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.cmdline.RestrictedArgRange 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.assembly_yaml.ChainData 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.mhc.docking_angles.DescriptiveAngles method) (schrodinger.application.bioluminate.mhc.docking_angles.ReceptorChainInfo 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.ResidueData 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.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.arkdb.ArkDb method) (schrodinger.application.desmond.arkdb.Datum method) (schrodinger.application.desmond.bennett.CalcBAR 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.measurement.Measurement method) (schrodinger.application.desmond.packages.analysis.AmorphousCrystalInter method) (schrodinger.application.desmond.packages.analysis.Angle method) (schrodinger.application.desmond.packages.analysis.AreaPerLipid method) (schrodinger.application.desmond.packages.analysis.AtomicPosition method) (schrodinger.application.desmond.packages.analysis.AxisDirector method) (schrodinger.application.desmond.packages.analysis.CenterOf method) (schrodinger.application.desmond.packages.analysis.Centroid method) (schrodinger.application.desmond.packages.analysis.Coc method) (schrodinger.application.desmond.packages.analysis.Com method) (schrodinger.application.desmond.packages.analysis.Dipole method) (schrodinger.application.desmond.packages.analysis.Distance method) (schrodinger.application.desmond.packages.analysis.FittedPlanarAngle method) (schrodinger.application.desmond.packages.analysis.Gyradius method) (schrodinger.application.desmond.packages.analysis.HalogenBondFinder method) (schrodinger.application.desmond.packages.analysis.HydrogenBondFinder method) (schrodinger.application.desmond.packages.analysis.HydrophobicInter method) (schrodinger.application.desmond.packages.analysis.HydrophobicInterFinder method) (schrodinger.application.desmond.packages.analysis.LigandRMSD method) (schrodinger.application.desmond.packages.analysis.LipidDirector method) (schrodinger.application.desmond.packages.analysis.MembraneDensityProfile method) (schrodinger.application.desmond.packages.analysis.MembraneThickness method) (schrodinger.application.desmond.packages.analysis.MetalInter method) (schrodinger.application.desmond.packages.analysis.MolecularSurfaceArea method) (schrodinger.application.desmond.packages.analysis.MomentOfInertia method) (schrodinger.application.desmond.packages.analysis.OrderParameter method) (schrodinger.application.desmond.packages.analysis.Pbc method) (schrodinger.application.desmond.packages.analysis.PlanarAngle method) (schrodinger.application.desmond.packages.analysis.PolarSurfaceArea method) (schrodinger.application.desmond.packages.analysis.PosAlign method) (schrodinger.application.desmond.packages.analysis.PosTrack method) (schrodinger.application.desmond.packages.analysis.ProteinSF method) (schrodinger.application.desmond.packages.analysis.ProtLigInter method) (schrodinger.application.desmond.packages.analysis.ProtLigPolarInter method) (schrodinger.application.desmond.packages.analysis.ProtProtHbondInter method) (schrodinger.application.desmond.packages.analysis.ProtProtInter method) (schrodinger.application.desmond.packages.analysis.ProtProtPiInter method) (schrodinger.application.desmond.packages.analysis.Ramachandran method) (schrodinger.application.desmond.packages.analysis.Rdf method) (schrodinger.application.desmond.packages.analysis.RMSD method) (schrodinger.application.desmond.packages.analysis.RMSF method) (schrodinger.application.desmond.packages.analysis.SaltBridgeFinder method) (schrodinger.application.desmond.packages.analysis.SecondaryStructure method) (schrodinger.application.desmond.packages.analysis.SmartsDirector method) (schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceArea method) (schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceAreaByResidue method) (schrodinger.application.desmond.packages.analysis.Torsion method) (schrodinger.application.desmond.packages.analysis.Vector method) (schrodinger.application.desmond.packages.analysis.VolumeMapper method) (schrodinger.application.desmond.packages.analysis.WatLigFragDistance method) (schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis method) (schrodinger.application.desmond.packages.staf.CustomMaestroAnalysis method) (schrodinger.application.desmond.packages.staf.DynamicAslAnalyzer method) (schrodinger.application.desmond.packages.staf.DynamicPositerAnalyzer method) (schrodinger.application.desmond.packages.staf.GeomAnalyzerBase method) (schrodinger.application.desmond.packages.staf.GeomCalc method) (schrodinger.application.desmond.packages.staf.Positer method) (schrodinger.application.desmond.packages.staf.UpdatedCmsFsysCtAnalysis method) (schrodinger.application.desmond.packages.topo.DuckFrame method) (schrodinger.application.desmond.packages.topo.FrameLoader method) (schrodinger.application.desmond.packages.traj.Frame method) (schrodinger.application.desmond.packages.traj.MaeFrameReader method) (schrodinger.application.desmond.packages.traj.MaeSource method) (schrodinger.application.desmond.packages.traj.MaestroFrame method) (schrodinger.application.desmond.packages.traj.Source method) (schrodinger.application.desmond.packages.traj.XtcSource method) 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(schrodinger.ui.qt.formlayout.FormTabWidget method) (schrodinger.ui.qt.formlayout.FormWidget method) (schrodinger.ui.qt.formlayout.PushLayout method) (schrodinger.ui.qt.formlayout.RadioLayout method) (schrodinger.ui.qt.formlayout.SliderLayout method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.jobwidgets.JobStatusButton method) (schrodinger.ui.qt.label_cursor.LabelCursor method) (schrodinger.ui.qt.label_cursor.LabelCursorAxes method) (schrodinger.ui.qt.label_cursor.MultiAxesLabelCursor method) (schrodinger.ui.qt.ligand_list.Ligand method) (schrodinger.ui.qt.ligand_list.LigandListModel method) (schrodinger.ui.qt.ligand_list.LigandListView method) (schrodinger.ui.qt.ligand_list.LigandListWidget method) (schrodinger.ui.qt.mapperwidgets.param_editor.ParamEditor method) (schrodinger.ui.qt.mapperwidgets.plptable.FieldColumn method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) 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(schrodinger.ui.qt.network_visualizer.ConnectionValidator method) (schrodinger.ui.qt.network_visualizer.Edge method) (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.network_visualizer.GraphSignals method) (schrodinger.ui.qt.network_visualizer.Node method) (schrodinger.ui.qt.pdb_dialog.PDBDialog method) (schrodinger.ui.qt.periodictable.ElementButton method) (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) (schrodinger.ui.qt.periodictable.PeriodicTableDialogMultipleClick method) (schrodinger.ui.qt.periodictable.PeriodicTableDialogSingleClick