Index

_

__contains__() (schrodinger.active_learning.bloom_filter_methods.BuiltInBloomFilter method) (schrodinger.application.bioluminate.anarci.loop_ranges.LoopRange method) (schrodinger.application.bioluminate.mutation.MutationSet method) (schrodinger.application.glide_ws.optimizer.WScoreOptimizerEnsemble method) (schrodinger.application.matsci.msutils.EnumMetaWithContains method) (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) (schrodinger.infra.canvas.ChmScaffold method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 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.BitBasedSet method) (schrodinger.utils.scollections.BitBasedSubset 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_driver.StopAfterRequest method) (schrodinger.active_learning.al_driver.StopAfterValidator 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.ActiveLearningHtmlReport 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.bloom_filter_methods.BuiltInBloomFilter 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_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.active_learning.scaffold_methods.ScaffoldData method) (schrodinger.active_learning.substruct_enrichment.SubstructEnrichCalculator method) (schrodinger.adapter.CaptureRDErrorLog method) (schrodinger.adapter.RDKitOptions 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.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.MutationSet 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.TCRPreset method) (schrodinger.application.bioluminate.pml_menus.TCRPresetAHo method) (schrodinger.application.bioluminate.pml_menus.TCRPresetIMGT method) (schrodinger.application.bioluminate.pml_menus.TCRPresetSubMenu 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.ProxyModel 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.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.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.cms_utils.MinimalFfioStructure 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) 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(schrodinger.infra.mm.FitParamInfo method) (schrodinger.infra.mm.LigandParameters method) (schrodinger.infra.mm.LigandScoreStructure method) (schrodinger.infra.mm.MetalSupportStatus method) (schrodinger.infra.mm.MinimizeResults method) (schrodinger.infra.mm.MmException method) (schrodinger.infra.mm.MMFfldAssign method) (schrodinger.infra.mm.MMFfldEsp method) (schrodinger.infra.mm.MMFfldEspData method) (schrodinger.infra.mm.MMFfldHandle method) (schrodinger.infra.mm.MMFfldInitializer method) (schrodinger.infra.mm.MMFileContext method) (schrodinger.infra.mm.MMFragHandle method) (schrodinger.infra.mm.MMPREF method) (schrodinger.infra.mm.OPLSArchive method) (schrodinger.infra.mm.OPLSArchiveError method) (schrodinger.infra.mm.OPLSDatafile method) (schrodinger.infra.mm.OPLSVersionHash method) (schrodinger.infra.mm.Preferences method) (schrodinger.infra.mm.RedirectMmerrToPythonStderr method) (schrodinger.infra.mm.ScoreAtom method) (schrodinger.infra.mm.UTT method) 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(schrodinger.infra.structure.AtomQueryParams method) (schrodinger.infra.structure.CellMatchAtom method) (schrodinger.infra.structure.ContactParams method) (schrodinger.infra.structure.DistanceCell method) (schrodinger.infra.structure.InteractionAtomPair method) (schrodinger.infra.structure.IOException method) (schrodinger.infra.structure.MaeReader method) (schrodinger.infra.structure.MaeWriter method) (schrodinger.infra.structure.MetalInteraction method) (schrodinger.infra.structure.MM_Bitset method) (schrodinger.infra.structure.MM_BitsetIterator method) (schrodinger.infra.structure.MmctSerializer method) (schrodinger.infra.structure.MmpdbxReader method) (schrodinger.infra.structure.MoleculeGraph method) (schrodinger.infra.structure.PBC method) (schrodinger.infra.structure.PiCationInteraction method) (schrodinger.infra.structure.PiCationParams method) (schrodinger.infra.structure.PiPiInteraction method) (schrodinger.infra.structure.PiPiParams method) (schrodinger.infra.structure.PyStructureReaderException method) (schrodinger.infra.structure.ResidueId method) (schrodinger.infra.structure.RingSpear method) (schrodinger.infra.structure.SaltBridge method) (schrodinger.infra.structure.SaltBridgeParams method) (schrodinger.infra.structure.Structure method) (schrodinger.infra.structure.StructureAtom method) (schrodinger.infra.structure.StructureCoordinates method) (schrodinger.infra.structure.StructureIterator method) (schrodinger.infra.structure.StructureReader method) (schrodinger.infra.structure.StructureReaderException method) (schrodinger.infra.structure.StructureRing method) (schrodinger.infra.structure.StructureWriter method) (schrodinger.infra.structure.TextBlockReader method) (schrodinger.infra.structure.TextBlockWriter method) (schrodinger.infra.structure.WorkflowMenuMaestroWriter method) (schrodinger.infra.table.Table method) (schrodinger.infra.table.TableRow method) (schrodinger.infra.unusable_module_importer.AbstractUnusableModuleFinder method) (schrodinger.infra.unusable_module_importer.DummyModule method) (schrodinger.infra.util.CreateWhenNeeded method) (schrodinger.job.cert.CertInfo method) (schrodinger.job.host_check.Error method) (schrodinger.job.jobcontrol.Host method) (schrodinger.job.jobcontrol.Job method) (schrodinger.job.jobhandler.AsyncJobHandler method) (schrodinger.job.jobwriter.OplsArchiveNotFoundError method) (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.JobSpecificationBuilder method) (schrodinger.job.launchapi.SpecificationKeyError method) (schrodinger.job.launchapi.TaskSpecification method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) (schrodinger.job.launcher.Launcher method) (schrodinger.job.launchparams.LaunchParameters method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) 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(schrodinger.maestro_utils.composer_agent.request_manager.network_manager.NetworkManager method) (schrodinger.maestro_utils.composer_agent.request_manager.network_manager.Query method) (schrodinger.maestro_utils.composer_agent.request_manager.network_manager.Response method) (schrodinger.maestro_utils.composer_agent.request_manager.network_manager.UserFeedbackQuery method) (schrodinger.maestro_utils.composer_agent.session_handler.ChatSessionHandler method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBar method) (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBarSketcherDialog method) (schrodinger.maestro_utils.maestro_sync.BaseMaestroSync method) (schrodinger.maestro_utils.maestro_sync.PLPTarget method) (schrodinger.maestro_utils.maestro_sync.ProjectEntryMaestroSync method) (schrodinger.maestro_utils.maestro_sync.TitleTarget method) (schrodinger.maestro_utils.surface_manager.delegates.ChildIndentDelegate method) (schrodinger.maestro_utils.surface_manager.info_tab.InfoTab method) (schrodinger.maestro_utils.surface_manager.menus.BaseSurfaceActionsMenu method) (schrodinger.maestro_utils.surface_manager.menus.EntryContextMenu method) (schrodinger.maestro_utils.surface_manager.menus.GlobalActionsMenu method) (schrodinger.maestro_utils.surface_manager.menus.MenuActionData method) (schrodinger.maestro_utils.surface_manager.menus.SurfaceActionsMenu method) (schrodinger.maestro_utils.surface_manager.menus.SurfaceContextMenu method) (schrodinger.maestro_utils.surface_manager.secondary_pane.SecondaryPane method) (schrodinger.maestro_utils.surface_manager.surface_info.SurfaceInfo method) (schrodinger.maestro_utils.surface_manager.surface_item.EntryNodeItem method) (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceItem method) (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceNodeItem method) (schrodinger.maestro_utils.surface_manager.surface_manager_panel.SurfaceManagerPanel 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(schrodinger.models.mappers.TargetSpec method) (schrodinger.models.parameters.BaseMutableParam method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.models.parameters.DictParam method) (schrodinger.models.parameters.EnumParam method) (schrodinger.models.parameters.HybridMethodsMixin method) (schrodinger.models.parameters.ItemClassMixin method) (schrodinger.models.parameters.ListParam method) (schrodinger.models.parameters.Param method) (schrodinger.models.parameters.ParamListParam method) (schrodinger.models.parameters.SetParam method) (schrodinger.models.presets.PresetManager method) (schrodinger.models.presets.TaskPanelPresetManager method) (schrodinger.pipeline.input.LinearWriter method) (schrodinger.pipeline.input.Writer method) (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) (schrodinger.pipeline.pipeline.Pipeline method) 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(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) (schrodinger.protein.protassign.changeables.WaterStateEnumerator method) (schrodinger.protein.protassign.hbond_cluster.hbond_cluster method) (schrodinger.protein.protassign.network_solver.NetworkSolver method) (schrodinger.protein.protassign.utils.Interactors method) (schrodinger.protein.protassign.utils.PropKaException method) (schrodinger.protein.reliability.ProteinCheckParameters method) (schrodinger.protein.reliability.Results method) (schrodinger.protein.residue.CombinedChainDisulfideBond method) (schrodinger.protein.residue.CombinedChainResidueWrapper method) (schrodinger.protein.residue.DisulfideBond method) 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method) (schrodinger.seam.testing.preemption.SubJobPreEmptionSimulator method) (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) (schrodinger.seam.testing.test_pipelines.BenchFlow method) (schrodinger.seam.testing.test_pipelines.GPUExampleWorkflow method) (schrodinger.seam.transforms.combiners.Smallest.Globally method) (schrodinger.seam.transforms.combiners.Smallest.PerGroupedValues method) (schrodinger.seam.transforms.combiners.Smallest.PerKey method) (schrodinger.seam.transforms.core.GroupIntoBatches method) (schrodinger.seam.transforms.core.TeeIf method) (schrodinger.seam.transforms.grouping.AssignNearestBinKey method) (schrodinger.seam.transforms.grouping.GroupIntoBins method) (schrodinger.seam.transforms.grouping.UnbinAndPartitionBoundaryValues method) (schrodinger.seam.transforms.partitioners.FixedSample method) (schrodinger.seam.transforms.partitioners.Top method) (schrodinger.seam.transforms.resources.requires_gpu method) (schrodinger.seam.transforms.resources.requires_local_execution method) (schrodinger.seam.transforms.samplers.RandomSample method) (schrodinger.seam.transforms.window.BatchWindows method) (schrodinger.seam.transforms.window.StringIDWindow method) (schrodinger.seam.transforms.window.StringIDWindows method) (schrodinger.seam.viz.inspect.PipelineDisplayInfo method) (schrodinger.seam.viz.inspect.TransformDisplayInfo method) (schrodinger.seam.viz.render.ColorByLicenseStyler method) (schrodinger.seam.viz.render.ColorByStageStatusStyler method) (schrodinger.seam.viz.render.ColorByStatusStyler method) (schrodinger.seam.viz.render.ColorByTransformCPUTimeStyler method) (schrodinger.seam.viz.render.PipelineRenderer method) (schrodinger.seam.viz.render.Styler method) (schrodinger.seam.viz.watcher.EndpointInfo method) (schrodinger.seam.viz.watcher.WatcherDirReader method) (schrodinger.seam.viz.watcher.WatcherWebServer method) (schrodinger.seam.viz.watcherd.Watcher method) (schrodinger.seam.yaml.schemad.SchemadDoFn method) (schrodinger.seam.yaml.schemad.SchemadParDo method) (schrodinger.seam.yaml.transforms.CreateMols method) (schrodinger.seam.yaml.transforms.CreateStructures method) (schrodinger.seam.yaml.transforms.GlideDock method) (schrodinger.seam.yaml.transforms.LigPrep method) (schrodinger.seam.yaml.transforms.MolToSmiles method) (schrodinger.seam.yaml.transforms.MolToStructure method) (schrodinger.seam.yaml.transforms.PrettyPrintJson method) (schrodinger.seam.yaml.transforms.QikProp method) (schrodinger.seam.yaml.transforms.ReadFromPDB method) (schrodinger.seam.yaml.transforms.ReadMolsFromFile method) (schrodinger.seam.yaml.transforms.ReadStructuresFromFile method) (schrodinger.seam.yaml.transforms.SmilesToMol method) (schrodinger.seam.yaml.transforms.SmilesToStructure method) (schrodinger.seam.yaml.transforms.StructureToMol method) (schrodinger.seam.yaml.transforms.WriteMolsToFile method) (schrodinger.seam.yaml.transforms.WriteStructuresToFile method) (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter method) (schrodinger.stepper.shims.ShimMapStep method) (schrodinger.stepper.shims.ShimReduceStep method) (schrodinger.stepper.sideinputs.ForkStep method) (schrodinger.stepper.stepper.ElapsedFormatter method) (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) (schrodinger.stepper.stepper.StepTaskMixin method) (schrodinger.stepper.stepper.UnbatchedChain method) (schrodinger.stepper.stepper.ValidationIssue method) (schrodinger.stepper.viz.AbstractPlot method) (schrodinger.stepper.viz.OutputsPlot method) (schrodinger.stepper.viz.TopologyChart method) (schrodinger.stepper.viz.VizWebpage method) (schrodinger.structure._AtomBondContainer method) (schrodinger.structure._AtomCollection method) (schrodinger.structure._Chain method) (schrodinger.structure._Molecule method) (schrodinger.structure._Ring method) (schrodinger.structure._StructureAtomContainer method) (schrodinger.structure._StructureAtomProperty method) (schrodinger.structure._StructureBondContainer method) (schrodinger.structure._StructureBondProperty method) (schrodinger.structure._StructureProperty method) (schrodinger.structure.MaestroReader method) (schrodinger.structure.MaestroTextReader method) (schrodinger.structure.MaestroWriter method) (schrodinger.structure.MMCIFWriter method) (schrodinger.structure.Mol2Writer method) (schrodinger.structure.MultiFileStructureReader method) (schrodinger.structure.MultiFileStructureWriter method) (schrodinger.structure.PDBReader method) (schrodinger.structure.PDBWriter method) (schrodinger.structure.PropertyName method) (schrodinger.structure.Residue method) (schrodinger.structure.SDWriter method) (schrodinger.structure.SmilesCsvReader method) (schrodinger.structure.SmilesCsvWriter method) (schrodinger.structure.SmilesReader method) (schrodinger.structure.SmilesStructure method) (schrodinger.structure.SmilesWriter method) (schrodinger.structure.Structure method) (schrodinger.structure.StructureAtom method) (schrodinger.structure.StructureBond method) (schrodinger.structure.StructureReader method) (schrodinger.structure.StructureWriter method) (schrodinger.structure.TextualStructure method) (schrodinger.structure.UnsupportedOption method) (schrodinger.structure.UnsupportedOptionValue method) (schrodinger.structutils.analyze.AslLigandSearcher method) (schrodinger.structutils.analyze.Ligand method) (schrodinger.structutils.analyze.MissingLoopFinder method) (schrodinger.structutils.check.AngleDistortion method) (schrodinger.structutils.check.BondDistortion method) (schrodinger.structutils.clash_resolution.ClashResolutionResult method) (schrodinger.structutils.clash_resolution.ReceptorLigandClashResolver method) (schrodinger.structutils.color.Color method) (schrodinger.structutils.color.ColorRamp method) (schrodinger.structutils.color.ColorScheme method) (schrodinger.structutils.color.RainbowColorRamp method) (schrodinger.structutils.createfragments.FragmentCreator method) (schrodinger.structutils.filter.Filter method) (schrodinger.structutils.filter.SinglePropFilter method) (schrodinger.structutils.filter.SingleSmartsFilter method) (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) (schrodinger.structutils.interactions.pi.CationPiInteraction method) (schrodinger.structutils.interactions.pi.Centroid method) (schrodinger.structutils.interactions.pi.PiPiInteraction method) (schrodinger.structutils.io.MultiFileWriter method) (schrodinger.structutils.measure.DistanceCellIterator method) (schrodinger.structutils.minimize.Minimizer method) (schrodinger.structutils.rgroup_enumerate.Concentration method) (schrodinger.structutils.rgroup_enumerate.RGroupEnumerator method) (schrodinger.structutils.rgroup_enumerate.RGroupSource method) (schrodinger.structutils.ringspear.Spear method) (schrodinger.structutils.ringspear.SpearRing method) (schrodinger.structutils.rmsd.ConformerRmsd method) (schrodinger.structutils.rmsd.ConformerRmsdX method) (schrodinger.structutils.sitealign.BindingSiteAligner method) (schrodinger.structutils.sitealign.SiteMatchLookup method) (schrodinger.structutils.smilesfilter.FilterReporter method) (schrodinger.structutils.smilesfilter.SmilesErrorHandler method) (schrodinger.structutils.sort.StructureFileSorter method) (schrodinger.structutils.structalign.StructAlign method) (schrodinger.surface.Surface method) (schrodinger.surface.Surface.Color method) (schrodinger.tasks.beamtasks.BeamTask method) (schrodinger.tasks.cli.TaskCLI method) (schrodinger.tasks.cmdline.ArgSpec method) (schrodinger.tasks.cmdline.ExtraWidthHelpFormatter method) (schrodinger.tasks.hosts.Gpu method) (schrodinger.tasks.hosts.Host method) (schrodinger.tasks.jobtasks.CmdJobTask method) (schrodinger.tasks.jobtasks.IncorporationParam method) (schrodinger.tasks.jobtasks.JobBackendCmdMixin method) (schrodinger.tasks.ldi.CsvColumn method) (schrodinger.tasks.ldi.DataColumn method) (schrodinger.tasks.ldi.InputColumn method) (schrodinger.tasks.ldi.LDI method) (schrodinger.tasks.ldi.PoseColumn method) (schrodinger.tasks.ldi.SdfColumn method) (schrodinger.tasks.param_cli.ParamCLI method) (schrodinger.tasks.provenance.TrackedValue method) (schrodinger.tasks.queue.TaskQueue method) (schrodinger.tasks.remote_modules.PatchInfo method) (schrodinger.tasks.slurmtasks.SlurmMonitor method) (schrodinger.tasks.taskmanager.TaskManager method) (schrodinger.tasks.tasks.ProcessingResult method) (schrodinger.tasks.tasks.QProcessError method) (schrodinger.tasks.tasks.SignalTask method) (schrodinger.tasks.tasks.SubprocessMixin method) (schrodinger.tasks.tasks.ThreadMixin method) (schrodinger.tasks.taskszmq.ZmqClient method) (schrodinger.tasks.taskszmq.ZmqServer method) (schrodinger.trajectory.pbc_manager.PBCMeasureMananger 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.trajectory.prody.pca.PCA method) (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner method) (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.NucleotideTorsions method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.ResiduesTorsions method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.SmallMoleculeTorsions method) (schrodinger.trajectory.trajectory_gui_dir.display_settings_data.DisplaySettingsData method) (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.FrameIntValidator method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameListItem method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) (schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets.PlotTitleLineEdit method) (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.SaveDefinitionsDialog method) (schrodinger.ui.chooseligand.ChooseLigandDialog method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.chooseligand.TestApp method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.DefinitionViewerDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.picking.MaestrolessLigandListModel method) (schrodinger.ui.picking.MaestrolessPickLigandDialog method) (schrodinger.ui.picking.MaestrolessPickResidueDialog method) (schrodinger.ui.picking.Pick3DObjectToggle method) (schrodinger.ui.picking.PickAslToggle method) (schrodinger.ui.picking.PickAtomsLassoToggle method) (schrodinger.ui.picking.PickAtomsToggle method) (schrodinger.ui.picking.PickAtomToggle method) (schrodinger.ui.picking.PickBondToggle method) (schrodinger.ui.picking.PickCategoryToggle method) (schrodinger.ui.picking.PickMixedToggle method) (schrodinger.ui.picking.PickPairToggle method) (schrodinger.ui.picking.PickResidueRow method) (schrodinger.ui.picking.PickResiduesToggle method) (schrodinger.ui.picking.PickTorsionToggle method) (schrodinger.ui.picking.ResidueRow method) (schrodinger.ui.qt.appframework.AppDockWidget method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework.CustomProgressBar method) (schrodinger.ui.qt.appframework.ReadDialog method) (schrodinger.ui.qt.appframework.WriteDialog method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.BaseBottomBar method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.af2.KBotFrame method) (schrodinger.ui.qt.appframework2.af2.KBotResponseWidget method) (schrodinger.ui.qt.appframework2.af2.MiniJobBottomBar method) (schrodinger.ui.qt.appframework2.af2.ProgressFrame method) (schrodinger.ui.qt.appframework2.af2.ResponseArea method) (schrodinger.ui.qt.appframework2.af2.SettingsButton method) (schrodinger.ui.qt.appframework2.af2.StatusBar method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) (schrodinger.ui.qt.appframework2.appmethods.MethodsDict method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.baseapp.DockWidget method) (schrodinger.ui.qt.appframework2.baseapp.ValidatedPanel method) (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) (schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method) (schrodinger.ui.qt.appframework2.debugcore.LogEntry method) (schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method) (schrodinger.ui.qt.appframework2.debugwidgets.BaseTable method) (schrodinger.ui.qt.appframework2.debugwidgets.ExecWidget method) 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__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.glide_ws.optimizer.WScoreOptimizerEnsemble 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.energy.VecMetalSystem method) (schrodinger.graphics3d.common.Group method) (schrodinger.infra.canvas.ChmAssignments method) (schrodinger.infra.canvas.ChmAtomIterator method) (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmBitsetIterator method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.canvas.ChmBondIterator method) (schrodinger.infra.canvas.ChmMatchExIterator method) (schrodinger.infra.canvas.ChmMatchIterator method) (schrodinger.infra.canvas.ChmPattern method) (schrodinger.infra.canvas.ChmSearchKey method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.infra.canvas.ChmValueAssignmentIterator method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.mmim.MMIMDict method) (schrodinger.infra.mmkv.MMKVArgList method) (schrodinger.infra.mmlist.mmlist method) (schrodinger.infra.structure.MM_Bitset method) (schrodinger.infra.structure.StructureCoordinates 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.BitBasedSet method) (schrodinger.utils.scollections.BitBasedSubset 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.geometry.PairPath attribute) 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) AA3_TO_1() (in module schrodinger.application.prepwizard2.tasks) 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) abCount (schrodinger.infra.canvas.ChmMCSRecord attribute) abeles() (in module schrodinger.application.matsci.gsas.GSASIIpwd) AbHumanizationTask (class in schrodinger.application.livedesign.tasks) AbHumanizationTask.Input (class in schrodinger.application.livedesign.tasks) AbHumanizationTask.JobConfig (class in schrodinger.application.livedesign.tasks) AbHumanizationTask.Output (class in schrodinger.application.livedesign.tasks) AbModelingTask (class in schrodinger.application.livedesign.tasks) AbModelingTask.Input (class in schrodinger.application.livedesign.tasks) AbModelingTask.JobConfig (class in schrodinger.application.livedesign.tasks) AbModelingTask.Output (class in schrodinger.application.livedesign.tasks) 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) aboutToShowProjectSettingsDialog (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin attribute) (schrodinger.ui.qt.forcefield.ffsettingsbutton.FFSettingsButton attribute) aboutToStartTask (schrodinger.ui.qt.tasks.taskwidgets.StartButton attribute) abraham_acid (schrodinger.application.jaguar.utils.JagSolventParams attribute) abraham_base (schrodinger.application.jaguar.utils.JagSolventParams 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) AbstractDockingMethod (class in schrodinger.application.glide.runner) 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) AbstractMinimizer (class in schrodinger.application.peptide_workflow.minimize) AbstractMover (class in schrodinger.application.peptide_workflow.moves) 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.propfilter.PropFilterDialog method) (schrodinger.application.bioluminate.propfilter.ValueSelectionDialog method) (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.matsci.chargegui.ChargeDialog method) (schrodinger.application.matsci.deswidgets.AdvancedMDOptions method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.NewPresetDialog method) (schrodinger.application.matsci.jagwidgets.SolventDialog method) (schrodinger.application.matsci.jobdirdlg.NewJobDirDialog method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.reordergui.ReorderAtomsDialog method) (schrodinger.application.matsci.reportutils.ReportOutputsDialog method) (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog method) (schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog method) (schrodinger.application.matsci.wfmanagement.WorkflowNamerDialog method) (schrodinger.ui.chooseligand.ChooseLigandDialog method) (schrodinger.ui.picking.MaestrolessPickLigandDialog method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) (schrodinger.ui.qt.formlayout.FormDialog method) (schrodinger.ui.qt.propertyselector.PropertySelectorDialog method) (schrodinger.ui.qt.rename_favorite_dialog.RenameFavoriteDialog method) (schrodinger.ui.qt.schart.AxesDialog method) (schrodinger.ui.qt.schart.BinsDialog method) (schrodinger.ui.qt.schart.SeriesDialog method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) (schrodinger.ui.qt.swidgets.NewNameDialog method) (schrodinger.ui.two_d_viewer.AtomPropertyDialog method) (schrodinger.ui.two_d_viewer.CtPropsDialog method) ACCEPT_MULTI (in module schrodinger.ui.qt.pop_up_widgets) accept_test() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) ACCEPT_TYPE (schrodinger.maestro_utils.composer_agent.request_manager.urls.PostQueryRequestKeys attribute) acceptableHeavyAtomsOverlap (schrodinger.infra.fast3d.Engine attribute) 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.constraints) 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) (schrodinger.infra.canvas.ChmSparseBitset 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) acentric_factor (schrodinger.application.jaguar.garza.SolventParams attribute) (schrodinger.application.jaguar.utils.JagSolventParams attribute) AcentricDipoleDirector (class in schrodinger.application.matsci.order_parameter_mod) ACETONITRILE (schrodinger.energy.Solvent attribute) 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.tasks.cmdline.ArgSpec attribute) (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) action_factory (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) action_name (schrodinger.maestro_utils.surface_manager.menus.MenuActionData 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) (schrodinger.utils.pythonpatch.Patch 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_entitlements (schrodinger.application.licensing.licserver.entitlement_status.EntitlementStatus attribute) active_grid_size (schrodinger.maestro_utils.surface_manager.surface_info.SurfaceInfo attribute) (schrodinger.project.surface.ProjectSurface property) 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) ActiveEntitlementFeature (class in schrodinger.application.licensing.licserver.entitlement_status) ActiveLearning (class in schrodinger.seam.examples.active_learning_weigher) ActiveLearningHtmlReport (class in schrodinger.active_learning.al_report) ActiveLearningJob (class in schrodinger.active_learning.al_driver) ActiveLearningNode (class in schrodinger.active_learning.al_node) ActiveLearningNodeSupplier (class in schrodinger.active_learning.al_node) ActiveOptimizationTab (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) actives (schrodinger.application.glide_ws.optimizer.WScoreOptimizer property) actives_data_file (schrodinger.application.glide_ws.nodes.OptimizeNode property) actives_libfile_per_node() (schrodinger.application.glide_ws.model.Model method) actives_ligfile (schrodinger.application.glide_ws.driver.GlideWSJob property) 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) adapter55039() (schrodinger.tasks.jobtasks.HostSettings class method) adapter70070() (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.OptResultSet method) (schrodinger.graphics3d.common.Group method) (schrodinger.infra.mm.OPLSArchive 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) add3DGenericEntityImportTask() (schrodinger.application.livedesign.ld_import_utils.LDImportTaskManager method) ADD_ALL (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute) add_analysis_argument() (in module schrodinger.application.matsci.equilibrium_md) add_anharmonic_parser_arguments() (in module schrodinger.application.matsci.anharmonic) add_annotator() (schrodinger.ui.qt.structure2d.structure_item method) add_annotator_function_return() (schrodinger.ui.qt.structure2d.structure_item method) 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_basic_formulations_parser_arguments() (in module schrodinger.application.matsci.parserutils) add_basic_model_to_job_spec() (in module schrodinger.application.matsci.ml_formulations_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_conformational_search_to_parser() (in module schrodinger.application.matsci.parserutils) add_core() (schrodinger.application.canvas.r_group.Data method) add_core_bonds() (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.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_dedup_geom_eps_parser_argument() (in module schrodinger.application.matsci.parserutils) add_describe_args() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.combinatorial_explorer.driver_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_dir_to_jobcontrol() (in module schrodinger.application.glide_ws.driver) add_disulfide_bond() (in module schrodinger.protein.residue) add_encryption_to_params() (in module schrodinger.application.matsci.cgforcefield) 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.shape_screen_reporter.option_utils) add_failed_triggers_to_ct() (schrodinger.application.glide_ws.trigger.TriggerSet method) add_feature_matching_args() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) add_file_handler() (schrodinger.application.livedesign.ldclient_proxy.LDClientLogger method) add_file_options_group() (in module schrodinger.application.glide.sort_parser_common) add_file_to_aljob_restart_dict() (in module schrodinger.active_learning.al_utils) add_files() (schrodinger.active_learning.bloom_filter_methods.BuiltInBloomFilter method) 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_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_geom_argument() (in module schrodinger.application.matsci.parserutils) 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_info_to_wscore_db() (in module schrodinger.application.glide_ws.db) add_input_file() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.glide.utils) add_input_property_data() (in module schrodinger.livedesign.biologics.registration) add_isub_option() (in module schrodinger.application.hitexpander) add_item_to_bit_mask_dict() (schrodinger.active_learning.bloom_filter_methods.BuiltInBloomFilter method) 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_keywords_parser_argument() (in module schrodinger.application.matsci.reaction_workflow_utils) add_jaguar_lic() (in module schrodinger.application.matsci.jobutils) add_job_to_db() (in module schrodinger.application.glide_ws.db) (schrodinger.application.glide_ws.driver.GlideWSJob method) add_jobcontrol_args() (in module schrodinger.application.bb_database.bb_arg_utils) add_jobcontrol_options() (in module schrodinger.utils.cmdline) add_jobs() (schrodinger.application.glide_ws.nodes.Node method) add_key_file_args() (in module schrodinger.application.bb_database.bb_arg_utils) add_keyword_parser_argument() (in module schrodinger.application.matsci.parserutils) add_kmc_flags() (in module schrodinger.application.matsci.kmc) add_labeled_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) add_ligand_sts() (in module schrodinger.protein.protassign.changeables) add_ligand_to_db() (in module schrodinger.application.glide_ws.db) add_list_args() (in module schrodinger.active_learning.al_utils) 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_max_i_freq_parser_arguments() (in module schrodinger.application.matsci.anharmonic) 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_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_missing_inter_residue_bonds (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) add_missing_inter_residue_bondsChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) add_missing_inter_residue_bondsReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) add_mlff_param_to_md_stage() (in module schrodinger.application.matsci.desconfig) add_mlff_param_to_task_stage() (in module schrodinger.application.matsci.desconfig) add_modes_group() (in module schrodinger.application.glide.sort_parser_common) ADD_MODULE_FUNCTIONS (schrodinger.tasks.param_cli.ParamCLI attribute) add_mopac_parser_argument() (in module schrodinger.application.matsci.parserutils) add_msd_arguments() (in module schrodinger.application.matsci.kmc) 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_node() (schrodinger.application.glide_ws.driver.GlideWSJob method) 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_peptide_bond() (in module schrodinger.application.prepwizard2.tasks) 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_poses_to_db() (in module schrodinger.application.glide_ws.db) add_position() (schrodinger.application.canvas.r_group.Data method) add_prepared_props() (in module schrodinger.application.prepwizard) add_print_args() (in module schrodinger.application.phase.shape_screen_reporter.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_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_RESET_THIS_TASK_OPTION (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin attribute) add_residue_atoms() (in module schrodinger.infra.structure) add_restart_parser_arguments() (in module schrodinger.application.matsci.parserutils) 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_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_screen_args() (in module schrodinger.application.combinatorial_explorer.driver_utils) add_signature() (schrodinger.application.licensing.flexlm.Feature method) add_signatures() (schrodinger.application.licensing.flexlm.License method) add_smarts_method_argument() (in module schrodinger.application.matsci.parserutils) add_smiles() (in module schrodinger.structutils.smilesfilter) add_solvation_entropy_arguments() (in module schrodinger.application.matsci.solvation_entropy_utils) add_standard_options() (in module schrodinger.utils.cmdline) add_structure_to_db() (in module schrodinger.application.glide_ws.db) add_subjob_files_to_backend() (in module schrodinger.application.matsci.jobutils) add_substance_group() (in module schrodinger.livedesign.biologics.rdmol_hierarchy) add_tag() (schrodinger.utils.sea.sea.Sea method) add_task_options() (in module schrodinger.tasks.cmdline) add_temp_hydrogen() (in module schrodinger.application.matsci.rxn_path) add_temp_press_parser_arguments() (in module schrodinger.application.matsci.solvation_entropy_utils) add_term_to_db() (in module schrodinger.application.glide_ws.db) 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_tracking_index_to_csv() (in module schrodinger.application.matsci.ml_formulations_utils) add_traj_analysis_parser_arguments() (in module schrodinger.application.matsci.parserutils) add_trigger() (schrodinger.application.glide_ws.trigger.TriggerSet method) add_trigger_set() (schrodinger.application.glide_ws.trigger.TriggerConfig method) add_ts_jaguar_keywords_parser_argument() (in module schrodinger.application.matsci.reaction_workflow_utils) add_undocumented_args() (in module schrodinger.application.glide.sort_parser_common) add_validator() (in module schrodinger.ui.qt.appframework2.validation) add_votca_logo() (in module schrodinger.application.matsci.kmcgui) add_wam_property() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) add_wam_to_cms() (in module schrodinger.application.matsci.jobutils) add_widget_to_menu() (in module schrodinger.ui.qt.utils) add_wmap_data_to_receptor_ct() (in module schrodinger.application.glide_ws.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) addAnharmonicJobs() (schrodinger.application.matsci.thermo_correction_utils.ThermoCorrection 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.infra.canvas.ChmMol method) (schrodinger.infra.structure.MoleculeGraph method) (schrodinger.infra.structure.Structure method) (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) addBeadProperties() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) addBidentateLigand() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) addBinderDummy() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) addBond() (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.structure.MoleculeGraph method) (schrodinger.infra.structure.Structure method) (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) addBondsToMetal() (schrodinger.application.matsci.vsepr.VSEPRFinder 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.qt.dendrogram.NewickNode method) addCIonBodies() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) addColumn() (schrodinger.ui.qt.swidgets.STableWidget method) addCOMAtoms() (schrodinger.application.matsci.clusterstruct.COMTracker method) addComment() (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) addConcentrationProperty() (schrodinger.structutils.rgroup_enumerate.Concentration method) addConnection() (schrodinger.livedesign.biologics.registration.BioPolymer method) addConsButtonPressed() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) addConsensusToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addConstantProperties() (schrodinger.application.matsci.cgforcefield.FFIOParam method) addConstraint() (schrodinger.application.glide.constraints.ConstraintGroup method) addConstraintGroup() (schrodinger.application.glide.job.Dock method) addContext() (schrodinger.application.bioluminate.actions.factory.Factory method) addControlButtons() (schrodinger.application.matsci.stage_widgets.MultiRowArea 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) 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) addDefaultSources() (schrodinger.infra.canvas.ChmCombinationOut32 method) (schrodinger.infra.canvas.ChmCombinationOut64 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) addDoubleBond() (schrodinger.infra.canvas.ChmMol 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) addEdge() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) addEdges() (schrodinger.application.matsci.permittivity.WorkflowParser method) (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) addEigenpair() (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.trajectory.prody.pca.PCA method) addElements() (schrodinger.protein.alignment.BaseAlignment method) addEnefileToAdditionalInfiles() (schrodinger.application.matsci.permittivity.MdPostAnalysis method) addEntry() (schrodinger.ui.qt.appframework2.debugwidgets.LogTable method) (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) addEnv() (schrodinger.job.launcher.Launcher method) addEtaDummy() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) addExcludedVolumes() (schrodinger.application.phase.phase_markers.PhaseXvolMarkers method) addExistingButton() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) addExpectedInput() (schrodinger.pipeline.stage.Stage method) addExpectedOutput() (schrodinger.pipeline.stage.Stage method) addext() (in module schrodinger.trajectory.prody.writenmd) addExtraFeatures() (in module schrodinger.active_learning.al_ligand_ml_utils) 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) (schrodinger.infra.canvas.ChmFPCombiner method) (schrodinger.infra.canvas.ChmFPCombiner64 method) addFilesToBackend() (schrodinger.application.matsci.desmondutils.SystemBuilder method) addFileToModel() (schrodinger.application.matsci.ml_formulations_utils.FormulationDriverMixin 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.automated_martini_mapping_protein.StructuralHarmonicRestraints method) (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.RowTemplateMixin method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) addHypoFromPT() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addHypoFromWorkspace() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addHypothesisFromEntry() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addIdealAnchors() (schrodinger.application.matsci.sculptcomplex.Sculptor method) addImportToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addIndicesToGroup() (schrodinger.application.matsci.atom_group.MSAtomGroupsBase method) addInputFile() (schrodinger.job.launcher.Launcher method) addInputFiles() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) addInputJsonToModel() (schrodinger.application.matsci.ml_formulations_utils.FormulationDriverMixin method) addIonProperties() (schrodinger.application.ligprep.ionizer.Ionizer method) addItem() (schrodinger.infra.canvas.ChmFPMapItem32 method) (schrodinger.infra.canvas.ChmFPMapItem64 method) (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) (schrodinger.tasks.slurmtasks.SlurmMonitor method) addJobsToJobDj() (schrodinger.application.matsci.permittivity.WorkflowParser method) addKBotButton() (schrodinger.ui.qt.appframework2.af2.StatusBar 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) addMetric() (schrodinger.seam.metric.UserMetrics method) addModule() (schrodinger.utils.pythonpatch.Patch method) addMoleculeRaw() (schrodinger.infra.canvas.ChmMol method) addMonitoringInfo() (schrodinger.seam.metric.UserMetrics 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.live_report_widget.LiveReportWidget 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) addParam() (schrodinger.infra.mm.UTT method) addParams() (schrodinger.application.matsci.cgforcefield.FFIOParam 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) addPosesFromDict() (schrodinger.application.glide_ws.optimizer.WScoreOptimizerLigand 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) (schrodinger.glide.CoreDefinition method) (schrodinger.glide.LigandConstraintData 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) addReleaseVersionToModel() (schrodinger.application.matsci.ml_formulations_utils.FormulationDriverMixin method) addReorgTerm() (schrodinger.application.glide_ws.scoring_report.WScoreSipPose method) addReorgTerms() (schrodinger.application.glide_ws.scoring_report.WScoreSipPose 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 (class in schrodinger.tasks.test.cli.customized_param_cli) address (schrodinger.job.cert.CertInfo attribute) (schrodinger.tasks.test.cli.customized_param_cli.User attribute) addressChanged (schrodinger.tasks.test.cli.customized_param_cli.User attribute) AddressError addressReplaced (schrodinger.tasks.test.cli.customized_param_cli.User attribute) addRestraints() (schrodinger.application.matsci.cgforcefield.RestraintAdaptationMixin method) addRGroups() (schrodinger.application.matsci.reaction_workflow_enum_utils.SculptMultiRGroup method) addRmsdPropToCT() (schrodinger.infra.mm.MMFfldEsp method) addRotationAtoms() (schrodinger.application.matsci.etarotamers.HapticLigand method) addRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.matsci.kmc.AtomsTable method) (schrodinger.application.matsci.kmc.FragmentsTable method) (schrodinger.application.matsci.kmc.FramesTable method) (schrodinger.application.matsci.kmc.MatSciSitesTable method) (schrodinger.application.matsci.kmc.MoleculesTable method) (schrodinger.application.matsci.kmc.PairsMixin method) (schrodinger.application.matsci.kmc.SchrodingerTable method) (schrodinger.application.matsci.kmc.SegmentsTable method) (schrodinger.application.matsci.kmc.SegmentTypesTable method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) (schrodinger.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) addSingleBond() (schrodinger.infra.canvas.ChmMol method) addSingleRestraint() (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints method) addSite() (schrodinger.application.matsci.sculptcomplex.CoordinationInfo method) addSites() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addSolvationEntropyJobs() (schrodinger.application.matsci.thermo_correction_utils.ThermoCorrection method) addSolventBodies() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) addSource() (schrodinger.application.fpsim.FPsimSearcher method) (schrodinger.infra.canvas.ChmCombinationOut32 method) (schrodinger.infra.canvas.ChmCombinationOut64 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) 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.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) addToParser() (schrodinger.tasks.cmdline.ArgSpec method) addToPlot() (schrodinger.application.matsci.reaction_workflow_utils.SiblingNode method) addToQueue() (schrodinger.application.matsci.fragments.NonUniqueTracker method) (schrodinger.application.matsci.fragments.UniqueTracker method) addToRestartFile() (schrodinger.active_learning.al_driver.ActiveLearningJob 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) addTripleBond() (schrodinger.infra.canvas.ChmMol method) addUndoRedoToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addVacuum() (schrodinger.application.matsci.nano.slab.Surface 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) addZeroOrderBond() (schrodinger.infra.canvas.ChmMol method) addZeros() (schrodinger.infra.canvas.ChmFPOut32 method) (schrodinger.infra.canvas.ChmFPOut64 method) Adenine (schrodinger.protein.helm.helm_renderer.HexColor attribute) adf() (schrodinger.application.macromodel.utils.ComUtil method) adj_list (schrodinger.energy.CoulPropagatorData attribute) 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) adjustOrderToTemplate() (schrodinger.application.matsci.vsepr.VSEPRFinder method) adjustRegionBounds() (schrodinger.application.bioluminate.classify.ProteinClass method) adjustSeeSawOrder() (schrodinger.application.matsci.vsepr.VSEPRFinder method) adjustSqPlanarOrder() (schrodinger.application.matsci.vsepr.VSEPRFinder method) adjustSqPyrOrder() (schrodinger.application.matsci.vsepr.VSEPRFinder method) adjustTorsion() (schrodinger.glide.Conformer method) adjustTrigBiPyrOrder() (schrodinger.application.matsci.vsepr.VSEPRFinder method) adjustTShapeOrder() (schrodinger.application.matsci.vsepr.VSEPRFinder 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) aggregate_scaffold_subjobs() (in module schrodinger.active_learning.scaffold_methods) AHEAD (schrodinger.application.matsci.nano.xtal.PBCBond attribute) 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_node_supplier (schrodinger.active_learning.al_driver.StopAfterRequest attribute) al_parse_args() (in module schrodinger.active_learning.fake_nodes) al_parse_input_file() (in module schrodinger.active_learning.fake_nodes) al_validate_args() (in module schrodinger.active_learning.fake_nodes) ALABFEPStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) 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) ALGlideStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) algorithm (schrodinger.application.licensing.licserver.client.LocalEntitlementValidation attribute) ALGORITHM_TYPE (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData attribute) alie_analysis() (in module schrodinger.application.jaguar.textparser) alie_analysis_precision (schrodinger.application.jaguar.results.JaguarResults attribute) alie_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) align (schrodinger.structutils.structalign2.Alignment attribute) align() (schrodinger.structutils.structalign.StructAlign method) align_after_download (schrodinger.protein.tasks.blast.BlastSettings attribute) align_after_downloadChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) align_after_downloadReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) align_alignment() (in module schrodinger.protein.sequence) align_all_molecules() (in module schrodinger.application.jaguar.autots_rmsd) align_all_to_reference() (in module schrodinger.livedesign.biologics.sequence) align_and_update_complex_cts() (in module schrodinger.application.glide_ws.model) align_and_update_wmap() (in module schrodinger.application.glide_ws.model) 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_input_st() (in module schrodinger.application.bioluminate.mhc.docking_angles) 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_path_strs() (in module schrodinger.application.jaguar.autots_rmsd) align_pos() (in module schrodinger.comparison.atom_mapper) 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_seqs_from_structs() (in module schrodinger.protein.align) 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) align_wmap_to_recep() (in module schrodinger.application.glide_ws.model) align_zprime2_asu() (in module schrodinger.comparison.struc) 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 (class in schrodinger.seam.yaml.transforms) 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) 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) AlkaneStructure() (in module schrodinger.seam.testing.benchmarks) 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.infra.mm.UTTPolicy 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.