze) lazy_import() (in module schrodinger.utils.imputils) lazy_product() (in module schrodinger.application.pathfinder.route) LazyIterable (class in schrodinger.application.pathfinder.route) LB() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) LC (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) LC1 (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) LC2 (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) LC_SEQ (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) lcm() (in module schrodinger.application.matsci.nano.xtal) lcm_approx() (in module schrodinger.application.matsci.nano.interface_mod) ld_client (schrodinger.application.livedesign.ld_export.ExportModel attribute) ld_clientChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) ld_clientReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) ld_data (schrodinger.application.livedesign.panel_components.LDDataCheckboxItem property) ld_destination (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) ld_destinationChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) ld_destinationReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) ld_endpoint (schrodinger.application.livedesign.export_models.DataExportSpec attribute) ld_endpointChanged (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) ld_endpointReplaced (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) ld_host (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) ld_input_file (schrodinger.tasks.ldtasks.LDInput attribute) ld_input_fileChanged (schrodinger.tasks.ldtasks.LDInput attribute) ld_input_fileReplaced (schrodinger.tasks.ldtasks.LDInput attribute) LD_LIBRARY_PATH (schrodinger.utils.openmpi.EnvVar attribute) ld_model (schrodinger.application.livedesign.export_models.DataExportSpec attribute) ld_modelChanged (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) ld_modelReplaced (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) ld_models (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ld_modelsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ld_modelsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) LDAPAuthenticationException LDClientConnectionError LDClientProxy (class in schrodinger.application.livedesign.ldclient_proxy) LDColumn (class in schrodinger.tasks.ldtasks) LDConnectionStatus (class in schrodinger.application.livedesign.ldclient_proxy) LDData (class in schrodinger.application.livedesign.data_classes) LDDataCheckboxItem (class in schrodinger.application.livedesign.panel_components) LDDataSelectionModel (class in schrodinger.application.livedesign.panel_components) LDDataSelectionTreeView (class in schrodinger.application.livedesign.panel_components) LDDataTreePopUp (class in schrodinger.application.livedesign.panel_components) LDDataTreePopUpButton (class in schrodinger.application.livedesign.panel_components) LDDestination (class in schrodinger.application.livedesign.export_models) LDError LDExportPanelMixin (class in schrodinger.application.livedesign.ld_export) LDExportSettingsMixin (class in schrodinger.application.livedesign.ld_settings) LDExportTaskMixin (class in schrodinger.application.livedesign.export_tasks) LDFolderTree (class in schrodinger.application.livedesign.ld_folder_tree) LDImportTask (class in schrodinger.application.livedesign.ld_import_utils) LDImportTaskManager (class in schrodinger.application.livedesign.ld_import_utils) LDInput (class in schrodinger.tasks.ldtasks) LDInputRow (class in schrodinger.tasks.ldtasks) LDLoginPanel (class in schrodinger.application.livedesign.login_gui2) LDLoginPanelModel (class in schrodinger.application.livedesign.login_gui2) LDMode (class in schrodinger.application.livedesign.ldclient_proxy) LDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) LDOutputRow (class in schrodinger.tasks.ldtasks) LDSelectionModel (class in schrodinger.application.livedesign.panel_components) LDSelectionTreeView (class in schrodinger.application.livedesign.panel_components) LDSettingsMixin (class in schrodinger.application.livedesign.ld_settings) LDTask (class in schrodinger.tasks.ldtasks) LDTask.Output (class in schrodinger.tasks.ldtasks) LDTreeItem (class in schrodinger.application.livedesign.panel_components) LE_WIDTH (schrodinger.application.desmond.gui.SimOptionsFrame attribute) (schrodinger.application.matsci.deswidgets.DesmondMDWEdit attribute) leaf_first_topo_sort() (in module schrodinger.thirdparty.networkx_algos) LEAK_VERSIONS (schrodinger.application.licensing.licadmin.LicenseResource attribute) least_square_method() (in module schrodinger.application.matsci.spectra) least_squares (schrodinger.application.phase.packages.ligand_aligner.AlignMethod attribute) leave_scope() (schrodinger.application.desmond.enhsamp.binding method) leaveEvent() (schrodinger.application.bioluminate.pml_menus.ColorLabel method) (schrodinger.application.matsci.builderwidgets.StructureLabel method) (schrodinger.ui.qt.swidgets.EllipsisPopUpButton method) (schrodinger.ui.qt.swidgets.HelpButton method) (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator method) leaving_atoms (schrodinger.structutils.rgroup_enumerate.RGroup attribute) LEAVING_MOL_WT (schrodinger.application.steps.enumerators.BaseDecorator attribute) LEFT (schrodinger.ui.qt.schart.SChart attribute) (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) Left (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.BtnPos attribute) LEFT_ARROW (schrodinger.ui.qt.standard.design_tokens.ScrollbarIcons attribute) left_axis (schrodinger.ui.qt.schart.SChart property) LeftHandedAlphaHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) LEG1 (schrodinger.application.matsci.kmc.FragmentsTable attribute) leg1_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) LEG2 (schrodinger.application.matsci.kmc.FragmentsTable attribute) leg2_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) leg2_names (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) leg2_names_short (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) LEG3 (schrodinger.application.matsci.kmc.FragmentsTable attribute) leg_names (schrodinger.application.desmond.new_fep_edge_data.FepData property) LEGACY (schrodinger.ui.qt.tasks.taskbar2.JobMonitorType attribute) LEGEND (schrodinger.ui.qt.schart.SChart attribute) LegProcess (class in schrodinger.application.desmond.physical_leg_infra) length (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue property) LENGTH (schrodinger.application.matsci.nano.tube.NanoTube attribute) length (schrodinger.structure.StructureBond property) (schrodinger.structutils.structalign2.Alignment attribute) LENGTH_COL (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame attribute) lengthAboutToChange (schrodinger.protein.sequence.AbstractSequence attribute) lengthChanged (schrodinger.protein.sequence.AbstractSequence attribute) LESS (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericOperator attribute) LESS_THAN (schrodinger.application.matsci.genetic_optimization.Property attribute) lessThan() (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) (schrodinger.ui.qt.table_helper.PythonSortProxyModel method) Let (class in schrodinger.application.desmond.enhsamp) Letter (schrodinger.application.phase.shape_screen_reporter.option_utils.PageSize attribute) LETTER_NUM (schrodinger.application.matsci.amorphous.PolymerFragments attribute) letUserSelectValues() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) Level (class in schrodinger.infra.mmerr) level (schrodinger.application.licensing.licerror.LicenseError property) LEVEL (schrodinger.application.matsci.crest.CrestTOML attribute) LewisAtomMapper (class in schrodinger.comparison.atom_mapper) LewisModes (class in schrodinger.application.jaguar.utils) LewisStructure (class in schrodinger.application.jaguar.utils) Lexer (class in schrodinger.application.desmond.antlr3.recognizers) lexical_ordering() (in module schrodinger.application.jaguar.nmr_utils) LFMM (schrodinger.energy.MonoMetalComplexType attribute) LFR (schrodinger.protein.annotation.AntibodyRegionLabel attribute) LG (schrodinger.ui.qt.standard.design_tokens.FontSizes attribute) LIB (schrodinger.job.util.DirectoryType attribute) LIC_TOKEN (schrodinger.application.matsci.appbase.BaseAnalysisGui attribute) License (class in schrodinger.application.licensing.flexlm) (class in schrodinger.utils.license) license_check() (in module schrodinger.application.livedesign.io_utils) license_class() (schrodinger.application.licensing.flexlm.License method) license_description() (schrodinger.application.licensing.flexlm.License method) license_directory() (in module schrodinger.application.licensing.licadmin) LICENSE_KEY (schrodinger.application.steps.licensing.LicenseMixin attribute) LicenseCheckoutError LicenseError, [1] (class in schrodinger.application.licensing.licerror) LicenseException LicenseFeature (class in schrodinger.application.licensing.licadmin) LicenseFileType (class in schrodinger.application.licensing.licserver.client) (class in schrodinger.application.licensing.licserver.install) LicenseLine (class in schrodinger.application.licensing.flexlm) LicenseMixin (class in schrodinger.application.steps.licensing) LicenseResource (class in schrodinger.application.licensing.licadmin) Licenses (schrodinger.job.jobcontrol.Job property) licenseSourceErrs (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) LicenseStatus (class in schrodinger.utils.license) LicenseVerificationError LicfileError licserver_dir() (in module schrodinger.application.licensing.licserver.server) lig_to_fullsys_aid() (in module schrodinger.application.desmond.automatic_analysis_generator) Ligand (class in schrodinger.application.matsci.buildcomplex) (class in schrodinger.application.matsci.mlearn.features) (class in schrodinger.application.matsci.siteselector.siteselector) (class in schrodinger.structutils.analyze) (class in schrodinger.ui.qt.ligand_list) LIGAND (schrodinger.application.bioluminate.pose_filtering.hdx_io.SubstructureType attribute) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) (schrodinger.application.desmond.constants.REST_COMPONENT attribute) ligand (schrodinger.application.desmond.struc.CompStruc attribute) LIGAND (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) ligand (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) (schrodinger.tasks.ldtasks.LDInputRow attribute) LIGAND (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute) ligand1_alchemical_atom_total (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_alchemical_mols (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_atomic_mass (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_cpx_asl (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_cpx_sid_lighb() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_molsa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_psa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_sasa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_waters() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) ligand1_fragments() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_hash (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_mol_formula (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_pdb_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_rot_bonds (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_smiles (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_sol_asl (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_sol_sid_lighb() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_molsa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_psa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_sasa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_st (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) ligand1_total_atoms (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_total_fragments (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_total_heavy (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand1_total_hot (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_alchemical_atom_total (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_alchemical_mols (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_atomic_mass (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_cpx_asl (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_cpx_sid_lighb() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_molsa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_psa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_sasa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_waters() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) ligand2_fragments() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_hash (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_mol_formula (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_pdb_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_rot_bonds (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_smiles (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_sol_asl (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_sol_sid_lighb() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_molsa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_psa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_sasa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_st (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) ligand2_total_atoms (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_total_fragments (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_total_heavy (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand2_total_hot (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) ligand_action (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar property) ligand_asl (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) (schrodinger.application.desmond.new_fep_edge_data.FepData property) (schrodinger.protein.tasks.kinase.KinaseConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) (schrodinger.structutils.analyze.Ligand property) ligand_aslChanged (schrodinger.protein.tasks.kinase.KinaseConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) ligand_aslReplaced (schrodinger.protein.tasks.kinase.KinaseConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) ligand_asls (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin property) ligand_charge (schrodinger.application.desmond.new_fep_edge_data.FepData property) LIGAND_FIELD (schrodinger.energy.MetalForceFieldComponent attribute) ligand_file (schrodinger.application.livedesign.tasks.LigandStrainTask.Input attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Input attribute) ligand_fileChanged (schrodinger.application.livedesign.tasks.LigandStrainTask.Input attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Input attribute) ligand_fileReplaced (schrodinger.application.livedesign.tasks.LigandStrainTask.Input attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Input attribute) ligand_fragments (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_gyration_radius (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_intrahbond_counts (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) ligand_molecular_formula (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_molecular_mass (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_molecular_sa (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_name() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method) ligand_num_fragments (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_num_hotatoms (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_num_rotatable_bonds (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_pdb_resname (schrodinger.application.desmond.new_fep_edge_data.FepData property) LIGAND_PLUS_BINDING_SITE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute) ligand_polar_sa (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_restraint (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) ligand_rmsd (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_rmsd_wrt_protein (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_sasa (schrodinger.application.desmond.new_fep_edge_data.FepData property) LIGAND_SELECTIVITY (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) ligand_smiles (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_st (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) (schrodinger.application.glide.ligand_designer.GridgenTask.Input attribute) ligand_st_mol_formula (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) ligand_stChanged (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) (schrodinger.application.glide.ligand_designer.GridgenTask.Input attribute) ligand_strain_args (schrodinger.application.livedesign.tasks.LigandStrainTask.Input attribute) ligand_strain_argsChanged (schrodinger.application.livedesign.tasks.LigandStrainTask.Input attribute) ligand_strain_argsReplaced (schrodinger.application.livedesign.tasks.LigandStrainTask.Input attribute) ligand_stReplaced (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) (schrodinger.application.glide.ligand_designer.GridgenTask.Input attribute) ligand_torsion_strain (schrodinger.application.desmond.new_fep_edge_data.FepData property) LIGAND_TORSION_TEXT (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) (schrodinger.application.desmond.fep_edge_report_maker.PRMEdgeReportMaker attribute) ligand_torsions (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) (schrodinger.application.desmond.new_fep_edge_data.FepData property) ligand_wateraround_counts (schrodinger.application.desmond.new_fep_edge_data.FepData property) LigandActionMixin (class in schrodinger.application.bioluminate.pml_menus) LigandAligner (class in schrodinger.application.phase.packages.ligand_aligner) LigandAlignerOptions (class in schrodinger.application.phase.packages.ligand_aligner) ligandChanged (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) LigandDetectionLink (class in schrodinger.ui.qt.swidgets) LigandInfo (class in schrodinger.application.matsci.buildcomplex) LigandListModel (class in schrodinger.ui.qt.ligand_list) LigandListView (class in schrodinger.ui.qt.ligand_list) LigandListWidget (class in schrodinger.ui.qt.ligand_list) LigandMLBackend (class in schrodinger.active_learning.mq_worker) LigandMLControl (class in schrodinger.application.vss.control) LigandMLEvalNode (class in schrodinger.active_learning.al_node) LigandMLScoreFilterChain (class in schrodinger.application.steps.filters) LigandMLScorer (class in schrodinger.application.steps.scorers) LigandMLScorer.Settings (class in schrodinger.application.steps.scorers) LigandMLTrainNode (class in schrodinger.active_learning.al_node) LigandMLZMQDriver (class in schrodinger.active_learning.mq_driver) LigandNumberIterator (class in schrodinger.application.glide.utils) LigandPrep (class in schrodinger.application.transforms.ligprep) LigandPrepper (class in schrodinger.application.steps.ligprep) LigandPreset (class in schrodinger.application.bioluminate.pml_menus) ligandReplaced (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) Ligands (class in schrodinger.application.livedesign.entry_types) ligands (schrodinger.application.bioluminate.antibody.grafting.GraftingInput attribute) (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) (schrodinger.application.prime.wrapper.PrimeTemplate property) (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin property) ligands_file (schrodinger.application.livedesign.tasks.AlignLigandsTask.Input attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Input attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) ligands_fileChanged (schrodinger.application.livedesign.tasks.AlignLigandsTask.Input attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Input attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) ligands_fileReplaced (schrodinger.application.livedesign.tasks.AlignLigandsTask.Input attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Input attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) ligandSelectionChanged (schrodinger.ui.qt.ligand_list.LigandListView attribute) LigandSelector (class in schrodinger.application.matsci.siteselector.siteselector) ligandSites() (schrodinger.application.matsci.sculptcomplex.CoordinationInfo method) LigandSitesSubMenu (class in schrodinger.application.bioluminate.pml_menus) LigandSketcherStructGetter (class in schrodinger.application.matsci.builderwidgets) ligandSource() (schrodinger.ui.qt.ligand_list.LigandListModel method) (schrodinger.ui.qt.ligand_list.LigandListWidget method) LigandStrainTask (class in schrodinger.application.livedesign.tasks) LigandStrainTask.Input (class in schrodinger.application.livedesign.tasks) LigandStrainTask.JobConfig (class in schrodinger.application.livedesign.tasks) LigandStrainTask.Output (class in schrodinger.application.livedesign.tasks) LigfilterFrame (class in schrodinger.ui.ligfilter) LigFilterStage (class in schrodinger.pipeline.stages.filtering) LigFilterTask (class in schrodinger.application.livedesign.tasks) LigFilterTask.Input (class in schrodinger.application.livedesign.tasks) LigFilterTask.JobConfig (class in schrodinger.application.livedesign.tasks) LigFilterTask.Output (class in schrodinger.application.livedesign.tasks) LIGHT (schrodinger.application.bioluminate.antibody.grafting.ChainTypes attribute) (schrodinger.application.bioluminate.antibody.models.VariableDomainType attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) LIGHT_COLS (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) LIGHT_FR_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute)

LIGHT_FR_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) light_heavy_heavy_light() (in module schrodinger.livedesign.biologics.registration) LIGHT_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) light_sequence (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) light_sequenceChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) light_sequenceReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) LIGHT_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) light_source_name (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) light_source_nameChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) light_source_nameReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) light_template_sequences (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) light_template_sequencesChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) light_template_sequencesReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) LightModeColors (class in schrodinger.ui.qt.standard.colors) lignum_reader() (in module schrodinger.application.glide.ensemble_selection) LigPrep (class in schrodinger.application.phase.packages.shape_ligprep) ligprep_args (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) ligprep_argsChanged (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) ligprep_argsReplaced (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) ligprep_filter_file (schrodinger.application.steps.docking.SmilesDockerSettings attribute) (schrodinger.application.steps.ligprep.LigPrepStep.Settings attribute) ligprep_filter_fileChanged (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) (schrodinger.application.steps.ligprep.LigPrepStep.Settings attribute) ligprep_filter_fileReplaced (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) (schrodinger.application.steps.ligprep.LigPrepStep.Settings attribute) ligprep_infile (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) ligprep_infileChanged (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) ligprep_infileReplaced (schrodinger.application.livedesign.tasks.LigPrepTask.Input attribute) LigPrepStage (class in schrodinger.pipeline.stages.ligprep) LigPrepStep (class in schrodinger.application.steps.ligprep) LigPrepStep.Settings (class in schrodinger.application.steps.ligprep) LigPrepTask (class in schrodinger.application.livedesign.tasks) LigPrepTask.Input (class in schrodinger.application.livedesign.tasks) LigPrepTask.JobConfig (class in schrodinger.application.livedesign.tasks) LigPrepTask.Output (class in schrodinger.application.livedesign.tasks) LigSource (class in schrodinger.ui.qt.ligand_list) Likely (schrodinger.protein.residue.HELIX_PROPENSITY attribute) limit_subjobs (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) limit_subjobsChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) limit_subjobsReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) limitModified() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) limitRangeToggled() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) lindh() (in module schrodinger.application.jaguar.hess_guess) LindhConstants (class in schrodinger.application.jaguar.hess_guess) line (schrodinger.application.desmond.antlr3.tree.CommonTree property) LINE (schrodinger.ui.qt.schart.SChart attribute) (schrodinger.ui.qt.schart.SeriesParams attribute) LINE_COL (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame attribute) LINE_EDIT_CLS (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUpDelegate attribute) LINE_LENGTH (schrodinger.application.matsci.reaction_workflow_utils.SiblingNode attribute) line_match_final_log() (in module schrodinger.application.desmond.replica_exchange_review) LINE_ORDER (schrodinger.application.matsci.desconfig.MSJStringer attribute) line_search_method (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) line_search_wolfe1() (schrodinger.application.matsci.mecp_mod.BFGS method) LINEAR (in module schrodinger.application.matsci.buildcomplex) linear_equation() (schrodinger.application.matsci.nano.tube.Rectangle method) LINEAR_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) linear_schedule (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) LinearError LinearRegressionModel (class in schrodinger.seam.examples.active_learning_weigher) LinearSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) LinearWriter (class in schrodinger.pipeline.input) LineEditDelegate (class in schrodinger.ui.qt.delegates) lineEditUpdated() (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.residueselector.MutationSelectorPopUp method) LineEditWithDisabledText (class in schrodinger.ui.qt.swidgets) LineEditWithPopUp (class in schrodinger.ui.qt.pop_up_widgets) LineEditWithSampleText (class in schrodinger.ui.qt.utils) LineHelmConnectorItem (class in schrodinger.protein.helm.helm_renderer) LinePlotFrame (class in schrodinger.application.matsci.density_analysis_widget) lineterminator (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) LINK (schrodinger.ui.qt.standard.colors.DarkModeColors attribute) (schrodinger.ui.qt.standard.colors.LightModeColors attribute) LINK_DISABLED (schrodinger.ui.qt.standard.colors.DarkModeColors attribute) (schrodinger.ui.qt.standard.colors.LightModeColors attribute) LINK_HOVERED (schrodinger.ui.qt.standard.colors.DarkModeColors attribute) (schrodinger.ui.qt.standard.colors.LightModeColors attribute) LINK_PRESSED (schrodinger.ui.qt.standard.colors.DarkModeColors attribute) (schrodinger.ui.qt.standard.colors.LightModeColors attribute) LINKAGE_TYPES (schrodinger.application.canvas.cluster.CanvasFingerprintCluster attribute) LinkButtonWithPopUp (class in schrodinger.ui.qt.pop_up_widgets) LinkDelegate (class in schrodinger.ui.qt.delegates) LinkedList (class in schrodinger.job.queue) LinkedListNode (class in schrodinger.job.queue) LINKER (schrodinger.protein.annotation.KinaseFeatureLabel attribute) linkFollowed() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) LinknodeEnumerable (class in schrodinger.application.scaffold_enumeration.linknode) LinknodeSgroup (class in schrodinger.application.scaffold_enumeration.linknode) linkSelectionAndInclusionToggled() (schrodinger.ui.two_d_viewer.TwoDViewer method) linux_setVisible_positioning_workaround() (in module schrodinger.ui.qt.utils) LIOUV_ZERO (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) LIPID_BILAYERS (class in schrodinger.application.desmond.constants) lipidImported (schrodinger.application.matsci.mswidgets.LipidImporter attribute) LipidImporter (class in schrodinger.application.matsci.mswidgets) lipo_smoothing() (in module schrodinger.application.bioluminate.patch_utils.msurfext) lipophilic_ChemScore_value() (in module schrodinger.application.bioluminate.interaction_calculator) LiposomeInputFile (class in schrodinger.application.matsci.packmol) List (class in schrodinger.utils.sea.sea) list (schrodinger.application.combinatorial_explorer.driver_utils.RouteSourceType attribute) list2jmonitorcmdline() (in module schrodinger.job.jobcontrol) list2str() (in module schrodinger.application.desmond.meta) list_features() (in module schrodinger.utils.featureflags.featureflags) LIST_SEPARATOR (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator attribute) list_to_csv() (in module schrodinger.structutils.rgroup_enumerate) list_to_string() (in module schrodinger.application.matsci.nano.interface_mod) list_widget_item_count (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel property) listAllNodes() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) listAvailableFiles() (schrodinger.application.matsci.jobdirdlg.InteractiveFileDownloader method) (schrodinger.application.matsci.jobutils.FileDownloader method) ListDiff (class in schrodinger.models.diffy) ListParam (class in schrodinger.models.parameters) listSelectionChanged() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) Lit (class in schrodinger.application.desmond.enhsamp) live_report_id (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel property) LiveDesignExportSummaryPanel (class in schrodinger.application.livedesign.summary) LiveDesignLoginDialog (class in schrodinger.application.livedesign.login_gui) LiveDesignProjectsCombo (class in schrodinger.application.livedesign.panel_components) liveReportDefaultsApplied (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) LiveReportModel (class in schrodinger.application.livedesign.live_report_widget) liveReportSelected (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelector attribute) LiveReportSelectionComboBox (class in schrodinger.application.livedesign.panel_components) LiveReportSelectionPopup (class in schrodinger.application.livedesign.panel_components) LiveReportSelector (class in schrodinger.application.livedesign.panel_components) LiveReportTemplateSelectorCombo (class in schrodinger.application.livedesign.panel_components) LiveReportType (class in schrodinger.application.livedesign.live_report_widget) LiveReportWidget (class in schrodinger.application.livedesign.live_report_widget) lj14_energy() (in module schrodinger.application.qsite.output) lj_energy() (in module schrodinger.application.qsite.output) llmd() (schrodinger.application.macromodel.utils.ComUtil method) lmdiag() (schrodinger.application.licensing.licadmin.LicenseResource method) lmgrd_lines() (in module schrodinger.application.licensing.licadmin) lmod() (schrodinger.application.macromodel.utils.ComUtil method) LMP2 (schrodinger.application.jaguar.constants.CalcType attribute) LMP2_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) LMP2_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) lmstat() (schrodinger.application.licensing.licadmin.LicenseResource method) Lnorm() (in module schrodinger.application.matsci.gsas.GSASIIlattice) LNQ (schrodinger.application.matsci.reaction_workflow_utils.DF_RATE_TYPE attribute) lo_precision (schrodinger.application.jaguar.results.JaguarResults attribute) load() (in module schrodinger.models.json) (schrodinger.analysis.transformations.TransformsRepository method) (schrodinger.application.desmond.test_utils.FileRegistry class method) (schrodinger.application.matsci.equilibrium_md.CmsModel method) (schrodinger.application.matsci.equilibrium_md.MaeModel method) (schrodinger.application.matsci.equilibrium_md.Model method) (schrodinger.application.matsci.permittivity.Config method) load_arrows() (in module schrodinger.trajectory.prody.test_arrow) load_cif() (in module schrodinger.comparison.struc) load_class_array() (in module schrodinger.application.jaguar.permutation_symmetry) load_data() (schrodinger.application.desmond.bennett.CalcBAR method) load_entries_for_panel() (in module schrodinger.application.matsci.gutils) load_force_field_parameters() (in module schrodinger.application.matsci.cgforcefield) LOAD_FROM_WORKSPACE (schrodinger.application.matsci.appbase.StructureLoadButton attribute) load_gui() (in module schrodinger.application.desmond.report_helper) load_job_into_panel() (in module schrodinger.application.matsci.gutils) load_job_products() (in module schrodinger.application.licensing.licadmin) load_job_reqs() (in module schrodinger.application.licensing.licadmin) load_keywords() (in module schrodinger.application.jaguar.keywordDB) load_structure() (in module schrodinger.application.matsci.mstest) load_yaml() (in module schrodinger.stepper.app) loadAccuracyAndInitialGuessSettings() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) loadAndProcessData() (schrodinger.application.matsci.kmcgui.PropertyCombo method) loadAndUpdateTaskProtocol() (schrodinger.application.matsci.permittivity.ConfigWriter method) loadAssayData() (schrodinger.application.livedesign.panel_components.ExportTableModel method) LoadCNSFile() (in module schrodinger.analysis.visanalysis.volumedataio) loadCommon() (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) loadConstraintCoordinates() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) LoadControls() (in module schrodinger.application.matsci.gsas.GSASIIfiles) loadConvergenceCriteriaSettings() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) loadConvergenceKeywords() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) loadConvergenceMethodsSettings() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) loadCurrentFile() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) loadData() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) (schrodinger.application.livedesign.panel_components.ExportTableModel method) (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.application.livedesign.panel_components.LDSelectionModel method) (schrodinger.application.livedesign.panel_components.StructSelectionModel method) (schrodinger.application.matsci.appbase.ViewerGuiMixin method) (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) (schrodinger.application.matsci.density_analysis_widget.DensityTab method) (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) loadDatabases() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) loadDataFromAllInOneFile() (schrodinger.application.matsci.equilibrium_md.MultiDriver method) loadDefaultPreset() (schrodinger.models.presets.PresetManager method) loadEndpointData() (schrodinger.application.livedesign.panel_components.ExportTableModel method) loadEntriesIntoStrucCombos() (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) loadEnumeration() (schrodinger.application.matsci.nano.slab.ParserWrapper method) LOADER (schrodinger.infra.unusable_module_importer.AbstractUnusableModuleFinder attribute) (schrodinger.infra.unusable_module_importer.MissingProductUnusableModuleFinder attribute) (schrodinger.infra.unusable_module_importer.NonPostTestUnusableModuleFinder attribute) LoadExportRoutines() (in module schrodinger.application.matsci.gsas.GSASIIfiles) loadFFCombo() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) loadFile() (schrodinger.analysis.transformations.TransformsRepository method) (schrodinger.ui.dendrogram.DendrogramTreeBuilder method) loadFromStructure() (schrodinger.application.matsci.espresso.qeinput.HybridType method) (schrodinger.application.matsci.espresso.qeinput.KpointsType method) loadHKLOptions() (schrodinger.application.matsci.nano.slab.ParserWrapper method) loadHotModels() (schrodinger.active_learning.mq_backend.Backend method) LoadImportRoutines() (in module schrodinger.application.matsci.gsas.GSASIIfiles) loadInfo() (schrodinger.application.matsci.kmcgui.DatabaseInfo method) loadIt() (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.particle.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.ParserWrapper method) (schrodinger.application.matsci.nano.xtal.ParserWrapper method) (schrodinger.application.matsci.rxn_path.ParserWrapper method) loadJobsIntoTable() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) loadLDFolderTree() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) loadLiveReports() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) loadMappings() (schrodinger.application.livedesign.panel_components.ExportTableModel method) loadMmJag() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) loadModel() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) loadModels() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) loadMol() (schrodinger.application.matsci.rdpattern.Pattern method) loadNewTask() (schrodinger.tasks.taskmanager.TaskManager method) loadNewWorkflow() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) LoadOptionalRestartFiles() (schrodinger.active_learning.al_driver.ActiveLearningJob method) LoadOptionalRestartFilesDict() (schrodinger.active_learning.al_driver.ActiveLearningJob method) loadOptions() (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) loadOrbitalsSettings() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) loadPanelState() (schrodinger.ui.qt.appframework2.settings.SettingsPanelMixin method) loadPanelStateFromNonPresetFile() (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) loadPerAtomSettings() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) loadPersistentOptions() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) loadPLP() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) loadPreset() (schrodinger.models.presets.PresetManager method) loadPresetFromFile() (schrodinger.models.presets.PresetManager method) LoadPreviousNodes() (schrodinger.active_learning.al_driver.ActiveLearningJob static method) loadQueue() (schrodinger.application.matsci.genetic_optimization.Jaguar method) loadRendererForCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) loadRequired() (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) LoadRestraintsFromStructure (class in schrodinger.application.desmond.stage.prepare.forcefield) loadResults() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) loadRow() (schrodinger.application.livedesign.panel_components.LDSelectionModel method) loadRows() (schrodinger.application.livedesign.panel_components.LDSelectionModel method) loads() (in module schrodinger.models.json) (schrodinger.analysis.transformations.TransformsRepository method) loadSelectedStructure() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) loadSettings() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MossbauerSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MullikenSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MultipoleSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.RamanSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.knime_af2.KnimeNodeMixin method) loadSettingsFromKeywords() (schrodinger.application.matsci.jagwidgets.EmbeddedSolventWidget method) loadSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.species.SpeciesCollection method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) LoadsTheoryMixin (class in schrodinger.application.jaguar.gui.tabs.base_tab) loadStruct() (schrodinger.application.matsci.appbase.StructureLoadButton method) loadStructure() (schrodinger.application.matsci.mswidgets.StructureLoader method) loadStructureIntoWorkspace() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) loadStructures() (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) loadTemplate() (schrodinger.application.matsci.builderwidgets.SketcherBox method) loadTemplateFile() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) loadToggled() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) loadTreeFromNewick() (schrodinger.ui.qt.dendrogram.Dendrogram method) LoadVisFile() (in module schrodinger.analysis.visanalysis.volumedataio) loadWorkflow() (schrodinger.application.matsci.permittivity.ConfigWriter method) loadWorkflowSettings() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) loadWorkspaceSelection() (schrodinger.ui.qt.atomselector.AtomSelector method) LOCAL (schrodinger.tasks.tasks.ResourceType attribute) (schrodinger.utils.cmdline.Options attribute) LOCAL_ENTITLEMENT (schrodinger.application.licensing.licserver.client.LicenseFileType attribute) (schrodinger.application.licensing.licserver.install.LicenseFileType attribute) LOCAL_ENTITLEMENT_BLOB (schrodinger.application.licensing.licserver.install.LicenseFileType attribute) local_server_files() (in module schrodinger.application.licensing.licadmin) local_server_resource() (in module schrodinger.application.licensing.licadmin) local_server_resources() (in module schrodinger.application.licensing.licadmin) local_st_file (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) local_st_fileChanged (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) local_st_fileReplaced (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) LocalEntitlement (class in schrodinger.application.licensing.licserver.client) localEntitlements (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) LocalEntitlementValidation (class in schrodinger.application.licensing.licserver.client) LOCALIZATION_METHODS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) LocalResourceError LocalServerProcess (class in schrodinger.application.licensing.licadmin) locate_darwin_pymol() (in module schrodinger.utils.fileutils) locate_file_from_link() (in module schrodinger.application.matsci.gutils) locate_pfx_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) locate_pymol() (in module schrodinger.utils.fileutils) locateAndRotate() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) locateVoids() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) LOCATION (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) location (schrodinger.protein.tasks.blast.BlastSettings attribute) location() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.licensing.licadmin.LicenseResource method) location_part() (schrodinger.application.matsci.cctbx.rot_mx.translation_part_info method) locationChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) locationReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) lock_marker_atom_in_place() (in module schrodinger.application.matsci.buildcomplex) lock_protonation() (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) lock_protonation_states() (schrodinger.protein.assignment.ProtAssign method) locked (schrodinger.protein.nonstandard_residues.AminoAcid property) LockedProjectException Locus (class in schrodinger.application.bioluminate.update_germline_db.translate_db) LOE (schrodinger.application.matsci.kmc.PairsTable attribute) LOG (schrodinger.tasks.queue.AutoFileMode attribute) (schrodinger.ui.qt.schart.SChart attribute) log() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) (in module schrodinger.application.matsci.order_parameter_mod) (in module schrodinger.application.matsci.reaction_workflow_utils) (in module schrodinger.application.matsci.textlogger) (in module schrodinger.pipeline.pipeline) (in module schrodinger.ui.qt.appframework2.debugcore) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) (schrodinger.application.matsci.equilibrium_md.MultiDriver method) (schrodinger.application.matsci.fragments.LoggerUser method) (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) (schrodinger.application.matsci.montecarlo.Metropolizer method) (schrodinger.application.matsci.permittivity.StepBase method) (schrodinger.application.matsci.smartsutils.SMARTSGroup method) (schrodinger.job.app.App method) (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) log_and_print_exception() (in module schrodinger.infra.exception_handler) log_banner() (in module schrodinger.utils.installation_check) log_build_progress() (in module schrodinger.application.combinatorial_explorer.driver_utils) log_debug() (in module schrodinger.application.matsci.amorphous) (in module schrodinger.application.matsci.equilibrium_md) (in module schrodinger.application.matsci.permittivity) (in module schrodinger.application.matsci.textlogger) log_deleted_lines() (schrodinger.application.licensing.flexlm.License method) log_displacements() (in module schrodinger.application.matsci.mecp_mod) log_energy_and_forces() (in module schrodinger.application.matsci.mecp_mod) log_error() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) (in module schrodinger.application.matsci.textlogger) (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) (schrodinger.application.matsci.equilibrium_md.MultiDriver method) log_file (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) log_file() (schrodinger.application.desmond.cmj.JobOutput method) log_fileChanged (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) log_fileReplaced (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) log_geometry() (in module schrodinger.application.matsci.mecp_mod) log_info() (in module schrodinger.application.matsci.mlearn.descriptor) (in module schrodinger.livedesign.cmdline) log_initial_data() (in module schrodinger.application.matsci.textlogger) log_interaction() (in module schrodinger.protein.assignment) log_into_livedesign() (in module schrodinger.application.livedesign.login_gui2) log_jobinfo() (in module schrodinger.application.matsci.textlogger) log_msg() (in module schrodinger.application.bb_database.bb_task_utils) (in module schrodinger.application.matsci.textlogger) log_namespace() (in module schrodinger.application.matsci.textlogger) log_results() (in module schrodinger.protein.process_enamine_db) log_sa (class in schrodinger.application.matsci.gsas.GSASIImath) log_structures_found() (in module schrodinger.application.matsci.jobutils) log_vector() (in module schrodinger.application.matsci.mecp_mod) logChanged() (schrodinger.ui.qt.schart.AxisParams method) logCoefficientsTable() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) logEnergyAndForces() (schrodinger.application.matsci.mecp_mod.MECPStep method) LogEntry (class in schrodinger.ui.qt.appframework2.debugcore) logError() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) logfile (schrodinger.application.glide.http_client.AbstractGlideServerManager property) logfile() (schrodinger.application.licensing.licadmin.LicenseResource method) logfiles (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) LogFiles (schrodinger.job.jobcontrol.Job property) logfilesChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) logfilesReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) LogFormatter (class in schrodinger.application.hitexpander) logFrequencyTable() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) logger (in module schrodinger.structutils.rgroup_enumerate) (schrodinger.application.prepwizard2.tasks.LoggerMixin attribute) (schrodinger.rdkit.rdkit_adapter.RdkitLoggerstate attribute) LoggerMixin (class in schrodinger.application.prepwizard2.tasks) (class in schrodinger.application.steps.basesteps) LoggerUser (class in schrodinger.application.matsci.fragments) logging_config() (in module schrodinger.utils.log) logging_summary_callback() (in module schrodinger.application.matsci.genetic_optimization) LoggingSubprocessJob (class in schrodinger.application.matsci.jobutils) logHeader() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) logHessianEigVals() (schrodinger.application.matsci.mecp_mod.MECPStep method) login() (schrodinger.application.matsci.qubec_utils.Qubec method) login_using_last_session_credentials() (in module schrodinger.application.livedesign.login_gui2) logInitialGeometry() (schrodinger.application.matsci.mecp_mod.MECPStep method) LoginManager (class in schrodinger.application.livedesign.login) logistic() (in module schrodinger.application.desmond.bennett) logistic_full() (in module schrodinger.application.desmond.bennett) logistic_function() (in module schrodinger.application.desmond.bennett) logistic_function_full() (in module schrodinger.application.desmond.bennett) logJobData() (schrodinger.application.matsci.mecp_mod.MECPStep method) logLnQTable() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) logn() (in module schrodinger.pipeline.pipeline) lognoret() (schrodinger.pipeline.stage.Stage method) lognotret() (schrodinger.job.app.App method) logout_from_livedesign() (in module schrodinger.application.livedesign.maestro_ld_connection) logP() (schrodinger.application.macromodel.utils.ComUtil method) logParams() (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) logPropertyTable() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) logReplicaInfo() (schrodinger.application.matsci.permittivity.WorkflowParser method) logResult() (schrodinger.structutils.smilesfilter.FilterReporter method) logS() (in module schrodinger.rdkit.filtering) logs_endpoint() (schrodinger.seam.viz.watcher.WatcherWebServer method) logScale (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute) logStepInfo() (schrodinger.application.matsci.mecp_mod.MECPStep method) logString() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) logSummary() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) (schrodinger.application.matsci.mecp_mod.MECPStep method) logSummaryHeader() (schrodinger.application.matsci.mecp_mod.MECPStep method) LogTable (class in schrodinger.ui.qt.appframework2.debugwidgets) LogTagTable (class in schrodinger.ui.qt.appframework2.debugwidgets) logToggled (schrodinger.ui.qt.schart.AxesDialog attribute) LOH (schrodinger.application.matsci.kmc.PairsTable attribute) long_code (schrodinger.protein.residue.Residue property) long_end (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule.RING_INFO attribute) LONG_ERROR_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) long_name (schrodinger.protein.sequence.CombinedChainProteinSequence property) long_range_dispersion_energy() (in module schrodinger.application.desmond.fepana) LONG_USAGE (schrodinger.application.desmond.multisimstartup.Help attribute) (schrodinger.application.desmond.multisimstartup.Startup.Help attribute) LongestConsecutiveRBCount() (in module schrodinger.rdkit.filtering) lookup_function() (in module schrodinger.application.jaguar.jagconvert) Loop (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data) loop() (schrodinger.application.macromodel.utils.ComUtil method) LOOP_1 (schrodinger.application.bioluminate.antibody.grafting.LoopTypes attribute) LOOP_2 (schrodinger.application.bioluminate.antibody.grafting.LoopTypes attribute) LOOP_3 (schrodinger.application.bioluminate.antibody.grafting.LoopTypes attribute) loop_databases (schrodinger.application.bioluminate.antibody.grafting.GraftingInput attribute) loop_grafting_inputs (schrodinger.application.bioluminate.antibody.grafting.GraftingInput attribute) loop_type (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) loopChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) LoopGraftingInput (class in schrodinger.application.bioluminate.antibody.grafting) LoopGraftingInstruction (class in schrodinger.application.bioluminate.antibody.grafting) LoopRange (class in schrodinger.application.bioluminate.anarci.loop_ranges) LoopTypes (class in schrodinger.application.bioluminate.antibody.grafting) LorchWeight() (in module schrodinger.application.matsci.gsas.GSASIIpwd) LOSSLESS (schrodinger.application.phase.packages.conformer_storage.Format attribute) Low (schrodinger.protein.annotation.KinaseConservation attribute) LOW (schrodinger.trajectory.trajectory_gui_dir.export_movie.Quality attribute) LOW_IDENTITY_ERROR (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) lowdin_charges() (in module schrodinger.application.jaguar.textparser) lowdin_spins() (in module schrodinger.application.jaguar.textparser) lower_bound (schrodinger.application.desmond.correlation_tau.ConfidenceInterval attribute) LOWEST (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor attribute) LOWEST_TIP (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor attribute) LowMemoryVolGraph (class in schrodinger.application.matsci.amorphous) LOWMODE (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute) LOWSCORE (schrodinger.protein.predictors.Disordered attribute) lr_column_ids (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) lr_column_idsChanged (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) lr_column_idsReplaced (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) lr_filter() (in module schrodinger.application.livedesign.live_report_widget) lr_id (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) lr_idChanged (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) lr_idReplaced (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) lr_input_type (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_input_typeChanged (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_input_typeReplaced (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_name (schrodinger.application.livedesign.export_models.LDDestination attribute) lr_nameChanged (schrodinger.application.livedesign.export_models.LDDestination attribute) lr_nameReplaced (schrodinger.application.livedesign.export_models.LDDestination attribute) lr_selection_mode (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_selection_modeChanged (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_selection_modeReplaced (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_sort_method (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_sort_methodChanged (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_sort_methodReplaced (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_template_id (schrodinger.application.livedesign.export_models.LDDestination attribute) lr_template_idChanged (schrodinger.application.livedesign.export_models.LDDestination attribute) lr_template_idReplaced (schrodinger.application.livedesign.export_models.LDDestination attribute) lr_url (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) lr_urlChanged (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) lr_urlReplaced (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) lr_user_text (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_user_textChanged (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_user_textReplaced (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) lr_widget_model (schrodinger.application.livedesign.ld_export.ExportModel attribute) lr_widget_modelChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) lr_widget_modelReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) LRInputType (class in schrodinger.application.livedesign.live_report_widget) LRSelectionMode (class in schrodinger.application.livedesign.live_report_widget) LRSort (class in schrodinger.application.livedesign.panel_components) LRSortCombo (class in schrodinger.application.livedesign.panel_components) LRSortMethodChanged (schrodinger.application.livedesign.panel_components.BaseLiveReportSelectionPopup attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelector attribute) (schrodinger.application.livedesign.panel_components.LRSortCombo attribute) LRUCacheData (class in schrodinger.application.matsci.cache) LST (schrodinger.application.jaguar.rotation_barriers_keywords.TSMethod attribute) LST_SEARCH_ALONG (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) LT() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.TokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) LT_token() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) LT_tree() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) luminance_level() (in module schrodinger.application.matsci.colorutils) lumo() (in module schrodinger.application.jaguar.textparser)

M

m (schrodinger.seam.examples.active_learning_weigher.LinearRegressionModel attribute) m2io_type_convert() (in module schrodinger.application.glide.utils) m2ioPropertyName() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method) m_glide_XPviz_exposure() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_hbonds() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_hexpairs() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_hexsp() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_blkpchg() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_charge() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_ddpen() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_polar() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_twistam() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penalties() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_phobcon_hb() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_phobpack() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_picat() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_rotbonds() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_stacking() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_water_ligand() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_water_protein() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_watmol() (in module schrodinger.application.glide.xpdes) m_hideAfterAnimation (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute) m_qn (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) machid (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) machineId (schrodinger.application.licensing.licserver.client.LocalEntitlement attribute) MacMultiComboBoxStyle (class in schrodinger.ui.qt.multi_combo_box) MACRO_COLUMN (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka attribute) MacroAtomSelectionDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) macrocycle (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) MACROCYCLE_COREHOPPING (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) macrocycleChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) MacrocycleForceFieldSelector (class in schrodinger.ui.qt.forcefield.ffselector) macrocycleReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) MacroKaInput (class in schrodinger.application.jaguar.macro_pka_input) MacroModel MacromodelConfSearchStep (class in schrodinger.application.matsci.jwsteps) MacromoleculeMutator (class in schrodinger.application.bioluminate.mutation) MAction (class in schrodinger.application.bioluminate.pml_menus) mADDOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MAE (schrodinger.application.livedesign.export_tasks.FileFormat attribute) mae() (in module schrodinger.application.jaguar.textparser) mae2coord() (in module schrodinger.application.xtb.utilities) MAE_CELL_ENDING (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) MAE_ENDING (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) mae_file (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) mae_fileChanged (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) mae_fileReplaced (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) mae_in() (in module schrodinger.application.jaguar.textparser) MAE_NOCELL_ENDING (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) mae_to_jin() (in module schrodinger.application.jaguar.jagconvert) MaeFileWriter (class in schrodinger.application.steps.converters) MaeFileWriter.Settings (class in schrodinger.application.steps.converters) MaeGlideDocker (class in schrodinger.application.steps.docking) MaeGlideDocker.Settings (class in schrodinger.application.steps.docking) MAEGZ (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) MaeInMixin (class in schrodinger.application.steps.dataclasses) MaeLigandPrepper (class in schrodinger.application.steps.ligprep) MaeMaeMixin (class in schrodinger.application.steps.dataclasses) MaeMaeWorkflow (class in schrodinger.application.steps.basesteps) MaeMapStep (class in schrodinger.application.steps.basesteps) MaeModel (class in schrodinger.application.matsci.equilibrium_md) MaeOutMixin (class in schrodinger.application.steps.dataclasses) MaeProductFilter (class in schrodinger.application.steps.filters) MaePropertyName (class in schrodinger.application.desmond.constants) MaeReduceStep (class in schrodinger.application.steps.basesteps) Maestro callbacks commands project table, [1] running scripts script installation workspace, [1] maestro (schrodinger.application.livedesign.export_tasks.ExportType attribute) MAESTRO (schrodinger.infra.structure.FileFormat attribute) Maestro (schrodinger.protein.sequence.AbstractSequence.ORIGIN attribute) MAESTRO (schrodinger.rdkit_extensions.Format attribute) MAESTRO_BANNER (schrodinger.application.jaguar.gui.input_tab_widgets_pka.MacroAtomSelectionDelegate attribute) MAESTRO_BANNER_ADD_H (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) MAESTRO_BANNER_REMOVE_H (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) maestro_check_callback (schrodinger.ui.qt.appframework2.maestro_callback.CallbackInfo attribute) maestro_command() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.bioluminate.protein_structure_quality) MAESTRO_EXPORT_MAP_DIR_PATH (schrodinger.application.livedesign.export_map_manager.ExportMapManager attribute) MAESTRO_LD_MAPPING_WIDGET_CLASS (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) maestro_properties (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) maestro_propertiesChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) maestro_propertiesReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) maestro_required() (in module schrodinger.ui.qt.utils) maestro_rotate_cell() (in module schrodinger.application.matsci.nano.slab) maestro_sdf (schrodinger.application.livedesign.export_tasks.ExportType attribute) MAESTRO_STATUS_MESSAGE (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) MaestroArrow (class in schrodinger.graphics3d.arrow) MaestroBox (class in schrodinger.graphics3d.box) MaestroCallbackMixin (class in schrodinger.ui.qt.appframework2.maestro_callback) MaestroCallbackModelMixin (class in schrodinger.ui.qt.appframework2.maestro_callback) MaestroCallbackWidgetMixin (class in schrodinger.ui.qt.appframework2.maestro_callback) MaestroCube (class in schrodinger.graphics3d.polyhedron) MaestroDockPanel (class in schrodinger.ui.qt.basewidgets) MaestroDockTaskPanel (class in schrodinger.ui.qt.basewidgets) MaestroDodecahedron (class in schrodinger.graphics3d.polyhedron) MaestroEllipsoid (class in schrodinger.graphics3d.ellipsoid) MaestroEntriesInfo (class in schrodinger.application.pymol.mae_sync) MaestroForceFieldSelector (class in schrodinger.ui.qt.forcefield.ffselector) MaestroHemisphere (class in schrodinger.graphics3d.hemisphere) MaestroIcosahedron (class in schrodinger.graphics3d.polyhedron) maestroJobPreferences() (schrodinger.ui.qt.appframework2.af2.SettingsButton method) MaestroLDMappingModel (class in schrodinger.application.livedesign.mapping_widgets) MaestroLDMappingWidget (class in schrodinger.application.livedesign.mapping_widgets) MaestrolessLigandListModel (class in schrodinger.ui.picking) MaestrolessPickLigandDialog (class in schrodinger.ui.picking) MaestrolessPickResidueDialog (class in schrodinger.ui.picking) MaestroLines (class in schrodinger.graphics3d.lines) MaestroNavToolbar (class in schrodinger.ui.qt.navtoolbar) MaestroNotAvailableError MaestroOctahedron (class in schrodinger.graphics3d.polyhedron) MaestroParallelepiped (class in schrodinger.graphics3d.box) MaestroPolygon (class in schrodinger.graphics3d.polygon) MaestroPolyhedronCore (class in schrodinger.graphics3d.polyhedron) MaestroPreferenceForceFieldSelector (class in schrodinger.ui.qt.forcefield.ffselector) MaestroPythonBannerManager (class in schrodinger.ui.qt.utils) MaestroReader (class in schrodinger.structure) MaestroSettingsModel (class in schrodinger.application.pymol.mae_sync) MaestroSphere (class in schrodinger.graphics3d.sphere) MaestroTetrahedron (class in schrodinger.graphics3d.polyhedron) MaestroTextReader (class in schrodinger.structure) MaestroTorus (class in schrodinger.graphics3d.torus) MaestroTube (class in schrodinger.graphics3d.tube) MaestroUnusableModuleFinder (class in schrodinger.infra.unusable_module_importer) MaestroViewSettingsModel (class in schrodinger.application.pymol.mae_sync) MaestroWriter (class in schrodinger.structure) MaeUniqueSmilesFilter (class in schrodinger.application.steps.filters) mag (schrodinger.application.matsci.espresso.utils.MagElement attribute) MagElement (class in schrodinger.application.matsci.espresso.utils) MagFF (in module schrodinger.application.matsci.gsas.atmdata) MagMod() (in module schrodinger.application.matsci.gsas.GSASIImath) MAGNIFY_FACTOR (schrodinger.protein.helm.helm_renderer.BBPhosphateMonomerBase attribute) (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin attribute) (schrodinger.protein.helm.helm_renderer.NABaseMonomerBase attribute) Magres (class in schrodinger.application.matsci.espresso.qeoutput) Magres.ATTR (class in schrodinger.application.matsci.espresso.qeoutput) MagresAtom (class in schrodinger.application.matsci.espresso.qeoutput) MagScatFac() (in module schrodinger.application.matsci.gsas.GSASIIElem) MagSGSym() (in module schrodinger.application.matsci.gsas.GSASIIspc) MagSpecies (class in schrodinger.application.matsci.espresso.utils) MagSSText2MTS() (in module schrodinger.application.matsci.gsas.GSASIIspc) MagSytSym() (in module schrodinger.application.matsci.gsas.GSASIIspc) MagText2MTS() (in module schrodinger.application.matsci.gsas.GSASIIspc) MAIN (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) main() (in module schrodinger.active_learning.mq_backend) (in module schrodinger.active_learning.mq_driver) (in module schrodinger.active_learning.mq_worker) (in module schrodinger.application.bioluminate.anarci.annotate) (in module schrodinger.application.bioluminate.epitope.driver) (in module schrodinger.application.bioluminate.methionine_oxidation) (in module schrodinger.application.bioluminate.peptide_sar.sar) (in module schrodinger.application.bioluminate.tcr.docking_angles) (in module schrodinger.application.bioluminate.update_germline_db.translate_db) (in module schrodinger.application.canvas.r_group_dee) (in module schrodinger.application.dendrogram.core_class) (in module schrodinger.application.desmond.bennett) (in module schrodinger.application.desmond.enhanced_sampling.mexpLexer) (in module schrodinger.application.desmond.enhanced_sampling.mexpParser) (in module schrodinger.application.desmond.gpgpu.test_gpgpu) (in module schrodinger.application.desmond.kinetics.cleanup) (in module schrodinger.application.desmond.kinetics.mtd_cleanup) (in module schrodinger.application.desmond.mxmd.mxmd_cleanup) (in module schrodinger.application.desmond.stage.run_method_parallel) (in module schrodinger.application.jaguar.check_headers) (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.licserver.main) (in module schrodinger.application.licensing.lmgrd_log_parser) (in module schrodinger.application.matsci.enumeration) (in module schrodinger.application.matsci.packmol) (in module schrodinger.application.matsci.reordergui) (in module schrodinger.application.mopac.mopac_backend) (in module schrodinger.application.mopac.mopac_startup) (in module schrodinger.application.phase.packages.phase_convert_MOE) (in module schrodinger.application.phase.packages.shape_screen_al_driver) (in module schrodinger.application.watermap.watermap_inp) (in module schrodinger.driver.structsubset) (in module schrodinger.forcefield.custom_params) (in module schrodinger.infra.epydoc_to_sphinx) (in module schrodinger.livedesign.cmdline) (in module schrodinger.protein.getpdb_utility) (in module schrodinger.protein.gpcr.update_gpcr_db) (in module schrodinger.protein.process_enamine_db) (in module schrodinger.protein.reliability) (in module schrodinger.seam.examples.active_learning_weigher) (in module schrodinger.seam.examples.haystack) (in module schrodinger.seam.examples.rescount) (in module schrodinger.seam.testing.benchmarks) (in module schrodinger.seam.viz.watcher) (in module schrodinger.seam.viz.watcherd) (in module schrodinger.stepper.viz) (in module schrodinger.structutils.sort) (in module schrodinger.ui.qt.mapperwidgets.param_editor) (in module schrodinger.ui.qt.tablewidget) (in module schrodinger.utils.compare) (in module schrodinger.utils.featureflags.featureflags) (in module schrodinger.utils.featureflags.write) (in module schrodinger.utils.installation_check) (in module schrodinger.utils.machid) (in module schrodinger.utils.postinstall) (schrodinger.stepper.app.StepperApplication class method) main_msj_fname (schrodinger.application.desmond.starter.generator.fep_residue_scanning.JobPreparedFiles attribute) main_st (schrodinger.application.matsci.species.SUB_STRUCT_INFO attribute) main_wrapper() (in module schrodinger.job.driver_decorator) (in module schrodinger.utils.cmdline) mainDone (schrodinger.tasks.tasks.SignalTask attribute) mainFunction() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask method) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask method) (schrodinger.application.glide.ligand_designer.BuildServerTask method) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask method) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask method) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask method) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask method) (schrodinger.application.livedesign.export_tasks.MasterExportTask method) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask method) (schrodinger.application.livedesign.ld_tasks.ImportTask method) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask method) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask method) (schrodinger.application.prepwizard2.tasks.CleanupTask method) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask method) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask method) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask method) (schrodinger.application.prepwizard2.tasks.PreprocessTask method) (schrodinger.protein.predictors.PredictorWrapperTask method) (schrodinger.protein.tasks.blast.BlastTask method) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask method) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask method) (schrodinger.protein.tasks.kinase.KinaseFeatureTask method) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask method) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager method) (schrodinger.stepper.stepper.StepJobTask method) (schrodinger.stepper.stepper.StepTaskMixin method) (schrodinger.tasks.ldtasks.LDTask method) mainLoop() (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) (schrodinger.active_learning.mq_worker.Worker method) mainProduct() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.prime.MMGBSAStage method) maintain_planarity (schrodinger.structutils.minimize.Minimizer property) maintainFileChoice() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) maintainVerticalScroll() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) major (schrodinger.application.livedesign.ldclient_proxy.Version attribute) make() (schrodinger.application.desmond.new_fep_edge_data.ResData static method) make_3D_grid() (in module schrodinger.application.mopac.mopac_surfaces) make_alignment_seq_with_analogs() (in module schrodinger.livedesign.biologics.sequence) make_backend_command() (in module schrodinger.application.phase.packages.phase_database_job_utils) make_canonical_solvent() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) make_cdr_shifts() (in module schrodinger.application.bioluminate.antibody.grafting) make_chorus_orthorhombic() (in module schrodinger.application.matsci.desmondutils) make_color_asl_for_element() (in module schrodinger.application.bioluminate.pml_menus) make_database() (in module schrodinger.application.vss.pilot) make_desres_about_button() (in module schrodinger.ui.qt.appframework) make_desres_layout() (in module schrodinger.ui.qt.appframework) make_dise_job() (in module schrodinger.application.vss.tasks) make_display_command() (in module schrodinger.application.phase.packages.phase_utils) make_empty_restraints() (in module schrodinger.application.desmond.cmj) make_fep_cmd() (in module schrodinger.application.desmond.fep_scholar_util) (in module schrodinger.application.desmond.feputils) make_fp_generator() (in module schrodinger.utils.multifpfile) make_fp_generator_from_canvas_fpfile() (in module schrodinger.application.hitexpander) make_get_job_spec_from_args() (in module schrodinger.tasks.cmdline) (in module schrodinger.tasks.ldtasks) make_glide_al_jobs() (in module schrodinger.application.vss.tasks) make_glide_jobs() (in module schrodinger.application.vss.tasks) make_job() (in module schrodinger.application.vss.tasks) make_ld_item_tree() (in module schrodinger.application.livedesign.panel_components) make_ligand_ml_jobs() (in module schrodinger.application.vss.tasks) make_ligand_ml_training_set() (in module schrodinger.application.vss.tasks) make_ligand_name() (in module schrodinger.protein.annotation) make_ligand_name_atom() (in module schrodinger.protein.annotation) make_local_protein() (schrodinger.protein.analysis.Report method) make_main() (in module schrodinger.tasks.cmdline) (in module schrodinger.tasks.ldtasks) make_mapper() (in module schrodinger.models.mappers) make_model() (in module schrodinger.tasks.ldtasks) make_my_signal() (schrodinger.application.jaguar.simple_spec.Peak method) make_nmr_acs_summary_string() (in module schrodinger.application.jaguar.simple_spec) make_one_letter_map() (in module schrodinger.protein.residue) make_outmaefile() (in module schrodinger.application.jaguar.file_logger) make_p1() (in module schrodinger.application.matsci.nano.xtal) make_parser_from_task_class() (in module schrodinger.tasks.cmdline) make_parser_from_task_class_dict() (in module schrodinger.tasks.cmdline) make_pos_restraints() (in module schrodinger.application.matsci.desmondutils) make_prop_dict() (in module schrodinger.application.livedesign.export_models) make_property() (in module schrodinger.application.desmond.ffiostructure) make_property_fepio() (in module schrodinger.application.desmond.ffiostructure) make_protocol() (in module schrodinger.tasks.ldtasks) make_recovery_table() (in module schrodinger.active_learning.al_report) make_regress_recovery_plots() (in module schrodinger.active_learning.al_report) make_reverse_mutation() (schrodinger.application.bioluminate.mutation.Mutation method) make_scheme_cb() (in module schrodinger.application.bioluminate.antibody.utils) make_score_hist_plot() (in module schrodinger.active_learning.al_report) make_scratch_dir() (in module schrodinger.application.mopac.utils) make_sequence() (in module schrodinger.protein.sequence) make_shape_jobs() (in module schrodinger.application.vss.tasks) make_smapfile() (in module schrodinger.application.jaguar.file_logger) make_standardized_df() (in module schrodinger.application.bioluminate.pose_filtering.test) make_structure_dummy() (in module schrodinger.application.desmond.util) make_task_from_parsed_args() (in module schrodinger.tasks.cmdline) make_three_letter_map() (in module schrodinger.protein.residue) make_train_report() (in module schrodinger.active_learning.al_report) make_validate_command() (in module schrodinger.application.phase.packages.phase_database_arg_utils) make_variants() (in module schrodinger.protein.residue) makeAndAddOutputRow() (schrodinger.tasks.ldtasks.LDTask method) makeAutoSpec() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec class method) makeBilbaoPhase() (in module schrodinger.application.matsci.gsas.GSASIIlattice) makeBinPoint() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) makeButton() (schrodinger.ui.qt.appframework2.af2.BaseBottomBar method) makeCartesianCoords() (schrodinger.application.jaguar.input.JaguarInput method) makeCmd() (schrodinger.application.desmond.feputils.ProteinReliabilityTask method) (schrodinger.application.glide.ligand_designer.GridgenTask method) (schrodinger.application.livedesign.tasks.AlignLigandsTask method) (schrodinger.application.livedesign.tasks.CanvasSearchTask method) (schrodinger.application.livedesign.tasks.CovDockTask method) (schrodinger.application.livedesign.tasks.EpikClassicTask method) (schrodinger.application.livedesign.tasks.EpikTask method) (schrodinger.application.livedesign.tasks.FlexAlignTask method) (schrodinger.application.livedesign.tasks.GlideTask method) (schrodinger.application.livedesign.tasks.LigandStrainTask method) (schrodinger.application.livedesign.tasks.LigFilterTask method) (schrodinger.application.livedesign.tasks.LigPrepTask method) (schrodinger.application.livedesign.tasks.MemPermTask method) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask method) (schrodinger.application.livedesign.tasks.QikPropTask method) (schrodinger.application.livedesign.tasks.RBSSTask method) (schrodinger.application.livedesign.tasks.StrainRescoreTask method) (schrodinger.application.livedesign.tasks.TugAlignTask method) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask method) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask method) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask method) (schrodinger.protein.predictors.AbstractPredictor method) (schrodinger.protein.predictors.AccproPredictor method) (schrodinger.protein.predictors.BetaproPredictor method) (schrodinger.protein.predictors.DiproPredictor method) (schrodinger.protein.predictors.DisproPredictor method) (schrodinger.protein.predictors.DomproPredictor method) (schrodinger.protein.predictors.SsproPredictor method) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask method) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask method) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask method) (schrodinger.protein.tasks.kinase.KinaseConservationTask method) (schrodinger.protein.tasks.pfam.PfamTask method) (schrodinger.protein.tasks.sta.STATask method) (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.jobtasks.JobBackendCmdMixin method) (schrodinger.tasks.tasks.AbstractCmdTask method) (schrodinger.tasks.tasks.AbstractComboTask method) MakeConsistent() (in module schrodinger.analysis.visanalysis.volumedatautils) makeCustomButtons() (schrodinger.ui.qt.appframework2.af2.BaseBottomBar method) makeDict() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog static method) makeEdge() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) makeEdges() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) makeFFTsizeList() (in module schrodinger.application.matsci.gsas.GSASIIpwd) makeFingerPrintInfile() (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) makeFpOptionsDict() (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) makeFragment() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) makeInitialModel() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.qt.tasks.configwidgets.ConfigWidgetMixin method) (schrodinger.ui.qt.tasks.taskbarwidgets.TaskWidgetMixin method) (schrodinger.ui.qt.tasks.taskwidgets.AbstractTaskBar method) makeInputArgsFile() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage method) makeInstDict() (in module schrodinger.application.matsci.gsas.GSASIIfiles) makeInternalCoords() (schrodinger.application.jaguar.input.JaguarInput method) makeIter() (schrodinger.structutils.rgroup_enumerate.RGroupSource method) makeJobSpec() (schrodinger.application.matsci.multiapp.MultiJobApp method) makeLauncher() (schrodinger.ui.qt.appframework2.af2.JobApp method) makeLigandASL() (schrodinger.application.bioluminate.pml_menus.LigandActionMixin method) makeListOf() (in module schrodinger.ui.qt.dendrogram) makeLogEntry() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) makeMaestroInfile() (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) makeMEMfile() (in module schrodinger.application.matsci.gsas.GSASIIpwd) makeMultiWalledTubes() (schrodinger.application.matsci.nano.tube.NanoTubes method) makeMutation() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator static method) (schrodinger.application.bioluminate.nucleic.mutator.NucleobaseMutator static method) makeNanoSheets() (schrodinger.application.matsci.nano.sheet.NanoSheets method) makeNestedRowVisible() (schrodinger.infra.table.Table method) makeNode() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) makeNodes() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) makePRFfile() (in module schrodinger.application.matsci.gsas.GSASIIpwd) MakeProjectEntry (class in schrodinger.application.bioluminate.pml_menus) makeQuat() (in module schrodinger.application.matsci.gsas.GSASIImath) Maker (class in schrodinger.application.matsci.etatoggle) MakeRDF() (in module schrodinger.application.matsci.gsas.GSASIIpwd) makeRefdFFT() (in module schrodinger.application.matsci.gsas.GSASIIpwd) makeReply() (schrodinger.tasks.taskszmq.ZmqServer method) makeReport() (schrodinger.tasks.queue.QueueResults method) makeRowObject() (schrodinger.application.combiglide.corehop.AttachmentPoint method) makeRxnComplex() (schrodinger.application.matsci.rxn_path.ReactionCoords method) makeSelection() (schrodinger.application.bioluminate.pml_menus.GenerateSelection method) makeSeqElement() (schrodinger.protein.sequence.AbstractSingleChainSequence class method) makeSingleWalledTubes() (schrodinger.application.matsci.nano.tube.NanoTubes method) makeSLDprofile() (in module schrodinger.application.matsci.gsas.GSASIIpwd) makeSpectrum() (schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor method) (schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum method) makeString() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog static method) makeTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) makeTsched() (in module schrodinger.application.matsci.gsas.GSASIImath) makeVariant() (schrodinger.protein.residue.ElementType method) makeWaves() (in module schrodinger.application.matsci.gsas.GSASIImath) makeWavesDerv() (in module schrodinger.application.matsci.gsas.GSASIImath) mALPHA() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) manage_failures_callback() (in module schrodinger.application.matsci.genetic_optimization) manage_skips_callback() (in module schrodinger.application.matsci.genetic_optimization) ManagePresetsDialog (class in schrodinger.ui.qt.presets.manage_presets_dialog) ManagePresetsModel (class in schrodinger.ui.qt.presets.manage_presets_dialog) ManagePresetsTableSpec (class in schrodinger.ui.qt.presets.manage_presets_dialog) manageTemplates() (schrodinger.application.matsci.builderwidgets.SketcherBox method) manageXvolIsOpen() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) MANUAL (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PickingModes attribute) MANUAL_SEQUENCE (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) Map (class in schrodinger.utils.sea.sea) map() (schrodinger.application.matsci.automated_cg_mapping.AutomatedCGMapping method) (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) (schrodinger.application.matsci.automated_cg_mapping.DpdMapper method) (schrodinger.application.matsci.automated_cg_mapping.MartiniMapper method) map_by_lone_element() (in module schrodinger.application.matsci.reorder) map_by_smarts() (in module schrodinger.application.matsci.reorder) map_by_smiles() (in module schrodinger.application.matsci.reorder) map_by_superposition() (in module schrodinger.application.matsci.reorder) map_chains() (in module schrodinger.application.bioluminate.antibody.assembly) map_corresponding_atoms_by_alignment() (in module schrodinger.structutils.structalign2) MAP_COUNTER_LABEL (schrodinger.application.matsci.reordergui.ReorderAtomFrame attribute) MAP_ERROR_MSG (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) MAP_EXISTS_MSG (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog attribute) map_file_path (schrodinger.application.livedesign.export_models.FileBatch attribute) map_file_pathChanged (schrodinger.application.livedesign.export_models.FileBatch attribute) map_file_pathReplaced (schrodinger.application.livedesign.export_models.FileBatch attribute) map_hydrogens() (in module schrodinger.application.matsci.reorder) map_neighboring_hydrogens() (in module schrodinger.application.matsci.reorder) map_reaction() (in module schrodinger.livedesign.setup_reaction) map_subparams() (in module schrodinger.models.paramtools) map_to_struct (schrodinger.application.jaguar.nmr_utils.NMRData attribute) mapAtom() (schrodinger.application.matsci.reordergui.ReferenceFrame method) (schrodinger.application.matsci.reordergui.StructureFrame method) mapCGStructure() (schrodinger.application.matsci.cg_mapping.CGMapper method) mapCompAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) mapFunction() (schrodinger.application.steps.converters.MolToSmilesConverter method) (schrodinger.application.steps.converters.MolToStructureConverter method) (schrodinger.application.steps.converters.SmilesToMolConverter method) (schrodinger.application.steps.converters.StructureToMolConverter method) (schrodinger.application.steps.docking.GlideDocker method) (schrodinger.application.steps.docking.MaeGlideDocker method) (schrodinger.application.steps.docking.SmilesDocker method) (schrodinger.application.steps.enumerators.Decorator method) (schrodinger.application.steps.enumerators.FastDecorator method) (schrodinger.application.steps.enumerators.FastFragmenter method) (schrodinger.application.steps.enumerators.RouteEnumerator method) (schrodinger.application.steps.enumerators.RouteEvaluator method) (schrodinger.application.steps.enumerators.TransformApplyer method) (schrodinger.application.steps.filters.ChiralCenterCountFilter method) (schrodinger.application.steps.filters.FepFilter method) (schrodinger.application.steps.filters.MaeUniqueSmilesFilter method) (schrodinger.application.steps.filters.MaxMolWtFilter method) (schrodinger.application.steps.filters.ProductFilterMixin method) (schrodinger.application.steps.filters.ProfileFilter method) (schrodinger.application.steps.filters.PropertyFilter method) (schrodinger.application.steps.filters.RangeFilter method) (schrodinger.application.steps.filters.SmartsFilter method) (schrodinger.application.steps.ligprep.LigandPrepper method) (schrodinger.application.steps.ligprep.LigPrepStep method) (schrodinger.application.steps.transformers.Standardizer method) (schrodinger.application.steps.transformers.StereoChemistryRemover method) (schrodinger.stepper.stepper.MapStep method) (schrodinger.stepper.stepper.UnbatchedMapStep method) MappableAtomSelector (class in schrodinger.ui.qt.atomselector) MappableButtonGroup (class in schrodinger.ui.qt.datamapper) mapPair() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) MAPPED_ATOM_INDEX (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer attribute) mappedParams() (schrodinger.models.mappers.MapperMixin method) (schrodinger.models.mappers.TargetParamMapper method) mapper() (schrodinger.application.matsci.automated_cg_mapping.MappingMethod static method) MAPPER_INDEX (schrodinger.comparison.atom_mapper.BaseAtomMapper attribute) mapper_params (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.MapperWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ProteinWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.SolubilityWorkflowParams attribute) MapperMixin (class in schrodinger.models.mappers) MapperMsjGenerator (in module schrodinger.application.desmond.msj_generator.common) MapperParams (class in schrodinger.application.desmond.msj_generator.workflow_params) MapperWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) Mapping (class in schrodinger.application.matsci.automated_cg_mapping) (class in schrodinger.utils.pymol) mapping_dist (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) mapping_distChanged (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) mapping_distReplaced (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) mapping_model (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) mapping_modelChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) mapping_modelReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) MappingAnnotator (class in schrodinger.application.desmond.fep_scholar_util) MappingError, [1] MappingManagerDialog (class in schrodinger.application.livedesign.export_map_manager) MappingMethod (class in schrodinger.application.matsci.automated_cg_mapping) MappingMode (class in schrodinger.application.livedesign.mapping_widgets) mappingSaved (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) MappingsComboBox (class in schrodinger.application.livedesign.export_map_manager) mappingSelected (schrodinger.application.livedesign.export_map_manager.MappingsComboBox attribute) MappingValidator (class in schrodinger.application.matsci.automated_cg_mapping) mapResidue() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) MapScore (class in schrodinger.application.jaguar.autots_rmsd) (class in schrodinger.comparison.atom_mapper) MapStep (class in schrodinger.stepper.stepper) mapSubgraph() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) mapSymmRingFragment() (schrodinger.application.matsci.automated_cg_mapping.MartiniMapper method) mapTaggedAtoms() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) mapToMaestroColor() (schrodinger.ui.qt.swidgets.ColorWidget method) MARGIN (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) (schrodinger.ui.qt.table_helper.SampleDataTableViewMixin attribute) mark() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.ui.two_d_viewer.TwoDViewer method) mark_atom() (in module schrodinger.application.desmond.maestro) (schrodinger.application.desmond.maestro.Workspace method) mark_eta_positions() (in module schrodinger.application.matsci.buildcomplex) mark_fullsystem_ct() (in module schrodinger.application.desmond.cms) mark_monomer_head_and_tail() (in module schrodinger.application.matsci.amorphous) mark_monomer_head_tail_ce_th() (in module schrodinger.application.matsci.amorphous) mark_monomer_head_tail_dummy() (in module schrodinger.application.matsci.amorphous) mark_monomer_head_tail_rx() (in module schrodinger.application.matsci.amorphous) mark_orig_atom_idx() (in module schrodinger.application.matsci.amorphous) markAtomMapped() (schrodinger.application.matsci.reordergui.ComparisonListWidget method) (schrodinger.application.matsci.reordergui.ReferenceListWidget method) (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.application.matsci.reordergui.StructurePic method) markAtomsBeforeSpearCheck() (schrodinger.structutils.ringspear.SpearRing static method) markAtomsInWS() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) markAtomUnmapped() (schrodinger.application.matsci.reordergui.ReferenceListWidget method) (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.application.matsci.reordergui.StructurePic method) markBackboneAtom() (schrodinger.application.matsci.amorphous.BaseMoiety method) markBond() (schrodinger.application.matsci.amorphous.BaseMoiety method) markBranchingFrag() (schrodinger.application.matsci.amorphous.PolymerFragment method) markCGBonds() (schrodinger.application.matsci.cg_mapping.CGMapper method) MARKER_SCALING_FACTOR (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama attribute) (schrodinger.ui.qt.rama.RamaScatterMixin attribute) MARKER_SETTINGS (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute) MARKER_TAB_CLASSES (schrodinger.application.jaguar.gui.base_panel.MarkerMixin attribute) (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin attribute) (schrodinger.application.jaguar.gui.base_panel.OptimizationTabMarkerMixin attribute) (schrodinger.application.jaguar.gui.base_panel.ScanTabMarkerMixin attribute) MarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) (class in schrodinger.ui.qt.appframework2.markers) markerTextToggled (schrodinger.application.phase.phase_markers.PhaseMarkers attribute) markForRestart() (schrodinger.job.queue.JobDJ method) markHeadTailLabels() (schrodinger.application.matsci.amorphous.BaseMoiety method) markMoietiesProps() (schrodinger.application.matsci.amorphous.PolymerFragments method) markOriginalAtomIds() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer static method) markParticleAtoms() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) markRAtomValues() (schrodinger.application.matsci.buildcomplex.ComplexSplitter static method) markShiftedDesignators() (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector method) markSidegroupFrag() (schrodinger.application.matsci.amorphous.PolymerFragment method) markSuggestedAtom() (schrodinger.application.matsci.reordergui.ComparisonListWidget method) markSuggestedAtomsInWS() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) markup (schrodinger.application.matsci.typography.TYPO_TYPE attribute) MartiniMapper (class in schrodinger.application.matsci.automated_cg_mapping) MartiniMolecule (class in schrodinger.application.matsci.automated_cg_mapping) MartiniMolecule.RING_INFO (class in schrodinger.application.matsci.automated_cg_mapping) MartiniProteinFFCleaner (class in schrodinger.application.matsci.cgforcefield) MartiniResidueData (class in schrodinger.application.matsci.automated_cg_mapping) mask() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) MASKED_COLOR (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) mass (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) MASS_DENSITY_KEY (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) MASS_H (schrodinger.application.steps.enumerators.FastFragmenter attribute) MASS_H2 (schrodinger.application.steps.enumerators.FastFragmenter attribute) massage_isub_option() (in module schrodinger.application.hitexpander) massChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) massReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) MasterExportTask (class in schrodinger.application.livedesign.export_tasks) MasterExportTask.Output (class in schrodinger.application.livedesign.export_tasks) match() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.matsci.smartsutils.SMARTSGroup method) match_by_cartesian_coordinates() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) match_by_distance() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) match_compounds_by (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) match_compounds_byChanged (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) match_compounds_byReplaced (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) match_compstr() (schrodinger.utils.ligfilter.Criterion method) match_core_hydrogens() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) match_hbond() (in module schrodinger.structutils.interactions.hbond) match_maestro_style (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) match_maestro_styleChanged (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) match_maestro_styleReplaced (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) match_prop_data_name (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) match_prop_data_nameChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) match_prop_data_nameReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) match_prop_user_name (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) match_prop_user_nameChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) match_prop_user_nameReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) matchAny() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) MatchCompoundsBy (class in schrodinger.application.livedesign.export_models) matched_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property) matched_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property) matches() (schrodinger.application.bioluminate.propfilter.StringDatabaseCriterion method) (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.utils.ligfilter.AslCriterion method) (schrodinger.utils.ligfilter.Criterion method) (schrodinger.utils.ligfilter.PredefinedCriterion method) (schrodinger.utils.ligfilter.PropertyCriterion method) (schrodinger.utils.ligfilter.SmartsCriterion method) matches_canonical_filename() (in module schrodinger.application.licensing.flexlm) matchesException() (schrodinger.tasks.tasks.FailureInfo method) matchesRequirement() (schrodinger.job.queue.ResourceHost method) MATCHING (schrodinger.trajectory.trajectory_gui_dir.display_settings_data.DisplayOnly attribute) matchIsomorphicGraphs() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) matchRange() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) matdynStr() (schrodinger.application.matsci.espresso.qeinput.KpointsType method) MATERIALS_SCIENCE (schrodinger.application.livedesign.ldclient_proxy.LDMode attribute) MatplotCanvas (class in schrodinger.ui.qt.matplot_widget) MatplotlibDelegate (class in schrodinger.ui.qt.delegates) MatplotWidget (class in schrodinger.ui.qt.matplot_widget) matrix_cofactor() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) matrix_matches (schrodinger.structutils.sitealign.BindingSiteAligner attribute) matrix_reciprocal() (in module schrodinger.application.canvas.topo_descriptors) matrix_to_vector() (in module schrodinger.application.matsci.mecp_mod) MATSCI_ABBE_NUMBER (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) MATSCI_ANALYSIS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) matsci_application_testfile() (in module schrodinger.application.matsci.mstest) MATSCI_ENGINE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) matsci_scripts_testfile() (in module schrodinger.application.matsci.mstest) MatSciAnalysis (class in schrodinger.application.desmond.stage.app.matsci) MatSciAppMixin (class in schrodinger.application.matsci.appbase) MatSciDatabaseManager (class in schrodinger.application.matsci.kmc) MatSciMDRelaxationStep (class in schrodinger.application.matsci.jwsteps) MatSciPairsTable (class in schrodinger.application.matsci.kmc) MatSciSitesTable (class in schrodinger.application.matsci.kmc) matter_is_conserved() (in module schrodinger.application.jaguar.autots_validation) MATURE_AFEP (schrodinger.application.desmond.systype.DesmondTyper attribute) MATURE_FEP (schrodinger.application.desmond.systype.DesmondTyper attribute) MATURE_REGULAR (schrodinger.application.desmond.systype.DesmondTyper attribute) max (schrodinger.application.desmond.new_fep_edge_data.TorsionPotential property) MAX (schrodinger.application.matsci.genetic_optimization.Property attribute) MAX_ANGLE (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) max_atom_count (schrodinger.structutils.analyze.AslLigandSearcher property) MAX_ATOM_NUM (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) max_atomic_displacement_and_rmsd() (in module schrodinger.application.glide.utils) max_b_factor (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin property) MAX_CARBOXYLIC_ACID_INTERACTION_DISTANCE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MAX_COL (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) max_complexity (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) max_complexityChanged (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) max_complexityReplaced (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) max_connect_distance() (in module schrodinger.application.matsci.nano.xtal) MAX_CUTOFF (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) MAX_DIEL_LOSS_FREQ_PROP (schrodinger.application.matsci.permittivity.ComplexPermittivity attribute) MAX_DIEL_LOSS_VAL_PROP (schrodinger.application.matsci.permittivity.ComplexPermittivity attribute) MAX_FILE_SIZE_GB (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin attribute) max_force_thr (schrodinger.application.matsci.espresso.qeinput.DimerNEBType attribute) MAX_FRAME_DURATION (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) max_frame_value (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator property) max_hac_diff (schrodinger.application.steps.filters.FepFilter.Settings attribute) max_hac_diffChanged (schrodinger.application.steps.filters.FepFilter.Settings attribute) max_hac_diffReplaced (schrodinger.application.steps.filters.FepFilter.Settings attribute) max_hbond_distance (schrodinger.protein.assignment.ProtAssign.changeable attribute) MAX_METAL_INTERACTION_DISTANCE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) max_mol_wt (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.filters.MaxMolWtFilter.Settings attribute) max_mol_wtChanged (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.filters.MaxMolWtFilter.Settings attribute) max_mol_wtReplaced (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.filters.MaxMolWtFilter.Settings attribute) MAX_N_CONFORMERS_LABEL (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection attribute) MAX_NUM_ATOMS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) MAX_NUM_TRACE (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) MAX_NUM_UNPRODUCTIVE_CYCLES (schrodinger.application.matsci.rxn_channel.ChannelDefinitions attribute) max_out (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) max_outChanged (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) max_outReplaced (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) max_pair_vdw_distance() (in module schrodinger.application.matsci.rxn_path) MAX_PEPTIDE_BOND_LENGTH (schrodinger.protein.analysis.Report.peptide_planarity_data_set attribute) MAX_PI_ARG_INTERACTION_DISTANCE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MAX_PI_CATION_INTERACTION_ANGLE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MAX_PI_CATION_INTERACTION_DISTANCE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MAX_PI_PI_INTERACTION_ANGLE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MAX_PI_PI_INTERACTION_DISTANCE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) max_pose_torsion_diff() (in module schrodinger.application.glide.utils) max_potential_energy (schrodinger.application.desmond.fep_edge_data.FEPTorsions property) max_products (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) max_productsChanged (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) max_productsReplaced (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) max_progress (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.tasks.tasks.AbstractTask attribute) max_progressChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) max_progressReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) MAX_REDUCED_DISPLACEMENT (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) MAX_REPLICATE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) MAX_ROW_COUNT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) max_running_tasks (schrodinger.tasks.queue.TaskQueue attribute) max_running_tasksChanged (schrodinger.tasks.queue.TaskQueue attribute) max_running_tasksReplaced (schrodinger.tasks.queue.TaskQueue attribute) max_score (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) max_scoreChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) max_scoreReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) max_selected_items (schrodinger.application.matsci.mswidgets.MultiComboWithCount property) max_stack_dist (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) max_stack_distChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) max_stack_distReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) max_states (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) max_statesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) max_statesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) MAX_STATIC_ACCEPTOR_INTERACTION_DISTANCE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MAX_STATIC_DONOR_INTERACTION_DISTANCE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) max_step (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) MAX_STEPS (schrodinger.application.matsci.desconfig.MSJStringer attribute) max_steps (schrodinger.structutils.minimize.Minimizer property) max_subgraph_size (schrodinger.application.jaguar.nmr_utils.NMRData attribute) (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) MAX_SUBJOBS_LABEL_TEXT (schrodinger.application.desmond.fep_dialog.FEPConfigDialog attribute) (schrodinger.application.matsci.configdlgs.PerStructDesmondSubhostConfigDialog attribute) MAX_SUBTASKS (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) MAX_THREAD_TASKS (schrodinger.tasks.tasks.ThreadMixin attribute) MAX_THUMBS (schrodinger.application.matsci.mswidgets.MultiSlider attribute) MAX_TIME (schrodinger.protein.assignment.NetworkSolver attribute) MAX_TITLE_LENGTH (schrodinger.application.matsci.appbase.StructureLoadButton attribute) MAX_UNIQUE_STR_PROPS (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) MAX_UPTAKE (schrodinger.application.bioluminate.pose_filtering.hdx_io.DynamXColumns attribute) max_value (schrodinger.application.steps.filters.ChiralCenterCountFilter.Settings attribute) (schrodinger.application.steps.filters.RangeFilter.Settings attribute) max_valueChanged (schrodinger.application.steps.filters.ChiralCenterCountFilter.Settings attribute) (schrodinger.application.steps.filters.RangeFilter.Settings attribute) max_valueReplaced (schrodinger.application.steps.filters.ChiralCenterCountFilter.Settings attribute) (schrodinger.application.steps.filters.RangeFilter.Settings attribute) max_walltime (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) max_with_none() (in module schrodinger.utils.withnone) maxFailuresReached() (schrodinger.application.desmond.queue.JobAdapter method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) MaxIdentityAligner (class in schrodinger.protein.align) maximum (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) MAXIMUM (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) maximum_identity (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput attribute) MAXIMUM_ITER_TEXT (schrodinger.application.jaguar.gui.theory_tab_widgets.HFExcitedStateWidget attribute) maximum_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) maximumChanged() (schrodinger.ui.qt.swidgets.MinMaxSpinBoxTether method) MaxIndex() (in module schrodinger.application.matsci.gsas.GSASIIlattice) MAXIT (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) MAXITG (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) MaxJobFailureError MaxMolWtFilter (class in schrodinger.application.steps.filters) MaxMolWtFilter.Settings (class in schrodinger.application.steps.filters) maxNum() (schrodinger.tasks.hosts.Host method) maxsize (schrodinger.application.matsci.cache.CacheInfo attribute) MaxSubjobsConfigDialog (class in schrodinger.application.matsci.configdlgs) mbaeCsLmod() (schrodinger.application.macromodel.utils.ComUtil method) mbaeCsMcmm() (schrodinger.application.macromodel.utils.ComUtil method) mbaeCsMcmmLmod() (schrodinger.application.macromodel.utils.ComUtil method) mbaeMiniEdiff() (schrodinger.application.macromodel.utils.ComUtil method) mbaeMiniInter() (schrodinger.application.macromodel.utils.ComUtil method) mBCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mBOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MBYTE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) mca (schrodinger.application.desmond.driver_utils.MPISettings attribute) mCCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MCG (class in schrodinger.application.scaffold_enumeration.cxsmiles) mcl() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) mclc1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) MCMM (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute) mcmm() (schrodinger.application.macromodel.utils.ComUtil method) mcmmllmd() (schrodinger.application.macromodel.utils.ComUtil method) mcmmlmod() (schrodinger.application.macromodel.utils.ComUtil method) mCOLON() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mCOMMA() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mCOMMENT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mCOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) McproTyper (class in schrodinger.application.desmond.systype) MCS (schrodinger.application.livedesign.tasks.CoreAtomsOptions attribute) mcs_timeout_no_skip (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) mcs_timeout_no_skipChanged (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) mcs_timeout_no_skipReplaced (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) mcsaSearch() (in module schrodinger.application.matsci.gsas.GSASIImath) mcsd() (schrodinger.application.macromodel.utils.ComUtil method) MCSFailure MD (schrodinger.application.bioluminate.methionine_oxidation.SamplingMode attribute) (schrodinger.application.desmond.constants.FepLegTypes attribute) (schrodinger.application.desmond.constants.KineticsLegTypes attribute) (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) md (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) MD (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.ui.qt.standard.design_tokens.FontSizes attribute) md5sum() (in module schrodinger.application.glide.ligand_designer) MD_COMPLEX_PERMITTIVITY_FILE_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) md_lic() (in module schrodinger.application.desmond.license) md_msj_fname (schrodinger.application.desmond.starter.generator.fep_residue_scanning.JobPreparedFiles attribute) md_sim_time (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) MdAnalyzer (class in schrodinger.application.bioluminate.methionine_oxidation) MDC_DEFAULT_HEIGHT (schrodinger.application.desmond.gui.AdvOptionsFrame attribute) MDC_DEFAULT_WIDTH (schrodinger.application.desmond.gui.AdvOptionsFrame attribute) MdcAdvancedDialog (class in schrodinger.application.desmond.gui) MdcMiscTab (class in schrodinger.application.desmond.gui) MDCustomMSJStep (class in schrodinger.application.matsci.jwsteps) MdGroup (class in schrodinger.application.desmond.gui) mDIGIT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mDIVOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MDL_MOLV2000 (schrodinger.rdkit_extensions.Format attribute) MDL_MOLV3000 (schrodinger.rdkit_extensions.Format attribute) MdlFileReader (class in schrodinger.application.scaffold_enumeration.mdl) MDMSJStringer (class in schrodinger.application.matsci.desconfig) MdPostAnalysis (class in schrodinger.application.matsci.permittivity) MdPostTrajectoryAnalysis (class in schrodinger.application.matsci.permittivity) MdStageModifier (class in schrodinger.application.matsci.permittivity) MdStats (class in schrodinger.application.bioluminate.methionine_oxidation) MdType (class in schrodinger.application.matsci.espresso.qeinput) mdyn() (schrodinger.application.macromodel.utils.ComUtil method) MDynePerAngstrom (schrodinger.application.jaguar.constants.Unit attribute) mean (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis.SysDipole attribute) mean_hydrophobicity (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) mean_isoelectric_point (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) mean_stress (schrodinger.application.matsci.elasticity.stress.Stress property) MeanConsecutiveRBCount() (in module schrodinger.rdkit.filtering) measure() (in module schrodinger.protein.assignment) (schrodinger.structure.Structure method) measure_angle_between_rings() (in module schrodinger.structutils.measure) measure_bond_angle() (in module schrodinger.structutils.measure) measure_dihedral_angle() (in module schrodinger.structutils.measure) measure_distance() (in module schrodinger.structutils.measure) measure_plane_angle() (in module schrodinger.structutils.measure) measure_vectors() (in module schrodinger.application.pathfinder.multiroute) measureDepth() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) (schrodinger.application.matsci.density_analysis_widget.CustomToolbar method) Measurement (class in schrodinger.application.desmond.measurement) MeasurementLine (class in schrodinger.application.matsci.density_analysis_widget) MeasurementMode (class in schrodinger.trajectory.trajectory_gui_dir.banners) MeasurementTableFrame (class in schrodinger.application.matsci.density_analysis_widget) MECP (class in schrodinger.application.matsci.mecp_mod) MECPStep (class in schrodinger.application.matsci.mecp_mod) median_sublimation_free_energy() (in module schrodinger.application.desmond.solubility_utils) MEDIUM (schrodinger.application.matsci.qualityslider.QualitySlider attribute) Medium (schrodinger.protein.annotation.KinaseConservation attribute) MEDIUM (schrodinger.trajectory.trajectory_gui_dir.export_movie.Quality attribute) MEDIUMSCORE (schrodinger.protein.predictors.Disordered attribute) mem_usage() (schrodinger.application.desmond.memory.MemoryGauger method) members (schrodinger.application.jaguar.simple_spec.Peak attribute) members_jnames (schrodinger.application.jaguar.simple_spec.Peak attribute) MEMBRANE (schrodinger.application.desmond.constants.REST_COMPONENT attribute) membrane (schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) (schrodinger.application.desmond.struc.CompStruc attribute) MEMBRANE (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) MEMBRANE_ENVIRON (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) Membrane_Model (class in schrodinger.protein.membrane) MEMO_RULE_FAILED (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) MEMO_RULE_UNKNOWN (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) memoize() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) memoized_method() (in module schrodinger.application.matsci.cache) MemoizeJac (class in schrodinger.application.jaguar.qrnn.temp_opt) memory_leak_server() (schrodinger.application.licensing.licadmin.LicenseResource method) MEMORY_MSG (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin attribute) memory_usage_psutil() (in module schrodinger.application.matsci.jobutils) MemoryEstimator (class in schrodinger.application.matsci.espresso.utils) MemoryGauger (class in schrodinger.application.desmond.memory) MemPermTask (class in schrodinger.application.livedesign.tasks) MemPermTask.Input (class in schrodinger.application.livedesign.tasks) MemPermTask.JobConfig (class in schrodinger.application.livedesign.tasks) MemPermTask.Output (class in schrodinger.application.livedesign.tasks) MEMupdateReflData() (in module schrodinger.application.matsci.gsas.GSASIIpwd) MenuLink (class in schrodinger.ui.qt.standard_widgets.hyperlink) menus (schrodinger.application.matsci.species.SC_TYPE_DATA attribute) mEQ() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) merge() (schrodinger.application.glide.sort_utils.GlideSortUtility method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.structure.Structure method) (schrodinger.ui.qt.network_visualizer.Graph method) merge_atom_group() (schrodinger.application.desmond.cms.Cms method) (schrodinger.application.desmond.stage.utils.SystemBuilder static method) merge_atom_group_from_asl() (schrodinger.application.desmond.cms.Cms method) merge_biologic_unit() (schrodinger.protein.getpdb_utility.Code method) merge_csv_files() (in module schrodinger.application.bioluminate.drivers.io) merge_ct() (in module schrodinger.application.desmond.ffiostructure) merge_dicts() (in module schrodinger.protein.residue) merge_files() (in module schrodinger.structutils.sort) merge_files_as_streams() (in module schrodinger.rdkit.molio) merge_files_in_memory() (in module schrodinger.rdkit.molio) merge_group() (schrodinger.application.desmond.cms.RestrainGroupContainer method) merge_ligand_files() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) merge_membrane_and_cosolvent_systems() (in module schrodinger.application.desmond.mxmd.mxmd_system_builder) merge_oned_data_files() (in module schrodinger.application.phase.packages.oned_task_utils) merge_oned_hits_files() (in module schrodinger.application.phase.packages.oned_task_utils) (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) merge_oplsdir() (in module schrodinger.forcefield.custom_params) merge_pv_files() (in module schrodinger.structutils.sort) merge_restrain() (schrodinger.application.desmond.stage.utils.SystemBuilder static method) merge_single() (schrodinger.application.desmond.cms.DictRestrainGroup method) (schrodinger.application.desmond.cms.PosRestrainArray method) (schrodinger.application.desmond.cms.RestrainGroup method) (schrodinger.application.desmond.cms.RestrainGroupContainer method) merge_st_iters() (in module schrodinger.structutils.sort) merge_subunit_sts() (in module schrodinger.structutils.build) merge_with() (schrodinger.application.desmond.cms.DictRestrainGroup method) (schrodinger.application.desmond.cms.PosRestrainArray method) (schrodinger.application.desmond.cms.Restrain method) (schrodinger.application.desmond.cms.RestrainGroup method) mergeByIndex() (schrodinger.application.canvas.utils.ChmCSVTools method) mergeByName() (schrodinger.application.canvas.utils.ChmCSVTools method) MergeDuplicatesStage (class in schrodinger.pipeline.stages.filtering) mergeGlideOutputs() (schrodinger.pipeline.stages.glide.DockingStage method) mergeNonbonds() (schrodinger.application.matsci.coarsegrain.Internals method) mergeRings() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) MergeStage (class in schrodinger.pipeline.stages.glide) MERIDIONAL (in module schrodinger.application.matsci.buildcomplex) mesh (schrodinger.surface.Style attribute) (schrodinger.surface.Surface.Style attribute) message (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.tasks.tasks.FailureInfo attribute) MessageBox (class in schrodinger.ui.qt.messagebox) MessageBoxMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) MessageButton (class in schrodinger.trajectory.trajectory_gui_dir.trajectory_messages) messageChanged (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.tasks.tasks.FailureInfo attribute) messageReplaced (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.tasks.tasks.FailureInfo attribute) MessageType (class in schrodinger.trajectory.trajectory_gui_dir.advanced_settings) Meta (class in schrodinger.application.desmond.enhsamp) (class in schrodinger.application.desmond.meta) META (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) meta (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) META_ASL (schrodinger.application.desmond.cms.Cms attribute) meta_sample() (in module schrodinger.application.pathfinder.multiroute) meta_template (schrodinger.application.desmond.meta.Meta attribute) meta_term() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) meta_well_tempered_template (schrodinger.application.desmond.meta.Meta attribute) MetaAtom (class in schrodinger.application.desmond.fep_scholar_util) metadata (schrodinger.application.phase.packages.shape_binary_utils.ShapeFileReader property) MetaDynamicsAnalysis (class in schrodinger.application.desmond.meta) MetadynamicsAnalysisJob (class in schrodinger.application.desmond.stage.analysis) METAL_BINDER_PROP (schrodinger.application.matsci.buildcomplex.ComplexSplitter attribute) metal_interactions() (schrodinger.protein.assignment.HistidinepKaPredictor method) metal_ligand_cutoff (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) METAL_OR_ION (schrodinger.application.prepwizard.HetType attribute) METAL_PKA_SHIFT (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MetalConstraint (class in schrodinger.application.glide.glide) MetalForceFieldComponent (class in schrodinger.energy) METALLOPROTEIN (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) MetalloproteinEdgeData (class in schrodinger.application.desmond.fep_edge_data) MetalloproteinMapperParams (class in schrodinger.application.desmond.msj_generator.workflow_params) MetalloproteinWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) MetalMsjGenerator (class in schrodinger.application.desmond.msj_generator.fep.metalloprotein) MetaSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) MetCoordConstraint (class in schrodinger.application.glide.glide) MethionineAnalyzer (class in schrodinger.application.bioluminate.methionine_oxidation) METHOD (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) method (schrodinger.application.matsci.espresso.qeinput.CustomNEBType attribute) (schrodinger.application.mopac.results_main.MopacResultsMain property) method() (in module schrodinger.application.mopac.results_main) METHOD_BUNDLE (schrodinger.application.matsci.automated_cg_mapping.MappingMethod attribute) method_changed (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin attribute) METHOD_NAMEMAP (schrodinger.application.desmond.gui.EnsembleTab attribute) method_synonyms (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain property) methodChanged() (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) MethodDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) methodFiltersChanged (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView attribute) MethodOptionAction (class in schrodinger.application.mopac.mopac_parser) METHODS (schrodinger.application.matsci.automated_cg_mapping.MappingMethod attribute) MethodsDict (class in schrodinger.ui.qt.appframework2.appmethods) methodToggled() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) metrics (schrodinger.seam.runners.events.StageFinished attribute) metricsChanged (schrodinger.seam.runners.events.StageFinished attribute) metricsReplaced (schrodinger.seam.runners.events.StageFinished attribute) Metropolizer (class in schrodinger.application.matsci.montecarlo) mEXP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mexpLexer (class in schrodinger.application.desmond.enhanced_sampling.mexpLexer) mexpLexer.DFA12 (class in schrodinger.application.desmond.enhanced_sampling.mexpLexer) mexpParser (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.atom_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.bind_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.block_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.comp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.decl_meta_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.decl_output_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.decl_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA1 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA15 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA17 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA18 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA19 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA20 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA21 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA22 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA24 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA25 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.expComp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.expr_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.exprOrBind_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.factor_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.fcnCall_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.header_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.if__return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.iter_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.meta_term_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.output_term_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.prog_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.series_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.signedExpComp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.static_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.varWithType_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) MExpressionSection (class in schrodinger.application.desmond.kinetics.enhanced_sampling) mg_ratio (schrodinger.application.jaguar.nmr_utils.IsotopeData attribute) mhz_to_tesla() (in module schrodinger.application.jaguar.nmr_utils) MicelleInputFile (class in schrodinger.application.matsci.packmol) Middle (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.BtnPos attribute) mIDENT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MIDFIX (schrodinger.application.matsci.nano.check.CheckInput attribute) MIDWAY (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) mif_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) might_be_system() (in module schrodinger.application.matsci.desmondutils) migrate_param() (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.deprecate.MustSkip method) (schrodinger.application.desmond.stage.simulate.Concatenate method) (schrodinger.application.desmond.stage.simulate.SimulateBase method) MIMAGE_KEY (schrodinger.application.matsci.espresso.qeinput.NEBPathType attribute) mimic() (schrodinger.application.pymol.pymol4maestro.panel method) MIN (schrodinger.application.matsci.genetic_optimization.Property attribute) min_angle (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) MIN_ANGLE (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) min_atom_count (schrodinger.structutils.analyze.AslLigandSearcher property) min_b_factor (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin property) MIN_CARBOXYLIC_ACID_INTERACTION_ANGLE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MIN_COL (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) min_edges (schrodinger.application.steps.filters.FepFilter.Settings attribute) min_edgesChanged (schrodinger.application.steps.filters.FepFilter.Settings attribute) min_edgesReplaced (schrodinger.application.steps.filters.FepFilter.Settings attribute) MIN_EMPTY_BANDS (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) MIN_FRAME_DURATION (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) min_func() (in module schrodinger.application.desmond.bennett) MIN_HYDROGEN_NONSTATIC_DONOR_DISTANCE (schrodinger.protein.assignment.WaterStateEnumerator attribute) MIN_MAX_DELTA (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka attribute) min_method (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) (schrodinger.structutils.minimize.Minimizer property) MIN_N_CONFORMERS_LABEL (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection attribute) min_nodes (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData attribute) min_passing_residues (schrodinger.application.bioluminate.pose_filtering.residue_filter.FilterCriteria attribute) MIN_POS_FREQ (schrodinger.application.matsci.espresso.qeoutput.PhDOS attribute) MIN_REF_FRAME (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) MIN_REPLICATE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) MIN_STATIC_ACCEPTOR_INTERACTION_ANGLE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MIN_STATIC_DONOR_INTERACTION_ANGLE (schrodinger.protein.assignment.HistidinepKaPredictor attribute) MIN_STEP (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) MIN_STEP_SIZE (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel attribute) min_structures (schrodinger.application.livedesign.entry_types.BaseEntryData attribute) (schrodinger.application.livedesign.entry_types.DockedPoses attribute) MIN_TAU_DATA_POINT_NUM (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) MIN_TERM_FRAGS (schrodinger.application.matsci.nano.constants.Constants attribute) MIN_TOKEN_INDEX (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream attribute) min_value (schrodinger.application.steps.filters.ChiralCenterCountFilter.Settings attribute) (schrodinger.application.steps.filters.RangeFilter.Settings attribute) min_valueChanged (schrodinger.application.steps.filters.ChiralCenterCountFilter.Settings attribute) (schrodinger.application.steps.filters.RangeFilter.Settings attribute) min_valueReplaced (schrodinger.application.steps.filters.ChiralCenterCountFilter.Settings attribute) (schrodinger.application.steps.filters.RangeFilter.Settings attribute) min_with_none() (in module schrodinger.utils.withnone) MinAdvancedDialog (class in schrodinger.application.desmond.gui) minCrossingSpringLayout() (schrodinger.ui.qt.network_visualizer.Graph method) MINDEX (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) MINDIST (schrodinger.application.desmond.kinetics.utils.MtdInfo attribute) mindist_cutoff (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) mini() (schrodinger.application.macromodel.utils.ComUtil method) MiniJobBottomBar (class in schrodinger.ui.qt.appframework2.af2) minimization Minimization (class in schrodinger.application.macromodel.input) MinimizationOptions (class in schrodinger.forcefield.ffld_options) MINIMIZE (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) minimize (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) minimize() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.matsci.mecp_mod.BFGS method) (schrodinger.structutils.minimize.Minimizer method) (schrodinger.ui.dendrogram.DendrogramGraphicTree method) minimize_adj_h (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) minimize_adj_hChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) minimize_adj_hReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) minimize_complex() (in module schrodinger.application.matsci.buildcomplex) minimize_complex_and_handle_errors() (in module schrodinger.application.matsci.buildcomplex) minimize_complexes() (in module schrodinger.application.matsci.buildcomplex) minimize_complexes_with_xtb() (in module schrodinger.application.matsci.buildcomplex) minimize_geometry() (in module schrodinger.application.matsci.rxn_channel) minimize_hydrogens() (schrodinger.protein.assignment.ProtAssign method) minimize_ligands() (in module schrodinger.forcefield.minimizer) minimize_new_bonds() (in module schrodinger.application.bioluminate.antibody.assembly) minimize_structure() (in module schrodinger.forcefield.minimizer) (in module schrodinger.structutils.minimize) minimize_structure_preassigned() (in module schrodinger.forcefield.minimizer) minimize_substructure() (in module schrodinger.forcefield.minimizer) minimize_volume (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) minimizeAlignment() (schrodinger.protein.alignment.BaseAlignment method) minimizeEtaPosition() (schrodinger.application.matsci.buildcomplex.Ligand method) minimizeIdealComplex() (schrodinger.application.matsci.sculptcomplex.Sculptor method) MinimizeInfo (class in schrodinger.application.matsci.buildcomplex) MinimizeMixin (class in schrodinger.application.matsci.builderwidgets) Minimizer (class in schrodinger.structutils.minimize) minimizer (schrodinger.application.bioluminate.protein.protein.PropertyCalculator property) minimizer_context() (in module schrodinger.structutils.minimize) MinimizerError minimizeVolume() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) minimum (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) MINIMUM (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) MINIMUM_IDENTITY (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) minimum_length (schrodinger.structutils.structalign.StructAlign property) minimum_similarity (schrodinger.structutils.structalign.StructAlign property) minimumChanged() (schrodinger.ui.qt.swidgets.MinMaxSpinBoxTether method) minimumLength (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute) minimumSizeHint() (schrodinger.ui.qt.swidgets.VerticalLabel method) miniumSizeHint() (schrodinger.ui.qt.rama.RamaFigure method) MinMaxNeighborWidgets (class in schrodinger.application.matsci.kmcgui) MinMaxSpinBoxTether (class in schrodinger.ui.qt.swidgets) minMaxValidate() (schrodinger.ui.qt.swidgets.SNoCommaMinMaxMixin method) MinMiscTab (class in schrodinger.application.desmond.gui) minor (schrodinger.application.livedesign.ldclient_proxy.Version attribute) MinSites (schrodinger.application.phase.phase_widgets.HypothesisColumns attribute) Minta (class in schrodinger.application.macromodel.input) minta() (schrodinger.application.macromodel.utils.ComUtil method) minTerminatingFragments() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) minTerminatingFrags() (schrodinger.application.matsci.nano.tube.NanoTube method) minus() (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) minus_unit_mx() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) misc_input_filenames (schrodinger.stepper.stepper.StepTaskInput attribute) misc_input_filenamesChanged (schrodinger.stepper.stepper.StepTaskInput attribute) misc_input_filenamesReplaced (schrodinger.stepper.stepper.StepTaskInput attribute) misc_input_folders (schrodinger.stepper.stepper.StepTaskInput attribute) misc_input_foldersChanged (schrodinger.stepper.stepper.StepTaskInput attribute) misc_input_foldersReplaced (schrodinger.stepper.stepper.StepTaskInput attribute) misc_output_filenames (schrodinger.stepper.stepper.StepTaskOutput attribute) misc_output_filenamesChanged (schrodinger.stepper.stepper.StepTaskOutput attribute) misc_output_filenamesReplaced (schrodinger.stepper.stepper.StepTaskOutput attribute) mismatch() (schrodinger.application.desmond.antlr3.tree.TreeParser method) MismatchedNotSetException MismatchedRangeException MismatchedSetException MismatchedTokenException MismatchedTreeNodeException mismatchIsMissingToken() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) mismatchIsUnwantedToken() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) miss (schrodinger.application.matsci.cache.CacheInfo attribute) missed_atom_ids (schrodinger.application.matsci.amorphous.ConnectionInfo attribute) MISSING (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute) missing (schrodinger.application.prepwizard2.diagnostics.Problems attribute) MISSING_PRODUCTS_ONLY (schrodinger.infra.unusable_module_importer.AbstractUnusableModuleFinder attribute) (schrodinger.infra.unusable_module_importer.MissingProductUnusableModuleFinder attribute) missingChanged (schrodinger.application.prepwizard2.diagnostics.Problems attribute) MissingColumnsError MissingDataError MissingExecutableError MissingHostsFileException MissingInputFileError, [1] MissingLicenseFile MissingLoopFinder (class in schrodinger.structutils.analyze) MissingModule (class in schrodinger.application.matsci.codeutils) missingOutput() (schrodinger.pipeline.stages.ligprep.LigPrepStage method) MissingParameterError MissingProductUnusableModuleFinder (class in schrodinger.infra.unusable_module_importer) MissingProductUnusableModuleLoader (class in schrodinger.infra.unusable_module_importer) missingReplaced (schrodinger.application.prepwizard2.diagnostics.Problems attribute) MissingResourceError MissingTokenException MissingValueError MITERTD (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) MIXED (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute) MixedAACGStructuresError MixedPairs (class in schrodinger.application.jaguar.input) MixedPotentialsException MixedSolventAnalysis (class in schrodinger.application.desmond.stage.app.mxmd) MixedSolventCleanup (class in schrodinger.application.desmond.stage.app.mxmd) MixedSolventMsjGenerator (class in schrodinger.application.desmond.msj_generator.mxmd) MixedSolventSetup (class in schrodinger.application.desmond.stage.app.mxmd) MixedSolventSimLegParams (class in schrodinger.application.desmond.msj_generator.workflow_params) MixedSolventWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) MIXPREVIOUS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) MIXPREVIOUSMAX (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) MIXPREVIOUSMIN (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) mkdir_p() (in module schrodinger.utils.fileutils) mktemp() (in module schrodinger.application.canvas.cluster) ml_file (schrodinger.application.steps.scorers.LigandMLScorer.Settings attribute) ml_fileChanged (schrodinger.application.steps.scorers.LigandMLScorer.Settings attribute) ml_fileReplaced (schrodinger.application.steps.scorers.LigandMLScorer.Settings attribute) ml_predict() (in module schrodinger.application.matsci.mlearn.descriptor) mLIT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mm (schrodinger.application.qsite.input.HydrogenCap property) mmatom (schrodinger.application.qsite.input.Cut property) mmc() (schrodinger.application.macromodel.utils.ComUtil method) MMCIF (schrodinger.infra.structure.FileFormat attribute) MMCIFWriter (class in schrodinger.structure) mmct() (in module schrodinger.infra.mminit) MmctSerializerException MmException mmexception_side_effect() (in module schrodinger.application.matsci.mstest) mmffld_environment() (in module schrodinger.forcefield.common) mmfile_path() (in module schrodinger.utils.fileutils) mmfrag() (in module schrodinger.infra.mminit) mmgbsa_blocksort() (in module schrodinger.application.livedesign.ld_mmgbsa_utils) MMGBSAStage (class in schrodinger.pipeline.stages.prime) MMIMArgList (class in schrodinger.infra.mmim) MMIMDict (class in schrodinger.infra.mmim) MmJag (class in schrodinger.application.jaguar.mmjag) mmjag_function() (in module schrodinger.application.jaguar.mmjag) mmjag_reset_connectivity() (in module schrodinger.application.jaguar.utils) mmjag_update_lewis() (in module schrodinger.application.jaguar.utils) MMJagManager (class in schrodinger.application.jaguar.mmjag) mmkey (schrodinger.application.qsite.input.QSiteInput property) MMKVArgList (class in schrodinger.infra.mmkv) mmlewis_apply() (in module schrodinger.application.matsci.msutils) MMLib() (in module schrodinger.infra.mminit) mmlist (class in schrodinger.infra.mmlist) MmObject (class in schrodinger.infra.mmobject) mmod (schrodinger.application.phase.packages.shape_generator.AtomTypes attribute) MmodEnergyKeys (class in schrodinger.application.matsci.reaction_workflow_utils) MMOK (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute) MMP3DScreener (class in schrodinger.application.phase.packages.mmp3dscreener) MMPDatabaseConnection (class in schrodinger.application.phase.packages.mmp2d) MMSHARE_DATA_DESMOND_DIR (schrodinger.application.desmond.envir.CONST attribute) MMSHARE_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute) MMSHARE_SYSTEM_BUILDER_DATA_DIR (schrodinger.application.desmond.envir.CONST attribute) MMSHARE_SYSTEM_BULDER_DATA_DIR (schrodinger.application.desmond.envir.CONST attribute) MMSHARE_VERSION (schrodinger.application.desmond.envir.CONST attribute) mmsmiles_initialized (schrodinger.structure.SmilesStructure attribute) mmsurf_lib() (in module schrodinger.infra.mminit) MMTypingFailure mMULTOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mmvisio() (in module schrodinger.infra.mminit) mmvol() (in module schrodinger.infra.mminit) mNEWLINE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mo_occupancies() (in module schrodinger.application.mopac.results_main) mob_keys (schrodinger.structutils.sitealign.SiteMatchLookup property) mock_job_backend() (in module schrodinger.seam.testing.fixtures) mock_json_load_from_fh() (in module schrodinger.application.matsci.mstest) mock_license_manager() (in module schrodinger.seam.testing.fixtures) mock_trial_fleet_task_type() (in module schrodinger.seam.testing.fixtures) mod_asl() (in module schrodinger.application.bioluminate.pml_menus) modalBannerClosed (schrodinger.ui.qt.utils.MaestroPythonBannerManager attribute) Mode (class in schrodinger.trajectory.prody.mode) mode (schrodinger.application.desmond.starter.ui.cmdline.BaseArgs property) (schrodinger.application.desmond.starter.ui.cmdline.FepArgs property) (schrodinger.application.desmond.starter.ui.constant_ph.Args property) (schrodinger.application.desmond.starter.ui.fep_residue_scanning.Args property) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) MODE (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) mode (schrodinger.maestro_utils.find_tool_bar.constants.SEARCH_OPTION_DETAILS attribute) Mode (schrodinger.ui.qt.tasks.configwidgets.IncorporationSelector attribute) MODE_CREATE (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) MODE_TEXT (schrodinger.ui.qt.tasks.configwidgets.IncorporationSelector attribute) MODE_UPDATE (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) MODE_VIEW (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) modeChanged (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel attribute) modeChanged() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.ui.qt.schart.BinsDialog method) Model (class in schrodinger.application.matsci.equilibrium_md) model (schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl attribute) (schrodinger.application.bioluminate.antibody.assembly.AtomPair attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Output attribute) MODEL (schrodinger.application.livedesign.constants.ModelSearchType attribute) model (schrodinger.models.mappers.MapperMixin property) MODEL (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) Model2CheckoutError model_base_class (schrodinger.models.advanced_mappers.ModelBaseClassMapperMixin attribute) (schrodinger.ui.qt.tasks.configwidgets.ConfigWidgetMixin attribute) model_changed_callback() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.EnsembleClassFrame method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.RelaxFrame method) model_class (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage attribute) MODEL_CLASS (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) model_class (schrodinger.application.jaguar.jaguar_config_dialog.JaguarHostSelector attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsDialog attribute) (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser attribute) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor attribute) (schrodinger.application.job_monitor.job_monitor_progress_bar.ProgressBar attribute) (schrodinger.application.job_monitor.job_monitor_widgets.JobBar attribute) (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane attribute) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget attribute) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane attribute) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.ServerRegistrationMixin attribute) (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog attribute) (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel attribute) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanel attribute) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget attribute) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel attribute) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel attribute) (schrodinger.application.livedesign.widgets.InvalidGEIdWarningDialog attribute) (schrodinger.application.pymol.export_to_pymol_gui.AdvancedSettingsPopUp attribute) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel attribute) (schrodinger.models.mappers.MapperMixin attribute) (schrodinger.models.presets.PresetManager attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget attribute) (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager attribute) (schrodinger.ui.qt.fp_selector_widget.FingerprintsSelectorWidget attribute) MODEL_CLASS (schrodinger.ui.qt.network_visualizer.AbstractNetworkView attribute) model_class (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog attribute) MODEL_CLASS (schrodinger.ui.qt.recent_completer.BrowseAndCreateCombo attribute) (schrodinger.ui.qt.recent_completer.BrowsePlaceholderRecentCombo attribute) (schrodinger.ui.qt.recent_completer.StringListModelInterface attribute) model_class (schrodinger.ui.qt.structure_selector.SlimStructureSelector attribute) (schrodinger.ui.qt.structure_selector.StructureSelector attribute) (schrodinger.ui.qt.tasks.configwidgets.HostSelector attribute) (schrodinger.ui.qt.tasks.taskwidgets.AbstractTaskBar attribute) model_classes (schrodinger.models.advanced_mappers.MultiModelClassMapperMixin attribute) (schrodinger.ui.qt.tasks.taskbarwidgets.TaskWidgetMixin attribute) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog attribute) model_edge (schrodinger.ui.qt.network_views.NetworkEdge property) model_fname (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) model_fnameChanged (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) model_fnameReplaced (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) MODEL_OPTION (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.genetic_optimization.DeepChem attribute) model_reset_method() (in module schrodinger.ui.qt.table_helper) model_scale (schrodinger.ui.qt.network_views.NetworkNode attribute) model_sts (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) model_stsChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) model_stsReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) MODEL_SYSTEM_TYPE (schrodinger.application.desmond.cms.Cms attribute) model_system_type() (schrodinger.application.desmond.cms.Cms method) ModelBaseClassMapperMixin (class in schrodinger.models.advanced_mappers) modelChanged (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Output attribute) (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) ModelIndexFilter (class in schrodinger.ui.qt.delegates) ModelingMode (class in schrodinger.application.bioluminate.antibody.io.csv_reader) ModellNotSupported modelPrep() (schrodinger.active_learning.mq_backend.Backend method) modelReplaced (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Output attribute) modelResetContext() (schrodinger.ui.qt.table_helper.ModelResetContextMixin method) ModelResetContextMixin (class in schrodinger.ui.qt.table_helper) ModelRestrainList (class in schrodinger.application.desmond.cms) Models (class in schrodinger.application.jaguar.qrnn.keywords) ModelSearchType (class in schrodinger.application.livedesign.constants) modeReplaced (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) ModeSet (class in schrodinger.trajectory.prody.modeset) Modified (schrodinger.ui.qt.appframework2.jobnames.JobnameType attribute) modified_sawtooth() (in module schrodinger.application.matsci.nano.xtal) modify() (schrodinger.application.qsite.input.QMRegion method) modify_df_for_testing() (in module schrodinger.application.matsci.mlearn.descriptor) modify_dihe (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) modify_enum_access() (in module schrodinger.infra.fix_sip6_enum_access) modify_fep_launcher_stage() (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.protein.CombinedProteinMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator method) modify_graph_fname() (schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator method) modify_graph_stage() (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.covalent_ligand.CovalentMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.metalloprotein.MetalMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.protein.CombinedProteinMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator method) modify_help_message() (in module schrodinger.application.matsci.parserutils) modify_multisim_stage() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) modify_params_protein_mapper() (schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator method) modify_params_protein_mutation_generation() (schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator method) modify_row_structure() (in module schrodinger.project.utils) modifyGraphForMartiniRings() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) modifyingStructure() (schrodinger.protein.alignment.BaseAlignment method) modifyMinimizer() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) modifyReplicaFirstStage() (schrodinger.application.matsci.permittivity.MultiStageMd method) modifyReplicaMsjHeader() (schrodinger.application.matsci.permittivity.MultiStageMd method) modifyReplicaStages() (schrodinger.application.matsci.permittivity.MultiStageMd method) modifyStageSettings() (schrodinger.application.matsci.permittivity.MultiStageMd class method) ModifySubMenu (class in schrodinger.application.bioluminate.pml_menus) Modulation() (in module schrodinger.application.matsci.gsas.GSASIImath) ModulationDerv() (in module schrodinger.application.matsci.gsas.GSASIImath) ModulationTw() (in module schrodinger.application.matsci.gsas.GSASIImath) module schrodinger schrodinger.active_learning schrodinger.active_learning.al_driver schrodinger.active_learning.al_node schrodinger.active_learning.al_report schrodinger.active_learning.al_utils schrodinger.active_learning.fake_nodes schrodinger.active_learning.mq_backend schrodinger.active_learning.mq_driver schrodinger.active_learning.mq_worker schrodinger.adapter schrodinger.analysis schrodinger.analysis.enrichment schrodinger.analysis.enrichment.calculator schrodinger.analysis.enrichment.enrichment_input schrodinger.analysis.enrichment.metrics schrodinger.analysis.enrichment.plotter schrodinger.analysis.reaction schrodinger.analysis.substructure schrodinger.analysis.transformations schrodinger.analysis.visanalysis schrodinger.analysis.visanalysis.vdaxis schrodinger.analysis.visanalysis.vdcoordinateframe schrodinger.analysis.visanalysis.vdexception schrodinger.analysis.visanalysis.volumedata schrodinger.analysis.visanalysis.volumedataio schrodinger.analysis.visanalysis.volumedatastructureutils schrodinger.analysis.visanalysis.volumedatautils schrodinger.application schrodinger.application.aacg schrodinger.application.aacg.utils schrodinger.application.bb_database schrodinger.application.bb_database.bb_arg_utils schrodinger.application.bb_database.bb_job_utils schrodinger.application.bb_database.bb_task_utils schrodinger.application.bindingsite schrodinger.application.bindingsite.atomtyping schrodinger.application.bindingsite.cavutils schrodinger.application.bindingsite.common schrodinger.application.bindingsite.intfield schrodinger.application.bindingsite.schema schrodinger.application.bioluminate schrodinger.application.bioluminate.actions schrodinger.application.bioluminate.actions.configs schrodinger.application.bioluminate.actions.factory schrodinger.application.bioluminate.actions.icons schrodinger.application.bioluminate.actions.icons_rc schrodinger.application.bioluminate.anarci schrodinger.application.bioluminate.anarci.anarci_adapter schrodinger.application.bioluminate.anarci.annotate schrodinger.application.bioluminate.anarci.loop_ranges schrodinger.application.bioluminate.antibody schrodinger.application.bioluminate.antibody.annotate schrodinger.application.bioluminate.antibody.annotation_constants schrodinger.application.bioluminate.antibody.antibody_homology_report_writer schrodinger.application.bioluminate.antibody.assembly schrodinger.application.bioluminate.antibody.grafting schrodinger.application.bioluminate.antibody.io schrodinger.application.bioluminate.antibody.io.csv_reader schrodinger.application.bioluminate.antibody.management schrodinger.application.bioluminate.antibody.models schrodinger.application.bioluminate.antibody.scaffold_search schrodinger.application.bioluminate.antibody.search_results_table schrodinger.application.bioluminate.antibody.sequence_indexer schrodinger.application.bioluminate.antibody.utils schrodinger.application.bioluminate.bwidgets schrodinger.application.bioluminate.classify schrodinger.application.bioluminate.drivers schrodinger.application.bioluminate.drivers.io schrodinger.application.bioluminate.epitope schrodinger.application.bioluminate.epitope.driver schrodinger.application.bioluminate.epitope.psc_workflow schrodinger.application.bioluminate.epitope.utils schrodinger.application.bioluminate.epitope.utils.esc_utils schrodinger.application.bioluminate.escomp schrodinger.application.bioluminate.interaction_calculator schrodinger.application.bioluminate.met_oxidation schrodinger.application.bioluminate.met_oxidation.hmc_sim_runner schrodinger.application.bioluminate.met_oxidation.md_sim_runner schrodinger.application.bioluminate.methionine_oxidation schrodinger.application.bioluminate.mutation schrodinger.application.bioluminate.nucleic schrodinger.application.bioluminate.nucleic.constants schrodinger.application.bioluminate.nucleic.mutator schrodinger.application.bioluminate.patch_utils schrodinger.application.bioluminate.patch_utils.msurfext schrodinger.application.bioluminate.patch_utils.patch_finder schrodinger.application.bioluminate.patch_utils.pre_analyze schrodinger.application.bioluminate.patch_utils.settings schrodinger.application.bioluminate.peptide_sar schrodinger.application.bioluminate.peptide_sar.encode schrodinger.application.bioluminate.peptide_sar.io schrodinger.application.bioluminate.peptide_sar.label schrodinger.application.bioluminate.peptide_sar.sar schrodinger.application.bioluminate.peptide_sar.statistics schrodinger.application.bioluminate.pml_menus schrodinger.application.bioluminate.pose_filtering schrodinger.application.bioluminate.pose_filtering.csv_filter schrodinger.application.bioluminate.pose_filtering.hdx_analysis schrodinger.application.bioluminate.pose_filtering.hdx_calc schrodinger.application.bioluminate.pose_filtering.hdx_io schrodinger.application.bioluminate.pose_filtering.operators schrodinger.application.bioluminate.pose_filtering.residue_filter schrodinger.application.bioluminate.pose_filtering.test schrodinger.application.bioluminate.propfilter schrodinger.application.bioluminate.propfilter_ui schrodinger.application.bioluminate.propka_parse schrodinger.application.bioluminate.protein schrodinger.application.bioluminate.protein.mutator schrodinger.application.bioluminate.protein.protein schrodinger.application.bioluminate.protein.utils schrodinger.application.bioluminate.protein_interaction schrodinger.application.bioluminate.protein_interaction.calculate schrodinger.application.bioluminate.protein_interaction.tasks schrodinger.application.bioluminate.protein_interaction.utils schrodinger.application.bioluminate.protein_protein_docking_shared schrodinger.application.bioluminate.protein_report_widget schrodinger.application.bioluminate.protein_structure_quality schrodinger.application.bioluminate.protein_structure_quality_ui schrodinger.application.bioluminate.reactive_residues schrodinger.application.bioluminate.residue_scanning schrodinger.application.bioluminate.residue_scanning.properties schrodinger.application.bioluminate.run_propka schrodinger.application.bioluminate.sliderchart schrodinger.application.bioluminate.ssv schrodinger.application.bioluminate.ssv.toolbars schrodinger.application.bioluminate.ssv.viewer schrodinger.application.bioluminate.surfcomp schrodinger.application.bioluminate.tcr schrodinger.application.bioluminate.tcr.annotate schrodinger.application.bioluminate.tcr.docking_angles schrodinger.application.bioluminate.update_germline_db schrodinger.application.bioluminate.update_germline_db.translate_db schrodinger.application.bioluminate.validate_imported_modules schrodinger.application.bioluminate.workspacelabeler schrodinger.application.canvas schrodinger.application.canvas.base schrodinger.application.canvas.cluster schrodinger.application.canvas.clustergui schrodinger.application.canvas.fingerprint schrodinger.application.canvas.fingerprintgui schrodinger.application.canvas.r_group schrodinger.application.canvas.r_group_dee schrodinger.application.canvas.similarity schrodinger.application.canvas.similaritygui schrodinger.application.canvas.topo_descriptors schrodinger.application.canvas.utils schrodinger.application.combiglide schrodinger.application.combiglide.connection_storage schrodinger.application.combiglide.corehop schrodinger.application.combiglide.packages schrodinger.application.combiglide.utils schrodinger.application.combinatorial_diversity schrodinger.application.combinatorial_diversity.diversity_fingerprinter schrodinger.application.combinatorial_diversity.diversity_selector schrodinger.application.combinatorial_diversity.diversity_splitter schrodinger.application.combinatorial_diversity.driver_utils schrodinger.application.combinatorial_diversity.splitter_utils schrodinger.application.combinatorial_explorer schrodinger.application.combinatorial_explorer.driver_utils schrodinger.application.combinatorial_explorer.route_screener schrodinger.application.combinatorial_screen schrodinger.application.combinatorial_screen.combinatorial_screener schrodinger.application.combinatorial_screen.driver_utils schrodinger.application.combinatorial_screen.fingerprint_utils schrodinger.application.dendrogram schrodinger.application.dendrogram.core_class schrodinger.application.dendrogram.gradientSelector schrodinger.application.dendrogram.proteinDendrogram schrodinger.application.dendrogram.randTestSet schrodinger.application.desmond schrodinger.application.desmond.ana schrodinger.application.desmond.antlr3 schrodinger.application.desmond.antlr3.compat schrodinger.application.desmond.antlr3.constants schrodinger.application.desmond.antlr3.debug schrodinger.application.desmond.antlr3.dfa schrodinger.application.desmond.antlr3.exceptions schrodinger.application.desmond.antlr3.recognizers schrodinger.application.desmond.antlr3.streams schrodinger.application.desmond.antlr3.tokens schrodinger.application.desmond.antlr3.tree schrodinger.application.desmond.antlr3.treewizard schrodinger.application.desmond.arkdb schrodinger.application.desmond.automatic_analysis_generator schrodinger.application.desmond.autopartition schrodinger.application.desmond.bennett schrodinger.application.desmond.bld_def schrodinger.application.desmond.bld_ver schrodinger.application.desmond.cmdline schrodinger.application.desmond.cmj 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schrodinger.ui.qt.appframework2.debugcore schrodinger.ui.qt.appframework2.debugwidgets schrodinger.ui.qt.appframework2.jobnames schrodinger.ui.qt.appframework2.jobs schrodinger.ui.qt.appframework2.knime_af2 schrodinger.ui.qt.appframework2.maestro_callback schrodinger.ui.qt.appframework2.markers schrodinger.ui.qt.appframework2.settings schrodinger.ui.qt.appframework2.validation schrodinger.ui.qt.appframework2.validators schrodinger.ui.qt.appframework2.wizards schrodinger.ui.qt.atom_weights_table_ui schrodinger.ui.qt.atom_weights_table_widget schrodinger.ui.qt.atomselector schrodinger.ui.qt.basewidgets schrodinger.ui.qt.borderless_popup_ui schrodinger.ui.qt.color_picker schrodinger.ui.qt.config_dialog schrodinger.ui.qt.config_dialog_open_mp_ui schrodinger.ui.qt.config_dialog_queue_ui schrodinger.ui.qt.datamapper schrodinger.ui.qt.decorators schrodinger.ui.qt.delegates schrodinger.ui.qt.dendrogram schrodinger.ui.qt.dialbox schrodinger.ui.qt.dialbox_dir schrodinger.ui.qt.dialbox_dir.dialbox_qrc schrodinger.ui.qt.directory_selector schrodinger.ui.qt.entryselector schrodinger.ui.qt.entryselector_ui schrodinger.ui.qt.figureoptions schrodinger.ui.qt.file_selector schrodinger.ui.qt.filedialog schrodinger.ui.qt.filter_dialog schrodinger.ui.qt.filter_dialog_dir schrodinger.ui.qt.filter_dialog_dir.filter_core schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui schrodinger.ui.qt.filter_dialog_dir.filter_widgets schrodinger.ui.qt.filter_dialog_ui schrodinger.ui.qt.filter_list schrodinger.ui.qt.forcefield schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget_ui schrodinger.ui.qt.forcefield.ffglobalpreferencewidget schrodinger.ui.qt.forcefield.ffglobalpreferencewidget_ui schrodinger.ui.qt.forcefield.ffprojectsettingsdlg schrodinger.ui.qt.forcefield.ffprojectsettingsdlg_ui schrodinger.ui.qt.forcefield.ffselector schrodinger.ui.qt.forcefield.ffsettingsbutton schrodinger.ui.qt.forcefield.forcefield schrodinger.ui.qt.forcefield.pathselectorwidget schrodinger.ui.qt.forcefield.stylesheet schrodinger.ui.qt.formlayout schrodinger.ui.qt.fp_selector_widget schrodinger.ui.qt.fp_selector_widget_ui schrodinger.ui.qt.icons schrodinger.ui.qt.icons_rc schrodinger.ui.qt.input_selector schrodinger.ui.qt.jobwidgets schrodinger.ui.qt.label schrodinger.ui.qt.label_cursor schrodinger.ui.qt.layout schrodinger.ui.qt.ligand_list schrodinger.ui.qt.mapperwidgets schrodinger.ui.qt.mapperwidgets.param_editor schrodinger.ui.qt.mapperwidgets.plptable schrodinger.ui.qt.matplot_widget schrodinger.ui.qt.messagebox schrodinger.ui.qt.multi_combo_box schrodinger.ui.qt.navtoolbar schrodinger.ui.qt.network_views schrodinger.ui.qt.network_visualizer schrodinger.ui.qt.pdb_dialog schrodinger.ui.qt.pdb_dialog_ui schrodinger.ui.qt.periodictable schrodinger.ui.qt.pop_up_widgets schrodinger.ui.qt.presets schrodinger.ui.qt.presets.manage_presets_dialog schrodinger.ui.qt.presets.manage_presets_dialog_ui schrodinger.ui.qt.presets.save_presets_dialog schrodinger.ui.qt.presets.save_presets_dialog_ui schrodinger.ui.qt.propertyselector schrodinger.ui.qt.protein_health_viewer schrodinger.ui.qt.protein_health_viewer_ui schrodinger.ui.qt.radial_plot schrodinger.ui.qt.rama schrodinger.ui.qt.rdmol_views schrodinger.ui.qt.recent_completer schrodinger.ui.qt.rename_favorite_dialog schrodinger.ui.qt.rename_favorite_dialog_ui schrodinger.ui.qt.schart schrodinger.ui.qt.schrodinger_ipython schrodinger.ui.qt.schrodingerstyle schrodinger.ui.qt.select_residues_dialog schrodinger.ui.qt.select_residues_dialog_ui schrodinger.ui.qt.smatplotlib schrodinger.ui.qt.standard schrodinger.ui.qt.standard.colors schrodinger.ui.qt.standard.constants schrodinger.ui.qt.standard.design_tokens schrodinger.ui.qt.standard.icons schrodinger.ui.qt.standard.icons.icons schrodinger.ui.qt.standard.panelx_stylesheet schrodinger.ui.qt.standard.widgets schrodinger.ui.qt.standard.widgets.group_boxes schrodinger.ui.qt.standard_widgets schrodinger.ui.qt.standard_widgets.buttons schrodinger.ui.qt.standard_widgets.combo_boxes schrodinger.ui.qt.standard_widgets.flat_button schrodinger.ui.qt.standard_widgets.hyperlink schrodinger.ui.qt.standard_widgets.labels schrodinger.ui.qt.standard_widgets.standard_widgets_rc schrodinger.ui.qt.standard_widgets.statusbar schrodinger.ui.qt.structtable schrodinger.ui.qt.structure2d schrodinger.ui.qt.structure_selector schrodinger.ui.qt.style schrodinger.ui.qt.stylesheet schrodinger.ui.qt.swidgets schrodinger.ui.qt.table schrodinger.ui.qt.table_helper schrodinger.ui.qt.table_speed_up schrodinger.ui.qt.tablewidget schrodinger.ui.qt.tasks schrodinger.ui.qt.tasks.config_dialog_ui schrodinger.ui.qt.tasks.config_info_ui schrodinger.ui.qt.tasks.configwidgets schrodinger.ui.qt.tasks.taskbar2 schrodinger.ui.qt.tasks.taskbar_ui schrodinger.ui.qt.tasks.taskbarwidgets schrodinger.ui.qt.tasks.taskwidgets schrodinger.ui.qt.tooltips schrodinger.ui.qt.utils schrodinger.ui.qt.widgetmixins schrodinger.ui.qt.widgetmixins.basicmixins schrodinger.ui.qt.widgetmixins.mock_ui schrodinger.ui.qt.widgetmixins.panelmixins schrodinger.ui.qt.xsignals schrodinger.ui.residueselector schrodinger.ui.sketcher schrodinger.ui.sketcher_extensions schrodinger.ui.sketcher_image schrodinger.ui.sketcher_smarts_dialog schrodinger.ui.sketcher_smarts_dialog_ui schrodinger.ui.two_d_viewer schrodinger.ui.two_d_viewer_ui schrodinger.utils schrodinger.utils.cgxutils schrodinger.utils.cmdline schrodinger.utils.colorscheme schrodinger.utils.compare schrodinger.utils.csv_unicode schrodinger.utils.deprecation schrodinger.utils.documentation schrodinger.utils.env schrodinger.utils.featureflags schrodinger.utils.featureflags.featureflags schrodinger.utils.featureflags.write schrodinger.utils.fileutils schrodinger.utils.funcchains schrodinger.utils.funcgroups schrodinger.utils.imputils schrodinger.utils.install_scripts schrodinger.utils.installation_check schrodinger.utils.license schrodinger.utils.ligfilter schrodinger.utils.log schrodinger.utils.machid schrodinger.utils.maestro_scripts_path schrodinger.utils.mmutil schrodinger.utils.moduleproxy schrodinger.utils.multifpfile schrodinger.utils.net schrodinger.utils.openmpi schrodinger.utils.platform schrodinger.utils.postinstall schrodinger.utils.preferences schrodinger.utils.profiling schrodinger.utils.pymol schrodinger.utils.qapplication schrodinger.utils.qt_utils schrodinger.utils.scollections schrodinger.utils.sea schrodinger.utils.sea.common schrodinger.utils.sea.evalor schrodinger.utils.sea.sea schrodinger.utils.singledashoptionparser schrodinger.utils.sshconfig schrodinger.utils.subproc schrodinger.utils.subprocess schrodinger.utils.sysinfo schrodinger.utils.thread_utils schrodinger.utils.typing schrodinger.utils.units schrodinger.utils.withnone