method) (schrodinger.ui.qt.pop_up_widgets.AddButtonWithIndicatorAndPopUp method) (schrodinger.ui.qt.pop_up_widgets.InfoButtonWithPopUp method) (schrodinger.ui.qt.pop_up_widgets.LineEditWithPopUp method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate method) (schrodinger.ui.qt.pop_up_widgets.ToolButtonWithPopUp method) (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.presets.save_presets_dialog.SavePresetsDialog method) (schrodinger.ui.qt.propertyselector.MyWindow method) (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.qt.propertyselector.PropertySelectorDialog method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) (schrodinger.ui.qt.propertyselector.PropertySelectorMenu method) (schrodinger.ui.qt.protein_health_viewer.BubbleTextItem method) (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) (schrodinger.ui.qt.radial_plot.Sector method) (schrodinger.ui.qt.rama.BackboneDihedral method) (schrodinger.ui.qt.rama.DihedralSpinBox method) (schrodinger.ui.qt.rama.Rama method) (schrodinger.ui.qt.rdmol_views.AbstractRDMolImageLabel method) (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) (schrodinger.ui.qt.rdmol_views.RDMolTooltipWithLabel method) (schrodinger.ui.qt.recent_completer.BrowseAndCreateCombo method) (schrodinger.ui.qt.recent_completer.BrowsePlaceholderRecentCombo method) (schrodinger.ui.qt.recent_completer.StringListModelInterface method) (schrodinger.ui.qt.rename_favorite_dialog.RenameFavoriteDialog method) (schrodinger.ui.qt.schart.AxesDialog method) (schrodinger.ui.qt.schart.AxisParams method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.BinsDialog method) (schrodinger.ui.qt.schart.Callout method) (schrodinger.ui.qt.schart.SChart method) (schrodinger.ui.qt.schart.SChartView method) (schrodinger.ui.qt.schart.SeriesData method) (schrodinger.ui.qt.schart.SeriesDialog method) (schrodinger.ui.qt.schart.SeriesParams method) (schrodinger.ui.qt.schart.SHistogramBarSeries method) (schrodinger.ui.qt.schart.SHistogramBarSet method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) (schrodinger.ui.qt.smatplotlib.SmatplotlibCanvas method) (schrodinger.ui.qt.standard_widgets.buttons.DoubleClickButtonMixin method) (schrodinger.ui.qt.standard_widgets.buttons.FlatButton method) (schrodinger.ui.qt.standard_widgets.buttons.SplitPushButton method) (schrodinger.ui.qt.standard_widgets.buttons.StyledButton method) (schrodinger.ui.qt.standard_widgets.hyperlink.ToggleLink method) (schrodinger.ui.qt.standard_widgets.labels.HeaderLabel method) (schrodinger.ui.qt.standard_widgets.labels.InfoTextLabel method) (schrodinger.ui.qt.structtable.StructureReaderDelegate method) (schrodinger.ui.qt.structtable.StructureViewerDelegate method) (schrodinger.ui.qt.structtable.ViewerTable method) (schrodinger.ui.qt.structure2d.AtomLabelAnnotator method) (schrodinger.ui.qt.structure2d.CgCoreAnnotator method) (schrodinger.ui.qt.structure2d.CircleAnnotator method) (schrodinger.ui.qt.structure2d.ColoredArrowAnnotator method) (schrodinger.ui.qt.structure2d.LabeledStructureToolTip method) (schrodinger.ui.qt.structure2d.MultiSquareAnnotator method) (schrodinger.ui.qt.structure2d.RedSquareAnnotator method) (schrodinger.ui.qt.structure2d.structure_item method) (schrodinger.ui.qt.structure2d.structure_view method) (schrodinger.ui.qt.structure2d.StructurePicture method) (schrodinger.ui.qt.structure2d.StructureToolTip method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) (schrodinger.ui.qt.swidgets.ActionComboBox method) (schrodinger.ui.qt.swidgets.ActionPushButton method) (schrodinger.ui.qt.swidgets.CenteringWidget method) (schrodinger.ui.qt.swidgets.CloseButton method) (schrodinger.ui.qt.swidgets.ColorWidget method) (schrodinger.ui.qt.swidgets.DeleteButton method) (schrodinger.ui.qt.swidgets.EditButton method) (schrodinger.ui.qt.swidgets.EditWithFocusOutEvent method) (schrodinger.ui.qt.swidgets.ElidedLabel method) (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) (schrodinger.ui.qt.swidgets.EllipsisPopUpButton method) (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.LeftElidedLabel 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.cmdline.RequireArgValue method) (schrodinger.utils.cmdline.RestrictedArgRange 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.cms.PosRestrainArray method) (schrodinger.application.desmond.packages.traj.MaeFrameReader 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) 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) 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) 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.ml_formulations_gui_utils.SketcherSMILESDialog 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_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.protassign.utils.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) 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) 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) adaptRestraints() (schrodinger.application.matsci.cgforcefield.RestraintAdaptationMixin method) add (schrodinger.ui.qt.appframework2.maestro_callback.CallbackInfo attribute) add() (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_analysis_argument() (in module schrodinger.application.matsci.equilibrium_md) 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_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_args() (in module schrodinger.application.phase.packages.shape_screen_oned_driver_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.protassign.changeables.changeable method) (schrodinger.protein.protassign.changeables.rotatable_changeable method) (schrodinger.protein.protassign.changeables.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_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_fv_modeling_mode() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) add_generate_arguments() (in module schrodinger.application.phase.packages.shape_screen_gpu_generate) add_geom_argument() (in module schrodinger.application.matsci.parserutils) 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_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) 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_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_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) (in module schrodinger.application.phase.packages.shape_screen_oned_driver_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_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.protassign.changeables) 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_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.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_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_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.protassign.changeables.