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.structure.MM_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_charged (schrodinger.glide.SpecialHBondPairData attribute) 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_ligand_gradients (schrodinger.energy.LfmmOutput attribute) 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) allH (schrodinger.infra.canvas.MCSsettings attribute) 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) allNumAsDouble() (schrodinger.infra.canvas.ChmPattern 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_amino_acid_only_molecules (schrodinger.infra.mm.LigandParameters 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_ion_only_molecules (schrodinger.infra.mm.LigandParameters attribute) ALLOW_MLFF (schrodinger.application.matsci.chargegui.ForceFieldDialog attribute) (schrodinger.application.matsci.chargegui.MLFFDialog 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_nucleic_acid_only_molecules (schrodinger.infra.mm.LigandParameters 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) allowDisconnect (schrodinger.infra.canvas.MCSsettings attribute) 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_keywords() (schrodinger.application.glide_ws.driver.GlideWSJob method) 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) allowRelative (schrodinger.infra.canvas.ChmMatcherData attribute) 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) 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) (schrodinger.energy.MorseParamKeys 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) already_printed_metal_ligand_warning (schrodinger.application.glide_ws.nodes.GlideBaseNode attribute) 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) AMESInput (class in schrodinger.application.jaguar.ames.ames_input) 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_full_name (schrodinger.protein.annotation.ImmuneReceptorDisplayNames attribute) anarci_shorthand (schrodinger.protein.annotation.ImmuneReceptorDisplayNames attribute) 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.glide.HBond attribute) (schrodinger.glide.Minimum attribute) (schrodinger.structutils.interactions.pi.CationPiInteraction property) (schrodinger.structutils.interactions.pi.PiPiInteraction property) ANGLE (schrodinger.trajectory.trajectory_gui_dir.banners.MeasurementMode attribute) angle() (schrodinger.infra.mm.Cartesian static method) 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) 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) AniEnergyOutput (class in schrodinger.energy) ANIIncompatibleException (class in schrodinger.energy) ANILINE (schrodinger.energy.Solvent 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) AniPredictor (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.ReferenceEnergyMethod 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) annotated_input_st (schrodinger.application.glide.runner.GlideDockingResult attribute) 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) AnnotationType (class in schrodinger.protein.annotation) ANTIBODY (schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType attribute) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) Antibody (schrodinger.protein.annotation.AnnotationType 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_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) AntibodyDisplayNames (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() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.structure.MM_Bitset method) any_atom_in_distance_cell() (in module schrodinger.structutils.measure) ANY_CONTACT (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) ANY_GPU (schrodinger.energy.AniPredictor 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.MetalParameterType attribute) (schrodinger.energy.MonoMetalComplexType attribute) aom_energy (schrodinger.energy.LfmmOutput attribute) (schrodinger.energy.MetalComplexOutput attribute) (schrodinger.energy.MetalForceFieldEnergy attribute) AomComplex (class in schrodinger.energy) AomComplex_create() (in module schrodinger.energy) AomParameter (class in schrodinger.energy) AomParamKeys (class in schrodinger.energy) aos_on_grid() (in module schrodinger.application.mopac.mopac_surfaces) api_data (schrodinger.energy.MlffDeviceConfig attribute) api_version (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) api_versionChanged (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) api_versionReplaced (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) 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) app_name (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALABFEPStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.ALGlideStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.BqQueryStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage attribute) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreStage attribute) 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() (in module schrodinger.infra.structure) (schrodinger.application.glide.csv_utils.RawCsvWriter method) (schrodinger.application.glide.phase_subset.PhaseSubsetWriter method) (schrodinger.application.glide.utils.PoseWriter method) (schrodinger.application.glide_ws.optimizer.WScoreOptimizerEnsemble method) (schrodinger.application.qsite.input.QMRegion method) (schrodinger.application.transforms.autosar.transforms.Combination method) (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.mmkv.MMKVArgList method) (schrodinger.infra.structure.MaeWriter method) (schrodinger.infra.structure.StructureWriter method) (schrodinger.infra.structure.TextBlockWriter 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) appendErr() (schrodinger.infra.canvas.ChmModelReporter 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) appendLog() (schrodinger.infra.canvas.ChmModelReporter method) appendMissedFrags() (schrodinger.application.matsci.amorphous.PolymerFragments method) appendReceptor() (schrodinger.application.glide.poseviewconvert.Complex method) appendRepository() (schrodinger.infra.fast3d.Engine 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) appendRule() (schrodinger.infra.fast3d.Generalizer 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) appendWarning() (schrodinger.infra.canvas.ChmModelReporter method) AppFramework (class in schrodinger.ui.qt.appframework) ApplicationMode (in module schrodinger.utils.qapplication) apply() (schrodinger.application.bioluminate.mutation.MutationSet method) (schrodinger.application.pathfinder.analysis.Transformer method) (schrodinger.application.pathfinder.reaction.Reaction method) (schrodinger.infra.mm.Cartesian 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_adc_mutations() (in module schrodinger.application.bioluminate.antibody.adc_mutator) apply_basic_style() (in module schrodinger.application.matsci.stylemanager) 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_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.maestro_utils.composer_agent.composer_gui.ComposerAgentPanel 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.maestro_utils.composer_agent.composer_gui.ComposerAgentPanel 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_style() (in module schrodinger.application.matsci.stylemanager) 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_symmetries() (in module schrodinger.comparison.struc) 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) apply_white_background() (in module schrodinger.application.matsci.stylemanager) 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) applyBondOrdersAndCharges() (schrodinger.infra.canvas.ChmMmctAdaptor static method) applyContextDependentDefaults() (schrodinger.application.glide.job.Dock method) (schrodinger.application.glide.job.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) applyStateToComplex() (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) applyToStructure() (schrodinger.infra.structure.PBC 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) approximateVolume() (schrodinger.application.matsci.amorphous.Scaffold static method) approxProgressPercent() (schrodinger.infra.structure.StructureReader method) AppTemplate (class in schrodinger.ui.qt.appframework2.af2_template) archive_filename (schrodinger.infra.mm.FFBundleVersionData attribute) archive_folder() (in module schrodinger.application.matsci.freevolume) archive_job_data() (in module schrodinger.application.matsci.jobutils) archive_license_file() (in module schrodinger.application.licensing.licserver.install) archive_logs() (schrodinger.application.glide_ws.nodes.Node method) 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_hbonded() (in module schrodinger.infra.structure) 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_ordered_isomers() (in module schrodinger.infra.structure) 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) areBonded() (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.structure.MoleculeGraph method) areBound() (schrodinger.structure.Structure method) areCompatible() (schrodinger.infra.canvas.ChmFPTypeInfo static method) areContiguous() (schrodinger.application.matsci.cg_mapping.CGMapperMixin 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) ArgSpec (class in schrodinger.tasks.cmdline) 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) ArNH (schrodinger.application.jaguar.ames.ames_constants.FORMULAE attribute) (schrodinger.application.jaguar.ames.ames_constants.INFILES attribute) ArNHOAc (schrodinger.application.jaguar.ames.ames_constants.FORMULAE attribute) (schrodinger.application.jaguar.ames.ames_constants.INFILES 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) aromaticity (schrodinger.application.jaguar.utils.JagSolventParams attribute) 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.glide_ws.model.Enrichment method) (schrodinger.application.glide_ws.trigger.Trigger method) (schrodinger.application.glide_ws.trigger.TriggerConfig method) (schrodinger.application.glide_ws.trigger.TriggerSet method) (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) as_string() (schrodinger.application.glide_ws.model.Model method) as_unit_vector() (schrodinger.infra.mm.Cartesian method) 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.application.glide.gui.GridSite attribute) (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) aslChanged (schrodinger.application.glide.gui.GridSite attribute) AslCriterion (class in schrodinger.utils.ligfilter) AslException asList() (schrodinger.application.bioluminate.mutation.MutationSet method) 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) aslMatcher() (schrodinger.application.matsci.automated_cg_mapping.UnsupportedMolChecker static method) aslModified (schrodinger.ui.qt.atomselector.AtomSelector attribute) ASLPopupMenu (class in schrodinger.ui.qt.atomselector) aslReplaced (schrodinger.application.glide.gui.GridSite attribute) 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_development_license_exists() (in module schrodinger.infra.mm) 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_pcoll_size_callable() (in module schrodinger.seam.testing.util) assert_same_struct() (in module schrodinger.application.matsci.mstest) assert_sanitization_passes() (in module schrodinger.livedesign.preprocessor) 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) assertStageEqual() (schrodinger.application.matsci.mstest.MSTestCase static method) assertStructAlmostEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertStructEqual() (schrodinger.application.matsci.mstest.MSTestCase method) assertTableContentsEqual() (schrodinger.application.matsci.mstest.MSTestCase method) asSif() (schrodinger.application.glide.job.GlideJob method) assign() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.seam.transforms.window.BatchWindows method) (schrodinger.seam.transforms.window.StringIDWindows 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_METAL_PROPERTIES_TYPE (schrodinger.infra.mm.OPLSDatafileType attribute) 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_pdb_names_to_residues() (in module schrodinger.protein.helm.monomer_db_converter) 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) assignAcceptors() (schrodinger.infra.canvas.ChmHbond method) assignCoordsForHiddenAtoms() (schrodinger.infra.canvas.Chm2DCoordGen static method) assignCoordsForNullAtoms() (schrodinger.infra.canvas.Chm2DCoordGen static method) assignDonors() (schrodinger.infra.canvas.ChmHbond method) assignLeaves() (in module schrodinger.ui.qt.dendrogram) assignLigandTypes() (schrodinger.energy.MetalForceFieldManager method) assignMetalTypes() (schrodinger.energy.MetalForceFieldManager method) assignMissingCoords() (schrodinger.infra.canvas.Chm2DCoordGen static method) AssignNearestBinKey (class in schrodinger.seam.transforms.grouping) assignParameters() (schrodinger.energy.MetalForceFieldManager method) assignPosenums() (schrodinger.glide.RefinedPoseEnsemble method) assignRingAtomIds() (schrodinger.application.matsci.amorphous.PolymerFragments 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_pg_sym_ops (schrodinger.comparison.dedup_utils.StructureClusterPair attribute) ASU_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) asVector() (schrodinger.infra.canvas.ChmAssignments method) (schrodinger.infra.canvas.ChmAtomIterator method) (schrodinger.infra.canvas.ChmBitsetIterator method) (schrodinger.infra.canvas.ChmBondIterator method) (schrodinger.infra.canvas.ChmMatchExIterator method) (schrodinger.infra.canvas.ChmMatchIterator method) (schrodinger.infra.canvas.ChmValueAssignmentIterator method) AsyncJobHandler (class in schrodinger.job.jobhandler) at() (schrodinger.infra.canvas.ChmAssignments method) (schrodinger.infra.canvas.ChmAtomIterator method) (schrodinger.infra.canvas.ChmBitsetIterator method) (schrodinger.infra.canvas.ChmBondIterator method) (schrodinger.infra.canvas.ChmMatchExIterator method) (schrodinger.infra.canvas.ChmMatchIterator method) (schrodinger.infra.canvas.ChmValueAssignmentIterator method) (schrodinger.infra.structure.MM_Bitset method) 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.BaseDiffusivitiyAnalysis 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.infra.mm.WaterMapStructure attribute) (schrodinger.structure._AtomCollection property) (schrodinger.structure.Structure attribute) (schrodinger.structure.StructureBond property) (schrodinger.structure.TextualStructure property) atom() (schrodinger.application.glide.constraints.MetalConstraint method) atom1 (schrodinger.glide.RotatableBond attribute) (schrodinger.glide.TorsionPenalty attribute) (schrodinger.infra.canvas.ChmChiralityInfo attribute) (schrodinger.infra.mm.UTT attribute) atom1() (schrodinger.infra.canvas.ChmBond method) atom2 (schrodinger.glide.RotatableBond attribute) (schrodinger.glide.TorsionPenalty attribute) (schrodinger.infra.canvas.ChmChiralityInfo attribute) (schrodinger.infra.mm.UTT attribute) atom2() (schrodinger.infra.canvas.ChmBond 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_id (schrodinger.glide.AtomPhob attribute) atom_idx (schrodinger.application.matsci.coarsegrain.AUTOMAPPED_ATOM_INFO attribute) (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) (schrodinger.glide.ConstraintWithAtom attribute) (schrodinger.infra.mm.UTTAtom 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_map_num (schrodinger.application.transforms.autosar.transforms.ComputeNormalizedPropertiesSettings 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.coarsegrain.AUTOMAPPED_ATOM_INFO attribute) atom_objects (schrodinger.structutils.analyze.Ligand property) ATOM_OVERLAP (schrodinger.glide.SkipReason attribute) 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_score (schrodinger.glide.AtomPhob attribute) 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) atomCount (schrodinger.infra.canvas.ChmMCSRecord attribute) AtomData (class in schrodinger.infra.canvas) AtomGroup (class in schrodinger.application.desmond.cms) AtomGroupData (class in schrodinger.application.matsci.clusterstruct) ATOMI_KEY (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) atomic_copyfile() (in module schrodinger.utils.fileutils) atomic_energies (schrodinger.energy.AniEnergyOutput attribute) (schrodinger.energy.QRNNEnergyOutput attribute) ATOMIC_NUMBER (schrodinger.glide.SkipReason attribute) 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) AtomicInvariant (class in schrodinger.infra.canvas) 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) ATOMJ_KEY (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) AtomLabelAnnotator (class in schrodinger.ui.qt.structure2d) AtomListEnumerable (class in schrodinger.application.scaffold_enumeration.atomlist) AtomListInfo (class in schrodinger.application.scaffold_enumeration.atomlist) atomLookingFrom (schrodinger.infra.canvas.ChmChiralityInfo attribute) 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) AtomPairWithValue (class in schrodinger.infra.structure) AtomPhob (class in schrodinger.glide) 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) AtomQueryParams (class in schrodinger.infra.structure) 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) (schrodinger.glide.Ring attribute) (schrodinger.infra.canvas.ChmAtomsAndBonds attribute) (schrodinger.infra.canvas.ChmMCSRecord attribute) ATOMS (schrodinger.infra.structure.SuperImposeBy attribute) atoms() (schrodinger.application.glide.constraints.MetalConstraint method) (schrodinger.infra.structure.MoleculeGraph method) atoms_in_ring() (in module schrodinger.application.jaguar.autots_bonding) atoms_phob (schrodinger.glide.GroupPhobscorePacking attribute) 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) atomTyping (schrodinger.infra.canvas.MCSsettings attribute) 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) AUTHORIZATION_KEY (schrodinger.maestro_utils.composer_agent.request_manager.urls.PostQueryRequestKeys attribute) authorized_project_ids (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) authorized_project_idsChanged (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) authorized_project_idsReplaced (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) 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_add_gridgen_node() (schrodinger.application.glide_ws.driver.GlideWSJob method) auto_add_wmap_node() (schrodinger.application.glide_ws.driver.GlideWSJob method) auto_align_complexes() (in module schrodinger.application.glide_ws.model) AUTO_DETECT (schrodinger.rdkit_extensions.Format attribute) auto_nstructs() (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode static method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) auto_recalculate (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) auto_recalculateChanged (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) auto_recalculateReplaced (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) auto_register_files() (in module schrodinger.tasks.queue) auto_shuffle_ligs() (schrodinger.application.glide_ws.nodes.ModelNode method) 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) autoIncreaseThreshold() (schrodinger.infra.fast3d.Engine method) autoMap() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) AUTOMAPPED_ATOM_INFO (class in schrodinger.application.matsci.coarsegrain) AUTOMAPPED_PARTICLE_INFO (class in schrodinger.application.matsci.coarsegrain) 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) autoScale() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) autoset_axis_range() (in module schrodinger.ui.qt.smatplotlib) autoSetGpuList() (schrodinger.tasks.hosts.Host method) 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_energy_info (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) avg_energy_key (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) avg_n_hydrox (schrodinger.application.bioluminate.methionine_oxidation.MdStats attribute) avg_n_waters (schrodinger.application.bioluminate.methionine_oxidation.MdStats attribute) avg_property_info (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty 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) axes (schrodinger.geometry.MomentsOfInertia attribute) AXES (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.geometry.PairPath attribute) 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) B3_LYSINE (schrodinger.protein.annotation.KinaseFeatureLabel attribute) 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) (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.structure.StructureCoordinates method) back_substitution_int() (in module schrodinger.application.matsci.cctbx.rot_mx) back_transparency (schrodinger.surface.Surface property) backbone() (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints method) backbone_dihedrals (in module schrodinger.protein.analysis_params) BACKBONE_INTERACTION (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) backbone_path_search() (in module schrodinger.application.matsci.geometry) 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) backboneRestraints() (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints method) BackButton (class in schrodinger.application.job_monitor.buttons) backClicked() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) 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) BACKGROUND_LIGHT_GRAY (schrodinger.application.matsci.stylemanager.SolidColors 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_ATOM (schrodinger.glide.SkipReason attribute) BAD_INTERNALS (schrodinger.application.jaguar.constants.FatalErrors attribute) BadComplex 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.tasks.slurmtasks.FooTask.Input attribute) BAR (schrodinger.ui.qt.schart.SeriesParams attribute) BAR_PADDING (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListPopUp attribute) barChanged (schrodinger.tasks.slurmtasks.FooTask.Input attribute) BAROSTAT_TAU (schrodinger.application.matsci.desconfig.MSJStringer attribute) barReplaced (schrodinger.tasks.slurmtasks.FooTask.Input 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) barycenterOf() (schrodinger.infra.canvas.ChmAtoms method) base() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) Base3DExportSpec (class in schrodinger.application.livedesign.export_models) 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) BaseCSVReader (class in schrodinger.application.matsci.ml_formulations_utils) 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) BaseDiffusivitiyAnalysis (class in schrodinger.application.matsci.equilibrium_md) 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) BaseMenu (class in schrodinger.maestro_utils.surface_manager.menus) 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) BasePLPSelectionTarget (class in schrodinger.ui.qt.mapperwidgets.plptarget) 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) BaseSurfaceActionsMenu (class in schrodinger.maestro_utils.surface_manager.menus) 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) 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.jaguar.xray.constants.KEYWORDS 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 (schrodinger.application.jaguar.xray.constants.DEFAULTS attribute) 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) BatchWindows (class in schrodinger.seam.transforms.window) baz (schrodinger.tasks.slurmtasks.FooTask.Output attribute) bazChanged (schrodinger.tasks.slurmtasks.FooTask.Output attribute) bazReplaced (schrodinger.tasks.slurmtasks.FooTask.Output attribute) BB (schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE attribute) BB_TASK (in module schrodinger.application.bb_database.bb_arg_utils) BBChemConfiguration (class in schrodinger.livedesign.bbchem_configuration) 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) BCC_OVERWRITE_TYPE (schrodinger.infra.mm.OPLSDatafileType attribute) 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) beads (schrodinger.application.matsci.automated_cg_mapping.MoleculeData.BEAD_TYPE attribute) BEAM_PIPELINE_STR (schrodinger.application.livedesign.models2.datamodels.definition.LogicType attribute) BeamTask (class in schrodinger.tasks.beamtasks) BeamTask.Input (class in schrodinger.tasks.beamtasks) BeamTask.Output (class in schrodinger.tasks.beamtasks) BEFORESUPERPOSITION (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) begin() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.structure.MM_Bitset method) (schrodinger.infra.structure.StructureCoordinates method) (schrodinger.infra.structure.StructureReader method) begin_node() (schrodinger.application.glide_ws.nodes.CrossNode method) (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) (schrodinger.application.glide_ws.nodes.GridGenNode method) (schrodinger.application.glide_ws.nodes.MMGBSAReceptorModelNode method) (schrodinger.application.glide_ws.nodes.ModelNode method) (schrodinger.application.glide_ws.nodes.Node method) beginGroup() (schrodinger.infra.mm.MMPREF method) (schrodinger.utils.preferences.Preferences method) beginOsAttribute() (schrodinger.infra.mm.MMPREF method) BEHIND (schrodinger.application.matsci.nano.xtal.PBCBond attribute) BehindMonomer (schrodinger.protein.helm.helm_renderer.ZOrder attribute) BenchFlow (class in schrodinger.seam.testing.test_pipelines) BenchFlow.LocalRandomStringsDoFn (class in schrodinger.seam.testing.test_pipelines) Benchmark (class in schrodinger.seam.testing.benchmarks) BenchmarkResult (class in schrodinger.seam.testing.benchmarks) bend_conj_amines (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) BEND_DAT (schrodinger.infra.mm.OPLSDatafileType attribute) BEND_INDEX_DAT (schrodinger.infra.mm.OPLSDatafileType attribute) BEND_TOLERANCE (schrodinger.application.matsci.atom_group.HelixArcAtomGroup attribute) bennett() (schrodinger.application.desmond.bennett.CalcBAR method) BENT (schrodinger.application.matsci.vsepr.VSEPRFinder attribute) BENZENE (schrodinger.energy.Solvent attribute) 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.application.glide.visualization.HistogramComponent attribute) 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) bit_reverse() (in module schrodinger.infra.canvas) BitBasedSet (class in schrodinger.utils.scollections) BitBasedSubset (class in schrodinger.utils.scollections) bitCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) bits() (schrodinger.infra.canvas.ChmSearchKey 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) bitwiseAnd() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) bitwiseNot() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) bitwiseOr() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) bitwiseXor() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) BLACK (schrodinger.application.matsci.stylemanager.SolidColors attribute) 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) blockReverse() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) BLOSUM45 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) BLOSUM62 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) BLOSUM80 (schrodinger.protein.tasks.blast.SimilarityMatrix attribute) BLUE() (in module schrodinger.utils.color) 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_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) bondCount (schrodinger.infra.canvas.ChmMCSRecord attribute) BondData (class in schrodinger.infra.canvas) 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) (schrodinger.infra.canvas.ChmAtomsAndBonds attribute) (schrodinger.infra.canvas.ChmMCSRecord attribute) bondSmallestRing() (schrodinger.infra.structure.MoleculeGraph method) bondsToAtoms() (schrodinger.infra.canvas.ChmBonds method) bondToH() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) BondType (class in schrodinger.structure) BONDWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) bool_flag (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) bool_flagChanged (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) bool_flagReplaced (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) BoolCriterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) BOOLEAN (schrodinger.application.livedesign.models2.datamodels.definition.InputType attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputType attribute) 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) BOOT_FAIL (schrodinger.tasks.slurmtasks.JobState attribute) bootstrap() (in module schrodinger.application.desmond.bennett) BootstrapNoiseHistogramData (class in schrodinger.application.matsci.uq_utils) BORDER_GRAY (schrodinger.application.matsci.stylemanager.SolidColors attribute) 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) 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) BOUNDARY_TAG (schrodinger.seam.transforms.grouping.UnbinAndPartitionBoundaryValues attribute) 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.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) BoxSettings (class in schrodinger.application.transforms.dockers.box) BoxWithInnerHull (class in schrodinger.application.matsci.amorphous) BqQueryStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) 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) breakTemplatePolymer() (schrodinger.application.matsci.amorphous.Monomer method) BRIDGE_ATTACH_1_PROP (schrodinger.application.matsci.buildcomplex.DimerComplexBuilder attribute) BRIDGE_ATTACH_2_PROP (schrodinger.application.matsci.buildcomplex.DimerComplexBuilder attribute) BRIDGE_LIGAND_PROP (schrodinger.application.matsci.buildcomplex.DimerComplexBuilder attribute) BRIDGE_MARK_2_PROP (schrodinger.application.matsci.buildcomplex.DimerComplexBuilder attribute) 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) BS (schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE attribute) bt (schrodinger.infra.mm.UTTEndAtom attribute) bt0 (schrodinger.infra.mm.UTTParamSpec attribute) bt3 (schrodinger.infra.mm.UTTParamSpec attribute) BTHR_FLAG (schrodinger.application.matsci.crest.CrestCSearch 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) build_spectrum() (in module schrodinger.application.jaguar.simple_spec) buildBestRotamer() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToRxnWF method) buildBilayer() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) buildCallbackDicts() (schrodinger.ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin method) buildCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) buildCellDriver() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) buildCGFromParticles() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) buildChain() (schrodinger.application.steps.basesteps.OptionalStepsMixin method) (schrodinger.application.steps.basesteps.Workflow method) (schrodinger.application.steps.enumerators.Synthesizer method) (schrodinger.application.steps.filters.InMemoryUniqueRandomSampleFilter method) (schrodinger.application.steps.filters.ScoreFilter method) (schrodinger.application.steps.filters.ScoreFilterChain method) (schrodinger.stepper.stepper.UnbatchedChain method) buildChannelStrDef() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) buildComplexBuild() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) buildCovariance() (schrodinger.trajectory.prody.pca.PCA method) buildCrystalSuperCell() (schrodinger.application.matsci.nano.xtal.Crystal method) buildCrystalUnitCell() (schrodinger.application.matsci.nano.xtal.Crystal method) buildCustomBar() (schrodinger.ui.qt.appframework2.af2.BaseBottomBar method) buildDerivedAttrs() (schrodinger.application.jaguar.results.DerivedAttrs method) buildDockedLigandsMap() (schrodinger.pipeline.stages.glide.DockingStage method) builder_opts (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) BuilderGrowInCellMixin (class in schrodinger.application.matsci.amorphous) BuilderWithClashDetection (class in schrodinger.application.matsci.amorphous) buildFragmentGraphs() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) buildingBlocksHaveRings() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) buildLattice() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) buildLayer() (schrodinger.application.matsci.nano.interface_mod.Interface method) buildLayers() (schrodinger.application.matsci.nano.interface_mod.Interface method) BuildMissingLoopsInput (class in schrodinger.application.prepwizard2.tasks) BuildMissingLoopsTask (class in schrodinger.application.prepwizard2.tasks) buildMultiWallTube() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) buildNanoTubeSheet() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) buildReorderList() (schrodinger.application.matsci.rxn_channel.Products method) buildResidueTypeCombo() (schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget.FindToolBar method) BuildServerTask (class in schrodinger.application.glide.ligand_designer) BuildServerTask.Input (class in schrodinger.application.glide.ligand_designer) BuildServerTask.Output (class in schrodinger.application.glide.ligand_designer) buildSlab() (schrodinger.application.matsci.nano.slab.Surface method) buildStandardBar() (schrodinger.ui.qt.appframework2.af2.BottomBar method) (schrodinger.ui.qt.appframework2.af2.JobBottomBar method) (schrodinger.ui.qt.appframework2.af2.MiniJobBottomBar method) (schrodinger.ui.qt.appframework2.af2.OKAndCancelBottomBar method) buildTemplateList() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) buildTree() (in module schrodinger.ui.qt.dendrogram) (schrodinger.ui.qt.dendrogram.Dendrogram method) buildTube() (schrodinger.application.matsci.nano.tube.NanoTube method) buildUnitCell() (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) built_in (schrodinger.protein.nonstandard_residues.AminoAcid property) builtin_dir (schrodinger.application.matsci.builderwidgets.TemplateFamily property) BUILTIN_WF_FILE (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.FreeVolumeStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.RDFStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) BuiltInBloomFilter (class in schrodinger.active_learning.bloom_filter_methods) BULK (schrodinger.application.matsci.msconst.DIMENSIONALITY attribute) bumpIndexes() (schrodinger.application.matsci.zmutils.ZAtom method) (schrodinger.application.matsci.zmutils.ZMatrix method) BURIED (schrodinger.protein.predictors.SolventAccessibility attribute) Buried (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) BURIED_VOLUME_VDW_SCALE (schrodinger.application.matsci.mlearn.features.Complex attribute) BUTTON_TEXT (schrodinger.application.job_monitor.job_monitor_widgets.JobBar attribute) (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar attribute) (schrodinger.application.job_monitor.job_monitor_widgets.TopLevelJobBar attribute) (schrodinger.application.matsci.mswidgets.StructureLoader attribute) (schrodinger.application.matsci.rdpattern_gui.SMARTSFrame attribute) BUTTON_TYPE (schrodinger.ui.qt.standard.design_tokens.PropertyNames attribute) ButtonAcceptsFocusMixin (class in schrodinger.ui.qt.utils) buttonChanged() (schrodinger.application.matsci.qualityslider.QualitySlider method) buttonChecked() (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) buttons() (schrodinger.ui.qt.datamapper.MappableButtonGroup method) ButtonTypes (class in schrodinger.ui.qt.standard.design_tokens) ButtonWithArrowMixin (class in schrodinger.ui.qt.standard_widgets.hyperlink) ButtonWithColorPicker (class in schrodinger.ui.qt.color_picker) bval (schrodinger.utils.sea.sea.Atom property) (schrodinger.utils.sea.sea.List property) (schrodinger.utils.sea.sea.Map property) BVECTOR (schrodinger.application.matsci.kmc.SchrodingerTable attribute) bytes() (schrodinger.infra.canvas.ChmSearchKey method) BytesSerializer (class in schrodinger.models.jsonable)

C

C (schrodinger.application.bioluminate.update_germline_db.translate_db.Gene attribute) (schrodinger.ui.qt.mapperwidgets.param_editor.MyEnum attribute) c1 (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) C1 (schrodinger.ui.qt.rama.BackboneDihedral attribute) c1Changed (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) c1Replaced (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) c2 (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) C2 (schrodinger.ui.qt.rama.BackboneDihedral attribute) c2Changed (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) c2Replaced (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) c6() (schrodinger.application.desmond.cms.Vdw method) C_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) C_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) c_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) c_v() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) C_VACUUM (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) CA (schrodinger.ui.qt.rama.BackboneDihedral attribute) cache_entity_IDs() (in module schrodinger.application.livedesign.import_utils) cache_hostname_plink() (in module schrodinger.utils.sshconfig) CACHE_LIMIT_BYTES (schrodinger.application.desmond.packages.traj.Source attribute) CACHE_SIZE (schrodinger.application.peptide_workflow.monte.MonteOptions attribute) cached_topo_descriptor() (in module schrodinger.application.canvas.topo_descriptors) cachedCoords (schrodinger.infra.canvas.AtomData attribute) CacheInfo (class in schrodinger.application.matsci.cache) (class in schrodinger.application.matsci.rxn_channel) CactusIdentifiers (class in schrodinger.application.matsci.rdpattern) CactusRes (class in schrodinger.application.matsci.rdpattern) calAbbeNum() (schrodinger.application.matsci.permittivity.RefractiveIndex class method) CALC (schrodinger.application.matsci.espresso.qeinput.TurboEelsType attribute) calc_accessible_cavities() (in module schrodinger.application.jaguar.garza) calc_acentric() (in module schrodinger.application.jaguar.garza) calc_ActivesInN() (in module schrodinger.analysis.enrichment.metrics) calc_ActivesInNStar() (in module schrodinger.analysis.enrichment.metrics) calc_AUAC() (in module schrodinger.analysis.enrichment.metrics) calc_AveNumberOutrankingDecoys() (in module schrodinger.analysis.enrichment.metrics) calc_average_vdw_coeff() (in module schrodinger.application.desmond.cms) calc_BEDROC() (in module schrodinger.analysis.enrichment.metrics) calc_buried_sasa_by_residue() (in module schrodinger.structutils.analyze) calc_cdr_shifts() (in module schrodinger.application.bioluminate.antibody.utils) calc_code (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) calc_code_version (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) calc_complementarity() (in module schrodinger.application.bioluminate.escomp) calc_complementarity_by_atom() (in module schrodinger.application.bioluminate.escomp) (in module schrodinger.application.bioluminate.surfcomp) calc_concentration_term() (in module schrodinger.application.jaguar.garza) calc_DEF() (in module schrodinger.analysis.enrichment.metrics) calc_DEFP() (in module schrodinger.analysis.enrichment.metrics) calc_DEFStar() (in module schrodinger.analysis.enrichment.metrics) calc_delta_residue_uptake() (in module schrodinger.application.bioluminate.pose_filtering.hdx_calc) calc_delta_sasa_by_res_id() (in module schrodinger.application.bioluminate.pose_filtering.hdx_analysis) calc_diffusion_tensor() (in module schrodinger.application.matsci.kmc) calc_drift_velocity() (in module schrodinger.application.matsci.kmc) calc_drift_velocity_tensor() (in module schrodinger.application.matsci.kmc) calc_EF() (in module schrodinger.analysis.enrichment.metrics) calc_EFF() (in module schrodinger.analysis.enrichment.metrics) calc_EFP() (in module schrodinger.analysis.enrichment.metrics) calc_EFStar() (in module schrodinger.analysis.enrichment.metrics) calc_entropy_translation() (in module schrodinger.application.jaguar.garza) calc_fluc_ct_energy_force_with_calculators() (in module schrodinger.energy) calc_FOD() (in module schrodinger.analysis.enrichment.metrics) calc_hbond_energy() (in module schrodinger.application.prepwizard) calc_HR() (in module schrodinger.analysis.enrichment.metrics) calc_intermediates() (in module schrodinger.application.jaguar.garza) calc_ligand_size() (in module schrodinger.application.glide.grid) calc_logd() (in module schrodinger.application.livedesign.ld_alogD_utils) calc_mobility_tensor_from_diffusion() (in module schrodinger.application.matsci.kmc) calc_mobility_tensor_from_drift_velocity() (in module schrodinger.application.matsci.kmc) calc_name (schrodinger.application.matsci.espresso.qeoutput.Magres.ATTR attribute) calc_property() (in module schrodinger.application.matsci.uq_utils) calc_rDsq() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsq2() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqT() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqTSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqZ() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rDsqZSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_residue_uptake() (in module schrodinger.application.bioluminate.pose_filtering.hdx_calc) calc_RIE() (in module schrodinger.analysis.enrichment.metrics) calc_rmsd() (in module schrodinger.application.glide_ws.entropy_score) calc_ROC() (in module schrodinger.analysis.enrichment.metrics) calc_rot_term() (in module schrodinger.application.jaguar.garza) calc_rV() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_rVsq() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calc_sasa_by_res_id() (in module schrodinger.application.bioluminate.pose_filtering.hdx_analysis) calc_sensitivity_with_rank() (in module schrodinger.analysis.enrichment.plotter) calc_shape_factor() (in module schrodinger.application.jaguar.garza) calc_specificity_with_rank() (in module schrodinger.analysis.enrichment.plotter) calc_spt() (in module schrodinger.application.jaguar.garza) calc_st_params() (in module schrodinger.application.jaguar.garza) calc_substructure_score() (in module schrodinger.application.bioluminate.pose_filtering.hdx_analysis) calc_substructure_scores() (in module schrodinger.application.bioluminate.pose_filtering.hdx_analysis) calc_total_complementarity() (in module schrodinger.application.bioluminate.escomp) (in module schrodinger.application.bioluminate.surfcomp) calc_type() (in module schrodinger.application.jaguar.textparser) calc_V() (in module schrodinger.application.matsci.gsas.GSASIIlattice) calcActivesInN() (schrodinger.analysis.enrichment.calculator.Calculator method) calcActivesInNStar() (schrodinger.analysis.enrichment.calculator.Calculator method) CalcAngle() (in module schrodinger.application.matsci.gsas.GSASIImath) calcAngle() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) CalcAngleDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) calcAntibodyTopography() (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) calcAUAC() (schrodinger.analysis.enrichment.calculator.Calculator method) calcAveNumberOutrankingDecoys() (schrodinger.analysis.enrichment.calculator.Calculator method) CalcBAR (class in schrodinger.application.desmond.bennett) calcBEDROC() (schrodinger.analysis.enrichment.calculator.Calculator method) calcBond() (in module schrodinger.application.matsci.gsas.GSASIImath) calcConsensusScore() (schrodinger.pipeline.stages.combine.DataFusionMergeStage method) calcCovariance() (in module schrodinger.trajectory.prody.crosscorrelation) calcCrossCorr() (in module schrodinger.trajectory.prody.crosscorrelation) calcDEF() (schrodinger.analysis.enrichment.calculator.Calculator method) calcDEFP() (schrodinger.analysis.enrichment.calculator.Calculator method) calcDEFStar() (schrodinger.analysis.enrichment.calculator.Calculator method) calcDihedral() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) CalcDist() (in module schrodinger.application.matsci.gsas.GSASIImath) calcDistance() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) CalcDistDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) calcEF() (schrodinger.analysis.enrichment.calculator.Calculator method) calcEFF() (schrodinger.analysis.enrichment.calculator.Calculator method) calcEFP() (schrodinger.analysis.enrichment.calculator.Calculator method) calcEFStar() (schrodinger.analysis.enrichment.calculator.Calculator method) calcFitZoomFactor() (schrodinger.ui.qt.network_views.NetworkViewer method) calcFOD() (schrodinger.analysis.enrichment.calculator.Calculator method) calcGasteigerCharges() (schrodinger.infra.canvas.ChmGasteigerCharge method) calcHR() (schrodinger.analysis.enrichment.calculator.Calculator method) calcIncident() (in module schrodinger.application.matsci.gsas.GSASIIpwd) calcItemZoomFactor() (schrodinger.ui.qt.network_views.NetworkViewer method) calcMinimumDiff() (schrodinger.application.desmond.packages.analysis.Pbc method) calcMinimumImage() (schrodinger.application.desmond.packages.analysis.Pbc method) calcModes() (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.trajectory.prody.pca.PCA method) CalcPDF() (in module schrodinger.application.matsci.gsas.GSASIIpwd) calcPlanarAngle() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) calcRamaEnergy() (in module schrodinger.application.matsci.gsas.GSASIImath) calcRIE() (schrodinger.analysis.enrichment.calculator.Calculator method) calcROC() (schrodinger.analysis.enrichment.calculator.Calculator method) calcScore() (schrodinger.glide.Conformer method) calcsDone() (schrodinger.application.matsci.jaguarworkflows.Step method) CalcStackingPWDR() (in module schrodinger.application.matsci.gsas.GSASIIpwd) CalcStackingSADP() (in module schrodinger.application.matsci.gsas.GSASIIpwd) calcStateScore() (schrodinger.application.prepwizard.HetState method) calcTorsionEnergy() (in module schrodinger.application.matsci.gsas.GSASIImath) CalcType (class in schrodinger.application.jaguar.constants) calculate() (schrodinger.active_learning.substruct_enrichment.SubstructEnrichCalculator method) (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) (schrodinger.application.canvas.r_group.RGroupFinder method) (schrodinger.structutils.rmsd.ConformerRmsd method) calculate1DDensity() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) calculate2DDensity() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) calculate_angle_term() (in module schrodinger.protein.protassign.hbond_cluster) calculate_bb_RMSD() (in module schrodinger.application.peptide_workflow.monte) calculate_binding_modes() (in module schrodinger.application.phase.hypothesis_binding_modes) calculate_ciexy() (in module schrodinger.application.matsci.colorutils) calculate_clash_term() (in module schrodinger.protein.protassign.hbond_cluster) calculate_cri() (in module schrodinger.application.matsci.colorutils) calculate_distance_term() (in module schrodinger.protein.protassign.hbond_cluster) calculate_enhanced_stereo() (in module schrodinger.livedesign.preprocessor) calculate_in_place_rmsd() (in module schrodinger.structutils.rmsd) calculate_interaction_matrix() (in module schrodinger.protein.assignment) calculate_interactions() (in module schrodinger.application.bioluminate.protein_interaction.calculate) calculate_kstest_results() (in module schrodinger.active_learning.al_report) calculate_nits() (in module schrodinger.application.matsci.colorutils) calculate_njobs() (in module schrodinger.job.jobcontrol) calculate_num_protons() (in module schrodinger.application.jaguar.gui.utils) calculate_principal_moments() (in module schrodinger.structutils.analyze) calculate_properties() (in module schrodinger.application.transforms.autosar.transforms) calculate_recovery_ratio() (in module schrodinger.active_learning.al_report) calculate_sasa() (in module schrodinger.structutils.analyze) calculate_sasa_by_atom() (in module schrodinger.structutils.analyze) calculate_sasa_by_residue() (in module schrodinger.structutils.analyze) calculate_statistics() (in module schrodinger.application.bioluminate.peptide_sar.statistics) calculate_stats() (schrodinger.application.glide.glideanalysis.PoseLibrary method) calculate_stress() (schrodinger.application.matsci.elasticity.elastic.NthOrderElasticTensor method) calculate_sts_rmsds() (in module schrodinger.application.glide.visualization) calculate_total_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) calculateArrow() (in module schrodinger.ui.qt.network_views) CalculateContainingVolume() (in module schrodinger.analysis.visanalysis.volumedatautils) calculateCoords() (schrodinger.graphics3d.arrow.MaestroArrow method) calculated (schrodinger.application.jaguar.garza.SolvEntropyParams attribute) CalculatedParams (class in schrodinger.application.jaguar.garza) calculateEnergy() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) calculateEnergyDifference() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) calculateForceFieldEnergy() (schrodinger.glide.ConformerTemplate method) calculateHelices() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) calculateHelixProp() (schrodinger.application.matsci.atom_group.HelixArc method) calculateInternalEnergy() (schrodinger.glide.ConformerTemplate method) calculatelnQs() (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties method) calculateMatrix() (schrodinger.structutils.sitealign.BindingSiteAligner method) calculateMeanAndStd() (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) calculateMembraneBox() (schrodinger.protein.membrane.Membrane_Model method) calculateMetric() (schrodinger.infra.canvas.ChmCustomMetric method) CalculateMolWt (class in schrodinger.seam.examples.active_learning_weigher) calculateMutationsList() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator method) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) calculateOverResidues() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) calculatePropertiesCoordinates() (schrodinger.ui.two_d_viewer.TwoDViewer method) calculatePropertyPrecisions() (schrodinger.ui.two_d_viewer.TwoDViewer method) calculateSASA() (schrodinger.infra.canvas.ChmMmctAdaptor static method) calculateSASAByAtom() (schrodinger.infra.canvas.ChmMmctAdaptor static method) calculateScalar() (schrodinger.infra.canvas.ChmAtomTyper method) (schrodinger.infra.canvas.ChmAtomTyperEstate method) CalculateScoreNodeFigs() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) CalculateScoreNodeMolDisplay() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) CalculateScoreNodeText() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) calculateSelfDensity() (schrodinger.glide.RefinedPoseEnsemble method) calculateSimilarity() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) calculateSpecificity() (schrodinger.analysis.enrichment.calculator.Calculator method) calculateTopologicalDescriptors() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method) calculateTorsionEnergy() (schrodinger.glide.ConformerTemplate method) calculateVolume() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) (schrodinger.infra.canvas.ChmMmctAdaptor static method) calculateWeightedScalar() (schrodinger.infra.canvas.ChmAtomTyper method) calculateXYZBox() (schrodinger.graphics3d.tube.MaestroTube method) CALCULATION (schrodinger.application.matsci.crest.CrestTOML attribute) CALCULATION_MODE (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget attribute) CALCULATIONS (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) Calculator (class in schrodinger.analysis.enrichment.calculator) calcZScores() (schrodinger.pipeline.stages.combine.DataFusionMergeStage method) calDensity() (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) call() (in module schrodinger.utils.subprocess) (schrodinger.ui.qt.formlayout.PushLayout method) call_func_and_wait_for_signal() (in module schrodinger.utils.qt_utils) callback (schrodinger.application.jaguar.textparser.TextParser attribute) (schrodinger.application.qsite.output.QSiteTextParser attribute) (schrodinger.application.xtb.textparser.TextParser attribute) callback() (in module schrodinger.application.jaguar.textparser) (in module schrodinger.application.mopac.results_main) (in module schrodinger.application.qsite.output) (in module schrodinger.application.xtb.textparser) callback_minimal (schrodinger.application.mopac.results_main.MopacMainTextParser attribute) callback_minimal() (in module schrodinger.application.mopac.results_main) callback_name (schrodinger.maestro_utils.surface_manager.menus.MenuActionData attribute) CallbackInfo (class in schrodinger.ui.qt.appframework2.maestro_callback) CallbackMonitor (class in schrodinger.ui.qt.appframework2.maestro_callback) callbacks (schrodinger.application.mopac.results_main.MopacMainTextParser attribute) calling_context (schrodinger.tasks.tasks.AbstractTask attribute) calling_contextChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.ld_tasks.StructureInfoTask attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask attribute) (schrodinger.application.livedesign.tasks.AbModelingTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.EventAnalysisTask attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MultisimTask attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.Trj2maeTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.BuildMissingLoopsTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.beamtasks.BeamTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.maptasks.MapTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.slurmtasks.ComboSlurmTask attribute) (schrodinger.tasks.slurmtasks.FooTask attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask attribute) (schrodinger.tasks.test.cli.preprocessor_cli.FooJobTask attribute) (schrodinger.ui.qt.pdb_dialog.Sf2MapConversionTask attribute) calling_contextReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.ld_tasks.StructureInfoTask attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask attribute) (schrodinger.application.livedesign.tasks.AbModelingTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.EventAnalysisTask attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MultisimTask attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.Trj2maeTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.BuildMissingLoopsTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.beamtasks.BeamTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.maptasks.MapTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.slurmtasks.ComboSlurmTask attribute) (schrodinger.tasks.slurmtasks.FooTask attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask attribute) (schrodinger.tasks.test.cli.preprocessor_cli.FooJobTask attribute) (schrodinger.ui.qt.pdb_dialog.Sf2MapConversionTask attribute) CallingContext (class in schrodinger.tasks.tasks) Callout (class in schrodinger.ui.qt.schart) can_atom_hydrogen_bond() (in module schrodinger.structutils.analyze) can_cache_more_frames() (schrodinger.application.desmond.packages.traj.MaestroFrame method) (schrodinger.application.desmond.packages.traj.Source method) CAN_CREATE_TRAJECTORY (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.CustomTrajectoryStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.MDCustomMSJStep