module (schrodinger.application.glide.client_module.GlideClientModuleAdapter attribute) ModuleInfo (class in schrodinger.application.matsci.codeutils) ModuleProxy (class in schrodinger.utils.moduleproxy) modules accessing your own installing Moieties (class in schrodinger.application.matsci.amorphous) MoietyError mol (schrodinger.application.jaguar.macro_pka_utils.RowData attribute) MOL (schrodinger.application.matsci.kmc.Table attribute) mol (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) (schrodinger.application.steps.dataclasses.ScoredMol attribute) MOL2 (schrodinger.infra.structure.FileFormat attribute) mol2image() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) mol2svg() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) Mol2Writer (class in schrodinger.structure) mol_atomic_mass (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_charge (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_formula (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_from_cxsmiles() (in module schrodinger.application.scaffold_enumeration.cxsmiles) mol_hash (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_index_str (schrodinger.application.jaguar.autots_constants.IndexString attribute) mol_name (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_num (schrodinger.structutils.analyze.Ligand property) mol_number (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) mol_number_carbon (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) mol_numbers (schrodinger.application.matsci.order_parameter_mod.PerMolOP attribute) mol_ops (schrodinger.application.matsci.order_parameter_mod.PerMolOP attribute) mol_pdb_name (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_smiles (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_st (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_to_nomap_cxsmiles() (in module schrodinger.application.pathfinder.route) mol_to_qpicture() (in module schrodinger.application.pathfinder.render) mol_to_structure() (in module schrodinger.application.steps.utils) mol_torsions (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_total (schrodinger.structure.Structure property) mol_total_atoms (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_total_fragments (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_total_heavy (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_total_rot_bonds (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) mol_weight() (in module schrodinger.application.jaguar.textparser) MOL_WEIGHT_KEY (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) mol_weight_precision (schrodinger.application.jaguar.output.JaguarOutput attribute) MOL_WEIGHT_PROP (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) MOL_WEIGHT_UNITS (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) molChanged (schrodinger.application.steps.dataclasses.ScoredMol attribute) MOLCHG (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) molchg() (in module schrodinger.application.jaguar.textparser) MolCoder (class in schrodinger.seam.coders) molecular (schrodinger.surface.MolSurfType attribute) MOLECULAR_DYNAMICS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) Molecular_formula() (in module schrodinger.utils.ligfilter) MOLECULAR_ORBITALS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) Molecular_weight() (in module schrodinger.utils.ligfilter) MolecularDynamicsStep (class in schrodinger.application.matsci.jwsteps) MolecularFormulaSignature (class in schrodinger.application.matsci.species) Molecule (schrodinger.application.glide.xpdes.TermKeywords attribute) MOLECULE (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) molecule (schrodinger.structure.Structure attribute) (schrodinger.structure.TextualStructure property) molecule() (schrodinger.application.matsci.automated_cg_mapping.MappingMethod static method) MOLECULE_1 (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute) molecule_history_callback() (in module schrodinger.application.matsci.genetic_optimization) molecule_indices (schrodinger.application.bioluminate.protein.protein.Consensus property) molecule_lists_are_conformers() (in module schrodinger.application.jaguar.autots_rmsd) MOLECULE_NUM (schrodinger.application.matsci.mswidgets.SystemInformationFrame attribute) molecule_number (schrodinger.comparison.neighbors.MoleculeNeighbor attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) (schrodinger.structure.Residue property) (schrodinger.structure.StructureAtom property) molecule_number_by_entry (schrodinger.structure.Residue property) (schrodinger.structure.StructureAtom property) MoleculeData (class in schrodinger.application.matsci.automated_cg_mapping) (class in schrodinger.application.matsci.kmc) MoleculeData.BEAD_TYPE (class in schrodinger.application.matsci.automated_cg_mapping) MoleculeData.MAPPED_BEAD_INFO (class in schrodinger.application.matsci.automated_cg_mapping) MoleculeData.NODE_GROUP_TYPE (class in schrodinger.application.matsci.automated_cg_mapping) MoleculeNeighbor (class in schrodinger.comparison.neighbors) moleculeNum() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) molecules (schrodinger.application.bioluminate.protein.protein.Consensus property) (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) molecules() (schrodinger.application.desmond.fep_struc.SchrodStruc method) MoleculeSpeciesFinder (class in schrodinger.application.matsci.species) MoleculesTable (class in schrodinger.application.matsci.kmc) MoleculeTab (class in schrodinger.application.jaguar.gui.tabs.molecule_tab) MoleculeTabBase (class in schrodinger.application.jaguar.gui.tabs.molecule_tab) MoleculeTabNoInputSelector (class in schrodinger.application.jaguar.gui.tabs.molecule_tab) MoleculeTabPka (class in schrodinger.application.jaguar.gui.tabs.molecule_tab) MOLFORM (schrodinger.application.matsci.kmc.SchrodingerTable attribute) molHasRing() (schrodinger.application.dendrogram.core_class.Utilities static method) molid (schrodinger.application.qsite.input.Cut property) MolInMixin (class in schrodinger.application.steps.dataclasses) MolMaeWorkflow (class in schrodinger.application.steps.basesteps) MolMapStep (class in schrodinger.application.steps.basesteps) MolMolMixin (class in schrodinger.application.steps.dataclasses) MolMolWorkflow (class in schrodinger.application.steps.basesteps) MolOutMixin (class in schrodinger.application.steps.dataclasses) MolReduceStep (class in schrodinger.application.steps.basesteps) molReplaced (schrodinger.application.steps.dataclasses.ScoredMol attribute) mols_analyzed (schrodinger.application.pathfinder.analysis.RetrosynthesisState attribute) MolSerializer (class in schrodinger.models.jsonable) MolSurfType (class in schrodinger.surface) MolToSmilesCoder (class in schrodinger.seam.coders) MolToSmilesConverter (class in schrodinger.application.steps.converters) MolToSmilesSerializer (class in schrodinger.application.steps.dataclasses) MolToStructureConverter (class in schrodinger.application.steps.converters) MolToStructureConverter.Settings (class in schrodinger.application.steps.converters) MolWriter (class in schrodinger.rdkit.molio) MOMENT_OF_INERTIA (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) MomentData (class in schrodinger.application.matsci.mlearn.features) MomentOfInertiaDirector (class in schrodinger.application.matsci.order_parameter_mod) momentum2Velocity() (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame method) MonitorAtomNumbering() (in module schrodinger.structure.atom_numbering_monitor) MonitoredCallbacks (class in schrodinger.ui.qt.appframework2.maestro_callback) monitorFiles() (schrodinger.application.matsci.jwsteps.BaseStep method) monitorJob() (schrodinger.ui.qt.appframework.AppFramework method) MONOCLINIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) MONODENTATE (in module schrodinger.application.matsci.buildcomplex) MonolayerInputFile (class in schrodinger.application.matsci.packmol) Monomer (class in schrodinger.application.matsci.amorphous) MONOMER (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) monomer_item_factory() (in module schrodinger.protein.helm.helm_renderer) monomer_string (schrodinger.livedesign.biologics.registration.BioPolymer attribute) MonomerSpeciesSelector (class in schrodinger.application.matsci.clusterstructgui) MonoMetalComplexType (class in schrodinger.energy) MONOSPECIFIC (schrodinger.application.bioluminate.antibody.io.csv_reader.ModelingMode attribute) MONOSPECIFIC_ANTIBODY (schrodinger.livedesign.entity_type.EntityClass attribute) MonteCarloMolecule (class in schrodinger.application.matsci.montecarlo) mopac (schrodinger.application.qsite.input.QSiteInput property) MOPAC_EXEC (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain attribute) MopacBasisError1 MopacBasisError2 MopacBasisError3 MopacBasisError4 MopacBasisError5 MopacConformerSelection (class in schrodinger.application.matsci.reaction_workflow_utils) MopacGradientParserError MopacIOError MopacLauncherMain (class in schrodinger.application.mopac.mopac_launchers) MopacMainTextParser (class in schrodinger.application.mopac.results_main) MopacNumericalError MopacPropertyError MopacResultsMain (class in schrodinger.application.mopac.results_main) MopacRuntimeError MopacUserFacingException more_columns_visible (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) more_columns_visibleChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) more_columns_visibleReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) MORSE (schrodinger.energy.MonoMetalComplexType attribute) MossbauerSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) MOST_RECENTLY_USED_LOCATIONS (schrodinger.ui.qt.forcefield.ffprojectsettingsdlg.FFProjectSettingsDlg attribute) MOUSE_CLICK_STARTS_EDIT (schrodinger.ui.qt.delegates.SpinBoxDelegate attribute) mouse_data (schrodinger.ui.qt.delegates.MouseTrackingDelegateMixin property) mouse_move() (schrodinger.ui.qt.navtoolbar.AtomInfoToolbar method) MOUSE_PRESS_STARTS_EDIT (schrodinger.ui.qt.delegates.ComboBoxDelegate attribute) mouseDoubleClickEvent() (schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets.PlotTitleLineEdit method) (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.standard_widgets.buttons.DoubleClickButtonMixin method) mouseMove() (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin method) mouseMoveEvent() (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_views.PosTextNetworkNode method) (schrodinger.ui.qt.swidgets.InstantToolTipTableView method) (schrodinger.ui.qt.table.SHeaderView method) (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator method) mousePressEvent() (schrodinger.application.bioluminate.pml_menus.ColorLabel method) (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView method) (schrodinger.application.livedesign.panel_components.InitialSuggestionLineEdit method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) (schrodinger.ui.qt.appframework.CustomProgressBar method) (schrodinger.ui.qt.dialbox.Dial method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.pop_up_widgets.LineEditWithPopUp method) (schrodinger.ui.qt.protein_health_viewer.BubbleTextItem method) (schrodinger.ui.qt.smatplotlib.SmatplotlibCanvas method) (schrodinger.ui.qt.structure2d.structure_item method) (schrodinger.ui.qt.table.PerColumnSortableHeaderView method) (schrodinger.ui.qt.table_helper.CheckableHeaderView method) (schrodinger.ui.qt.tasks.taskwidgets.SpinnerLabel method) (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator method) mouseReleaseEvent() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) (schrodinger.application.job_monitor.job_monitor_table.HorizontalHeader method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.ui.qt.label.ClickableLabel method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.smatplotlib.SmatplotlibCanvas method) (schrodinger.ui.qt.table.PerColumnSortableHeaderView method) (schrodinger.ui.qt.table.SHeaderView method) mouseRightButtonClicked (schrodinger.ui.qt.radial_plot.RadialRingHistogram attribute) MouseTrackingDelegateMixin (class in schrodinger.ui.qt.delegates) MOVABLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) MOVE (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) move_alchemical_ions() (in module schrodinger.application.desmond.move_alchem_ions) move_atoms_into_cell() (in module schrodinger.application.matsci.nano.xtal) move_atoms_next_to_xyz() (in module schrodinger.application.matsci.clusterstruct) MOVE_DOWN_LB (schrodinger.ui.qt.standard.design_tokens.GeneralIcons attribute) move_group() (in module schrodinger.project.utils) move_ions_in_file() (in module schrodinger.application.desmond.move_alchem_ions) move_ions_to_ligands() (in module schrodinger.application.desmond.move_alchem_ions) move_row() (in module schrodinger.project.utils) move_solvent_cts_back() (schrodinger.application.desmond.cms.Cms method) MOVE_UP_LB (schrodinger.ui.qt.standard.design_tokens.GeneralIcons attribute) moveAuxSelectedDown() (schrodinger.ui.qt.propertyselector.PropertySelector method) moveAuxSelectedUp() (schrodinger.ui.qt.propertyselector.PropertySelector method) moveBack() (schrodinger.application.matsci.sliceplot.SlicePlot method) moveBrowserToBottom() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) moveCell() (schrodinger.ui.two_d_viewer.TwoDTableModel method) moveColumn() (schrodinger.infra.table.Table method) moveCursorToBeginning() (schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets.PlotTitleLineEdit method) moved (schrodinger.models.diffy.ListDiff attribute) moveDown() (schrodinger.application.matsci.mswidgets.StageFrame method) moveEvent() (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) moveForward() (schrodinger.application.matsci.sliceplot.SlicePlot method) moveHeadToOrigin() (schrodinger.application.matsci.amorphous.BaseMoiety method) moveNodesBetweenBeads() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) moveNodesInIteration() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) moveOldTemplates() (schrodinger.application.matsci.builderwidgets.ComplexTemplateSketcher method) movePreset() (schrodinger.models.presets.PresetManager method) moveRows() (schrodinger.infra.table.Table method) moveRowsToGroup() (schrodinger.project.project.Project method) moveStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) moveStageDown() (schrodinger.application.matsci.mswidgets.MultiStageArea method) moveStageUp() (schrodinger.application.matsci.mswidgets.MultiStageArea method) moveTo() (schrodinger.application.dendrogram.gradientSelector.ColorSelector method) moveToGroup() (schrodinger.project.manager.EntryGroupManager method) (schrodinger.project.project.ProjectRow method) moveToPosition() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) MoveToUnitCell() (in module schrodinger.application.matsci.gsas.GSASIIspc) moveUp() (schrodinger.application.matsci.mswidgets.StageFrame method) MOVEXBY (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) MOVEYBY (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) movie_settings (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) movie_settingsChanged (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) movie_settingsReplaced (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) MovieExportMode (class in schrodinger.application.pymol.gui_models) MovieSettingsModel (class in schrodinger.application.pymol.gui_models) mp (schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinMapperParams attribute) mp2() (in module schrodinger.application.jaguar.textparser) mPCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MPISettings (class in schrodinger.application.desmond.driver_utils) MPmcsaSearch() (in module schrodinger.application.matsci.gsas.GSASIImath) mPOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mro() (schrodinger.ui.qt.table_speed_up.AbstractFlagCacheProxyMixinMetaclass method) ms (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) MS_ADSORPTION_ENERGY (schrodinger.infra.structure.WorkflowType attribute) MS_AMORPHOUS_DIELECTRIC (schrodinger.infra.structure.WorkflowType attribute) MS_BAND_STRUCTURE (schrodinger.infra.structure.WorkflowType attribute) MS_BANDSHAPE (schrodinger.infra.structure.WorkflowType attribute) MS_BOND_DISSOCIATION (schrodinger.infra.structure.WorkflowType attribute) MS_CG_FF_ASSIGNMENT (schrodinger.infra.structure.WorkflowType attribute) MS_CG_FF_BUILDER (schrodinger.infra.structure.WorkflowType attribute) MS_CLUSTER_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) MS_CONVERGENCE_TESTS (schrodinger.infra.structure.WorkflowType attribute) MS_DENSITY_OF_STATES (schrodinger.infra.structure.WorkflowType attribute) MS_DIELECTRIC_FUNCTION (schrodinger.infra.structure.WorkflowType attribute) MS_DIFFUSION_COEFFICIENT (schrodinger.infra.structure.WorkflowType attribute) MS_DISORDERED_NO_SYSTEM (schrodinger.infra.structure.WorkflowType attribute) MS_DISORDERED_SYSTEM (schrodinger.infra.structure.WorkflowType attribute) MS_DROPLET_CONTACT (schrodinger.infra.structure.WorkflowType attribute) MS_ELASTIC_CONSTANTS (schrodinger.infra.structure.WorkflowType attribute) MS_ELECTROLYTE_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) MS_ELECTROPORATION (schrodinger.infra.structure.WorkflowType attribute) MS_EQUATION_OF_STATE (schrodinger.infra.structure.WorkflowType attribute) MS_ESM_DENSITY_POTENTIAL (schrodinger.infra.structure.WorkflowType attribute) MS_EVAPORATION_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) MS_EXCITED_STATE_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) MS_FREE_VOLUME (schrodinger.infra.structure.WorkflowType attribute) MS_GENETIC_OPTIMIZATION (schrodinger.infra.structure.WorkflowType attribute) MS_KMC_CHARGE_HOPPING (schrodinger.infra.structure.WorkflowType attribute) MS_KMC_CHARGE_MOBILITY (schrodinger.infra.structure.WorkflowType attribute) MS_MD_BUILDERS_CMS (schrodinger.infra.structure.WorkflowType attribute) MS_MD_BUILDERS_MAE (schrodinger.infra.structure.WorkflowType attribute) MS_MD_TRAJ_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) MS_MECP_VIEWER (schrodinger.infra.structure.WorkflowType attribute) MS_MICROKINETICS (schrodinger.infra.structure.WorkflowType attribute) MS_MORPHOLOGY (schrodinger.infra.structure.WorkflowType attribute) MS_NANOREACTOR (schrodinger.infra.structure.WorkflowType attribute) MS_OPTO_FILM_PROPS (schrodinger.infra.structure.WorkflowType attribute) MS_OPTOELECTRONICS (schrodinger.infra.structure.WorkflowType attribute) MS_ORDER_PARAMETER (schrodinger.infra.structure.WorkflowType attribute) MS_PENETRANT_LOADING (schrodinger.infra.structure.WorkflowType attribute) MS_PHONON_DENSITY_OF_STATES (schrodinger.infra.structure.WorkflowType attribute) MS_PHONON_DISPERSION (schrodinger.infra.structure.WorkflowType attribute) MS_POLYMER_BUILDER (schrodinger.infra.structure.WorkflowType attribute) MS_POLYMER_CHAIN_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) MS_POLYMER_CROSSLINK (schrodinger.infra.structure.WorkflowType attribute) MS_POWDER_DIFFRACTION_PATTERN (schrodinger.infra.structure.WorkflowType attribute) MS_PREPARE_FOR_MD (schrodinger.infra.structure.WorkflowType attribute) MS_PROJECTED_DENSITY_OF_STATES (schrodinger.infra.structure.WorkflowType attribute) MS_RELAX (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) MS_SIMULATION_PROFILE (schrodinger.infra.structure.WorkflowType attribute) MS_SOLID_ELECTOLYTE_INTERPHASE (schrodinger.infra.structure.WorkflowType attribute) MS_SOLVATION_BUILDER (schrodinger.infra.structure.WorkflowType attribute) MS_STRESS_STRAIN (schrodinger.infra.structure.WorkflowType attribute) MS_STRUCTURE_FACTOR (schrodinger.infra.structure.WorkflowType attribute) MS_SURFACE_TENSION (schrodinger.infra.structure.WorkflowType attribute) MS_SURFACES_INTERFACES (schrodinger.infra.structure.WorkflowType attribute) MS_SURFACTANT_TILT (schrodinger.infra.structure.WorkflowType attribute) MS_TG (schrodinger.infra.structure.WorkflowType attribute) MS_THERMAL_CONDUCTIVITY (schrodinger.infra.structure.WorkflowType attribute) MS_THIN_PLANE_SHEAR (schrodinger.infra.structure.WorkflowType attribute) MS_TORSION_PROFILE_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) MS_TRAJECTORY_ESP_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute) MS_TST_RATE_VIEWER (schrodinger.infra.structure.WorkflowType attribute) MS_UNCERTIANTY_QUANTIFICATION (schrodinger.infra.structure.WorkflowType attribute) ms_use_rdkit_ff_helper() (in module schrodinger.application.matsci.mstest) MS_VISCOSITY (schrodinger.infra.structure.WorkflowType attribute) MS_VISCOSITY_DIFFUSION (schrodinger.infra.structure.WorkflowType attribute) MSAnalysisMSJStringer (class in schrodinger.application.matsci.desconfig) MSAtom (class in schrodinger.application.matsci.atom_group) MSAtomGroup (class in schrodinger.application.matsci.atom_group) MSAtomGroupsBase (class in schrodinger.application.matsci.atom_group) MSAtomSelector (class in schrodinger.application.matsci.mswidgets) MSD_ANG2 (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) MsdTrajBase (class in schrodinger.application.matsci.equilibrium_md) MsdTrajBase.DIFFUSIVITY (class in schrodinger.application.matsci.equilibrium_md) mSEMI() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MSForceFieldSelector (class in schrodinger.application.matsci.mswidgets) msg (schrodinger.job.queue.MaxJobFailureError attribute) MSGWIDTH (schrodinger.application.matsci.genetic_optimization.GeneticOptimization attribute) (schrodinger.application.matsci.nano.interface_mod.Interface attribute) (schrodinger.application.matsci.nano.particle.Nanoparticle attribute) (schrodinger.application.matsci.nano.sheet.NanoSheets attribute) (schrodinger.application.matsci.nano.slab.Surface attribute) (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) (schrodinger.application.matsci.nano.tube.NanoTubes attribute) (schrodinger.application.matsci.nano.xtal.Crystal attribute) Msj (class in schrodinger.application.desmond.multisim.parser) msj2cfg() (in module schrodinger.application.desmond.gconfig) msj2sea() (in module schrodinger.application.desmond.cmj) msj2sea_full() (in module schrodinger.application.desmond.cmj) MSJ_BASE (schrodinger.application.matsci.desconfig.MSJStringer attribute) MSJ_LAST (schrodinger.application.matsci.desconfig.MSJStringer attribute) MSJStringer (class in schrodinger.application.matsci.desconfig) MSJSTRINGERS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) MSMoleculeAtomGroups (class in schrodinger.application.matsci.atom_group) MSMoleculeSelector (class in schrodinger.application.matsci.mswidgets) MSRingAtomGroup (class in schrodinger.application.matsci.atom_group) MSTestCase (class in schrodinger.application.matsci.mstest) mSTRING() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mSUBTROP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) msys (schrodinger.application.matsci.desmondutils.DesmondModel attribute) msys_model (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame attribute) MT2text() (in module schrodinger.application.matsci.gsas.GSASIIspc) mT__45() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__46() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__47() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__48() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__49() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__50() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__51() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__52() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__53() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__54() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__55() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__56() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__57() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__58() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mtd_time (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) MtdInfo (class in schrodinger.application.desmond.kinetics.utils) MtdOption (class in schrodinger.application.desmond.kinetics.enhanced_sampling) MtdStatus (class in schrodinger.application.desmond.kinetics.utils) mTokens() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mtype (schrodinger.application.matsci.kmc.MoleculeData attribute) mu (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) Muiso2Shkl() (in module schrodinger.application.matsci.gsas.GSASIIspc) mulliken_charge() (in module schrodinger.application.mopac.results_main) mulliken_charges() (in module schrodinger.application.jaguar.textparser) mulliken_electronegativity() (in module schrodinger.application.mopac.results_main) mulliken_spins() (in module schrodinger.application.jaguar.textparser) MullikenSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) mult() (schrodinger.application.macromodel.utils.ComUtil method) MULT_TIP (schrodinger.application.matsci.mswidgets.Stepper attribute) multi_inputconfig() (in module schrodinger.application.glide.utils) multi_validator() (in module schrodinger.ui.qt.appframework2.validation) multi_value_keywords (schrodinger.application.livedesign.tasks.CovDockTask attribute) MultiAxesLabelCursor (class in schrodinger.ui.qt.label_cursor) MultiBasisSelectorDialog (class in schrodinger.application.jaguar.gui.input_tab_widgets) MulticenterSgroup (class in schrodinger.application.scaffold_enumeration.posvarbond) MultiCmdJobApp (class in schrodinger.application.matsci.multiapp) MultiComboBox (class in schrodinger.ui.qt.multi_combo_box) MultiComboWithCount (class in schrodinger.application.matsci.mswidgets) MultiDesmondJobApp (class in schrodinger.application.matsci.multiapp) MultiDriver (class in schrodinger.application.matsci.equilibrium_md) MultiEnvironmentContext (class in schrodinger.utils.env) MultiFileReader (class in schrodinger.utils.fileutils) MultiFileStructureReader (class in schrodinger.structure) MultiFileStructureWriter (class in schrodinger.structure) MultiFileWriter (class in schrodinger.structutils.io) MultiFPFile (class in schrodinger.utils.multifpfile) multifpfile_fpreader() (in module schrodinger.application.hitexpander) MultiFPFileWriter (class in schrodinger.utils.multifpfile) MultiJobApp (class in schrodinger.application.matsci.multiapp) MultijobDriver (class in schrodinger.application.matsci.jobutils) multijobDriver() (schrodinger.application.matsci.jobutils.MultijobDriver method) multiJobStart() (schrodinger.application.matsci.multiapp.CmdJobMixin method) (schrodinger.application.matsci.multiapp.MultiJobApp method) multimae_to_jin() (in module schrodinger.application.jaguar.jagconvert) MultiModelClassMapperMixin (class in schrodinger.models.advanced_mappers) MULTIP (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) multip() (in module schrodinger.application.jaguar.textparser) MultiPanelWizard (class in schrodinger.ui.qt.appframework2.wizards) Multiple (schrodinger.ui.qt.config_dialog.GpuHostProductMode attribute) multiple_align() (in module schrodinger.livedesign.biologics.sequence) multiple_align_ct() (in module schrodinger.application.ska) MULTIPLE_STRUC_JOB_TITLE (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin attribute) MULTIPLE_STRUC_PICK_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) MULTIPLE_STRUC_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) MultipleChainsError MultipleOnlyGpu (schrodinger.ui.qt.config_dialog.GpuHostProductMode attribute) MultipleProteinInteractions (class in schrodinger.application.bioluminate.protein_interaction.tasks) MultipleRolesRoleModelMixin (class in schrodinger.ui.qt.table_speed_up) MultipleRolesRoleProxyMixin (class in schrodinger.ui.qt.table_speed_up) MultipleRolesRoleProxyPassthroughMixin (class in schrodinger.ui.qt.table_speed_up) MultipleSpeedUpDelegatesViewMixin (class in schrodinger.ui.qt.table_speed_up) MultipleStructSplitterStep (class in schrodinger.application.matsci.jwsteps) MULTIPLICITIES_KEY (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) MULTIPLICITIES_TITLE (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) multiplicity (schrodinger.application.jaguar.nmr_utils.IsotopeData attribute) multiply() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) multipole_esp() (in module schrodinger.application.jaguar.textparser) multipole_moments() (in module schrodinger.application.jaguar.textparser) multipole_mulliken() (in module schrodinger.application.jaguar.textparser) multipole_qm() (in module schrodinger.application.jaguar.textparser) MultipoleSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) MultiReportWithChart (class in schrodinger.application.bioluminate.protein_structure_quality) MultiRouteEnumerator (class in schrodinger.application.pathfinder.multiroute) Multisim (class in schrodinger.application.desmond.stage.launcher) MULTISIM_EXEC (schrodinger.application.desmond.envir.CONST attribute) MultiSlider (class in schrodinger.application.matsci.mswidgets) MultiSquareAnnotator (class in schrodinger.ui.qt.structure2d) MultiStageArea (class in schrodinger.application.matsci.mswidgets) MultiStageMd (class in schrodinger.application.matsci.permittivity) MultiStructureMixin (class in schrodinger.application.jaguar.gui.base_panel) MultiStructurePanel (class in schrodinger.application.jaguar.gui.base_panel) MultiStructurePanelMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) MultiStructureTab (class in schrodinger.application.jaguar.gui.tabs.multi_structure_tab) MultiTheorySelectorDialog (class in schrodinger.application.jaguar.gui.input_tab_widgets) MultiToOneConverter (class in schrodinger.application.matsci.equilibrium_md) MultiWalledNanoTube (class in schrodinger.application.matsci.nano.tube) MuscleJob (class in schrodinger.protein.tasks.muscle) MuShklMean() (in module schrodinger.application.matsci.gsas.GSASIIspc) must_register_input_file() (in module schrodinger.application.phase.packages.phase_utils) must_run_classic_screen() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) MustrainCoeff() (in module schrodinger.application.matsci.gsas.GSASIIspc) MustrainNames() (in module schrodinger.application.matsci.gsas.GSASIIspc) MustSkip (class in schrodinger.application.desmond.stage.deprecate) MUT (schrodinger.application.desmond.constants.FEP_STATE_KEYS attribute) mut (schrodinger.application.desmond.new_fep_edge_data.FepData property) (schrodinger.application.desmond.new_fep_edge_data.FepLambdas attribute) mut_asl (schrodinger.application.desmond.replica_sid_generator.AlchemAsl attribute) mut_frag_name (schrodinger.application.bioluminate.mutation.Mutation property) (schrodinger.application.bioluminate.nucleic.mutator.NucleobaseMutation property) mut_frag_st (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) mut_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) mut_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) mut_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) mut_solv_asl (schrodinger.application.desmond.replica_sid_generator.AlchemAsl attribute) mut_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) mutate() (in module schrodinger.structutils.build) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) MUTATE_METHOD_NAMES (schrodinger.models.parameters.BaseMutableParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.SetParam attribute) mutate_nucleic_acid() (in module schrodinger.structutils.build) Mutated (schrodinger.models.parameters.SignalType attribute) mutateResidues() (schrodinger.protein.alignment.BaseAlignment method) Mutation (class in schrodinger.application.bioluminate.mutation) MUTATION_CHAIN (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsStructure attribute) mutation_chain_asl (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) mutation_filename (schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams attribute) mutations (schrodinger.application.bioluminate.mutation.MacromoleculeMutator property) mutations_filename (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) MUTATIONS_PROPERTY (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) MutationSelectorComboBox (class in schrodinger.ui.residueselector) MutationSelectorFrame (class in schrodinger.ui.residueselector) MutationSelectorLineEdit (class in schrodinger.ui.residueselector) MutationSelectorMixin (class in schrodinger.ui.residueselector) MutationSelectorPopUp (class in schrodinger.ui.residueselector) MutationStructureMap (class in schrodinger.application.bioluminate.mutation) mutator (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) MUTS_FILE_REGEX (schrodinger.application.bioluminate.nucleic.mutator.NucleobaseMutator attribute) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) muts_str_to_list() (in module schrodinger.ui.residueselector) MUVT (schrodinger.application.desmond.constants.Ensembles attribute) MVCorrMW() (in module schrodinger.rdkit.filtering) MWidgetAction (class in schrodinger.application.bioluminate.pml_menus) mWS() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MXMD (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) MxmdArgs (class in schrodinger.application.desmond.starter.ui.mxmd) my_csv_reader() (in module schrodinger.active_learning.al_utils) my_file_exists() (in module schrodinger.active_learning.al_utils) my_uuid() (in module schrodinger.active_learning.mq_driver) (in module schrodinger.active_learning.mq_worker) myDataChanged() (schrodinger.ui.qt.table.StructureDataViewerModel method) MyEnum (class in schrodinger.ui.qt.mapperwidgets.param_editor) mylayout (schrodinger.ui.qt.swidgets.SLabeledComboBox attribute) (schrodinger.ui.qt.swidgets.SLabeledDoubleSpinBox attribute) (schrodinger.ui.qt.swidgets.SLabeledSpinBox attribute) myResetMethod() (schrodinger.application.matsci.jobdirdlg.DownloadingMonitorMixin method) mysplit() (in module schrodinger.utils.ligfilter) myStartMethod() (schrodinger.application.matsci.appbase.ProcessPtStructuresApp method) MyWindow (class in schrodinger.ui.qt.propertyselector) (class in schrodinger.ui.qt.tablewidget)

N

n (schrodinger.application.steps.filters.InMemoryRandomSampleFilter.Settings attribute) (schrodinger.application.steps.filters.InMemoryUniqueRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.RandomSampleFilter.Settings attribute) n() (schrodinger.ui.qt.formlayout.CountLayout method) N1 (schrodinger.ui.qt.rama.BackboneDihedral attribute) N2 (schrodinger.ui.qt.rama.BackboneDihedral attribute) N_ATOMS_KEY (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) n_blocks (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) N_CUTOFF (schrodinger.seam.transforms.samplers.RandomSample attribute) N_DIMS (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer attribute) N_fab (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) N_MOLECULES (schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder attribute) n_points (schrodinger.application.matsci.anharmonic.SeqData attribute) n_qn (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) n_segments (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) n_structures (schrodinger.application.bioluminate.methionine_oxidation.HmcStats attribute) n_win (schrodinger.application.desmond.fep_schedule.FepSchedule attribute) NA (schrodinger.application.desmond.fep_edge_data_classifier.Rating attribute) (schrodinger.application.jaguar.gui.utils.SpinTreatment attribute) (schrodinger.livedesign.biologics.fasta.PolymerType attribute) (schrodinger.protein.alignment.ResidueSimilarity attribute) NABackBone (schrodinger.protein.helm.helm_renderer.HexColor attribute) NABackboneBaseConnectorItem (class in schrodinger.protein.helm.helm_renderer) NABackboneConnectorItem (class in schrodinger.protein.helm.helm_renderer) NABaseConnectorItem (class in schrodinger.protein.helm.helm_renderer) NABaseMonomerBase (class in schrodinger.protein.helm.helm_renderer) nactive_gids (schrodinger.application.desmond.cms.Cms property) name (schrodinger.application.bioluminate.anarci.anarci_adapter.InputSequence attribute) NAME (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) name (schrodinger.application.bioluminate.peptide_sar.io.ScoredSeq attribute) (schrodinger.application.dendrogram.core_class.RingSysInfo attribute) NAME (schrodinger.application.desmond.cmj.StageBase attribute) (schrodinger.application.desmond.constants.BUILD_GEOMETRY attribute) (schrodinger.application.desmond.kinetics.utils.ResultsCols attribute) name (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot property) NAME (schrodinger.application.desmond.simulation_block_test.BoxSize attribute) (schrodinger.application.desmond.simulation_block_test.E_f attribute) (schrodinger.application.desmond.simulation_block_test.E_k attribute) (schrodinger.application.desmond.simulation_block_test.E_x attribute) (schrodinger.application.desmond.simulation_block_test.Energy attribute) (schrodinger.application.desmond.simulation_block_test.Job_Details attribute) (schrodinger.application.desmond.simulation_block_test.PotentialEnergy attribute) (schrodinger.application.desmond.simulation_block_test.Pressure attribute) (schrodinger.application.desmond.simulation_block_test.T_0 attribute) (schrodinger.application.desmond.simulation_block_test.Temperature attribute) (schrodinger.application.desmond.simulation_block_test.V attribute) (schrodinger.application.desmond.stage.analysis.Analysis attribute) (schrodinger.application.desmond.stage.analysis.FepAnalysis attribute) (schrodinger.application.desmond.stage.analysis.PLAnalysis attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer attribute) (schrodinger.application.desmond.stage.app.constant_ph.ConstantpHAnalysis attribute) (schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer attribute) (schrodinger.application.desmond.stage.app.kinetics.PathUnbinding attribute) (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingAnalysis attribute) (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup attribute) (schrodinger.application.desmond.stage.app.kinetics.RamdCleanup attribute) (schrodinger.application.desmond.stage.app.kinetics.RamdGenerateUnbindingPath attribute) (schrodinger.application.desmond.stage.app.kinetics.RamdSetup attribute) (schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD attribute) (schrodinger.application.desmond.stage.app.kinetics.ValidateStability attribute) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper attribute) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher attribute) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsSplitReceptor attribute) (schrodinger.application.desmond.stage.app.lambda_dynamics_analysis.LambdaDynamicsAnalysis attribute) (schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob attribute) (schrodinger.application.desmond.stage.app.matsci.AverageCell attribute) (schrodinger.application.desmond.stage.app.matsci.DeformCell attribute) (schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem attribute) (schrodinger.application.desmond.stage.app.matsci.FrozenPhononCorrection attribute) (schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis attribute) (schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent attribute) (schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder attribute) (schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture attribute) (schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox attribute) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis attribute) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup attribute) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup attribute) (schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures attribute) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis attribute) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher attribute) (schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher attribute) (schrodinger.application.desmond.stage.app.watermap.WaterMapCluster attribute) (schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis attribute) (schrodinger.application.desmond.stage.deprecate.AlignCore attribute) (schrodinger.application.desmond.stage.deprecate.FepMapperReport attribute) (schrodinger.application.desmond.stage.deprecate.ForcefieldBuilder attribute) (schrodinger.application.desmond.stage.deprecate.MustSkip attribute) (schrodinger.application.desmond.stage.deprecate.SolvatePocket attribute) (schrodinger.application.desmond.stage.deprecate.VacuumReport attribute) (schrodinger.application.desmond.stage.fep_mapper.CalcDdg attribute) (schrodinger.application.desmond.stage.fep_mapper.CombinedProteinFepMapper attribute) (schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper attribute) (schrodinger.application.desmond.stage.fep_mapper.FepMapper attribute) (schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup attribute) (schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper attribute) (schrodinger.application.desmond.stage.launcher.FepLauncher attribute) (schrodinger.application.desmond.stage.launcher.FepMembraneLauncher attribute) (schrodinger.application.desmond.stage.launcher.Multisim attribute) (schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge attribute) (schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield attribute) (schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule attribute) (schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher attribute) (schrodinger.application.desmond.stage.prepare.forcefield.LambdaDynamicsAssignForcefield attribute) (schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure attribute) (schrodinger.application.desmond.stage.prepare.structure.BuildGeometry attribute) (schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder attribute) (schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure attribute) (schrodinger.application.desmond.stage.prepare.structure.ExtractStructures attribute) (schrodinger.application.desmond.stage.prepare.structure.GroupWaters attribute) (schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle attribute) (schrodinger.application.desmond.stage.prepare.structure.LambdaDynamicsBuildGeometry attribute) (schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator attribute) (schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure attribute) (schrodinger.application.desmond.stage.simulate.Concatenate attribute) (schrodinger.application.desmond.stage.simulate.DesmondExtend attribute) (schrodinger.application.desmond.stage.simulate.FepVrun attribute) (schrodinger.application.desmond.stage.simulate.LambdaHopping attribute) (schrodinger.application.desmond.stage.simulate.ReInit attribute) (schrodinger.application.desmond.stage.simulate.ReplicaExchange attribute) (schrodinger.application.desmond.stage.simulate.Simulate attribute) (schrodinger.application.desmond.stage.simulate.Vrun attribute) (schrodinger.application.desmond.stage.utils.SystemBuilder attribute) (schrodinger.application.desmond.stage.workflow.Concluder attribute) (schrodinger.application.desmond.stage.workflow.Extern attribute) (schrodinger.application.desmond.stage.workflow.Primer attribute) (schrodinger.application.desmond.stage.workflow.Stop attribute) (schrodinger.application.desmond.stage.workflow.Task attribute) (schrodinger.application.desmond.stage.workflow.Trim attribute) name (schrodinger.application.desmond.starter.ui.cmdline.Option attribute) NAME (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.desmond.systype.TyperBase attribute) (schrodinger.application.desmond.systype.WatermapTyper attribute) name (schrodinger.application.glide.glide.Constraint property) NAME (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) name (schrodinger.application.jaguar.gui.utils.Solvent attribute) (schrodinger.application.jaguar.input.JaguarInput property) (schrodinger.application.jaguar.macro_pka_utils.RowData attribute) (schrodinger.application.jaguar.simple_spec.Peak attribute) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword property) (schrodinger.application.livedesign.entry_types.BaseEntryData attribute) (schrodinger.application.livedesign.entry_types.Complexes attribute) (schrodinger.application.livedesign.entry_types.CovalentDockingComplexes attribute) (schrodinger.application.livedesign.entry_types.DockedPoses attribute) (schrodinger.application.livedesign.entry_types.GenericEntities attribute) (schrodinger.application.livedesign.entry_types.Ligands attribute) (schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.BEAD_TYPE attribute) (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.MAPPED_BEAD_INFO attribute) (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) (schrodinger.application.matsci.cg_mapping.ATOM_DEFINITION attribute) (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) (schrodinger.application.matsci.codeutils.ModuleInfo attribute) NAME (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) name (schrodinger.application.matsci.kmc.MoleculeData attribute) NAME (schrodinger.application.matsci.kmc.Table attribute) name (schrodinger.application.matsci.msutils.Forcefield attribute) (schrodinger.application.matsci.packmol.SolventInfo attribute) (schrodinger.application.matsci.packmol.SurfactantInfo attribute) NAME (schrodinger.application.matsci.reaction_workflow_utils.JMSWFConformerSelection attribute) (schrodinger.application.matsci.reaction_workflow_utils.MopacConformerSelection attribute) name (schrodinger.application.matsci.reaction_workflow_utils.ReactProdTS attribute) (schrodinger.application.matsci.reaction_workflow_utils.SameTypeGSTS attribute) NAME (schrodinger.application.matsci.reaction_workflow_utils.XtbConformerSelection attribute) (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Slab attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) name (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) NAME (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) name (schrodinger.application.mopac.results_main.MopacResultsMain property) (schrodinger.application.pathfinder.route.ReactionInstance property) (schrodinger.application.prime.wrapper.BasePrimeAlignment property) NAME (schrodinger.application.vss.control.DiseControl attribute) (schrodinger.application.vss.control.GlideALControl attribute) (schrodinger.application.vss.control.GlideControl attribute) (schrodinger.application.vss.control.LigandMLControl attribute) (schrodinger.application.vss.control.ShapeControl attribute) Name (schrodinger.job.jobcontrol.Job property) name (schrodinger.project.manager.EntryGroupManager property) (schrodinger.project.project.EntryGroup property) (schrodinger.project.surface.ProjectSurface property) (schrodinger.protein.nonstandard_residues.AminoAcid property) (schrodinger.protein.sequence.AbstractSingleChainSequence property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) (schrodinger.stepper.stepper.Topic attribute) (schrodinger.structure._Chain property) (schrodinger.structure.StructureAtom property) (schrodinger.surface.Surface property) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.ui.qt.network_visualizer.Edge property) (schrodinger.ui.qt.network_visualizer.Node property) name0 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute) name1 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute) (schrodinger.application.matsci.cgforcefield.ShadowData attribute) name2 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute) (schrodinger.application.matsci.cgforcefield.ShadowData attribute) name3a (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute) name3b (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute) name4 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute) name5 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute) name6 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute) NAME_COL (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame attribute) NAME_FIELDS (schrodinger.rdkit.molio.BaseCsvMolReader attribute) NAME_NOT_UNIQUE_MSG (schrodinger.tasks.taskmanager.TaskManager attribute) name_num (schrodinger.application.desmond.new_fep_edge_data.ResData property) nameChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.sequence.AbstractSequence attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.stepper.stepper.Topic attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) nameContextCallback() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) NAMED_PROPERTIES (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) (schrodinger.application.matsci.cgforcefield.FFIOSite attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwType attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) NameLineEdit (class in schrodinger.ui.qt.tasks.taskbarwidgets) nameNum() (schrodinger.application.desmond.fep_edge_data.ResData method) namer (schrodinger.tasks.taskmanager.TaskManager attribute) namerChanged (schrodinger.tasks.taskmanager.TaskManager attribute) nameReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.stepper.stepper.Topic attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) namerReplaced (schrodinger.tasks.taskmanager.TaskManager attribute) NAMES (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) names (schrodinger.application.matsci.coarsegrain.InternalInfo attribute) (schrodinger.application.matsci.jwsteps.ParentPathInfo attribute) nameUpdated (schrodinger.ui.qt.tasks.configwidgets.JobnameWidget attribute) Nanoparticle (class in schrodinger.application.matsci.nano.particle) NanoSheet (class in schrodinger.application.matsci.nano.tube) NanoSheets (class in schrodinger.application.matsci.nano.sheet) NanoTube (class in schrodinger.application.matsci.nano.tube) NanoTubes (class in schrodinger.application.matsci.nano.tube) NanoTubeSheet (class in schrodinger.application.matsci.nano.tube) narcs (schrodinger.application.matsci.atom_group.HelixData attribute) NASequence (class in schrodinger.protein.sequence) NAStandardBaseMonomerItem (class in schrodinger.protein.helm.helm_renderer) NativeColors (class in schrodinger.ui.qt.standard.colors) natoms (schrodinger.application.jaguar.hess_guess.CoordinateManager attribute) NATOMS_KEY (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) NATOMS_PROP (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) natural_analog_sequence (schrodinger.livedesign.biologics.sequence.AlignedSequence attribute) natural_analog_similarity (schrodinger.protein.nonstandard_residues.AminoAcid property) NAUnnaturalBaseMonomerItem (class in schrodinger.protein.helm.helm_renderer) NavToolbar (class in schrodinger.ui.qt.navtoolbar) nb_cutoff() (in module schrodinger.application.qsite.output) nb_update() (in module schrodinger.application.qsite.output) nbasis() (in module schrodinger.application.jaguar.textparser) nbeta (schrodinger.application.matsci.espresso.utils.PseudoData attribute) NBILAYERS (schrodinger.application.matsci.nano.constants.Constants attribute) nbo_charges() (in module schrodinger.application.jaguar.textparser) nbo_mem_failure() (in module schrodinger.application.jaguar.textparser) NCELL1 (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) NCELL2 (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) NCELLA (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) NCELLB (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) NCELLC (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) NCELLS (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) nChanged (schrodinger.application.steps.filters.InMemoryRandomSampleFilter.Settings attribute) (schrodinger.application.steps.filters.InMemoryUniqueRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.RandomSampleFilter.Settings attribute) nconmm() (in module schrodinger.application.qsite.output) NCScattDen() (in module schrodinger.application.matsci.gsas.GSASIImath) ncuts() (in module schrodinger.application.qsite.output) NDDO (schrodinger.application.jaguar.constants.CalcType attribute) nddo_atoms() (in module schrodinger.application.qsite.output) nddo_hcaps() (in module schrodinger.application.qsite.output) NEAR_METHOD_NAMEMAP (schrodinger.application.desmond.gui.InteractionTab attribute) NEAR_RESIDUES (schrodinger.ui.picking.MaestrolessPickResidueDialog attribute) nearbyRes() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) nearest_asl_atom (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) nearest_atom_distance() (schrodinger.application.bindingsite.intfield.Field method) nearest_atom_indices (schrodinger.surface.Surface property) nearest_rotatable_bonds() (in module schrodinger.application.matsci.amorphous) NEBInputType (class in schrodinger.application.matsci.espresso.qeinput) NEBPathType (class in schrodinger.application.matsci.espresso.qeinput) need_msys (schrodinger.application.desmond.cms.Cms property) need_server() (schrodinger.application.licensing.flexlm.License method) needs_restart() (in module schrodinger.application.matsci.jaguar_restart) needsExplicitJobname() (schrodinger.job.launchapi.TaskSpecification method) needsHistogram() (schrodinger.active_learning.al_node.ActiveLearningNode method) needVisibilityUpdate() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) NEG_HESS_TOL (schrodinger.application.matsci.mecp_mod.BFGS attribute) negative (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute) Negative (schrodinger.protein.residue.RESIDUE_CHARGE attribute) negative_salt (schrodinger.application.desmond.struc.CompStruc attribute) NEGATIVE_SALT (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) negligible() (in module schrodinger.application.jaguar.nmr_utils) Neighbor (class in schrodinger.application.matsci.clusterstruct) neighbor (schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams attribute) neighbor() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) neighbor_atom (schrodinger.application.matsci.clusterstruct.Neighbor attribute) neighbor_max_dist (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) neighbor_max_distChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) neighbor_max_distReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) NeighborAtom (class in schrodinger.application.bioluminate.methionine_oxidation) neighbors (schrodinger.livedesign.biologics.registration.BioPolymer attribute) NeighborsTab (class in schrodinger.application.matsci.kmcgui) NeighborTreatment (class in schrodinger.application.matsci.chargegui) NeighborType (class in schrodinger.application.matsci.nano.sheet) nelectron() (in module schrodinger.application.jaguar.textparser) NELEMENTS_KEY (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) NELEMENTS_PROP (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) NetsuiteError, [1] NetsuiteKeyExhausted NetworkConnectionLabel (class in schrodinger.ui.qt.network_views) NetworkEdge (class in schrodinger.ui.qt.network_views) NetworkLoopError NetworkNode (class in schrodinger.ui.qt.network_views) NetworkSolver (class in schrodinger.protein.assignment) NetworkViewer (class in schrodinger.ui.qt.network_views) neutral (schrodinger.application.desmond.struc.FormHashes attribute) (schrodinger.application.desmond.struc.FormMols attribute) Neutral (schrodinger.protein.residue.RESIDUE_CHARGE attribute) NeutralHydrophilic (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) NeutralHydrophobicAliphatic (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) NeutralHydrophobicAromatic (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) NEUTRALIZE (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) neutralize() (in module schrodinger.livedesign.preprocessor) neutralize_mol() (in module schrodinger.application.pathfinder.synthesis) neutralize_structure() (in module schrodinger.structutils.build) neutralizeToggled() (schrodinger.ui.two_d_viewer.TwoDViewer method) NEW (schrodinger.application.desmond.constants.UiMode attribute) (schrodinger.application.livedesign.export_models.EntityRegistrationStatus attribute) (schrodinger.ui.qt.tasks.taskbar2.JobMonitorType attribute) new_best() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) new_data_available (schrodinger.application.matsci.jobdirdlg.JobManager attribute) NEW_DATA_TEXT (schrodinger.application.matsci.jobdirdlg.JobManager attribute) new_denominator() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) NEW_ENTRIES (schrodinger.application.matsci.appbase.ProcessPtStructuresApp attribute) new_method_selected (schrodinger.application.matsci.jagwidgets.TheorySelector attribute) new_page() (in module schrodinger.application.desmond.rl_helper) new_pymol_window (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) new_pymol_windowChanged (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) new_pymol_windowReplaced (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) NEW_STRUC_DIFF_WARNING (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) NEW_STRUCTURE (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute)

new_temperature() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) newAssaySelected (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) newDataAlert() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) NewDipro (schrodinger.protein.predictors.DiproPredictor.DiproFormat attribute) NewEntry (class in schrodinger.application.desmond.maestro) NewEntryGroup (class in schrodinger.application.desmond.maestro) NewickNode (class in schrodinger.ui.qt.dendrogram) newIteration() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) NewJobDirDialog (class in schrodinger.application.matsci.jobdirdlg) NewJobDirFrame (class in schrodinger.application.matsci.jobdirdlg) newLiveReportSelected (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelector attribute) newLocationSelected (schrodinger.ui.qt.forcefield.pathselectorwidget.PathSelectorWidget attribute) newMolecularSurface() (schrodinger.project.project.ProjectRow method) (schrodinger.project.surface.ProjectSurface class method) (schrodinger.surface.Surface class method) NewNameDialog (class in schrodinger.ui.qt.swidgets) newParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) newPreset() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) NewPresetDialog (class in schrodinger.application.matsci.jagwidgets) newTaskLoaded (schrodinger.tasks.taskmanager.TaskManager attribute) newValueSelected (schrodinger.application.livedesign.panel_components.AbstractSelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp attribute) next() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) (schrodinger.ui.dendrogram.DendrogramNodeBFIterator method) next_prime() (in module schrodinger.application.desmond.autopartition) next_sphere_id (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) nextButton() (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) nextGeom() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom method) nextMatchRequested (schrodinger.ui.qt.swidgets.TextSearchBar attribute) nextNode() (schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method) nextNumber() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) nextOutFile() (schrodinger.pipeline.stages.ligprep.PostLigPrepStage method) nextStructure() (schrodinger.ui.two_d_viewer.TwoDViewer method) nextTask() (schrodinger.tasks.taskmanager.TaskManager method) nextToken() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.TokenSource method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method) (schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer method) nextTree() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) NFFTX (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) nfrzmm() (in module schrodinger.application.qsite.output) nhcaps() (in module schrodinger.application.qsite.output) NICE (schrodinger.utils.cmdline.Options attribute) NIGGLI_REDUCE (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) niggli_reduce_cell() (in module schrodinger.comparison.struc) nil() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) nilNode() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) NIMAGE_KEY (schrodinger.application.matsci.espresso.qeinput.NEBPathType attribute) NINDEX (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) NITROGEN_PDBNAMES (schrodinger.protein.assignment.HistidinepKaPredictor attribute) (schrodinger.protein.assignment.ProtAssign.amide_changeable attribute) NJOBS (schrodinger.utils.cmdline.Options attribute) NM (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) NMA (class in schrodinger.trajectory.prody.nma) nmodels (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) nmr_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) NMRData (class in schrodinger.application.jaguar.nmr_utils) NMRSpectrum (class in schrodinger.application.matsci.spectra) nn_gas_energy() (in module schrodinger.application.jaguar.textparser) nn_optimize() (in module schrodinger.application.jaguar.neural_network_optimizer) nn_sol_energy() (in module schrodinger.application.jaguar.textparser) NO (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput attribute) no (schrodinger.structutils.clash_resolution.ClashResolutionResult attribute) no_cm1a_bcc (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) NO_DATA_CHANGED (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) no_debug_flags_from_env() (in module schrodinger.seam.testing.fixtures) no_debug_flags_from_env_impl() (in module schrodinger.seam.testing.fixtures) NO_DOUBLE_BONDS (schrodinger.application.matsci.nano.constants.Constants attribute) NO_FAILURE_MSG (schrodinger.tasks.tasks.FailureInfo attribute) NO_FEATURE (schrodinger.protein.annotation.KinaseFeatureLabel attribute) NO_INV_KEY (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) NO_ISOMER (in module schrodinger.application.matsci.buildcomplex) NO_MINIMIZATION (schrodinger.application.matsci.rxn_channel.Constants attribute) NO_MORE_LICENSES (schrodinger.application.steps.licensing.LicenseMixin attribute) NO_PARALLEL (schrodinger.seam.debug.DebugFlag attribute) NO_REACTIVE_H (schrodinger.application.matsci.rxn_channel.Constants attribute) no_restrain_zob (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) NO_SOLVENT_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) no_stack() (in module schrodinger.application.jaguar) (in module schrodinger.application.mopac) (in module schrodinger.application.xtb) NO_STRUCT_LABEL (schrodinger.application.matsci.appbase.StructureLoadButton attribute) NO_TIME (schrodinger.application.jaguar.gui.timing.TimingResults attribute) NO_UNITS (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) NO_VALUE (schrodinger.application.desmond.arkdb.DSC attribute) NO_WORKFLOWS (schrodinger.application.matsci.wfmanagement.WorkflowFinder attribute) no_zob_restrain (schrodinger.structutils.minimize.Minimizer property) NoArgCustomAction (class in schrodinger.application.matsci.parserutils) noautofit_call() (in module schrodinger.application.desmond.maestro) NoBlastHitsError NoContact (schrodinger.protein.annotation.BINDING_SITE attribute) NoCustomIACCGOptimizationTab (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) Node (class in schrodinger.application.desmond.enhsamp) (class in schrodinger.application.pathfinder.route) (class in schrodinger.ui.qt.network_visualizer) node() (schrodinger.ui.dendrogram.DendrogramNodeBFIterator method) node_ids (schrodinger.application.desmond.new_fep_edge_data.FepData property) node_run_timer() (in module schrodinger.active_learning.al_utils) node_str (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData attribute) (schrodinger.application.livedesign.entry_types.Complexes attribute) (schrodinger.application.livedesign.entry_types.DockedPoses attribute) (schrodinger.application.livedesign.entry_types.Ligands attribute) (schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute) nodeCount() (schrodinger.ui.qt.network_visualizer.Graph method) nodeHovered() (schrodinger.ui.qt.network_views.NetworkViewer method) nodeIntersectionPoint() (schrodinger.ui.qt.network_views.NetworkEdge method) nodeMenu() (schrodinger.ui.qt.network_views.NetworkViewer method) nodes (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData.RING_NODE_TYPE attribute) (schrodinger.ui.qt.network_visualizer.Edge property) NODES (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) nodes() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) (schrodinger.ui.qt.dendrogram.Dendrogram method) NODES_ADDED (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) NODES_CHANGED (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) NODES_DELETED (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) nodesAdded (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) nodesChanged (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) nodesDeleted (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) nodeUnhovered() (schrodinger.ui.qt.network_views.NetworkViewer method) NoDomain (schrodinger.protein.annotation.Domains attribute) NOEConstraint (class in schrodinger.application.glide.glide) NOFAIL (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) nofail_geopt() (in module schrodinger.application.jaguar.textparser) nofail_geopt_restart() (in module schrodinger.application.jaguar.textparser) nofail_mode() (in module schrodinger.application.jaguar.textparser) NofailResult (class in schrodinger.application.jaguar.results) nofitgrow_call() (in module schrodinger.application.desmond.maestro) NoFpClass() (in module schrodinger.application.combinatorial_diversity.diversity_fingerprinter) NoGpus (schrodinger.ui.qt.config_dialog.GpuHostProductMode attribute) NoInputTabJobMixin (class in schrodinger.application.jaguar.gui.base_panel) noJobAction() (schrodinger.application.matsci.jwsteps.BaseStep method) NOJOBID (schrodinger.utils.cmdline.Options attribute) NOLAUNCH (schrodinger.utils.cmdline.Options attribute) NOLOCAL (schrodinger.utils.cmdline.Options attribute) NoMetalError NOMM (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute) noMoreLigs (schrodinger.application.glide.http_client.ZmqClient attribute) NON_ANALYTICAL_SCF_ACCURACIES (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) NON_AROMATIC_RES (schrodinger.application.bioluminate.interaction_calculator.PiStackFinder attribute) NON_BONDED_ELEC (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) NON_BONDED_VDW (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) non_default_print_options() (in module schrodinger.application.jaguar.textparser) NON_EPV_RECEP (schrodinger.application.glide.sort_utils.StructureType attribute) NON_PARAMETERIZED_MODEL (schrodinger.application.livedesign.constants.ModelSearchType attribute) non_pri (schrodinger.application.livedesign.constants.CompoundSource attribute) NON_RETRIABLE_FAILURE (schrodinger.application.desmond.cmj.JobStatus attribute) NON_WATER_SOLVENT (schrodinger.application.prepwizard.HetType attribute) NonAtom (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomType attribute) NonBlockingBackendChecker (class in schrodinger.application.glide.http_client) NonBlockingGlideServerManager (class in schrodinger.application.glide.http_client) NonBlockingGlideServerManagerZmq (class in schrodinger.application.glide.http_client) NonBlockingHTTPClient (class in schrodinger.application.glide.http_client) nonbond_cutoff (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) nonbonded_cutoff (schrodinger.structutils.minimize.Minimizer property) NonContiguousBondingError NONE (schrodinger.application.desmond.constants.DRUDE_INVERSE_FORCE_CONSTANT_SCALING attribute) (schrodinger.application.jaguar.results.InputDeviation attribute) (schrodinger.application.job_monitor.job_monitor_models.RequestedStatus attribute) (schrodinger.energy.Solvent attribute) (schrodinger.infra.structure.WorkflowType attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.livedesign.preprocessor.GenerateCoordinates attribute) (schrodinger.tasks.ldtasks.Status attribute) (schrodinger.tasks.queue.AutoFileMode attribute) (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.MessageType attribute) (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Loop attribute) (schrodinger.ui.qt.tasks.taskbar2.JobMonitorType attribute) nonEmittingUpdate() (schrodinger.ui.qt.schart.BarSeriesSizeSpinBox method) NoneSkipper (class in schrodinger.rdkit.molio) NonHydrogen (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomType attribute) NonParamAttribute (class in schrodinger.models.parameters) nonpolarHydrogensChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) NonPostTestUnusableModuleFinder (class in schrodinger.infra.unusable_module_importer) NonPostTestUnusableModuleLoader (class in schrodinger.infra.unusable_module_importer) NONRAD_DECAYS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) Nonstandard (schrodinger.protein.nonstandard_residues.StructureSource attribute) NonUniqueTracker (class in schrodinger.application.matsci.fragments) noPosesDocked (schrodinger.application.glide.http_client.NonBlockingGlideServerManager attribute) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) (schrodinger.application.glide.http_client.NonBlockingHTTPClient attribute) (schrodinger.application.glide.http_client.ZmqClient attribute) NoPropensity (schrodinger.protein.residue.BETA_STRAND_PROPENSITY attribute) (schrodinger.protein.residue.HELIX_PROPENSITY attribute) (schrodinger.protein.residue.TURN_PROPENSITY attribute) NOPS (schrodinger.application.jaguar.results.InputDeviation attribute) nops (schrodinger.application.jaguar.results.NofailResult attribute) NOPS_AND_CUT20 (schrodinger.application.jaguar.results.InputDeviation attribute) nops_off() (in module schrodinger.application.jaguar.textparser) nops_on() (in module schrodinger.application.jaguar.textparser) NOPS_OPT_SWITCH (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) nops_setting() (in module schrodinger.application.jaguar.textparser) norm() (in module schrodinger.application.desmond.cms) norm_gen (class in schrodinger.application.matsci.gsas.GSASIIpwd) NORM_INDICES (schrodinger.application.matsci.elasticity.strain.DeformedStructureSet attribute) NORM_STRAINS (schrodinger.application.matsci.elasticity.strain.DeformedStructureSet attribute) NORM_STRAINS_KEY (schrodinger.application.matsci.espresso.qeinput.ElasticControlType attribute) normal (schrodinger.application.livedesign.upload_utils.CommandType attribute) NORMAL (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.phase.phase_markers.FontStyles attribute) normal_mode (schrodinger.application.matsci.bandshape_utils.NormalMode attribute) NORMAL_TOPOLOGY (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) normalize_and_join_paths() (in module schrodinger.application.job_monitor.job_monitor_file_browser) normalize_probe_occupancy_grid() (in module schrodinger.application.desmond.stage.app.mxmd) normalize_rgb_color() (in module schrodinger.application.matsci.maestrocmds) NormalMode (class in schrodinger.application.jaguar.results) (class in schrodinger.application.matsci.bandshape_utils) NormalModeAnalysis (class in schrodinger.application.matsci.bandshape_utils) NormalModeAnalysisException normest() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) normQ() (in module schrodinger.application.matsci.gsas.GSASIImath) NORMTHRESH (schrodinger.application.matsci.rxn_path.ReactionPath attribute) NoRotatableBondsError NORXNCOMPLEX (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) NoSave (schrodinger.job.launchparams.SaveMode attribute) NoSideChainChem (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) NoSteric (schrodinger.protein.residue.STERIC_GROUP attribute) not_conserved (schrodinger.protein.annotation.Consensus attribute) NOT_HETERO_ATOM_NUMS (schrodinger.application.matsci.automated_cg_mapping.StructData attribute) NOT_LOADED (schrodinger.application.matsci.mswidgets.StructureLoader attribute) NOT_LOADED_TIP (schrodinger.application.matsci.mswidgets.StructureLoader attribute) NOT_OK (schrodinger.application.matsci.chargegui.ForceFieldDialog attribute) NOT_SIGNED_IN (schrodinger.application.livedesign.ldclient_proxy.LDConnectionStatus attribute) NOT_STARTED (schrodinger.application.fragment_virtual_screening.frag_vs_utils.StageStatus attribute) NotCDR (schrodinger.protein.annotation.AntibodyCDRLabel attribute) NoTendency (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) notHBond() (schrodinger.application.steps.enumerators.FastFragmenter method) noViableAlt() (schrodinger.application.desmond.antlr3.dfa.DFA method) NoViableAltException NoWritableDirectoryError npacosd() (in module schrodinger.application.matsci.gsas.GSASIIpwd) npair() (in module schrodinger.application.jaguar.textparser) nparent (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) npasind() (in module schrodinger.application.matsci.gsas.GSASIIpwd) npatan2d() (in module schrodinger.application.matsci.gsas.GSASIIpwd) npatand() (in module schrodinger.application.matsci.gsas.GSASIIpwd) npcosd() (in module schrodinger.application.matsci.gsas.GSASIIpwd) (in module schrodinger.application.matsci.gsas.GSASIIspc) NPgammaT (schrodinger.application.desmond.constants.Ensembles attribute) NPO (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) nproc (schrodinger.application.desmond.driver_utils.MPISettings attribute) npsind() (in module schrodinger.application.matsci.gsas.GSASIIpwd) (in module schrodinger.application.matsci.gsas.GSASIIspc) NPT (schrodinger.application.desmond.constants.Ensembles attribute) npT2q() (in module schrodinger.application.matsci.gsas.GSASIIpwd) npT2stl() (in module schrodinger.application.matsci.gsas.GSASIIpwd) nptand() (in module schrodinger.application.matsci.gsas.GSASIIpwd) NPX (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) NPY (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) NPZ (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) NR (schrodinger.protein.tasks.blast.BlastDatabase attribute) nReplaced (schrodinger.application.steps.filters.InMemoryRandomSampleFilter.Settings attribute) (schrodinger.application.steps.filters.InMemoryUniqueRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.RandomSampleFilter.Settings attribute) nreplicas_mtd (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) nreplicas_ramd (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) nring_sys (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) nstates (schrodinger.protein.assignment.ProtAssign.ligand_changeable property) (schrodinger.protein.assignment.ProtAssign.water_changeable property) nsteps (schrodinger.application.matsci.espresso.qeinput.CustomNEBType attribute) (schrodinger.application.matsci.espresso.qeinput.DimerNEBType attribute) NSTRUCTS (schrodinger.utils.cmdline.Options attribute) NTerm (schrodinger.protein.annotation.GPCRSegmentLabel attribute) NthOrderElasticTensor (class in schrodinger.application.matsci.elasticity.elastic) nthreads() (in module schrodinger.application.jaguar.textparser) ntop_poses (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) ntop_posesChanged (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) ntop_posesReplaced (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) NU (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) nuclear_magnetic_dipole_moment_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) nuclear_spin_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) NucleicAcidAlignment (class in schrodinger.protein.alignment) NucleicAcidAssembler (class in schrodinger.livedesign.biologics.fasta) NucleicAcidSequence (class in schrodinger.protein.sequence) NucleicAcidSequenceAnnotations (class in schrodinger.protein.annotation) NucleicSequenceMeta (class in schrodinger.protein.sequence) NucleobaseMutation (class in schrodinger.application.bioluminate.nucleic.mutator) NucleobaseMutator (class in schrodinger.application.bioluminate.nucleic.mutator) Nucleotide (class in schrodinger.protein.residue) NucleotideTorsions (class in schrodinger.trajectory.trajectory_gui_dir.custom_analyzers) NucleotideType (class in schrodinger.protein.residue) nucrep1() (in module schrodinger.application.jaguar.textparser) nucrep2() (in module schrodinger.application.jaguar.textparser) nucrep_precision (schrodinger.application.jaguar.results.JaguarResults attribute) null() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) NULL_ALLOWED (schrodinger.application.matsci.kmc.SchrodingerTable attribute) (schrodinger.application.matsci.kmc.Table attribute) NULL_Y_LIM (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute) NUM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) num (schrodinger.application.matsci.mswidgets.Stepper.StepperData attribute) num() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) num_alignments (schrodinger.protein.tasks.blast.BlastSettings attribute) num_alignmentsChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) num_alignmentsReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) Num_aliphatic_rings() (in module schrodinger.utils.ligfilter) Num_aromatic_rings() (in module schrodinger.utils.ligfilter) num_atoms (schrodinger.application.desmond.new_fep_edge_data.FepData property) Num_atoms() (in module schrodinger.utils.ligfilter) num_atoms_alchemical_solvent (schrodinger.application.desmond.new_fep_edge_data.FepData property) num_basis_functions() (in module schrodinger.application.jaguar.gui.basis_selector) NUM_BITS_PER_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) NUM_CENTERING_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) num_centering_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) Num_chiral_centers() (in module schrodinger.utils.ligfilter) num_choices (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) num_clusters_selected (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog attribute) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog attribute) NUM_COLS (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) num_columns (schrodinger.protein.alignment.BaseAlignment property) NUM_CONSTRAINT (schrodinger.application.desmond.cms.Constraint attribute) num_constraint() (schrodinger.application.desmond.cms.Constraint method) num_cpu() (in module schrodinger.application.desmond.config_utils) NUM_CRU_PROP (schrodinger.application.matsci.permittivity.StepBase attribute) NUM_DECIMAL_COORDS (schrodinger.application.matsci.nano.xtal.Crystal attribute) num_done_tasks (schrodinger.tasks.queue.QueueReport attribute) num_done_tasksChanged (schrodinger.tasks.queue.QueueReport attribute) num_done_tasksReplaced (schrodinger.tasks.queue.QueueReport attribute) num_electrons() (in module schrodinger.application.mopac.results_main) NUM_EQUIV_SETS (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) num_failed_tasks (schrodinger.tasks.queue.QueueReport attribute) num_failed_tasksChanged (schrodinger.tasks.queue.QueueReport attribute) num_failed_tasksReplaced (schrodinger.tasks.queue.QueueReport attribute) num_failure (schrodinger.application.livedesign.export_models.AttachmentTaskOutput attribute) (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) num_failureChanged (schrodinger.application.livedesign.export_models.AttachmentTaskOutput attribute) (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) num_failureReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskOutput attribute) (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) num_glide_workers() (in module schrodinger.application.glide.ligand_designer) Num_heavy_atoms() (in module schrodinger.utils.ligfilter) Num_heteroaromatic_rings() (in module schrodinger.utils.ligfilter) NUM_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) NUM_IMAGES (schrodinger.ui.qt.dialbox.Dial attribute) num_iterations (schrodinger.protein.tasks.blast.BlastSettings attribute) num_iterationsChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) num_iterationsReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) num_lambda_window() (in module schrodinger.application.desmond.config_utils) num_models (schrodinger.application.bioluminate.antibody.grafting.GraftingInput attribute) Num_molecules() (in module schrodinger.utils.ligfilter) Num_negative_atoms() (in module schrodinger.utils.ligfilter) num_of_shape_screen_tokens() (in module schrodinger.application.phase.license) num_poses (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) num_posesChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) num_posesReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) Num_positive_atoms() (in module schrodinger.utils.ligfilter) NUM_PRIMARY_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) num_primary_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) num_products (schrodinger.livedesign.check_reaction.RxnCheckResult attribute) num_pt_entries (schrodinger.application.pymol.mae_sync.MaestroEntriesInfo attribute) num_pt_sel_entries (schrodinger.application.pymol.mae_sync.MaestroEntriesInfo attribute) num_pubsub_workers (schrodinger.stepper.stepper.BatchSettings attribute) num_pubsub_workersChanged (schrodinger.stepper.stepper.BatchSettings attribute) num_pubsub_workersReplaced (schrodinger.stepper.stepper.BatchSettings attribute) NUM_RANDOM_CHANNELS (schrodinger.application.matsci.rxn_channel.Constants attribute) NUM_RANDOM_CHANNELS_METAVAR (schrodinger.application.matsci.rxn_channel.Constants attribute) num_reactants (schrodinger.livedesign.check_reaction.RxnCheckResult attribute) num_replica() (in module schrodinger.application.desmond.config_utils) num_replicas (schrodinger.application.desmond.new_fep_edge_data.FepData property) Num_residues() (in module schrodinger.utils.ligfilter) Num_rings() (in module schrodinger.utils.ligfilter) num_rl_groups (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) Num_rotatable_bonds() (in module schrodinger.utils.ligfilter) num_salt_atoms (schrodinger.application.desmond.new_fep_edge_data.FepData property) num_scaffolds (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput attribute) NUM_SCALING (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) num_scenes (schrodinger.application.pymol.mae_sync.MaestroEntriesInfo attribute) num_solvation_legs (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) NUM_SPACE_GROUPS (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute) num_steps (schrodinger.application.jaguar.utils.ScanCoord attribute) num_subjobs (schrodinger.tasks.jobtasks.HostSettings attribute) num_subjobs_sb (schrodinger.ui.qt.tasks.configwidgets.HostSelector property) num_subjobsChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) (schrodinger.tasks.jobtasks.HostSettings attribute) num_subjobsReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarHostSettings attribute) (schrodinger.tasks.jobtasks.HostSettings attribute) num_substructure_matches() (in module schrodinger.livedesign.bbchem_endpoints) num_subtasks (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) num_success (schrodinger.application.livedesign.export_models.AttachmentTaskOutput attribute) (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) num_successChanged (schrodinger.application.livedesign.export_models.AttachmentTaskOutput attribute) (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) num_successReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskOutput attribute) (schrodinger.application.livedesign.export_models.GETaskOutput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) NUM_SYM_ATOMS (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) NUM_SYMMETRY_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) num_symmetry_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) num_tasks (schrodinger.tasks.queue.QueueReport attribute) num_tasksChanged (schrodinger.tasks.queue.QueueReport attribute) num_tasksReplaced (schrodinger.tasks.queue.QueueReport attribute) NUM_TRACEBACK_LINES (in module schrodinger.tasks.tasks) num_trajectory_frames (schrodinger.application.desmond.new_fep_edge_data.FepData property) num_undefined_chiralities() (in module schrodinger.ui.sketcher_extensions) NUM_UNIQUE_EDGES (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) NUM_UNIQUE_FACES (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) num_uploaded_msgs (schrodinger.stepper.stepper.Topic attribute) num_uploaded_msgsChanged (schrodinger.stepper.stepper.Topic attribute) num_uploaded_msgsReplaced (schrodinger.stepper.stepper.Topic attribute) num_water_molecules (schrodinger.application.desmond.new_fep_edge_data.FepData property) num_wildcard() (schrodinger.utils.sea.sea.Atom static method) num_ws_entries (schrodinger.application.pymol.mae_sync.MaestroEntriesInfo attribute) NumAlkyne() (in module schrodinger.rdkit.filtering) NUMATOMS (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) numAtoms() (schrodinger.trajectory.prody.ensemble.Ensemble method) (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) number (schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo attribute) (schrodinger.application.bioluminate.classify.NumberedResidue attribute) (schrodinger.application.livedesign.summary.SummaryTableSpec attribute) NUMBER (schrodinger.application.matsci.packmol.PackmolKw attribute) number (schrodinger.application.matsci.packmol.SolventInfo attribute) (schrodinger.application.matsci.packmol.SurfactantInfo attribute) (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) (schrodinger.structure._Molecule property) number_by_entry (schrodinger.structure._Molecule property) (schrodinger.structure.StructureAtom property) number_by_molecule (schrodinger.structure.StructureAtom property) number_with_ins_code (schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo property) (schrodinger.application.bioluminate.classify.NumberedResidue property) number_with_ins_code_and_chain_id (schrodinger.application.bioluminate.classify.NumberedResidue property) numberDistribution() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) NumberedCanvas (class in schrodinger.application.desmond.rl_helper) NumberedResidue (class in schrodinger.application.bioluminate.classify) NumberedSequence (class in schrodinger.application.bioluminate.classify) numberFiles() (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) numbering (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciDomainResult attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering property) (schrodinger.application.bioluminate.classify.ProteinClass attribute) numbering_params (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput attribute) numbering_scheme (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) numbering_schemeChanged (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) numbering_schemeReplaced (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportData attribute) numbering_strings (schrodinger.application.bioluminate.classify.ProteinClass property) numbering_strings_with_chain_id (schrodinger.application.bioluminate.classify.ProteinClass property) NumberingScheme (class in schrodinger.application.bioluminate.antibody.scaffold_search) numberstr (schrodinger.application.matsci.cg_mapping.ATOM_DEFINITION attribute) numBins() (schrodinger.ui.qt.schart.SHistogramBarSeries method) numCells() (schrodinger.ui.two_d_viewer.TwoDTableModel method) NumChiralCenters() (in module schrodinger.rdkit.filtering) numChoices() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) numClashs() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numConfs() (schrodinger.trajectory.prody.ensemble.Ensemble method) NUMDECIMAL (schrodinger.application.matsci.nano.tube.NanoTube attribute) NUMDENSEPOINTS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) NUMDIGITS (schrodinger.application.matsci.nano.slab.Surface attribute) numDisulfides() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numDOF() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) numerical_diff_is_acceptable() (in module schrodinger.utils.compare) numerical_freqs() (in module schrodinger.application.jaguar.textparser) NumericalDatabaseCriterion (class in schrodinger.application.bioluminate.propfilter) NumericCriterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) NumericLineEdit (class in schrodinger.application.bioluminate.bwidgets) NumericOperator (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) NumFiveFiveRings() (in module schrodinger.rdkit.filtering) numForceFields() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) numHbonds() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numModes() (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) NumNonSpiroCR4() (in module schrodinger.rdkit.filtering) numPiStacks() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numPointsChanged() (schrodinger.application.matsci.mswidgets.Stepper method) numPos() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) NumProcsSpinBox (class in schrodinger.ui.qt.config_dialog) numpy_equal() (schrodinger.application.matsci.mstest.MSTestCase method) numResources() (schrodinger.application.licensing.licadmin.LocalServerProcess method) numSaltBridges() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) NumSAtoms() (in module schrodinger.rdkit.filtering) numSelected() (schrodinger.trajectory.prody.ensemble.Ensemble method) numSelectedCells() (schrodinger.ui.two_d_viewer.TwoDViewer method) numSelectedRowsChanged (schrodinger.application.livedesign.panel_components.AbstractSelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) numsOfSharedNodes() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) numSpecificInteractions() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) NVE (schrodinger.application.desmond.constants.Ensembles attribute) NVT (schrodinger.application.desmond.constants.Ensembles attribute) NWALLS (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube attribute) nwfc (schrodinger.application.matsci.espresso.utils.PseudoData attribute) NY (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute)

O

obj (schrodinger.application.watermap.shapes.ShapeFactory property) ObjectClass (schrodinger.models.jsonable.AbstractJsonSerializer attribute) (schrodinger.models.jsonable.BytesSerializer attribute) (schrodinger.models.jsonable.DateTimeSerializer attribute) (schrodinger.models.jsonable.MolSerializer attribute) (schrodinger.models.jsonable.SetSerializer attribute) (schrodinger.models.jsonable.StructureSerializer attribute) (schrodinger.models.jsonable.TupleSerializer attribute) ObjectFreeContextSubMenu (class in schrodinger.application.bioluminate.pml_menus) objectFromJson() (schrodinger.models.jsonable.AbstractJsonSerializer class method) objectFromJsonable() (schrodinger.models.jsonable.AbstractJsonSerializer class method) (schrodinger.models.jsonable.BytesSerializer class method) (schrodinger.models.jsonable.DateTimeSerializer class method) (schrodinger.models.jsonable.MolSerializer class method) (schrodinger.models.jsonable.SetSerializer class method) (schrodinger.models.jsonable.StructureSerializer class method) (schrodinger.models.jsonable.TupleSerializer class method) Oblique() (in module schrodinger.application.matsci.gsas.GSASIIpwd) ObsoleteAction (class in schrodinger.application.glide.sort_parser_common) OCCP_SING (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) OCCP_TRIP (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) OCCPE (schrodinger.application.matsci.kmc.SitesMixin attribute) OCCPH (schrodinger.application.matsci.kmc.SitesMixin attribute) occupation (schrodinger.application.jaguar.input.GuessOrbital attribute) OCTAHEDRAL (in module schrodinger.application.matsci.buildcomplex) OCTAHEDRAL_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) OctahedralSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) Octahedron (class in schrodinger.application.matsci.shapes) octahedron() (schrodinger.application.watermap.shapes.ShapeFactory method) OCTANOL (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute) OdfChk() (in module schrodinger.application.matsci.gsas.GSASIIlattice) offset (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) OFFSET (schrodinger.ui.qt.label_cursor.LabelCursorAxes attribute) offset_indices() (in module schrodinger.protein.sequence) offset_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) offsetAtomData() (schrodinger.application.matsci.nano.xtal.PBCBond method) offsetForChain() (schrodinger.protein.sequence.CombinedChainProteinSequence method) OH_LENGTH (schrodinger.protein.assignment.WaterStateEnumerator attribute) OK (schrodinger.application.desmond.kinetics.utils.MtdStatus attribute) (schrodinger.application.jaguar.output.JaguarOutput attribute) (schrodinger.application.jaguar.utils.GenOptions attribute) (schrodinger.application.matsci.chargegui.ForceFieldDialog attribute) (schrodinger.application.xtb.output.XTBOutput attribute) Ok (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.StdBtn attribute) ok_pattern (schrodinger.infra.mmcheck.ReturnCode attribute) OKAndCancelBottomBar (class in schrodinger.ui.qt.appframework2.af2) okClicked() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) okPressed() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) okToWrite() (schrodinger.application.matsci.reportutils.ReportInfo method) OmitMap() (in module schrodinger.application.matsci.gsas.GSASIImath) on_complex() (in module schrodinger.application.desmond.new_fep_edge_data) on_complex_lambda_0() (in module schrodinger.application.desmond.new_fep_edge_data) on_complex_lambdas() (in module schrodinger.application.desmond.new_fep_edge_data) on_complex_solvent() (in module schrodinger.application.desmond.new_fep_edge_data) on_complex_solvent_lambda_0() (in module schrodinger.application.desmond.new_fep_edge_data) on_complex_solvent_lambdas() (in module schrodinger.application.desmond.new_fep_edge_data) ON_HETERO_AND_KEEP_WEDGED (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute) on_jobs_list (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel property) on_move() (schrodinger.application.desmond.fep_edge_report_maker.ABFEPReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) on_same_drive_letter() (in module schrodinger.utils.fileutils) onActiveConstraintsChkChanged() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab method) onActiveJobsOnlyChanged() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) onApplyToRowsClicked() (schrodinger.application.livedesign.panel_components.AbstractSelectionLineEdit method) onAssaySelected() (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) onBackClicked() (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) onBiologicalUnitToggled() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) onCancelClicked() (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) onCategoryChanged() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) onCellChanged() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) onClicked() (schrodinger.ui.qt.tasks.taskwidgets.StartButton method) onCommitDataToSelected() (schrodinger.application.livedesign.panel_components.ExportTableView method) onContextMenuRequested() (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget method) onCurrentIndexChanged() (schrodinger.application.livedesign.panel_components.LRSortCombo method) onCurrentJobChanged() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) onDataChanged() (schrodinger.ui.qt.filter_list.FilterListPopUp method) onDialogDismissed() (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) onDraw() (schrodinger.ui.qt.label_cursor.MultiAxesLabelCursor method) onDynamicStateChanged() (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) ONE_BY_ARMCHAIR_BASE (schrodinger.application.matsci.nano.sheet.Grow attribute) ONE_BY_ZIGZAG_BASE (schrodinger.application.matsci.nano.sheet.Grow attribute) one_e_terms() (in module schrodinger.application.jaguar.textparser) one_hot() (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer method) ONE_PER_STEP_IN_RANGE (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute) OneIndexedList (class in schrodinger.infra.util) onEneGrpIntervalChanged() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) onEneSeqIntervalChanged() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) onEnsembleChanged() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) onFileIndexChanged() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) onFileListChanged() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) onFindCheckToggled() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) onFinishedTask() (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) onHessianRefinementToggled() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) onHostMenuChanged() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) onInclusionChanged() (schrodinger.ui.qt.table_helper.PtRowBasedTableModel method) onKeyPressed() (schrodinger.ui.qt.network_views.NetworkViewer method) onLiveReportSelected() (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) onLoadClicked() (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) onLRSortMethodChanged() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) Only (schrodinger.ui.qt.table_helper.Include attribute) ONLY_CURRENT_FRAME (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute) ONLY_INIT (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) only_lowest_energy (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) onlyDifferByAHydrogen() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) onMethodChanged() (schrodinger.application.jaguar.gui.base_panel.AutomaticJobnameMixin method) onModelParamChanged() (schrodinger.models.mappers.TargetSpec method) onMotion() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) onMove() (schrodinger.ui.qt.label_cursor.MultiAxesLabelCursor method) onNewAssaySelected() (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) onNextBtnClicked() (schrodinger.ui.qt.swidgets.TextSearchBar method) onNextClicked() (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) onNumOfFramesChanged() (schrodinger.application.desmond.gui.SimOptionsFrame method) onOKPressed() (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) onPickModeChanged() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) onPickModeComboChanged() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) onPress() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) onPrevBtnClicked() (schrodinger.ui.qt.swidgets.TextSearchBar method) onProcUnitComboIndexChanged() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) onProgressChanged() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask method) onProjectChanged() (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) onProjectClosed() (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) (schrodinger.ui.qt.table_helper.PtRowBasedTableModel method) onProjectSelected() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) onProjectUpdate() (schrodinger.project.manager.EntryGroupManager method) onProjectUpdated() (schrodinger.application.livedesign.maestro_sync.EntrySelectionMaestroSync method) (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync method) (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) (schrodinger.maestro_utils.maestro_sync.ProjectEntryMaestroSync method) (schrodinger.ui.qt.table_helper.PtRowBasedTableModel method) onProjFilterChanged() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) onPtensorIntervalChanged() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) onRefreshClicked() (schrodinger.application.livedesign.panel_components.LiveReportSelectionPopup method) onRefreshCompleted() (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionPopup method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) onRegisterClicked() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) onRelease() (schrodinger.application.bioluminate.sliderchart.SlidableLine method) onRetrieveFromLocalToggled() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) onReturnPressed() (schrodinger.ui.qt.filter_list.FilterListPopUp method) ONSAGER_FILE_EXT (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) onSearchMethodChanged() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) onSelectionChanged() (schrodinger.ui.qt.network_views.NetworkViewer method) onServerTimeout() (schrodinger.application.glide.http_client.NonBlockingBackendChecker method) onShowComboIndexChanged() (schrodinger.ui.picking.MaestrolessPickResidueDialog method) onShowHideActionsToggled() (schrodinger.ui.two_d_viewer.TwoDViewer method) onSimTimeChanged() (schrodinger.application.desmond.gui.SimOptionsFrame method) onStatementExecuted() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) onStaticStateChanged() (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) onStatusBarUpdate() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) onStrucListingsUpdated() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) onStructureChanged() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) onSubJobBack() (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) onTargetSignal() (schrodinger.models.mappers.TargetSpec method) onTaskStatusChanged() (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsDialog method) onTimeChanged() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) onTimestepChanged() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) onTopLevelBack() (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) onTrajIntervalChanged() (schrodinger.application.desmond.gui.SimOptionsFrame method) onTrjIntervalChanged() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) onUsernameOrPasswordChanged() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.ServerRegistrationMixin method) onValueSelected() (schrodinger.application.livedesign.panel_components.AbstractSelectionLineEdit method) (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit method) onWizardFinish() (schrodinger.application.livedesign.ld_export_gui.ExportPanelWizard method) onWorkflowSelected() (schrodinger.application.matsci.wfmanagement.WorkflowManagerMixin method) onWorkspaceChanged() (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) onWorkspaceChangedWithActiveProj() (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) onWriteRequested() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) OPACITY_DEFAULT (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager attribute) OPACITY_SELECTED (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager attribute) OPAL_PREFIX (schrodinger.utils.openmpi.EnvVar attribute) opdiv() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) open() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) open_bonding_sites() (in module schrodinger.application.matsci.rxn_channel) open_database() (in module schrodinger.protein.gpcr.sql) open_databases() (in module schrodinger.application.bioluminate.antibody.utils) OPEN_EXT_VALUES (schrodinger.protein.tasks.blast.BlastSettings attribute) open_file() (in module schrodinger.application.mopac.utils) open_filename() (in module schrodinger.protein.getpdb) open_maybe_compressed() (in module schrodinger.utils.fileutils) open_mmzip() (in module schrodinger.project.project) open_project() (in module schrodinger.project.project) open_url() (in module schrodinger.utils.documentation) openAdvancedDialog() (schrodinger.application.desmond.gui.AdvOptionsFrame method) openAxesDialog() (schrodinger.ui.qt.schart.SChart method) openBinsDialog() (schrodinger.ui.qt.schart.SChart method) openColorSelector() (schrodinger.ui.qt.swidgets.ColorWidget method) OpenDirAsFileDialog (class in schrodinger.ui.qt.filedialog) openDisplayPreferences() (schrodinger.ui.two_d_viewer.TwoDViewer method) openExportMap() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) openFile() (in module schrodinger.trajectory.prody.writenmd) (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.WholePDB method) openFiles() (schrodinger.protein.getpdb_utility.Code method) openHelp() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) openMapping() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) openMenu() (schrodinger.application.bioluminate.ssv.toolbars.ImportToolBar method) OpenMPIVersion (class in schrodinger.utils.openmpi) openRequested (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog attribute) openSelectDialog() (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) openSelectedExportMap() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) openSeriesDialog() (schrodinger.ui.qt.schart.SChart method) openTempURL() (in module schrodinger.utils.documentation) oper_multiply() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) operate() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.canvas.Canvas2DSimilarityStage method) (schrodinger.pipeline.stages.combine.CombineStage method) (schrodinger.pipeline.stages.combine.DataFusionMergeStage method) (schrodinger.pipeline.stages.example.ExampleStage method) (schrodinger.pipeline.stages.filtering.ChargeFilterStage method) (schrodinger.pipeline.stages.filtering.DrugLikeSplitStage method) (schrodinger.pipeline.stages.filtering.GeneratePropsStage method) (schrodinger.pipeline.stages.filtering.LigFilterStage method) (schrodinger.pipeline.stages.filtering.MergeDuplicatesStage method) (schrodinger.pipeline.stages.filtering.SubSetStage method) (schrodinger.pipeline.stages.gencodes.RecombineStage method) (schrodinger.pipeline.stages.gencodes.RestoreTitlesStage method) (schrodinger.pipeline.stages.glide.DockingStage method) (schrodinger.pipeline.stages.glide.GlideSortStage method) (schrodinger.pipeline.stages.glide.GridgenStage method) (schrodinger.pipeline.stages.glide.MergeStage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) (schrodinger.pipeline.stages.ligprep.PostLigPrepStage method) (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) (schrodinger.pipeline.stages.phase.DBConfSitesStage method) (schrodinger.pipeline.stages.phase.DBExportStage method) (schrodinger.pipeline.stages.phase.DBManageStage method) (schrodinger.pipeline.stages.phase.PhaseShapeStage method) (schrodinger.pipeline.stages.prime.MMGBSAStage method) (schrodinger.pipeline.stages.prime.PrimeStage method) (schrodinger.pipeline.stages.pull.PullStage method) (schrodinger.pipeline.stages.qikprop.QikPropStage method) (schrodinger.pipeline.stages.rmsd.RmsdStage method) (schrodinger.pipeline.stages.semiemp.SemiEmpStage method) operater2Changed() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) operator() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) operator1Changed() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) operator_name (schrodinger.application.bioluminate.pose_filtering.csv_filter.FilterParameters attribute) (schrodinger.application.bioluminate.pose_filtering.residue_filter.SasaResidueFilter attribute) opls (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) OPLS5ForceFieldSelector (class in schrodinger.application.matsci.mswidgets) OPLS_ENERGY_KEY (schrodinger.application.matsci.rxn_channel.Channels attribute) opls_force_field() (in module schrodinger.forcefield.common) OPLS_VERSION (schrodinger.application.matsci.rxn_channel.Channels attribute) oplsChanged (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) OPLSDIR (schrodinger.utils.cmdline.Options attribute) OPLSDirResult (class in schrodinger.ui.qt.forcefield.forcefield) oplsReplaced (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) OPLSValidator (class in schrodinger.ui.qt.forcefield.forcefield) Opposite() (in module schrodinger.application.matsci.gsas.GSASIIspc) OPS_PRESET (schrodinger.application.matsci.mlearn.features.CrystalNNFeatures attribute) OpsfromStringOps() (in module schrodinger.application.matsci.gsas.GSASIIspc) OPT_ATTR (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) (schrodinger.application.matsci.permittivity.JaguarFinerCalculation attribute) opt_method (schrodinger.application.matsci.espresso.qeinput.CustomNEBType attribute) OPT_STUCK (schrodinger.application.jaguar.constants.FatalErrors attribute) opt_success() (in module schrodinger.application.xtb.textparser) optimal_solution() (schrodinger.protein.assignment.NetworkSolver method) OPTIMIZATION (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin attribute) OPTIMIZATION_KEYWORDS (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) OptimizationAndScanMixin (class in schrodinger.application.jaguar.gui.base_panel) OptimizationFailure, [1] OptimizationTab (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) OptimizationTabMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) optimize() (schrodinger.application.jaguar.qrnn.temp_opt.Brent method) (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.protein.assignment.ProtAssign method) (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) optimize_cluster() (schrodinger.protein.assignment.ProtAssign method) optimize_key() (in module schrodinger.application.desmond.gconfig) OptimizeAlignmentTask (class in schrodinger.protein.tasks.optimize_alignment) OptimizeAlignmentTask.Input (class in schrodinger.protein.tasks.optimize_alignment) OptimizeAlignmentTask.Output (class in schrodinger.protein.tasks.optimize_alignment) optimizeGeometry() (schrodinger.application.matsci.genetic_optimization.StructureGenome method) OptimizeHBondInput (class in schrodinger.application.prepwizard2.tasks) OptimizeHBondTask (class in schrodinger.application.prepwizard2.tasks) OptimizePDF() (in module schrodinger.application.matsci.gsas.GSASIIpwd) OptimizeResult (class in schrodinger.application.jaguar.qrnn.temp_opt) OptimizeWarning Option (class in schrodinger.active_learning.al_driver) (class in schrodinger.application.desmond.starter.ui.cmdline) (class in schrodinger.application.desmond.task) option (schrodinger.application.livedesign.export_models.DataExportSpec attribute) option_parser() (in module schrodinger.application.jaguar.jagconvert) OPTION_TEXT (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) OPTIONAL_SETTINGS_MAP (schrodinger.application.steps.basesteps.OptionalStepsMixin attribute) OptionalInputSelector (class in schrodinger.application.matsci.mswidgets) OptionalStepsMixin (class in schrodinger.application.steps.basesteps) optionChanged (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) OptionError (class in schrodinger.structure) optionfile() (schrodinger.application.licensing.flexlm.Vendor method) optionReplaced (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) Options (class in schrodinger.application.jaguar.jagconvert) (class in schrodinger.utils.cmdline) options (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) (schrodinger.application.desmond.task.Task property) Options (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) options_file() (in module schrodinger.application.licensing.licadmin) options_quit() (schrodinger.ui.qt.rama.Rama method) optionsChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) optionsReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) optionsToStage() (schrodinger.application.matsci.permittivity.MultiStageMd class method) optionsToTaskProtocols() (schrodinger.application.matsci.permittivity.CMSParser class method) (schrodinger.application.matsci.permittivity.DipoleAnalysis class method) (schrodinger.application.matsci.permittivity.DisorderSystemBuilder class method) (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) (schrodinger.application.matsci.permittivity.JaguarCalculation class method) (schrodinger.application.matsci.permittivity.JaguarMerge class method) (schrodinger.application.matsci.permittivity.MultiStageMd class method) (schrodinger.application.matsci.permittivity.PolymerBuilder class method) (schrodinger.application.matsci.permittivity.RefractiveIndex class method) (schrodinger.application.matsci.permittivity.StepBase class method) optoelectronics_evaluator() (in module schrodinger.application.matsci.genetic_optimization) OptStep (class in schrodinger.application.matsci.jaguarworkflows) ORANGE (schrodinger.ui.qt.standard.colors.NativeColors attribute) orbe_precision (schrodinger.application.jaguar.results.DerivedAttrs attribute) ORBFILE (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) Orbital (class in schrodinger.application.jaguar.results) orbital_energies() (in module schrodinger.application.jaguar.textparser) orbitalsChanged() (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) OrbSpec (class in schrodinger.application.jaguar.input) orc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orcc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orcf1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orcf2() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orcf3() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orchestrate() (schrodinger.application.matsci.nano.xtal.Crystal method) (schrodinger.application.matsci.rxn_channel.Channels method) orci() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) order (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) (schrodinger.application.glide.sort_utils.SortCriterion attribute) (schrodinger.application.matsci.elasticity.elastic.NthOrderElasticTensor property) (schrodinger.application.matsci.packmol.PDBdata attribute) (schrodinger.structure.StructureBond property) order() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) order_atoms() (in module schrodinger.application.jaguar.autots_rmsd) order_contiguous() (in module schrodinger.protein.residue) order_internal_by_name() (in module schrodinger.application.matsci.coarsegrain) order_ring_or_chain() (in module schrodinger.structutils.assignbondorders) OrderBy (class in schrodinger.structutils.interactions.salt_bridge) orderedMatches() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) OrderedOctahedralSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) OrderedResidueDict (class in schrodinger.application.bioluminate.protein.protein) OrderedSquarePlanarSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) OrderParameter (class in schrodinger.application.matsci.order_parameter_mod) orders_assigned() (in module schrodinger.structutils.assignbondorders) organize_ld_data_tree() (in module schrodinger.application.livedesign.panel_components) OrganometallicCompounds (class in schrodinger.application.livedesign.entry_types) Orient (class in schrodinger.application.bioluminate.pml_menus) ORIG_ATOM_INDEX (schrodinger.structutils.ringspear.SpearRing attribute) orig_idx_to_cur_idx() (in module schrodinger.trajectory.prody.writenmd) orig_index_prop (schrodinger.structutils.rmsd.ConformerRmsd attribute) orig_key() (schrodinger.utils.sea.sea.Key method) Origin (class in schrodinger.application.bioluminate.pml_menus) ORIGIN (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) origin (schrodinger.protein.sequence.AbstractSingleChainSequence property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) origin_normal (schrodinger.structutils.ringspear.SpearRing attribute) origin_shift() (schrodinger.application.matsci.cctbx.rot_mx.translation_part_info method) origin_shift_maestro() (in module schrodinger.application.matsci.nano.tools) origin_to_point() (in module schrodinger.graphics3d.polyhedron) ORIGINAL_ATOM_INDEX (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer attribute) ORIGINAL_MOLNUM_PROP (schrodinger.application.matsci.clusterstruct.COMTracker attribute) original_phi (schrodinger.ui.qt.rama.BackboneDihedral attribute) original_psi (schrodinger.ui.qt.rama.BackboneDihedral attribute) originalStructFile() (schrodinger.ui.qt.input_selector.InputSelector method) OrigLaunchDir (schrodinger.job.jobcontrol.Job property) OrigLaunchHost (schrodinger.job.jobcontrol.Job property) ORTHORHOMBIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) osc_precision (schrodinger.application.jaguar.results.DerivedAttrs attribute) (schrodinger.application.jaguar.results.JaguarResults attribute) OSCILLATE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Loop attribute) OSS (schrodinger.application.jaguar.constants.CalcType attribute) OTHER (schrodinger.application.bioluminate.methionine_oxidation.NeighborAtom attribute) (schrodinger.application.desmond.constants.SystemType attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) (schrodinger.application.prepwizard.HetType attribute) Other (schrodinger.protein.annotation.GPCRSegmentLabel attribute) (schrodinger.protein.helm.helm_renderer.HexColor attribute) other_name (schrodinger.application.matsci.reaction_workflow_utils.ReactProdTS attribute) (schrodinger.application.matsci.reaction_workflow_utils.SameTypeGSTS attribute) (schrodinger.protein.tasks.binding_site_align.Result attribute) other_ok (schrodinger.protein.align.ASLResult attribute) Other_Partition_F (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) OTHER_RELAX_STAGE_TRJ_INTVL (schrodinger.application.matsci.permittivity.MdStageModifier attribute) other_seq (schrodinger.protein.align.AbstractStructureAligner.Result attribute) Other_Sibling (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) other_skips (schrodinger.protein.align.ASLResult attribute) other_sse (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute) other_string (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute)

OtherAminoAcidMonomerItem (class in schrodinger.protein.helm.helm_renderer) otherAtom() (schrodinger.structure.StructureBond method) OTHERS (schrodinger.application.matsci.desconfig.MSJStringer attribute) out_csv (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) out_csvChanged (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) out_csvReplaced (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) OUT_EXT (schrodinger.application.matsci.genetic_optimization.ChemInformatics attribute) (schrodinger.application.matsci.genetic_optimization.Jaguar attribute) out_file (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) out_fileChanged (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) out_fileReplaced (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) out_fname (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) OUT_ST2_EXT (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) OUT_ST2_PROP (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) outcfg_file() (schrodinger.application.desmond.cmj.JobInput method) outcomes (schrodinger.application.vss.tasks.JobAndOutcomes attribute) outComFile() (schrodinger.application.macromodel.utils.ComUtil static method) outdated_server() (schrodinger.application.licensing.licadmin.LicenseResource method) OUTFILE_EXT (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) (schrodinger.application.matsci.permittivity.AveCellAnalysis attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) (schrodinger.application.matsci.permittivity.JaguarMerge attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) (schrodinger.application.matsci.permittivity.StepBase attribute) outfileExist() (schrodinger.application.matsci.permittivity.StepBase method) OutfileNameAttributes (class in schrodinger.application.glide.utils) outfiles (schrodinger.application.matsci.jwsteps.ParentPathInfo attribute) OUTLIER (schrodinger.ui.qt.rama.RamaClassification attribute) Output (class in schrodinger.application.matsci.espresso.qeoutput) output (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) OUTPUT (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) (schrodinger.application.matsci.packmol.PackmolKw attribute) output (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) Output (schrodinger.application.steps.converters.MaeFileWriter attribute) (schrodinger.application.steps.converters.MolToSmilesConverter attribute) (schrodinger.application.steps.dataclasses.MaeOutMixin attribute) (schrodinger.application.steps.dataclasses.MolOutMixin attribute) (schrodinger.application.steps.dataclasses.ScoredMolOutMixin attribute) (schrodinger.application.steps.dataclasses.ScorerMixin attribute) (schrodinger.application.steps.enumerators.RouteDeduplicator attribute) (schrodinger.application.steps.enumerators.RouteEnumerator attribute) (schrodinger.application.steps.enumerators.SmilesTransformPairer attribute) output (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) Output (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter attribute) (schrodinger.stepper.core_steps.DeduplicationStep attribute) (schrodinger.stepper.core_steps.RandomSampleFilter attribute) output (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.stepper.stepper.StepTaskMixin attribute) Output (schrodinger.stepper.stepper.UnbatchedChain property) (schrodinger.tasks.jobtasks.CmdJobTask attribute) output (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) output() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) OUTPUT_COLUMN_MAP (schrodinger.tasks.ldtasks.LDTask attribute) output_file (schrodinger.application.mopac.results_main.MopacResultsMain property) (schrodinger.stepper.stepper.StepTaskOutput attribute) OUTPUT_FILE_NAME (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) output_file_names (schrodinger.application.matsci.jwsteps.BaseStep property) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin property) output_fileChanged (schrodinger.stepper.stepper.StepTaskOutput attribute) output_filename (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) output_filenameChanged (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) output_filenameReplaced (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) output_fileReplaced (schrodinger.stepper.stepper.StepTaskOutput attribute) output_filesChanged (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) output_filesReplaced (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) output_pcoll_counts (schrodinger.seam.metric.ExecutionMetrics attribute) output_term() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) outputChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) OutputFiles (schrodinger.job.jobcontrol.Job property) outputReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) outputRequested() (schrodinger.pipeline.stage.Stage method) OutputRow (schrodinger.tasks.ldtasks.LDTask attribute) outputs() (schrodinger.stepper.sideinputs.JoinFromFileStep method) (schrodinger.stepper.sideinputs.JoinStep method) (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) OUTPUTS_CMS (schrodinger.application.matsci.jwsteps.BaseDesmondStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.CustomCmsToMaeStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) OutputSerializer (schrodinger.application.steps.dataclasses.MolOutMixin attribute) (schrodinger.application.steps.dataclasses.ScoredMolOutMixin attribute) (schrodinger.application.steps.dataclasses.ScorerMixin attribute) (schrodinger.application.steps.enumerators.RouteDeduplicator attribute) (schrodinger.application.steps.enumerators.RouteEnumerator attribute) (schrodinger.stepper.stepper.UnbatchedChain property) OutputsPlot (class in schrodinger.stepper.viz) outputStructure() (schrodinger.protein.captermini.CapTermini method) outputStructurePath() (schrodinger.application.matsci.jwsteps.HOFStep method) OutputTab (class in schrodinger.application.desmond.gui) (class in schrodinger.application.jaguar.gui.tabs.output_tab) outputTypeChanged() (schrodinger.application.matsci.appbase.ProcessPtStructuresApp method) overlap_matrix() (in module schrodinger.application.mopac.results_main) overlap_ratio_cutoff (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) overlap_ratio_cutoffChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) overlap_ratio_cutoffReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) overlapping (schrodinger.application.prepwizard2.diagnostics.Problems attribute) overlappingChanged (schrodinger.application.prepwizard2.diagnostics.Problems attribute) overlappingReplaced (schrodinger.application.prepwizard2.diagnostics.Problems attribute) OverrideKeywords (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) OVERWRITE (schrodinger.infra.structure.WriteMode attribute) overwrite_data (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) overwrite_hotatoms() (in module schrodinger.application.desmond.stage.app.absolute_binding.restraint) OVERWRITE_QUESTION_KEY (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) overwriteVertices() (schrodinger.application.matsci.nano.particle.Nanoparticle method) Owner (schrodinger.application.livedesign.panel_components.LRSort attribute) owner() (schrodinger.models.parameters.Param class method) ownerChain() (schrodinger.models.parameters.Param class method) OXYGEN_PDBNAMES (schrodinger.protein.assignment.AsparticAcidpKaPredictor attribute) (schrodinger.protein.assignment.GlutamicAcidpKaPredictor attribute) (schrodinger.protein.assignment.ProtAssign.amide_changeable attribute)