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_reporting_args() (in module schrodinger.application.phase.packages.shape_screen_arg_utils) (in module schrodinger.application.phase.packages.shape_screen_oned_driver_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) (in module schrodinger.application.phase.packages.shape_screen_oned_driver_utils) ADD_RESET_THIS_TASK_OPTION (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin attribute) add_restart_parser_arguments() (in module schrodinger.application.matsci.parserutils) 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_screening_args() (in module schrodinger.application.phase.packages.shape_screen_oned_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_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_standard_confgen_options() (in module schrodinger.application.phase.packages.conformer_reader) add_standard_options() (in module schrodinger.utils.cmdline) 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_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_verbose_flag() (in module schrodinger.application.phase.packages.phase_database_arg_utils) add_votca_logo() (in module schrodinger.application.matsci.kmcgui) add_wam_to_cms() (in module schrodinger.application.matsci.jobutils) 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) addAnalyzer() (schrodinger.application.desmond.packages.staf.GeomCalc 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) addAngle() (schrodinger.application.desmond.packages.staf.GeomCalc 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) addAtomProps() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) addAtoms() (schrodinger.structure.Structure method) addBackmapping() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder 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.application.matsci.automated_martini_mapping_protein.CGStructBuilder method) (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.ui.dendrogram.DendrogramNode method) (schrodinger.ui.qt.dendrogram.NewickNode method) addCIonBodies() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) addColor() (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) addColorStop() (schrodinger.application.dendrogram.gradientSelector.GradientSelectorView method) addColumn() (schrodinger.ui.qt.swidgets.STableWidget method) addCOMAtoms() (schrodinger.application.matsci.clusterstruct.COMTracker method) addComment() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) addCompositionRow() (schrodinger.application.matsci.ml_formulations_gui_utils.FormulationRowManager 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) addControlButtons() (schrodinger.application.matsci.stage_widgets.RowFrame 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) addCustom() (schrodinger.application.desmond.packages.staf.GeomCalc method) addCustomSites() (schrodinger.application.phase.phase_markers.PhaseMarkers 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) addDataColumnWidget() (schrodinger.application.matsci.ml_formulations_gui_utils.DataRowWidget 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) addDistance() (schrodinger.application.desmond.packages.staf.GeomCalc method) addDistanceRestraint() (schrodinger.structutils.minimize.Minimizer method) addDisulfideBond() (schrodinger.protein.alignment.ProteinAlignment method) addDummyAtomAnchors() (schrodinger.application.matsci.reaction_workflow_enum_utils.SculptMultiRGroup 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) addEditColumnWidget() (schrodinger.application.matsci.ml_formulations_gui_utils.DataRowWidget 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) addFittedPlanarAngle() (schrodinger.application.desmond.packages.staf.GeomCalc 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.TagFullStructure 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) addImportGenericEntityTask() (schrodinger.application.livedesign.ld_import_utils.LDImportTaskManager method) addImportToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addIndicesToGroup() (schrodinger.application.matsci.atom_group.MSAtomGroupsBase method) addInputFile() (schrodinger.job.launcher.Launcher method) addInputFiles() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) addIonProperties() (schrodinger.application.ligprep.ionizer.Ionizer 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_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) addLDImportTask() (schrodinger.application.livedesign.ld_import_utils.LDImportTaskManager 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.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) 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) addNewSite() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder 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) addOneItem() (schrodinger.ui.qt.multi_combo_box.MultiComboBox 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) 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) addPlanarAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method) addPointsToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addPosFrozen() (schrodinger.structutils.minimize.Minimizer method) addPosition() (schrodinger.application.desmond.packages.staf.GeomCalc 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) addPropertiesRow() (schrodinger.application.matsci.ml_formulations_gui_utils.FormulationRowManager method) addProperty() (schrodinger.application.matsci.ml_formulations_gui_utils.FormulationData 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) addRDFFile() (schrodinger.application.matsci.jwsteps.RDFStep 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) addRGroups() (schrodinger.application.matsci.reaction_workflow_enum_utils.SculptMultiRGroup 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.ml_formulations_gui_utils.ScrollableAreaManager method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) (schrodinger.application.matsci.stage_widgets.MultiRowArea 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) 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) addShadow() (schrodinger.application.matsci.mlearn.features.Complex 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) addStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) (schrodinger.pipeline.input.LinearWriter method) (schrodinger.pipeline.input.Writer method) addStatsToPlot() (schrodinger.application.matsci.ml_formulations_gui_utils.FormulationPlotFrame 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) 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.