attribute) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) can_show_online_docs() (in module schrodinger.utils.documentation) can_skip_line() (in module schrodinger.utils.compare) can_write_file() (in module schrodinger.application.licensing.licadmin) canBeChiral() (schrodinger.infra.canvas.ChmAtom method) canBroaden() (schrodinger.application.matsci.espresso.qeoutput.DOS method) CANCEL (schrodinger.application.job_monitor.job_monitor_models.RequestedStatus attribute) (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.MessageButton attribute) (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) Cancel (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.StdBtn attribute) cancel() (schrodinger.application.glide.http_client.ZmqClient method) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) (schrodinger.application.matsci.qubec_utils.Job method) (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.protein.tasks.clustal.AbstractAlignmentJob method) (schrodinger.ui.qt.pdb_dialog.PDBDialog method) cancelBatch() (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) cancelClicked() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) CANCELED (schrodinger.job.jobcontrol.DisplayStatus attribute) CANCELLED (schrodinger.tasks.slurmtasks.JobState attribute) cancelRequested (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget attribute) cancelSelected() (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) cancelSubmitted() (schrodinger.job.queue.JobControlJob method) CancelSubmittedStatus (class in schrodinger.job.queue) canDriverUseUmbrella() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) canonical (schrodinger.application.desmond.struc.FormHashes attribute) (schrodinger.application.desmond.struc.FormMols attribute) canonical_filename() (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.licensing.licadmin.LicenseResource method) CANONICAL_STRUCTURAL (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes attribute) CANONICAL_STRUCTURAL_RES (schrodinger.application.bioluminate.antibody.annotate.Properties attribute) Canonicalize (class in schrodinger.adapter) canonicalize() (schrodinger.application.matsci.deprecated_pattern.SmilesGenerator method) (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) (schrodinger.infra.fast3d.Canonicalizer method) (schrodinger.infra.mm.UTT method) canonicalize_atom_names() (in module schrodinger.application.jaguar.autots_bonding) canonicalize_R_labels() (in module schrodinger.application.scaffold_enumeration.markush) canonicalizePositions() (schrodinger.infra.fast3d.Canonicalizer method) Canonicalizer (class in schrodinger.infra.fast3d) canorb() (in module schrodinger.application.jaguar.textparser) canRestrainCore() (schrodinger.glide.LigandConstraintData method) CANRIGID (schrodinger.application.matsci.kmc.FramesTable attribute) (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) canSnapCore() (schrodinger.glide.LigandConstraintData method) canStart() (schrodinger.application.matsci.jaguarworkflows.Step method) CantAccessModelError CantAlignException CantCreateQApplicationError canvas (schrodinger.application.matsci.msconst.SMARTS_METHOD attribute) Canvas2DSimilarityStage (class in schrodinger.pipeline.stages.canvas) canvas_size_units (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) canvas_size_unitsChanged (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) canvas_size_unitsReplaced (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) CanvasFingerprintCluster (class in schrodinger.application.canvas.cluster) CanvasFingerprintClusterCLI (class in schrodinger.application.canvas.cluster) CanvasFingerprintClusterGUI (class in schrodinger.application.canvas.clustergui) CanvasFingerprintGenerator (class in schrodinger.application.canvas.fingerprint) CanvasFingerprintGeneratorCLI (class in schrodinger.application.canvas.fingerprint) CanvasFingerprintGeneratorGUI (class in schrodinger.application.canvas.fingerprintgui) CanvasFingerprintSimilarity (class in schrodinger.application.canvas.similarity) CanvasFingerprintSimilarityCLI (class in schrodinger.application.canvas.similarity) CanvasFingerprintSimilarityGUI (class in schrodinger.application.canvas.similaritygui) canvasfp_fpreader() (in module schrodinger.application.hitexpander) canvasFPGen (schrodinger.infra.canvas.ChmDescriptorSourceMapper attribute) CanvasKPLS (class in schrodinger.application.matsci.genetic_optimization) canvasMolDescriptors (schrodinger.infra.canvas.ChmDescriptorSourceMapper attribute) CanvasPattern (class in schrodinger.application.matsci.rdpattern) CanvasSearchTask (class in schrodinger.application.livedesign.tasks) CanvasSearchTask.Input (class in schrodinger.application.livedesign.tasks) CanvasSearchTask.JobConfig (class in schrodinger.application.livedesign.tasks) CanvasSearchTask.Output (class in schrodinger.application.livedesign.tasks) CanvasSimilarityNotImplemented CanvasWithHeaderAndFooter (class in schrodinger.application.matsci.reportutils) cap_termini (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_termini() (in module schrodinger.protein.captermini) cap_termini_min_atoms (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_termini_min_atomsChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_termini_min_atomsReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_terminiChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) cap_terminiReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) capability (schrodinger.gpgpu.DeviceInfo attribute) capacity() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) cappedResidues() (schrodinger.protein.captermini.CapTermini method) cappedSites() (schrodinger.application.matsci.sculptcomplex.CoordinationInfo method) CAPPING_BOND_LENGTH (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) CAPPINGELEMENT (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) capResidues() (schrodinger.protein.captermini.CapTermini method) capSequences() (schrodinger.protein.captermini.CapTermini method) CapTermini (class in schrodinger.protein.captermini) CAPTION (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) Capture (class in schrodinger.infra.mmerr) CaptureMMErr (class in schrodinger.infra.mm) CaptureRDErrorLog (class in schrodinger.adapter) CARBON_PDBNAME (schrodinger.protein.protassign.pka_prediction.AsparticAcidpKaPredictor attribute) (schrodinger.protein.protassign.pka_prediction.GlutamicAcidpKaPredictor attribute) CARBON_PDBNAMES (schrodinger.protein.protassign.changeables.amide_changeable attribute) (schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor attribute) CarbonCount (class in schrodinger.application.transforms.template.starter) CarbonCountingWorkflow (class in schrodinger.application.transforms.template.starter) carboxyl_changeable (class in schrodinger.protein.protassign.changeables) carboxyl_interactions() (schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor method) CARBOXYLIC_ACID_PKA_SHIFT (schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor attribute) carrier_avg_diffusion_tensor() (in module schrodinger.application.matsci.kmc) carrier_avg_drift_velocity() (in module schrodinger.application.matsci.kmc) carrier_avg_mobility_tensor_from_diffusion() (in module schrodinger.application.matsci.kmc) carrier_avg_mobility_tensor_from_drift_velocity() (in module schrodinger.application.matsci.kmc) carrier_avg_tensors() (in module schrodinger.application.matsci.kmc) CARRIERTYPE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) Cartesian (class in schrodinger.infra.mm) CARTESIAN (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) Cartesian_angle() (in module schrodinger.infra.mm) Cartesian_dihedral() (in module schrodinger.infra.mm) Cartesian_distance() (in module schrodinger.infra.mm) cartesian_hessian() (in module schrodinger.application.jaguar.hess_guess) Cartesian_square_distance() (in module schrodinger.infra.mm) CARTESIANWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) Cascader (class in schrodinger.application.matsci.amorphous) CascadingCheckboxItem (class in schrodinger.application.livedesign.panel_components) case_insensitive_file_exists() (in module schrodinger.application.matsci.wfmanagement) CaseInsensitiveString (class in schrodinger.application.jaguar.jaguar_diff) cast_type (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) cast_validation_result() (in module schrodinger.ui.qt.appframework2.validation) cat() (in module schrodinger.utils.fileutils) cat_csv_files() (in module schrodinger.rdkit.molio) cat_flat_files() (in module schrodinger.utils.fileutils) CATALYTIC_LOOP (schrodinger.protein.annotation.KinaseFeatureLabel attribute) catch_error_for_dialog() (in module schrodinger.ui.qt.utils) catch_jag_errors() (in module schrodinger.application.jaguar.gui.utils) catch_last_added() (in module schrodinger.application.bioluminate.ssv.viewer) catch_subprocess_errors() (in module schrodinger.utils.sysinfo) categories (schrodinger.application.matsci.builderwidgets.BaseTemplateListWidgetItem property) (schrodinger.application.matsci.builderwidgets.CustomListWidgetItem property) (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) categorize_entries_by_locus() (in module schrodinger.application.bioluminate.update_germline_db.translate_db) categorizeBonds() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) categorizeServers() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) categorizeSymmetryMappings() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) CATEGORY (schrodinger.ui.qt.schart.SChart attribute) category_keys (schrodinger.application.matsci.builderwidgets.TemplateFamily attribute) (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) CategoryOrderError cation_centroid (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) cation_pi_interactions() (schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor method) cation_structure (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) CationPiInteraction (class in schrodinger.structutils.interactions.pi) CatPiFinder (class in schrodinger.application.desmond.packages.analysis) CatPiInteraction (in module schrodinger.application.desmond.packages.analysis) cauchy_gen (class in schrodinger.application.matsci.gsas.GSASIIpwd) cav (schrodinger.application.jaguar.results.ThermoComponents attribute) Cavity (class in schrodinger.application.bindingsite.cavutils) cavity (schrodinger.application.jaguar.results.SolvThermoProp attribute) cavity_depth (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) CB_TEXT (schrodinger.ui.qt.forcefield.forcefield.ValidateOplsDirMessageBox attribute) CC_SLIDER (schrodinger.application.matsci.mswidgets.MultiSlider attribute) ccd_assign_by_names_and_bonds() (in module schrodinger.structutils.ccd) CCDAtomMapper (class in schrodinger.structutils.ccd) CCDStructureMismatchError cd() (in module schrodinger.utils.installation_check) cdock (schrodinger.application.livedesign.tasks.CovDockTask attribute) cdock_file (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cdock_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cdock_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cdr_name (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput property) CDXML (schrodinger.rdkit_extensions.Format attribute) cealign() (in module schrodinger.geometry) (in module schrodinger.structutils.rmsd) (in module schrodinger.structutils.structalign2) Cell (class in schrodinger.ui.qt.tablewidget) (class in schrodinger.ui.two_d_viewer) cell (schrodinger.application.matsci.clusterstruct.ComInfo attribute) (schrodinger.ui.qt.tablewidget.Column property) (schrodinger.ui.qt.tablewidget.Row property) cell2A() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cell2AB() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cell2Gmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cell2GS() (in module schrodinger.application.matsci.gsas.GSASIIlattice) CELL_DOFREE_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_DOFREE_XML (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_DYNAMICS_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_FACTOR_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_PADDING (schrodinger.application.report2d.PicturePrinter attribute) CellAbsorption() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cellAspectRatio() (schrodinger.ui.qt.structtable.ViewerTable method) CellBlock() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cellClearData() (schrodinger.infra.table.Table method) cellClicked() (schrodinger.ui.two_d_viewer.TwoDViewer method) CellContextualMenu (class in schrodinger.ui.two_d_viewer) CellControlType (class in schrodinger.application.matsci.espresso.qeinput) cellDijFill() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cellDoubleClicked() (schrodinger.ui.two_d_viewer.TwoDViewer method) cellHasData() (schrodinger.infra.table.Table method) CellIterator (class in schrodinger.ui.qt.tablewidget) CellMatchAtom (class in schrodinger.infra.structure) CellRunInfo (class in schrodinger.application.matsci.jobutils) cellWidget() (schrodinger.ui.qt.swidgets.STableWidget method) CentCheck() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Center (class in schrodinger.application.bioluminate.pml_menus) center (schrodinger.application.glide.gui.GridSite attribute) CENTER (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) center (schrodinger.application.scaffold_enumeration.cxsmiles.MCG attribute) (schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup attribute) (schrodinger.math.multi_parameter_optimization.Transition attribute) Center (schrodinger.ui.qt.pop_up_widgets.PopUpAlignment attribute) center() (in module schrodinger.application.desmond.packages.topo) (schrodinger.infra.canvas.Chm2DCoordGen static method) (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) center_cms() (in module schrodinger.application.desmond.packages.topo) center_com() (in module schrodinger.comparison.struc) center_ct() (in module schrodinger.application.desmond.packages.staf) center_fr() (in module schrodinger.application.desmond.packages.staf) center_fr_along_z() (in module schrodinger.application.desmond.packages.staf) center_of_mass() (in module schrodinger.application.matsci.cg_mapping) (in module schrodinger.geometry) (in module schrodinger.structutils.analyze) center_rotation (schrodinger.application.pymol.mae_sync.MaestroSettingsModel attribute) center_widget_in_table_cell() (in module schrodinger.ui.qt.swidgets) center_xyz (schrodinger.glide.RefinedPose attribute) centerAndRescale() (schrodinger.infra.canvas.Chm2DCoordGen static method) centerChanged (schrodinger.application.glide.gui.GridSite attribute) CenteredIconDelegate (class in schrodinger.ui.qt.delegates) CenteredSoluteAnalysis (class in schrodinger.application.desmond.packages.staf) CENTERING (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute) CENTERING_OPERATIONS_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) CENTERING_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) centering_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) centering_opers_strs (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) CenteringWidget (class in schrodinger.ui.qt.swidgets) CenterOf (class in schrodinger.application.desmond.packages.analysis) centerOf() (schrodinger.infra.canvas.ChmAtoms method) CenterOfMotion (in module schrodinger.application.desmond.packages.analysis) centerPos() (schrodinger.ui.qt.network_views.NetworkNode method) centerReplaced (schrodinger.application.glide.gui.GridSite attribute) centerStruct() (schrodinger.application.matsci.desmondutils.SystemBuilder method) central_bt (schrodinger.infra.mm.UTT attribute) centralAtom (schrodinger.infra.canvas.ChmChiralityInfo attribute) centrality (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule.RING_INFO attribute) Centroid (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.structutils.interactions.pi) centroid (schrodinger.structutils.analyze.Ligand property) (schrodinger.structutils.ringspear.SpearRing attribute) centroid() (in module schrodinger.geometry) CentroidBanner (class in schrodinger.trajectory.trajectory_gui_dir.banners) centroids (schrodinger.comparison.dedup_utils.CrystalData attribute) centroidsPicked (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner attribute) cert (schrodinger.application.licensing.licserver.client.LocalEntitlementValidation attribute) (schrodinger.job.cert.CertInfo attribute) CertInfo (class in schrodinger.job.cert) CFG_FILE (schrodinger.application.matsci.permittivity.MultiStageMd attribute) cflt_file (schrodinger.application.steps.filters.ProductFilterMixin.Settings attribute) cflt_fileChanged (schrodinger.application.steps.filters.ProductFilterMixin.Settings attribute) cflt_fileReplaced (schrodinger.application.steps.filters.ProductFilterMixin.Settings attribute) CG_AA_ELEMENT_SYMBOL (schrodinger.application.matsci.nano.constants.Constants attribute) CG_CAPPING_ELEMENT (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) CG_ELEMENT1 (schrodinger.application.matsci.nano.constants.Constants attribute) CG_ELEMENT2 (schrodinger.application.matsci.nano.constants.Constants attribute) cg_substructure_matches() (in module schrodinger.rdkit.substructure) CgCoreAnnotator (class in schrodinger.ui.qt.structure2d) cgen() (schrodinger.application.macromodel.utils.ComUtil method) CGFFIOStructure (class in schrodinger.application.matsci.cgforcefield) CGForceFieldSelector (class in schrodinger.application.matsci.cgforcefieldgui) CGGraphHelper (class in schrodinger.application.matsci.automated_cg_mapping) CGMapper (class in schrodinger.application.matsci.cg_mapping) CGMapperMixin (class in schrodinger.application.matsci.cg_mapping) CGStructBuilder (class in schrodinger.application.matsci.automated_martini_mapping_protein) CH (schrodinger.protein.annotation.AntibodyRegionLabel attribute) CH2CL2 (schrodinger.energy.Solvent attribute) Chain (class in schrodinger.protein.getpdb_utility) (class in schrodinger.stepper.stepper) chain (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch attribute) CHAIN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain (schrodinger.application.bioluminate.mutation.Mutation attribute) CHAIN (schrodinger.application.bioluminate.pose_filtering.hdx_io.StandardColumns attribute) chain (schrodinger.application.bioluminate.protein_interaction.utils.Residue attribute) (schrodinger.application.glide.utils.ResidueId attribute) (schrodinger.application.glide.utils.ResidueInteraction attribute) (schrodinger.application.licensing.licserver.client.LocalEntitlementValidation attribute) CHAIN (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule attribute) chain (schrodinger.application.qsite.input.Cut property) (schrodinger.protein.residue.Residue property) (schrodinger.protein.residue.ResidueKey attribute) (schrodinger.protein.sequence.AbstractSingleChainSequence property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.structure.Residue property) (schrodinger.structure.Structure attribute) (schrodinger.structure.StructureAtom property) (schrodinger.structure.TextualStructure property) Chain (schrodinger.ui.picking.PickResidueColumns attribute) chain (schrodinger.ui.qt.rama.BackboneDihedral attribute) chain1 (schrodinger.application.bioluminate.mhc.docking_angles.ReceptorChainInfo attribute) chain2 (schrodinger.application.bioluminate.mhc.docking_angles.ReceptorChainInfo attribute) CHAIN_FR_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) CHAIN_FR_SIM (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain_id (schrodinger.application.bioluminate.classify.NumberedResidue attribute) CHAIN_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain_name (schrodinger.application.matsci.packmol.PDBdata attribute) (schrodinger.structure.StructureAtom property) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) chain_offsets (schrodinger.protein.sequence.CombinedChainProteinSequence property) CHAIN_SIM (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain_type (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) chainAdded() (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) ChainAlignment (class in schrodinger.application.bioluminate.anarci.anarci_adapter) ChainData (class in schrodinger.application.bioluminate.antibody.assembly_yaml) ChainHitsTable (class in schrodinger.application.bioluminate.anarci.anarci_adapter) chainKey() (schrodinger.protein.residue.ResidueKey method) ChainNumbering (class in schrodinger.application.bioluminate.anarci.anarci_adapter) chainRemoved() (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) chains (schrodinger.protein.sequence.CombinedChainProteinSequence property) ChainTypes (class in schrodinger.application.bioluminate.antibody.grafting) CHANGE_CREATION_DEFAULTS (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) change_current_pick() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.Rama method) change_directory() (in module schrodinger.application.bioluminate.methionine_oxidation) CHANGE_DISPLAY (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) change_empirical_pka() (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.rotatable_changeable method) change_pka() (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.rotatable_changeable method) change_to_rgroup() (in module schrodinger.rdkit.rgroup) CHANGE_VIEW_SETTINGS (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) change_working_directory() (in module schrodinger.utils.fileutils) changeable (class in schrodinger.protein.protassign.changeables) changeAxisFontSize() (schrodinger.ui.qt.schart.SChart static method) changeBasis() (schrodinger.application.matsci.nano.tube.NanoSheet method) changeBFactorPlot() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) changeButtonState() (schrodinger.application.matsci.sliceplot.SlicePlot method) changeCoord() (schrodinger.application.matsci.zmutils.ZAtom method) Changed (schrodinger.models.parameters.SignalType attribute) changeEvent() (schrodinger.ui.qt.swidgets.LineEditWithDisabledText method) (schrodinger.ui.qt.swidgets.SCheckBox method) changeGroup() (schrodinger.utils.preferences.Preferences method) changeIcon() (schrodinger.ui.qt.color_picker.ButtonWithColorPicker method) changeLayer() (schrodinger.application.matsci.sliceplot.SlicePlot method) changeLimitsEnd() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) changeLimitsStart() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) changeMarkerAtomsToTempElement() (schrodinger.application.matsci.builderwidgets.SketcherStructureMixin method) changeModel() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) changeMoleculeForParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) changePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) changeParameterValuesByIndex() (in module schrodinger.infra.mm) changePreset() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) changeProtein() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) changeScaling() (schrodinger.ui.qt.dendrogram.GuiPanel method) changesSaved() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) changeTemplateDirectory() (schrodinger.application.matsci.builderwidgets.TemplateManager method) changeThickness() (schrodinger.ui.qt.dendrogram.GuiPanel method) changeToolTip() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) CHANNEL_FILE (schrodinger.application.matsci.rxn_channel.Constants attribute) ChannelDefinition (class in schrodinger.application.matsci.rxn_channel) ChannelDefinitions (class in schrodinger.application.matsci.rxn_channel) Channels (class in schrodinger.application.matsci.rxn_channel) CHAR_TO_ACC_MAP (schrodinger.protein.predictors.AccproPredictor attribute) CHARGE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) charge (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) CHARGE (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) charge (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) CHARGE (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) charge (schrodinger.application.jaguar.utils.ChgAt attribute) CHARGE (schrodinger.application.jaguar.xray.constants.KEYWORDS attribute) charge (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule.MAPPED_BEAD_INFO attribute) (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) (schrodinger.application.matsci.cgforcefield.VDWData attribute) (schrodinger.application.matsci.coarsegrain.AUTOMAPPED_PARTICLE_INFO attribute) CHARGE (schrodinger.application.matsci.crest.CrestTOML attribute) (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute) charge (schrodinger.protein.residue.Residue property) charge_correction (schrodinger.glide.EnergyOptions attribute) charge_idx (schrodinger.application.matsci.kmc.MSDInfo attribute) charge_is_conserved() (in module schrodinger.application.jaguar.autots_validation) charge_is_consistent() (in module schrodinger.application.jaguar.workflow_validation) charge_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) CHARGE_SPIN_INCONSISTANT_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) CHARGE_TRANSFER (schrodinger.energy.MetalForceFieldComponent attribute) charge_transfer_matrix (schrodinger.energy.FlucCTIntermediateOutput attribute) ChargeConstraint (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) ChargeConstraintRow (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsColumns (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints) ChargeConstraintsTableView (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) charged (schrodinger.application.matsci.kmcgui.PlotInfo attribute) charged_charged (schrodinger.glide.HBonds attribute) CHARGED_CHARGED (schrodinger.glide.HBondType attribute) charged_ligand_atom_score (schrodinger.glide.VisualizationData attribute) CHARGED_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) CHARGED_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) CHARGED_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) ChargeDialog (class in schrodinger.application.matsci.chargegui) ChargedNHpKaFilter (class in schrodinger.application.transforms.filters) chargedStrucsPresent() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) ChargeFilterStage (class in schrodinger.pipeline.stages.filtering) ChargeFlip() (in module schrodinger.application.matsci.gsas.GSASIImath) ChargePropertySelector (class in schrodinger.application.matsci.chargegui) charges (schrodinger.application.jaguar.utils.LewisStructure attribute) charges_from_ct (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) (schrodinger.structutils.minimize.Minimizer property) ChargeSelectorDelegate (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeSelectorLineEdit (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector) ChargeVectorizer (in module schrodinger.application.bioluminate.peptide_sar.encode) ChatSessionHandler (class in schrodinger.maestro_utils.composer_agent.session_handler) CHCL3 (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute) (schrodinger.energy.Solvent attribute) chdir (class in schrodinger.application.matsci.permittivity) (class in schrodinger.utils.fileutils) chdir() (in module schrodinger.application.desmond.util) check() (schrodinger.application.glide_ws.trigger.Trigger method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.packmol.BilayerInputFile method) (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) check_anharmonic() (in module schrodinger.application.matsci.thermo_correction_utils) check_args() (schrodinger.application.glide_ws.driver.GlideWSJob method) check_attachment_point() (in module schrodinger.structutils.rgroup_enumerate) check_attachment_points_changed() (in module schrodinger.livedesign.preprocessor) check_bond_vec_proj() (in module schrodinger.application.matsci.nano.xtal) CHECK_BOX_COLUMN (schrodinger.maestro_utils.surface_manager.constants.SurfaceColumnType attribute) check_call() (in module schrodinger.utils.subprocess) check_canvas_license() (in module schrodinger.application.canvas.topo_descriptors) check_centroid_rep() (in module schrodinger.application.matsci.reaction_workflow_utils) check_cg_license() (in module schrodinger.application.matsci.jobutils) check_charge_and_multiplicity() (in module schrodinger.application.matsci.jaguarworkflows) check_cms_trj_properties_are_found() (in module schrodinger.application.matsci.deswidgets) check_command() (in module schrodinger.application.desmond.util) check_config() (in module schrodinger.livedesign.cmdline) check_conflicts() (in module schrodinger.application.jaguar.ames.ames_validation) (in module schrodinger.application.jaguar.autots_validation) (in module schrodinger.application.jaguar.distributed_frequencies.validation) (in module schrodinger.application.jaguar.hydrokinetic_validation) (in module schrodinger.application.jaguar.macro_pka_validation) (in module schrodinger.application.jaguar.mlff.validation) (in module schrodinger.application.jaguar.rotation_barriers_validation) (in module schrodinger.application.jaguar.solvation_validation) check_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) (in module schrodinger.application.peptide_workflow.driver_utils) check_connection() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) check_consistency() (in module schrodinger.application.desmond.packages.topo) check_coordinates_changed() (in module schrodinger.application.matsci.freevolume) check_cpu_features() (in module schrodinger.utils.sysinfo) check_cstate_changed() (in module schrodinger.livedesign.preprocessor) check_ct() (schrodinger.application.glide_ws.trigger.TriggerConfig method) (schrodinger.application.glide_ws.trigger.TriggerSet method) check_cts() (schrodinger.application.glide_ws.trigger.TriggerConfig method) (schrodinger.application.glide_ws.trigger.TriggerSet method) check_directrunner_license_checkouts() (in module schrodinger.seam.testing.fixtures) check_directrunner_license_checkouts_impl() (in module schrodinger.seam.testing.fixtures) check_driver_disk_space() (in module schrodinger.active_learning.al_utils) check_enamine_subclass() (in module schrodinger.protein.process_enamine_db) check_ensemble_size() (schrodinger.application.glide_ws.nodes.CrossNode method) check_excited_calc() (schrodinger.application.jaguar.input.JaguarInput method) check_external_calc() (schrodinger.application.jaguar.input.JaguarInput method) check_feature_string() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) check_ff_assignment() (in module schrodinger.application.matsci.reaction_workflow_utils) check_file_formats() (in module schrodinger.application.glide.sort_parser_common) check_finite_molecules() (in module schrodinger.application.matsci.equilibrium_md) check_for_metal_ligand_interaction() (schrodinger.application.glide_ws.nodes.GlideBaseNode method) check_for_queue_execs() (in module schrodinger.autoinstall.misc) check_for_spears() (in module schrodinger.structutils.ringspear) check_fp_availability() (in module schrodinger.application.hitexpander) check_grid_for_unsupported_waters() (schrodinger.application.glide_ws.nodes.GridGenNode method) check_hbond() (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method) (schrodinger.protein.analysis.Report.steric_clash_data_set method) check_if_backbone_atom() (in module schrodinger.application.bioluminate.protein_interaction.calculate) check_if_comparable() (in module schrodinger.protein.residue) check_if_hips_needs_pka_recalculated() (schrodinger.protein.assignment.ProtAssign method) check_if_lattice_properties_exist() (in module schrodinger.application.matsci.nano.particle) check_imaginary_frequencies() (in module schrodinger.application.matsci.anharmonic) check_jaguar_license() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) check_jaguar_output() (in module schrodinger.application.matsci.thermo_correction_utils) check_kekulization() (in module schrodinger.livedesign.preprocessor) check_key_pair() (in module schrodinger.utils.sshconfig) check_libfile() (schrodinger.application.glide_ws.nodes.GlideBaseNode method) check_libfiles() (schrodinger.application.glide_ws.nodes.GlideBaseNode method) check_license() (in module schrodinger.active_learning.al_ligand_ml_utils) (in module schrodinger.application.matsci.jobutils) (schrodinger.application.glide_ws.driver.GlideWSJob method) check_licenses() (in module schrodinger.application.matsci.jobutils) check_ligand_file() (in module schrodinger.application.livedesign.io_utils) check_map() (in module schrodinger.utils.sea.evalor) check_memory_use() (in module schrodinger.application.mopac.results_main) check_missing_data() (in module schrodinger.application.matsci.kmc) check_mlff_keyword_is_valid() (in module schrodinger.application.matsci.jaguarworkflows) check_model_version() (in module schrodinger.application.matsci.ml_formulations_utils) check_modes() (in module schrodinger.application.glide.sort_parser_common) check_module() (in module schrodinger.application.bioluminate.validate_imported_modules) check_moved_variables() (in module schrodinger.application.matsci.codeutils) CHECK_MSG (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.genetic_optimization.ChemInformatics attribute) check_options() (in module schrodinger.application.matsci.equilibrium_md) check_output() (in module schrodinger.utils.subprocess) check_params() (schrodinger.application.jaguar.garza.SolventParams method) check_permitted_features_string() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) check_property_sign() (in module schrodinger.application.matsci.uq_utils) check_qrnn() (schrodinger.application.jaguar.input.JaguarInput method) check_reaction() (in module schrodinger.livedesign.bbchem_endpoints) check_reaction_wf_structures() (in module schrodinger.application.matsci.reaction_workflow_utils) check_required_gridfiles() (in module schrodinger.application.glide.grid) check_required_modules() (in module schrodinger.active_learning.al_utils) check_residue_flip_state() (in module schrodinger.protein.assignment) check_restart_host() (in module schrodinger.active_learning.al_utils) check_ring_spears() (in module schrodinger.application.matsci.packmol) check_running_as_root() (in module schrodinger.utils.installation_check) check_rxn() (in module schrodinger.livedesign.check_reaction) check_sanity() (in module schrodinger.application.desmond.cms) check_seamrunner_license_checkouts() (in module schrodinger.seam.testing.fixtures) check_seamrunner_license_checkouts_impl() (in module schrodinger.seam.testing.fixtures) check_slm_status() (in module schrodinger.autoinstall.misc) check_slurm_job() (in module schrodinger.tasks.slurmtasks) check_slurm_jobs() (in module schrodinger.tasks.slurmtasks) check_solvation() (schrodinger.application.jaguar.input.JaguarInput method) check_strict_config() (in module schrodinger.livedesign.preprocessor) check_subjob_output() (schrodinger.pipeline.stages.glide.DockingStage method) check_subset_existence() (in module schrodinger.pipeline.stages.phase) check_tau_options() (in module schrodinger.application.matsci.equilibrium_md) check_triggers() (schrodinger.application.glide_ws.nodes.NativeNode method) check_ts_vetting() (in module schrodinger.application.matsci.thermo_correction_utils) check_user_query() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) check_valid_key() (in module schrodinger.job.launchapi) check_watermap_good_for_grid() (in module schrodinger.application.glide_ws.utils) check_xtb() (schrodinger.application.jaguar.input.JaguarInput method) check_xtb_solvent() (in module schrodinger.energy) CHECKABLE_COLS (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) CHECKABLE_ITEM (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) CheckableHeaderView (class in schrodinger.ui.qt.table_helper) checkAgainstTemplate() (schrodinger.application.matsci.vsepr.VSEPRFinder method) checkAlignment() (schrodinger.application.matsci.nano.particle.CheckInput method) checkAll() (schrodinger.application.matsci.nano.sheet.CheckInput method) (schrodinger.application.matsci.nano.tube.CheckInput method) checkAndmarkPolymerProp() (schrodinger.application.matsci.amorphous.PolymerFragments method) checkAndProcessAllowAdsorptionOnto() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkArgs() (schrodinger.structutils.createfragments.FragmentCreator method) checkASL() (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) (schrodinger.application.matsci.mswidgets.MSAtomSelector method) checkASU() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkAtomUniqueness() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) checkAtomZeroIndex() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) checkBasisSets() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetProxyModel method) checkBilayerSep() (schrodinger.application.matsci.nano.check.CheckInput method) checkBilayerShift() (schrodinger.application.matsci.nano.check.CheckInput method) checkBilayerStackType() (schrodinger.application.matsci.nano.check.CheckInput method) checkBondingAndTranslate() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkBondlength() (schrodinger.application.matsci.nano.check.CheckInput method) CheckboxDelegate (class in schrodinger.ui.qt.delegates) CheckboxIcons (class in schrodinger.ui.qt.standard.design_tokens) checkBoxText() (schrodinger.ui.qt.swidgets.SCheckBoxEdit method) checkCanvasElementsLicense() (in module schrodinger.infra.canvas) checkCellDims() (schrodinger.application.matsci.nano.check.CheckInput method) checkChannelDefs() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkChannelDefsVsReactants() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkChannelUniqueness() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkChargesMultiplicitiesStates() (schrodinger.application.matsci.mecp_mod.CheckInput static method) checkConflicts() (schrodinger.application.glide.job.Dock method) (schrodinger.application.glide.job.GlideJob method) checkConformationalSearch() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkConnectivity() (schrodinger.application.matsci.rxn_path.CheckInput method) checkConstantVol() (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) checkConstraintCoords() (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) checkCoords() (schrodinger.infra.canvas.ChmMol method) checkCorrectionParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) checkCustomKeysForTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) checkDeadlines() (schrodinger.active_learning.mq_worker.Worker method) checkDefinition() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) checkDefStrFormat() (schrodinger.application.matsci.rxn_channel.ChannelDefinition method) checkDict() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) checkDielectric() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) checkDissociationBondLength() (schrodinger.application.matsci.rxn_channel.CheckInput method) CHECKED_DEFAULT (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) CHECKED_DISABLED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) CHECKED_HOVER (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) CHECKED_PRESSED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) (schrodinger.ui.qt.standard.design_tokens.RadioButtonIcons attribute) checkedFeatures() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) checkEdgetypes() (schrodinger.application.matsci.nano.check.CheckInput method) checkedText() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) CheckElement() (in module schrodinger.application.matsci.gsas.GSASIIElem) checkElements() (schrodinger.application.matsci.nano.check.CheckInput method) checkElitism() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkEntryDatabase() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) checkExcitedStatesType() (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController method) checkExistingFile() (schrodinger.application.matsci.nano.check.CheckInput method) checkFile() (schrodinger.pipeline.stage.Stage method) checkFileExists() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkFiles() (schrodinger.pipeline.stage.Stage method) checkFinalPointRange() (schrodinger.application.matsci.density_analysis_widget.MeasurementLine method) checkFit() (schrodinger.application.matsci.kmc.MSDFit method) checkForClashes() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) checkForCompletion() (schrodinger.pipeline.stages.qikprop.QikPropStage method) checkForInterStructureClashes() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) checkForIntraStructureClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) checkForMatch() (schrodinger.application.bioluminate.propfilter.BooleanDatabaseCriterion method) (schrodinger.application.bioluminate.propfilter.NumericalDatabaseCriterion method) (schrodinger.application.bioluminate.propfilter.StringDatabaseCriterion method) checkForNAN() (schrodinger.infra.canvas.Chm2DCoordGen static method) checkForOneInputSource() (schrodinger.tasks.maptasks.MapTaskMixin method) checkForRings() (schrodinger.application.matsci.montecarlo.ClashChecker method) checkFractionalRedundancies() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkFragmentLibs() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkFreezers() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkGenerations() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkGridfile() (schrodinger.application.glide.ligand_designer.GridgenTask method) checkGuess() (schrodinger.application.matsci.rxn_path.CheckInput method) checkHKLextc() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkHost() (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) checkIfNotAdsorbable() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkIfNotSimpleBond() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkin() (schrodinger.utils.license.License method) checkIndicies() (schrodinger.application.matsci.nano.check.CheckInput method) checkInitialPopulation() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkInLicenses() (schrodinger.glide.LicenseManager method) checkInoculate() (schrodinger.application.matsci.genetic_optimization.CheckInput method) CheckInput (class in schrodinger.application.matsci.genetic_optimization) (class in schrodinger.application.matsci.mecp_mod) (class in schrodinger.application.matsci.nano.check) (class in schrodinger.application.matsci.nano.particle) (class in schrodinger.application.matsci.nano.sheet) (class in schrodinger.application.matsci.nano.tube) (class in schrodinger.application.matsci.nano.xtal) (class in schrodinger.application.matsci.rxn_channel) (class in schrodinger.application.matsci.rxn_path) checkInput() (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) checkInputFile() (schrodinger.application.matsci.nano.xtal.CheckInput method) (schrodinger.application.matsci.rxn_channel.CheckInput method) checkInputFiles() (schrodinger.application.matsci.rxn_path.CheckInput method) checkInputfileTasktypeDriverpaths() (schrodinger.application.matsci.permittivity.ConfigWriter method) checkInputParams() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) (schrodinger.application.matsci.nano.xtal.Crystal method) (schrodinger.application.matsci.rxn_channel.Channels method) checkInputs() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.glide.DockingStage method) checkInterpolation() (schrodinger.application.matsci.rxn_path.CheckInput method) checkIntersectingBond() (schrodinger.application.matsci.nano.particle.Nanoparticle method) checkIsBest() (schrodinger.application.matsci.custom_lipid_prep.StretchMol method) checkJMSWFOutputs() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) checkJob() (schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelection method) checkJobName() (schrodinger.application.matsci.rxn_path.CheckInput method) checkKeywordsLE() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) checkLatticeAngleValues() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkLatticeMaxVolume() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkLatticeParameters() (schrodinger.application.matsci.nano.xtal.CheckInput method) CheckLayout (class in schrodinger.ui.qt.formlayout) checkLicense() (in module schrodinger.infra.canvas) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) checkLigands() (schrodinger.application.livedesign.entry_types.Complexes method) checkLocalDatabase() (schrodinger.protein.tasks.blast.BlastTask method) checkMaeExt() (schrodinger.application.matsci.nano.check.CheckInput method) checkMaeFile() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkMagextc() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkMatchesContained() (schrodinger.application.matsci.automated_martini_mapping_protein.Mapper method) checkMemoryLimit() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) checkMillerIndices() (schrodinger.application.matsci.nano.plane.CrystalPlane method) checkMixPrevious() (schrodinger.application.matsci.rxn_path.CheckInput method) checkMLFFLicense() (schrodinger.application.matsci.multiapp.MlffValidationMixin static method) checkModelFiles() (schrodinger.application.matsci.genetic_optimization.ChemInformatics class method) checkModule() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) checkMoleculeRings() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) checkMultipleMappings() (in module schrodinger.application.canvas.r_group) checkMultiplicity() (schrodinger.application.jaguar.gui.base_panel.ExcitedStateValidatorMixin method) checkMultiplicityProperty() (schrodinger.application.jaguar.gui.base_panel.PropertiesValidatorMixin method) checkNewCoordinate() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) checkNoRxnComplex() (schrodinger.application.matsci.rxn_path.CheckInput method) checkNumBilayers() (schrodinger.application.matsci.nano.check.CheckInput method) checkNumCells() (schrodinger.application.matsci.nano.check.CheckInput method) checkNumEntries() (schrodinger.application.livedesign.entry_types.BaseEntryData method) (schrodinger.application.livedesign.entry_types.Complexes method) checkNumRandomChannels() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkNumUnitCellParams() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkNumWalls() (schrodinger.application.matsci.nano.check.CheckInput method) checkOK() (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.Code method) (schrodinger.protein.getpdb_utility.WholePDB method) checkOperators() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkOrigin() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkOSFileLimit() (schrodinger.active_learning.al_driver.ActiveLearningJob method) checkout() (schrodinger.application.licensing.licadmin.LicenseResource method) checkout_phase_dbsearch_tokens() (in module schrodinger.application.phase.license) checkout_shape_screen_tokens() (in module schrodinger.application.phase.license) checkOutcome() (schrodinger.active_learning.al_node.LigandMLEvalNode method) (schrodinger.active_learning.al_node.LigandMLTrainNode method) (schrodinger.active_learning.al_node.PrepareSmilesNode method) (schrodinger.active_learning.al_node.ScoreProviderNode method) checkOutDocking() (schrodinger.glide.LicenseManager method) checkOutGridgen() (schrodinger.glide.LicenseManager method) checkOutputFile() (schrodinger.application.matsci.rxn_channel.Channels method) checkParameters() (schrodinger.pipeline.stage.Stage method) checkPkaAtom() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) checkPkaAtoms() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) CHECKPOINT (schrodinger.application.matsci.desconfig.MSJStringer attribute) checkpoint() (schrodinger.utils.profiling.Timer method) checkPopulationParam() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkPresumedTs() (schrodinger.application.matsci.rxn_path.CheckInput method) checkProducts() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) checkProperties() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkProperty() (schrodinger.application.matsci.genetic_optimization.Property method) checkPropertyType() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) checkPropTableForTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) checkRandomChannelsInput() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkRandomSeed() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkRandomTypes() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkRates() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkReactants() (schrodinger.application.matsci.rxn_channel.CheckInput method) checkReactions() (schrodinger.application.pathfinder.route.RouteNode method) checkReflig() (schrodinger.application.glide.ligand_designer.GridgenTask method) checkReorder() (schrodinger.application.matsci.rxn_path.CheckInput method) checkRepresentatives() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) checkRequiredProperties() (schrodinger.application.matsci.amorphous.BaseMoiety method) checkResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method) checkReverseInterpolation() (schrodinger.application.matsci.rxn_path.CheckInput method) checkRunning() (schrodinger.application.licensing.licadmin.LocalServerProcess method) checkRxnWFStructures() (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) checkSample() (schrodinger.application.matsci.rxn_path.CheckInput method) checkScaling() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkScanCoords() (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) checkSelection() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkSetTimeInterval() (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis method) (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) checkShapeParams() (schrodinger.application.matsci.nano.particle.CheckInput method) checkSizingPolicies() (schrodinger.ui.qt.table.DataViewerTable method) checkSmarts() (schrodinger.tasks.test.cli.preprocessor_cli.PreprocessorCLI method) checkSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) checkSpaceGroup() (schrodinger.application.matsci.nano.xtal.CheckInput method) CheckSpin() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkSSextc() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkSSLaue() (in module schrodinger.application.matsci.gsas.GSASIIspc) checkState() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) (schrodinger.ui.qt.tablewidget.Cell method) checkStereo() (schrodinger.infra.canvas.ChmMol method) checkStructure() (schrodinger.structutils.filter.Filter method) (schrodinger.structutils.filter.SingleFilter method) (schrodinger.structutils.filter.SinglePropFilter method) (schrodinger.structutils.filter.SingleSmartsFilter method) checkStructurePairs() (schrodinger.application.matsci.rxn_path.CheckInput method) checkStructurePrep() (in module schrodinger.ui.qt.utils) checkStructures() (schrodinger.application.matsci.rxn_path.CheckInput method) checkTargets() (schrodinger.application.livedesign.entry_types.Complexes method) checkTau() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis method) (schrodinger.application.matsci.equilibrium_md.TrjBase method) checkTermFrag() (schrodinger.application.matsci.nano.check.CheckInput method) checkTerminationParams() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkTournamentSize() (schrodinger.application.matsci.genetic_optimization.CheckInput method) checkUnsupportedTypes() (schrodinger.application.matsci.automated_cg_mapping.UnsupportedMolChecker method) checkUpToIndex() (schrodinger.application.matsci.nano.check.CheckInput method) checkUserNames() (schrodinger.application.bioluminate.propfilter.PropertySelectorWithRanges method) (schrodinger.ui.qt.propertyselector.PropertySelector method) checkUserOutputs() (schrodinger.pipeline.pipeline.Pipeline method) checkValidateSettings() (in module schrodinger.application.steps.test) checkValidOneLetterCodes() (schrodinger.application.matsci.amorphous.Moieties method) checkValidWeights() (schrodinger.application.matsci.amorphous.Moieties method) checkVel() (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis method) (schrodinger.application.matsci.equilibrium_md.TrjBase method) checkVsdbFile() (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask method) checkWallSep() (schrodinger.application.matsci.nano.check.CheckInput method) checkWeights() (in module schrodinger.trajectory.prody.ensemble) (schrodinger.application.matsci.rxn_path.CheckInput method) Chem (schrodinger.protein.helm.helm_renderer.HexColor attribute) ChemConnectorItem (class in schrodinger.protein.helm.helm_renderer) CHEMICAL_INFORMATION (schrodinger.livedesign.custom_entity.registration.EntityComponent attribute) ChemInformatics (class in schrodinger.application.matsci.genetic_optimization) ChemMonomerItem (class in schrodinger.protein.helm.helm_renderer) chemscore_clash (schrodinger.glide.ScoreDescriptors attribute) ChgAt (class in schrodinger.application.jaguar.utils) CHI (schrodinger.energy.FlucCTParamKeys attribute) child_data (schrodinger.livedesign.registration.RegistrationData attribute) child_inheritance_mode (schrodinger.application.livedesign.models2.datamodels.instance.InputInst attribute) child_inheritance_modeChanged (schrodinger.application.livedesign.models2.datamodels.instance.InputInst attribute) child_inheritance_modeReplaced (schrodinger.application.livedesign.models2.datamodels.instance.InputInst attribute) CHILD_NODE_INDEXES (schrodinger.application.matsci.permittivity.WorkflowParser attribute) ChildDataComponent (class in schrodinger.livedesign.custom_entity.registration) ChildIndentDelegate (class in schrodinger.maestro_utils.surface_manager.delegates) ChildInheritanceMode (class in schrodinger.application.livedesign.models2.datamodels.instance) children (schrodinger.application.jaguar.simple_spec.Peak attribute) CHILDREN (schrodinger.livedesign.custom_entity.registration.EntityComponent attribute) CHIRAL_FLAG_0_MEANING (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) chiral_mol (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) chiral_res (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) ChiralCenterCountFilter (class in schrodinger.application.steps.filters) ChiralCenterCountFilter.Settings (class in schrodinger.application.steps.filters) chiralCenters() (schrodinger.infra.canvas.ChmMol method) ChiralFlag0Meaning (class in schrodinger.livedesign.preprocessor) chirality (schrodinger.structure.StructureAtom property) ChiralityMismatchError chiralityString() (schrodinger.infra.structure.StructureAtom method) Chm2DCoordGen (class in schrodinger.infra.canvas) Chm2DCoordGen_assignCoordsForHiddenAtoms() (in module schrodinger.infra.canvas) Chm2DCoordGen_assignCoordsForNullAtoms() (in module schrodinger.infra.canvas) Chm2DCoordGen_assignMissingCoords() (in module schrodinger.infra.canvas) Chm2DCoordGen_center() (in module schrodinger.infra.canvas) Chm2DCoordGen_centerAndRescale() (in module schrodinger.infra.canvas) Chm2DCoordGen_checkForNAN() (in module schrodinger.infra.canvas) Chm2DCoordGen_exportCoordinatesFromMinimizer() (in module schrodinger.infra.canvas) Chm2DCoordGen_flipHorizontal() (in module schrodinger.infra.canvas) Chm2DCoordGen_flipVertical() (in module schrodinger.infra.canvas) Chm2DCoordGen_generateAndApply() (in module schrodinger.infra.canvas) Chm2DCoordGen_generateCoordinates() (in module schrodinger.infra.canvas) Chm2DCoordGen_generateFromTemplateAndApply() (in module schrodinger.infra.canvas) Chm2DCoordGen_generateFromTemplateAndApply2() (in module schrodinger.infra.canvas) Chm2DCoordGen_getBounds() (in module schrodinger.infra.canvas) Chm2DCoordGen_getScale() (in module schrodinger.infra.canvas) Chm2DCoordGen_hasCorrectScale() (in module schrodinger.infra.canvas) Chm2DCoordGen_initializeMinimizerFromMolecule() (in module schrodinger.infra.canvas) Chm2DCoordGen_isAvailable() (in module schrodinger.infra.canvas) Chm2DCoordGen_rotate() (in module schrodinger.infra.canvas) Chm2DCoordGen_rotateAbout() (in module schrodinger.infra.canvas) Chm2DCoordGen_sketcherBondStereoFromChmBond() (in module schrodinger.infra.canvas) Chm2DCoordGen_sketcherChiralityFromChmChirality() (in module schrodinger.infra.canvas) Chm2DCoordGen_translate() (in module schrodinger.infra.canvas) Chm2DCoordGen_visibleAtomsAtOrigin() (in module schrodinger.infra.canvas) chm_bluebird (class in schrodinger.application.canvas.utils) chm_excel (class in schrodinger.application.canvas.utils) CHM_FORCE2D() (in module schrodinger.infra.canvas) chm_sparse_bitset_from_string() (in module schrodinger.structutils.interactionfp) chmacos() (in module schrodinger.infra.canvas) ChmAssignments (class in schrodinger.infra.canvas) ChmAtom (class in schrodinger.infra.canvas) ChmAtomHybridizationTyper (class in schrodinger.infra.canvas) ChmAtomIterator (class in schrodinger.infra.canvas) ChmAtomOption (class in schrodinger.infra.canvas) ChmAtoms (class in schrodinger.infra.canvas) ChmAtomsAndBonds (class in schrodinger.infra.canvas) ChmAtomTyper (class in schrodinger.infra.canvas) ChmAtomTyperAlogP (class in schrodinger.infra.canvas) ChmAtomTyperEstate (class in schrodinger.infra.canvas) ChmAtomTyperEstateBinned (class in schrodinger.infra.canvas) ChmAtomTyperMR (class in schrodinger.infra.canvas) ChmAtomTyperPolarMiller (class in schrodinger.infra.canvas) ChmAtomTyperPSA (class in schrodinger.infra.canvas) ChmBitComparable32 (class in schrodinger.infra.canvas) ChmBitComparable64 (class in schrodinger.infra.canvas) ChmBitset (class in schrodinger.infra.canvas) ChmBitset64 (class in schrodinger.infra.canvas) ChmBitset64_fromBinary() (in module schrodinger.infra.canvas) ChmBitset64_fromBlob() (in module schrodinger.infra.canvas) ChmBitset64_fromHex() (in module schrodinger.infra.canvas) ChmBitset_fromBinary() (in module schrodinger.infra.canvas) ChmBitset_fromBlob() (in module schrodinger.infra.canvas) ChmBitsetIterator (class in schrodinger.infra.canvas) ChmBitsetVector (class in schrodinger.infra.canvas) ChmBond (class in schrodinger.infra.canvas) ChmBondIterator (class in schrodinger.infra.canvas) ChmBonds (class in schrodinger.infra.canvas) ChmChiralityInfo (class in schrodinger.infra.canvas) ChmClusterGrouper (class in schrodinger.infra.canvas) ChmColumnUIDFilter (class in schrodinger.infra.canvas) ChmColumnUIDFilter_fromFile() (in module schrodinger.infra.canvas) ChmCombinationOut32 (class in schrodinger.infra.canvas) ChmCombinationOut64 (class in schrodinger.infra.canvas) ChmCompressedBitset (class in schrodinger.infra.canvas) ChmCompressedBitset64 (class in schrodinger.infra.canvas) ChmCompressedBitset64_fromString() (in module schrodinger.infra.canvas) ChmCompressedBitset_fromString() (in module schrodinger.infra.canvas) ChmCompressedBitsetIterator (class in schrodinger.infra.canvas) ChmCompressedBitsetIterator64 (class in schrodinger.infra.canvas) ChmCompressedBitsetWordIterator (class in schrodinger.infra.canvas) ChmCompressedBitsetWordIterator64 (class in schrodinger.infra.canvas) ChmCoordGenOption (class in schrodinger.infra.canvas) chmcos() (in module schrodinger.infra.canvas) ChmCSVBinaryOut (class in schrodinger.infra.canvas) ChmCSVBinaryOut_parseHeader() (in module schrodinger.infra.canvas) ChmCSVBinaryOut_parseHeader64() (in module schrodinger.infra.canvas) ChmCustomMetric (class in schrodinger.infra.canvas) ChmCustomOut32 (class in schrodinger.infra.canvas) ChmCustomOut64 (class in schrodinger.infra.canvas) ChmDelimitedPatterns (class in schrodinger.infra.canvas) ChmDelimitedPatterns_getDelimiter() (in module schrodinger.infra.canvas) ChmDelimitedPatterns_getDelimiterAndQualifier() (in module schrodinger.infra.canvas) ChmDendriticOut32 (class in schrodinger.infra.canvas) ChmDendriticOut64 (class in schrodinger.infra.canvas) ChmDenseFPOut (class in schrodinger.infra.canvas) ChmDescriptorInfo (class in schrodinger.infra.canvas) ChmDescriptorMarshaler (class in schrodinger.infra.canvas) ChmDescriptorSourceMapper (class in schrodinger.infra.canvas) ChmDescriptorSourceMapper_getInfo() (in module schrodinger.infra.canvas) ChmDescriptorSourceMapper_getInfoAll() (in module schrodinger.infra.canvas) ChmDescriptorSourceMapper_sourceToString() (in module schrodinger.infra.canvas) chmendl() (in module schrodinger.infra.canvas) ChmEstateDescriptors (class in schrodinger.infra.canvas) ChmEstateKey (class in schrodinger.infra.canvas) ChmException ChmFingerprints (class in schrodinger.infra.canvas) ChmFingerprints_getRGACodes() (in module schrodinger.infra.canvas) ChmFPCombiner (class in schrodinger.infra.canvas) ChmFPCombiner64 (class in schrodinger.infra.canvas) ChmFPIn32 (class in schrodinger.infra.canvas) ChmFPIn32_isCorrectPrecision() (in module schrodinger.infra.canvas) ChmFPIn64 (class in schrodinger.infra.canvas) ChmFPIn64_isCorrectPrecision() (in module schrodinger.infra.canvas) ChmFPMap32 (class in schrodinger.infra.canvas) ChmFPMap64 (class in schrodinger.infra.canvas) ChmFPMapItem32 (class in schrodinger.infra.canvas) ChmFPMapItem64 (class in schrodinger.infra.canvas) ChmFPOut32 (class in schrodinger.infra.canvas) ChmFPOut64 (class in schrodinger.infra.canvas) ChmFPSplitter (class in schrodinger.infra.canvas) ChmFPTypeInfo (class in schrodinger.infra.canvas) ChmFPTypeInfo_areCompatible() (in module schrodinger.infra.canvas) ChmFPTypeInfo_fromFile() (in module schrodinger.infra.canvas) ChmFPWrapper (class in schrodinger.infra.canvas) ChmGasteigerCharge (class in schrodinger.infra.canvas) ChmHbond (class in schrodinger.infra.canvas) ChmHierarchicalClustering (class in schrodinger.infra.canvas) ChmKPLSParser (class in schrodinger.infra.canvas) ChmLicenseAutoQsar (class in schrodinger.infra.canvas) ChmLicenseAutoQsar_isValid() (in module schrodinger.infra.canvas) ChmLicenseElements (class in schrodinger.infra.canvas) ChmLicenseElements_isValid() (in module schrodinger.infra.canvas) ChmLicenseElementsOrFull (class in schrodinger.infra.canvas) ChmLicenseFull (class in schrodinger.infra.canvas) ChmLicenseFull_isValid() (in module schrodinger.infra.canvas) ChmLicenseFullOrMain (class in schrodinger.infra.canvas) ChmLicenseMain (class in schrodinger.infra.canvas) ChmLicenseMain_isValid() (in module schrodinger.infra.canvas) ChmLicenseMatSci (class in schrodinger.infra.canvas) ChmLicenseMatSci_isValid() (in module schrodinger.infra.canvas) ChmLicenseShared (class in schrodinger.infra.canvas) ChmLicenseShared_isValid() (in module schrodinger.infra.canvas) ChmLicenseXCluster (class in schrodinger.infra.canvas) ChmLicenseXCluster_isValid() (in module schrodinger.infra.canvas) ChmLinearOut32 (class in schrodinger.infra.canvas) ChmLinearOut64 (class in schrodinger.infra.canvas) ChmMaccsOut32 (class in schrodinger.infra.canvas) ChmMaccsOut64 (class in schrodinger.infra.canvas) ChmMatch (class in schrodinger.infra.canvas) ChmMatcherData (class in schrodinger.infra.canvas) ChmMatches (class in schrodinger.infra.canvas) ChmMatchesEx (class in schrodinger.infra.canvas) ChmMatchEx (class in schrodinger.infra.canvas) ChmMatchExIterator (class in schrodinger.infra.canvas) ChmMatchIterator (class in schrodinger.infra.canvas) ChmMatrixUnsignedInt (class in schrodinger.infra.canvas) ChmMCSRecord (class in schrodinger.infra.canvas) ChmMinimalRPParser (class in schrodinger.infra.canvas) ChmMmctAdaptor (class in schrodinger.infra.canvas) ChmMmctAdaptor_applyBondOrdersAndCharges() (in module schrodinger.infra.canvas) ChmMmctAdaptor_calculateSASA() (in module schrodinger.infra.canvas) ChmMmctAdaptor_calculateSASAByAtom() (in module schrodinger.infra.canvas) ChmMmctAdaptor_calculateVolume() (in module schrodinger.infra.canvas) ChmMmctAdaptor_collectMaeProperties() (in module schrodinger.infra.canvas) ChmMmctAdaptor_estimateRecordCount() (in module schrodinger.infra.canvas) ChmMmctAdaptor_getComponents() (in module schrodinger.infra.canvas) ChmMmctAdaptor_safeDelete() (in module schrodinger.infra.canvas) ChmMmctSmilesGenerator (class in schrodinger.infra.canvas) ChmModelParser (class in schrodinger.infra.canvas) ChmModelParser_getResultsParser() (in module schrodinger.infra.canvas) ChmModelReporter (class in schrodinger.infra.canvas) ChmModelReporter_translateCode() (in module schrodinger.infra.canvas) ChmModelTypeInfo (class in schrodinger.infra.canvas) ChmMol (class in schrodinger.infra.canvas) ChmMol_fromMAE() (in module schrodinger.infra.canvas) ChmMol_fromMDL() (in module schrodinger.infra.canvas) ChmMol_fromSMILES() (in module schrodinger.infra.canvas) ChmMolprint2D32 (class in schrodinger.infra.canvas) ChmMolprint2D64 (class in schrodinger.infra.canvas) ChmMultiYDelimitedPatterns (class in schrodinger.infra.canvas) ChmObjChmAtomImpl (class in schrodinger.infra.canvas) ChmObjChmAtomTyperImpl (class in schrodinger.infra.canvas) ChmObjChmMatcherImpl (class in schrodinger.infra.canvas) ChmObjChmQueryImpl (class in schrodinger.infra.canvas) ChmPairwiseFPIn (class in schrodinger.infra.canvas) ChmPairwiseFPOut (class in schrodinger.infra.canvas) ChmPairwiseFPOut32 (class in schrodinger.infra.canvas) ChmPairwiseFPOut64 (class in schrodinger.infra.canvas) ChmPairwiseOut32 (class in schrodinger.infra.canvas) ChmPairwiseOut64 (class in schrodinger.infra.canvas) ChmPathTools (class in schrodinger.infra.canvas) ChmPathTools_classifyAtoms() (in module schrodinger.infra.canvas) ChmPathTools_computeLaplacian() (in module schrodinger.infra.canvas) ChmPathTools_computePathsUpToLength() (in module schrodinger.infra.canvas) ChmPathTools_computeShortestPaths() (in module schrodinger.infra.canvas) ChmPathTools_deriveMapping() (in module schrodinger.infra.canvas) ChmPathTools_fuseRings() (in module schrodinger.infra.canvas) ChmPathTools_getComponentCount() (in module schrodinger.infra.canvas) ChmPathTools_getComponents() (in module schrodinger.infra.canvas) ChmPathTools_getComponentsMappings() (in module schrodinger.infra.canvas) ChmPathTools_getCoreAtoms() (in module schrodinger.infra.canvas) ChmPathTools_getDistancesToCentroid() (in module schrodinger.infra.canvas) ChmPathTools_getFeaturePaths() (in module schrodinger.infra.canvas) ChmPathTools_getmmsymLikeGroup() (in module schrodinger.infra.canvas) ChmPathTools_getShortestPathsBetweenAtoms() (in module schrodinger.infra.canvas) ChmPathTools_getShortestPathsBetweenAtomsWithSideChains() (in module schrodinger.infra.canvas) ChmPathTools_getSSSR() (in module schrodinger.infra.canvas) ChmPathTools_getSSSRAndAcyclicAtoms() (in module schrodinger.infra.canvas) ChmPathTools_getSymmetryGroups() (in module schrodinger.infra.canvas) ChmPathTools_isConnected() (in module schrodinger.infra.canvas) ChmPathTools_scoreConnections() (in module schrodinger.infra.canvas) ChmPathTools_strip() (in module schrodinger.infra.canvas) ChmPathTools_stripToScaffold() (in module schrodinger.infra.canvas) ChmPattern (class in schrodinger.infra.canvas) ChmPatterns (class in schrodinger.infra.canvas) ChmPLSParser (class in schrodinger.infra.canvas) ChmProfiler (class in schrodinger.infra.canvas) ChmProfiler_get_num_aromatic_rings() (in module schrodinger.infra.canvas) ChmProfiler_get_num_rotatable_bonds() (in module schrodinger.infra.canvas) ChmQuartetOut32 (class in schrodinger.infra.canvas) ChmQuartetOut64 (class in schrodinger.infra.canvas) ChmQuery (class in schrodinger.infra.canvas) ChmQuery_fromMDL() (in module schrodinger.infra.canvas) ChmQuery_fromMDLFile() (in module schrodinger.infra.canvas) ChmQuery_fromSMARTS() (in module schrodinger.infra.canvas) ChmQuery_fromStream() (in module schrodinger.infra.canvas) ChmQuery_validateSMARTS() (in module schrodinger.infra.canvas) ChmQueryMatcher (class in schrodinger.infra.canvas) ChmRadialOut32 (class in schrodinger.infra.canvas) ChmRadialOut64 (class in schrodinger.infra.canvas) ChmRandom (class in schrodinger.infra.canvas) ChmRandom_fromSeed() (in module schrodinger.infra.canvas) ChmRangeFilter (class in schrodinger.infra.canvas) ChmRangeFilter_fromSubFormat() (in module schrodinger.infra.canvas) ChmRangeFilter_makeFilter() (in module schrodinger.infra.canvas) ChmRangeUIDFilter (class in schrodinger.infra.canvas) ChmRangeUIDFilter_fromBlob() (in module schrodinger.infra.canvas) ChmRangeUIDFilter_fromFile() (in module schrodinger.infra.canvas) chmround() (in module schrodinger.infra.canvas) ChmRowUIDFilter (class in schrodinger.infra.canvas) ChmRowUIDFilter_fromFile() (in module schrodinger.infra.canvas) ChmScaffold (class in schrodinger.infra.canvas) ChmScaffoldFinder (class in schrodinger.infra.canvas) ChmScaffoldMatcher (class in schrodinger.infra.canvas) ChmSDReader (class in schrodinger.infra.canvas) ChmSDReader_estimateRecordCount() (in module schrodinger.infra.canvas) ChmSDReaderImpl (class in schrodinger.infra.canvas) ChmSearchKey (class in schrodinger.infra.canvas) ChmSearchKey_fromBinary() (in module schrodinger.infra.canvas) ChmSearchKey_fromHex() (in module schrodinger.infra.canvas) chmsin() (in module schrodinger.infra.canvas) ChmSMARTSOut32 (class in schrodinger.infra.canvas) ChmSMARTSOut64 (class in schrodinger.infra.canvas) ChmSmiles (class in schrodinger.infra.canvas) ChmSmilesFileReader (class in schrodinger.infra.canvas) ChmSmilesGenerator (class in schrodinger.infra.canvas) ChmSparseBitset (class in schrodinger.infra.canvas) ChmSparseBitset64 (class in schrodinger.infra.canvas) ChmSparseBitset64_createModal() (in module schrodinger.infra.canvas) ChmSparseBitset64_fromBlob() (in module schrodinger.infra.canvas) ChmSparseBitset64_fromString() (in module schrodinger.infra.canvas) ChmSparseBitset_createModal() (in module schrodinger.infra.canvas) ChmSparseBitset_fromBlob() (in module schrodinger.infra.canvas) ChmSparseBitset_fromString() (in module schrodinger.infra.canvas) ChmSymmetricMatrixUnsignedInt (class in schrodinger.infra.canvas) ChmTautomericAtomTyper (class in schrodinger.infra.canvas) ChmTopologicalTorsionOut32 (class in schrodinger.infra.canvas) ChmTopologicalTorsionOut64 (class in schrodinger.infra.canvas) chmtostring() (schrodinger.infra.canvas.ChmAssignments method) (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmAtomIterator method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmBitsetIterator method) (schrodinger.infra.canvas.ChmBond method) (schrodinger.infra.canvas.ChmBondIterator method) (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) (schrodinger.infra.canvas.ChmFPMapItem32 method) (schrodinger.infra.canvas.ChmFPMapItem64 method) (schrodinger.infra.canvas.ChmMatchExIterator method) (schrodinger.infra.canvas.ChmMatchIterator method) (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmObjChmAtomImpl method) (schrodinger.infra.canvas.ChmObjChmAtomTyperImpl method) (schrodinger.infra.canvas.ChmObjChmMatcherImpl method) (schrodinger.infra.canvas.ChmObjChmQueryImpl method) (schrodinger.infra.canvas.ChmPattern method) (schrodinger.infra.canvas.ChmRangeFilter method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) (schrodinger.infra.canvas.ChmSDReaderImpl method) (schrodinger.infra.canvas.ChmSearchKey method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.infra.canvas.ChmValueAssignment method) (schrodinger.infra.canvas.ChmValueAssignmentIterator method) ChmTripletOut32 (class in schrodinger.infra.canvas) ChmTripletOut64 (class in schrodinger.infra.canvas) ChmUniqueSmilesGenerator (class in schrodinger.infra.canvas) ChmValueAssignment (class in schrodinger.infra.canvas) ChmValueAssignmentIterator (class in schrodinger.infra.canvas) CHOICE_OFF (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) CHOICE_ON (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) choiceChanged (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector attribute) Choices (class in schrodinger.application.jaguar.workflow_keywords) choices (schrodinger.tasks.cmdline.ArgSpec attribute) CHOOSE_ATOMS (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) CHOOSE_CANONICAL_TAUTOMER (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) choose_color() (schrodinger.ui.qt.formlayout.ColorButton method) choose_ligand() (in module schrodinger.ui.chooseligand) choose_template_map() (schrodinger.application.jaguar.autots_rmsd.AutoTSTemplateAtomMapper method) chooseFromList() (schrodinger.ui.qt.propertyselector.PropertySelectorDialog method) chooseFromPT() (schrodinger.ui.qt.propertyselector.PropertySelectorDialog method) ChooseLigandDialog (class in schrodinger.ui.chooseligand) ChooseLigandModel (class in schrodinger.ui.chooseligand) chooseSolvent() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) chop() (in module schrodinger.utils.cgxutils) CHORUS_BOX_A_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_B_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BASE_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_C_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_KEY_VECTORS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) chorus_to_lower_triangle() (in module schrodinger.application.matsci.nano.xtal) (in module schrodinger.comparison.struc) ciexy_to_cie1960uv() (in module schrodinger.application.matsci.colorutils) ciexy_to_upvp() (in module schrodinger.application.matsci.colorutils) CIF (schrodinger.application.livedesign.export_tasks.FileFormat attribute) (schrodinger.infra.structure.FileFormat attribute) cion_name (schrodinger.application.matsci.packmol.SurfactantInfo attribute) cion_st (schrodinger.application.matsci.packmol.SurfactantInfo attribute) CircleAnnotator (class in schrodinger.ui.qt.structure2d) CIS (in module schrodinger.application.matsci.buildcomplex) cis_excitation_energies() (in module schrodinger.application.jaguar.textparser) CISPRO (schrodinger.ui.qt.rama.RamaResidueType attribute) cisTransBonds() (schrodinger.infra.canvas.ChmMol method) city (schrodinger.tasks.test.cli.customized_param_cli.Address attribute) cityChanged (schrodinger.tasks.test.cli.customized_param_cli.Address attribute) cityReplaced (schrodinger.tasks.test.cli.customized_param_cli.Address attribute) CL (schrodinger.protein.annotation.AntibodyRegionLabel attribute) CLASH (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) clash_iterator() (in module schrodinger.structutils.interactions.steric_clash) clash_volume() (in module schrodinger.structutils.interactions.steric_clash) ClashChecker (class in schrodinger.application.matsci.montecarlo) clashers (schrodinger.protein.protassign.utils.Interactors attribute) clashes (schrodinger.structutils.clash_resolution.ClashResolutionResult attribute) ClashResolutionResult (class in schrodinger.structutils.clash_resolution) class_evaluator (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) class_kwargs (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) CLASS_NUM (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) classandinstancemethod() (in module schrodinger.models.parameters) ClassEvaluator (class in schrodinger.application.matsci.genetic_optimization) classify_ab_assembly() (in module schrodinger.livedesign.biologics.registration) classify_antibody() (in module schrodinger.livedesign.biologics.registration) classify_nucleotide_polymer() (in module schrodinger.livedesign.biologics.registration) classify_overall_molecule() (in module schrodinger.livedesign.biologics.registration) classify_polymer() (in module schrodinger.livedesign.biologics.registration) classify_protein() (in module schrodinger.livedesign.biologics.registration) classifyAtoms() (schrodinger.infra.canvas.ChmPathTools static method) classifyMartiniFragments() (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule method) classifyNodeClusters() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) classifyRingNodeTypes() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) Clean (class in schrodinger.application.bioluminate.pml_menus) clean() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) (schrodinger.application.bioluminate.protein.protein.Refiner method) (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) clean_basisname() (in module schrodinger.application.jaguar.jaguar_keyword_utils) clean_beam_traceback() (in module schrodinger.seam.testing.fixtures) clean_beam_traceback_impl() (in module schrodinger.seam.testing.fixtures) clean_ct_properties() (schrodinger.application.desmond.cms.Cms static method) clean_st() (in module schrodinger.application.jaguar.autots_bonding) clean_string() (in module schrodinger.application.matsci.jobutils) clean_up() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) clean_up_polymer_brackets() (in module schrodinger.livedesign.preprocessor) clean_values() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) clean_xtb_input() (in module schrodinger.application.xtb.runner) cleanAndUniquify() (schrodinger.application.matsci.jobutils.StringCleaner method) cleanArrowAndPlanes() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) cleanAtomProperties() (schrodinger.application.matsci.desmondutils.SystemBuilder method) cleanBoolCheck() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) cleanFiles() (schrodinger.application.matsci.jobutils.FileDownloader method) cleanHTerminals() (schrodinger.application.matsci.automated_martini_mapping_protein.Mapper method) CleanOptionsCheckbox (class in schrodinger.application.matsci.builderwidgets) cleanPostSculpt() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) CleanStateMixin (class in schrodinger.ui.qt.widgetmixins.panelmixins) cleanStructProperties() (schrodinger.application.matsci.desmondutils.SystemBuilder method) cleanup (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) cleanup() (in module schrodinger.infra.canvas) cleanUp() (schrodinger.active_learning.mq_driver.LigandMLZMQDriver method) (schrodinger.active_learning.mq_worker.Worker method) cleanup() (schrodinger.application.glide.constraints.ConstraintGroup method) (schrodinger.application.glide.job.Dock method) (schrodinger.application.glide.job.GlideJob method) (schrodinger.application.glide.job.Gridgen method) (schrodinger.application.glide_ws.driver.GlideWSJob method) (schrodinger.application.licensing.flexlm.License method) cleanUp() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) (schrodinger.application.steps.enumerators.RouteEnumerator method) (schrodinger.application.steps.ligprep.LigPrepStep method) cleanup() (schrodinger.protein.assignment.ProtAssign method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) cleanup_after_prep_calculation() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) cleanup_external() (in module schrodinger.application.mopac.utils) cleanup_martini_protein() (in module schrodinger.application.matsci.cgforcefield) cleanup_resources() (schrodinger.structutils.minimize.Minimizer method) cleanupChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) cleanUpCompletePipelinesDir() (schrodinger.seam.viz.watcherd.Watcher method) CleanupInput (class in schrodinger.application.prepwizard2.tasks) cleanupIntermediateFiles() (schrodinger.pipeline.pipeline.Pipeline method) cleanUpPBCBonds() (schrodinger.application.matsci.nano.xtal.PBCBonds method) cleanupReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) CleanupTask (class in schrodinger.application.prepwizard2.tasks) cleanupTempFiles() (schrodinger.application.matsci.reportutils.PDFBuilder method) clear() (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.matsci.cache.BaseCacheData method) (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.phase.featureselector.FeatureSelector method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.energy.VecMetalSystem method) (schrodinger.graphics3d.common.Group method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.infra.canvas.ChmModelParser method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmQuery method) (schrodinger.infra.canvas.ChmQueryMatcher method) (schrodinger.infra.canvas.ChmSearchKey method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.Preferences method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.membrane.Membrane_Model method) (schrodinger.seam.io.jobfilesystem.JobFileSystem method) (schrodinger.structure._StructureAtomProperty method) (schrodinger.structure._StructureProperty method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) (schrodinger.ui.qt.propertyselector.PropertySelectorMenu method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) (schrodinger.ui.qt.structure2d.structure_item method) (schrodinger.ui.qt.swidgets.SFilteredListWidget method) (schrodinger.ui.qt.swidgets.SMARTSEdit method) (schrodinger.ui.qt.table_speed_up.DataCache method) (schrodinger.ui.residueselector.MutationSelectorMixin method) (schrodinger.utils.preferences.Preferences method) (schrodinger.utils.scollections.IdDict method) clear_all_tag() (schrodinger.utils.sea.sea.Sea method) clear_annotations() (in module schrodinger.livedesign.biologics.registration) (schrodinger.application.jaguar.simple_spec.Peak method) clear_annotators() (schrodinger.ui.qt.structure2d.structure_item method) clear_asu_and_fractional_properties() (in module schrodinger.application.matsci.nano.xtal) clear_autots_atom_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_bond_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_st_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_bond_arrows() (schrodinger.ui.qt.structure2d.ColoredArrowAnnotator method) clear_cache() (schrodinger.application.desmond.packages.traj.Source method) clear_glide_props() (in module schrodinger.glide) clear_global_state_file() (in module schrodinger.glide) clear_group_properties() (in module schrodinger.glide) CLEAR_INVALID_WEDGE_BONDS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) clear_layout() (in module schrodinger.ui.qt.utils) clear_ld_library_path() (in module schrodinger.application.livedesign.pse_helpers) clear_marker_properties() (in module schrodinger.application.matsci.buildcomplex) clear_model_cache() (in module schrodinger.application.matsci.ml_formulations_utils) clear_restrain() (schrodinger.application.desmond.cms.Cms method) clear_selection() (schrodinger.ui.qt.rama.Rama method) clear_structure_properties() (in module schrodinger.infra.structure) clear_wedge_bonds_from_achiral_centers() (in module schrodinger.livedesign.preprocessor) clearActions() (schrodinger.application.bioluminate.actions.factory.Factory method) clearAlignment() (schrodinger.ui.two_d_viewer.Cell method) clearAllCaching() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinAlignmentAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.protein.sequence.ProteinSequence method) clearAllConstraints() (schrodinger.application.jaguar.input.JaguarInput method) clearAllSources() (schrodinger.infra.canvas.ChmCombinationOut32 method) (schrodinger.infra.canvas.ChmCombinationOut64 method) clearAnchors() (schrodinger.protein.alignment.BaseAlignment method) clearAslText() (schrodinger.application.matsci.mswidgets.MSAtomSelector method) clearAtom() (schrodinger.ui.qt.structure2d.RedSquareAnnotator method) clearAtomicBases() (schrodinger.application.jaguar.input.JaguarInput method) clearAtomProperty() (schrodinger.infra.canvas.ChmMol method) clearAtoms() (schrodinger.ui.qt.structure2d.CircleAnnotator method) clearAutQsarModel() (schrodinger.ui.two_d_viewer.TwoDViewer method) clearBondDirectionHint() (schrodinger.infra.canvas.ChmBond method) clearBrowserText() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) clearCache() (schrodinger.application.matsci.rdpattern.Pattern method) (schrodinger.ui.qt.structtable.StructureViewerDelegate method) (schrodinger.ui.qt.table.StructureDataViewerDelegate method) clearChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) clearConfs() (schrodinger.infra.canvas.ChmMol method) clearConstraintsIfMultiStrucTab() (schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin method) clearConstraintsIfProject() (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin method) clearConstraintsIfWorkspace() (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) clearCoords() (schrodinger.infra.canvas.ChmMol method) clearData() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method) clearDataForEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) clearDataFrame() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) clearDefaultPreset() (schrodinger.models.presets.PresetManager method) clearDescriptors() (schrodinger.protein.sequence.AbstractSequence method) clearDisulfideBondsCache() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) clearEntryID() (schrodinger.infra.structure.Structure method) clearFiles() (schrodinger.infra.canvas.ChmFPCombiner method) (schrodinger.infra.canvas.ChmFPCombiner64 method) clearFilters() (schrodinger.ui.qt.filter_list.FilterListPopUp method) (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp method) (schrodinger.ui.qt.swidgets.SelectorWithPopUp method) clearFirstLevelParentChildJobs() (schrodinger.application.matsci.permittivity.WorkflowParser method) clearFromStructure() (schrodinger.infra.structure.PBC static method) clearGraph() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) (schrodinger.ui.qt.rama.Rama method) clearHoverLabel() (schrodinger.ui.qt.schart.SChartView method) clearImageCache() (schrodinger.ui.qt.delegates.PictureDelegate method) ClearInitialSuggestionLineEdit (class in schrodinger.application.livedesign.panel_components) clearJobs() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) clearLabels() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) clearLigands() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) clearMessage() (schrodinger.ui.qt.appframework2.af2.StatusBar method) clearModifications() (schrodinger.ui.qt.rdmol_views.AbstractRDMolImageLabel method) clearPfam() (schrodinger.protein.sequence.AbstractSequence method) clearPicked() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) clearProject() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) clearProperties() (schrodinger.infra.canvas.ChmMol method) clearProps() (in module schrodinger.application.matsci.equilibrium_md) clearReferenceHighlighting() (schrodinger.ui.two_d_viewer.TwoDTableModel method) clearResources() (schrodinger.application.licensing.licadmin.LocalServerProcess method) ClearResults() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) clearRowIfEmpty() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate method) clearRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) clearSelected() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) clearSelection() (schrodinger.application.livedesign.export_map_manager.MappingsComboBox method) (schrodinger.application.phase.featureselector.FeatureModel method) (schrodinger.application.phase.phase_markers.PhaseMarkers method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) clearSettings() (schrodinger.infra.mm.MMPREF method) clearSketcher() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) clearSpheres() (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager method) clearStatusMessage() (schrodinger.ui.qt.widgetmixins.basicmixins.StatusBarMixin method) clearStructs() (schrodinger.ui.qt.table.ViewerModel method) clearTable() (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.two_d_viewer.TwoDViewer method) clearTransformations() (schrodinger.ui.two_d_viewer.Cell method) clearUndoHistory() (schrodinger.ui.qt.network_visualizer.Graph method) click() (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) click_to_run (schrodinger.application.livedesign.upload_utils.CommandType attribute) ClickableLabel (class in schrodinger.ui.qt.label) clicked (schrodinger.application.job_monitor.job_monitor_table.JobDetailsArrowDelegate attribute) (schrodinger.ui.qt.delegates.PushButtonDelegate attribute) (schrodinger.ui.qt.label.ClickableLabel attribute) (schrodinger.ui.qt.tasks.taskwidgets.SpinnerLabel attribute) client (schrodinger.application.glide.http_client.AbstractGlideServerManager property) (schrodinger.application.glide.http_client.GlideServerManager property) (schrodinger.application.glide.http_client.NonBlockingGlideServerManager property) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq property) client_module (schrodinger.application.glide.http_client.GlideServerManager attribute) ClientUsage (class in schrodinger.application.licensing.licserver.entitlement_status) climb (schrodinger.application.matsci.espresso.qeinput.CustomNEBType attribute) clone() (schrodinger.application.matsci.genetic_optimization.StructureGenome method) (schrodinger.application.qsite.input.Cut method) (schrodinger.application.qsite.input.HydrogenCap method) (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmQuery method) (schrodinger.infra.canvas.ChmQueryMatcher method) (schrodinger.infra.canvas.ChmSmilesGenerator method) (schrodinger.infra.canvas.ChmUniqueSmilesGenerator method) (schrodinger.utils.sea.sea.Map method) clone_workspace_selection() (in module schrodinger.trajectory.utils) cloneProperties() (schrodinger.infra.canvas.ChmMol method) cloneWithNewCoords() (schrodinger.glide.GridArchive method) CLOSABLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) close() (in module schrodinger.ui.qt.appframework2.appmethods) (schrodinger.active_learning.bloom_filter_methods.BuiltInBloomFilter method) (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.desmond.packages.traj.Source method) (schrodinger.application.glide.utils.PoseWriter method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmDenseFPOut method) (schrodinger.infra.canvas.ChmFPOut32 method) (schrodinger.infra.canvas.ChmFPOut64 method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) (schrodinger.infra.mm.RedirectMmerrToPythonStderr method) (schrodinger.infra.structure.StructureWriter method) (schrodinger.infra.structure.TextBlockReader method) (schrodinger.infra.structure.TextBlockWriter method) (schrodinger.project.project.Project method) (schrodinger.rdkit.molio.BaseCsvMolReader method) (schrodinger.rdkit.molio.BasePfxMolReader method) (schrodinger.rdkit.molio.CsvMolWriter method) (schrodinger.rdkit.molio.PfxMolWriter method) (schrodinger.rdkit.molio.RdkitMolWriter method) (schrodinger.seam.io.filesystems.FSStructureReader method) (schrodinger.seam.io.filesystems.FSStructureWriter method) (schrodinger.structure.MaestroReader method) (schrodinger.structure.MaestroTextReader method) (schrodinger.structure.MaestroWriter method) (schrodinger.structure.MultiFileStructureWriter method) (schrodinger.structure.PDBReader method) (schrodinger.structure.PDBWriter method) (schrodinger.structure.SmilesCsvReader method) (schrodinger.structure.SmilesCsvWriter method) (schrodinger.structure.SmilesWriter method) (schrodinger.structure.StructureReader method) (schrodinger.structure.StructureWriter method) (schrodinger.utils.cgxutils.FragmentLibrary method) (schrodinger.utils.fileutils.MultiFileReader method) (schrodinger.utils.multifpfile.MultiFPFile method) (schrodinger.utils.multifpfile.MultiFPFileWriter method) (schrodinger.utils.pymol.PymolInstance method) (schrodinger.utils.pymol.PymolScriptInstance method) close_logger_file_handlers() (in module schrodinger.application.matsci.textlogger) close_output() (schrodinger.application.desmond.bennett.CalcBAR method) closeBanner (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner attribute) (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner attribute) closeBanner() (schrodinger.ui.qt.utils.MaestroPythonBannerManager method) closeBlockIfNecessary() (schrodinger.structure.Structure method) (schrodinger.structure.TextualStructure method) CloseButton (class in schrodinger.ui.qt.swidgets) CloseContact (schrodinger.protein.annotation.BINDING_SITE attribute) closed (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector attribute) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel attribute) closeEvent() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) (schrodinger.application.matsci.chargegui.ChargeDialog method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) (schrodinger.application.matsci.sliceplot.SlicePlot method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) (schrodinger.ui.qt.appframework.AppDockWidget method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.baseapp.DockWidget method) (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer method) (schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackMixin method) (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) closeFeatureEditDialog (schrodinger.application.phase.phase_markers.PhaseMarkers attribute) closeFile() (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.WholePDB method) closeFiles() (schrodinger.protein.getpdb_utility.Code method) closeKnimePanel() (schrodinger.ui.qt.appframework2.knime_af2.KnimeNodeMixin method)

closePanel() (schrodinger.application.bioluminate.pml_menus.ResultsWindow method) (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) closeWindow() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) clustal (schrodinger.utils.fileutils.SeqFormat attribute) ClustalAligner (class in schrodinger.protein.align) ClustalJob (class in schrodinger.protein.tasks.clustal) cluster (schrodinger.comparison.dedup_utils.StructureClusterPair attribute) cluster() (in module schrodinger.application.desmond.packages.analysis) (schrodinger.infra.canvas.ChmHierarchicalClustering method) (schrodinger.protein.assignment.ProtAssign method) cluster_hits() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) cluster_hits_by_features() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) cluster_hits_by_scaffold() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) ClusterAnalysisStep (class in schrodinger.application.matsci.jwsteps) ClusterBy (class in schrodinger.application.phase.shape_screen_reporter.option_utils) clusterDM() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) clusterFP() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) clustering (schrodinger.application.livedesign.upload_utils.CommandType attribute) CLUSTERING_CUTOFF (schrodinger.application.peptide_workflow.monte.MonteOptions attribute) clusterSelection() (schrodinger.glide.RefinedPoseEnsemble method) ClusterStatisticsPlotDialog (class in schrodinger.application.canvas.clustergui) CluUtil (class in schrodinger.application.macromodel.utils) CM_TO_ANGSTROM (schrodinger.application.matsci.nano.xtal.Crystal attribute) CMAP_DAT (schrodinger.infra.mm.OPLSDatafileType attribute) CMAP_TYPE (schrodinger.infra.mm.OPLSDatafileType attribute) cmd (schrodinger.application.glide_ws.nodes.Subjob attribute) (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.application.matsci.multiapp.CMD_DRIVER_DATA attribute) (schrodinger.tasks.tasks.SubprocessMixin attribute) cmd_dir (schrodinger.application.glide_ws.nodes.Subjob attribute) CMD_DRIVER_DATA (class in schrodinger.application.matsci.multiapp) CmdJobMixin (class in schrodinger.application.matsci.multiapp) CmdJobTask (class in schrodinger.tasks.jobtasks) CMDLINE (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.CallingContext attribute) CMDLINE_GEOMETRIES (in module schrodinger.application.matsci.buildcomplex) CMDLINE_TO_GEOMETRY (in module schrodinger.application.matsci.buildcomplex) cmdlist_to_cmd() (in module schrodinger.job.jobwriter) CmlFileReader (class in schrodinger.application.scaffold_enumeration.rdcml) cmp() (schrodinger.application.jaguar.results.BondCharge method) (schrodinger.application.jaguar.results.Dipole method) (schrodinger.application.jaguar.results.Orbital method) (schrodinger.application.jaguar.results.ThermoProp method) Cms (class in schrodinger.application.desmond.cms) CMS (schrodinger.application.livedesign.export_tasks.FileFormat attribute) cms (schrodinger.application.matsci.desmondutils.DesmondModel attribute) CMS (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) cms2pdb() (in module schrodinger.application.desmond.cms_utils) cms_atom() (in module schrodinger.application.desmond.packages.topo) cms_atom_index() (in module schrodinger.application.desmond.packages.topo) CMS_ENDING (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) cms_file (schrodinger.application.livedesign.tasks.Trj2maeTask.Input attribute) (schrodinger.project.project.ProjectRow property) cms_fileChanged (schrodinger.application.livedesign.tasks.Trj2maeTask.Input attribute) cms_fileReplaced (schrodinger.application.livedesign.tasks.Trj2maeTask.Input attribute) cms_model (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame attribute) CMS_PARSER (schrodinger.application.matsci.permittivity.CMSParser attribute) cms_structure_reader (schrodinger.project.project.ProjectRow property) cms_trj_optional_job_spec() (in module schrodinger.application.matsci.jobutils) cms_writer() (in module schrodinger.application.matsci.desmondutils) CmsModel (class in schrodinger.application.matsci.equilibrium_md) cmsModels() (schrodinger.ui.qt.input_selector.InputSelector method) CMSParser (class in schrodinger.application.matsci.permittivity) CN_PRESET (schrodinger.application.matsci.mlearn.features.CrystalNNFeatures attribute) CNSData (class in schrodinger.application.desmond.cns_io) COARSE (schrodinger.application.matsci.qualityslider.QualitySlider attribute) CoarseGrainBond (class in schrodinger.application.matsci.cg_mapping) CoarseGrainNameEdit (class in schrodinger.application.matsci.atomicsymbolsgui) Coc (class in schrodinger.application.desmond.packages.analysis) Code (class in schrodinger.protein.getpdb_utility) code (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.infra.canvas.ChmMCSRecord attribute) (schrodinger.protein.nonstandard_residues.AminoAcid property) col_inputs (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) col_inputsChanged (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) col_inputsReplaced (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) COL_NAMES (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame attribute) COL_NUM_POS (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis attribute) (schrodinger.application.matsci.equilibrium_md.TrajectoryFrame attribute) col_outputs (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) col_outputsChanged (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) col_outputsReplaced (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) CollagenHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) collapseAll() (schrodinger.application.matsci.mswidgets.MultiStageArea method) collapsed (schrodinger.project.project.EntryGroup property) collect_bbkeys() (in module schrodinger.application.bb_database.bb_task_utils) collect_diagnostics() (in module schrodinger.application.licensing.licserver.client) collect_unique_structures() (in module schrodinger.application.matsci.coarsegrain) collectAfterBond (schrodinger.infra.canvas.MCSsettings attribute) collectAnharmonicFrequencies() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) collectData() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) collectDiagnosticsRequested (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget attribute) collectEnergies() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) collectFits() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) collectInternals() (schrodinger.application.matsci.rxn_path.ReactionCoords method) collection() (in module schrodinger.application.scaffold_enumeration.layered) collectIonCandidates() (schrodinger.application.ligprep.ionizer.Ionizer method) collectionChanged() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) CollectJobDiagnosticsDialog (class in schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) CollectJobDiagnosticsModel (class in schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) CollectJobDiagnosticsTask (class in schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) CollectJobDiagnosticsTask.output (class in schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) collectMaeProperties() (schrodinger.infra.canvas.ChmMmctAdaptor static method) Color (class in schrodinger.structutils.color) color (schrodinger.structure.StructureAtom property) (schrodinger.surface.Surface property) (schrodinger.ui.qt.color_picker.ButtonWithColorPicker property) (schrodinger.ui.qt.formlayout.ColorButton attribute) color() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) color_arg_to_rgb() (in module schrodinger.graphics3d.common) color_atom_groups() (in module schrodinger.application.matsci.maestrocmds) color_atoms() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.matsci.maestrocmds) color_atoms_rgb() (in module schrodinger.application.bioluminate.pml_menus) color_by_element() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.matsci.maestrocmds) color_chainbow_groups() (in module schrodinger.application.bioluminate.pml_menus) color_changed (schrodinger.ui.qt.swidgets.ColorWidget attribute) COLOR_DEFAULT (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager attribute) color_dict (in module schrodinger.application.bioluminate.pml_menus) color_distance() (in module schrodinger.application.matsci.colorutils) COLOR_GRADIENT (schrodinger.seam.viz.render.ColorByTransformCPUTimeStyler attribute) color_potential_surface() (in module schrodinger.application.bioluminate.escomp) color_scheme (schrodinger.surface.Surface property) COLOR_SELECTED (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager attribute) color_source (schrodinger.surface.Surface property) color_temperature() (in module schrodinger.application.matsci.colorutils) color_text() (in module schrodinger.application.matsci.gutils) colorAtoms() (schrodinger.application.bioluminate.pml_menus.AutoColorObjects method) (schrodinger.application.bioluminate.pml_menus.AutoCycleColor method) (schrodinger.application.bioluminate.pml_menus.RegionInfo method) ColorAtomsByBFactor (class in schrodinger.application.bioluminate.pml_menus) ColorAtomsBySpectrum (class in schrodinger.application.bioluminate.pml_menus) ColorButton (class in schrodinger.ui.qt.formlayout) ColorBy (class in schrodinger.surface) ColorByElementSubMenu (class in schrodinger.application.bioluminate.pml_menus) ColorByLicenseStyler (class in schrodinger.seam.viz.render) colorByMolecule() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) colorByRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) ColorByStageStatusStyler (class in schrodinger.seam.viz.render) ColorByStatusStyler (class in schrodinger.seam.viz.render) ColorBySubstructure (class in schrodinger.application.bioluminate.pml_menus) colorByThreshold() (schrodinger.ui.qt.dendrogram.GuiPanel method) ColorByTransformCPUTimeStyler (class in schrodinger.seam.viz.render) ColorCalphasByBFactor (class in schrodinger.application.bioluminate.pml_menus) ColorCalphasBySpectrum (class in schrodinger.application.bioluminate.pml_menus) ColorCarbons (class in schrodinger.application.bioluminate.pml_menus) ColorCarbonsBySpectrum (class in schrodinger.application.bioluminate.pml_menus) ColorChainbows (class in schrodinger.application.bioluminate.pml_menus) ColorChains (class in schrodinger.application.bioluminate.pml_menus) colorChains() (schrodinger.application.bioluminate.pml_menus.ColorChains method) ColorChainsByCalpha (class in schrodinger.application.bioluminate.pml_menus) ColorChainsByCarbon (class in schrodinger.application.bioluminate.pml_menus) ColorChainSubMenu (class in schrodinger.application.bioluminate.pml_menus) colorChanged (schrodinger.ui.qt.formlayout.ColorButton attribute) ColorChooserPanel (class in schrodinger.application.bioluminate.pml_menus) ColorContext (class in schrodinger.livedesign.draw) ColorCycle (class in schrodinger.application.matsci.stylemanager) ColoredArrowAnnotator (class in schrodinger.ui.qt.structure2d) ColorFrom (class in schrodinger.surface) ColorGradients (class in schrodinger.ui.qt.standard.design_tokens) ColorHNOS (class in schrodinger.application.bioluminate.pml_menus) ColorHydrogens (class in schrodinger.application.bioluminate.pml_menus) coloring() (schrodinger.surface.Surface method) ColoringStyle (class in schrodinger.livedesign.draw) ColorLabel (class in schrodinger.application.bioluminate.pml_menus) ColorLayout (class in schrodinger.ui.qt.formlayout) ColorMenu (class in schrodinger.application.bioluminate.pml_menus) ColorObject (class in schrodinger.application.bioluminate.pml_menus) ColorPairFrame (class in schrodinger.application.matsci.reaction_workflow_gui_utils) ColorParam (class in schrodinger.ui.qt.color_picker) ColorProvider (class in schrodinger.application.matsci.stylemanager) ColorRamp (class in schrodinger.structutils.color) ColorRecentCarbons (class in schrodinger.application.bioluminate.pml_menus) ColorRecentHydrogens (class in schrodinger.application.bioluminate.pml_menus) ColorRecentObjects (class in schrodinger.application.bioluminate.pml_menus) ColorRibbonMixin (class in schrodinger.application.bioluminate.pml_menus) colors (schrodinger.application.matsci.stylemanager.ShadeDefinition attribute) COLORS (schrodinger.structutils.color.RainbowColorRamp attribute) (schrodinger.ui.qt.schart.SChart