P

p_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) P_VALUE (schrodinger.application.desmond.kinetics.utils.ResultsCols attribute) pack_stage() (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.simulate.SimulateBase method) Package (class in schrodinger.application.licensing.flexlm) package_TGC_models() (in module schrodinger.active_learning.al_utils) PACKAGE_TO_PRODUCT_NAME (schrodinger.infra.unusable_module_importer.AbstractUnusableModuleFinder attribute) packing_pct (schrodinger.application.matsci.packmol.SolventInfo attribute) (schrodinger.application.matsci.packmol.SurfactantInfo attribute) packingFraction() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) PackmolInputFile (class in schrodinger.application.matsci.packmol) PackmolInputFileException PackmolKw (class in schrodinger.application.matsci.packmol) PackRot() (in module schrodinger.application.matsci.gsas.GSASIIspc) pad_asl_if_invalid() (in module schrodinger.application.desmond.kinetics.utils) padAlignment() (schrodinger.protein.alignment.BaseAlignment method) PADDING (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.ui.qt.schart.SChartView attribute) paddingFactor() (schrodinger.ui.qt.delegates.PictureDelegate method) PaddingSizes (class in schrodinger.ui.qt.standard.design_tokens) PAGE_MARGIN (schrodinger.application.report2d.PicturePrinter attribute) PageSize (class in schrodinger.application.phase.shape_screen_reporter.option_utils) paint() (schrodinger.application.dendrogram.gradientSelector.ColorSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.application.job_monitor.job_monitor_table.JobDetailsArrowDelegate method) (schrodinger.application.job_monitor.job_monitor_table.JobProgressDelegate method) (schrodinger.application.job_monitor.job_monitor_table.JobTableDelegate method) (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUpDelegate method) (schrodinger.application.livedesign.panel_components.ExportTableDataColumnDelegate method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.SeparatorItemDelegate method) (schrodinger.protein.helm.helm_renderer.AminoAcidMonomerBase method) (schrodinger.ui.qt.delegates.CenteredIconDelegate method) (schrodinger.ui.qt.delegates.CheckboxDelegate method) (schrodinger.ui.qt.delegates.ComboBoxDelegate method) (schrodinger.ui.qt.delegates.DefaultMessageDelegate method) (schrodinger.ui.qt.delegates.LineEditDelegate method) (schrodinger.ui.qt.delegates.LinkDelegate method) (schrodinger.ui.qt.delegates.MatplotlibDelegate method) (schrodinger.ui.qt.delegates.PictureDelegate method) (schrodinger.ui.qt.delegates.ProgressBarDelegate method) (schrodinger.ui.qt.delegates.PushButtonDelegate method) (schrodinger.ui.qt.delegates.RadioButtonDelegate method) (schrodinger.ui.qt.delegates.ToolTipIconDelegate method) (schrodinger.ui.qt.delegates.WorkspaceInclusionDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) (schrodinger.ui.qt.schart.Callout method) (schrodinger.ui.qt.structure2d.structure_item method) (schrodinger.ui.qt.table.GenericViewerDelegate method) (schrodinger.ui.two_d_viewer.TwoDTableDelegate method) paint_asl() (in module schrodinger.application.desmond.maestro) (schrodinger.application.desmond.maestro.Workspace method) paint_mol() (schrodinger.application.desmond.maestro.Workspace method) paint_progress() (in module schrodinger.application.job_monitor.job_monitor_progress_bar) PAINT_ROLES (schrodinger.ui.qt.table_speed_up.SpeedUpDelegate attribute) paint_scene() (in module schrodinger.protein.helm.image_generation) paintCell() (schrodinger.ui.qt.structtable.StructureViewerDelegate method) (schrodinger.ui.qt.table.StructureDataViewerDelegate method) paintEvent() (schrodinger.application.bioluminate.bwidgets.RowActionItem method) (schrodinger.application.jaguar.gui.utils.WorkspaceInclusionCheckBox method) (schrodinger.application.job_monitor.job_monitor_progress_bar.ProgressBar method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.ui.qt.dialbox.Dial method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.rdmol_views.AbstractRDMolImageLabel method) (schrodinger.ui.qt.schart.SChartView method) (schrodinger.ui.qt.standard_widgets.combo_boxes.ItalicsPlaceholderComboBox method) (schrodinger.ui.qt.standard_widgets.hyperlink.ButtonWithArrowMixin method) (schrodinger.ui.qt.structure2d.StructureToolTip method) (schrodinger.ui.qt.swidgets.ImageLabel method) (schrodinger.ui.qt.swidgets.PlaceholderComboMixin method) (schrodinger.ui.qt.swidgets.ResizablePictureLabel method) (schrodinger.ui.qt.swidgets.StyleMixin method) (schrodinger.ui.qt.swidgets.VerticalLabel method) (schrodinger.ui.two_d_viewer.ZoomWidget method) paintItemBackground() (schrodinger.ui.qt.delegates.AbstractCustomDelegate method) paintOneCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) paintPicture() (schrodinger.ui.qt.delegates.PictureDelegate method) (schrodinger.ui.qt.delegates.RdMolDelegate method) paintSection() (schrodinger.ui.qt.table_helper.CheckableHeaderView method) (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator method) paintStructure() (schrodinger.ui.qt.table.StructureDataViewerDelegate method) paintText() (schrodinger.ui.qt.delegates.PictureDelegate method) paintWait() (schrodinger.ui.qt.table.GenericViewerDelegate method) PAIR_DISTANCE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) PAIR_ELEC (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) PAIR_TYPE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) PAIR_VDW (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) PAIRS (schrodinger.application.matsci.rxn_path.CheckInput attribute) PAIRS_TABLE (schrodinger.application.matsci.kmc.BaseDatabaseManager attribute) (schrodinger.application.matsci.kmc.MatSciDatabaseManager attribute) (schrodinger.application.matsci.kmc.VotcaDatabaseManager attribute) pairs_table_has_com() (in module schrodinger.application.matsci.kmc) PairsMixin (class in schrodinger.application.matsci.kmc) PairsTable (class in schrodinger.application.matsci.kmc) pairwise_align_ct() (in module schrodinger.application.ska) pairwise_constraints (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) PAM30 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) PAM70 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) pan() (schrodinger.application.matsci.density_analysis_widget.CustomToolbar method) (schrodinger.ui.qt.navtoolbar.MaestroNavToolbar method) panel (class in schrodinger.application.pymol.pymol4maestro) Panel (class in schrodinger.ui.qt.basewidgets) PANEL (schrodinger.ui.qt.standard.design_tokens.BackgroundColors attribute) panel() (in module schrodinger.application.bioluminate.protein_report_widget) (in module schrodinger.application.livedesign.login_gui) (in module schrodinger.application.livedesign.login_gui2) (in module schrodinger.application.matsci.reordergui) (in module schrodinger.ui.qt.atomselector) (in module schrodinger.ui.qt.structure_selector) (schrodinger.application.matsci.appbase.MatSciAppMixin class method) (schrodinger.ui.qt.appframework2.af2.App class method) (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard class method) (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin class method) PANEL_TASKS (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin attribute) panelLabelChanged (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) PanelMixin (class in schrodinger.ui.qt.widgetmixins.panelmixins) PanelPreset (class in schrodinger.models.presets) PanelState (class in schrodinger.ui.qt.appframework2.settings) Parallelepiped (class in schrodinger.application.matsci.shapes) ParallelPleatedSheet (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) Param (class in schrodinger.models.parameters) PARAM (schrodinger.application.desmond.cmj.StageBase attribute) (schrodinger.application.desmond.stage.analysis.Analysis attribute) (schrodinger.application.desmond.stage.analysis.FepAnalysis attribute) (schrodinger.application.desmond.stage.analysis.PLAnalysis attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepLauncher attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingLauncherBase attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher attribute) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer attribute) (schrodinger.application.desmond.stage.app.constant_ph.ConstantpHAnalysis attribute) (schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer attribute) (schrodinger.application.desmond.stage.app.kinetics.PathUnbinding attribute) (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingAnalysis attribute) (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup attribute) (schrodinger.application.desmond.stage.app.kinetics.RamdCleanup attribute) (schrodinger.application.desmond.stage.app.kinetics.RamdGenerateUnbindingPath attribute) (schrodinger.application.desmond.stage.app.kinetics.RamdSetup attribute) (schrodinger.application.desmond.stage.app.kinetics.RandomAcceleratedMD attribute) (schrodinger.application.desmond.stage.app.kinetics.ValidateStability attribute) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper attribute) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher attribute) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsSplitReceptor attribute) (schrodinger.application.desmond.stage.app.lambda_dynamics_analysis.LambdaDynamicsAnalysis attribute) (schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob attribute) (schrodinger.application.desmond.stage.app.matsci.AverageCell attribute) (schrodinger.application.desmond.stage.app.matsci.DeformCell attribute) (schrodinger.application.desmond.stage.app.matsci.ExtractSubSystem attribute) (schrodinger.application.desmond.stage.app.matsci.FrozenPhononCorrection attribute) (schrodinger.application.desmond.stage.app.matsci.MatSciAnalysis attribute) (schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent attribute) (schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder attribute) (schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture attribute) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventAnalysis attribute) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup attribute) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventSetup attribute) (schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures attribute) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis attribute) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepLauncher attribute) (schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher attribute) (schrodinger.application.desmond.stage.app.watermap.WaterMapCluster attribute) (schrodinger.application.desmond.stage.app.watermap.WaterMapPostAnalysis attribute) (schrodinger.application.desmond.stage.fep_mapper.CalcDdg attribute) (schrodinger.application.desmond.stage.fep_mapper.CombinedProteinFepMapper attribute) (schrodinger.application.desmond.stage.fep_mapper.CovalentFepMapper attribute) (schrodinger.application.desmond.stage.fep_mapper.FepMapper attribute) (schrodinger.application.desmond.stage.fep_mapper.FepMapperCleanup attribute) (schrodinger.application.desmond.stage.fep_mapper.ProteinFepMapper attribute) (schrodinger.application.desmond.stage.launcher.FepLauncher attribute) (schrodinger.application.desmond.stage.launcher.FepMembraneLauncher attribute) (schrodinger.application.desmond.stage.launcher.Multisim attribute) (schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge attribute) (schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield attribute) (schrodinger.application.desmond.stage.prepare.forcefield.AssignLambdaSchedule attribute) (schrodinger.application.desmond.stage.prepare.forcefield.ForcefieldBuilderLauncher attribute) (schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure attribute) (schrodinger.application.desmond.stage.prepare.structure.BuildGeometry attribute) (schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder attribute) (schrodinger.application.desmond.stage.prepare.structure.ExtractStructures attribute) (schrodinger.application.desmond.stage.prepare.structure.GroupWaters attribute) (schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator attribute) (schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure attribute) (schrodinger.application.desmond.stage.simulate.Concatenate attribute) param (schrodinger.application.desmond.stage.simulate.Concatenate property) PARAM (schrodinger.application.desmond.stage.simulate.DesmondExtend attribute) (schrodinger.application.desmond.stage.simulate.FepVrun attribute) (schrodinger.application.desmond.stage.simulate.GCMCCapable attribute) (schrodinger.application.desmond.stage.simulate.LambdaHopping attribute) (schrodinger.application.desmond.stage.simulate.ReInit attribute) (schrodinger.application.desmond.stage.simulate.ReplicaExchange attribute) (schrodinger.application.desmond.stage.simulate.SimulateBase attribute) (schrodinger.application.desmond.stage.simulate.Vrun attribute) (schrodinger.application.desmond.stage.simulate.VrunBase attribute) (schrodinger.application.desmond.stage.utils.SystemBuilder attribute) (schrodinger.application.desmond.stage.workflow.Extern attribute) (schrodinger.application.desmond.stage.workflow.Task attribute) (schrodinger.application.desmond.stage.workflow.Trim attribute) PARAM_ORDER (schrodinger.application.matsci.cgforcefield.FFIOBond attribute) (schrodinger.application.matsci.cgforcefield.FFIOImproper attribute) (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) param_to_yaml_file() (in module schrodinger.models.yaml_utils) param_to_yaml_str() (in module schrodinger.models.yaml_utils) ParamAttributeError ParamColumn (class in schrodinger.ui.qt.mapperwidgets.plptable) ParamDict (class in schrodinger.models.parameters) paramDict() (schrodinger.application.bioluminate.interaction_calculator.InteractionParams method) ParamEditor (class in schrodinger.ui.qt.mapperwidgets.param_editor) parameter_string (schrodinger.application.desmond.stage.prepare.forcefield.AssignForcefield attribute) (schrodinger.application.desmond.stage.simulate.SimulateBase attribute) ParameterData (class in schrodinger.application.matsci.cgforcefieldgui) PARAMETERIZABLE (schrodinger.application.livedesign.constants.ModelSearchType attribute) PARAMETERIZED (schrodinger.application.livedesign.constants.ModelSearchType attribute) ParameterLine (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) Parameters (class in schrodinger.application.jaguar.spin_simulator_v2) ParamListParam (class in schrodinger.models.parameters) ParamModel (in module schrodinger.models.parameters) paramName() (schrodinger.models.parameters.Param class method) ParamTargetSpec (class in schrodinger.models.mappers) ParamToConfigObj (class in schrodinger.models.adapters.inputconfig) ParamToInputConfig (class in schrodinger.models.adapters.inputconfig) ParamType (class in schrodinger.models.parameters) ParchTrajectoryForAbsoluteFep (class in schrodinger.application.desmond.task) ParchTrajectoryForFep (class in schrodinger.application.desmond.task) ParchTrajectoryForFepLambda (class in schrodinger.application.desmond.task) ParchTrajectoryForSolubilityFep (class in schrodinger.application.desmond.task) parent (schrodinger.application.jaguar.simple_spec.Peak attribute) PARENT (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) parent() (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.utils.sea.sea.Sea method) PARENT2PSEUDO (schrodinger.application.desmond.constants.IdConversion attribute) parent_d (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) parent_dir() (in module schrodinger.application.desmond.util) parent_group (schrodinger.project.manager.EntryGroupManager property) parent_group_name (schrodinger.project.manager.EntryGroupManager property) parent_job_id (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) parent_job_idChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) parent_job_idReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) PARENT_NODE_INDEXES (schrodinger.application.matsci.permittivity.WorkflowParser attribute) PARENT_OUTFILE_MASK (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CommandLine attribute) parent_script_path (schrodinger.application.matsci.builderwidgets.TemplateFamily attribute) ParentJobId (schrodinger.job.jobcontrol.Job property) ParentPathInfo (class in schrodinger.application.matsci.jwsteps) parents (schrodinger.application.matsci.codeutils.ModuleInfo attribute) ParentStageData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) pargph() (in module schrodinger.application.desmond.rl_helper) parr_and_pople() (in module schrodinger.application.mopac.results_main) parse() (in module schrodinger.application.desmond.multisim.parser) (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.application.jaguar.scan.Scan static method) (schrodinger.application.jaguar.textparser.TextParser method) (schrodinger.application.mopac.results_main.MopacMainTextParser method) (schrodinger.application.xtb.textparser.TextParser method) (schrodinger.utils.ligfilter.CriterionParser method) (schrodinger.utils.ligfilter.DefinitionParser method) parse_and_delete_output_file() (schrodinger.protein.assignment.NetworkSolver method) parse_and_drop_xmlns() (in module schrodinger.application.scaffold_enumeration.rdcml) parse_antibody_rescode() (in module schrodinger.protein.annotation) parse_args() (in module schrodinger.active_learning.mq_backend) (in module schrodinger.active_learning.mq_driver) (in module schrodinger.active_learning.mq_worker) (in module schrodinger.application.bioluminate.anarci.annotate) (in module schrodinger.application.bioluminate.methionine_oxidation) (in module schrodinger.application.bioluminate.peptide_sar.sar) (in module schrodinger.application.bioluminate.tcr.docking_angles) (in module schrodinger.application.bioluminate.update_germline_db.translate_db) (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.lmgrd_log_parser) (in module schrodinger.application.mopac.mopac_parser) (in module schrodinger.application.phase.packages.shape_screen_al_driver) (in module schrodinger.forcefield.custom_params) (in module schrodinger.protein.process_enamine_db) (in module schrodinger.seam.examples.haystack) (in module schrodinger.seam.examples.rescount) (in module schrodinger.utils.featureflags.featureflags) (in module schrodinger.utils.installation_check) (in module schrodinger.utils.postinstall) (schrodinger.application.matsci.parserutils.DriverParser method) (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method) parse_arguments() (in module schrodinger.protein.getpdb_utility) (in module schrodinger.structutils.sort) parse_basis() (in module schrodinger.application.jaguar.basis) parse_bond_reactions() (in module schrodinger.application.pathfinder.route) parse_cmd() (in module schrodinger.application.desmond.kinetics.cleanup) (in module schrodinger.application.desmond.kinetics.mtd_cleanup) (in module schrodinger.application.desmond.mxmd.mxmd_cleanup) parse_combined_exclusion_str() (in module schrodinger.application.matsci.coarsegrain) parse_components() (in module schrodinger.application.licensing.flexlm) parse_CSV() (in module schrodinger.application.matsci.stress_strain) parse_csv_line() (in module schrodinger.application.glide.utils) parse_csv_props_file() (in module schrodinger.application.glide.utils) parse_cvseq() (in module schrodinger.application.desmond.meta) parse_cx_extensions() (in module schrodinger.application.scaffold_enumeration.cxsmiles) parse_database_prop() (in module schrodinger.application.matsci.kmc) parse_date() (in module schrodinger.application.licensing.flexlm) parse_datetime() (in module schrodinger.application.licensing.lmgrd_log_parser) parse_edge_file() (in module schrodinger.application.desmond.util) parse_ene_file() (in module schrodinger.application.desmond.ene_utils) parse_enegrp_file() (in module schrodinger.application.desmond.ene_utils) parse_eneseq() (in module schrodinger.application.desmond.fepana) parse_events() (in module schrodinger.application.licensing.lmgrd_log_parser) parse_expiration() (in module schrodinger.application.licensing.flexlm) parse_feature_rules() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) parse_feature_tol() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) parse_fep_data() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) parse_field_prop() (in module schrodinger.application.matsci.kmc) parse_filter_expression() (in module schrodinger.structutils.filter) parse_frozen_atoms() (in module schrodinger.application.pathfinder.analysis) parse_gibbs_energies() (in module schrodinger.application.jaguar.utils) parse_glide_results() (in module schrodinger.application.livedesign.ld_glide_utils) parse_halogen_interactions() (in module schrodinger.application.desmond.sid_plots.pl_interactions) parse_helm() (in module schrodinger.protein.helm) parse_hunt_args() (in module schrodinger.job.hunt_stub) parse_indices() (in module schrodinger.application.desmond.enhsamp) parse_input() (in module schrodinger.active_learning.mq_driver) parse_input_file() (in module schrodinger.application.phase.packages.shape_screen_al_driver) parse_inverse_tags() (in module schrodinger.application.pathfinder.reaction) parse_keyword_list() (in module schrodinger.application.matsci.parserutils) parse_kinase_conservation() (in module schrodinger.protein.tasks.kinase) parse_known_options() (in module schrodinger.application.desmond.starter.ui.cmdline) parse_lambda() (in module schrodinger.application.desmond.config_utils) parse_lewis_data() (in module schrodinger.application.jaguar.utils) parse_license_server_env() (in module schrodinger.application.licensing.licserver.client) parse_license_sources() (in module schrodinger.application.licensing.licserver.client) parse_ligand_file() (in module schrodinger.application.desmond.util) parse_ligand_strain_results() (in module schrodinger.application.livedesign.ld_ligand_strain_utils) parse_line() (in module schrodinger.application.licensing.flexlm) parse_lmdiag_entry() (in module schrodinger.application.licensing.licadmin) parse_lmdiag_output() (in module schrodinger.application.licensing.licadmin) parse_lmgrd_event() (in module schrodinger.application.licensing.licadmin) parse_lmgrd_lines() (in module schrodinger.application.licensing.licadmin) parse_lmgrd_log() (in module schrodinger.application.licensing.licadmin) parse_lmhostid_output() (in module schrodinger.application.licensing.licadmin) parse_lmstat_output() (in module schrodinger.application.licensing.licadmin) parse_local_entitlement() (in module schrodinger.application.licensing.licserver.client) parse_logfile() (in module schrodinger.application.licensing.lmgrd_log_parser) parse_matrix() (in module schrodinger.application.matsci.jaguarworkflows) parse_mcg() (in module schrodinger.application.scaffold_enumeration.cxsmiles) parse_meta() (in module schrodinger.application.desmond.meta) parse_mexpr() (in module schrodinger.application.desmond.enhsamp) parse_mmgbsa_results() (in module schrodinger.application.livedesign.ld_mmgbsa_utils) parse_mobility_or_velocity_prop() (in module schrodinger.application.matsci.kmc) parse_msj() (in module schrodinger.application.desmond.cmj) parse_multi_entity_fasta() (in module schrodinger.livedesign.biologics.fasta) parse_multiple_jobs() (schrodinger.application.mopac.results_main.MopacMainTextParser method) parse_name() (schrodinger.application.bioluminate.update_germline_db.translate_db.GermlineEntry static method) parse_nodefile() (in module schrodinger.application.desmond.driver_utils) parse_novel_sdf_file() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF static method) parse_options() (in module schrodinger.application.desmond.starter.ui.cmdline) parse_output_structure_properties() (in module schrodinger.application.desmond.solubility_utils) parse_overlap_mat() (in module schrodinger.application.jaguar.output) parse_pathfinder_data() (in module schrodinger.application.pathfinder.reaction) parse_prm_tag() (in module schrodinger.application.desmond.replica_sid_generator) parse_reaction_data() (in module schrodinger.application.pathfinder.reaction) parse_reagent_classes_data() (in module schrodinger.application.pathfinder.reaction) parse_report() (in module schrodinger.application.desmond.solubility_utils) parse_res() (in module schrodinger.application.desmond.util) parse_res_name_with_atoms() (in module schrodinger.application.desmond.sid_plots.pl_interactions) parse_res_tag() (in module schrodinger.application.desmond.fep_edge_report_maker) parse_resstr() (in module schrodinger.application.bioluminate.protein_interaction.utils) parse_restart_parameters_file() (in module schrodinger.application.matsci.jobutils) parse_rgmol() (in module schrodinger.livedesign.rgfile_parse) parse_route_data() (in module schrodinger.application.pathfinder.route) parse_sba() (in module schrodinger.application.desmond.simulation_block_data) parse_sbt() (in module schrodinger.application.desmond.simulation_block_test) parse_sea() (in module schrodinger.application.desmond.fep_edge_data) parse_server_identifier() (in module schrodinger.application.licensing.licserver.client) parse_shape_screen_options() (in module schrodinger.application.phase.packages.phase_option_utils) parse_sid() (in module schrodinger.application.desmond.fep_edge_data) parse_single_entity_fasta() (in module schrodinger.livedesign.biologics.fasta) parse_size() (in module schrodinger.application.glide.utils) parse_sru() (in module schrodinger.application.scaffold_enumeration.cxsmiles) parse_stage_data() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) parse_strain_rescore_results() (in module schrodinger.application.livedesign.ld_strain_rescore_utils) parse_string (class in schrodinger.application.matsci.cctbx.rot_mx) parse_symm_op() (schrodinger.application.matsci.cctbx.rot_mx.parse_string method) parse_task_output_ids() (in module schrodinger.application.livedesign.tasks) parse_timedelta() (in module schrodinger.application.licensing.lmgrd_log_parser) parse_tokens() (in module schrodinger.application.licensing.flexlm) parse_xvol_file() (in module schrodinger.application.glide.utils) parse_yes_no_setting() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) parseArgs() (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.particle.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.ParserWrapper method) (schrodinger.application.matsci.nano.xtal.ParserWrapper method) (schrodinger.application.matsci.rxn_path.ParserWrapper method) (schrodinger.stepper.app.StepperApplication class method) parseAtomText() (schrodinger.application.matsci.reordergui.StructureListWidget method) parseAvailableFiles() (schrodinger.application.matsci.jobutils.FileDownloader method) parseBlock_F() (schrodinger.application.glide.xpdes.XpPVParser method) parseBlock_SL() (schrodinger.application.glide.xpdes.XpPVParser method) parseConservationOutput() (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask method) parsed_inp_file (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) parsed_inp_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) parsed_inp_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) parseDataLine() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) parseDomains() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) ParseError parseHP() (schrodinger.application.matsci.espresso.qeoutput.Output static method) parseKeyval() (schrodinger.application.glide.utils.DictAction method) parseLabel() (in module schrodinger.application.desmond.sid_plots.pl_lid) parseLine() (schrodinger.utils.ligfilter.Criterion method) parseMsjStr() (schrodinger.application.matsci.permittivity.MultiStageMd method) parseNewickString() (in module schrodinger.ui.qt.dendrogram) parseNode() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method) parseOptions() (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method) parseOutput() (schrodinger.protein.tasks.kinase.KinaseConservationTask method) parsePropertyString() (schrodinger.application.matsci.genetic_optimization.Property method) Parser (class in schrodinger.application.desmond.antlr3.recognizers) parser (schrodinger.application.livedesign.tasks.CovDockTask attribute) ParserRuleReturnScope (class in schrodinger.application.desmond.antlr3.recognizers) parserUserInput() (schrodinger.application.matsci.permittivity.TaskProtocol method) ParserWrapper (class in schrodinger.application.matsci.nano.interface_mod) (class in schrodinger.application.matsci.nano.particle) (class in schrodinger.application.matsci.nano.slab) (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) (class in schrodinger.application.matsci.nano.xtal) (class in schrodinger.application.matsci.rxn_path) parseSiblings() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) parseStr() (in module schrodinger.application.desmond.enhsamp) parseTree() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method) PARSING_EXCEPTIONS (schrodinger.application.jaguar.output.JaguarOutput attribute) PARTIAL (schrodinger.application.jaguar.utils.GenOptions attribute) partial_charge (schrodinger.structure.StructureAtom property) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) partial_to_custom_charges() (in module schrodinger.application.matsci.desmondutils) PARTIALLY_COMPLETED (schrodinger.seam.viz.inspect.TransformStatus attribute) participants (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab property) ParticipantView (class in schrodinger.application.jaguar.gui.tabs.reaction_tab) Particle (class in schrodinger.application.matsci.cg_mapping) particle_total (schrodinger.application.desmond.cms.Cms property) ParticleInfo (class in schrodinger.application.matsci.coarsegrain) particleNameToProxy() (schrodinger.application.matsci.rdpattern.Pattern method) partition_scores() (in module schrodinger.application.combinatorial_diversity.splitter_utils) partition_values() (in module schrodinger.application.phase.packages.phase_utils) partitionAtoms() (schrodinger.application.matsci.nano.particle.Nanoparticle method) pascal_case_to_snake() (in module schrodinger.ui.qt.standard.design_tokens) pass_errors (schrodinger.structure.MultiFileStructureReader attribute) pass_prop_filter() (in module schrodinger.application.combinatorial_explorer.route_screener) password (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationInput attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) passwordChanged (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationInput attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) passwordReplaced (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationInput attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) Patch (class in schrodinger.application.bioluminate.patch_utils.patch_finder) patch_count (schrodinger.surface.Surface property) patch_vertices (schrodinger.surface.Surface property) PatchAnalysis (class in schrodinger.application.bioluminate.patch_utils.patch_finder) PatchFinder (class in schrodinger.application.bioluminate.patch_utils.patch_finder) PatchSettings (class in schrodinger.application.bioluminate.patch_utils.settings) PatchType (class in schrodinger.application.bioluminate.patch_utils.settings) PatchTypeSettings (class in schrodinger.application.bioluminate.patch_utils.settings) PATH, [1] (schrodinger.application.desmond.kinetics.utils.ResultsCols attribute) path (schrodinger.application.desmond.test_utils.FileRegistration attribute) (schrodinger.application.desmond.test_utils.FileRegistry attribute) PATH (schrodinger.application.licensing.licserver.client.ServerIdentifierSourceType attribute) path (schrodinger.application.matsci.espresso.qeinput.DataType attribute) PATH (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) path (schrodinger.seam.viz.watcher.EndpointInfo attribute) PATH (schrodinger.utils.openmpi.EnvVar attribute) PATH_DROP (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) path_geometry() (in module schrodinger.application.jaguar.textparser) path_join() (in module schrodinger.application.matsci.permittivity) PATH_ONLY (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) path_optimize() (in module schrodinger.application.desmond.kinetics.utils) path_prune() (in module schrodinger.application.desmond.kinetics.utils) path_rmsd_matrix() (in module schrodinger.application.desmond.kinetics.utils) path_satisfies_mindist() (in module schrodinger.application.desmond.kinetics.utils) path_smooth() (in module schrodinger.application.desmond.kinetics.utils) path_structures (schrodinger.application.jaguar.output.JaguarOutput property) path_thr (schrodinger.application.matsci.espresso.qeinput.CustomNEBType attribute) PATH_TRACE (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) path_trace() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) pathChanged (schrodinger.application.matsci.kmcgui.DatabaseInfo attribute) PATHCV_Z_WALL (schrodinger.application.desmond.kinetics.enhanced_sampling.MtdOption attribute) pathcv_z_wall (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) PathExists (class in schrodinger.ui.qt.appframework2.validators) PathFailure pathModified() (schrodinger.application.desmond.cwidget.FileEntry method) pathname() (schrodinger.application.licensing.flexlm.Vendor method) (schrodinger.application.licensing.licadmin.LicenseResource method) PathSelectorWidget (class in schrodinger.ui.qt.forcefield.pathselectorwidget) PathTreeDict (class in schrodinger.application.livedesign.panel_components) PathUnbinding (class in schrodinger.application.desmond.stage.app.kinetics) PathUnbindingAnalysis (class in schrodinger.application.desmond.stage.app.kinetics) PathUnbindingCleanup (class in schrodinger.application.desmond.stage.app.kinetics) pathWidth() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) pathWidthEneg() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) patient_file_deletions() (in module schrodinger.utils.fileutils) Pattern (class in schrodinger.application.matsci.rdpattern) PATTERN (schrodinger.application.matsci.rxn_channel.ChannelDefinition attribute) pattern (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) pattern() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method) PatternModel (class in schrodinger.ui.ligfilter) PATTERNS (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) patternTranslate() (schrodinger.application.matsci.rdpattern.Pattern static method) PauliMatrices (class in schrodinger.application.jaguar.nmr_utils) payloadless_stage_pipeline (schrodinger.seam.runners.events.PipelineStarted attribute) payloadless_stage_pipelineChanged (schrodinger.seam.runners.events.PipelineStarted attribute) payloadless_stage_pipelineReplaced (schrodinger.seam.runners.events.PipelineStarted attribute) payloadless_user_pipeline (schrodinger.seam.runners.events.PipelineStarted attribute) payloadless_user_pipelineChanged (schrodinger.seam.runners.events.PipelineStarted attribute) payloadless_user_pipelineReplaced (schrodinger.seam.runners.events.PipelineStarted attribute) pbc (schrodinger.structure.Structure property) (schrodinger.structutils.ringspear.SpearRing attribute) PBC_BOND_COLOR (schrodinger.application.matsci.nano.xtal.PBCBond attribute) PBC_BOND_COLOR_KEY (schrodinger.application.matsci.nano.xtal.PBCBond attribute) PBC_BOND_KEY (schrodinger.application.matsci.nano.xtal.PBCBond attribute) PBC_BOND_THRESHOLD (schrodinger.application.matsci.nano.xtal.PBCBond attribute) PBC_BONDING (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) pbc_ring_coords (schrodinger.structutils.ringspear.SpearRing attribute) PBCBond (class in schrodinger.application.matsci.nano.xtal) PBCBonds (class in schrodinger.application.matsci.nano.xtal) PBCMeasureMananger (class in schrodinger.trajectory.pbc_manager) PBF (schrodinger.application.jaguar.rotation_barriers_keywords.SolvationMethod attribute) PBF_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) PCA (class in schrodinger.trajectory.prody.pca) PCM (schrodinger.application.jaguar.rotation_barriers_keywords.SolvationMethod attribute) PCM_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) PCM_MODELS (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) PCM_RADII (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) pcolls (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine attribute) PDB (schrodinger.infra.structure.FileFormat attribute) (schrodinger.protein.tasks.blast.BlastDatabase attribute) (schrodinger.rdkit_extensions.Format attribute) pdb_id (schrodinger.protein.sequence.CombinedChainProteinSequence property) pdb_name (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) pdb_nameChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) pdb_nameReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) PDB_RES (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) PDB_STRING (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) pdbcode (schrodinger.structure.StructureAtom property) PDBdata (class in schrodinger.application.matsci.packmol) PDBDialog (class in schrodinger.ui.qt.pdb_dialog) pdbid (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch property) pdbname (schrodinger.application.matsci.packmol.PDBdata attribute) (schrodinger.structure.StructureAtom property) PDBReader (class in schrodinger.structure) pdbres (schrodinger.application.matsci.packmol.PDBdata attribute) (schrodinger.structure.Residue property) (schrodinger.structure.StructureAtom property) (schrodinger.structutils.analyze.Ligand property) PDBRES_NAMES (schrodinger.protein.assignment.AsparticAcidpKaPredictor attribute) (schrodinger.protein.assignment.GlutamicAcidpKaPredictor attribute) PDBWriter (class in schrodinger.application.matsci.packmol) (class in schrodinger.structure) pdf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method) (schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method) (schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method) PDF_FILE_ENDING (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter attribute) PDFBuilder (class in schrodinger.application.matsci.reportutils) PDFPeakFit() (in module schrodinger.application.matsci.gsas.GSASIIpwd) pdfRequested() (schrodinger.application.matsci.reportutils.ReportInfo method) PDFWrite() (in module schrodinger.application.matsci.gsas.GSASIIfiles) pdist_vec_row_col() (in module schrodinger.application.matsci.nano.xtal) PDOS (class in schrodinger.application.matsci.espresso.qeoutput) Peak (class in schrodinger.application.jaguar.simple_spec) PeaksEquiv() (in module schrodinger.application.matsci.gsas.GSASIImath) PeaksUnique() (in module schrodinger.application.matsci.gsas.GSASIImath) pearson_by_set() (in module schrodinger.application.bioluminate.escomp) Penalties (schrodinger.application.glide.xpdes.TermKeywords attribute) PENALTYWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) PENDING (schrodinger.seam.viz.inspect.TransformStatus attribute) PenetrantLoadingStep (class in schrodinger.application.matsci.jwsteps) PENTAGONAL_BIPYRAMIDAL (in module schrodinger.application.matsci.buildcomplex) PENTAGONAL_BIPYRAMIDAL_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) PEPTIDE (schrodinger.application.bioluminate.mutation.PolymerType attribute) (schrodinger.livedesign.entity_type.EntityClass attribute) peptide_name() (schrodinger.application.desmond.fep_edge_data.PRMEdgeData static method) PER_FRAME (schrodinger.trajectory.trajectory_gui_dir.export_movie.DurationType attribute) PER_FRAME_ALLOWED_DECIMALS (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) PER_FRAME_MAX_VALUE (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) PER_FRAME_MIN_VALUE (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) per_mol_op (schrodinger.application.matsci.order_parameter_mod.Result attribute) PER_STRUCTURE (schrodinger.infra.structure.WorkflowType attribute) perAtomBasisChanged() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) perAtomBasisForEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel method) PerAtomBasisPopUp (class in schrodinger.application.jaguar.gui.tabs.transition_state_tab) PerAtomBasisRow (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) perAtomBasisSetsPresent() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) PerAtomMaker (class in schrodinger.application.matsci.etatoggle) PERCENT_D (schrodinger.application.bioluminate.pose_filtering.hdx_io.HDExaminerColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.StandardColumns attribute) Percent_helix() (in module schrodinger.utils.ligfilter) Percent_loop() (in module schrodinger.utils.ligfilter) percent_sasa_cutoff (schrodinger.application.bioluminate.pose_filtering.residue_filter.SasaResidueFilter attribute) Percent_strand() (in module schrodinger.utils.ligfilter) PERCENT_TO_AVG (schrodinger.application.matsci.desconfig.AveCellMSJStringer attribute) PercentScreenPlotter (class in schrodinger.analysis.enrichment.plotter) PerColumnSortableHeaderView (class in schrodinger.ui.qt.table) PerColumnSortableTableView (class in schrodinger.ui.qt.table) perEntryData() (schrodinger.application.jaguar.gui.timing.TimingResults method) perform_ks_test() (in module schrodinger.active_learning.al_report) perform_transmutations() (in module schrodinger.application.matsci.enumeration) perform_ttest() (in module schrodinger.active_learning.al_report) performMovement() (schrodinger.application.matsci.montecarlo.Metropolizer method) performSVD() (schrodinger.trajectory.prody.pca.PCA method) performSwapping() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) performTransmutation() (schrodinger.application.matsci.enumeration.Alchemist method) (schrodinger.application.matsci.enumeration.ElementAlchemist method) (schrodinger.application.matsci.enumeration.VacancyAlchemist method) period_start() (in module schrodinger.application.licensing.lmgrd_log_parser) PERIODIC_Z (schrodinger.application.matsci.kmc.PairsMixin attribute) periodicMaintenance() (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.jwsteps.BaseStep method) PeriodicTableDialog (class in schrodinger.ui.qt.periodictable) PeriodicTableDialogMultipleClick (class in schrodinger.ui.qt.periodictable) PeriodicTableDialogSingleClick (class in schrodinger.ui.qt.periodictable) PERMANENT_LICENSE_FAILURE (schrodinger.application.desmond.cmj.JobStatus attribute) permeability_args (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) permeability_argsChanged (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) permeability_argsReplaced (schrodinger.application.livedesign.tasks.MemPermTask.Input attribute) permissive_issubclass() (in module schrodinger.models.parameters) permittivity_transform() (in module schrodinger.application.matsci.permittivity) PerMolOP (class in schrodinger.application.matsci.order_parameter_mod) permutations() (in module schrodinger.application.matsci.gsas.GSASIIlattice) perp() (in module schrodinger.ui.qt.network_visualizer) PersistentMenu (class in schrodinger.ui.qt.swidgets) perspective (schrodinger.application.pymol.mae_sync.MaestroViewSettingsModel attribute) PerStrucConfigDialog (class in schrodinger.application.matsci.configdlgs) PerStrucSingleGpuConfigDialog (class in schrodinger.application.matsci.configdlgs) PerStructDesmondSubhostConfigDialog (class in schrodinger.application.matsci.configdlgs) perturb (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) pfam (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) pfamChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractSequence attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) pfamReplaced (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) PfamTask (class in schrodinger.protein.tasks.pfam) PfamTask.Input (class in schrodinger.protein.tasks.pfam) PfamTask.Output (class in schrodinger.protein.tasks.pfam) PfxMolIterator (class in schrodinger.rdkit.molio) PfxMolReader (class in schrodinger.rdkit.molio) PfxMolWriter (class in schrodinger.rdkit.molio) pH (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) (schrodinger.application.prepwizard.PrepWizardSettings attribute) PH_DEPENDENCE (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) ph_md (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) pH_pop (schrodinger.application.jaguar.macro_pka_utils.RowData attribute) pharma_testfile() (in module schrodinger.application.phase.packages.test) PHASE_COMMON_PH4 (schrodinger.infra.structure.WorkflowType attribute) PhaseDatabaseOpenDialog (class in schrodinger.ui.qt.filedialog) PhaseDB (class in schrodinger.pipeline.pipeio) PhaseFeatureMarker (class in schrodinger.application.phase.phase_markers) PhaseHypothesis (class in schrodinger.application.phase.hypothesis) PhaseHypothesisFromLigand (class in schrodinger.application.phase.hypothesis) PhaseHypothesisHybrid (class in schrodinger.application.phase.hypothesis) PhaseHypothesisInputConfig (class in schrodinger.application.phase.input) PhaseHypothesisMonitor (class in schrodinger.application.phase.pt_hypothesis) PhaseHypothesisStandard (class in schrodinger.application.phase.hypothesis) PhaseHypothesisStatic (class in schrodinger.application.phase.hypothesis) PhaseMarkers (class in schrodinger.application.phase.phase_markers) PhaseShapeStage (class in schrodinger.pipeline.stages.phase) PhaseSphere (class in schrodinger.application.phase.phase_markers) PhaseSphereMarkers (class in schrodinger.application.phase.phase_markers) PhaseTextMarker (class in schrodinger.application.phase.phase_markers) PhaseTolMarkers (class in schrodinger.application.phase.phase_markers) PhaseWtSum() (in module schrodinger.application.matsci.gsas.GSASIIpwd) PhaseXvolMarkers (class in schrodinger.application.phase.phase_markers) pHChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) PHControlType (class in schrodinger.application.matsci.espresso.qeinput) phdb_fpreader() (in module schrodinger.application.hitexpander) phdb_mol_reader() (in module schrodinger.application.hitexpander) PhDOS (class in schrodinger.application.matsci.espresso.qeoutput) PhDOS.Thermo (class in schrodinger.application.matsci.espresso.qeoutput) PhDOSTensors (class in schrodinger.application.matsci.espresso.qeoutput) PHDynmatType (class in schrodinger.application.matsci.espresso.qeinput) phi (schrodinger.ui.qt.rama.BackboneDihedral attribute) PHInputType (class in schrodinger.application.matsci.espresso.qeinput) Phob_pack (schrodinger.application.glide.xpdes.TermKeywords attribute) Phobcon_HB (schrodinger.application.glide.xpdes.TermKeywords attribute) PhpException PhpMOEConverter (class in schrodinger.application.phase.packages.phase_convert_MOE) PhPopulations (class in schrodinger.application.jaguar.macro_pka_utils) pHReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) phs (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) PhysicalFlag (class in schrodinger.application.matsci.parserutils) PhysicalLegTypes (class in schrodinger.application.desmond.constants) PI_CATION_PKA_SHIFT (schrodinger.protein.assignment.HistidinepKaPredictor attribute) pi_centroid (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) pi_pi_interactions() (schrodinger.protein.assignment.HistidinepKaPredictor method) PI_PI_PKA_SHIFT (schrodinger.protein.assignment.HistidinepKaPredictor attribute) PI_STACK (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) pi_stacking (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) pi_stackingChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) pi_stackingReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) pi_structure (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) Picat (schrodinger.application.glide.xpdes.TermKeywords attribute) Pick3DObjectToggle (class in schrodinger.ui.picking) pick_by_atom() (schrodinger.ui.qt.rama.Rama method) pick_by_point() (schrodinger.ui.qt.rama.Rama method) PICK_CATEGORY() (in module schrodinger.application.phase.constants) PICK_MAX_ATOMS (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker attribute) PICK_RADIUS (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama attribute) PickAslToggle (class in schrodinger.ui.picking) PickAtomsLassoToggle (class in schrodinger.ui.picking) PickAtomsToggle (class in schrodinger.ui.picking) PickAtomToggle (class in schrodinger.ui.picking) PickBondToggle (class in schrodinger.ui.picking) PickCategoryToggle (class in schrodinger.ui.picking) pickCompleted (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker attribute) pickCompleted() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) Picked (schrodinger.ui.picking.PickResidueColumns attribute) picked() (schrodinger.application.bioluminate.pml_menus.ColorChooserPanel method) pickInclude() (schrodinger.ui.qt.navtoolbar.MaestroNavToolbar method) pickingMessage() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.MacroAtomSelectionDelegate method) pickingModeChanged (schrodinger.ui.qt.network_views.NetworkViewer attribute) PickingModes (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) pickLabel() (schrodinger.ui.qt.navtoolbar.MaestroNavToolbar method) Picklable (class in schrodinger.application.desmond.picklejar) PicklableMetaClass (class in schrodinger.application.desmond.picklejar) PickleJar (class in schrodinger.application.desmond.picklejar) PickleState (class in schrodinger.application.desmond.picklejar) PickMixedToggle (class in schrodinger.ui.picking) PickModelClass (schrodinger.ui.picking.MaestrolessPickResidueDialog attribute) pickMolecule() (schrodinger.application.matsci.mswidgets.MSAtomSelector method) PickPairToggle (class in schrodinger.ui.picking) PickPairToggleIntermediate (class in schrodinger.application.matsci.reordergui) pickProjTableAtom() (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) PickRandomly (class in schrodinger.seam.examples.active_learning_weigher) pickResidueAtom() (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) PickResidueColumns (class in schrodinger.ui.picking) PickResidueModel (class in schrodinger.ui.picking) PickResidueRow (class in schrodinger.ui.picking) PickResiduesChangedMixin (class in schrodinger.ui.picking) PickResiduesToggle (class in schrodinger.ui.picking) pickSelect() (schrodinger.ui.qt.navtoolbar.MaestroNavToolbar method) pickThisAtom() (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) pickToggled() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) PickTopScoring (class in schrodinger.seam.examples.active_learning_weigher) PickTorsionToggle (class in schrodinger.ui.picking) PictureDelegate (class in schrodinger.ui.qt.delegates) PicturePrinter (class in schrodinger.application.report2d) PiHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) PilotScoreNode (class in schrodinger.application.phase.packages.shape_screen_al_node) PINK (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker attribute) pinv() (in module schrodinger.application.matsci.gsas.GSASIImath) piola_kirchoff_1() (schrodinger.application.matsci.elasticity.stress.Stress method) piola_kirchoff_2() (schrodinger.application.matsci.elasticity.stress.Stress method) PipeIO (class in schrodinger.pipeline.pipeio) Pipeline (class in schrodinger.pipeline.pipeline) pipeline_id (schrodinger.seam.runners.events.SeamEvent attribute) pipeline_idChanged (schrodinger.seam.runners.events.PipelineFinished attribute) (schrodinger.seam.runners.events.PipelineStarted attribute) (schrodinger.seam.runners.events.SeamEvent attribute) (schrodinger.seam.runners.events.StageFailed attribute) (schrodinger.seam.runners.events.StageFinished attribute) (schrodinger.seam.runners.events.StageStarted attribute) pipeline_idReplaced (schrodinger.seam.runners.events.PipelineFinished attribute) (schrodinger.seam.runners.events.PipelineStarted attribute) (schrodinger.seam.runners.events.SeamEvent attribute) (schrodinger.seam.runners.events.StageFailed attribute) (schrodinger.seam.runners.events.StageFinished attribute) (schrodinger.seam.runners.events.StageStarted attribute) pipeline_info_endpoint() (schrodinger.seam.viz.watcher.WatcherWebServer method) pipeline_init_wrapper() (in module schrodinger.pipeline.compiled_functions) PipelineDisplayInfo (class in schrodinger.seam.viz.inspect) PipelineFinished (class in schrodinger.seam.runners.events) PipelineRenderer (class in schrodinger.seam.viz.render) pipelines_endpoint() (schrodinger.seam.viz.watcher.WatcherWebServer method) PipelineStarted (class in schrodinger.seam.runners.events) PipelineStatus (class in schrodinger.seam.viz.inspect) PIPERConstraint (class in schrodinger.application.bioluminate.protein_protein_docking_shared) PIPERDistanceConstraintPair (class in schrodinger.application.bioluminate.protein_protein_docking_shared) PiPiInteraction (class in schrodinger.structutils.interactions.pi) pir (schrodinger.utils.fileutils.SeqFormat attribute) PiStackFinder (class in schrodinger.application.bioluminate.interaction_calculator) piStacksIterator() (schrodinger.application.bioluminate.interaction_calculator.PiStackFinder method) pitch (schrodinger.application.matsci.atom_group.HelixData attribute) pk50 (schrodinger.application.jaguar.pk50_report.Pk50Factory property) Pk50Factory (class in schrodinger.application.jaguar.pk50_report) PKA (schrodinger.application.desmond.constants.CorrectionTerm attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) pka_atom (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) PKA_ATOM_ADD (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) PKA_ATOM_PROP (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) PKA_ATOM_REMOVE (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) PKA_COLUMN_INVALID (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) PKA_COLUMNS (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) pka_indexes (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTupleMacroPka attribute) PKA_INVALID (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) PKA_MISSING (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) PKA_VALID (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) PkaEditDialog (class in schrodinger.application.jaguar.gui.edit_dialog) PkaPage (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) pl_contact_data0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) pl_contact_data1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) pl_interaction_similarity_matrix0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) pl_interaction_similarity_matrix1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) place_rgroups() (in module schrodinger.application.scaffold_enumeration.layered) (in module schrodinger.application.scaffold_enumeration.markush) placeFromExplicitMembrane() (schrodinger.protein.membrane.Membrane_Model method) PlaceHolder (class in schrodinger.structutils.markush_enumerate) PLACEHOLDER_TEXT (schrodinger.application.livedesign.panel_components.LiveReportTemplateSelectorCombo attribute) PLACEHOLDER_TEXTS (schrodinger.ui.qt.tasks.configwidgets.HostSelector attribute) PlaceholderComboMixin (class in schrodinger.ui.qt.swidgets) PlaceholderRecentCombo (class in schrodinger.ui.qt.recent_completer) placeholderSelected (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo attribute) placeOneIniInCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) placeStructureInCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) PLAnalysis (class in schrodinger.application.desmond.stage.analysis) planarAnglesPicked (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner attribute) PlanarBanner (class in schrodinger.trajectory.trajectory_gui_dir.banners) planckian_locus() (in module schrodinger.application.matsci.colorutils) planckian_radiator() (in module schrodinger.application.matsci.colorutils) PLANE_SCALE (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) PlaneIntercepts() (in module schrodinger.application.matsci.gsas.GSASIIlattice) PlaneSelectorMixin (class in schrodinger.application.matsci.mswidgets) platform_specific (schrodinger.ui.qt.swidgets.ActionPushButton attribute) PlaybackSettings (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings) PlaybackSettingsData (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data) playDirectionChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) plot() (schrodinger.application.desmond.fep_edge_data.FEPTorsions method) (schrodinger.application.desmond.stage.analysis.Reporter method) plot_1d() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) plot_2d() (schrodinger.application.desmond.stage.analysis.Reporter method) plot_3d_data() (in module schrodinger.application.mopac.mopac_surfaces) plot_convergence() (in module schrodinger.application.desmond.fepana) plot_correlation() (in module schrodinger.active_learning.al_report) PLOT_DATA_TYPE (schrodinger.ui.qt.delegates.MatplotlibDelegate attribute) plot_descriptors() (in module schrodinger.application.desmond.kinetics.utils) plot_height (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) plot_lambda_window_overlap() (in module schrodinger.application.desmond.fepana) plot_mat() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) plot_mos() (in module schrodinger.application.mopac.mopac_surfaces) plot_mtd_report() (in module schrodinger.application.desmond.kinetics.utils) plot_path_matrices() (in module schrodinger.application.desmond.kinetics.utils) plot_recovery() (in module schrodinger.active_learning.al_report) plot_regression() (in module schrodinger.active_learning.al_report) plot_sim_mat() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) plot_spectra() (in module schrodinger.application.jaguar.simple_spec) plot_subgraphs() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) plot_tau_fitting() (in module schrodinger.application.desmond.kinetics.utils) PLOT_TYPE (schrodinger.application.matsci.density_analysis_widget.ImagePlotFrame attribute) (schrodinger.application.matsci.density_analysis_widget.LinePlotFrame attribute) PLOT_TYPES (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog attribute) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog attribute) plot_width (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) plotContour() (schrodinger.application.matsci.mlearn.features.Complex method) plotData() (schrodinger.application.matsci.density_analysis_widget.ImagePlotFrame method) (schrodinger.application.matsci.density_analysis_widget.LinePlotFrame method) (schrodinger.application.matsci.sliceplot.SlicePlot method) plotDiagram() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) plotFitting() (schrodinger.application.matsci.plotwidgets.SliderchartVLFitStdPlot method) PlotInfo (class in schrodinger.application.matsci.kmcgui) plotParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) plotPotentials() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) Plotter (class in schrodinger.analysis.enrichment.plotter) plotter() (in module schrodinger.application.matsci.anharmonic) PlotTitleLineEdit (class in schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets) plotYSTd() (schrodinger.application.matsci.plotwidgets.SliderchartVLFitStdPlot method) PLPColumn (class in schrodinger.ui.qt.mapperwidgets.plptable) PLPMutated (schrodinger.maestro_utils.maestro_sync.PLPTarget attribute) PLPTableWidget (class in schrodinger.ui.qt.mapperwidgets.plptable) PLPTarget (class in schrodinger.maestro_utils.maestro_sync) pluralize_no_text() (in module schrodinger.utils.qt_utils) pluralize_text() (in module schrodinger.utils.qt_utils) PLUS_TIP_WITH_SAVE (schrodinger.application.matsci.mswidgets.MSAtomSelector attribute) PLYM (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) pmf_coefficients_fname (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) PMLContextMenu (class in schrodinger.application.bioluminate.pml_menus) PMLMenu (class in schrodinger.application.bioluminate.pml_menus) pmode() (schrodinger.utils.sea.sea.Sea method) PNG (schrodinger.livedesign.draw.Format attribute) PNG_FILE_ENDING (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter attribute) Point (class in schrodinger.application.matsci.rxn_path) point_group() (in module schrodinger.application.jaguar.textparser) POINT_GROUP_NAME (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) point_group_name (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) POINT_GROUP_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) point_group_used() (in module schrodinger.application.jaguar.textparser) pointInside() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.application.matsci.shapes.Cylinder method) (schrodinger.application.matsci.shapes.Sphere method) pointVectorAwayFromStructure() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) Polar (schrodinger.protein.residue.STERIC_GROUP attribute) POLAR_ALPHA (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) polar_decomposition() (schrodinger.application.matsci.elasticity.tensors.SquareTensor method) POLAR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) POLAR_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) POLAR_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) PolarContactsObject (class in schrodinger.application.bioluminate.pml_menus) PolarContactsOnlyMainchain (class in schrodinger.application.bioluminate.pml_menus) PolarContactsOnlySidechain (class in schrodinger.application.bioluminate.pml_menus) PolarContactsSubMenu (class in schrodinger.application.bioluminate.pml_menus) PolarContactsToAnyAtoms (class in schrodinger.application.bioluminate.pml_menus) PolarContactsToAnyNonSolvent (class in schrodinger.application.bioluminate.pml_menus) PolarContactsToEntry (class in schrodinger.application.bioluminate.pml_menus) PolarContactsToEntryWithoutSolvent (class in schrodinger.application.bioluminate.pml_menus) PolarContactsWithoutIntraMainchain (class in schrodinger.application.bioluminate.pml_menus) PolarContactsWithoutMainchain (class in schrodinger.application.bioluminate.pml_menus) PolarContactsWithoutSolvent (class in schrodinger.application.bioluminate.pml_menus) PolarContactsWithSidechains (class in schrodinger.application.bioluminate.pml_menus) PolarContactsWithSolvent (class in schrodinger.application.bioluminate.pml_menus) PolarityVectorizer (in module schrodinger.application.bioluminate.peptide_sar.encode) PolarizabilitySubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) Polarization() (in module schrodinger.application.matsci.gsas.GSASIIpwd) polfcal() (in module schrodinger.application.matsci.gsas.GSASIIlattice) poly_chiral_mol (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) poly_mol (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) polydispersity() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) polyfit() (in module schrodinger.math.mathutils) polygonize_structures() (in module schrodinger.application.matsci.nano.tools) PolylineHelmConnectorItem (class in schrodinger.protein.helm.helm_renderer) POLYMER_BUILDER (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) polymer_id (schrodinger.livedesign.biologics.registration.BioPolymer attribute) POLYMER_INT_KEYWORDS_DIFF (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) POLYMER_SUBTYPES (schrodinger.livedesign.biologics.fasta.AntibodyAssembler attribute) (schrodinger.livedesign.biologics.fasta.NucleicAcidAssembler attribute) (schrodinger.livedesign.biologics.fasta.PolymerAssembler attribute) polymer_type (schrodinger.application.bioluminate.mutation.Mutation attribute) (schrodinger.protein.helm.helm_renderer.HelmConnector property) PolymerAssembler (class in schrodinger.livedesign.biologics.fasta) PolymerBuilder (class in schrodinger.application.matsci.permittivity) PolymerBuilderStep (class in schrodinger.application.matsci.jwsteps) PolymerChainAnalysisStep (class in schrodinger.application.matsci.jwsteps) PolymerCrosslinkStep (class in schrodinger.application.matsci.jwsteps) PolymerDescriptor (class in schrodinger.application.matsci.mlearn.descriptor) PolymerDescriptorError PolymerFragment (class in schrodinger.application.matsci.amorphous) PolymerFragments (class in schrodinger.application.matsci.amorphous) PolymerSmilesSignature (class in schrodinger.application.matsci.species) PolymerType (class in schrodinger.application.bioluminate.mutation) (class in schrodinger.livedesign.biologics.fasta) pop (schrodinger.application.jaguar.macro_pka_utils.RowData attribute) pop() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) (schrodinger.infra.util.OneIndexedList method) (schrodinger.job.queue.PriorityQueue method) (schrodinger.utils.sea.sea.List method) (schrodinger.utils.sea.sea.Map method) pop_level() (in module schrodinger.infra.mmerr) pop_properties() (in module schrodinger.livedesign.bbchem_endpoints) POP_UP_CLASS (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterListToolButton attribute) (schrodinger.application.jaguar.gui.solvent_selector.SolventSelectorFilterListToolButton attribute) (schrodinger.application.jaguar.gui.theory_selector.DftTheorySelectorFilterListToolButton attribute) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListToolButton attribute) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListToolButton attribute) (schrodinger.application.matsci.builderwidgets.TemplateToolButton attribute) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp attribute) pop_up_visible (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin property) POPC (schrodinger.application.desmond.constants.LIPID_BILAYERS attribute) POPE (schrodinger.application.desmond.constants.LIPID_BILAYERS attribute) Popen() (in module schrodinger.utils.subprocess) popLocalClashes() (schrodinger.application.matsci.amorphous.PolymerFragments method) populate() (schrodinger.structutils.markush_enumerate.Scaffold method) populate_nonstandard_residues_data() (in module schrodinger.maestro_utils.nonstandard_residue_utils) populate_ppdb_from_dir() (in module schrodinger.application.matsci.espresso.ppdb) populate_smarts_edit() (in module schrodinger.application.matsci.smartsutilsgui) populate_with_charges() (in module schrodinger.application.matsci.clusterstruct) populateExcitedStatesType() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) populateList() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) populatePickCombo() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker method) populateResidueTypeCombo() (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBar method) populateSaveExportMenu() (schrodinger.ui.two_d_viewer.TwoDViewer method) populateTableAndSummary() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) populateTableFromStructures() (schrodinger.ui.two_d_viewer.TwoDViewer method) populateTableWithProgress() (schrodinger.ui.two_d_viewer.TwoDViewer method) populateTypeCombo() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker method) populateViewMenu() (schrodinger.ui.two_d_viewer.TwoDViewer method) POPULATION (schrodinger.application.desmond.constants.CorrectionTerm attribute) PopUp (class in schrodinger.ui.qt.pop_up_widgets) POPUP_CLS (schrodinger.application.livedesign.panel_components.AbstractSelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUpDelegate attribute) POPUP_LINK (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) PopUpAlignment (class in schrodinger.ui.qt.pop_up_widgets) popupClosed (schrodinger.ui.qt.multi_combo_box.MultiComboBox attribute) popUpClosed() (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate method) popUpClosing (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin attribute) PopUpDelegate (class in schrodinger.ui.qt.pop_up_widgets) PopUpLink (class in schrodinger.ui.qt.standard_widgets.buttons) PopUpMode (class in schrodinger.ui.qt.pop_up_widgets) popUpResized (schrodinger.ui.qt.pop_up_widgets.PopUp attribute) popUpUpdated() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit method) (schrodinger.application.jaguar.gui.theory_selector.FilterTheorySelectorReadOnlyLineEdit method) (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) port (schrodinger.active_learning.mq_driver.Worker attribute) port() (schrodinger.application.licensing.flexlm.Vendor method) POS (schrodinger.application.desmond.constants.RestrainTypes attribute) pos() (schrodinger.ui.qt.network_visualizer.Node method) Pos2dsp() (in module schrodinger.application.matsci.gsas.GSASIIlattice) POS_FBHW (schrodinger.application.desmond.constants.RestrainTypes attribute) pos_frozen_idxs (schrodinger.application.matsci.buildcomplex.MinimizeInfo attribute) posBlock() (in module schrodinger.application.matsci.gsas.GSASIImath) POSE (schrodinger.application.glide.sort_utils.StructureType attribute) pose_name_custom_text (schrodinger.application.livedesign.export_models.TaskInput attribute) pose_name_custom_textChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) pose_name_custom_textReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) pose_name_model (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) pose_name_modelChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) pose_name_modelReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) pose_name_propname (schrodinger.application.livedesign.export_models.TaskInput attribute) pose_name_propnameChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) pose_name_propnameReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) pose_name_text (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) pose_name_textChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) pose_name_textReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) POSE_VIEWER (schrodinger.infra.structure.WorkflowType attribute) PoseColumn (class in schrodinger.tasks.ldtasks) PoseColumn.Pose (class in schrodinger.tasks.ldtasks) PoseLibrary (class in schrodinger.application.glide.glideanalysis) PoseNameEditModel (class in schrodinger.application.livedesign.export_models) PoseNameEditPanel (class in schrodinger.application.livedesign.pose_name_panel) Poses() (schrodinger.application.transforms.dock.Dock static method) poses_per_lig (schrodinger.application.steps.docking.GlideSettings attribute) poses_per_ligChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) poses_per_ligReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) POSES_TAG (schrodinger.application.transforms.dock.Dock attribute) posesDocked (schrodinger.application.glide.http_client.NonBlockingGlideServerManager attribute) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) (schrodinger.application.glide.http_client.NonBlockingHTTPClient attribute) (schrodinger.application.glide.http_client.ZmqClient attribute) PoseWriter (class in schrodinger.application.glide.utils) poseWriter() (schrodinger.application.glide.client_module.GlideClientModuleAdapter method) posFourier() (in module schrodinger.application.matsci.gsas.GSASIImath) PositionalConstraint (class in schrodinger.application.glide.glide) positionChanged (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) positionPopup() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) positive (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute) Positive (schrodinger.protein.residue.RESIDUE_CHARGE attribute) positive_int() (in module schrodinger.active_learning.al_utils) positive_salt (schrodinger.application.desmond.struc.CompStruc attribute) POSITIVE_SALT (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) PosResDelegate (class in schrodinger.application.desmond.gui) PosResModel (class in schrodinger.application.desmond.gui) PosResRow (class in schrodinger.application.desmond.gui) PosRestrainArray (class in schrodinger.application.desmond.cms) possible_gap_open (schrodinger.protein.tasks.blast.BlastSettings attribute) possible_gap_openChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) possible_gap_openReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) post() (schrodinger.application.bioluminate.pml_menus.PMLContextMenu method) post_process_server_identifiers() (in module schrodinger.application.licensing.licserver.client) postCommand() (schrodinger.application.matsci.jobutils.LoggingSubprocessJob method) (schrodinger.application.matsci.packmol.StdInJob method) (schrodinger.job.queue.BaseJob method) PosTextNetworkNode (class in schrodinger.ui.qt.network_views) PostLigPrepStage (class in schrodinger.pipeline.stages.ligprep) postProcess() (schrodinger.application.matsci.genetic_optimization.Jaguar method) postprocess() (schrodinger.protein.predictors.AbstractPredictor method) postProcess() (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) postprocess_conformational_search() (in module schrodinger.application.matsci.reaction_workflow_utils) postprocess_traj() (in module schrodinger.application.desmond.process_fep_traj) postprocess_valence_error (schrodinger.application.prepwizard2.tasks.PPWorkflowOutput attribute) postprocess_valence_errorChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowOutput attribute) postprocess_valence_errorReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowOutput attribute) postProcessCms() (schrodinger.application.matsci.desmondutils.SystemBuilder method) postprocessing() (schrodinger.active_learning.al_driver.ActiveLearningJob method) postProcessOptimization() (schrodinger.application.matsci.mecp_mod.MECP method) postprocessors() (schrodinger.tasks.tasks.AbstractTask method) postProcessStructures() (schrodinger.application.livedesign.ld_tasks.ImportTask method) poststage() (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.analysis.FepAnalysis method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingMdLauncher method) (schrodinger.application.desmond.stage.app.kinetics.PathUnbindingCleanup method) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup method) (schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher method) (schrodinger.application.desmond.stage.workflow.Stop method) postTreatBuiltCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) postTreatMinimizedStructure() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) PosVarBondEnumerable (class in schrodinger.application.scaffold_enumeration.posvarbond) posx (schrodinger.application.matsci.kmc.MoleculeData attribute) POSX (schrodinger.application.matsci.kmc.Table attribute) posy (schrodinger.application.matsci.kmc.MoleculeData attribute) POSY (schrodinger.application.matsci.kmc.Table attribute) posz (schrodinger.application.matsci.kmc.MoleculeData attribute) POSZ (schrodinger.application.matsci.kmc.Table attribute) posZigZag() (in module schrodinger.application.matsci.gsas.GSASIImath) POT (schrodinger.application.desmond.kinetics.enhanced_sampling.MExpressionSection attribute) POT_NTICKS (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute) potential() (schrodinger.application.desmond.torsion_related.BondRotator method) POTENTIAL_ENERGY (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) potential_energy (schrodinger.application.desmond.fep_edge_data.FEPTorsions property) PotentialEnergy (class in schrodinger.application.desmond.simulation_block_test) PotGrid (class in schrodinger.application.bioluminate.escomp) PowderDiffractionException PowderDiffractionFile (class in schrodinger.application.matsci.spectra) PP_HEADER_TAG (schrodinger.application.matsci.espresso.utils.PPHeaderHTMLParser attribute) pp_type (schrodinger.application.matsci.espresso.utils.PseudoData attribute) PP_TYPE_NC (schrodinger.application.matsci.espresso.utils.UPFParser attribute) PP_TYPE_PAW (schrodinger.application.matsci.espresso.utils.UPFParser attribute) PP_TYPES (schrodinger.application.matsci.espresso.utils.UPFParser attribute) PPBatchWorkflowInput (class in schrodinger.application.prepwizard2.tasks) PPBatchWorkflowTask (class in schrodinger.application.prepwizard2.tasks) PPBatchWorkflowTask.JobConfig (class in schrodinger.application.prepwizard2.tasks) PPBatchWorkflowTask.Output (class in schrodinger.application.prepwizard2.tasks) PPHeaderHTMLParser (class in schrodinger.application.matsci.espresso.utils) PPlotType (class in schrodinger.application.matsci.espresso.qeinput) ppm_to_hz() (in module schrodinger.application.jaguar.nmr_utils) PPSpecies (class in schrodinger.application.matsci.espresso.utils) PPWorkflowInput (class in schrodinger.application.prepwizard2.tasks) PPWorkflowOutput (class in schrodinger.application.prepwizard2.tasks) PPWorkflowSettings (class in schrodinger.application.prepwizard2.tasks) PPWorkflowTask (class in schrodinger.application.prepwizard2.tasks) PR_NAME (schrodinger.application.desmond.stage.analysis.TimeSeriesAnalysisJob attribute) pre_analyze() (in module schrodinger.application.bioluminate.patch_utils.pre_analyze) PRE_REFRESH_TEXT (schrodinger.application.livedesign.panel_components.LiveReportSelectionPopup attribute) pre_score_pairs() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) pre_score_self() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) pre_treat() (schrodinger.protein.assignment.ProtAssign.changeable method) pre_treat_1() (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) pre_treat_2() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) pre_treat_changeables() (in module schrodinger.protein.assignment) PreAnalyzer (class in schrodinger.application.bioluminate.patch_utils.patch_finder) preciseGradientUpdated (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView attribute) PRECISION (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) precision (schrodinger.application.jaguar.results.BondCharge attribute) (schrodinger.application.jaguar.results.Dipole attribute) (schrodinger.application.jaguar.results.FukuiIndices attribute) PRECISION (schrodinger.application.jaguar.results.HsoSingletTripletElement attribute) precision (schrodinger.application.jaguar.results.Orbital attribute) (schrodinger.application.jaguar.results.ThermoCollection attribute) (schrodinger.application.jaguar.results.ThermoProp attribute) (schrodinger.application.jaguar.results.ZVariables attribute) (schrodinger.application.jaguar.scan.Scan attribute) PRECISION (schrodinger.protein.assignment.NetworkSolver attribute) (schrodinger.utils.profiling.Timer attribute) preCommand() (schrodinger.job.queue.BaseJob method) precursors (schrodinger.application.pathfinder.route.RouteNode property) pred_accessibility (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) PRED_ANNOTATION_TYPES (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) pred_disordered (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) pred_disulfide_bond (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) pred_disulfide_bonds (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.protein.sequence.ProteinSequence property) pred_domain_arr (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) PRED_RES_TIME (schrodinger.application.desmond.kinetics.utils.ResultsCols attribute) pred_secondary_structure (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) pred_secondary_structures (schrodinger.protein.sequence.AbstractProteinSequenceMixin property) preDeepCopy() (schrodinger.application.matsci.amorphous.PolymerFragment method) PREDEFINED_PATTERNS (schrodinger.application.matsci.automated_cg_mapping.StructData attribute) (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer attribute)

PREDEFINED_WIDGET_INDEX (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) PredefinedCriterion (class in schrodinger.utils.ligfilter) PredefinedFiltersPopUp (class in schrodinger.ui.qt.filter_list) predict() (schrodinger.active_learning.mq_backend.Backend method) (schrodinger.application.desmond.antlr3.dfa.DFA method) (schrodinger.protein.assignment.HistidinepKaPredictor method) (schrodinger.seam.examples.active_learning_weigher.LinearRegressionModel method) predict_correlation() (in module schrodinger.application.desmond.correlation_tau) predict_disordered_regions() (in module schrodinger.protein.predictors) predict_disulfide_bond() (in module schrodinger.protein.predictors) predict_domain_arrangement() (in module schrodinger.protein.predictors) predict_expected_slope() (in module schrodinger.application.desmond.correlation_tau) predict_kendall_tau() (in module schrodinger.application.desmond.correlation_tau) predict_memory_utilization() (in module schrodinger.application.desmond.util) predict_secondary_structure() (in module schrodinger.protein.predictors) predict_solvent_accessibility() (in module schrodinger.protein.predictors) predict_temperature() (in module schrodinger.application.desmond.predict_remd_temp) predict_temperature_ladder() (in module schrodinger.application.desmond.remd) predict_with_bagged_models() (in module schrodinger.application.matsci.mlearn.descriptor) predict_with_nreplica_and_exch() (in module schrodinger.application.desmond.remd) predict_with_temp_and_exch() (in module schrodinger.application.desmond.remd) predict_with_temp_and_nreplica() (in module schrodinger.application.desmond.remd) prediction() (schrodinger.protein.predictors.AbstractPredictor method) (schrodinger.protein.predictors.AccproPredictor method) (schrodinger.protein.predictors.BetaproPredictor method) (schrodinger.protein.predictors.DiproPredictor method) (schrodinger.protein.predictors.DisproPredictor method) (schrodinger.protein.predictors.DomproPredictor method) (schrodinger.protein.predictors.SsproPredictor method) predictionsChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractProteinSequenceMixin attribute) PREDICTOR_NAME (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) PredictorWrapperTask (class in schrodinger.protein.predictors) PREF_GROUP (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel attribute) (schrodinger.application.livedesign.ld_settings.LDSettingsMixin attribute) PREF_KEY (schrodinger.application.matsci.mswidgets.MSAtomSelector attribute) (schrodinger.ui.qt.swidgets.ItemsManagerMixin attribute) (schrodinger.ui.qt.swidgets.SavedItemsManager attribute) (schrodinger.ui.qt.swidgets.SavedSMARTSManager attribute) prefac (schrodinger.application.matsci.espresso.qeinput.FreePositionsType.PWallType attribute) Preferences (class in schrodinger.utils.preferences) PREFERENCES (schrodinger.utils.postinstall.CustomConfigFiles attribute) PREFERENCES_KEY (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin property) prefix (schrodinger.application.desmond.driver_utils.MPISettings attribute) preflight() (schrodinger.application.jaguar.input.JaguarInput method) Premise (class in schrodinger.application.desmond.task) premises (schrodinger.application.desmond.task.Task property) preoptimizeIsChecked() (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab method) prepActive() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) prepAntibodyLoop() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) prepare() (schrodinger.application.desmond.systype.SysType method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) (schrodinger.application.matsci.rxn_path.ReactionCoords method) prepare_adaptive_ligand_restraints() (in module schrodinger.application.desmond.stage.app.absolute_binding.restraint) prepare_building_block() (in module schrodinger.application.matsci.amorphous) prepare_cg_for_rdkit() (in module schrodinger.rdkit.coarsegrain) prepare_cms_properties_for_writing() (in module schrodinger.application.matsci.desmondutils) prepare_command() (schrodinger.application.desmond.rest_inp.RestInput method) prepare_command_for_launch() (in module schrodinger.application.desmond.launch_utils) prepare_command_for_restart() (in module schrodinger.application.desmond.launch_utils) prepare_ct() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) prepare_files_and_command_for_fep_restart_extend() (in module schrodinger.application.desmond.starter.generator.common) prepare_files_and_command_for_restart() (in module schrodinger.application.desmond.starter.generator.common) prepare_for_backend() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) prepare_for_epik() (in module schrodinger.application.prepwizard) prepare_for_parsing() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) prepare_input_structures() (in module schrodinger.application.desmond.stage.app.absolute_binding.struc) prepare_inputs() (in module schrodinger.application.desmond.starter.generator.fep_absolute_binding) (in module schrodinger.application.desmond.starter.generator.fep_solubility) prepare_ions() (in module schrodinger.application.desmond.move_alchem_ions) prepare_job_spec_builder() (in module schrodinger.application.matsci.jobutils) prepare_ligand_restraints() (in module schrodinger.application.desmond.stage.app.absolute_binding.restraint) prepare_md_structures() (in module schrodinger.application.desmond.stage.app.absolute_binding.struc) prepare_msj() (schrodinger.application.desmond.rest_inp.RestInput method) prepare_multisim_files_for_restart() (in module schrodinger.application.desmond.launch_utils) prepare_next_generation_dirs_callback() (in module schrodinger.application.matsci.genetic_optimization) prepare_res_st_for_prime() (in module schrodinger.protein.nonstandard_residues) prepare_restart_dirs() (in module schrodinger.application.matsci.jaguar_restart) prepare_structure() (in module schrodinger.application.prepwizard) (schrodinger.application.desmond.rest_inp.RestInput method) prepare_system() (in module schrodinger.application.desmond.kinetics.utils) prepareBuildGeometryInput() (schrodinger.application.matsci.desmondutils.SystemBuilder method) prepareCTSTOutput() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) prepareForClose() (schrodinger.application.matsci.kmcgui.NeighborsTab method) (schrodinger.application.matsci.kmcgui.Tab method) prepareInput() (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask method) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask method) prepareInputLigands() (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) prepareJMSWFOutput() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) prepareOutput() (schrodinger.application.matsci.qubec_utils.Qubec method) preparePbcAndParams() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) PrepareSmilesNode (class in schrodinger.active_learning.al_node) prepareStructure() (schrodinger.application.phase.packages.shape_ligprep.LigPrep method) prepareStructureForMinimization() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) prepareStructures() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) prepareTangledChainBlocks() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) prepareWaterModel() (schrodinger.application.matsci.desmondutils.SystemBuilder method) prepBldStruct() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) prepend_hypos() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) prepend_mmfile_path() (in module schrodinger.application.ligprep.ionizer) prepend_path() (in module schrodinger.utils.env) prepend_schrodinger_run() (in module schrodinger.job.jobcontrol) prepend_sys_path() (in module schrodinger.utils.env) prepEnergy() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) PrepForMDStep (class in schrodinger.application.matsci.jwsteps) prepLoop() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) prepMinimize() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) prepResidue() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) PREPRO (schrodinger.ui.qt.rama.RamaResidueType attribute) preprocess (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) preprocess() (in module schrodinger.livedesign.preprocessor) preprocess_delete_far_waters (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) preprocess_delete_far_watersChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) preprocess_delete_far_watersReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) preprocess_infile() (in module schrodinger.application.jaguar.user_config) preprocess_molblock() (in module schrodinger.livedesign.preprocessor) preprocess_st() (in module schrodinger.comparison.struc) preprocess_watdist (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) preprocess_watdistChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) preprocess_watdistReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) preprocessChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) PreprocessInput (class in schrodinger.application.prepwizard2.tasks) PreprocessInput.ABOOptions (class in schrodinger.application.prepwizard2.tasks) preprocessInputStruct() (schrodinger.application.matsci.fragments.FragmentReactor method) preprocessMatchAtoms() (schrodinger.application.matsci.nano.tube.NanoTube method) preprocessor_options (schrodinger.livedesign.registration.RegistrationOptions attribute) PreprocessorOptions (class in schrodinger.livedesign.preprocessor) preprocessors() (schrodinger.tasks.tasks.AbstractTask method) preprocessReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) PreprocessTask (class in schrodinger.application.prepwizard2.tasks) prepSidechain() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) prepSidechainBB() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) prepSidechainCBeta() (schrodinger.application.bioluminate.protein.protein.PrimeConfig method) PrepWizardSettings (class in schrodinger.application.prepwizard) preserve_bonds() (in module schrodinger.application.matsci.nano.xtal) PRESERVE_ENHANCED_STEREO_GROUP_IDS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) preserve_selection() (in module schrodinger.project.utils) preserve_st_titles (schrodinger.application.prepwizard.PrepWizardSettings attribute) preserve_st_titlesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) preserve_st_titlesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) preset_name (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec attribute) (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) preset_nameChanged (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) preset_nameReplaced (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) preset_names (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsModel attribute) preset_namesChanged (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsModel attribute) preset_namesReplaced (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsModel attribute) PresetAction (class in schrodinger.application.bioluminate.pml_menus) PresetManager (class in schrodinger.models.presets) PresetRowModel (class in schrodinger.ui.qt.presets.manage_presets_dialog) PRESETS_FEATURE_FLAG (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin attribute) PresetsDialog (class in schrodinger.application.matsci.jagwidgets) PresetSubMenu (class in schrodinger.application.bioluminate.pml_menus) PRESS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) press_n (schrodinger.application.matsci.reaction_workflow_utils.PressData attribute) press_start (schrodinger.application.matsci.reaction_workflow_utils.PressData attribute) press_step (schrodinger.application.matsci.reaction_workflow_utils.PressData attribute) PRESS_TENSOR (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) PressData (class in schrodinger.application.matsci.reaction_workflow_utils) PRESSED (schrodinger.ui.qt.standard.design_tokens.BorderColors attribute) (schrodinger.ui.qt.standard.design_tokens.StateColors attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) PRESSED_BUTTON_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) PRESSED_HORIZONTAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) PRESSED_VERTICAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) Pressure (class in schrodinger.application.desmond.simulation_block_test) PRESSURE (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) pressure (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) Pressure_atm (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) PRESSURE_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) PRESSURE_TENSOR (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute) prestage() (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.simulate.SimulateBase method) (schrodinger.application.desmond.stage.workflow.Stop method) prestart() (in module schrodinger.ui.qt.appframework2.appmethods) PRESUMED_TS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) PRESUMED_TS_CHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) pretty_time_delta() (in module schrodinger.application.matsci.textlogger) PrettyPubPreset (class in schrodinger.application.bioluminate.pml_menus) Prev (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom.NextGeomFrom attribute) PREV_BACKBONE_SITE_PROP (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner attribute) prevent_overlapping_x_labels() (in module schrodinger.application.bioluminate.sliderchart) (in module schrodinger.application.desmond.mplchart) preventUnwantedReactions() (schrodinger.application.matsci.fragments.FragmentReactor method) preview() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) previous_lr_user_text (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) previous_lr_user_textChanged (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) previous_lr_user_textReplaced (schrodinger.application.livedesign.live_report_widget.LiveReportModel attribute) previously_aligned (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) previously_alignedChanged (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) previously_alignedReplaced (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) previousStructure() (schrodinger.ui.two_d_viewer.TwoDViewer method) prevMatchRequested (schrodinger.ui.qt.swidgets.TextSearchBar attribute) prewrite() (in module schrodinger.ui.qt.appframework2.appmethods) pri (schrodinger.application.livedesign.constants.CompoundSource attribute) PRIMARY (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute) (schrodinger.ui.qt.standard.design_tokens.PrimaryColors attribute) PRIMARY_BUTTON (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) PRIMARY_LINK (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) PRIMARY_OPERATIONS_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) PRIMARY_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) primary_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) primary_opers_strs (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) PrimaryColors (class in schrodinger.ui.qt.standard.design_tokens) PrimaryThiol (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) Prime (class in schrodinger.application.prime.input) PRIME_ANTIB_LOOP_PRED (schrodinger.application.bioluminate.protein.protein.Refiner attribute) PRIME_HOMOLOGY (schrodinger.infra.structure.WorkflowType attribute) PRIME_LOOP_PRED (schrodinger.application.bioluminate.protein.protein.Refiner attribute) PRIME_MINIMIZE (schrodinger.application.bioluminate.protein.protein.Refiner attribute) prime_mmgbsa_args (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) prime_mmgbsa_argsChanged (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) prime_mmgbsa_argsReplaced (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) PRIME_RESIDUE (schrodinger.application.bioluminate.protein.protein.Refiner attribute) PRIME_SIDECHAIN (schrodinger.application.bioluminate.protein.protein.Refiner attribute) PRIME_SIDECHAIN_BB (schrodinger.application.bioluminate.protein.protein.Refiner attribute) PRIME_SIDECHAIN_CBETA (schrodinger.application.bioluminate.protein.protein.Refiner attribute) PrimeConfig (class in schrodinger.application.bioluminate.protein.protein) (class in schrodinger.application.prime.wrapper) PrimeMMGBSATask (class in schrodinger.application.livedesign.tasks) PrimeMMGBSATask.Input (class in schrodinger.application.livedesign.tasks) PrimeMMGBSATask.JobConfig (class in schrodinger.application.livedesign.tasks) PrimeMMGBSATask.Output (class in schrodinger.application.livedesign.tasks) Primer (class in schrodinger.application.desmond.stage.workflow) PrimeSTAAligner (class in schrodinger.protein.align) PrimeStage (class in schrodinger.pipeline.stages.prime) PrimeStructure (class in schrodinger.application.bioluminate.protein.protein) PrimeTemplate (class in schrodinger.application.prime.wrapper) Primitive (class in schrodinger.graphics3d.common) principal_invariants (schrodinger.application.matsci.elasticity.tensors.SquareTensor property) PRINT (schrodinger.application.jaguar.utils.LewisModes attribute) print_allow_adsorption_onto() (in module schrodinger.application.matsci.rxn_channel) print_attachment_points() (schrodinger.application.canvas.r_group.Data method) print_attachment_points_ct() (schrodinger.application.canvas.r_group.Data method) print_bad_jobs() (in module schrodinger.application.matsci.genetic_optimization) print_cpu_features() (in module schrodinger.utils.machid) print_debug() (in module schrodinger.application.desmond.cmj) print_deprecate() (in module schrodinger.application.watermap.watermap_inp) print_fields() (in module schrodinger.utils.machid) (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.LicenseLine method) (schrodinger.application.licensing.flexlm.Package method) (schrodinger.application.licensing.flexlm.Server method) (schrodinger.application.licensing.flexlm.Vendor method) print_help() (schrodinger.application.desmond.multisimstartup.Help method) (schrodinger.application.desmond.multisimstartup.Startup.Help method) print_hosts() (in module schrodinger.application.desmond.driver_utils) print_images() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) PRINT_INFO (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) print_installation_check() (in module schrodinger.utils.installation_check) print_job_info() (in module schrodinger.application.macromodel.paraUtils) print_pathway() (in module schrodinger.application.desmond.fepana) print_proclamation() (in module schrodinger.application.jaguar.nmr_utils) print_product_versions() (in module schrodinger.utils.machid) print_quiet() (in module schrodinger.application.desmond.cmj) print_report() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) print_silent() (in module schrodinger.application.desmond.cmj) print_tonull() (in module schrodinger.application.desmond.cmj) print_usage() (in module schrodinger.application.desmond.simulation_block_data) (in module schrodinger.application.desmond.simulation_block_test) (schrodinger.application.desmond.multisimstartup.Startup method) (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method) print_val() (schrodinger.application.desmond.simulation_block_test.Test method) print_verbose() (in module schrodinger.application.desmond.cmj) print_version() (in module schrodinger.utils.cmdline) (schrodinger.application.desmond.multisimstartup.Help method) (schrodinger.application.desmond.multisimstartup.Startup method) (schrodinger.application.desmond.multisimstartup.Startup.Help method) PrintableStatus (class in schrodinger.job.queue) printAction() (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.pipeline.StageJob method) printAllChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) printAllSpgInfo() (schrodinger.application.matsci.nano.space_groups.SpaceGroups method) printChannelDefs() (schrodinger.application.matsci.rxn_channel.Channels method) printCrystalParams() (schrodinger.application.matsci.nano.xtal.Crystal method) printDatabaseEntry() (schrodinger.application.matsci.nano.space_groups.SpaceGroup method) printDebug() (schrodinger.tasks.tasks.AbstractTask method) printException() (schrodinger.utils.qt_utils.EventLoop method) printFailureMessage() (schrodinger.pipeline.pipeline.StageJob method) printFiltered() (schrodinger.application.matsci.rxn_channel.Channels method) printInfo() (schrodinger.application.desmond.replica_dE.replica_container method) printingOutputToTerminal() (schrodinger.tasks.tasks.SubprocessMixin method) printInternals() (schrodinger.application.matsci.rxn_path.InternalCoords method) printit() (schrodinger.application.jaguar.simple_spec.Peak method) printJobParams() (schrodinger.application.matsci.nano.sheet.NanoSheets method) (schrodinger.application.matsci.nano.tube.NanoTubes method) printMultiWalledTubes() (schrodinger.application.matsci.nano.tube.NanoTubes method) printNotMinimized() (schrodinger.application.matsci.rxn_channel.Channels method) printout() (schrodinger.application.inputconfig.InputConfig method) (schrodinger.ui.qt.config_dialog.JobParameters method) printParameters() (schrodinger.structutils.minimize.Minimizer method) printParams() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.slab.Surface method) printProperties() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) printProps() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) (schrodinger.application.matsci.nano.tube.NanoTube method) printRho() (in module schrodinger.application.matsci.gsas.GSASIImath) printRxnReprs() (schrodinger.application.matsci.rxn_channel.Channels method) printSingleWalledTubes() (schrodinger.application.matsci.nano.tube.NanoTubes method) printStatus() (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.job.queue.JobDJ method) printSymmetryOpers() (schrodinger.application.matsci.nano.space_groups.SpaceGroup method) printTree() (schrodinger.ui.ligfilter.DefinitionViewerDialog method) prioritizeBackbone() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) prioritizeSameMonomers() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) priority() (schrodinger.application.licensing.licadmin.LicenseResource method) PriorityQueue (class in schrodinger.job.queue) PRM_LIGAND_BINDING (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) prm_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) PRM_PROTEIN_BINDING (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) PRM_THERMOSTABILITY (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) PRMEdgeData (class in schrodinger.application.desmond.fep_edge_data) PRMEdgeReportMaker (class in schrodinger.application.desmond.fep_edge_report_maker) probe_checkpoint() (in module schrodinger.application.desmond.cmj) probe_mass (schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent property) probe_mols (schrodinger.application.desmond.mxmd.mxmd_cleanup.Spot property) probe_name (schrodinger.application.desmond.mxmd.mxmd_cleanup.Spot property) probe_nheavy (schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent property) probe_pdbres (schrodinger.application.desmond.mxmd.mxmd_system_builder.Cosolvent property) Problems (class in schrodinger.application.prepwizard2.diagnostics) process_atom_selection() (in module schrodinger.application.desmond.kinetics.utils) process_attributes() (in module schrodinger.application.licensing.licadmin) process_bennett_log() (schrodinger.application.desmond.replica_dE.replica_container method) process_chunks() (in module schrodinger.application.desmond.simulation_block_test) process_completed_job() (schrodinger.application.desmond.cmj.Job method) process_detected_ligands (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_detected_ligandsChanged (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_detected_ligandsReplaced (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_docstring() (in module schrodinger.infra.epydoc_to_sphinx) process_enamine_db() (in module schrodinger.protein.process_enamine_db) process_events() (in module schrodinger.utils.qapplication) process_highlights() (in module schrodinger.utils.pymol) process_homology_search_results() (in module schrodinger.application.bioluminate.antibody.scaffold_search) process_hypothesis() (in module schrodinger.utils.pymol) process_input() (in module schrodinger.livedesign.cmdline) process_interactions() (in module schrodinger.utils.pymol) process_ld_import_request() (in module schrodinger.application.livedesign.ld_import_utils) process_livedesign_request() (in module schrodinger.application.livedesign.ld_maestro_actions) process_loaded_model() (in module schrodinger.application.desmond.gui) process_measurements() (in module schrodinger.utils.pymol) process_metals_and_ions (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_metals_and_ionsChanged (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_metals_and_ionsReplaced (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_namespace() (in module schrodinger.seam.viz.watcherd) process_non_water_solvents (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_non_water_solventsChanged (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_non_water_solventsReplaced (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_nonchange_diffs() (in module schrodinger.utils.compare) process_one_aa() (in module schrodinger.protein.process_enamine_db) process_option_strings() (schrodinger.utils.singledashoptionparser.SingleDashOption method) process_other_hets (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_other_hetsChanged (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_other_hetsReplaced (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) process_prj() (in module schrodinger.utils.pymol) process_res_selection_str() (in module schrodinger.application.bioluminate.methionine_oxidation) process_row() (in module schrodinger.utils.pymol) process_salt_and_ions() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) process_sequence() (in module schrodinger.protein.helix) process_strain_rescore_outfiles() (in module schrodinger.application.livedesign.ld_strain_rescore_utils) process_structure() (in module schrodinger.protein.pdbname) process_surface() (in module schrodinger.utils.pymol) process_trajectory() (in module schrodinger.utils.pymol) process_watermap() (in module schrodinger.utils.pymol) processAnharmonic() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) processBack() (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) ProcessBusyDialog (class in schrodinger.application.matsci.mswidgets) processContextAction() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView method) processEpsilonFile() (schrodinger.application.matsci.espresso.qeoutput.Output method) processEvents() (schrodinger.ui.qt.appframework.AppFramework method) processFile() (schrodinger.application.matsci.espresso.qeoutput.Output method) processFuncChain() (schrodinger.utils.funcchains.FuncChainMixin method) ProcessingResult (class in schrodinger.tasks.tasks) processJobOutputs() (schrodinger.pipeline.stages.filtering.GeneratePropsStage method) (schrodinger.pipeline.stages.filtering.LigFilterStage method) (schrodinger.pipeline.stages.glide.DockingStage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) (schrodinger.pipeline.stages.prime.MMGBSAStage method) (schrodinger.pipeline.stages.prime.PrimeStage method) (schrodinger.pipeline.stages.qikprop.QikPropStage method) (schrodinger.pipeline.stages.semiemp.SemiEmpStage method) processMoleculeInfo() (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule method) (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) processNext() (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) processOldDBs() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseDialog method) processorName() (schrodinger.tasks.tasks.ProcessingResult method) Processors (schrodinger.job.jobcontrol.Job property) processOutput() (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.TgStep method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask method) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask method) processPanel() (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) processPrevPanel() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) processProducts() (schrodinger.application.matsci.rxn_channel.Channels method) ProcessPtStructuresApp (class in schrodinger.application.matsci.appbase) processSmapInfo() (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) processStructure() (schrodinger.application.matsci.appbase.ProcessPtStructuresApp method) processSwapPair() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) processUtilityDescriptorOutputs() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) PROCS (schrodinger.application.matsci.jwsteps.BaseNoJobStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) procText() (in module schrodinger.application.desmond.enhsamp) prodMGMT() (in module schrodinger.application.matsci.gsas.GSASIIlattice) prodQQ() (in module schrodinger.application.matsci.gsas.GSASIImath) prodQVQ() (in module schrodinger.application.matsci.gsas.GSASIImath) PRODUCT (class in schrodinger.application.desmond.constants) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) PRODUCT_HOSTS_KEY (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) product_installed() (in module schrodinger.application.phase.packages.phase_screen_utils) PRODUCT_LIKE (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) PRODUCT_NAME_BASE (schrodinger.application.matsci.rxn_channel.Products attribute) product_of_ranges() (in module schrodinger.application.scaffold_enumeration.common) ProductFilter (class in schrodinger.application.steps.filters) (class in schrodinger.application.transforms.filters) ProductFilterMixin (class in schrodinger.application.steps.filters) ProductFilterMixin.Settings (class in schrodinger.application.steps.filters) ProductNotAvailableError PRODUCTPREFIX (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) Products (class in schrodinger.application.matsci.rxn_channel) PRODUCTS (schrodinger.application.matsci.fragments.FragmentReactor attribute) profile_call() (in module schrodinger.utils.profiling) profile_memory() (in module schrodinger.utils.profiling) ProfileFilter (class in schrodinger.application.steps.filters) ProfileFilter.Settings (class in schrodinger.application.steps.filters) Profiler (class in schrodinger.utils.profiling) ProfileSettings (class in schrodinger.application.steps.filters) prog() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) prog_for_argparse() (in module schrodinger.application.hitexpander) progname (schrodinger.protein.tasks.blast.BlastSettings attribute) prognameChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) prognameReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) program (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) Program (schrodinger.job.jobcontrol.Job property) PROGRAM_NAME (schrodinger.application.desmond.starter.ui.cmdline.FepArgs attribute) (schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args attribute) (schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs attribute) (schrodinger.application.desmond.starter.ui.fep_solubility.FepSolubilityArgs attribute) (schrodinger.application.matsci.jwsteps.CombinerStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) programChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) programReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) Progress (class in schrodinger.application.glide.utils) progress (schrodinger.application.bioluminate.protein.protein.PropertyCalculator attribute) (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) (schrodinger.tasks.tasks.AbstractTask attribute) progress_string (schrodinger.tasks.tasks.AbstractTask attribute) progress_stringChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) progress_stringReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) PROGRESS_STRUCT_COUNT (schrodinger.ui.two_d_viewer.TwoDViewer attribute) ProgressBar (class in schrodinger.application.job_monitor.job_monitor_progress_bar) (class in schrodinger.ui.qt.tasks.taskwidgets) ProgressBarDelegate (class in schrodinger.ui.qt.delegates) progressChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) ProgressDialog (class in schrodinger.ui.qt.tasks.taskwidgets) ProgressFrame (class in schrodinger.ui.qt.appframework2.af2) progressMade (schrodinger.protein.tasks.clustal.AbstractAlignmentJob attribute) progressReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) proj_id (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) proj_idChanged (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) proj_idReplaced (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) proj_name (schrodinger.application.livedesign.export_models.LDDestination attribute) proj_nameChanged (schrodinger.application.livedesign.export_models.LDDestination attribute) proj_nameReplaced (schrodinger.application.livedesign.export_models.LDDestination attribute) Project (class in schrodinger.project.project) project (schrodinger.application.phase.packages.phase_screen_driver_utils.SourceFormat attribute) Project (schrodinger.job.jobcontrol.Job property) project table Maestro, [1] project_changed() (in module schrodinger.ui.qt.appframework2.maestro_callback) project_close() (in module schrodinger.application.phase.phase_markers) (in module schrodinger.ui.qt.appframework2.maestro_callback) project_id (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel property) project_name (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel property) project_nameChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) project_nameReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) PROJECT_TABLE (schrodinger.application.pymol.gui_models.ProjectExportMode attribute) (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportToOption attribute) (schrodinger.ui.qt.input_selector.InputSelector attribute) project_updated() (in module schrodinger.ui.qt.appframework2.maestro_callback) project_vec_onto_plane() (in module schrodinger.application.jaguar.utils) projectChanged() (schrodinger.ui.qt.ligand_list.LigandListWidget method) projectClose() (schrodinger.ui.qt.ligand_list.LigandListWidget method) projectClosed() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) ProjectDisposition (class in schrodinger.job.launchparams) ProjectEntryMaestroSync (class in schrodinger.maestro_utils.maestro_sync) ProjectExportMode (class in schrodinger.application.pymol.gui_models) projectModel() (schrodinger.application.phase.phase_markers.PhaseMarkers method) ProjectOpenDialog (class in schrodinger.ui.qt.filedialog) ProjectRow (class in schrodinger.project.project) projectSelected (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo attribute) ProjectStructure (class in schrodinger.project.utils) ProjectSurface (class in schrodinger.project.surface) ProjectTableAll (schrodinger.application.pymol.pymol4maestro.EntryMode attribute) ProjectTableButton (class in schrodinger.ui.qt.swidgets) ProjectTableExportMode (class in schrodinger.application.pymol.gui_models) ProjectTableSelected (schrodinger.application.pymol.pymol4maestro.EntryMode attribute) projectUpdated() (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) (schrodinger.ui.qt.input_selector.InputSelector method) ProjEntry (class in schrodinger.application.jaguar.gui.input_tab_widgets) ProjEntryMacroPkaByCharge (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) ProjEntryMacroPkaByPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) ProjEntryPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) ProjEntryTuple (class in schrodinger.application.jaguar.gui.input_tab_widgets) ProjEntryTupleMacroPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) ProjEntryTuplePka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) PROJET_TABLE (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) ProjTableLikeView (class in schrodinger.application.jaguar.gui.utils) projUpdated (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) promoteShowToolTip() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) PROP (schrodinger.application.matsci.genetic_optimization.GlassTransitionTemperature attribute) (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) prop (schrodinger.application.matsci.kmcgui.PlotInfo attribute) PROP (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) PROP_BASE_NAME (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.ChemInformatics attribute) (schrodinger.application.matsci.genetic_optimization.DeepChem attribute) PROP_CHOP (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) PROP_CMS (schrodinger.application.desmond.cms.Cms attribute) prop_dicts (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) PROP_KEYS (schrodinger.application.matsci.permittivity.WorkflowParser attribute) prop_name (schrodinger.application.glide.sort_utils.SortCriterion attribute) (schrodinger.application.matsci.cg_mapping.ATOM_DEFINITION attribute) PROP_NORM (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) PROP_SOURCE (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) PROP_TRJ (schrodinger.application.desmond.cms.Cms attribute) prop_type (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion property) prop_value (schrodinger.application.desmond.simulation_block_data.Array_Prop attribute) PROP_ZERO (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) propagate_chain_data_from_atom() (in module schrodinger.application.matsci.amorphous) propagator() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) Properties (class in schrodinger.adapter) (class in schrodinger.application.bioluminate.antibody.annotate) PROPERTIES (schrodinger.application.matsci.espresso.qeoutput.Output attribute) (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) PropertiesMixin (class in schrodinger.application.jaguar.gui.base_panel) PropertiesTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) PropertiesTabBase (class in schrodinger.application.jaguar.gui.tabs.properties_tab) PropertiesTableWidget (class in schrodinger.application.jaguar.gui.utils) PropertiesValidatorMixin (class in schrodinger.application.jaguar.gui.base_panel) Property (class in schrodinger.application.matsci.genetic_optimization) property (schrodinger.application.matsci.equilibrium_md.Model property) (schrodinger.application.phase.hypothesis.PhaseHypothesis property) (schrodinger.application.steps.scorers.PropertyScorer.Settings attribute) (schrodinger.project.project.ProjectRow property) (schrodinger.structure.Structure property) (schrodinger.structure.StructureAtom property) (schrodinger.structure.StructureBond property) (schrodinger.structure.TextualStructure property) property_export_specs (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) property_export_specsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) property_export_specsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) property_filters (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) property_filtersChanged (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) property_filtersReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) property_key (schrodinger.application.jaguar.utils.FreeEnergy attribute) (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) PROPERTY_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab attribute) property_name (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.protein.properties.SequenceProperty attribute) property_name_final (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) property_name_finalChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) property_name_finalReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) property_nameChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.protein.properties.SequenceProperty attribute) property_nameReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.protein.properties.SequenceProperty attribute) property_names (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) property_namesChanged (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) property_namesReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) property_ranges (schrodinger.application.steps.filters.ProfileSettings attribute) (schrodinger.application.steps.filters.PropertyRangeSettings attribute) property_rangesChanged (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) (schrodinger.application.steps.filters.ProfileSettings attribute) (schrodinger.application.steps.filters.PropertyRangeSettings attribute) property_rangesReplaced (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) (schrodinger.application.steps.filters.ProfileSettings attribute) (schrodinger.application.steps.filters.PropertyRangeSettings attribute) property_source (schrodinger.protein.properties.SequenceProperty attribute) property_sourceChanged (schrodinger.protein.properties.SequenceProperty attribute) property_sourceReplaced (schrodinger.protein.properties.SequenceProperty attribute) property_string() (in module schrodinger.ui.two_d_viewer) property_type (schrodinger.protein.properties.SequenceProperty attribute) property_typeChanged (schrodinger.protein.properties.SequenceProperty attribute) property_typeReplaced (schrodinger.protein.properties.SequenceProperty attribute) property_user_name (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) property_user_nameChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) property_user_nameReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) PropertyCalculator (class in schrodinger.application.bioluminate.protein.protein) propertyChanged (schrodinger.application.steps.scorers.PropertyScorer.Settings attribute) PropertyCombo (class in schrodinger.application.matsci.kmcgui) PropertyCriterion (class in schrodinger.utils.ligfilter) PropertyExportSpec (class in schrodinger.application.livedesign.export_models) PropertyFilter (class in schrodinger.application.combinatorial_diversity.diversity_selector) (class in schrodinger.application.steps.filters) PropertyFilter.Settings (class in schrodinger.application.steps.filters) PropertyInfo (class in schrodinger.application.matsci.genetic_optimization) PropertyName (class in schrodinger.structure) PropertyNameError PropertyNames (class in schrodinger.ui.qt.standard.design_tokens) PropertyRangeSettings (class in schrodinger.application.steps.filters) propertyReplaced (schrodinger.application.steps.scorers.PropertyScorer.Settings attribute) PropertyScorer (class in schrodinger.application.steps.scorers) PropertyScorer.Settings (class in schrodinger.application.steps.scorers) PropertySelector (class in schrodinger.ui.qt.propertyselector) PropertySelectorDialog (class in schrodinger.ui.qt.propertyselector) PropertySelectorList (class in schrodinger.ui.qt.propertyselector) PropertySelectorMenu (class in schrodinger.ui.qt.propertyselector) PropertySelectorWithRanges (class in schrodinger.application.bioluminate.propfilter) PropertySource (class in schrodinger.protein.properties) PropertySyntaxError propertyTableSelectionChanged() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) PropertyType (class in schrodinger.application.combinatorial_diversity.diversity_fingerprinter) (class in schrodinger.protein.properties) PropertyWidget (class in schrodinger.application.dendrogram.gradientSelector) PropFilter (class in schrodinger.structutils.filter) PropFilterDialog (class in schrodinger.application.bioluminate.propfilter) propka_pH (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) propka_pHChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) propka_pHReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) PropkaError PropKaException props (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) propsChanged (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) propsChanged() (schrodinger.ui.two_d_viewer.TwoDViewer method) propsDialog() (schrodinger.ui.qt.propertyselector.MyWindow method) propsReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) prot_ids (schrodinger.application.desmond.stage.app.constant_ph.SiteAndProtonationIds attribute) ProtAssign (class in schrodinger.protein.assignment) ProtAssign.amide_changeable (class in schrodinger.protein.assignment) ProtAssign.amine_changeable (class in schrodinger.protein.assignment) ProtAssign.carboxyl_changeable (class in schrodinger.protein.assignment) ProtAssign.changeable (class in schrodinger.protein.assignment) ProtAssign.hbond_cluster (class in schrodinger.protein.assignment) ProtAssign.histidine_changeable (class in schrodinger.protein.assignment) ProtAssign.ligand_changeable (class in schrodinger.protein.assignment) ProtAssign.rotatable_changeable (class in schrodinger.protein.assignment) ProtAssign.water_changeable (class in schrodinger.protein.assignment) protassign_max_cluster_size (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) protassign_max_cluster_sizeChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) protassign_max_cluster_sizeReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) protassign_number_sequential_cycles (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) protassign_number_sequential_cyclesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) protassign_number_sequential_cyclesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) protect_painter() (in module schrodinger.protein.helm.helm_renderer) PROTECTED_PATTERN_BIT (schrodinger.application.matsci.rdpattern.Pattern attribute) PROTEIN (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute) PROTEIN_CATEGORY (schrodinger.application.bioluminate.antibody.annotate.Properties attribute) PROTEIN_DOCKING_POSE (schrodinger.infra.structure.WorkflowType attribute) protein_family (schrodinger.protein.tasks.sta.STATask.Input attribute) protein_familyChanged (schrodinger.protein.tasks.sta.STATask.Input attribute) protein_familyReplaced (schrodinger.protein.tasks.sta.STATask.Input attribute) protein_file (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Input attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) protein_fileChanged (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Input attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) protein_fileReplaced (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Input attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) protein_mutation_lics() (in module schrodinger.application.desmond.license) PROTEIN_PREP (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) protein_present_image (schrodinger.ui.qt.structure2d.StructureToolTip attribute) protein_residue() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method) protein_secondary_structure (schrodinger.application.desmond.new_fep_edge_data.FepData property) PROTEIN_SELECTIVITY (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) protein_sequences (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer property) PROTEIN_STABILITY (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) PROTEIN_STATE (schrodinger.application.bioluminate.pose_filtering.hdx_io.DynamXColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.HDExaminerColumns attribute) protein_states_lig (schrodinger.application.bioluminate.pose_filtering.hdx_io.HdxMsProperties attribute) protein_states_recep (schrodinger.application.bioluminate.pose_filtering.hdx_io.HdxMsProperties attribute) ProteinAlignment (class in schrodinger.protein.alignment) ProteinAlignmentAnnotations (class in schrodinger.protein.annotation) ProteinAlignmentAnnotations.ANNOTATION_TYPES (class in schrodinger.protein.annotation) ProteinCheckParameters (class in schrodinger.protein.reliability) ProteinCheckSpinnerWidget (class in schrodinger.application.desmond.feputils) ProteinClass (class in schrodinger.application.bioluminate.classify) ProteinFeature (class in schrodinger.application.prepwizard2.tasks) ProteinFepMapper (class in schrodinger.application.desmond.stage.fep_mapper) ProteinHealthViewer (class in schrodinger.ui.qt.protein_health_viewer) ProteinInteractionInput (class in schrodinger.application.bioluminate.protein_interaction.tasks) ProteinInteractionOptions (class in schrodinger.application.bioluminate.protein_interaction.tasks) ProteinInteractionOutput (class in schrodinger.application.bioluminate.protein_interaction.tasks) ProteinInteractionSubTask (class in schrodinger.application.bioluminate.protein_interaction.tasks) ProteinInteractionTask (class in schrodinger.application.bioluminate.protein_interaction.tasks) ProteinMapperMsjGenerator (class in schrodinger.application.desmond.msj_generator.fep.protein) ProteinMapperParams (class in schrodinger.application.desmond.msj_generator.workflow_params) ProteinMutationGenerator (class in schrodinger.application.desmond.stage.prepare.structure) ProteinMutator (class in schrodinger.application.bioluminate.protein.mutator) proteinOnlyChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) ProteinProperties (class in schrodinger.application.bioluminate.patch_utils.patch_finder) ProteinRefinementInput (class in schrodinger.application.prepwizard2.tasks) ProteinRefinementTask (class in schrodinger.application.prepwizard2.tasks) ProteinReliabilityTask (class in schrodinger.application.desmond.feputils) ProteinReliabilityTask.Input (class in schrodinger.application.desmond.feputils) ProteinReliabilityTask.Output (class in schrodinger.application.desmond.feputils) ProteinReport (class in schrodinger.application.desmond.replica_sid_generator) ProteinSequence (class in schrodinger.protein.sequence) ProteinSequenceAnnotations (class in schrodinger.protein.annotation) ProteinSequenceAnnotations.ANNOTATION_TYPES (class in schrodinger.protein.annotation) ProteinSequenceMeta (class in schrodinger.protein.sequence) ProteinStructureQualityViewer (class in schrodinger.application.bioluminate.protein_structure_quality) ProteinWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) Protocol (class in schrodinger.application.matsci.permittivity) PROTOCOL (schrodinger.application.livedesign.constants.ModelSearchType attribute) PROTOCOL_VERSION (schrodinger.application.desmond.antlr3.debug.DebugEventListener attribute) protonate_histidine() (in module schrodinger.protein.assignment) protonation_states (schrodinger.application.jaguar.pk50_report.Pk50Factory property) ProvidesBasisMixin (class in schrodinger.application.jaguar.gui.tabs.base_tab) ProvidesStructuresMixin (class in schrodinger.application.jaguar.gui.tabs.base_tab) ProvidesTheoryMixin (class in schrodinger.application.jaguar.gui.tabs.base_tab) ProvidesTheoryTheoryTab (class in schrodinger.application.jaguar.gui.tabs.theory_tab) ProvidesTheoryTheoryTabNoSoZora (class in schrodinger.application.jaguar.gui.tabs.theory_tab) proximity_constraints (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) PROXY_CLASS (schrodinger.application.bioluminate.antibody.search_results_table.FullTable attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) PROXY_MODEL_CLASS (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom attribute) proxyToParticleName() (schrodinger.application.matsci.rdpattern.Pattern method) prune_couplings() (in module schrodinger.application.jaguar.simple_spec) pruneIt() (schrodinger.application.matsci.nano.slab.Surface method) psc_workflow (class in schrodinger.application.bioluminate.epitope.psc_workflow) psd (schrodinger.protein.align.AbstractStructureAligner.Result attribute) (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute) Pseudo (class in schrodinger.application.desmond.cms) PSEUDO2PARENT (schrodinger.application.desmond.constants.IdConversion attribute) PSEUDO_END (schrodinger.application.desmond.constants.IdConversion attribute) PseudoData (class in schrodinger.application.matsci.espresso.utils) PseudopotentialsType (class in schrodinger.application.matsci.espresso.qeinput) pseudospectral() (in module schrodinger.application.jaguar.textparser) psi (schrodinger.ui.qt.rama.BackboneDihedral attribute) PSIBLAST (schrodinger.protein.tasks.blast.BlastAlgorithm attribute) pt_entry_id (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant property) pt_export_mode (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) pt_export_modeChanged (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) pt_export_modeReplaced (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) PT_IMPORT_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) ptensor (schrodinger.application.matsci.deswidgets.DesmondMDWidgets.NUM_FRMS_TYPE attribute) PTENSOR_NFRM_LABEL (schrodinger.application.matsci.deswidgets.DesmondMDWidgets attribute) PtRowBasedCustomRole (in module schrodinger.ui.qt.table_helper) PtRowBasedTableModel (class in schrodinger.ui.qt.table_helper) publish_data (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) publish_dataChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) publish_dataReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) PubsubEnabledStepMixin (class in schrodinger.stepper.stepper) pull_ligand() (in module schrodinger.application.glide.http_server) (schrodinger.application.glide.client_module.GlideClientModule method) pullCompounds() (schrodinger.pipeline.stages.pull.PullStage method) PullStage (class in schrodinger.pipeline.stages.pull) pulse_acquire() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) PureEd25519 (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) purgeRecord() (schrodinger.job.jobcontrol.Job method) push() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.queue.Queue method) (schrodinger.job.queue.PriorityQueue method) push_level() (in module schrodinger.infra.mmerr) push_ligand() (in module schrodinger.application.glide.http_server) (schrodinger.application.glide.client_module.GlideClientModule method) PushButtonDelegate (class in schrodinger.ui.qt.delegates) PushButtonWithIndicatorAndPopUp (class in schrodinger.ui.qt.pop_up_widgets) PushButtonWithPopUp (class in schrodinger.ui.qt.pop_up_widgets) PushLayout (class in schrodinger.ui.qt.formlayout) pushpop() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) put() (schrodinger.application.desmond.arkdb.ArkDb method) (schrodinger.application.desmond.multisim.parser.Msj method) put_to() (schrodinger.application.desmond.arkdb.Datum method) putToM2ioFile() (schrodinger.structure.Structure method) (schrodinger.structure.TextualStructure method) pv_file (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) pv_fileChanged (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) pv_fileReplaced (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) py38StrEnum (class in schrodinger) PyMOL (schrodinger.protein.sequence.AbstractSequence.ORIGIN attribute) pymol_location (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) pymol_locationChanged (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) pymol_locationReplaced (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) PymolInstance (class in schrodinger.utils.pymol) PyMOLMaestroSync (class in schrodinger.application.pymol.mae_sync) PymolScriptInstance (class in schrodinger.utils.pymol) PyStructureReaderException PYTHON_EXE (in module schrodinger.utils.sysinfo) PYTHON_MINIMIZE (schrodinger.application.bioluminate.protein.protein.Refiner attribute) PYTHONPATH, [1], [2], [3], [4], [5], [6] PythonSortProxyModel (class in schrodinger.ui.qt.table_helper)

Q

Q2AV() (in module schrodinger.application.matsci.gsas.GSASIImath) Q2AVdeg() (in module schrodinger.application.matsci.gsas.GSASIImath) Q2Mat() (in module schrodinger.application.matsci.gsas.GSASIImath) Q_GIPAW (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) Q_MESH (schrodinger.application.matsci.espresso.qeinput.TurboEelsType attribute) qCleanupResources() (in module schrodinger.application.bioluminate.actions.icons_rc) (in module schrodinger.application.job_monitor.job_monitor_icons_rc) (in module schrodinger.application.jobserver_cert_gui_dir.jobserver_cert_gui_icons_rc) (in module schrodinger.application.livedesign.icons_rc) (in module schrodinger.application.matsci.controlicons_rc) (in module schrodinger.trajectory.trajectory_gui_dir.icons_rc) (in module schrodinger.ui.images_rc) (in module schrodinger.ui.qt.dialbox_dir.dialbox_qrc) (in module schrodinger.ui.qt.icons_rc) (in module schrodinger.ui.qt.standard_widgets.standard_widgets_rc) QEMDCms (class in schrodinger.application.matsci.cgforcefield) QFileDialog (in module schrodinger.ui.qt.filedialog) qfont_to_tuple() (in module schrodinger.ui.qt.formlayout) QikPropStage (class in schrodinger.pipeline.stages.qikprop) QikPropTask (class in schrodinger.application.livedesign.tasks) QikPropTask.Input (class in schrodinger.application.livedesign.tasks) QikPropTask.JobConfig (class in schrodinger.application.livedesign.tasks) QikPropTask.Output (class in schrodinger.application.livedesign.tasks) qInitResources() (in module schrodinger.application.bioluminate.actions.icons_rc) (in module schrodinger.application.job_monitor.job_monitor_icons_rc) (in module schrodinger.application.jobserver_cert_gui_dir.jobserver_cert_gui_icons_rc) (in module schrodinger.application.livedesign.icons_rc) (in module schrodinger.application.matsci.controlicons_rc) (in module schrodinger.trajectory.trajectory_gui_dir.icons_rc) (in module schrodinger.ui.images_rc) (in module schrodinger.ui.qt.dialbox_dir.dialbox_qrc) (in module schrodinger.ui.qt.icons_rc) (in module schrodinger.ui.qt.standard_widgets.standard_widgets_rc) qm (schrodinger.application.qsite.input.HydrogenCap property) qm_atoms() (in module schrodinger.application.jaguar.textparser) (in module schrodinger.application.qsite.output) qmatom (schrodinger.application.qsite.input.Cut property) QMConformerSelection (class in schrodinger.application.matsci.reaction_workflow_utils) QMConformerSelectionException QMID (schrodinger.application.matsci.kmc.AtomsTable attribute) qmmm_bend_energy() (in module schrodinger.application.qsite.output) qmmm_electrostatic_energy() (in module schrodinger.application.qsite.output) qmmm_stretch_energy() (in module schrodinger.application.qsite.output) qmmm_torsion_energy() (in module schrodinger.application.qsite.output) QMMoleculeKeywords (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) QMPOSX (schrodinger.application.matsci.kmc.AtomsTable attribute) QMPOSY (schrodinger.application.matsci.kmc.AtomsTable attribute) QMPOSZ (schrodinger.application.matsci.kmc.AtomsTable attribute) QMPreOptimization (class in schrodinger.application.matsci.reaction_workflow_gui_utils) QMRegion (class in schrodinger.application.qsite.input) qmregion (schrodinger.application.qsite.input.QSiteInput property) qp_args (schrodinger.application.livedesign.tasks.QikPropTask.Input attribute) qp_argsChanged (schrodinger.application.livedesign.tasks.QikPropTask.Input attribute) qp_argsReplaced (schrodinger.application.livedesign.tasks.QikPropTask.Input attribute) qp_csv_file (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qp_csv_fileChanged (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qp_csv_fileReplaced (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qp_out_file (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qp_out_fileChanged (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qp_out_fileReplaced (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qp_qpsa_file (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qp_qpsa_fileChanged (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qp_qpsa_fileReplaced (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) qprocess (schrodinger.tasks.tasks.SubprocessMixin attribute) QProcessCrashedError QProcessError QProcessFailedToStartError QProcessReadError QProcessTimedout QProcessUnknownError QProcessWriteError QPTS_MESH_KEY (schrodinger.application.matsci.espresso.qeinput.HPType attribute) (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) QPTS_SPACING_KEY (schrodinger.application.matsci.espresso.qeinput.HPType attribute) (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) QRNN (schrodinger.application.jaguar.constants.CalcType attribute) QRNN_1 (schrodinger.application.jaguar.rotation_barriers_keywords.ExternalMethod attribute) QRNN_2 (schrodinger.application.jaguar.rotation_barriers_keywords.ExternalMethod attribute) QRNN_3 (schrodinger.application.jaguar.rotation_barriers_keywords.ExternalMethod attribute) QRNN_4 (schrodinger.application.jaguar.rotation_barriers_keywords.ExternalMethod attribute) QRNN_TB (schrodinger.application.jaguar.constants.CalcType attribute) QRNN_TB_TRANSFER (schrodinger.application.jaguar.constants.CalcType attribute) QRNN_TRANSFER (schrodinger.application.jaguar.constants.CalcType attribute) QRNNInput (class in schrodinger.application.jaguar.qrnn.input) QRNNModel (class in schrodinger.energy) QRNNSupportError qsar (schrodinger.application.phase.packages.shape_generator.AtomTypes attribute) QSI() (in module schrodinger.ui.qt.entryselector) QSiteInput (class in schrodinger.application.qsite.input) QSiteOutput (class in schrodinger.application.qsite.output) QSiteResults (class in schrodinger.application.qsite.output)

QSiteTextParser (class in schrodinger.application.qsite.output) QSliderIcons (class in schrodinger.ui.qt.standard.design_tokens) QSM_MAX (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) QST3 (schrodinger.application.jaguar.rotation_barriers_keywords.TSMethod attribute) qst_geometries() (in module schrodinger.application.jaguar.textparser) qst_initial_geometry() (in module schrodinger.application.jaguar.textparser) QST_SEARCH_ALONG (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) qthread (schrodinger.tasks.tasks.ThreadMixin attribute) quadratic_1() (in module schrodinger.application.matsci.mecp_mod) quadratic_2() (in module schrodinger.application.matsci.mecp_mod) quadratic_3() (in module schrodinger.application.matsci.mecp_mod) qualify() (schrodinger.pipeline.stages.filtering.DrugLikeSplitStage method) Quality (class in schrodinger.trajectory.trajectory_gui_dir.export_movie) QualitySlider (class in schrodinger.application.matsci.qualityslider) Qubec (class in schrodinger.application.matsci.qubec_utils) qubec_error() (in module schrodinger.application.matsci.qubec_utils) QubecException query() (in module schrodinger.application.fpsim) (schrodinger.application.fpsim.FPsimSearcher method) (schrodinger.seam.metric.SeamMetrics method) query_asl_1 (schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) query_asl_1Changed (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) query_asl_1Replaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) query_asl_2 (schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) query_asl_2Changed (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) query_asl_2Replaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) query_chain_sequence (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput attribute) query_end (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) query_file (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) query_fileChanged (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) query_fileReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) query_monomers() (in module schrodinger.application.matsci.rxn_channel) query_name (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) query_registry() (in module schrodinger.utils.sysinfo) query_seq (schrodinger.protein.tasks.sta.STATask.Input attribute) query_seqChanged (schrodinger.protein.tasks.sta.STATask.Input attribute) query_seqReplaced (schrodinger.protein.tasks.sta.STATask.Input attribute) query_sequence (schrodinger.application.prime.wrapper.BasePrimeAlignment property) (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastTask.Input attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask.Input attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) query_sequenceChanged (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastTask.Input attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask.Input attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) query_sequenceReplaced (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastTask.Input attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask.Input attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) query_start (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) QueryError QueryOptions (class in schrodinger.rdkit.substructure) queryTemplateName() (schrodinger.application.matsci.builderwidgets.SketcherBox method) question() (in module schrodinger.ui.qt.appframework) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.swidgets.SDialog method) (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) QuestionMessageBox (class in schrodinger.ui.qt.messagebox) Queue (class in schrodinger.application.desmond.queue) queue_config_diffs() (in module schrodinger.utils.installation_check) queue_config_file_pairs() (in module schrodinger.utils.installation_check) queue_config_files_diff() (in module schrodinger.utils.installation_check) queue_inst_file() (in module schrodinger.utils.installation_check) queue_orig_dir() (in module schrodinger.utils.installation_check) queue_orig_file() (in module schrodinger.utils.installation_check) queueDone (schrodinger.tasks.queue.TaskQueue attribute) queuedTaskFinished (schrodinger.tasks.queue.TaskQueue attribute) QueueHost (schrodinger.job.jobcontrol.Job property) QueueReport (class in schrodinger.tasks.queue) QueueResults (class in schrodinger.tasks.queue) QUICK (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute) quick_append() (schrodinger.utils.sea.sea.List method) QuickHelpButton (class in schrodinger.application.bioluminate.bwidgets) quicktest_model() (in module schrodinger.tasks.ldtasks) quickWeedAtoms() (schrodinger.structutils.ringspear.SpearRing method) quietlySelectSite() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) Quit (class in schrodinger.application.bioluminate.pml_menus) quit() (in module schrodinger.application.bioluminate.protein_report_widget) (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) quit_application() (in module schrodinger.utils.qapplication) quitPanel() (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.two_d_viewer.TwoDViewer method) quotechar (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) quoting (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute)