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) addTorsion() (schrodinger.application.desmond.packages.staf.GeomCalc 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) addVector() (schrodinger.application.desmond.packages.staf.GeomCalc 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) addWidgetToCell() (schrodinger.application.matsci.stage_widgets.RowFrame 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) adjustHelixTerminal() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder 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) af2SettingsGetValue() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox 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.application.livedesign.panel_components.LiveReportSelectionComboBox 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) aid_match() (in module schrodinger.application.desmond.packages.topo) AIDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) aids (schrodinger.application.matsci.atom_group.HelixData attribute) (schrodinger.application.matsci.species.SUB_STRUCT_INFO attribute) aids2gids() (in module schrodinger.application.desmond.packages.topo) 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) alchemical_water (schrodinger.application.desmond.struc.CompStruc attribute) Alchemist (class in schrodinger.application.matsci.enumeration) ALDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) Alessandro (schrodinger.protein.predictors.DiproPredictor.DiproFormat attribute) 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_asl (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction attribute) (schrodinger.application.livedesign.tasks.Trj2maeTask.Input attribute) align_aslChanged (schrodinger.application.livedesign.tasks.Trj2maeTask.Input attribute) align_aslReplaced (schrodinger.application.livedesign.tasks.Trj2maeTask.Input 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_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.application.desmond.packages.analysis) (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) aligned_rmsd() (in module schrodinger.application.desmond.packages.msys.pfx) 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.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_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_STRUCS (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) all_structures (schrodinger.protein.alignment.BaseAlignment 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) ALPB (schrodinger.energy.SolventModel 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) 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) 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) amide_changeable (class in schrodinger.protein.protassign.changeables) amin (schrodinger.application.matsci.reaction_workflow_gui_utils.SequenceData attribute) amine_changeable (class in schrodinger.protein.protassign.changeables) 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) AmorphousCrystalInter (class in schrodinger.application.desmond.packages.analysis) AMU_TO_GRAM (schrodinger.application.desmond.packages.analysis.MembraneDensityProfile attribute) 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) AnalysisMSJStringer (class in schrodinger.application.matsci.desconfig) analyze() (in module schrodinger.application.desmond.packages.analysis) (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) 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.desmond.packages.analysis) (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_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) angstroms (schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.MockOpenMM.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) 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.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.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.protassign.changeables) annotate_ligand_rotatable_hydrogens() (in module schrodinger.protein.protassign.changeables) 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.protassign.changeables) (in module schrodinger.protein.protassign.utils) 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.immunebuilder.immunebuilder_adapter.ImmuneBuilderType attribute) (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_DRUG_CONJUGATE (schrodinger.livedesign.entity_type.EntityClass 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) AntibodyFormat (class in schrodinger.application.bioluminate.antibody.assembly_yaml) 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) 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.ui.qt.appframework2.af2) app (schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.MockOpenMM attribute) AppDockWidget (class in schrodinger.ui.qt.appframework) APPEND (schrodinger.application.matsci.mswidgets.MultiStageArea attribute) (schrodinger.infra.structure.WriteMode attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.tasks.jobtasks.IncorporationMode attribute) append() (schrodinger.application.glide.phase_subset.PhaseSubsetWriter 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.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_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) ApplicationMode (in module schrodinger.utils.qapplication) apply() (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_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() (in module schrodinger.protein.protassign.utils) 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.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.application.matsci.stage_widgets.RowFrame method) (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) 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_torsion_safe_bonded() (schrodinger.application.jaguar.hess_guess.CoordinateManager method) area (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) AreaPerLipid (class in schrodinger.application.desmond.packages.analysis) 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_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.protassign.pka_prediction.HistidinepKaPredictor method) argparser_set_defaults() (in module schrodinger.application.matsci.parserutils) ArgumentParserError ArgumentParserNoExit (class in schrodinger.application.matsci.espresso.utils) 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) Aromaticize (schrodinger.ui.sketcher_smarts_dialog.SmartsSearchOption attribute) 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) ArrayCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) 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.protassign.changeables.amide_changeable attribute) (schrodinger.protein.protassign.changeables.amine_changeable attribute) (schrodinger.protein.protassign.changeables.carboxyl_changeable attribute) (schrodinger.protein.protassign.changeables.changeable attribute) (schrodinger.protein.protassign.changeables.histidine_changeable attribute) (schrodinger.protein.protassign.changeables.rotatable_changeable attribute) (schrodinger.protein.protassign.changeables.water_changeable attribute) asl2gids() (in module schrodinger.application.desmond.packages.topo) 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_NOT_ALLOWED (schrodinger.application.matsci.mswidgets.MSAtomSelector 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) 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) 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.protassign.pka_prediction) 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.