attribute) ColorScheme (class in schrodinger.structutils.color) ColorSpectrumSubMenu (class in schrodinger.application.bioluminate.pml_menus) ColorSubstructureSubMenu (class in schrodinger.application.bioluminate.pml_menus) colorSurfByPatches() (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) ColorWidget (class in schrodinger.ui.qt.swidgets) cols() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.infra.canvas.ChmPairwiseFPIn method) Column (class in schrodinger.ui.qt.table_helper) (class in schrodinger.ui.qt.tablewidget) COLUMN (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullTable attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitTable attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesModelHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.RelaxedScanCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetTableView attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute) Column (schrodinger.application.livedesign.panel_components.ExportTableModel attribute) (schrodinger.application.livedesign.panel_components.ExportTableView property) (schrodinger.application.phase.featureselector.FeatureModel attribute) (schrodinger.application.phase.phase_widgets.HypothesisModel attribute) (schrodinger.ui.picking.PickResidueModel attribute) COLUMN (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) Column (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) column (schrodinger.ui.qt.tablewidget.Cell property) column() (schrodinger.application.livedesign.panel_components.ColumnCheckboxItem method) column_count() (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) column_id (schrodinger.application.livedesign.models2.datamodels.execution_record.ColumnVar attribute) column_idChanged (schrodinger.application.livedesign.models2.datamodels.execution_record.ColumnVar attribute) column_idReplaced (schrodinger.application.livedesign.models2.datamodels.execution_record.ColumnVar attribute) column_ids (schrodinger.application.livedesign.ld_tasks.StructureInfoTask.Input attribute) column_idsChanged (schrodinger.application.livedesign.ld_tasks.StructureInfoTask.Input attribute) column_idsReplaced (schrodinger.application.livedesign.ld_tasks.StructureInfoTask.Input attribute) column_name (schrodinger.application.bioluminate.pose_filtering.csv_filter.FilterParameters attribute) COLUMN_STRETCH (schrodinger.application.matsci.stage_widgets.BaseTableWidgetDefinition attribute) COLUMN_TYPE (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUpDelegate attribute) columnActionSelected() (schrodinger.ui.two_d_viewer.TwoDViewer method) columnChanged() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) ColumnCheckboxItem (class in schrodinger.application.livedesign.panel_components) columnCount() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.table.ViewerModel method) (schrodinger.ui.qt.table_helper.RowBasedListModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) columnCountChanged() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) ColumnData (class in schrodinger.application.matsci.kmc) columnGetDataName() (schrodinger.infra.table.Table method) columnGetDataType() (schrodinger.infra.table.Table method) columnGetName() (schrodinger.infra.table.Table method) columnGetPersistent() (schrodinger.infra.table.Table method) columnGetProperty() (schrodinger.infra.table.Table method) columnGetVisible() (schrodinger.infra.table.Table method) columnGetWidth() (schrodinger.infra.table.Table method) columnHasAllSameResidues() (schrodinger.protein.alignment.BaseAlignment method) ColumnIterator (class in schrodinger.ui.qt.tablewidget) columnResized() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) COLUMNS (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.kmc.AtomsTable attribute) (schrodinger.application.matsci.kmc.FragmentsTable attribute) (schrodinger.application.matsci.kmc.FramesTable attribute) (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) (schrodinger.application.matsci.kmc.MoleculesTable attribute) (schrodinger.application.matsci.kmc.PairsTable attribute) (schrodinger.application.matsci.kmc.SchrodingerTable attribute) (schrodinger.application.matsci.kmc.SegmentsTable attribute) (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) (schrodinger.application.matsci.kmc.SuperExchangeTable attribute) (schrodinger.application.matsci.kmc.Table attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.SpectrumFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) columns (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec attribute) columns() (schrodinger.protein.alignment.BaseAlignment method) columnsChanged (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) (schrodinger.application.livedesign.summary.SummaryTableSpec attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec attribute) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec attribute) ColumnSelectionModel (class in schrodinger.application.livedesign.panel_components) ColumnSelectionProxyModel (class in schrodinger.application.livedesign.panel_components) ColumnSeries (class in schrodinger.ui.qt.mapperwidgets.plptable) columnSetName() (schrodinger.infra.table.Table method) columnSetPersistent() (schrodinger.infra.table.Table method) columnSetProperty() (schrodinger.infra.table.Table method) columnSetVisible() (schrodinger.infra.table.Table method) columnSetWidth() (schrodinger.infra.table.Table method) columnsInserted() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) columnsMoved() (schrodinger.ui.qt.table.DataViewerTable method) columnsRemoved() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) columnsReplaced (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) (schrodinger.application.livedesign.summary.SummaryTableSpec attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec attribute) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec attribute) columnStateChanged (schrodinger.ui.qt.table_helper.CheckableHeaderView attribute) ColumnVar (class in schrodinger.application.livedesign.models2.datamodels.execution_record) columnWidth() (schrodinger.ui.two_d_viewer.TwoDTableView method) Com (class in schrodinger.application.desmond.packages.analysis) com_cell_atoms() (in module schrodinger.comparison.neighbors) COM_DRX (schrodinger.application.matsci.kmc.PairsMixin attribute) COM_DRY (schrodinger.application.matsci.kmc.PairsMixin attribute) COM_DRZ (schrodinger.application.matsci.kmc.PairsMixin attribute) COMBIGLD_REPLACEMENTS (schrodinger.application.matsci.rxn_path.CheckInput attribute) Combination (class in schrodinger.application.transforms.autosar.transforms) combinations() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (schrodinger.structutils.rgroup_enumerate.RGroupEnumerator method) CombinatorialScreener (class in schrodinger.application.combinatorial_screen.combinatorial_screener) combine() (schrodinger.infra.canvas.ChmFPCombiner method) (schrodinger.infra.canvas.ChmFPCombiner64 method) combine_diverse_structures() (in module schrodinger.application.combinatorial_diversity.driver_utils) combine_fingerprints() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) combine_helm() (in module schrodinger.livedesign.biologics.registration) combine_log_files() (in module schrodinger.active_learning.mq_worker) (in module schrodinger.application.combinatorial_screen.driver_utils) combine_output_files() (in module schrodinger.rdkit.molio) combine_sentences() (in module schrodinger.application.jaguar.gui.basis_selector) combine_trajectories() (in module schrodinger.application.matsci.desmondutils) combine_two_structures() (in module schrodinger.application.matsci.genetic_optimization) combine_vdw() (in module schrodinger.application.desmond.cms) combineAndReorder() (schrodinger.application.matsci.rxn_channel.Products method) combined_reader() (in module schrodinger.application.glide_ws.utils) CombinedChainDisulfideBond (class in schrodinger.protein.residue) CombinedChainProteinAlignment (class in schrodinger.protein.alignment) CombinedChainProteinSequence (class in schrodinger.protein.sequence) CombinedChainProteinSequenceAnnotations (class in schrodinger.protein.annotation) CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES (class in schrodinger.protein.annotation) CombinedChainResidueWrapper (class in schrodinger.protein.residue) CombinedChainSequenceAnnotationMeta (class in schrodinger.protein.annotation) CombinedChainSequenceMeta (class in schrodinger.protein.sequence) combinedResForSplitRes() (schrodinger.protein.alignment.CombinedChainProteinAlignment method) CombinedRunner (class in schrodinger.application.glide.runner) combinedSeqForSplitSeq() (schrodinger.protein.alignment.CombinedChainProteinAlignment method) CombinedUi (class in schrodinger.application.jaguar.gui.tabs.base_tab) combineFunction() (schrodinger.tasks.beamtasks.BeamTask method) (schrodinger.tasks.maptasks.MapTask method) (schrodinger.tasks.maptasks.MapTaskMixin method) combineInOrder() (schrodinger.infra.canvas.ChmFPCombiner method) (schrodinger.infra.canvas.ChmFPCombiner64 method) combineMapWith() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) COMBINER (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.CombinerStep attribute) CombinerStep (class in schrodinger.application.matsci.jwsteps) CombineStage (class in schrodinger.pipeline.stages.combine) combineTrace() (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) combo (schrodinger.application.matsci.kmcgui.PlotInfo attribute) combo_find_data() (in module schrodinger.ui.qt.utils) COMBO_TEXT (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) ComboBlockingFunctionTask (class in schrodinger.tasks.tasks) COMBOBOX_ROLE (schrodinger.ui.qt.delegates.ComboBoxDelegate attribute) ComboBoxDelegate (class in schrodinger.ui.qt.delegates) ComboBoxSpec (class in schrodinger.ui.qt.mapperwidgets.plpcombobox) ComboBoxWithPopUp (class in schrodinger.ui.qt.pop_up_widgets) ComboJobMixin (class in schrodinger.tasks.jobtasks) ComboJobTask (class in schrodinger.tasks.jobtasks) ComboRadioSelector (class in schrodinger.application.jaguar.gui.tabs.theory_tab) ComboSlurmTask (class in schrodinger.tasks.slurmtasks) ComboSlurmTask.JobConfig (class in schrodinger.tasks.slurmtasks) ComboSubprocessTask (class in schrodinger.tasks.tasks) ComInfo (class in schrodinger.application.matsci.clusterstruct) Command (class in schrodinger.application.transforms.autosar.config) command() (schrodinger.application.bioluminate.pml_menus.AddHydrogens method) (schrodinger.application.bioluminate.pml_menus.AntibodyPreset method) (schrodinger.application.bioluminate.pml_menus.Around method) (schrodinger.application.bioluminate.pml_menus.AutoColorCarbons method) (schrodinger.application.bioluminate.pml_menus.AutoColorObjects method) (schrodinger.application.bioluminate.pml_menus.AutoCycleCarbonColor method) (schrodinger.application.bioluminate.pml_menus.AutoCycleColor method) (schrodinger.application.bioluminate.pml_menus.BAndSPreset method) (schrodinger.application.bioluminate.pml_menus.BFactorPreset method) (schrodinger.application.bioluminate.pml_menus.Center method) (schrodinger.application.bioluminate.pml_menus.Clean method) (schrodinger.application.bioluminate.pml_menus.ColorAtomsByBFactor method) (schrodinger.application.bioluminate.pml_menus.ColorAtomsBySpectrum method) (schrodinger.application.bioluminate.pml_menus.ColorBySubstructure method) (schrodinger.application.bioluminate.pml_menus.ColorCalphasByBFactor method) (schrodinger.application.bioluminate.pml_menus.ColorCalphasBySpectrum method) (schrodinger.application.bioluminate.pml_menus.ColorCarbons method) (schrodinger.application.bioluminate.pml_menus.ColorCarbonsBySpectrum method) (schrodinger.application.bioluminate.pml_menus.ColorChainbows method) (schrodinger.application.bioluminate.pml_menus.ColorChains method) (schrodinger.application.bioluminate.pml_menus.ColorChainsByCalpha method) (schrodinger.application.bioluminate.pml_menus.ColorChainsByCarbon method) (schrodinger.application.bioluminate.pml_menus.ColorHNOS method) (schrodinger.application.bioluminate.pml_menus.ColorHydrogens method) (schrodinger.application.bioluminate.pml_menus.ColorObject method) (schrodinger.application.bioluminate.pml_menus.ColorRecentCarbons method) (schrodinger.application.bioluminate.pml_menus.ColorRecentHydrogens method) (schrodinger.application.bioluminate.pml_menus.ColorRecentObjects method) (schrodinger.application.bioluminate.pml_menus.ComputeSurfaceArea method) (schrodinger.application.bioluminate.pml_menus.CountAtoms method) (schrodinger.application.bioluminate.pml_menus.CreateEntry method) (schrodinger.application.bioluminate.pml_menus.DefaultPreset method) (schrodinger.application.bioluminate.pml_menus.DeleteAll method) (schrodinger.application.bioluminate.pml_menus.DeleteAtoms method) (schrodinger.application.bioluminate.pml_menus.DeleteProject method) (schrodinger.application.bioluminate.pml_menus.DeleteSelections method) (schrodinger.application.bioluminate.pml_menus.DeleteWS method) (schrodinger.application.bioluminate.pml_menus.Disable method) (schrodinger.application.bioluminate.pml_menus.Duplicate method) (schrodinger.application.bioluminate.pml_menus.ExcludeFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludeInorganicFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludeOrganicFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludePolymerFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludeSolventFromSelection method) (schrodinger.application.bioluminate.pml_menus.ExcludeVisibleFromSelection method) (schrodinger.application.bioluminate.pml_menus.Expand method) (schrodinger.application.bioluminate.pml_menus.Extend method) (schrodinger.application.bioluminate.pml_menus.GenerateInterfaceSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateLigandSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateSurfResSelection method) (schrodinger.application.bioluminate.pml_menus.GenerateSymmetryMates method) (schrodinger.application.bioluminate.pml_menus.HideAllOthers method) (schrodinger.application.bioluminate.pml_menus.HideAtoms method) (schrodinger.application.bioluminate.pml_menus.HideEverything method) (schrodinger.application.bioluminate.pml_menus.HideHydrogens method) (schrodinger.application.bioluminate.pml_menus.HideLabel method) (schrodinger.application.bioluminate.pml_menus.HideMainChain method) (schrodinger.application.bioluminate.pml_menus.HideNonBonded method) (schrodinger.application.bioluminate.pml_menus.HidePolarHydrogens method) (schrodinger.application.bioluminate.pml_menus.HideRibbons method) (schrodinger.application.bioluminate.pml_menus.HideSideChain method) (schrodinger.application.bioluminate.pml_menus.HideSurface method) (schrodinger.application.bioluminate.pml_menus.HideSymmetryMates method) (schrodinger.application.bioluminate.pml_menus.HideWaters method) (schrodinger.application.bioluminate.pml_menus.IncludeInSelection method) (schrodinger.application.bioluminate.pml_menus.IncludeVisibleInSelection method) (schrodinger.application.bioluminate.pml_menus.InterfacePreset method) (schrodinger.application.bioluminate.pml_menus.LabelAtom method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByProp method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByStereo method) (schrodinger.application.bioluminate.pml_menus.LabelChains method) (schrodinger.application.bioluminate.pml_menus.LabelResidues method) (schrodinger.application.bioluminate.pml_menus.LigandPreset method) (schrodinger.application.bioluminate.pml_menus.MAction method) (schrodinger.application.bioluminate.pml_menus.MakeProjectEntry method) (schrodinger.application.bioluminate.pml_menus.MWidgetAction method) (schrodinger.application.bioluminate.pml_menus.Orient method) (schrodinger.application.bioluminate.pml_menus.Origin method) (schrodinger.application.bioluminate.pml_menus.PolarContactsObject method) (schrodinger.application.bioluminate.pml_menus.PolarContactsOnlyMainchain method) (schrodinger.application.bioluminate.pml_menus.PolarContactsOnlySidechain method) (schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyAtoms method) (schrodinger.application.bioluminate.pml_menus.PolarContactsToAnyNonSolvent method) (schrodinger.application.bioluminate.pml_menus.PolarContactsToEntry method) (schrodinger.application.bioluminate.pml_menus.PolarContactsToEntryWithoutSolvent method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutIntraMainchain method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutMainchain method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithoutSolvent method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithSidechains method) (schrodinger.application.bioluminate.pml_menus.PolarContactsWithSolvent method) (schrodinger.application.bioluminate.pml_menus.PrettyPubPreset method) (schrodinger.application.bioluminate.pml_menus.Quit method) (schrodinger.application.bioluminate.pml_menus.Ray method) (schrodinger.application.bioluminate.pml_menus.Reinitialize method) (schrodinger.application.bioluminate.pml_menus.RemoveHydrogens method) (schrodinger.application.bioluminate.pml_menus.RemovePC method) (schrodinger.application.bioluminate.pml_menus.RemoveWaters method) (schrodinger.application.bioluminate.pml_menus.Rename method) (schrodinger.application.bioluminate.pml_menus.RestrictSelection method) (schrodinger.application.bioluminate.pml_menus.RestrictToInorganic method) (schrodinger.application.bioluminate.pml_menus.RestrictToOrganic method) (schrodinger.application.bioluminate.pml_menus.RestrictToPolymer method) (schrodinger.application.bioluminate.pml_menus.RestrictToSolvent method) (schrodinger.application.bioluminate.pml_menus.RestrictToVisible method) (schrodinger.application.bioluminate.pml_menus.Select method) (schrodinger.application.bioluminate.pml_menus.SelectWithinAny method) (schrodinger.application.bioluminate.pml_menus.SelectWithinCalpha method) (schrodinger.application.bioluminate.pml_menus.SelectWithinChain method) (schrodinger.application.bioluminate.pml_menus.SelectWithinEntry method) (schrodinger.application.bioluminate.pml_menus.SelectWithinMolecule method) (schrodinger.application.bioluminate.pml_menus.SelectWithinResidue method) (schrodinger.application.bioluminate.pml_menus.ShowBAndS method) (schrodinger.application.bioluminate.pml_menus.ShowCartoonOrRibbon method) (schrodinger.application.bioluminate.pml_menus.ShowLabel method) (schrodinger.application.bioluminate.pml_menus.ShowLigandLines method) (schrodinger.application.bioluminate.pml_menus.ShowLigandSpheres method) (schrodinger.application.bioluminate.pml_menus.ShowLigandTubes method) (schrodinger.application.bioluminate.pml_menus.ShowLines method) (schrodinger.application.bioluminate.pml_menus.ShowMesh method) (schrodinger.application.bioluminate.pml_menus.ShowNonBonded method) (schrodinger.application.bioluminate.pml_menus.ShowNonBondedSpheres method) (schrodinger.application.bioluminate.pml_menus.ShowSpheres method) (schrodinger.application.bioluminate.pml_menus.ShowSurface method) (schrodinger.application.bioluminate.pml_menus.ShowTubes method) (schrodinger.application.bioluminate.pml_menus.SimplePreset method) (schrodinger.application.bioluminate.pml_menus.SumFormalCharge method) (schrodinger.application.bioluminate.pml_menus.SumPartialCharge method) (schrodinger.application.bioluminate.pml_menus.TCRPreset method) (schrodinger.application.bioluminate.pml_menus.TechnicalPreset method) (schrodinger.application.bioluminate.pml_menus.ToggleState method) (schrodinger.application.bioluminate.pml_menus.Zoom method) (schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) (schrodinger.application.glide_ws.nodes.GlideBaseNode method) (schrodinger.application.glide_ws.nodes.MMGBSAReceptorBaseNode method) (schrodinger.application.glide_ws.nodes.Node method) (schrodinger.application.glide_ws.nodes.OptimizeNode method) (schrodinger.application.glide_ws.nodes.WmapGenNode method) (schrodinger.ui.chooseligand.TestApp method) command_option (schrodinger.maestro_utils.find_tool_bar.constants.SEARCH_OPTION_DETAILS attribute) commandCallback() (schrodinger.ui.two_d_viewer.TwoDViewer method) CommandError commandify() (in module schrodinger.application.desmond.util) CommandLine (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) Commandline (schrodinger.job.jobcontrol.Job property) commandLineArgs() (schrodinger.ui.qt.config_dialog.StartDialogParams method) commandLineOptions() (schrodinger.application.jaguar.utils.GenOptions method) (schrodinger.ui.qt.config_dialog.StartDialogParams method) commands (schrodinger.maestro_utils.composer_agent.request_manager.network_manager.Response attribute) CommandType (class in schrodinger.application.livedesign.upload_utils) COMMENT (schrodinger.application.matsci.packmol.PackmolKw attribute) comment (schrodinger.infra.mm.UTT attribute) (schrodinger.infra.mm.UTTDefSpec attribute) (schrodinger.infra.mm.UTTParameter attribute) (schrodinger.infra.mm.UTTParamSpec attribute) (schrodinger.maestro_utils.composer_agent.request_manager.network_manager.UserFeedbackQuery attribute) COMMENT (schrodinger.maestro_utils.composer_agent.request_manager.urls.PostUserFeedbackPayloadKey attribute) comment (schrodinger.maestro_utils.surface_manager.surface_info.SurfaceInfo attribute) (schrodinger.surface.Surface property) commitDataToSelected (schrodinger.application.jaguar.gui.input_tab_widgets.CommitMultipleDelegate attribute) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate attribute) commitDataToSelected() (schrodinger.application.jaguar.gui.utils.ProjTableLikeView method) CommitMultipleDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) COMMON_COLUMNS (schrodinger.application.matsci.kmc.SitesMixin attribute) common_get_job_spec_from_args() (in module schrodinger.active_learning.al_driver) common_parse_args() (in module schrodinger.active_learning.al_driver) common_validate_args() (in module schrodinger.active_learning.al_driver) comp_atom_total (schrodinger.application.desmond.cms.Cms property) comp_atoms() (in module schrodinger.application.desmond.packages.topo) COMP_SCORE (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) CompactSolventSelector (class in schrodinger.application.matsci.jagwidgets) ComparableMol (class in schrodinger.rdkit.filtering) comparator() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) compare() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) compare_a_none() (in module schrodinger.application.jaguar.jaguar_diff) compare_angle() (in module schrodinger.application.jaguar.jaguar_diff) compare_base_features() (in module schrodinger.application.phase.compare_utils) compare_diff_chunks() (in module schrodinger.utils.compare) compare_diff_lines() (in module schrodinger.utils.compare) compare_float() (in module schrodinger.application.jaguar.jaguar_diff) compare_hypo_add_cts() (in module schrodinger.application.phase.compare_utils) compare_hypo_cnst() (in module schrodinger.application.phase.compare_utils) compare_hypo_masks() (in module schrodinger.application.phase.compare_utils) compare_hypo_qsar() (in module schrodinger.application.phase.compare_utils) compare_hypo_rad() (in module schrodinger.application.phase.compare_utils) compare_hypo_ref() (in module schrodinger.application.phase.compare_utils) compare_hypo_rules() (in module schrodinger.application.phase.compare_utils) compare_hypo_sites() (in module schrodinger.application.phase.compare_utils) compare_hypo_tol() (in module schrodinger.application.phase.compare_utils) compare_hypo_vol() (in module schrodinger.application.phase.compare_utils) compare_hypos() (in module schrodinger.application.phase.compare_utils) compare_molecular_formulas() (in module schrodinger.application.matsci.reorder) compare_property_wrapper() (in module schrodinger.comparison.dedup_utils) compare_screen_results() (in module schrodinger.application.phase.compare_utils) compare_sites() (in module schrodinger.application.phase.compare_utils) compare_sphere_lists() (in module schrodinger.application.phase.compare_utils) compare_spheres() (in module schrodinger.application.phase.compare_utils) compare_structure_coordinates() (in module schrodinger.application.phase.compare_utils) compare_structure_coordinates_subset() (in module schrodinger.application.phase.compare_utils) compare_transformations() (in module schrodinger.application.phase.compare_utils) ComparisonFrame (class in schrodinger.application.matsci.reordergui) ComparisonListWidget (class in schrodinger.application.matsci.reordergui) compatibleChildNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) compAtomFromRefAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) compile_instructions_for_format() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) compile_scoring_data() (in module schrodinger.application.glide_ws.entropy_score) compile_slurm() (in module schrodinger.autoinstall.slurm_install) compileDict() (schrodinger.application.glide.job.GlideJob method) compileOneToManyResults() (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) compileOneToOneResults() (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) COMPLEMENT_FN (schrodinger.protein.sequence.NucleicAcidSequence attribute) COMPLEMENT_FN() (schrodinger.protein.sequence.DNASequence static method) (schrodinger.protein.sequence.RNASequence static method) COMPLETED (schrodinger.job.jobcontrol.DisplayStatus attribute) (schrodinger.seam.viz.inspect.PipelineStatus attribute) (schrodinger.seam.viz.inspect.TransformStatus attribute) (schrodinger.tasks.slurmtasks.JobState attribute) completedJobids() (schrodinger.utils.installation_check.TestJobDJ method) CompleteLinkage (schrodinger.infra.canvas.ChmHierarchicalClustering attribute) completePolymer() (schrodinger.application.matsci.amorphous.Initiator method) CompleteSubMenu (class in schrodinger.application.bioluminate.pml_menus) COMPLETING (schrodinger.tasks.slurmtasks.JobState attribute) Complex (class in schrodinger.application.glide.poseviewconvert) (class in schrodinger.application.glide_ws.model) (class in schrodinger.application.matsci.mlearn.features) complex_allowed_keywords() (schrodinger.application.glide_ws.driver.GlideWSJob method) complex_config_spec() (schrodinger.application.glide_ws.driver.GlideWSJob method) complex_gridfiles() (schrodinger.application.glide_ws.nodes.Node method) complex_id (schrodinger.application.glide_ws.optimizer.WScoreOptimizerPose attribute) (schrodinger.application.glide_ws.optimizer.WScoreOptimizerReceptor attribute) complex_ids (schrodinger.application.glide_ws.optimizer.WScoreOptimizerEnsemble property) complex_input_prereqs() (schrodinger.application.glide_ws.nodes.GridGenNode method) (schrodinger.application.glide_ws.nodes.Node method) complex_job_generator() (schrodinger.application.glide_ws.nodes.DistributedJobMixin method) (schrodinger.application.glide_ws.nodes.GridGenNode method) (schrodinger.application.glide_ws.nodes.SerialJobMixin method) complex_ligfiles() (schrodinger.application.glide_ws.nodes.Node method) complex_name (schrodinger.application.glide_ws.optimizer.WScoreOptimizerPose attribute) (schrodinger.application.glide_ws.optimizer.WScoreOptimizerReceptor attribute) complex_names (schrodinger.application.glide_ws.model.Model property) (schrodinger.application.glide_ws.optimizer.WScoreOptimizerEnsemble property) complex_offset_iterator() (schrodinger.application.glide_ws.nodes.ComplexLoopMixin method) (schrodinger.application.glide_ws.nodes.ModelLoopMixin method) COMPLEX_PERMITTIVITY (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) COMPLEX_PERMITTIVITY_DATA_HEADER (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) COMPLEX_PERMITTIVITY_FILE_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) complex_recepfiles() (schrodinger.application.glide_ws.nodes.Node method) COMPLEX_SIZE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) complex_wmapfiles() (schrodinger.application.glide_ws.nodes.Node method) ComplexBuilder (class in schrodinger.application.matsci.buildcomplex) ComplexConformerRmsd (class in schrodinger.application.matsci.buildcomplex) ComplexDockingMover (class in schrodinger.application.peptide_workflow.moves) Complexes (class in schrodinger.application.livedesign.entry_types) complexes_are_aligned() (in module schrodinger.application.glide_ws.model) complexes_to_run() (schrodinger.application.glide_ws.nodes.ComplexLoopMixin method) (schrodinger.application.glide_ws.nodes.ModelLoopMixin method) ComplexFeatures (class in schrodinger.application.matsci.mlearn.features) ComplexLigandRxMixin (class in schrodinger.application.matsci.builderwidgets) ComplexLoopMixin (class in schrodinger.application.glide_ws.nodes) ComplexPermittivity (class in schrodinger.application.matsci.permittivity) ComplexSdfToMae (class in schrodinger.application.matsci.buildcomplex2d) ComplexSdfToMaeException ComplexSdfToRxnWF (class in schrodinger.application.matsci.buildcomplex2d) ComplexSplitter (class in schrodinger.application.matsci.buildcomplex) ComplexTemplateSketcher (class in schrodinger.application.matsci.builderwidgets) compliance_tensor (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) ComplianceTensor (class in schrodinger.application.matsci.elasticity.elastic) component (schrodinger.application.glide.visualization.HistogramComponent attribute) (schrodinger.application.matsci.kmc.MSDInfo attribute) component_name (schrodinger.application.glide.visualization.HistogramComponent attribute) component_structures() (in module schrodinger.application.desmond.struc) components (schrodinger.application.matsci.mlearn.features.MomentData attribute) ComposerAgentPanel (class in schrodinger.maestro_utils.composer_agent.composer_gui) ComposerAgentSettingsModel (class in schrodinger.maestro_utils.composer_agent.gui_models) CompositeAnalyzer (class in schrodinger.application.desmond.packages.staf) CompositeDynamicAslAnalyzer (class in schrodinger.application.desmond.packages.staf) CompositeKeySyntaxError composition (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) COMPOUND (schrodinger.application.livedesign.live_report_widget.LiveReportType attribute) compound_batches (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) CompoundParam (class in schrodinger.models.parameters) compoundparam_dill_reduce() (in module schrodinger.models.parameters) CompoundParamMeta (class in schrodinger.models.parameters) CompoundParamMixin (class in schrodinger.models.parameters) CompoundSource (class in schrodinger.application.livedesign.constants) COMPRESS (schrodinger.application.matsci.desconfig.MSJStringer attribute) compress() (in module schrodinger.pipeline.stages.glide) (in module schrodinger.pipeline.stages.ligprep) compress_structure() (in module schrodinger.application.glide_ws.db) CompressionType (class in schrodinger.rdkit_extensions) COMPRESSIVE (schrodinger.application.matsci.permittivity.MultiStageMd attribute) COMPRESSIVE_PROTOCOL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) COMPRESSIVE_RELAX (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) CompressiveRelaxationStep (class in schrodinger.application.matsci.jwsteps) CompStruc (class in schrodinger.application.desmond.struc) ComptonFac() (in module schrodinger.application.matsci.gsas.GSASIIElem) compute() (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.DiversityFingerprinter method) (schrodinger.infra.canvas.ChmProfiler method) compute_alogp() (in module schrodinger.application.medchem.property) compute_and_populate_charges() (in module schrodinger.application.matsci.clusterstruct) compute_common_check_state() (in module schrodinger.maestro_utils.surface_manager.utils) compute_cpu_times() (schrodinger.application.glide_ws.driver.GlideWSJob method) compute_data() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) compute_domain_data() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) compute_energy() (in module schrodinger.structutils.minimize) compute_esp_charges() (in module schrodinger.application.matsci.clusterstruct) compute_factor_scores() (in module schrodinger.application.combinatorial_diversity.splitter_utils) compute_filter_score() (in module schrodinger.application.combinatorial_diversity.diversity_selector) compute_max_internal_distance() (in module schrodinger.application.matsci.coarsegrain) compute_medchem_properties() (in module schrodinger.application.medchem.property) compute_mode (schrodinger.gpgpu.DeviceInfo attribute) compute_mw() (in module schrodinger.application.medchem.property) compute_num_hbond_acceptors() (in module schrodinger.application.medchem.property) compute_num_hbond_donors() (in module schrodinger.application.medchem.property) compute_num_rot_bonds() (in module schrodinger.application.medchem.property) compute_polar_surf_area() (in module schrodinger.application.medchem.property) compute_real_moment_components() (in module schrodinger.application.matsci.jaguarworkflows) compute_rmsdn() (in module schrodinger.comparison.neighbors) compute_sim_to_probes() (in module schrodinger.application.combinatorial_diversity.splitter_utils) compute_similarity() (in module schrodinger.rdkit.filtering) compute_smiles() (in module schrodinger.application.medchem.property) compute_std_conc_gibbs_energy() (in module schrodinger.application.jaguar.utils) compute_strain_energy() (in module schrodinger.glide) compute_template_data() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) compute_thermochemical_properties() (in module schrodinger.application.jaguar.thermochemical_properties) compute_tick_interval() (in module schrodinger.ui.qt.schart) compute_title() (in module schrodinger.application.medchem.property) computeBedrocForEnsemble() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) computeBindingAffinityRMSD() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) computeCapability() (schrodinger.gpgpu.CudaDevice method) computeCostFunction() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) computed_data (schrodinger.livedesign.registration.RegistrationData attribute) computeDensity() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) computeEmodels() (schrodinger.glide.RefinedPoseEnsemble method) computeLaplacian() (schrodinger.infra.canvas.ChmPathTools static method) computeMode() (schrodinger.gpgpu.CudaDevice method) ComputeNormalizedProperties (class in schrodinger.application.transforms.autosar.transforms) ComputeNormalizedPropertiesSettings (class in schrodinger.application.transforms.autosar.transforms) computeOnsagerCoefficients() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis method) computeOnsagerLambda() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis method) computePathsUpToLength() (schrodinger.infra.canvas.ChmPathTools static method) computePlaneFromAtoms() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) computePlaneFromEntry() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) ComputeRequirement (class in schrodinger.job.resource) computeScore() (schrodinger.glide.Pose method) computeShortestPaths() (schrodinger.infra.canvas.ChmPathTools static method) computeStats() (schrodinger.application.matsci.kmcgui.NeighborsTab method) ComputeSubMenu (class in schrodinger.application.bioluminate.pml_menus) ComputeSurfaceArea (class in schrodinger.application.bioluminate.pml_menus) computeTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) ComputeType (class in schrodinger.job.resource) COMTracker (class in schrodinger.application.matsci.clusterstruct) ComUtil (class in schrodinger.application.macromodel.utils) ComUtil_2010 (class in schrodinger.application.macromodel.utils) ComUtilAppSci (class in schrodinger.application.macromodel.utils) conc (schrodinger.application.jaguar.garza.SolvEntropyProps attribute) (schrodinger.application.jaguar.results.ThermoComponents attribute) concat() (in module schrodinger.application.desmond.packages.traj) CONCATENATE (schrodinger.application.matsci.desconfig.MSJStringer attribute) concatenate_logs() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.glide.utils) ConcatMSJStringer (class in schrodinger.application.matsci.desconfig) Concentration (class in schrodinger.structutils.rgroup_enumerate) concentration (schrodinger.application.jaguar.results.SolvThermoProp attribute) CONCENTRATIONS_FILE (schrodinger.application.matsci.kmc.SchrodingerTable attribute) CONCRETE (schrodinger.models.parameters.ParamType attribute) concrete_only() (in module schrodinger.models.parameters) ConcreteMetalSystem (class in schrodinger.energy) cond_1d_dist_mat() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) condensed_hosts_list() (in module schrodinger.application.glide_ws.utils) conf (schrodinger.glide.RefinedPose attribute) CONF_CLEANUP_TORSION_TYPE (schrodinger.infra.mm.OPLSDatafileType attribute) ConfFilters (class in schrodinger.application.jaguar.esol_constants) CONFGEN (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute) (schrodinger.glide.SkipReason attribute) CONFGEN_TORSION_TYPE (schrodinger.infra.mm.OPLSDatafileType attribute) Config (class in schrodinger.application.matsci.permittivity) (class in schrodinger.application.vss.config) (class in schrodinger.glide) config (schrodinger.active_learning.mq_driver.LigandMLZMQDriver property) (schrodinger.application.glide.http_client.AbstractGlideServerManager property) (schrodinger.application.glide_ws.driver.GlideWSJob property) (schrodinger.ui.qt.tasks.configwidgets.ConfigWidgetMixin property) config_ext (schrodinger.application.glide.http_client.AbstractGlideServerManager attribute) (schrodinger.application.glide.http_client.GlideServerManager attribute) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) config_file (schrodinger.application.livedesign.tasks.MultisimTask.Input attribute) config_fileChanged (schrodinger.application.livedesign.tasks.MultisimTask.Input attribute) config_fileReplaced (schrodinger.application.livedesign.tasks.MultisimTask.Input attribute) config_slurm() (in module schrodinger.autoinstall.slurm_install) config_spec() (schrodinger.application.glide_ws.driver.GlideWSJob method) ConfigDialog (class in schrodinger.ui.qt.config_dialog) (class in schrodinger.ui.qt.tasks.configwidgets) configDialogSettings() (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.knime_af2.KnimeNodeMixin method) ConfigDialogWithPlatformValidation (class in schrodinger.application.matsci.configdlgs) configuration_problem (schrodinger.infra.canvas.MCSsettings attribute) configure() (schrodinger.active_learning.al_driver.ActiveLearningJob method) (schrodinger.application.glide_ws.nodes.CrossNode method) (schrodinger.application.glide_ws.nodes.DecoysNode method) (schrodinger.application.glide_ws.nodes.GridGenNode method) (schrodinger.application.glide_ws.nodes.ModelNode method) (schrodinger.application.glide_ws.nodes.Node method) (schrodinger.application.glide_ws.nodes.SPDecoysNode method) (schrodinger.application.glide_ws.nodes.TestSetNode method) (schrodinger.application.glide_ws.nodes.WmapGenNode method) (schrodinger.glide.LoggerConfig method) configure_dise_args() (in module schrodinger.active_learning.al_utils) configure_local_ssh_setup() (in module schrodinger.utils.sshconfig) configure_mq_run() (in module schrodinger.active_learning.al_utils) configure_no_input_splitting() (in module schrodinger.active_learning.al_utils) configure_subplots() (schrodinger.ui.qt.navtoolbar.NavToolbar method) configure_taskdirs() (in module schrodinger.tasks.queue) configureBonds() (schrodinger.application.matsci.nano.particle.Nanoparticle method) configured_servers() (in module schrodinger.job.cert) configureForSystem() (schrodinger.energy.IterativeMlffModel method) configureParam() (schrodinger.application.livedesign.ld_export.ExportModel class method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel class method) (schrodinger.application.prepwizard2.tasks.PreprocessInput class method) (schrodinger.models.parameters.CompoundParam class method) CONFIGURING (schrodinger.tasks.slurmtasks.JobState attribute) ConfigWidgetMixin (class in schrodinger.ui.qt.tasks.configwidgets) ConfigWriter (class in schrodinger.application.matsci.permittivity) confirm_all_pcoll_data_deleted() (in module schrodinger.seam.testing.fixtures) ConformationalSearch (class in schrodinger.application.matsci.reaction_workflow_gui_utils) ConformationalSearchException ConformationalSearchMixin (class in schrodinger.application.matsci.reaction_workflow_utils) ConformationSampler (class in schrodinger.application.peptide_workflow.moves) Conformer (class in schrodinger.glide) conformer (schrodinger.glide.RoughPose attribute) (schrodinger.structutils.clash_resolution.ClashResolutionResult attribute) conformer_groups (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) ConformerEnsemble (class in schrodinger.glide) ConformerError ConformerRmsd (class in schrodinger.structutils.rmsd) ConformerRmsdX (class in schrodinger.structutils.rmsd) CONFORMERS_XYZ_OUT (schrodinger.application.matsci.crest.CrestCSearchJob attribute) ConformerSelection (class in schrodinger.application.matsci.reaction_workflow_gui_utils) ConformerTemplate (class in schrodinger.glide) ConfSearch (class in schrodinger.application.macromodel.input) ConfSearchStage (class in schrodinger.pipeline.stages.macromodel) conglomerate_rings() (in module schrodinger.application.canvas.r_group) connect (schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup attribute) connect() (in module schrodinger.structutils.build) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) (schrodinger.application.livedesign.login.LoginManager class method) (schrodinger.utils.qt_utils.SignalAndSlot method) connect_atoms() (in module schrodinger.application.matsci.nano.xtal) connect_close_atoms() (in module schrodinger.infra.structure) connect_job_manager_signals() (in module schrodinger.job.jobhandler) connect_signals() (in module schrodinger.ui.qt.table_helper) connect_to_livedesign() (in module schrodinger.application.livedesign.maestro_ld_connection) connect_to_workspacehub() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) connect_variable_attachment_points() (in module schrodinger.livedesign.preprocessor) connectAction() (schrodinger.application.bioluminate.actions.factory.Factory method) connectConfigDialogToTimer() (schrodinger.application.jaguar.gui.timing.TimerMixin method) CONNECTED (schrodinger.application.livedesign.ldclient_proxy.LDConnectionStatus attribute) ConnectedMoleculeChain (class in schrodinger.analysis.substructure) connectInfo (class in schrodinger.infra.canvas) connecting_atom_ids (schrodinger.application.matsci.amorphous.ConnectionInfo attribute) connectionChanged (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy attribute) ConnectionError connectionFailed (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy attribute) ConnectionInfo (class in schrodinger.application.matsci.amorphous) connections (schrodinger.livedesign.biologics.registration.BioPolymer attribute) ConnectionStorage (class in schrodinger.application.combiglide.connection_storage) ConnectionValidator (class in schrodinger.ui.qt.network_visualizer) ConnectivityAtomMapper (class in schrodinger.comparison.atom_mapper) CONNECTIVITYCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) connectNVEInitialVelocity() (schrodinger.application.matsci.permittivity.MdStageModifier method) connector_item_factory() (in module schrodinger.protein.helm.helm_renderer) connectReplicaNode() (schrodinger.application.matsci.permittivity.WorkflowParser method) connectSignal() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) connectSignalAndSlot() (schrodinger.models.mappers.TargetParamMapper method) connectSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) connectSlot() (schrodinger.application.bioluminate.actions.factory.SAction method) connectToBasicTabForUpdates() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) connectToCells() (schrodinger.application.matsci.nano.xtal.PBCBonds method) connectToJobHub() (schrodinger.application.matsci.jobdirdlg.JobManager method) connectToLD() (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) connectToLiveDesignRequested (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy attribute) connectToViewPositionTabForUpdates() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) cons_file (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cons_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) cons_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) Consensus (class in schrodinger.application.bioluminate.protein.protein) (class in schrodinger.protein.annotation) consensus_freq (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) consensus_seq (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) consensus_symbols (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) CONSENSUS_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) ConsensusConfig (class in schrodinger.application.prime.wrapper) consensusCounterions() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) consensusLigands() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) ConsensusToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) consensusWaters() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) consider() (schrodinger.math.sampling.ReservoirSampler method) considersOffBits() (in module schrodinger.infra.canvas) CONSOLV_TYPE (schrodinger.infra.mm.OPLSDatafileType attribute) const (schrodinger.tasks.cmdline.ArgSpec attribute) const_type (schrodinger.application.jaguar.utils.ScanCoord attribute) CONSTANT_PROPERTIES (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) (schrodinger.application.matsci.cgforcefield.FFIOSite attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) Constants (class in schrodinger.application.matsci.nano.constants) (class in schrodinger.application.matsci.rxn_channel) CONSTRAIN (schrodinger.application.jaguar.rotation_barriers_keywords.TSMethod attribute) constrainAll() (schrodinger.application.matsci.zmutils.ZAtom method) (schrodinger.application.matsci.zmutils.ZMatrix method) constrainAtomXYZ() (schrodinger.application.jaguar.input.JaguarInput method) constrainCoord() (schrodinger.application.matsci.zmutils.ZAtom method) constrained (schrodinger.infra.canvas.AtomData attribute) constrainInternal() (schrodinger.application.jaguar.input.JaguarInput method) Constraint (class in schrodinger.application.desmond.cms) (class in schrodinger.application.glide.constraints) (class in schrodinger.application.glide_ws.model) (class in schrodinger.forcefield.minimizer) CONSTRAINT (schrodinger.application.matsci.crest.CrestTOML attribute) constraint (schrodinger.glide.ConstraintWithAtom attribute) CONSTRAINT_FC (schrodinger.application.matsci.crest.CrestTOML attribute) CONSTRAINT_SCORE (schrodinger.protein.align.AbstractNWPairwiseAligner attribute) constraint_tuple (schrodinger.glide.RefinedPose attribute) constraint_type (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) CONSTRAINT_TYPE (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile attribute) (schrodinger.application.matsci.packmol.MicelleInputFile attribute) (schrodinger.application.matsci.packmol.MonolayerInputFile attribute) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile attribute) constraint_typeChanged (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) constraint_typeReplaced (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) ConstraintCoordinateColumns (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinateData (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesDelegate (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesModel (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesProxyModel (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) constraintCount() (schrodinger.application.jaguar.input.JaguarInput method) ConstraintError ConstraintFormatError ConstraintGroup (class in schrodinger.application.glide.constraints) (class in schrodinger.application.glide_ws.model) CONSTRAINTS (schrodinger.application.matsci.crest.CrestTOML attribute) constraints (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) (schrodinger.protein.tasks.sta.STATask.Input attribute) constraints() (schrodinger.application.jaguar.input.JaguarInput method) CONSTRAINTS_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab attribute) constraintsChanged (schrodinger.protein.tasks.sta.STATask.Input attribute) constraintsReplaced (schrodinger.protein.tasks.sta.STATask.Input attribute) ConstraintWithAtom (class in schrodinger.glide) constructHostArg() (schrodinger.job.launchparams.LaunchParameters method) consumeCommandLine() (schrodinger.job.launchparams.LaunchParameters method) CONTACT_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) ContactParams (class in schrodinger.infra.structure) Contained (schrodinger.ui.qt.pop_up_widgets.PopUpMode attribute) containmentGroup (schrodinger.infra.canvas.ChmMCSRecord attribute) CONTAINS (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.TextOperator attribute) contains() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) (schrodinger.infra.canvas.ChmScaffold method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.infra.mm.OPLSArchive method) (schrodinger.utils.preferences.Preferences method) contains_batch() (schrodinger.active_learning.bloom_filter_methods.BuiltInBloomFilter method) contains_built_in_aa() (in module schrodinger.protein.process_enamine_db) containsFuzzy() (schrodinger.infra.canvas.ChmScaffold method) containsKey() (schrodinger.infra.canvas.ChmRangeUIDFilter method) containsMultipleCores() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) content (schrodinger.application.livedesign.models2.datamodels.definition.Logic attribute) CONTENT_TYPE (schrodinger.maestro_utils.composer_agent.request_manager.urls.PostQueryRequestKeys attribute) contentChanged (schrodinger.application.livedesign.models2.datamodels.definition.Logic attribute) contentReplaced (schrodinger.application.livedesign.models2.datamodels.definition.Logic attribute) Context (class in schrodinger.tasks.taskszmq) contextMenuEvent() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) contextMenuIndicatorClicked (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator attribute) continueResBackbone() (schrodinger.application.matsci.amorphous.PolymerFragments method) continuous() (schrodinger.infra.mm.WaterMapStructure method) CONTOURS_DIR (schrodinger.application.matsci.mlearn.features.Complex attribute) contract() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) contract_by_molecule() (in module schrodinger.application.matsci.clusterstruct) contract_by_molecule2() (in module schrodinger.application.matsci.clusterstruct) contract_slab_z() (in module schrodinger.application.matsci.clusterstruct) contract_structure() (in module schrodinger.application.matsci.clusterstruct) contract_structure2() (in module schrodinger.application.matsci.clusterstruct) contract_structure_pfx() (in module schrodinger.application.matsci.clusterstruct) ControlType (class in schrodinger.application.matsci.espresso.qeinput) ConvCriteria (class in schrodinger.application.jaguar.results) ConvenientSelectorWithPopUp (class in schrodinger.application.matsci.mswidgets) converge_search() (in module schrodinger.application.macromodel.apps) converged (schrodinger.infra.mm.MinimizeResults attribute) convergence_category() (in module schrodinger.application.jaguar.textparser) CONVERGENCE_CRITERIA (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) CONVERGENCE_SCHEME_OPTS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) convergenceTypeChanged() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) CONVERSION (schrodinger.application.matsci.reaction_workflow_utils.JMSWFConformerSelection attribute) (schrodinger.application.matsci.reaction_workflow_utils.MopacConformerSelection attribute) convert() (in module schrodinger.application.glide_ws.ml_featurizer) (in module schrodinger.livedesign.convert) (schrodinger.application.matsci.etatoggle.DummyMaker method) (schrodinger.application.matsci.etatoggle.PerAtomMaker method) (schrodinger.models.adapters.abstractadapter.AbstractAdapter class method) convert2DTo3DAndMinimize() (schrodinger.application.matsci.builderwidgets.MinimizeMixin method) convert_attachment_point() (in module