R

R (schrodinger.application.jaguar.hess_guess.LindhConstants attribute) r() (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method) r2 (schrodinger.application.matsci.equilibrium_md.MsdTrajBase.DIFFUSIVITY attribute) R_1280X720 (schrodinger.trajectory.trajectory_gui_dir.export_movie.Resolution attribute) R_1920X1080 (schrodinger.trajectory.trajectory_gui_dir.export_movie.Resolution attribute) R_3840X2160 (schrodinger.trajectory.trajectory_gui_dir.export_movie.Resolution attribute) R_CUSTOM (schrodinger.trajectory.trajectory_gui_dir.export_movie.Resolution attribute) R_CUT (schrodinger.application.jaguar.hess_guess.LindhConstants attribute) R_GROUP_FRAGMENT (schrodinger.livedesign.entity_type.EntityClass attribute) R_GROUP_SD_KEY_PATTERN (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF attribute) r_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) RAD_DECAYS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) RadialRingHistogram (class in schrodinger.ui.qt.radial_plot) Radian (schrodinger.application.jaguar.constants.Unit attribute) RadioButtonDelegate (class in schrodinger.ui.qt.delegates) RadioButtonIcons (class in schrodinger.ui.qt.standard.design_tokens) RadioLayout (class in schrodinger.ui.qt.formlayout) radius (schrodinger.application.jaguar.gui.utils.Solvent attribute) (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) (schrodinger.application.matsci.freevolume.GridRadius attribute) RADIUS (schrodinger.application.matsci.nano.tube.NanoTube attribute) (schrodinger.application.matsci.packmol.PackmolKw attribute) radius (schrodinger.graphics3d.arrow.MaestroArrow property) (schrodinger.graphics3d.hemisphere.MaestroHemisphere property) (schrodinger.graphics3d.sphere.MaestroSphere property) (schrodinger.graphics3d.torus.MaestroTorus property) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) (schrodinger.structure.StructureAtom property) (schrodinger.structutils.ringspear.SpearRing attribute) radius_of_gyration() (in module schrodinger.application.matsci.geometry) (in module schrodinger.structutils.analyze) RADIUS_TOLERANCE (schrodinger.application.matsci.atom_group.HelixArcAtomGroup attribute) radiusChanged (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) radiusReplaced (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) RainbowColorRamp (class in schrodinger.structutils.color) raise_deprecation_error() (in module schrodinger.utils.deprecation) raise_voluptuous_exception() (in module schrodinger.application.jaguar.workflow_validation) raiseProcessError() (schrodinger.application.matsci.jobutils.FileDownloader method) Rama (class in schrodinger.ui.qt.rama) RamaClassification (class in schrodinger.ui.qt.rama) RamaContourMixin (class in schrodinger.ui.qt.rama) RamaFigure (class in schrodinger.ui.qt.rama) RAMAN_ACT_KEY (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) RAMAN_ACT_TITLE (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) raman_activity_precision (schrodinger.application.jaguar.results.NormalMode attribute) RAMAN_INT_KEY (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) RAMAN_INT_TITLE (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) raman_intensity_precision (schrodinger.application.jaguar.results.NormalMode attribute) RamanSpectrum (class in schrodinger.application.matsci.spectra) RamanSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) RamaResidueType (class in schrodinger.ui.qt.rama) RamaScatterMixin (class in schrodinger.ui.qt.rama) RAMD (schrodinger.application.desmond.constants.KineticsLegTypes attribute) ramd_fk_increase_rate (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) ramd_only (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) ramd_spring_fk (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) RamdCleanup (class in schrodinger.application.desmond.stage.app.kinetics) RamdGenerateUnbindingPath (class in schrodinger.application.desmond.stage.app.kinetics) RamdSetup (class in schrodinger.application.desmond.stage.app.kinetics) ramp_colors (schrodinger.utils.pymol.Mapping attribute) rand_seed (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) RANDOM_ALL_TO_ON_THE_FLY_THRESH (schrodinger.application.matsci.rxn_channel.ChannelDefinitions attribute) random_choice() (in module schrodinger.application.matsci.rxn_channel) random_filtering() (in module schrodinger.active_learning.al_utils) random_rotation() (in module schrodinger.application.matsci.amorphous) RANDOM_SEED (schrodinger.application.matsci.rxn_channel.Constants attribute) random_split() (in module schrodinger.active_learning.al_utils) random_string() (in module schrodinger.application.desmond.util) RANDOM_TYPES_CHOICES (schrodinger.application.matsci.rxn_channel.Constants attribute) RandomAcceleratedMD (class in schrodinger.application.desmond.stage.app.kinetics) randomAVdeg() (in module schrodinger.application.matsci.gsas.GSASIImath) RANDOMIZE_VEL (schrodinger.application.matsci.desconfig.MSJStringer attribute) RANDOMIZE_VELOCITY (schrodinger.application.matsci.permittivity.MdStageModifier attribute) RANDOMIZE_VELOCITY_DOT_FIRST (schrodinger.application.matsci.permittivity.MdStageModifier attribute) RANDOMIZE_VELOCITY_DOT_SEED (schrodinger.application.matsci.permittivity.MdStageModifier attribute) randomlyRotate() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) randomlyTranslate() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) randomQ() (in module schrodinger.application.matsci.gsas.GSASIImath) RandomSample (class in schrodinger.seam.transforms.samplers) RandomSampleFilter (class in schrodinger.stepper.core_steps) RandomSampleFilter.Settings (class in schrodinger.stepper.core_steps) RandomSampleIterator (class in schrodinger.application.pathfinder.synthesis) RandomSeedWidget (class in schrodinger.application.matsci.mswidgets) randomSelect() (schrodinger.active_learning.al_node.PrepareSmilesNode method) RandVelFrame (class in schrodinger.application.desmond.gui) range (schrodinger.protein.annotation.TupleWithRange property) Range (schrodinger.ui.qt.table_helper.Include attribute) range() (schrodinger.infra.mmbitset.Bitset method) RANGE_COLUMNS (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) RANGE_LIMITS (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka attribute) range_max (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTupleMacroPka attribute) range_min (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTupleMacroPka attribute) RANGE_SEPARATOR (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator attribute) RangeFilter (class in schrodinger.application.steps.filters) RangeFilter.Settings (class in schrodinger.application.steps.filters) rank_reactants() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) ranks (schrodinger.application.matsci.elasticity.tensors.TensorCollection property) rate (schrodinger.math.multi_parameter_optimization.Transition attribute) rate() (in module schrodinger.application.desmond.fep_edge_data_classifier) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) RATE12E (schrodinger.application.matsci.kmc.PairsMixin attribute) RATE12H (schrodinger.application.matsci.kmc.PairsMixin attribute) RATE21E (schrodinger.application.matsci.kmc.PairsMixin attribute) RATE21H (schrodinger.application.matsci.kmc.PairsMixin attribute) RATE_COLUMNS (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) Rate_Constant (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) Rate_Constant_Type (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) Rate_Constant_Units (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) RateConstants (class in schrodinger.application.matsci.reaction_workflow_gui_utils) RATEFILE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) Rating (class in schrodinger.application.desmond.fep_edge_data_classifier) ratioCount() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) ratioIonicity() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) RAW_AFEP (schrodinger.application.desmond.systype.DesmondTyper attribute) RAW_FEP (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) RAW_MD_KEYS (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) RAW_POTENTIAL (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) RAW_REGULAR (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.desmond.systype.WatermapTyper attribute) raw_val (schrodinger.utils.sea.sea.Atom property) (schrodinger.utils.sea.sea.List property) (schrodinger.utils.sea.sea.Map property) RAW_WEBSVC_RESPONSE (schrodinger.application.licensing.licserver.install.LicenseFileType attribute) rawPrediction() (schrodinger.protein.predictors.AccproPredictor method) (schrodinger.protein.predictors.DisproPredictor method) (schrodinger.protein.predictors.DomproPredictor method) (schrodinger.protein.predictors.SsproPredictor method) Ray (class in schrodinger.application.bioluminate.pml_menus) rb_potential_from_struct() (in module schrodinger.application.desmond.torsion_related) rbss_yaml (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) rbss_yamlChanged (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) rbss_yamlReplaced (schrodinger.application.livedesign.tasks.RBSSTask.Input attribute) RBSSTask (class in schrodinger.application.livedesign.tasks) RBSSTask.Input (class in schrodinger.application.livedesign.tasks) RBSSTask.JobConfig (class in schrodinger.application.livedesign.tasks) RBSSTask.Output (class in schrodinger.application.livedesign.tasks) RCE (class in schrodinger.application.macromodel.input) rdk_mol_from_cml_element() (in module schrodinger.application.scaffold_enumeration.rdcml) rdkit (schrodinger.application.matsci.msconst.SMARTS_METHOD attribute) rdkit_reaction_from_smarts() (in module schrodinger.analysis.transformations) rdkit_to_sdf() (in module schrodinger.livedesign.convert) RdkitLoggerstate (class in schrodinger.rdkit.rdkit_adapter) RdkitMergeHandler (class in schrodinger.rdkit.molio) RdkitMolWriter (class in schrodinger.rdkit.molio) RDMOL_BINARY_BASE64 (schrodinger.rdkit_extensions.Format attribute) RdMolDelegate (class in schrodinger.ui.qt.delegates) RDMolStructureItem (class in schrodinger.ui.qt.rdmol_views) RDMolTooltipWithLabel (class in schrodinger.ui.qt.rdmol_views) RDPatternSMARTSEdit (class in schrodinger.application.matsci.rdpattern_gui) rdsq2d() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIIpwd) REACTANT (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) (schrodinger.application.livedesign.live_report_widget.LiveReportType attribute) (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) REACTANT_LIKE (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) REACTANT_NAME_BASE (schrodinger.application.matsci.rxn_channel.CheckInput attribute) ReactantMolecule (class in schrodinger.application.matsci.rxn_channel) REACTANTPREFIX (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) Reactants (class in schrodinger.application.matsci.rxn_channel) REACTANTS (schrodinger.application.matsci.fragments.FragmentReactor attribute) Reaction (class in schrodinger.application.matsci.fragments) (class in schrodinger.application.pathfinder.reaction) reaction (schrodinger.application.pathfinder.route.RouteNode property) reaction_instance (schrodinger.application.pathfinder.route.RouteNode property) reaction_is_excluded() (in module schrodinger.application.pathfinder.analysis) reaction_is_supported() (in module schrodinger.application.jaguar.autots_validation) reaction_smarts (schrodinger.application.jaguar.autots_input.AutoTSInput property) reaction_type (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) reaction_typeChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) reaction_typeReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) REACTIONANGLETHRESH (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) REACTIONBONDTHRESH (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) ReactionCoords (class in schrodinger.application.matsci.rxn_path) ReactionDict (class in schrodinger.application.pathfinder.reaction) REACTIONDIHEDRALTHRESH (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) ReactionFailureTracker (class in schrodinger.application.pathfinder.synthesis) ReactionInstance (class in schrodinger.application.pathfinder.route) ReactionMoleculesTab (class in schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab) ReactionParticipant (class in schrodinger.application.jaguar.gui.tabs.reaction_tab) reactionParticipantAdded (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) reactionParticipantRemoved (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) reactionParticipantStructChanged (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) ReactionPath (class in schrodinger.application.matsci.rxn_path) ReactionPropertiesTab (class in schrodinger.application.jaguar.gui.tabs.reaction_properties_tab) ReactionTab (class in schrodinger.application.jaguar.gui.tabs.reaction_tab) ReactionWorkflow (class in schrodinger.application.matsci.reaction_workflow_utils) ReactionWorkflowEnergyAnalysis (class in schrodinger.application.matsci.reaction_workflow_utils) ReactionWorkflowException ReactionWorkflowFile (class in schrodinger.application.matsci.reaction_workflow_utils) ReactionWorkflowFileException ReactionWorkflowFrame (class in schrodinger.application.matsci.reaction_workflow_gui_utils) REACTIVEATOM (schrodinger.application.matsci.rxn_path.ReactionPath attribute) ReactiveResidues (class in schrodinger.application.bioluminate.reactive_residues) ReactProdTS (class in schrodinger.application.matsci.reaction_workflow_utils) reactWith() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) read() (in module schrodinger.application.jaguar.input) (in module schrodinger.ui.qt.appframework2.appmethods) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchAnalysis class method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder class method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.jaguar.autots_input.AutoTSInput method) (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.solvation_input.SolvationInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.project.surface.ProjectSurface class method) (schrodinger.structure.MaestroReader method) (schrodinger.structure.MaestroTextReader static method) (schrodinger.structure.Structure static method) (schrodinger.structure.StructureReader static method) (schrodinger.structure.TextualStructure static method) (schrodinger.surface.Surface class method) read_all_ct() (in module schrodinger.application.desmond.struc) read_all_st_from_file() (in module schrodinger.active_learning.al_utils) read_all_structures() (in module schrodinger.application.desmond.struc) read_archive_data() (schrodinger.application.desmond.kinetics.cleanup.CleanUp method) (schrodinger.application.desmond.kinetics.mtd_cleanup.CleanUp method) (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) read_args_yaml() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) read_asl_file() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) read_build_time() (in module schrodinger.utils.machid) read_canvas_fingerprint_matrix() (in module schrodinger.protein.natural_analog) read_ccd_structures() (in module schrodinger.structutils.ccd) read_cfg() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) read_checkpoint_file() (in module schrodinger.application.desmond.launch_utils) read_cluster_file() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) read_cms() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) read_constraints() (in module schrodinger.application.glide.glide) read_constraints_file() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint static method) read_csv() (in module schrodinger.application.jaguar.nmr_utils) read_csv_columns() (in module schrodinger.application.livedesign.io_utils) read_data_from_log_file() (in module schrodinger.application.desmond.replica_exchange_review) read_dE_file() (in module schrodinger.application.desmond.fepana) read_dE_Replicas() (schrodinger.application.desmond.replica_dE.replica_container method) read_density_from_eaf() (in module schrodinger.application.matsci.desmondutils) read_fasta() (in module schrodinger.application.bioluminate.anarci.annotate) read_FEP_REST_energetics() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_FEPSimulation() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_file() (in module schrodinger.livedesign.cmdline) read_git_hash() (in module schrodinger.utils.machid) read_hdf() (in module schrodinger.application.matsci.hdfutils) read_input() (in module schrodinger.application.jaguar.simple_spec) read_input_file() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) (in module schrodinger.application.matsci.qubec_utils) read_json() (in module schrodinger.application.glide.utils) read_json_data() (in module schrodinger.utils.featureflags.write) read_json_file() (in module schrodinger.application.glide.ligand_designer) read_keys() (in module schrodinger.utils.ligfilter) read_keywords_file() (in module schrodinger.application.glide.glide) read_keywords_file_as_dict() (in module schrodinger.application.glide.glide) read_license_file() (in module schrodinger.application.licensing.flexlm) read_LigandInfo() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_lines_in_file() (in module schrodinger.application.phase.packages.phase_utils) read_mae_files() (in module schrodinger.application.jaguar.autots_input) read_meta_cfg() (in module schrodinger.application.desmond.meta) read_minimal_caps_file() (in module schrodinger.application.pathfinder.reaction) read_mode (schrodinger.structure.MaestroTextReader attribute) read_nmr_input() (in module schrodinger.application.jaguar.nmr_utils) read_only (schrodinger.project.project.ProjectRow property) read_pathfinder_data() (in module schrodinger.application.pathfinder.reaction) read_paths_listed_in_file() (in module schrodinger.active_learning.al_driver) read_properties() (in module schrodinger.application.combinatorial_diversity.driver_utils) read_properties_from_csv_file() (in module schrodinger.application.combinatorial_diversity.driver_utils) read_properties_from_fp_file() (in module schrodinger.application.combinatorial_diversity.driver_utils) read_property_filters() (in module schrodinger.application.combinatorial_diversity.driver_utils) (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) read_property_filters_from_iterable() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) read_ProteinInfo() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_query_catalog() (in module schrodinger.application.bb_database.bb_task_utils) read_query_cmd() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) read_reactant_fps() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) read_reactions_file() (in module schrodinger.application.pathfinder.reaction) read_reagent_classes_file() (in module schrodinger.application.pathfinder.reaction) read_REST_exchanges() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_restraints() (in module schrodinger.forcefield.minimizer) read_route_file() (in module schrodinger.application.pathfinder.route) read_rxn_file() (in module schrodinger.application.pathfinder.reaction) read_safe_yaml_file() (in module schrodinger.application.matsci.yamlutils) read_scaffold() (in module schrodinger.structutils.markush_enumerate) read_score() (in module schrodinger.active_learning.al_utils) read_scored_ligands() (in module schrodinger.active_learning.al_utils) read_sdf() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae static method) read_seqres_from_ct() (in module schrodinger.structutils.analyze) read_split_query() (in module schrodinger.application.bb_database.bb_task_utils) read_stage_datafile() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) read_structs_from_tgz() (in module schrodinger.application.desmond.kinetics.utils) read_structures_as_conformations() (in module schrodinger.utils.cgxutils) read_text() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) read_trj_void_file() (in module schrodinger.application.matsci.freevolume) read_trj_volume_file() (in module schrodinger.application.matsci.freevolume) read_unique_field() (in module schrodinger.pipeline.pipeutils) read_void_file() (in module schrodinger.application.matsci.freevolume) read_volume_file() (in module schrodinger.application.matsci.freevolume) read_workflow_metadata() (in module schrodinger.application.matsci.wfmanagement) read_xy_spectrum_data_file() (in module schrodinger.application.matsci.spectra) read_yaml() (in module schrodinger.application.glide.glide) readActionSelected() (schrodinger.application.desmond.gui.GuiApp method) readAgain() (schrodinger.application.glide.http_client.SubprocessJobAdapter method) (schrodinger.job.jobcontrol.Job method) ReadAllStructuresFromFile (class in schrodinger.seam.io.chemio) readAndRun() (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer class method) readColMetadata() (in module schrodinger.application.matsci.gsas.GSASIIfiles) readColMetadataLabels() (in module schrodinger.application.matsci.gsas.GSASIIfiles) readCommand() (schrodinger.application.desmond.gui.GuiApp method) readConsKeywords() (schrodinger.application.glide.glide.Dock method) readd_hydrogens (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) readd_hydrogensChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) readd_hydrogensReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) readDatabaseFile() (schrodinger.protein.nonstandard_residues.ResidueDatabase method) ReadDialog (class in schrodinger.ui.qt.appframework) ReadEditMixin (class in schrodinger.application.jaguar.gui.base_panel) reader (schrodinger.structure.MultiFileStructureReader attribute) reader_class (schrodinger.structure.MultiFileStructureReader attribute) reader_open() (in module schrodinger.utils.csv_unicode) readFile() (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.structutils.filter.Filter method) (schrodinger.structutils.filter.PropFilter method) (schrodinger.structutils.filter.SmartsFilter method) ReadFileDialog (class in schrodinger.application.jaguar.gui.filedialog) readFileName() (schrodinger.structutils.filter.Filter method) readFilterCriteria() (schrodinger.ui.ligfilter.LigfilterFrame method) readFragmentLibrary() (schrodinger.application.ligprep.ionizer.Ionizer method) readFrameSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) readFromDatabase() (schrodinger.application.matsci.kmcgui.NeighborsTab method) readFromStructure() (schrodinger.application.matsci.amorphous.BaseMoiety method) (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Monomer method) readHDF() (schrodinger.application.matsci.hdfutils.HDFIO method) (schrodinger.application.matsci.hdfutils.HDFProxyPickleIO method) readJobAndUpdateProgress() (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) readJobsFromDatabase() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) readjustHoverLabel() (schrodinger.ui.qt.schart.SChartView method) readMapFile() (schrodinger.application.livedesign.export_map_manager.ExportMap method) readMasks() (in module schrodinger.application.matsci.gsas.GSASIIfiles) ReadMolsFromFile (class in schrodinger.seam.io.chemio) readNewFormat() (schrodinger.pipeline.pipeline.Pipeline method) readNewFormatStage() (schrodinger.pipeline.pipeline.Pipeline method) readNewFormatVariable() (schrodinger.pipeline.pipeline.Pipeline method) readonly_cached_property (class in schrodinger.application.matsci.cache) readOutputFiles() (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask method) ReadPowderInstprm() (in module schrodinger.application.matsci.gsas.GSASIIfiles) readsec() (in module schrodinger.application.jaguar.textparser) readSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) readShFile() (schrodinger.ui.qt.appframework2.af2.App method) readSpecFile() (schrodinger.application.ligprep.ionizer.Ionizer method) readStdItems() (schrodinger.ui.qt.swidgets.SavedItemsManager method) readStructsFromFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) ReadStructuresFromFile (class in schrodinger.seam.io.chemio) readTemplateStructure() (schrodinger.application.matsci.builderwidgets.SketcherBox method) readTrj() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) (schrodinger.application.matsci.equilibrium_md.TrjBase method) readValueList() (schrodinger.pipeline.stages.filtering.SubSetStage method) readyToRun() (schrodinger.pipeline.pipeline.StageJob method) reagent_lib (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) reagent_libChanged (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) reagent_libReplaced (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) ReagentClass (class in schrodinger.application.pathfinder.reaction) ReagentNode (class in schrodinger.application.pathfinder.route) ReagentSource (class in schrodinger.application.pathfinder.synthesis) real (schrodinger.utils.profiling.SystemResourceTimes attribute) REAL_SIZE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) real_to_int() (in module schrodinger.application.desmond.gconfig) RealColumn (class in schrodinger.tasks.ldtasks) realSpaceGridInit() (schrodinger.application.matsci.espresso.utils.MemoryEstimator method) realtime (schrodinger.application.livedesign.upload_utils.CommandType attribute) realUnitCoordinate() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) reassignHets() (schrodinger.application.prime.primefix.FixForPrime method) reassignResNums() (schrodinger.application.prime.primefix.FixForPrime method) rebuild_chunk() (in module schrodinger.application.bb_database.bb_task_utils) recalculate() (schrodinger.application.matsci.kmcgui.NeighborsTab method) recalculate_empirical_pkas() (schrodinger.protein.assignment.ProtAssign method) recalculate_propka_pkas() (schrodinger.protein.assignment.ProtAssign method) recalculateGradient() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) recalculateShape() (schrodinger.ui.qt.network_views.NetworkEdge method) recalculateTableSize() (schrodinger.ui.qt.structtable.StructureReaderDelegate method) RecentCarbonColorSubMenu (class in schrodinger.application.bioluminate.pml_menus) RecentColorSubMenu (class in schrodinger.application.bioluminate.pml_menus) RecentCombo (class in schrodinger.ui.qt.recent_completer) RecentCompleter (class in schrodinger.ui.qt.recent_completer) recentered() (schrodinger.ui.dendrogram.DendrogramNode method) RecentHydrogenColorSubMenu (class in schrodinger.application.bioluminate.pml_menus) RecentObjectColorSubMenu (class in schrodinger.application.bioluminate.pml_menus) RECEPTOR (schrodinger.application.bioluminate.pose_filtering.hdx_io.SubstructureType attribute) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) (schrodinger.application.desmond.constants.REST_COMPONENT attribute) receptor (schrodinger.application.desmond.new_fep_edge_data.FepData property) (schrodinger.application.desmond.struc.CompStruc attribute) RECEPTOR (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) receptor (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) receptor_asl (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) receptor_b_factor (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_backbone_rmsd (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_backbone_rmsf (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_chain_names (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_file (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) receptor_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) receptor_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) receptor_issue_msg (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Output attribute) receptor_issue_msgChanged (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Output attribute) receptor_issue_msgReplaced (schrodinger.application.desmond.feputils.ProteinReliabilityTask.Output attribute) receptor_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) receptor_num_atoms (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_num_heavy_atoms (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_num_residues (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_num_residues_per_chain (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_residue_b_factor (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_residue_sequence (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_residues_interaction_ligand1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_residues_interaction_ligand2 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_sid_rmsd_backbone_lambda0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_sid_rmsd_backbone_lambda1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_sid_rmsd_ligand_lambda0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_sid_rmsd_ligand_lambda1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_sid_rmsf_backbone_lambda0 (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) receptor_sid_rmsf_backbone_lambda1 (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) receptor_st (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) (schrodinger.application.glide.ligand_designer.GridgenTask.Input attribute) receptor_stChanged (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) (schrodinger.application.glide.ligand_designer.GridgenTask.Input attribute) receptor_stReplaced (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) (schrodinger.application.glide.ligand_designer.GridgenTask.Input attribute) receptor_title (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.new_fep_edge_data.FepData property) receptor_total_atom (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_total_heavy (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_total_residues (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptor_total_residues_in_chains (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) receptorChanged (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) receptorHealthChanged (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget attribute) ReceptorLigandClashResolver (class in schrodinger.structutils.clash_resolution) ReceptorLigandGroup (class in schrodinger.application.livedesign.data_classes) ReceptorLigandMap (class in schrodinger.application.livedesign.data_classes) ReceptorLigandPair (class in schrodinger.application.livedesign.data_classes) receptorReplaced (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) receptors (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) ReceptorTable (class in schrodinger.application.glide.sort_utils) reciprocal_bohr_to_angstrom() (in module schrodinger.application.matsci.mecp_mod) RecognitionException recognitionException() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) RecognizerSharedState (class in schrodinger.application.desmond.antlr3.recognizers) recolorPlot() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) recombine_solutions() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) recombineInputLigands() (schrodinger.pipeline.stages.glide.DockingStage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.qikprop.QikPropStage method) (schrodinger.pipeline.stages.semiemp.SemiEmpStage method) RecombineStage (class in schrodinger.pipeline.stages.gencodes) recompute_stereo() (in module schrodinger.utils.cgxutils) record() (schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) record_error() (schrodinger.utils.sea.evalor.Evalor method) record_failures() (in module schrodinger.application.livedesign.io_utils) recordChange() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) RecordDebugEventListener (class in schrodinger.application.desmond.antlr3.debug) recordFailureStatus() (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) RecordingTimer (class in schrodinger.utils.profiling) recover() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) RECOVER_KEY (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) recoverFromMismatchedSet() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) recoverFromMismatchedToken() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) Rectangle (class in schrodinger.application.matsci.nano.tube) rectangular (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute) recur_caller (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute) recurse_include() (in module schrodinger.application.matsci.cgforcefield) recurse_neighbors() (in module schrodinger.protein.pdbname) RECURSIVE (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) recursivelySort() (schrodinger.application.matsci.coarsegrain.Internals method) recv() (schrodinger.active_learning.mq_backend.Backend method) (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) (schrodinger.active_learning.mq_worker.Worker method) RED (schrodinger.ui.qt.standard.colors.NativeColors attribute) redefineLatticeVecs() (schrodinger.application.matsci.nano.tube.NanoTubeSheet static method) redirect (schrodinger.ui.qt.appframework2.debugcore.DebugStderr attribute) (schrodinger.ui.qt.appframework2.debugcore.DebugStdout attribute) redisplayAtoms() (schrodinger.application.matsci.sliceplot.SlicePlot method) redo() (schrodinger.ui.qt.network_visualizer.Graph method) redraw (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) redraw() (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) RedSquareAnnotator (class in schrodinger.ui.qt.structure2d) reduce() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.NucleotideTorsions method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.ResiduesTorsions method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.SmallMoleculeTorsions method) reduce_and_optimize_path() (in module schrodinger.application.desmond.kinetics.utils) reduce_hkl() (in module schrodinger.application.matsci.nano.plane) reduce_settings_for_group() (in module schrodinger.ui.qt.appframework2.af2) reduce_vec() (schrodinger.application.matsci.order_parameter_mod.ReduceVecMixin method) (schrodinger.application.matsci.order_parameter_mod.UniqueSmartsDirector method) reduce_vector() (in module schrodinger.application.matsci.nano.xtal) reduced (schrodinger.application.desmond.struc.FormHashes attribute) (schrodinger.application.desmond.struc.FormMols attribute) reduced_mass_precision (schrodinger.application.jaguar.results.NormalMode attribute) reducedUnitNumpyPos() (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame method) reduceFunction() (schrodinger.application.steps.basesteps.LoggerMixin method) (schrodinger.application.steps.converters.MaeFileWriter method) (schrodinger.application.steps.enumerators.RouteDeduplicator method) (schrodinger.application.steps.enumerators.SmilesTransformPairer method) (schrodinger.application.steps.filters.InMemoryRandomSampleFilter method) (schrodinger.application.steps.filters.InMemoryUniqueSmilesFilter method) (schrodinger.application.steps.licensing.LicenseMixin method) (schrodinger.application.steps.scorers.LigandMLScorer method) (schrodinger.application.steps.scorers.PropertyScorer method) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter method) (schrodinger.stepper.core_steps.DeduplicationStep method) (schrodinger.stepper.core_steps.RandomSampleFilter method) (schrodinger.stepper.sideinputs.ForkStep method) (schrodinger.stepper.stepper.ReduceStep method) (schrodinger.stepper.stepper.UnbatchedChain method) (schrodinger.stepper.stepper.UnbatchedMapStep method) (schrodinger.stepper.stepper.UnbatchedReduceStep method) ReduceStep (class in schrodinger.stepper.stepper) reduceToSingleOperationPerIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) ReduceVecMixin (class in schrodinger.application.matsci.order_parameter_mod) reduceVector() (schrodinger.application.matsci.order_parameter_mod.AcentricDipoleDirector static method) (schrodinger.application.matsci.order_parameter_mod.ReduceVecMixin static method) redundancy_tolerance (schrodinger.protein.assignment.ProtAssign.water_changeable attribute) redundant_server() (schrodinger.application.licensing.flexlm.License method) reEnableColumnResize() (schrodinger.ui.qt.table.DataViewerTable method) ref (schrodinger.application.desmond.cms.Restrain property) (schrodinger.application.desmond.new_fep_edge_data.FepData property) (schrodinger.application.desmond.new_fep_edge_data.FepLambdas attribute) ref_asl (schrodinger.application.desmond.replica_sid_generator.AlchemAsl attribute) ref_file (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) ref_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) ref_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) ref_indices (schrodinger.application.bioluminate.antibody.sequence_indexer.SingleDomainAbSequenceIndexer property) ref_keys (schrodinger.structutils.sitealign.SiteMatchLookup property) ref_ligand_file (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) ref_ligand_fileChanged (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) ref_ligand_fileReplaced (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) ref_mols (schrodinger.application.steps.filters.FepFilter.Settings attribute) ref_molsChanged (schrodinger.application.steps.filters.FepFilter.Settings attribute) ref_molsReplaced (schrodinger.application.steps.filters.FepFilter.Settings attribute) ref_ok (schrodinger.protein.align.ASLResult attribute) ref_seq (schrodinger.protein.align.AbstractStructureAligner.Result attribute) (schrodinger.protein.tasks.sta.STATask.Input attribute) ref_seqChanged (schrodinger.protein.tasks.sta.STATask.Input attribute) ref_seqReplaced (schrodinger.protein.tasks.sta.STATask.Input attribute) ref_solv_asl (schrodinger.application.desmond.replica_sid_generator.AlchemAsl attribute) ref_sse (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute) ref_string (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute) refAtomFromCompAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) REFDModelFxn() (in module schrodinger.application.matsci.gsas.GSASIIpwd) REFDRefine() (in module schrodinger.application.matsci.gsas.GSASIIpwd) REFERENCE_FILTERS (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) reference_struct (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) reference_structChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) reference_structReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) referenceChanged() (schrodinger.ui.two_d_viewer.TwoDViewer method) ReferenceFrame (class in schrodinger.application.matsci.reordergui) ReferenceListWidget (class in schrodinger.application.matsci.reordergui) ReferenceResidueInfo (class in schrodinger.application.bioluminate.antibody.sequence_indexer) refill() (schrodinger.application.jaguar.gui.timing.EntryTimingTable method) refilterJobs() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) refine_hypo_sites() (in module schrodinger.application.phase.packages.hypo_refine.screen_utils) refine_hypo_xvol() (in module schrodinger.application.phase.packages.hypo_refine.screen_utils) refine_rotation() (schrodinger.application.matsci.elasticity.tensors.SquareTensor method) refinePrime() (schrodinger.application.bioluminate.protein.protein.Refiner method) Refiner (class in schrodinger.application.bioluminate.protein.protein) refit() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) refligs_file (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) refligs_fileChanged (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) refligs_fileReplaced (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) REFOLD_POS_KEY (schrodinger.application.matsci.espresso.qeinput.IonControlType attribute) reform_barely_broken_bonds() (in module schrodinger.application.jaguar.autots_rmsd) REFRACTIVE_INDEX (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) REFRACTIVE_INDEX_PROP (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) RefractiveIndex (class in schrodinger.application.matsci.genetic_optimization) (class in schrodinger.application.matsci.permittivity) refresh() (in module schrodinger.application.licensing.licadmin) (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget method) (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) REFRESHING_TEXT (schrodinger.application.livedesign.panel_components.LiveReportSelectionPopup attribute) refreshJobTable() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) refreshLiveReportSelector() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) refreshMarkers (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) refreshPlot() (schrodinger.application.matsci.sliceplot.SlicePlot method) refreshRequested (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelectionPopup attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelector attribute) refreshTable() (schrodinger.project.project.Project method) (schrodinger.ui.two_d_viewer.TwoDViewer method) refreshTables() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) reg_checking() (in module schrodinger.application.desmond.cmj) reg_data (schrodinger.livedesign.biologics.registration.BioPolymer attribute) reg_xcheck() (in module schrodinger.utils.sea.evalor) regenerate_with_box_fix() (in module schrodinger.comparison.struc) regeneratePicture() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant method) Region (class in schrodinger.protein.annotation) region_bounds (schrodinger.application.bioluminate.classify.ProteinClass attribute) region_to_replace (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction attribute) RegionInfo (class in schrodinger.application.bioluminate.pml_menus) register() (schrodinger.application.desmond.image_generator.ImageGenerator method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) register_driver_log() (in module schrodinger.application.matsci.jobutils) register_file() (in module schrodinger.application.jaguar.file_logger) (in module schrodinger.application.jaguar.macro_pka_utils) (schrodinger.application.jaguar.file_logger.FileLogger method) register_float_field() (schrodinger.ui.qt.formlayout.FormDialog method) register_inputs() (in module schrodinger.active_learning.mq_driver) register_job_output() (in module schrodinger.job.jobcontrol) register_md_outfiles() (in module schrodinger.application.matsci.desmondutils) register_required_field() (schrodinger.ui.qt.formlayout.FormDialog method) register_task_output_files() (in module schrodinger.application.livedesign.tasks) registerCmsAndTrjToJob() (schrodinger.application.matsci.permittivity.MdPostTrajectoryAnalysis class method) REGISTERED (schrodinger.application.livedesign.export_models.EntityRegistrationStatus attribute) registerHostSelectorForHostUpdates() (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) registerJob() (schrodinger.ui.qt.appframework2.af2.JobApp method) registerJobcontrolInputs() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.BqQueryStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreStage method) registerLogFilename() (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) registerOutputFile() (schrodinger.stepper.app.StepperApplication class method) registerOutputFolder() (schrodinger.stepper.app.StepperApplication class method) registerSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) RegistrationData (class in schrodinger.livedesign.registration) RegistrationInput (class in schrodinger.application.jobserver_cert_gui_dir.registration_dialogs) RegistrationOptions (class in schrodinger.livedesign.registration) RegistrationPanel (class in schrodinger.application.jobserver_cert_gui_dir.registration_dialogs) registry (schrodinger.application.desmond.test_utils.FileRegistry attribute) regularize_indices() (schrodinger.application.jaguar.hess_guess.Bond static method) (schrodinger.application.jaguar.hess_guess.GenericAngle static method) (schrodinger.application.jaguar.hess_guess.InternalCoordinate static method) (schrodinger.application.jaguar.hess_guess.Wag static method) regularize_value() (schrodinger.application.jaguar.hess_guess.Bond static method) (schrodinger.application.jaguar.hess_guess.GenericAngle static method) (schrodinger.application.jaguar.hess_guess.InternalCoordinate static method) ReInit (class in schrodinger.application.desmond.stage.simulate) REINIT (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) reinit (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) REINIT_GVECS (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) Reinitialize (class in schrodinger.application.bioluminate.pml_menus) REJECT (in module schrodinger.ui.qt.pop_up_widgets) reject() (schrodinger.application.bioluminate.propfilter.ValueSelectionDialog method) (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.mswidgets.ProcessBusyDialog method) (schrodinger.application.matsci.reordergui.ReorderAtomsDialog method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.basewidgets.BaseOptionsDialog method) (schrodinger.ui.qt.formlayout.FormDialog method) (schrodinger.ui.qt.rename_favorite_dialog.RenameFavoriteDialog method) (schrodinger.ui.qt.schart.BinsDialog method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) rejected() (schrodinger.ui.ligfilter.AddDefinitionDialog method) relative (schrodinger.application.matsci.reaction_workflow_utils.MmodEnergyKeys attribute) relative_id (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) relative_idChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) relative_idReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) relative_path() (in module schrodinger.application.jaguar.file_logger) RELATIVE_PERMITTIVITY_INF_PROP (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) RELATIVE_POT_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) RELATIVE_STATIC_PERMITTIVITY_PROP (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) RELATIVE_STATIC_PERMITTIVITY_STORE_PROP (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) RELAXATION_MAP (schrodinger.application.matsci.permittivity.MultiStageMd attribute) RelaxedScanCoordinatesProxyModel (class in schrodinger.application.jaguar.gui.tabs.scan_tab) RelaxFrame (class in schrodinger.application.desmond.gui) RELAY_KEYS (schrodinger.application.desmond.stage.launcher.Multisim attribute) release() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.workflow.Concluder method) released (schrodinger.application.matsci.siteselector.siteselector.SiteRadioButton attribute) released() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) reload (schrodinger.application.jaguar.input.JaguarInput attribute) reload() (schrodinger.application.livedesign.export_map_manager.MappingsComboBox method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBar method) RELOAD_STRUCTURE (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) reloadSpecies() (schrodinger.application.matsci.speciesgui.SpeciesSelector method) reloadTemplateList() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) relocateEtaMarkers() (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) relocateFailedMol() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) relpath() (in module schrodinger.application.desmond.util) remap() (schrodinger.protein.assignment.Interactors method) REMD (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) remd (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) remediate_ct() (in module schrodinger.protein.remediate) remote_command() (in module schrodinger.job.remote_command) remote_file_name (schrodinger.application.livedesign.export_models.AttachmentItem attribute) remote_file_nameChanged (schrodinger.application.livedesign.export_models.AttachmentItem attribute) remote_file_nameReplaced (schrodinger.application.livedesign.export_models.AttachmentItem attribute) remote_modules (schrodinger.tasks.tasks.AbstractComboTask attribute) REMOVE (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.MessageButton attribute) remove (schrodinger.ui.qt.appframework2.maestro_callback.CallbackInfo attribute) remove() (schrodinger.application.bioluminate.sliderchart.SlidableLine method) (schrodinger.application.desmond.cmj.JobOutput method) (schrodinger.graphics3d.common.Group method) (schrodinger.job.queue.LinkedList method) (schrodinger.job.queue.PriorityQueue method) (schrodinger.job.queue.RunningJobs method) (schrodinger.ui.qt.tablewidget.Column method) (schrodinger.ui.qt.tablewidget.Row method) (schrodinger.utils.fileutils.tempfilename method) (schrodinger.utils.preferences.Preferences method) remove_agostic_bonds() (in module schrodinger.application.jaguar.autots_bonding) REMOVE_ALL (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute) remove_all_pka_markers (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) remove_alternate_positions() (in module schrodinger.structutils.build) remove_atom_alternate_positions() (in module schrodinger.structutils.build) remove_atom_property() (in module schrodinger.application.matsci.msutils) remove_atoms_by_asl() (in module schrodinger.application.bioluminate.antibody.assembly) remove_bad_poses() (in module schrodinger.application.glide.utils) remove_basename_ext() (in module schrodinger.application.matsci.genetic_optimization) remove_cert() (in module schrodinger.job.cert) remove_changeable_interactors() (in module schrodinger.protein.assignment) remove_cms_atom_property() (in module schrodinger.application.matsci.msutils) remove_cts_property() (schrodinger.application.desmond.cms.Cms method) remove_disulfide_bond() (in module schrodinger.protein.residue) remove_driver_log_file() (in module schrodinger.application.matsci.jaguar_restart) remove_dummy_atoms() (in module schrodinger.application.matsci.msutils) remove_dupes() (in module schrodinger.structutils.smilesfilter) remove_duplicate_poses() (in module schrodinger.application.glide.utils) remove_entries() (in module schrodinger.project.utils) remove_explicit_hydrogens() (in module schrodinger.livedesign.preprocessor) remove_extra_rotable_atoms() (in module schrodinger.application.desmond.r_group_asl) remove_file() (in module schrodinger.application.desmond.util) remove_formal_charges() (in module schrodinger.application.jaguar.autots_bonding) remove_fragments() (in module schrodinger.livedesign.preprocessor) remove_gibbs_energies() (in module schrodinger.application.jaguar.utils) remove_grow_properties() (in module schrodinger.application.matsci.rxn_channel) remove_H_atoms() (in module schrodinger.comparison.struc) remove_handlers() (in module schrodinger.utils.log) remove_inactive_solvent() (in module schrodinger.application.desmond.gcmc_utils) remove_inactive_solvent_file() (in module schrodinger.application.desmond.gcmc_utils) remove_input_file_paths() (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) remove_invalid_config_options() (in module schrodinger.livedesign.preprocessor) remove_jaguar_file_properties() (in module schrodinger.application.matsci.jaguarworkflows) remove_last_atom_highlight() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) remove_option() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method) remove_output_files() (in module schrodinger.application.phase.packages.hypo_refine.job_utils) (in module schrodinger.application.phase.packages.phase_screen_driver_utils) REMOVE_OVERLAPPED_SOLVENT (schrodinger.application.desmond.constants.BUILD_GEOMETRY attribute) remove_pbc() (in module schrodinger.application.matsci.nano.tube) remove_pbc_props() (in module schrodinger.application.matsci.pbcutils) remove_plugin() (in module schrodinger.application.desmond.config_utils) remove_preference_key() (in module schrodinger.ui.qt.appframework2.settings) remove_project_table_group_info() (in module schrodinger.application.matsci.msutils) REMOVE_PROPERTIES (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) remove_properties() (in module schrodinger.application.matsci.msutils) (in module schrodinger.livedesign.preprocessor) remove_react_atom_props() (in module schrodinger.rdkit.molio) remove_ring_spear_dummies() (in module schrodinger.application.matsci.packmol) remove_spacers() (in module schrodinger.application.matsci.gutils) remove_ssl_ld_library_path() (in module schrodinger.utils.env) remove_stale_props() (in module schrodinger.application.matsci.amorphous) remove_stereo_annotation() (in module schrodinger.structutils.smiles) remove_structure_wam() (in module schrodinger.application.matsci.jobutils) remove_subset_clusters() (schrodinger.application.jaguar.nmr_basis.Basis static method) remove_tag() (schrodinger.utils.sea.sea.Sea method) remove_temp_dir() (in module schrodinger.application.desmond.mplchart) remove_unconn_core_atoms() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) remove_validator() (in module schrodinger.ui.qt.appframework2.validation) remove_vals_below_thresh() (in module schrodinger.application.jaguar.nmr_utils) remove_wiggly_bonds_around_double_bonds() (in module schrodinger.livedesign.preprocessor) remove_zero_order_bonds() (schrodinger.protein.assignment.ProtAssign method) removeAction() (schrodinger.application.bioluminate.actions.factory.Factory method) (schrodinger.ui.qt.swidgets.PersistentMenu method) removeAlignments() (schrodinger.ui.two_d_viewer.CellContextualMenu method) removeAllCallbacks() (schrodinger.ui.qt.input_selector.InputSelector method) removeAllCheckableColumns() (schrodinger.ui.qt.table_helper.CheckableHeaderView method) removeAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAllFeaturesForEntry() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAllGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) removeAllJaguarMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) removeAllJaguarMarkersForEntry() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) removeAllMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) removeAllPkaMarkers() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) removeAllRefCtMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAllRows() (schrodinger.ui.qt.appframework2.debugwidgets.BaseTable method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) removeAllTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAllXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAminoAcids() (in module schrodinger.application.desmond.automatic_analysis_generator) removeAnchors() (schrodinger.protein.alignment.BaseAlignment method) removeAndRenumber() (schrodinger.application.matsci.nano.particle.Nanoparticle method) removeAtom() (schrodinger.ui.qt.structure2d.CircleAnnotator method) removeBadOptions() (in module schrodinger.application.bioluminate.workspacelabeler) removeButton() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) removeCallback() (schrodinger.ui.qt.input_selector.InputSelector method) removeChain() (schrodinger.protein.sequence.CombinedChainProteinSequence method) removeChains() (schrodinger.protein.sequence.CombinedChainProteinSequence method) removeClosestMLine() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) removeColor() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) removeColorsForMissingPoints() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) removeColumn() (schrodinger.application.desmond.gui.TableModel method) (schrodinger.ui.qt.table.StructureDataViewerModel method) removeColumns() (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) removeCom() (schrodinger.application.matsci.permittivity.MdStageModifier method) removeCoordinate() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) removeCriterion (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion attribute) removeCriterion() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) removeCurrentPage() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) removed (schrodinger.models.diffy.DictDiff attribute) (schrodinger.models.diffy.ListDiff attribute) (schrodinger.models.diffy.SetDiff attribute) removeDisulfideBond() (schrodinger.protein.alignment.ProteinAlignment method) RemovedStageError removeDummyFields() (schrodinger.application.matsci.permittivity.MdStageModifier method) removeDuplicates() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) removeEdge() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) removeEdges() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) removeElements() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) removeFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeFFProperties() (schrodinger.application.matsci.builderwidgets.ItemRow method) removeFinishedPolymer() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) removeFlag() (schrodinger.application.matsci.jobutils.MultijobDriver method) removeGapsFromChainStartsAndEnds() (schrodinger.protein.sequence.CombinedChainProteinSequence method) removeHighlights() (schrodinger.application.matsci.kmcgui.MinMaxNeighborWidgets method) (schrodinger.application.matsci.kmcgui.NeighborsTab method) RemoveHydrogens (class in schrodinger.application.bioluminate.pml_menus) removeHydrogens() (schrodinger.application.matsci.nano.tube.NanoTube method) removeIgnoredClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) removeIgnorePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) removeIncomingProperties() (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep method) removeInternalsWithNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) removeIsFromTable() (schrodinger.ui.two_d_viewer.TwoDTableModel method) removeItem() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.swidgets.SListWidget method) removeItemByText() (schrodinger.ui.qt.swidgets.SComboBox method) (schrodinger.ui.qt.swidgets.SListWidget method) removeJaguarMarker (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute) removeJaguarMarker() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) removeJaguarMarkerForAtoms() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) removeJaguarMarkerForRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel method) removeKey() (schrodinger.utils.ligfilter.Definition method) removeLocalFiles() (schrodinger.application.livedesign.export_models.FFCExportSpec method) removeMapping() (schrodinger.ui.qt.datamapper.TrackingDataWidgetMapper method) removeMarker() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) RemoveMetalBonds (class in schrodinger.application.matsci.buildcomplex2d) removeMissingPoints() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) removeNode() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) removeNodeFromGroup() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) removeNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) removeOneRow() (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) removePABJaguarMarker() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) removeParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) RemovePC (class in schrodinger.application.bioluminate.pml_menus) removePerSubjobUnwantedKeywords() (schrodinger.application.matsci.jobutils.MultijobDriver method) removePkaMarkers() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) removeProcessors() (schrodinger.job.queue.ResourceHost method) removeProperties() (schrodinger.application.matsci.genetic_optimization.StructureGenome method) removeRefCtMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeReference() (schrodinger.ui.two_d_viewer.TwoDTableModel method) removeRow() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.table.StructureDataViewerModel method) removeRows() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) removeRowsByIndices() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) removeRowsByRowNumbers() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) removeSelectedEntriesItem() (schrodinger.application.jaguar.gui.input_tab_widgets.UseFromCombo method) removeSelectedFromTable() (schrodinger.ui.two_d_viewer.TwoDViewer method) removeSelectedItems() (schrodinger.ui.qt.swidgets.SListWidget method) removeSelectedParams() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) removeSelectedRows() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) removeSeq() (schrodinger.protein.alignment.BaseAlignment method) removeSeqs() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.alignment.CombinedChainProteinAlignment method) removeSeqsFromAlnSet() (schrodinger.protein.alignment.BaseAlignment method) RemovesInitialGCMCSolvent (class in schrodinger.application.desmond.stage.simulate) removeSliders() (schrodinger.application.matsci.plotwidgets.SliderchartVLPlot method) removeSpheres() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) removeStaleProps() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) removeStartingJobs() (schrodinger.application.matsci.permittivity.WorkflowParser method) removeStruct() (schrodinger.ui.qt.table.ViewerModel method) removeStructurelessResidues() (schrodinger.protein.sequence.ProteinSequence method) removeSubalignment() (schrodinger.protein.alignment.BaseAlignment method) removeSubTabMarker() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) removeSubview() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) removeTask() (schrodinger.tasks.taskmanager.TaskManager method) removeTerminalGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) removeThumb() (schrodinger.application.matsci.mswidgets.MultiSlider method) removeTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) removeTrajProp() (schrodinger.application.matsci.equilibrium_md.CmsModel method) (schrodinger.application.matsci.equilibrium_md.MaeModel method) removeTree() (schrodinger.ui.qt.dendrogram.DendrogramSyncer method) removeUnwantedKeywords() (schrodinger.application.matsci.jobutils.MultijobDriver method) RemoveWaters (class in schrodinger.application.bioluminate.pml_menus) removeXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeXvolMarkersWithIDs() (schrodinger.application.phase.phase_markers.PhaseMarkers method) Rename (class in schrodinger.application.bioluminate.pml_menus) rename() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.project.surface.ProjectSurface method) (schrodinger.surface.Surface method) rename_chain_in_asl() (in module schrodinger.application.bioluminate.antibody.assembly) rename_chains_in_bonds() (in module schrodinger.application.bioluminate.antibody.assembly) rename_chains_in_structure() (in module schrodinger.application.bioluminate.antibody.assembly) rename_favorite() (in module schrodinger.ui.qt.rename_favorite_dialog) renameAlnSet() (schrodinger.protein.alignment.BaseAlignment method) renameColumn() (schrodinger.ui.qt.swidgets.STableWidget method) RenameFavoriteDialog (class in schrodinger.ui.qt.rename_favorite_dialog) renderSurface() (schrodinger.application.bioluminate.pml_menus.SurfaceRender method) renderToFile() (schrodinger.application.pathfinder.render.RouteRenderer method) renumber_ab_residues (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) renumber_ab_residuesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) renumber_ab_residuesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) renumber_conformer() (in module schrodinger.structutils.rmsd) renumber_residues() (in module schrodinger.protein.pdbname) renumber_st_chain() (in module schrodinger.application.bioluminate.classify) renumber_tcr_residues (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) renumber_tcr_residuesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) renumber_tcr_residuesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) renumber_tcr_structure() (in module schrodinger.application.bioluminate.tcr.annotate) renumberAtomLists() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) renumberByMolecule() (schrodinger.application.prime.primefix.FixForPrime method) renumberBySymmetry() (schrodinger.structutils.rmsd.ConformerRmsd method) renumberResGetM2PMap() (schrodinger.application.matsci.amorphous.PolymerFragments method) renumberResidues() (schrodinger.protein.sequence.ProteinSequence method) renumberWorkingStructures() (schrodinger.application.matsci.buildcomplex.ComplexConformerRmsd method) (schrodinger.structutils.rmsd.ConformerRmsd method) reord_st (schrodinger.comparison.atom_mapper.MapScore attribute) REORDER (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) reorder_atoms() (in module schrodinger.structutils.build) reorder_cluster_atoms() (in module schrodinger.comparison.struc) reorder_protein_atoms_by_sequence() (in module schrodinger.structutils.build) reorder_solute() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) reorder_structures() (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper method) (schrodinger.comparison.atom_mapper.BaseAtomMapper method) reorder_water() (in module schrodinger.structutils.build) ReorderAtomFrame (class in schrodinger.application.matsci.reordergui) ReorderAtomPanel (class in schrodinger.application.matsci.reordergui) ReorderAtomsDialog (class in schrodinger.application.matsci.reordergui) reorderSequences() (schrodinger.protein.alignment.BaseAlignment method) rep (schrodinger.application.dendrogram.core_class.RingSysInfo attribute) repair_box_vector() (in module schrodinger.application.desmond.repair_cms) repeatingMethod() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) repeats (schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup attribute) REPLACE (schrodinger.application.livedesign.export_models.InvalidGEIdHandlingPolicy attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.tasks.jobtasks.IncorporationMode attribute) replace() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) replace_arg_value() (in module schrodinger.pipeline.stages.ligprep) REPLACE_ATOM_SD_KEY (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF attribute) replace_base_chains() (in module schrodinger.livedesign.biologics.registration) replace_calcd_pKas_with_expts() (schrodinger.application.jaguar.macro_pka_utils.PhPopulations method) replace_coords_with_zmat() (in module schrodinger.application.matsci.zmutils) replace_domain() (in module schrodinger.application.bioluminate.antibody.assembly) REPLACE_ENTRIES (schrodinger.application.matsci.appbase.ProcessPtStructuresApp attribute) REPLACE_FIT (schrodinger.job.launchparams.ProjectDisposition attribute) replace_generic_h_queries() (in module schrodinger.rdkit.substructure) REPLACE_METHOD_NAME (schrodinger.models.parameters.BaseMutableParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.SetParam attribute) replace_reactant_file_name() (in module schrodinger.application.combinatorial_screen.driver_utils) replace_reactant_file_names() (in module schrodinger.application.combinatorial_screen.driver_utils) replace_rgroups_with_dummy_atoms() (in module schrodinger.livedesign.rgroup_decomposition) replace_rxnwf_file_suffix() (in module schrodinger.application.matsci.reaction_workflow_utils) replace_slot() (in module schrodinger.application.bioluminate.actions.factory) replaceChildren() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) Replaced (schrodinger.models.parameters.SignalType attribute) ReplaceOp (class in schrodinger.application.desmond.antlr3.streams) replaceResiduesWithGaps() (schrodinger.protein.alignment.BaseAlignment method) replaceRows() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) replaceSubalignment() (schrodinger.protein.alignment.BaseAlignment method) replaceValue() (schrodinger.application.matsci.jobutils.MultijobDriver method) replica_container (class in schrodinger.application.desmond.replica_dE) REPLICA_DELIM (schrodinger.application.matsci.permittivity.WorkflowParser attribute) replica_energy (class in schrodinger.application.desmond.replica_dE) replica_name() (in module schrodinger.application.desmond.report_helper) REPLICA_TAG (schrodinger.application.matsci.permittivity.StepBase attribute) ReplicaExchange (class in schrodinger.application.desmond.stage.simulate) replicas_monitor (class in schrodinger.application.desmond.replica_dE) replicate() (in module schrodinger.comparison.struc) (schrodinger.tasks.tasks.AbstractTask method) ReplicateMakerMixin (class in schrodinger.application.matsci.jwsteps) ReplicateStructure (class in schrodinger.application.desmond.stage.prepare.structure) replot() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) (schrodinger.application.matsci.plotwidgets.SideHistogram method) (schrodinger.application.matsci.plotwidgets.SliderchartVLFitStdPlot method) replotChart() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) replySent (schrodinger.tasks.taskszmq.ZmqServer attribute) repopulateSearchAlongCombo() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) Report (class in schrodinger.protein.analysis) report() (in module schrodinger.protein.assignment) (schrodinger.active_learning.al_report.ALPilotReportMaker method) (schrodinger.active_learning.al_report.ALScreenReportMaker method) (schrodinger.analysis.enrichment.calculator.Calculator method) (schrodinger.application.desmond.fep_edge_report_maker.ABFEPReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.PRMEdgeReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker method) (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.protein.analysis.Report.data_set method) (schrodinger.stepper.sideinputs.ForkStep method) (schrodinger.stepper.stepper.UnbatchedChain method) Report.backbone_dihedral_data_set (class in schrodinger.protein.analysis) Report.Bfactor_data_set (class in schrodinger.protein.analysis) Report.bond_angle_data_set (class in schrodinger.protein.analysis) Report.bond_length_data_set (class in schrodinger.protein.analysis) Report.chirality_data_set (class in schrodinger.protein.analysis) Report.data_set (class in schrodinger.protein.analysis) Report.data_set.data_point (class in schrodinger.protein.analysis) Report.gamma_Bfactor_data_set (class in schrodinger.protein.analysis) Report.Gfactor_summary_data_set (class in schrodinger.protein.analysis) Report.improper_torsion_data_set (class in schrodinger.protein.analysis) Report.local_atom (class in schrodinger.protein.analysis) Report.local_protein (class in schrodinger.protein.analysis) Report.local_residue (class in schrodinger.protein.analysis) Report.missing_atoms_data_set (class in schrodinger.protein.analysis) Report.peptide_planarity_data_set (class in schrodinger.protein.analysis) Report.primex_steric_clash_data_set (class in schrodinger.protein.analysis) Report.sidechain_dihedral_data_set (class in schrodinger.protein.analysis) Report.sidechain_planarity_data_set (class in schrodinger.protein.analysis) Report.steric_clash_data_set (class in schrodinger.protein.analysis) Report2D (class in schrodinger.application.report2d) report_add_logo() (in module schrodinger.application.desmond.rl_helper) report_add_ms_logo() (in module schrodinger.application.desmond.rl_helper) report_data_points() (schrodinger.protein.analysis.Report.data_set method) REPORT_FILE_NAME (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) report_level (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) report_levelChanged (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) report_levelReplaced (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) report_strain_energy (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) report_strain_energyChanged (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) report_strain_energyReplaced (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) report_t() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) report_total_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) report_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) ReportData (class in schrodinger.application.bioluminate.antibody.antibody_homology_report_writer) Reporter (class in schrodinger.application.desmond.stage.analysis) reportError() (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) reportFinalResults() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) ReportFrame (class in schrodinger.application.bioluminate.protein_report_widget) ReportInfo (class in schrodinger.application.matsci.reportutils) reportLigandsDetails() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) ReportOutputsDialog (class in schrodinger.application.matsci.reportutils) reportParameters() (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.stage.Stage method) reportProteinDetails() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportReplicaExchanges() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportReplicaPairEnergies() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportSimulationDetails() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportValidation() (schrodinger.ui.qt.appframework2.validation.ValidationMixin method) ReportWriter (class in schrodinger.application.bioluminate.antibody.antibody_homology_report_writer) REPRESENTATIVE (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) representative_conformers (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) representative_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) representativeConformers() (schrodinger.application.matsci.reaction_workflow_utils.RepresentativeConformersMixin method) RepresentativeConformersMixin (class in schrodinger.application.matsci.reaction_workflow_utils) REPULSION (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) request() (schrodinger.tasks.taskszmq.ZmqClient method) request_ff_preference_widget() (in module schrodinger.ui.qt.forcefield.ffglobalpreferencewidget) request_schema (schrodinger.seam.viz.watcher.EndpointInfo attribute) requestCpus() (schrodinger.pipeline.pipeline.Pipeline method) requested_descriptors (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Input attribute) requested_descriptorsChanged (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Input attribute) requested_descriptorsReplaced (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Input attribute) requested_status (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) requested_statusChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) requested_statusReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) RequestedAction (class in schrodinger.ui.qt.config_dialog) RequestedStatus (class in schrodinger.application.job_monitor.job_monitor_models) requestInterruption() (schrodinger.tasks.tasks.AbstractTask method) requestReceived (schrodinger.tasks.taskszmq.ZmqServer attribute) requestRestoreSelection() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) requests_retry_session() (in module schrodinger.protein.getpdb) RequestType (class in schrodinger.application.livedesign.ld_maestro_actions_constants) requeue() (schrodinger.application.desmond.cmj.Job method) require_application() (in module schrodinger.utils.qapplication) required_basis() (in module schrodinger.application.jaguar.jaguar_keyword_utils) required_valid() (schrodinger.ui.qt.formlayout.FormDialog method) requiredProduct() (schrodinger.pipeline.stage.Stage method) requiredProductRuntime() (schrodinger.pipeline.stage.Stage method) REQUIRES (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) requires_3d (schrodinger.application.livedesign.data_classes.LDData property) REQUIRES_CMS_INPUT (schrodinger.application.matsci.jwsteps.BaseDesmondStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) requires_ffc (schrodinger.application.livedesign.data_classes.LDData property) requires_local_execution() (in module schrodinger.seam.transforms.resources) requires_structure_getter() (in module schrodinger.maestro_utils.maestro_sync) REQUIRES_TRAJECTORY_INPUT (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) RequireValue (class in schrodinger.application.phase.packages.phase_utils) RereadImageData() (in module schrodinger.application.matsci.gsas.GSASIIfiles) res (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) res_asl() (schrodinger.application.bioluminate.mutation.Mutation method) res_can_be_capped() (in module schrodinger.protein.captermini) RES_CODE (schrodinger.application.bioluminate.pose_filtering.hdx_calc.AnalysisColumns attribute) RES_FILE_REGEX (schrodinger.application.bioluminate.nucleic.mutator.NucleobaseMutator attribute) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) res_id (schrodinger.application.bioluminate.mutation.Mutation property) res_id_set_by_domain_type (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueZone property) res_ids (schrodinger.application.bioluminate.pose_filtering.residue_filter.FilterCriteria attribute) res_ids_h (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueZone attribute) res_ids_l (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueZone attribute) res_list (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) res_listChanged (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) res_listReplaced (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) RES_MATCH_BONUS (schrodinger.protein.align.AbstractNWPairwiseAligner attribute) RES_MISMATCH_PENALTY (schrodinger.protein.align.AbstractNWPairwiseAligner attribute) res_name (schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo attribute) res_num (schrodinger.application.bioluminate.mutation.Mutation attribute) RES_NUM (schrodinger.application.bioluminate.pose_filtering.hdx_calc.AnalysisColumns attribute) res_pair (schrodinger.protein.residue.DisulfideBond property) RES_PROPENSITY_ANNOTATIONS (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) res_type (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueZone attribute) RES_TYPES (schrodinger.application.bioluminate.patch_utils.patch_finder.Patch attribute) resBackbone() (schrodinger.application.matsci.amorphous.PolymerFragments method) rescale() (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) rescale_ff() (in module schrodinger.application.desmond.remd) rescale_ff_solute_tempering() (in module schrodinger.application.desmond.remd) resCapped() (schrodinger.protein.captermini.CapTermini method) rescode (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) RescodeAligner (class in schrodinger.protein.align) RescoreNode (class in schrodinger.application.phase.packages.shape_screen_al_node) ResData (class in schrodinger.application.desmond.fep_edge_data) (class in schrodinger.application.desmond.new_fep_edge_data) (in module schrodinger.application.bioluminate.patch_utils.patch_finder) reservoir_sampling() (in module schrodinger.active_learning.al_utils) ReservoirSampler (class in schrodinger.math.sampling) RESET (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.MessageButton attribute) Reset (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.StdBtn attribute) reset() (in module schrodinger.ui.qt.appframework2.appmethods) (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.antibody.search_results_table.TableView method) (schrodinger.application.bioluminate.pml_menus.PresetAction method) (schrodinger.application.bioluminate.sliderchart.SliderPlot method) (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) (schrodinger.application.desmond.cmj.Engine method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.InputGroup method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.desmond.util.Counter method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.jaguar.gui.timing.TimingResults method) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword method) (schrodinger.application.livedesign.panel_components.BaseSelectionPopUp method) (schrodinger.application.livedesign.panel_components.ExportTableModel method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) (schrodinger.application.matsci.appbase.ProcessPtStructuresApp method) (schrodinger.application.matsci.appbase.StructureLoadButton method) (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox method) (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) (schrodinger.application.matsci.builderwidgets.TemplateSelector method) (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) (schrodinger.application.matsci.chargegui.ChargeDialog method) (schrodinger.application.matsci.chargegui.ChargePropertySelector method) (schrodinger.application.matsci.chargegui.ForceFieldDialog method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) (schrodinger.application.matsci.density_analysis_widget.CustomToolbar method) (schrodinger.application.matsci.density_analysis_widget.DensityTab method) (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame method) (schrodinger.application.matsci.deswidgets.AdvancedMDOptions method) (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) (schrodinger.application.matsci.jagwidgets.BasisSetSelector method) (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) (schrodinger.application.matsci.jagwidgets.EmbeddedSolventWidget method) (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.TheorySelector method) (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) (schrodinger.application.matsci.kmcgui.DatabaseInfo method) (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) (schrodinger.application.matsci.kmcgui.MinMaxNeighborWidgets method) (schrodinger.application.matsci.kmcgui.NeighborsTab method) (schrodinger.application.matsci.kmcgui.PropertyCombo method) (schrodinger.application.matsci.kmcgui.Tab method) (schrodinger.application.matsci.mswidgets.ConvenientSelectorWithPopUp method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.mswidgets.LipidImporter method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.application.matsci.mswidgets.MultiStageArea method) (schrodinger.application.matsci.mswidgets.SaveDesmondFilesWidget method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.mswidgets.Stepper method) (schrodinger.application.matsci.mswidgets.StructureLoader method) (schrodinger.application.matsci.mswidgets.SystemInformationFrame method) (schrodinger.application.matsci.plotwidgets.SideHistogram method) (schrodinger.application.matsci.plotwidgets.SliderchartVLFitStdPlot method) (schrodinger.application.matsci.qualityslider.QualitySlider method) (schrodinger.application.matsci.rdpattern_gui.SMARTSFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ColorPairFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Jaguar method) (schrodinger.application.matsci.reaction_workflow_gui_utils.QMPreOptimization method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.UniformSequence method) (schrodinger.application.matsci.reaction_workflow_gui_utils.WorkspaceSuperpositionFrame method) (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.application.matsci.reordergui.StructurePic method) (schrodinger.application.matsci.sliceplot.SlicePlot method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) (schrodinger.application.phase.featureselector.FeatureSelector method) (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) (schrodinger.application.prepwizard2.tasks.PreprocessInput method) (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.protein.nonstandard_residues.ResidueDatabase method) (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.ui.picking.PickAtomsToggle method) (schrodinger.ui.qt.appframework2.debugwidgets.BaseTable method) (schrodinger.ui.qt.appframework2.maestro_callback.MonitoredCallbacks method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.atomselector.AtomSelector method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.StringCriterion method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) (schrodinger.ui.qt.schart.SChart method) (schrodinger.ui.qt.swidgets.ActionComboBox method) (schrodinger.ui.qt.swidgets.ColorWidget method) (schrodinger.ui.qt.swidgets.SCheckBox method) (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) (schrodinger.ui.qt.swidgets.SCheckBoxWithSubWidget method) (schrodinger.ui.qt.swidgets.SComboBox method) (schrodinger.ui.qt.swidgets.SDialog method) (schrodinger.ui.qt.swidgets.SDoubleSpinBox method) (schrodinger.ui.qt.swidgets.SGroupBox method) (schrodinger.ui.qt.swidgets.SLabel method) (schrodinger.ui.qt.swidgets.SLabeledComboBox method) (schrodinger.ui.qt.swidgets.SLabeledDoubleSpinBox method) (schrodinger.ui.qt.swidgets.SLabeledEdit method) (schrodinger.ui.qt.swidgets.SLabeledRadioButtonGroup method) (schrodinger.ui.qt.swidgets.SLabeledSlider method) (schrodinger.ui.qt.swidgets.SLabeledSpinBox method) (schrodinger.ui.qt.swidgets.SLineEdit method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) (schrodinger.ui.qt.swidgets.SRadioButton method) (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) (schrodinger.ui.qt.swidgets.SRadioButtonWithSubWidget method) (schrodinger.ui.qt.swidgets.SSpinBox method) (schrodinger.ui.qt.swidgets.STableWidget method) (schrodinger.ui.qt.swidgets.STabWidget method) (schrodinger.ui.qt.swidgets.SValidIndicator method) (schrodinger.ui.qt.table.ViewerModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method)

reset_clicked (schrodinger.ui.qt.appframework2.af2.StatusBar attribute) reset_colors() (in module schrodinger.application.combiglide.connection_storage) reset_tag() (schrodinger.utils.sea.sea.Sea method) reset_tddft_excitation_energies() (in module schrodinger.application.jaguar.textparser) resetAcceptedRow() (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) resetAdvancedWidgets() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) resetAll() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) resetAllFeatures() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) resetAnnotation() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) resetAtomGroupTable() (schrodinger.application.desmond.gui.AtomGroupFrame method) resetAxisLabels() (schrodinger.ui.qt.schart.SChart method) resetBaseName() (schrodinger.tasks.taskmanager.TaskManager method) resetBasisForRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) resetBasisOfSelectedRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) resetBatch() (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) ResetButton (class in schrodinger.ui.qt.swidgets) resetCallNumber() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) resetData() (schrodinger.ui.ligfilter.CriteriaListModel method) resetDefinitions() (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.SaveDefinitionsDialog method) resetEditor() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) resetEnsClass() (schrodinger.application.desmond.gui.EnsembleTab method) resetFiniteDiffCall() (schrodinger.application.matsci.mecp_mod.BFGS method) resetfp() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) resetFragDihedralPool() (schrodinger.application.matsci.amorphous.PolymerFragment method) resetFrame() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) resetFromModel() (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.MdcMiscTab method) (schrodinger.application.desmond.gui.RestraintsTab method) resetGroup() (schrodinger.utils.preferences.Preferences method) resetJMSWF() (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) resetKey() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.xtb.input.XTBInput method) resetLabelOptions() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) resetLimitRange() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) resetMap() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) resetMappedParams() (schrodinger.models.mappers.MapperMixin method) (schrodinger.models.mappers.TargetParamMapper method) resetMaxStepSize() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) resetMeasureBtn() (schrodinger.application.matsci.density_analysis_widget.CustomToolbar method) resetModel() (schrodinger.application.desmond.gui.GuiApp method) resetNestingLevel() (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) resetPAB() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) resetPanBtn() (schrodinger.application.matsci.density_analysis_widget.CustomToolbar method) resetPanel() (schrodinger.application.matsci.appbase.BaseAnalysisGui method) (schrodinger.application.matsci.appbase.ViewerGuiMixin method) (schrodinger.application.matsci.deswidgets.TrajAnalysisGuiMixin method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) resetPanZoom() (schrodinger.ui.qt.navtoolbar.NavToolbar method) resetParentProperties() (schrodinger.application.matsci.genetic_optimization.StructureGenome method) resetPosResTable() (schrodinger.application.desmond.gui.RestraintsTab method) resetRange() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) resetSelected() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) resetSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) resetSlots() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) resetStats() (schrodinger.application.matsci.kmcgui.NeighborsTab method) resetStructure() (schrodinger.application.jaguar.input.JaguarInput method) resetTable() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) resetTheoryForRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) resetTheoryOfSelectedRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) resetToDB() (schrodinger.application.matsci.kmcgui.NeighborsTab method) resetView() (schrodinger.ui.qt.schart.SChart method) resetWidgets() (schrodinger.application.livedesign.panel_components.BaseSearchTreeWidgetHelper method) resetZoomBtn() (schrodinger.application.matsci.density_analysis_widget.CustomToolbar method) reshowPkaMarkers() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) RESIDENCE_TIME_CUTOFF (schrodinger.application.desmond.kinetics.enhanced_sampling.MtdOption attribute) residence_time_cutoff (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) ResidualPotential (class in schrodinger.application.bioluminate.escomp) Residue (class in schrodinger.application.bioluminate.protein_interaction.utils) (class in schrodinger.protein.residue) (class in schrodinger.structure) residue (schrodinger.application.bioluminate.classify.NumberedResidue attribute) RESIDUE (schrodinger.application.matsci.automated_cg_mapping.MoleculeData attribute) Residue (schrodinger.protein.properties.PropertySource attribute) (schrodinger.protein.properties.SequenceProperty attribute) residue (schrodinger.protein.sequence.StructureSequence property) (schrodinger.structure._Chain property) (schrodinger.structure._Molecule property) (schrodinger.structure.Structure property) (schrodinger.structure.TextualStructure property) Residue (schrodinger.ui.picking.PickResidueColumns attribute) residue() (schrodinger.application.matsci.automated_cg_mapping.MappingMethod static method) residue_asl (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) residue_aslChanged (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) residue_aslReplaced (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) RESIDUE_CALCULATIONS (schrodinger.application.bioluminate.protein.protein.PropertyCalculator attribute) RESIDUE_CHARGE (class in schrodinger.protein.residue) residue_charge (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) residue_file (schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams attribute) residue_hydrophobicity (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) residue_indices (schrodinger.application.bioluminate.protein.protein.Consensus property) residue_interaction_counts (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) residue_interaction_countsChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) residue_interaction_countsReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) residue_is_nonpolar() (in module schrodinger.application.bioluminate.protein.protein) residue_is_polar() (in module schrodinger.application.bioluminate.protein.protein) residue_names (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) residue_position (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) RESIDUE_SCANNING (schrodinger.infra.structure.WorkflowType attribute) residue_to_label() (in module schrodinger.protein.assignment) residue_type (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) ResidueChainKey (class in schrodinger.protein.residue) ResidueData (class in schrodinger.application.bioluminate.reactive_residues) (class in schrodinger.application.matsci.automated_cg_mapping) ResidueDatabase (class in schrodinger.protein.nonstandard_residues) ResidueFilter (class in schrodinger.application.bioluminate.pose_filtering.residue_filter) ResidueGroups (class in schrodinger.ui.residueselector) residueIsInZone() (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueZone method) ResidueKey (class in schrodinger.protein.residue) ResidueRow (class in schrodinger.ui.picking) residues (schrodinger.application.bioluminate.protein.protein.Consensus property) residues() (schrodinger.protein.sequence.AbstractSequence method) residues_around_ligand (schrodinger.application.desmond.new_fep_edge_data.FepData property) residues_around_ligand_both_lambda_states (schrodinger.application.desmond.new_fep_edge_data.FepData property) residues_centroid_changed (schrodinger.ui.picking.PickResiduesChangedMixin attribute) residues_changed (schrodinger.ui.picking.PickResiduesChangedMixin attribute) residuesAboutToBeRemoved (schrodinger.protein.alignment.AlignmentSignals attribute) residuesAdded (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractSequence attribute) residuesChanged (schrodinger.protein.nonstandard_residues.ResidueDatabase attribute) (schrodinger.protein.sequence.AbstractSequence attribute) residueSelectionChanged() (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) ResidueSimilarity (class in schrodinger.protein.alignment) ResiduesModel (class in schrodinger.ui.qt.select_residues_dialog) residuesModelUpdated() (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) ResidueSpeciesFinder (class in schrodinger.application.matsci.species) residuesRemoved (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractSequence attribute) ResiduesTorsions (class in schrodinger.trajectory.trajectory_gui_dir.custom_analyzers) ResidueType (class in schrodinger.protein.residue) ResidueVectorizer (in module schrodinger.application.bioluminate.peptide_sar.encode) ResInfo (class in schrodinger.application.bioluminate.anarci.anarci_adapter) (class in schrodinger.application.bioluminate.patch_utils.patch_finder) ResizablePictureLabel (class in schrodinger.ui.qt.swidgets) ResizableRDMolImageLabel (class in schrodinger.ui.qt.rdmol_views) Resize() (in module schrodinger.analysis.visanalysis.volumedatautils) resize() (schrodinger.infra.mmbitset.Bitset method) (schrodinger.ui.qt.table.ViewerModel method) resizeColumns() (schrodinger.ui.qt.table.ViewerModel method) resizeColumnsToContents() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) resizeDialog() (schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog method) resizeEvent() (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) (schrodinger.ui.qt.rdmol_views.ResizableRDMolImageLabel method) (schrodinger.ui.qt.structtable.ViewerTable method) (schrodinger.ui.qt.structure2d.structure_view method) (schrodinger.ui.qt.swidgets.ElidedLabel method) (schrodinger.ui.qt.swidgets.SLineEdit method) (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) (schrodinger.ui.two_d_viewer.TwoDTableView method) resizeHeaders() (schrodinger.ui.qt.swidgets.STableWidget method) resizeRows() (schrodinger.ui.qt.table.ViewerModel method) resizeRowsToContents() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) resizeToContents() (schrodinger.ui.qt.tablewidget.Column method) (schrodinger.ui.qt.tablewidget.Row method) resKey() (schrodinger.application.prime.residue_interaction.InteractionReader static method) resname (schrodinger.application.bioluminate.protein_interaction.utils.Residue attribute) RESNAME (schrodinger.application.matsci.kmc.AtomsTable attribute) resname (schrodinger.ui.qt.rama.BackboneDihedral attribute) RESNR (schrodinger.application.matsci.kmc.AtomsTable attribute) resnum (schrodinger.application.bioluminate.protein_interaction.utils.Residue attribute) (schrodinger.application.matsci.packmol.PDBdata attribute) (schrodinger.application.qsite.input.Cut property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) (schrodinger.protein.residue.ResidueChainKey attribute) (schrodinger.protein.residue.ResidueKey attribute) (schrodinger.structure.Residue property) (schrodinger.structure.StructureAtom property) Resnum (schrodinger.ui.picking.PickResidueColumns attribute) resnum (schrodinger.ui.qt.rama.BackboneDihedral attribute) resnum_with_inscode (schrodinger.application.bioluminate.mutation.Mutation property) Resolution (class in schrodinger.trajectory.trajectory_gui_dir.export_movie) RESOLUTION_DEFAULT (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager attribute) RESOLVE_AMBIGUOUS_TAUTOMERS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) resolve_atomsel() (in module schrodinger.application.desmond.enhsamp) (schrodinger.application.desmond.enhsamp.FcnCall method) (schrodinger.application.desmond.enhsamp.Node method) resolve_conflict() (in module schrodinger.comparison.struc) resolve_to_abspath() (in module schrodinger.job.launchapi) resolveClashes() (schrodinger.structutils.clash_resolution.ReceptorLigandClashResolver method) resolveCoordsConflict() (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) resolvePaths() (schrodinger.application.glide.glide.GlideJob method) resolveTriangularGroup() (schrodinger.structutils.assignbondorders.AssignBondOrders method) RESONANCE (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) RESOURCE (schrodinger.application.matsci.jwsteps.BaseDesmondStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) (schrodinger.application.matsci.permittivity.Step attribute) resource_summary() (in module schrodinger.application.licensing.licadmin) ResourceError ResourceHost (class in schrodinger.job.queue) resources() (in module schrodinger.application.licensing.licadmin) resources_from_list() (in module schrodinger.application.licensing.licadmin) resources_from_path() (in module schrodinger.application.licensing.licadmin) ResourceType (class in schrodinger.tasks.tasks) respaBondChanged() (schrodinger.application.desmond.gui.IntegrationTab method) ResPatchData (class in schrodinger.application.bioluminate.patch_utils.patch_finder) respondToChangeSelection() (schrodinger.ui.qt.dendrogram.DendrogramSyncer method) respondToUpdatePositions() (schrodinger.ui.qt.dendrogram.DendrogramSyncer method) response_type (schrodinger.seam.viz.watcher.EndpointInfo attribute) ResponseType (class in schrodinger.seam.viz.watcher) rest_asl (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) REST_COMPONENT (class in schrodinger.application.desmond.constants) rest_enabled (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) REST_PROPERTIES (class in schrodinger.application.desmond.constants) REST_REGION_RULE (class in schrodinger.application.desmond.constants) RESTART (schrodinger.application.desmond.constants.UiMode attribute) restart (schrodinger.application.jaguar.input.JaguarInput property) (schrodinger.application.jaguar.output.JaguarOutput property) RESTART (schrodinger.utils.cmdline.Options attribute) Restart() (in module schrodinger.pipeline.pipeline) (in module schrodinger.pipeline.stage) restart() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage static method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage static method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreStage static method) (schrodinger.pipeline.pipeline.StageJob method) restart_args_handler() (in module schrodinger.active_learning.al_driver) restart_edges() (schrodinger.application.desmond.stage.launcher.FepLauncher method) restart_files (schrodinger.active_learning.al_driver.ActiveLearningJob property) restart_for_backend_error() (schrodinger.application.desmond.cmj.JobErrorHandler static method) RESTART_MODE_KEY (schrodinger.application.matsci.espresso.qeinput.ControlType attribute) restart_name() (in module schrodinger.application.jaguar.utils) restart_subjobs() (schrodinger.application.desmond.cmj.StageBase method) (schrodinger.application.desmond.stage.app.solubility.SolubilityMdLauncher method) (schrodinger.application.desmond.stage.launcher.FepLauncher method) (schrodinger.application.desmond.stage.launcher.Multisim method) (schrodinger.application.desmond.stage.simulate.DesmondExtend method) (schrodinger.application.desmond.stage.simulate.LambdaHopping method) (schrodinger.application.desmond.stage.simulate.ReplicaExchange method) (schrodinger.application.desmond.stage.simulate.SimulateBase method) restart_supported() (in module schrodinger.application.phase.packages.phase_database_job_utils) RESTARTABLE (schrodinger.application.desmond.cmj.StageBase attribute) (schrodinger.application.desmond.stage.launcher.Multisim attribute) (schrodinger.application.desmond.stage.simulate.SimulateBase attribute) RESTARTED (schrodinger.job.queue.PrintableStatus attribute) RestartException RESTARTING (schrodinger.job.queue.PrintableStatus attribute) RestInput (class in schrodinger.application.desmond.rest_inp) restore() (schrodinger.protein.rotamers.Rotamers method) restore_cursor() (in module schrodinger.application.bioluminate.pml_menus) restore_included_entries() (in module schrodinger.project.utils) restore_stages() (schrodinger.application.desmond.cmj.Engine method) restore_workspace (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) restore_zobs() (schrodinger.protein.assignment.ProtAssign method) restoreAdditionalSettings() (schrodinger.application.livedesign.ld_settings.LDExportSettingsMixin method) (schrodinger.application.livedesign.ld_settings.LDSettingsMixin method) restoreCompleted (schrodinger.application.livedesign.ld_settings.LDSettingsMixin attribute) restoreCursor() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.two_d_viewer.TwoDViewer method) restoreDefaultVisibility() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) restoreIonCenterProps() (schrodinger.application.ligprep.ionizer.Ionizer method) restoreLabelOptions() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) restoreLastValidValue() (schrodinger.ui.qt.swidgets.EnforcingValidatorMixin method) restoreLDSettings() (schrodinger.application.livedesign.ld_settings.LDSettingsMixin method) restorePanelSettings() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) restorePreviouslyIncludedEntry() (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) restoreSelection() (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget method) restoreSettings() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) RestoreTitlesStage (class in schrodinger.pipeline.stages.gencodes) Restrain (class in schrodinger.application.desmond.cms) restrain_force_constant() (in module schrodinger.application.desmond.gconfig) RESTRAINED_FRAGMENT_HYDRATION (schrodinger.application.desmond.constants.FepLegTypes attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) RestrainGroup (class in schrodinger.application.desmond.cms) RestrainGroupContainer (class in schrodinger.application.desmond.cms) Restraint (class in schrodinger.application.desmond.fepana) (class in schrodinger.forcefield.minimizer) restraint_enabled (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator property) RESTRAINT_PROP (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner attribute) RestraintAdaptationMixin (class in schrodinger.application.matsci.cgforcefield) restraints (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) restraints_file (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) restraints_incompatible() (in module schrodinger.application.desmond.cmj) RestraintsTab (class in schrodinger.application.desmond.gui) RestrainTypes (class in schrodinger.application.desmond.constants) restrict_nested_syncing() (in module schrodinger.ui.qt.network_visualizer) restrictByChains() (schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart method) Restricted (schrodinger.application.jaguar.gui.utils.SpinTreatment attribute) RestrictedRange (class in schrodinger.application.phase.packages.phase_utils) restrictJaguarTheoryOptions() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) RestrictSelection (class in schrodinger.application.bioluminate.pml_menus) RestrictSubMenu (class in schrodinger.application.bioluminate.pml_menus) RestrictToInorganic (class in schrodinger.application.bioluminate.pml_menus) RestrictToOrganic (class in schrodinger.application.bioluminate.pml_menus) RestrictToPolymer (class in schrodinger.application.bioluminate.pml_menus) RestrictToSolvent (class in schrodinger.application.bioluminate.pml_menus) RestrictToVisible (class in schrodinger.application.bioluminate.pml_menus) ResTuple (class in schrodinger.application.bioluminate.interaction_calculator) Result (class in schrodinger.application.matsci.order_parameter_mod) (class in schrodinger.comparison.results) (class in schrodinger.protein.tasks.binding_site_align) result_urls (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) result_urlsChanged (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) result_urlsReplaced (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) Results (class in schrodinger.application.matsci.jaguarworkflows) (class in schrodinger.protein.reliability) (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator property) results (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain property) results_cache (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget attribute) results_csv (schrodinger.tasks.ldtasks.LDTask.Output attribute) results_csvChanged (schrodinger.tasks.ldtasks.LDTask.Output attribute) results_csvReplaced (schrodinger.tasks.ldtasks.LDTask.Output attribute) ResultsCols (class in schrodinger.application.desmond.kinetics.utils) ResultSet (class in schrodinger.comparison.results) ResultsWindow (class in schrodinger.application.bioluminate.pml_menus) RETAIN (schrodinger.application.desmond.constants.EXISTING_RESTRAINT attribute) retain_ref_single() (schrodinger.application.desmond.cms.DictRestrainGroup method) (schrodinger.application.desmond.cms.PosRestrainArray method) (schrodinger.application.desmond.cms.RestrainGroup method) retain_refs() (schrodinger.application.desmond.cms.DictRestrainGroup method) (schrodinger.application.desmond.cms.PosRestrainArray method) (schrodinger.application.desmond.cms.RestrainGroup method) retranslateUi() (schrodinger.application.bioluminate.propfilter_ui.Ui_Form method) (schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form method) (schrodinger.application.desmond.desmond_advanced_tab_ui.Ui_Dialog method) (schrodinger.application.desmond.input_group_ui.Ui_Form method) (schrodinger.application.desmond.rest_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up.per_atom_basis_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.config_dialog_jaguar_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui.Ui_Dialog method) (schrodinger.application.jaguar.gui.ui.define_smarts_panel_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.edit_dialog_ui.Ui_MainWindow method) (schrodinger.application.jaguar.gui.ui.excited_state_widget_ui.Ui_Widget method) (schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_hb_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_pka_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_std_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.irc_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.irc_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.multi_structures_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.optimization_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.output_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.pka_smarts_page_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.properties_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scan_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scf_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvent_pka_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvent_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui.Ui_Widget method) (schrodinger.application.jaguar.gui.ui.theory_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.transition_state_top_ui.Ui_Form method) (schrodinger.application.jaguar.update_pka_settings_ui.Ui_UpdatePKASettingsDlg method) (schrodinger.application.job_monitor.diagnostics_dialog_ui.Ui_Form method) (schrodinger.application.job_monitor.file_browser_ui.Ui_Form method) (schrodinger.application.job_monitor.job_info_view_ui.Ui_Form method) (schrodinger.application.job_monitor.top_level_view_ui.Ui_Form method) (schrodinger.application.jobserver_cert_gui_dir.registration_panel_ui.Ui_Dialog method) (schrodinger.application.livedesign.export_setup_ui.Ui_Form method) (schrodinger.application.livedesign.export_ui.Ui_Form method) (schrodinger.application.livedesign.invalid_ge_id_warning_ui.Ui_Form method) (schrodinger.application.livedesign.live_report_widget_ui.Ui_Form method) (schrodinger.application.livedesign.login2_ui.Ui_Form method) (schrodinger.application.livedesign.login_ui.Ui_Dialog method) (schrodinger.application.livedesign.maestro_ld_mapping_ui.Ui_Form method) (schrodinger.application.livedesign.mappings_manager_ui.Ui_Form method) (schrodinger.application.livedesign.pose_name_panel_ui.Ui_Form method) (schrodinger.application.livedesign.save_mapping_dialog_ui.Ui_Form method) (schrodinger.application.livedesign.selection_pop_up_ui.Ui_Form method) (schrodinger.application.livedesign.summary_ui.Ui_Form method) (schrodinger.application.prime.gui.ui.analyze_energy_ui.Ui_Form method) (schrodinger.application.prime.gui.ui.environment_options_ui.Ui_Form method) (schrodinger.application.pymol.pymol4maestro_ui.Ui_Dialog method) (schrodinger.application.pymol.ui.advanced_settings_wdg_ui.Ui_Form method) (schrodinger.application.pymol.ui.export_to_pymol_dlg_ui.Ui_pymol_dlg method) (schrodinger.infra.exception_handler_dir.exception_dialog_ui.Ui_Dialog method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_ui.Ui_FindToolBar method) (schrodinger.trajectory.traj_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.advanced_plot_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.collapsible_plot_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.conf_wheel_plot_panel_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.energy_plot_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.export_movie_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.export_structures_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.job_settings_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.rdf_plot_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.shortcut_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui.Ui_snapshot_panel method) (schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui.Ui_trajectory_form method) (schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog method) (schrodinger.ui.ligfilter_ui.Ui_Form method) (schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.qt.appframework2.debug_gui_ui.Ui_Form method) (schrodinger.ui.qt.atom_weights_table_ui.Ui_Form method) (schrodinger.ui.qt.borderless_popup_ui.Ui_Frame method) (schrodinger.ui.qt.config_dialog_open_mp_ui.Ui_Form method) (schrodinger.ui.qt.config_dialog_queue_ui.Ui_Form method) (schrodinger.ui.qt.entryselector_ui.Ui_Dialog method) (schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui.Ui_Form method) (schrodinger.ui.qt.filter_dialog_ui.Ui_Dialog method) (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget_ui.Ui_customoplssettingwidget method) (schrodinger.ui.qt.forcefield.ffglobalpreferencewidget_ui.Ui_FFGlobalPreferencesWidget method) (schrodinger.ui.qt.forcefield.ffprojectsettingsdlg_ui.Ui_FFProjectSettingsDlg method) (schrodinger.ui.qt.fp_selector_widget_ui.Ui_Form method) (schrodinger.ui.qt.pdb_dialog_ui.Ui_PdbDialog method) (schrodinger.ui.qt.presets.manage_presets_dialog_ui.Ui_Form method) (schrodinger.ui.qt.presets.save_presets_dialog_ui.Ui_Form method) (schrodinger.ui.qt.protein_health_viewer_ui.Ui_Form method) (schrodinger.ui.qt.rename_favorite_dialog_ui.Ui_Dialog method) (schrodinger.ui.qt.select_residues_dialog_ui.Ui_Dialog method) (schrodinger.ui.qt.tasks.config_dialog_ui.Ui_Form method) (schrodinger.ui.qt.tasks.config_info_ui.Ui_Form method) (schrodinger.ui.qt.tasks.taskbar_ui.Ui_Form method) (schrodinger.ui.qt.widgetmixins.mock_ui.Ui_Form method) (schrodinger.ui.sketcher_smarts_dialog_ui.Ui_SketcherDialog method) (schrodinger.ui.two_d_viewer_ui.Ui_Form method) RETRIABLE_FAILURE (schrodinger.application.desmond.cmj.JobStatus attribute) RETRIES (schrodinger.utils.cmdline.Options attribute) retrieve_and_read_pdb() (in module schrodinger.application.prepwizard) retrieve_ent() (in module schrodinger.protein.getpdb) retrieve_license_file() (in module schrodinger.application.licensing.netsuiteapi) retrieve_licserver_license_file() (in module schrodinger.application.licensing.netsuiteapi) retrieve_pdb() (in module schrodinger.protein.getpdb) RetroSynthesisNode (class in schrodinger.application.pathfinder.route) RetrosynthesisState (class in schrodinger.application.pathfinder.analysis) retrosynthesize() (in module schrodinger.application.pathfinder.analysis) retrosynthesize_gen() (in module schrodinger.application.pathfinder.analysis) retryFailure() (schrodinger.application.matsci.jobutils.RobustSubmissionJob method) (schrodinger.job.queue.JobControlJob method) ReturnCode (class in schrodinger.infra.mmcheck) retype() (schrodinger.structure.Structure method) (schrodinger.structure.StructureAtom method) rev_one_hot() (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer method) REVERSE_COMPLEMENT_FN (schrodinger.protein.sequence.NucleicAcidSequence attribute) REVERSE_COMPLEMENT_FN() (schrodinger.protein.sequence.DNASequence static method) (schrodinger.protein.sequence.RNASequence static method) REVERSE_INTERPOLATION (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) reverse_iter() (schrodinger.job.queue.LinkedList method) revert() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) revert_to_original() (schrodinger.ui.qt.rama.Rama method) revert_to_saved() (schrodinger.ui.qt.rama.Rama method) reviseIonizedGroup() (schrodinger.application.ligprep.ionizer.Ionizer method) REVOLUTION (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) REVOLUTIONTHRESH (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) rewind() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) rewrite() (schrodinger.application.canvas.utils.ChmCSVTools method) rewriteByIndex() (schrodinger.application.canvas.utils.ChmCSVTools method) RewriteCardinalityException RewriteEarlyExitException RewriteEmptyStreamException RewriteOperation (class in schrodinger.application.desmond.antlr3.streams) RewriteRuleElementStream (class in schrodinger.application.desmond.antlr3.tree) RewriteRuleNodeStream (class in schrodinger.application.desmond.antlr3.tree) RewriteRuleSubtreeStream (class in schrodinger.application.desmond.antlr3.tree) RewriteRuleTokenStream (class in schrodinger.application.desmond.antlr3.tree) rgb (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) rgb_float (schrodinger.structutils.color.Color property) (schrodinger.surface.Surface.Color property) rgb_to_hex() (in module schrodinger.structutils.color) RGroup (class in schrodinger.structutils.rgroup_enumerate) rgroup_atom_smarts (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) rgroup_atom_smartsChanged (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) rgroup_atom_smartsReplaced (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) rgroup_decompose() (in module schrodinger.livedesign.bbchem_endpoints) (in module schrodinger.livedesign.rgroup_decomposition) rgroup_file (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) rgroup_fileChanged (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) rgroup_fileReplaced (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) rgroup_st (schrodinger.application.matsci.reaction_workflow_utils.Source attribute) RGroupEnumerator (class in schrodinger.structutils.rgroup_enumerate) RgroupEnumerator (in module schrodinger.structutils.rgroup_enumerate) RGroupError RgroupError (in module schrodinger.structutils.rgroup_enumerate) RGroupException RGroupFileFrame (class in schrodinger.application.matsci.reaction_workflow_gui_utils) RGroupFinder (class in schrodinger.application.canvas.r_group) RGroupSource (class in schrodinger.structutils.rgroup_enumerate) RGroupStructureToolTip (class in schrodinger.application.matsci.builderwidgets) Rh2Hx() (in module schrodinger.application.matsci.gsas.GSASIIlattice) rhl1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) rhl2() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) RI_CAP (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) RIBBON_SCHEME (schrodinger.application.bioluminate.pml_menus.ShowCartoon attribute) (schrodinger.application.bioluminate.pml_menus.ShowCartoonOrRibbon attribute) (schrodinger.application.bioluminate.pml_menus.ShowRibbon attribute) RibonucleotideType (class in schrodinger.protein.residue) Right (schrodinger.ui.qt.pop_up_widgets.PopUpAlignment attribute) RIGHT (schrodinger.ui.qt.schart.SChart attribute) (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) Right (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.BtnPos attribute) RIGHT_ARROW (schrodinger.ui.qt.standard.design_tokens.ScrollbarIcons attribute) right_axis (schrodinger.ui.qt.schart.SChart property) rimp2_energies() (in module schrodinger.application.jaguar.textparser) RIMP2_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab attribute) ring (schrodinger.structure.Structure attribute) (schrodinger.structure.TextualStructure property) (schrodinger.ui.qt.radial_plot.Sector attribute) ring_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) ring_graph (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule.RING_INFO attribute) ring_indexes (schrodinger.structutils.ringspear.Spear attribute) ring_size (schrodinger.structutils.ringspear.SpearRing attribute) ring_sys_d (schrodinger.application.dendrogram.core_class.RingSysStorage attribute) ringAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) RINGCHAIN (schrodinger.application.jaguar.utils.LewisModes attribute) RingFlipError RingSysInfo (class in schrodinger.application.dendrogram.core_class) RingSysStorage (class in schrodinger.application.dendrogram.core_class) rise (schrodinger.application.matsci.atom_group.HelixData attribute) rl_group_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) rl_groups (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) rmKwargs() (schrodinger.application.matsci.genetic_optimization.Property static method) rmReplicaKeywords() (schrodinger.application.matsci.permittivity.TaskProtocol method) rmsd (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) (schrodinger.protein.align.AbstractStructureAligner.Result attribute) (schrodinger.protein.tasks.binding_site_align.Result attribute) (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute) (schrodinger.structutils.structalign2.Alignment attribute) rmsd_cutoff (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) rmsd_precision (schrodinger.application.jaguar.output.JaguarOutput attribute) rmsd_rows (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) rmsd_rowsChanged (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) rmsd_rowsReplaced (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) RMSD_THRESH (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper attribute) (schrodinger.application.jaguar.autots_rmsd.AutoTSTemplateAtomMapper attribute) (schrodinger.comparison.atom_mapper.CSPAtomMapper attribute) rmsdChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) RMSDnError rmsdReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) RmsdSelection (class in schrodinger.application.desmond.kinetics.utils) RmsdStage (class in schrodinger.pipeline.stages.rmsd) RMSDSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) RNA (schrodinger.application.bioluminate.mutation.PolymerType attribute) RNA_ANTISENSE (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) RNA_SENSE (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) RNASequence (class in schrodinger.protein.sequence) robust_log() (in module schrodinger.application.matsci.kmcgui) RobustSubmissionJob (class in schrodinger.application.matsci.jobutils) rock_workspace() (in module schrodinger.application.bioluminate.pml_menus) RockData (class in schrodinger.application.bioluminate.pml_menus) RODFT (schrodinger.application.jaguar.constants.CalcType attribute) ROHF (schrodinger.application.jaguar.constants.CalcType attribute) ROHFLMP2 (schrodinger.application.jaguar.constants.CalcType attribute) rollback() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) RootJob (schrodinger.job.launchparams.SaveMode attribute) RootJobAndFailedSubjobs (schrodinger.job.launchparams.SaveMode attribute) RootJobAndSubjobs (schrodinger.job.launchparams.SaveMode attribute) rosen() (in module schrodinger.application.jaguar.qrnn.temp_opt) (in module schrodinger.application.matsci.mecp_mod) rosen_der() (in module schrodinger.application.jaguar.qrnn.temp_opt) rosen_hess() (in module schrodinger.application.jaguar.qrnn.temp_opt) rosen_hess_prod() (in module schrodinger.application.jaguar.qrnn.temp_opt) Rot_bonds (schrodinger.application.glide.xpdes.TermKeywords attribute) rot_mx (class in schrodinger.application.matsci.cctbx.rot_mx) rot_mx_info (class in schrodinger.application.matsci.cctbx.rot_mx) ROT_STR_KEY (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) ROT_STR_TITLE (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) Rotamers (class in schrodinger.protein.rotamers) rotamers (schrodinger.protein.rotamers.Rotamers property) rotatable_bonds_iterator() (in module schrodinger.structutils.analyze) rotatableBondsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) ROTATE (schrodinger.application.matsci.montecarlo.Metropolizer attribute) rotate() (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) rotate_2D() (in module schrodinger.rdkit.alignment) rotate_hydrogens_along_axis() (schrodinger.protein.assignment.WaterStateEnumerator method) rotate_pointgroup_symmetry_ops() (in module schrodinger.comparison.struc) rotate_structure() (in module schrodinger.structutils.transform) rotate_xyz() (in module schrodinger.comparison.struc) rotateIcon() (schrodinger.ui.qt.swidgets.Spinner method) rotateLeft() (schrodinger.ui.two_d_viewer.TwoDViewer method) rotateNanoSheet() (schrodinger.application.matsci.nano.tube.NanoSheet method) rotateProteinToMembrane() (schrodinger.protein.membrane.Membrane_Model method) RotateRBXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath) rotateRight() (schrodinger.ui.two_d_viewer.TwoDViewer method) rotateRigidBodyCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) rotateTube() (schrodinger.application.matsci.nano.tube.NanoTube method) rotation (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) rotation_matrix() (in module schrodinger.application.matsci.zmutils) rotational_constants() (in module schrodinger.application.jaguar.textparser) rotational_strength_precision (schrodinger.application.jaguar.results.NormalMode attribute) RotationalStrength (schrodinger.application.jaguar.constants.Unit attribute) RotationBarriersInput (class in schrodinger.application.jaguar.rotation_barriers_input) rotationChanged (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) RotationError rotationReplaced (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) rotdMat() (in module schrodinger.application.matsci.gsas.GSASIIlattice) rotdMat4() (in module schrodinger.application.matsci.gsas.GSASIIlattice) rotomers() (schrodinger.application.matsci.amorphous.TorsionAngler method) ROUGH_CUT_DISTANCE (in module schrodinger.structutils.ringspear) round_value() (in module schrodinger.math.mathutils) roundup() (in module schrodinger.math.mathutils) RouteDeduplicator (class in schrodinger.application.steps.enumerators) RouteEnumerator (class in schrodinger.application.steps.enumerators) RouteEnumerator.Settings (class in schrodinger.application.steps.enumerators) RouteEvaluator (class in schrodinger.application.steps.enumerators) RouteEvaluator.Settings (class in schrodinger.application.steps.enumerators) RouteNode (class in schrodinger.application.pathfinder.route) RouteNodeCoder (class in schrodinger.seam.coders) RouteRenderer (class in schrodinger.application.pathfinder.render) RouteScreener (class in schrodinger.application.combinatorial_explorer.route_screener) RouteSerializer (class in schrodinger.application.steps.enumerators) RouteSourceType (class in schrodinger.application.combinatorial_explorer.driver_utils) routine_time() (in module schrodinger.application.jaguar.textparser) RoutineTimes (class in schrodinger.application.jaguar.results) Row (class in schrodinger.ui.qt.tablewidget) row (schrodinger.ui.qt.tablewidget.Cell property) row_charge (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry property) ROW_CLASS (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) (schrodinger.application.livedesign.panel_components.ExportTableModel attribute) (schrodinger.application.phase.featureselector.FeatureModel attribute) (schrodinger.application.phase.phase_widgets.HypothesisModel attribute) (schrodinger.ui.picking.PickResidueModel attribute) (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) row_keys (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) row_keysChanged (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) row_keysReplaced (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Input attribute) ROW_LIST_OFFSET (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) row_number (schrodinger.project.project.ProjectRow property) row_nums (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) row_numsChanged (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) row_numsReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) row_structures (schrodinger.application.livedesign.export_models.AttachmentItem attribute) row_structuresChanged (schrodinger.application.livedesign.export_models.AttachmentItem attribute) row_structuresReplaced (schrodinger.application.livedesign.export_models.AttachmentItem attribute) RowActionItem (class in schrodinger.application.bioluminate.bwidgets) RowBasedListModel (class in schrodinger.ui.qt.table_helper) RowBasedModelMixin (class in schrodinger.ui.qt.table_helper) RowBasedTableModel (class in schrodinger.ui.qt.table_helper) rowByText() (schrodinger.ui.qt.swidgets.SListWidget method) rowChanged() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) rowCount() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.table.ViewerModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) rowCountChanged() (schrodinger.ui.qt.table.DataViewerTable method) RowData (class in schrodinger.application.jaguar.macro_pka_utils) rowGetExpanded() (schrodinger.infra.table.Table method) rowGetVisible() (schrodinger.infra.table.Table method) rowHeight() (schrodinger.ui.two_d_viewer.TwoDTableView method) RowIterator (class in schrodinger.ui.qt.tablewidget) RowProxy (class in schrodinger.utils.pymol) rowResized() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) rows (schrodinger.ui.qt.table_helper.RowBasedModelMixin property) rows() (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) rowSetExpanded() (schrodinger.infra.table.Table method) rowSetVisible() (schrodinger.infra.table.Table method) rowsForEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) rowsInserted() (schrodinger.ui.qt.table.DataViewerTable method) rowsMoved() (schrodinger.ui.qt.table.DataViewerTable method) rowsRemoved() (schrodinger.ui.qt.table.DataViewerTable method) rrho() (schrodinger.application.macromodel.utils.ComUtil method) rsh_put_cmd() (in module schrodinger.job.remote_command) rsh_test() (in module schrodinger.job.remote_command) rt_mx (class in schrodinger.application.matsci.cctbx.rot_mx) rubberband_method() (in module schrodinger.application.matsci.spectra) Ruland() (in module schrodinger.application.matsci.gsas.GSASIIpwd) RULE (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.desmond.systype.TyperBase attribute) (schrodinger.application.desmond.systype.WatermapTyper attribute) rule_file (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) rule_fileChanged (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) rule_fileReplaced (schrodinger.application.livedesign.tasks.CanvasSearchTask.Input attribute) rulePostProcessing() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) RuleReturnScope (class in schrodinger.application.desmond.antlr3.recognizers) Run (schrodinger.ui.qt.config_dialog.RequestedAction attribute) run() (in module schrodinger.application.bioluminate.met_oxidation.hmc_sim_runner) (in module schrodinger.application.bioluminate.met_oxidation.md_sim_runner) (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.matsci.packmol) (schrodinger.active_learning.mq_backend.Backend method) (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) (schrodinger.active_learning.mq_worker.Worker method) (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator class method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) (schrodinger.application.desmond.cmj.StructureStageBase method) (schrodinger.application.desmond.kinetics.cleanup.CleanUp method) (schrodinger.application.desmond.kinetics.mtd_cleanup.CleanUp method) (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) (schrodinger.application.desmond.queue.Queue method) (schrodinger.application.desmond.rest_inp.RestInput method) (schrodinger.application.desmond.stage.analysis.AnalysisJob method) (schrodinger.application.desmond.stage.analysis.FepanaJob method) (schrodinger.application.desmond.stage.analysis.MetadynamicsAnalysisJob method) (schrodinger.application.desmond.stage.analysis.SeaJob method) (schrodinger.application.desmond.stage.analysis.TimeSeriesAnalysisJob method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingFepPrimer method) (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingStructurePrimer method) (schrodinger.application.desmond.stage.app.fragment_linking.stage.FragmentLinkingPrimer method) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper method) (schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsSplitReceptor method) (schrodinger.application.desmond.stage.app.matsci.AverageCell method) (schrodinger.application.desmond.stage.app.matsci.DeformCell method) (schrodinger.application.desmond.stage.app.matsci.ScaleEffectiveSolvent method) (schrodinger.application.desmond.stage.app.matsci.SolvateSlabBuilder method) (schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox method) (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) (schrodinger.application.desmond.stage.prepare.forcefield.AssignCustomCharge method) (schrodinger.application.desmond.stage.prepare.forcefield.LoadRestraintsFromStructure method) (schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder method) (schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure method) (schrodinger.application.desmond.stage.prepare.structure.ExtractStructures method) (schrodinger.application.desmond.stage.prepare.structure.GroupWaters method) (schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle method) (schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure method) (schrodinger.application.desmond.starter.starter.Starter method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.desmond.util.TestSuite method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.BqQueryStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreStage method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportPanelWizard method) (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF method) (schrodinger.application.matsci.crest.Crest method) (schrodinger.application.matsci.desmondutils.SystemBuilder method) (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) (schrodinger.application.matsci.equilibrium_md.MultiDriver method) (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) (schrodinger.application.matsci.order_parameter_mod.OrderParameter method) (schrodinger.application.matsci.permittivity.ConfigWriter method) (schrodinger.application.matsci.permittivity.MdStageModifier method) (schrodinger.application.matsci.qubec_utils.Qubec method) (schrodinger.application.matsci.rdpattern.EvaluateSMARTS method) (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) (schrodinger.application.matsci.reaction_workflow_utils.EnumerateReactionWorkflow method) (schrodinger.application.matsci.reaction_workflow_utils.EnumerateSwap method) (schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelection method) (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain method) (schrodinger.application.mopac.structure_launchers.StructureLauncher method) (schrodinger.application.pathfinder.synthesis.Synthesizer method) (schrodinger.application.report2d.PicturePrinter method) (schrodinger.application.watermap.watermap_inp.WaterMapInput method) (schrodinger.job.app.App method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobDJ method) (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.stage.Stage method) (schrodinger.protein.align.AbstractAligner method) (schrodinger.protein.align.AbstractPairwiseAligner method) (schrodinger.protein.align.ClustalAligner method) (schrodinger.protein.align.CustomASLStructureAligner method) (schrodinger.protein.align.FamilyPairwiseAligner method) (schrodinger.protein.align.MaxIdentityAligner method) (schrodinger.protein.align.PrimeSTAAligner method) (schrodinger.protein.align.RescodeAligner method) (schrodinger.protein.align.StructureAligner method) (schrodinger.protein.align.StructurelessGapAligner method) (schrodinger.protein.tasks.clustal.AbstractAlignmentJob method) (schrodinger.protein.tasks.clustal.ClustalJob method) (schrodinger.protein.tasks.muscle.MuscleJob method) (schrodinger.seam.testing.benchmarks.Benchmark method) (schrodinger.seam.testing.benchmarks.ExecStagesWithSlowCoder method) (schrodinger.seam.testing.benchmarks.FlattenWithSlowCoder method) (schrodinger.seam.testing.benchmarks.GroupByKey method) (schrodinger.seam.testing.benchmarks.GroupByKeyWithSlowCoder method) (schrodinger.structutils.analyze.MissingLoopFinder method) (schrodinger.tasks.tasks.AbstractCmdTask method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.tasks.tasks.SignalTask method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.CleanStateMixin method) (schrodinger.utils.installation_check.TestJob method) run_align() (in module schrodinger.application.ska) run_analysis() (schrodinger.protein.analysis.Report.steric_clash_data_set method) run_antibody_model() (in module schrodinger.livedesign.biologics.modeling) run_apbs() (in module schrodinger.application.desmond.fep_net_charge) run_application() (in module schrodinger.utils.qapplication) run_bedroc_screen() (in module schrodinger.application.phase.packages.hypo_refine.screen_utils) run_bennett() (in module schrodinger.application.desmond.fepana) run_bq_query_task() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) run_bq_query_task_restart() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) RUN_BUTTON_TEXT (schrodinger.application.matsci.appbase.ProcessPtStructuresApp attribute) run_check() (in module schrodinger.protein.reliability) run_check_config() (in module schrodinger.livedesign.cmdline) run_cleanup() (in module schrodinger.application.mopac.utils) RUN_DICT (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) run_distributed() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) run_diversity_filter() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) run_dj() (in module schrodinger.active_learning.mq_worker) run_epik (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) run_epikChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) run_epikReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) run_fep_mapper_cleanup() (in module schrodinger.application.desmond.stage.fep_mapper) run_filters() (in module schrodinger.application.bioluminate.pose_filtering.residue_filter) (in module schrodinger.application.phase.shape_screen_reporter.task_utils) run_format_convert() (in module schrodinger.livedesign.cmdline) run_full_workflow() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) run_glide_sort() (in module schrodinger.application.phase.packages.phase_screen_utils) run_image_generation() (in module schrodinger.livedesign.cmdline) run_impref (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) run_imprefChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) run_imprefReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) run_info (schrodinger.stepper.stepper.StepTaskOutput attribute) run_infoChanged (schrodinger.stepper.stepper.StepTaskOutput attribute) run_infoReplaced (schrodinger.stepper.stepper.StepTaskOutput attribute) run_installation_check() (in module schrodinger.utils.installation_check) run_jobdj_and_add_files() (in module schrodinger.application.matsci.jobutils) run_jobs_with_update_logging() (in module schrodinger.application.matsci.textlogger) run_kwargs (schrodinger.application.jaguar.input.JaguarInput attribute) run_lmdiag() (in module schrodinger.application.licensing.licadmin) run_lmstat() (in module schrodinger.application.licensing.licadmin) run_model() (in module schrodinger.tasks.ldtasks) run_multiple_inputs() (in module schrodinger.application.bioluminate.escomp) run_multiple_sequence_alignment() (in module schrodinger.livedesign.cmdline) run_oned_screen() (in module schrodinger.application.phase.packages.oned_task_utils) run_parent_method() (in module schrodinger.application.matsci.gutils) run_phase_database_job() (in module schrodinger.pipeline.stages.phase) run_pilot() (in module schrodinger.application.vss.tasks) run_postmortem() (in module schrodinger.utils.installation_check) run_production() (in module schrodinger.application.vss.tasks) run_property_filter() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) run_propka() (in module schrodinger.application.bioluminate.run_propka) (schrodinger.protein.assignment.ProtAssign method) run_protassign (schrodinger.application.prepwizard.PrepWizardSettings attribute) run_protassignChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) run_protassignReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) run_protein_reliability() (in module schrodinger.application.desmond.feputils) run_query() (in module schrodinger.application.bb_database.bb_task_utils) run_quick_check() (in module schrodinger.protein.reliability) run_reaction() (in module schrodinger.livedesign.bbchem_endpoints) (in module schrodinger.livedesign.run_reaction) run_reaction_with_filters() (in module schrodinger.livedesign.run_reaction) run_registration() (in module schrodinger.livedesign.cmdline) run_requested (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) run_search_service() (in module schrodinger.livedesign.cmdline) run_set_family() (schrodinger.application.desmond.cmj.Engine method) run_simulation() (schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer method) run_single_subjob() (in module schrodinger.application.matsci.jobutils) run_smarts_filter() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) run_stage_method_in_parallel() (in module schrodinger.application.desmond.stage.utils) run_system_builder() (in module schrodinger.application.matsci.desmondutils) run_task() (in module schrodinger.application.livedesign.tasks) run_tasks_in_parallel() (in module schrodinger.tasks.queue) run_tasks_on_dj() (in module schrodinger.tasks.queue) run_tasks_on_queue() (in module schrodinger.tasks.queue) run_test_jobs() (in module schrodinger.utils.installation_check) run_workflows() (in module schrodinger.application.matsci.jaguarworkflows) run_xtb() (in module schrodinger.application.xtb.runner) runAddJob() (schrodinger.pipeline.stages.phase.DBManageStage method) runALABFEP() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage method) runALGlide() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage static method) runAllSlots() (schrodinger.models.mappers.MapperMixin method) runAnharmonic() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) runBackend() (schrodinger.tasks.drivers.BaseDriverTask method) (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.jobtasks.ComboJobTask method) (schrodinger.tasks.tasks.AbstractComboTask method) (schrodinger.tasks.tasks.ComboSubprocessTask method) runBuildGeometry() (schrodinger.application.matsci.desmondutils.SystemBuilder method) runCanvas() (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) runCluFile() (schrodinger.application.macromodel.utils.CluUtil method) runCmd() (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask method) (schrodinger.tasks.tasks.AbstractCmdTask method) (schrodinger.tasks.tasks.ComboBlockingFunctionTask method) (schrodinger.tasks.tasks.SubprocessMixin method) runCTST() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) runCurrentPanel() (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) runDescriptors() (schrodinger.application.matsci.reaction_workflow_utils.DescriptorsMixin method) runEditedInput() (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) runEnumerateRXNWF() (schrodinger.application.matsci.reaction_workflow_utils.EnumerateSwapMixin method) runFeature() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) runForceFieldAssignment() (schrodinger.application.matsci.desmondutils.SystemBuilder method) runFrequencyJob() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) runInProcess() (schrodinger.tasks.tasks.AbstractComboTask method) runIt() (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) (schrodinger.application.matsci.genetic_optimization.ClassEvaluator method) (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator method) (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) (schrodinger.application.matsci.genetic_optimization.Jaguar method) (schrodinger.application.matsci.genetic_optimization.RefractiveIndex method) (schrodinger.application.matsci.genetic_optimization.StructureEvaluator method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.slab.Surface method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) (schrodinger.application.matsci.rxn_path.ReactionPath method) runJaguar() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) runJMSWF() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) runJob() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.matsci.reaction_workflow_utils.JMSWFConformerSelection method) (schrodinger.application.matsci.reaction_workflow_utils.MopacConformerSelection method) runJobDJ() (schrodinger.pipeline.stage.Stage method) runJobs() (schrodinger.application.matsci.fragments.FragmentReactor method) (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) runKnime() (schrodinger.ui.qt.appframework2.af2.App class method) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin class method) runLigandMLMerge() (schrodinger.active_learning.al_node.LigandMLTrainNode method) runMaestro() (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) runMerge() (schrodinger.application.phase.packages.shape_screen_gpu_update.ShapeDataUpdateDriver method) runMode() (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) RUNNER_LOGLEVEL_DEBUG (schrodinger.seam.debug.DebugFlag attribute) RUNNER_LOGLEVEL_INFO (schrodinger.seam.debug.DebugFlag attribute) RunnerControl (class in schrodinger.application.vss.control) RUNNING (schrodinger.application.desmond.cmj.JobStatus attribute) (schrodinger.job.jobcontrol.DisplayStatus attribute) (schrodinger.seam.viz.inspect.PipelineStatus attribute) (schrodinger.seam.viz.inspect.TransformStatus attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.Status attribute) running_jobs (schrodinger.application.desmond.queue.Queue property) RUNNING_MESSAGE (schrodinger.application.glide.ligand_designer.GridgenTask attribute) running_message (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute) RunningJobs (class in schrodinger.job.queue) runNode() (schrodinger.active_learning.al_node.KnownScoreProviderNode method) (schrodinger.active_learning.al_node.LigandMLEvalNode method) (schrodinger.active_learning.al_node.LigandMLTrainNode method) (schrodinger.active_learning.al_node.PrepareSmilesNode method) (schrodinger.active_learning.fake_nodes.DummyCalculateScoreNode method) (schrodinger.active_learning.fake_nodes.DummyPilotScoreNode method) (schrodinger.active_learning.fake_nodes.DummyRescoreNode method) (schrodinger.application.phase.packages.shape_screen_al_node.CalculateScoreNode method) (schrodinger.application.phase.packages.shape_screen_al_node.PilotScoreNode method) (schrodinger.application.phase.packages.shape_screen_al_node.RescoreNode method) runNodes() (schrodinger.active_learning.al_driver.ActiveLearningJob method) runOnEachGraphicNode() (schrodinger.ui.qt.dendrogram.Dendrogram method) runPipeline() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) runpKa() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) runPrediction() (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) runPreprocessing() (schrodinger.tasks.tasks.AbstractTask method) runPrimeLoopPrediction() (schrodinger.application.bioluminate.protein.protein.Refiner method) runPrimeMinimization() (schrodinger.application.bioluminate.protein.protein.Refiner method) runPrimeResidue() (schrodinger.application.bioluminate.protein.protein.Refiner method) runPrimeSidechain() (schrodinger.application.bioluminate.protein.protein.Refiner method) runPrimeSidechainBB() (schrodinger.application.bioluminate.protein.protein.Refiner method) runPrimeSidechainCBeta() (schrodinger.application.bioluminate.protein.protein.Refiner method) runPythonMinimize() (schrodinger.application.bioluminate.protein.protein.Refiner method) runQMConformerSelection() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) runRefinement() (schrodinger.application.bioluminate.protein.protein.Refiner method) runShapeScreen() (schrodinger.application.phase.packages.shape_screen_al_node.ShapeScreenJob method) runSinglePointJobs() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) runSingleStruc() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) runsLocally() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) runSmartsSearch() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) runStandalone() (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) runStructureAlignment() (in module schrodinger.protein.tasks.structure_alignment) runStub() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator method) runSubjobs() (schrodinger.application.matsci.equilibrium_md.MultiDriver method) runSubpanel() (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) runSuperposition() (schrodinger.application.matsci.rxn_path.ReactionCoords method) runSwapFragments() (schrodinger.application.matsci.reaction_workflow_utils.EnumerateSwapMixin method) runTabValidation() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) RUNTIME (schrodinger.application.matsci.kmc.SchrodingerTable attribute) RuntimeParametersError RuntimeParametersKeyError runtimize_paths() (in module schrodinger.application.phase.packages.shape_creation_logic) runTransmutations() (schrodinger.application.matsci.enumeration.Alchemist method) (schrodinger.application.matsci.enumeration.StructureAlchemist method) runValidation() (schrodinger.ui.qt.appframework2.validation.ValidationMixin method) runWorkflow() (schrodinger.stepper.app.StepperApplication class method) runXCluFile() (schrodinger.application.macromodel.utils.CluUtil method) RX_PROP (schrodinger.application.matsci.amorphous.BaseMoiety attribute) rxn_coord_precision (schrodinger.application.jaguar.results.JaguarResults attribute) RXN_REPRESENTATION_KEY (schrodinger.application.matsci.rxn_channel.Products attribute) rxn_validated (schrodinger.livedesign.check_reaction.RxnCheckResult attribute) RxnCheckResult (class in schrodinger.livedesign.check_reaction) RXNCOORD (schrodinger.application.matsci.rxn_path.ReactionPath attribute) RXNINDEX (schrodinger.application.matsci.rxn_path.ReactionPath attribute) RxnNetworkGraph (class in schrodinger.application.matsci.reaction_workflow_utils) RxnNetworkGraphException