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.protassign.hbond_cluster.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.protassign.changeables.amide_changeable method) (schrodinger.protein.protassign.changeables.amine_changeable method) (schrodinger.protein.protassign.changeables.carboxyl_changeable method) (schrodinger.protein.protassign.changeables.changeable method) (schrodinger.protein.protassign.changeables.histidine_changeable method) (schrodinger.protein.protassign.changeables.ligand_changeable method) (schrodinger.protein.protassign.changeables.rotatable_changeable method) (schrodinger.protein.protassign.changeables.water_changeable method) assign_state_gap() (schrodinger.protein.protassign.changeables.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) assignGroupDoubleBonds() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignGroupTripleBonds() (schrodinger.structutils.assignbondorders.AssignBondOrders method) 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) 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_time_ge() (in module schrodinger.application.desmond.packages.msys.molfile.findframe) at_time_gt() (in module schrodinger.application.desmond.packages.msys.molfile.findframe) at_time_le() (in module schrodinger.application.desmond.packages.msys.molfile.findframe) at_time_lt() (in module schrodinger.application.desmond.packages.msys.molfile.findframe) at_time_near() (in module schrodinger.application.desmond.packages.msys.molfile.findframe) 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) 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) atom() (schrodinger.application.glide.glide.MetalConstraint method) atom_1 (schrodinger.application.matsci.mlearn.features.ProjBondData attribute) atom_2 (schrodinger.application.matsci.mlearn.features.ProjBondData attribute) 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_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_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_property (schrodinger.application.desmond.cms.AtomGroup property) atom_style (schrodinger.structure.StructureAtom property) atom_symtype() (in module schrodinger.application.mopac.results_main) atom_total (schrodinger.application.jaguar.results.JaguarResults property) (schrodinger.structure.Structure property) (schrodinger.structure.TextualStructure property) atom_type (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) AtomGroupData (class in schrodinger.application.matsci.clusterstruct) 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) AtomicPosition (class in schrodinger.application.desmond.packages.analysis) atomicsec() (in module schrodinger.application.jaguar.textparser) AtomIndexType (schrodinger.application.desmond.packages.traj.Frame attribute) 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.infra.structure.SuperImposeBy 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) 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) 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) 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.desmond.packages.traj.Fmt attribute) (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_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) AutomatedMartiniProteinMapping (class in schrodinger.application.matsci.automated_martini_mapping_protein) 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) 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_CELL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) AVERAGE_JEFF (schrodinger.application.matsci.kmc.SchrodingerTable attribute) averageable (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) averageAndSort() (schrodinger.application.matsci.coarsegrain.Internals method) 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) AxisDirector (class in schrodinger.application.desmond.packages.analysis) 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) b2fs() (in module schrodinger.application.matsci.espresso.qeinput) B3LYP (schrodinger.application.matsci.permittivity.JaguarCalculation 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_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_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) backup_file() (in module schrodinger.job.queue) 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_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) 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) BAROSTAT_TAU (schrodinger.application.matsci.desconfig.MSJStringer attribute) 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) 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) 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) 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) 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) BaseRelaxationStep (class in schrodinger.application.matsci.jwsteps) BaseResidueFilter (class in schrodinger.application.bioluminate.pose_filtering.residue_filter) BaseSearchTreeWidgetHelper (class in schrodinger.application.livedesign.panel_components) BaseSelectionPopUp (class in schrodinger.application.livedesign.panel_components) BaseSignature (class in schrodinger.application.matsci.species) BaseSquareAnnotator (class in schrodinger.ui.qt.structure2d) BaseStep (class in schrodinger.application.matsci.jwsteps) BaseStructureExportTask (class in schrodinger.application.livedesign.export_tasks) BaseStructureExportTask.Output (class in schrodinger.application.livedesign.export_tasks) BaseStructureExportTask86 (class in schrodinger.application.livedesign.export_tasks) BaseSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab) (class in schrodinger.application.jaguar.gui.tabs.properties_tab) BaseTab (class in schrodinger.application.jaguar.gui.tabs.base_tab) BaseTable (class in schrodinger.ui.qt.appframework2.debugwidgets) BaseTableWidgetDefinition (class in schrodinger.application.matsci.stage_widgets) BaseTemplateListWidgetItem (class in schrodinger.application.matsci.builderwidgets) BaseTextValidator (class in schrodinger.ui.qt.appframework2.validators) BaseTogglableCellWidget (class in schrodinger.application.matsci.stage_widgets) BaseWidget (class in schrodinger.ui.qt.basewidgets) BaseWizardPanel (class in schrodinger.ui.qt.appframework2.wizards) BaseWorkflow (class in schrodinger.application.matsci.jwsteps) BaseWorkflowFinderDialog (class in schrodinger.application.matsci.wfmanagement) Basic (schrodinger.protein.helm.helm_renderer.HexColor attribute) BASIC (schrodinger.trajectory.trajectory_gui_dir.playback_settings.Tab attribute) basic_windows_path() (in module schrodinger.application.jaguar.utils) BasicHydrophilic (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) BasicStatsAccumulator (class in schrodinger.application.phase.packages.oned_task_utils) Basis (class in schrodinger.application.jaguar.gui.input_tab_widgets) (class in schrodinger.application.jaguar.nmr_basis) BASIS (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) basis (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) BASIS (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) basis_changed (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin attribute) basis_is_supported_for_functional() (in module schrodinger.application.jaguar.jaguar_keyword_utils) basis_of_invariant() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method) basis_of_mirror_plane_with_normal() (in module schrodinger.application.matsci.cctbx.rot_mx) basis_set() (in module schrodinger.application.jaguar.textparser) basis_set_is_valid() (in module schrodinger.application.jaguar.workflow_validation) basisChanged (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) basisFiltersChanged (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView attribute) basisModel() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) basisname_in_list() (in module schrodinger.application.jaguar.jaguar_keyword_utils) BasisSelector (class in schrodinger.application.jaguar.gui.basis_selector) BasisSelectorFilterList (class in schrodinger.application.jaguar.gui.input_tab_widgets) BasisSelectorFilterListToolButton (class in schrodinger.application.jaguar.gui.basis_selector) BasisSelectorFilterPopUp (class in schrodinger.application.jaguar.gui.basis_selector) BasisSelectorLineEdit (class in schrodinger.application.jaguar.gui.basis_selector) BasisSet (class in schrodinger.application.jaguar.basis) BasisSetColumns (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) BasisSetListWidgetItem (class in schrodinger.application.jaguar.gui.basis_selector) BasisSetModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetProxyModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetSelector (class in schrodinger.application.matsci.jagwidgets) BasisSetSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set) BasisSetTableView (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSizeException BasisType (class in schrodinger.application.matsci.espresso.qeinput) batchFinished (schrodinger.application.glide.http_client.NonBlockingGlideServerManager attribute) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) BatchId (schrodinger.job.jobcontrol.Job property) BatchSettings (class in schrodinger.stepper.stepper) BB (schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE attribute) BB_TASK (in module schrodinger.application.bb_database.bb_arg_utils) BBModifiedPhosphateMonomerItem (class in schrodinger.protein.helm.helm_renderer) BBModifiedSugarMonomerItem (class in schrodinger.protein.helm.helm_renderer) BBPhosphateMonomerBase (class in schrodinger.protein.helm.helm_renderer) BBStandardPhosphateMonomerItem (class in schrodinger.protein.helm.helm_renderer) BBStandardSugarMonomerItem (class in schrodinger.protein.helm.helm_renderer) BBSugarMonomerBase (class in schrodinger.protein.helm.helm_renderer) BBValidationError BC_EFIELD_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) BC_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) bc_type (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) BC_W_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) bcc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) bctet1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) bctet2() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) BDEStep (class in schrodinger.application.matsci.jwsteps) bead_graph (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.BEAD_TYPE attribute) bead_names (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.NODE_GROUP_TYPE attribute) bead_nums (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.NODE_GROUP_TYPE attribute) beads (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.BEAD_TYPE attribute) BedrocScreener (class in schrodinger.application.phase.packages.bedroc_screener) BEFORESUPERPOSITION (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) beginGroup() (schrodinger.utils.preferences.Preferences method) BEHIND (schrodinger.application.matsci.nano.xtal.PBCBond attribute) BehindMonomer (schrodinger.protein.helm.helm_renderer.ZOrder attribute) Benchmark (class in schrodinger.seam.testing.benchmarks) BenchmarkResult (class in schrodinger.seam.testing.benchmarks) bend_conj_amines (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) BEND_TOLERANCE (schrodinger.application.matsci.atom_group.HelixArcAtomGroup attribute) bennett() (schrodinger.application.desmond.bennett.CalcBAR method) BessIn() (in module schrodinger.application.matsci.gsas.GSASIImath) BessJn() (in module schrodinger.application.matsci.gsas.GSASIImath) best_scoring_element() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) BestPoseFilter (class in schrodinger.application.glide.sort_utils) BETA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) beta_au() (in module schrodinger.application.jaguar.utils) beta_fdpolar() (in module schrodinger.application.jaguar.textparser) beta_homo_lumo_energy() (in module schrodinger.application.mopac.results_main) beta_kcalmol() (in module schrodinger.application.jaguar.utils) BETA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) beta_mix (schrodinger.application.jaguar.input.MixedPairs attribute) BETA_ORBITALS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) BETA_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) beta_polar() (in module schrodinger.application.jaguar.textparser) beta_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute) beta_somo_lumo_energy() (in module schrodinger.application.mopac.results_main) BETA_STRAND_PROPENSITY (class in schrodinger.protein.residue) beta_strand_propensity (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) betaij2Uij() (in module schrodinger.application.matsci.gsas.GSASIIlattice) BetaproPredictor (class in schrodinger.protein.predictors) BetaproPredictor.Input (class in schrodinger.protein.predictors) BETTER_LABELS (schrodinger.ui.qt.navtoolbar.SchrodingerSubplotTool attribute) BETWEEN (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericOperator attribute) beyondBindingSiteChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) BFactorPreset (class in schrodinger.application.bioluminate.pml_menus) BFGS (class in schrodinger.application.matsci.mecp_mod) BFR (schrodinger.protein.annotation.TCRRegionLabel attribute) bias (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) BIDENTATE (in module schrodinger.application.matsci.buildcomplex) BilayerInputFile (class in schrodinger.application.matsci.packmol) BILAYERSEP (schrodinger.application.matsci.nano.constants.Constants attribute) BILAYERSHIFT (schrodinger.application.matsci.nano.constants.Constants attribute) BilinearHistogramData (class in schrodinger.application.matsci.uq_utils) bin_b_factors() (in module schrodinger.application.bioluminate.pml_menus) bin_by_geometry() (in module schrodinger.application.matsci.reaction_workflow_utils) bin_structures_by_property() (in module