schrodinger.structutils.rgroup_enumerate) convert_csv_to_smi() (in module schrodinger.active_learning.al_utils) convert_diff_token_to_float() (in module schrodinger.utils.compare) convert_file() (in module schrodinger.infra.epydoc_to_sphinx) convert_flags_to_underscore() (in module schrodinger.application.glide.utils) convert_gaps_to_dots() (in module schrodinger.application.prime.wrapper) convert_gaps_to_tildes() (in module schrodinger.application.prime.wrapper) convert_gibbs_energy_to_std_conc() (in module schrodinger.application.jaguar.utils) convert_log_to_exception() (in module schrodinger.rdkit.rdkit_adapter) convert_muts_file() (in module schrodinger.application.bioluminate.mutation) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_n_features() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) convert_nm_and_wavenumber() (in module schrodinger.application.matsci.spectra) convert_old_marker_props_to_new() (in module schrodinger.application.matsci.buildcomplex) convert_path_to_unix() (in module schrodinger.utils.fileutils) convert_project_hypotheses() (in module schrodinger.application.phase.pt_hypothesis) convert_qzip_to_tar_gz_model() (in module schrodinger.active_learning.al_utils) convert_res_file() (in module schrodinger.application.bioluminate.mutation) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_res_list() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_res_to_muts() (in module schrodinger.application.bioluminate.mutation) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_residue_list() (in module schrodinger.application.bioluminate.mutation) (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) convert_sdf_to_rxnwf() (in module schrodinger.application.matsci.buildcomplex2d) convert_selenomethionines() (in module schrodinger.application.prepwizard) convert_sf_cif_to_cns() (in module schrodinger.protein.getpdb) convert_sparse_dict_to_list() (in module schrodinger.application.mopac.utils) convert_strain_to_deformation() (in module schrodinger.application.matsci.elasticity.strain) convert_string() (in module schrodinger.infra.mmim) convert_structure_sequence_for_pattern_search() (in module schrodinger.protein.sequence) convert_tar_gz_to_qzip_model() (in module schrodinger.active_learning.al_utils) convert_to_acs_label() (in module schrodinger.application.jaguar.nmr_utils) convert_to_gids() (schrodinger.application.desmond.cms.Cms method) convert_to_ieee() (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) convert_to_local_timezone() (in module schrodinger.application.job_monitor.util) convertAlternateHtoCaps() (schrodinger.application.matsci.automated_martini_mapping_protein.Mapper static method) ConvertBondsToDative (class in schrodinger.application.matsci.buildcomplex) convertCOMToAtomCluster() (schrodinger.application.matsci.clusterstruct.COMTracker method) convertMultiToOne() (schrodinger.application.matsci.equilibrium_md.MultiDriver method) convertMutsFile() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertResFile() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertResidueList() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertResList() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertResToMuts() (schrodinger.application.bioluminate.mutation.MacromoleculeMutator class method) convertSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) convertToCartesian() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) convertToClassToken() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) convertToEnv() (schrodinger.job.launchparams.LaunchParameters method) convertToJLaunchOptions() (schrodinger.job.launchparams.LaunchParameters method) convertToMMSortFieldsList() (in module schrodinger.project.project) convertToZMatrix() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) ConvertZOBToSingle (class in schrodinger.application.matsci.buildcomplex) ConvexPolyhedron (class in schrodinger.application.matsci.shapes) Coord (class in schrodinger.application.matsci.rxn_path) (class in schrodinger.tasks.test.cli.customized_cli) (class in schrodinger.ui.qt.mapperwidgets.param_editor) coord (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) coord2mae() (in module schrodinger.application.xtb.utilities) coord_in_ring() (in module schrodinger.application.jaguar.autots_bonding) COORD_LETTERS (schrodinger.application.matsci.zmutils.ZAtom attribute) COORD_NAME (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) COORD_TYPE (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) coord_type (schrodinger.application.jaguar.utils.ScanCoord attribute) coordChanged (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) COORDFILE (schrodinger.application.matsci.kmc.SegmentTypesTable attribute) Coordinate (class in schrodinger.application.jaguar.autots_bonding) COORDINATE_ANGLE_OFFSET (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_ANGLE_STEP_SIZE (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_DISTANCE_OFFSET (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_DISTANCE_STEP_SIZE (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_FUNCS (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_OPTS (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) coordinateAdded (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinateData (class in schrodinger.application.jaguar.gui.tabs.coordinates) coordinateDeleted (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) coordinateDeselected (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinateDialog (class in schrodinger.application.jaguar.gui.base_panel) CoordinateFrame (schrodinger.analysis.visanalysis.volumedata.VolumeData property) CoordinateManager (class in schrodinger.application.jaguar.hess_guess) CoordinateMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) CoordinatePicker (class in schrodinger.application.jaguar.gui.tabs.coordinates) Coordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) coordinateSelected (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinatesModel (class in schrodinger.application.jaguar.gui.tabs.coordinates) CoordinateTab (class in schrodinger.application.jaguar.gui.tabs.coordinates) coordinateTypeChanged() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker method) coordinatingAtoms() (schrodinger.application.matsci.sculptcomplex.Sculptor method) coordination (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) CoordinationInfo (class in schrodinger.application.matsci.sculptcomplex) CoordinationSite (class in schrodinger.application.matsci.siteselector.siteselector) coordReplaced (schrodinger.ui.qt.mapperwidgets.param_editor.Atom attribute) coords (schrodinger.application.matsci.espresso.qeoutput.KptLegend attribute) coords_all_zero() (in module schrodinger.livedesign.preprocessor) coords_frozen1() (in module schrodinger.application.jaguar.textparser) coords_frozen2() (in module schrodinger.application.jaguar.textparser) coords_harmonic() (in module schrodinger.application.jaguar.textparser) coords_ind() (in module schrodinger.application.jaguar.textparser) coords_nred() (in module schrodinger.application.jaguar.textparser) coords_opt() (in module schrodinger.application.jaguar.textparser) coords_outside_1st_cell() (in module schrodinger.application.matsci.nano.xtal) Copy (schrodinger.adapter.Properties attribute) (schrodinger.adapter.StereoChemistry attribute) COPY (schrodinger.ui.qt.schart.SChart attribute) copy() (in module schrodinger.infra.structure) (schrodinger.application.bioluminate.mutation.MutationSet method) (schrodinger.application.desmond.packages.traj.Frame method) (schrodinger.application.glide_ws.optimizer.WScoreOptimizerEnsemble method) (schrodinger.application.glide_ws.optimizer.WScoreOptimizerReceptor method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.PerAtomBasisRow method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow method) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) (schrodinger.application.matsci.genetic_optimization.StructureGenome method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.structure.MM_Bitset method) (schrodinger.infra.util.OneIndexedList method) (schrodinger.models.jsonable.JsonableSet method) (schrodinger.seam.io.jobfilesystem.JobFileSystem method) (schrodinger.structure.Structure method) (schrodinger.structutils.color.ColorScheme method) (schrodinger.surface.Surface method) (schrodinger.ui.qt.swidgets.STableWidgetItem method) (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.scollections.IdSet method) copy_and_compress_files() (in module schrodinger.application.desmond.util) copy_atom_constr() (in module schrodinger.application.matsci.espresso.utils) copy_atom_properties() (in module schrodinger.application.matsci.desmondutils) copy_autots_atom_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_bond_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_st_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_bonding() (in module schrodinger.application.jaguar.autots_bonding) copy_chorus_box_props() (in module schrodinger.application.matsci.nano.xtal) copy_cms_and_trj() (in module schrodinger.application.matsci.deswidgets) copy_csv_file() (in module schrodinger.rdkit.molio) copy_ct() (in module schrodinger.infra.structure) copy_custom_config_file() (in module schrodinger.utils.postinstall) copy_customized_files() (in module schrodinger.utils.postinstall) copy_file() (in module schrodinger.application.jaguar.file_logger) copy_from() (schrodinger.utils.sea.evalor.Evalor method) copy_lewis_structure_and_hydrogens() (in module schrodinger.livedesign.preprocessor) copy_maestro_properties() (in module schrodinger.infra.structure) copy_msj_and_cfg() (in module schrodinger.application.matsci.desconfig) copy_opls_archive_to_job_dir() (in module schrodinger.job.jobwriter) copy_rates_csv_to_db() (in module schrodinger.application.matsci.kmc) copy_residue_properties() (in module schrodinger.infra.structure) COPY_RESOLUTION (schrodinger.ui.qt.schart.SChart attribute) copy_sql_data() (in module schrodinger.application.matsci.kmc) copy_st_props() (in module schrodinger.application.matsci.msutils) copy_structure_bonding() (in module schrodinger.application.jaguar.utils) copy_style() (in module schrodinger.infra.structure) copy_to_autorxnwf_file() (in module schrodinger.application.matsci.reaction_workflow_utils) copyalgn() (schrodinger.application.macromodel.utils.ComUtil method) copyAllStructsIntoCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) copyAndCalculateSelfDensity() (schrodinger.glide.RefinedPoseEnsemble method) copyAndClusterSelection() (schrodinger.glide.RefinedPoseEnsemble method) copyAndComputeEmodels() (schrodinger.glide.RefinedPoseEnsemble method) copyAndCreateConstraintCopies() (schrodinger.glide.RefinedPoseEnsemble method) copyAndFilterByCoreRmsd() (schrodinger.glide.RefinedPoseEnsemble method) copyAndMinimizePoses() (schrodinger.glide.RefinedPoseEnsemble method) copyAndResampleConformers() (schrodinger.glide.RefinedPoseEnsemble method) copyAndTruncate() (schrodinger.glide.RefinedPoseEnsemble method) copyCfgFiles() (schrodinger.application.matsci.permittivity.MultiStageMd method) copyChargeMultBasisFromModel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) copyFiles() (schrodinger.application.matsci.permittivity.StepBase method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) copyImageToClipboard() (schrodinger.ui.qt.navtoolbar.NavToolbar method) (schrodinger.ui.qt.table.DataViewerTable method) copyMaskTargetIfNeeded() (schrodinger.application.matsci.jwsteps.BaseStep method) copyModelFiles() (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) copyReagentFile() (schrodinger.application.pathfinder.reaction.ReagentClass method) copyRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel method) copyStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) copyTo() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) copyToClipboard() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) (schrodinger.ui.qt.schart.SChart method) (schrodinger.ui.two_d_viewer.CellContextualMenu method) (schrodinger.ui.two_d_viewer.TwoDViewer method) copyTransformations() (schrodinger.ui.two_d_viewer.Cell method) CORE (schrodinger.glide.RotType attribute) core_atoms (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_atomsChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_atomsReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_complexity (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) core_complexityChanged (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) core_complexityReplaced (schrodinger.application.steps.filters.ProfileFilter.Settings attribute) core_constraint_smarts (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_constraint_smartsChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_constraint_smartsReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) CORE_LOCALIZATION_METHODS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) core_restraint_index (schrodinger.glide.EnergyOptions attribute) core_rmsd (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_rmsdChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_rmsdReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) core_smarts (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.SmartsFilter.Settings attribute) core_smartsChanged (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.SmartsFilter.Settings attribute) core_smartsReplaced (schrodinger.application.steps.enumerators.BaseDecorator.Settings attribute) (schrodinger.application.steps.enumerators.FastFragmenter.Settings attribute) (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) (schrodinger.application.steps.filters.SmartsFilter.Settings attribute) CoreAtomsOptions (class in schrodinger.application.livedesign.tasks) CoreDefinition (class in schrodinger.glide) cores (schrodinger.gpgpu.DeviceInfo attribute) cores() (schrodinger.gpgpu.CudaDevice method) corp_id (schrodinger.application.livedesign.export_models.GEExportItem attribute) (schrodinger.application.livedesign.export_models.MatchCompoundsBy attribute) corp_id_match_prop (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) corp_id_match_propChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) corp_id_match_propReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) corp_idChanged (schrodinger.application.livedesign.export_models.GEExportItem attribute) corp_idReplaced (schrodinger.application.livedesign.export_models.GEExportItem attribute) corp_ids (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) corp_idsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) corp_idsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask.Output attribute) correct_arginine_sidechain_charge() (in module schrodinger.protein.assignment) correct_sgroup_coordinates() (in module schrodinger.livedesign.preprocessor) corrected_mass() (in module schrodinger.application.glide_ws.entropy_score) correlation_type() (in module schrodinger.application.jaguar.textparser) CosAngle() (in module schrodinger.application.matsci.gsas.GSASIIlattice) cosd() (in module schrodinger.application.matsci.gsas.GSASIIlattice) (in module schrodinger.application.matsci.gsas.GSASIImath) (in module schrodinger.application.matsci.gsas.GSASIIpwd) COSMO (schrodinger.energy.SolventModel attribute) COSMO_PCM_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) cosolvent (schrodinger.application.desmond.struc.CompStruc attribute) CosSinAngle() (in module schrodinger.application.matsci.gsas.GSASIIlattice) coul (schrodinger.application.glide.utils.ResidueInteraction attribute) (schrodinger.glide.EnergyComponents attribute) coul_weight (schrodinger.glide.EnergyOptions attribute) (schrodinger.glide.StrainCorrectionOptions attribute) COULOMB_METHOD (schrodinger.application.matsci.desconfig.MSJStringer attribute) CoulPropagatorData (class in schrodinger.energy) count (schrodinger.active_learning.scaffold_methods.ScaffoldData attribute) (schrodinger.application.jaguar.simple_spec.Peak attribute) (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.application.licensing.licserver.entitlement_status.ClientUsage attribute) (schrodinger.application.matsci.species.SpeciesData property) COUNT (schrodinger.livedesign.custom_entity.registration.ChildDataComponent attribute) (schrodinger.livedesign.custom_entity.registration.EntityComponent attribute) count() (in module schrodinger.application.macromodel.tools) (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) (schrodinger.infra.canvas.ChmRangeFilter method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) (schrodinger.infra.canvas.ChmSearchKey method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.structure.MM_Bitset method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.ui.qt.swidgets.ActionComboBox method) count_atom_hbonds() (in module schrodinger.protein.captermini) count_clashes_of_het_state() (in module schrodinger.application.prepwizard) count_intramolecular_hbonds() (in module schrodinger.glide) count_ligands() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.hitexpander) count_lines() (in module schrodinger.utils.fileutils) count_num_strucs() (in module schrodinger.application.jaguar.gui.utils) count_protons() (in module schrodinger.application.jaguar.nmr_utils) count_residues_in_model() (in module schrodinger.livedesign.biologics.registration) count_species_in_cms() (in module schrodinger.application.matsci.clusterstructgui) count_structures() (in module schrodinger.structure) (schrodinger.application.vss.database.Database method) count_waters() (in module schrodinger.application.matsci.msutils) CountAtoms (class in schrodinger.application.bioluminate.pml_menus) countAtoms() (schrodinger.infra.structure.MoleculeGraph method) countBonds() (schrodinger.infra.structure.MoleculeGraph method) countChanged (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) countClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection static method) countCommonOff() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) countCommonOn() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) countDifference() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) Counter (class in schrodinger.application.desmond.util) counters (schrodinger.seam.metric.UserMetrics attribute) CountLayout (class in schrodinger.ui.qt.formlayout) countMetalsInBox() (schrodinger.glide.Receptor method) countNeighborsByAtomicNumber() (schrodinger.infra.canvas.ChmAtom method) countRoots() (in module schrodinger.pipeline.pipeutils) counts_file (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) counts_fileChanged (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) counts_fileReplaced (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) counts_to_formula() (in module schrodinger.application.matsci.atomicsymbols) countStructures() (schrodinger.infra.structure.MaeReader static method) (schrodinger.infra.structure.MmpdbxReader static method) (schrodinger.infra.structure.StructureReader static method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.structure_selector.StructureSelector method) coupler (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) COUPLER_AT_ORIGIN (schrodinger.application.matsci.amorphous.BaseMoiety attribute) coupler_marker (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) COUPLING_COLUMNS (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) (schrodinger.application.matsci.kmc.PairsTable attribute) couplings (schrodinger.application.jaguar.nmr_utils.NMRData attribute) CouplingStrength (class in schrodinger.application.jaguar.nmr_interactions) COV_FACTOR (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) COV_MIN (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) COV_OFFSET (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) CovalentDockingComplexes (class in schrodinger.application.livedesign.entry_types) covdock_inp_file (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) covdock_inp_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) covdock_inp_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Input attribute) covdock_opts (schrodinger.application.livedesign.tasks.CovDockTask attribute) CovDockTask (class in schrodinger.application.livedesign.tasks) CovDockTask.Input (class in schrodinger.application.livedesign.tasks) CovDockTask.JobConfig (class in schrodinger.application.livedesign.tasks) CovDockTask.Output (class in schrodinger.application.livedesign.tasks) CPCM_PCM_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) Cpu (schrodinger.energy.MlffDeviceType attribute) CPU (schrodinger.job.resource.ComputeType attribute) CPU_AND_GPU (schrodinger.tasks.jobtasks.AllowedHostTypes attribute) CPU_AND_GPU_PLACEHOLDER_ARG (schrodinger.tasks.jobtasks.HostSettings attribute) cpu_count (schrodinger.gpgpu.MIGInfo attribute) CPU_ONLY (schrodinger.tasks.jobtasks.AllowedHostTypes attribute) CPU_PLACEHOLDER_ARG (schrodinger.tasks.jobtasks.HostSettings attribute) cpu_time (schrodinger.seam.viz.inspect.PipelineDisplayInfo attribute) cpu_time() (in module schrodinger.application.jaguar.textparser) CPU_UNIT_LABEL (schrodinger.application.matsci.configdlgs.PerStrucConfigDialog attribute) (schrodinger.application.matsci.configdlgs.PerStrucSingleGpuConfigDialog attribute) (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) cpus (schrodinger.application.jaguar.gui.timing.TimingResults.PER_ENTRY_DATA attribute) cpus3Edited() (schrodinger.ui.qt.config_dialog.ConfigDialog method) cputime (schrodinger.seam.viz.inspect.TransformDisplayInfo attribute) cputime_seconds (schrodinger.seam.metric.ExecutionMetrics attribute) CPUTransform (class in schrodinger.seam.testing.test_pipelines) CPUTYPE (schrodinger.tasks.hosts.Host attribute) cradius (schrodinger.application.matsci.elementalprops.ElementalProperties property) crankshaft_move() (in module schrodinger.application.peptide_workflow.moves) crankshaft_move_for_complex_cycles() (in module schrodinger.application.peptide_workflow.moves) CREATE (schrodinger.application.livedesign.mapping_widgets.MappingMode attribute) create() (schrodinger.application.matsci.desconfig.BarrierInfo class method) (schrodinger.application.matsci.kmc.Table method) (schrodinger.energy.AomComplex static method) (schrodinger.energy.DummyComplex static method) (schrodinger.energy.LfmmComplex static method) (schrodinger.energy.MorseComplex static method) (schrodinger.infra.canvas.ChmMmctAdaptor method) (schrodinger.infra.mm.OPLSArchive static method) (schrodinger.infra.structure.MM_Bitset method) (schrodinger.seam.io.jobfilesystem.JobFileSystem method) create_2d_img() (in module schrodinger.application.livedesign.two_d_render) create_acc_db() (in module schrodinger.autoinstall.slurm_install) create_action_menu() (in module schrodinger.application.bioluminate.pml_menus) create_alignment_from_chains() (in module schrodinger.protein.sequence) create_archive_file() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.licserver.client) create_archive_from_oplsdir() (in module schrodinger.forcefield.custom_params) create_argument_parser() (in module schrodinger.utils.cmdline) create_autots_template_file() (in module schrodinger.application.jaguar.hydrokinetic_input) create_biounits() (in module schrodinger.ui.qt.pdb_dialog) create_blast_db() (in module schrodinger.protein.gpcr.update_gpcr_db) create_bonds() (in module schrodinger.application.bioluminate.antibody.assembly) create_center_of_mass_info() (in module schrodinger.application.matsci.clusterstruct) create_cg_molecule_name() (in module schrodinger.application.matsci.coarsegrain) create_cg_system() (in module schrodinger.application.matsci.cgforcefield) create_child_group() (in module schrodinger.project.utils) create_chmmol_from_structure() (in module schrodinger.application.matsci.deprecated_pattern) create_clib_archive() (in module schrodinger.application.combinatorial_screen.driver_utils) create_cluster_hypo() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) create_colorbyele_menu() (in module schrodinger.application.bioluminate.pml_menus) create_combined_ab_data() (in module schrodinger.livedesign.biologics.registration) create_config_dir() (in module schrodinger.utils.postinstall) create_conformer_files_and_config() (in module schrodinger.application.peptide_workflow.driver_utils) create_conn() (in module schrodinger.protein.gpcr.sql) create_constraint_supporting_info() (in module schrodinger.glide) create_cpu_and_gpu_hosts() (in module schrodinger.job.queue) create_cpu_gpu_queue() (in module schrodinger.application.matsci.jobutils) create_csv() (in module schrodinger.application.livedesign.io_utils) create_database() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) create_debug_logger() (in module schrodinger.application.matsci.textlogger) create_dimer_structures() (in module schrodinger.application.matsci.clusterstruct) create_directories() (in module schrodinger.glide) create_distance_cell() (in module schrodinger.application.matsci.clusterstruct) (in module schrodinger.structutils.measure) (in module schrodinger.structutils.ringspear) create_disulfide_bonds() (in module schrodinger.application.prepwizard) create_empty_ffio_block() (in module schrodinger.application.desmond.cms_utils) create_entry_database() (in module schrodinger.protein.gpcr.update_gpcr_db) create_epv_from_lib() (in module schrodinger.application.glide_ws.utils) create_fluc_ct_calculators_and_guesses() (in module schrodinger.energy) create_fragment_structure() (in module schrodinger.structutils.rgroup_enumerate) create_frame_from_coords() (in module schrodinger.application.desmond.packages.traj) create_glycosylation_bonds() (in module schrodinger.application.prepwizard) create_guesses() (in module schrodinger.application.jaguar.input) create_hard_link() (in module schrodinger.utils.fileutils) create_hbond_clusters_from_changeables() (in module schrodinger.protein.protassign.hbond_cluster) create_hide_menu() (in module schrodinger.application.bioluminate.pml_menus) create_hybrid() (schrodinger.protein.protassign.hbond_cluster.hbond_cluster method) create_hypo (schrodinger.application.phase.input.InputSpecs attribute) create_icon_button() (in module schrodinger.application.matsci.gutils) create_interaction_distance() (in module schrodinger.utils.pymol) create_interactions_group() (in module schrodinger.utils.pymol) create_invalid_structure() (schrodinger.infra.structure.Structure static method) create_isosurface_from_grid_data() (in module schrodinger.surface) create_iterative_mlff() (in module schrodinger.energy) create_job() (in module schrodinger.application.matsci.jaguarworkflows) create_job_spec_function() (in module schrodinger.application.matsci.jobutils) create_jobs_table() (in module schrodinger.application.glide_ws.db) create_label_menu() (in module schrodinger.application.bioluminate.pml_menus) create_lid() (in module schrodinger.application.livedesign.ld_glide_utils) create_ligands_table() (in module schrodinger.application.glide_ws.db) create_live_report() (in module schrodinger.application.livedesign.export_tasks) create_logger() (in module schrodinger.application.matsci.textlogger) create_minimizer_if_needed() (in module schrodinger.application.matsci.msminimize) create_mlff() (in module schrodinger.energy) CREATE_MODE_PAGE (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUp attribute) create_modify_menu() (in module schrodinger.application.bioluminate.pml_menus) create_module() (schrodinger.infra.unusable_module_importer.UnusableModuleLoader class method) create_movie (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) create_movieChanged (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) create_movieReplaced (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) create_msj() (in module schrodinger.application.matsci.desconfig) create_nearest_neighbor_cluster() (in module schrodinger.application.matsci.clusterstruct) CREATE_NEW (schrodinger.ui.qt.recent_completer.BrowseAndCreateStringModel attribute) create_new_box() (in module schrodinger.application.matsci.nano.xtal) create_new_database() (in module schrodinger.application.bb_database.bb_task_utils) create_new_structure() (in module schrodinger.structure) create_non_pbc_cluster() (in module schrodinger.application.matsci.clusterstruct) create_nonbonded_extents() (in module schrodinger.application.matsci.nano.xtal) create_normal() (in module schrodinger.graphics3d.common) create_nx_graph() (in module schrodinger.structutils.analyze) create_oligomer() (in module schrodinger.application.matsci.mlearn.descriptor) create_palmitoylation_bonds() (in module schrodinger.application.prepwizard) create_pbc() (in module schrodinger.application.matsci.clusterstruct) (in module schrodinger.structutils.ringspear) create_peptide_files_and_config() (in module schrodinger.application.peptide_workflow.driver_utils) create_pi_cation_interaction_distance() (in module schrodinger.utils.pymol) create_pi_pi_interaction_distance() (in module schrodinger.utils.pymol) create_polymer_name() (in module schrodinger.application.matsci.polymer) create_poses_table() (in module schrodinger.application.glide_ws.db) create_postmortem() (in module schrodinger.application.livedesign.io_utils) create_postmortem_args() (in module schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) create_properties_table() (in module schrodinger.application.glide_ws.db) create_queue() (in module schrodinger.application.matsci.jobutils) CREATE_RADIOBUTTON_NAMES (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) create_reactant_files() (in module schrodinger.application.combinatorial_screen.driver_utils) create_reactant_fp_file() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) create_reagent_library() (in module schrodinger.application.pathfinder.synthesis) create_registration_data() (in module schrodinger.livedesign.biologics.registration) create_restart_jobcmd() (in module schrodinger.application.matsci.jobutils) create_restart_launcher() (in module schrodinger.application.matsci.jobutils) create_rotated_complexes() (in module schrodinger.application.matsci.etarotamers) create_run_dir() (in module schrodinger.application.matsci.jobutils) create_selection() (in module schrodinger.utils.pymol) create_show_menu() (in module schrodinger.application.bioluminate.pml_menus) create_show_organic_menu() (in module schrodinger.application.bioluminate.pml_menus) create_show_substructure_menu() (in module schrodinger.application.bioluminate.pml_menus) create_sim_cormat() (in module schrodinger.application.combinatorial_diversity.splitter_utils) create_smap() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) create_structure() (in module schrodinger.infra.structure) create_structures_table() (in module schrodinger.application.glide_ws.db) create_stub_license() (in module schrodinger.application.licensing.licadmin) create_subgroup() (in module schrodinger.project.utils) create_subjob() (in module schrodinger.application.matsci.jobutils) create_surface() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.bioluminate.surfcomp) create_surface_from_void() (in module schrodinger.application.matsci.freevolume) create_task() (schrodinger.application.livedesign.tasks.AbHumanizationTask class method) (schrodinger.application.livedesign.tasks.AbModelingTask class method) (schrodinger.application.livedesign.tasks.AlignLigandsTask class method) (schrodinger.application.livedesign.tasks.CanvasSearchTask class method) (schrodinger.application.livedesign.tasks.CovDockTask class method) (schrodinger.application.livedesign.tasks.EpikClassicTask class method) (schrodinger.application.livedesign.tasks.EpikTask class method) (schrodinger.application.livedesign.tasks.EventAnalysisTask class method) (schrodinger.application.livedesign.tasks.FFBuilderTask class method) (schrodinger.application.livedesign.tasks.FlexAlignTask class method) (schrodinger.application.livedesign.tasks.GlideTask class method) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask class method) (schrodinger.application.livedesign.tasks.LigandStrainTask class method) (schrodinger.application.livedesign.tasks.LigFilterTask class method) (schrodinger.application.livedesign.tasks.LigPrepTask class method) (schrodinger.application.livedesign.tasks.MCSDockingTask class method) (schrodinger.application.livedesign.tasks.MemPermTask class method) (schrodinger.application.livedesign.tasks.MultisimTask class method) (schrodinger.application.livedesign.tasks.PeptideDockingTask class method) (schrodinger.application.livedesign.tasks.PhaseScreenTask class method) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask class method) (schrodinger.application.livedesign.tasks.QikPropTask class method) (schrodinger.application.livedesign.tasks.RBSSTask class method) (schrodinger.application.livedesign.tasks.StrainRescoreTask class method) (schrodinger.application.livedesign.tasks.Trj2maeTask class method) (schrodinger.application.livedesign.tasks.TugAlignTask class method) create_term_data_table() (in module schrodinger.application.glide_ws.db) create_user_hypo() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) create_workflows() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) create_wscore_database_tables() (in module schrodinger.application.glide_ws.db) create_xvol (schrodinger.application.phase.input.InputSpecs attribute) createActions() (schrodinger.application.bioluminate.actions.factory.Factory method) createAlignFile() (schrodinger.application.bioluminate.protein.protein.PrimeStructure method) createAllGrowthSpaces() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) createAllReactions() (schrodinger.application.matsci.fragments.FragmentReactor method) createArrow() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) createAttachmentItems() (schrodinger.application.livedesign.export_models.FFCExportSpec method) createAxis() (schrodinger.ui.qt.schart.SChart method) createBaseParser() (schrodinger.tasks.param_cli.ParamCLI method) createBasicStructure() (schrodinger.application.matsci.sculptcomplex.Sculptor method) createBeadForManyOutboundNodes() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMapper method) createBeadForTwoOutboundNodes() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMapper method) createBeadsFromFragment() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMapper method) createBottomBar() (schrodinger.ui.qt.appframework2.af2.App method) (schrodinger.ui.qt.appframework2.af2.JobApp method) createCell() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) createCGStruct() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder method) createChargeProperties() (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) createCmd() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) createCommand() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) createComplex() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) createConformers() (schrodinger.application.matsci.reaction_workflow_utils.ConformationalSearchMixin method) createConstraintCopies() (schrodinger.glide.RefinedPoseEnsemble method) createControlButtons() (schrodinger.application.matsci.mswidgets.StageFrame method) createCriterionForProp() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) createCycleMappings() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) createDimer() (schrodinger.application.matsci.buildcomplex.DimerComplexBuilder method) createDisplayModeWidgets() (schrodinger.application.matsci.stage_widgets.BaseTogglableCellWidget method) createDummies() (schrodinger.application.matsci.etatoggle.DummyMaker method) createEdge() (schrodinger.ui.qt.network_views.NetworkViewer method) createEditableFrame() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) createEditModeWidgets() (schrodinger.application.matsci.stage_widgets.BaseTogglableCellWidget method) createEditor() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBoxDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate method) (schrodinger.ui.qt.delegates.CheckboxDelegate method) (schrodinger.ui.qt.delegates.ComboBoxDelegate method) (schrodinger.ui.qt.delegates.MatplotlibDelegate method) (schrodinger.ui.qt.delegates.MouseTrackingDelegateMixin method) (schrodinger.ui.qt.delegates.ProgressBarDelegate method) (schrodinger.ui.qt.delegates.SketcherDelegate method) (schrodinger.ui.qt.delegates.SpinBoxDelegate method) (schrodinger.ui.qt.delegates.WorkspaceInclusionDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate method) createElementsToken() (in module schrodinger.infra.canvas) createEndSubFragment() (schrodinger.application.matsci.amorphous.PolymerFragments method) CreateEntry (class in schrodinger.application.bioluminate.pml_menus) createExcludedVolumeClash() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createExcludedVolumeReceptor() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createExcludedVolumeShell() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createFamilies() (schrodinger.ui.qt.propertyselector.PropertySelector method) createFragForInitiator() (schrodinger.application.matsci.amorphous.PolymerFragments method) createFromSize() (schrodinger.infra.structure.MM_Bitset static method) createGroupMapping() (schrodinger.application.matsci.automated_cg_mapping.StructData method) createGuessZeros() (schrodinger.energy.FlucCTCalculator method) createImportWidget() (schrodinger.application.bioluminate.bwidgets.ImportWidget method) CreateInpFile() (schrodinger.application.livedesign.tasks.CovDockTask method) createInputSelector() (schrodinger.ui.qt.appframework2.af2.App method) createInputSt2() (schrodinger.application.matsci.permittivity.AnalyzeSimulation method) createInterfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) createIter() (schrodinger.application.bioluminate.interaction_calculator.PiStackFinder class method) createJob() (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) createJobDir() (schrodinger.ui.qt.appframework2.af2.JobApp method) createLabel() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) createLabels() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.SmallMoleculeTorsions method) createLigandStructures() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) CreateLike() (in module schrodinger.analysis.visanalysis.volumedatautils) createLipidSkeleton() (schrodinger.application.matsci.custom_lipid_prep.FindHeadTail method) createMatMinerDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createMenus() (schrodinger.ui.qt.appframework.AppFramework method) createMimic() (schrodinger.application.matsci.clusterstruct.COMTracker method) createModal() (schrodinger.infra.canvas.ChmSparseBitset static method) (schrodinger.infra.canvas.ChmSparseBitset64 static method) createModifiedGuess() (schrodinger.application.jaguar.input.JaguarInput method) CreateMols (class in schrodinger.seam.yaml.transforms) createMols() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createMorganDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createMSJ() (schrodinger.application.matsci.permittivity.MultiStageMd method) createNewGroup() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) (schrodinger.project.project.Project method) createNewSelected (schrodinger.ui.qt.recent_completer.BrowseAndCreateCombo attribute) createNewSipTerm() (schrodinger.application.glide_ws.scoring_report.WScoreSipTerm static method) createNewSite() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder method) createObject() (schrodinger.graphics3d.tube.MaestroTube method) CreateOrEditMappingsDialog (class in schrodinger.application.livedesign.mapping_widgets) CreateOrEditMappingsModel (class in schrodinger.application.livedesign.mapping_widgets) createPixmaps() (schrodinger.ui.qt.swidgets.SValidIndicator method) createPlane() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) createPolymerDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createProductGroups() (schrodinger.application.matsci.fragments.FragmentReactor method) createQJobFromCommand() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) createRawTrainingCsvFile() (schrodinger.active_learning.al_node.LigandMLTrainNode method) createRdkitDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) createReactantTracker() (schrodinger.application.matsci.fragments.FragmentReactor method) createReorderedEntry() (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) CreateReplicates (class in schrodinger.application.peptide_workflow.beam_adapter) createResourceHost() (schrodinger.job.queue.JobDJ static method) createRestraints() (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints method) createRotatedStructures() (schrodinger.application.matsci.etarotamers.HapticLigand method) CreateScreeningDBTask (class in schrodinger.application.phase.shape_screen_reporter.tasks) CreateScreeningDBTask.Input (class in schrodinger.application.phase.shape_screen_reporter.tasks) createSection() (schrodinger.application.jaguar.input.JaguarInput method) createSegmentInfo() (schrodinger.application.matsci.custom_lipid_prep.RenumberLipid method) createSequence() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) createSketcher() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) createSlab() (schrodinger.application.matsci.sliceplot.SlicePlot method) createSmilesStructure() (schrodinger.structure.SmilesReader method) createSourceLayout() (schrodinger.ui.qt.structure_selector.StructureSelector method) createStage() (schrodinger.pipeline.pipeline.Pipeline method) createStateReactions() (schrodinger.application.matsci.fragments.FragmentReactor method) createStereoStructure() (schrodinger.application.matsci.custom_lipid_prep.SetStereochemistry method) createString() (schrodinger.application.matsci.desconfig.MSJStringer method) CreateStructures (class in schrodinger.seam.yaml.transforms) createSubsetForCompsWithoutSites() (schrodinger.pipeline.stages.phase.DBConfSitesStage method) createSubWidgets() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) createSurfaces() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) createTemplateFile() (schrodinger.application.bioluminate.protein.protein.PrimeStructure method) createTextSequence() (schrodinger.application.bioluminate.pml_menus.AntibodyPreset method) createTip4pFfio() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) createTopFrame() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) createTrendLine() (schrodinger.ui.qt.schart.SeriesData method) createUniqueElement() (schrodinger.application.matsci.espresso.utils.MagSpecies method) createViewFrame() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) CreateWhenNeeded (class in schrodinger.infra.util) createWidget() (schrodinger.application.matsci.wfmanagement.BaseWorkflowFinderDialog method) (schrodinger.application.matsci.wfmanagement.WorkflowFinderDialog method) (schrodinger.application.matsci.wfmanagement.WorkflowManagerDialog method) createWidgets() (schrodinger.application.matsci.stage_widgets.RowFrame method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.StringCriterion method) CREATION_COMMAND (schrodinger.application.matsci.kmc.Table attribute) creator (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) CREATOR (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) creatorChanged (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) creatorReplaced (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) CREDENTIALS (schrodinger.application.livedesign.login_gui2.AuthenticationMode attribute) credentials_host (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) credentials_hostChanged (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) credentials_hostReplaced (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) Crest (class in schrodinger.application.matsci.crest) CrestCSearch (class in schrodinger.application.matsci.crest) CrestCSearchJob (class in schrodinger.application.matsci.crest) CrestException CrestJob (class in schrodinger.application.matsci.crest) CrestTOML (class in schrodinger.application.matsci.crest) criteriaChanged (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget attribute) CriteriaLayout (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) CriteriaListModel (class in schrodinger.application.bioluminate.propfilter) (class in schrodinger.ui.ligfilter) Criterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_core) (class in schrodinger.utils.ligfilter) criterion_changed (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector attribute) CRITERION_CHOICES (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion attribute) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolCriterion attribute) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion attribute) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.StringCriterion attribute) criterionChanged (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion attribute) criterionChanged() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) CriterionParser (class in schrodinger.utils.ligfilter) criterionTypeChanged() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion method) critical_points() (schrodinger.application.jaguar.discretized_1d_function.DiscretelySampledFunction method) criticalEllipse() (in module schrodinger.application.matsci.gsas.GSASIIlattice) CriticalPointsFailure cross() (schrodinger.infra.mm.Cartesian method) cross_angle (schrodinger.application.bioluminate.mhc.docking_angles.DescriptiveAngles attribute) cross_libfile (schrodinger.application.glide_ws.model.Model property) CROSSHAIR_COLOR (schrodinger.ui.qt.rama.RamaContourMixin attribute) CROSSHAIR_LINEWIDTH (schrodinger.ui.qt.rama.RamaContourMixin attribute) CrossNode (class in schrodinger.application.glide_ws.nodes) crossover (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) crossprod() (in module schrodinger.application.desmond.cms) CrsAng() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Crystal (class in schrodinger.application.matsci.nano.xtal) CRYSTAL (schrodinger.application.matsci.kmc.SchrodingerTable attribute) CRYSTAL_ENVIRON (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) CRYSTAL_SYSTEM (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) crystal_system (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) CRYSTAL_SYSTEM_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) CRYSTAL_SYSTEMS (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute) CRYSTAL_VECTOR (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) crystal_water (schrodinger.application.desmond.struc.CompStruc attribute) CrystalData (class in schrodinger.comparison.dedup_utils) CrystalNNFeatures (class in schrodinger.application.matsci.mlearn.features) CrystalPlane (class in schrodinger.application.matsci.nano.plane) crystals_are_duplicates() (in module schrodinger.comparison.dedup_utils) CrystalSystems (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Cubic (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Hexagonal (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Monoclinic (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Orthorhombic (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Tetragonal (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Triclinic (class in schrodinger.application.matsci.nano.space_groups) CrystalSystems.Trigonal (class in schrodinger.application.matsci.nano.space_groups) crystalVectorPicked() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) CS2 (schrodinger.energy.Solvent attribute) CS_METHOD (class in schrodinger.application.jaguar.csrch_input_constants) csearchEngineChanged() (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch method) CSPAtomMapper (class in schrodinger.comparison.atom_mapper) CSPError CSTART (schrodinger.application.matsci.cgforcefield.FFIODihedral attribute) (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) csv (schrodinger.application.livedesign.io_utils.SupportedFormats attribute) (schrodinger.utils.fileutils.SeqFormat attribute) csv_file (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) csv_fileChanged (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) csv_filename (schrodinger.application.glide_ws.model.Model property) csv_fileReplaced (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) CSV_HEADER_3D (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) CSV_HEADER_AXIS (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) CSV_HEADER_PLANE (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) csv_index (schrodinger.active_learning.mq_driver.Worker attribute) csv_mol_reader_class (schrodinger.rdkit.molio.PfxMolIterator attribute) (schrodinger.rdkit.molio.PfxMolReader attribute) CSV_OUT_EXT (schrodinger.application.matsci.permittivity.JaguarMerge attribute) csv_writer_mode (schrodinger.application.glide_ws.nodes.MMGBSANode attribute) (schrodinger.application.glide_ws.nodes.MMGBSATestsetNode attribute) CsvColumn (class in schrodinger.tasks.ldi) CsvMergeHandler (class in schrodinger.rdkit.molio) CsvMolIterator (class in schrodinger.rdkit.molio) CsvMolReader (class in schrodinger.rdkit.molio) CsvMolWriter (class in schrodinger.rdkit.molio) CsvSmilesFile (class in schrodinger.application.vss.csvsmiles) ct_to_multipart() (schrodinger.application.glide.http_client.AbstractHTTPClient method) CtAssertion CTerm (schrodinger.protein.annotation.GPCRSegmentLabel attribute) CtException CtMsgException ctPropertiesChanged (schrodinger.ui.two_d_viewer.CtPropsDialog attribute) CtPropsDialog (class in schrodinger.ui.two_d_viewer) CtRdrException Cube (class in schrodinger.application.matsci.shapes) Cubeoctahedron (class in schrodinger.application.matsci.shapes) cubic() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) CUBIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) Cuda (schrodinger.energy.MlffDeviceType attribute) CudaDevice (class in schrodinger.gpgpu) CURRENT (schrodinger.trajectory.trajectory_gui_dir.display_settings_data.DisplayOnly attribute) current_file (schrodinger.ui.qt.input_selector.InputSelector attribute) current_filename (schrodinger.structure.MultiFileStructureReader attribute) CURRENT_FRAME_WITH_COMPONENT_CTS (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute) current_job (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_jobChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_jobReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) CURRENT_MAGNITUDE_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_MAGNITUDE_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) current_opls_metadata() (in module schrodinger.infra.mm) current_progress (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) current_progress_display() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) current_progressChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) current_progressReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) current_project_jobs_only (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_jobs_onlyChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_jobs_onlyReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_name (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_nameChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_project_nameReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_source (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) current_sourceChanged (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) current_sourceReplaced (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) current_top_level_job (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_top_level_jobChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) current_top_level_jobReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) CURRENT_VAL (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) CURRENT_X_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_X_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_Y_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_Y_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_Z_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) CURRENT_Z_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) currentCategory() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) currentChoice() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) currentCriterion() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) currentData() (schrodinger.ui.qt.swidgets.SComboBox