S

S (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) s (schrodinger.application.matsci.espresso.qeoutput.PhDOS.Thermo attribute) s2() (in module schrodinger.application.jaguar.textparser) s_min_eval() (in module schrodinger.application.jaguar.textparser) s_opls_version() (in module schrodinger.forcefield.test.fixtures) SA_ACTIVE (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_LOWEST_BOND_STRETCH (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_LOWEST_HESSIAN (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_LOWEST_NON_TORSIONAL (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_RP_PATH (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_USER (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SAction (class in schrodinger.application.bioluminate.actions.factory) safe_data_export() (in module schrodinger.application.matsci.gutils) safe_extractall_tar() (in module schrodinger.utils.fileutils) safe_extractall_zip() (in module schrodinger.utils.fileutils) safe_filename() (in module schrodinger.application.licensing.licserver.client) safe_mkdir() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) safe_server_address_filename() (in module schrodinger.utils.net) safely_set_property() (in module schrodinger.application.livedesign.ld_utils) SALT_BRIDGE (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) salt_bridge_max_dist (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) salt_bridge_max_distChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) salt_bridge_max_distReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) salt_bridges (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) salt_bridgesChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) salt_bridgesReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) salt_concentration (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) (schrodinger.application.desmond.new_fep_edge_data.FepData property) SamAng() (in module schrodinger.application.matsci.gsas.GSASIIlattice) SAME_STRUCTURE (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) SAME_VECTOR_THRESH (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) sameSizeAndThreshold() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) SameTypeGSTS (class in schrodinger.application.matsci.reaction_workflow_utils) sample_by_scaffold (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) sample_by_scaffoldChanged (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) sample_by_scaffoldReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) SAMPLE_DATA (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) (schrodinger.ui.qt.table_helper.SampleDataTableViewMixin attribute) SAMPLE_DEFAULT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) SAMPLE_SIZE (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData attribute) SampleDataTableView (class in schrodinger.ui.qt.table_helper) SampleDataTableViewMixin (class in schrodinger.ui.qt.table_helper) SampleRingsStage (class in schrodinger.pipeline.stages.macromodel) samplewater (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) samplewaterChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) samplewaterReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) sampling_fraction (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) sampling_fractionChanged (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) sampling_fractionReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) SAMPLING_MODE (schrodinger.application.bioluminate.methionine_oxidation.HmcAnalyzer attribute) (schrodinger.application.bioluminate.methionine_oxidation.MdAnalyzer attribute) (schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer attribute) SamplingMode (class in schrodinger.application.bioluminate.methionine_oxidation) Sanitize (class in schrodinger.adapter) sanitize_dest_table_id() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) sanitize_for_viparr() (schrodinger.application.desmond.cms.Cms method) sanitize_permitted() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) sanitizeCustomOPLSDir() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) sanitized (schrodinger.application.matsci.rdpattern.Pattern property) sanitizeJobnameText() (schrodinger.ui.qt.appframework2.af2.JobApp method) sanityCheckParentAndChildIndexes() (schrodinger.application.desmond.antlr3.tree.BaseTree method) sasa (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) SasaResidueFilter (class in schrodinger.application.bioluminate.pose_filtering.residue_filter) SAsciiOnlyValidator (class in schrodinger.ui.qt.swidgets) SASLValidator (class in schrodinger.ui.qt.swidgets) SAVE (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) (schrodinger.utils.cmdline.Options attribute) save() (schrodinger.application.desmond.rl_helper.NumberedCanvas method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.xtb.input.XTBInput method) (schrodinger.seam.metric.SeamMetrics method) (schrodinger.ui.qt.rama.Rama method) save_2d_annotated_img() (in module schrodinger.application.desmond.report_helper) save_figure() (in module schrodinger.application.matsci.reportutils) save_hypo_for_job() (in module schrodinger.application.phase.packages.hypo_refine.job_utils) save_hypo_with_score() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils) save_image_file() (in module schrodinger.ui.sketcher_image) save_images() (in module schrodinger.application.matsci.reportutils) save_mat_csv() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) save_matplotlib_figure() (in module schrodinger.application.matsci.reportutils) save_mkdir() (in module schrodinger.application.bioluminate.epitope.psc_workflow) save_new_color() (in module schrodinger.application.bioluminate.pml_menus) save_plot() (in module schrodinger.analysis.enrichment.plotter) save_sym_mat_csv() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) saveAdditionalSettings() (schrodinger.application.livedesign.ld_settings.LDExportSettingsMixin method) (schrodinger.application.livedesign.ld_settings.LDSettingsMixin method) saveAs() (schrodinger.application.jaguar.input.JaguarInput method) saveASL() (schrodinger.application.matsci.mswidgets.MSAtomSelector method) SaveButton (class in schrodinger.ui.qt.swidgets) SaveCCP4File() (in module schrodinger.analysis.visanalysis.volumedataio) saveCleanState() (schrodinger.ui.qt.widgetmixins.panelmixins.CleanStateMixin method) saveCoefficients() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) saveConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) saved_phi (schrodinger.ui.qt.rama.BackboneDihedral attribute) saved_psi (schrodinger.ui.qt.rama.BackboneDihedral attribute) SavedASLItem (class in schrodinger.application.matsci.mswidgets) saveDatabase() (schrodinger.protein.nonstandard_residues.ResidueDatabase method) SaveDefinitionsDialog (class in schrodinger.trajectory.trajectory_gui_dir.trajectory_messages) SaveDesmondFilesWidget (class in schrodinger.application.matsci.mswidgets) saveDistanceConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) SavedItemsManager (class in schrodinger.ui.qt.swidgets) SavedMenuItem (class in schrodinger.ui.qt.swidgets) SavedSMARTSManager (class in schrodinger.ui.qt.swidgets) saveExpansionBFS() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) saveImage() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) saveIonCenterProps() (schrodinger.application.ligprep.ionizer.Ionizer method) saveItem() (schrodinger.ui.qt.swidgets.SavedItemsManager method) saveLabelOptions() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) saveLDSettings() (schrodinger.application.livedesign.ld_settings.LDSettingsMixin method) saveLocalStructs() (schrodinger.application.matsci.amorphous.PolymerFragments method) saveMapping() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) SaveMode (class in schrodinger.job.launchparams) saveMsdTxt() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) saveMsjStages() (schrodinger.application.matsci.permittivity.MdStageModifier method) saveNewMapping() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) saveOptions() (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) savePanelSettings() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) savePersistentOptions() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) savePlot() (schrodinger.analysis.enrichment.calculator.Calculator method) savePotentialWallConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) savePreset() (schrodinger.models.presets.PresetManager method) SavePresetsDialog (class in schrodinger.ui.qt.presets.save_presets_dialog) savePresetToFile() (schrodinger.models.presets.PresetManager method) savePressed() (schrodinger.ui.qt.config_dialog.ConfigDialog method) savePropAndCms() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) saveSelection() (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget method) saveSettings() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) saveTemplate() (schrodinger.application.matsci.builderwidgets.SketcherBox method) saveTorsionConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) SaveVisFile() (in module schrodinger.analysis.visanalysis.volumedataio) savgol_method() (in module schrodinger.application.matsci.spectra) SB (schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE attribute) SB_CMD (schrodinger.application.desmond.stage.utils.SystemBuilder attribute) SbcUtil (class in schrodinger.application.macromodel.utils) SC_GROOVE (schrodinger.application.matsci.mswidgets.MultiSlider attribute) SC_HANDLE (schrodinger.application.matsci.mswidgets.MultiSlider attribute) SC_TYPE_DATA (class in schrodinger.application.matsci.species) Scaffold (class in schrodinger.application.matsci.amorphous) (class in schrodinger.structutils.markush_enumerate) scaffold (schrodinger.application.bioluminate.antibody.grafting.GraftingInput attribute) ScaffoldError ScaffoldMatch (class in schrodinger.application.bioluminate.antibody.scaffold_search) scaffolds (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchOutput attribute) (schrodinger.application.phase.shape_screen_reporter.option_utils.ClusterBy attribute) ScaffoldSearchInput (class in schrodinger.application.bioluminate.antibody.scaffold_search) ScaffoldSearchOutput (class in schrodinger.application.bioluminate.antibody.scaffold_search) scalar_search_wolfe1() (schrodinger.application.matsci.mecp_mod.BFGS method) scale (schrodinger.application.jaguar.simple_spec.Peak attribute) scale() (schrodinger.application.matsci.automated_cg_mapping.MappingMethod static method) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) scale_cell() (in module schrodinger.application.matsci.cgforcefield) (in module schrodinger.application.matsci.nano.xtal) scale_for_diversity_job() (in module schrodinger.active_learning.al_utils) scale_vertices() (in module schrodinger.graphics3d.polyhedron) ScaleEffectiveSolvent (class in schrodinger.application.desmond.stage.app.matsci) scaleFactor (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute) scalePosFromModel() (schrodinger.ui.qt.network_views.NetworkNode method) scalePosToModel() (schrodinger.ui.qt.network_views.NetworkNode method) scaleSmoother() (schrodinger.ui.qt.network_views.NetworkViewer method) Scan (class in schrodinger.application.jaguar.scan) SCAN (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin attribute) scan() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) scan_coordinates() (in module schrodinger.application.jaguar.textparser) scan_step (schrodinger.application.jaguar.output.JaguarOutput property) ScanCoord (class in schrodinger.application.jaguar.utils) ScanCoordinateColumns (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanCoordinateData (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanCoordinatesDelegate (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanCoordinatesModel (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanCoordinatesProxyModel (class in schrodinger.application.jaguar.gui.tabs.scan_tab) scanCount() (schrodinger.application.jaguar.input.JaguarInput method) scanSignals() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) ScanTab (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanTabMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) ScanTabNextGeom (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanTabNextGeom.NextGeomFrom (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScatFac() (in module schrodinger.application.matsci.gsas.GSASIIElem) SCATTER (schrodinger.ui.qt.schart.SChart attribute) (schrodinger.ui.qt.schart.SeriesParams attribute) SCENE_LOOP (schrodinger.application.pymol.gui_models.MovieExportMode attribute) SCENES (schrodinger.application.pymol.gui_models.ProjectExportMode attribute) scenes (schrodinger.application.pymol.mae_sync.MaestroSettingsModel attribute) scenesChecked() (schrodinger.application.pymol.pymol4maestro.panel method) SCF_MAX_ITERS (schrodinger.application.jaguar.constants.FatalErrors attribute) scfe() (in module schrodinger.application.jaguar.textparser) ScfIteration (class in schrodinger.application.jaguar.results) ScfTab (class in schrodinger.application.jaguar.gui.tabs.scf_tab) ScfTabConsistentOrbitals (class in schrodinger.application.jaguar.gui.tabs.scf_tab) SCFVSequenceIndexer (class in schrodinger.application.bioluminate.antibody.sequence_indexer) SChart (class in schrodinger.ui.qt.schart) SChartView (class in schrodinger.ui.qt.schart) SCheckBox (class in schrodinger.ui.qt.swidgets) SCheckBoxEdit (class in schrodinger.ui.qt.swidgets) SCheckBoxToggle (class in schrodinger.ui.qt.swidgets) SCheckBoxWithSubWidget (class in schrodinger.ui.qt.swidgets) Schedule (class in schrodinger.application.desmond.constants) schedule() (schrodinger.application.desmond.config_utils.LambdaSchedule class method) ScheduleAngleAttachment (class in schrodinger.application.desmond.config_utils) ScheduleAngleCoreDummy (class in schrodinger.application.desmond.config_utils) ScheduleAngleCorePhysical (class in schrodinger.application.desmond.config_utils) ScheduleBondCoreDummy (class in schrodinger.application.desmond.config_utils) ScheduleBondCorePhysical (class in schrodinger.application.desmond.config_utils) ScheduleLinear (class in schrodinger.application.desmond.config_utils) SCHEMA (schrodinger.application.vss.control.DiseControl attribute) (schrodinger.application.vss.control.GlideALControl attribute) (schrodinger.application.vss.control.GlideControl attribute) (schrodinger.application.vss.control.LigandMLControl attribute) (schrodinger.application.vss.control.ShapeControl attribute) (schrodinger.application.vss.csvsmiles.CsvSmilesFile attribute) scheme (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput attribute) SCHEMES (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar attribute) schlegel_hessian() (in module schrodinger.application.jaguar.hess_guess) schlegel_to_cartesian() (in module schrodinger.application.jaguar.hess_guess) SchlegelConstants (class in schrodinger.application.jaguar.hess_guess) ScholarStructureItem (class in schrodinger.application.desmond.fep_scholar_util) schrod_port() (schrodinger.application.licensing.licadmin.LicenseResource method) SchrodImageGenerator (class in schrodinger.application.desmond.image_generator) SCHRODINGER schrodinger (schrodinger.application.desmond.envir.CONST attribute) (schrodinger.energy.ANIModel attribute) module schrodinger.active_learning module schrodinger.active_learning.al_driver module schrodinger.active_learning.al_node module schrodinger.active_learning.al_report module schrodinger.active_learning.al_utils module schrodinger.active_learning.fake_nodes module schrodinger.active_learning.mq_backend module schrodinger.active_learning.mq_driver module schrodinger.active_learning.mq_worker module schrodinger.adapter module schrodinger.analysis module schrodinger.analysis.enrichment module schrodinger.analysis.enrichment.calculator module schrodinger.analysis.enrichment.enrichment_input module schrodinger.analysis.enrichment.metrics module schrodinger.analysis.enrichment.plotter module schrodinger.analysis.reaction module schrodinger.analysis.substructure module schrodinger.analysis.transformations module schrodinger.analysis.visanalysis module schrodinger.analysis.visanalysis.vdaxis module schrodinger.analysis.visanalysis.vdcoordinateframe module schrodinger.analysis.visanalysis.vdexception module schrodinger.analysis.visanalysis.volumedata module schrodinger.analysis.visanalysis.volumedataio module schrodinger.analysis.visanalysis.volumedatastructureutils module schrodinger.analysis.visanalysis.volumedatautils module schrodinger.application module schrodinger.application.aacg module schrodinger.application.aacg.utils module schrodinger.application.bb_database module schrodinger.application.bb_database.bb_arg_utils module schrodinger.application.bb_database.bb_job_utils module schrodinger.application.bb_database.bb_task_utils module schrodinger.application.bindingsite module schrodinger.application.bindingsite.atomtyping module schrodinger.application.bindingsite.cavutils module schrodinger.application.bindingsite.common module schrodinger.application.bindingsite.intfield module schrodinger.application.bindingsite.schema module schrodinger.application.bioluminate module schrodinger.application.bioluminate.actions module schrodinger.application.bioluminate.actions.configs module schrodinger.application.bioluminate.actions.factory module schrodinger.application.bioluminate.actions.icons module schrodinger.application.bioluminate.actions.icons_rc module schrodinger.application.bioluminate.anarci module schrodinger.application.bioluminate.anarci.anarci_adapter module schrodinger.application.bioluminate.anarci.annotate module schrodinger.application.bioluminate.anarci.loop_ranges module schrodinger.application.bioluminate.antibody module schrodinger.application.bioluminate.antibody.annotate module schrodinger.application.bioluminate.antibody.annotation_constants module schrodinger.application.bioluminate.antibody.antibody_homology_report_writer module schrodinger.application.bioluminate.antibody.assembly module schrodinger.application.bioluminate.antibody.grafting module schrodinger.application.bioluminate.antibody.io module schrodinger.application.bioluminate.antibody.io.csv_reader module schrodinger.application.bioluminate.antibody.management module schrodinger.application.bioluminate.antibody.models module schrodinger.application.bioluminate.antibody.scaffold_search module schrodinger.application.bioluminate.antibody.search_results_table module schrodinger.application.bioluminate.antibody.sequence_indexer module schrodinger.application.bioluminate.antibody.utils module schrodinger.application.bioluminate.bwidgets module schrodinger.application.bioluminate.classify module schrodinger.application.bioluminate.drivers module schrodinger.application.bioluminate.drivers.io module schrodinger.application.bioluminate.epitope module schrodinger.application.bioluminate.epitope.driver module schrodinger.application.bioluminate.epitope.psc_workflow module schrodinger.application.bioluminate.epitope.utils module schrodinger.application.bioluminate.epitope.utils.esc_utils module schrodinger.application.bioluminate.escomp module schrodinger.application.bioluminate.interaction_calculator module schrodinger.application.bioluminate.met_oxidation module schrodinger.application.bioluminate.met_oxidation.hmc_sim_runner module schrodinger.application.bioluminate.met_oxidation.md_sim_runner module schrodinger.application.bioluminate.methionine_oxidation module schrodinger.application.bioluminate.mutation module schrodinger.application.bioluminate.nucleic module schrodinger.application.bioluminate.nucleic.constants module schrodinger.application.bioluminate.nucleic.mutator module schrodinger.application.bioluminate.patch_utils module schrodinger.application.bioluminate.patch_utils.msurfext module schrodinger.application.bioluminate.patch_utils.patch_finder module schrodinger.application.bioluminate.patch_utils.pre_analyze module schrodinger.application.bioluminate.patch_utils.settings module schrodinger.application.bioluminate.peptide_sar module schrodinger.application.bioluminate.peptide_sar.encode module schrodinger.application.bioluminate.peptide_sar.io module schrodinger.application.bioluminate.peptide_sar.label module schrodinger.application.bioluminate.peptide_sar.sar module schrodinger.application.bioluminate.peptide_sar.statistics module schrodinger.application.bioluminate.pml_menus module schrodinger.application.bioluminate.pose_filtering module schrodinger.application.bioluminate.pose_filtering.csv_filter module schrodinger.application.bioluminate.pose_filtering.hdx_analysis module schrodinger.application.bioluminate.pose_filtering.hdx_calc module schrodinger.application.bioluminate.pose_filtering.hdx_io module schrodinger.application.bioluminate.pose_filtering.operators module schrodinger.application.bioluminate.pose_filtering.residue_filter module schrodinger.application.bioluminate.pose_filtering.test module schrodinger.application.bioluminate.propfilter module schrodinger.application.bioluminate.propfilter_ui module schrodinger.application.bioluminate.propka_parse module schrodinger.application.bioluminate.protein module schrodinger.application.bioluminate.protein.mutator module schrodinger.application.bioluminate.protein.protein module schrodinger.application.bioluminate.protein.utils module schrodinger.application.bioluminate.protein_interaction module schrodinger.application.bioluminate.protein_interaction.calculate module schrodinger.application.bioluminate.protein_interaction.tasks module schrodinger.application.bioluminate.protein_interaction.utils module schrodinger.application.bioluminate.protein_protein_docking_shared module schrodinger.application.bioluminate.protein_report_widget module schrodinger.application.bioluminate.protein_structure_quality module schrodinger.application.bioluminate.protein_structure_quality_ui module schrodinger.application.bioluminate.reactive_residues module schrodinger.application.bioluminate.residue_scanning module schrodinger.application.bioluminate.residue_scanning.properties module schrodinger.application.bioluminate.run_propka module schrodinger.application.bioluminate.sliderchart module schrodinger.application.bioluminate.ssv module schrodinger.application.bioluminate.ssv.toolbars module schrodinger.application.bioluminate.ssv.viewer module schrodinger.application.bioluminate.surfcomp module schrodinger.application.bioluminate.tcr module schrodinger.application.bioluminate.tcr.annotate module schrodinger.application.bioluminate.tcr.docking_angles module schrodinger.application.bioluminate.update_germline_db module schrodinger.application.bioluminate.update_germline_db.translate_db module schrodinger.application.bioluminate.validate_imported_modules module schrodinger.application.bioluminate.workspacelabeler module schrodinger.application.canvas module schrodinger.application.canvas.base module schrodinger.application.canvas.cluster module schrodinger.application.canvas.clustergui module schrodinger.application.canvas.fingerprint module schrodinger.application.canvas.fingerprintgui module schrodinger.application.canvas.r_group module schrodinger.application.canvas.r_group_dee module schrodinger.application.canvas.similarity module schrodinger.application.canvas.similaritygui module schrodinger.application.canvas.topo_descriptors module schrodinger.application.canvas.utils module schrodinger.application.combiglide module schrodinger.application.combiglide.connection_storage module schrodinger.application.combiglide.corehop module schrodinger.application.combiglide.packages module schrodinger.application.combiglide.utils module schrodinger.application.combinatorial_diversity module schrodinger.application.combinatorial_diversity.diversity_fingerprinter module schrodinger.application.combinatorial_diversity.diversity_selector module schrodinger.application.combinatorial_diversity.diversity_splitter module schrodinger.application.combinatorial_diversity.driver_utils module schrodinger.application.combinatorial_diversity.splitter_utils module schrodinger.application.combinatorial_explorer module schrodinger.application.combinatorial_explorer.driver_utils module schrodinger.application.combinatorial_explorer.route_screener module schrodinger.application.combinatorial_screen module schrodinger.application.combinatorial_screen.combinatorial_screener module schrodinger.application.combinatorial_screen.driver_utils module schrodinger.application.combinatorial_screen.fingerprint_utils module schrodinger.application.dendrogram module schrodinger.application.dendrogram.core_class module schrodinger.application.dendrogram.gradientSelector module schrodinger.application.dendrogram.proteinDendrogram module schrodinger.application.dendrogram.randTestSet module schrodinger.application.desmond module schrodinger.application.desmond.ana module schrodinger.application.desmond.antlr3 module schrodinger.application.desmond.antlr3.compat module schrodinger.application.desmond.antlr3.constants module schrodinger.application.desmond.antlr3.debug module schrodinger.application.desmond.antlr3.dfa module schrodinger.application.desmond.antlr3.exceptions module schrodinger.application.desmond.antlr3.recognizers module schrodinger.application.desmond.antlr3.streams module schrodinger.application.desmond.antlr3.tokens module schrodinger.application.desmond.antlr3.tree module schrodinger.application.desmond.antlr3.treewizard module schrodinger.application.desmond.arkdb module schrodinger.application.desmond.automatic_analysis_generator module schrodinger.application.desmond.autopartition module schrodinger.application.desmond.bennett module schrodinger.application.desmond.bld_def module schrodinger.application.desmond.bld_ver module schrodinger.application.desmond.cmdline module schrodinger.application.desmond.cmj module schrodinger.application.desmond.cms module schrodinger.application.desmond.cms_utils module schrodinger.application.desmond.cns_io module schrodinger.application.desmond.config_utils module schrodinger.application.desmond.constants module schrodinger.application.desmond.correlation_tau module schrodinger.application.desmond.cwidget module schrodinger.application.desmond.deltaE module schrodinger.application.desmond.depictor module schrodinger.application.desmond.desmond_advanced_tab_ui module schrodinger.application.desmond.driver_utils module schrodinger.application.desmond.ene_utils module schrodinger.application.desmond.enhanced_sampling module schrodinger.application.desmond.enhanced_sampling.FcnTypes module schrodinger.application.desmond.enhanced_sampling.mexpLexer module schrodinger.application.desmond.enhanced_sampling.mexpParser module schrodinger.application.desmond.enhsamp module schrodinger.application.desmond.envir module schrodinger.application.desmond.event_analysis module schrodinger.application.desmond.event_analysis.pl_image_tools module schrodinger.application.desmond.fep_dialog module schrodinger.application.desmond.fep_edge_data module schrodinger.application.desmond.fep_edge_data_classifier module schrodinger.application.desmond.fep_edge_report_maker module schrodinger.application.desmond.fep_mapping module schrodinger.application.desmond.fep_net_charge module schrodinger.application.desmond.fep_reporter module schrodinger.application.desmond.fep_schedule module schrodinger.application.desmond.fep_scholar_msj_generator module schrodinger.application.desmond.fep_scholar_rules module schrodinger.application.desmond.fep_scholar_util module schrodinger.application.desmond.fep_struc module schrodinger.application.desmond.fep_util module schrodinger.application.desmond.fepana module schrodinger.application.desmond.feputils module schrodinger.application.desmond.ffiostructure module schrodinger.application.desmond.file_utils module schrodinger.application.desmond.frag_snap module schrodinger.application.desmond.gaussian_filter module schrodinger.application.desmond.gchart module schrodinger.application.desmond.gcmc_utils module schrodinger.application.desmond.gconfig module schrodinger.application.desmond.gpgpu module schrodinger.application.desmond.gpgpu.test_gpgpu module schrodinger.application.desmond.gui module schrodinger.application.desmond.image_generator module schrodinger.application.desmond.input_group_ui module schrodinger.application.desmond.keep_struc_tags module schrodinger.application.desmond.kinetics module schrodinger.application.desmond.kinetics.cleanup module schrodinger.application.desmond.kinetics.enhanced_sampling module schrodinger.application.desmond.kinetics.mtd_cleanup module schrodinger.application.desmond.kinetics.utils module schrodinger.application.desmond.lambda_dynamics_utils module schrodinger.application.desmond.launch_utils module schrodinger.application.desmond.license module schrodinger.application.desmond.license_utils module schrodinger.application.desmond.maestro module schrodinger.application.desmond.measurement module schrodinger.application.desmond.membrane_utils module schrodinger.application.desmond.memory module schrodinger.application.desmond.meta module schrodinger.application.desmond.move_alchem_ions module schrodinger.application.desmond.mplchart module schrodinger.application.desmond.msj_defaults module schrodinger.application.desmond.msj_generator module schrodinger.application.desmond.msj_generator.common module schrodinger.application.desmond.msj_generator.constant_ph module schrodinger.application.desmond.msj_generator.fep module schrodinger.application.desmond.msj_generator.fep.absolute_binding module schrodinger.application.desmond.msj_generator.fep.covalent_ligand module schrodinger.application.desmond.msj_generator.fep.metalloprotein module schrodinger.application.desmond.msj_generator.fep.protein module schrodinger.application.desmond.msj_generator.fep.small_molecule module schrodinger.application.desmond.msj_generator.fep.solubility module schrodinger.application.desmond.msj_generator.keep_struc_tags module schrodinger.application.desmond.msj_generator.lambda_dynamics module schrodinger.application.desmond.msj_generator.msj_constants module schrodinger.application.desmond.msj_generator.mxmd module schrodinger.application.desmond.msj_generator.subjob_msj module schrodinger.application.desmond.msj_generator.unbinding_kinetics module schrodinger.application.desmond.msj_generator.workflow_params module schrodinger.application.desmond.multisim module schrodinger.application.desmond.multisim.parser module schrodinger.application.desmond.multisimstartup module schrodinger.application.desmond.mxmd module schrodinger.application.desmond.mxmd.mxmd_cleanup module schrodinger.application.desmond.mxmd.mxmd_system_builder module schrodinger.application.desmond.new_fep_edge_data module schrodinger.application.desmond.physical_leg_infra module schrodinger.application.desmond.picklejar module schrodinger.application.desmond.platforms module schrodinger.application.desmond.predict_remd_temp module schrodinger.application.desmond.process_fep_traj module schrodinger.application.desmond.queue module schrodinger.application.desmond.r_group_asl module schrodinger.application.desmond.remd module schrodinger.application.desmond.repair_cms module schrodinger.application.desmond.replica_dE module schrodinger.application.desmond.replica_exchange_review module schrodinger.application.desmond.replica_sid_generator module schrodinger.application.desmond.report_helper module schrodinger.application.desmond.rest_inp module schrodinger.application.desmond.rest_tab_ui module schrodinger.application.desmond.rl_helper module schrodinger.application.desmond.sid_plots module schrodinger.application.desmond.sid_plots.pl_interactions module schrodinger.application.desmond.sid_plots.pl_lid module schrodinger.application.desmond.simulation_block_data module schrodinger.application.desmond.simulation_block_test module schrodinger.application.desmond.skip_fep_utils module schrodinger.application.desmond.smarts module schrodinger.application.desmond.solubility_utils module schrodinger.application.desmond.stage module schrodinger.application.desmond.stage.analysis module schrodinger.application.desmond.stage.app module schrodinger.application.desmond.stage.app.absolute_binding module schrodinger.application.desmond.stage.app.absolute_binding.restraint module schrodinger.application.desmond.stage.app.absolute_binding.stage module schrodinger.application.desmond.stage.app.absolute_binding.struc module schrodinger.application.desmond.stage.app.constant_ph module schrodinger.application.desmond.stage.app.fragment_linking module schrodinger.application.desmond.stage.app.fragment_linking.stage module schrodinger.application.desmond.stage.app.fragment_linking.utils module schrodinger.application.desmond.stage.app.kinetics module schrodinger.application.desmond.stage.app.lambda_dynamics module schrodinger.application.desmond.stage.app.lambda_dynamics_analysis module schrodinger.application.desmond.stage.app.matsci module schrodinger.application.desmond.stage.app.mxmd module schrodinger.application.desmond.stage.app.solubility module schrodinger.application.desmond.stage.app.watermap module schrodinger.application.desmond.stage.constants module schrodinger.application.desmond.stage.deprecate module schrodinger.application.desmond.stage.fep_mapper module schrodinger.application.desmond.stage.jobs module schrodinger.application.desmond.stage.launcher module schrodinger.application.desmond.stage.prepare module schrodinger.application.desmond.stage.prepare.forcefield module schrodinger.application.desmond.stage.prepare.structure module schrodinger.application.desmond.stage.run_method_parallel module schrodinger.application.desmond.stage.simulate module schrodinger.application.desmond.stage.utils module schrodinger.application.desmond.stage.workflow module schrodinger.application.desmond.starter module schrodinger.application.desmond.starter.generator module schrodinger.application.desmond.starter.generator.common module schrodinger.application.desmond.starter.generator.constant_ph module schrodinger.application.desmond.starter.generator.fep_absolute_binding module schrodinger.application.desmond.starter.generator.fep_plus module schrodinger.application.desmond.starter.generator.fep_residue_scanning module schrodinger.application.desmond.starter.generator.fep_solubility module schrodinger.application.desmond.starter.generator.mxmd module schrodinger.application.desmond.starter.generator.unbinding_kinetics module schrodinger.application.desmond.starter.starter module schrodinger.application.desmond.starter.ui module schrodinger.application.desmond.starter.ui.cmdline module schrodinger.application.desmond.starter.ui.constant_ph module schrodinger.application.desmond.starter.ui.fep_absolute_binding module schrodinger.application.desmond.starter.ui.fep_plus module schrodinger.application.desmond.starter.ui.fep_residue_scanning module schrodinger.application.desmond.starter.ui.fep_solubility module schrodinger.application.desmond.starter.ui.mxmd module schrodinger.application.desmond.starter.ui.unbinding_kinetics module schrodinger.application.desmond.struc module schrodinger.application.desmond.system_builder_inp module schrodinger.application.desmond.system_builder_util module schrodinger.application.desmond.systype module schrodinger.application.desmond.task module schrodinger.application.desmond.test_utils module schrodinger.application.desmond.torsion_related module schrodinger.application.desmond.typing_utils module schrodinger.application.desmond.util module schrodinger.application.epik module schrodinger.application.fpsim module schrodinger.application.fragment_virtual_screening module schrodinger.application.fragment_virtual_screening.bq_query_task module schrodinger.application.fragment_virtual_screening.frag_vs_stages module schrodinger.application.fragment_virtual_screening.frag_vs_utils module schrodinger.application.glide module schrodinger.application.glide.client_module module schrodinger.application.glide.ensemble_selection module schrodinger.application.glide.glide module schrodinger.application.glide.glideanalysis module schrodinger.application.glide.gui module schrodinger.application.glide.http_client module schrodinger.application.glide.http_server module schrodinger.application.glide.ligand_designer module schrodinger.application.glide.packages module schrodinger.application.glide.poseviewconvert module schrodinger.application.glide.property_names module schrodinger.application.glide.sort_parser_common module schrodinger.application.glide.sort_utils module schrodinger.application.glide.utils module schrodinger.application.glide.xpdes module schrodinger.application.hitexpander module schrodinger.application.inputconfig module schrodinger.application.jaguar module schrodinger.application.jaguar.autots_bonding module schrodinger.application.jaguar.autots_constants module schrodinger.application.jaguar.autots_exceptions module schrodinger.application.jaguar.autots_input module schrodinger.application.jaguar.autots_input_constants module schrodinger.application.jaguar.autots_keywords module schrodinger.application.jaguar.autots_rmsd module schrodinger.application.jaguar.autots_validation module schrodinger.application.jaguar.basis module schrodinger.application.jaguar.check_headers module schrodinger.application.jaguar.constants module schrodinger.application.jaguar.csrch_input_constants module schrodinger.application.jaguar.discretized_1d_function module schrodinger.application.jaguar.esol_constants module schrodinger.application.jaguar.esol_input module schrodinger.application.jaguar.esol_keywords module schrodinger.application.jaguar.esol_validation module schrodinger.application.jaguar.exceptions module schrodinger.application.jaguar.file_logger module schrodinger.application.jaguar.global_macros module schrodinger.application.jaguar.gui module schrodinger.application.jaguar.gui.base_panel module schrodinger.application.jaguar.gui.basis_selector module schrodinger.application.jaguar.gui.edit_dialog module schrodinger.application.jaguar.gui.filedialog module schrodinger.application.jaguar.gui.input_tab_widgets module schrodinger.application.jaguar.gui.input_tab_widgets_hb module schrodinger.application.jaguar.gui.input_tab_widgets_pka module schrodinger.application.jaguar.gui.solvent_selector module schrodinger.application.jaguar.gui.tabs module schrodinger.application.jaguar.gui.tabs.base_tab module schrodinger.application.jaguar.gui.tabs.coordinates module schrodinger.application.jaguar.gui.tabs.input_sub_tabs module schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab module schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set module schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints module schrodinger.application.jaguar.gui.tabs.input_tab module schrodinger.application.jaguar.gui.tabs.irc_tab module schrodinger.application.jaguar.gui.tabs.molecule_tab module schrodinger.application.jaguar.gui.tabs.multi_structure_tab module schrodinger.application.jaguar.gui.tabs.optimization_tab module schrodinger.application.jaguar.gui.tabs.output_tab module schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up module schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up.per_atom_basis_ui module schrodinger.application.jaguar.gui.tabs.properties_tab module schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab module schrodinger.application.jaguar.gui.tabs.reaction_properties_tab module schrodinger.application.jaguar.gui.tabs.reaction_tab module schrodinger.application.jaguar.gui.tabs.scan_tab module schrodinger.application.jaguar.gui.tabs.scf_tab module schrodinger.application.jaguar.gui.tabs.solvation_tab module schrodinger.application.jaguar.gui.tabs.sub_tab_widgets module schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets module schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets module schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets module schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector module schrodinger.application.jaguar.gui.tabs.theory_tab module schrodinger.application.jaguar.gui.tabs.transition_state_tab module schrodinger.application.jaguar.gui.theory_selector module schrodinger.application.jaguar.gui.theory_tab_widgets module schrodinger.application.jaguar.gui.timing module schrodinger.application.jaguar.gui.ui module schrodinger.application.jaguar.gui.ui.config_dialog_jaguar_ui module schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui module schrodinger.application.jaguar.gui.ui.define_smarts_panel_ui module schrodinger.application.jaguar.gui.ui.edit_dialog_ui module schrodinger.application.jaguar.gui.ui.excited_state_widget_ui module schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui module schrodinger.application.jaguar.gui.ui.input_hb_top_ui module schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui module schrodinger.application.jaguar.gui.ui.input_pka_top_ui module schrodinger.application.jaguar.gui.ui.input_std_bottom_ui module schrodinger.application.jaguar.gui.ui.input_sub_tabs module schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui module schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui module schrodinger.application.jaguar.gui.ui.input_top_ui module schrodinger.application.jaguar.gui.ui.irc_bottom_ui module schrodinger.application.jaguar.gui.ui.irc_top_ui module schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui module schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui module schrodinger.application.jaguar.gui.ui.molecule_top_ui module schrodinger.application.jaguar.gui.ui.multi_structures_ui module schrodinger.application.jaguar.gui.ui.optimization_tab_ui module schrodinger.application.jaguar.gui.ui.output_tab_ui module schrodinger.application.jaguar.gui.ui.pka_smarts_page_ui module schrodinger.application.jaguar.gui.ui.properties_tab_ui module schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui module schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui module schrodinger.application.jaguar.gui.ui.reaction_tab_ui module schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui module schrodinger.application.jaguar.gui.ui.scan_tab_ui module schrodinger.application.jaguar.gui.ui.scf_tab_ui module schrodinger.application.jaguar.gui.ui.solvent_pka_tab_ui module schrodinger.application.jaguar.gui.ui.solvent_tab_ui module schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui module schrodinger.application.jaguar.gui.ui.theory_tab_ui module schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui module schrodinger.application.jaguar.gui.ui.transition_state_top_ui module schrodinger.application.jaguar.gui.utils module schrodinger.application.jaguar.hess_guess module schrodinger.application.jaguar.hydrokinetic_constants module schrodinger.application.jaguar.hydrokinetic_input module schrodinger.application.jaguar.hydrokinetic_input_constants module schrodinger.application.jaguar.hydrokinetic_keywords module schrodinger.application.jaguar.hydrokinetic_validation module schrodinger.application.jaguar.input module schrodinger.application.jaguar.jagconvert module schrodinger.application.jaguar.jaguar_config_dialog module schrodinger.application.jaguar.jaguar_diff module schrodinger.application.jaguar.jaguar_keyword_utils module schrodinger.application.jaguar.jaguar_tasks module schrodinger.application.jaguar.keywordDB module schrodinger.application.jaguar.kinetics module schrodinger.application.jaguar.macro_pka_constants module schrodinger.application.jaguar.macro_pka_input module schrodinger.application.jaguar.macro_pka_keywords module schrodinger.application.jaguar.macro_pka_utils module schrodinger.application.jaguar.macro_pka_validation module schrodinger.application.jaguar.mmjag module schrodinger.application.jaguar.neural_network_optimizer module schrodinger.application.jaguar.nmr_basis module schrodinger.application.jaguar.nmr_interactions module schrodinger.application.jaguar.nmr_utils module schrodinger.application.jaguar.output module schrodinger.application.jaguar.permutation_symmetry module schrodinger.application.jaguar.pk50_report module schrodinger.application.jaguar.qrnn module schrodinger.application.jaguar.qrnn.constants module schrodinger.application.jaguar.qrnn.input module schrodinger.application.jaguar.qrnn.keywords module schrodinger.application.jaguar.qrnn.temp_opt module schrodinger.application.jaguar.qrnn.validation module schrodinger.application.jaguar.results module schrodinger.application.jaguar.rotation_barriers_input module schrodinger.application.jaguar.rotation_barriers_keywords module schrodinger.application.jaguar.rotation_barriers_validation module schrodinger.application.jaguar.scan module schrodinger.application.jaguar.simple_spec module schrodinger.application.jaguar.solvation_input module schrodinger.application.jaguar.solvation_keywords module schrodinger.application.jaguar.solvation_validation module schrodinger.application.jaguar.spectroscopy_defaults module schrodinger.application.jaguar.spin_simulator_v2 module schrodinger.application.jaguar.textparser module schrodinger.application.jaguar.update_pka_settings module schrodinger.application.jaguar.update_pka_settings_ui module schrodinger.application.jaguar.user_config module schrodinger.application.jaguar.utils module schrodinger.application.jaguar.validation module schrodinger.application.jaguar.workflow_input module schrodinger.application.jaguar.workflow_keywords module schrodinger.application.jaguar.workflow_validation module schrodinger.application.job_monitor module schrodinger.application.job_monitor.buttons module schrodinger.application.job_monitor.diagnostics_dialog_ui module schrodinger.application.job_monitor.file_browser_ui module schrodinger.application.job_monitor.job_info_view_ui module schrodinger.application.job_monitor.job_monitor_diagnostics_dialog module schrodinger.application.job_monitor.job_monitor_file_browser module schrodinger.application.job_monitor.job_monitor_gui module schrodinger.application.job_monitor.job_monitor_icons_rc module schrodinger.application.job_monitor.job_monitor_models module schrodinger.application.job_monitor.job_monitor_progress_bar module schrodinger.application.job_monitor.job_monitor_stylesheets module schrodinger.application.job_monitor.job_monitor_table module schrodinger.application.job_monitor.job_monitor_widgets module schrodinger.application.job_monitor.top_level_view_ui module schrodinger.application.job_monitor.util module schrodinger.application.jobserver_cert_gui_dir module schrodinger.application.jobserver_cert_gui_dir.jobserver_cert_gui_icons_rc module schrodinger.application.jobserver_cert_gui_dir.registration_dialogs module schrodinger.application.jobserver_cert_gui_dir.registration_panel_ui module schrodinger.application.licensing module schrodinger.application.licensing.flexlm module schrodinger.application.licensing.licadmin module schrodinger.application.licensing.licerror module schrodinger.application.licensing.licserver module schrodinger.application.licensing.licserver.client module schrodinger.application.licensing.licserver.exceptions module schrodinger.application.licensing.licserver.install module schrodinger.application.licensing.licserver.main module schrodinger.application.licensing.licserver.server module schrodinger.application.licensing.lmgrd_log_parser module schrodinger.application.licensing.netsuiteapi module schrodinger.application.ligprep module schrodinger.application.ligprep.ionizer module schrodinger.application.livedesign module schrodinger.application.livedesign.constants module schrodinger.application.livedesign.data_classes module schrodinger.application.livedesign.entry_types module schrodinger.application.livedesign.export_map_manager module schrodinger.application.livedesign.export_models module schrodinger.application.livedesign.export_setup_ui module schrodinger.application.livedesign.export_tasks module schrodinger.application.livedesign.export_ui module schrodinger.application.livedesign.icons_rc module schrodinger.application.livedesign.import_utils module schrodinger.application.livedesign.invalid_ge_id_warning_ui module schrodinger.application.livedesign.io_utils module schrodinger.application.livedesign.ld_base_classes module schrodinger.application.livedesign.ld_connection_checker module schrodinger.application.livedesign.ld_export module schrodinger.application.livedesign.ld_export_gui module schrodinger.application.livedesign.ld_folder_tree module schrodinger.application.livedesign.ld_glide_utils module schrodinger.application.livedesign.ld_import module schrodinger.application.livedesign.ld_import_utils module schrodinger.application.livedesign.ld_ligand_strain_utils module schrodinger.application.livedesign.ld_maestro_actions module schrodinger.application.livedesign.ld_maestro_actions_constants module schrodinger.application.livedesign.ld_mmgbsa_utils module schrodinger.application.livedesign.ld_model_input module schrodinger.application.livedesign.ld_settings module schrodinger.application.livedesign.ld_strain_rescore_utils module schrodinger.application.livedesign.ld_tasks module schrodinger.application.livedesign.ld_utils module schrodinger.application.livedesign.ldclient_proxy module schrodinger.application.livedesign.lid module schrodinger.application.livedesign.live_report_widget module schrodinger.application.livedesign.live_report_widget_ui module schrodinger.application.livedesign.login module schrodinger.application.livedesign.login2_ui module schrodinger.application.livedesign.login_gui module schrodinger.application.livedesign.login_gui2 module schrodinger.application.livedesign.login_ui module schrodinger.application.livedesign.maestro_ld_connection module schrodinger.application.livedesign.maestro_ld_mapping_ui module schrodinger.application.livedesign.maestro_sync module schrodinger.application.livedesign.mapping_widgets module schrodinger.application.livedesign.mappings_manager_ui module schrodinger.application.livedesign.panel_components module schrodinger.application.livedesign.pose_name_panel module schrodinger.application.livedesign.pose_name_panel_ui module schrodinger.application.livedesign.pse_helpers module schrodinger.application.livedesign.save_mapping_dialog_ui module schrodinger.application.livedesign.selection_pop_up_ui module schrodinger.application.livedesign.summary module schrodinger.application.livedesign.summary_ui module schrodinger.application.livedesign.tasks module schrodinger.application.livedesign.two_d_render module schrodinger.application.livedesign.upload_utils module schrodinger.application.livedesign.widgets module schrodinger.application.macromodel module schrodinger.application.macromodel.apps module schrodinger.application.macromodel.input module schrodinger.application.macromodel.packages module schrodinger.application.macromodel.paraUtils module schrodinger.application.macromodel.tools module schrodinger.application.macromodel.utils module schrodinger.application.matsci module schrodinger.application.matsci.amorphous module schrodinger.application.matsci.anharmonic module schrodinger.application.matsci.appbase module schrodinger.application.matsci.aseutils module schrodinger.application.matsci.atom_group module schrodinger.application.matsci.atomicsymbols module schrodinger.application.matsci.atomicsymbolsgui module schrodinger.application.matsci.automated_cg_mapping module schrodinger.application.matsci.bandshape_utils module schrodinger.application.matsci.basiselements module schrodinger.application.matsci.boltzmann_avg_props module schrodinger.application.matsci.buildcomplex module schrodinger.application.matsci.buildcomplex2d module schrodinger.application.matsci.builderwidgets module schrodinger.application.matsci.cache module schrodinger.application.matsci.cctbx module schrodinger.application.matsci.cctbx.rot_mx module schrodinger.application.matsci.cg_mapping module schrodinger.application.matsci.cgforcefield module schrodinger.application.matsci.cgforcefieldgui module schrodinger.application.matsci.chargegui module schrodinger.application.matsci.clusterstruct module schrodinger.application.matsci.clusterstructgui module schrodinger.application.matsci.coarsegrain module schrodinger.application.matsci.codeutils module schrodinger.application.matsci.colorutils module schrodinger.application.matsci.configdlgs module schrodinger.application.matsci.controlicons_rc module schrodinger.application.matsci.crest module schrodinger.application.matsci.density_analysis module schrodinger.application.matsci.density_analysis_widget module schrodinger.application.matsci.desconfig module schrodinger.application.matsci.desmondutils module schrodinger.application.matsci.deswidgets module schrodinger.application.matsci.elasticity module schrodinger.application.matsci.elasticity.elastic module schrodinger.application.matsci.elasticity.strain module schrodinger.application.matsci.elasticity.stress module schrodinger.application.matsci.elasticity.tensors module schrodinger.application.matsci.elementalprops module schrodinger.application.matsci.enc module schrodinger.application.matsci.enumeration module schrodinger.application.matsci.equilibrium_md module schrodinger.application.matsci.espresso module schrodinger.application.matsci.espresso.ppdb module schrodinger.application.matsci.espresso.qeinput module schrodinger.application.matsci.espresso.qeoutput module schrodinger.application.matsci.espresso.utils module schrodinger.application.matsci.etarotamers module schrodinger.application.matsci.etatoggle module schrodinger.application.matsci.fragments module schrodinger.application.matsci.freevolume module schrodinger.application.matsci.genetic_optimization module schrodinger.application.matsci.geometry module schrodinger.application.matsci.graph module schrodinger.application.matsci.gsas module schrodinger.application.matsci.gsas.atmdata module schrodinger.application.matsci.gsas.ElementTable module schrodinger.application.matsci.gsas.GSASIIElem module schrodinger.application.matsci.gsas.GSASIIfiles module schrodinger.application.matsci.gsas.GSASIIlattice module schrodinger.application.matsci.gsas.GSASIImath module schrodinger.application.matsci.gsas.GSASIIpwd module schrodinger.application.matsci.gsas.GSASIIspc module schrodinger.application.matsci.gutils module schrodinger.application.matsci.hdfutils module schrodinger.application.matsci.jaguar_multistage_workflow_utils module schrodinger.application.matsci.jaguar_restart module schrodinger.application.matsci.jaguarworkflows module schrodinger.application.matsci.jagwidgets module schrodinger.application.matsci.jobdirdlg module schrodinger.application.matsci.jobutils module schrodinger.application.matsci.jwsteps module schrodinger.application.matsci.kmc module schrodinger.application.matsci.kmcgui module schrodinger.application.matsci.maestrocmds module schrodinger.application.matsci.mecp_mod module schrodinger.application.matsci.mlearn module schrodinger.application.matsci.mlearn.base module schrodinger.application.matsci.mlearn.descriptor module schrodinger.application.matsci.mlearn.features module schrodinger.application.matsci.mlearn.sklearn_json module schrodinger.application.matsci.mlearn.sklearn_json.classification module schrodinger.application.matsci.mlearn.sklearn_json.common module schrodinger.application.matsci.mlearn.sklearn_json.csr module schrodinger.application.matsci.mlearn.sklearn_json.decomposition module schrodinger.application.matsci.mlearn.sklearn_json.regression module schrodinger.application.matsci.montecarlo module schrodinger.application.matsci.msconst module schrodinger.application.matsci.msminimize module schrodinger.application.matsci.msprops module schrodinger.application.matsci.mstest module schrodinger.application.matsci.msutils module schrodinger.application.matsci.mswidgets module schrodinger.application.matsci.multiapp module schrodinger.application.matsci.nano module schrodinger.application.matsci.nano.check module schrodinger.application.matsci.nano.constants module schrodinger.application.matsci.nano.interface_mod module schrodinger.application.matsci.nano.particle module schrodinger.application.matsci.nano.plane module schrodinger.application.matsci.nano.sheet module schrodinger.application.matsci.nano.slab module schrodinger.application.matsci.nano.space_groups module schrodinger.application.matsci.nano.surfaces_interfaces_mod module schrodinger.application.matsci.nano.tools module schrodinger.application.matsci.nano.tube module schrodinger.application.matsci.nano.util module schrodinger.application.matsci.nano.xtal module schrodinger.application.matsci.optoelectronics module schrodinger.application.matsci.order_parameter_mod module schrodinger.application.matsci.packmol module schrodinger.application.matsci.parserutils module schrodinger.application.matsci.pbcutils module schrodinger.application.matsci.permittivity module schrodinger.application.matsci.plotwidgets module schrodinger.application.matsci.pmgutils module schrodinger.application.matsci.polymer module schrodinger.application.matsci.qualityslider module schrodinger.application.matsci.qubec_utils module schrodinger.application.matsci.rdpattern module schrodinger.application.matsci.rdpattern_gui module schrodinger.application.matsci.reaction_workflow_gui_utils module schrodinger.application.matsci.reaction_workflow_utils module schrodinger.application.matsci.reorder module schrodinger.application.matsci.reordergui module schrodinger.application.matsci.reportutils module schrodinger.application.matsci.rxn_channel module schrodinger.application.matsci.rxn_path module schrodinger.application.matsci.sculptcomplex module schrodinger.application.matsci.shapes module schrodinger.application.matsci.siteselector module schrodinger.application.matsci.siteselector.siteselector module schrodinger.application.matsci.sliceplot module schrodinger.application.matsci.smartsutils module schrodinger.application.matsci.smartsutilsgui module schrodinger.application.matsci.species module schrodinger.application.matsci.speciesgui module schrodinger.application.matsci.spectra module schrodinger.application.matsci.stress_strain module schrodinger.application.matsci.swap_fragments_utils module schrodinger.application.matsci.textlogger module schrodinger.application.matsci.typography module schrodinger.application.matsci.uq_utils module schrodinger.application.matsci.wfmanagement module schrodinger.application.matsci.xrd module schrodinger.application.matsci.yamlutils module schrodinger.application.matsci.zmutils module schrodinger.application.medchem module schrodinger.application.medchem.property module schrodinger.application.mopac module schrodinger.application.mopac.exceptions module schrodinger.application.mopac.mopac_backend module schrodinger.application.mopac.mopac_launchers module schrodinger.application.mopac.mopac_parser module schrodinger.application.mopac.mopac_startup module schrodinger.application.mopac.mopac_surfaces module schrodinger.application.mopac.results_main module schrodinger.application.mopac.structure_launchers module schrodinger.application.mopac.utils module schrodinger.application.pathfinder module schrodinger.application.pathfinder.aligner module schrodinger.application.pathfinder.analysis module schrodinger.application.pathfinder.multiroute module schrodinger.application.pathfinder.reaction module schrodinger.application.pathfinder.render module schrodinger.application.pathfinder.route module schrodinger.application.pathfinder.synthesis module schrodinger.application.phase module schrodinger.application.phase.compare_utils module schrodinger.application.phase.constants module schrodinger.application.phase.create_xvol module schrodinger.application.phase.featureselector module schrodinger.application.phase.hypothesis module schrodinger.application.phase.hypothesis_binding_modes module schrodinger.application.phase.input module schrodinger.application.phase.license module schrodinger.application.phase.packages module schrodinger.application.phase.packages.align_ligands_driver_options module schrodinger.application.phase.packages.bedroc_screener module schrodinger.application.phase.packages.cat_hypo_converter module schrodinger.application.phase.packages.conformer_reader module schrodinger.application.phase.packages.conformer_storage module schrodinger.application.phase.packages.hypo_refine module schrodinger.application.phase.packages.hypo_refine.hypo_utils module schrodinger.application.phase.packages.hypo_refine.job_utils module schrodinger.application.phase.packages.hypo_refine.option_utils module schrodinger.application.phase.packages.hypo_refine.project_utils module schrodinger.application.phase.packages.hypo_refine.screen_utils module schrodinger.application.phase.packages.ligand_aligner module schrodinger.application.phase.packages.mmp2d module schrodinger.application.phase.packages.mmp3d_driver_utils module schrodinger.application.phase.packages.mmp3dscreener module schrodinger.application.phase.packages.mmp_compare_utils module schrodinger.application.phase.packages.oned_app_utils module schrodinger.application.phase.packages.oned_option_utils module schrodinger.application.phase.packages.oned_task_utils module schrodinger.application.phase.packages.phase_convert_MOE module schrodinger.application.phase.packages.phase_database_arg_utils module schrodinger.application.phase.packages.phase_database_job_utils module schrodinger.application.phase.packages.phase_option_utils module schrodinger.application.phase.packages.phase_screen_driver_utils module schrodinger.application.phase.packages.phase_screen_utils module schrodinger.application.phase.packages.phase_utils module schrodinger.application.phase.packages.shape_binary_utils module schrodinger.application.phase.packages.shape_creation_logic module schrodinger.application.phase.packages.shape_diversity module schrodinger.application.phase.packages.shape_generator module schrodinger.application.phase.packages.shape_ligprep module schrodinger.application.phase.packages.shape_screen_al_driver module schrodinger.application.phase.packages.shape_screen_al_node module schrodinger.application.phase.packages.shape_screen_al_utils module schrodinger.application.phase.packages.shape_screen_arg_utils module schrodinger.application.phase.packages.shape_screen_gpu_generate module schrodinger.application.phase.packages.shape_screen_gpu_update module schrodinger.application.phase.packages.shape_screen_job_utils module schrodinger.application.phase.packages.shape_screen_oned_driver_utils module schrodinger.application.phase.packages.test module schrodinger.application.phase.phase_markers module schrodinger.application.phase.phase_widgets module schrodinger.application.phase.pt_hypothesis module schrodinger.application.phase.shape_screen_reporter module schrodinger.application.phase.shape_screen_reporter.option_utils module schrodinger.application.phase.shape_screen_reporter.prop_utils module schrodinger.application.phase.shape_screen_reporter.task_utils module schrodinger.application.phase.shape_screen_reporter.tasks module schrodinger.application.phase.utils module schrodinger.application.prepwizard module schrodinger.application.prepwizard2 module schrodinger.application.prepwizard2.diagnostics module schrodinger.application.prepwizard2.tasks module schrodinger.application.prime module schrodinger.application.prime.gui module schrodinger.application.prime.gui.analyze_energy module schrodinger.application.prime.gui.ui module schrodinger.application.prime.gui.ui.analyze_energy_ui module schrodinger.application.prime.gui.ui.environment_options_ui module schrodinger.application.prime.input module schrodinger.application.prime.primefix module schrodinger.application.prime.residue_interaction module schrodinger.application.prime.wrapper module schrodinger.application.pymol module schrodinger.application.pymol.constants module schrodinger.application.pymol.export_handler module schrodinger.application.pymol.export_to_pymol_gui module schrodinger.application.pymol.gui_models module schrodinger.application.pymol.mae_sync module schrodinger.application.pymol.pymol4maestro module schrodinger.application.pymol.pymol4maestro_ui module schrodinger.application.pymol.ui module schrodinger.application.pymol.ui.advanced_settings_wdg_ui module schrodinger.application.pymol.ui.export_to_pymol_dlg_ui module schrodinger.application.pymol.utils module schrodinger.application.qsite module schrodinger.application.qsite.input module schrodinger.application.qsite.output module schrodinger.application.report2d module schrodinger.application.scaffold_enumeration module schrodinger.application.scaffold_enumeration.atomlist module schrodinger.application.scaffold_enumeration.common module schrodinger.application.scaffold_enumeration.cxsmiles module schrodinger.application.scaffold_enumeration.layered module schrodinger.application.scaffold_enumeration.linknode module schrodinger.application.scaffold_enumeration.markush module schrodinger.application.scaffold_enumeration.mdl module schrodinger.application.scaffold_enumeration.posvarbond module schrodinger.application.scaffold_enumeration.rdcml module schrodinger.application.ska module schrodinger.application.steps module schrodinger.application.steps.basesteps module schrodinger.application.steps.converters module schrodinger.application.steps.dataclasses module schrodinger.application.steps.docking module schrodinger.application.steps.enumerators module schrodinger.application.steps.env_keys module schrodinger.application.steps.filters module schrodinger.application.steps.licensing module schrodinger.application.steps.ligprep module schrodinger.application.steps.scorers module schrodinger.application.steps.test module schrodinger.application.steps.transformers module schrodinger.application.steps.utils module schrodinger.application.transforms module schrodinger.application.transforms.chem module schrodinger.application.transforms.chemio module schrodinger.application.transforms.dock module schrodinger.application.transforms.dofn_utils module schrodinger.application.transforms.enumerators module schrodinger.application.transforms.filters module schrodinger.application.transforms.ligprep module schrodinger.application.transforms.template module schrodinger.application.transforms.template.starter module schrodinger.application.transforms.template.workflow module schrodinger.application.transforms.test module schrodinger.application.transforms.validators module schrodinger.application.utils module schrodinger.application.vss module schrodinger.application.vss.config module schrodinger.application.vss.control module schrodinger.application.vss.csvsmiles module schrodinger.application.vss.database module schrodinger.application.vss.dise module schrodinger.application.vss.pilot module schrodinger.application.vss.tasks module schrodinger.application.watermap module schrodinger.application.watermap.shapes module schrodinger.application.watermap.utils module schrodinger.application.watermap.watermap_inp module schrodinger.application.watermap.watermap_scoring module schrodinger.application.xtb module schrodinger.application.xtb.constants module schrodinger.application.xtb.input module schrodinger.application.xtb.keywords module schrodinger.application.xtb.output module schrodinger.application.xtb.runner module schrodinger.application.xtb.textparser module schrodinger.application.xtb.utilities module schrodinger.cloud module schrodinger.comparison module schrodinger.comparison.atom_mapper module schrodinger.comparison.chirality module schrodinger.comparison.comparison module schrodinger.comparison.constants module schrodinger.comparison.exceptions module schrodinger.comparison.neighbors module schrodinger.comparison.results module schrodinger.comparison.struc module schrodinger.driver module schrodinger.driver.structsubset module schrodinger.energy module schrodinger.forcefield module schrodinger.forcefield.common module schrodinger.forcefield.constants module schrodinger.forcefield.custom_params module schrodinger.forcefield.ffld_options module schrodinger.forcefield.minimizer module schrodinger.forcefield.packages module schrodinger.forcefield.test module schrodinger.forcefield.test.fixtures module schrodinger.genericfp module schrodinger.geometry module schrodinger.gpgpu module schrodinger.graphics3d module schrodinger.graphics3d.arrow module schrodinger.graphics3d.box module schrodinger.graphics3d.common module schrodinger.graphics3d.ellipsoid module schrodinger.graphics3d.gridbox module schrodinger.graphics3d.hemisphere module schrodinger.graphics3d.lines module schrodinger.graphics3d.polygon module schrodinger.graphics3d.polyhedron module schrodinger.graphics3d.sphere module schrodinger.graphics3d.torus module schrodinger.graphics3d.tube module schrodinger.infra module schrodinger.infra.ark module schrodinger.infra.epydoc_to_sphinx module schrodinger.infra.exception_handler module schrodinger.infra.exception_handler_dir module schrodinger.infra.exception_handler_dir.exception_dialog module schrodinger.infra.exception_handler_dir.exception_dialog_ui module schrodinger.infra.fast3d module schrodinger.infra.fix_sip6_enum_access module schrodinger.infra.gpgpu_utils module schrodinger.infra.growthspace module schrodinger.infra.jobhub module schrodinger.infra.licensing module schrodinger.infra.mm module schrodinger.infra.mmbitset module schrodinger.infra.mmcheck module schrodinger.infra.mmerr module schrodinger.infra.mmim module schrodinger.infra.mminit module schrodinger.infra.mmjob module schrodinger.infra.mmkv module schrodinger.infra.mmlist module schrodinger.infra.mmobject module schrodinger.infra.mmproj module schrodinger.infra.mmreflect module schrodinger.infra.mmsurf module schrodinger.infra.phase module schrodinger.infra.projectmodel module schrodinger.infra.qt_message_handler module schrodinger.infra.structure module schrodinger.infra.table module schrodinger.infra.test module schrodinger.infra.unusable_module_importer module schrodinger.infra.util module schrodinger.job module schrodinger.job.app module schrodinger.job.cert module schrodinger.job.download module schrodinger.job.driver_decorator module schrodinger.job.files module schrodinger.job.host_check module schrodinger.job.hunt_stub module schrodinger.job.jobcontrol module schrodinger.job.jobhandler module schrodinger.job.jobwriter module schrodinger.job.launchapi module schrodinger.job.launcher module schrodinger.job.launchparams module schrodinger.job.queue module schrodinger.job.remote_command module schrodinger.job.resource module schrodinger.job.server module schrodinger.job.util module schrodinger.livedesign module schrodinger.livedesign.bbchem_endpoints module schrodinger.livedesign.biologics module schrodinger.livedesign.biologics.fasta module schrodinger.livedesign.biologics.modeling module schrodinger.livedesign.biologics.registration module schrodinger.livedesign.biologics.sequence module schrodinger.livedesign.check_reaction module schrodinger.livedesign.cmdline module schrodinger.livedesign.convert module schrodinger.livedesign.draw module schrodinger.livedesign.entity_type module schrodinger.livedesign.preprocessor module schrodinger.livedesign.registration module schrodinger.livedesign.rgfile_parse module schrodinger.livedesign.rgroup_decomposition module schrodinger.livedesign.run_reaction module schrodinger.livedesign.search module schrodinger.livedesign.setup_reaction module schrodinger.maestro module schrodinger.maestro.commands module schrodinger.maestro.maestro module schrodinger.maestro.maestro_job_callbacks module schrodinger.maestro.markers module schrodinger.maestro.workspace_panels module schrodinger.maestro_utils module schrodinger.maestro_utils.find_tool_bar module schrodinger.maestro_utils.find_tool_bar.constants module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_ui module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget module schrodinger.maestro_utils.find_tool_bar.stylesheet module schrodinger.maestro_utils.maestro_sync module schrodinger.maestro_utils.nonstandard_residue_utils module schrodinger.math module schrodinger.math.mathutils module schrodinger.math.multi_parameter_optimization module schrodinger.math.sampling module schrodinger.models module schrodinger.models.adapters module schrodinger.models.adapters.abstractadapter module schrodinger.models.adapters.inputconfig module schrodinger.models.advanced_mappers module schrodinger.models.diffy module schrodinger.models.json module schrodinger.models.jsonable module schrodinger.models.mappers module schrodinger.models.parameters module schrodinger.models.paramtools module schrodinger.models.presets module schrodinger.models.yaml_utils module schrodinger.pipeline module schrodinger.pipeline.compiled_functions module schrodinger.pipeline.input module schrodinger.pipeline.pipeio module schrodinger.pipeline.pipeline module schrodinger.pipeline.pipeutils module schrodinger.pipeline.stage module schrodinger.pipeline.stages module schrodinger.pipeline.stages.canvas module schrodinger.pipeline.stages.combine module schrodinger.pipeline.stages.example module schrodinger.pipeline.stages.filtering module schrodinger.pipeline.stages.gencodes module schrodinger.pipeline.stages.glide module schrodinger.pipeline.stages.ligprep module schrodinger.pipeline.stages.macromodel module schrodinger.pipeline.stages.phase module schrodinger.pipeline.stages.prime module schrodinger.pipeline.stages.pull module schrodinger.pipeline.stages.qikprop module schrodinger.pipeline.stages.rmsd module schrodinger.pipeline.stages.semiemp module schrodinger.project module schrodinger.project.manager module schrodinger.project.pandasutils module schrodinger.project.project module schrodinger.project.surface module schrodinger.project.utils module schrodinger.protein module schrodinger.protein.align module schrodinger.protein.alignment module schrodinger.protein.analysis module schrodinger.protein.analysis_params module schrodinger.protein.annotation module schrodinger.protein.assignment module schrodinger.protein.biounit module schrodinger.protein.buildpeptide module schrodinger.protein.captermini module schrodinger.protein.constants module schrodinger.protein.findhets module schrodinger.protein.getpdb module schrodinger.protein.getpdb_utility module schrodinger.protein.gpcr module schrodinger.protein.gpcr.annotate module schrodinger.protein.gpcr.gpcrdb module schrodinger.protein.gpcr.sql module schrodinger.protein.gpcr.tasks module schrodinger.protein.gpcr.update_gpcr_db module schrodinger.protein.helix module schrodinger.protein.helm module schrodinger.protein.helm.helm_renderer module schrodinger.protein.helm.image_generation module schrodinger.protein.membrane module schrodinger.protein.natural_analog module schrodinger.protein.nonstandard_residues module schrodinger.protein.pdbname module schrodinger.protein.predictors module schrodinger.protein.process_enamine_db module schrodinger.protein.properties module schrodinger.protein.reliability module schrodinger.protein.remediate module schrodinger.protein.renumber_residues module schrodinger.protein.residue module schrodinger.protein.rotamers module schrodinger.protein.seqres module schrodinger.protein.sequence module schrodinger.protein.tasks module schrodinger.protein.tasks.binding_site_align module schrodinger.protein.tasks.blast module schrodinger.protein.tasks.clustal module schrodinger.protein.tasks.descriptors module schrodinger.protein.tasks.hit_align module schrodinger.protein.tasks.kinase module schrodinger.protein.tasks.mock_blast_output module schrodinger.protein.tasks.muscle module schrodinger.protein.tasks.optimize_alignment module schrodinger.protein.tasks.pfam module schrodinger.protein.tasks.sta module schrodinger.protein.tasks.structure_alignment module schrodinger.rdkit module schrodinger.rdkit.alignment module schrodinger.rdkit.coarsegrain module schrodinger.rdkit.filtering module schrodinger.rdkit.mesomerizer module schrodinger.rdkit.molio module schrodinger.rdkit.rdkit_adapter module schrodinger.rdkit.rgroup module schrodinger.rdkit.sorted_molwriter module schrodinger.rdkit.substructure module schrodinger.rdkit_extensions module schrodinger.seam module schrodinger.seam.coders module schrodinger.seam.debug module schrodinger.seam.examples module schrodinger.seam.examples.active_learning_weigher module schrodinger.seam.examples.haystack module schrodinger.seam.examples.rescount module schrodinger.seam.io module schrodinger.seam.io.chemio module schrodinger.seam.io.textio module schrodinger.seam.metric module schrodinger.seam.options module schrodinger.seam.options.pipeline_options module schrodinger.seam.runners module schrodinger.seam.runners.events module schrodinger.seam.runners.urns module schrodinger.seam.testing module schrodinger.seam.testing.benchmarks module schrodinger.seam.testing.fixtures module schrodinger.seam.testing.stateful module schrodinger.seam.testing.util module schrodinger.seam.testing.utils module schrodinger.seam.transforms module schrodinger.seam.transforms.core module schrodinger.seam.transforms.partitioners module schrodinger.seam.transforms.resources module schrodinger.seam.transforms.samplers module schrodinger.seam.viz module schrodinger.seam.viz.inspect module schrodinger.seam.viz.render module schrodinger.seam.viz.watcher module schrodinger.seam.viz.watcherd module schrodinger.shape module schrodinger.sitemap module schrodinger.stepper module schrodinger.stepper.app module schrodinger.stepper.core_steps module schrodinger.stepper.shims module schrodinger.stepper.sideinputs module schrodinger.stepper.stepper module schrodinger.stepper.viz module schrodinger.structure module schrodinger.structure.atom_numbering_monitor module schrodinger.structure.structure module schrodinger.structure.workflow_action_menu module schrodinger.structutils module schrodinger.structutils.analyze module schrodinger.structutils.assignbondorders module schrodinger.structutils.block_data module schrodinger.structutils.build module schrodinger.structutils.ccd module schrodinger.structutils.check module schrodinger.structutils.clash_resolution module schrodinger.structutils.color module schrodinger.structutils.createfragments module schrodinger.structutils.filter module schrodinger.structutils.interactionfp module schrodinger.structutils.interactions module schrodinger.structutils.interactions.hbond module schrodinger.structutils.interactions.pi module schrodinger.structutils.interactions.protein_protein_interactions module schrodinger.structutils.interactions.salt_bridge module schrodinger.structutils.interactions.ssbond module schrodinger.structutils.interactions.steric_clash module schrodinger.structutils.io module schrodinger.structutils.markush_enumerate module schrodinger.structutils.measure module schrodinger.structutils.minimize module schrodinger.structutils.pbc_tools module schrodinger.structutils.residue module schrodinger.structutils.rgroup_enumerate module schrodinger.structutils.rings module schrodinger.structutils.ringspear module schrodinger.structutils.rmsd module schrodinger.structutils.shuffle module schrodinger.structutils.sitealign module schrodinger.structutils.smiles module schrodinger.structutils.smilesfilter module schrodinger.structutils.sort module schrodinger.structutils.standard_nuclear_orientation module schrodinger.structutils.structalign module schrodinger.structutils.structalign2 module schrodinger.structutils.transform module schrodinger.surface module schrodinger.tasks module schrodinger.tasks.cmdline module schrodinger.tasks.drivers module schrodinger.tasks.gui module schrodinger.tasks.hosts module schrodinger.tasks.jobtasks module schrodinger.tasks.ldtasks module schrodinger.tasks.queue module schrodinger.tasks.remote_modules module schrodinger.tasks.taskmanager module schrodinger.tasks.tasks module schrodinger.tasks.taskszmq module schrodinger.thirdparty module schrodinger.thirdparty.networkx_algos module schrodinger.trajectory module schrodinger.trajectory.pbc_manager module schrodinger.trajectory.prody module schrodinger.trajectory.prody.crosscorrelation module schrodinger.trajectory.prody.ensemble module schrodinger.trajectory.prody.mode module schrodinger.trajectory.prody.modeset module schrodinger.trajectory.prody.nma module schrodinger.trajectory.prody.pca module schrodinger.trajectory.prody.test_arrow module schrodinger.trajectory.prody.writenmd module schrodinger.trajectory.traj_dialog_ui module schrodinger.trajectory.trajectory_gui_dir module schrodinger.trajectory.trajectory_gui_dir.advanced_plot_ui module schrodinger.trajectory.trajectory_gui_dir.advanced_settings module schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui module schrodinger.trajectory.trajectory_gui_dir.banners module schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui module schrodinger.trajectory.trajectory_gui_dir.collapsible_plot_ui module schrodinger.trajectory.trajectory_gui_dir.conf_wheel_plot_panel_ui module schrodinger.trajectory.trajectory_gui_dir.custom_analyzers module schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui module schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui module schrodinger.trajectory.trajectory_gui_dir.display_settings_data module schrodinger.trajectory.trajectory_gui_dir.display_settings_manager module schrodinger.trajectory.trajectory_gui_dir.energy_plot_ui module schrodinger.trajectory.trajectory_gui_dir.export_movie module schrodinger.trajectory.trajectory_gui_dir.export_movie_ui module schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures module schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui module schrodinger.trajectory.trajectory_gui_dir.export_structure_enums module schrodinger.trajectory.trajectory_gui_dir.export_structures module schrodinger.trajectory.trajectory_gui_dir.export_structures_ui module schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter module schrodinger.trajectory.trajectory_gui_dir.icons_rc module schrodinger.trajectory.trajectory_gui_dir.job_settings_dialog_ui module schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui module schrodinger.trajectory.trajectory_gui_dir.playback_settings module schrodinger.trajectory.trajectory_gui_dir.playback_settings_data module schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui module schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui module schrodinger.trajectory.trajectory_gui_dir.rdf_plot_ui module schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui module schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data module schrodinger.trajectory.trajectory_gui_dir.shortcut_ui module schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings module schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui module schrodinger.trajectory.trajectory_gui_dir.snapshot_panel module schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui module schrodinger.trajectory.trajectory_gui_dir.stylesheet module schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui module schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets module schrodinger.trajectory.trajectory_gui_dir.trajectory_messages module schrodinger.trajectory.trajectoryviewer module schrodinger.trajectory.utils module schrodinger.trajectory.validate_trajectory module schrodinger.ui module schrodinger.ui.chooseligand module schrodinger.ui.dendrogram module schrodinger.ui.images_rc module schrodinger.ui.ligfilter module schrodinger.ui.ligfilter_definition_dialog_ui module schrodinger.ui.ligfilter_ui module schrodinger.ui.maestro_ui module schrodinger.ui.picking module schrodinger.ui.picking_dir module schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui module schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui module schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui module schrodinger.ui.qt module schrodinger.ui.qt.appframework module schrodinger.ui.qt.appframework2 module schrodinger.ui.qt.appframework2.af2 module schrodinger.ui.qt.appframework2.af2_template module schrodinger.ui.qt.appframework2.application module schrodinger.ui.qt.appframework2.appmethods module schrodinger.ui.qt.appframework2.baseapp module schrodinger.ui.qt.appframework2.debug module schrodinger.ui.qt.appframework2.debug_gui module schrodinger.ui.qt.appframework2.debug_gui_ui module schrodinger.ui.qt.appframework2.debugcore module schrodinger.ui.qt.appframework2.debugwidgets module schrodinger.ui.qt.appframework2.jobnames module schrodinger.ui.qt.appframework2.jobs module schrodinger.ui.qt.appframework2.knime_af2 module schrodinger.ui.qt.appframework2.maestro_callback module schrodinger.ui.qt.appframework2.markers module schrodinger.ui.qt.appframework2.settings module schrodinger.ui.qt.appframework2.validation module schrodinger.ui.qt.appframework2.validators module schrodinger.ui.qt.appframework2.wizards module schrodinger.ui.qt.atom_weights_table_ui module schrodinger.ui.qt.atom_weights_table_widget module schrodinger.ui.qt.atomselector module schrodinger.ui.qt.basewidgets module schrodinger.ui.qt.borderless_popup_ui module schrodinger.ui.qt.color_picker module schrodinger.ui.qt.config_dialog module schrodinger.ui.qt.config_dialog_open_mp_ui module schrodinger.ui.qt.config_dialog_queue_ui module schrodinger.ui.qt.datamapper module schrodinger.ui.qt.decorators module schrodinger.ui.qt.delegates module schrodinger.ui.qt.dendrogram module schrodinger.ui.qt.dialbox module schrodinger.ui.qt.dialbox_dir module schrodinger.ui.qt.dialbox_dir.dialbox_qrc module schrodinger.ui.qt.directory_selector module schrodinger.ui.qt.entryselector module schrodinger.ui.qt.entryselector_ui module schrodinger.ui.qt.figureoptions module schrodinger.ui.qt.file_selector module schrodinger.ui.qt.filedialog module schrodinger.ui.qt.filter_dialog module schrodinger.ui.qt.filter_dialog_dir module schrodinger.ui.qt.filter_dialog_dir.filter_core module schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui module schrodinger.ui.qt.filter_dialog_dir.filter_widgets module schrodinger.ui.qt.filter_dialog_ui module schrodinger.ui.qt.filter_list module schrodinger.ui.qt.forcefield module schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget module schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget_ui module schrodinger.ui.qt.forcefield.ffglobalpreferencewidget module schrodinger.ui.qt.forcefield.ffglobalpreferencewidget_ui module schrodinger.ui.qt.forcefield.ffprojectsettingsdlg module schrodinger.ui.qt.forcefield.ffprojectsettingsdlg_ui module schrodinger.ui.qt.forcefield.ffselector module schrodinger.ui.qt.forcefield.ffsettingsbutton module schrodinger.ui.qt.forcefield.forcefield module schrodinger.ui.qt.forcefield.pathselectorwidget module schrodinger.ui.qt.forcefield.stylesheet module schrodinger.ui.qt.formlayout module schrodinger.ui.qt.fp_selector_widget module schrodinger.ui.qt.fp_selector_widget_ui module schrodinger.ui.qt.icons module schrodinger.ui.qt.icons_rc module schrodinger.ui.qt.input_selector module schrodinger.ui.qt.jobwidgets module schrodinger.ui.qt.label module schrodinger.ui.qt.label_cursor module schrodinger.ui.qt.layout module schrodinger.ui.qt.ligand_list module schrodinger.ui.qt.mapperwidgets module schrodinger.ui.qt.mapperwidgets.param_editor module schrodinger.ui.qt.mapperwidgets.plptable module schrodinger.ui.qt.matplot_widget module schrodinger.ui.qt.messagebox module schrodinger.ui.qt.multi_combo_box module schrodinger.ui.qt.navtoolbar module schrodinger.ui.qt.network_views module schrodinger.ui.qt.network_visualizer module schrodinger.ui.qt.pdb_dialog module schrodinger.ui.qt.pdb_dialog_ui module schrodinger.ui.qt.periodictable module schrodinger.ui.qt.pop_up_widgets module schrodinger.ui.qt.presets module schrodinger.ui.qt.presets.manage_presets_dialog module schrodinger.ui.qt.presets.manage_presets_dialog_ui module schrodinger.ui.qt.presets.save_presets_dialog module schrodinger.ui.qt.presets.save_presets_dialog_ui module schrodinger.ui.qt.propertyselector module schrodinger.ui.qt.protein_health_viewer module schrodinger.ui.qt.protein_health_viewer_ui module schrodinger.ui.qt.radial_plot module schrodinger.ui.qt.rama module schrodinger.ui.qt.rdmol_views module schrodinger.ui.qt.recent_completer module schrodinger.ui.qt.rename_favorite_dialog module schrodinger.ui.qt.rename_favorite_dialog_ui module schrodinger.ui.qt.schart module schrodinger.ui.qt.schrodinger_ipython module schrodinger.ui.qt.schrodingerstyle module schrodinger.ui.qt.select_residues_dialog module schrodinger.ui.qt.select_residues_dialog_ui module schrodinger.ui.qt.smatplotlib module schrodinger.ui.qt.standard module schrodinger.ui.qt.standard.colors module schrodinger.ui.qt.standard.constants module schrodinger.ui.qt.standard.design_tokens module schrodinger.ui.qt.standard.icons module schrodinger.ui.qt.standard.icons.icons module schrodinger.ui.qt.standard.panelx_stylesheet module schrodinger.ui.qt.standard.widgets module schrodinger.ui.qt.standard.widgets.group_boxes module schrodinger.ui.qt.standard_widgets module schrodinger.ui.qt.standard_widgets.buttons module schrodinger.ui.qt.standard_widgets.combo_boxes module schrodinger.ui.qt.standard_widgets.flat_button module schrodinger.ui.qt.standard_widgets.hyperlink module schrodinger.ui.qt.standard_widgets.labels module schrodinger.ui.qt.standard_widgets.standard_widgets_rc module schrodinger.ui.qt.standard_widgets.statusbar module schrodinger.ui.qt.structtable module schrodinger.ui.qt.structure2d module schrodinger.ui.qt.structure_selector module schrodinger.ui.qt.style module schrodinger.ui.qt.stylesheet module schrodinger.ui.qt.swidgets module schrodinger.ui.qt.table module schrodinger.ui.qt.table_helper module schrodinger.ui.qt.table_speed_up module schrodinger.ui.qt.tablewidget module schrodinger.ui.qt.tasks module schrodinger.ui.qt.tasks.config_dialog_ui module schrodinger.ui.qt.tasks.config_info_ui module schrodinger.ui.qt.tasks.configwidgets module schrodinger.ui.qt.tasks.taskbar2 module schrodinger.ui.qt.tasks.taskbar_ui module schrodinger.ui.qt.tasks.taskbarwidgets module schrodinger.ui.qt.tasks.taskwidgets module schrodinger.ui.qt.tooltips module schrodinger.ui.qt.utils module schrodinger.ui.qt.widgetmixins module schrodinger.ui.qt.widgetmixins.basicmixins module schrodinger.ui.qt.widgetmixins.mock_ui module schrodinger.ui.qt.widgetmixins.panelmixins module schrodinger.ui.qt.xsignals module schrodinger.ui.residueselector module schrodinger.ui.sketcher module schrodinger.ui.sketcher_extensions module schrodinger.ui.sketcher_image module schrodinger.ui.sketcher_smarts_dialog module schrodinger.ui.sketcher_smarts_dialog_ui module schrodinger.ui.two_d_viewer module schrodinger.ui.two_d_viewer_ui module schrodinger.utils module schrodinger.utils.cgxutils module schrodinger.utils.cmdline module schrodinger.utils.colorscheme module schrodinger.utils.compare module schrodinger.utils.csv_unicode module schrodinger.utils.deprecation module schrodinger.utils.documentation module schrodinger.utils.env module schrodinger.utils.featureflags module schrodinger.utils.featureflags.featureflags module schrodinger.utils.featureflags.write module schrodinger.utils.fileutils module schrodinger.utils.funcchains module schrodinger.utils.funcgroups module schrodinger.utils.imputils module schrodinger.utils.install_scripts module schrodinger.utils.installation_check module schrodinger.utils.license module schrodinger.utils.ligfilter module schrodinger.utils.log module schrodinger.utils.machid module schrodinger.utils.maestro_scripts_path module schrodinger.utils.mmutil module schrodinger.utils.moduleproxy module schrodinger.utils.multifpfile module schrodinger.utils.net module schrodinger.utils.openmpi module schrodinger.utils.platform module schrodinger.utils.postinstall module schrodinger.utils.preferences module schrodinger.utils.profiling module schrodinger.utils.pymol module schrodinger.utils.qapplication module schrodinger.utils.qt_utils module schrodinger.utils.scollections module schrodinger.utils.sea module schrodinger.utils.sea.common module schrodinger.utils.sea.evalor module schrodinger.utils.sea.sea module schrodinger.utils.singledashoptionparser module schrodinger.utils.sshconfig module schrodinger.utils.subproc module schrodinger.utils.subprocess module schrodinger.utils.sysinfo module schrodinger.utils.thread_utils module schrodinger.utils.typing module schrodinger.utils.units module schrodinger.utils.withnone module SCHRODINGER_ANI (schrodinger.application.jaguar.constants.CalcType attribute) SCHRODINGER_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute) schrodinger_license_dir() (in module schrodinger.application.licensing.licserver.client) SCHRODINGER_OPENMPI (schrodinger.utils.openmpi.EnvVar attribute) SCHRODINGER_PYTHONPATH, [1] SCHRODINGER_SCRIPTS, [1], [2] SCHRODINGER_UTILITIES (schrodinger.application.desmond.envir.CONST attribute) schrodingerInstallation (schrodinger.job.server.ServerInfo attribute) SchrodingerPairwiseAligner (class in schrodinger.protein.align) SchrodingerStyleMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) SchrodingerSubplotTool (class in schrodinger.ui.qt.navtoolbar) SchrodingerTable (class in schrodinger.application.matsci.kmc) SchrodStruc (class in schrodinger.application.desmond.fep_struc) SComboBox (class in schrodinger.ui.qt.swidgets) score (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch property) (schrodinger.application.bioluminate.peptide_sar.io.ScoredSeq attribute) (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot property) (schrodinger.application.desmond.mxmd.mxmd_cleanup.Spot property) (schrodinger.application.jaguar.autots_rmsd.MapScore attribute) (schrodinger.application.jaguar.utils.LewisStructure attribute) (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData.RING_NODE_TYPE attribute) (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) (schrodinger.application.steps.dataclasses.ScoredMol attribute) (schrodinger.comparison.atom_mapper.MapScore attribute) (schrodinger.structutils.structalign2.Alignment attribute) score_acceptor_acceptor() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_combination() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_donor_acceptor() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_exhaustively() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_filter (schrodinger.application.steps.filters.ScoreFilter.Settings attribute) score_filterChanged (schrodinger.application.steps.filters.ScoreFilter.Settings attribute) score_filterReplaced (schrodinger.application.steps.filters.ScoreFilter.Settings attribute) score_filters (schrodinger.application.steps.filters.ScoreFilterChain.Settings attribute) score_filtersChanged (schrodinger.application.steps.filters.ScoreFilterChain.Settings attribute) score_filtersReplaced (schrodinger.application.steps.filters.ScoreFilterChain.Settings attribute) score_is_equivalent() (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper method) (schrodinger.comparison.atom_mapper.BaseAtomMapper method) (schrodinger.comparison.atom_mapper.ConnectivityAtomMapper method) (schrodinger.comparison.atom_mapper.CSPAtomMapper method) (schrodinger.comparison.atom_mapper.LewisAtomMapper method) score_ligand() (in module schrodinger.application.watermap.watermap_scoring) score_mapping() (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper method) (schrodinger.application.jaguar.autots_rmsd.AutoTSTemplateAtomMapper method) (schrodinger.comparison.atom_mapper.BaseAtomMapper method) (schrodinger.comparison.atom_mapper.ConnectivityAtomMapper method) (schrodinger.comparison.atom_mapper.CSPAtomMapper method) (schrodinger.comparison.atom_mapper.LewisAtomMapper method) (schrodinger.structutils.ccd.CCDAtomMapper method) score_metal_donor() (schrodinger.protein.assignment.ProtAssign.hbond_cluster static method) score_pair() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_sequentially() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) scoreChanged (schrodinger.application.steps.dataclasses.ScoredMol attribute) scored_csv_file_list (schrodinger.active_learning.al_driver.ActiveLearningJob property) ScoredMol (class in schrodinger.application.steps.dataclasses) ScoredMolInMixin (class in schrodinger.application.steps.dataclasses) ScoredMolOutMixin (class in schrodinger.application.steps.dataclasses) ScoredMolSerializer (class in schrodinger.application.steps.dataclasses) ScoredSeq (class in schrodinger.application.bioluminate.peptide_sar.io) ScoreFilter (class in schrodinger.application.steps.filters) ScoreFilter.Settings (class in schrodinger.application.steps.filters) ScoreFilterChain (class in schrodinger.application.steps.filters) ScoreFilterChain.Settings (class in schrodinger.application.steps.filters) ScoreProviderNode (class in schrodinger.active_learning.al_node) SCORER_CLASS (schrodinger.application.steps.filters.LigandMLScoreFilterChain attribute) (schrodinger.application.steps.filters.ScoreFilter attribute) (schrodinger.application.steps.filters.ScoreFilterChain attribute) scoreReplaced (schrodinger.application.steps.dataclasses.ScoredMol attribute) ScorerMixin (class in schrodinger.application.steps.dataclasses) screen() (schrodinger.application.combinatorial_explorer.route_screener.RouteScreener method) (schrodinger.application.combinatorial_screen.combinatorial_screener.CombinatorialScreener method) (schrodinger.application.phase.packages.bedroc_screener.BedrocScreener method) (schrodinger.application.phase.packages.mmp3dscreener.MMP3DScreener method) SCREEN_PARAM_KEY (schrodinger.application.matsci.espresso.qeinput.HybridType attribute) screen_structure_file() (in module schrodinger.application.phase.packages.oned_app_utils) screening_db_file (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) screening_db_fileChanged (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) screening_db_fileReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) SCRIPT (schrodinger.application.desmond.multisimstartup.Startup attribute) script_dir() (in module schrodinger.application.jaguar) scrollBarChanged() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) ScrollbarIcons (class in schrodinger.ui.qt.standard.design_tokens) scrollToItemWithPath() (schrodinger.application.livedesign.panel_components.LDSelectionTreeView method) sculpt() (schrodinger.application.matsci.sculptcomplex.Sculptor method) sculptComplexBuild() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) SculptingError Sculptor (class in schrodinger.application.matsci.sculptcomplex) sd (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis.SysDipole attribute) SD (schrodinger.infra.structure.FileFormat attribute) SD_EXT (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) SD_PROP_PATTERN (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae attribute) SD_PROP_STARTER (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae attribute) sdf (schrodinger.application.livedesign.export_tasks.ExportType attribute) sdf_file_path (schrodinger.application.livedesign.export_models.FileBatch attribute) sdf_file_pathChanged (schrodinger.application.livedesign.export_models.FileBatch attribute) sdf_file_pathReplaced (schrodinger.application.livedesign.export_models.FileBatch attribute) SdfFile (class in schrodinger.tasks.ldtasks) sdFromDisplacement() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) SDialog (class in schrodinger.ui.qt.swidgets) SDoubleSpinBox (class in schrodinger.ui.qt.swidgets) SDWriter (class in schrodinger.structure) Sea (class in schrodinger.utils.sea.sea) sea_filter() (in module schrodinger.utils.sea.sea) SeaJob (class in schrodinger.application.desmond.stage.analysis) SeamEvent (class in schrodinger.seam.runners.events) SeamMetrics (class in schrodinger.seam.metric) SeamOptions (class in schrodinger.seam.options.pipeline_options) search() (schrodinger.structutils.analyze.AslLigandSearcher method) SEARCH_ALONG_VALUES (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) search_and_scan() (schrodinger.application.desmond.torsion_related.BondRotator method) search_antibody() (in module schrodinger.application.bioluminate.antibody.utils) search_by_sequence() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) search_cluster_radius() (in module schrodinger.comparison.neighbors) SEARCH_LST (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) SEARCH_MODE_PAGE (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp attribute) SEARCH_OPTION_DETAILS (class in schrodinger.maestro_utils.find_tool_bar.constants) search_path() (in module schrodinger.application.licensing.licserver.client) SEARCH_QST (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) SEARCH_STANDARD (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SEARCH_TEXT (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUp attribute) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUp attribute) searchAlongChanged() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) SearchError SearchForDataPointsWithin() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) SearchForDataPointsWithinL() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) searchKeyPressed() (schrodinger.ui.qt.swidgets.TextSearchBar method) SearchMap() (in module schrodinger.application.matsci.gsas.GSASIImath) searchMethodChanged (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) searchTextChanged() (schrodinger.application.livedesign.panel_components.BaseSearchTreeWidgetHelper method) SEasySDTable (class in schrodinger.ui.qt.table) sec2HMS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) SECOND_SEP (schrodinger.application.matsci.rxn_channel.ChannelDefinition attribute) SECONDARY_BUTTON (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) SECONDARY_LINK (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) SECONDARY_SORT_COLUMNS (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) SECONDARY_STRUCTURE (class in schrodinger.protein.buildpeptide) secondary_structure (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) (schrodinger.structure.Residue property) (schrodinger.structure.StructureAtom property) secondary_structures (schrodinger.protein.sequence.AbstractProteinSequenceMixin property) secondaryStructureCacheCleared (schrodinger.protein.sequence.ProteinSequence attribute) secondaryStructureChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractProteinSequenceMixin attribute) SecondaryStructureData (class in schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data) SECONDS_PER_HOUR (schrodinger.application.jaguar.gui.timing.TimingResults attribute) sectionDefined() (schrodinger.application.jaguar.input.JaguarInput method) Sector (class in schrodinger.ui.qt.radial_plot) sectorClicked (schrodinger.ui.qt.radial_plot.RadialRingHistogram attribute) SECULAR (schrodinger.application.jaguar.nmr_interactions.CouplingStrength attribute) SEED (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.application.matsci.kmc.SchrodingerTable attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) seed (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.InMemoryRandomSampleFilter.Settings attribute) (schrodinger.application.steps.filters.InMemoryUniqueRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.RandomSampleFilter.Settings attribute) seed_random_number_generator() (in module schrodinger.application.matsci.jobutils) SEED_STRINGER (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) seedChanged (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.InMemoryRandomSampleFilter.Settings attribute) (schrodinger.application.steps.filters.InMemoryUniqueRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.RandomSampleFilter.Settings attribute) seedRandom() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method) seedReplaced (schrodinger.application.steps.enumerators.RouteEvaluator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.InMemoryRandomSampleFilter.Settings attribute) (schrodinger.application.steps.filters.InMemoryUniqueRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter.Settings attribute) (schrodinger.stepper.core_steps.RandomSampleFilter.Settings attribute) seek() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.structure.MaestroReader method) SEG (schrodinger.application.matsci.kmc.Table attribute) SEG1 (schrodinger.application.matsci.kmc.PairsTable attribute) SEG2 (schrodinger.application.matsci.kmc.PairsTable attribute) seg_intersect() (in module schrodinger.ui.qt.network_visualizer) SegmentsTable (class in schrodinger.application.matsci.kmc) SegmentTypesTable (class in schrodinger.application.matsci.kmc) sel_features (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) sel_featuresChanged (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) sel_featuresReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) Select (class in schrodinger.application.bioluminate.pml_menus) select() (schrodinger.application.combinatorial_diversity.diversity_selector.DiversitySelector method) (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) (schrodinger.ui.qt.propertyselector.PropertySelectorMenu method) (schrodinger.ui.qt.tablewidget.Cell method) (schrodinger.ui.qt.tablewidget.Column method) (schrodinger.ui.qt.tablewidget.Row method) select_all_atoms() (in module schrodinger.application.matsci.maestrocmds) select_atom() (schrodinger.application.desmond.cms.Cms method) select_atom_comp() (schrodinger.application.desmond.cms.Cms method) select_atoms() (in module schrodinger.application.matsci.maestrocmds) select_data() (in module schrodinger.application.desmond.arkdb) select_dictionary() (in module schrodinger.application.phase.packages.mmp2d) SELECT_ITEM (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) select_probes() (in module schrodinger.application.combinatorial_diversity.splitter_utils) select_shape_gpu_hits() (in module schrodinger.application.phase.packages.shape_diversity) select_surf_asl() (in module schrodinger.utils.pymol) selectAddRows() (schrodinger.infra.table.Table method) selectAll() (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.residueselector.MutationSelectorMixin method) selectAllItems() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) selectAllSignals() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) selectAtom() (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.application.matsci.reordergui.StructurePic method) selectAtomGroupAsl() (schrodinger.application.desmond.gui.AtomGroupFrame method) selectAtoms() (schrodinger.application.matsci.chargegui.ChargeDialog method) selectConformers() (schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelection method) selected (schrodinger.application.jaguar.gui.input_tab_widgets.UseFrom attribute) (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite attribute) SELECTED (schrodinger.application.pymol.gui_models.ProjectTableExportMode attribute) (schrodinger.project.pandasutils.WhichRows attribute) selected (schrodinger.ui.qt.ligand_list.LigSource attribute) selected_atoms() (in module schrodinger.application.desmond.struc) SELECTED_COLOR (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) SELECTED_ENTRIES (schrodinger.ui.qt.input_selector.InputSelector attribute) selected_maestro_properties (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) selected_maestro_propertiesChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) selected_maestro_propertiesReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) selected_names (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsModel attribute) selected_namesChanged (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsModel attribute) selected_namesReplaced (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsModel attribute) selected_rows (schrodinger.project.project.EntryGroup property) (schrodinger.project.project.Project property) selected_sequences (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer property) selected_st (schrodinger.trajectory.prody.ensemble.Ensemble property) selected_sts_info (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) selected_sts_infoChanged (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) selected_sts_infoReplaced (schrodinger.application.livedesign.ld_tasks.ImportTaskInput attribute) selected_weights (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) selected_weightsChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) selected_weightsReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) SelectedAtomContextActionSubMenu (class in schrodinger.application.bioluminate.pml_menus) selectedCharge() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) selectedEdges() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.Graph method) SelectedEntries (schrodinger.ui.qt.structure_selector.InputSource attribute) selectedFeaturesCount() (schrodinger.application.phase.featureselector.FeatureModel method) selectedIndex() (schrodinger.application.matsci.reordergui.ReferenceFrame method) selectedLigands() (schrodinger.ui.qt.ligand_list.LigandListView method) selectedNodes() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.Graph method) selectedOption() (schrodinger.application.jaguar.gui.filedialog.FileDialogWithExtraCombo method) selectedParams() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) selectedText() (schrodinger.ui.qt.swidgets.SListWidget method) selectedWorkflowBasename() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) selectedWorkflowName() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) selectedWorkflowPath() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) selectEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) selectFirstAllowedPropertyRow() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) selectIfNoSelection() (schrodinger.ui.qt.ligand_list.LigandListView method) SelectingFilteredListWidget (class in schrodinger.application.bioluminate.propfilter) selectInitialModel() (schrodinger.application.matsci.mswidgets.WaterTypesComboBox method) selection (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog property) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog property) SELECTION_MACRO_TEXT (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) SELECTION_MICRO_TEXT (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) selection_type_changed (schrodinger.application.matsci.speciesgui.GroupingMethodSelector attribute) selectionChanged (schrodinger.application.matsci.mswidgets.ConvenientSelectorWithPopUp attribute) (schrodinger.application.phase.featureselector.FeatureSelector attribute) (schrodinger.ui.dendrogram.DendrogramGraphicTree attribute) (schrodinger.ui.qt.datamapper.MappableButtonGroup attribute) (schrodinger.ui.qt.dendrogram.Dendrogram attribute) (schrodinger.ui.qt.multi_combo_box.MultiComboBox attribute) (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync attribute) selectionChanged() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) (schrodinger.application.livedesign.panel_components.LDSelectionTreeView method) (schrodinger.application.matsci.builderwidgets.TemplateSelector method) (schrodinger.application.matsci.jagwidgets.BasisSetSelector method) (schrodinger.application.matsci.jagwidgets.TheorySelector method) (schrodinger.ui.qt.ligand_list.LigandListView method) (schrodinger.ui.qt.swidgets.SelectorWithPopUp method) selectionChangedCallback() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) selectionCommand() (schrodinger.application.jaguar.gui.utils.ProjTableLikeView method) selectionContainsNonDefaultBasisSets() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) selectionContainsNonDefaultMethod() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) SelectionListView (class in schrodinger.application.livedesign.panel_components) selections() (in module schrodinger.application.matsci.gsas.GSASIIlattice) SelectionSubMenu (class in schrodinger.application.bioluminate.pml_menus) selectItems() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) selective_set_value() (in module schrodinger.models.paramtools) selectJob() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) selectLigandsFromAtoms() (schrodinger.ui.qt.ligand_list.LigandListView method) selectLigandsFromWorkspaceAtomNums() (schrodinger.ui.qt.ligand_list.LigandListView method) selectNewValue() (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp method) selectNoSignals() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) selectOnly() (schrodinger.project.project.ProjectRow method) (schrodinger.ui.qt.tablewidget.Row method) selectOnlyByEntry() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) selectOnlyBySeqs() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) selectOnlyCellI() (schrodinger.ui.two_d_viewer.TwoDViewer method) selectOnlyCellIndex() (schrodinger.ui.two_d_viewer.TwoDViewer method) selectOnlyRows() (schrodinger.ui.qt.swidgets.STableWidget method) SELECTORS (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog attribute) SelectorWithPopUp (class in schrodinger.ui.qt.swidgets) selectPattern() (schrodinger.ui.ligfilter.LigfilterFrame method) selectPlaceholderItem() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) selectPosResAsl() (schrodinger.application.desmond.gui.RestraintsTab method) selectPredefined() (schrodinger.ui.ligfilter.LigfilterFrame method) selectProperty() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) selectRefAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) SelectResiduesDialog (class in schrodinger.ui.qt.select_residues_dialog) selectResidueToggle() (schrodinger.ui.residueselector.MutationSelectorMixin method) selectRows() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) (schrodinger.infra.table.Table method) (schrodinger.project.project.Project method) selectSet() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) SelectWithinAny (class in schrodinger.application.bioluminate.pml_menus) SelectWithinCalpha (class in schrodinger.application.bioluminate.pml_menus) SelectWithinChain (class in schrodinger.application.bioluminate.pml_menus) SelectWithinEntry (class in schrodinger.application.bioluminate.pml_menus) SelectWithinMolecule (class in schrodinger.application.bioluminate.pml_menus) SelectWithinResidue (class in schrodinger.application.bioluminate.pml_menus) selenomethionines (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) selenomethioninesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) selenomethioninesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) SELF_ENERGY_ONLY (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute) self_polarizability() (in module schrodinger.application.mopac.results_main) SelfContainedTable (class in schrodinger.ui.qt.tablewidget) selfReorganize (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute) selftestlist (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIIspc) semanticPredicate() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) SEMI_CRYSTALLINE1_RELAX (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) SEMI_CRYSTALLINE2_RELAX (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) SEMI_ISOTROPIC (schrodinger.application.desmond.constants.IsotropyPolicy attribute) SemiCrystalRelaxation1Step (class in schrodinger.application.matsci.jwsteps) SemiCrystalRelaxation2Step (class in schrodinger.application.matsci.jwsteps) SemiEmpStage (class in schrodinger.pipeline.stages.semiemp) SEmittingScrollBar (class in schrodinger.ui.qt.swidgets) send() (schrodinger.application.pymol.pymol4maestro.panel method) send_entries() (schrodinger.application.pymol.pymol4maestro.panel method) send_maestro_settings() (in module schrodinger.utils.pymol) send_scenes() (schrodinger.application.pymol.pymol4maestro.panel method) send_settings() (schrodinger.application.pymol.pymol4maestro.panel method) send_workspace() (schrodinger.application.pymol.pymol4maestro.panel method) sendCSV() (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) sendHostsToUse() (schrodinger.pipeline.pipeline.StageJob method) sendPredictions() (schrodinger.active_learning.mq_backend.Backend method) sendPredsToDriver() (schrodinger.active_learning.mq_worker.Worker method) sendToBackend() (schrodinger.active_learning.mq_worker.Worker method) sendToDriver() (schrodinger.active_learning.mq_worker.Worker method) sendVersionCheck() (schrodinger.utils.pymol.PymolInstance method) sense() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method) sense_of_rotation() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method) SENTINEL (schrodinger.protein.align.CustomASLStructureAligner attribute) separate_complex() (in module schrodinger.application.livedesign.entry_types) SEPARATOR (schrodinger.application.matsci.genetic_optimization.ClassEvaluator attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.steps.dataclasses.ScoredMolSerializer attribute) SeparatorItemDelegate (class in schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) SeparatorStringModel (class in schrodinger.ui.qt.recent_completer) seq (schrodinger.application.bioluminate.peptide_sar.io.ScoredSeq attribute) (schrodinger.protein.annotation.AbstractRegionFinder attribute) (schrodinger.protein.predictors.AbstractPredictor.Input attribute) (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask.Input attribute) (schrodinger.protein.tasks.pfam.PfamTask.Input attribute) seq_align_match() (in module schrodinger.structutils.analyze) seq_annotations (schrodinger.protein.alignment.BaseAlignment property) seq_from_chain() (in module schrodinger.application.bioluminate.antibody.sequence_indexer) seq_type_from_chain() (in module schrodinger.application.bioluminate.antibody.sequence_indexer) seqChanged (schrodinger.protein.predictors.AbstractPredictor.Input attribute) (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask.Input attribute) (schrodinger.protein.tasks.pfam.PfamTask.Input attribute) SeqData (class in schrodinger.application.matsci.anharmonic) SeqFormat (class in schrodinger.utils.fileutils) seqMatchesRefType() (schrodinger.protein.alignment.BaseAlignment method) seqReplaced (schrodinger.protein.predictors.AbstractPredictor.Input attribute) (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask.Input attribute) (schrodinger.protein.tasks.pfam.PfamTask.Input attribute) seqres_only (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) seqs (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Input attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Input attribute) seqsChanged (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Input attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Input attribute) seqsReplaced (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Input attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Input attribute) SeqTypeMixin (class in schrodinger.protein.annotation) Sequence (class in schrodinger.protein.sequence) sequence (schrodinger.application.bioluminate.anarci.anarci_adapter.InputSequence attribute) (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult attribute) SEQUENCE (schrodinger.application.bioluminate.pose_filtering.hdx_io.DynamXColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.HDExaminerColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.StandardColumns attribute) sequence (schrodinger.livedesign.biologics.sequence.AlignedSequence attribute) (schrodinger.protein.annotation.AbstractSequenceAnnotations attribute) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations attribute) Sequence (schrodinger.protein.properties.PropertySource attribute) (schrodinger.protein.properties.SequenceProperty attribute) sequence (schrodinger.protein.residue.AbstractSequenceElement property) (schrodinger.protein.residue.CombinedChainResidueWrapper property) sequence_logo (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) SEQUENCE_PROP (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) SequenceAnnotations (class in schrodinger.protein.annotation) sequenceContextCallback() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) sequenceCopied (schrodinger.protein.sequence.AbstractSingleChainSequence attribute) SequenceData (class in schrodinger.application.matsci.reaction_workflow_gui_utils) SequenceDescriptorsTask (class in schrodinger.protein.tasks.descriptors) SequenceDescriptorsTask.Input (class in schrodinger.protein.tasks.descriptors) SequenceDescriptorsTask.Output (class in schrodinger.protein.tasks.descriptors) SequenceDockWidget (class in schrodinger.application.bioluminate.ssv.viewer) SequenceFileDialog (class in schrodinger.application.bioluminate.bwidgets) sequenceNameChanged (schrodinger.protein.alignment.AlignmentSignals attribute) SequenceProperty (class in schrodinger.protein.properties) sequenceResiduesChanged (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesAboutToBeInserted (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesAboutToBeRemoved (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesAboutToBeReordered (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesImported (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) sequencesInserted (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesRemoved (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesReordered (schrodinger.protein.alignment.AlignmentSignals attribute) sequenceStructureChanged (schrodinger.protein.alignment.AlignmentSignals attribute) sequenceVisibilityChanged (schrodinger.protein.alignment.AlignmentSignals attribute) serial_split() (in module schrodinger.application.macromodel.tools) SerializableShapeGenerator (class in schrodinger.application.phase.packages.shape_generator) SerializationError serialize() (schrodinger.application.desmond.cmj.Engine method) (schrodinger.application.desmond.picklejar.PickleJar static method) (schrodinger.application.desmond.stage.workflow.Extern method) (schrodinger.stepper.stepper.Serializer method) (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method) serialize_bernoulli_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_bytes() (schrodinger.application.desmond.cmj.Engine method) serialize_compact() (in module schrodinger.application.phase.packages.conformer_storage) serialize_complement_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_conformations() (in module schrodinger.utils.cgxutils) serialize_csr_matrix() (in module schrodinger.application.matsci.mlearn.sklearn_json.csr) serialize_decision_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_decision_tree_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_dummy_classifier() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_dummy_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_gaussian_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_gradient_boosting() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_gradient_boosting_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_het_states() (in module schrodinger.application.prepwizard) serialize_label_binarizer() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_lasso_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_lda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_linear_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_logistic_regression() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_lossless() (in module schrodinger.application.phase.packages.conformer_storage) serialize_mlp() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_mlp_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_model() (in module schrodinger.application.matsci.mlearn.sklearn_json) serialize_multinomial_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_params_random_state() (in module schrodinger.application.matsci.mlearn.sklearn_json.common) serialize_pca() (in module schrodinger.application.matsci.mlearn.sklearn_json.decomposition) serialize_perceptron() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_qda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_random_forest() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_random_forest_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_ridge_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_svm() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) serialize_svr() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialize_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) serialized_panel (schrodinger.models.presets.PanelPreset attribute) serialized_panelChanged (schrodinger.models.presets.PanelPreset attribute) serialized_panelReplaced (schrodinger.models.presets.PanelPreset attribute) serialized_rdmol (schrodinger.livedesign.registration.RegistrationData attribute) serializeNode() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) Serializer (class in schrodinger.stepper.stepper) serializer (in module schrodinger.models.jsonable) serializeToken() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) Series (class in schrodinger.application.desmond.enhsamp) SERIES (schrodinger.ui.qt.schart.SChart attribute) series() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) SeriesData (class in schrodinger.ui.qt.schart) SeriesDialog (class in schrodinger.ui.qt.schart) seriesHovered() (schrodinger.ui.qt.schart.SChart method) SeriesParams (class in schrodinger.ui.qt.schart) Server (class in schrodinger.application.licensing.flexlm) server (schrodinger.application.glide.ligand_designer.BuildServerTask.Output attribute) SERVER (schrodinger.utils.postinstall.CustomConfigFiles attribute) SERVER_ENTITLEMENT (schrodinger.application.licensing.licserver.install.LicenseFileType attribute) SERVER_ENTITLEMENT_BLOB (schrodinger.application.licensing.licserver.install.LicenseFileType attribute) server_host() (schrodinger.application.licensing.flexlm.License method) server_host_and_port() (schrodinger.application.licensing.licadmin.LicenseResource method) server_hostid() (schrodinger.application.licensing.licadmin.LicenseResource method) server_hostids() (schrodinger.application.licensing.licadmin.LicenseResource method) server_hostnames() (schrodinger.application.licensing.licadmin.LicenseResource method) server_hostport() (schrodinger.application.licensing.flexlm.License method) SERVER_IDENTIFIER (schrodinger.application.licensing.licserver.client.LicenseFileType attribute) (schrodinger.application.licensing.licserver.install.LicenseFileType attribute) server_log() (in module schrodinger.application.licensing.licadmin) server_pathname() (schrodinger.application.licensing.licadmin.LicenseResource method) SERVER_ROOT (schrodinger.seam.viz.watcher.WatcherWebServer attribute) server_version() (schrodinger.application.licensing.licadmin.LicenseResource method) serverAddress (schrodinger.application.licensing.licserver.client.ServerIdentifier attribute) serverChanged (schrodinger.application.glide.ligand_designer.BuildServerTask.Output attribute) ServerError ServerIdentifier (class in schrodinger.application.licensing.licserver.client) serverIdentifiers (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) ServerIdentifierSourceType (class in schrodinger.application.licensing.licserver.client) ServerInfo (class in schrodinger.application.licensing.licadmin) (class in schrodinger.job.server) ServerRegistrationMixin (class in schrodinger.application.jobserver_cert_gui_dir.registration_dialogs) serverReplaced (schrodinger.application.glide.ligand_designer.BuildServerTask.Output attribute) servers_without_registration() (in module schrodinger.job.cert) ServerTimedOutError serves_as_backbone_bond() (in module schrodinger.application.matsci.rxn_channel) serves_as_sidechain_bond() (in module schrodinger.application.matsci.rxn_channel) sessiontokenHasAccess() (schrodinger.seam.viz.watcher.WatcherWebServer method) set() (schrodinger.application.desmond.cmj.JobStatus method) (schrodinger.application.matsci.builderwidgets.StructureLabel method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.ui.qt.config_dialog.DialogParameters method) (schrodinger.utils.preferences.Preferences method) set3DDataSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) set_1_buried_sasa (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_1_buried_sasaChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_1_buried_sasaReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_1_residue (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_1_residueChanged (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_1_residueReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_2_buried_sasa (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_2_buried_sasaChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_2_buried_sasaReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_2_residue (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_2_residueChanged (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_2_residueReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) set_active_databases() (in module schrodinger.application.bioluminate.antibody.utils) set_all_atoms_entry_id_from_entry_id_property() (in module schrodinger.structure) set_all_databases() (in module schrodinger.application.bioluminate.antibody.utils) set_all_st_group_hierarchies() (in module schrodinger.application.desmond.kinetics.utils) set_alpha() (schrodinger.ui.qt.label_cursor.LabelCursorAxes method) set_angle_potential_type() (in module schrodinger.application.matsci.coarsegrain) set_antibody_scheme() (in module schrodinger.application.bioluminate.antibody.utils) set_as_coarse_grain() (in module schrodinger.application.matsci.coarsegrain) set_atom_cart_constr() (in module schrodinger.application.matsci.espresso.utils) set_atom_coarse_grain_properties() (in module schrodinger.application.matsci.coarsegrain) set_atom_elements() (in module schrodinger.application.scaffold_enumeration.atomlist) set_atom_ffio_velocity() (in module schrodinger.application.matsci.desmondutils) set_atom_group() (schrodinger.application.desmond.cms.Cms method) (schrodinger.application.desmond.stage.utils.SystemBuilder static method) set_atom_group_from_asl() (schrodinger.application.desmond.cms.Cms method) set_atom_properties() (in module schrodinger.application.desmond.struc) set_atom_reference_coordinates() (in module schrodinger.application.desmond.struc) set_atom_type() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) set_ballnstick_repr() (in module schrodinger.application.matsci.maestrocmds) set_box_buffer_width() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator static method) set_bracket() (schrodinger.application.jaguar.qrnn.temp_opt.Brent method) set_color() (schrodinger.application.desmond.torsion_related.TorsionPotential method) (schrodinger.ui.qt.formlayout.ColorButton method) set_colormap() (schrodinger.ui.qt.structure2d.structure_item method) set_column_constant() (in module schrodinger.application.matsci.kmc) set_connection_status() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) set_corp_id_properties() (in module schrodinger.application.livedesign.ld_utils) set_ct_reference_coordinates() (in module schrodinger.application.desmond.struc) set_cts_property() (schrodinger.application.desmond.cms.Cms method) set_cursor() (schrodinger.ui.qt.navtoolbar.NavToolbar method) set_custom_scoring_function_from_args() (in module schrodinger.application.glide.sort_parser_common) set_debug_flag() (in module schrodinger.seam.debug) set_default_template_file() (schrodinger.application.jaguar.autots_input.AutoTSInput method) (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) set_defaults() (schrodinger.application.matsci.parserutils.DriverParser method) set_deletable() (schrodinger.application.desmond.maestro.NewEntry method) set_dimensionality_to_st() (in module schrodinger.application.matsci.pbcutils) set_dummy_atoms_as_attachment_points() (in module schrodinger.rdkit.rgroup) set_e_and_g() (in module schrodinger.application.matsci.mecp_mod) set_edge_skip_fep() (in module schrodinger.application.desmond.skip_fep_utils) set_entries_included() (in module schrodinger.project.utils) set_entries_marked() (in module schrodinger.project.utils) set_entries_pinned() (in module schrodinger.project.utils) set_entry_included() (in module schrodinger.project.utils) set_entry_locked() (in module schrodinger.project.utils) set_entry_pinned() (in module schrodinger.project.utils) set_entry_property() (in module schrodinger.application.phase.phase_markers) set_exception_handler() (in module schrodinger.infra.exception_handler) set_excluded_volume_visible() (in module schrodinger.application.phase.phase_markers) set_expires() (schrodinger.application.licensing.licadmin.LicenseFeature method) set_extra_energy_props() (in module schrodinger.application.matsci.reaction_workflow_utils) set_family() (schrodinger.application.desmond.stage.workflow.Task method) set_feature_flag() (in module schrodinger.application.matsci.mstest) set_feature_labels_visible() (in module schrodinger.application.phase.phase_markers) set_feature_tolerance_visible() (in module schrodinger.application.phase.phase_markers) set_features() (in module schrodinger.utils.featureflags.featureflags) set_ff() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) set_file_logger() (in module schrodinger.application.licensing.flexlm) set_files_from_args() (in module schrodinger.application.glide.sort_parser_common) set_filters_from_args() (in module schrodinger.application.glide.sort_parser_common) set_find_toolbar_enabled() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) set_find_toolbar_visible() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) set_freestyle_site_type() (in module schrodinger.application.phase.phase_markers) set_freezing_atommass() (in module schrodinger.application.desmond.remd) set_from_atom() (schrodinger.application.canvas.r_group.TempAtom method) set_gas_phase_zpe_props() (in module schrodinger.application.matsci.reaction_workflow_utils) set_globals() (in module schrodinger.infra.mm) set_highlight() (in module schrodinger.livedesign.draw) set_hkl() (in module schrodinger.application.matsci.nano.slab) set_hostid() (schrodinger.application.licensing.licadmin.LicenseFeature method) set_hotregion() (in module schrodinger.application.desmond.r_group_asl) set_id() (schrodinger.application.desmond.fep_struc.Struc method) set_included() (in module schrodinger.application.matsci.maestrocmds) set_input_and_output_files() (in module schrodinger.application.bb_database.bb_job_utils) (in module schrodinger.application.phase.packages.phase_database_job_utils) (in module schrodinger.application.phase.packages.shape_screen_job_utils) set_installation_feature() (in module schrodinger.utils.featureflags.featureflags) set_interaction_label() (in module schrodinger.protein.assignment) set_isosurface() (in module schrodinger.application.desmond.mxmd.mxmd_cleanup) set_job_builder_opts() (in module schrodinger.application.matsci.espresso.utils) set_jsb_input_file() (in module schrodinger.application.bb_database.bb_job_utils) (in module schrodinger.application.phase.packages.phase_utils) set_lambda_hopping() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) set_lattice_properties() (in module schrodinger.application.matsci.nano.xtal) set_layout_margins() (in module schrodinger.ui.qt.swidgets) set_ligand_from() (schrodinger.application.desmond.torsion_related.TorsionPotential method) set_ligand_to() (schrodinger.application.desmond.torsion_related.TorsionPotential method) set_logger() (in module schrodinger.application.licensing.flexlm) set_loggerstates() (in module schrodinger.rdkit.rdkit_adapter) set_macro_dict() (in module schrodinger.utils.sea.sea) set_mag_hubbu() (in module schrodinger.application.matsci.espresso.utils) set_marker_properties() (in module schrodinger.application.matsci.buildcomplex) set_match_atom() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) set_member_names() (schrodinger.application.jaguar.simple_spec.Peak method) set_message() (schrodinger.ui.qt.navtoolbar.AtomInfoToolbar method) (schrodinger.ui.qt.navtoolbar.NavToolbar method) set_min_dimensions() (in module schrodinger.application.matsci.gutils) set_mmffld_option() (in module schrodinger.forcefield.common) set_mps_factor() (schrodinger.application.desmond.starter.ui.cmdline.BaseArgs method) set_nactive_gids() (schrodinger.application.desmond.cms.Cms method) set_neighbor_atoms_basis_set() (in module schrodinger.application.matsci.clusterstruct) set_nonbond_potential_type() (in module schrodinger.application.matsci.coarsegrain) set_nresamples() (schrodinger.application.desmond.bennett.CalcBAR method) set_obj_value() (in module schrodinger.ui.qt.appframework2.settings) set_option() (in module schrodinger.application.matsci.jobutils) set_output() (schrodinger.application.desmond.bennett.CalcBAR method) set_output_options_from_args() (in module schrodinger.application.glide.sort_parser_common) set_parent() (schrodinger.utils.sea.sea.Sea method) set_parent_stylesheet() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) set_pbc() (in module schrodinger.application.matsci.packmol) set_pbc_properties() (in module schrodinger.application.matsci.nano.xtal) set_persistent_value() (in module schrodinger.ui.qt.appframework2.settings) set_physical_properties() (in module schrodinger.application.matsci.desmondutils) (in module schrodinger.application.matsci.nano.xtal) set_pka() (in module schrodinger.protein.assignment) set_pka_marker (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) set_pmode() (schrodinger.utils.sea.sea.Sea method) set_preference() (in module schrodinger.utils.preferences) set_project_group_hierarchy() (in module schrodinger.application.matsci.msutils) set_project_preference_custom_opls_path() (in module schrodinger.ui.qt.forcefield.forcefield) set_prop() (in module schrodinger.application.pathfinder.synthesis) set_prop_list() (schrodinger.application.canvas.r_group.Data method) set_properties() (in module schrodinger.application.matsci.mecp_mod) (in module schrodinger.livedesign.bbchem_endpoints) (in module schrodinger.livedesign.convert) set_property_labels_visible() (in module schrodinger.application.phase.phase_markers) set_pt_subgroup_info() (in module schrodinger.application.matsci.fragments) set_pymol_location_preference() (in module schrodinger.application.pymol.utils) set_random_seed() (in module schrodinger.application.desmond.kinetics.utils) set_range() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) set_rank() (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot method) set_rbpotential() (schrodinger.application.desmond.torsion_related.TorsionPotential method) set_readonly() (schrodinger.application.desmond.maestro.NewEntry method) set_rect() (schrodinger.ui.qt.structure2d.structure_item method) set_reference_ligand_visible() (in module schrodinger.application.phase.phase_markers) set_relative_restrain_scaling() (in module schrodinger.application.desmond.gconfig) set_representation() (in module schrodinger.application.matsci.nano.particle) set_representation_bond() (in module schrodinger.application.matsci.nano.xtal) set_res_name() (in module schrodinger.protein.process_enamine_db) set_restart_input_files() (in module schrodinger.application.matsci.jaguar_restart) set_restrain() (schrodinger.application.desmond.cms.Cms method) (schrodinger.application.desmond.stage.utils.SystemBuilder static method) set_rgroup_highlight() (in module schrodinger.livedesign.draw) set_schrodinger_db_value() (in module schrodinger.application.matsci.kmc) set_seed() (schrodinger.application.desmond.bennett.CalcBAR method) set_seqres() (in module schrodinger.protein.seqres) set_server_refresh() (in module schrodinger.application.licensing.licadmin) set_sgroups() (in module schrodinger.application.scaffold_enumeration.common) set_sh_file_flags() (in module schrodinger.job.jobwriter) (in module schrodinger.ui.qt.appframework2.jobs) set_significant_figures() (in module schrodinger.math.mathutils) set_smart_distribution_from_environ() (in module schrodinger.application.matsci.jobutils) set_sort_criteria_from_args() (in module schrodinger.application.glide.sort_parser_common) set_sort_index() (schrodinger.application.licensing.flexlm.Feature method) set_source_path() (in module schrodinger.application.matsci.jobutils) set_starts() (schrodinger.application.licensing.licadmin.LicenseFeature method) set_state_coordinates() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) set_struct_file() (schrodinger.application.desmond.cmj.JobOutput method) set_structure() (in module schrodinger.ui.sketcher_extensions) (schrodinger.ui.qt.structure2d.structure_item method) set_structure_file() (in module schrodinger.application.jaguar.file_logger) set_structure_index() (in module schrodinger.application.bioluminate.protein_interaction.tasks) set_structure_properties() (in module schrodinger.application.desmond.struc) set_structure_skip_fep() (in module schrodinger.application.desmond.skip_fep_utils) set_structure_soluble() (in module schrodinger.application.desmond.solubility_utils) set_structure_wam() (in module schrodinger.application.matsci.jobutils) set_symbol_size() (schrodinger.ui.qt.rama.RamaScatterMixin method) set_table_expire() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) set_temp_press_props() (in module schrodinger.application.matsci.reaction_workflow_utils)