schrodinger.application.matsci.reaction_workflow_utils) BIND_PROP (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae attribute) BINDING_SITE (class in schrodinger.protein.annotation) binding_site_cutoff (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) binding_site_cutoffChanged (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) binding_site_cutoffReplaced (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Input attribute) binding_site_residues (schrodinger.protein.annotation.ProteinSequenceAnnotations property) binding_sites (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) BindingSiteAligner (class in schrodinger.structutils.sitealign) BindingSiteAlignmentTask (class in schrodinger.protein.tasks.binding_site_align) BindingSiteAlignmentTask.Input (class in schrodinger.protein.tasks.binding_site_align) BindingSiteAlignmentTask.Output (class in schrodinger.protein.tasks.binding_site_align) BINS (schrodinger.ui.qt.schart.BinsDialog attribute) (schrodinger.ui.qt.schart.SChart attribute) bins() (schrodinger.application.desmond.packages.analysis.Rdf method) binsChanged (schrodinger.ui.qt.schart.SHistogramBarSeries attribute) BinsDialog (class in schrodinger.ui.qt.schart) bio_class (schrodinger.livedesign.biologics.registration.BioPolymer property) BioPolymer (class in schrodinger.livedesign.biologics.registration) BiopythonPairwiseAligner (class in schrodinger.protein.align) BiounitOverrunError biounits_from_structure() (in module schrodinger.protein.biounit) BISPECIFIC (schrodinger.application.bioluminate.antibody.assembly_yaml.AntibodyFormat attribute) (schrodinger.application.bioluminate.antibody.io.csv_reader.ModelingMode attribute) BISPECIFIC_ANTIBODY (schrodinger.livedesign.entity_type.EntityClass attribute) BIT_EXT (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) bitCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method)

bitscore (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) Bitset (class in schrodinger.infra.mmbitset) bitset_to_list() (in module schrodinger.utils.multifpfile) bitSetOff() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) bitSetOn() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) Black (schrodinger.protein.helm.helm_renderer.HexColor attribute) BLACK (schrodinger.ui.qt.standard.colors.NativeColors attribute) (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) BLANK_PATTERN (schrodinger.application.matsci.rxn_channel.ChannelDefinitions attribute) BlankableSpinBox (class in schrodinger.application.jaguar.gui.input_tab_widgets) BlankableSpinBoxDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) BLAST (schrodinger.protein.tasks.blast.BlastAlgorithm attribute) BlastAlgorithm (class in schrodinger.protein.tasks.blast) BlastDatabase (class in schrodinger.protein.tasks.blast) BlastSettings (class in schrodinger.protein.tasks.blast) BlastTask (class in schrodinger.protein.tasks.blast) BlastTask.Input (class in schrodinger.protein.tasks.blast) bld_align_file (schrodinger.application.bioluminate.antibody.grafting.GraftingInput property) bld_scaffold_file (schrodinger.application.bioluminate.antibody.grafting.GraftingInput property) BlenResCW() (in module schrodinger.application.matsci.gsas.GSASIIElem) BlenResTOF() (in module schrodinger.application.matsci.gsas.GSASIIElem) BlindedCompoundError BLKSIZE (schrodinger.pipeline.pipeutils.BackwardsReader attribute) blobs() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) BLOCK_NAME (schrodinger.application.prime.residue_interaction.InteractionReader attribute) block_signal_propagation() (schrodinger.models.parameters.CompoundParam method) BlockingFunctionTask (class in schrodinger.tasks.tasks) BlockingMixin (class in schrodinger.tasks.tasks) BLOSUM45 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) BLOSUM62 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) BLOSUM80 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) Bohr (schrodinger.application.jaguar.constants.Unit attribute) BOLD (schrodinger.application.phase.phase_markers.FontStyles attribute) (schrodinger.ui.qt.standard.design_tokens.FontWeights attribute) BOLD_ITALIC (schrodinger.application.phase.phase_markers.FontStyles attribute) BOLTZMANN (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor attribute) boltzmann_probability() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) BOLTZMANN_TIP (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor attribute) Bond (class in schrodinger.application.jaguar.hess_guess) BOND (schrodinger.application.matsci.rxn_path.Coord attribute) bond (schrodinger.structure.Structure attribute) (schrodinger.structure.StructureAtom property) BOND_A (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) BOND_B (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) bond_clicked (schrodinger.ui.qt.structure2d.structure_view attribute) bond_crossover() (in module schrodinger.application.matsci.genetic_optimization) bond_in_ring() (in module schrodinger.application.canvas.r_group) bond_iter() (schrodinger.structure._StructureBondContainer static method) bond_iterator() (in module schrodinger.structutils.analyze) bond_length_cache (schrodinger.application.matsci.amorphous.BaseMoiety attribute) bond_order (schrodinger.structutils.rgroup_enumerate.RGroup attribute) BOND_ORDERS_CHOICES (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BOND_ORDERS_DEFAULT (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) bond_stretch_energy() (in module schrodinger.application.qsite.output) bond_total (schrodinger.structure.StructureAtom property) BondCharge (class in schrodinger.application.jaguar.results) bondchg_repulsion_energy() (in module schrodinger.application.qsite.output) BondDistortion (class in schrodinger.structutils.check) bonded_atoms (schrodinger.structure.StructureAtom property) bondedAtomIdInSameRes() (schrodinger.application.matsci.amorphous.PolymerFragments method) BondEnergies (class in schrodinger.application.matsci.fragments) BondError BONDI_PCM_RADII (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) BONDING_CHOICES (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BONDING_DEFAULT (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BONDLENGTH (schrodinger.application.matsci.nano.constants.Constants attribute) bondLigandsToMetal() (schrodinger.application.matsci.sculptcomplex.Sculptor method) bondMatchingEdges() (schrodinger.application.matsci.nano.tube.NanoTube method) BondOrderMismatch bondPair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) BONDPENALTYTHRESH (schrodinger.application.matsci.rxn_path.ReactionPath attribute) bondRemainingNodes() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) bondRingPlaneIntersection() (schrodinger.structutils.ringspear.SpearRing method) BondRotator (class in schrodinger.application.desmond.torsion_related) bonds properties bonds (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction attribute) (schrodinger.application.jaguar.hess_guess.CoordinateManager property) (schrodinger.application.jaguar.utils.LewisStructure attribute) bondToH() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) BondType (class in schrodinger.structure) BONDWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) BoolCriterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) boolean() (in module schrodinger.utils.sea.common) BooleanDatabaseCriterion (class in schrodinger.application.bioluminate.propfilter) BoolOperator (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) BoolParam (class in schrodinger.models.parameters) bootstrap() (in module schrodinger.application.desmond.bennett) BootstrapNoiseHistogramData (class in schrodinger.application.matsci.uq_utils) BorderColors (class in schrodinger.ui.qt.standard.design_tokens) BorderlessPopUpFrame (class in schrodinger.ui.qt.utils) BorderSizes (class in schrodinger.ui.qt.standard.design_tokens) both_bond_types_exist() (in module schrodinger.application.matsci.nano.xtal) BOTTOM (schrodinger.ui.qt.schart.SChart attribute) (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) bottom_axis (schrodinger.ui.qt.schart.SChart property) BOTTOM_DATOR (schrodinger.application.matsci.deswidgets.DesmondMDWEdit attribute) bottom_reached (schrodinger.application.matsci.ml_formulations_gui_utils.ScrollableAreaWidget attribute) BottomBar (class in schrodinger.ui.qt.appframework2.af2) BottomButtonMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) BottomButtonMixin.BtnPos (class in schrodinger.ui.qt.widgetmixins.basicmixins) BottomButtonMixin.StdBtn (class in schrodinger.ui.qt.widgetmixins.basicmixins) bound_hydrogen() (in module schrodinger.application.jaguar.autots_bonding) BoundaryType (class in schrodinger.application.matsci.espresso.qeinput) boundingBoxCallback() (schrodinger.graphics3d.common.Group method) BoundingInformation() (in module schrodinger.analysis.visanalysis.volumedatastructureutils) BoundingInformationL() (in module schrodinger.analysis.visanalysis.volumedatastructureutils) boundingRect() (schrodinger.application.dendrogram.gradientSelector.ColorSelector method) (schrodinger.application.dendrogram.gradientSelector.GradientSelector method) (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) (schrodinger.ui.qt.schart.Callout method) (schrodinger.ui.qt.structure2d.structure_item method) Box (class in schrodinger.application.matsci.amorphous) box (schrodinger.application.desmond.packages.analysis.Pbc property) (schrodinger.application.desmond.packages.topo.DuckFrame property) (schrodinger.application.desmond.packages.traj.Frame property) BOX (schrodinger.application.matsci.packmol.PackmolKw attribute) box() (schrodinger.application.watermap.shapes.ShapeFactory method) BOX11 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX12 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX13 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX21 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX22 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX23 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX31 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX32 (schrodinger.application.matsci.kmc.FramesTable attribute) BOX33 (schrodinger.application.matsci.kmc.FramesTable attribute) box_letter() (in module schrodinger.protein.residue) BoxWithInnerHull (class in schrodinger.application.matsci.amorphous) bracket() (in module schrodinger.application.jaguar.qrnn.temp_opt) bracket_zeros() (in module schrodinger.application.jaguar.discretized_1d_function) break_infinite_segment() (in module schrodinger.application.matsci.graph) BREAK_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) BreakingBond (class in schrodinger.application.matsci.fragments) breakIntoFragments() (schrodinger.application.matsci.amorphous.PolymerFragments method) breakIntoMols() (schrodinger.application.matsci.amorphous.PolymerFragments method) breakSeqIntoLoops() (schrodinger.application.bioluminate.antibody.antibody_homology_report_writer.ReportWriter method) breakTemplatePolymer() (schrodinger.application.matsci.amorphous.Monomer method) Brent (class in schrodinger.application.jaguar.qrnn.temp_opt) brent() (in module schrodinger.application.jaguar.qrnn.temp_opt) brokenBonds() (schrodinger.application.pathfinder.route.RouteNode method) BROWNIAN_DYNAMICS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) BROWNIE (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) BrownieMSJStringer (class in schrodinger.application.matsci.desconfig) BROWSE (schrodinger.ui.qt.recent_completer.BrowseAndCreateStringModel attribute) (schrodinger.ui.qt.recent_completer.BrowseStringModel attribute) browse() (schrodinger.application.pymol.pymol4maestro.panel method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) BrowseAndCreateCombo (class in schrodinger.ui.qt.recent_completer) BrowseAndCreateStringModel (class in schrodinger.ui.qt.recent_completer) browseDirectory() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) browseFiles() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) (schrodinger.ui.qt.input_selector.InputSelector method) BrowsePlaceholderRecentCombo (class in schrodinger.ui.qt.recent_completer) browseSelected (schrodinger.ui.qt.recent_completer.BrowseAndCreateCombo attribute) (schrodinger.ui.qt.recent_completer.BrowsePlaceholderRecentCombo attribute) BrowseStringModel (class in schrodinger.ui.qt.recent_completer) brute() (in module schrodinger.application.jaguar.qrnn.temp_opt) BS (schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE attribute) BubbleTextItem (class in schrodinger.ui.qt.protein_health_viewer) build() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) (schrodinger.application.matsci.reportutils.PDFBuilder method) build_ab() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) build_ab_log_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) build_antibody_models() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) build_cell() (in module schrodinger.application.matsci.nano.sheet) build_chain_settings() (in module schrodinger.application.bioluminate.antibody.grafting) build_coupling_tensors() (schrodinger.application.jaguar.nmr_interactions.Interactions method) build_crystal() (in module schrodinger.application.matsci.maestrocmds) build_database() (in module schrodinger.application.bb_database.bb_task_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) build_irreps() (schrodinger.application.jaguar.nmr_basis.Basis method) build_kwargs() (in module schrodinger.application.matsci.nano.particle) build_natural_analog_dict() (in module schrodinger.protein.natural_analog) build_peptide() (in module schrodinger.protein.buildpeptide) build_peptide_bonds() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) build_polymer_graph() (in module schrodinger.livedesign.biologics.registration) build_ref_charges_and_bonds_cache() (in module schrodinger.structutils.ccd)