method) currentDBInfo() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) currentDir (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) currentFrameOnly() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) currentFrameWithComponentStructures() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) currentHost() (schrodinger.ui.qt.config_dialog.ConfigDialog method) currentIndex() (schrodinger.ui.qt.formlayout.CountLayout method) (schrodinger.ui.qt.formlayout.RadioLayout method) currentIndexChanged (schrodinger.ui.qt.swidgets.SComboBox attribute) currentLabel() (schrodinger.ui.qt.swidgets.STabWidget method) currentPanel() (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard method) currentProjectID() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) currentProjectName() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) currentProjectSelector() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) currentScheme() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) currentSelection (schrodinger.ui.qt.datamapper.MappableButtonGroup attribute) currentSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.clusterstructgui.SpeciesCombo method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) currentText() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) currsize (schrodinger.application.matsci.cache.CacheInfo attribute) curvatures() (schrodinger.surface.Surface method) CUSTOM (schrodinger.application.livedesign.tasks.CoreAtomsOptions attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) Custom (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) (schrodinger.protein.nonstandard_residues.StructureSource attribute) CUSTOM (schrodinger.protein.tasks.blast.BlastDatabase attribute) Custom (schrodinger.ui.qt.appframework2.jobnames.JobnameType attribute) (schrodinger.ui.two_d_viewer.DpiMode attribute) custom() (in module schrodinger.ui.qt.appframework2.appmethods) custom_aln (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) custom_alnChanged (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) custom_alnReplaced (schrodinger.protein.tasks.hit_align.CustomFamilyTask.Input attribute) custom_annotation (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) CUSTOM_CLASS_FILE_OPTION (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) custom_color_dicts (in module schrodinger.application.bioluminate.pml_menus) custom_config_file_exists() (in module schrodinger.utils.postinstall) custom_database_path (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastSettings attribute) custom_database_pathChanged (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastSettings attribute) custom_database_pathReplaced (schrodinger.protein.gpcr.tasks.GPCRTask.Input attribute) (schrodinger.protein.tasks.blast.BlastSettings attribute) custom_dpi (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) custom_dpiChanged (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) custom_dpiReplaced (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) CUSTOM_ENTITY (schrodinger.rdkit_extensions.Format attribute) custom_fasta_file (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) custom_fasta_fileChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) custom_fasta_fileReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) custom_functional() (in module schrodinger.application.jaguar.textparser) CUSTOM_HYPO_TEXT (schrodinger.application.phase.featureselector.FeatureModel attribute) custom_is_list() (in module schrodinger.application.inputconfig) custom_is_string_list() (in module schrodinger.application.inputconfig) custom_menu_item() (in module schrodinger.ui.qt.appframework2.appmethods) CUSTOM_MSJ (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) custom_path (schrodinger.infra.mm.FfldSpec attribute) CUSTOM_RESOLUTION_INDEX (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) CUSTOM_SELECTION (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute) custom_text (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_text_final (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_text_finalChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_text_finalReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_textChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_textReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) custom_weight (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) custom_weightChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) custom_weightReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) CUSTOM_WIDGET_INDEX (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) CustomAngles (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) CustomASLStructureAligner (class in schrodinger.protein.align) CustomClassEvaluator (class in schrodinger.application.matsci.genetic_optimization) CustomCmsStep (class in schrodinger.application.matsci.jwsteps) CustomCmsToMaeStep (class in schrodinger.application.matsci.jwsteps) CustomColor (class in schrodinger.application.bioluminate.pml_menus) CustomConfigFiles (class in schrodinger.utils.postinstall) customDirChanged (schrodinger.application.matsci.builderwidgets.TemplateManager attribute) CustomDisplaySettings (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings) CustomExternalForce (schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.MockOpenMM attribute) CustomFamilyTask (class in schrodinger.protein.tasks.hit_align) CustomFamilyTask.Input (class in schrodinger.protein.tasks.hit_align) CustomFileDialog (class in schrodinger.ui.qt.filedialog) customize() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) CustomizedCLI (class in schrodinger.tasks.test.cli.customized_cli) customizeFuncResult() (schrodinger.utils.funcchains.FuncChainMarker method) customizeInputAndCommand() (schrodinger.application.matsci.permittivity.JaguarCalculation method) customizeParamArgs() (schrodinger.tasks.ldi.LDI method) (schrodinger.tasks.param_cli.ParamCLI method) (schrodinger.tasks.test.cli.customized_cli.CustomizedCLI method) (schrodinger.tasks.test.cli.customized_param_cli.UserCLI method) customizeParser() (schrodinger.tasks.ldi.LDI method) (schrodinger.tasks.param_cli.ParamCLI method) (schrodinger.tasks.test.cli.customized_cli.CustomizedCLI method) CustomLipidPrep (class in schrodinger.application.matsci.custom_lipid_prep) CustomLipidPrepException CustomListWidgetItem (class in schrodinger.application.matsci.builderwidgets) CustomMaeStep (class in schrodinger.application.matsci.jwsteps) CustomMaestroAnalysis (class in schrodinger.application.desmond.packages.staf) CustomMaeToCmsStep (class in schrodinger.application.matsci.jwsteps) CustomMDType (class in schrodinger.application.matsci.espresso.qeinput) CustomNEBType (class in schrodinger.application.matsci.espresso.qeinput) customOPLSDir() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) customOPLSDirForModel() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) customOPLSPathChanged (schrodinger.ui.qt.forcefield.ffglobalpreferencewidget.FFGlobalPreferenceWidget attribute) customProcessParsedArgs() (schrodinger.tasks.ldi.LDI method) (schrodinger.tasks.param_cli.ParamCLI method) (schrodinger.tasks.test.cli.customized_cli.CustomizedCLI method) CustomProgressBar (class in schrodinger.ui.qt.appframework) CustomRecentColor (class in schrodinger.application.bioluminate.pml_menus) CustomResMutationSelectorFrame (class in schrodinger.ui.residueselector) CustomResMutationSelectorMixin (class in schrodinger.ui.residueselector) CustomResMutationSelectorPopUp (class in schrodinger.ui.residueselector) CustomScoringFunction (class in schrodinger.application.glide.sort_utils) CustomScriptLine (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) CustomSideBarMixin (class in schrodinger.ui.qt.filedialog) CustomToolbar (class in schrodinger.application.matsci.density_analysis_widget) CustomTorsionForce (schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.MockOpenMM attribute) CustomTrajectoryStep (class in schrodinger.application.matsci.jwsteps) Cut (class in schrodinger.application.qsite.input) CUT20 (schrodinger.application.jaguar.results.InputDeviation attribute) cut20 (schrodinger.application.jaguar.results.NofailResult attribute) cutAwayExcess() (schrodinger.application.matsci.nano.particle.Nanoparticle method) Cutoff (class in schrodinger.application.transforms.autosar.util) cutoff (schrodinger.application.matsci.espresso.qeinput.FreePositionsType.PWallType attribute) (schrodinger.comparison.results.OptResultSet property) CUTOFF_COMBO_ITEMS (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) cutoff_config_filename() (schrodinger.application.glide_ws.nodes.ModelNode method) CUTOFF_RADIUS (schrodinger.application.matsci.desconfig.MSJStringer attribute) cutoff_server_logfile() (schrodinger.application.glide_ws.nodes.ModelNode method) cutoffChanged (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider attribute) cutoffChanged() (schrodinger.application.matsci.kmcgui.NeighborsTab method) cutOutNanoSheet() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) Cv (schrodinger.application.jaguar.results.ThermoCollection attribute) cv (schrodinger.application.matsci.espresso.qeoutput.PhDOS.Thermo attribute) cvdw_coeff (schrodinger.application.glide.sort_utils.CustomScoringFunction attribute) CVECTOR (schrodinger.application.matsci.kmc.SchrodingerTable attribute) CYAN() (in module schrodinger.utils.color) cycle() (schrodinger.ui.qt.swidgets.SpinnerIcon method) cycle_feature_flag() (in module schrodinger.application.matsci.mstest) cycle_shades() (in module schrodinger.application.matsci.stylemanager) Cylinder (class in schrodinger.application.matsci.shapes) Cytosine (schrodinger.protein.helm.helm_renderer.HexColor attribute)

D

D (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) (schrodinger.application.bioluminate.update_germline_db.translate_db.Gene attribute) D1d (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) D3Dispersion (schrodinger.energy.MlffFixedInteractionType attribute) DAminoAcidMonomerItem (class in schrodinger.protein.helm.helm_renderer) DARK_BLUE (schrodinger.application.matsci.stylemanager.SolidColors attribute) DARK_GRAY (schrodinger.application.matsci.stylemanager.SolidColors attribute) (schrodinger.ui.qt.standard.colors.NativeColors attribute) darken_colors_by_cavity_depth (schrodinger.surface.Surface property) DarkModeColors (class in schrodinger.ui.qt.standard.colors) DarkRed (schrodinger.protein.helm.helm_renderer.HexColor attribute) Data (class in schrodinger.application.canvas.r_group) (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) data (schrodinger.application.matsci.coarsegrain.InternalInfo attribute) (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) (schrodinger.comparison.results.OptResultSet property) DATA (schrodinger.job.util.DirectoryType attribute) data (schrodinger.ui.qt.radial_plot.Sector attribute) data() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.livedesign.panel_components.EndpointSelectionModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) (schrodinger.ui.qt.network_visualizer.Edge method) (schrodinger.ui.qt.recent_completer.SeparatorStringModel method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) (schrodinger.ui.qt.table_helper.DataMethodDecoratorMixin method) (schrodinger.ui.qt.table_helper.DataMethodDecoratorProxyMixin method) (schrodinger.ui.qt.table_helper.PtRowBasedTableModel method) (schrodinger.ui.qt.table_speed_up.MultipleRolesRoleModelMixin method) (schrodinger.ui.qt.table_speed_up.MultipleRolesRoleProxyMixin method) (schrodinger.ui.qt.table_speed_up.MultipleRolesRoleProxyPassthroughMixin method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) DATA_CACHE_SIZE (schrodinger.ui.qt.table_speed_up.MultipleSpeedUpDelegatesViewMixin attribute) data_changed (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase attribute) DATA_CLASSES (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData attribute) data_column (schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart attribute) data_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) data_field_names (schrodinger.livedesign.registration.RegistrationOptions attribute) DATA_MAX (schrodinger.ui.qt.rama.RamaContourMixin attribute) data_method() (in module schrodinger.ui.qt.table_helper) DATA_MIN (schrodinger.ui.qt.rama.RamaContourMixin attribute) data_name (schrodinger.application.livedesign.data_classes.LDData property) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) data_nameChanged (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) data_nameReplaced (schrodinger.application.livedesign.export_models.Base3DExportSpec attribute) (schrodinger.application.livedesign.export_models.DataExportSpec attribute) (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) (schrodinger.application.livedesign.export_models.PropertyExportSpec attribute) (schrodinger.application.livedesign.export_models.Standard3DExportSpec attribute) data_violations (schrodinger.application.bioluminate.antibody.io.csv_reader.InvalidRowError property) Database (class in schrodinger.application.vss.database) DATABASE (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase attribute) database_changed (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase attribute) database_name (schrodinger.protein.tasks.blast.BlastSettings attribute) database_nameChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) database_nameReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) database_parameter_key (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) databaseComboChanged() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) DatabaseInfo (class in schrodinger.application.matsci.kmcgui) databases (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput attribute) DATABASES (schrodinger.infra.licensing.SimilarityEndpoint attribute) databaseType (schrodinger.job.server.ServerInfo attribute) DataCache (class in schrodinger.ui.qt.table_speed_up) dataChanged (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates attribute) (schrodinger.ui.qt.pop_up_widgets.PopUp attribute) (schrodinger.ui.residueselector.MutationSelectorMixin attribute) (schrodinger.ui.residueselector.MutationSelectorPopUp attribute) dataChanged() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView method) DataClass (schrodinger.models.parameters.BaseMutableParam attribute) (schrodinger.models.parameters.CompoundParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.Param attribute) (schrodinger.models.parameters.ParamListParam attribute) (schrodinger.models.parameters.SetParam attribute) (schrodinger.ui.qt.color_picker.ColorParam attribute) dataclass_to_compoundparam() (in module schrodinger.models.param_class_convertors) DataColumn (class in schrodinger.tasks.ldi) datadir (schrodinger.application.glide_ws.driver.GlideWSJob property) dataDir() (schrodinger.infra.fast3d.Engine static method) DataExportSpec (class in schrodinger.application.livedesign.export_models) DataFile (class in schrodinger.application.transforms.dofn_utils) DataFiles (class in schrodinger.glide) DataFusionMergeStage (class in schrodinger.pipeline.stages.combine) DataMethodDecoratorMixin (class in schrodinger.ui.qt.table_helper) DataMethodDecoratorProxyMixin (class in schrodinger.ui.qt.table_helper) DataModel (class in schrodinger.application.bioluminate.protein_report_widget) DataModelWithChart (class in schrodinger.application.bioluminate.protein_structure_quality) dataName() (schrodinger.structure.PropertyName method) dataName2ViewName() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion class method) dataNameIterator() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) DataPointLocator (class in schrodinger.analysis.visanalysis.volumedatautils) dataRequested() (schrodinger.application.matsci.reportutils.ReportInfo method) DataType (class in schrodinger.application.matsci.espresso.qeinput) (schrodinger.application.steps.dataclasses.MolToSmilesSerializer attribute) (schrodinger.application.steps.dataclasses.ScoredMolSerializer attribute) (schrodinger.application.steps.enumerators.RouteSerializer attribute) (schrodinger.stepper.stepper.Serializer attribute) DataViewerTable (class in schrodinger.ui.qt.table) DataViolation (class in schrodinger.application.bioluminate.antibody.io.csv_reader) date_created (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) date_createdChanged (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) date_createdReplaced (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) date_edited (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) date_editedChanged (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) date_editedReplaced (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) date_executed (schrodinger.application.livedesign.models2.datamodels.execution_record.ModelExecution attribute) date_executedChanged (schrodinger.application.livedesign.models2.datamodels.execution_record.ModelExecution attribute) date_executedReplaced (schrodinger.application.livedesign.models2.datamodels.execution_record.ModelExecution attribute) DateTimeSerializer (class in schrodinger.models.jsonable) Dative (schrodinger.structure.BondType attribute) Datum (class in schrodinger.application.desmond.arkdb) daylight_locus() (in module schrodinger.application.matsci.colorutils) daylight_radiator() (in module schrodinger.application.matsci.colorutils) DB_LB (schrodinger.application.matsci.stylemanager.Gradients attribute) DBConfSitesStage (class in schrodinger.pipeline.stages.phase) DBExportStage (class in schrodinger.pipeline.stages.phase) DBManageStage (class in schrodinger.pipeline.stages.phase) dbscan_cluster() (in module schrodinger.math.mathutils) dbTestIdentity() (schrodinger.infra.canvas.ChmSearchKey method) dbTestSubstructure() (schrodinger.infra.canvas.ChmSearchKey method) dbTestSuperstructure() (schrodinger.infra.canvas.ChmSearchKey method) DCCompoundParam (class in schrodinger.models.param_class_convertors) DCCompoundParamMeta (class in schrodinger.models.param_class_convertors) deactivate() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) deactivateTabs() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) debug (schrodinger.application.glide.glideanalysis.PoseLibrary attribute) (schrodinger.application.jaguar.nmr_utils.NMRData attribute) DEBUG (schrodinger.utils.cmdline.Options attribute) debug() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.infra.canvas.ChmObjChmAtomImpl method) (schrodinger.infra.canvas.ChmObjChmAtomTyperImpl method) (schrodinger.infra.canvas.ChmObjChmMatcherImpl method) (schrodinger.infra.canvas.ChmObjChmQueryImpl method) (schrodinger.infra.canvas.ChmQuery method) (schrodinger.infra.canvas.ChmSDReaderImpl method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.qt.widgetmixins.basicmixins.ExecutionMixin method) debug_func() (in module schrodinger.ui.qt.appframework2.debugcore) debug_func_args() (in module schrodinger.ui.qt.appframework2.debugcore) debug_mode (schrodinger.stepper.stepper.StepTaskInput attribute) debug_modeChanged (schrodinger.stepper.stepper.StepTaskInput attribute) debug_modeReplaced (schrodinger.stepper.stepper.StepTaskInput attribute) debug_mols() (in module schrodinger.application.pathfinder.reaction) debug_outfile (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) debug_print() (in module schrodinger.utils.sea.common) debugEnabled() (schrodinger.job.launchapi.JobSpecification method) DebugFlag (class in schrodinger.seam.debug) DEBUGGER (schrodinger.utils.cmdline.Options attribute) debugPrint() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) debugReactants() (schrodinger.application.pathfinder.reaction.Reaction method) DebugStderr (class in schrodinger.ui.qt.appframework2.debugcore) DebugStdout (class in schrodinger.ui.qt.appframework2.debugcore) DebugViewer (class in schrodinger.ui.qt.appframework2.debug_gui) Debye (schrodinger.application.jaguar.constants.Unit attribute) Decimal (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) decimals (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) declareAromatic (schrodinger.infra.canvas.AtomData attribute) decode() (in module schrodinger.models.json) (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer class method) (schrodinger.seam.coders.MolCoder method) (schrodinger.seam.coders.MolToSmilesCoder method) (schrodinger.seam.coders.RouteNodeCoder method) (schrodinger.seam.coders.StructureCoder method) (schrodinger.seam.transforms.window.StringIDWindowCoder method) decode_base64_cmd() (in module schrodinger.application.matsci.textlogger) decode_position_vector() (in module schrodinger.application.bioluminate.peptide_sar.encode) decode_str() (in module schrodinger.application.desmond.cms) decode_string_from_structure_property() (in module schrodinger.application.desmond.struc) decode_to_server_info() (in module schrodinger.job.server) decode_value() (in module schrodinger.application.bioluminate.peptide_sar.encode) (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer class method) decoder() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) decomp_rawfep_structure() (in module schrodinger.application.desmond.cms) deconverge() (schrodinger.protein.protassign.hbond_cluster.hbond_cluster method) Decorate (class in schrodinger.application.transforms.enumerators.decorate) decorateAxes() (schrodinger.application.matsci.sliceplot.SlicePlot method) Decorator (class in schrodinger.application.steps.enumerators) decoy_ligs (schrodinger.application.glide_ws.driver.GlideWSJob property) decoys (schrodinger.application.glide_ws.optimizer.WScoreOptimizer property) decoys_data_file (schrodinger.application.glide_ws.nodes.OptimizeNode property) decoys_libfile (schrodinger.application.glide_ws.model.Model property) DecoysNode (class in schrodinger.application.glide_ws.nodes) decreaseSpeed() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) decrement_state_of_changeable() (schrodinger.protein.assignment.ProtAssign method) decrementNestingLevel() (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) decrypt_cms() (in module schrodinger.application.matsci.enc) dedup_frags() (schrodinger.active_learning.substruct_enrichment.SubstructEnrichCalculator static method) DedupeAndRandomSampleFilter (class in schrodinger.stepper.core_steps) DedupeAndRandomSampleFilter.Settings (class in schrodinger.stepper.core_steps) deduplicate_crystals() (in module schrodinger.comparison.dedup_utils) deduplicate_routes (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) deduplicate_routesChanged (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) deduplicate_routesReplaced (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) deduplicate_sequences() (in module schrodinger.livedesign.biologics.modeling) deduplicate_strain_rescore_input() (in module schrodinger.application.livedesign.ld_strain_rescore_utils) deduplicate_xy_data() (in module schrodinger.math.mathutils) DeduplicateRoutes (class in schrodinger.application.transforms.enumerators.synthesize) deduplication_hash (schrodinger.livedesign.biologics.registration.BioPolymer property) (schrodinger.livedesign.registration.RegistrationData attribute) DeduplicationStep (class in schrodinger.stepper.core_steps) DEE_Backtracking (class in schrodinger.application.canvas.r_group_dee) DEE_EnergyMatrix (class in schrodinger.application.canvas.r_group_dee) deep_find_signals() (in module schrodinger.ui.qt.appframework2.debugwidgets) deep_update_dict() (in module schrodinger.application.matsci.msutils) DeepChem (class in schrodinger.application.matsci.genetic_optimization) deepCopy() (schrodinger.application.matsci.amorphous.PolymerFragment method) deepFindSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) DEF2_SVPD (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) def_str (schrodinger.infra.mm.UTTDefSpec attribute) default (schrodinger.application.glide.sort_utils.SortCriterion attribute) (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute) (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute) (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute) DEFAULT (schrodinger.application.jaguar.hess_guess.SchlegelConstants attribute) default (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword property) (schrodinger.application.matsci.cgforcefieldgui.ParameterData attribute) (schrodinger.application.matsci.kmc.ColumnData attribute) (schrodinger.application.matsci.reaction_workflow_utils.JaguarKeyStructPropData attribute) DEFAULT (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Slab attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) (schrodinger.forcefield.constants.ReferenceEnergyMethod attribute) Default (schrodinger.infra.canvas.ChmCoordGenOption attribute) default (schrodinger.tasks.cmdline.ArgSpec attribute) DEFAULT (schrodinger.ui.qt.forcefield.forcefield.OPLSDirResult attribute) (schrodinger.ui.qt.standard.design_tokens.BorderColors attribute) (schrodinger.ui.qt.standard.design_tokens.BorderSizes attribute) (schrodinger.ui.qt.standard.design_tokens.FontSizes attribute) (schrodinger.ui.qt.standard.design_tokens.FontWeights attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) default() (schrodinger.application.glide_ws.utils.ObjectEncoder method) DEFAULT_ALLOWED_MODES (schrodinger.tasks.jobtasks.IncorporationParam attribute) DEFAULT_ALPHA_CEILING (schrodinger.ui.qt.color_picker.AlphaLimitedColorPickerButton attribute) default_args() (in module schrodinger.active_learning.al_utils) DEFAULT_ATOM_TYPING_SCHEMES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) DEFAULT_AXIS_BUFFER_PCT (schrodinger.ui.qt.schart.SChart attribute) DEFAULT_AXIS_FONT_SIZE (schrodinger.ui.qt.schart.SChart attribute) default_basis (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel property) DEFAULT_BASIS_SET (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) DEFAULT_BIN_WIDTH (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) DEFAULT_CATEGORY_LABEL_ANGLE (schrodinger.ui.qt.schart.SChart attribute) DEFAULT_COULOMB (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) default_custom_fraglib() (in module schrodinger.utils.cgxutils) DEFAULT_DATA (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) DEFAULT_DENSITY (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) DEFAULT_ENVIRON (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) DEFAULT_FC (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) DEFAULT_FILTERS (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) (schrodinger.application.glide.sort_utils.GlideSortUtility attribute) DEFAULT_GROUP_NAME (schrodinger.application.matsci.appbase.ProcessPtStructuresApp attribute) DEFAULT_HEADERS (schrodinger.application.matsci.mswidgets.SystemInformationFrame attribute) DEFAULT_HORIZONTAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) DEFAULT_IPOLAR (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) default_jaguar_basis() (in module schrodinger.application.jaguar.basis) DEFAULT_JAGUAR_OPTIONS (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) (schrodinger.application.matsci.permittivity.JaguarFinerCalculation attribute) DEFAULT_JOB_NAME (schrodinger.application.matsci.reaction_workflow_utils.DescriptorsMixin attribute) DEFAULT_JOBNAME (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) (schrodinger.application.matsci.permittivity.AveCellAnalysis attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) (schrodinger.application.matsci.permittivity.CMSParser attribute) (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) (schrodinger.application.matsci.permittivity.JaguarMerge attribute) (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) DEFAULT_KWARGS (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) default_label() (schrodinger.application.transforms.enumerators.substitute.SubstructureSubstitute method) DEFAULT_LEGEND_CB (schrodinger.ui.qt.schart.SChart attribute) default_logging_config() (in module schrodinger.utils.log) DEFAULT_MAE_EXT (schrodinger.application.matsci.nano.constants.Constants attribute) DEFAULT_MARKER_SIZE (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama attribute) (schrodinger.ui.qt.rama.RamaScatterMixin attribute) default_method (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain property) DEFAULT_MIN_ENRICH (schrodinger.active_learning.substruct_enrichment.SubstructEnrichCalculator attribute) DEFAULT_MIN_RATIO (schrodinger.active_learning.substruct_enrichment.SubstructEnrichCalculator attribute) DEFAULT_MOSS_ATNUM (schrodinger.application.jaguar.gui.tabs.properties_tab.MossbauerSubTab attribute) DEFAULT_MOSS_NUC_QUADRUPOLE_MOMENT (schrodinger.application.jaguar.gui.tabs.properties_tab.MossbauerSubTab attribute) DEFAULT_MOVE_AMPLITUDE (schrodinger.application.peptide_workflow.monte.MonteOptions attribute) DEFAULT_MSJ_HEADER (schrodinger.application.matsci.permittivity.MultiStageMd attribute) default_name (schrodinger.application.glide_ws.nodes.CrossNode attribute) (schrodinger.application.glide_ws.nodes.DecoysNode attribute) (schrodinger.application.glide_ws.nodes.GridGenNode attribute) (schrodinger.application.glide_ws.nodes.MMGBSACrossNode attribute) (schrodinger.application.glide_ws.nodes.MMGBSADecoysNode attribute) (schrodinger.application.glide_ws.nodes.MMGBSANode attribute) (schrodinger.application.glide_ws.nodes.MMGBSAReceptorComplexNode attribute) (schrodinger.application.glide_ws.nodes.MMGBSAReceptorModelNode attribute) (schrodinger.application.glide_ws.nodes.MMGBSATestsetNode attribute) (schrodinger.application.glide_ws.nodes.ModelNode attribute) (schrodinger.application.glide_ws.nodes.NativeNode attribute) (schrodinger.application.glide_ws.nodes.Node attribute) (schrodinger.application.glide_ws.nodes.OptimizeNode attribute) (schrodinger.application.glide_ws.nodes.SPDecoysNode attribute) (schrodinger.application.glide_ws.nodes.TestSetNode attribute) (schrodinger.application.glide_ws.nodes.WmapGenNode attribute) default_nodes() (schrodinger.application.glide_ws.driver.GlideWSJob static method) DEFAULT_NONCATEGORY_LABEL_ANGLE (schrodinger.ui.qt.schart.SChart attribute) DEFAULT_NUMBER_OF_MOLECULES (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) DEFAULT_NUMBER_OF_POLYMERS (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) DEFAULT_ORBITAL (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) DEFAULT_P_VALUE_CUT (schrodinger.active_learning.substruct_enrichment.SubstructEnrichCalculator attribute) DEFAULT_POP_UP_MODE (schrodinger.ui.qt.pop_up_widgets.ComboBoxWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.LineEditWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.LinkButtonWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.PushButtonWithIndicatorAndPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.PushButtonWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.ToolButtonWithPopUp attribute) (schrodinger.ui.qt.pop_up_widgets.WidgetWithPopUpMixin attribute) (schrodinger.ui.residueselector.MutationSelectorLineEdit attribute) DEFAULT_RANDOM_TYPES (schrodinger.application.matsci.rxn_channel.Constants attribute) DEFAULT_RANGE (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka attribute) DEFAULT_RC (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) DEFAULT_REF (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis attribute) default_size_factor (schrodinger.ui.qt.network_views.NetworkNode attribute) DEFAULT_SORT_COLUMN (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel attribute) DEFAULT_SORT_CRITERIA (schrodinger.application.glide.sort_utils.GlideSortUtility attribute) DEFAULT_SORT_ORDER (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) DEFAULT_START_FRAME (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) DEFAULT_STEP_SIZE (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel attribute) DEFAULT_SUB_TAB_VISIBILITY (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) DEFAULT_TASKDIR_SETTING (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.stepper.stepper.StepTaskMixin attribute) (schrodinger.tasks.tasks.AbstractTask attribute) default_text (schrodinger.application.livedesign.panel_components.AddNewLineEdit attribute) default_theory (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel property) DEFAULT_THEORY (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) DEFAULT_TOOLBARS (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) DEFAULT_TOOLS (schrodinger.ui.qt.schart.SChart attribute) DEFAULT_TOOLTIP (schrodinger.ui.qt.atomselector.AtomSelector attribute) DEFAULT_TRANSPARENCY (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings attribute) default_val (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) default_valChanged (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) default_valReplaced (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) DEFAULT_VERSION (schrodinger.infra.structure.MmctSerializer attribute) DEFAULT_VERTICAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) DEFAULT_WEIGHT (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow attribute) default_weight (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) default_weightChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) default_weightReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings attribute) DEFAULT_X_RADIUS (schrodinger.protein.helm.helm_renderer.DAminoAcidMonomerItem attribute) (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin attribute) DEFAULT_Y_RADIUS (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin attribute) defaultConfig() (schrodinger.infra.fast3d.Volumizer static method) defaultCustomRepository() (schrodinger.infra.fast3d.Engine static method) DefaultFactoryDict (class in schrodinger.utils.scollections) DefaultFactoryDictMixin (class in schrodinger.utils.scollections) DefaultIdDict (class in schrodinger.utils.scollections) defaultLogicalSize (schrodinger.infra.canvas.ChmCompressedBitset attribute) (schrodinger.infra.canvas.ChmCompressedBitset64 attribute) DefaultMessageDelegate (class in schrodinger.ui.qt.delegates) DefaultMonomerItem (schrodinger.protein.helm.helm_renderer.ZOrder attribute) DEFAULTMSG (schrodinger.application.matsci.nano.check.CheckInput attribute) DefaultPreset (class in schrodinger.application.bioluminate.pml_menus) defaultRepositories() (schrodinger.infra.fast3d.Engine static method) DEFAULTS (class in schrodinger.application.jaguar.xray.constants) (schrodinger.application.matsci.deswidgets.DesmondMDWidgets attribute) (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) (schrodinger.application.matsci.espresso.qeinput.BasisType attribute) (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) (schrodinger.application.matsci.espresso.qeinput.ControlType attribute) (schrodinger.application.matsci.espresso.qeinput.CustomMDType attribute) (schrodinger.application.matsci.espresso.qeinput.DftType attribute) (schrodinger.application.matsci.espresso.qeinput.DftUType attribute) (schrodinger.application.matsci.espresso.qeinput.ElasticControlType attribute) (schrodinger.application.matsci.espresso.qeinput.ElasticType attribute) (schrodinger.application.matsci.espresso.qeinput.ElectronControlType attribute) (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) (schrodinger.application.matsci.espresso.qeinput.FPhononControlType attribute) (schrodinger.application.matsci.espresso.qeinput.FreePositionsType attribute) (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) (schrodinger.application.matsci.espresso.qeinput.HPType attribute) (schrodinger.application.matsci.espresso.qeinput.HybridType attribute) (schrodinger.application.matsci.espresso.qeinput.IonControlType attribute) (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) (schrodinger.application.matsci.espresso.qeinput.MdType attribute) (schrodinger.application.matsci.espresso.qeinput.NEBPathType attribute) (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) (schrodinger.application.matsci.espresso.qeinput.PHDynmatType attribute) (schrodinger.application.matsci.espresso.qeinput.PPlotType attribute) (schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType attribute) (schrodinger.application.matsci.espresso.qeinput.SpinType attribute) (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboEelsType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboLanczosType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) (schrodinger.application.matsci.espresso.qeinput.VdwType attribute) (schrodinger.infra.mm.OPLSDatafileType attribute) (schrodinger.protein.tasks.blast.BlastSettings attribute) DEFAULTS_DAT (schrodinger.infra.mm.OPLSDatafileType attribute) defaultValue() (schrodinger.models.parameters.CompoundParam class method) (schrodinger.models.parameters.Param class method) DefineASLDialog (class in schrodinger.application.matsci.mswidgets) defineAtom() (schrodinger.application.matsci.cg_mapping.Particle method) defineBins() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) defineBox() (schrodinger.application.matsci.amorphous.Scaffold method) defineBoxFromNonPBCStruct() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineBoxFromPBC() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineBoxFromScaffold() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineCustomSettings() (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) defineDimensions() (schrodinger.application.matsci.nano.tube.NanoSheet method) definedShadowBonds() (schrodinger.application.matsci.cgforcefield.ForceField static method) defineIgnoredParams() (schrodinger.models.presets.PresetManager method) (schrodinger.models.presets.TaskPanelPresetManager method) defineInputParams() (schrodinger.models.presets.PresetManager method) defineInternals() (schrodinger.application.matsci.cgforcefield.ForceField method) defineJobControlOptions() (schrodinger.tasks.cli.TaskCLI method) defineMappings() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage method) (schrodinger.application.jaguar.jaguar_config_dialog.JaguarHostSelector method) (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.job_monitor.job_monitor_progress_bar.ProgressBar method) (schrodinger.application.job_monitor.job_monitor_widgets.JobBar method) (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.ServerRegistrationMixin method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export.LDExportPanelMixin method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfoDialog method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel method) (schrodinger.application.livedesign.widgets.InvalidGEIdWarningDialog method) (schrodinger.application.pymol.export_to_pymol_gui.AdvancedSettingsPopUp method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.maestro_utils.composer_agent.composer_gui.ComposerAgentPanel method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget method) (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager method) (schrodinger.ui.qt.fp_selector_widget.FingerprintsSelectorWidget method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.tasks.configwidgets.IncorporationSelector method) (schrodinger.ui.qt.tasks.configwidgets.JobnameWidget method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressBar method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.StartButton method) (schrodinger.ui.qt.tasks.taskwidgets.StatusLabel method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) (schrodinger.ui.two_d_viewer.SaveImagesDialog method) DefineMappingsException defineNewNormal() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) definePanelSettings() (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.ui.qt.appframework2.settings.SettingsPanelMixin method) definePipeline() (schrodinger.tasks.beamtasks.BeamTask static method) defines_integer_atom_props() (in module schrodinger.application.matsci.smartsutils) defineTaskPostprocessors() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) defineTaskPreprocessors() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) defineTorsionIndexes() (schrodinger.application.matsci.etarotamers.HapticLigand method) defineVectors() (schrodinger.application.matsci.nano.tube.NanoSheet method) defineVoids() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) Definition (class in schrodinger.utils.ligfilter) definition_id (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) DEFINITION_ID (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) definition_id (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) definition_idChanged (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) definition_idReplaced (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) DefinitionMetadata (class in schrodinger.application.livedesign.models2.datamodels.definition) DefinitionParser (class in schrodinger.utils.ligfilter) DefinitionViewerDialog (class in schrodinger.ui.ligfilter) deform_cms_model() (in module schrodinger.application.matsci.desmondutils) Deformation (class in schrodinger.application.matsci.elasticity.strain) deformation_matrix (schrodinger.application.matsci.elasticity.strain.Strain property) DeformedStructureSet (class in schrodinger.application.matsci.elasticity.strain) Degree (schrodinger.application.jaguar.constants.Unit attribute) degree (schrodinger.ui.qt.network_visualizer.Node property) degree() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) degree_seconds_mapping_dict (schrodinger.application.pymol.pymol4maestro.panel attribute) degreeOfPolymerization() (schrodinger.application.matsci.amorphous.FlorySchulzDistribution method) degreesCurrentIndexChanged() (schrodinger.application.pymol.pymol4maestro.panel method) dehydrated_step (schrodinger.stepper.stepper.StepTaskInput attribute) dehydrated_stepChanged (schrodinger.stepper.stepper.StepTaskInput attribute) dehydrated_stepReplaced (schrodinger.stepper.stepper.StepTaskInput attribute) del_from() (schrodinger.application.desmond.arkdb.Datum method) del_key() (schrodinger.utils.sea.sea.Map method) DelayedInputValidation() (schrodinger.active_learning.al_driver.ActiveLearningJob method) delChiralMatchAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) delConnectivity() (schrodinger.application.matsci.amorphous.PolymerFragments method) delDanglingTermAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) delegate() (schrodinger.ui.qt.structtable.ViewerTable method) DELEGATE_CLASS (schrodinger.ui.qt.table_speed_up.SpeedUpDelegateViewMixin attribute) DelegatingIndentedHelpFormatter (class in schrodinger.utils.singledashoptionparser) deletable (schrodinger.project.project.ProjectRow property) DELETE (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) delete() (schrodinger.application.desmond.arkdb.ArkDb method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.project.project.ProjectRow method) (schrodinger.project.surface.ProjectSurface method) (schrodinger.seam.io.jobfilesystem.JobFileSystem method) (schrodinger.structure.StructureBond method) (schrodinger.surface.Surface method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) DELETE_ALL (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) delete_all_atom_group() (schrodinger.application.desmond.cms.Cms method) delete_all_pbc_bonds() (in module schrodinger.application.matsci.nano.xtal) delete_all_rows() (in module schrodinger.application.matsci.kmc) delete_atom_group() (schrodinger.application.desmond.cms.Cms method) delete_atom_properties() (in module schrodinger.application.desmond.struc) delete_atoms() (schrodinger.protein.assignment.ProtAssign method) delete_bonds() (in module schrodinger.structutils.build) delete_bonds_to_atoms() (in module schrodinger.structutils.build) DELETE_BOTH (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) DELETE_CONSTRAINT (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) delete_duplicate_atoms() (in module schrodinger.application.matsci.nano.xtal) delete_far_waters (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_far_waters() (in module schrodinger.application.prepwizard) delete_far_watersChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_far_watersReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_fepio() (in module schrodinger.application.desmond.cms) delete_ffio_ff() (in module schrodinger.application.desmond.struc) delete_ghosts() (in module schrodinger.application.jaguar.utils) delete_group() (in module schrodinger.application.matsci.maestrocmds) delete_group_properties() (in module schrodinger.application.matsci.smartsutils) delete_hydrogens() (in module schrodinger.structutils.build) DELETE_MAPPING_PREFKEY (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog attribute) delete_molecules_from_aa_model() (in module schrodinger.application.matsci.desmondutils) delete_molecules_from_cg_model() (in module schrodinger.application.matsci.desmondutils) delete_molecules_from_comps() (in module schrodinger.application.matsci.desmondutils) delete_molecules_from_model() (in module schrodinger.application.matsci.desmondutils) delete_non_bridging_waters() (in module schrodinger.application.prepwizard) delete_nonbridging_waters (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_nonbridging_watersChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_nonbridging_watersReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delete_pbc_bonds() (in module schrodinger.application.matsci.nano.xtal) DELETE_PROPERTY (schrodinger.application.matsci.enumeration.VacancyAlchemist attribute) delete_ring_bond() (in module schrodinger.application.peptide_workflow.moves) DELETE_SCAN (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) delete_structure_properties() (in module schrodinger.application.desmond.struc) delete_substitution_site_bonds() (schrodinger.application.matsci.reaction_workflow_enum_utils.Sites static method) delete_surface() (in module schrodinger.maestro_utils.surface_manager.commands) delete_temp_project_directory() (in module schrodinger.project.project) DELETE_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) delete_workflow_metadata() (in module schrodinger.application.matsci.wfmanagement) delete_zobs() (in module schrodinger.structutils.build) DeleteAll (class in schrodinger.application.bioluminate.pml_menus) deleteAll() (schrodinger.application.matsci.stage_widgets.MultiRowArea method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) deleteAllPredictions() (schrodinger.protein.sequence.AbstractSingleChainSequence method) deleteAllRestraints() (schrodinger.structutils.minimize.Minimizer method) deleteAllRows() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.infra.table.Table method) (schrodinger.ui.qt.swidgets.STableWidget method) deleteAnchors() (schrodinger.application.matsci.sculptcomplex.Sculptor method) deleteAngles() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) DeleteAtoms (class in schrodinger.application.bioluminate.pml_menus) deleteAtoms() (schrodinger.application.matsci.enumeration.VacancyAlchemist method) (schrodinger.infra.structure.Structure method) (schrodinger.structure.Structure method) deleteBond() (schrodinger.infra.structure.Structure method) (schrodinger.structure.Structure method) (schrodinger.structure.StructureAtom method) DeleteButton (class in schrodinger.ui.qt.swidgets) deleteByEntry() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) deleteBySequences() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) deleteClicked (schrodinger.application.matsci.mswidgets.SavedASLItem attribute) (schrodinger.ui.qt.swidgets.SavedMenuItem attribute) deleteColumn() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.swidgets.STableWidget method) deleteCurrentRow() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) deleteEntry() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) deleteExtraAngles() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) deleteFiles() (schrodinger.infra.canvas.ChmFPCombiner method) (schrodinger.infra.canvas.ChmFPCombiner64 method) deleteGroup() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) deleteInput (schrodinger.infra.canvas.MCSsettings attribute) deleteItems() (schrodinger.ui.qt.network_visualizer.Graph method) deleteJobRecordRequested (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget attribute) deleteJobs() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) deleteKey() (schrodinger.application.jaguar.input.JaguarInput method) deleteKeys() (schrodinger.application.jaguar.input.JaguarInput method) deleteMapping() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) deleteNode() (schrodinger.application.matsci.automated_cg_mapping.Mapping method) deleteOtherBranches() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) deletePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) deleteParticipant (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) deletePrediction() (schrodinger.protein.sequence.AbstractSingleChainSequence method) deletePreset() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) (schrodinger.models.presets.PresetManager method) DeleteProject (class in schrodinger.application.bioluminate.pml_menus) deleteProperty() (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.structure.Structure method) (schrodinger.infra.structure.StructureAtom method) deletePropertyFromAllAtoms() (schrodinger.infra.structure.Structure method) (schrodinger.structure.Structure method) deleteRow() (schrodinger.application.matsci.stage_widgets.MultiRowArea method) (schrodinger.infra.table.Table method) (schrodinger.project.project.Project method) deleteRowSignal (schrodinger.application.matsci.stage_widgets.MultiRowArea attribute) deleteSavedItem() (schrodinger.ui.qt.swidgets.ItemsManagerMixin method) deleteSection() (schrodinger.application.jaguar.input.JaguarInput method) deleteSelectedItems() (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.Graph method) deleteSelectedRows() (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) (schrodinger.ui.qt.swidgets.STableWidget method) DeleteSelections (class in schrodinger.application.bioluminate.pml_menus) deleteStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) deleteStructure() (schrodinger.application.jaguar.input.JaguarInput method) deleteSurfaces() (schrodinger.maestro_utils.surface_manager.surface_model.SurfaceModel method) deleteTemplate() (schrodinger.application.matsci.builderwidgets.TemplateManager method) deleteTmpHydrogens() (schrodinger.application.matsci.rxn_channel.Products method) DeleteWatersTask (class in schrodinger.application.prepwizard2.tasks) deleteWorkflow() (schrodinger.application.matsci.wfmanagement.WorkflowManagerMixin method) DeleteWS (class in schrodinger.application.bioluminate.pml_menus) deletion_penalty (schrodinger.structutils.structalign.StructAlign property) delFromAuxListbox() (schrodinger.ui.qt.propertyselector.PropertySelector method) DELIM (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) delimiter (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) delKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) delta (schrodinger.application.bindingsite.cavutils.Grid property) DELTA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) (schrodinger.application.jaguar.mlff.constants.QRNNModels attribute) DELTA_2022_1 (schrodinger.energy.QRNNModel attribute) DELTA_TRANSFER (schrodinger.application.jaguar.mlff.constants.QRNNModels attribute) DELTA_TRANSFER_2022_1 (schrodinger.energy.QRNNModel attribute) DELTAE_12E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DELTAE_12H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DELTAE_21E (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DELTAE_21H (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) DELTAE_COLUMNS (schrodinger.application.matsci.kmc.MatSciPairsTable attribute) deltaGIsChecked() (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab method) delTempHydrogens() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) delwater_hbond_cutoff (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delwater_hbond_cutoffChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delwater_hbond_cutoffReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) delZigZagMatchAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) den() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) Den2Vol() (in module schrodinger.application.matsci.gsas.GSASIImath) Dendrogram (class in