set_text() (schrodinger.ui.qt.structure2d.structure_item method) set_thread_name() (in module schrodinger.utils.thread_utils) set_title() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) set_title_to_stoichiometry() (in module schrodinger.application.matsci.genetic_optimization) set_tokens() (schrodinger.application.licensing.licadmin.LicenseFeature method) set_trajectory_path() (in module schrodinger.trajectory.utils) set_unique_pdb_atom_names() (in module schrodinger.application.matsci.packmol) set_unique_pdb_res_names() (in module schrodinger.application.matsci.packmol) set_up_logger() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) set_user_states() (schrodinger.protein.assignment.ProtAssign method) set_val() (schrodinger.application.desmond.simulation_block_test.Test method) set_value() (schrodinger.utils.sea.sea.Map method) set_value_fast() (schrodinger.utils.sea.sea.Map method) set_visible() (schrodinger.ui.qt.label_cursor.LabelCursorAxes method) (schrodinger.ui.qt.label_cursor.MultiAxesLabelCursor method) set_wa_dont_show_on_screen() (in module schrodinger.application.matsci.mstest) set_wait_cursor() (in module schrodinger.application.bioluminate.pml_menus) set_zob_to_sob() (in module schrodinger.application.matsci.rxn_channel) setAbbeNum() (schrodinger.application.matsci.permittivity.RefractiveIndex static method) setAbstractColumns() (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) setAcceptableContraintEids() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) setActions() (schrodinger.application.bioluminate.actions.factory.Factory method) (schrodinger.ui.qt.tasks.taskwidgets.SettingsButton method) setActive() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) setActiveCoord() (schrodinger.application.jaguar.input.JaguarInput method) setActiveTask() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) setAddAlchemicalIons() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setADProjectedPointsChecked() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) setAlias() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) setAliasedValue() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) setAliases() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) setAlignment() (schrodinger.application.prime.wrapper.ConsensusConfig method) (schrodinger.application.prime.wrapper.PrimeConfig method) (schrodinger.ui.qt.delegates.PictureDelegate method) setAllAssayData() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) setAllData() (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) setAllfragments() (schrodinger.application.matsci.amorphous.PolymerFragments method) setAllItemsSelected() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) setAllowedPrograms() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) setAllowMovement() (schrodinger.ui.qt.network_views.NetworkViewer method) setAllPairs() (schrodinger.application.matsci.coarsegrain.Internals method) setAllTransBackbone() (schrodinger.application.matsci.amorphous.Monomer method) setAlpha() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) setAlphaCeiling() (schrodinger.ui.qt.color_picker.AlphaLimitedColorPickerButton method) setAndMarkResidues() (schrodinger.application.matsci.amorphous.PolymerFragments method) setAngleNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setAngles() (schrodinger.application.matsci.coarsegrain.Internals method) setAnnotators() (schrodinger.ui.qt.structure2d.StructurePicture method) setAntibodyNumberingToolBarVisible() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) setAppendLogs() (schrodinger.job.launcher.Launcher method) setArea() (schrodinger.application.matsci.shapes.Face method) setArrowhead() (schrodinger.ui.qt.network_views.NetworkEdge method) setAsFragment() (schrodinger.application.matsci.amorphous.BaseMoiety method) (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Monomer method) setASL() (schrodinger.application.desmond.gui.OutputTab method) setAsl() (schrodinger.ui.qt.atomselector.AtomSelector method) setAsOneFragment() (schrodinger.application.matsci.amorphous.PolymerFragments method) setAspectRatioPolicy() (schrodinger.ui.qt.table.DataViewerTable method) setAsReference() (schrodinger.ui.two_d_viewer.CellContextualMenu method) setAsuAtomsFalse() (schrodinger.application.matsci.nano.xtal.Crystal method) setAsWorkspace() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView method) setAtom() (schrodinger.ui.qt.structure2d.RedSquareAnnotator method) setAtomBondTyping() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) setAtomGroups() (schrodinger.application.matsci.atom_group.HelixGroups method) (schrodinger.application.matsci.atom_group.MSAtomGroupsBase method) (schrodinger.application.matsci.atom_group.MSMoleculeAtomGroups method) setAtomHighlights() (schrodinger.ui.qt.rdmol_views.AbstractRDMolImageLabel method) (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) setAtomicBasis() (schrodinger.application.jaguar.input.JaguarInput method) setAtomicCharge() (schrodinger.application.jaguar.input.JaguarInput method) setAtomicMultiplicity() (schrodinger.application.jaguar.input.JaguarInput method) setAtomicWeight() (schrodinger.application.matsci.cg_mapping.Particle method) setAtomLabels() (schrodinger.ui.qt.rdmol_views.AbstractRDMolImageLabel method) setAtomNum() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit method) setAtomProps() (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) setAtomType() (schrodinger.application.matsci.cg_mapping.Particle method) setAttributes() (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam method) (schrodinger.application.matsci.genetic_optimization.Property method) setAutoFit() (schrodinger.ui.qt.ligand_list.LigandListView method) setAutoInclude() (schrodinger.ui.qt.ligand_list.LigandListView method) setAutoQsarModel() (schrodinger.ui.two_d_viewer.TwoDViewer method) setAutoResize() (schrodinger.ui.qt.structtable.ViewerTable method) setAutoSizing() (schrodinger.ui.qt.table.DataViewerTable method) setAxisAutoRange() (schrodinger.ui.qt.schart.SChart method) setAxisLabels() (schrodinger.application.matsci.density_analysis_widget.ImagePlotFrame method) (schrodinger.application.matsci.density_analysis_widget.LinePlotFrame method) setAxisMinMax() (schrodinger.ui.qt.schart.SChart method) setAxisMSD() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase method) setBackboneAndSideGroup() (schrodinger.application.matsci.amorphous.PolymerFragments method) setBackend() (schrodinger.application.glide.http_client.NonBlockingBackendChecker method) SetBackgroundParms() (in module schrodinger.application.matsci.gsas.GSASIIpwd) setBacktrackingLevel() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) setBaroMethod() (schrodinger.application.desmond.gui.EnsembleTab method) setBaroRelaxationMethod() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) setBaroStyle() (schrodinger.application.desmond.gui.EnsembleTab method) setBaseName() (schrodinger.application.matsci.nano.interface_mod.Interface method) setBasic() (schrodinger.application.matsci.coarsegrain.Internals method) setBasis() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterListToolButton method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit method) (schrodinger.application.matsci.jagwidgets.BasisSetSelector method) setBasisForRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) setBasisFromText() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) setBasisSafe() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) setBasisVectors() (schrodinger.application.matsci.zmutils.ZMatrix method) setBestXtalVectorProperty() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) setBeta() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) setBindingSiteASL() (schrodinger.protein.reliability.ProteinCheckParameters method) setBindingSiteAtoms() (schrodinger.structutils.sitealign.BindingSiteAligner method) setBins() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) setBinVolume() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) setBlankBasisAllowed() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) setBoltzmannDistribution() (schrodinger.application.matsci.amorphous.EnergySurface method) setBondNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setBondOrder() (schrodinger.structutils.assignbondorders.AssignBondOrders method) setBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setBoundaryCondition() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setBoundingRect() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) setBox() (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame method) setBoxes() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) setBranchColor() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) setBranchReplicaNode() (schrodinger.application.matsci.permittivity.WorkflowParser method) setBranchWidth() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) setBrowserText() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) setButtonColor() (schrodinger.ui.qt.swidgets.ColorWidget method) setButtonEnabled() (schrodinger.ui.qt.appframework.AppFramework method) setButtonIcon() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) setButtonMethods() (schrodinger.ui.qt.appframework2.appmethods.MethodsDict method) setButtonState() (schrodinger.ui.qt.appframework.AppFramework method) setButtonToolTip() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) setCallbacksActive() (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) setCell() (schrodinger.ui.qt.swidgets.STableWidget method) setCellAsReference() (schrodinger.ui.two_d_viewer.TwoDViewer method) SetCellAtoms() (in module schrodinger.application.matsci.gsas.GSASIIpwd) setCells() (schrodinger.ui.two_d_viewer.TwoDTableModel method) setCellsForTangledChain() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setCellValue() (schrodinger.ui.qt.table.StructureDataViewerModel method) setCGBondLengths() (in module schrodinger.application.matsci.coarsegrain) setChanged() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) setChannel() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setChannelAttrs() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) setCharge() (schrodinger.application.matsci.crest.CrestTOML method) setChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) setCharges() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) setCharPositionInLine() (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setCharStream() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) setCheckable() (schrodinger.ui.qt.tablewidget.Cell method) setCheckableColumns() (schrodinger.ui.qt.table_helper.CheckableHeaderView method) setCheckBoxText() (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) setChecked() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.swidgets.SCheckBox method) setCheckedData() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) setCheckedMaestroProperties() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) setCheckState() (schrodinger.ui.qt.tablewidget.Cell method) setChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setChildIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setChiralHash() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond method) setChmmol() (schrodinger.application.desmond.fep_scholar_util.FEPStructureObject method) setChorusBoxProps() (schrodinger.application.matsci.desmondutils.SystemBuilder method) setChorusProperties() (schrodinger.application.matsci.nano.xtal.Crystal method) setClassKwargs() (schrodinger.application.matsci.genetic_optimization.Property method) setClearButton() (schrodinger.ui.qt.swidgets.SLineEdit method) setClickable() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) setColor() (schrodinger.application.dendrogram.gradientSelector.ColorSelector method) (schrodinger.graphics3d.tube.MaestroTube method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) (schrodinger.ui.qt.structure2d.CircleAnnotator method) (schrodinger.ui.qt.structure2d.RedSquareAnnotator method) setColoring() (schrodinger.project.surface.ProjectSurface method) (schrodinger.surface.Surface method) setColormap() (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) setColorModeAction() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) setColorRGB() (schrodinger.structure.StructureAtom method) setColors() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) setColumnCount() (schrodinger.ui.qt.swidgets.STableWidget method) setColumnIsGanged() (schrodinger.ui.qt.table.DataViewerTable method) setColumns() (schrodinger.application.desmond.gui.TableModel method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) setColumnWidth() (schrodinger.ui.qt.table.VStackedDataViewerTable method) setCombiningRule() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) setComboToSelect() (schrodinger.application.livedesign.panel_components.LiveReportSelector method) setCommandLine() (schrodinger.job.launchapi.TaskSpecificationBuilder method) setComponent() (schrodinger.application.matsci.kmc.AxisData method) setCompStr() (schrodinger.utils.ligfilter.Criterion method) setConfigDialog() (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.AbstractTaskBar method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) setConfigDialogSettings() (schrodinger.ui.qt.appframework2.af2.JobApp method) setConfs() (schrodinger.trajectory.prody.ensemble.Ensemble method) setConnectionFile() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConnectionMaxLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConnectionMinLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConnectionName() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConnectionSize() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConstants() (schrodinger.application.jaguar.autots_input.AutoTSInput method) setConstraint() (schrodinger.application.jaguar.input.JaguarInput method) setConstraints() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.matsci.crest.CrestTOML method) setConversion() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) setCoordinates() (schrodinger.ui.dendrogram.DendrogramGraphicNode method) setCoords() (schrodinger.graphics3d.hemisphere.MaestroHemisphere method) (schrodinger.graphics3d.sphere.MaestroSphere method) (schrodinger.graphics3d.torus.MaestroTorus method) (schrodinger.trajectory.prody.ensemble.Ensemble method) setCoorGenMode() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) setCorpIds() (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask method) setCovariance() (schrodinger.trajectory.prody.pca.PCA method) setCrystalSymmetry() (schrodinger.application.matsci.nano.xtal.Crystal method) setCurrentChoice() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) setCurrentData() (schrodinger.ui.qt.swidgets.SComboBox method) setCurrentFile() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) setCurrentIndex() (schrodinger.ui.qt.swidgets.SComboBox method) setCurrentJob() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) setCurrentLabel() (schrodinger.ui.qt.swidgets.STabWidget method) setCurrentLR() (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) setCurrentMmJagData() (schrodinger.application.jaguar.gui.utils.EnhancedComboBox method) setCurrentSelection() (schrodinger.ui.qt.datamapper.MappableButtonGroup method) setCurrentSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.clusterstructgui.SpeciesCombo method) setCurrentText() (schrodinger.ui.qt.swidgets.SComboBox method) setCurrentTopLevelJob() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) setCursor() (schrodinger.application.matsci.kmc.Table method) setCustomBaseName() (schrodinger.tasks.taskmanager.TaskManager method) setCustomTemplateDir() (schrodinger.application.matsci.builderwidgets.SketcherBox method) setCVals() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) setDarkStyle() (schrodinger.ui.qt.atomselector.AtomSelector method) setData() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart method) (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) (schrodinger.application.matsci.amorphous.TorsionAngler method) (schrodinger.application.matsci.hdfutils.HDFIO method) (schrodinger.application.matsci.hdfutils.HDFProxyPickleIO method) (schrodinger.application.matsci.mswidgets.AtomNameWidgetItem method) (schrodinger.livedesign.rgfile_parse.ForwardRGMolSupplier method) (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) (schrodinger.ui.qt.mapperwidgets.plptable.FieldColumn method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) (schrodinger.ui.qt.network_visualizer.Edge method) (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.network_visualizer.Node method) (schrodinger.ui.qt.table_helper.PtRowBasedTableModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) (schrodinger.ui.qt.tablewidget.Cell method) setDatabase() (schrodinger.application.matsci.kmcgui.NeighborsTab method) (schrodinger.application.matsci.kmcgui.Tab method) setDebug() (schrodinger.infra.table.Table static method) (schrodinger.project.project.Project static method) setDebugLevel() (schrodinger.job.launchparams.LaunchParameters method) setDebugListener() (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) setDefault() (schrodinger.ui.qt.filter_list.FilterCheckBox method) setdefault() (schrodinger.utils.scollections.DefaultIdDict method) (schrodinger.utils.scollections.IdDict method) setDefaultAnalysisParams() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) setDefaultBasis() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) setDefaultCheckedItems() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportPanelWizard method) setDefaultItems() (schrodinger.application.matsci.mswidgets.SystemInformationFrame method) setDefaultParticleLabels() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond method) setDefaultPreset() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) (schrodinger.models.presets.PresetManager method) setDefaultRangeLimit() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) setDefaults() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) (schrodinger.application.livedesign.panel_components.LiveReportTemplateSelectorCombo method) (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.two_d_viewer.TwoDViewer method) setDefaultScale() (schrodinger.ui.qt.network_views.NetworkViewer method) setDefaultText() (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp method) setDefaultTheory() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) setDefinitions() (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.SaveDefinitionsDialog method) setDelegate() (schrodinger.ui.qt.structtable.ViewerTable method) (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.StructureDataViewerModel method) setDelegates() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka method) setDeleteAfterIncorporation() (schrodinger.job.launchparams.LaunchParameters method) setDelimiter() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) setDeltasToNeighboringCells() (schrodinger.application.matsci.nano.xtal.PBCBond method) (schrodinger.application.matsci.nano.xtal.PBCBonds method) setDensityIncreaseAllowed() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) setDescription() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) setDielectricConstant() (schrodinger.application.matsci.cgforcefield.FFIOSite method) SetDiff (class in schrodinger.models.diffy) setDihedralNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setDihedrals() (schrodinger.application.matsci.amorphous.PolymerFragment method) (schrodinger.application.matsci.coarsegrain.Internals method) setDiheInit() (schrodinger.application.matsci.amorphous.PolymerFragments method) setDirecional() (schrodinger.application.matsci.amorphous.Monomer method) setDirective() (schrodinger.application.jaguar.input.JaguarInput method) setDirectoryPath() (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) setDisabledIconPath() (schrodinger.ui.qt.standard_widgets.buttons.FlatButton method) setDisorderedRegionsPredictions() (schrodinger.protein.sequence.AbstractSingleChainSequence method) setDisplayAtomsASL() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) setDisplayedEids() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) setDisplayNames() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) setDistance() (schrodinger.ui.dendrogram.DendrogramNode method) (schrodinger.ui.dendrogram.DendrogramTreeBuilder method) setDistanceCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setDistanceMatrixCallback() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) setDivergencies() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) setDomainArrangementPredictions() (schrodinger.protein.sequence.AbstractSingleChainSequence method) setDoneAdding() (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) setDOSFromFile() (schrodinger.application.matsci.espresso.qeoutput.Output method) setDownstreamWidgetsEnabled() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) setDraggableThumb() (schrodinger.application.matsci.mswidgets.MultiSlider method) setDriverReservesCores() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setDurationTextEditBox() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) setDurationValidator() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) setEdges() (schrodinger.ui.qt.schart.SHistogramBarSeries method) setEdgeValidator() (schrodinger.ui.qt.network_visualizer.Graph method) setEditable() (schrodinger.application.matsci.kmcgui.NeighborsTab method) (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) (schrodinger.ui.qt.tablewidget.Cell method) setEditablePkaAtomDelegate() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka method) setEditEnabled() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) setEditorData() (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.TempItemDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBoxDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeSelectorDelegate method) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUpDelegate method) (schrodinger.ui.qt.delegates.ComboBoxDelegate method) (schrodinger.ui.qt.delegates.SpinBoxDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate method) setEigens() (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.trajectory.prody.pca.PCA method) setEmptyOK() (schrodinger.ui.qt.swidgets.SMARTSEdit method) setEnabled() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) (schrodinger.application.matsci.kmcgui.PropertyCombo method) (schrodinger.application.matsci.mswidgets.OptionalInputSelector method) (schrodinger.application.matsci.reaction_workflow_gui_utils.UniformSequence method) (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.qt.standard_widgets.buttons.SplitPushButton method) (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) (schrodinger.ui.qt.swidgets.SCheckBoxWithSubWidget method) (schrodinger.ui.qt.swidgets.SLabeledComboBox method) (schrodinger.ui.qt.swidgets.SLabeledDoubleSpinBox method) (schrodinger.ui.qt.swidgets.SLabeledEdit method) (schrodinger.ui.qt.swidgets.SLabeledRadioButtonGroup method) (schrodinger.ui.qt.swidgets.SLabeledSlider method) (schrodinger.ui.qt.swidgets.SLabeledSpinBox method) (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) (schrodinger.ui.qt.swidgets.SRadioButtonWithSubWidget method) (schrodinger.ui.qt.swidgets.VerticalLabel method) (schrodinger.ui.qt.tablewidget.Cell method) setEnabledCurrentFrameOptions() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) setEnabledExceptSimulationTime() (schrodinger.application.desmond.gui.MdGroup method) (schrodinger.application.desmond.gui.SimOptionsFrame method) setEnabledState() (schrodinger.application.matsci.chargegui.ChargeDialog method) setEndFrameValue() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) setEnergiesAndForces() (schrodinger.application.matsci.mecp_mod.MECPStep method) setEnergiesAndForcesData() (schrodinger.application.matsci.mecp_mod.MECPStep method) setEntryId() (schrodinger.application.matsci.kmcgui.MinMaxNeighborWidgets method) setEntryID() (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.tube.MaestroTube method) setError() (schrodinger.application.jaguar.gui.timing.TimingResults method) (schrodinger.ui.qt.appframework.CustomProgressBar method) setErrorStatusMessage() (schrodinger.ui.qt.widgetmixins.basicmixins.StatusBarMixin method) setExcitedStateCheckBoxText() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) setExcludeLocation() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setExclusive() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) setExpandedRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) setExpansionBFS() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) setExportMapManager() (schrodinger.application.livedesign.export_map_manager.MappingsComboBox method) setExtraColumnsVisible() (schrodinger.application.livedesign.panel_components.ExportTableView method) setF16Only() (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) setFeatureLabelVisible() (schrodinger.application.phase.phase_markers.PhaseMarkers method) setFeatures() (schrodinger.application.phase.featureselector.FeatureSelector method) setFeatureSelection() (schrodinger.application.phase.phase_markers.PhaseMarkers method) setFFCDataSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) setFFType() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) setFigures() (schrodinger.application.matsci.reportutils.ReportInfo method) setFile() (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.structtable.StructureReaderDelegate method) setFileLabelText() (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.structure_selector.StructureSelector method) setFileList() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) setFilePath() (schrodinger.ui.qt.file_selector.FileSelector method) setFilePaths() (schrodinger.ui.qt.file_selector.FileSelector method) setFilesUsingExt() (schrodinger.application.matsci.appbase.ViewerGuiMixin method) setFilesUsingStProp() (schrodinger.application.matsci.appbase.ViewerGuiMixin method) setFillPolicy() (schrodinger.ui.qt.table.DataViewerTable method) setFinalDisplacement() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setFinalDisplacementCenter() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setFinalDisplacementNoCenter() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setFingerprint() (schrodinger.ui.qt.fp_selector_widget.FingerprintsPopUp method) setFirstNode() (schrodinger.ui.qt.network_visualizer.ConnectionValidator method) setFitFunction() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method) setFitViewPolicy() (schrodinger.ui.qt.table.DataViewerTable method) setFixed() (schrodinger.application.macromodel.utils.SbcUtil method) setFixedWidth() (schrodinger.ui.qt.table.VStackedDataViewerTable method) setFloatable() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) setFloatableMovable() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) setFloatableMovableClosable() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) setFloatMaximum() (schrodinger.ui.qt.swidgets.SLabeledSlider method) setFloatMinimum() (schrodinger.ui.qt.swidgets.SLabeledSlider method) setFloatValue() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) (schrodinger.ui.qt.swidgets.SLabeledSlider method) setForceConstant() (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) setForceDummy() (schrodinger.infra.unusable_module_importer.AbstractUnusableModuleFinder method) setForceField() (schrodinger.ui.qt.forcefield.ffselector.MaestroForceFieldSelector method) setForceFieldDir() (schrodinger.application.matsci.desmondutils.SystemBuilder method) setFormalCharge() (schrodinger.application.matsci.cg_mapping.Particle method) (schrodinger.structutils.assignbondorders.AssignBondOrders method) setFormula() (schrodinger.application.matsci.cg_mapping.Particle method) setFrame() (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame method) setFrameSSData() (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method) setFromCommandLineFlags() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) (schrodinger.application.matsci.mswidgets.RandomSeedWidget method) (schrodinger.application.matsci.mswidgets.SaveDesmondFilesWidget method) setFrozen() (schrodinger.application.macromodel.utils.SbcUtil method) setFrozenAtoms() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) setFusedRingNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setGangPolicy() (schrodinger.ui.qt.table.DataViewerTable method) setGapPenalties() (schrodinger.protein.tasks.clustal.AbstractAlignmentJob method) setGids() (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame method) setGidsAndMass() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) setGlobalPosition() (schrodinger.ui.qt.structure2d.LabeledStructureToolTip method) (schrodinger.ui.qt.structure2d.StructureToolTip method) setGlowColor() (schrodinger.graphics3d.common.Primitive method) setGPCRAnnotations() (schrodinger.protein.sequence.ProteinSequence method) setGpuList() (schrodinger.tasks.hosts.Host method) setGraphEnergies() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) setGridSize() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) setGroup() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) setGrpMass() (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame method) setGuiState() (schrodinger.application.desmond.gui.SimOptionsFrame method) setHasStructureSpecificSites() (schrodinger.application.matsci.reaction_workflow_utils.EnumerateReactionWorkflow method) setHbondParameters() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setHeader() (schrodinger.ui.qt.tablewidget.Column method) (schrodinger.ui.qt.tablewidget.Row method) setHeaderData() (schrodinger.ui.qt.table.StructureDataViewerModel method) setHeaderToolTip() (schrodinger.ui.qt.tablewidget.Column method) setHeight() (schrodinger.ui.qt.tablewidget.Row method) setHelmMolecule() (schrodinger.protein.helm.helm_renderer.HelmScene method) setHelpTopic() (schrodinger.ui.qt.swidgets.HelpButton method) setHessian() (schrodinger.application.jaguar.input.JaguarInput method) setHighlighted() (schrodinger.ui.qt.standard_widgets.buttons.StyledButton method) setHKL() (schrodinger.application.matsci.nano.interface_mod.Interface method) setHorizontalHeaderLabels() (schrodinger.ui.qt.swidgets.STableWidget method) setHost() (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.job.jobcontrol.Host method) setHostList() (schrodinger.job.queue.JobDJ method) setHostname() (schrodinger.job.launchparams.LaunchParameters method) setHostSelectorOrder() (schrodinger.ui.qt.tasks.configwidgets.HostLayoutWidget method) setHovered() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) setHoverIconPath() (schrodinger.ui.qt.standard_widgets.buttons.FlatButton method) setHoverLabelFormat() (schrodinger.ui.qt.schart.SChartView method) setIcon() (schrodinger.ui.qt.swidgets.LargeSpinner method) setIconPath() (schrodinger.ui.qt.standard_widgets.buttons.FlatButton method) setIconSize_() (schrodinger.ui.qt.standard_widgets.buttons.FlatButton method) setIds() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setIgnorePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setImage() (schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method) (schrodinger.ui.qt.swidgets.ImageLabel method) (schrodinger.ui.qt.tasks.taskwidgets.SpinnerLabel method) (schrodinger.ui.qt.tasks.taskwidgets.SpinnerStartButton method) setImageDelegate() (schrodinger.ui.qt.rdmol_views.AbstractRDMolImageLabel method) (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) (schrodinger.ui.qt.rdmol_views.RDMolTooltipWithLabel method) setImageSize() (schrodinger.ui.qt.rdmol_views.FixedSizeRDMolImageLabel method) (schrodinger.ui.qt.rdmol_views.RDMolTooltipWithLabel method) setImpropers() (schrodinger.application.matsci.coarsegrain.Internals method) setIncludeAcceptor() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeAromatic() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeBackbone() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeCharged() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeContact() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncluded() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) setIncludedExcludedNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setIncludeDonor() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeHydrophobic() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludePolar() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeSidechain() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIndex() (schrodinger.structure.StructureReader method) setIndexEnabled() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) setIndexSelected() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) setIndicator() (schrodinger.ui.qt.swidgets.SLabeledEdit method) setIndices() (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) setIniFrags() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setIniFragsOnebyOne() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setInitialStatus() (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask method) setInitiatorResidue() (schrodinger.application.matsci.amorphous.PolymerFragments method) setInput() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.matsci.crest.CrestTOML method) (schrodinger.pipeline.stage.Stage method) setInputDirectory() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) setInputFile() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) (schrodinger.stepper.stepper.UnbatchedChain method) setInputFiles() (schrodinger.job.launchapi.JobSpecificationBuilder method) setInputLoaded() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) setInputs() (schrodinger.stepper.stepper.UnbatchedChain method) setInputSelector() (schrodinger.application.jaguar.gui.basis_selector.BasisSelector method) setInputSource() (schrodinger.ui.qt.structure_selector.StructureSelector method) setInputSourceComboVisible() (schrodinger.ui.qt.input_selector.InputSelector method) setInputSourceEnabled() (schrodinger.ui.qt.structure_selector.StructureSelector method) setInputState() (schrodinger.ui.qt.input_selector.InputSelector method) setInputStream() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setInputTopic() (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) setInTemplates() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.matsci.mecp_mod.MECPStep method) setInteractionCutoff() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setInterfaceLatticeProperties() (schrodinger.application.matsci.nano.interface_mod.Interface method) setInterfaceProperties() (schrodinger.application.matsci.nano.interface_mod.Interface method) setInternals() (schrodinger.application.matsci.coarsegrain.Internals method) setIonLocation() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setIsGlowing() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.graphics3d.common.Primitive method) setIsInfinite() (schrodinger.application.matsci.nano.interface_mod.Interface method) setIsotropicMSD() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase method) setItemChecked() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) setItemDelegate() (schrodinger.ui.qt.table.DataViewerTable method) setItemDelegateForColumn() (schrodinger.application.jaguar.gui.utils.ProjTableLikeView method) setItemEnabled() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) setItemKey() (schrodinger.application.livedesign.export_models.ThreeDExportItem method) setItems() (schrodinger.ui.ligfilter.PatternModel method) setItemsChecked() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) setItemSelected() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) setItemsEnabled() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) setItemsTooltip() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) setItemTooltip() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) setItUp() (schrodinger.application.matsci.textlogger.GetLogger method) setJaguarKwargs() (schrodinger.application.matsci.mecp_mod.MECP method) setJaguarValue() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) setJaguarValues() (schrodinger.application.jaguar.autots_input.AutoTSInput method) (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.solvation_input.SolvationInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) setJob() (schrodinger.tasks.jobtasks.ComboJobMixin method) setJobData() (schrodinger.application.matsci.mecp_mod.MECPStep method) setJobDJOptions() (schrodinger.pipeline.stage.Stage method) setJobname() (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) setJobName() (schrodinger.job.app.App method) setJobname() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.JobSpecificationBuilder method) (schrodinger.job.launchparams.LaunchParameters method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) setJobOptions() (schrodinger.pipeline.stage.Stage method) SetJobRuntimeError setJobUsesTPP() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setKey() (schrodinger.application.matsci.cg_mapping.Particle method) setKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) setKeywords() (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.KeywordEdit method) (schrodinger.application.matsci.qualityslider.QualitySlider method) setKinaseConservation() (schrodinger.protein.sequence.ProteinSequence method) setKinaseFeatures() (schrodinger.protein.sequence.ProteinSequence method) setLabel() (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.ui.dendrogram.DendrogramGraphicNode method) (schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method) (schrodinger.ui.dendrogram.DendrogramNode method) (schrodinger.ui.qt.network_views.NetworkEdge method) setLabelPixmap() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) setLabelsVisible() (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) setLabelText() (schrodinger.ui.qt.directory_selector.DirectorySelector method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) setLabelToolTip() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) setLambdaDynamics() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) setLastRewriteTokenIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) setLatticeProperties() (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) setLaunchDirectory() (schrodinger.job.launchparams.LaunchParameters method) setLayerLabelSize() (schrodinger.application.matsci.sliceplot.SlicePlot method) setLayerWidgetStates() (schrodinger.application.matsci.sliceplot.SlicePlot method) setLeaf() (schrodinger.ui.dendrogram.DendrogramNode method) setLeaves() (schrodinger.ui.qt.dendrogram.Dendrogram method) setLigandCleanupOptions() (schrodinger.structutils.minimize.Minimizer method) setLigandCorpID() (schrodinger.application.livedesign.export_models.ThreeDExportItem method) setLigandDistance() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) setLigands() (schrodinger.application.matsci.mlearn.features.Complex method) setLigandSource() (schrodinger.ui.qt.ligand_list.LigandListModel method) (schrodinger.ui.qt.ligand_list.LigandListWidget method) setLigRange() (schrodinger.application.glide.glide.Dock method) setLimits() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.StringCriterion method) setLine() (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setLinkage() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) setLiveReport() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) setLiveReportDefaults() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) setLiveReportTemplateDefaults() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) setLocalStructAtomIds() (schrodinger.application.matsci.amorphous.PolymerFragments method) setLocalStructs() (schrodinger.application.matsci.amorphous.PolymerFragments method) setLogger() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method) setLogTag() (schrodinger.application.matsci.permittivity.StepBase method) setLRC() (schrodinger.application.matsci.espresso.qeinput.HybridType method) setMaestroProjectDisposition() (schrodinger.job.launchparams.LaunchParameters method) setMaestroProjectName() (schrodinger.job.launchparams.LaunchParameters method) setMaestroViewname() (schrodinger.job.launchparams.LaunchParameters method) SetMagnetic() (in module schrodinger.application.matsci.gsas.GSASIIspc) setMainProduct() (schrodinger.pipeline.stage.Stage method) setMakeWholeState() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setMapping() (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) setMarkerColor() (schrodinger.ui.qt.ligand_list.LigandListView method) setMarkerHighlighting (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) setMarkersEnabled() (schrodinger.ui.qt.atomselector.AtomSelector method) setMarkSelectedLigands() (schrodinger.ui.qt.ligand_list.LigandListView method) setMass() (schrodinger.application.matsci.cgforcefield.QEMDCms method) (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame method) setMaxCutoff() (schrodinger.application.matsci.kmcgui.NeighborsTab method) setMaxFrame() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) setMaximum() (schrodinger.application.desmond.fep_dialog.CustomGPUComboBox method) (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) (schrodinger.ui.qt.swidgets.SLabeledSlider method) setMaxRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) setMembrane() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMembranePatch() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMembranize() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMergeReplicaNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) setMetadata() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) setMetalAtom() (schrodinger.application.matsci.mlearn.features.Complex method) setMethod() (schrodinger.application.jaguar.gui.theory_selector.FilterTheorySelectorReadOnlyLineEdit method) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListPopUp method) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListToolButton method) setMethodFromText() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) setMetric() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) setMetricCB() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) setMinMaxBox() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) setMinRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) setMMFepioMapModeOption() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMMFepioRetainAngleOption() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMode() (schrodinger.application.livedesign.login.LoginManager method) setModel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.panel_components.ExportTableView method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.models.mappers.TargetParamMapper method) (schrodinger.ui.qt.ligand_list.LigandListView method) (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.table_helper.SampleDataTableViewMixin method) (schrodinger.ui.qt.table_speed_up.MultipleSpeedUpDelegatesViewMixin method) (schrodinger.ui.qt.table_speed_up.SpeedUpDelegate method) (schrodinger.ui.qt.table_speed_up.SpeedUpDelegateViewMixin method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskbarwidgets.NameLineEdit method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressBar method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) (schrodinger.ui.qt.widgetmixins.panelmixins.CleanStateMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) setModelData() (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.TempItemDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBoxDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeSelectorDelegate method) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUpDelegate method) (schrodinger.ui.qt.delegates.ComboBoxDelegate method) (schrodinger.ui.qt.delegates.SpinBoxDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate method) setModelStringList() (schrodinger.ui.qt.recent_completer.RecentCombo method) (schrodinger.ui.qt.recent_completer.StringListModelInterface method) setModelSyncEnabled() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) setModelWithoutSlots() (schrodinger.models.mappers.MapperMixin method) SetMolCent() (in module schrodinger.application.matsci.gsas.GSASIImath) setMoleculeCompletion() (schrodinger.application.matsci.nano.particle.Nanoparticle method) setMonomerGrowAtoms() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) setMonomialConstraint() (schrodinger.application.jaguar.input.JaguarInput method) setMultipleNodePos() (schrodinger.ui.qt.network_visualizer.Graph method) setMultiplePatternCriterionState() (schrodinger.ui.ligfilter.LigfilterFrame method) setMultiplePredefinedCriterionState() (schrodinger.ui.ligfilter.LigfilterFrame method) setMultiplePropCriterionState() (schrodinger.ui.ligfilter.LigfilterFrame method) setName() (schrodinger.application.matsci.cg_mapping.Particle method) (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) setNamespace() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) (schrodinger.ui.qt.appframework2.debugwidgets.ExecWidget method) setNameToTypeMap() (schrodinger.application.matsci.permittivity.Config method) setNanoparticleProperties() (schrodinger.application.matsci.nano.particle.Nanoparticle method) setNBands() (schrodinger.application.matsci.espresso.qeinput.BandsType method) setNegativeIon() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setNetworkNodeDefaultClass() (schrodinger.ui.qt.network_views.NetworkViewer method) setNeutralize() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setNewData() (schrodinger.application.matsci.mswidgets.ProcessBusyDialog method) setNextTask() (schrodinger.tasks.taskmanager.TaskManager method) setNodeDeletion() (schrodinger.ui.qt.network_views.NetworkViewer method) setNodesOpacity() (schrodinger.ui.qt.network_views.NetworkViewer method) setNoLaunch() (schrodinger.job.launcher.Launcher method) setNonAngleNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setNonAngleNonDihedralNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setNonExportableData() (schrodinger.application.livedesign.panel_components.ExportTableModel method) setNormal() (schrodinger.application.matsci.shapes.Face method) setNoStrucAllowed() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) setNotes() (schrodinger.application.jaguar.input.JaguarInput method) setNRequired() (schrodinger.application.glide.glide.Dock method) setNumberOfProcessorsManyNodes() (schrodinger.job.launchparams.LaunchParameters method) setNumberOfProcessorsOneNode() (schrodinger.job.launchparams.LaunchParameters method) setNumberOfSubjobs() (schrodinger.job.launchparams.LaunchParameters method) setNumClusters() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) setNumColumns() (schrodinger.ui.two_d_viewer.TwoDViewer method) setNumSelectedRows() (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp method) setNumThumbs() (schrodinger.application.matsci.mswidgets.MultiSlider method) setObjValue() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) setOffset() (schrodinger.ui.qt.structure2d.StructureToolTip method) setOpcdArgs() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.SbcUtil method) setOperatorNames() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) setOplsaaVersion() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setOPLSDir() (schrodinger.job.launchparams.LaunchParameters method) setOption() (schrodinger.structure._BaseWriter method) (schrodinger.structure.StructureWriter method) setOptions() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method) (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.structutils.minimize.Minimizer method) setOptionsFromRepresentativeStructure() (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) setOrigin() (schrodinger.application.matsci.nano.xtal.Crystal method) setOriginalData() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method) setOutfile() (schrodinger.application.matsci.permittivity.AnalyzeSimulation method) (schrodinger.application.matsci.permittivity.StepBase method) setOutput() (schrodinger.pipeline.stage.Stage method) setOutputFile() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setOutputFiles() (schrodinger.job.launchapi.JobSpecificationBuilder method) setOutputName() (schrodinger.pipeline.stage.Stage method) setOutputPaths() (schrodinger.application.livedesign.tasks.AlignLigandsTask method) (schrodinger.application.livedesign.tasks.CanvasSearchTask method) (schrodinger.application.livedesign.tasks.CovDockTask method) (schrodinger.application.livedesign.tasks.EpikClassicTask method) (schrodinger.application.livedesign.tasks.EpikTask method) (schrodinger.application.livedesign.tasks.FlexAlignTask method) (schrodinger.application.livedesign.tasks.GlideTask method) (schrodinger.application.livedesign.tasks.LigandStrainTask method) (schrodinger.application.livedesign.tasks.LigFilterTask method) (schrodinger.application.livedesign.tasks.LigPrepTask method) (schrodinger.application.livedesign.tasks.MemPermTask method) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask method) (schrodinger.application.livedesign.tasks.QikPropTask method) (schrodinger.application.livedesign.tasks.RBSSTask method) (schrodinger.application.livedesign.tasks.StrainRescoreTask method) (schrodinger.application.livedesign.tasks.TugAlignTask method) setOutputTopic() (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) setPABJaguarMarkerHighlighting() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) setPaddingFactor() (schrodinger.ui.qt.delegates.PictureDelegate method) setPaintWait() (schrodinger.ui.qt.table.GenericViewerDelegate method) setPanelOptions() (schrodinger.application.jaguar.gui.base_panel.AutomaticJobnameMixin method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.matsci.appbase.ProcessPtStructuresApp method) (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) (schrodinger.ui.qt.appframework2.af2_template.SettingsInJobNamesTemplate method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.filter_dialog.FilterDialog method) setPanelState() (schrodinger.ui.qt.appframework2.settings.SettingsPanelMixin method) SetParam (class in schrodinger.models.parameters) setParam() (schrodinger.ui.qt.mapperwidgets.param_editor.ParamEditor method) setParamValue() (schrodinger.models.parameters.Param class method) setParent() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setParentBondsHash() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond method) setParentChildJobs() (schrodinger.application.matsci.permittivity.WorkflowParser method) setParentCutBonds() (schrodinger.application.matsci.cg_mapping.Particle method) setParentData() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond method) setParentIndices() (schrodinger.application.matsci.cg_mapping.Particle method) setParentStructure() (schrodinger.application.matsci.cg_mapping.Particle method) setParentStructureStr() (schrodinger.application.matsci.cg_mapping.Particle method) setPartialCharge() (schrodinger.application.matsci.cg_mapping.Particle method) setPath() (schrodinger.application.matsci.kmcgui.DatabaseInfo method) setPathtoBranchingAtom() (schrodinger.application.matsci.amorphous.PolymerFragments method) setPatternOptions() (schrodinger.ui.ligfilter.LigfilterFrame method) setPBCBonds() (schrodinger.application.matsci.nano.xtal.PBCBonds method) setPeakparms() (in module schrodinger.application.matsci.gsas.GSASIImath) setPerAtom() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit method) setPerAtomBasisModel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) setPeriodicStyle() (schrodinger.ui.qt.periodictable.ElementButton method) setPersistent() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) setPfam() (schrodinger.protein.sequence.AbstractSequence method) setPickAtom() (schrodinger.ui.picking.PickMixedToggle method) setPickBond() (schrodinger.ui.picking.PickMixedToggle method) setPickingMode() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.ui.qt.network_views.NetworkViewer method) setPickMethodToAuto() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) setPickMethodToManual() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) setPicture() (schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method) setPixmap() (schrodinger.application.desmond.feputils.LabelSpinner method) setPkaAtomsForEid() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) setpKaData() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) setPkaMarkers() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) setPlaneMSD() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase method) setPlaybackSettingsData() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) setPlotType() (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) setPLP() (schrodinger.maestro_utils.maestro_sync.PLPTarget method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) setPoints() (schrodinger.graphics3d.tube.MaestroTube method) setPolymerFragments() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setPopUp() (schrodinger.application.livedesign.panel_components.LDDataTreePopUpButton method) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp method) (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) setPopUpClass() (schrodinger.application.matsci.builderwidgets.TemplateToolButton method) (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) setPopupHalign() (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) setPopupValign() (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) setPos() (schrodinger.ui.qt.network_visualizer.Node method) setPosition() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) setPositiveIon() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) SetPowderInstParms() (in module schrodinger.application.matsci.gsas.GSASIIfiles) setPrecision() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) setPrefGroup() (schrodinger.application.livedesign.ld_settings.LDSettingsMixin method) setPressedIconPath() (schrodinger.ui.qt.standard_widgets.buttons.FlatButton method) setPrintingOutputToTerminal() (schrodinger.tasks.tasks.SubprocessMixin method) setProgramName() (schrodinger.job.app.App method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setProgress() (schrodinger.ui.qt.appframework.AppFramework method) setProgressError() (schrodinger.ui.qt.appframework.AppFramework method) setProperties() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) (schrodinger.ui.qt.propertyselector.PropertySelectorMenu method) setProperty() (schrodinger.application.matsci.equilibrium_md.CmsModel method) (schrodinger.application.matsci.equilibrium_md.MaeModel method) (schrodinger.application.matsci.equilibrium_md.Model method) setPropertyLabelVisible() (schrodinger.application.phase.phase_markers.PhaseMarkers method) setProtein() (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) SetPWDRscan() (in module schrodinger.application.matsci.gsas.GSASIIpwd) setQubecJob() (schrodinger.application.matsci.qubec_utils.Job method) setQueue() (schrodinger.application.matsci.genetic_optimization.ClassEvaluator method) setRadius() (schrodinger.graphics3d.tube.MaestroTube method) (schrodinger.ui.qt.structure2d.CircleAnnotator method) setRange() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) setRawScale() (schrodinger.ui.qt.network_views.NetworkViewer method) setRDMol() (schrodinger.ui.qt.rdmol_views.AbstractRDMolImageLabel method) (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) (schrodinger.ui.qt.rdmol_views.RDMolTooltipWithLabel method) setReactionInstance() (schrodinger.application.pathfinder.route.RouteNode method) setReactiveInds() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) setReactiveMolecules() (schrodinger.application.matsci.rxn_channel.Reactants method) setRecalcButtonState() (schrodinger.application.matsci.kmcgui.NeighborsTab method) setReceptorStructure() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setReference() (schrodinger.models.parameters.CompoundParam class method) setReferenceLigand() (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.glide.http_client.HTTPClient method) setReferenceSeq() (schrodinger.protein.alignment.BaseAlignment method) setReferenceToIndex() (schrodinger.ui.two_d_viewer.TwoDTableModel method) setRefFrameValidator() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) setRefractiveIndexProperty() (schrodinger.application.matsci.genetic_optimization.RefractiveIndex class method) setRelaxAndProductionIndexes() (schrodinger.application.matsci.permittivity.MdStageModifier method) setRelaxRandomVel() (schrodinger.application.matsci.permittivity.MdStageModifier method) setRemoveIntBlocksFromStruct() (schrodinger.application.matsci.espresso.qeinput.PHDynmatType method) setRemoveOverlappedCrystalWater() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setRemoveOverlappedSolvent() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setReplica() (schrodinger.application.matsci.permittivity.WorkflowParser method) setReplicateErrorWarningIcon() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) setReplicaType() (schrodinger.application.matsci.permittivity.WorkflowParser method) setRepresentatives() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) setResidue() (schrodinger.ui.residueselector.CustomResidueMixin method) setResidueConnectivity() (schrodinger.application.matsci.amorphous.PolymerFragments method) setResidueMap() (schrodinger.protein.sequence.AbstractSingleChainSequence method) setResidues() (schrodinger.application.bioluminate.protein.protein.Refiner method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method) setResizablePolicy() (schrodinger.ui.qt.table.DataViewerTable method) setResProperties() (schrodinger.application.matsci.amorphous.PolymerFragments method) setResults() (schrodinger.application.jaguar.gui.timing.TimingResults method) setRGBColor() (schrodinger.application.matsci.cg_mapping.Particle method) setRGroupStructures() (schrodinger.application.matsci.reaction_workflow_utils.EnumerateReactionWorkflow method) setRightClickHandler() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) setRightClickOnGObject() (schrodinger.graphics3d.common.Primitive method) setRingData() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) setRingsForOneMol() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setRole() (schrodinger.ui.qt.delegates.PushButtonDelegate method) setRootLoggerForPyEvolve() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) setRotatableBond() (schrodinger.application.matsci.amorphous.PolymerFragments method) setRow() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setRowIsGanged() (schrodinger.ui.qt.table.DataViewerTable method) setRows() (schrodinger.application.bioluminate.antibody.management.ActiveDatabaseTable method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) setRowValues() (schrodinger.application.matsci.kmc.PairsMixin class method) SETS_IACCG_CUSTOM (schrodinger.application.jaguar.gui.tabs.optimization_tab.NoCustomIACCGOptimizationTab attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) SETS_REQUIRED (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner attribute) setSaltNegativeIon() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSaltPositiveIon() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSampleData() (schrodinger.ui.qt.table_helper.SampleDataTableViewMixin method) setSampleSize() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method) setSampleText() (schrodinger.ui.qt.utils.LineEditWithSampleText method) setSaveMode() (schrodinger.job.launchparams.LaunchParameters method) setScale() (schrodinger.ui.qt.network_views.NetworkViewer method) setScanCoordinate() (schrodinger.application.jaguar.input.JaguarInput method) setSCFGS() (schrodinger.application.matsci.mecp_mod.MECP method) setSectorData() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) setSelectable() (schrodinger.ui.qt.tablewidget.Cell method) setSelected() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphere method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.ui.dendrogram.DendrogramGraphicNode method) setSelectedElements() (schrodinger.ui.qt.periodictable.PeriodicTableDialogMultipleClick method) setSelectedFeatures() (schrodinger.application.phase.featureselector.FeatureSelector method) (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) setSelectedIndexes() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) setSelectedItems() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) setSelectedMutations() (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) (schrodinger.ui.residueselector.MutationSelectorMixin method) setSelectedObjs() (schrodinger.ui.qt.network_visualizer.Graph method) setSelectedParams() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) setSelectedThumb() (schrodinger.application.matsci.mswidgets.MultiSlider method) setSelectedValues() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) setSelection() (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog method) (schrodinger.application.matsci.builderwidgets.TemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListToolButton method) (schrodinger.application.matsci.mswidgets.ConvenientSelectorWithPopUp method) (schrodinger.application.phase.phase_markers.PhaseMarkers method) setSelectionAndLoadTrj() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setSelectionForceField() (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) setSelectorEnabled() (schrodinger.application.jaguar.gui.tabs.theory_tab.DFTComboRadioSelector method) setSelfMethods() (schrodinger.ui.qt.appframework2.appmethods.MethodsDict method) SetSerializer (class in schrodinger.models.jsonable) setSeriesSize() (schrodinger.ui.qt.schart.SChart static method) setSets() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) setSettingsMenuActions() (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.AbstractTaskBar method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) setShape() (schrodinger.protein.helm.helm_renderer.AminoAcidMonomerBase method) (schrodinger.protein.helm.helm_renderer.BBPhosphateMonomerBase method) (schrodinger.protein.helm.helm_renderer.BBSugarMonomerBase method) (schrodinger.protein.helm.helm_renderer.ChemMonomerItem method) (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin method) (schrodinger.protein.helm.helm_renderer.NABaseMonomerBase method) setShiftLeft() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) setSingleRxAtom() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) setSiteClickable() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) setSiteMatches() (schrodinger.structutils.sitealign.BindingSiteAligner method) setSites() (schrodinger.application.matsci.coarsegrain.Internals method) setSize() (schrodinger.infra.mmkv.MMKVArgList method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) (schrodinger.ui.qt.table.StructureDataViewerModel method) setSketcherStructure() (schrodinger.application.matsci.builderwidgets.SketcherBox method) setSlotOrder() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) setSmartDistribution() (schrodinger.job.queue.JobDJ method) setSmartsToSketcher() (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) setSmiles() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond method) setSolute() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSoluteAlignment() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSoluteCoords() (schrodinger.trajectory.prody.ensemble.Ensemble method) setSolvate() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSolvent() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.jaguar.gui.solvent_selector.SolventSelectorFilterListPopUp method) (schrodinger.application.jaguar.gui.solvent_selector.SolventSelectorFilterListToolButton method) setSolventAccessibilityPredictions() (schrodinger.protein.sequence.AbstractSingleChainSequence method) setSortingEnabled() (schrodinger.ui.qt.swidgets.STableWidget method) (schrodinger.ui.qt.table.DataViewerTable method) setSource() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) setSourceLabelText() (schrodinger.ui.qt.structure_selector.StructureSelector method) setSourceModel() (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) (schrodinger.ui.qt.table_speed_up.AbstractFlagCacheProxyMixin method) setSourceObj() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) setSpec() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) setSpeciesCollection() (schrodinger.application.matsci.speciesgui.GroupingMethodSelector method) setSphereRadiusAndCoords() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) setSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) setSquaredDisplacement() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setSquaredDisplacementTimeserial() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setSSA() (schrodinger.protein.sequence.AbstractSingleChainSequence method) setSSAPredictions() (schrodinger.protein.sequence.AbstractSingleChainSequence method) SetStackingClay() (in module schrodinger.application.matsci.gsas.GSASIIpwd) SetStackingSF() (in module schrodinger.application.matsci.gsas.GSASIIpwd) SetStackingTrans() (in module schrodinger.application.matsci.gsas.GSASIIpwd) setStageOptions() (schrodinger.pipeline.pipeline.Pipeline method) setStages() (schrodinger.application.matsci.permittivity.MdStageModifier method) setStandardBaseName() (schrodinger.tasks.taskmanager.TaskManager method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) setStartAndEnd() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) setStartAndEndEnabled() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) setStartFrameValue() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) setStartingStep() (schrodinger.stepper.stepper.UnbatchedChain method) setState() (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.swidgets.SValidIndicator method) setStatus() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.ui.qt.appframework2.af2.StatusBar method) (schrodinger.ui.qt.tasks.taskwidgets.StatusLabel method) setStderr() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setStdout() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setStdOutErrFile() (schrodinger.job.launcher.Launcher method) setStep() (schrodinger.stepper.stepper.StepTaskMixin method) setStepSize() (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) setStoppable() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setStrainedAdsorptionLatticeProperties() (schrodinger.application.matsci.nano.interface_mod.Interface method) setStretchLastSection() (schrodinger.ui.qt.tablewidget.HorizontalHeader method) (schrodinger.ui.qt.tablewidget.VerticalHeader method) setStringList() (schrodinger.ui.qt.recent_completer.BrowseAndCreateStringModel method) (schrodinger.ui.qt.recent_completer.BrowseStringModel method) setStruct() (schrodinger.ui.qt.table.ViewerModel method) setStructOrCMSProperty() (schrodinger.application.matsci.jwsteps.BaseStep method) setStructure() (schrodinger.application.desmond.fep_scholar_util.FEPStructureObject method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterListToolButton method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.espresso.qeinput.PHControlType method) (schrodinger.application.matsci.jagwidgets.BasisSetSelector method) (schrodinger.application.matsci.kmcgui.NeighborsTab method) (schrodinger.application.matsci.kmcgui.Tab method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.application.matsci.reordergui.StructurePic method) (schrodinger.project.project.ProjectRow method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.structutils.minimize.Minimizer method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) setStructureAndUpdateBorder() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) setStructureDict() (schrodinger.application.matsci.mswidgets.LipidImporter method) setStructureFile() (schrodinger.application.qsite.input.QSiteInput method) setStructureGetter() (schrodinger.maestro_utils.maestro_sync.ProjectEntryMaestroSync method) setStructureMonitorFile() (schrodinger.job.launcher.Launcher method) setStructureOutput() (schrodinger.pipeline.input.Writer method) setStructureOutputFile() (schrodinger.job.launcher.Launcher method) setStructureOutputFileBE() (schrodinger.job.app.App method) setStructureOutputFileFE() (schrodinger.job.app.App method) setStructureProperties() (schrodinger.application.matsci.nano.xtal.Crystal method) setStructures() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) (schrodinger.application.matsci.reordergui.PickPairToggleIntermediate method) (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) setStructureSelectorsEnabled() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) setStructureType() (schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType method) setStyle() (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) (schrodinger.structure.StructureBond method) (schrodinger.ui.qt.standard_widgets.buttons.StyledButton method) setStyler() (schrodinger.seam.viz.render.PipelineRenderer method) setStyleSheet() (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.formlayout.CheckLayout method) (schrodinger.ui.qt.formlayout.ColorLayout method) (schrodinger.ui.qt.formlayout.CountLayout method) (schrodinger.ui.qt.formlayout.FileLayout method) (schrodinger.ui.qt.formlayout.FontLayout method) (schrodinger.ui.qt.formlayout.RadioLayout method) (schrodinger.ui.qt.formlayout.SliderLayout method) (schrodinger.ui.qt.widgetmixins.basicmixins.SchrodingerStyleMixin method) setSubDir() (schrodinger.application.matsci.jwsteps.SubdirectoryStepMixin method) setSubjobDependence() (schrodinger.application.matsci.permittivity.WorkflowParser method) setSubs() (schrodinger.application.macromodel.utils.SbcUtil method) setSubstrateSpearRings() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setSubTabMarkerHighlighting() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) setSubTabsVisible() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) setSuggestions() (schrodinger.ui.qt.recent_completer.StringListModelInterface method) setSurfaceProperties() (schrodinger.application.matsci.nano.slab.Surface method) setSystemInfo() (schrodinger.application.matsci.mswidgets.SystemInformationFrame method) setTable() (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) setTabVisibleByLabel() (schrodinger.ui.qt.swidgets.STabWidget method) setTargetFunction() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method) setTask() (schrodinger.ui.qt.tasks.taskbarwidgets.TaskWidgetMixin method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) setTauFrame() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase method) setTauRange() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) setTemplate() (schrodinger.application.prime.wrapper.BasePrimeAlignment method) setTemplateResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method) setTemplates() (schrodinger.application.livedesign.panel_components.LiveReportTemplateSelectorCombo method) setTemplateStructures() (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget method) setTemporaryPixmap() (schrodinger.application.desmond.feputils.LabelSpinner method) setTempRangeToSlider() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) setTempTrajRange() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) setText() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.desmond.cwidget.EntryField method) (schrodinger.application.desmond.cwidget.FileEntry method) (schrodinger.application.desmond.fep_dialog.CustomGPUComboBox method) (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) (schrodinger.ui.qt.swidgets.ActionComboBox method) (schrodinger.ui.qt.swidgets.ElidedLabel method) (schrodinger.ui.qt.swidgets.ImageLabel method) (schrodinger.ui.qt.swidgets.LineEditWithDisabledText method) (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) (schrodinger.ui.qt.swidgets.SLineEdit method) (schrodinger.ui.qt.swidgets.SMARTSEdit method) (schrodinger.ui.qt.tablewidget.Cell method) (schrodinger.ui.qt.tasks.configwidgets.JobnameWidget method) setTextAlignment() (schrodinger.ui.qt.tablewidget.Cell method) setTextChecked() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) setTextElide() (schrodinger.ui.qt.delegates.PictureDelegate method) setTextSelected() (schrodinger.ui.qt.swidgets.SListWidget method) setTextVisibile() (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) setTheory() (schrodinger.application.matsci.jagwidgets.TheorySelector method) setTheoryForRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) setTheoryLevel() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) setThermoMethod() (schrodinger.application.desmond.gui.EnsembleTab method) setThermoRelaxationMethod() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) setThreadingReplicaNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) setThreadName() (schrodinger.utils.thread_utils.ThreadTool method) setThreads() (schrodinger.application.matsci.crest.CrestTOML method) setTimeSlider() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) Setting (class in schrodinger.application.jaguar.keywordDB) setting_model() (schrodinger.models.mappers.MapperMixin method) (schrodinger.models.mappers.TargetParamMapper method) SETTING_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) setting_to_bool() (in module schrodinger.application.matsci.msutils) SETTINGS (schrodinger.application.matsci.desconfig.MSJStringer attribute) settings (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput attribute) (schrodinger.protein.tasks.blast.BlastTask.Input attribute) SETTINGS_DICT (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) SETTINGS_ONLY (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) SettingsButton (class in schrodinger.ui.qt.appframework2.af2) (class in schrodinger.ui.qt.tasks.taskwidgets) settingsChanged (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput attribute) (schrodinger.protein.tasks.blast.BlastTask.Input attribute) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings attribute) SettingsError SettingsInJobNamesTemplate (class in schrodinger.ui.qt.appframework2.af2_template) SettingsMixin (class in schrodinger.ui.qt.appframework2.settings) SettingsPanelMixin (class in schrodinger.ui.qt.appframework2.settings) settingsReplaced (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput attribute) (schrodinger.protein.tasks.blast.BlastTask.Input attribute) SettingsWarning setTitle() (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.nma.NMA method) setToAlwaysValid() (schrodinger.ui.qt.swidgets.SLineEdit method) setToken() (schrodinger.application.livedesign.login.LoginManager method) setTokenBoundaries() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setTokenIndex() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setTokenSource() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) setTokenStartIndex() (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) setTokenStopIndex() (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) setTokenStream() (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) setTokenTypeChannel() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) setToMinStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) setToolbarMessage() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) setToolBars() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) setToolTip() (schrodinger.ui.qt.swidgets.SLabeledSlider method) (schrodinger.ui.qt.swidgets.SLabeledSpinBox method) (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.tablewidget.Cell method) setToolTipSize() (schrodinger.ui.qt.table.DataViewerTable method) setTopLevelJobs() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) setTPP() (schrodinger.job.launchparams.LaunchParameters method) setTrajLimits() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) setTransparency() (schrodinger.surface.Surface method) setTreeAdaptor() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) setTreeNodeStream() (schrodinger.application.desmond.antlr3.tree.TreeParser method) setType() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setUhf() (schrodinger.application.matsci.crest.CrestTOML method) setUndoPoint() (schrodinger.ui.qt.network_visualizer.Graph method) setUniformDistribution() (schrodinger.application.matsci.amorphous.EnergySurface method) setUniqueNavigationNodes() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) setUnknownTokenBoundaries() (schrodinger.application.desmond.antlr3.tree.CommonTree method) setup() (in module schrodinger.infra.epydoc_to_sphinx) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.SimOptionsFrame method) (schrodinger.application.glide.glide.ConstraintGroup method) (schrodinger.application.glide.http_server.GlideHTTPHandler method) (schrodinger.application.jaguar.gui.base_panel.AutomaticJobnameMixin method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.ExcitedStateValidatorMixin method) (schrodinger.application.jaguar.gui.base_panel.InputMultiplicityMixin method) (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) (schrodinger.application.jaguar.gui.base_panel.MarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) (schrodinger.application.jaguar.gui.base_panel.OptimizationTabMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.PropertiesValidatorMixin method) (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) (schrodinger.application.jaguar.gui.base_panel.ScanTabMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) (schrodinger.application.jaguar.gui.base_panel.UseConsistentOrbitalsMixin method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabCoordinateScan method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTabNoOptimized method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.PerAtomBasisPopUp method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.jaguar.gui.timing.ArchPopUp method) (schrodinger.application.jaguar.gui.timing.TimerMixin method) (schrodinger.application.livedesign.ld_export_gui.ExportPanelWizard method) (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp method) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUp method) (schrodinger.application.livedesign.panel_components.BaseSelectionPopUp method) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUp method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.application.macromodel.input.ConfSearch method) (schrodinger.application.macromodel.input.EmbraceConfSearch method) (schrodinger.application.macromodel.input.EmbraceMinimization method) (schrodinger.application.macromodel.input.EnergyListing method) (schrodinger.application.macromodel.input.Minimization method) (schrodinger.application.macromodel.input.Minta method) (schrodinger.application.macromodel.input.RCE method) setUp() (schrodinger.application.matsci.appbase.ProcessPtStructuresApp method) setup() (schrodinger.application.matsci.equilibrium_md.SingleMDJob method) setUp() (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) setup() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) (schrodinger.application.matsci.mswidgets.OptionalInputSelector method) (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) (schrodinger.application.matsci.permittivity.AnalyzeSimulation method) (schrodinger.application.matsci.permittivity.AveCellAnalysis method) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis method) (schrodinger.application.matsci.permittivity.DensityAnalysis method) (schrodinger.application.matsci.permittivity.JaguarCalculation method) (schrodinger.application.matsci.permittivity.MdPostAnalysis method) (schrodinger.application.matsci.permittivity.MultiStageMd method) (schrodinger.application.matsci.permittivity.StaticPermittivity method) (schrodinger.application.matsci.permittivity.StepBase method) (schrodinger.application.matsci.permittivity.SusceptibilityMerge method) (schrodinger.application.matsci.permittivity.TwoFileInput method) setUp() (schrodinger.application.matsci.permittivity.WorkflowParser method) setup() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) (schrodinger.application.pymol.export_to_pymol_gui.AdvancedSettingsPopUp method) setUp() (schrodinger.application.steps.enumerators.BaseDecorator method) (schrodinger.application.steps.enumerators.FastFragmenter method) (schrodinger.application.steps.enumerators.RouteDeduplicator method) (schrodinger.application.steps.enumerators.RouteEnumerator method) (schrodinger.application.steps.enumerators.RouteEvaluator method) (schrodinger.application.steps.filters.FepFilter method) (schrodinger.application.steps.filters.MaeUniqueSmilesFilter method) (schrodinger.application.steps.filters.ProductFilterMixin method) (schrodinger.application.steps.filters.ProfileFilter method) (schrodinger.application.steps.filters.PropertyFilter method) (schrodinger.application.steps.filters.SmartsFilter method) (schrodinger.application.steps.transformers.Standardizer method) setup() (schrodinger.job.queue.BaseJob method) (schrodinger.protein.assignment.ProtAssign method) (schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin method) (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin method) (schrodinger.protein.helm.helm_renderer.LineHelmConnectorItem method) (schrodinger.protein.helm.helm_renderer.PolylineHelmConnectorItem method) (schrodinger.seam.testing.benchmarks.Benchmark method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) (schrodinger.ui.ligfilter.LigfilterFrame method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.BaseBottomBar method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.af2.MiniJobBottomBar method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) (schrodinger.ui.qt.appframework2.af2_template.SettingsInJobNamesTemplate method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.debugwidgets.BaseTable method) (schrodinger.ui.qt.appframework2.debugwidgets.LogTable method) (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) (schrodinger.ui.qt.filter_dialog.FilterDialog method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) (schrodinger.ui.qt.filter_list.FilterListPopUp method) (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) (schrodinger.ui.qt.formlayout.FormComboWidget method) (schrodinger.ui.qt.formlayout.FormTabWidget method) (schrodinger.ui.qt.formlayout.FormWidget method) (schrodinger.ui.qt.fp_selector_widget.FingerprintsPopUp method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.residueselector.GridLayoutPopUp method) (schrodinger.ui.residueselector.MutationSelectorPopUp method) setup_alchem_properties() (in module schrodinger.application.desmond.replica_sid_generator) (schrodinger.application.desmond.replica_sid_generator.FEPReport method) setup_arrow() (in module schrodinger.trajectory.prody.test_arrow) setup_atom() (in module schrodinger.trajectory.prody.writenmd) setup_connection_with_maestro() (in module schrodinger.application.livedesign.maestro_ld_connection) setup_counters() (schrodinger.ui.qt.rama.Rama method) setup_db_screen() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) setup_distributed_align_pairs() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) setup_distributed_mask_screens() (in module schrodinger.application.phase.packages.hypo_refine.screen_utils) setup_distributed_screen() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) setup_distributed_smiles_to_3d() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) setup_distributed_tol_direct_screens() (in module schrodinger.application.phase.packages.hypo_refine.screen_utils) setup_distributed_tol_probe_screens() (in module schrodinger.application.phase.packages.hypo_refine.screen_utils) setup_fixed_file_screen() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) setup_local_static() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) setup_local_static_alt() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) setup_md_job() (in module schrodinger.application.matsci.equilibrium_md) setup_mol() (in module schrodinger.livedesign.preprocessor) setup_mtd_mexpr() (in module schrodinger.application.desmond.kinetics.enhanced_sampling) setup_nonstandard_residue_map_signal() (in module schrodinger.maestro_utils.nonstandard_residue_utils) setup_panel_ui() (in module schrodinger.ui.qt.widgetmixins.basicmixins) setup_player_toolbar() (in module schrodinger.trajectory.trajectoryviewer) setup_project_close() (in module schrodinger.application.phase.phase_markers) setup_project_screen() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) setup_protein() (schrodinger.protein.analysis.Report method) setup_ramd_mexpr() (in module schrodinger.application.desmond.kinetics.enhanced_sampling) setup_reaction() (in module schrodinger.livedesign.bbchem_endpoints) (in module schrodinger.livedesign.setup_reaction) setup_rgroup_rxn_map_nums() (in module schrodinger.livedesign.check_reaction) setup_screen() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) setup_simulation() (schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer method) setup_snapshot_panel() (in module schrodinger.trajectory.trajectoryviewer) setup_split_file_screen() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) setup_toulbar2_inputs() (schrodinger.protein.assignment.NetworkSolver method) setup_xtal() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) setupAset() (schrodinger.application.macromodel.utils.ComUtil method) setupBasicTab() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) setupBuildGeometryMSJ() (schrodinger.application.matsci.desmondutils.SystemBuilder method) setUpButtonBox() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) setUpDefaults() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) setupDialogConnections() (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) setUpFast3D() (schrodinger.application.matsci.rxn_channel.Channels method) setupFetchingOptions() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) setupFFBuilderOptions() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) setupGravity() (schrodinger.application.matsci.montecarlo.Metropolizer method) setupHostCombo() (schrodinger.ui.qt.config_dialog.ConfigDialog method) setupHostLayout() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) setUpInputFiles() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) setupInWorkspaceColumn() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) setUpIterationLaunchDir() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) setUpJaguarJobs() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) setupJobCmd() (schrodinger.application.matsci.multiapp.MultiCmdJobApp method) (schrodinger.ui.qt.appframework2.af2.JobApp method) setupJobParameters() (schrodinger.ui.qt.appframework.AppFramework method) setupJobs() (schrodinger.pipeline.stages.filtering.GeneratePropsStage method) (schrodinger.pipeline.stages.filtering.LigFilterStage method) (schrodinger.pipeline.stages.glide.DockingStage method) (schrodinger.pipeline.stages.glide.GridgenStage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) (schrodinger.pipeline.stages.prime.MMGBSAStage method) (schrodinger.pipeline.stages.prime.PrimeStage method) (schrodinger.pipeline.stages.qikprop.QikPropStage method) (schrodinger.pipeline.stages.semiemp.SemiEmpStage method) setupJson() (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.glide.glide.Gridgen method) setUpLaunchDir() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) setUpLayout() (schrodinger.application.livedesign.panel_components.BaseLiveReportSelectionPopup method) (schrodinger.application.livedesign.panel_components.BaseSearchTreeWidgetHelper method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionPopup method) setupLDClient() (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) SetupLigandsFromZippedDir() (schrodinger.active_learning.al_driver.ActiveLearningJob method) setUpMain() (schrodinger.tasks.queue.TaskQueue method) (schrodinger.tasks.tasks.SignalTask method) setUpMembrane() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) setUpMembraneRelaxation() (schrodinger.application.desmond.gui.GuiApp method) setupPanel() (schrodinger.ui.two_d_viewer.TwoDViewer method) SetupPDFEval() (in module schrodinger.application.matsci.gsas.GSASIIpwd) setupPickToggle() (schrodinger.ui.qt.atomselector.AtomSelector method) setupPlusButton() (schrodinger.ui.qt.atomselector.AtomSelector method) setUpPreferences() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) setUpQue() (schrodinger.application.matsci.equilibrium_md.MultiDriver method) setupSaveWidgets() (schrodinger.application.matsci.mswidgets.MSAtomSelector method) setupSubHostCombo() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) setupSubHostLayout() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) setupTable() (schrodinger.ui.qt.tablewidget.MyWindow method) setupTacticity() (schrodinger.application.matsci.amorphous.Monomer method) setUpTestUserDict() (schrodinger.stepper.app.StepperApplication class method) setupTextLabel() (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin method) setupToggles() (schrodinger.ui.residueselector.CustomResMutationSelectorMixin method) (schrodinger.ui.residueselector.MutationSelectorMixin method) setupToolBar() (schrodinger.ui.qt.schart.SChart method) setupToolTips() (schrodinger.ui.residueselector.MutationSelectorMixin method) setupUi() (schrodinger.application.bioluminate.propfilter_ui.Ui_Form method) (schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form method) (schrodinger.application.desmond.desmond_advanced_tab_ui.Ui_Dialog method) (schrodinger.application.desmond.input_group_ui.Ui_Form method) (schrodinger.application.desmond.rest_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up.per_atom_basis_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.config_dialog_jaguar_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui.Ui_Dialog method) (schrodinger.application.jaguar.gui.ui.define_smarts_panel_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.edit_dialog_ui.Ui_MainWindow method) (schrodinger.application.jaguar.gui.ui.excited_state_widget_ui.Ui_Widget method) (schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_hb_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_pka_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_std_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.irc_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.irc_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.multi_structures_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.optimization_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.output_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.pka_smarts_page_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.properties_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scan_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scf_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvent_pka_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvent_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui.Ui_Widget method) (schrodinger.application.jaguar.gui.ui.theory_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.transition_state_top_ui.Ui_Form method) (schrodinger.application.jaguar.update_pka_settings_ui.Ui_UpdatePKASettingsDlg method) (schrodinger.application.job_monitor.diagnostics_dialog_ui.Ui_Form method) (schrodinger.application.job_monitor.file_browser_ui.Ui_Form method) (schrodinger.application.job_monitor.job_info_view_ui.Ui_Form method) (schrodinger.application.job_monitor.top_level_view_ui.Ui_Form method) (schrodinger.application.jobserver_cert_gui_dir.registration_panel_ui.Ui_Dialog method) (schrodinger.application.livedesign.export_setup_ui.Ui_Form method) (schrodinger.application.livedesign.export_ui.Ui_Form method) (schrodinger.application.livedesign.invalid_ge_id_warning_ui.Ui_Form method) (schrodinger.application.livedesign.live_report_widget_ui.Ui_Form method) (schrodinger.application.livedesign.login2_ui.Ui_Form method) (schrodinger.application.livedesign.login_ui.Ui_Dialog method) (schrodinger.application.livedesign.maestro_ld_mapping_ui.Ui_Form method) (schrodinger.application.livedesign.mappings_manager_ui.Ui_Form method) (schrodinger.application.livedesign.pose_name_panel_ui.Ui_Form method) (schrodinger.application.livedesign.save_mapping_dialog_ui.Ui_Form method) (schrodinger.application.livedesign.selection_pop_up_ui.Ui_Form method) (schrodinger.application.livedesign.summary_ui.Ui_Form method) (schrodinger.application.prime.gui.ui.analyze_energy_ui.Ui_Form method) (schrodinger.application.prime.gui.ui.environment_options_ui.Ui_Form method) (schrodinger.application.pymol.pymol4maestro_ui.Ui_Dialog method) (schrodinger.application.pymol.ui.advanced_settings_wdg_ui.Ui_Form method) (schrodinger.application.pymol.ui.export_to_pymol_dlg_ui.Ui_pymol_dlg method) (schrodinger.infra.exception_handler_dir.exception_dialog_ui.Ui_Dialog method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_ui.Ui_FindToolBar method) (schrodinger.trajectory.traj_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.advanced_plot_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.collapsible_plot_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.conf_wheel_plot_panel_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.energy_plot_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.export_movie_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.export_structures_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.job_settings_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.rdf_plot_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.shortcut_ui.Ui_Form method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui.Ui_Dialog method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui.Ui_snapshot_panel method) (schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui.Ui_trajectory_form method) (schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog method) (schrodinger.ui.ligfilter_ui.Ui_Form method) (schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.qt.appframework2.debug_gui_ui.Ui_Form method) (schrodinger.ui.qt.atom_weights_table_ui.Ui_Form method) (schrodinger.ui.qt.borderless_popup_ui.Ui_Frame method) (schrodinger.ui.qt.config_dialog_open_mp_ui.Ui_Form method) (schrodinger.ui.qt.config_dialog_queue_ui.Ui_Form method) (schrodinger.ui.qt.entryselector_ui.Ui_Dialog method) (schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui.Ui_Form method) (schrodinger.ui.qt.filter_dialog_ui.Ui_Dialog method) (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget_ui.Ui_customoplssettingwidget method) (schrodinger.ui.qt.forcefield.ffglobalpreferencewidget_ui.Ui_FFGlobalPreferencesWidget method) (schrodinger.ui.qt.forcefield.ffprojectsettingsdlg_ui.Ui_FFProjectSettingsDlg method) (schrodinger.ui.qt.fp_selector_widget_ui.Ui_Form method) (schrodinger.ui.qt.pdb_dialog_ui.Ui_PdbDialog method) (schrodinger.ui.qt.presets.manage_presets_dialog_ui.Ui_Form method) (schrodinger.ui.qt.presets.save_presets_dialog_ui.Ui_Form method) (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.qt.protein_health_viewer_ui.Ui_Form method) (schrodinger.ui.qt.rename_favorite_dialog_ui.Ui_Dialog method) (schrodinger.ui.qt.select_residues_dialog_ui.Ui_Dialog method) (schrodinger.ui.qt.tasks.config_dialog_ui.Ui_Form method) (schrodinger.ui.qt.tasks.config_info_ui.Ui_Form method) (schrodinger.ui.qt.tasks.taskbar_ui.Ui_Form method) (schrodinger.ui.qt.widgetmixins.mock_ui.Ui_Form method) (schrodinger.ui.sketcher_smarts_dialog_ui.Ui_SketcherDialog method) (schrodinger.ui.two_d_viewer_ui.Ui_Form method) setupValueLabel() (schrodinger.ui.qt.swidgets.SLabeledSlider method) setupViewer() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) setupViewPositionTab() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) setUpWidgets() (schrodinger.application.livedesign.panel_components.BaseLiveReportSelectionPopup method) (schrodinger.application.livedesign.panel_components.BaseSearchTreeWidgetHelper method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionPopup method) setUseAlchemicalWater() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setUseCustomizedVersionCBState() (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin method) setUseCustomOPLS() (schrodinger.ui.qt.forcefield.ffsettingsbutton.FFSettingsButton method) setUsedHosts() (schrodinger.pipeline.pipeline.StageJob method) setUsername() (schrodinger.application.livedesign.login.LoginManager method) setValidator() (schrodinger.application.desmond.cwidget.EntryField method) setValue() (schrodinger.application.desmond.fep_dialog.CustomGPUComboBox method) (schrodinger.application.jaguar.autots_bonding.Coordinate method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword method) (schrodinger.application.xtb.input.XTBInput method) (schrodinger.models.mappers.AttrTargetSpec method) (schrodinger.models.mappers.ParamTargetSpec method) (schrodinger.models.mappers.TargetSpec method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) setValues() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.matsci.kmcgui.MinMaxNeighborWidgets method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) setVarianceEdit() (schrodinger.application.matsci.plotwidgets.SliderchartVLFitStdPlot method) setVDWRadius() (schrodinger.application.matsci.cg_mapping.Particle method) setVdwScalingFactor() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setVerticalHeadersSortable() (schrodinger.ui.qt.table.StructureDataViewerModel method) setViewname() (schrodinger.ui.qt.jobwidgets.JobStatusButton method) setViewSize() (schrodinger.protein.helm.helm_renderer.HelmWidget method) setVisible() (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.matsci.chargegui.ChargePropertySelector method) (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) (schrodinger.application.matsci.mswidgets.RandomSeedWidget method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) (schrodinger.ui.qt.swidgets.SCheckBoxWithSubWidget method) (schrodinger.ui.qt.swidgets.SLabeledComboBox method) (schrodinger.ui.qt.swidgets.SLabeledDoubleSpinBox method) (schrodinger.ui.qt.swidgets.SLabeledEdit method) (schrodinger.ui.qt.swidgets.SLabeledRadioButtonGroup method) (schrodinger.ui.qt.swidgets.SLabeledSlider method) (schrodinger.ui.qt.swidgets.SLabeledSpinBox method) (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) (schrodinger.ui.qt.swidgets.SRadioButtonWithSubWidget method) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) setVolGraphAndBitset() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setVsliderPosition() (schrodinger.application.matsci.plotwidgets.SliderchartVLPlot method) setWaitCursor() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.two_d_viewer.TwoDViewer method) setWam() (schrodinger.application.matsci.equilibrium_md.CmsModel method) setWAMProperty() (schrodinger.application.matsci.jwsteps.BaseStep method) setWarningStatus() (schrodinger.ui.qt.appframework2.af2.StatusBar method) setWeight() (schrodinger.trajectory.prody.ensemble.Ensemble method) setWeights() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector.ChargeSelectorLineEdit method) setWidgetLayout() (schrodinger.ui.qt.widgetmixins.basicmixins.DockableMixinCollection method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) setWidgetStylePropertyValue() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) setWidth() (schrodinger.ui.qt.tablewidget.Column method) setWindowFlags() (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) setWindowFlagsForRun() (schrodinger.ui.qt.widgetmixins.basicmixins.DockableMixinCollection method) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) setWindowTitle() (schrodinger.ui.qt.messagebox.MessageBox method) setWorkflow() (schrodinger.application.matsci.permittivity.Config method) setWorkingDirectory() (schrodinger.application.prime.wrapper.BasePrimeAlignment method) setWriteG96File() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteMaeffFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteMaeFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteOneMaeFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWritePdbFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteTopFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteXyzFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setX() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) (schrodinger.ui.qt.network_visualizer.Node method) setXAutoRange() (schrodinger.ui.qt.schart.SChart method) setXBiasFunction() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method) setXMinMax() (schrodinger.ui.qt.schart.SChart method) setXvolSelected() (schrodinger.application.phase.phase_markers.PhaseMarkers method) setXY() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) setXYYStd() (schrodinger.application.matsci.plotwidgets.SliderchartVLFitStdPlot method) setXYZ() (schrodinger.application.matsci.cg_mapping.Particle method) (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame method) (schrodinger.structure.Structure method) setXYZCoords() (schrodinger.graphics3d.ellipsoid.MaestroEllipsoid method) (schrodinger.graphics3d.hemisphere.MaestroHemisphere method) (schrodinger.graphics3d.sphere.MaestroSphere method) setY() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) (schrodinger.ui.qt.network_visualizer.Node method) setYAutoRange() (schrodinger.ui.qt.schart.SChart method) setYMinMax() (schrodinger.ui.qt.schart.SChart method) SFilteredListWidget (class in schrodinger.ui.qt.swidgets) sfloat() (in module schrodinger.application.matsci.gsas.GSASIIfiles) SFrame (class in schrodinger.ui.qt.swidgets) sg_t_den (schrodinger.application.matsci.cctbx.rot_mx.tr_vec attribute) sgequiv_2002_orthorhombic (in module schrodinger.application.matsci.gsas.GSASIIspc) SGErrors() (in module schrodinger.application.matsci.gsas.GSASIIspc) SGpolar() (in module schrodinger.application.matsci.gsas.GSASIIspc) SGPrint() (in module schrodinger.application.matsci.gsas.GSASIIspc) SGProd() (in module schrodinger.application.matsci.gsas.GSASIIspc) SGPtGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc) SGridLayout (class in schrodinger.ui.qt.swidgets) SGroupBox (class in schrodinger.ui.qt.swidgets) sh_mut_coord (schrodinger.application.desmond.stage.jobs.SnapcoreCoordinates attribute) sh_ref_coord (schrodinger.application.desmond.stage.jobs.SnapcoreCoordinates attribute) SHA256WithRSA (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) SHA256WithRSAPSS (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) SHA384WithRSA (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) SHA384WithRSAPSS (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) SHA512WithRSA (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) SHA512WithRSAPSS (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) SHADE_10 (schrodinger.ui.qt.standard.design_tokens.PrimaryColors attribute) SHADE_20 (schrodinger.ui.qt.standard.design_tokens.PrimaryColors attribute) SHADE_60 (schrodinger.ui.qt.standard.design_tokens.PrimaryColors attribute) ShadowData (class in schrodinger.application.matsci.cgforcefield) shape_based (schrodinger.application.phase.packages.ligand_aligner.AlignMethod attribute) shape_generate() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) ShapeControl (class in schrodinger.application.vss.control) ShapeCreator (class in schrodinger.application.phase.packages.shape_creation_logic) ShapeDataUpdateDriver (class in schrodinger.application.phase.packages.shape_screen_gpu_update) ShapeFactory (class in schrodinger.application.watermap.shapes) ShapeFileReader (class in schrodinger.application.phase.packages.shape_binary_utils) ShapeFileWriter (class in schrodinger.application.phase.packages.shape_binary_utils) ShapeGenerator (class in schrodinger.application.phase.packages.shape_generator) SHAPES (schrodinger.ui.qt.schart.SeriesParams attribute) ShapeScreenJob (class in schrodinger.application.phase.packages.shape_screen_al_node) shared_tags (schrodinger.analysis.transformations.TransformsRepository property) shareNodes() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) sharingNodesInSymmRing() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) SharingViolationError SHBoxLayout (class in schrodinger.ui.qt.swidgets) SHeaderView (class in schrodinger.ui.qt.table) SHEAR_INDICES (schrodinger.application.matsci.elasticity.strain.DeformedStructureSet attribute) SHEAR_STRAINS (schrodinger.application.matsci.elasticity.strain.DeformedStructureSet attribute) SHEAR_STRAINS_KEY (schrodinger.application.matsci.espresso.qeinput.ElasticControlType attribute) SHEET_OUT_MAE_NAME (schrodinger.application.matsci.nano.constants.Constants attribute) shell() (in module schrodinger.job.remote_command) shift (schrodinger.application.jaguar.simple_spec.Peak attribute) shift() (schrodinger.application.matsci.espresso.qeoutput.MagresAtom method) shift_pka() (in module schrodinger.protein.assignment) shifts (schrodinger.application.jaguar.nmr_utils.NMRData attribute) ShimMapStep (class in schrodinger.stepper.shims) ShimReduceStep (class in schrodinger.stepper.shims) SHistogramBarSeries (class in schrodinger.ui.qt.schart) SHistogramBarSet (class in schrodinger.ui.qt.schart) SHLine (class in schrodinger.ui.qt.swidgets) short() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.LicenseLine method) (schrodinger.application.licensing.flexlm.Package method) short_code (schrodinger.protein.residue.Residue property) short_end (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule.RING_INFO attribute) SHORT_FINGERPRINT_TYPES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) short_hash (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) SHORT_HERMANN_MAUGUIN_SYMBOL (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) SHORT_NAME (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) short_name (schrodinger.seam.metric.ExecutionMetrics attribute) SHORT_NAME_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) SHORT_RADIUS (schrodinger.application.matsci.packmol.PackmolKw attribute) SHORT_RADIUS_SCALE (schrodinger.application.matsci.packmol.PackmolKw attribute) SHORT_USAGE (schrodinger.application.desmond.multisimstartup.Help attribute) (schrodinger.application.desmond.multisimstartup.Startup.Help attribute) shorten_name() (in module schrodinger.application.desmond.fep_edge_data) shorthost() (in module schrodinger.application.licensing.flexlm) (in module schrodinger.utils.net) shortname (schrodinger.project.project.Project property) should_edge_skip_fep() (in module schrodinger.application.desmond.skip_fep_utils) should_paint_progress() (in module schrodinger.application.job_monitor.job_monitor_progress_bar) should_restart_from_checkpoint() (schrodinger.application.desmond.cmj.JobStatus method) should_structure_skip_fep() (in module schrodinger.application.desmond.skip_fep_utils) shouldMinimize() (schrodinger.application.matsci.builderwidgets.ItemRow method) shouldRelax() (schrodinger.application.desmond.gui.RelaxFrame method) shouldRestoreVisibility() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) shouldShowSectorAnnotation() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) shouldUpdateVisibility() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) show() (in module schrodinger.ui.qt.appframework2.appmethods) (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.gridbox.GridBox method) (schrodinger.protein.membrane.Membrane_Model method) (schrodinger.surface.Surface method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.qt.rename_favorite_dialog.RenameFavoriteDialog method) (schrodinger.ui.qt.structure2d.LabeledStructureToolTip method) (schrodinger.ui.qt.structure2d.StructureToolTip method) (schrodinger.ui.qt.swidgets.EllipsisPopUpButton method) (schrodinger.ui.qt.tablewidget.Row method) (schrodinger.ui.qt.tooltips.TooltipMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin method) (schrodinger.ui.two_d_viewer.CellContextualMenu method) show2DStructures() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) show_all_feature_labels() (in module schrodinger.application.phase.phase_markers) show_all_marker_labels_if_property_checked() (in module schrodinger.application.phase.phase_markers) show_all_property_labels() (in module schrodinger.application.phase.phase_markers) SHOW_AS_WINDOW (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel attribute) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel attribute) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog attribute) (schrodinger.ui.qt.widgetmixins.basicmixins.DockableMixinCollection attribute) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin attribute) (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin attribute) show_attached_hydrogen() (in module schrodinger.application.desmond.depictor) show_contact_info() (in module schrodinger.utils.documentation) show_entry() (schrodinger.application.desmond.maestro.Workspace method) show_error() (in module schrodinger.ui.qt.messagebox) show_ff_project_settings_dlg() (in module schrodinger.ui.qt.forcefield.ffprojectsettingsdlg) show_info() (in module schrodinger.ui.qt.messagebox) show_invalid_structure_dlg() (in module schrodinger.trajectory.trajectory_gui_dir.trajectory_messages) show_invalid_trajectory_file_dlg() (in module schrodinger.trajectory.trajectory_gui_dir.trajectory_messages) show_job_launch_failure_dialog() (in module schrodinger.ui.qt.utils) show_knowledge_base() (in module schrodinger.utils.documentation) show_known_issues() (in module schrodinger.utils.documentation) show_ld_connector() (in module schrodinger.application.livedesign.login_gui2) show_local_doc() (in module schrodinger.utils.documentation) show_message() (in module schrodinger.utils.documentation) show_message_box() (in module schrodinger.ui.qt.messagebox) show_msv_annotation() (in module schrodinger.application.bioluminate.anarci.annotate) show_network_error_popup() (in module schrodinger.application.livedesign.maestro_ld_connection) show_new_features() (in module schrodinger.utils.documentation) show_new_maestro_features() (in module schrodinger.utils.documentation) show_online_tutorials() (in module schrodinger.utils.documentation) show_only() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) show_only_entry() (schrodinger.application.desmond.maestro.Workspace method) show_options() (in module schrodinger.application.jaguar.qrnn.temp_opt) show_panel() (in module schrodinger.application.pymol.pymol4maestro) show_phase_hover_markers() (in module schrodinger.application.phase.phase_markers) SHOW_POSE_PAGE (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget attribute) show_product_missing_info() (in module schrodinger.ui.qt.messagebox) show_question() (in module schrodinger.ui.qt.messagebox) show_result() (in module schrodinger.application.bioluminate.pml_menus) SHOW_ROW_NUMBERS (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) show_simplified_stereo_annotation (schrodinger.livedesign.draw.ImageGenOptions attribute) show_snapshot_atom_limit_warning() (in module schrodinger.trajectory.trajectory_gui_dir.trajectory_messages) show_stereo_annotation (schrodinger.livedesign.draw.ImageGenOptions attribute) show_terminal_methyl (schrodinger.livedesign.draw.ImageGenOptions attribute) show_tool_tip (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) show_topic() (in module schrodinger.utils.documentation) show_warning() (in module schrodinger.ui.qt.messagebox) show_wiggly_bonds (schrodinger.livedesign.draw.ImageGenOptions attribute) show_workspace_phase_markers() (in module schrodinger.application.phase.phase_markers) showAdjustWindow() (schrodinger.ui.qt.navtoolbar.NavToolbar method) showAdvancedSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) showAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) showAllFeaturesForEntry() (schrodinger.application.phase.phase_markers.PhaseMarkers method) showAllFeaturesForEntryByType() (schrodinger.application.phase.phase_markers.PhaseMarkers method) showAllJaguarMarkers() (schrodinger.application.jaguar.gui.base_panel.MarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) showAllMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) showAtoms() (schrodinger.application.bioluminate.pml_menus.ShowNonBonded method) showAuxProperties() (schrodinger.ui.qt.propertyselector.PropertySelector method) showBadEdge() (schrodinger.ui.qt.network_views.NetworkEdge method) ShowBAndS (class in schrodinger.application.bioluminate.pml_menus) showBanner() (schrodinger.ui.qt.utils.MaestroPythonBannerManager method) ShowCartoon (class in schrodinger.application.bioluminate.pml_menus) ShowCartoonOrRibbon (class in schrodinger.application.bioluminate.pml_menus) showChargeDialog() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) showConfigDialog() (schrodinger.application.jaguar.gui.timing.TimerInfoDialog method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) showContextMenu() (schrodinger.ui.two_d_viewer.TwoDViewer method) showCrystalMateClashesToggled() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) showDefineButton() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) showDendrogramPlot() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) showDescription() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) showDistanceMatrixPlot() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) showDlg() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) showEntryIds() (schrodinger.ui.two_d_viewer.TwoDViewer method) showEvent() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) (schrodinger.application.jaguar.gui.timing.TimerInfoDialog method) (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.matsci.sliceplot.SlicePlot method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackMixin method) (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.atomselector.AtomSelector method) (schrodinger.ui.qt.forcefield.ffselector.ffComboBox method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) (schrodinger.ui.qt.periodictable.PeriodicTableDialogMultipleClick method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.swidgets.SEmittingScrollBar method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) (schrodinger.ui.qt.table.EmittingScrollBar method) showExportSnapshotStructuresDlg() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) showExportStructuresDlg() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) showFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) showFFDialog() (schrodinger.application.matsci.chargegui.FFInfo method) showForEdit() (schrodinger.application.matsci.deswidgets.AdvancedMDOptions method) (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) showHelp() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) showHTMLResult (schrodinger.application.jaguar.update_pka_settings.UpdatePKASettingsDlg attribute) showJobsList() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) ShowLabel (class in schrodinger.application.bioluminate.pml_menus) showLabels() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) showLaunchStatus() (schrodinger.application.matsci.multiapp.MultiJobApp method) showLeaves() (schrodinger.ui.qt.dendrogram.Dendrogram method) showLegend() (schrodinger.ui.qt.schart.SChart method) ShowLigandLines (class in schrodinger.application.bioluminate.pml_menus) ShowLigandSpheres (class in schrodinger.application.bioluminate.pml_menus) ShowLigandTubes (class in schrodinger.application.bioluminate.pml_menus) ShowLines (class in schrodinger.application.bioluminate.pml_menus) ShowMenu (class in schrodinger.application.bioluminate.pml_menus) ShowMesh (class in schrodinger.application.bioluminate.pml_menus) showMessage() (schrodinger.application.bioluminate.pml_menus.ResultsWindow method) (schrodinger.ui.qt.appframework2.af2.StatusBar method) (schrodinger.ui.qt.standard_widgets.statusbar.StatusBar method) showMessageBox() (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) showMoleculeWidgetForParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) shown (schrodinger.ui.qt.table.EmittingScrollBar attribute) showNewStructure() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) ShowNonBonded (class in schrodinger.application.bioluminate.pml_menus) ShowNonBondedSpheres (class in schrodinger.application.bioluminate.pml_menus) ShowOrganicMenu (class in schrodinger.application.bioluminate.pml_menus) showOrHideEntryDBFrame() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) showPage() (schrodinger.application.desmond.rl_helper.NumberedCanvas method) showPopup() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.pop_up_widgets.ComboBoxWithPopUp method) (schrodinger.ui.qt.swidgets.ActionComboBox method) showPresets() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) showProgress() (schrodinger.ui.qt.appframework2.af2.StatusBar method) showProgressBarForJob() (schrodinger.ui.qt.appframework2.af2.App method) showPropNames() (schrodinger.ui.two_d_viewer.TwoDViewer method) showProteinHealthReport() (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) showPT() (schrodinger.ui.qt.navtoolbar.MaestroNavToolbar method) ShowRibbon (class in schrodinger.application.bioluminate.pml_menus) showScheme() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) showSeriesInLegend() (schrodinger.ui.qt.schart.SChart method) showSettingsMenu() (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) showSketcher() (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) showSmartsSelector() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelectorButton method) showSphere() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) ShowSpheres (class in schrodinger.application.bioluminate.pml_menus) showStatisticsPlot() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) showStructures (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame attribute) showSTUDialog() (schrodinger.ui.qt.appframework2.af2.JobApp method) ShowSubstructureMenu (class in schrodinger.application.bioluminate.pml_menus) showSubwidgets() (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) showSuperposed() (schrodinger.application.matsci.reaction_workflow_gui_utils.WorkspaceSuperpositionFrame method) ShowSurface (class in schrodinger.application.bioluminate.pml_menus) showTimingDialog() (schrodinger.application.jaguar.gui.timing.TimerMixin method) showTolMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) (schrodinger.application.phase.phase_markers.PhaseTolMarkers method) showToolTip() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin method) showTrajRangeSelectorDialog() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) showTree() (schrodinger.ui.qt.dendrogram.Dendrogram method) ShowTubes (class in schrodinger.application.bioluminate.pml_menus) showtype() (in module schrodinger.application.desmond.enhanced_sampling.FcnTypes) (in module schrodinger.application.desmond.enhsamp) showUnavailable() (schrodinger.application.livedesign.panel_components.ColumnSelectionProxyModel method) showZoomCellStatus() (schrodinger.ui.two_d_viewer.TwoDViewer method) shrink_box() (in module schrodinger.application.desmond.mxmd.mxmd_system_builder) shrink_panel() (in module schrodinger.application.matsci.gutils) shrinkRowHeight() (schrodinger.application.jaguar.gui.utils.PropertiesTableWidget method) shuffle_merge() (in module schrodinger.structutils.shuffle) shuffle_structs() (in module schrodinger.structutils.shuffle) ShuffleException shutdown() (schrodinger.tasks.taskszmq.ZmqClient method) (schrodinger.tasks.taskszmq.ZmqServer method) shutdown_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) shutdown_server() (schrodinger.application.glide.http_client.AbstractHTTPClient method) (schrodinger.application.glide.http_client.HTTPClient method) (schrodinger.application.glide.http_client.NonBlockingHTTPClient method) (schrodinger.application.glide.http_client.ZmqClient method) Sibling (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) sibling_group (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) SiblingNode (class in schrodinger.application.matsci.reaction_workflow_utils) SIDE_CHAIN_ATOMS (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner attribute) SIDE_CHAIN_CHEM (class in schrodinger.protein.residue) side_chain_chem (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) SIDECHAIN (schrodinger.application.desmond.constants.ConfRestraintType attribute) sidechain_dihedral_atomnames (in module schrodinger.protein.analysis_params) sidechain_dihedrals (in module schrodinger.protein.analysis_params) SIDECHAIN_INTERACTION (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) SIDECHAIN_PDBNAMES (schrodinger.protein.assignment.AsparticAcidpKaPredictor attribute) (schrodinger.protein.assignment.GlutamicAcidpKaPredictor attribute) SIDECHAIN_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) sidechains() (schrodinger.protein.getpdb_utility.Code method) SIDECHAINS_PDBNAMES (schrodinger.protein.assignment.HistidinepKaPredictor attribute) SidedError (class in schrodinger.application.desmond.constants) SideHistogram (class in schrodinger.application.matsci.plotwidgets) SIDEMAX (schrodinger.application.matsci.packmol.PackmolKw attribute) sifValue() (schrodinger.application.glide.glide.MetalConstraint method) (schrodinger.application.glide.glide.MetCoordConstraint method) (schrodinger.application.glide.glide.NOEConstraint method) (schrodinger.application.glide.glide.PositionalConstraint method) sig_fig_round() (in module schrodinger.math.mathutils) Sigmoid (class in schrodinger.math.multi_parameter_optimization) SignalAndSlot (class in schrodinger.utils.qt_utils) SignalsAndSlotsException SignalTable (class in schrodinger.ui.qt.appframework2.debugwidgets) SignalTask (class in schrodinger.tasks.tasks) SignalTimeoutException SignalType (class in schrodinger.models.parameters) signature (schrodinger.application.licensing.licserver.client.LocalEntitlementValidation attribute) (schrodinger.application.matsci.species.SC_TYPE_DATA attribute) signature() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) SignatureAlgorithm (class in schrodinger.application.licensing.licserver.client) signedExpComp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) significant() (in module schrodinger.application.jaguar.nmr_utils) sigterm_handler() (in module schrodinger.active_learning.mq_driver) (in module schrodinger.active_learning.mq_worker) silentlySetItems() (schrodinger.application.matsci.builderwidgets.TemplateCombo method) silentlySetItemsAndSelectText() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) silentlySetTemplates() (schrodinger.application.matsci.builderwidgets.FilteredTemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelector method) silentlyTryToSelectTemplate() (schrodinger.application.matsci.builderwidgets.TemplateSelector method) silentlyTryToSelectText() (schrodinger.application.matsci.builderwidgets.TemplateCombo method) sim2dist() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) SIM_BOX (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) sim_charge (schrodinger.application.desmond.new_fep_edge_data.FepData property) sim_ensemble (schrodinger.application.desmond.new_fep_edge_data.FepData property) sim_ff (schrodinger.application.desmond.new_fep_edge_data.FepData property) sim_params (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.SolubilityWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsWorkflowParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams attribute) sim_temperature (schrodinger.application.desmond.new_fep_edge_data.FepData property) SIM_TIME (schrodinger.application.desmond.kinetics.utils.MtdInfo attribute) (schrodinger.application.desmond.kinetics.utils.ResultsCols attribute) sim_time (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) (schrodinger.application.desmond.new_fep_edge_data.FepData property) sim_time_complex (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) sim_time_fragment (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) sim_time_solvent (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) sim_time_vacuum (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) SIM_TYPE (schrodinger.application.matsci.permittivity.MultiStageMd attribute) simBuser() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simCosine() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simDice() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simDixon() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simEuclidean() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simHamann() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simHamming() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) Similar (schrodinger.protein.alignment.ResidueSimilarity attribute) similar_coordinate() (schrodinger.application.jaguar.autots_bonding.Coordinate method) similar_neigh (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData.RING_NODE_TYPE attribute) similarity (schrodinger.livedesign.biologics.sequence.AlignedSequence attribute) similarity_fingerprint() (in module schrodinger.livedesign.search) similarity_matrix (schrodinger.protein.tasks.blast.BlastSettings attribute) similarity_matrix_by_protein_ligand_interactions (schrodinger.application.desmond.new_fep_edge_data.FepData property) similarity_matrixChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) similarity_matrixReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) SIMILARITY_METRICS (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity attribute) SIMILARITY_SCORE (schrodinger.livedesign.search.FingerprintUse attribute) SimilarityEndpoint (class in schrodinger.infra.licensing) SimilarityMatrix (class in schrodinger.protein.tasks.blast) simKulczynski() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) SimLegParams (class in schrodinger.application.desmond.msj_generator.workflow_params) simMatching() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simMcConnaughey() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simMinMax() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simModifiedTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) SimOptionsFrame (class in schrodinger.application.desmond.gui) simPatternDifference() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simPearson() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simPetke() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) SimpleLink (class in schrodinger.ui.qt.standard_widgets.hyperlink) SimplePreset (class in schrodinger.application.bioluminate.pml_menus) SimpleSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) simplified_pH (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) simplified_pHChanged (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) simplified_pHReplaced (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) SimplifiedSequenceViewer (class in schrodinger.application.bioluminate.ssv.viewer) simplify_structure() (in module schrodinger.application.jaguar.autots_bonding) simRogersTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) SIMS (schrodinger.application.desmond.kinetics.utils.ResultsCols attribute) simShape() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simSimpson() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simSize() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simSoergel() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simTversky() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) Simulate (class in schrodinger.application.desmond.stage.simulate) SIMULATE (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) simulate() (schrodinger.application.matsci.montecarlo.Metropolizer method) simulate_spectrum() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) SimulateBase (class in schrodinger.application.desmond.stage.simulate) SimulatedAnnealing (class in schrodinger.application.canvas.r_group_dee) simulateTreeConstruction() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) SIMULATION (schrodinger.application.desmond.constants.DefaultFEPSimulationTimes attribute) SIMULATION_BOX (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute) SIMULATION_PROTOCOL (class in schrodinger.application.desmond.constants) SIMULATION_RUNNER (schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer attribute) SIMULATION_RUNNER() (schrodinger.application.bioluminate.methionine_oxidation.HmcAnalyzer static method) (schrodinger.application.bioluminate.methionine_oxidation.MdAnalyzer static method) SimulationParams (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) SimulationProfileStep (class in schrodinger.application.matsci.jwsteps) simVariance() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simYule() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) sind() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIImath) SINGLE (schrodinger.application.livedesign.login_gui2.AuthenticationMode attribute) (schrodinger.energy.ANIPrecision attribute) Single (schrodinger.structure.BondType attribute) SINGLE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Loop attribute) Single (schrodinger.ui.qt.config_dialog.GpuHostProductMode attribute) SINGLE_DISPLACEMENT_TYPE (schrodinger.application.matsci.rxn_channel.Constants attribute) SINGLE_DOMAIN (schrodinger.application.bioluminate.antibody.io.csv_reader.ModelingMode attribute) single_point() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) single_point_cluster() (schrodinger.protein.assignment.ProtAssign method) SINGLE_PRECISION (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) single_sign_on_host (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) single_sign_on_hostChanged (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) single_sign_on_hostReplaced (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) SINGLE_STRUC (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) SingleBrownieStep (class in schrodinger.application.matsci.jwsteps) singleClicked (schrodinger.ui.qt.standard_widgets.buttons.DoubleClickButtonMixin attribute) SingleCpuMultipleGpu (schrodinger.ui.qt.config_dialog.GpuHostProductMode attribute) SingleDashOption (class in schrodinger.utils.singledashoptionparser) SingleDashOptionParser (class in schrodinger.utils.singledashoptionparser) SingleDomainAbSequenceIndexer (class in schrodinger.application.bioluminate.antibody.sequence_indexer) SingleFilter (class in schrodinger.structutils.filter) SingleGpuDesmondGuiConfigDialog (class in schrodinger.application.desmond.gui) SingleMDJob (class in schrodinger.application.matsci.equilibrium_md) SingleMDStep (class in schrodinger.application.matsci.jwsteps) SingleOnlyGpu (schrodinger.ui.qt.config_dialog.GpuHostProductMode attribute) SingleOptionAction (class in schrodinger.application.desmond.starter.ui.cmdline) SinglePropFilter (class in schrodinger.structutils.filter) SingleProteinInteractions (class in schrodinger.application.bioluminate.protein_interaction.tasks) singleR1Atom() (schrodinger.application.matsci.amorphous.Moieties method) SingleSmartsFilter (class in schrodinger.structutils.filter) singlet (schrodinger.application.jaguar.gui.tabs.theory_tab.ExcitedStateInfo attribute) singleton() (in module schrodinger.application.desmond.depictor) SingularShapeFileReader (class in schrodinger.application.phase.packages.shape_binary_utils) Site (class in schrodinger.application.desmond.cms) (class in schrodinger.application.matsci.reaction_workflow_utils) site() (schrodinger.application.desmond.cms.Cms method) SITE1 (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) (schrodinger.application.matsci.kmc.PairsTable attribute) SITE2 (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) (schrodinger.application.matsci.kmc.PairsTable attribute) SITE_ATOM_KEY (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF attribute) site_idxs (schrodinger.application.matsci.reaction_workflow_utils.Source attribute) site_info (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) site_iterator() (in module schrodinger.application.matsci.coarsegrain) SITE_KEYWORDS (schrodinger.application.matsci.kmc.SchrodingerTable attribute) site_matches (schrodinger.structutils.sitealign.BindingSiteAligner attribute) site_state_is_hidden() (in module schrodinger.utils.featureflags.featureflags) SiteAndProtonationIds (class in schrodinger.application.desmond.stage.app.constant_ph) SiteAtom (class in schrodinger.application.matsci.sculptcomplex) siteDeselected() (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog method) SITEMAP_CMD (schrodinger.application.desmond.stage.app.matsci.Aacg_SiteMap_Multijob attribute) SiteMatchLookup (class in schrodinger.structutils.sitealign) sitename (schrodinger.application.desmond.stage.app.constant_ph.SiteAndProtonationIds attribute) sitePicked() (schrodinger.application.matsci.siteselector.siteselector.SiteRadioButton method) SiteRadioButton (class in schrodinger.application.matsci.siteselector.siteselector) Sites (class in schrodinger.application.matsci.reaction_workflow_utils) sites_keyword (schrodinger.application.glide.glide.MetCoordConstraint attribute) SITES_TABLE (schrodinger.application.matsci.kmc.BaseDatabaseManager attribute) (schrodinger.application.matsci.kmc.MatSciDatabaseManager attribute) (schrodinger.application.matsci.kmc.VotcaDatabaseManager attribute) siteSelected() (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog method) SiteSelectionDialog (class in schrodinger.application.matsci.siteselector.siteselector) siteSifValue() (schrodinger.application.glide.glide.MetCoordConstraint method) SitesMixin (class in schrodinger.application.matsci.kmc) siteUnpicked() (schrodinger.application.matsci.siteselector.siteselector.SiteRadioButton method) SIZE (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) size (schrodinger.stepper.stepper.BatchSettings attribute) size() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.pathfinder.reaction.ReagentClass method) (schrodinger.infra.mmbitset.Bitset method) sizeChanged (schrodinger.stepper.stepper.BatchSettings attribute) (schrodinger.ui.qt.table.ViewerModel attribute) sizeHint() (schrodinger.application.desmond.fep_scholar_util.FEPStructureObject method) (schrodinger.application.jaguar.gui.utils.PropertiesTableWidget method) (schrodinger.application.job_monitor.job_monitor_progress_bar.ProgressBar method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.SeparatorItemDelegate method) (schrodinger.ui.qt.delegates.CheckboxDelegate method) (schrodinger.ui.qt.delegates.ProgressBarDelegate method) (schrodinger.ui.qt.delegates.PushButtonDelegate method) (schrodinger.ui.qt.dialbox.Dial method) (schrodinger.ui.qt.navtoolbar.NavToolbar method) (schrodinger.ui.qt.rama.RamaFigure method) (schrodinger.ui.qt.schart.SChartView method) (schrodinger.ui.qt.standard_widgets.hyperlink.ButtonWithArrowMixin method) (schrodinger.ui.qt.structure2d.StructurePicture method) (schrodinger.ui.qt.swidgets.ImageLabel method) (schrodinger.ui.qt.swidgets.VerticalLabel method) (schrodinger.ui.qt.table.StructureDataViewerDelegate method) (schrodinger.ui.qt.table_helper.SampleDataTableViewMixin method) (schrodinger.ui.qt.utils.LineEditWithSampleText method) sizeHintForColumn() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) (schrodinger.ui.qt.table_helper.SampleDataTableViewMixin method) sizeHintForRow() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) sizeHintForText() (schrodinger.ui.qt.delegates.PushButtonDelegate method) sizePolicy() (schrodinger.ui.qt.swidgets.ImageLabel method) sizeReplaced (schrodinger.stepper.stepper.BatchSettings attribute) SizeVectorizer (in module schrodinger.application.bioluminate.peptide_sar.encode) ska_pairwise_align() (in module schrodinger.structutils.structalign2) SketchDialog (class in schrodinger.application.matsci.builderwidgets) SketcherBox (class in schrodinger.application.matsci.builderwidgets) SketcherSMARTSDialog (class in schrodinger.ui.sketcher_smarts_dialog) SketcherStructureMixin (class in schrodinger.application.matsci.builderwidgets) sketchStructure() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) SKIP (schrodinger.application.livedesign.export_models.InvalidGEIdHandlingPolicy attribute) skip() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) skip_assigned_residues (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput.ABOOptions attribute) skip_assigned_residuesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput.ABOOptions attribute) skip_assigned_residuesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput.ABOOptions attribute) skip_csv (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) skip_csvChanged (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) skip_csvReplaced (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) skip_eq_check() (schrodinger.models.parameters.CompoundParam method) skip_fep_cutoff_rmsd (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) skip_funcnames (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute) skip_if() (in module schrodinger.infra.util) skip_legacy_spacing_style() (in module schrodinger.ui.qt.style) skip_legs (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) SkipFepReason (class in schrodinger.application.desmond.constants) skipinitialspace (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) skipOffTokenChannels() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) skipOffTokenChannelsReverse() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) skippedStWriter() (schrodinger.application.glide.client_module.GlideClientModuleAdapter method) Slab (class in schrodinger.application.matsci.shapes) SLAB_THRESHOLD (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) SLAB_XY (schrodinger.application.matsci.msconst.DIMENSIONALITY attribute) SLabel (class in schrodinger.ui.qt.swidgets) SLabeledComboBox (class in schrodinger.ui.qt.swidgets) SLabeledDoubleSpinBox (class in schrodinger.ui.qt.swidgets) SLabeledEdit (class in schrodinger.ui.qt.swidgets) SLabeledRadioButtonGroup (class in schrodinger.ui.qt.swidgets) SLabeledSlider (class in schrodinger.ui.qt.swidgets) SLabeledSpinBox (class in schrodinger.ui.qt.swidgets) SlicePlot (class in schrodinger.application.matsci.sliceplot) SLICES (schrodinger.application.matsci.density_analysis_widget.ImagePlotFrame attribute) (schrodinger.application.matsci.density_analysis_widget.LinePlotFrame attribute) SlidableHLine (class in schrodinger.application.bioluminate.sliderchart) SlidableLine (class in schrodinger.application.bioluminate.sliderchart) SlidableVLine (class in schrodinger.application.bioluminate.sliderchart) sliderChange() (schrodinger.ui.qt.dialbox.Dial method) SliderchartVLFitStdPlot (class in schrodinger.application.matsci.plotwidgets) SliderchartVLPlot (class in schrodinger.application.matsci.plotwidgets) SliderLayout (class in schrodinger.ui.qt.formlayout) sliderMoved() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) SliderPlot (class in schrodinger.application.bioluminate.sliderchart) slidersMoved() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) SlimFileSelector (class in schrodinger.ui.qt.file_selector) SlimStructureSelector (class in schrodinger.ui.qt.structure_selector) SLineEdit (class in schrodinger.ui.qt.swidgets) SListWidget (class in schrodinger.ui.qt.swidgets) slot() (schrodinger.models.mappers.TargetSpec method) SLOT_BLOCKLIST (schrodinger.protein.residue.Residue attribute) slotSend() (schrodinger.application.pymol.pymol4maestro.panel method) slugify() (in module schrodinger.application.jaguar.file_logger) (in module schrodinger.utils.fileutils) SM6_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) SM8 (schrodinger.application.jaguar.rotation_barriers_keywords.SolvationMethod attribute) SM8_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) sm_geometry() (in module schrodinger.application.jaguar.textparser) Small (schrodinger.protein.residue.STERIC_GROUP attribute) SMALL_MATRIX (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) SMALL_MOLECULE (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) (schrodinger.livedesign.entity_type.EntityClass attribute) SmallCloseButton (class in schrodinger.ui.qt.swidgets) SmallMoleculeMsjGenerator (class in schrodinger.application.desmond.msj_generator.fep.small_molecule) SmallMoleculeReport (class in schrodinger.application.desmond.replica_sid_generator) SmallMoleculeTorsions (class in schrodinger.trajectory.trajectory_gui_dir.custom_analyzers) SmallMoleculeWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) SMARTS (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PickingModes attribute) smarts (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsPageModel attribute) SMARTS (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) smarts (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.BEAD_TYPE attribute) (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.MAPPED_BEAD_INFO attribute) SMARTS (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) smarts (schrodinger.application.matsci.rdpattern.Pattern property) SMARTS (schrodinger.rdkit_extensions.Format attribute) smarts() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) smarts_data_changed (schrodinger.ui.qt.swidgets.SMARTSEdit attribute) smarts_filters (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) smarts_filtersChanged (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) smarts_filtersReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Input attribute) SMARTS_KEY (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) SMARTS_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) SMARTS_METHOD (class in schrodinger.application.matsci.msconst) SMARTS_NONUNIQUE_BONDS (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) SMARTS_PATTERN_SEPARATOR (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) SMARTS_PROP (schrodinger.application.matsci.genetic_optimization.StructureEvaluator attribute) SMARTS_TOOLTIP (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) SMARTS_UNIQUE_PAIR (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) SMARTS_UNIQUE_TRIPLE_NORMAL (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) SMARTS_WILDCARD (schrodinger.application.matsci.rxn_channel.Constants attribute) smartsChanged (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsPageModel attribute) SMARTSComplexity (class in schrodinger.application.matsci.smartsutils) SmartsCriterion (class in schrodinger.utils.ligfilter) SmartsDirector (class in schrodinger.application.matsci.order_parameter_mod) SMARTSEdit (class in schrodinger.ui.qt.swidgets) SmartsException SmartsFilter (class in schrodinger.application.steps.filters) (class in schrodinger.structutils.filter) SmartsFilter.Settings (class in schrodinger.application.steps.filters) SMARTSFrame (class in schrodinger.application.matsci.rdpattern_gui) SMARTSGroup (class in schrodinger.application.matsci.smartsutils) SMARTSGroupData (class in schrodinger.application.matsci.smartsutils) SMARTSGroupError SMARTSNameValidator (class in schrodinger.application.matsci.smartsutilsgui) SmartsPageModel (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) SMARTSParseError smartsReplaced (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsPageModel attribute) SmartsSelector (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) SmartsSelectorButton (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) SmatplotlibCanvas (class in schrodinger.ui.qt.smatplotlib) SmatplotlibToolbar (class in schrodinger.ui.qt.smatplotlib) SMD (schrodinger.application.jaguar.rotation_barriers_keywords.SolvationMethod attribute) SMD_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) SmearAbeles() (in module schrodinger.application.matsci.gsas.GSASIIpwd) SMEARTYPES (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) smi (schrodinger.application.steps.enumerators.SmilesTransformPair attribute) (schrodinger.application.transforms.enumerators.SmilesTransformPair attribute) smiChanged (schrodinger.application.steps.enumerators.SmilesTransformPair attribute) smiles (schrodinger.application.matsci.rdpattern.Pattern property) SMILES (schrodinger.rdkit_extensions.Format attribute) smiles() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) smiles2image() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) smiles2mol() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) smiles2svg() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) smiles_to_3d (schrodinger.application.phase.packages.mmp3d_driver_utils.SubjobType attribute) smiles_to_3d_structure() (in module schrodinger.adapter) smiles_to_fingerprint() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) smiles_to_fingerprints() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) SmilesCsvReader (class in schrodinger.structure) SmilesCsvWriter (class in schrodinger.structure) SmilesDocker (class in schrodinger.application.steps.docking) SmilesDocker.Settings (class in schrodinger.application.steps.docking) SmilesDockerSettings (class in schrodinger.application.steps.docking) SmilesErrorHandler (class in schrodinger.structutils.smilesfilter) SmilesGenerateError SmilesGenerator (class in schrodinger.structutils.smiles) SmilesNetworkNode (class in schrodinger.ui.qt.network_views) SmilesReader (class in schrodinger.structure) SmilesSignature (class in schrodinger.application.matsci.species) SmilesStructure (class in schrodinger.structure) SmilesToMolConverter (class in schrodinger.application.steps.converters) SmilesTransformPair (class in schrodinger.application.steps.enumerators) (class in schrodinger.application.transforms.enumerators) SmilesTransformPairer (class in schrodinger.application.steps.enumerators) SmilesTransformPairer.Settings (class in schrodinger.application.steps.enumerators) SmilesWriter (class in schrodinger.structure) SmiMergeHandler (class in schrodinger.rdkit.molio) smiReplaced (schrodinger.application.steps.enumerators.SmilesTransformPair attribute) smooth_grid_values() (in module schrodinger.application.bioluminate.patch_utils.msurfext) smoothColors() (schrodinger.surface.Surface method) smoothingChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) Sn2Failure snap_core (schrodinger.application.phase.packages.ligand_aligner.AlignMethod attribute) SnapcoreCoordinates (class in schrodinger.application.desmond.stage.jobs) SNAPSHOT_FRAMES (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute) SNAPSHOT_VIEWER (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportMode attribute) SnapshotPanel (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_panel) SNoCommaDoubleValidator (class in schrodinger.ui.qt.swidgets) SNoCommaIntValidator (class in schrodinger.ui.qt.swidgets) SNoCommaMinMaxMixin (class in schrodinger.ui.qt.swidgets) SNonEmptyStringValidator (class in schrodinger.ui.qt.swidgets) SNonNegativeIntValidator (class in schrodinger.ui.qt.swidgets) SNonNegativeRealValidator (class in schrodinger.ui.qt.swidgets) SNumberListValidator (class in schrodinger.ui.qt.swidgets) socket() (schrodinger.tasks.taskszmq.Context method) SocketAuthenticationException SODFT (schrodinger.application.jaguar.constants.CalcType attribute) softcore_enabled (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams attribute) sol_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_forward (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_forward_dg (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_end_time_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_ensemble (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_ff (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_rest_exchanges (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_result (schrodinger.application.desmond.fep_edge_data.FEPTorsions property) sol_salt_info (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_salt_molecules (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_sid_snapshot_times_ps (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_sim_time (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_start_time_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_temperature (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_timestep_interval (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_timestep_list (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_total_atoms (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_total_replicas (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_total_waters (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sol_user_restraint (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) solid (schrodinger.surface.Style attribute) (schrodinger.surface.Surface.Style attribute) SOLUBILITY (schrodinger.application.desmond.constants.FEP_TYPES attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) solubility_dg (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) SOLUBILITY_SOLVATION (schrodinger.application.desmond.constants.PhysicalLegTypes attribute) SolubilityFepAnalysis (class in schrodinger.application.desmond.stage.app.solubility) SolubilityFEPEdgeData (class in schrodinger.application.desmond.fep_edge_data) SolubilityFepLauncher (class in schrodinger.application.desmond.stage.app.solubility) SolubilityMdLauncher (class in schrodinger.application.desmond.stage.app.solubility) SolubilityMsjGenerator (class in schrodinger.application.desmond.msj_generator.fep.solubility) SolubilityReportMaker (class in schrodinger.application.desmond.fep_edge_report_maker) SolubilitySimLegParams (class in schrodinger.application.desmond.msj_generator.workflow_params) SolubilityWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) solute (schrodinger.application.desmond.struc.CompStruc attribute) solute_st (schrodinger.trajectory.prody.ensemble.Ensemble property) solution_phase() (in module schrodinger.application.jaguar.textparser) solvate_with_cosolvent() (in module schrodinger.application.desmond.mxmd.mxmd_system_builder) SolvatePocket (class in schrodinger.application.desmond.stage.deprecate) SolvateSlabBuilder (class in schrodinger.application.desmond.stage.app.matsci) SOLVATION (schrodinger.application.desmond.constants.FepLegTypes attribute) (schrodinger.application.desmond.constants.PhysicalLegTypes attribute) (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget attribute) solvation() (in module schrodinger.application.jaguar.textparser) solvation_charge (schrodinger.structure.StructureAtom property) solvation_fep_sim_time (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) solvation_job() (in module schrodinger.application.jaguar.textparser) solvation_only (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) SOLVATION_RADIUS_KEY (schrodinger.application.matsci.desmondutils.SystemBuilder attribute) SolvationInput (class in schrodinger.application.jaguar.solvation_input) SolvationMethod (class in schrodinger.application.jaguar.rotation_barriers_keywords) SolvationTab (class in schrodinger.application.jaguar.gui.tabs.solvation_tab) SolvationTabNoOptimized (class in schrodinger.application.jaguar.gui.tabs.solvation_tab) solve_network_exact_and_diversify() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) SOLVENT (class in schrodinger.application.jaguar.csrch_input_constants) Solvent (class in schrodinger.application.jaguar.gui.utils) (class in schrodinger.energy) SOLVENT (schrodinger.application.desmond.constants.FepLegTypes attribute) solvent (schrodinger.application.desmond.new_fep_edge_data.FepLegs attribute) SOLVENT (schrodinger.application.desmond.stage.prepare.structure.BuildGeometry attribute) (schrodinger.application.desmond.stage.utils.SystemBuilder attribute) solvent (schrodinger.application.desmond.struc.CompStruc attribute) SOLVENT (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) solvent_asl (schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams attribute) solvent_composition (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) solvent_dg (schrodinger.application.desmond.stage.app.absolute_binding.stage.AbsoluteBindingResult attribute) SOLVENT_EXPOSURE_TENDENCY (class in schrodinger.protein.residue) solvent_fullsystem_ct (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) SOLVENT_HOTREGION (schrodinger.application.desmond.constants.REST_PROPERTIES attribute) SOLVENT_MODELS (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) solvent_template_structure (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) SolventAccessibility (class in schrodinger.protein.predictors) solventChanged (schrodinger.application.jaguar.gui.solvent_selector.SolventSelectorFilterListToolButton attribute) (schrodinger.application.matsci.jagwidgets.CompactSolventSelector attribute) SolventDialog (class in schrodinger.application.matsci.jagwidgets) SolventInfo (class in schrodinger.application.matsci.packmol) solventKeywordsChanged() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) SolventListWidgetItem (class in schrodinger.application.jaguar.gui.solvent_selector) solventModelChanged() (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) (schrodinger.application.matsci.jagwidgets.EmbeddedSolventWidget method) SolventPkaTab (class in schrodinger.application.jaguar.gui.tabs.solvation_tab) SOLVENTS (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab attribute) SolventSelectorFilterListPopUp (class in schrodinger.application.jaguar.gui.solvent_selector) SolventSelectorFilterListToolButton (class in schrodinger.application.jaguar.gui.solvent_selector) solventsOnlyChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) SolventTab (class in schrodinger.application.jaguar.gui.tabs.solvation_tab) sort() (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart method) (schrodinger.application.glide.sort_utils.GlideSortUtility method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.structutils.sort.StructureFileSorter method) (schrodinger.ui.qt.table.StructureDataViewerModel method) SORT_ASC (schrodinger.ui.qt.swidgets.STableWidget attribute) sort_atoms() (in module schrodinger.application.desmond.automatic_analysis_generator) sort_by_centroid_distance() (in module schrodinger.application.jaguar.autots_rmsd) sort_file() (in module schrodinger.structutils.sort) sort_file_in_memory() (in module schrodinger.structutils.sort) sort_group_include_row() (in module schrodinger.application.matsci.maestrocmds) sort_index() (schrodinger.application.licensing.flexlm.Feature method) sort_key() (schrodinger.structutils.analyze.Ligand method) sort_order() (in module schrodinger.ui.qt.appframework2.appmethods) sort_output_file() (in module schrodinger.application.glide.utils) sort_residue_pair() (in module schrodinger.application.bioluminate.protein_interaction.utils) SORT_ROLE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) (schrodinger.ui.qt.table_helper.PythonSortProxyModel attribute) sort_role() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec method) sort_with_none() (in module schrodinger.utils.withnone) SortAction (class in schrodinger.application.glide.sort_parser_common) sortAlphabetically() (schrodinger.ui.qt.propertyselector.PropertySelector method) sortArray() (in module schrodinger.application.matsci.gsas.GSASIImath) sortBondableAtomsByGroups() (schrodinger.structutils.assignbondorders.AssignBondOrders method) sortBy() (schrodinger.ui.qt.tablewidget.Column method) sortByColumn() (schrodinger.ui.qt.table.StructureDataViewerModel method) sortByInitialOrder() (schrodinger.ui.qt.propertyselector.PropertySelector method) sortByProperties() (schrodinger.application.glide.glideanalysis.PoseLibrary method) sortByProperty() (schrodinger.protein.alignment.BaseAlignment method) sortByVerticalHeader() (schrodinger.ui.qt.table.StructureDataViewerModel method) SortCriterion (class in schrodinger.application.glide.sort_utils) sorted_func_groups (schrodinger.application.matsci.automated_cg_mapping.StructData property) sorted_hypo_structures() (in module schrodinger.application.phase.hypothesis) sorted_with_none() (in module schrodinger.utils.withnone) SortedMolWriter (class in schrodinger.rdkit.sorted_molwriter) sortEntries() (schrodinger.project.project.Project method) sortEntryCheck() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) sortEntryGroups() (schrodinger.project.project.Project method) sortFirstThreeOfGroup() (schrodinger.structutils.assignbondorders.AssignBondOrders method) sortHeaderKey() (schrodinger.ui.qt.table.StructureDataViewerModel method) sortHeaderKeyUnsorted() (schrodinger.ui.qt.table.StructureDataViewerModel method) sortHKLd() (in module schrodinger.application.matsci.gsas.GSASIIlattice) sortInterTitle() (schrodinger.application.glide.glideanalysis.PoseLibrary method) sortIntraTitle() (schrodinger.application.glide.glideanalysis.PoseLibrary method) sortKey() (schrodinger.ui.qt.table.StructureDataViewerModel method) sortKeyUnsorted() (schrodinger.ui.qt.table.StructureDataViewerModel method) sortMappedBeads() (schrodinger.application.matsci.automated_cg_mapping.AutomatedCGMapping static method) SortOrder (class in schrodinger.application.glide.sort_utils) sortPoses() (schrodinger.application.glide.glideanalysis.PoseLibrary method) sortResultByScore() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage static method) sortRows() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.swidgets.STableWidget method) sortStages() (schrodinger.application.matsci.permittivity.Config method) SortValidator (class in schrodinger.application.glide.sort_utils) sortWriteResults() (schrodinger.active_learning.mq_backend.Backend method) Source (class in schrodinger.application.matsci.reaction_workflow_utils) source() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) source_changed (schrodinger.ui.qt.input_selector.InputSelector attribute) source_color (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) source_index (schrodinger.structutils.rgroup_enumerate.RGroup attribute) source_lbl_text (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) source_lbl_textChanged (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) source_lbl_textReplaced (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) source_pdb (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) sourceChanged (schrodinger.ui.qt.structure_selector.StructureSelector attribute) SourceFormat (class in schrodinger.application.phase.packages.phase_screen_driver_utils) sources (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) sourcesChanged (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) sourcesReplaced (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) sourceType (schrodinger.application.licensing.licserver.client.ServerIdentifier attribute) sourceType() (schrodinger.ui.qt.input_selector.InputSelector method) sourceValue (schrodinger.application.licensing.licserver.client.LocalEntitlement attribute) (schrodinger.application.licensing.licserver.client.ServerIdentifier attribute) sp3AtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) SPACE_GROUP (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) space_group_full_name (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) SPACE_GROUP_ID (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) space_group_id (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) SPACE_GROUP_ID_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) SPACE_GROUP_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) SPACE_GROUP_SETTING (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) space_group_short_name (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) SpaceGroup (class in schrodinger.application.matsci.nano.space_groups) SpaceGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc) SpaceGroupNumber() (in module schrodinger.application.matsci.gsas.GSASIIspc) SpaceGroups (class in schrodinger.application.matsci.nano.space_groups) SPC (schrodinger.application.desmond.constants.WATER_MODELS attribute) SPCE (schrodinger.application.desmond.constants.WATER_MODELS attribute) SpcGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc) Spear (class in schrodinger.structutils.ringspear) spear_indexes (schrodinger.structutils.ringspear.Spear attribute) SpearRing (class in schrodinger.structutils.ringspear) spears (schrodinger.structutils.clash_resolution.ClashResolutionResult attribute) Spec (class in schrodinger.application.ligprep.ionizer) spec (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget property) SPEC_BUFFER (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) spec_description (schrodinger.job.launchapi.JobSpecificationKeyError attribute) (schrodinger.job.launchapi.RuntimeParametersKeyError attribute) (schrodinger.job.launchapi.SpecificationKeyError attribute) (schrodinger.job.launchapi.TaskSpecificationKeyError attribute) SpecialResidueTypes (class in schrodinger.application.bioluminate.antibody.annotate) SpecialResidueZone (class in schrodinger.application.bioluminate.antibody.annotate) specialStateTransition() (schrodinger.application.desmond.antlr3.dfa.DFA method) species (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) SPECIES (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) species_changed (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector attribute) (schrodinger.application.matsci.speciesgui.SpeciesSelector attribute) species_collection (schrodinger.application.matsci.speciesgui.SpeciesSelector property) species_collection_type (schrodinger.application.matsci.speciesgui.SpeciesSelector property) species_updated (schrodinger.application.matsci.speciesgui.SpeciesSelector attribute) speciesChanged() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) SpeciesCollection (class in schrodinger.application.matsci.species) SpeciesCollectionTypes (class in schrodinger.application.matsci.species) SpeciesCombo (class in schrodinger.application.matsci.clusterstructgui) SpeciesData (class in schrodinger.application.matsci.clusterstruct) (class in schrodinger.application.matsci.species) SpeciesSelector (class in schrodinger.application.matsci.speciesgui) speciesUpdated() (schrodinger.application.matsci.speciesgui.SpeciesSelector method) SPECIFIC_RESTART_LOCATOR_MAP (schrodinger.application.matsci.permittivity.WorkflowParser attribute) SpecificationKeyError specifyTaskDir() (schrodinger.tasks.tasks.AbstractTask method) specs (schrodinger.application.prime.wrapper.ConsensusConfig attribute) (schrodinger.application.prime.wrapper.PrimeConfig attribute) SpectatorMoleculeError SPECTRUM_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) spectrum_npoints (schrodinger.application.jaguar.nmr_utils.NMRData attribute) (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) SPECTRUM_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) spectrum_type (schrodinger.application.jaguar.nmr_utils.NMRData attribute) (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) SpectrumDataException SpectrumFile (class in schrodinger.application.matsci.spectra) speed_percentage (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings property) SpeedUpDelegate (class in schrodinger.ui.qt.table_speed_up) SpeedUpDelegateViewMixin (class in schrodinger.ui.qt.table_speed_up) spg2origins (in module schrodinger.application.matsci.gsas.GSASIIspc) spg_setting (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) spgbyNum (in module schrodinger.application.matsci.gsas.GSASIIspc) spglist (in module schrodinger.application.matsci.gsas.GSASIIspc) Sphere (class in schrodinger.application.matsci.shapes) sphere() (schrodinger.application.watermap.shapes.ShapeFactory method) SPHERE_COLOR (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) (schrodinger.application.phase.phase_markers.PhaseTolMarkers attribute) (schrodinger.application.phase.phase_markers.PhaseXvolMarkers attribute) SPHERE_OPACITY (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) (schrodinger.application.phase.phase_markers.PhaseTolMarkers attribute) (schrodinger.application.phase.phase_markers.PhaseXvolMarkers attribute) sphere_overlap_volume() (in module schrodinger.structutils.interactions.steric_clash) SPHERE_RADII (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) SPHERE_RESOLUTION (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) SphereCore (class in schrodinger.graphics3d.sphere) spherical_atomic_cluster() (in module schrodinger.comparison.neighbors) Spin (class in schrodinger.application.jaguar.simple_spec) SPIN_AUTOMATIC (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) SPIN_LSDA_ID (schrodinger.application.matsci.espresso.qeinput.SpinType attribute) SPIN_MULT (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) spin_mult (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) SPIN_MULT (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) spin_mult (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) spin_multiplicity() (in module schrodinger.application.matsci.fragments) SPIN_NON_LSDA_ID (schrodinger.application.matsci.espresso.qeinput.SpinType attribute) SPIN_RESTRICTED (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) spin_splitting_precision (schrodinger.application.jaguar.results.JaguarResults attribute) spin_splitting_score() (in module schrodinger.application.jaguar.textparser) SPIN_UNRESTRICTED (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) SPINBOX_ADJUST_THRESH (schrodinger.ui.qt.rama.Rama attribute) SPINBOX_LIMITS_ROLE (schrodinger.ui.qt.delegates.SpinBoxDelegate attribute) SpinBoxDelegate (class in schrodinger.ui.qt.delegates) SpinBoxDoubleSlider (class in schrodinger.ui.qt.swidgets) SpinExcitedStateController (class in schrodinger.application.jaguar.gui.theory_tab_widgets) Spinner (class in schrodinger.ui.qt.swidgets) SpinnerIcon (class in schrodinger.ui.qt.swidgets) SpinnerLabel (class in schrodinger.ui.qt.tasks.taskwidgets) SpinnerStartButton (class in schrodinger.ui.qt.tasks.taskwidgets) SpinSpinCoupling (class in schrodinger.application.jaguar.results) SpinSystem (class in schrodinger.application.jaguar.spin_simulator_v2) SpinTreatment (class in schrodinger.application.jaguar.gui.utils) spinTreatmentChanged (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget attribute) SpinTreatmentWidget (class in schrodinger.application.jaguar.gui.theory_tab_widgets) SpinType (class in schrodinger.application.matsci.espresso.qeinput) SPLAT (schrodinger.application.jaguar.output.JaguarOutput attribute) (schrodinger.application.xtb.output.XTBOutput attribute) SPLINE_PS (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) SPLINE_PS_KEY (schrodinger.application.matsci.espresso.qeinput.BasisType attribute) split_and_shuffle() (in module schrodinger.structutils.shuffle) split_by (schrodinger.application.jaguar.simple_spec.Peak attribute) split_by_hierarchy() (in module schrodinger.livedesign.biologics.sequence) split_ct() (in module schrodinger.application.desmond.remd) split_data_blocks() (in module schrodinger.livedesign.bbchem_endpoints) split_ext_pv() (in module schrodinger.utils.fileutils) split_file() (in module schrodinger.structutils.sort) split_file_round_robin() (in module schrodinger.utils.fileutils) split_fingerprints() (in module schrodinger.application.combinatorial_diversity.driver_utils) split_fragments() (in module schrodinger.livedesign.bbchem_endpoints) split_hits() (in module schrodinger.application.phase.packages.shape_diversity) split_input_and_run_subjobs() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) split_inputs() (in module schrodinger.application.phase.packages.mmp3d_driver_utils) split_into_spots() (in module schrodinger.application.desmond.mxmd.mxmd_cleanup) split_isotope (schrodinger.application.jaguar.simple_spec.Peak attribute) split_jag_ext() (in module schrodinger.application.jaguar.utils) split_lig() (in module schrodinger.active_learning.al_utils) split_list() (in module schrodinger.utils.scollections) split_numbers_by_region() (in module schrodinger.application.bioluminate.anarci.annotate) split_oned_data_file() (in module schrodinger.application.phase.packages.oned_task_utils) split_outfile() (in module schrodinger.application.mopac.results_main) split_peak() (schrodinger.application.jaguar.simple_spec.Peak method) split_populations() (in module schrodinger.application.bioluminate.peptide_sar.statistics) split_queries() (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) split_query() (in module schrodinger.application.bb_database.bb_task_utils) split_res (schrodinger.protein.residue.CombinedChainResidueWrapper property) split_route_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) split_sequence (schrodinger.protein.residue.CombinedChainResidueWrapper property) split_shadow_bond_tag() (in module schrodinger.application.matsci.coarsegrain) split_shape_data_file() (in module schrodinger.application.phase.packages.shape_screen_gpu_update) split_smi_line() (in module schrodinger.active_learning.al_utils) split_spin_state() (in module schrodinger.application.matsci.fragments) split_string() (in module schrodinger.application.phase.packages.phase_utils) split_structure_file() (in module schrodinger.application.phase.packages.oned_task_utils) split_structure_files() (in module schrodinger.application.jaguar.input) split_structures() (in module schrodinger.application.combinatorial_diversity.driver_utils) split_type_name() (in module schrodinger.application.matsci.cgforcefield) split_unique (schrodinger.application.matsci.species.SC_TYPE_DATA attribute) split_using_composition() (in module schrodinger.application.matsci.species) splitByComponentChanged() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) SplitColumns (class in schrodinger.application.bioluminate.antibody.search_results_table) splitComponents() (schrodinger.application.matsci.desmondutils.SystemBuilder method) (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) splitext() (in module schrodinger.utils.fileutils) splitFingerprints() (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method) splitGroupByArc() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) splitGroupByChecks() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) splitGroupByLine() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) splitGroupByRadius() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) spliting_bonds (schrodinger.application.jaguar.simple_spec.Peak attribute) splitInputfiles() (schrodinger.active_learning.al_driver.ActiveLearningJob method) splitIntoComponents() (schrodinger.application.matsci.rxn_channel.Reactants method) splitIntoLigands() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) splitJobOutputs() (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) splitNameAndType() (schrodinger.application.matsci.permittivity.Config method) SplitProxyModel (class in schrodinger.application.bioluminate.antibody.search_results_table) SplitPushButton (class in schrodinger.ui.qt.standard_widgets.buttons) splitSSsym() (in module schrodinger.application.matsci.gsas.GSASIIspc) SplitStyledButton (class in schrodinger.ui.qt.standard_widgets.buttons) SplitTable (class in schrodinger.application.bioluminate.antibody.search_results_table) SPLITTER (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep attribute) splitting_label (schrodinger.application.jaguar.simple_spec.Peak attribute) spmc() (schrodinger.application.macromodel.utils.ComUtil method) SPosIntListValidator (class in schrodinger.ui.qt.swidgets) Spot (class in schrodinger.application.desmond.mxmd.mxmd_cleanup) spring_layout() (in module schrodinger.ui.qt.network_visualizer) springLayout() (schrodinger.ui.qt.network_visualizer.Graph method) SPushButton (class in schrodinger.ui.qt.swidgets) SQID (schrodinger.application.matsci.kmc.Table attribute) sql_command() (in module schrodinger.application.matsci.kmc) SQL_ID (schrodinger.application.matsci.kmc.Table attribute) SQLCreationError SQLCursor (class in schrodinger.application.matsci.kmc) sqlite_path (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) sqlite_pathChanged (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) sqlite_pathReplaced (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) SQUARE (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) SQUARE_ANTIPRISMATIC (in module schrodinger.application.matsci.buildcomplex) SQUARE_ANTIPRISMATIC_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) SQUARE_PLANAR (in module schrodinger.application.matsci.buildcomplex) SQUARE_PLANAR_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) SQUARE_PYRAMIDAL (in module schrodinger.application.matsci.buildcomplex) SQUARE_PYRAMIDAL_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) squared_centroid_distance() (in module schrodinger.structutils.interactions.pi) SquarePlanarSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) SquareTensor (class in schrodinger.application.matsci.elasticity.tensors) SRadioButton (class in schrodinger.ui.qt.swidgets) SRadioButtonGroup (class in schrodinger.ui.qt.swidgets) SRadioButtonWithSubWidget (class in schrodinger.ui.qt.swidgets) SRealValidator (class in schrodinger.ui.qt.swidgets) SRegularExpressionValidator (class in schrodinger.ui.qt.swidgets) SRetainableMenu (class in schrodinger.ui.qt.swidgets) SRU (class in schrodinger.application.scaffold_enumeration.cxsmiles) SS (schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE attribute) SS_DNA (schrodinger.livedesign.entity_type.EntityClass attribute) ss_prediction (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) ss_prediction_psipred (schrodinger.protein.residue.Residue property) ss_prediction_sspro (schrodinger.protein.residue.Residue property) ss_predictionChanged (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) ss_predictionReplaced (schrodinger.protein.predictors.BetaproPredictor.Input attribute) (schrodinger.protein.predictors.SsAccDependentPredictors.Input attribute) SS_RNA (schrodinger.livedesign.entity_type.EntityClass attribute) SsAccDependentPredictors (class in schrodinger.protein.predictors) SsAccDependentPredictors.Input (class in schrodinger.protein.predictors) ssccb() (in module schrodinger.application.jaguar.textparser) ssccb_summary() (in module schrodinger.application.jaguar.textparser) SSChargeFlip() (in module schrodinger.application.matsci.gsas.GSASIImath) SSChoice() (in module schrodinger.application.matsci.gsas.GSASIIspc) sse_limits_lambda0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) sse_limits_lambda1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData property) SSGModCheck() (in module schrodinger.application.matsci.gsas.GSASIIspc) SSGPrint() (in module schrodinger.application.matsci.gsas.GSASIIspc) ssh_check() (in module schrodinger.job.host_check) SSLatt2text() (in module schrodinger.application.matsci.gsas.GSASIIspc) SSMT2text() (in module schrodinger.application.matsci.gsas.GSASIIspc) SSpaceGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc) SSpcGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc) SSpinBox (class in schrodinger.ui.qt.swidgets) SSplitter (class in schrodinger.ui.qt.swidgets) SsproPredictor (class in schrodinger.protein.predictors) SSVPE_PCM_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) st (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch attribute) (schrodinger.application.livedesign.export_models.GEExportItem attribute) (schrodinger.application.matsci.packmol.SolventInfo attribute) (schrodinger.application.matsci.packmol.SurfactantInfo attribute) (schrodinger.application.prime.wrapper.PrimeTemplate property) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.structutils.analyze.Ligand property) st0 (schrodinger.comparison.results.Result attribute) ST2_EXT (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) st_changed() (schrodinger.protein.nonstandard_residues.AminoAcid method) st_from_blob() (in module schrodinger.application.glide.http_client) st_from_mol() (in module schrodinger.application.pathfinder.multiroute) st_matches_criteria() (in module schrodinger.utils.ligfilter) st_matches_round_trip_hash() (in module schrodinger.application.livedesign.ld_utils) st_path_map (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) st_to_graph() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) st_to_rdmol_without_hydrogens() (in module schrodinger.ui.two_d_viewer) stability_sim_time (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) STableView (class in schrodinger.ui.qt.swidgets) STableWidget (class in schrodinger.ui.qt.swidgets) STableWidgetItem (class in schrodinger.ui.qt.swidgets) STabWidget (class in schrodinger.ui.qt.swidgets) STACK_DIRECTION (schrodinger.application.matsci.nano.sheet.HoneycombBilayers attribute) stackBilayers() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) StackSim() (in module schrodinger.application.matsci.gsas.GSASIIpwd) STACKTYPES (schrodinger.application.matsci.nano.constants.Constants attribute) Stage (class in schrodinger.pipeline.stage) stage (schrodinger.application.desmond.multisim.parser.Msj property) stage_cls (schrodinger.application.desmond.cmj.StageBase attribute) STAGE_DELETED (schrodinger.application.matsci.mswidgets.StageFrame attribute) stage_name (schrodinger.seam.runners.events.StageFailed attribute) (schrodinger.seam.runners.events.StageFinished attribute) (schrodinger.seam.runners.events.StageStarted attribute) stage_nameChanged (schrodinger.seam.runners.events.StageFailed attribute) (schrodinger.seam.runners.events.StageFinished attribute) (schrodinger.seam.runners.events.StageStarted attribute) stage_nameReplaced (schrodinger.seam.runners.events.StageFailed attribute) (schrodinger.seam.runners.events.StageFinished attribute) (schrodinger.seam.runners.events.StageStarted attribute) stage_obj (schrodinger.application.desmond.cmj.StageBase attribute) StageBase (class in schrodinger.application.desmond.cmj) StageControlButton (class in schrodinger.application.matsci.mswidgets) StageData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) StageFailed (class in schrodinger.seam.runners.events) StageFinished (class in schrodinger.seam.runners.events) StageFrame (class in schrodinger.application.matsci.mswidgets) StageInfo (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) StageInfoLine (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) StageJob (class in schrodinger.pipeline.pipeline) StageKeywords (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) stagePipelineFromSeamEvents() (schrodinger.seam.viz.render.PipelineRenderer class method) STAGES (schrodinger.application.matsci.desconfig.ConcatMSJStringer attribute) StageStarted (class in schrodinger.seam.runners.events) StageStatus (class in schrodinger.application.fragment_virtual_screening.frag_vs_utils) STANDARD (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants attribute) standard (schrodinger.protein.nonstandard_residues.AminoAcid property) Standard (schrodinger.protein.nonstandard_residues.StructureSource attribute) (schrodinger.ui.qt.appframework2.jobnames.JobnameType attribute) (schrodinger.ui.qt.standard_widgets.buttons.StyledButton.Style attribute) Standard3DExportSpec (class in schrodinger.application.livedesign.export_models) STANDARD_BACKGROUND (schrodinger.ui.qt.standard.colors.LightModeColors attribute) STANDARD_BORDER (schrodinger.ui.qt.standard.colors.LightModeColors attribute) STANDARD_BUTTON_BACKGROUND (schrodinger.ui.qt.standard.colors.LightModeColors attribute) STANDARD_BUTTON_BORDER_DISABLED (schrodinger.ui.qt.standard.colors.LightModeColors attribute) STANDARD_BUTTON_BORDER_ENABLED (schrodinger.ui.qt.standard.colors.LightModeColors attribute) STANDARD_BUTTON_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) STANDARD_COLUMNS (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) standard_nuclear_orientation() (in module schrodinger.structutils.standard_nuclear_orientation) STANDARD_PRESSED_BUTTON_BACKGROUND_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) STANDARD_SEARCH_ALONG (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) STANDARD_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) STANDARD_TIP (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants attribute) StandardAminoAcidMonomerItem (class in schrodinger.protein.helm.helm_renderer) StandardColumns (class in schrodinger.application.bioluminate.pose_filtering.hdx_io) Standardize (class in schrodinger.application.transforms.chem) standardize_args() (in module schrodinger.application.phase.packages.phase_database_arg_utils) Standardizer (class in schrodinger.application.steps.transformers) StandardizeSpcName() (in module schrodinger.application.matsci.gsas.GSASIIspc) StandardPanel (class in schrodinger.application.jaguar.gui.base_panel) StandardPanelNoInputTab (class in schrodinger.application.jaguar.gui.base_panel) StandardStatusMixin (class in schrodinger.application.jaguar.gui.base_panel) STAR_TOPOLOGY (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) START (schrodinger.application.bioluminate.pose_filtering.hdx_io.DynamXColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.HDExaminerColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.StandardColumns attribute) start (schrodinger.application.matsci.anharmonic.SeqData attribute) START (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) start (schrodinger.application.matsci.mswidgets.Stepper.StepperData attribute) (schrodinger.protein.annotation.AntibodyCDR attribute) (schrodinger.protein.annotation.Region attribute) (schrodinger.protein.helm.helm_renderer.HelmConnector attribute) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) START (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) (schrodinger.ui.qt.config_dialog.StartDialog attribute) start() (in module schrodinger.application.glide.http_server) (in module schrodinger.ui.qt.appframework2.appmethods) (in module schrodinger.ui.qt.appframework2.debugcore) (schrodinger.active_learning.mq_worker.LigandMLBackend method) (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) (schrodinger.application.desmond.feputils.LabelSpinner method) (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) (schrodinger.application.desmond.stage.workflow.Primer method) (schrodinger.application.glide.client_module.GlideClientModule method) (schrodinger.application.glide.http_client.AbstractGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) (schrodinger.application.jaguar.gui.base_panel.InputTabJobMixin method) (schrodinger.application.jaguar.gui.base_panel.NoInputTabJobMixin method) (schrodinger.application.jaguar.gui.base_panel.UseConsistentOrbitalsMixin method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.seam.viz.watcherd.Watcher method) (schrodinger.stepper.stepper.ElapsedFormatter method) (schrodinger.tasks.queue.TaskQueue method) (schrodinger.tasks.tasks.AbstractComboTask method) (schrodinger.tasks.tasks.AbstractTask method) start_application() (in module schrodinger.utils.qapplication) start_btn (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 property) start_file_debug() (in module schrodinger.ui.qt.appframework2.debug) start_geometry() (in module schrodinger.application.jaguar.textparser) start_gridgen (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) start_gridgenChanged (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) start_gridgenReplaced (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) start_gui_debug() (in module schrodinger.ui.qt.appframework2.debug) start_index (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering attribute) (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult attribute) START_IRR_KEY (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) start_job_manager() (in module schrodinger.application.matsci.jobdirdlg) start_ld_ping_task() (in module schrodinger.application.livedesign.ld_connection_checker) start_of_program() (in module schrodinger.application.jaguar.textparser) start_progress() (in module schrodinger.application.bioluminate.pml_menus) start_residue (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) start_simple_http_server() (schrodinger.seam.viz.watcher.WatcherWebServer static method) start_stdout_debug() (in module schrodinger.ui.qt.appframework2.debug) start_str() (schrodinger.application.licensing.flexlm.Feature method) START_TAG (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser.HTMLType attribute) start_task() (in module schrodinger.tasks.gui) start_time (schrodinger.seam.viz.inspect.PipelineDisplayInfo attribute) START_VAL (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) start_wrapper_timeout (schrodinger.ui.qt.appframework.AppFramework attribute) startAnimation() (schrodinger.ui.qt.swidgets.LargeSpinner method) (schrodinger.ui.qt.swidgets.Spinner method) startBackend() (schrodinger.active_learning.mq_worker.Worker method) StartButton (class in schrodinger.ui.qt.tasks.taskwidgets) startChanged() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) startCommand() (schrodinger.application.desmond.gui.GuiApp method) startCompletion() (schrodinger.application.livedesign.panel_components.InitialSuggestionLineEdit method) startDate (schrodinger.application.licensing.licserver.client.LocalEntitlement attribute) startDebug() (schrodinger.ui.qt.appframework2.af2.JobApp method) StartDialog (class in schrodinger.ui.qt.config_dialog) StartDialogParams (class in schrodinger.ui.qt.config_dialog) STARTED (schrodinger.application.fragment_virtual_screening.frag_vs_utils.StageStatus attribute) (schrodinger.job.queue.PrintableStatus attribute) startedEditingSMARTS() (schrodinger.ui.qt.swidgets.SMARTSEdit method) Starter (class in schrodinger.application.desmond.starter.starter) startFilter() (schrodinger.ui.qt.swidgets.SFilteredListWidget method) starting_conformation (schrodinger.application.desmond.fep_edge_data.FEPTorsions property) STARTINGPOT_KEY (schrodinger.application.matsci.espresso.qeinput.ElectronControlType attribute) STARTINGWFC_KEY (schrodinger.application.matsci.espresso.qeinput.ElectronControlType attribute) startJob() (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) startMonitoring() (schrodinger.ui.qt.appframework2.maestro_callback.CallbackMonitor method) startPicking() (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner method) (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner method) startPressed() (schrodinger.ui.qt.config_dialog.ConfigDialog method) startRangeModified() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) startReadyStages() (schrodinger.pipeline.pipeline.Pipeline method) startRequested (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog attribute) (schrodinger.ui.qt.tasks.taskwidgets.AbstractTaskBar attribute) startSpinner() (schrodinger.ui.qt.swidgets.SpinnerIcon method) startStreaming() (schrodinger.application.job_monitor.job_monitor_file_browser.SubprocessStdOutStreamer method) startTask() (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsDialog method) StartTime (schrodinger.job.jobcontrol.Job property) Startup (class in schrodinger.application.desmond.multisimstartup) startUp() (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) startup() (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) Startup.Help (class in schrodinger.application.desmond.multisimstartup) startValidate() (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) stat_info (class in schrodinger.application.licensing.licadmin) STATask (class in schrodinger.protein.tasks.sta) STATask.Input (class in schrodinger.protein.tasks.sta) state (schrodinger.job.queue.BaseJob property) state() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) STATE_PENALTY (schrodinger.application.desmond.constants.CorrectionTerm attribute) StateColors (class in schrodinger.ui.qt.standard.design_tokens) StatefulBeamPipelineMachine (class in schrodinger.seam.testing.stateful) StatefulBeamPipelineMachineTestCase() (in module schrodinger.seam.testing.stateful) statementExecuted (schrodinger.ui.qt.appframework2.debugwidgets.ExecWidget attribute) statevec() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) STATIC (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) (schrodinger.tasks.tasks.ResourceType attribute) static() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) static_acceptor_interactions() (schrodinger.protein.assignment.HistidinepKaPredictor method) static_at_index_str (schrodinger.application.jaguar.autots_constants.IndexString attribute) static_donor_interactions() (schrodinger.protein.assignment.HistidinepKaPredictor method) STATIC_DONOR_PKA_SHIFT (schrodinger.protein.assignment.HistidinepKaPredictor attribute) static_mol_index_str (schrodinger.application.jaguar.autots_constants.IndexString attribute) STATIC_PERMITTIVITY (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) StaticPermittivity (class in schrodinger.application.matsci.permittivity) StaticResourceError STATISTICS_CSV_EX (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) STATISTICS_FILE_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) Status (class in schrodinger.application.licensing.licadmin) (class in schrodinger.tasks.ldtasks) (class in schrodinger.tasks.tasks) STATUS (schrodinger.application.desmond.kinetics.utils.MtdInfo attribute) Status (schrodinger.application.glide.http_client.SubprocessJobAdapter property) status (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) Status (schrodinger.job.jobcontrol.Job property) status (schrodinger.seam.viz.inspect.PipelineDisplayInfo attribute) (schrodinger.tasks.ldtasks.LDOutputRow attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractTask attribute) status() (in module schrodinger.application.xtb.textparser) (schrodinger.ui.qt.appframework2.af2.StatusBar method) (schrodinger.ui.two_d_viewer.TwoDViewer method) status_message (schrodinger.tasks.ldtasks.LDOutputRow attribute) status_messageChanged (schrodinger.tasks.ldtasks.LDOutputRow attribute) status_messageReplaced (schrodinger.tasks.ldtasks.LDOutputRow attribute) status_shrunk (schrodinger.ui.qt.appframework2.af2.StatusBar attribute) StatusBar (class in schrodinger.ui.qt.appframework2.af2) (class in schrodinger.ui.qt.standard_widgets.statusbar) StatusBarDialog (class in schrodinger.application.livedesign.panel_components) StatusBarMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) statusChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDOutputRow attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) StatusChangeReason (schrodinger.job.jobcontrol.Job property) StatusIcon (class in schrodinger.application.job_monitor.job_monitor_widgets) StatusLabel (class in schrodinger.ui.qt.tasks.taskwidgets) statusOk (schrodinger.application.mopac.results_main.MopacResultsMain property) statusReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.desmond.feputils.ProteinReliabilityTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.ldtasks.LDOutputRow attribute) (schrodinger.tasks.ldtasks.LDTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) StatusTime (schrodinger.job.jobcontrol.Job property) staying_atom (schrodinger.structutils.rgroup_enumerate.RGroup attribute) stChanged (schrodinger.application.livedesign.export_models.GEExportItem attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) STD (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute) (schrodinger.application.jaguar.utils.LewisModes attribute) std_dev (schrodinger.application.matsci.equilibrium_md.MsdTrajBase.DIFFUSIVITY attribute) STD_DEV (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) std_dev (schrodinger.application.phase.packages.oned_task_utils.BasicStatsAccumulator property) STDEV (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) STDEV_ANG2 (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) StdInJob (class in schrodinger.application.matsci.packmol) StdMenuItem (class in schrodinger.ui.qt.swidgets) stdNeighborCount() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) stdNeighborIon() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) StdoutDebugViewer (class in schrodinger.ui.qt.appframework2.debugcore) Step (class in schrodinger.application.matsci.jaguarworkflows) (class in schrodinger.application.matsci.permittivity) step (schrodinger.application.jaguar.utils.ScanCoord attribute) (schrodinger.application.matsci.anharmonic.SeqData attribute) STEP (schrodinger.application.matsci.kmc.FramesTable attribute) step (schrodinger.application.matsci.reaction_workflow_gui_utils.SequenceData attribute) step() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) STEP_NAME (schrodinger.application.matsci.jwsteps.BaseRelaxationStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.CompressiveRelaxationStep attribute) (schrodinger.application.matsci.jwsteps.CustomCmsStep attribute) (schrodinger.application.matsci.jwsteps.CustomCmsToMaeStep attribute) (schrodinger.application.matsci.jwsteps.CustomMaeStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.FreeVolumeStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.MatSciMDRelaxationStep attribute) (schrodinger.application.matsci.jwsteps.MDCustomMSJStep attribute) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation1Step attribute) (schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation2Step attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.SingleBrownieStep attribute) (schrodinger.application.matsci.jwsteps.SingleMDStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) (schrodinger.application.matsci.jwsteps.VoidStep attribute) step_size (schrodinger.application.jaguar.scan.Scan property) (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) StepBase (class in schrodinger.application.matsci.permittivity) stepBy() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) stepChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) StepContract (class in schrodinger.application.steps.test) STEPDENSEPOINTS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) stepEnabled() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) StepJobTask (class in schrodinger.stepper.stepper) Stepper (class in schrodinger.application.matsci.mswidgets) Stepper.StepperData (class in schrodinger.application.matsci.mswidgets) StepperApplication (class in schrodinger.stepper.app) StepperFile (class in schrodinger.stepper.stepper) StepperFolder (class in schrodinger.stepper.stepper) STEPS (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) steps (schrodinger.application.jaguar.scan.Scan property) STEPS (schrodinger.application.steps.basesteps.Workflow attribute) steps() (schrodinger.application.pathfinder.route.RouteNode method) StepsError, [1] stepsInWriteOrder() (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) stepsize (schrodinger.application.matsci.mswidgets.Stepper.StepperData attribute) StepSubprocessTask (class in schrodinger.stepper.stepper) StepTaskInput (class in schrodinger.stepper.stepper) StepTaskMixin (class in schrodinger.stepper.stepper) StepTaskOutput (class in schrodinger.stepper.stepper) StereoChemistry (class in schrodinger.adapter) StereoChemistryRemover (class in schrodinger.application.steps.transformers) stereomethods (schrodinger.utils.pymol.Mapping attribute) stereospecific (schrodinger.rdkit.substructure.QueryOptions attribute) STERIC_GROUP (class in schrodinger.protein.residue) steric_group (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) stockholder_charges() (in module schrodinger.application.jaguar.textparser) stoichiometry() (in module schrodinger.application.jaguar.textparser) SToolButton (class in schrodinger.ui.qt.swidgets) Stop (class in schrodinger.application.desmond.stage.workflow) STOP (schrodinger.application.job_monitor.job_monitor_models.RequestedStatus attribute) stop() (in module schrodinger.application.glide.http_server) (in module schrodinger.ui.qt.appframework2.debugcore) (schrodinger.application.desmond.feputils.BaseSpinnerWidget method) (schrodinger.application.desmond.feputils.LabelSpinner method) (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) (schrodinger.application.desmond.queue.Queue method) (schrodinger.application.glide.client_module.GlideClientModule method) (schrodinger.application.glide.http_client.AbstractGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) (schrodinger.job.jobcontrol.Job method) stop_debug() (in module schrodinger.ui.qt.appframework2.debug) stop_player_and_exit_snapshot_mode() (in module schrodinger.trajectory.trajectoryviewer) stop_rocking() (in module schrodinger.application.bioluminate.pml_menus) STOP_RXN_FAIL (schrodinger.application.jaguar.constants.FatalErrors attribute) StopAndRestartRequest stopAnimation() (schrodinger.ui.qt.swidgets.LargeSpinner method) (schrodinger.ui.qt.swidgets.Spinner method) stopBackend() (schrodinger.active_learning.mq_worker.Worker method) stopChecking() (schrodinger.application.glide.http_client.NonBlockingBackendChecker method) stopMonitoring() (schrodinger.ui.qt.appframework2.maestro_callback.CallbackMonitor method) STOPPED (schrodinger.job.jobcontrol.DisplayStatus attribute) stopPicking() (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner method) (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner method) stopPickingConnection (schrodinger.ui.qt.network_views.NetworkViewer attribute) stopping_optimization() (in module schrodinger.application.jaguar.textparser) StopRequest stopRequested (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget attribute) stopSelected() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) stopSignalTracing() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) stopSpinner() (schrodinger.ui.qt.swidgets.SpinnerIcon method) stopStreaming() (schrodinger.application.job_monitor.job_monitor_file_browser.SubprocessStdOutStreamer method) StopTime (schrodinger.job.jobcontrol.Job property) store_chorus_box_props() (in module schrodinger.application.matsci.desmondutils) (in module schrodinger.application.matsci.nano.xtal) store_mae_to_db() (in module schrodinger.active_learning.al_utils) store_prefs() (schrodinger.application.pymol.pymol4maestro.panel method) store_schrodinger_job_props() (in module schrodinger.application.matsci.kmc) StoreDictKeyPair (class in schrodinger.application.matsci.parserutils) storeFilenames() (schrodinger.application.matsci.jaguarworkflows.Step method) storeIfLowestEnergy() (schrodinger.application.matsci.fragments.BondEnergies method) STR (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute) str() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) str2hexid() (in module schrodinger.application.desmond.util) str_compare_error() (in module schrodinger.application.jaguar.jaguar_diff) STR_PROP_PREFIX (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) str_remove_suffix() (in module schrodinger.application.livedesign.io_utils) Strain (class in schrodinger.application.matsci.elasticity.strain) strain (schrodinger.application.desmond.fep_edge_data.FEPTorsions property) STRAIN_DEFO_KEY (schrodinger.application.matsci.espresso.qeinput.ElasticType attribute) strain_rescore_args (schrodinger.application.livedesign.tasks.StrainRescoreTask.Input attribute) strain_rescore_argsChanged (schrodinger.application.livedesign.tasks.StrainRescoreTask.Input attribute) strain_rescore_argsReplaced (schrodinger.application.livedesign.tasks.StrainRescoreTask.Input attribute) StrainRescoreTask (class in schrodinger.application.livedesign.tasks) StrainRescoreTask.Input (class in schrodinger.application.livedesign.tasks) StrainRescoreTask.JobConfig (class in schrodinger.application.livedesign.tasks) StrainRescoreTask.Output (class in schrodinger.application.livedesign.tasks) STRAND (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) STRAND_COLOR (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) StrandBreaking (schrodinger.protein.residue.BETA_STRAND_PROPENSITY attribute) STRANDED (schrodinger.application.desmond.cmj.JobStatus attribute) StrandForming (schrodinger.protein.residue.BETA_STRAND_PROPENSITY attribute) stReader() (schrodinger.application.glide.client_module.GlideClientModuleAdapter method) streamingDone (schrodinger.application.job_monitor.job_monitor_file_browser.SubprocessStdOutStreamer attribute) StrEnum (class in schrodinger) stReplaced (schrodinger.application.livedesign.export_models.GEExportItem attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) Stress (class in schrodinger.application.matsci.elasticity.stress) StressStrainStep (class in schrodinger.application.matsci.jwsteps) STRETCH_FBHW (schrodinger.application.desmond.constants.RestrainTypes attribute) stretch_index() (schrodinger.application.jaguar.hess_guess.LindhConstants static method) (schrodinger.application.jaguar.hess_guess.SchlegelConstants static method) STRICT (schrodinger.utils.cmdline.Options attribute) String (class in schrodinger.application.desmond.enhsamp) STRING (schrodinger.application.desmond.cmj.JobStatus attribute) (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.desmond.systype.TyperBase attribute) (schrodinger.application.desmond.systype.WatermapTyper attribute) string() (schrodinger.application.licensing.flexlm.LicenseLine method) (schrodinger.application.licensing.flexlm.Vendor method) (schrodinger.application.matsci.cctbx.rot_mx.parse_string method) string2measurement() (in module schrodinger.application.desmond.measurement) string_to_value() (in module schrodinger.application.matsci.jobutils) StringCleaner (class in schrodinger.application.matsci.jobutils) StringColumn (class in schrodinger.tasks.ldtasks) StringCriterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) StringDatabaseCriterion (class in schrodinger.application.bioluminate.propfilter) STRINGED_RESPONSES (schrodinger.ui.qt.messagebox.MessageBox attribute) STRINGER_CLASS (schrodinger.application.matsci.jwsteps.SingleBrownieStep attribute) (schrodinger.application.matsci.jwsteps.SingleMDStep attribute) stringList() (schrodinger.ui.qt.recent_completer.BrowseAndCreateStringModel method) (schrodinger.ui.qt.recent_completer.BrowseStringModel method) StringListModelInterface (class in schrodinger.ui.qt.recent_completer) StringOpsProd() (in module schrodinger.application.matsci.gsas.GSASIIspc) StringParam (class in schrodinger.models.parameters) StringSearchFilterProxyModel (class in schrodinger.application.livedesign.panel_components) StringStream (in module schrodinger.application.desmond.antlr3.streams) STRIP_AND_GROUPS_ON_SINGLE_ATOM (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) strip_capping_groups() (in module schrodinger.protein.nonstandard_residues) strip_extension() (in module schrodinger.utils.fileutils) strip_gpu_from_localhost() (in module schrodinger.tasks.hosts) strip_lines() (in module schrodinger.application.jaguar.check_headers) strip_r() (in module schrodinger.application.canvas.utils) STRIP_SALTS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) strip_salts() (in module schrodinger.livedesign.preprocessor) strip_stereo_and() (in module schrodinger.livedesign.preprocessor) stripBrackets() (schrodinger.application.dendrogram.core_class.Utilities static method) stripSideStructs() (schrodinger.application.matsci.amorphous.Monomer method) strongly_conserved (schrodinger.protein.annotation.Consensus attribute) Struc (class in schrodinger.application.desmond.fep_struc) struc (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTupleMacroPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) (schrodinger.ui.qt.ligand_list.Ligand property) struc_iter() (in module schrodinger.application.desmond.struc) struc_merge() (in module schrodinger.application.desmond.struc) strucComboSelectionChanged() (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) strucSourceChanged (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) struct (schrodinger.application.matsci.clusterstruct.ComInfo attribute) (schrodinger.application.prepwizard2.tasks.StructureInput attribute) struct2spglib() (in module schrodinger.application.matsci.espresso.utils) struct_file (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput attribute) struct_file() (schrodinger.application.desmond.cmj.JobOutput method) struct_fileChanged (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput attribute) struct_fileReplaced (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput attribute) struct_has_ffio_ct_type() (in module schrodinger.application.matsci.desmondutils) struct_idx (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) struct_idxChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) struct_idxReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) struct_prop (schrodinger.application.matsci.reaction_workflow_utils.JaguarKeyStructPropData attribute) StructAlign (class in schrodinger.structutils.structalign) StructAlignResult (class in schrodinger.protein.tasks.structure_alignment) structChanged (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) (schrodinger.application.prepwizard2.tasks.StructureInput attribute) structCount() (schrodinger.ui.qt.table.ViewerModel method) StructData (class in schrodinger.application.matsci.automated_cg_mapping) structFile() (schrodinger.ui.qt.input_selector.InputSelector method) structFiles() (schrodinger.ui.qt.input_selector.InputSelector method) StructInfo (class in schrodinger.application.report2d) structReplaced (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) (schrodinger.application.prepwizard2.tasks.StructureInput attribute) structs (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowOutput attribute) structsChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowOutput attribute) StructSelectionModel (class in schrodinger.application.livedesign.panel_components) structsReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowOutput attribute) structToOriginByFrag() (schrodinger.application.matsci.amorphous.PolymerFragments method) StructuralInteractionFingerprintGenerator (class in schrodinger.structutils.interactionfp) structure adjustment creation i/o measurement minimization properties substructure searching Structure (class in schrodinger.structure) structure (schrodinger.application.jaguar.hess_guess.CoordinateManager property) (schrodinger.application.livedesign.export_models.MatchCompoundsBy attribute) STRUCTURE (schrodinger.application.matsci.packmol.PackmolKw attribute) structure (schrodinger.application.mopac.results_main.MopacResultsMain property) (schrodinger.project.project.ProjectRow property) Structure (schrodinger.protein.properties.PropertySource attribute) (schrodinger.protein.properties.SequenceProperty attribute) structure (schrodinger.structure._AtomCollection property) (schrodinger.structure.StructureAtom property) structure_chain (schrodinger.protein.residue.Residue property) structure_changed (schrodinger.application.matsci.mswidgets.StructureLoader attribute) structure_evaluator() (in module schrodinger.application.matsci.genetic_optimization) structure_file (schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams attribute) STRUCTURE_FILE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) structure_file_reader() (in module schrodinger.application.hitexpander) STRUCTURE_FILTERS (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) structure_fpreader() (in module schrodinger.application.hitexpander) structure_idx (schrodinger.application.matsci.reaction_workflow_utils.Site attribute) structure_index_map (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) structure_infos (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Output attribute) structure_infosChanged (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Output attribute) structure_infosReplaced (schrodinger.application.livedesign.ld_import_utils.StructureInfoTask.Output attribute) structure_is_open_shell() (in module schrodinger.application.matsci.genetic_optimization) structure_item (class in schrodinger.ui.qt.structure2d) STRUCTURE_PATH (schrodinger.application.matsci.kmc.SchrodingerTable attribute) structure_reader() (in module schrodinger.application.matsci.msutils) structure_reader_to_3d() (in module schrodinger.application.matsci.msutils) structure_scene (class in schrodinger.ui.qt.structure2d) structure_sequences (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer property) structure_title (schrodinger.application.jaguar.nmr_utils.NMRData attribute) structure_to_mol() (in module schrodinger.application.steps.utils) structure_to_rdkit_smiles() (in module schrodinger.analysis.transformations) structure_tuple() (in module schrodinger.ui.qt.delegates) structure_view (class in schrodinger.ui.qt.structure2d) StructureAlchemist (class in schrodinger.application.matsci.enumeration) StructureAligner (class in schrodinger.protein.align) StructureAnalyzer (class in schrodinger.application.matsci.automated_cg_mapping) StructureAtom (class in schrodinger.structure) StructureBond (class in schrodinger.structure) structureCbToggled() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) structureChanged (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant attribute) (schrodinger.protein.sequence.AbstractSequence attribute) structureChanged() (schrodinger.application.jaguar.gui.basis_selector.BasisSelector method) StructureCoder (class in schrodinger.seam.coders) StructureColumn (class in schrodinger.tasks.ldtasks) StructureCount (schrodinger.infra.structure.FileSplitStrategy attribute) StructureDataViewerDelegate (class in schrodinger.ui.qt.table) StructureDataViewerModel (class in schrodinger.ui.qt.table) StructureDelegate (class in schrodinger.ui.qt.delegates) StructureDescriptorsTask (class in schrodinger.protein.tasks.descriptors) StructureDescriptorsTask.Input (class in schrodinger.protein.tasks.descriptors) StructureDescriptorsTask.Output (class in schrodinger.protein.tasks.descriptors) StructuredLiquidInputFile (class in schrodinger.application.matsci.packmol) structuredResidueCount() (schrodinger.protein.sequence.AbstractSequence method) StructuredResidueError StructureEvaluator (class in schrodinger.application.matsci.genetic_optimization) StructureFactorStep (class in schrodinger.application.matsci.jwsteps) StructureFileSorter (class in schrodinger.structutils.sort) StructureFrame (class in schrodinger.application.matsci.reordergui) StructureGenome (class in schrodinger.application.matsci.genetic_optimization) StructureInfoTask (class in schrodinger.application.livedesign.ld_import_utils) StructureInfoTask.Input (class in schrodinger.application.livedesign.ld_import_utils) StructureInfoTask.Output (class in schrodinger.application.livedesign.ld_import_utils) StructureInput (class in schrodinger.application.prepwizard2.tasks) StructureLabel (class in schrodinger.application.matsci.builderwidgets) StructureLauncher (class in schrodinger.application.mopac.structure_launchers) StructureLauncherError StructurelessGapAligner (class in schrodinger.protein.align) StructureListWidget (class in schrodinger.application.matsci.reordergui) StructureLoadButton (class in schrodinger.application.matsci.appbase) (class in schrodinger.ui.qt.structure_selector) StructureLoader (class in schrodinger.application.matsci.mswidgets) StructureMergeHandler (class in schrodinger.rdkit.molio) StructureOutputFile (schrodinger.job.jobcontrol.Job property) StructureParam (class in schrodinger.models.parameters) StructurePic (class in schrodinger.application.matsci.reordergui) StructurePicture (class in schrodinger.ui.qt.structure2d) StructureProperty (schrodinger.protein.properties.PropertyType attribute) (schrodinger.protein.properties.SequenceProperty attribute) StructurePropertyFilter (class in schrodinger.application.transforms.filters) StructurePropertyInput (class in schrodinger.application.phase.shape_screen_reporter.tasks) StructurePropertyTask (class in schrodinger.application.phase.shape_screen_reporter.tasks) StructurePropertyTask.Output (class in schrodinger.application.phase.shape_screen_reporter.tasks) StructureReader (class in schrodinger.structure) StructureReaderAdapter (class in schrodinger.rdkit.molio) StructureReaderDelegate (class in schrodinger.ui.qt.structtable) Structures (class in schrodinger.pipeline.pipeio) structures (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property) structures() (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.structure_selector.StructureSelector method) structures_for_2d_export (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) structures_for_2d_exportChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) structures_for_2d_exportReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) structures_missing (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) structures_missingChanged (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) structures_missingReplaced (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) StructureSelector (class in schrodinger.ui.qt.structure_selector) StructureSelectorMaestroSync (class in schrodinger.ui.qt.structure_selector) StructureSelectorModel (class in schrodinger.ui.qt.structure_selector) StructureSelectorWithImportButton (class in schrodinger.ui.qt.structure_selector) StructureSequence (class in schrodinger.protein.sequence) StructureSerializer (class in schrodinger.models.jsonable) StructureSource (class in schrodinger.protein.nonstandard_residues) StructureStageBase (class in schrodinger.application.desmond.cmj) StructureToMolConverter (class in schrodinger.application.steps.converters) StructureToolTip (class in schrodinger.ui.qt.structure2d) StructureTooltipMixin (class in schrodinger.ui.qt.matplot_widget) StructureType (class in schrodinger.application.glide.sort_utils) (class in schrodinger.application.matsci.espresso.qeinput) structureUpdated() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) StructureView (class in schrodinger.application.matsci.reordergui) StructureViewerDelegate (class in schrodinger.ui.qt.structtable) StructureWriter (class in schrodinger.structure) sts (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) stsChanged (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) stsReplaced (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) stub_license() (schrodinger.application.licensing.licadmin.LicenseResource method) STwoButtonBox (class in schrodinger.ui.qt.swidgets) Style (class in schrodinger.surface) style (schrodinger.structure.StructureAtom property) (schrodinger.structure.StructureBond property) (schrodinger.surface.Surface property) style() (schrodinger.seam.viz.render.ColorByLicenseStyler method) (schrodinger.seam.viz.render.ColorByStageStatusStyler method) (schrodinger.seam.viz.render.ColorByStatusStyler method) (schrodinger.seam.viz.render.ColorByTransformCPUTimeStyler method) (schrodinger.seam.viz.render.PipelineRenderer method) (schrodinger.seam.viz.render.Styler method) STYLE_NAMEMAP (schrodinger.application.desmond.gui.EnsembleTab attribute) STYLE_SHEET (schrodinger.ui.qt.swidgets.ActionPushButton attribute) StyledAcceptsFocusPushButton (class in schrodinger.ui.qt.tasks.taskbarwidgets) StyledButton (class in schrodinger.ui.qt.standard_widgets.buttons) StyledButton.Style (class in schrodinger.ui.qt.standard_widgets.buttons) StyleMixin (class in schrodinger.ui.qt.swidgets) Styler (class in schrodinger.seam.viz.render) STYLESHEET (schrodinger.ui.qt.standard_widgets.labels.InfoTextLabel attribute) SUB_BUTTON_STYLESHEET (schrodinger.ui.qt.standard_widgets.buttons.SplitPushButton attribute) sub_charge (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_forward (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_end_time_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_ensemble (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_ff (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_formula() (in module schrodinger.application.matsci.gutils) sub_interactions() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) sub_job_ids (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) sub_job_idsChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) sub_job_idsReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) sub_log_file (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) sub_log_fileChanged (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) sub_log_fileReplaced (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) sub_median_delta_g (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_mol_number (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) SUB_OPTIONS (schrodinger.application.matsci.genetic_optimization.Property attribute) sub_rest_exchanges (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_script() (in module schrodinger.application.matsci.reportutils) sub_sid_molsa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) sub_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_sid_psa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) sub_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) sub_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) sub_sid_sasa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method) sub_sid_snapshot_times_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_sim_time (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_st (schrodinger.application.matsci.species.SUB_STRUCT_INFO attribute) sub_start_time_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) SUB_STRUCT_INFO (class in schrodinger.application.matsci.species) SUB_TAB_NAME (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) sub_temperature (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) SUB_TEXT() (in module schrodinger.ui.qt.swidgets) sub_total_atoms (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_total_replicas (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) sub_total_waters (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property) subControlRect() (schrodinger.ui.qt.multi_combo_box.MacMultiComboBoxStyle method) SubdirectoryStepMixin (class in schrodinger.application.matsci.jwsteps) subdirs (schrodinger.application.matsci.jwsteps.ParentPathInfo attribute) subhost (schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams attribute) (schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams attribute) SUBHOST (schrodinger.utils.cmdline.Options attribute) SUBJOB_RESOURCE (schrodinger.application.matsci.jwsteps.BaseDesmondStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) SubJobBar (class in schrodinger.application.job_monitor.job_monitor_widgets) SubjobInfo (in module schrodinger.application.matsci.jobutils) subjobs (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) SUBJOBS (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) SubJobs (schrodinger.job.jobcontrol.Job property) subjobsChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) subjobsReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) SubJobTableWidget (class in schrodinger.application.job_monitor.job_monitor_table) SubjobType (class in schrodinger.application.phase.packages.mmp3d_driver_utils) sublatticePackingFraction() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) SUBLIMATION (schrodinger.application.desmond.constants.FepLegTypes attribute) sublimation_fep_sim_time (schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams attribute) submit_jobdj() (in module schrodinger.active_learning.mq_worker) submit_jobs() (schrodinger.application.desmond.cmj.JobManager method) SubprocessCmdTask (class in schrodinger.tasks.tasks) SubprocessJob (class in schrodinger.job.queue) SubprocessJobAdapter (class in schrodinger.application.glide.http_client) SubprocessMixin (class in schrodinger.tasks.tasks) SubprocessStdOutStreamer (class in schrodinger.application.job_monitor.job_monitor_file_browser) subscript (schrodinger.application.scaffold_enumeration.cxsmiles.SRU attribute) subscript_cg_formula() (in module schrodinger.application.matsci.gutils) subscript_chemical_formula() (in module schrodinger.application.matsci.gutils) subscript_digits() (in module schrodinger.application.matsci.typography) SubscriptableNameSpace (class in schrodinger.application.matsci.parserutils) SubSetStage (class in schrodinger.pipeline.stages.filtering) SubstCoreDatabase (class in schrodinger.application.combiglide.corehop) Substitute (class in schrodinger.application.transforms.enumerators) substitute() (in module schrodinger.application.matsci.reaction_workflow_utils) SubstrateRestraintGroupBox (class in schrodinger.application.matsci.deswidgets) substring() (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) substructure_fingerprint() (in module schrodinger.livedesign.search) substructure_matches() (in module schrodinger.rdkit.substructure) SUBSTRUCTURE_SEARCH (schrodinger.livedesign.search.FingerprintUse attribute) SubstructureContextSubMenu (class in schrodinger.application.bioluminate.pml_menus) SubstructureSubstitute (class in schrodinger.application.transforms.enumerators) SubstructureType (class in schrodinger.application.bioluminate.pose_filtering.hdx_io) subTabChanged (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) SubTabMixin (class in schrodinger.application.jaguar.gui.base_panel) SubTabModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets) SubTabProxyModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets) SubTabRow (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets) subTabsVisible() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) SubTabTableView (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets) SubtaskExecutionError subtract_host_lists() (in module schrodinger.pipeline.pipeline) SubWidget (class in schrodinger.ui.qt.swidgets) subWidgetHasFocus() (schrodinger.ui.qt.filter_list.FilterListPopUp method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) succeeded() (schrodinger.job.jobcontrol.Job method) SUCCESS (schrodinger.application.desmond.cmj.JobStatus attribute) success (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask.output attribute) SUCCESS (schrodinger.application.matsci.mswidgets.ProcessBusyDialog attribute) (schrodinger.job.queue.CancelSubmittedStatus attribute) SUCCESS_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) successChanged (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask.output attribute) successReplaced (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask.output attribute) suffix (schrodinger.application.glide.utils.OutfileNameAttributes attribute) suggestCloseAtom() (schrodinger.application.matsci.reordergui.ComparisonFrame method) suggestedIndex() (schrodinger.application.matsci.reordergui.ComparisonFrame method) suggestion_limit (schrodinger.ui.qt.recent_completer.StringListModelInterface property) suggestReagentClasses() (schrodinger.application.pathfinder.reaction.Reaction method) SUITE (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) sum_atomic_weights() (in module schrodinger.application.matsci.atomicsymbols) SumFormalCharge (class in schrodinger.application.bioluminate.pml_menus) summarize() (schrodinger.structutils.smilesfilter.FilterReporter method) summarize_archive() (in module schrodinger.application.combinatorial_screen.driver_utils) summarize_pkas() (schrodinger.protein.assignment.ProtAssign method) summarize_properties() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) summarize_property_filters() (in module schrodinger.application.combinatorial_diversity.driver_utils) summarize_traj_with_com_st() (in module schrodinger.application.desmond.kinetics.utils) summary() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.job.jobcontrol.Job method) summary_model (schrodinger.application.livedesign.ld_export.ExportModel attribute) summary_modelChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) summary_modelReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) SummaryModel (class in schrodinger.application.livedesign.export_models) SummaryTableSpec (class in schrodinger.application.livedesign.summary) SumPartialCharge (class in schrodinger.application.bioluminate.pml_menus) SUP_TEXT() (in module schrodinger.ui.qt.swidgets) Super (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer attribute) (schrodinger.ui.qt.appframework2.debugwidgets.LogTable attribute) (schrodinger.ui.qt.appframework2.debugwidgets.LogTagTable attribute) (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable attribute) super_script() (in module schrodinger.application.matsci.reportutils) SuperExchangeTable (class in schrodinger.application.matsci.kmc) superimpose() (in module schrodinger.structutils.rmsd) superimpose_bond() (in module schrodinger.structutils.rmsd) superimpose_substructure_molecules() (in module schrodinger.structutils.rmsd) SUPERIMPOSED_PROPERTY (schrodinger.structutils.sitealign.SiteMatchLookup attribute) superimposeOnParent() (schrodinger.application.matsci.fragments.UniqueTracker method) superimposition superpose() (schrodinger.trajectory.prody.ensemble.Ensemble method) SUPERPOSITION_ATOM_SD_KEY (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF attribute) SuperpositionAligner (class in schrodinger.protein.align) superscript (schrodinger.application.scaffold_enumeration.cxsmiles.SRU attribute) supersedes() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) supported_basis_sets() (in module schrodinger.application.jaguar.jaguar_keyword_utils) SUPPORTED_BUILD_RESIDUES (schrodinger.application.bioluminate.nucleic.mutator.NucleobaseMutator attribute) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) SUPPORTED_FEP_TYPES (schrodinger.application.desmond.starter.ui.cmdline.FepArgs attribute) (schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args attribute) (schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs attribute) (schrodinger.application.desmond.starter.ui.fep_solubility.FepSolubilityArgs attribute) SUPPORTED_GEOMETRIES (in module schrodinger.application.matsci.buildcomplex) SUPPORTED_IN_EXTS (schrodinger.application.matsci.rxn_channel.Constants attribute) SUPPORTED_OPLS_VERSIONS (schrodinger.application.desmond.starter.ui.cmdline.BaseArgs attribute) (schrodinger.application.desmond.starter.ui.fep_residue_scanning.Args attribute) supported_output_format() (in module schrodinger.rdkit.molio) SUPPORTED_TYPES (schrodinger.ui.qt.schart.SeriesParams attribute) SUPPORTEDINEXTS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) supports_struct_group_search() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) suppress_options() (in module schrodinger.application.desmond.starter.ui.cmdline) suppress_rdkit_log() (in module schrodinger.rdkit.rdkit_adapter) suppress_signals (class in schrodinger.utils.qt_utils) Surface (class in schrodinger.application.matsci.nano.slab) (class in schrodinger.surface) surface (schrodinger.project.project.ProjectRow property) Surface (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) surface (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) Surface.Color (class in schrodinger.surface) Surface.ColorBy (class in schrodinger.surface) Surface.ColorFrom (class in schrodinger.surface) Surface.Style (class in schrodinger.surface) surface_area (schrodinger.surface.Surface property) surface_cmd (schrodinger.utils.pymol.Mapping attribute) surface_complementarity (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) surface_complementarityChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) surface_complementarityReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) surface_type (schrodinger.surface.Surface property) SURFACE_TYPE_NAME (schrodinger.surface.Surface attribute) surface_volume (schrodinger.surface.Surface property) SurfaceAreaSubMenu (class in schrodinger.application.bioluminate.pml_menus) SurfaceDict (class in schrodinger.project.surface) SurfaceRender (class in schrodinger.application.bioluminate.pml_menus) SurfaceRough() (in module schrodinger.application.matsci.gsas.GSASIIpwd) SurfaceRoughDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd) Surfaces (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) surfaces (schrodinger.project.project.ProjectRow property) SURFACES_ORBITAL_HOMOMINUS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) SURFACES_ORBITAL_LUMOPLUS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) SurfacesInterfaces (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) SurfacesSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) SurfaceTensionStep (class in schrodinger.application.matsci.jwsteps) SURFACTANT_BOTTOM_ATOM_CONSTRAINT (schrodinger.application.matsci.packmol.MicelleInputFile attribute) (schrodinger.application.matsci.packmol.MonolayerInputFile attribute) SURFACTANT_TOP_ATOM_CONSTRAINT (schrodinger.application.matsci.packmol.MicelleInputFile attribute) (schrodinger.application.matsci.packmol.MonolayerInputFile attribute) SurfactantInfo (class in schrodinger.application.matsci.packmol) surfnet_gaps_supplier() (in module schrodinger.application.bindingsite.cavutils) sus (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) SUSCEPT_CAP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SUSCEPTIBILITY (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SusceptibilityMerge (class in schrodinger.application.matsci.permittivity) suspendAnchors() (schrodinger.protein.alignment.BaseAlignment method) suspendCallbacks() (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) sval (schrodinger.utils.sea.sea.Atom property) (schrodinger.utils.sea.sea.Sea property) SValidIndicator (class in schrodinger.ui.qt.swidgets) SVBoxLayout (class in schrodinger.ui.qt.swidgets) SVG (schrodinger.livedesign.draw.Format attribute) SwallowEnterFilter (class in schrodinger.application.livedesign.live_report_widget) swap_atoms() (schrodinger.protein.assignment.ProtAssign.changeable method) swap_ld_library_path() (in module schrodinger.utils.env) swapBeads() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) SwapFragmentsException SwapIndx() (in module schrodinger.application.matsci.gsas.GSASIIlattice) swapInSourceModel() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) swapOrder() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) sweep (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) swissprot (schrodinger.utils.fileutils.SeqFormat attribute) switchPair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) switchSubJob() (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) switchTopLevelJob() (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) sym_groups (schrodinger.application.jaguar.nmr_utils.NMRData attribute) sym_spins (schrodinger.application.jaguar.nmr_utils.NMRData attribute) SYMATOMS (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) SYMBOL_START (in module schrodinger.application.matsci.atomicsymbols) symbol_to_number() (in module schrodinger.application.matsci.rdpattern) symlink() (in module schrodinger.application.desmond.util) symm (schrodinger.application.jaguar.input.GuessOrbital attribute) SYMM_KEY (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) SYMM_TITLE (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) symmetric_difference() (schrodinger.utils.scollections.IdSet method) symmetric_difference_update() (schrodinger.utils.scollections.IdSet method) symmetrized (schrodinger.application.matsci.elasticity.tensors.Tensor property) (schrodinger.application.matsci.elasticity.tensors.TensorCollection property) symmetrized_geometry() (in module schrodinger.application.jaguar.textparser) SYMMETRY (schrodinger.application.matsci.kmc.FragmentsTable attribute) (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute) symmetry_group() (in module schrodinger.application.jaguar.permutation_symmetry) SYMMETRY_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) SYMMETRY_LABEL_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) symmetry_number() (in module schrodinger.application.jaguar.textparser) SYMMETRY_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) symmetry_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) symmetry_opers_strs (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) symmetry_reduce() (in module schrodinger.application.matsci.elasticity.tensors) SYMMETRY_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) SymmetryEquiv (class in schrodinger.application.matsci.nano.sheet) SymmetryType (class in schrodinger.application.matsci.espresso.qeinput) SymmRingFragmentData (class in schrodinger.application.matsci.automated_cg_mapping) SymmRingFragmentData.RING_NODE_TYPE (class in schrodinger.application.matsci.automated_cg_mapping) sync() (schrodinger.utils.preferences.Preferences method) sync_dummy_atoms() (in module schrodinger.application.jaguar.utils) sync_pbc() (in module schrodinger.application.matsci.espresso.utils) (in module schrodinger.application.matsci.nano.xtal) sync_pbc2() (in module schrodinger.application.matsci.nano.xtal) syncAll() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) syncConfigDialog() (schrodinger.ui.qt.appframework2.af2.JobApp method) syncEdges() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) synchFromFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) synchronize_fsys_ct() (schrodinger.application.desmond.cms.Cms method) synchronizePreferencesFromMaestro() (schrodinger.ui.two_d_viewer.TwoDViewer method) SyncLevels (class in schrodinger.ui.qt.network_visualizer) syncModel() (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.network_views.PosTextNetworkNode method) (schrodinger.ui.qt.network_views.TextNetworkNode method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) syncNodes() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) syncNodesAdded() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) syncNodesChanged() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) syncNodesDeleted() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) syncPanelInfoWithMaestro() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) syncRecursive() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) syncSelection() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) Syntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) Synthesize (class in schrodinger.application.transforms.enumerators) synthesizeCombinations() (schrodinger.application.pathfinder.synthesis.Synthesizer method) Synthesizer (class in schrodinger.application.pathfinder.synthesis) (class in schrodinger.application.steps.enumerators) Synthesizer.Settings (class in schrodinger.application.steps.enumerators) synthesizeRandomSample() (schrodinger.application.pathfinder.synthesis.Synthesizer method) SYSBUILD (schrodinger.application.matsci.desconfig.MSJStringer attribute) SysbuildMSJStringer (class in schrodinger.application.matsci.desconfig) system (schrodinger.utils.profiling.SystemResourceTimes attribute) SYSTEM_BUILDER_INP (class in schrodinger.application.desmond.constants) system_file (schrodinger.analysis.transformations.TransformsRepository attribute) system_has_charged_particles() (in module schrodinger.application.matsci.coarsegrain) system_hosts_file() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.licserver.client) system_license_dir() (in module schrodinger.application.licensing.licserver.client) system_resource_times (schrodinger.utils.profiling.SystemResourceTimer property) SystematicIterator (class in schrodinger.application.pathfinder.synthesis) SystematicSampler (class in schrodinger.math.sampling) SystematicSynthesize (class in schrodinger.application.transforms.enumerators) SystemBuilder (class in schrodinger.application.desmond.stage.utils) (class in schrodinger.application.matsci.desmondutils) SystemBuilderInput (class in schrodinger.application.desmond.system_builder_inp) SystemInformationFrame (class in schrodinger.application.matsci.mswidgets) SystemResourceTimer (class in schrodinger.utils.profiling) SystemResourceTimes (class in schrodinger.utils.profiling) SystemType (class in schrodinger.application.desmond.constants) SYSTEMWIDE_DIPOLE (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SYSTEMWIDE_DIPOLE_PROPS (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SYSTEMWIDE_DIPOLE_STD_PROPS (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SYSTEMWIDE_DIPOLE_X_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SYSTEMWIDE_DIPOLE_X_STD_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SYSTEMWIDE_DIPOLE_Y_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SYSTEMWIDE_DIPOLE_Y_STD_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SYSTEMWIDE_DIPOLE_Z_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) SYSTEMWIDE_DIPOLE_Z_STD_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) systrait_is() (in module schrodinger.application.desmond.stage.workflow) SysType (class in schrodinger.application.desmond.systype) systype_is() (in module schrodinger.application.desmond.stage.workflow) SytSym() (in module schrodinger.application.matsci.gsas.GSASIIspc) sz2() (in module schrodinger.application.jaguar.textparser)

