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 schroding