T

t() (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method) T_0 (class in schrodinger.application.desmond.simulation_block_test) t_cell_receptor (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) t_intrinsic_part() (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method) t_location_part() (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method) Tab (class in schrodinger.application.matsci.kmcgui) (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings) tabBarClicked() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) tabChanged() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) TabHeaderLink (class in schrodinger.ui.qt.standard_widgets.hyperlink) Table (class in schrodinger.application.matsci.kmc) (class in schrodinger.infra.table) TABLE_CLASSES (schrodinger.application.matsci.kmc.MatSciDatabaseManager attribute) (schrodinger.application.matsci.kmc.VotcaDatabaseManager attribute) table_data (schrodinger.application.jaguar.nmr_utils.NMRData attribute) table_exists() (in module schrodinger.application.phase.packages.mmp2d) table_getter (schrodinger.application.matsci.kmcgui.PlotInfo attribute) TABLE_MODEL_CLASS (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab attribute) (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) TABLE_NAME (schrodinger.application.matsci.kmc.AtomsTable attribute) (schrodinger.application.matsci.kmc.FragmentsTable attribute) (schrodinger.application.matsci.kmc.FramesTable attribute) (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) (schrodinger.application.matsci.kmc.MoleculesTable attribute) (schrodinger.application.matsci.kmc.PairsTable attribute) (schrodinger.application.matsci.kmc.SchrodingerTable attribute) (schrodinger.application.matsci.kmc.SegmentsTable attribute) (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) (schrodinger.application.matsci.kmc.SuperExchangeTable attribute) (schrodinger.application.matsci.kmc.Table attribute) table_rows() (in module schrodinger.application.matsci.kmc) TABLE_VIEW_CLASS (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) TableModel (class in schrodinger.application.desmond.gui) TableProxy (class in schrodinger.application.job_monitor.job_monitor_table) TableRow (class in schrodinger.infra.table) tableSelected() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) tableSelectionChanged() (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) (schrodinger.ui.two_d_viewer.TwoDViewer method) TableSpec (class in schrodinger.ui.qt.mapperwidgets.plptable) TableView (class in schrodinger.application.bioluminate.antibody.search_results_table) tableViewClicked() (schrodinger.ui.chooseligand.ChooseLigandDialog method) TableWidget (class in schrodinger.ui.qt.tablewidget) TABS (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) tabs() (schrodinger.ui.qt.swidgets.STabWidget method) tabSelected() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) TAG (schrodinger.application.desmond.stage.app.absolute_binding.stage.FepAbsoluteBindingAnalysis attribute) (schrodinger.application.desmond.stage.app.mxmd.MixedSolventCleanup attribute) (schrodinger.application.desmond.stage.app.solubility.GenerateSolubilityFepStructures attribute) (schrodinger.application.desmond.stage.app.solubility.SolubilityFepAnalysis attribute) (schrodinger.application.desmond.stage.prepare.structure.ExtractStructures attribute) tag (schrodinger.application.licensing.licerror.LicenseError property) TAG (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) tag() (schrodinger.utils.sea.sea.Sea method) tag_gcmc_ligand() (in module schrodinger.application.desmond.gcmc_utils) tag_gcmc_ligand_file() (in module schrodinger.application.desmond.gcmc_utils) tag_gcmc_near_ligand() (in module schrodinger.application.desmond.gcmc_utils) tag_gcmc_near_ligand_file() (in module schrodinger.application.desmond.gcmc_utils) tag_mol_indexes() (in module schrodinger.livedesign.preprocessor) tag_protein() (in module schrodinger.application.desmond.fep_edge_data) TAG_RE (schrodinger.application.matsci.espresso.qeoutput.Magres attribute) tag_sim_map() (in module schrodinger.application.desmond.msj_defaults) TAG_SPECS (class in schrodinger.application.desmond.msj_defaults) tag_st_het_num_prop() (in module schrodinger.application.prepwizard) tags (schrodinger.analysis.transformations.TransformsRepository property) (schrodinger.application.desmond.test_utils.FileRegistration attribute) TAGS (schrodinger.application.matsci.espresso.qeoutput.Magres attribute) (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) TagSpec (class in schrodinger.application.desmond.msj_defaults) tand() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIImath) (in module schrodinger.application.matsci.gsas.GSASIIpwd) TanimotoFilter (class in schrodinger.application.transforms.filters) tar_files() (in module schrodinger.utils.fileutils) TARGET_CLASS (schrodinger.models.mappers.TargetParamMapper attribute) target_seq (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Output attribute) target_seqChanged (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Output attribute) target_seqReplaced (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Output attribute) target_str (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData attribute) (schrodinger.application.livedesign.entry_types.Complexes attribute) (schrodinger.application.livedesign.entry_types.DockedPoses attribute) TARGET_VAL (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) target_validate() (schrodinger.ui.qt.appframework2.validators.Validator method) targetChanged (schrodinger.models.mappers.TargetSpec attribute) targetGetValue() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.maestro_utils.maestro_sync.PLPTarget method) (schrodinger.maestro_utils.maestro_sync.TitleTarget method) (schrodinger.models.mappers.TargetMixin method) (schrodinger.tasks.taskmanager.TaskManager method) (schrodinger.ui.qt.atomselector.MappableAtomSelector method) (schrodinger.ui.qt.color_picker.ButtonWithColorPicker method) (schrodinger.ui.qt.directory_selector.DirectorySelector method) (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.mapperwidgets.param_editor.ParamEditor method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) (schrodinger.ui.residueselector.MutationSelectorFrame method) TargetlessBase (class in schrodinger.application.livedesign.entry_types) TargetMixin (class in schrodinger.models.mappers) TargetParamMapper (class in schrodinger.models.mappers) targetSetValue() (schrodinger.application.job_monitor.job_monitor_widgets.StatusIcon method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.maestro_utils.maestro_sync.PLPTarget method) (schrodinger.maestro_utils.maestro_sync.TitleTarget method) (schrodinger.models.mappers.TargetMixin method) (schrodinger.tasks.taskmanager.TaskManager method) (schrodinger.ui.qt.atomselector.MappableAtomSelector method) (schrodinger.ui.qt.color_picker.ButtonWithColorPicker method) (schrodinger.ui.qt.directory_selector.DirectorySelector method) (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.jobwidgets.JobStatusButton method) (schrodinger.ui.qt.mapperwidgets.param_editor.ParamEditor method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) (schrodinger.ui.residueselector.MutationSelectorFrame method) TargetSpec (class in schrodinger.models.mappers) targetValueChanged (schrodinger.models.mappers.TargetMixin attribute) Task (class in schrodinger.application.desmond.stage.workflow) (class in schrodinger.application.desmond.task) task_class (schrodinger.stepper.stepper.BatchSettings attribute) task_classChanged (schrodinger.stepper.stepper.BatchSettings attribute) task_classReplaced (schrodinger.stepper.stepper.BatchSettings attribute) TASK_DRIVER_PATH (schrodinger.application.matsci.permittivity.WorkflowParser attribute) task_list (schrodinger.tasks.taskmanager.TaskManager attribute) task_listChanged (schrodinger.tasks.taskmanager.TaskManager attribute) task_listReplaced (schrodinger.tasks.taskmanager.TaskManager attribute) TASK_NAME (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) (schrodinger.application.matsci.permittivity.WorkflowParser attribute) TASK_REPLICA (schrodinger.application.matsci.permittivity.WorkflowParser attribute) task_rl_map (schrodinger.application.livedesign.ld_export.ExportModel attribute) task_rl_mapChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) task_rl_mapReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) TASK_SUBCLASS (schrodinger.application.matsci.permittivity.WorkflowParser attribute) TASK_SUBJOB (schrodinger.application.matsci.permittivity.WorkflowParser attribute) TASK_TUPLE (in module schrodinger.application.phase.packages.phase_database_arg_utils) TASK_TYPE (schrodinger.application.matsci.permittivity.WorkflowParser attribute) TASK_TYPE_TO_SUBCLASS (schrodinger.application.matsci.permittivity.WorkflowParser attribute) TaskBar (class in schrodinger.ui.qt.tasks.taskwidgets) TaskBar2 (class in schrodinger.ui.qt.tasks.taskbar2) TaskClass (schrodinger.tasks.taskmanager.TaskManager attribute) TaskClassChanged (schrodinger.tasks.taskmanager.TaskManager attribute) TaskClassReplaced (schrodinger.tasks.taskmanager.TaskManager attribute) TaskDirNotFoundError TaskDirSetting (class in schrodinger.tasks.tasks) taskDirSetting() (schrodinger.tasks.tasks.AbstractTask method) TaskDJ (class in schrodinger.tasks.queue) taskDone (schrodinger.tasks.tasks.AbstractTask attribute) taskEnded (schrodinger.tasks.taskmanager.TaskManager attribute) taskFailed (schrodinger.tasks.tasks.AbstractTask attribute) TaskFailure TaskFile (class in schrodinger.tasks.tasks) TaskFolder (class in schrodinger.tasks.tasks) TaskInput (class in schrodinger.application.livedesign.export_models) TaskKilled TaskManager (class in schrodinger.tasks.taskmanager) TaskPanel (class in schrodinger.ui.qt.basewidgets) TaskPanelMixin (class in schrodinger.ui.qt.widgetmixins.panelmixins) TaskPanelPresetManager (class in schrodinger.models.presets) TaskProtocol (class in schrodinger.application.matsci.permittivity) TaskQueue (class in schrodinger.tasks.queue) TaskSpecification (class in schrodinger.job.launchapi) TaskSpecificationBuilder (class in schrodinger.job.launchapi) TaskSpecificationError TaskSpecificationKeyError taskStarted (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractTask attribute) taskStatusChanged (schrodinger.tasks.taskmanager.TaskManager attribute) TaskStatusMixin (class in schrodinger.application.jaguar.gui.base_panel) TaskType (class in schrodinger.application.livedesign.export_tasks) TaskWidgetMixin (class in schrodinger.ui.qt.tasks.taskbarwidgets) TaskWithLicenseManager (class in schrodinger.seam.testing.fixtures) taskWritten (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin attribute) TAU (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) TAU_END_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) TAU_ESTIMATE_SEC (schrodinger.application.desmond.kinetics.utils.MtdInfo attribute) TAU_PS (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) TAU_PS_INDEX (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) TAU_START_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) tautomer_insensitive (schrodinger.rdkit.substructure.QueryOptions attribute) TCR (schrodinger.application.prepwizard2.tasks.ProteinFeature attribute) TCR_A (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType attribute) TCR_B (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType attribute) tcr_cdr_scheme (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) tcr_cdr_schemeChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) tcr_cdr_schemeReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) TCR_D (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType attribute) TCR_G (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType attribute) tcr_regions (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) TcrChainIds (class in schrodinger.application.bioluminate.tcr.docking_angles) TCRRegionFinder (class in schrodinger.protein.annotation) TCRRegionLabel (class in schrodinger.protein.annotation) tddft_excitation_properties() (in module schrodinger.application.jaguar.textparser) tddft_geopt_energy() (in module schrodinger.application.jaguar.textparser) tdm_precision (schrodinger.application.jaguar.results.Dipole attribute) (schrodinger.application.jaguar.results.JaguarResults attribute) teardown() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) TechnicalPreset (class in schrodinger.application.bioluminate.pml_menus) temp (schrodinger.application.jaguar.utils.FreeEnergy attribute) TEMP (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) TEMP_DIR (schrodinger.application.matsci.appbase.ProcessPtStructuresApp attribute) temp_n (schrodinger.application.matsci.reaction_workflow_utils.TempData attribute) TEMP_ONLY (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) TEMP_PROP (schrodinger.application.matsci.permittivity.MdPostAnalysis attribute) TEMP_REPLICA_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) TEMP_REPLICA_PROP_REX (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) temp_start (schrodinger.application.matsci.reaction_workflow_utils.TempData attribute) TEMP_STD_PROP (schrodinger.application.matsci.permittivity.MdPostAnalysis attribute) TEMP_STD_REPLICA_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) temp_step (schrodinger.application.matsci.reaction_workflow_utils.TempData attribute) TEMP_TASKDIR (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.TaskDirSetting attribute) temp_unzip_project() (in module schrodinger.project.project) TempAtom (class in schrodinger.application.canvas.r_group) TempData (class in schrodinger.application.matsci.reaction_workflow_utils) Temperature (class in schrodinger.application.desmond.simulation_block_test) TEMPERATURE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) (schrodinger.application.matsci.permittivity.MdStageModifier attribute) temperature (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) temperature_factor (schrodinger.structure._AtomCollection property) (schrodinger.structure.StructureAtom property) Temperature_K (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) tempfilename (class in schrodinger.utils.fileutils) TempFileNameIterator (class in schrodinger.application.glide.sort_utils) TempItemDelegate (class in schrodinger.application.desmond.gui) template (schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl attribute) (schrodinger.application.bioluminate.antibody.assembly.AtomPair attribute) (schrodinger.application.prime.wrapper.BasePrimeAlignment property) (schrodinger.job.queue.MissingResourceError attribute) TEMPLATE_MD_MSJ (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator attribute) TEMPLATE_MSJ (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator attribute) template_path (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) template_seq (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Output attribute) template_seqChanged (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Output attribute) template_seqReplaced (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Input attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask.Output attribute) template_sequence (schrodinger.application.prime.wrapper.BasePrimeAlignment property) template_st (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings property) template_sts (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings property) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget property) template_stsChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) TemplateAtomMapFailure TemplateCombo (class in schrodinger.application.matsci.builderwidgets) TemplateFamily (class in schrodinger.application.matsci.builderwidgets) TemplateGuessFailure TemplateListWidgetItem (class in schrodinger.application.matsci.builderwidgets) TemplateManager (class in schrodinger.application.matsci.builderwidgets) templateSelected (schrodinger.application.livedesign.panel_components.LiveReportTemplateSelectorCombo attribute) TemplateSelector (class in schrodinger.application.matsci.builderwidgets) TemplateSelectorFilterListPopUp (class in schrodinger.application.matsci.builderwidgets) TemplateSelectorFilterListToolButton (class in schrodinger.application.matsci.builderwidgets) TemplateSelectorPopUp (class in schrodinger.application.matsci.builderwidgets) templatesUpdated (schrodinger.application.matsci.builderwidgets.SketcherBox attribute) TemplateToolButton (class in schrodinger.application.matsci.builderwidgets) temporary_directory() (in module schrodinger.application.licensing.licadmin) TEMPORARY_LICENSE_FAILURE (schrodinger.application.desmond.cmj.JobStatus attribute) TempStructureFile (class in schrodinger.utils.fileutils) Tensor (class in schrodinger.application.matsci.elasticity.tensors) TensorCollection (class in schrodinger.application.matsci.elasticity.tensors) tensors() (schrodinger.application.matsci.espresso.qeoutput.PhDOSTensors method) TERMDICT (schrodinger.application.matsci.nano.constants.Constants attribute) TERMFRAG (schrodinger.application.matsci.nano.constants.Constants attribute) TERMFRAGS (schrodinger.application.matsci.nano.constants.Constants attribute) TERMINAL_INFILE_NUM (schrodinger.application.matsci.permittivity.StepBase attribute) (schrodinger.application.matsci.permittivity.TwoFileInput attribute) terminate() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.jaguar.mmjag.MmJag static method) (schrodinger.application.matsci.mecp_mod.MECPStep method) (schrodinger.infra.mminit.Initializer method) (schrodinger.infra.mmlist.mmlist static method) (schrodinger.infra.table.Table static method) (schrodinger.project.project.Project static method) TerminateException terminateLattice() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) Terminator (class in schrodinger.application.matsci.amorphous) TERMINDICIES (schrodinger.application.matsci.nano.sheet.Grow attribute) TermKeywords (class in schrodinger.application.glide.xpdes) termMaestroWriter() (schrodinger.application.matsci.rxn_channel.Channels method) TERMMAP (schrodinger.application.matsci.nano.constants.Constants attribute) TERMNONE (schrodinger.application.matsci.nano.constants.Constants attribute) tesla_to_mhz() (in module schrodinger.application.jaguar.nmr_utils) Test (class in schrodinger.application.desmond.simulation_block_test) test() (in module schrodinger.ui.chooseligand) test0() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIIpwd) (in module schrodinger.application.matsci.gsas.GSASIIspc) test1() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIIpwd) (in module schrodinger.application.matsci.gsas.GSASIIspc) test2() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIIpwd) (in module schrodinger.application.matsci.gsas.GSASIIspc) test3() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIIpwd) (in module schrodinger.application.matsci.gsas.GSASIIspc) test4() (in module schrodinger.application.matsci.gsas.GSASIIlattice) test5() (in module schrodinger.application.matsci.gsas.GSASIIlattice) test6() (in module schrodinger.application.matsci.gsas.GSASIIlattice) test7() (in module schrodinger.application.matsci.gsas.GSASIIlattice) test8() (in module schrodinger.application.matsci.gsas.GSASIIlattice) test9() (in module schrodinger.application.matsci.gsas.GSASIIlattice) test_deps() (in module schrodinger.utils.installation_check) test_dict (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_dictChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_dictReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_enum (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_enum2 (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_enum2Changed (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_enum2Replaced (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_enumChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_enumReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_envvars() (in module schrodinger.application.desmond.gpgpu.test_gpgpu) test_get_available_devices() (in module schrodinger.application.desmond.gpgpu.test_gpgpu) test_getLicenseRequirements() (schrodinger.application.steps.test.StepContract method) test_getOutputs() (schrodinger.application.steps.test.StepContract method) test_is_any_gpu_available() (in module schrodinger.application.desmond.gpgpu.test_gpgpu) test_list (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_listChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_listReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) test_minimum_nvml_driver() (in module schrodinger.application.desmond.gpgpu.test_gpgpu) test_nvml_driver_supported() (in module schrodinger.application.desmond.gpgpu.test_gpgpu) test_print_gpgpu_devices() (in module schrodinger.application.desmond.gpgpu.test_gpgpu) test_query_gpgpu() (in module schrodinger.application.desmond.gpgpu.test_gpgpu) test_validateSettings() (schrodinger.application.steps.test.StepContract method) TestApp (class in schrodinger.ui.chooseligand) testASL() (schrodinger.application.matsci.chargegui.ChargeDialog method) TestData() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIIpwd) TestJob (class in schrodinger.utils.installation_check) TestJobDJ (class in schrodinger.utils.installation_check) TestStdException (class in schrodinger.ui.dendrogram) testString() (schrodinger.application.jaguar.utils.GenOptions static method) TestSuite (class in schrodinger.application.desmond.util) tet() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) TETRAGONAL_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) TETRAHEDRAL (in module schrodinger.application.matsci.buildcomplex) tetrahedral_bonding_vector() (in module schrodinger.application.matsci.rxn_channel) TETRAHEDRAL_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) TetrahedralSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) Tetrahedron (class in schrodinger.application.matsci.shapes) tetrahedron() (schrodinger.application.watermap.shapes.ShapeFactory method) Text (class in schrodinger.pipeline.pipeio) text (schrodinger.application.desmond.antlr3.recognizers.Lexer property) (schrodinger.application.desmond.antlr3.tokens.CommonToken property) (schrodinger.application.desmond.antlr3.tree.CommonTree property) (schrodinger.application.matsci.reportutils.Footer attribute) TEXT (schrodinger.seam.viz.watcher.ResponseType attribute) (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser.HTMLType attribute) text() (schrodinger.application.desmond.cwidget.EntryField method) (schrodinger.application.desmond.cwidget.FileEntry method) (schrodinger.application.desmond.fep_dialog.CustomGPUComboBox method) (schrodinger.ui.qt.formlayout.ColorLayout method) (schrodinger.ui.qt.formlayout.CountLayout method) (schrodinger.ui.qt.formlayout.FileLayout method) (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) (schrodinger.ui.qt.tablewidget.Cell method) Text2MT() (in module schrodinger.application.matsci.gsas.GSASIIspc) text_alignment_role() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) TEXT_MARGIN (schrodinger.ui.qt.delegates.PictureDelegate attribute) text_offset (schrodinger.ui.qt.network_views.TextNetworkNode attribute) TEXT_OFFSET_DIVISOR (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter attribute) text_size (schrodinger.ui.qt.network_views.PosTextNetworkNode attribute) (schrodinger.ui.qt.network_views.SmilesNetworkNode attribute) (schrodinger.ui.qt.network_views.TextNetworkNode attribute) TEXT_SIZE (schrodinger.ui.qt.rama.RamaContourMixin attribute) text_to_qcolor() (in module schrodinger.ui.qt.formlayout) text_y_pos (schrodinger.ui.qt.network_views.SmilesNetworkNode attribute) (schrodinger.ui.qt.network_views.TextNetworkNode attribute) textAppended (schrodinger.application.job_monitor.job_monitor_file_browser.SubprocessStdOutStreamer attribute) TextColors (class in schrodinger.ui.qt.standard.design_tokens) textElide() (schrodinger.ui.qt.delegates.PictureDelegate method) textFromValue() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) TextGen() (in module schrodinger.application.matsci.gsas.GSASIIspc) TextNetworkNode (class in schrodinger.ui.qt.network_views) TextOperator (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) TextOps() (in module schrodinger.application.matsci.gsas.GSASIIspc) TextParser (class in schrodinger.application.jaguar.textparser) (class in schrodinger.application.xtb.textparser) textparser_trace() (in module schrodinger.application.jaguar.textparser) TextSearchBar (class in schrodinger.ui.qt.swidgets) TextualStructure (class in schrodinger.structure) textUpdated() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.ui.qt.pop_up_widgets.LineEditWithPopUp method) textureIndex() (in module schrodinger.application.matsci.gsas.GSASIIlattice) TgStep (class in schrodinger.application.matsci.jwsteps) THEORY (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) theory (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) THEORY (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) theory (schrodinger.application.qsite.input.Cut property) (schrodinger.application.qsite.input.HydrogenCap property) THEORY_COMBO_DFT (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_COMBO_HF (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_COMBO_LMP2 (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_COMBO_RIMP2 (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_INDICES (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_TO_INDEX (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) theoryChanged (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) theoryChanged() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) TheoryListWidgetItem (class in schrodinger.application.jaguar.gui.theory_selector) theoryOrBasisUpdated() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) TheorySelector (class in schrodinger.application.matsci.jagwidgets) TheorySelectorFilterList (class in schrodinger.application.jaguar.gui.input_tab_widgets) TheorySelectorFilterListPopUp (class in schrodinger.application.jaguar.gui.theory_selector) TheorySelectorFilterListToolButton (class in schrodinger.application.jaguar.gui.theory_selector) TheoryTab (class in schrodinger.application.jaguar.gui.tabs.theory_tab) TheoryTabNoSoZora (class in schrodinger.application.jaguar.gui.tabs.theory_tab) TheoryTabOptimization (class in schrodinger.application.jaguar.gui.tabs.theory_tab) TheoryTabWithSoZora (class in schrodinger.application.jaguar.gui.tabs.theory_tab) theoryToInput() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) theoryUpdated() (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MultipoleSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) THERMAL_SMEARING_OPTS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) thermalSmearingChanged() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) thermo() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) thermo_helper() (in module schrodinger.application.jaguar.textparser) ThermoCollection (class in schrodinger.application.jaguar.results) thermoMethodChanged() (schrodinger.application.desmond.gui.EnsembleTab method) ThermoProp (class in schrodinger.application.jaguar.results) theta_0 (schrodinger.ui.qt.radial_plot.Sector attribute) theta_1 (schrodinger.ui.qt.radial_plot.Sector attribute) THICKNESS (schrodinger.application.matsci.mswidgets.MultiSlider attribute) Thiol (schrodinger.protein.helm.helm_renderer.HexColor attribute) THOROUGH (schrodinger.application.jaguar.utils.LewisModes attribute) THREAD_FLAG (schrodinger.application.matsci.crest.Crest attribute) thread_print() (in module schrodinger.utils.thread_utils) ThreadFunctionTask (class in schrodinger.tasks.tasks) ThreadMixin (class in schrodinger.tasks.tasks) ThreadOnlyConfigDialog (class in schrodinger.application.matsci.configdlgs) threadPrint() (schrodinger.utils.thread_utils.ThreadTool method) THREADS (schrodinger.application.matsci.crest.CrestTOML attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) ThreadsAndMaxSubjobsConfigDialog (class in schrodinger.application.matsci.configdlgs) ThreadSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) ThreadTool (class in schrodinger.utils.thread_utils) three_d (schrodinger.application.livedesign.export_tasks.TaskType attribute) three_d_export_items (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) three_d_export_itemsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) three_d_export_itemsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) three_d_file_path (schrodinger.application.livedesign.export_models.FileBatch attribute) three_d_file_pathChanged (schrodinger.application.livedesign.export_models.FileBatch attribute) three_d_file_pathReplaced (schrodinger.application.livedesign.export_models.FileBatch attribute) three_d_specs (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) three_d_specsChanged (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) three_d_specsReplaced (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) ThreeDExportItem (class in schrodinger.application.livedesign.export_models) ThreeTenHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) thresh_prec (schrodinger.application.jaguar.results.ConvCriteria attribute) throwBadAlloc() (schrodinger.ui.dendrogram.TestStdException method) throwLogicError() (schrodinger.ui.dendrogram.TestStdException method) throwOutOfRange() (schrodinger.ui.dendrogram.TestStdException method) throwRuntimeError() (schrodinger.ui.dendrogram.TestStdException method) Thymine (schrodinger.protein.helm.helm_renderer.HexColor attribute) TICK_LABEL_SIZE (schrodinger.ui.qt.rama.RamaContourMixin attribute) TICK_SPACING (schrodinger.ui.qt.rama.RamaContourMixin attribute) tickets (schrodinger.application.desmond.test_utils.FileRegistration attribute) tileParticipants() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) time (schrodinger.application.desmond.ene_utils.ENEGRP_VALUE attribute) (schrodinger.application.jaguar.gui.timing.TimingResults.PER_ENTRY_DATA attribute) (schrodinger.application.licensing.lmgrd_log_parser.event attribute) (schrodinger.application.matsci.atom_group.HelixData attribute) TIME (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.application.matsci.kmc.FramesTable attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) time_duration() (in module schrodinger.application.desmond.util) TIME_FORMAT (schrodinger.application.matsci.jobdirdlg.JobManager attribute) (schrodinger.utils.profiling.Timer attribute) time_in_seconds (schrodinger.seam.testing.benchmarks.BenchmarkResult attribute) TIME_SERIAL (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) TIME_SERIAL_CAPITALIZE (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) TIME_SERIAL_FILE_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) TIME_SERIAL_LABELS (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) TIME_SLICE (schrodinger.application.bioluminate.pose_filtering.hdx_io.DynamXColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.HDExaminerColumns attribute) time_slices (schrodinger.application.bioluminate.pose_filtering.hdx_io.HdxMsProperties attribute) time_stage() (schrodinger.application.desmond.cmj.StageBase method) TIME_TEXT (schrodinger.application.jaguar.gui.timing.TimerMixin attribute) time_weighted_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) TIMED_PROPERTIES (schrodinger.application.jaguar.gui.timing.TimerMixin attribute) timeit_logger_debug() (in module schrodinger.application.matsci.textlogger) TimelinePlot (class in schrodinger.stepper.viz) TimeoutError, [1] Timer (class in schrodinger.utils.profiling) timer() (in module schrodinger.application.glide.utils) TimerInfoDialog (class in schrodinger.application.jaguar.gui.timing) TimerMixin (class in schrodinger.application.jaguar.gui.timing) TimeSanityException TimeSeriesAnalysisJob (class in schrodinger.application.desmond.stage.analysis) timestamp (schrodinger.active_learning.mq_driver.Worker attribute) (schrodinger.seam.runners.events.SeamEvent attribute) timestamp() (in module schrodinger.job.jobcontrol) timestampChanged (schrodinger.seam.runners.events.PipelineFinished attribute) (schrodinger.seam.runners.events.PipelineStarted attribute) (schrodinger.seam.runners.events.SeamEvent attribute) (schrodinger.seam.runners.events.StageFailed attribute) (schrodinger.seam.runners.events.StageFinished attribute) (schrodinger.seam.runners.events.StageStarted attribute) timestampReplaced (schrodinger.seam.runners.events.PipelineFinished attribute) (schrodinger.seam.runners.events.PipelineStarted attribute) (schrodinger.seam.runners.events.SeamEvent attribute) (schrodinger.seam.runners.events.StageFailed attribute) (schrodinger.seam.runners.events.StageFinished attribute) (schrodinger.seam.runners.events.StageStarted attribute) TIMESTEP (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) timestep_npoints (schrodinger.application.jaguar.nmr_utils.NMRData attribute) (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) timingEnabled() (schrodinger.application.jaguar.gui.timing.TimerMixin method) timingImpacted() (schrodinger.application.jaguar.gui.timing.TimerMixin method) TimingResults (class in schrodinger.application.jaguar.gui.timing) TimingResults.PER_ENTRY_DATA (class in schrodinger.application.jaguar.gui.timing) TINT_30 (schrodinger.ui.qt.standard.design_tokens.PrimaryColors attribute) TINT_50 (schrodinger.ui.qt.standard.design_tokens.PrimaryColors attribute) TINT_90 (schrodinger.ui.qt.standard.design_tokens.PrimaryColors attribute) tip (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) TIP3P (schrodinger.application.desmond.constants.WATER_MODELS attribute) TIP3P_CHARMM (schrodinger.application.desmond.constants.WATER_MODELS attribute) TIP4P (schrodinger.application.desmond.constants.WATER_MODELS attribute) TIP4P2005 (schrodinger.application.desmond.constants.WATER_MODELS attribute) TIP4PD (schrodinger.application.desmond.constants.WATER_MODELS attribute) TIP4PEW (schrodinger.application.desmond.constants.WATER_MODELS attribute) TIP5P (schrodinger.application.desmond.constants.WATER_MODELS attribute) TITLE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) title (schrodinger.application.jaguar.gui.timing.TimingResults.PER_ENTRY_DATA attribute) (schrodinger.application.livedesign.live_report_widget.LRInputType attribute) (schrodinger.application.livedesign.summary.SummaryTableSpec attribute) (schrodinger.application.matsci.kmcgui.PlotInfo attribute) (schrodinger.application.phase.hypothesis.PhaseHypothesis property) (schrodinger.project.manager.EntryGroupManager property) (schrodinger.project.project.EntryGroup property) (schrodinger.project.project.ProjectRow property) (schrodinger.structure.SmilesStructure property) (schrodinger.structure.Structure property) (schrodinger.ui.qt.appframework2.baseapp.BasePanel property) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel property) TITLE (schrodinger.ui.qt.forcefield.forcefield.ValidateOplsDirMessageBox attribute) title() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) TITLE_BASE (schrodinger.application.livedesign.ld_export.LDExportPanelMixin attribute) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel attribute) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel attribute) title_case() (in module schrodinger.application.matsci.typography) TITLE_KEY (schrodinger.application.matsci.nano.xtal.CheckInput attribute) (schrodinger.application.matsci.rxn_channel.CheckInput attribute) titleChanged (schrodinger.protein.annotation.AbstractSequenceAnnotations attribute) TITLEKEY (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) (schrodinger.application.matsci.rxn_path.CheckInput attribute) TITLENAME (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) TitleTarget (class in schrodinger.maestro_utils.maestro_sync) TLS2Uij() (in module schrodinger.application.matsci.gsas.GSASIImath) tls_names (schrodinger.application.licensing.licserver.exceptions.TLSHostnameError attribute) TLSHostnameError tlsServerName (schrodinger.application.licensing.licserver.client.ServerIdentifier attribute) TLSVerifyError TM (schrodinger.protein.annotation.GPCRSegmentLabel attribute) TM_METAL_LIST (in module schrodinger.application.matsci.atomicsymbols) TM_METAL_SET (in module schrodinger.application.matsci.atomicsymbols) TMLigandRowMixin (class in schrodinger.application.matsci.builderwidgets) TMPDIR (schrodinger.utils.cmdline.Options attribute) to_binary() (in module schrodinger.livedesign.registration) to_coarse_grain() (in module schrodinger.protein.helm) to_deprecate_no_stereo_hash (schrodinger.livedesign.registration.RegistrationData attribute) to_deprecate_sdf (schrodinger.livedesign.registration.RegistrationData attribute) to_dict() (in module schrodinger.application.matsci.mlearn.sklearn_json) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.StageInfo method) (schrodinger.application.vss.csvsmiles.CsvSmilesFile method) to_dot() (schrodinger.seam.viz.render.PipelineRenderer method) to_fingerprint() (in module schrodinger.livedesign.bbchem_endpoints) to_float() (in module schrodinger.ui.qt.utils)

to_format() (in module schrodinger.livedesign.bbchem_endpoints) to_hostentry() (schrodinger.job.jobcontrol.Host method) to_idx (schrodinger.application.matsci.reaction_workflow_utils.Site attribute) to_image() (in module schrodinger.livedesign.bbchem_endpoints) to_json() (in module schrodinger.application.matsci.mlearn.sklearn_json) to_measurement() (schrodinger.application.desmond.correlation_tau.ConfidenceInterval method) to_rdkit() (in module schrodinger.rdkit.rdkit_adapter) to_registration_data() (in module schrodinger.livedesign.bbchem_endpoints) to_res_3l (schrodinger.application.bioluminate.mutation.Mutation attribute) to_sequence_viewer_data() (in module schrodinger.livedesign.bbchem_endpoints) to_smarts() (in module schrodinger.adapter) (in module schrodinger.application.matsci.rdpattern) to_smiles() (in module schrodinger.adapter) (in module schrodinger.application.matsci.rdpattern) to_smiles_canonical_atom_order() (in module schrodinger.adapter) to_string() (in module schrodinger.application.steps.utils) (schrodinger.application.desmond.measurement.Measurement method) to_style (schrodinger.structure.StructureBond property) to_text_string() (in module schrodinger.ui.qt.formlayout) to_type_hint() (schrodinger.seam.coders.MolCoder method) (schrodinger.seam.coders.RouteNodeCoder method) (schrodinger.seam.coders.StructureCoder method) to_yaml() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) toArgparse() (schrodinger.active_learning.al_driver.Option method) ToArrayCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) ToArrayCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) toAtom() (schrodinger.application.matsci.espresso.qeoutput.MagresAtom method) toClustalFile() (schrodinger.protein.alignment.ProteinAlignment method) toCmdArg() (schrodinger.tasks.jobtasks.HostSettings method) toConfig() (schrodinger.livedesign.preprocessor.PreprocessorOptions method) toConfigObj() (schrodinger.active_learning.al_driver.Option method) toDebugString() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) toDict() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method) (schrodinger.application.phase.packages.shape_generator.SerializableShapeGenerator method) (schrodinger.models.parameters.CompoundParam method) TOF2dsp() (in module schrodinger.application.matsci.gsas.GSASIIlattice) toFastaFile() (schrodinger.protein.alignment.ProteinAlignment method) toFastaString() (schrodinger.protein.alignment.ProteinAlignment method) toFastaStringList() (schrodinger.protein.alignment.ProteinAlignment method) toFile() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method) Toggle (schrodinger.ui.qt.table_helper.Include attribute) toggle_maestro_mouse() (schrodinger.application.pymol.pymol4maestro.panel method) toggle_structure() (in module schrodinger.application.matsci.etatoggle) toggle_table (in module schrodinger.application.bioluminate.pml_menus) toggleActiveFilter() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) toggleAllowed() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) toggleControls() (schrodinger.ui.qt.navtoolbar.MaestroNavToolbar method) toggleCounterions() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) toggleDisallowed() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) toggleFavorable() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) toggleLigands() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) ToggleLink (class in schrodinger.ui.qt.standard_widgets.hyperlink) toggleLogAxis() (schrodinger.ui.qt.schart.SChart method) toggleProjectFilter() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) toggleRelaxModel() (schrodinger.application.desmond.gui.RelaxFrame method) toggleSelection() (schrodinger.application.phase.featureselector.FeatureModel method) ToggleState (class in schrodinger.application.bioluminate.pml_menus) toggleStateMain() (schrodinger.application.matsci.appbase.BaseAnalysisGui method) (schrodinger.application.matsci.deswidgets.TrajAnalysisGuiMixin method) ToggleStateSubMenu (class in schrodinger.application.bioluminate.pml_menus) toggleTimer() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) toggleVisibility() (schrodinger.application.matsci.mswidgets.StageFrame method) toggleWaters() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) toggleZoomView() (schrodinger.ui.two_d_viewer.TwoDViewer method) toInt() (schrodinger.ui.qt.swidgets.SLabeledSlider method) toJson() (schrodinger.application.glide.http_client.GlideResult method) (schrodinger.models.json.JsonableClassMixin method) toJsonImplementation() (schrodinger.application.bioluminate.pose_filtering.residue_filter.BaseResidueFilter method) (schrodinger.application.livedesign.data_classes.LDData method) (schrodinger.application.livedesign.export_models.JsonablePropertyName method) (schrodinger.application.livedesign.panel_components.BaseLDTreeItemWrapper method) (schrodinger.application.livedesign.panel_components.ExportRow method) (schrodinger.application.livedesign.panel_components.ExportTableModel method) (schrodinger.application.prepwizard.JsonableHetStates method) (schrodinger.models.json.JsonableClassMixin method) (schrodinger.models.jsonable.JsonableBytes method) (schrodinger.models.jsonable.JsonableEnum method) (schrodinger.models.jsonable.JsonableIntEnum method) (schrodinger.models.jsonable.JsonableSet method) (schrodinger.models.jsonable.JsonableStructure method) (schrodinger.models.jsonable.JsonableTuple method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.protein.alignment.ProteinAlignment method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES method) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES method) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES method) (schrodinger.protein.residue.Gap method) (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.ProteinSequence method) (schrodinger.seam.metric.ExecutionMetrics method) (schrodinger.seam.runners.events.SeamEvent method) (schrodinger.tasks.hosts.Gpu method) (schrodinger.tasks.hosts.Host method) (schrodinger.tasks.jobtasks.HostSettings method) Token (class in schrodinger.application.desmond.antlr3.tokens) token (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) token_link (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) token_linkChanged (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) token_linkReplaced (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) tokenChanged (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) tokenNames (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) tokenReplaced (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) TokenRewriteStream (class in schrodinger.application.desmond.antlr3.streams) tokens (schrodinger.application.licensing.lmgrd_log_parser.event attribute) tokens() (in module schrodinger.application.licensing.licadmin) (schrodinger.application.licensing.licadmin.LicenseResource method) tokens_str() (schrodinger.application.licensing.flexlm.Feature method) TokenSource (class in schrodinger.application.desmond.antlr3.recognizers) tokenStartIndex (schrodinger.application.desmond.antlr3.tree.CommonTree property) tokenStopIndex (schrodinger.application.desmond.antlr3.tree.CommonTree property) TokenStream (class in schrodinger.application.desmond.antlr3.streams) TolerableError TOLERANCE (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) TOML_DICT (schrodinger.application.matsci.crest.CrestCSearch attribute) toNetworkX() (schrodinger.ui.qt.network_visualizer.Graph method) TOO_SLOW (schrodinger.application.desmond.kinetics.utils.MtdInfo attribute) (schrodinger.application.desmond.kinetics.utils.MtdStatus attribute) TOOL_BUTTON_CLASS (schrodinger.application.matsci.builderwidgets.TemplateSelector attribute) (schrodinger.application.matsci.jagwidgets.BasisSetSelector attribute) (schrodinger.application.matsci.jagwidgets.TheorySelector attribute) TOOL_ITEMS (schrodinger.ui.qt.navtoolbar.NavToolbar attribute) TOOL_TIP_INSTRUCTIONS (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) TOOL_TIP_WRONG_EID (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) TOOLBAR_CLASS (schrodinger.ui.qt.smatplotlib.SmatplotlibCanvas attribute) toolbar_feedback_override() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) ToolButtonWithFilterListPopUp (class in schrodinger.ui.qt.filter_list) ToolButtonWithPopUp (class in schrodinger.ui.qt.pop_up_widgets) tooltip (schrodinger.maestro_utils.find_tool_bar.constants.SEARCH_OPTION_DETAILS attribute) (schrodinger.protein.annotation.Consensus property) tooltip_calculating (schrodinger.application.desmond.feputils.BaseSpinnerWidget attribute) (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget attribute) TOOLTIP_CLEAR_SKETCHER (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox attribute) tooltip_for_aa() (in module schrodinger.ui.qt.tooltips) TOOLTIP_FRAME_WIDTH (schrodinger.ui.qt.delegates.MatplotlibDelegate attribute) TOOLTIP_HIDE_DELAY (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin attribute) TOOLTIP_PLOT (schrodinger.ui.qt.delegates.MatplotlibDelegate attribute) TOOLTIP_PLOT_HEIGHT (schrodinger.ui.qt.delegates.MatplotlibDelegate attribute) TOOLTIP_PLOT_WIDTH (schrodinger.ui.qt.delegates.MatplotlibDelegate attribute) TOOLTIP_SELECTOR (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox attribute) TOOLTIP_SHOW_DELAY (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin attribute) TOOLTIP_TEXT (schrodinger.application.desmond.gui.EnsembleClassFrame attribute) ToolTipFilter (class in schrodinger.ui.qt.table) ToolTipIconDelegate (class in schrodinger.ui.qt.delegates) TooltipMixin (class in schrodinger.ui.qt.tooltips) TOOLTIPS (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) TooManyGroupsError toOriginalString() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) Top (class in schrodinger.seam.transforms.partitioners) TOP (schrodinger.application.desmond.constants.SidedError attribute) (schrodinger.application.matsci.kmc.Table attribute) (schrodinger.ui.qt.schart.SChart attribute) (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) top_axis (schrodinger.ui.qt.schart.SChart property) top_level_jobs (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) top_level_jobsChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) top_level_jobsReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) TopBorderGroupBox (class in schrodinger.ui.qt.standard.widgets.group_boxes) Topic (class in schrodinger.stepper.stepper) TOPIC (schrodinger.application.desmond.multisimstartup.Help attribute) (schrodinger.application.desmond.multisimstartup.Startup.Help attribute) topic_prefix (schrodinger.stepper.stepper.PubsubEnabledStepMixin property) topic_suffix (schrodinger.stepper.stepper.PubsubEnabledStepMixin property) TopLevelJobBar (class in schrodinger.application.job_monitor.job_monitor_widgets) TopoError TopologicalDescriptors (class in schrodinger.application.canvas.topo_descriptors) TOPOLOGY (schrodinger.application.desmond.constants.IdConversion attribute) TopologyChart (class in schrodinger.stepper.viz) TORBNRS (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) toRdIndices() (schrodinger.application.matsci.rdpattern.Pattern method) tors_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property) TORSION_A (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) TORSION_B (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) torsion_energy() (in module schrodinger.application.qsite.output) torsion_iterator() (in module schrodinger.structutils.analyze) TorsionAngler (class in schrodinger.application.matsci.amorphous) torsionEnergySurf() (schrodinger.application.matsci.amorphous.PolymerFragments method) TorsionPotential (class in schrodinger.application.desmond.new_fep_edge_data) (class in schrodinger.application.desmond.torsion_related) TORSIONS_PER_PAGE (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker attribute) TORUS_RADII (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) TORUS_TUBE_RADII (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) TorusCore (class in schrodinger.graphics3d.torus) toSmarts() (schrodinger.application.matsci.rdpattern.Pattern method) toSmiles() (schrodinger.application.matsci.rdpattern.Pattern method) (schrodinger.rdkit.molio.CsvMolWriter method) toStIndices() (schrodinger.application.matsci.rdpattern.Pattern method) toString() (in module schrodinger.infra.ark) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.DeleteOp method) (schrodinger.application.desmond.antlr3.streams.ReplaceOp method) (schrodinger.application.desmond.antlr3.streams.RewriteOperation method) (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) (schrodinger.application.desmond.antlr3.streams.TokenStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) (schrodinger.application.desmond.antlr3.treewizard.TreePattern method) (schrodinger.application.jaguar.results.ScfIteration method) (schrodinger.application.jaguar.utils.GenOptions method) tostring() (schrodinger.application.matsci.wfmanagement.WorkflowMetadata method) toString() (schrodinger.application.steps.dataclasses.MolToSmilesSerializer method) (schrodinger.application.steps.dataclasses.ScoredMolSerializer method) (schrodinger.application.steps.enumerators.RouteSerializer method) (schrodinger.stepper.stepper.Serializer method) (schrodinger.utils.profiling.SystemResourceTimes method) toStrings() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) toStringTree() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) toStructure() (schrodinger.application.matsci.espresso.qeoutput.Magres method) toSubparser() (schrodinger.active_learning.al_driver.Option method) TOT_CHARGE_KEY (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) TOT_MAG_KEY (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) total (schrodinger.application.licensing.licadmin.stat_info attribute) TOTAL (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) total_active (schrodinger.job.queue.JobDJ property) total_added (schrodinger.job.queue.JobDJ property) total_atoms() (in module schrodinger.application.qsite.output) TOTAL_CHARGE (schrodinger.application.matsci.mswidgets.SystemInformationFrame attribute) total_charge() (in module schrodinger.application.desmond.fep_net_charge) Total_charge() (in module schrodinger.utils.ligfilter) total_charge() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) TOTAL_ENERGY (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) total_energy() (in module schrodinger.application.mopac.results_main) (in module schrodinger.application.qsite.output) total_failed (schrodinger.job.queue.JobDJ property) total_file_arguments_length() (in module schrodinger.job.jobcontrol) total_finished (schrodinger.job.queue.JobDJ property) TOTAL_FREE_ENERGY (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter attribute) total_kinetic_energy() (in module schrodinger.application.qsite.output) total_lo_correction() (in module schrodinger.application.jaguar.textparser) total_mutations (schrodinger.application.bioluminate.mutation.MacromoleculeMutator property) total_nucleophilic_superdelocalizability() (in module schrodinger.application.mopac.results_main) total_op (schrodinger.application.matsci.order_parameter_mod.Result attribute) total_potential_energy() (in module schrodinger.application.qsite.output) TOTAL_TIME (schrodinger.application.jaguar.gui.timing.TimerInfoDialog attribute) total_tokens() (schrodinger.application.licensing.licadmin.LicenseResource method) TOTAL_WEIGHT (schrodinger.application.matsci.mswidgets.SystemInformationFrame attribute) total_weight (schrodinger.structure.Structure property) totalAngle (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute) totalColumnWidth() (schrodinger.ui.qt.table.DataViewerTable method) totalRowHeight() (schrodinger.ui.qt.table.DataViewerTable method) toTree() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method) touch() (in module schrodinger.utils.fileutils) TOULBAR2 (schrodinger.protein.assignment.NetworkSolver attribute) ToWorldCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) ToWorldCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) TPP (schrodinger.application.matsci.genetic_optimization.Jaguar attribute) (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) TPSAIncludeSandP() (in module schrodinger.rdkit.filtering) tr_vec (class in schrodinger.application.matsci.cctbx.rot_mx) TRACE_FILE_EXT (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) TRACE_HEADER (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis attribute) traceback_str (schrodinger.tasks.tasks.FailureInfo attribute) traceback_strChanged (schrodinger.tasks.tasks.FailureInfo attribute) traceback_strReplaced (schrodinger.tasks.tasks.FailureInfo attribute) TraceDebugEventListener (class in schrodinger.application.desmond.antlr3.debug) traceIn() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) traceOut() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) track_leaked_loghandlers() (in module schrodinger.seam.testing.fixtures) trackAbleState() (schrodinger.ui.qt.swidgets.SCheckBox method) tracker (schrodinger.application.matsci.clusterstruct.ComInfo attribute) TrackingDataWidgetMapper (class in schrodinger.ui.qt.datamapper) trackJobProgress() (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) train() (schrodinger.seam.examples.active_learning_weigher.LinearRegressionModel method) TRAJ_MASK (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CommandLine attribute) TrajAnalysisGuiMixin (class in schrodinger.application.matsci.deswidgets) Trajectory TRAJECTORY (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) trajectory_intervals (schrodinger.application.desmond.new_fep_edge_data.FepData property) trajectory_not_found_dlg() (in module schrodinger.trajectory.trajectory_gui_dir.trajectory_messages) trajectory_not_loaded_dlg() (in module schrodinger.trajectory.trajectory_gui_dir.trajectory_messages) trajectory_timelines (schrodinger.application.desmond.new_fep_edge_data.FepData property) TRAJECTORY_VIEWER (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportMode attribute) TrajectoryCompoundParam (class in schrodinger.application.matsci.deswidgets) TrajectoryForSolubilityFep (class in schrodinger.application.desmond.task) TrajectoryFrame (class in schrodinger.application.matsci.equilibrium_md) TrajectoryMovieDoubleValidator (class in schrodinger.trajectory.trajectory_gui_dir.export_movie) TrajectoryTimeSlider (class in schrodinger.application.matsci.deswidgets) trajFrames() (schrodinger.application.matsci.equilibrium_md.TrjBase method) TrajRangeSelectorDialog (class in schrodinger.application.matsci.deswidgets) TrajRangeSelectorFrame (class in schrodinger.application.matsci.deswidgets) TRANS (in module schrodinger.application.matsci.buildcomplex) trans (schrodinger.application.matsci.elasticity.tensors.SquareTensor property) Trans2Text() (in module schrodinger.application.matsci.gsas.GSASIIspc) trans_cart_to_frac_from_vecs() (in module schrodinger.application.matsci.nano.xtal) trans_cart_to_fract() (in module schrodinger.application.matsci.nano.xtal) trans_frac_to_cart_from_vecs() (in module schrodinger.application.matsci.nano.xtal) trans_fract_to_cart() (in module schrodinger.application.matsci.nano.xtal) transfer_subjob_files() (in module schrodinger.application.jaguar.file_logger) transferAnnotationToQuerySeq() (schrodinger.protein.gpcr.tasks.GPCRTask method) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask method) (schrodinger.protein.tasks.hit_align.CustomFamilyTask method) transform (schrodinger.application.transforms.enumerators.SmilesTransformPair attribute) transform() (in module schrodinger.livedesign.preprocessor) (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) (schrodinger.application.matsci.mlearn.base.BaseFeaturizer method) (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) transform_atom_coordinates() (in module schrodinger.structutils.transform) transform_attributes() (schrodinger.seam.viz.render.PipelineRenderer method) transform_conformer() (in module schrodinger.rdkit.alignment) transform_file (schrodinger.application.steps.enumerators.SmilesTransformPair attribute) transform_fileChanged (schrodinger.application.steps.enumerators.SmilesTransformPair attribute) transform_fileReplaced (schrodinger.application.steps.enumerators.SmilesTransformPair attribute) transform_folders (schrodinger.application.steps.enumerators.SmilesTransformPairer.Settings attribute) transform_foldersChanged (schrodinger.application.steps.enumerators.SmilesTransformPairer.Settings attribute) transform_foldersReplaced (schrodinger.application.steps.enumerators.SmilesTransformPairer.Settings attribute) transform_matrix (schrodinger.structutils.structalign2.Alignment attribute) transform_pbc() (in module schrodinger.application.matsci.nano.xtal) transform_structure() (in module schrodinger.application.ska) (in module schrodinger.structutils.transform) transform_watermap() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) TransformApplyer (class in schrodinger.application.steps.enumerators) TRANSFORMATIONS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) TransformCell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Transformer (class in schrodinger.application.pathfinder.analysis) TransformError TransformPhase() (in module schrodinger.application.matsci.gsas.GSASIIlattice) TransformsRepository (class in schrodinger.analysis.transformations) TransformStatus (class in schrodinger.seam.viz.inspect) TransformU6() (in module schrodinger.application.matsci.gsas.GSASIIlattice) transformVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) transformWaterMapTrajectory() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) TransformXYZ() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Transition (class in schrodinger.application.matsci.bandshape_utils) (class in schrodinger.math.multi_parameter_optimization) TRANSITION_STATE (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) TransitionStateBasisSetSubTab (class in schrodinger.application.jaguar.gui.tabs.transition_state_tab) TransitionStateMixin (class in schrodinger.application.jaguar.gui.tabs.transition_state_tab) TransitionStateTab (class in schrodinger.application.jaguar.gui.tabs.transition_state_tab) TRANSLATE (schrodinger.application.matsci.montecarlo.Metropolizer attribute) translate_atom_to_origin() (in module schrodinger.structutils.transform) translate_atoms() (in module schrodinger.application.matsci.nano.xtal) translate_center_to_origin() (in module schrodinger.structutils.transform) translate_centroid_to_origin() (in module schrodinger.structutils.transform) TRANSLATE_CHOICES (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) TRANSLATE_DEFAULT (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) translate_mdl_enumerable_features() (in module schrodinger.application.scaffold_enumeration.mdl) translate_molecules() (in module schrodinger.application.matsci.nano.xtal) translate_nan_tokens_in_line() (in module schrodinger.utils.compare) translate_output_file_names() (in module schrodinger.application.desmond.config_utils) translate_output_file_names_helper() (in module schrodinger.application.desmond.config_utils) translate_rdkit_props_dict() (in module schrodinger.rdkit.rdkit_adapter) translate_structure() (in module schrodinger.structutils.transform) translate_to_1st_cell() (in module schrodinger.application.matsci.nano.xtal) translate_to_cell() (in module schrodinger.application.matsci.nano.xtal) translate_to_hb_cell() (in module schrodinger.application.matsci.pbcutils) translate_to_origin() (in module schrodinger.structutils.transform) translate_tube() (in module schrodinger.application.matsci.nano.tube) translateCentroidToOrigin() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize static method) translated_record (schrodinger.application.bioluminate.update_germline_db.translate_db.GermlineEntry property) translateLayers() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) translateMappingToProps() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) translateToFirstUnitCellChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) translateToPlane() (schrodinger.application.matsci.nano.particle.Nanoparticle method) translateTopLayer() (schrodinger.application.matsci.nano.interface_mod.Interface method) translateVertices() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) translation_part_info (class in schrodinger.application.matsci.cctbx.rot_mx) Transmission() (in module schrodinger.application.matsci.gsas.GSASIIpwd) transmit() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) transmute_atom() (in module schrodinger.application.matsci.buildcomplex) TRANSPARENT_STDOUT (schrodinger.seam.debug.DebugFlag attribute) transpose() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) transposeHKLF() (in module schrodinger.application.matsci.gsas.GSASIIlattice) TRANSPRO (schrodinger.ui.qt.rama.RamaResidueType attribute) TrashButton (class in schrodinger.ui.qt.swidgets) traverse_model_rows() (in module schrodinger.ui.qt.utils) treat_disulfides (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_disulfidesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_disulfidesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_glycosylation (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_glycosylationChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_glycosylationReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_metals (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_metalsChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_metalsReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_palmitoylation (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_palmitoylationChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treat_palmitoylationReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) treatSolventFromSolute() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) Tree (class in schrodinger.application.desmond.antlr3.tree) tree (schrodinger.application.pathfinder.analysis.RetrosynthesisState attribute) TreeAdaptor (class in schrodinger.application.desmond.antlr3.tree) treeAsString() (schrodinger.application.pathfinder.route.Node method) treeContextCallback() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) TreeNodeStream (class in schrodinger.application.desmond.antlr3.tree) TreeParser (class in schrodinger.application.desmond.antlr3.tree) TreePattern (class in schrodinger.application.desmond.antlr3.treewizard) TreePatternLexer (class in schrodinger.application.desmond.antlr3.treewizard) TreePatternParser (class in schrodinger.application.desmond.antlr3.treewizard) TreePatternTreeAdaptor (class in schrodinger.application.desmond.antlr3.treewizard) TreeRuleReturnScope (class in schrodinger.application.desmond.antlr3.tree) TreeVisitor (class in schrodinger.application.desmond.antlr3.tree) TreeWizard (class in schrodinger.application.desmond.antlr3.treewizard) tria() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) triangle_areas() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) TRICAPPED_TRIGONAL_PRISMATIC (in module schrodinger.application.matsci.buildcomplex) TRICAPPED_TRIGONAL_PRISMATIC_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) TRICLINIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) TRIGONAL_BIPYRAMIDAL (in module schrodinger.application.matsci.buildcomplex) TRIGONAL_BIPYRAMIDAL_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) trigonal_bonding_vector() (in module schrodinger.application.matsci.rxn_channel) TRIGONAL_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) TRIGONAL_PLANAR (in module schrodinger.application.matsci.buildcomplex) TRIGONAL_PLANAR_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) TrigonalBipyramidalSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) TrigonalPlanarSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) Trim (class in schrodinger.application.desmond.stage.workflow) trim_redundant_combinations() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) trim_str() (in module schrodinger.application.matsci.typography) trimDefinitionDict() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) Triple (schrodinger.structure.BondType attribute) tripleRingAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) triplet (schrodinger.application.jaguar.gui.tabs.theory_tab.ExcitedStateInfo attribute) trj (schrodinger.application.matsci.deswidgets.DesmondMDWidgets.NUM_FRMS_TYPE attribute) (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) TRJ_INTVL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) trj_max (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) trj_maxChanged (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) trj_maxReplaced (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) trj_min (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) trj_minChanged (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) trj_minReplaced (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) TRJ_NFRM_LABEL (schrodinger.application.matsci.deswidgets.DesmondMDWidgets attribute) trj_step (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) trj_stepChanged (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) trj_stepReplaced (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) TRJ_WRITE_VEL (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) TrjBase (class in schrodinger.application.matsci.equilibrium_md) trjChanged (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) trjFrames() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) TRJINT (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) TRJINT_STRINGER (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) trjReplaced (schrodinger.application.matsci.deswidgets.TrajectoryCompoundParam attribute) TRUE (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolOperator attribute) truncate_hits() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) truncate_label() (in module schrodinger.application.desmond.feputils) truncate_solvate_protein() (in module schrodinger.application.desmond.system_builder_util) truncateProtein() (in module schrodinger.application.desmond.system_builder_util) try_access_bq_table() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) try_import() (in module schrodinger.utils.moduleproxy) try_login_using_last_session_credential() (in module schrodinger.application.livedesign.maestro_ld_connection) TS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) ts_component_precision (schrodinger.application.jaguar.results.JaguarResults attribute) TS_NAME (schrodinger.application.desmond.stage.analysis.TimeSeriesAnalysisJob attribute) TS_Partition_F (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) TS_Sibling (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) TSDisplacementError TSEnergyError TSFailure TSFrequencyError TSMethod (class in schrodinger.application.jaguar.rotation_barriers_keywords) tst_rate_constant() (in module schrodinger.application.jaguar.kinetics) TUBE_OUT_MAE_NAME (schrodinger.application.matsci.nano.constants.Constants attribute) tube_radius (schrodinger.graphics3d.torus.MaestroTorus property) tubularizeNanoTubeSheet() (schrodinger.application.matsci.nano.tube.NanoTube method) tug_align_args (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) tug_align_argsChanged (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) tug_align_argsReplaced (schrodinger.application.livedesign.tasks.TugAlignTask.Input attribute) TugAlignTask (class in schrodinger.application.livedesign.tasks) TugAlignTask.Input (class in schrodinger.application.livedesign.tasks) TugAlignTask.Output (class in schrodinger.application.livedesign.tasks) tuple_to_qfont() (in module schrodinger.ui.qt.formlayout) TupleParam (class in schrodinger.models.parameters) TupleSafeLoader (class in schrodinger.application.matsci.yamlutils) TupleSerializer (class in schrodinger.models.jsonable) TupleWithRange (class in schrodinger.protein.annotation) TurboEelsType (class in schrodinger.application.matsci.espresso.qeinput) TurboLanczosType (class in schrodinger.application.matsci.espresso.qeinput) TurboSpectrumType (class in schrodinger.application.matsci.espresso.qeinput) turn_off_unwanted_wheel_events() (in module schrodinger.application.matsci.gutils) TURN_PROPENSITY (class in schrodinger.protein.residue) turn_propensity (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) TurnBreaking (schrodinger.protein.residue.TURN_PROPENSITY attribute) TurnForming (schrodinger.protein.residue.TURN_PROPENSITY attribute) tutorialRequested (schrodinger.ui.qt.swidgets.HelpButton attribute) twist (schrodinger.application.matsci.atom_group.HelixData attribute) two_d (schrodinger.application.livedesign.export_tasks.TaskType attribute) two_e_terms() (in module schrodinger.application.jaguar.textparser) TWO_THETA_KEY (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) TWO_THETA_TITLE (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) TWOD (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath attribute) TwoDTableDelegate (class in schrodinger.ui.two_d_viewer) TwoDTableModel (class in schrodinger.ui.two_d_viewer) TwoDTableView (class in schrodinger.ui.two_d_viewer) TwoDViewer (class in schrodinger.ui.two_d_viewer) TwoFileInput (class in schrodinger.application.matsci.permittivity) type (schrodinger.application.bioluminate.classify.ProteinClass attribute) (schrodinger.application.desmond.antlr3.tree.CommonTree property) TYPE (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) type (schrodinger.application.matsci.kmc.ColumnData attribute) TYPE (schrodinger.application.matsci.kmc.Table attribute) (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) type (schrodinger.protein.assignment.ProtAssign.amine_changeable attribute) (schrodinger.protein.assignment.ProtAssign.ligand_changeable attribute) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) (schrodinger.structure.StructureBond property) type() (schrodinger.application.glide.glide.Constraint method) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method) TYPE1NEIGHBOR (schrodinger.application.matsci.nano.sheet.Grow attribute) TYPE2NEIGHBOR (schrodinger.application.matsci.nano.sheet.Grow attribute) type_asl() (in module schrodinger.application.matsci.parserutils) type_cast_jaguar_keywords() (in module schrodinger.application.matsci.reaction_workflow_utils) type_cast_novel_sdf_file() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF static method) type_cast_reaction_wf_input() (in module schrodinger.application.matsci.reaction_workflow_utils) type_cast_sdf_file() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae static method) type_cms_file() (in module schrodinger.application.matsci.parserutils) type_cms_with_trj() (in module schrodinger.application.matsci.parserutils) type_csv_file() (in module schrodinger.application.matsci.parserutils) type_desmond_cfg() (in module schrodinger.application.matsci.parserutils) type_desmond_ensemble() (in module schrodinger.application.matsci.parserutils) type_desmond_msj() (in module schrodinger.application.matsci.parserutils) type_element() (in module schrodinger.application.matsci.parserutils) type_element_comma_list() (in module schrodinger.application.matsci.parserutils) type_exclusive_percent() (in module schrodinger.application.matsci.parserutils) type_field() (in module schrodinger.application.matsci.kmc) type_file() (in module schrodinger.application.matsci.parserutils) type_float_comma_list() (in module schrodinger.application.matsci.parserutils) type_forcefield() (in module schrodinger.application.matsci.parserutils) type_forcefield_and_get_number() (in module schrodinger.application.matsci.parserutils) type_host() (in module schrodinger.application.matsci.parserutils) type_input() (in module schrodinger.application.matsci.qubec_utils) type_json_file() (in module schrodinger.application.matsci.parserutils) type_keywords_to_dict() (in module schrodinger.application.matsci.parserutils) type_keywords_to_string() (in module schrodinger.application.matsci.parserutils) TYPE_LABEL (schrodinger.application.matsci.clusterstruct.AtomGroupData attribute) (schrodinger.application.matsci.clusterstruct.SpeciesData attribute) TYPE_MAX (schrodinger.application.matsci.cg_mapping.CGMapper attribute) type_model_file() (in module schrodinger.application.matsci.equilibrium_md) type_msj() (in module schrodinger.application.matsci.parserutils) type_negative_float() (in module schrodinger.application.matsci.parserutils) type_nonnegative_float() (in module schrodinger.application.matsci.parserutils) type_nonnegative_float_comma_list() (in module schrodinger.application.matsci.parserutils) type_nonnegative_int() (in module schrodinger.application.matsci.parserutils) type_nonpositive_float() (in module schrodinger.application.matsci.parserutils) type_nonzero_percent() (in module schrodinger.application.matsci.parserutils) type_num_colon_list() (in module schrodinger.application.matsci.parserutils) type_num_comma_list() (in module schrodinger.application.matsci.parserutils) type_num_list() (in module schrodinger.application.matsci.parserutils) type_out_file() (in module schrodinger.application.matsci.parserutils) type_percentage() (in module schrodinger.application.matsci.parserutils) type_positive_float() (in module schrodinger.application.matsci.parserutils) type_positive_int() (in module schrodinger.application.matsci.parserutils) type_positive_integer_comma_list() (in module schrodinger.application.matsci.parserutils) type_random_seed() (in module schrodinger.application.matsci.parserutils) type_ranged_int() (in module schrodinger.application.matsci.parserutils) type_ranged_num() (in module schrodinger.application.matsci.parserutils) type_smarts() (in module schrodinger.application.matsci.parserutils) type_structure_file() (in module schrodinger.application.matsci.parserutils) type_toml_file() (in module schrodinger.application.matsci.parserutils) type_xyz_file() (in module schrodinger.application.matsci.parserutils) type_yaml_file() (in module schrodinger.application.matsci.parserutils) TYPEAANEIGHBOR (schrodinger.application.matsci.nano.sheet.Grow attribute) typeChanged() (schrodinger.application.matsci.mswidgets.StructureLoader method) TYPED_RESPONSES (schrodinger.ui.qt.messagebox.MessageBox attribute) typer_cls (schrodinger.application.desmond.systype.TyperBase attribute) TyperBase (class in schrodinger.application.desmond.systype) TYPES (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) TYPES_TO_CLASSES (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) typeTest() (schrodinger.application.matsci.mstest.MSTestCase method) TYPEZZNEIGHBOR (schrodinger.application.matsci.nano.sheet.Grow attribute) TYPO_TYPE (class in schrodinger.application.matsci.typography)

U

u (schrodinger.application.matsci.espresso.qeoutput.PhDOS.Thermo attribute) u() (in module schrodinger.ui.qt.formlayout) U2Uij() (in module schrodinger.application.matsci.gsas.GSASIIspc) U6toUij() (in module schrodinger.application.matsci.gsas.GSASIIlattice) UDFT (schrodinger.application.jaguar.constants.CalcType attribute) udpateCmd() (schrodinger.application.matsci.permittivity.SusceptibilityMerge method) (schrodinger.application.matsci.permittivity.TwoFileInput method) udpateToolTip() (schrodinger.application.matsci.deswidgets.AdvancedMDOptions method) UFF_PCM_RADII (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) UFFFailure UHF (schrodinger.application.jaguar.constants.CalcType attribute) (schrodinger.application.matsci.crest.CrestTOML attribute) UHF_LABELS (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) ui() (in module schrodinger.application.desmond.starter.ui.constant_ph) (in module schrodinger.application.desmond.starter.ui.fep_absolute_binding) (in module schrodinger.application.desmond.starter.ui.fep_plus) (in module schrodinger.application.desmond.starter.ui.fep_residue_scanning) (in module schrodinger.application.desmond.starter.ui.fep_solubility) (in module schrodinger.application.desmond.starter.ui.mxmd) (in module schrodinger.application.desmond.starter.ui.unbinding_kinetics) Ui_customoplssettingwidget (class in schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget_ui) Ui_Dialog (class in schrodinger.application.desmond.desmond_advanced_tab_ui) (class in schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui) (class in schrodinger.application.jobserver_cert_gui_dir.registration_panel_ui) (class in schrodinger.application.livedesign.login_ui) (class in schrodinger.application.pymol.pymol4maestro_ui) (class in schrodinger.infra.exception_handler_dir.exception_dialog_ui) (class in schrodinger.trajectory.traj_dialog_ui) (class in schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui) (class in schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui) (class in schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui) (class in schrodinger.trajectory.trajectory_gui_dir.export_movie_ui) (class in schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui) (class in schrodinger.trajectory.trajectory_gui_dir.export_structures_ui) (class in schrodinger.trajectory.trajectory_gui_dir.job_settings_dialog_ui) (class in schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui) (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui) (class in schrodinger.ui.ligfilter_definition_dialog_ui) (class in schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui) (class in schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui) (class in schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui) (class in schrodinger.ui.qt.entryselector_ui) (class in schrodinger.ui.qt.filter_dialog_ui) (class in schrodinger.ui.qt.rename_favorite_dialog_ui) (class in schrodinger.ui.qt.select_residues_dialog_ui) Ui_FFGlobalPreferencesWidget (class in schrodinger.ui.qt.forcefield.ffglobalpreferencewidget_ui) Ui_FFProjectSettingsDlg (class in schrodinger.ui.qt.forcefield.ffprojectsettingsdlg_ui) Ui_FindToolBar (class in schrodinger.maestro_utils.find_tool_bar.find_tool_bar_ui) Ui_Form (class in schrodinger.application.bioluminate.propfilter_ui) (class in schrodinger.application.bioluminate.protein_structure_quality_ui) (class in schrodinger.application.desmond.input_group_ui) (class in schrodinger.application.desmond.rest_tab_ui) (class in schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up.per_atom_basis_ui) (class in schrodinger.application.jaguar.gui.ui.config_dialog_jaguar_ui) (class in schrodinger.application.jaguar.gui.ui.define_smarts_panel_ui) (class in schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.input_hb_top_ui) (class in schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.input_pka_top_ui) (class in schrodinger.application.jaguar.gui.ui.input_std_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui) (class in schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui) (class in schrodinger.application.jaguar.gui.ui.input_top_ui) (class in schrodinger.application.jaguar.gui.ui.irc_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.irc_top_ui) (class in schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.molecule_top_ui) (class in schrodinger.application.jaguar.gui.ui.multi_structures_ui) (class in schrodinger.application.jaguar.gui.ui.optimization_tab_ui) (class in schrodinger.application.jaguar.gui.ui.output_tab_ui) (class in schrodinger.application.jaguar.gui.ui.pka_smarts_page_ui) (class in schrodinger.application.jaguar.gui.ui.properties_tab_ui) (class in schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui) (class in schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui) (class in schrodinger.application.jaguar.gui.ui.reaction_tab_ui) (class in schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui) (class in schrodinger.application.jaguar.gui.ui.scan_tab_ui) (class in schrodinger.application.jaguar.gui.ui.scf_tab_ui) (class in schrodinger.application.jaguar.gui.ui.solvent_pka_tab_ui) (class in schrodinger.application.jaguar.gui.ui.solvent_tab_ui) (class in schrodinger.application.jaguar.gui.ui.theory_tab_ui) (class in schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.transition_state_top_ui) (class in schrodinger.application.job_monitor.diagnostics_dialog_ui) (class in schrodinger.application.job_monitor.file_browser_ui) (class in schrodinger.application.job_monitor.job_info_view_ui) (class in schrodinger.application.job_monitor.top_level_view_ui) (class in schrodinger.application.livedesign.export_setup_ui) (class in schrodinger.application.livedesign.export_ui) (class in schrodinger.application.livedesign.invalid_ge_id_warning_ui) (class in schrodinger.application.livedesign.live_report_widget_ui) (class in schrodinger.application.livedesign.login2_ui) (class in schrodinger.application.livedesign.maestro_ld_mapping_ui) (class in schrodinger.application.livedesign.mappings_manager_ui) (class in schrodinger.application.livedesign.pose_name_panel_ui) (class in schrodinger.application.livedesign.save_mapping_dialog_ui) (class in schrodinger.application.livedesign.selection_pop_up_ui) (class in schrodinger.application.livedesign.summary_ui) (class in schrodinger.application.prime.gui.ui.analyze_energy_ui) (class in schrodinger.application.prime.gui.ui.environment_options_ui) (class in schrodinger.application.pymol.ui.advanced_settings_wdg_ui) (class in schrodinger.trajectory.trajectory_gui_dir.advanced_plot_ui) (class in schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui) (class in schrodinger.trajectory.trajectory_gui_dir.collapsible_plot_ui) (class in schrodinger.trajectory.trajectory_gui_dir.conf_wheel_plot_panel_ui) (class in schrodinger.trajectory.trajectory_gui_dir.energy_plot_ui) (class in schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui) (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui) (class in schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui) (class in schrodinger.trajectory.trajectory_gui_dir.rdf_plot_ui) (class in schrodinger.trajectory.trajectory_gui_dir.shortcut_ui) (class in schrodinger.ui.ligfilter_ui) (class in schrodinger.ui.qt.appframework2.debug_gui_ui) (class in schrodinger.ui.qt.atom_weights_table_ui) (class in schrodinger.ui.qt.config_dialog_open_mp_ui) (class in schrodinger.ui.qt.config_dialog_queue_ui) (class in schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui) (class in schrodinger.ui.qt.fp_selector_widget_ui) (class in schrodinger.ui.qt.presets.manage_presets_dialog_ui) (class in schrodinger.ui.qt.presets.save_presets_dialog_ui) (class in schrodinger.ui.qt.protein_health_viewer_ui) (class in schrodinger.ui.qt.tasks.config_dialog_ui) (class in schrodinger.ui.qt.tasks.config_info_ui) (class in schrodinger.ui.qt.tasks.taskbar_ui) (class in schrodinger.ui.qt.widgetmixins.mock_ui) (class in schrodinger.ui.two_d_viewer_ui) Ui_Frame (class in schrodinger.ui.qt.borderless_popup_ui) Ui_MainWindow (class in schrodinger.application.jaguar.gui.ui.edit_dialog_ui) ui_module (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector attribute) UI_MODULE (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab attribute) ui_module (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsDialog attribute) (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser attribute) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget attribute) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane attribute) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel attribute) (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog attribute) (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel attribute) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget attribute) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel attribute) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel attribute) (schrodinger.application.livedesign.widgets.InvalidGEIdWarningDialog attribute) (schrodinger.application.pymol.export_to_pymol_gui.AdvancedSettingsPopUp attribute) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel attribute) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBar attribute) (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner attribute) (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget attribute) (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingWidget attribute) (schrodinger.ui.qt.fp_selector_widget.FingerprintsSelectorWidget attribute) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog attribute) (schrodinger.ui.qt.presets.save_presets_dialog.SavePresetsDialog attribute) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog attribute) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 attribute) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin attribute) (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog attribute) UI_MODULES (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) Ui_PdbDialog (class in schrodinger.ui.qt.pdb_dialog_ui) Ui_pymol_dlg (class in schrodinger.application.pymol.ui.export_to_pymol_dlg_ui) Ui_SketcherDialog (class in schrodinger.ui.sketcher_smarts_dialog_ui) Ui_snapshot_panel (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui) Ui_trajectory_form (class in schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui) Ui_UpdatePKASettingsDlg (class in schrodinger.application.jaguar.update_pka_settings_ui) Ui_Widget (class in schrodinger.application.jaguar.gui.ui.excited_state_widget_ui) (class in schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui) Uij2betaij() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Uij2U() (in module schrodinger.application.matsci.gsas.GSASIIspc) Uij2Ueqv() (in module schrodinger.application.matsci.gsas.GSASIIlattice) UijtoU6() (in module schrodinger.application.matsci.gsas.GSASIIlattice) UiMode (class in schrodinger.application.desmond.constants) unarchive_surf_data() (in module schrodinger.application.matsci.freevolume) UNAVAIL_VALUE_TYPES (schrodinger.application.livedesign.panel_components.ColumnCheckboxItem attribute) UnavailableFingerprintType UnbatchedChain (class in schrodinger.stepper.stepper) UnbatchedMapStep (class in schrodinger.stepper.stepper) UnbatchedReduceStep (class in schrodinger.stepper.stepper) UNBIND (schrodinger.application.desmond.constants.KineticsLegTypes attribute) UnbindingKineticsArgs (class in schrodinger.application.desmond.starter.ui.unbinding_kinetics) UnbindingKineticsMsjGenerator (class in schrodinger.application.desmond.msj_generator.unbinding_kinetics) UnbindingKineticsSimLegParams (class in schrodinger.application.desmond.msj_generator.workflow_params) UnbindingKineticsWorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) UNBOUND_SIMS (schrodinger.application.desmond.kinetics.utils.ResultsCols attribute) uncapped_smi (schrodinger.application.dendrogram.core_class.RingSysInfo attribute) uncapped_st (schrodinger.application.dendrogram.core_class.RingSysInfo attribute) uncertaintySelect() (schrodinger.active_learning.al_node.PrepareSmilesNode method) Uncharge (class in schrodinger.application.transforms.chem) uncheckAll() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) UNCHECKED_DEFAULT (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) UNCHECKED_DISABLED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) UNCHECKED_HOVER (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) unchecked_map (schrodinger.utils.sea.evalor.Evalor property) UNCHECKED_PRESSED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) UndefinedBondOperation UndefinedStereochemistry (class in schrodinger.structure) under_job_control() (in module schrodinger.job.jobcontrol) undo() (schrodinger.ui.qt.network_visualizer.Graph method) undo_block() (in module schrodinger.ui.qt.utils) UNDO_REDO_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) undoblock_cm() (in module schrodinger.application.matsci.maestrocmds) undoPointSet (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) UNEDITABLE (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) UNEDITABLE_COLS (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) unexpectedType (schrodinger.application.desmond.antlr3.exceptions.RecognitionException property) unexported_items (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) unexported_itemsChanged (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) unexported_itemsReplaced (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) UNFOLDED_PROPERTY (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) UNFOLDED_PROPERTY_PRIME (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) ungroup() (schrodinger.project.project.ProjectRow method) UNGROUPED_ARE_ABSOLUTE (schrodinger.livedesign.preprocessor.ChiralFlag0Meaning attribute) UNGROUPED_ARE_RACEMIC (schrodinger.livedesign.preprocessor.ChiralFlag0Meaning attribute) UNGROUPED_ARE_RELATIVE (schrodinger.livedesign.preprocessor.ChiralFlag0Meaning attribute) unicode (schrodinger.application.matsci.typography.TYPO_TYPE attribute) unicode_to_str() (in module schrodinger.livedesign.preprocessor) UniformSequence (class in schrodinger.application.matsci.reaction_workflow_gui_utils) union() (schrodinger.utils.scollections.IdSet method) UNIQUE (schrodinger.application.matsci.rxn_channel.Constants attribute) unique() (in module schrodinger.application.desmond.util) unique_job_name() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) unique_smiles (schrodinger.structutils.analyze.Ligand property) uniqueCombinations() (in module schrodinger.application.matsci.gsas.GSASIIlattice) UniqueFilter (class in schrodinger.adapter) UniqueGeomMixin (class in schrodinger.application.matsci.reaction_workflow_utils) UniqueSmartsDirector (class in schrodinger.application.matsci.order_parameter_mod) uniquesmiler() (in module schrodinger.utils.cgxutils) UniqueTracker (class in schrodinger.application.matsci.fragments) uniquifiyTaskName() (schrodinger.tasks.taskmanager.TaskManager method) uniquify() (in module schrodinger.ui.qt.appframework2.jobnames) uniquify_mols() (in module schrodinger.application.pathfinder.synthesis) uniquify_titles_callback() (in module schrodinger.application.matsci.genetic_optimization) UniquifyResults() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) Unit (class in schrodinger.application.jaguar.constants) UNIT_CELL_DENSITY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) UNIT_CELL_FORMULA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) UNIT_CELL_VOLUME_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) unit_vector() (in module schrodinger.structutils.interactions.pi) unit_vector_points() (in module schrodinger.structutils.interactions.pi) UNITCELLINDEX (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) units (schrodinger.application.livedesign.export_models.DataExportSpec attribute) Units (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) UNITS (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) (schrodinger.application.matsci.espresso.qeoutput.Magres attribute) units (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) UNITS (schrodinger.application.matsci.genetic_optimization.ChemInformatics attribute) (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) (schrodinger.application.matsci.genetic_optimization.GlassTransitionTemperature attribute) units (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) UNITS (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) units (schrodinger.application.matsci.mlearn.features.MomentData attribute) units() (schrodinger.tasks.hosts.Host method) UNITS_DICT (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) units_lbl (schrodinger.ui.qt.tasks.configwidgets.HostSelector property) unitsChanged (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) unitsReplaced (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) universal_anisotropy (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) UNK (schrodinger.application.matsci.automated_cg_mapping.MoleculeData attribute) UNKNOWN (in module schrodinger.ui.qt.pop_up_widgets) (schrodinger.application.desmond.constants.CorrectionTerm attribute) (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.jaguar.output.JaguarOutput attribute) (schrodinger.application.xtb.output.XTBOutput attribute) (schrodinger.livedesign.entity_type.EntityClass attribute) (schrodinger.rdkit_extensions.CompressionType attribute) UNKNOWN_BIOLOGIC (schrodinger.livedesign.entity_type.EntityClass attribute) UnknownAppError UnknownChiralityError UnknownPropertySuboptionError UnknownRuleError unlock_entries() (in module schrodinger.project.utils) unmapAtom() (schrodinger.application.matsci.reordergui.StructureFrame method) unmapPair() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) unmask() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) unmaskCommand() (schrodinger.application.matsci.jwsteps.BaseStep method) unmatched_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property) unmatched_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property) unpack() (schrodinger.application.desmond.antlr3.dfa.DFA class method) unpackModel() (schrodinger.active_learning.mq_backend.Backend method) unpaired (schrodinger.application.jaguar.utils.LewisStructure attribute) unproductive() (in module schrodinger.application.matsci.genetic_optimization) UnreadableHostsFileException UnregisteredFile (class in schrodinger.application.desmond.test_utils) UnregisteredFileError Unrestricted (schrodinger.application.jaguar.gui.utils.SpinTreatment attribute) unrestrictedAvailable() (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) (schrodinger.application.jaguar.gui.utils.SpinTreatment method) unroll_pos() (in module schrodinger.trajectory.utils) unselectRows() (schrodinger.infra.table.Table method) UnserializableMolError unset() (schrodinger.application.matsci.builderwidgets.StructureLabel method) (schrodinger.infra.mmbitset.Bitset method) unset_unique_pdb_res_names() (in module schrodinger.application.matsci.packmol) unsign() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.licensing.flexlm.LicenseLine method) (schrodinger.application.licensing.flexlm.Package method) UNSORTABLE_COLS (schrodinger.ui.qt.table.PerColumnSortableTableView attribute) UnsupportedConversionException UnsupportedElementError UnsupportedFormat UnsupportedOption (class in schrodinger.structure) UnsupportedOptionValue (class in schrodinger.structure) UnsupportedReaction UnsupportedStructureError, [1] UNUSABLE_PACKAGES (schrodinger.infra.unusable_module_importer.AbstractUnusableModuleFinder attribute) (schrodinger.infra.unusable_module_importer.MaestroUnusableModuleFinder attribute) (schrodinger.infra.unusable_module_importer.NonPostTestUnusableModuleFinder attribute) UnusableModuleLoader (class in schrodinger.infra.unusable_module_importer) UnwantedTokenException unwrap_lines() (in module schrodinger.application.jaguar.check_headers) unwrapReducedDisplacement() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) unzip_and_get_membrane_test_files() (in module schrodinger.application.desmond.test_utils) unzip_grids() (in module schrodinger.application.glide.utils) unzip_project() (in module schrodinger.project.project) unzip_query() (in module schrodinger.application.bb_database.bb_task_utils) UP (schrodinger.models.presets.Direction attribute) UP_ARROW (schrodinger.ui.qt.standard.design_tokens.ScrollbarIcons attribute) UP_TO_MINDEX (schrodinger.application.matsci.nano.constants.Constants attribute) UP_TO_NINDEX (schrodinger.application.matsci.nano.constants.Constants attribute) update() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.desmond.rest_inp.RestInput method) (schrodinger.application.desmond.stage.simulate.ConcatParam method) (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) (schrodinger.application.glide.sort_utils.ReceptorTable method) (schrodinger.application.glide.utils.Progress method) (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) (schrodinger.application.matsci.automated_cg_mapping.Mapping method) (schrodinger.application.matsci.crest.CrestCSearchJob method) (schrodinger.application.matsci.crest.CrestJob method) (schrodinger.application.matsci.permittivity.TaskProtocol method) (schrodinger.application.watermap.watermap_inp.WaterMapInput method) (schrodinger.comparison.results.ResultSet method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.project.project.Project method) (schrodinger.ui.qt.config_dialog.DialogParameters method) (schrodinger.ui.qt.config_dialog.StartDialogParams method) (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) (schrodinger.ui.qt.formlayout.SliderLayout method) (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.scollections.IdSet method) (schrodinger.utils.sea.sea.Atom method) (schrodinger.utils.sea.sea.List method) (schrodinger.utils.sea.sea.Map method) update_atom_indices() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) update_basedir() (schrodinger.application.desmond.cmj.JobOutput method) update_buttons() (schrodinger.ui.qt.formlayout.FormDialog method) update_color() (schrodinger.ui.qt.formlayout.ColorLayout method) update_display() (schrodinger.ui.qt.rama.Rama method) update_guess() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) (schrodinger.application.matsci.gsas.GSASIImath.fast_sa method) (schrodinger.application.matsci.gsas.GSASIImath.log_sa method) update_hydrogen_xyz_from_state() (schrodinger.protein.assignment.ProtAssign.ligand_changeable method) update_hypothesis_entry() (in module schrodinger.application.phase.phase_markers) (in module schrodinger.application.phase.pt_hypothesis) update_index_properties() (in module schrodinger.application.matsci.reaction_workflow_utils) update_input_file_paths() (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) update_internal_coords_to_vector_atoms() (schrodinger.protein.membrane.Membrane_Model method) update_jobname() (in module schrodinger.ui.qt.appframework2.jobnames) update_ligand_rotatables_annotation() (in module schrodinger.protein.assignment) update_macro_dict() (in module schrodinger.utils.sea.sea) update_membrane_relaxation_protocol() (in module schrodinger.application.desmond.gui) update_mol_groups() (in module schrodinger.livedesign.preprocessor) update_once() (in module schrodinger.structure) update_params() (in module schrodinger.application.prepwizard2.tasks) (in module schrodinger.application.steps.utils) update_pass_fail() (schrodinger.application.desmond.simulation_block_test.Test method) update_pdb_pbc() (in module schrodinger.application.matsci.desmondutils) update_phase_markers_label_font() (in module schrodinger.application.phase.phase_markers) update_pipeline_jobs() (schrodinger.seam.viz.watcherd.Watcher method) update_point_faces() (schrodinger.ui.qt.rama.RamaScatterMixin method) update_point_xval() (schrodinger.ui.qt.rama.RamaScatterMixin method) update_point_yval() (schrodinger.ui.qt.rama.RamaScatterMixin method) update_progress() (in module schrodinger.application.bioluminate.pml_menus) update_props() (in module schrodinger.application.mopac.results_main) update_required_licenses() (in module schrodinger.application.livedesign.ld_glide_utils) update_rotatable_changeable_indices() (in module schrodinger.protein.assignment) update_sgroup_indexes() (in module schrodinger.livedesign.preprocessor) update_sgroups() (in module schrodinger.livedesign.preprocessor) update_simulation_box() (in module schrodinger.trajectory.trajectoryviewer) update_stage_user_keys() (schrodinger.application.jaguar.esol_input.EsolInput method) update_stereo_groups() (in module schrodinger.livedesign.preprocessor) update_task_from_settings() (in module schrodinger.application.prepwizard) update_temp() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) (schrodinger.application.matsci.gsas.GSASIImath.fast_sa method) (schrodinger.application.matsci.gsas.GSASIImath.log_sa method) update_text() (schrodinger.ui.qt.formlayout.ColorLayout method) update_title() (in module schrodinger.protein.process_enamine_db) update_widget_style() (in module schrodinger.ui.qt.utils) update_with_frame() (schrodinger.application.desmond.cms.Cms method) update_workflow_metadata() (in module schrodinger.application.matsci.wfmanagement) updateAdjustPositionCheckBox() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateAdjustViewPositioning() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateAllAtomIndexMaps() (schrodinger.application.matsci.amorphous.PolymerFragments method) updateAllConstraintsPB() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) updateAllNumFrames() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) updateAllResidues() (schrodinger.ui.residueselector.ResidueGroups method) updateAndCheckMmJag() (schrodinger.application.jaguar.gui.base_panel.NoInputTabJobMixin method) updateAnimation() (schrodinger.application.desmond.feputils.LabelSpinner method) updateAnimationSize() (schrodinger.application.desmond.feputils.LabelSpinner method) updateArrowAndPlane() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) updateAtomGroupButtons() (schrodinger.application.desmond.gui.AtomGroupFrame method) updateAtomNames() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow method) updateAtomSelectorWidget() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) updateAtomWeights() (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings method) updateAVPAsl() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateAVPAslOption() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateAVPAslOptionLabel() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateAVPOption() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateAxes() (schrodinger.ui.qt.schart.SHistogramBarSeries method) updateBasicDataFromUI() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateBasicTab() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateBeyondBindingSite() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateBidningSiteRadius() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) updateBindingSiteTooltip() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method)

updateBins() (schrodinger.ui.qt.schart.BinsDialog method) updateButtonStates() (schrodinger.ui.qt.propertyselector.PropertySelector method) updateButtonText() (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) updateChannelDefReprs() (schrodinger.application.matsci.rxn_channel.Channels method) updateCheckState() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) updateClearButton() (schrodinger.ui.qt.swidgets.SLineEdit method) updateColumnNames() (schrodinger.ui.qt.swidgets.STableWidget method) updateCoordinates() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) (schrodinger.structutils.minimize.Minimizer method) (schrodinger.ui.qt.dendrogram.GuiPanel method) updateCPULimits() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) updateCrystalPropertiesIfRequired() (schrodinger.project.project.Project method) updateCurrentFrameLabel() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) updateCustomOplsDir() (schrodinger.ui.qt.forcefield.ffglobalpreferencewidget.FFGlobalPreferenceWidget method) updated (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) (schrodinger.models.diffy.DictDiff attribute) updated_display() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) updated_font() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) updated_foreground() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) updated_sort_role() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) UPDATED_TEXT (schrodinger.application.matsci.jobdirdlg.JobManager attribute) updated_tooltip_display() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) updateData() (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame method) updateDefinitionState() (schrodinger.ui.ligfilter.AddDefinitionDialog method) updateDefParts() (schrodinger.application.matsci.rxn_channel.Reactants method) updateDescriptors() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) updateDialogKeys() (schrodinger.application.desmond.gui.AdvOptionsFrame method) updateDipoleInterval() (schrodinger.application.matsci.permittivity.MdStageModifier method) updateDlg() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) updateDownloadButton() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) updatedTasks() (schrodinger.tasks.queue.TaskDJ method) updateEdge() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) updateEdges() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) updateEditorGeometry() (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.TempItemDelegate method) (schrodinger.ui.qt.delegates.SpinBoxDelegate method) updateEnabled() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) (schrodinger.ui.qt.tasks.taskwidgets.StartButton method) updateEnabledExportableData() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) updateEnsClassFromKey() (schrodinger.application.desmond.gui.EnsembleClassFrame method) updateEnsembleParameters() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) updateEntryCountLabels() (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) updateEntryTitles() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) updateExportButton() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) updateFeatureNames() (schrodinger.application.phase.featureselector.FeatureModel method) updateFileDependentOptions() (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) updateFilterObj() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) updateFontForAllLabels() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) updateForMethod() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) updateForRangeType() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) updateFrameLog() (schrodinger.application.matsci.atom_group.MSAtomGroupsBase method) updateFramesOption() (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) updateFramesOptionAndResetButton() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) updateFramesStackedWidget() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) updateFromDump() (schrodinger.pipeline.pipeline.StageJob method) updateFromIterable() (schrodinger.utils.scollections.IdDict method) updateFromKey() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.EnsembleClassFrame method) (schrodinger.application.desmond.gui.EnsembleTab method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.IntegrationTab method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.OutputTab method) (schrodinger.application.desmond.gui.RandVelFrame method) (schrodinger.application.desmond.gui.RelaxFrame method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.gui.SimOptionsFrame method) updateFunctionalGroups() (schrodinger.application.matsci.automated_cg_mapping.StructData method) updateFusedRingIdxsForNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) updateGUI() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) updateHideAtoms() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) updateHideAtomsDataFromUI() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateHistogram() (schrodinger.ui.qt.schart.SHistogramBarSet method) updateHistograms() (schrodinger.ui.qt.schart.SHistogramBarSeries method) updateHostsList() (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) updateHoverLabel() (schrodinger.ui.qt.schart.SChartView method) updateHypothesisFromEntry() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) updateInclExclState() (schrodinger.ui.ligfilter.AddDefinitionDialog method) updateInfileAndCommand() (schrodinger.application.matsci.permittivity.StepBase method) updateInfoLabel() (schrodinger.ui.two_d_viewer.TwoDViewer method) updateInternalsForNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) updateItems() (schrodinger.application.bioluminate.pml_menus.EntrySubMenu method) (schrodinger.application.bioluminate.pml_menus.RecentCarbonColorSubMenu method) (schrodinger.application.bioluminate.pml_menus.RecentColorSubMenu method) (schrodinger.application.bioluminate.pml_menus.RecentHydrogenColorSubMenu method) (schrodinger.application.bioluminate.pml_menus.RecentObjectColorSubMenu method) (schrodinger.application.bioluminate.pml_menus.SelectionSubMenu method) updateJaguarUserKeywords() (schrodinger.application.jaguar.autots_input.AutoTSInput method) updateJobdj() (schrodinger.pipeline.stage.Stage method) updateJobname() (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.JobApp method) updateJobs() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) updateKey() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.EnsembleClassFrame method) (schrodinger.application.desmond.gui.EnsembleTab method) (schrodinger.application.desmond.gui.IntegrationTab method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.OutputTab method) (schrodinger.application.desmond.gui.RandVelFrame method) (schrodinger.application.desmond.gui.RelaxFrame method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.gui.SimOptionsFrame method) updateKeywordEdit() (schrodinger.application.matsci.qualityslider.QualitySlider method) updateLabel() (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.mswidgets.StructureLoader method) (schrodinger.application.matsci.siteselector.siteselector.SiteRadioButton method) (schrodinger.ui.qt.label_cursor.LabelCursorAxes method) updateLastStage() (schrodinger.application.matsci.permittivity.MdStageModifier method) updateLatticeBonding() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) updateLatticeProperties() (schrodinger.application.matsci.nano.xtal.Crystal method) updateLaunchParams() (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) updateLegend() (schrodinger.application.matsci.plotwidgets.SliderchartVLFitStdPlot method) updateLigandList() (schrodinger.ui.qt.ligand_list.LigandListModel method) updateLightColVisibility() (schrodinger.application.bioluminate.antibody.search_results_table.FullTable method) updateLimitFrame() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) updateLineEdit() (schrodinger.application.matsci.mswidgets.ConvenientSelectorWithPopUp method) updateLoop() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateLoopTooltip() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateMaestroProperties() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) updateMapCounter() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) updateMapperWidgets() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) updateMatches() (schrodinger.application.matsci.rdpattern.EvaluateSMARTS method) updateMatchLabel() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) updateMaxjobsDefault() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.application.matsci.configdlgs.PerStructDesmondSubhostConfigDialog method) UpdateMCSAxyz() (in module schrodinger.application.matsci.gsas.GSASIImath) updateMenu() (schrodinger.ui.qt.swidgets.SavedItemsManager method) updateMetadata() (schrodinger.application.matsci.wfmanagement.WorkflowManagerMixin method) updateModel() (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.MdcMiscTab method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.models.mappers.TargetParamMapper method) updateMovieDurationTime() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) updateMovieOptions() (schrodinger.application.pymol.pymol4maestro.panel method) updateMultiStructureOptions() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) updateNConformersLabel() (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection method) updateNode() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) updateNodes() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) updateNonpolarHydrogens() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateNonpolarHydrogensTooltip() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) updateNonStandardResidues() (schrodinger.ui.residueselector.ResidueGroups method) updateNumCPUsLabel() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) updateNumFrames() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) updateNumPickedResiduesLabel() (schrodinger.ui.picking.MaestrolessPickResidueDialog method) updateOpenMPInfo() (schrodinger.application.jaguar.gui.base_panel.JaguarConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) updateOpenMPLabel() (schrodinger.ui.qt.config_dialog.ConfigDialog method) updateOrigAtomIdx() (schrodinger.application.matsci.amorphous.PolymerFragments method) updatePagination() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) updatePanel() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) updatePanelLabel() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) updatePanelTitle() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) updatePBC() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) updatePBCBondOrders() (schrodinger.application.matsci.nano.xtal.PBCBonds method) updatePermanentPic() (schrodinger.application.desmond.feputils.LabelSpinner method) updatePkaAtomsFromSmarts() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) UpdatePKASettingsDlg (class in schrodinger.application.jaguar.update_pka_settings) updatePlayDirection() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updatePlayDirectionToolTip() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updatePlusButtonStyle() (schrodinger.ui.qt.atomselector.AtomSelector method) updatePositions() (schrodinger.ui.dendrogram.DendrogramGraphicTree method) updatePosresButtons() (schrodinger.application.desmond.gui.RestraintsTab method) updatePreferences() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) updatePreviousAndNextButtons() (schrodinger.ui.two_d_viewer.TwoDViewer method) updateProductGeometries() (schrodinger.application.matsci.fragments.Reaction method) updateProductStageTempAndPress() (schrodinger.application.matsci.permittivity.MdStageModifier method) updateProgress() (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressBar method) updateProjectLabelVisibility() (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) updateProperties() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF method) (schrodinger.application.matsci.chargegui.ChargeDialog method) (schrodinger.application.matsci.chargegui.ChargePropertySelector method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.application.matsci.rxn_channel.Products method) updatePropertiesTab() (schrodinger.application.jaguar.gui.base_panel.PropertiesMixin method) updatePropertiesTable() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) updateProteinOnly() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateProteinTooltip() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) updateQueueResources() (schrodinger.ui.qt.config_dialog.ConfigDialog method) updateRangeLabel() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) updateRangeLineEditStyle() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) updateRangeStyle() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) UpdateRBUIJ() (in module schrodinger.application.matsci.gsas.GSASIImath) UpdateRBXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath) updateRecentTemplateFile() (schrodinger.application.matsci.builderwidgets.SketcherBox method) updateRecommendationLabel() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) updateReferenceMenu() (schrodinger.ui.two_d_viewer.TwoDViewer method) updateRefFrame() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateReflig() (schrodinger.application.glide.ligand_designer.GridgenTask method) updateRelativeChargeInfo() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) updateRelativeID() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) updateRelaxStageTempAndPress() (schrodinger.application.matsci.permittivity.MdStageModifier method) updateReplicaNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) updateReplicaSeed() (schrodinger.application.matsci.permittivity.MultiStageMd method) updateReplicatedAtomTotalStatus() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) updateResults() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) updateSartupJobs() (schrodinger.application.matsci.permittivity.WorkflowParser method) updateSavedASLs() (schrodinger.application.matsci.mswidgets.MSAtomSelector method) updateScatterPlot() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.RamaScatterMixin method) updateScenesRB() (schrodinger.application.pymol.pymol4maestro.panel method) updateSelectability() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) updateSelectedElements() (schrodinger.ui.qt.periodictable.PeriodicTableDialogMultipleClick method) updateSelectedEntries() (schrodinger.application.livedesign.maestro_sync.EntrySelectionMaestroSync method) updateSelections() (schrodinger.ui.residueselector.MutationSelectorMixin method) updateShape() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) updateSlider() (schrodinger.application.matsci.plotwidgets.SliderchartVLPlot method) updateSliderPosition() (schrodinger.application.matsci.mswidgets.MultiSlider method) updateSmoothing() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateSolventsOnly() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateSolventsTooltip() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) updateSpecifiedASLButton() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) updateSpeedIcons() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateSpheres() (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager method) updateSpinBox() (schrodinger.application.matsci.mswidgets.MultiSlider method) updateSpinBoxLimits() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage method) updateStageCpus() (schrodinger.pipeline.pipeline.StageJob method) updateStageDict() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage method) updateStageLabels() (schrodinger.application.matsci.mswidgets.MultiStageArea method) updateStagesCpus() (schrodinger.pipeline.pipeline.Pipeline method) updateStartAndEndFrames() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) updateStatus() (schrodinger.application.matsci.jobdirdlg.JobManager method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressBar method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) updateStatusBar (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsDialog attribute) (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser attribute) updateStatusBar() (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.JobApp method) updateStatusLabel() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) updateStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateStopCancelButtons() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) updateStrucCbsState() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) updateStructureProperties() (schrodinger.application.matsci.genetic_optimization.StructureGenome method) updateStyleSheet() (schrodinger.ui.qt.standard_widgets.buttons.FlatButton method) (schrodinger.ui.qt.standard_widgets.buttons.SplitStyledButton method) (schrodinger.ui.qt.standard_widgets.buttons.StyledButton method) UpdateSytSym() (in module schrodinger.application.matsci.gsas.GSASIIspc) updateTables() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) updateTarget() (schrodinger.models.mappers.TargetParamMapper method) updateTargetIndexMap() (schrodinger.application.pathfinder.route.RouteNode method) updateTaskReplicaSettings() (schrodinger.application.matsci.permittivity.CMSParser method) (schrodinger.application.matsci.permittivity.DisorderSystemBuilder method) (schrodinger.application.matsci.permittivity.ElectricPolarizability method) (schrodinger.application.matsci.permittivity.PolymerBuilder method) (schrodinger.application.matsci.permittivity.StepBase method) updateTempFromKey() (schrodinger.application.desmond.gui.EnsembleClassFrame method) updateTemplatePolymerResidue() (schrodinger.application.matsci.amorphous.Monomer method) updateTemplates() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) updateTemplateSelectorImportButton() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) updateText() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets.UseFromCombo method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) updateThreadingNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) updateToggled() (schrodinger.ui.qt.schart.BinsDialog method) updateToolbarFromModelOptions() (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBar method) updateToolTips() (schrodinger.application.desmond.feputils.ProteinCheckSpinnerWidget method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) updateTotalStructures() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) updateToWorkspace() (schrodinger.application.desmond.maestro.NewEntry method) updateTrajectoryDependentOptions() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) updateTrajectoryRangeLabel() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) updateTranslateToFirstUnitCellCheckBox() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateTranslateToFirstUnitCellPosition() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateTrj() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) updateTrjIntvel() (schrodinger.application.matsci.permittivity.MdStageModifier method) updateValidWaterModels() (schrodinger.application.matsci.mswidgets.WaterTypesComboBox method) updateValueLabel() (schrodinger.ui.qt.swidgets.SLabeledSlider method) updateVerticalStructure() (schrodinger.application.matsci.fragments.NonUniqueTracker method) (schrodinger.application.matsci.fragments.UniqueTracker method) updateVertices() (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) updateView() (schrodinger.ui.two_d_viewer.CellContextualMenu method) updateViewPositionDataFromUI() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateViewPositionTab() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) updateWidget() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) updateWidgets() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) updateWithData() (schrodinger.application.matsci.espresso.qeinput.GenericType method) updateWorkspaceView() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) updateXvolMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) UPDATING_TEXT (schrodinger.application.matsci.jobdirdlg.JobManager attribute) updating_values() (schrodinger.models.mappers.TargetParamMapper method) UPF2_TRUE (schrodinger.application.matsci.espresso.utils.UPFParser attribute) UPFParser (class in schrodinger.application.matsci.espresso.utils) upgrade_oplsdir() (in module schrodinger.forcefield.custom_params) upload_ld_attachment() (in module schrodinger.application.livedesign.upload_utils) upload_ld_model() (in module schrodinger.application.livedesign.upload_utils) upper_bound (schrodinger.application.desmond.correlation_tau.ConfidenceInterval attribute) UpperCaseValidator (class in schrodinger.application.jaguar.gui.basis_selector) UPTAKE (schrodinger.application.bioluminate.pose_filtering.hdx_io.DynamXColumns attribute) Uracil (schrodinger.protein.helm.helm_renderer.HexColor attribute) urlencode() (in module schrodinger.application.desmond.gchart) URN (schrodinger.seam.runners.events.PipelineFinished attribute) (schrodinger.seam.runners.events.PipelineStarted attribute) (schrodinger.seam.runners.events.SeamEvent attribute) (schrodinger.seam.runners.events.StageFailed attribute) (schrodinger.seam.runners.events.StageFinished attribute) (schrodinger.seam.runners.events.StageStarted attribute) usage() (in module schrodinger.application.jaguar.jagconvert) UsageError, [1] UsageException USE_ALL_FRAC_KEY (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) use_ccd (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput.ABOOptions attribute) use_ccdChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput.ABOOptions attribute) use_ccdReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput.ABOOptions attribute) use_centroid (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) use_confgenx (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) use_confgenxChanged (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) use_confgenxReplaced (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) USE_CONV_KEY (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) use_custom_opls_dir_preference() (in module schrodinger.ui.qt.forcefield.forcefield) use_custom_oplsdir() (in module schrodinger.application.desmond.util) use_custom_weights (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) use_custom_weightsChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) use_custom_weightsReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) USE_ENTRY_DB (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase attribute) use_epikx (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) use_epikxChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) use_epikxReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) use_existing (schrodinger.application.livedesign.live_report_widget.LRSelectionMode attribute) use_fp (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) use_fpChanged (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) use_fpReplaced (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) use_gfactors (in module schrodinger.protein.analysis) use_glide_sort() (in module schrodinger.application.phase.packages.shape_screen_job_utils) USE_GPU (schrodinger.application.desmond.cmj.Job attribute) (schrodinger.application.desmond.stage.jobs.DesmondBackendJob attribute) USE_IN_SCREEN (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) USE_JC (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) USE_LOOP_DB (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInstruction attribute) use_maestro_mouse (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) use_maestro_mouseChanged (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) use_maestro_mouseReplaced (schrodinger.application.pymol.gui_models.AdvancedSettingsModel attribute) use_monomer_charges() (in module schrodinger.application.matsci.desmondutils) use_native_file_dialog() (in module schrodinger.ui.qt.filedialog) USE_NMR_MACROSCOPIC_SHAPE (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) use_pandas_utils() (in module schrodinger.project.pandasutils) use_PDB_pH (schrodinger.application.prepwizard.PrepWizardSettings attribute) use_pdb_ph_if_available (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) use_pdb_ph_if_availableChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) use_pdb_ph_if_availableReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) use_PDB_pHChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) use_PDB_pHReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) use_pl_interactions (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) use_pose_name (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) use_pose_nameChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) use_pose_nameReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) use_pot (schrodinger.application.matsci.espresso.qeinput.CustomNEBType attribute) USE_PRIM_KEY (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) use_propka (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) use_propkaChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) use_propkaReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) use_pubsub (schrodinger.stepper.stepper.BatchSettings attribute) use_pubsubChanged (schrodinger.stepper.stepper.BatchSettings attribute) use_pubsubReplaced (schrodinger.stepper.stepper.BatchSettings attribute) use_representative_frame() (in module schrodinger.application.desmond.stage.app.absolute_binding.restraint) use_representative_structure (schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams attribute) USE_SCAFFOLD_LOOP (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInstruction attribute) use_scanning_alignment (schrodinger.structutils.structalign.StructAlign property) USE_STRUCTURE (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInstruction attribute) USE_SYMM_KEY (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) use_titration (schrodinger.application.desmond.cms.Cms property) use_wfc (schrodinger.application.matsci.espresso.qeinput.CustomNEBType attribute) useADProjectedPointsChecked() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) UseConsistentOrbitalsMixin (class in schrodinger.application.jaguar.gui.base_panel) useConstraint() (schrodinger.application.glide.glide.Dock method) useCustomForceFieldToggled (schrodinger.ui.qt.forcefield.ffglobalpreferencewidget.FFGlobalPreferenceWidget attribute) (schrodinger.ui.qt.forcefield.ffselector.MaestroForceFieldSelector attribute) useCustomParameterStateChanged (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin attribute) useCustomSettings() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) useCustomTemplate() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) used (schrodinger.application.licensing.licadmin.stat_info attribute) useDefaultTemplateDirectory() (schrodinger.application.matsci.builderwidgets.TemplateManager method) useEntryDatabaseToggled() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) useFF() (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox method) UseFrom (class in schrodinger.application.jaguar.gui.input_tab_widgets) UseFromCombo (class in schrodinger.application.jaguar.gui.input_tab_widgets) useFromComboChanged() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) useLocalDriver() (schrodinger.job.app.App method) UseModernStereoPerception() (in module schrodinger.rdkit_extensions) useParallelArg() (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) USER (schrodinger.application.jaguar.constants.CalcType attribute) user (schrodinger.application.licensing.lmgrd_log_parser.event attribute) User (schrodinger.job.jobcontrol.Job property) user (schrodinger.utils.profiling.SystemResourceTimes attribute) user_labels (schrodinger.seam.metric.ExecutionMetrics attribute) user_name (schrodinger.application.livedesign.data_classes.LDData property) USER_TO_FLAG_VALUE (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox attribute) userData() (schrodinger.application.matsci.mswidgets.AtomNameWidgetItem method) username (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationInput attribute) (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) userName() (schrodinger.structure.PropertyName method) usernameChanged (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationInput attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) usernameReplaced (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationInput attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) userNameWithFamily() (schrodinger.structure.PropertyName method) userOutput() (schrodinger.pipeline.input.Writer method) userPipelineFromSeamEvents() (schrodinger.seam.viz.render.PipelineRenderer class method) UserRolesEnumMeta (class in schrodinger.ui.qt.table_helper) users_default_template_filename() (in module schrodinger.application.jaguar.autots_input) (in module schrodinger.application.jaguar.hydrokinetic_input) userWorkflow() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) USES_JC (schrodinger.application.matsci.jwsteps.BaseNoJobStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.CustomCmsStep attribute) (schrodinger.application.matsci.jwsteps.CustomMaeStep attribute) USES_MULTI_SUBJOBS (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.CustomCmsStep attribute) (schrodinger.application.matsci.jwsteps.CustomMaeStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) USES_THREADS (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.CustomCmsStep attribute) (schrodinger.application.matsci.jwsteps.CustomMaeStep attribute) useSchrodingerProduct() (schrodinger.job.launchapi.TaskSpecification method) useSchrodingerRun() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) UseServer (class in schrodinger.application.licensing.flexlm) useShowHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) usesJobServer() (schrodinger.job.queue.JobControlJob method) useStructure() (schrodinger.application.matsci.builderwidgets.SketchDialog method) useSubhost() (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog method) useTrajectorySettings() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) useXTB() (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox method) usingExistingDatabase() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) usingPubsub() (schrodinger.stepper.sideinputs.JoinFromFileStep method) (schrodinger.stepper.sideinputs.JoinStep method) (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) usingSelected() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) util_scripts_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) Utilities (class in schrodinger.application.dendrogram.core_class) UVVis_Spectrum (class in schrodinger.application.matsci.spectra)

V

V (class in schrodinger.application.desmond.simulation_block_test) (schrodinger.application.bioluminate.update_germline_db.translate_db.Gene attribute) va_ (schrodinger.application.desmond.util.Counter property) VacancyAlchemist (class in schrodinger.application.matsci.enumeration) VACUUM (schrodinger.application.desmond.constants.FepLegTypes attribute) vacuum (schrodinger.application.desmond.new_fep_edge_data.FepLegs attribute) VacuumReport (class in schrodinger.application.desmond.stage.deprecate) val (schrodinger.application.desmond.arkdb.ArkDb property) (schrodinger.application.desmond.correlation_tau.ConfidenceInterval attribute) (schrodinger.application.desmond.util.Counter property) (schrodinger.utils.sea.sea.Atom property) (schrodinger.utils.sea.sea.List property) (schrodinger.utils.sea.sea.Map property) valence_error (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) valence_errorChanged (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) valence_errorReplaced (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) VALENCE_LOCALIZATION_METHODS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) ValEsd() (in module schrodinger.application.matsci.gsas.GSASIImath) VALID (schrodinger.ui.qt.forcefield.forcefield.OPLSDirResult attribute) valid_asl() (in module schrodinger.application.bioluminate.protein.protein) valid_chiral_comp() (in module schrodinger.comparison.chirality) valid_forcefield_info() (in module schrodinger.application.matsci.parserutils) VALID_LABEL_PUNCTUATION (schrodinger.application.matsci.atomicsymbolsgui.AtomNameLabelValidator attribute) (schrodinger.application.matsci.smartsutilsgui.SMARTSNameValidator attribute) valid_mapping (schrodinger.livedesign.check_reaction.RxnCheckResult attribute) valid_methods (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain property) valid_polymer_monomer_double_displacement_rxn() (in module schrodinger.application.matsci.rxn_channel) valid_rgroups (schrodinger.livedesign.check_reaction.RxnCheckResult attribute) valid_smarts() (in module schrodinger.application.jaguar.workflow_validation) VALID_STATE_PROP (schrodinger.ui.qt.tasks.configwidgets.HostSelector attribute) valid_type (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword property) validate (schrodinger.analysis.transformations.TransformsRepository attribute) validate() (schrodinger.application.bioluminate.bwidgets.NumericLineEdit method) (schrodinger.application.desmond.cmj.AslValidator method) (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.application.desmond.gui.AtomGroupRow method) (schrodinger.application.desmond.gui.DesmondBasicConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.application.desmond.gui.PosResRow method) (schrodinger.application.desmond.starter.ui.cmdline.BaseArgs method) (schrodinger.application.desmond.starter.ui.cmdline.FepArgs method) (schrodinger.application.desmond.starter.ui.constant_ph.Args method) (schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args method) (schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs method) (schrodinger.application.desmond.starter.ui.fep_residue_scanning.Args method) (schrodinger.application.desmond.starter.ui.fep_solubility.FepSolubilityArgs method) (schrodinger.application.desmond.starter.ui.mxmd.MxmdArgs method) (schrodinger.application.desmond.starter.ui.unbinding_kinetics.UnbindingKineticsArgs method) (schrodinger.application.jaguar.autots_input.AutoTSInput method) (schrodinger.application.jaguar.esol_input.EsolInput method) (schrodinger.application.jaguar.gui.basis_selector.UpperCaseValidator method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateData method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.macro_pka_input.MacroKaInput method) (schrodinger.application.jaguar.qrnn.input.QRNNInput method) (schrodinger.application.jaguar.rotation_barriers_input.RotationBarriersInput method) (schrodinger.application.jaguar.solvation_input.SolvationInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.matsci.atomicsymbolsgui.AtomNameLabelValidator method) (schrodinger.application.matsci.atomicsymbolsgui.ElementListValidator method) (schrodinger.application.matsci.atomicsymbolsgui.ElementValidator method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.application.matsci.configdlgs.ConfigDialogWithPlatformValidation method) (schrodinger.application.matsci.configdlgs.PerStructDesmondSubhostConfigDialog method) (schrodinger.application.matsci.crest.Crest static method) (schrodinger.application.matsci.jagwidgets.BasisSetSelector method) (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) (schrodinger.application.matsci.kmcgui.Tab method) (schrodinger.application.matsci.mswidgets.OptionalInputSelector method) (schrodinger.application.matsci.mswidgets.StructureLoader method) (schrodinger.application.matsci.nano.xtal.ParserWrapper method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch method) (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) (schrodinger.application.matsci.reaction_workflow_utils.EnumerateReactionWorkflow method) (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) (schrodinger.application.steps.docking.GlideSettings method) (schrodinger.application.steps.docking.SmilesDockerSettings method) (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) (schrodinger.application.steps.filters.ProfileFilter.Settings method) (schrodinger.application.steps.filters.PropertyRangeSettings method) (schrodinger.application.vss.csvsmiles.CsvSmilesFile method) (schrodinger.application.vss.database.Database method) (schrodinger.application.xtb.input.XTBInput method) (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) (schrodinger.livedesign.biologics.fasta.PolymerAssembler class method) (schrodinger.seam.options.pipeline_options.SeamOptions method) (schrodinger.stepper.app.StepperApplication class method) (schrodinger.trajectory.trajectory_gui_dir.export_movie.TrajectoryMovieDoubleValidator method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.network_visualizer.ConnectionValidator method) (schrodinger.ui.qt.swidgets.EnforcingValidatorMixin method) (schrodinger.ui.qt.swidgets.FileBaseNameValidator method) (schrodinger.ui.qt.swidgets.SAsciiOnlyValidator method) (schrodinger.ui.qt.swidgets.SASLValidator method) (schrodinger.ui.qt.swidgets.SNoCommaDoubleValidator method) (schrodinger.ui.qt.swidgets.SNoCommaIntValidator method) (schrodinger.ui.qt.swidgets.SNonEmptyStringValidator method) (schrodinger.ui.qt.swidgets.SNumberListValidator method) validate_absolute_source_path() (in module schrodinger.application.phase.packages.oned_option_utils) validate_actives_decoys() (in module schrodinger.application.phase.packages.hypo_refine.option_utils) validate_all_auto_reaction_workflow_options() (in module schrodinger.application.matsci.reaction_workflow_utils) validate_alpha_aa() (in module schrodinger.protein.nonstandard_residues) validate_args() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.combinatorial_diversity.driver_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) (in module schrodinger.application.combinatorial_screen.driver_utils) (in module schrodinger.application.phase.packages.align_ligands_driver_options) (in module schrodinger.application.phase.packages.hypo_refine.option_utils) (in module schrodinger.application.phase.packages.mmp3d_driver_utils) (in module schrodinger.application.phase.packages.oned_option_utils) (in module schrodinger.application.phase.packages.phase_database_arg_utils) (in module schrodinger.application.phase.packages.phase_screen_driver_utils) (in module schrodinger.application.phase.packages.shape_creation_logic) (in module schrodinger.application.phase.packages.shape_screen_al_driver) (in module schrodinger.application.phase.packages.shape_screen_arg_utils) (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) (in module schrodinger.application.phase.shape_screen_reporter.option_utils) validate_asl() (in module schrodinger.structutils.analyze) validate_asl_expr() (in module schrodinger.application.desmond.cmj) validate_atom_classes() (in module schrodinger.application.jaguar.autots_validation) validate_auto_reaction_workflow_files() (in module schrodinger.application.matsci.reaction_workflow_utils) validate_auto_reaction_workflow_options() (in module schrodinger.application.matsci.reaction_workflow_utils) validate_bbkeys() (in module schrodinger.application.bb_database.bb_arg_utils) validate_box_size() (in module schrodinger.application.matsci.desmondutils) VALIDATE_BROWNIE_MINIMIZE (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) validate_build_args() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) validate_charges() (in module schrodinger.application.jaguar.workflow_validation) validate_child_widgets() (in module schrodinger.application.matsci.gutils) validate_chirality() (in module schrodinger.protein.process_enamine_db) validate_cluster_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) VALIDATE_CONCAT (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) validate_conf_pkas() (in module schrodinger.application.jaguar.esol_validation) validate_confgen_conflicts() (in module schrodinger.application.phase.packages.conformer_reader) validate_confgen_nddo() (in module schrodinger.application.phase.packages.conformer_reader) validate_conformer_related_compatibility() (in module schrodinger.application.phase.packages.shape_screen_gpu_update) validate_connection() (in module schrodinger.utils.net) validate_constraints() (in module schrodinger.application.jaguar.autots_validation) validate_coord_flag() (in module schrodinger.application.matsci.sculptcomplex) validate_core_smarts() (in module schrodinger.application.steps.utils) validate_covalent_fmp() (in module schrodinger.application.desmond.starter.generator.fep_plus) validate_create_args() (in module schrodinger.application.phase.packages.oned_option_utils) (in module schrodinger.application.phase.shape_screen_reporter.option_utils) validate_crest_options() (in module schrodinger.application.matsci.reaction_workflow_utils) validate_csv_header() (in module schrodinger.active_learning.al_utils) validate_custom_rate_with_extra_stages() (in module schrodinger.application.matsci.reaction_workflow_utils) validate_database_args() (in module schrodinger.application.combinatorial_explorer.driver_utils) validate_dbpath() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.bb_database.bb_task_utils) validate_dbsites() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) validate_describe_args() (in module schrodinger.application.combinatorial_explorer.driver_utils) (in module schrodinger.application.phase.packages.oned_option_utils) validate_energy_property_names() (in module schrodinger.application.matsci.reaction_workflow_utils) validate_export_args() (in module schrodinger.application.phase.packages.oned_option_utils) (in module schrodinger.application.phase.shape_screen_reporter.option_utils) validate_feature_matching_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) validate_ff_and_water_model() (in module schrodinger.application.matsci.desmondutils) validate_ff_name_and_get_number() (in module schrodinger.application.matsci.desmondutils) validate_file() (in module schrodinger.application.steps.utils) validate_file_formats() (in module schrodinger.application.glide.sort_utils) validate_filter_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) validate_folder() (in module schrodinger.application.steps.utils) validate_fragment() (in module schrodinger.structutils.markush_enumerate) VALIDATE_GCMC (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) validate_generate_args() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) validate_global_database() (in module schrodinger.application.bb_database.bb_task_utils) validate_hypo() (in module schrodinger.application.phase.packages.hypo_refine.option_utils) (in module schrodinger.application.phase.packages.phase_screen_driver_utils) validate_input_files() (in module schrodinger.active_learning.al_utils) validate_input_mae() (in module schrodinger.active_learning.al_utils) validate_input_smiles() (in module schrodinger.active_learning.al_utils) validate_input_zipfile() (in module schrodinger.active_learning.al_utils) validate_is_not_builtin() (in module schrodinger.protein.process_enamine_db) validate_jag_keys() (in module schrodinger.application.jaguar.autots_validation) validate_jaguar_keywords() (schrodinger.application.jaguar.autots_input.AutoTSInput method) (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.rotation_barriers_input.RotationBarriersInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) validate_jaguarlike_stages() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) validate_jobcontrol_args() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) validate_key_files() (in module schrodinger.application.bb_database.bb_task_utils) validate_le_float_input() (in module schrodinger.application.jaguar.gui.utils) validate_license_host_port() (in module schrodinger.application.licensing.licadmin) validate_ligprep_arguments() (in module schrodinger.application.phase.packages.shape_ligprep) validate_ligprep_options() (in module schrodinger.application.phase.packages.shape_ligprep) validate_localhost() (in module schrodinger.application.desmond.platforms) validate_localhost_platform_compatibility() (in module schrodinger.utils.platform) validate_mappings() (in module schrodinger.livedesign.biologics.fasta) VALIDATE_MD (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) validate_merge_args() (in module schrodinger.application.phase.packages.oned_option_utils) (in module schrodinger.application.phase.packages.shape_screen_gpu_update) VALIDATE_META (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) validate_metalike_stages() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) VALIDATE_MINIMIZE (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) validate_model (schrodinger.application.steps.scorers.LigandMLScorer.Settings attribute) validate_modelChanged (schrodinger.application.steps.scorers.LigandMLScorer.Settings attribute) validate_modelReplaced (schrodinger.application.steps.scorers.LigandMLScorer.Settings attribute) validate_mutated_residues() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) validate_name() (in module schrodinger.application.matsci.smartsutils) validate_no_cg() (in module schrodinger.application.matsci.coarsegrain) validate_no_dummy_atoms() (in module schrodinger.application.matsci.msutils) validate_non_empty_smiles_path() (in module schrodinger.application.transforms.validators) validate_nonzero_positive_int() (in module schrodinger.application.transforms.validators) validate_nonzero_positive_number() (in module schrodinger.application.transforms.validators) validate_obj() (in module schrodinger.ui.qt.appframework2.validation) validate_oned_data_file() (in module schrodinger.application.phase.packages.oned_option_utils) validate_oned_data_file_attributes() (in module schrodinger.application.phase.packages.oned_option_utils) validate_oned_data_file_source() (in module schrodinger.application.phase.packages.oned_option_utils) validate_opls_dir() (in module schrodinger.ui.qt.forcefield.forcefield) validate_optional_int() (in module schrodinger.application.transforms.validators) validate_options() (in module schrodinger.application.jaguar.esol_validation) (in module schrodinger.application.macromodel.paraUtils) (in module schrodinger.application.matsci.cgforcefield) (in module schrodinger.application.matsci.nano.check) (in module schrodinger.application.matsci.reaction_workflow_utils) validate_params() (in module schrodinger.application.livedesign.ld_maestro_actions) validate_path_exists() (in module schrodinger.application.transforms.validators) validate_pdb_id() (in module schrodinger.ui.qt.pdb_dialog) validate_pfx_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) validate_platform() (in module schrodinger.application.matsci.crest) validate_positive_int() (in module schrodinger.application.transforms.validators) validate_print_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) validate_project_creation_options() (in module schrodinger.application.phase.packages.hypo_refine.option_utils) validate_project_fd() (in module schrodinger.application.phase.packages.hypo_refine.option_utils) validate_project_sites() (in module schrodinger.application.phase.packages.hypo_refine.option_utils) validate_properties() (in module schrodinger.application.combinatorial_diversity.driver_utils) validate_property_filters() (in module schrodinger.application.combinatorial_explorer.driver_utils) validate_property_names() (in module schrodinger.application.phase.packages.oned_option_utils) validate_property_ranges() (in module schrodinger.application.transforms.validators) validate_qrun_args() (in module schrodinger.application.bb_database.bb_arg_utils) validate_qsplit_args() (in module schrodinger.application.bb_database.bb_arg_utils) validate_range() (in module schrodinger.application.transforms.validators) validate_refinement_options() (in module schrodinger.application.phase.packages.hypo_refine.option_utils) VALIDATE_REINIT (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) VALIDATE_REMD (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) validate_request_from_ld() (in module schrodinger.application.livedesign.ld_maestro_actions) validate_restart_stage() (in module schrodinger.application.desmond.launch_utils) validate_routes() (in module schrodinger.application.combinatorial_explorer.driver_utils) validate_run_args() (in module schrodinger.application.phase.packages.oned_option_utils) validate_scaffold() (in module schrodinger.structutils.markush_enumerate) validate_screen_args() (in module schrodinger.application.combinatorial_explorer.driver_utils) validate_server_for_auth() (in module schrodinger.job.cert) validate_shape_data_file_metadata() (in module schrodinger.application.phase.packages.shape_creation_logic) validate_shape_data_file_metadata_compatibility() (in module schrodinger.application.phase.packages.shape_creation_logic) validate_shape_gen_options() (in module schrodinger.application.phase.packages.shape_generator) validate_shape_generator_dict() (in module schrodinger.application.phase.packages.shape_generator) validate_shape_generator_dict_compatibility() (in module schrodinger.application.phase.packages.shape_generator) validate_shape_screen_report_args() (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) validate_slice_limits() (in module schrodinger.application.bb_database.bb_arg_utils) validate_smarts() (in module schrodinger.application.matsci.rdpattern) (in module schrodinger.application.transforms.validators) (in module schrodinger.structutils.analyze) validate_smarts_canvas() (in module schrodinger.structutils.analyze) validate_smarts_for_mol() (in module schrodinger.application.transforms.validators) validate_smarts_for_structure() (in module schrodinger.application.transforms.validators) validate_smasher_file() (in module schrodinger.application.steps.utils) validate_source() (in module schrodinger.application.phase.packages.phase_screen_driver_utils) validate_source_dbs() (in module schrodinger.application.phase.packages.phase_screen_utils) validate_split_args() (in module schrodinger.application.phase.packages.oned_option_utils) (in module schrodinger.application.phase.packages.shape_screen_gpu_update) validate_stage_user_keys() (in module schrodinger.application.jaguar.esol_validation) validate_stages() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) validate_stoichiometry() (in module schrodinger.application.jaguar.utils) validate_stop_after() (in module schrodinger.active_learning.al_driver) validate_structure_file() (in module schrodinger.application.phase.packages.oned_option_utils) validate_structure_property_name() (in module schrodinger.application.steps.utils) (in module schrodinger.application.transforms.validators) validate_structure_property_ranges() (in module schrodinger.application.transforms.validators) validate_structures() (in module schrodinger.application.jaguar.autots_validation) (in module schrodinger.application.jaguar.esol_validation) (in module schrodinger.application.jaguar.hydrokinetic_validation) (in module schrodinger.application.jaguar.macro_pka_validation) (in module schrodinger.application.jaguar.qrnn.validation) (in module schrodinger.application.jaguar.rotation_barriers_validation) (in module schrodinger.application.jaguar.solvation_validation) validate_subclass() (in module schrodinger.protein.process_enamine_db) validate_subset() (in module schrodinger.application.phase.packages.phase_screen_utils) validate_title_option() (in module schrodinger.application.phase.packages.conformer_reader) validate_trajectory_path() (in module schrodinger.trajectory.validate_trajectory) validate_value() (in module schrodinger.application.matsci.espresso.qeinput) VALIDATE_VRUN (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) validate_workflow_name() (in module schrodinger.application.matsci.wfmanagement) validateAllAssigned() (schrodinger.application.matsci.cg_mapping.CGMapper method) validateAndAccept() (schrodinger.ui.qt.config_dialog.ConfigDialog method) validateAnharmonic() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) validateASL() (schrodinger.application.matsci.chargegui.ChargeDialog method) (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) validateAsl() (schrodinger.application.matsci.mswidgets.MSAtomSelector method) validateAtom() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.MacroAtomSelectionDelegate method) validateBarriers() (schrodinger.application.matsci.desconfig.BarrierHeader static method) validateBasisSet() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) validateBeads() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) validateBlockTau() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) validateBuildGeometryMsj() (schrodinger.application.matsci.desmondutils.SystemBuilder static method) validateChain() (schrodinger.stepper.stepper.UnbatchedChain method) validateCMS() (schrodinger.application.matsci.deswidgets.TrajAnalysisGuiMixin method) validateCoordinateScanRange() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) validateDBAndStructure() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) ValidatedPanel (class in schrodinger.ui.qt.appframework2.baseapp) validateEntries() (schrodinger.ui.qt.input_selector.InputSelector method) validateFuncGroups() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) validateGapIndices() (schrodinger.protein.sequence.AbstractSequence method) validateGapsToRemoveFromChainStartAndEnds() (schrodinger.protein.sequence.CombinedChainProteinSequence method) validateGpuHosts() (schrodinger.application.matsci.permittivity.ConfigWriter method) validateHost() (schrodinger.application.matsci.configdlgs.ConfigDialogWithPlatformValidation method) validateInput() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) (schrodinger.application.prepwizard2.tasks.CleanupTask method) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask method) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask method) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask method) (schrodinger.application.prepwizard2.tasks.PreprocessTask method) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask method) (schrodinger.protein.predictors.PredictorWrapperTask method) validateJobCount() (schrodinger.application.matsci.multiapp.MultiJobApp method) validateKeywords() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageInfoLine method) (schrodinger.application.matsci.jagwidgets.KeywordEdit method) (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) validateLicenses() (schrodinger.application.prepwizard2.tasks.GenerateStatesTask method) validateMacroSettings() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) validateMapping() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) validateMicroSettings() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) validateModelLoaded() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) validateMSJPath() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams method) validateMutatedResidues() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator static method) validateMutations() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator static method) validateNodes() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method)

validateNumCpus() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) validateNumGpus() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) validateNumOpenMP() (schrodinger.ui.qt.config_dialog.ConfigDialog method) validateNumProcs() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) validateOPLSDir() (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.forcefield.forcefield.OPLSValidator method) ValidateOplsDirMessageBox (class in schrodinger.ui.qt.forcefield.forcefield) validateOutputs() (schrodinger.active_learning.mq_backend.Backend method) validatePanel() (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) validatePlatform() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) validatePredefinedMapping() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) validateRateConstants() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) validateRAtomIdentity() (schrodinger.application.matsci.builderwidgets.ComplexLigandRxMixin method) (schrodinger.application.matsci.builderwidgets.SketcherStructureMixin method) validateRAtomStructure() (schrodinger.application.matsci.builderwidgets.ComplexLigandRxMixin method) (schrodinger.application.matsci.builderwidgets.SketcherStructureMixin method) validateResidueName() (schrodinger.ui.residueselector.ResidueGroups method) validateSecondVal() (schrodinger.ui.qt.network_visualizer.ConnectionValidator method) validateSettings() (schrodinger.application.steps.converters.MaeFileWriter method) (schrodinger.application.steps.enumerators.BaseDecorator method) (schrodinger.application.steps.enumerators.FastFragmenter method) (schrodinger.application.steps.enumerators.RouteEnumerator method) (schrodinger.application.steps.enumerators.RouteEvaluator method) (schrodinger.application.steps.enumerators.SmilesTransformPairer method) (schrodinger.application.steps.filters.ChiralCenterCountFilter method) (schrodinger.application.steps.filters.FepFilter method) (schrodinger.application.steps.filters.InMemoryRandomSampleFilter method) (schrodinger.application.steps.filters.MaxMolWtFilter method) (schrodinger.application.steps.filters.ProductFilterMixin method) (schrodinger.application.steps.filters.ProfileFilter method) (schrodinger.application.steps.filters.PropertyFilter method) (schrodinger.application.steps.filters.RangeFilter method) (schrodinger.application.steps.filters.ScoreFilterChain method) (schrodinger.application.steps.filters.SmartsFilter method) (schrodinger.application.steps.ligprep.LigPrepStep method) (schrodinger.application.steps.scorers.LigandMLScorer method) (schrodinger.application.steps.scorers.PropertyScorer method) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter method) (schrodinger.stepper.core_steps.RandomSampleFilter method) (schrodinger.stepper.stepper.UnbatchedChain method) (schrodinger.ui.qt.filter_dialog.FilterDialog method) validateSharesWithNeighbors() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) validateSitesData() (schrodinger.application.matsci.reaction_workflow_utils.Sites static method) validateSitesFormat() (schrodinger.application.matsci.reaction_workflow_utils.Sites static method) validateSmarts() (schrodinger.application.matsci.rdpattern.Pattern method) validateSMARTS() (schrodinger.ui.qt.swidgets.SMARTSEdit method) ValidateStability (class in schrodinger.application.desmond.stage.app.kinetics) validateStage() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage static method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage static method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.BqQueryStage static method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.FragmentVSStage static method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage static method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage static method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreStage static method) validateStrucCombos() (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) validateStruct() (schrodinger.application.matsci.espresso.qeinput.StructureType method) validateSubHost() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) (schrodinger.application.matsci.configdlgs.PerStructDesmondSubhostConfigDialog method) validateSubhost() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) validateSubjobs() (schrodinger.application.desmond.fep_dialog.FEPConfigDialog method) validateText() (schrodinger.ui.qt.appframework2.validators.BaseTextValidator method) (schrodinger.ui.qt.appframework2.validators.FileExists method) (schrodinger.ui.qt.appframework2.validators.IsInteger method) (schrodinger.ui.qt.appframework2.validators.JobName method) (schrodinger.ui.qt.appframework2.validators.PathExists method) validateTOFs() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) validateUnsharedNeighbors() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) validateValues() (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.inputconfig.InputConfig method) (schrodinger.pipeline.stage.Stage method) validateWorkspace() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) validating (schrodinger.ui.qt.forcefield.forcefield.OPLSValidator property) validation_specs() (in module schrodinger.application.glide.glide) VALIDATION_STYLE_SHEET (schrodinger.ui.qt.tasks.configwidgets.HostSelector attribute) validationEnabled() (schrodinger.ui.qt.appframework2.validators.Validator method) ValidationError ValidationIssue ValidationMixin (class in schrodinger.ui.qt.appframework2.validation) ValidationResult (class in schrodinger.ui.qt.appframework2.validation) ValidationResults (class in schrodinger.ui.qt.appframework2.validation) Validator (class in schrodinger.ui.qt.appframework2.validators) validator() (in module schrodinger.ui.qt.appframework2.validation) validForceFieldSelectorCustomOPLSDir() (schrodinger.ui.qt.appframework2.af2.JobApp method) validProtein() (in module schrodinger.application.matsci.gsas.GSASIImath) vals_by_prop (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask.Output attribute) vals_by_propChanged (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask.Output attribute) vals_by_propReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask.Output attribute) value (schrodinger.application.bioluminate.pose_filtering.csv_filter.FilterParameters attribute) (schrodinger.application.desmond.ene_utils.ENEGRP_VALUE attribute) (schrodinger.application.jaguar.hess_guess.InternalCoordinate property) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword property) (schrodinger.application.matsci.reaction_workflow_gui_utils.SequenceData attribute) (schrodinger.protein.annotation.Region attribute) VALUE (schrodinger.ui.qt.schart.SChart attribute) value() (schrodinger.application.desmond.fep_dialog.CustomGPUComboBox method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) (schrodinger.ui.qt.formlayout.SliderLayout method) value_is_type() (in module schrodinger.application.jaguar.validation) VALUE_MAP (schrodinger.protein.annotation.AbstractRegionFinder attribute) (schrodinger.protein.annotation.AntibodyRegionsFinder attribute) (schrodinger.protein.annotation.GPCRSegmentFinder attribute) (schrodinger.protein.annotation.TCRRegionFinder attribute) VALUE_PATTERN (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) valueAt() (schrodinger.application.matsci.mswidgets.MultiSlider method) valueChanged (schrodinger.application.matsci.mswidgets.MultiSlider attribute) (schrodinger.models.parameters.CompoundParam attribute) valueChanged() (schrodinger.application.matsci.qualityslider.QualitySlider method) valueFromText() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) valueMatches() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Criterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) values (schrodinger.application.jaguar.workflow_input.WorkflowInput property) (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) (schrodinger.application.matsci.mswidgets.MultiSlider property) values() (schrodinger.application.desmond.cms.PosRestrainArray method) (schrodinger.application.desmond.cms.RestrainGroup method) (schrodinger.application.matsci.mswidgets.Stepper method) (schrodinger.ui.qt.dialbox.XYZDialBox method) (schrodinger.ui.qt.formlayout.CheckLayout method) (schrodinger.utils.sea.sea.Map method) Values2Dict() (in module schrodinger.application.matsci.gsas.GSASIIpwd) values_changed (schrodinger.application.matsci.kmcgui.PropertyCombo attribute) valueSelected (schrodinger.application.livedesign.panel_components.AbstractSelectionLineEdit attribute) ValueSelectionDialog (class in schrodinger.application.bioluminate.propfilter) Var (class in schrodinger.application.desmond.enhsamp) var() (in module schrodinger.job.launchapi) var_name (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) var_nameChanged (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) var_nameReplaced (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) VariableDomainType (class in schrodinger.application.bioluminate.antibody.models) VariablePolar (schrodinger.protein.helm.helm_renderer.HexColor attribute) variationChanged() (schrodinger.application.matsci.plotwidgets.SliderchartVLFitStdPlot method) varWithType() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) vbox() (in module schrodinger.ui.qt.layout) vbr2() (schrodinger.application.macromodel.utils.ComUtil method) VCD_Spectrum (class in schrodinger.application.matsci.spectra) VCENTER (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) VDException Vdw (class in schrodinger.application.desmond.cms) vdw (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property) (schrodinger.application.desmond.fep_schedule.FepScheduleBinding property) (schrodinger.application.matsci.espresso.qeinput.DftType property) (schrodinger.surface.MolSurfType attribute) vdw_clash (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) vdw_clashChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) vdw_clashReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) vdw_radius (schrodinger.structure.StructureAtom property) vdwA (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property) (schrodinger.application.desmond.fep_schedule.FepScheduleBinding property) vdwB (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property) (schrodinger.application.desmond.fep_schedule.FepScheduleBinding property) VDWData (class in schrodinger.application.matsci.cgforcefield) VDWMask() (in module schrodinger.analysis.visanalysis.volumedatastructureutils) VDWSCALE (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) VdwType (class in schrodinger.application.matsci.espresso.qeinput) vecnorm() (in module schrodinger.application.jaguar.qrnn.temp_opt) Vector (class in schrodinger.trajectory.prody.mode) vector_cross() (in module schrodinger.graphics3d.torus) VECTOR_DELIM (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) VECTOR_DELIM_WITH_SPACE (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) vector_to_matrix() (in module schrodinger.application.matsci.mecp_mod) VectorBase (class in schrodinger.trajectory.prody.mode) Vectorizer (class in schrodinger.application.bioluminate.peptide_sar.encode) vectorizer_class_factory() (in module schrodinger.application.bioluminate.peptide_sar.encode) vectorStr() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase class method) Vendor (class in schrodinger.application.licensing.flexlm) vendor() (schrodinger.application.licensing.flexlm.Vendor method) verbose (schrodinger.application.desmond.driver_utils.MPISettings attribute) VERBOSE (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMakerBase attribute) (schrodinger.application.desmond.fep_edge_report_maker.SolubilityReportMaker attribute) verbose (schrodinger.structutils.minimize.Minimizer property) verify() (schrodinger.job.launchparams.LaunchParameters method) verify_args_validate() (in module schrodinger.application.desmond.starter.ui.cmdline) verify_cert() (in module schrodinger.job.cert) verify_cfg_files_exist() (in module schrodinger.application.matsci.desconfig) verify_file_exists() (in module schrodinger.application.desmond.util) verify_license() (in module schrodinger.application.licensing.licserver.client) verify_template_has_coordinates() (in module schrodinger.rdkit.substructure) verify_traj_exists() (in module schrodinger.application.desmond.util) verifyJaguarOutfiles() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) verifySettings() (schrodinger.application.desmond.gui.GuiApp method) VERNIER (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes attribute) VERNIER_RES (schrodinger.application.bioluminate.antibody.annotate.Properties attribute) Version (class in schrodinger.application.livedesign.ldclient_proxy) VERSION (schrodinger.application.desmond.multisimstartup.Help attribute) (schrodinger.application.desmond.multisimstartup.Startup.Help attribute) (schrodinger.application.matsci.kmc.SchrodingerTable attribute) version (schrodinger.application.matsci.msutils.Forcefield attribute) (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) Version (schrodinger.job.jobcontrol.Job property) version() (in module schrodinger.application.xtb.textparser) VERSION_1_6_5 (schrodinger.utils.openmpi.OpenMPIVersion attribute) version_at_least() (in module schrodinger) version_at_most() (in module schrodinger) version_compatible() (in module schrodinger) version_str_to_tuple() (in module schrodinger.application.desmond.antlr3) version_string() (in module schrodinger.utils.singledashoptionparser) version_uptodate() (in module schrodinger.application.licensing.licadmin) versionString (schrodinger.job.server.ServerInfo attribute) VERT_NO_BORDER (schrodinger.ui.qt.standard.design_tokens.PaddingSizes attribute) VERT_W_BORDER (schrodinger.ui.qt.standard.design_tokens.PaddingSizes attribute) Vertex (class in schrodinger.application.matsci.shapes) vertex (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) vertex_colors (schrodinger.surface.Surface property) vertex_coords (schrodinger.surface.Surface property) vertex_count (schrodinger.surface.Surface property) vertex_normals (schrodinger.surface.Surface property) VERTICAL_ALIGNS (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) VERTICAL_SPACING_DIVISOR (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter attribute) VerticalHeader (class in schrodinger.ui.qt.tablewidget) VerticalLabel (class in schrodinger.ui.qt.swidgets) VERTICES (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) VeryHigh (schrodinger.protein.annotation.KinaseConservation attribute) VeryLow (schrodinger.protein.annotation.KinaseConservation attribute) vibr() (schrodinger.application.macromodel.utils.ComUtil method) VIBRATION_MASS_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VIBRATION_SCALING_AUTO (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VIBRATION_SCALING_CUSTOM (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VIBRATION_SCALING_NONE (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VIBRATION_SCALING_PULAY (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VibrationalSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) VibState (class in schrodinger.application.matsci.bandshape_utils) view() (schrodinger.ui.ligfilter.AddDefinitionDialog method) VIEW_CLASS (schrodinger.application.bioluminate.antibody.search_results_table.FullTable attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) view_settings (schrodinger.application.pymol.mae_sync.MaestroSettingsModel attribute) viewAllProteins() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) viewAtomLabels() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) viewer() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer class method) ViewerGuiMixin (class in schrodinger.application.matsci.appbase) ViewerModel (class in schrodinger.ui.qt.structtable) (class in schrodinger.ui.qt.table) ViewerTable (class in schrodinger.ui.qt.structtable) ViewerWindow (class in schrodinger.application.bioluminate.ssv.viewer) viewFirstProtein() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) viewJobDetails() (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) Viewname (schrodinger.job.jobcontrol.Job property) viewname (schrodinger.tasks.jobtasks.JobConfig attribute) VIEWNAME (schrodinger.utils.cmdline.Options attribute) viewnameChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) viewnameReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) viewPattern() (schrodinger.ui.ligfilter.LigfilterFrame method) VIEWPOSITION (schrodinger.trajectory.trajectory_gui_dir.playback_settings.Tab attribute) viewPositioningChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) VIRIAL (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) virtualenv VirtualLibrary (class in schrodinger.structutils.markush_enumerate) ViscosityStep (class in schrodinger.application.matsci.jwsteps) visibility (schrodinger.protein.sequence.AbstractSingleChainSequence property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) visibilityChanged (schrodinger.protein.sequence.AbstractSequence attribute) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel attribute) (schrodinger.ui.qt.pop_up_widgets.PopUp attribute) VISIBLE (schrodinger.project.pandasutils.WhichColumns attribute) visible (schrodinger.protein.properties.SequenceProperty attribute) (schrodinger.structure.StructureAtom property) (schrodinger.surface.Surface property) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameListItem property) VISIBLE_COLUMNS (schrodinger.application.jaguar.gui.tabs.scan_tab.RelaxedScanCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel attribute) visibleChanged (schrodinger.protein.properties.SequenceProperty attribute) visibleFeatureLabels() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visiblePropLabels() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visibleRefCt() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visibleReplaced (schrodinger.protein.properties.SequenceProperty attribute) visibleTabs() (schrodinger.ui.qt.swidgets.STabWidget method) visibleTol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visibleXvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visit() (schrodinger.application.desmond.antlr3.tree.TreeVisitor method) (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) VisRecord (class in schrodinger.utils.pymol) VisRecordVol (class in schrodinger.utils.pymol) visualize_pipelines() (in module schrodinger.seam.testing.fixtures) (in module schrodinger.seam.testing.utils) VizWebpage (class in schrodinger.stepper.viz) Void (class in schrodinger.application.matsci.freevolume) VoidInfo (class in schrodinger.application.matsci.freevolume) voids() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) VoidStep (class in schrodinger.application.matsci.jwsteps) voigt (schrodinger.application.matsci.elasticity.tensors.Tensor property) (schrodinger.application.matsci.elasticity.tensors.TensorCollection property) voigt_symmetrized (schrodinger.application.matsci.elasticity.tensors.Tensor property) Vol2Den() (in module schrodinger.application.matsci.gsas.GSASIImath) volPerAnion() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) VOLUME (schrodinger.application.desmond.ene_utils.EneGrpProp attribute) volume (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot property) (schrodinger.application.desmond.mxmd.mxmd_cleanup.Spot property) (schrodinger.application.matsci.amorphous.Scaffold property) VOLUME (schrodinger.application.matsci.kmc.SchrodingerTable attribute) volume (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) volume_name (schrodinger.surface.Surface property) volume_range() (in module schrodinger.application.mopac.mopac_surfaces) VolumeData (class in schrodinger.analysis.visanalysis.volumedata) VolumeMemoryError volumeOfGraph() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) von_mises (schrodinger.application.matsci.elasticity.stress.Stress property) von_mises_strain (schrodinger.application.matsci.elasticity.strain.Strain property) VotcaDatabaseManager (class in schrodinger.application.matsci.kmc) Vrun (class in schrodinger.application.desmond.stage.simulate) VRUN (schrodinger.application.desmond.msj_defaults.DEFAULT_SETTING attribute) vrun (schrodinger.application.desmond.msj_defaults.TAG_SPECS attribute) VrunBase (class in schrodinger.application.desmond.stage.simulate) vsdb_file (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) vsdb_fileChanged (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) vsdb_fileReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyInput attribute) VStackedDataViewerTable (class in schrodinger.ui.qt.table) VSubDataViewerTable (class in schrodinger.ui.qt.table) vtype (schrodinger.application.matsci.cgforcefield.VDWData attribute)

W

w (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) Wag (class in schrodinger.application.jaguar.hess_guess) WAG (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) wags (schrodinger.application.jaguar.hess_guess.CoordinateManager property) WAIT (schrodinger.utils.cmdline.Options attribute) wait() (schrodinger.application.glide.http_client.NonBlockingBackendChecker method) (schrodinger.job.jobcontrol.Job method) (schrodinger.tasks.taskmanager.TaskManager method) (schrodinger.tasks.tasks.AbstractTask method) wait_before_kill() (schrodinger.job.jobcontrol.Job method) wait_for_signal() (in module schrodinger.utils.qt_utils) waitForSchrodDaemon() (schrodinger.application.licensing.licadmin.LocalServerProcess method) WAITING (schrodinger.application.desmond.cmj.JobStatus attribute) (schrodinger.job.jobcontrol.DisplayStatus attribute) (schrodinger.job.queue.JobState attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.Status attribute) waiting_jobs (schrodinger.job.queue.JobDJ property) waitUntilReady() (schrodinger.application.glide.http_client.AbstractGlideServerManager method) WALLSEP (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube attribute) walltime_seconds (schrodinger.seam.metric.ExecutionMetrics attribute) WAM_LOAD_INCLUDED (schrodinger.application.matsci.appbase.MatSciAppMixin attribute) WAM_LOAD_SELECTED (schrodinger.application.matsci.appbase.MatSciAppMixin attribute) warn_about_mmjag_unknowns() (in module schrodinger.application.jaguar.gui.utils) warning (schrodinger.application.desmond.gui.AtomGroupModel attribute) (schrodinger.application.desmond.gui.PosResModel attribute) WARNING (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.MessageType attribute) warning() (in module schrodinger.structutils.assignbondorders) (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.prepwizard2.tasks.LoggerMixin method) (schrodinger.application.report2d.Report2D method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework.WriteDialog method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.schart.SChart method) (schrodinger.ui.qt.swidgets.SDialog method) (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) (schrodinger.ui.two_d_viewer.TwoDViewer method) warning_dialog() (in module schrodinger.application.desmond.gui) WARNING_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) Watcher (class in schrodinger.seam.viz.watcherd) WatcherDirReader (class in schrodinger.seam.viz.watcher) WatcherWebServer (class in schrodinger.seam.viz.watcher) watdist (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) watdistChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) watdistReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) WATER (schrodinger.application.bioluminate.methionine_oxidation.NeighborAtom attribute) (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute) water_action (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar property) water_model (schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams attribute) WATER_MODELS (class in schrodinger.application.desmond.constants) water_mol() (in module schrodinger.application.desmond.fep_edge_data) WATER_NAMES (schrodinger.application.prime.wrapper.PrimeTemplate attribute) watermap (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) WATERMAP_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute) watermap_lic() (in module schrodinger.application.desmond.license) WATERMAP_VERSION (schrodinger.application.desmond.envir.CONST attribute) WaterMapAnaJob (class in schrodinger.application.desmond.stage.app.watermap) watermapChanged (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) WaterMapCluster (class in schrodinger.application.desmond.stage.app.watermap) WaterMapInput (class in schrodinger.application.watermap.watermap_inp) WaterMapPostAnalysis (class in schrodinger.application.desmond.stage.app.watermap) watermapReplaced (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) WatermapTyper (class in schrodinger.application.desmond.systype) waters (schrodinger.application.prime.wrapper.PrimeTemplate property) WaterStateEnumerator (class in schrodinger.protein.assignment) WaterTypesComboBox (class in schrodinger.application.matsci.mswidgets) WAV_EP_FILE_PROP (schrodinger.application.matsci.permittivity.JaguarMerge attribute) WAV_IR_FILE_PROP (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) wavekE() (in module schrodinger.application.matsci.gsas.GSASIImath) wChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) WEAK (schrodinger.application.jaguar.nmr_interactions.CouplingStrength attribute) Weak (schrodinger.protein.residue.HELIX_PROPENSITY attribute) weakly_conserved (schrodinger.protein.annotation.Consensus attribute) WeakRefAttribute (class in schrodinger.infra.util) web_cie_to_rgb() (in module schrodinger.application.matsci.colorutils) webServerSecret (schrodinger.job.server.ServerInfo attribute) wedge_clean() (in module schrodinger.livedesign.preprocessor) WEDGE_TWO_BONDS_AROUND_CHIRAL_ATOMS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) WEIGHT (schrodinger.application.bioluminate.pose_filtering.hdx_calc.AnalysisColumns attribute) weight (schrodinger.application.jaguar.gui.utils.Solvent attribute) WEIGHT (schrodinger.application.matsci.kmc.AtomsTable attribute) weight (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) weight_color() (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec method) weight_font() (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec method) weightChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) weightDistribution() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) weightReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) weightsByNum() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow method) WeightSphereManager (class in schrodinger.ui.qt.atom_weights_table_widget) wf_stability_eigenvalues() (in module schrodinger.application.jaguar.textparser) WfcType (class in schrodinger.application.matsci.espresso.qeoutput) wheelEvent() (schrodinger.ui.qt.structure2d.structure_view method) WheelEventFilterer (class in schrodinger.application.matsci.gutils) where_sorted_array() (in module schrodinger.application.jaguar.nmr_utils) which() (in module schrodinger.job.remote_command) WhichColumns (class in schrodinger.project.pandasutils) WhichRows (class in schrodinger.project.pandasutils) White (schrodinger.protein.helm.helm_renderer.HexColor attribute) WHITE (schrodinger.ui.qt.standard.colors.NativeColors attribute) (schrodinger.ui.qt.standard.design_tokens.BackgroundColors attribute) (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) WhiteGroupBox (class in schrodinger.ui.qt.standard.widgets.group_boxes) WHOLE_FILE (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) whole_ring_test() (in module schrodinger.application.desmond.r_group_asl) WholePDB (class in schrodinger.protein.getpdb_utility) wholePDB() (schrodinger.protein.getpdb_utility.Code method) widget (schrodinger.ui.qt.swidgets.SubWidget attribute) widgetChanged (schrodinger.ui.qt.datamapper.TrackingDataWidgetMapper attribute) widgets() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) widgetStateIsValid() (schrodinger.ui.qt.structure_selector.StructureSelector method) WidgetWithPopUpMixin (class in schrodinger.ui.qt.pop_up_widgets) width (schrodinger.livedesign.draw.ImageGenOptions attribute) WILDCARD_PATTERN (schrodinger.utils.sea.sea.Atom attribute) WildcardTreePattern (class in schrodinger.application.desmond.antlr3.treewizard) wilson_b_matrix() (in module schrodinger.application.jaguar.hess_guess) WINDMILL_TOPOLOGY (schrodinger.application.desmond.test_utils.FileRegistrationTag attribute) window() (schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackModelMixin method) window_hydrophobicity (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) window_isoelectric_point (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) window_length (schrodinger.structutils.structalign.StructAlign property) WINDOW_TITLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) with_disabled_panel() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) with_global_as() (in module schrodinger.application.matsci.msutils) with_license_requirements() (in module schrodinger.seam.transforms.resources) WithCount() (schrodinger.seam.transforms.samplers.RandomSample method) within_three_bonds() (schrodinger.protein.analysis.Report.steric_clash_data_set method) withinFilter() (schrodinger.ui.qt.swidgets.SFilteredListWidget method) without_trial_fleet() (in module schrodinger.seam.testing.fixtures) word_size (schrodinger.protein.tasks.blast.BlastSettings attribute) word_sizeChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) word_sizeReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) Worker (class in schrodinger.active_learning.mq_driver) (class in schrodinger.active_learning.mq_worker) worker() (in module schrodinger.application.matsci.gsas.GSASIImath) WorkFlow (class in schrodinger.application.matsci.jaguarworkflows) Workflow (class in schrodinger.application.steps.basesteps) workflow_name (schrodinger.application.jaguar.autots_input.AutoTSInput attribute) (schrodinger.application.jaguar.esol_input.EsolInput attribute) (schrodinger.application.jaguar.macro_pka_input.MacroKaInput attribute) (schrodinger.application.jaguar.qrnn.input.QRNNInput attribute) (schrodinger.application.jaguar.rotation_barriers_input.RotationBarriersInput attribute) (schrodinger.application.jaguar.solvation_input.SolvationInput attribute) (schrodinger.application.jaguar.workflow_input.WorkflowInput attribute) (schrodinger.application.xtb.input.XTBInput attribute) workflow_requires_fep_license() (in module schrodinger.application.desmond.license_utils) workflow_selection_changed (schrodinger.application.matsci.wfmanagement.WorkflowFinder attribute) WorkflowConservationError WorkflowError WorkflowFilterWidget (class in schrodinger.application.matsci.wfmanagement) WorkflowFinder (class in schrodinger.application.matsci.wfmanagement) WorkflowFinderDialog (class in schrodinger.application.matsci.wfmanagement) WorkflowInput (class in schrodinger.application.jaguar.workflow_input) WorkflowKeyword (class in schrodinger.application.jaguar.workflow_keywords) WorkflowKeywordConflictError WorkflowKeywordError WorkflowKeywordException WorkflowKeywordFormatError WorkflowKeywordValueError WorkflowKeywordValueTypeError WorkflowManager (class in schrodinger.application.matsci.wfmanagement) WorkflowManagerDialog (class in schrodinger.application.matsci.wfmanagement) WorkflowManagerMixin (class in schrodinger.application.matsci.wfmanagement) WorkflowMetadata (class in schrodinger.application.matsci.wfmanagement) WorkflowMetadataFrame (class in schrodinger.application.matsci.wfmanagement) workflowMetadataMode() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) (schrodinger.application.matsci.wfmanagement.WorkflowManagerMixin method) WorkflowNamerDialog (class in schrodinger.application.matsci.wfmanagement) WorkflowParams (class in schrodinger.application.desmond.msj_generator.workflow_params) WorkflowParamsCls (schrodinger.application.desmond.msj_generator.common.BaseMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.constant_ph.ConstantpHMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.fep.covalent_ligand.CovalentMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.fep.metalloprotein.MetalMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.fep.protein.CombinedProteinMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.fep.protein.ProteinMapperMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.mxmd.MixedSolventMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.subjob_msj.BaseMsjGenerator attribute) (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator attribute) WorkflowParser (class in schrodinger.application.matsci.permittivity) WorkflowProtocol (class in schrodinger.application.matsci.permittivity) WorkflowType (class in schrodinger.infra.structure) working_directory() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.matsci.jobutils) workspace Maestro Workspace (class in schrodinger.application.desmond.maestro) WORKSPACE (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) (schrodinger.application.matsci.mswidgets.StructureLoader attribute) (schrodinger.application.pymol.gui_models.ProjectExportMode attribute) Workspace (schrodinger.application.pymol.pymol4maestro.EntryMode attribute) WORKSPACE (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.ui.qt.input_selector.InputSelector attribute) workspace, Maestro workspace_changed() (in module schrodinger.ui.qt.appframework2.maestro_callback) workspace_changed_active_project() (in module schrodinger.ui.qt.appframework2.maestro_callback) workspace_ct (schrodinger.ui.picking.PickAtomsToggle property) WORKSPACE_DISPLAY_TEXT (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) workspace_get() (schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro method) WORKSPACE_RESOLUTION_INDEX (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) workspaceChanged() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.two_d_viewer.TwoDViewer method) WorkspaceIdMapper (class in schrodinger.utils.pymol) WorkspaceInclusionCheckBox (class in schrodinger.application.jaguar.gui.utils) WorkspaceInclusionDelegate (class in schrodinger.ui.qt.delegates) WorkspaceLabeler (class in schrodinger.application.bioluminate.workspacelabeler) workspaceMarkersChanged (schrodinger.application.phase.phase_markers.PhaseMarkers attribute) WorkspaceSuperpositionFrame (class in schrodinger.application.matsci.reaction_workflow_gui_utils) WorldCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) WormlikeMicelleInputFile (class in schrodinger.application.matsci.packmol) worst_saved_score() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) wrap_html_tag() (in module schrodinger.ui.qt.utils) wrap_module() (in module schrodinger.infra.mmcheck) wrap_qt_tag() (in module schrodinger.ui.qt.utils) wrap_trajectory() (in module schrodinger.trajectory.utils) WrappedObjDeletedError wrapper_build_attach_structure() (in module schrodinger.application.matsci.rxn_channel) wrapUp() (schrodinger.application.matsci.appbase.ProcessPtStructuresApp method) wReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) writable_server_log() (in module schrodinger.application.licensing.licadmin) WRITE (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) Write (schrodinger.ui.qt.config_dialog.RequestedAction attribute) write() (in module schrodinger.ui.qt.appframework2.appmethods) (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportWriter method) (schrodinger.application.bioluminate.antibody.grafting.GraftingOutput method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchAnalysis method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint static method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.arkdb.ArkDb method) (schrodinger.application.desmond.cms.Cms method) (schrodinger.application.desmond.cns_io.CNSData method) (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) (schrodinger.application.desmond.ffiostructure.FFIOStructure method) (schrodinger.application.desmond.gaussian_filter.GaussianFilter method) (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.desmond.rest_inp.RestInput method) (schrodinger.application.desmond.stage.analysis.Reporter method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.glide.glideanalysis.PoseLibrary method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.matsci.amorphous.BaseMoiety class method) (schrodinger.application.matsci.amorphous.Cascader class method) (schrodinger.application.matsci.amorphous.Monomer class method) (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF method) (schrodinger.application.matsci.cgforcefield.QEMDCms method) (schrodinger.application.matsci.crest.CrestTOML method) (schrodinger.application.matsci.equilibrium_md.CmsModel method) (schrodinger.application.matsci.equilibrium_md.MaeModel method) (schrodinger.application.matsci.fragments.NonUniqueTracker method) (schrodinger.application.matsci.fragments.UniqueTracker method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.BaseWorkflow method) (schrodinger.application.matsci.jwsteps.CombinerStep method) (schrodinger.application.matsci.packmol.PackmolInputFile method) (schrodinger.application.matsci.packmol.PDBWriter method) (schrodinger.application.matsci.permittivity.ConfigWriter method) (schrodinger.application.matsci.spectra.SpectrumFile method) (schrodinger.application.mopac.structure_launchers.StructureLauncher method) (schrodinger.application.pathfinder.route.RouteNode method) (schrodinger.application.phase.hypothesis.PhaseHypothesis method) (schrodinger.application.prime.input.Prime method) (schrodinger.application.qsite.input.QSiteInput method) (schrodinger.application.watermap.watermap_inp.WaterMapInput method) (schrodinger.pipeline.input.Writer method) (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.Code method) (schrodinger.protein.getpdb_utility.WholePDB method) (schrodinger.stepper.viz.VizWebpage method) (schrodinger.structure.MMCIFWriter method) (schrodinger.structure.PDBWriter method) (schrodinger.structure.SmilesStructure method) (schrodinger.structure.Structure method) (schrodinger.structure.StructureWriter static method) (schrodinger.structure.TextualStructure method) (schrodinger.structutils.sort.StructureFileSorter method) (schrodinger.surface.Surface method) (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.ui.qt.appframework2.debugcore.DebugStderr class method) (schrodinger.ui.qt.appframework2.debugcore.DebugStdout class method) (schrodinger.ui.qt.appframework2.knime_af2.KnimeNodeMixin method)

write_alignment_file() (in module schrodinger.application.bioluminate.antibody.grafting) write_angle_csv() (in module schrodinger.application.bioluminate.tcr.docking_angles) write_annotated_fasta() (in module schrodinger.application.bioluminate.anarci.annotate) write_antibody_modeling_fasta() (in module schrodinger.livedesign.biologics.modeling) write_apbs_input_with_ligand() (in module schrodinger.application.desmond.fep_net_charge) write_apbs_input_with_protein() (in module schrodinger.application.desmond.fep_net_charge) write_argfile() (in module schrodinger.job.jobcontrol) write_asl_file() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) write_attachment_block() (in module schrodinger.application.combiglide.corehop) write_blocks() (in module schrodinger.structutils.block_data) write_canvas_fingerprint() (in module schrodinger.protein.natural_analog) write_canvas_fingerprint_matrix() (in module schrodinger.protein.natural_analog) write_checkpoint() (schrodinger.application.desmond.cmj.Engine method) write_cms() (in module schrodinger.application.desmond.ffiostructure) write_cms_to_string() (in module schrodinger.application.desmond.ffiostructure) write_cms_with_wam() (in module schrodinger.application.matsci.jobutils) write_cns() (in module schrodinger.application.desmond.cns_io) (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot method) write_com_file() (in module schrodinger.application.matsci.reaction_workflow_utils) write_complex_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator method) write_config() (in module schrodinger.application.glide.http_server) write_core_only() (in module schrodinger.application.canvas.r_group) write_csv_from_dicts() (in module schrodinger.application.matsci.msutils) write_csv_record_to_string() (in module schrodinger.application.glide.utils) write_ct_to_sd_string() (in module schrodinger.structure) write_ct_to_string() (in module schrodinger.structure) write_cts() (in module schrodinger.structure) write_data() (in module schrodinger.application.bioluminate.methionine_oxidation) (schrodinger.application.desmond.bennett.CalcBAR method) write_dE() (in module schrodinger.application.desmond.deltaE) write_desmond_cells() (in module schrodinger.application.matsci.packmol) write_elec_block() (in module schrodinger.application.desmond.fep_net_charge) write_empty_file() (in module schrodinger.application.glide.sort_utils) write_encrypted_file() (in module schrodinger.application.matsci.enc) write_encrypted_text() (in module schrodinger.application.matsci.enc) write_events_csv() (in module schrodinger.application.licensing.lmgrd_log_parser) write_features_json() (in module schrodinger.utils.featureflags.write) write_fep_msj() (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator method) write_ff_solute_tempering() (in module schrodinger.application.desmond.remd) write_file() (in module schrodinger.application.licensing.licadmin) (schrodinger.ui.qt.rama.Rama method) write_force_field_to_json() (in module schrodinger.application.matsci.cgforcefield) write_fragment_msj() (schrodinger.application.desmond.msj_generator.fep.protein.CombinedProteinMsjGenerator method) write_glide_input_file() (schrodinger.pipeline.stages.glide.DockingStage method) write_hits() (in module schrodinger.application.combinatorial_screen.driver_utils) write_hotspot_files() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) write_hst_file() (in module schrodinger.application.macromodel.utils) write_idfile() (in module schrodinger.application.matsci.jobutils) write_image_to_file() (in module schrodinger.livedesign.cmdline) write_input() (in module schrodinger.application.bioluminate.escomp) write_input_file() (in module schrodinger.application.matsci.qubec_utils) write_job_cmd() (in module schrodinger.job.jobwriter) write_ligand_file() (in module schrodinger.application.desmond.util) write_list_to_file() (in module schrodinger.application.phase.packages.phase_utils) write_mae() (schrodinger.application.desmond.mxmd.mxmd_cleanup.Hotspot method) write_mae_with_wam() (in module schrodinger.application.matsci.jobutils) write_maestro_project() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) write_main_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator method) (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator method) (schrodinger.application.desmond.msj_generator.mxmd.MixedSolventMsjGenerator method) (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) write_md_msj() (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator method) (schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator method) (schrodinger.application.desmond.msj_generator.mxmd.MixedSolventMsjGenerator method) (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) write_membrane_msj() (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) write_modules_config() (in module schrodinger.tasks.remote_modules) write_mop_file() (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain method) write_msj() (in module schrodinger.application.desmond.cmj) (schrodinger.application.desmond.msj_generator.constant_ph.ConstantpHMsjGenerator method) write_msj_file() (in module schrodinger.application.bioluminate.met_oxidation.md_sim_runner) write_mtd_unbinding_path_summary() (in module schrodinger.application.desmond.kinetics.utils) write_n_ct() (in module schrodinger.application.desmond.util) write_natural_analog_res_db() (in module schrodinger.protein.natural_analog) write_oned_data_file_row_count() (in module schrodinger.application.phase.packages.oned_task_utils) write_output() (in module schrodinger.application.canvas.r_group) (in module schrodinger.application.glide.sort_utils) write_overall_usage_csv() (in module schrodinger.application.licensing.lmgrd_log_parser) write_packmol_input_file() (in module schrodinger.application.matsci.packmol) write_pk50_report() (in module schrodinger.application.jaguar.pk50_report) write_populations_report() (in module schrodinger.application.jaguar.macro_pka_utils) write_powder_diffraction_pattern() (in module schrodinger.application.matsci.spectra) write_pqr() (in module schrodinger.application.bioluminate.escomp) (in module schrodinger.application.desmond.fep_net_charge) write_pqrs() (in module schrodinger.application.desmond.fep_net_charge) write_preprocessed_tmp_db() (in module schrodinger.protein.process_enamine_db) write_probe_files() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) write_products() (in module schrodinger.application.pathfinder.multiroute) write_props_to_csv() (in module schrodinger.application.bioluminate.residue_scanning.properties) write_ramd_clustering_summary() (in module schrodinger.application.desmond.kinetics.utils) write_ramd_msj() (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) write_random_smi_subset() (in module schrodinger.application.combinatorial_diversity.driver_utils) write_reactions_file() (in module schrodinger.application.pathfinder.reaction) write_readme() (in module schrodinger.application.glide.utils) write_readme_file() (in module schrodinger.application.bb_database.bb_task_utils) write_reagent_classes_file() (in module schrodinger.application.pathfinder.reaction) write_recentered_traj() (in module schrodinger.application.desmond.replica_sid_generator) write_ref_receptor() (schrodinger.application.desmond.mxmd.mxmd_cleanup.CleanUp method) write_res_log_file() (in module schrodinger.protein.process_enamine_db) write_residues_to_file() (in module schrodinger.protein.process_enamine_db) write_restart_parameters_file() (in module schrodinger.application.matsci.jobutils) write_restraints() (in module schrodinger.forcefield.minimizer) write_result_row() (in module schrodinger.application.livedesign.ld_glide_utils) (in module schrodinger.application.livedesign.ld_strain_rescore_utils) write_results() (schrodinger.application.desmond.bennett.CalcBAR method) write_row_data() (in module schrodinger.ui.qt.table) write_sba_file() (in module schrodinger.application.desmond.simulation_block_data) write_script() (in module schrodinger.application.desmond.feputils) write_sea2msj() (in module schrodinger.application.desmond.cmj) (in module schrodinger.application.matsci.msutils) write_seq_stats() (in module schrodinger.application.bioluminate.peptide_sar.io) write_sequences_to_fasta() (in module schrodinger.application.prepwizard) write_simplified_transitions_file() (in module schrodinger.application.matsci.bandshape_utils) write_site_features_json() (in module schrodinger.utils.featureflags.write) write_solvent_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.absolute_binding.AbsoluteBindingMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator method) write_st_from_db_by_smiles() (in module schrodinger.active_learning.al_utils) write_stages_file() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) write_string_to_file() (in module schrodinger.application.phase.packages.phase_utils) write_structure() (schrodinger.protein.membrane.Membrane_Model method) write_structures() (in module schrodinger.application.desmond.struc) write_structures_subset_to_new_file() (in module schrodinger.driver.structsubset) write_subjob_msjs() (schrodinger.application.desmond.msj_generator.common.FepBaseMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.protein.CombinedProteinMsjGenerator method) (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator method) write_subjob_selections() (in module schrodinger.application.combinatorial_diversity.driver_utils) write_substructure_constraints_file() (in module schrodinger.application.matsci.crest) write_task() (in module schrodinger.tasks.gui) write_to_file() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) write_to_stdout() (schrodinger.protein.analysis.Report method) write_to_string() (schrodinger.application.desmond.cms.Cms method) write_trajectory_data() (in module schrodinger.application.livedesign.ld_utils) write_translated_gene_fastas() (in module schrodinger.application.bioluminate.update_germline_db.translate_db) write_unbind_msj() (schrodinger.application.desmond.msj_generator.unbinding_kinetics.UnbindingKineticsMsjGenerator method) write_unbinding_paths() (schrodinger.application.desmond.kinetics.cleanup.CleanUp method) write_unbinding_paths_summary() (schrodinger.application.desmond.kinetics.mtd_cleanup.CleanUp method) write_unbinding_statistics() (schrodinger.application.desmond.kinetics.mtd_cleanup.CleanUp method) write_unencrypted_file() (in module schrodinger.application.matsci.enc) write_unique_ligands() (in module schrodinger.application.livedesign.io_utils) write_usage_csv() (in module schrodinger.application.licensing.lmgrd_log_parser) write_vacuum_msj() (schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator method) write_vectors_to_pml() (in module schrodinger.application.bioluminate.tcr.docking_angles) write_vis_file() (in module schrodinger.application.mopac.mopac_surfaces) write_vis_files() (schrodinger.application.mopac.results_main.MopacResultsMain method) write_watermap() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) write_yaml() (in module schrodinger.stepper.app) writeAlignData() (schrodinger.structutils.sitealign.BindingSiteAligner method) writeAnalyzeDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AnalyzeStageData static method) writeAutoQSARInFile() (schrodinger.application.matsci.genetic_optimization.AutoQSAR method) writeBarriersToStructure() (schrodinger.application.matsci.desconfig.BarrierHeader method) WriteBatchesOfStructures (class in schrodinger.application.transforms.chemio) writeBestStereos() (schrodinger.pipeline.stages.ligprep.PostLigPrepStage method) writeCluFile() (schrodinger.application.macromodel.utils.CluUtil method) writeCMS() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) writeCms() (schrodinger.application.matsci.permittivity.MdPostAnalysis method) writeCom() (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) writeComFile() (schrodinger.application.macromodel.utils.ComUtil method) writeCommand() (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.structutils.rmsd.ConformerRmsd method) writeCommandFile() (schrodinger.ui.qt.appframework2.knime_af2.KnimeNodeMixin method) writeCompressedPredictions() (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) writeConfig() (schrodinger.application.matsci.permittivity.WorkflowParser class method) (schrodinger.application.prime.wrapper.ConsensusConfig method) (schrodinger.application.prime.wrapper.PrimeConfig method) writeConfiguration() (schrodinger.stepper.app.StepperApplication class method) WriteControls() (in module schrodinger.application.matsci.gsas.GSASIIfiles) writeCSVFile() (schrodinger.active_learning.mq_worker.Worker method) (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) writeData() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint static method) writeDataFiles() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) WriteDialog (class in schrodinger.ui.qt.appframework) writeDictDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords static method) writeDihedralDis() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) writeDstFile() (schrodinger.application.macromodel.utils.CluUtil method) writeEnergiesToCSV() (schrodinger.application.matsci.mecp_mod.MECP method) writeFailure() (schrodinger.application.pathfinder.synthesis.ReactionFailureTracker method) writeFES() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis static method) writeFile() (schrodinger.application.transforms.dofn_utils.DataFile method) (schrodinger.ui.qt.structure_selector.StructureSelector method) writeFiles() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) writeFingerprintFiles() (schrodinger.application.matsci.mlearn.features.ComplexFeatures static method) writeFPFile() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) writeFrameWater() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) writeGrd() (schrodinger.application.jaguar.output.JaguarOutput method) writeGridData() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) writeHSWater() (schrodinger.application.desmond.stage.app.watermap.WaterMapAnaJob method) writeInheritableParentDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParentStageData static method) writeInput() (schrodinger.application.matsci.crest.Crest method) (schrodinger.application.matsci.fragments.UniqueTracker method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.CombinerStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) (schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelection method) writeInputFile() (schrodinger.application.inputconfig.InputConfig method) writeInputFiles() (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask method) writeInputForConsensus() (schrodinger.application.prime.wrapper.BasePrimeAlignment method) writeInputForPrime() (schrodinger.application.prime.wrapper.BasePrimeAlignment method) writeInputTOML() (schrodinger.application.matsci.crest.Crest method) (schrodinger.application.matsci.crest.CrestCSearch method) writeInputXYZs() (schrodinger.application.matsci.crest.Crest method) writeInteractionsFile() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) writeInterfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) writeJobCmd() (schrodinger.ui.qt.appframework2.af2.JobApp method) writeJSON() (schrodinger.application.glide.glide.GlideJob method) writeKeyStringToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.OverrideKeywords static method) writeKeywordsToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords static method) writeLigand() (schrodinger.application.glide.poseviewconvert.Complex method) writeLogEntry() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) (schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method) (schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method) writeMae() (schrodinger.application.matsci.desmondutils.SystemBuilder method) writeMaefile() (schrodinger.application.jaguar.input.JaguarInput method) writeMapToFile() (schrodinger.application.livedesign.export_map_manager.ExportMap method) writeMatrixData() (schrodinger.structutils.sitealign.BindingSiteAligner method) WriteMode (class in schrodinger.infra.structure) writeModelDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint static method) writeModelFiles() (schrodinger.active_learning.mq_worker.Worker method) WriteMolsToFile (class in schrodinger.seam.io.chemio) writeMsj() (schrodinger.application.matsci.desmondutils.SystemBuilder method) writeMSJ() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) writeMSJFile() (schrodinger.application.matsci.jwsteps.MDCustomMSJStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) writeNMD() (in module schrodinger.trajectory.prody.writenmd) writeNMDmae() (in module schrodinger.trajectory.prody.writenmd) writeNonInheritableParentDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParentStageData static method) writeOnsagerCoefficients() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) writeOutput() (schrodinger.application.matsci.crest.Crest method) (schrodinger.application.matsci.crest.CrestCSearch method) writeOutputCmsAndData() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) writeOutputCsv() (schrodinger.tasks.ldtasks.LDTask method) writePanelState() (schrodinger.ui.qt.appframework2.settings.SettingsPanelMixin method) writeParagraphs() (schrodinger.application.matsci.reportutils.PDFBuilder method) writeParameterLine() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine class method) writePDB() (schrodinger.application.prime.wrapper.PrimeTemplate method) writePressed() (schrodinger.ui.qt.appframework.WriteDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) writePrimeInput() (schrodinger.application.bioluminate.protein.protein.Refiner method) writePrimeProperties() (schrodinger.protein.membrane.Membrane_Model method) writePTEntries() (schrodinger.application.matsci.mswidgets.OptionalInputSelector method) (schrodinger.ui.qt.input_selector.InputSelector method) writePv() (schrodinger.application.glide.poseviewconvert.Complex method) Writer (class in schrodinger.pipeline.input) writer_open() (in module schrodinger.utils.csv_unicode) writeReadableCmdComment() (schrodinger.ui.qt.appframework2.af2.JobApp method) writeReceptor() (schrodinger.application.glide.poseviewconvert.Complex method) writeRoot() (schrodinger.pipeline.stages.filtering.DrugLikeSplitStage method) writeSbcFile() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.SbcUtil method) writeSchemeFile() (schrodinger.structutils.color.ColorScheme method) writeScoreCsv() (schrodinger.active_learning.al_node.ScoreProviderNode method) (schrodinger.application.phase.packages.shape_screen_al_node.CalculateScoreNode method) writeSectionsToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ExtraSectionData static method) writeSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) writeSIFFile() (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) writeSimplified() (schrodinger.application.glide.glide.GlideJob method) writeSingleStructures() (schrodinger.application.matsci.fragments.FragmentReactor method) writeSmap() (schrodinger.application.matsci.jwsteps.BaseWorkflow method) writeStateAndClose() (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.knime_af2.KnimeNodeMixin method) writeStructures() (schrodinger.structutils.rmsd.ConformerRmsd method) (schrodinger.structutils.sitealign.BindingSiteAligner method) WriteStructuresToFile (class in schrodinger.seam.io.chemio) writeSurfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) writeTOFFile() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow static method) writeTopNFromBlock() (schrodinger.structutils.sort.StructureFileSorter method) writeTopPoses() (schrodinger.application.glide.glideanalysis.PoseLibrary method) writeToString() (schrodinger.structure.Structure method) WriteToText (class in schrodinger.seam.io.textio) writeValidPoses() (schrodinger.application.glide.glideanalysis.PoseLibrary method) writeVibFile() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis class method) written_count (schrodinger.rdkit.molio.PfxMolWriter property) (schrodinger.rdkit.molio.RdkitMolWriter property) WrongFileType ws_coordinate_center (schrodinger.application.pymol.mae_sync.MaestroViewSettingsModel attribute) ws_index (schrodinger.application.matsci.sculptcomplex.SiteAtom attribute) ws_translation (schrodinger.application.pymol.mae_sync.MaestroViewSettingsModel attribute) ws_view_matrix (schrodinger.application.pymol.mae_sync.MaestroViewSettingsModel attribute) ws_viewing_volume (schrodinger.application.pymol.mae_sync.MaestroViewSettingsModel attribute) WSCORE_GROUP_DATA (schrodinger.infra.structure.WorkflowType attribute) WScoreSIPStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) WScoreStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) WT (schrodinger.application.desmond.constants.FEP_STATE_KEYS attribute) wt_frag_st (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) wt_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) wt_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) wt_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property) wt_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)

X

x (schrodinger.application.jaguar.macro_pka_utils.GraphData attribute) X (schrodinger.application.matsci.amorphous.Box attribute) (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.matsci.espresso.qeinput.StructureType attribute) (schrodinger.application.matsci.nano.xtal.AXIS attribute) x (schrodinger.comparison.results.Result attribute) (schrodinger.graphics3d.ellipsoid.MaestroEllipsoid property) (schrodinger.graphics3d.hemisphere.MaestroHemisphere property) (schrodinger.graphics3d.sphere.MaestroSphere property) (schrodinger.structure.StructureAtom property) (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) x() (schrodinger.ui.qt.network_visualizer.Node method) x0 (schrodinger.graphics3d.torus.MaestroTorus property) x1 (schrodinger.graphics3d.torus.MaestroTorus property) X_ALIAS (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) X_BIAS_F() (in module schrodinger.application.matsci.uq_utils) X_GAP (schrodinger.application.matsci.reaction_workflow_utils.SiblingNode attribute) X_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) x_key (schrodinger.ui.qt.network_visualizer.Node attribute) X_TITLE (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) XAnomAbs() (in module schrodinger.application.matsci.gsas.GSASIImath) xChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute)

xhead (schrodinger.graphics3d.arrow.MaestroArrow property) XL (schrodinger.ui.qt.standard.design_tokens.FontSizes attribute) xmerNum() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) xmerProbability() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) XP_SCORE (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) XpPVParser (class in schrodinger.application.glide.xpdes) XRDCalculator (class in schrodinger.application.matsci.xrd) xReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) XScattDen() (in module schrodinger.application.matsci.gsas.GSASIImath) XSignal (class in schrodinger.ui.qt.xsignals) xtail (schrodinger.graphics3d.arrow.MaestroArrow property) xtal (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) xtalChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) xtalReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) XTB (schrodinger.application.jaguar.constants.CalcType attribute) (schrodinger.application.jaguar.rotation_barriers_keywords.ExternalMethod attribute) (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox attribute) XtbConformerSelection (class in schrodinger.application.matsci.reaction_workflow_utils) XTBError xTBFailure XTBInput (class in schrodinger.application.xtb.input) XTBKeyword (class in schrodinger.application.xtb.keywords) XTBOutput (class in schrodinger.application.xtb.output) XTBParseError XVOL_TEXT (schrodinger.application.phase.featureselector.FeatureModel attribute) xyz (schrodinger.application.desmond.fep_scholar_util.MetaAtom property) XYZ (schrodinger.infra.structure.FileFormat attribute) (schrodinger.rdkit_extensions.Format attribute) xyz (schrodinger.structure.StructureAtom property) xyz_to_sdf() (in module schrodinger.utils.fileutils) xyzasu (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) XYZDialBox (class in schrodinger.ui.qt.dialbox) XYZVolumeGraph (class in schrodinger.application.matsci.amorphous)

Y

y (schrodinger.application.jaguar.macro_pka_utils.GraphData attribute) Y (schrodinger.application.matsci.amorphous.Box attribute) (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.matsci.espresso.qeinput.StructureType attribute) (schrodinger.application.matsci.nano.xtal.AXIS attribute) y (schrodinger.graphics3d.ellipsoid.MaestroEllipsoid property) (schrodinger.graphics3d.hemisphere.MaestroHemisphere property) (schrodinger.graphics3d.sphere.MaestroSphere property) (schrodinger.structure.StructureAtom property) (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) y() (schrodinger.ui.qt.network_visualizer.Node method) y0 (schrodinger.graphics3d.torus.MaestroTorus property) y1 (schrodinger.graphics3d.torus.MaestroTorus property) Y_ALIAS (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) Y_AXIS_SCALE (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute) Y_HEADERS (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) Y_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute)

y_key (schrodinger.ui.qt.network_visualizer.Node attribute) Y_MARKER (schrodinger.application.desmond.stage.analysis.TimeSeriesAnalysisJob attribute) y_mod (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) Y_TITLE (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) yaml_file_to_param() (in module schrodinger.models.yaml_utils) yaml_str_to_param() (in module schrodinger.models.yaml_utils) yaml_tuple_constructor() (in module schrodinger.application.matsci.yamlutils) yaml_tuple_representer() (in module schrodinger.application.matsci.yamlutils) yChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) YES (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput attribute) yhead (schrodinger.graphics3d.arrow.MaestroArrow property) yield_enum_and_typed_val() (in module schrodinger.forcefield.ffld_options) yield_input (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) yield_inputChanged (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) yield_inputReplaced (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) yieldStructures() (schrodinger.application.phase.packages.shape_ligprep.LigPrep method) yReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) ytail (schrodinger.graphics3d.arrow.MaestroArrow property)

Z

Z (schrodinger.application.matsci.amorphous.Box attribute) (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) (schrodinger.application.matsci.espresso.qeinput.StructureType attribute) (schrodinger.application.matsci.nano.xtal.AXIS attribute) z (schrodinger.graphics3d.ellipsoid.MaestroEllipsoid property) (schrodinger.graphics3d.hemisphere.MaestroHemisphere property) (schrodinger.graphics3d.sphere.MaestroSphere property) (schrodinger.structure.StructureAtom property) (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) z0 (schrodinger.graphics3d.torus.MaestroTorus property) z1 (schrodinger.graphics3d.torus.MaestroTorus property) Z_INDEX (schrodinger.ui.qt.label_cursor.LabelCursorAxes attribute) Z_KEY (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) Z_TITLE (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) z_variables() (in module schrodinger.application.jaguar.textparser) ZAtom (class in schrodinger.application.matsci.zmutils) zChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) Zero (schrodinger.structure.BondType attribute) ZERO_NORM_TANGENT (schrodinger.application.jaguar.constants.FatalErrors attribute) zero_order_metal_bonds() (in module schrodinger.application.jaguar.autots_bonding) zero_point_energy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) zeroed() (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) ZEROVEC (schrodinger.application.matsci.nano.sheet.HoneycombBilayers attribute) (schrodinger.application.matsci.nano.tube.NanoTubeSheet attribute) zhead (schrodinger.graphics3d.arrow.MaestroArrow property) ZIGZAG (schrodinger.application.matsci.nano.constants.Constants attribute) ZIGZAG_BY_ONE_BASE (schrodinger.application.matsci.nano.sheet.Grow attribute) zip (schrodinger.application.combinatorial_explorer.driver_utils.RouteSourceType attribute) ZIP (schrodinger.seam.viz.watcher.ResponseType attribute) zip_and_set_incorporation() (in module schrodinger.application.matsci.jobutils) zip_files() (in module schrodinger.utils.fileutils)

zip_files_or_directory() (in module schrodinger.application.matsci.jobutils) zip_library_dir() (in module schrodinger.application.combinatorial_screen.driver_utils) zip_project() (in module schrodinger.application.phase.packages.hypo_refine.project_utils) (in module schrodinger.project.project) zip_query() (in module schrodinger.application.bb_database.bb_task_utils) ZMATNUMBER (schrodinger.application.matsci.rxn_path.InternalCoords attribute) ZMatrix (class in schrodinger.application.matsci.zmutils) ZmqClient (class in schrodinger.application.glide.http_client) (class in schrodinger.tasks.taskszmq) ZmqServer (class in schrodinger.tasks.taskszmq) Zoom (class in schrodinger.application.bioluminate.pml_menus) ZOOM (schrodinger.ui.qt.schart.SChart attribute) zoom() (schrodinger.application.matsci.density_analysis_widget.CustomToolbar method) (schrodinger.ui.qt.navtoolbar.MaestroNavToolbar method) zoomContextMenuRequested() (schrodinger.ui.two_d_viewer.TwoDViewer method) zoomItem() (schrodinger.ui.qt.network_views.NetworkViewer method) ZoomWidget (class in schrodinger.ui.two_d_viewer) ZORA_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab attribute) ZOrder (class in schrodinger.protein.helm.helm_renderer) zpe (schrodinger.application.matsci.espresso.qeoutput.PhDOS.Thermo attribute) zpe() (in module schrodinger.application.jaguar.textparser) zpe_precision (schrodinger.application.jaguar.results.JaguarResults attribute) zReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Coord attribute) ZSTD (schrodinger.rdkit_extensions.CompressionType attribute) ztail (schrodinger.graphics3d.arrow.MaestroArrow property) zte() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) ZTE_MAXDEN (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) ZTE_NSTEPS (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) ZTE_TOL (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) zval (schrodinger.application.matsci.espresso.utils.MagElement attribute) (schrodinger.application.matsci.espresso.utils.PPSpecies attribute) (schrodinger.application.matsci.espresso.utils.PseudoData attribute) ZVariables (class in schrodinger.application.jaguar.results)