schrodinger.ui.qt.dendrogram) DendrogramPlotDialog (class in schrodinger.application.canvas.clustergui) DendrogramSyncer (class in schrodinger.ui.qt.dendrogram) denscore_gaussian_resolution (schrodinger.glide.EnergyOptions attribute) denscore_radius (schrodinger.glide.EnergyOptions attribute) DENSE_MATRIX (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) DENSEAROUND (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) density (schrodinger.application.jaguar.garza.SolventParams attribute) (schrodinger.application.jaguar.gui.utils.Solvent attribute) (schrodinger.application.jaguar.utils.JagSolventParams attribute) DENSITY (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) density() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) DENSITY_EXT (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) density_precision (schrodinger.application.jaguar.results.JaguarResults attribute) DENSITY_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_REPLICA_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_REPLICA_PROP_REX (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_STD_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) DENSITY_STD_REPLICA_PROP (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) density_weight (schrodinger.glide.EnergyOptions attribute) DensityAnalysis (class in schrodinger.application.matsci.permittivity) DensityAnalysisMixin (class in schrodinger.application.matsci.density_analysis) DensityTab (class in schrodinger.application.matsci.density_analysis_widget) DEOXY_SUBTYPES (schrodinger.livedesign.biologics.fasta.NucleicAcidAssembler attribute) DeoxyribonucleotideType (class in schrodinger.protein.residue) depletion_at_t12() (in module schrodinger.application.jaguar.kinetics) deploymentCheck() (schrodinger.stepper.app.StepperApplication class method) deprecate_module() (in module schrodinger.utils.deprecation) deprecated() (in module schrodinger.utils.deprecation) DeprecationError depth (schrodinger.application.matsci.cgforcefield.ShadowData attribute) (schrodinger.application.pathfinder.analysis.RetrosynthesisState attribute) (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) depth() (schrodinger.application.pathfinder.route.RouteNode method) depthChanged (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) depthReplaced (schrodinger.application.steps.enumerators.RouteEnumerator.Settings attribute) (schrodinger.application.steps.enumerators.Synthesizer.Settings attribute) deregisterSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) derive_token_name() (in module schrodinger.ui.qt.standard.design_tokens) DerivedAttrs (class in schrodinger.application.jaguar.results) deriveMapping() (schrodinger.infra.canvas.ChmPathTools static method) deriveReferenceResidueInfo() (schrodinger.application.bioluminate.antibody.sequence_indexer.DVDSequenceIndexer method) (schrodinger.application.bioluminate.antibody.sequence_indexer.SCFVSequenceIndexer method) (schrodinger.application.bioluminate.antibody.sequence_indexer.SingleDomainAbSequenceIndexer method) Desalt (class in schrodinger.application.transforms.chem) desalt_mol() (in module schrodinger.application.pathfinder.synthesis) desalt_structure() (in module schrodinger.structutils.build) DESCENDING (schrodinger.application.glide.sort_utils.SortOrder attribute) describe_database() (in module schrodinger.application.bb_database.bb_task_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) description (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword property) (schrodinger.application.licensing.licerror.LicenseError property) (schrodinger.application.livedesign.entry_types.BaseEntryData attribute) (schrodinger.application.livedesign.entry_types.Complexes attribute) (schrodinger.application.livedesign.entry_types.CovalentDockingComplexes attribute) (schrodinger.application.livedesign.entry_types.DockedPoses attribute) (schrodinger.application.livedesign.entry_types.Ligands attribute) (schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute) (schrodinger.application.livedesign.export_models.AttachmentData attribute) DESCRIPTION (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) description (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfo attribute) (schrodinger.application.livedesign.models2.datamodels.definition.DefinitionMetadata attribute) (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) DESCRIPTION (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Slab attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame attribute) description (schrodinger.protein.nonstandard_residues.AminoAcid property) (schrodinger.protein.properties.SequenceProperty attribute) description() (schrodinger.gpgpu.CudaDevice method) descriptionChanged (schrodinger.application.livedesign.export_models.AttachmentData attribute) (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfo attribute) (schrodinger.application.livedesign.models2.datamodels.definition.DefinitionMetadata attribute) (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) (schrodinger.protein.properties.SequenceProperty attribute) descriptionReplaced (schrodinger.application.livedesign.export_models.AttachmentData attribute) (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfo attribute) (schrodinger.application.livedesign.models2.datamodels.definition.DefinitionMetadata attribute) (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) (schrodinger.protein.properties.SequenceProperty attribute) DescriptiveAngles (class in schrodinger.application.bioluminate.mhc.docking_angles) Descriptor (class in schrodinger.application.canvas.topo_descriptors) (class in schrodinger.application.matsci.order_parameter_mod) (class in schrodinger.application.matsci.reaction_workflow_gui_utils) DESCRIPTOR (schrodinger.models.parameters.ParamType attribute) Descriptor (schrodinger.protein.properties.PropertyType attribute) (schrodinger.protein.properties.SequenceProperty attribute) DESCRIPTOR_DICT (schrodinger.application.matsci.rxn_channel.ChannelDefinitions attribute) descriptor_only() (in module schrodinger.models.parameters) DESCRIPTORS (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor attribute) descriptors (schrodinger.glide.ScoreInfo attribute) (schrodinger.protein.residue.Residue property) (schrodinger.protein.sequence.AbstractSequence property) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) descriptorsChanged (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) descriptorsCleared (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.AbstractSequence attribute) DescriptorsMixin (class in schrodinger.application.matsci.reaction_workflow_utils) descriptorsReplaced (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) DescriptorUtility (in module schrodinger.application.matsci.mlearn.features) deselect() (schrodinger.ui.qt.tablewidget.Cell method) (schrodinger.ui.qt.tablewidget.Row method) deselectAll() (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.residueselector.MutationSelectorMixin method) deselected (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite attribute) deselectEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) deselectOtherEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) deselectSelectedSites() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) deserialize() (schrodinger.application.steps.dataclasses.MolToSmilesSerializer method) (schrodinger.stepper.stepper.Serializer method) deserialize_bernoulli_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_complement_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_conformations() (in module schrodinger.utils.cgxutils) deserialize_csr_matrix() (in module schrodinger.application.matsci.mlearn.sklearn_json.csr) deserialize_decision_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_decision_tree_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_gaussian_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_gradient_boosting() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_gradient_boosting_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_het_states() (in module schrodinger.application.prepwizard) deserialize_label_binarizer() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_lasso_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_lda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_linear_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_logistic_regression() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_mlp() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_mlp_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_model() (in module schrodinger.application.matsci.mlearn.sklearn_json) deserialize_multinomial_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_params_random_state() (in module schrodinger.application.matsci.mlearn.sklearn_json.common) deserialize_pca() (in module schrodinger.application.matsci.mlearn.sklearn_json.decomposition) deserialize_perceptron() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_qda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_random_forest() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_random_forest_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_ridge_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_svm() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) deserialize_svr() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserialize_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification) (in module schrodinger.application.matsci.mlearn.sklearn_json.regression) deserializeCT() (schrodinger.infra.structure.MmctSerializer static method) deserializeStructure() (schrodinger.infra.structure.MmctSerializer static method) Desmond DESMOND (schrodinger.energy.ANIModel attribute) DESMOND_EXCLUSIONS (schrodinger.energy.MlffModelType attribute) DESMOND_UNIT_CONVERTERS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) DesmondBoxSize (class in schrodinger.application.desmond.system_builder_util) DesmondMDWEdit (class in schrodinger.application.matsci.deswidgets) DesmondMDWidgets (class in schrodinger.application.matsci.deswidgets) DesmondMDWidgets.NUM_FRMS_TYPE (class in schrodinger.application.matsci.deswidgets) DesmondModel (class in schrodinger.application.matsci.desmondutils) DesmondSubhostConfigDialog (class in schrodinger.application.matsci.configdlgs) dest (schrodinger.tasks.cmdline.ArgSpec attribute) destroyAtom() (schrodinger.infra.canvas.ChmMol method) destroyBond() (schrodinger.infra.canvas.ChmMol method) det (schrodinger.application.matsci.elasticity.tensors.SquareTensor property) Detached (schrodinger.ui.qt.pop_up_widgets.PopUpMode attribute) DetailBitset (schrodinger.infra.canvas.ChmMCSRecord attribute) detailed_atom_smarts() (in module schrodinger.application.matsci.rdpattern) DetailMapping (schrodinger.infra.canvas.ChmMCSRecord attribute) DetailNone (schrodinger.infra.canvas.ChmMCSRecord attribute) detailsData() (schrodinger.application.bioluminate.patch_utils.patch_finder.Patch method) detect_custom_mmffld_data() (in module schrodinger.application.matsci.amorphous)

detect_license_file_type() (in module schrodinger.application.licensing.licserver.install) detect_property_types() (in module schrodinger.application.combinatorial_diversity.driver_utils) detect_symmetry_in_het() (in module schrodinger.application.prepwizard) detect_tetrahedral() (in module schrodinger.application.matsci.rxn_channel) DETECTED_LIGAND (schrodinger.application.prepwizard.HetType attribute) determinant() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) determine_active_bonds_info() (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper method) determine_attachment_bonds() (in module schrodinger.application.canvas.r_group) determine_attachments() (in module schrodinger.application.canvas.r_group) determine_box_size() (in module schrodinger.application.matsci.desmondutils) determine_ccd_pdbres() (in module schrodinger.structutils.ccd) determine_gap() (schrodinger.protein.protassign.hbond_cluster.hbond_cluster method) determine_his_ccd_pdbres() (in module schrodinger.structutils.ccd) determine_jobtype() (in module schrodinger.application.inputconfig) (in module schrodinger.ui.qt.appframework2.jobnames) determine_multiplicity() (in module schrodinger.energy) determine_na_type() (in module schrodinger.livedesign.biologics.registration) determine_rgroup_indexes() (in module schrodinger.application.canvas.r_group) determine_rings_in_attachments() (in module schrodinger.application.canvas.r_group) determine_source_path() (in module schrodinger.application.matsci.jobutils) determine_vsepr_geometries_from_file() (in module schrodinger.application.matsci.vsepr) determine_vsepr_geometry() (in module schrodinger.application.matsci.vsepr) determineBasisVectors() (schrodinger.application.matsci.nano.xtal.Crystal method) determineCouplerLocation() (schrodinger.application.matsci.amorphous.BaseMoiety method) determineLatticeNumbering() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) determineMapping() (schrodinger.application.matsci.automated_martini_mapping_protein.Mapper method) determineQueueResource() (schrodinger.application.matsci.jwsteps.BaseNoJobStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) dev_keywords() (in module schrodinger.application.glide.utils) dev_principal_invariants (schrodinger.application.matsci.elasticity.stress.Stress property) development_license_exists() (in module schrodinger.infra.mm) deviator_stress (schrodinger.application.matsci.elasticity.stress.Stress property) DEVICE (schrodinger.application.livedesign.live_report_widget.LiveReportType attribute) DeviceInfo (class in schrodinger.gpgpu) deviceToStr() (schrodinger.energy.MlffDeviceConfig static method) DfCustomEqColumns (class in schrodinger.application.matsci.reaction_workflow_utils) DfCustomRateColumns (class in schrodinger.application.matsci.reaction_workflow_utils) DFG (schrodinger.protein.annotation.KinaseFeatureLabel attribute) DFT (schrodinger.application.jaguar.constants.CalcType attribute) (schrodinger.forcefield.constants.ReferenceEnergyMethod attribute) DFT_BASE_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab attribute) dft_functional (schrodinger.application.matsci.espresso.utils.PseudoData attribute) DFT_GRID_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFT_ONLY (schrodinger.application.jaguar.gui.theory_selector.DftTheorySelectorFilterListPopUp attribute) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListPopUp attribute) DFT_ONLY_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFT_OR_HF_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFTComboRadioSelector (class in schrodinger.application.jaguar.gui.tabs.theory_tab) DFTD3_TBD_KEY (schrodinger.application.matsci.espresso.qeinput.VdwType attribute) DFTNAME (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) dftnames_markup() (in module schrodinger.application.jaguar.jaguar_keyword_utils) DftTheorySelectorFilterListPopUp (class in schrodinger.application.jaguar.gui.theory_selector) DftTheorySelectorFilterListToolButton (class in schrodinger.application.jaguar.gui.theory_selector) DftType (class in schrodinger.application.matsci.espresso.qeinput) dftu (schrodinger.application.matsci.espresso.qeinput.DftType property) DftUType (class in schrodinger.application.matsci.espresso.qeinput) DIAG (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) DIAG_TYPE (schrodinger.application.matsci.espresso.qeinput.GIPAWType attribute) DiagnosticsCollectionError diagonalize_symmat() (in module schrodinger.application.combinatorial_diversity.splitter_utils) Dial (class in schrodinger.ui.qt.dialbox) dial_changed_delta (schrodinger.ui.qt.dialbox.Dial attribute) (schrodinger.ui.qt.dialbox.XYZDialBox attribute) DIAL_NAMES (schrodinger.ui.qt.dialbox.XYZDialBox attribute) dialChangedDelta() (schrodinger.ui.qt.dialbox.XYZDialBox method) dialog() (schrodinger.ui.qt.appframework.ReadDialog method) DIALOG_ID (schrodinger.application.matsci.mswidgets.StructureLoader attribute) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame attribute) DIALOG_SIZE (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog attribute) DialogParameters (class in schrodinger.ui.qt.config_dialog) diameter (schrodinger.application.matsci.atom_group.HelixData attribute) Dict2Values() (in module schrodinger.application.matsci.gsas.GSASIIpwd) dict_delete_and_decrement_keys() (in module schrodinger.application.matsci.rxn_channel) dict_to_str() (in module schrodinger.application.matsci.nano.particle) DictAction (class in schrodinger.application.glide.utils) DictDiff (class in schrodinger.models.diffy) DictParam (class in schrodinger.models.parameters) DictRestrainGroup (class in schrodinger.application.desmond.cms) die() (in module schrodinger.application.glide_ws.merge) died() (schrodinger.pipeline.pipeline.StageJob method) dielco (schrodinger.glide.EnergyOptions attribute) (schrodinger.glide.StrainCorrectionOptions attribute) dielectric (schrodinger.application.jaguar.gui.utils.Solvent attribute) (schrodinger.application.matsci.cgforcefield.VDWData attribute) DIELECTRIC (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) dielectric_293K (schrodinger.application.jaguar.utils.JagSolventParams attribute) dielectric_298K (schrodinger.application.jaguar.utils.JagSolventParams attribute) dielectric_constant (schrodinger.application.jaguar.garza.SolventParams attribute) (schrodinger.structutils.minimize.Minimizer property) dielectricConstant() (schrodinger.infra.fast3d.Volumizer method) DIETHYL_ETHER (schrodinger.energy.Solvent attribute) diff() (in module schrodinger.utils.sea.sea) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.jaguar.results.DerivedAttrs method) (schrodinger.application.jaguar.results.JaguarAtomicResults method) (schrodinger.application.jaguar.results.JaguarResults method) (schrodinger.application.jaguar.results.RoutineTimes method) DiffCompareArgumentParser (class in schrodinger.utils.compare) difference() (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.utils.scollections.IdSet method) difference_update() (schrodinger.utils.scollections.IdSet method) different() (in module schrodinger.application.jaguar.gui.tabs.solvation_tab) DIFFHIGHVAL (schrodinger.application.matsci.rxn_path.ReactionPath attribute) DIFFLOWTHRESH (schrodinger.application.matsci.rxn_path.ReactionPath attribute) DIFFUSION_COL_MAP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSION_FILE_EXT (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis attribute) (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis attribute) DIFFUSION_FILE_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSION_PROPS_MAP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DiffusionGKStep (class in schrodinger.application.matsci.jwsteps) DiffusionMSDStep (class in schrodinger.application.matsci.jwsteps) diffusivity (schrodinger.application.matsci.equilibrium_md.MsdTrajBase.DIFFUSIVITY attribute) DIFFUSIVITY_1D_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_1D_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_1D_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_2D_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_2D_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_2D_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_3D_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_3D_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_3D_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_VECTOR_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_X_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_X_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_X_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Y_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Y_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Y_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Z_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Z_R2_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIFFUSIVITY_Z_SD_PROP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DiffusivityMsdAnalysis (class in schrodinger.application.matsci.equilibrium_md) digest() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) dih (schrodinger.application.desmond.torsion_related.TorsionPotential attribute) Dihedral (class in schrodinger.application.jaguar.hess_guess) DIHEDRAL (schrodinger.application.matsci.rxn_path.Coord attribute) dihedral() (schrodinger.infra.mm.Cartesian static method) dihedral_type (schrodinger.ui.qt.rama.BackboneDihedral attribute) dihedrals (schrodinger.application.jaguar.hess_guess.CoordinateManager property) DihedralSpinBox (class in schrodinger.ui.qt.rama) DIHEDRALWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) DIMENSION_MAP (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) DIMENSIONALITY (class in schrodinger.application.matsci.msconst) Dimer (class in schrodinger.application.matsci.clusterstruct) DimerComplexBuilder (class in schrodinger.application.matsci.buildcomplex) DimerNEBType (class in schrodinger.application.matsci.espresso.qeinput) DimerSpeciesSelector (class in schrodinger.application.matsci.clusterstructgui) DIPEPTIDE_SASA (schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceAreaByResidue attribute) Dipole (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.application.jaguar.results) DIPOLE (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) dipole() (in module schrodinger.application.mopac.results_main) DIPOLE_CAP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) dipole_esp() (in module schrodinger.application.mopac.results_main) DIPOLE_INTERVAL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) DIPOLE_SQ (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SQ_INDEX (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SQ_MEAN (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SQ_MEAN_INDEX (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) dipole_strength_precision (schrodinger.application.jaguar.results.NormalMode attribute) DIPOLE_SUSCEPTIBILITY_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SUSCEPTIBILITY_STD_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) DIPOLE_SUSCEPTIBILITY_STORE_PROP (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) dipole_xyz() (in module schrodinger.application.mopac.results_main) DipoleAnalysis (class in schrodinger.application.matsci.permittivity) DipoleDirector (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.application.matsci.order_parameter_mod) DipoleStrength (schrodinger.application.jaguar.constants.Unit attribute) DiproPredictor (class in schrodinger.protein.predictors) DiproPredictor.DiproFormat (class in schrodinger.protein.predictors) dir (schrodinger.application.combinatorial_explorer.driver_utils.RouteSourceType attribute) DIR (schrodinger.application.matsci.desconfig.MSJStringer attribute) Dir (schrodinger.job.jobcontrol.Job property) DIR_SELECTOR_ID (schrodinger.application.matsci.reportutils.ReportOutputsDialog attribute) DIRECT (schrodinger.application.jaguar.mlff.constants.QRNNModels attribute) DIRECT_2022_1 (schrodinger.energy.QRNNModel attribute) DIRECT_TRANSFER (schrodinger.application.jaguar.mlff.constants.QRNNModels attribute) DIRECT_TRANSFER_2022_3 (schrodinger.energy.QRNNModel attribute) Direction (class in schrodinger.models.presets) (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data) DIRECTION (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) direction (schrodinger.infra.canvas.ChmChiralityInfo attribute) directionChanged() (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) directionDown (schrodinger.infra.canvas.ChmBond attribute) directionNone (schrodinger.infra.canvas.ChmBond attribute) DIRECTIONS (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) directionUp (schrodinger.infra.canvas.ChmBond attribute) Director (class in schrodinger.application.matsci.order_parameter_mod) directories (schrodinger.application.licensing.licserver.exceptions.NoWritableDirectoryError attribute) directory (schrodinger.application.glide_ws.model.Model property) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) directoryChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.ui.qt.directory_selector.DirectorySelector attribute) directoryReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) DirectorySelector (class in schrodinger.ui.qt.directory_selector) DirectoryType (class in schrodinger.job.util) Disable (class in schrodinger.application.bioluminate.pml_menus) (schrodinger.adapter.Canonicalize attribute) (schrodinger.adapter.Generate2DCoordinates attribute) (schrodinger.adapter.LabelAtoms attribute) (schrodinger.adapter.Sanitize attribute) (schrodinger.adapter.UniqueFilter attribute) disable() (schrodinger.project.project.Project method) disable_core() (in module schrodinger.utils.sysinfo) disable_dummy_maestro_imports() (in module schrodinger.infra.unusable_module_importer) disable_dummy_missing_product_imports() (in module schrodinger.infra.unusable_module_importer) disable_dummy_non_post_test_imports() (in module schrodinger.infra.unusable_module_importer) DISABLE_LICENSE_SANITY_CHECK (schrodinger.seam.debug.DebugFlag attribute) disable_local_gpu_check() (in module schrodinger.tasks.hosts) disable_lr_columns (schrodinger.application.livedesign.panel_components.ExportTableModel property) disable_memwatcher_task() (in module schrodinger.seam.testing.fixtures) disable_mmerr (class in schrodinger.infra.mmerr) disable_table_sort() (in module schrodinger.application.matsci.gutils) DISABLE_TYPE_KEY (schrodinger.application.matsci.espresso.qeinput.HPType attribute) disableCapture() (schrodinger.glide.LoggerConfig method) disableConnectCloseAtoms() (schrodinger.infra.structure.MmpdbxReader method) DISABLED (schrodinger.ui.qt.standard.design_tokens.BorderColors attribute) (schrodinger.ui.qt.standard.design_tokens.StateColors attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) disableD3Dispersion() (schrodinger.energy.MlffFixedInteractions method) DISABLED_BUTTON (schrodinger.ui.qt.standard.design_tokens.BackgroundColors attribute) DISABLED_BUTTON_BACKGROUND (schrodinger.ui.qt.standard.colors.LightModeColors attribute) DISABLED_BUTTON_BORDER (schrodinger.ui.qt.standard.colors.LightModeColors attribute) DISABLED_BUTTON_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) DISABLED_FORM_FIELD (schrodinger.ui.qt.standard.design_tokens.BackgroundColors attribute) DISABLED_STYLE (schrodinger.ui.qt.delegates.LinkDelegate attribute) DISABLED_TEXTS (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget attribute) DisabledSymmetryWarning disableDuplicatesElimination() (schrodinger.infra.fast3d.Engine method) disableDyncalc() (schrodinger.application.desmond.packages.staf.GeomAnalyzerBase method) disableResidue() (schrodinger.ui.residueselector.MutationSelectorMixin method) disableResidues() (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) (schrodinger.ui.residueselector.MutationSelectorMixin method) disableSidechainPacking() (schrodinger.protein.reliability.ProteinCheckParameters method) disableSmartDistribution() (schrodinger.job.queue.JobDJ method) disableTestingMode() (schrodinger.infra.structure.MmpdbxReader method) disableUnselectedItems() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) disallow_grpc_workers() (in module schrodinger.seam.testing.fixtures) disallowCisAmides() (schrodinger.infra.fast3d.Engine method) disallowedMutations() (schrodinger.ui.residueselector.ResidueGroups method) discard() (schrodinger.utils.scollections.IdSet method) discard_lewis_data() (in module schrodinger.comparison.atom_mapper) discard_named_m2io_block() (in module schrodinger.infra.structure) discardChanges() (schrodinger.ui.qt.widgetmixins.panelmixins.CleanStateMixin method) disconnect() (schrodinger.application.glide.http_client.ZmqClient method) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.utils.qt_utils.SignalAndSlot method) disconnect_from_workspacehub() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) disconnect_signals() (in module schrodinger.ui.qt.table_helper) DISCONNECTED (schrodinger.application.livedesign.ldclient_proxy.LDConnectionStatus attribute) disconnected (schrodinger.application.livedesign.live_report_widget.LiveReportWidget attribute) disconnectOrigNode() (schrodinger.application.matsci.permittivity.WorkflowParser method) disconnectSignal() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) disconnectSignals() (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable method) disconnectSlots() (schrodinger.application.bioluminate.actions.factory.SAction method) discountedCores() (schrodinger.gpgpu.CudaDevice method) DiscretelySampledFunction (class in schrodinger.application.jaguar.discretized_1d_function) DISE (schrodinger.active_learning.al_utils.SelectionRule attribute) dise_select_ligands() (in module schrodinger.active_learning.al_utils) DiseControl (class in schrodinger.application.vss.control) diseSelect() (schrodinger.active_learning.al_node.PrepareSmilesNode method) DISORDER_SYSTEM (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) Disordered (class in schrodinger.protein.predictors) DisorderedSystemBuilderStep (class in schrodinger.application.matsci.jwsteps) DisorderSystemBuilder (class in schrodinger.application.matsci.permittivity) DISP_COORD_KEY (schrodinger.application.matsci.espresso.qeinput.FPhononControlType attribute) DISP_KEY (schrodinger.application.matsci.espresso.qeinput.FPhononControlType attribute) dispersity() (in module schrodinger.application.matsci.amorphous) displacement_prec (schrodinger.application.jaguar.results.ConvCriteria attribute) display() (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.qt.filter_dialog.FilterDialog method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) display_atoms() (in module schrodinger.application.bioluminate.pml_menus) display_atoms_as() (in module schrodinger.application.bioluminate.pml_menus) DISPLAY_DATA_CLASS (schrodinger.ui.qt.delegates.PictureDelegate attribute) (schrodinger.ui.qt.delegates.RdMolDelegate attribute) (schrodinger.ui.qt.delegates.StructureDelegate attribute) display_image() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.livedesign.cmdline) display_name (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputDef attribute) (schrodinger.application.matsci.builderwidgets.BaseTemplateListWidgetItem property) (schrodinger.application.matsci.builderwidgets.CustomListWidgetItem property) (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem property) (schrodinger.infra.mm.FFVersionData attribute) (schrodinger.protein.properties.SequenceProperty attribute) display_nameChanged (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputDef attribute) (schrodinger.protein.properties.SequenceProperty attribute) display_nameReplaced (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputDef attribute) (schrodinger.protein.properties.SequenceProperty attribute) display_residue() (schrodinger.ui.qt.rama.Rama method) display_ribbons() (in module schrodinger.application.bioluminate.pml_menus) display_string (schrodinger.livedesign.registration.RegistrationData attribute) display_structure() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.Rama method) displayDefault() (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec method) displayedEntryIds() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) displayedSurfacesUpdated (schrodinger.maestro_utils.surface_manager.surface_model.SurfaceModel attribute) (schrodinger.maestro_utils.surface_manager.surface_table.SurfaceTable attribute) displayLocalAtoms() (schrodinger.application.matsci.sliceplot.SlicePlot method) DisplayOnly (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_data) displayProperties() (schrodinger.ui.qt.propertyselector.PropertySelector method) displayPropsDialog() (schrodinger.ui.two_d_viewer.TwoDViewer method) DisplaySettingsData (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_data) DisplaySettingsManager (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_manager) DisplayStatus (class in schrodinger.job.jobcontrol) (schrodinger.job.jobcontrol.Job property) displayTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) DisproPredictor (class in schrodinger.protein.predictors) Dissimilar (schrodinger.protein.alignment.ResidueSimilarity attribute) dissociate() (schrodinger.application.matsci.rxn_channel.ReactantMolecule method) DISSOCIATION_BOND_LENGTH (schrodinger.application.matsci.rxn_channel.Constants attribute) DISSOCIATION_TYPE (schrodinger.application.matsci.rxn_channel.Constants attribute) dist (schrodinger.application.glide.utils.ResidueInteraction attribute) dist3() (in module schrodinger.application.bindingsite.cavutils) dist_cell_iterator() (in module schrodinger.structutils.measure) DIST_KEY (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) Distance (class in schrodinger.application.desmond.packages.analysis) distance (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) DISTANCE (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) distance (schrodinger.application.qsite.input.HydrogenCap property) (schrodinger.structutils.interactions.pi.CationPiInteraction property) (schrodinger.structutils.interactions.pi.PiPiInteraction property) DISTANCE (schrodinger.trajectory.trajectory_gui_dir.banners.MeasurementMode attribute) distance() (schrodinger.infra.mm.Cartesian static method) distance_cutoff (schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter attribute) (schrodinger.energy.MetalForceFieldTyperPolicy attribute) distance_from_planckian() (in module schrodinger.application.matsci.colorutils) DISTANCE_THRESH (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) distance_vectors() (in module schrodinger.application.jaguar.hess_guess) DistanceCell (class in schrodinger.infra.structure) DistanceCellIterator (class in schrodinger.structutils.measure) distanceChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) DistanceMatrixPlotDialog (class in schrodinger.application.canvas.clustergui) distanceReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) distanceTo() (schrodinger.infra.canvas.ChmAtoms method) distDixon() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) distEuclidean() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) distHamming() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) DISTINCT_SCAFFOLDS (schrodinger.active_learning.al_utils.SelectionRule attribute) DistinctStructures (class in schrodinger.application.transforms.filters) Distortion (class in schrodinger.structutils.check) distPatternDifference() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) distributeCpus() (schrodinger.pipeline.pipeline.Pipeline method) DistributedFrequenciesInput (class in schrodinger.application.jaguar.distributed_frequencies.input) DistributedGlideBaseNode (class in schrodinger.application.glide_ws.nodes) DistributedJobMixin (class in schrodinger.application.glide_ws.nodes) DistributedMMGBSABaseNode (class in schrodinger.application.glide_ws.nodes) distributions (schrodinger.seam.metric.UserMetrics attribute) distShape() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) distSize() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) distSoergel() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) distSquaredEuclidean() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) distTanimoto() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) distVariance() (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) DISULFIDE (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) disulfide_bond (schrodinger.protein.residue.CombinedChainResidueWrapper property) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) disulfide_bonds (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.sequence.AbstractProteinSequenceMixin property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.protein.sequence.ProteinSequence property) DisulfideBond (class in schrodinger.protein.residue) disulfideBondsCacheCleared (schrodinger.protein.sequence.AbstractProteinSequenceMixin attribute) DisulfideConnectorMixin (class in schrodinger.protein.helm.helm_renderer) DisulfideCyclicConnectorItem (class in schrodinger.protein.helm.helm_renderer) DisulfideLinearConnectorItem (class in schrodinger.protein.helm.helm_renderer) DISULFIDES (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) disulfides (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) disulfidesChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) disulfidesReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) DIVERSITY (schrodinger.active_learning.al_utils.SelectionRule attribute) DiversityFingerprinter (class in schrodinger.application.combinatorial_diversity.diversity_fingerprinter) diversitySelect() (schrodinger.active_learning.al_node.PrepareSmilesNode method) DiversitySelector (class in schrodinger.application.combinatorial_diversity.diversity_selector) DiversitySplitter (class in schrodinger.application.combinatorial_diversity.diversity_splitter) divide() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) Divider (class in schrodinger.application.matsci.mswidgets) DLG_TITLE (schrodinger.application.matsci.jobdirdlg.InteractiveFileDownloader attribute) dlst() (schrodinger.application.macromodel.utils.ComUtil method) DMF (schrodinger.energy.Solvent attribute) DMSO (schrodinger.energy.Solvent attribute) DNA (schrodinger.application.bioluminate.mutation.PolymerType attribute) DNA_ANTISENSE (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) DNA_SENSE (schrodinger.livedesign.biologics.fasta.FastaHeader attribute) DNASequence (class in schrodinger.protein.sequence) do() (schrodinger.utils.pymol.PymolInstance method) do_any_residues_have_missing_side_chains() (in module schrodinger.application.prepwizard) do_cleanup (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_cleanupChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_cleanupReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_force (schrodinger.energy.MlffPostProcessSteps attribute) do_GET() (schrodinger.application.glide.http_server.GlideHTTPHandler method) do_hbond (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_hbondChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_hbondReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) DO_NOT_CHECK_PATH (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) do_nothing() (schrodinger.application.bioluminate.protein_structure_quality.FakeMaestro method) do_POST() (schrodinger.application.glide.http_server.GlideHTTPHandler method) do_preprocess (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_preprocessChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_preprocessReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) do_virial (schrodinger.energy.MlffPostProcessSteps attribute) doAnd() (in module schrodinger.infra.canvas) doApplyClustering() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) doBonding() (schrodinger.application.matsci.crest.CrestCSearch method) (schrodinger.application.matsci.nano.xtal.Crystal method) doBondOrders() (schrodinger.application.matsci.nano.tube.NanoTube method) (schrodinger.application.matsci.nano.xtal.Crystal method) doc (schrodinger.project.project.ProjectRow attribute) DoCalibInst() (in module schrodinger.application.matsci.gsas.GSASIIpwd) Dock (class in schrodinger.application.glide.job) (class in schrodinger.application.transforms.dock) dock() (schrodinger.application.glide.http_client.AbstractHTTPClient method) (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.glide.http_client.HTTPClient method) (schrodinger.application.glide.http_client.NonBlockingHTTPClient method) (schrodinger.application.glide.http_client.ZmqClient method) dock_from_structures() (in module schrodinger.application.glide.runner) dock_widget (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) DockableMixinCollection (class in schrodinger.ui.qt.widgetmixins.basicmixins) dockBatch() (schrodinger.application.glide.http_client.NonBlockingGlideServerManager method) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) dockConformerEnsemble() (schrodinger.glide.Docker method) DockedPoses (class in schrodinger.application.livedesign.entry_types) Docker (class in schrodinger.glide) docking_config_setup() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage method) docking_job() (schrodinger.application.glide_ws.model.Complex method) docking_keywords (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) docking_keywordsChanged (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) docking_keywordsReplaced (schrodinger.application.glide.ligand_designer.BuildServerTask.Input attribute) docking_params (schrodinger.application.transforms.dockers.multi_receptor_dock.MultiReceptorDockSettings attribute) (schrodinger.application.transforms.dockers.redock.ReDockSettings attribute) docking_params() (schrodinger.application.glide_ws.driver.GlideWSJob method) docking_sif() (schrodinger.application.glide_ws.model.Complex method) DockingLicense() (in module schrodinger.glide) DockingLicenseRequirements (class in schrodinger.application.glide.license_requirements) DockingStage (class in schrodinger.pipeline.stages.glide) DockingWorkflowOptions (class in schrodinger.application.glide.runner) dockSmiles() (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.glide.http_client.HTTPClient method) (schrodinger.application.glide.http_client.NonBlockingHTTPClient method) DockWidget (class in schrodinger.ui.qt.appframework2.baseapp) doCluster() (schrodinger.application.macromodel.utils.CluUtil method) doCommand() (schrodinger.application.matsci.jobutils.LoggingSubprocessJob method) (schrodinger.application.matsci.packmol.StdInJob method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.utils.installation_check.TestJob method) docstring (schrodinger.application.livedesign.models2.datamodels.definition.DefinitionMetadata attribute) (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputDef attribute) docstringChanged (schrodinger.application.livedesign.models2.datamodels.definition.DefinitionMetadata attribute) (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputDef attribute) docstringReplaced (schrodinger.application.livedesign.models2.datamodels.definition.DefinitionMetadata attribute) (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputDef attribute) doctype() (schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method) documentationRequested (schrodinger.ui.qt.swidgets.HelpButton attribute) Dodecahedron (class in schrodinger.application.matsci.shapes) dodecahedron() (schrodinger.application.watermap.shapes.ShapeFactory method) doEnumeration() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) does_res_have_missing_side_chains() (in module schrodinger.application.prepwizard) doGroup() (schrodinger.utils.pymol.RowProxy method) domain (schrodinger.application.bioluminate.antibody.sequence_indexer.DVDSequenceIndexer property) (schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo attribute) (schrodinger.application.bioluminate.antibody.sequence_indexer.SingleDomainAbSequenceIndexer property) Domain (schrodinger.protein.annotation.Domains attribute) domain_structure (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction attribute) DomainAlignment (class in schrodinger.application.bioluminate.anarci.anarci_adapter) DomainArrangement (class in schrodinger.protein.predictors) DomainAssemblyInstruction (class in schrodinger.application.bioluminate.antibody.assembly) DomainForming (schrodinger.protein.predictors.DomainArrangement attribute) DomainNumbering (class in schrodinger.application.bioluminate.anarci.anarci_adapter) Domains (class in schrodinger.protein.annotation) domains (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) domainsChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin attribute) DomproPredictor (class in schrodinger.protein.predictors) donateNodes() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) done (schrodinger.application.pathfinder.analysis.RetrosynthesisState attribute) DONE (schrodinger.job.queue.JobState attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.Status attribute) done_jobs (schrodinger.job.queue.JobDJ property) done_tasks (schrodinger.tasks.queue.QueueResults attribute) done_tasksChanged (schrodinger.tasks.queue.QueueResults attribute) done_tasksReplaced (schrodinger.tasks.queue.QueueResults attribute) doneEditingSMARTS() (schrodinger.ui.qt.swidgets.SMARTSEdit method) doneReordering() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) doNonLinearFit() (schrodinger.application.matsci.rxn_path.ReactionPath method) donor_atom (schrodinger.glide.HBond attribute) donor_attractive (schrodinger.glide.SiteGridDescriptors attribute) DONOR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) donor_repulsive (schrodinger.glide.SiteGridDescriptors attribute) DonorConstraint (class in schrodinger.application.glide.constraints) donors (schrodinger.protein.protassign.utils.Interactors attribute) DoNothing (schrodinger.ui.qt.config_dialog.RequestedAction attribute) dont_ignore_stereo() (in module schrodinger.application.glide.utils) doOr() (in module schrodinger.infra.canvas) DoPeakFit() (in module schrodinger.application.matsci.gsas.GSASIIpwd) doPropertyEvaluation() (schrodinger.application.matsci.nano.xtal.Crystal method) doPropsMatch() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method) doQuery() (schrodinger.ui.qt.appframework2.af2.KBotFrame method) DOS (class in schrodinger.application.matsci.espresso.qeoutput) DOS_FREQ_DEGAUSS (schrodinger.application.matsci.espresso.qeoutput.PhDOS attribute) DOS_FREQ_GRID_SPACING (schrodinger.application.matsci.espresso.qeoutput.PhDOS attribute) doStateOptimizations() (schrodinger.application.matsci.mecp_mod.MECP method) DOT (schrodinger.application.matsci.desconfig.MSJStringer attribute) dot (schrodinger.surface.Style attribute) (schrodinger.surface.Surface.Style attribute) dot() (schrodinger.pipeline.pipeutils.DotPrinter method) dot_endpoint() (schrodinger.seam.viz.watcher.WatcherWebServer method) doTermination() (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.slab.Surface method) (schrodinger.application.matsci.nano.tube.NanoTube method) DotPrinter (class in schrodinger.pipeline.pipeutils) dotprod() (in module schrodinger.application.desmond.cms) doTranslation() (schrodinger.application.matsci.nano.xtal.Crystal method) DOUBLE (schrodinger.energy.ANIPrecision attribute) Double (schrodinger.energy.MlffPrecision attribute) (schrodinger.structure.BondType attribute) DOUBLE_DISPLACEMENT_TYPE (schrodinger.application.matsci.rxn_channel.Constants attribute) DOUBLE_PRECISION (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) DOUBLE_SIDED_HBOND_PKA_SHIFT (schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor attribute) doubleCenter() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) DoubleClickButtonMixin (class in schrodinger.ui.qt.standard_widgets.buttons) doubleClicked (schrodinger.ui.qt.standard_widgets.buttons.DoubleClickButtonMixin attribute) DoubleClickSplitStyledButton (class in schrodinger.ui.qt.standard_widgets.buttons) doublequote (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) doubleRingAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) DoubleSigmoid (class in schrodinger.math.multi_parameter_optimization) doubted_geom() (in module schrodinger.application.jaguar.textparser) DOWN (schrodinger.models.presets.Direction attribute) DOWN_ARROW (schrodinger.ui.qt.standard.design_tokens.ScrollbarIcons attribute) download() (schrodinger.job.jobcontrol.Job method) download_all_entry_data() (in module schrodinger.protein.gpcr.gpcrdb) download_and_decompress() (in module schrodinger.application.pathfinder.multiroute) download_blob() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) download_cif() (in module schrodinger.protein.getpdb) download_definition() (in module schrodinger.application.livedesign.models2.io.definition) download_em_map() (in module schrodinger.protein.getpdb) download_exported_csv_from_bucket() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) download_fasta() (in module schrodinger.protein.getpdb) download_file() (in module schrodinger.protein.getpdb) DOWNLOAD_FILE_ENDINGS (schrodinger.application.matsci.jobdirdlg.DownloadingMonitorMixin attribute) download_format() (in module schrodinger.protein.getpdb_utility) download_from_url() (in module schrodinger.autoinstall.misc) download_icon_tooltip() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) download_instance() (in module schrodinger.application.livedesign.models2.io.instance) download_job() (in module schrodinger.job.download) download_ld_client() (in module schrodinger.application.livedesign.login) download_linux_packages_requirement() (in module schrodinger.utils.installation_check) download_nodelocked_license() (in module schrodinger.application.licensing.licadmin) download_pdb() (in module schrodinger.protein.getpdb) DOWNLOAD_PENDING (schrodinger.application.job_monitor.job_monitor_models.DownloadStatus attribute) download_release() (in module schrodinger.autoinstall.suite_install) download_server_license() (in module schrodinger.application.licensing.licadmin) download_sf() (in module schrodinger.protein.getpdb) download_slurm() (in module schrodinger.autoinstall.slurm_install) download_status (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) download_statusChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) download_statusReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) download_structures (schrodinger.protein.tasks.blast.BlastSettings attribute) download_structuresChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) download_structuresReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) DOWNLOADED (schrodinger.application.job_monitor.job_monitor_models.DownloadStatus attribute) downloadFile() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) downloadFilesToDir() (schrodinger.application.matsci.jobdirdlg.InteractiveFileDownloader method) DownloadingMonitorMixin (class in schrodinger.application.matsci.jobdirdlg) downloadJobFiles() (schrodinger.application.matsci.jobdirdlg.DownloadingMonitorMixin method) downloadJobFilesIfNecessary() (schrodinger.application.matsci.jobdirdlg.DownloadingMonitorMixin method) downloadJobFileToTemp() (schrodinger.application.matsci.jobdirdlg.InteractiveFileDownloader method) (schrodinger.application.matsci.jobutils.FileDownloader method) DownloadRandomSmiles (class in schrodinger.seam.examples.lipinski) DownloadStatus (class in schrodinger.application.job_monitor.job_monitor_models) doXCluster() (schrodinger.application.macromodel.utils.CluUtil method) doXor() (in module schrodinger.infra.canvas) DpdMapper (class in schrodinger.application.matsci.automated_cg_mapping) DpdMolecule (class in schrodinger.application.matsci.automated_cg_mapping) dpi (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) Dpi150 (schrodinger.ui.two_d_viewer.DpiMode attribute) Dpi300 (schrodinger.ui.two_d_viewer.DpiMode attribute) dpi_mode (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) dpi_modeChanged (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) dpi_modeReplaced (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) DpiMode (class in schrodinger.ui.two_d_viewer) dpiRadioToggled() (schrodinger.ui.two_d_viewer.SaveImagesDialog method) DRACO_PCM_RADII (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) drag() (schrodinger.ui.qt.rama.Rama method) dragEnterEvent() (schrodinger.ui.two_d_viewer.TwoDTableView method) draw() (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.application.matsci.permittivity.WorkflowParser method) draw2DPicture() (schrodinger.ui.qt.structure2d.LabeledStructureToolTip method) draw_axes() (schrodinger.ui.qt.rama.RamaContourMixin method) draw_image() (in module schrodinger.livedesign.draw) draw_picture_into_rect() (in module schrodinger.ui.qt.structtable) (in module schrodinger.ui.qt.swidgets) draw_regions() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.RamaContourMixin method) DRAW_STYLE (schrodinger.ui.qt.delegates.CheckboxDelegate attribute) (schrodinger.ui.qt.delegates.ProgressBarDelegate attribute) (schrodinger.ui.qt.delegates.RadioButtonDelegate attribute) DRAW_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) drawAndUpdate() (schrodinger.ui.qt.smatplotlib.SmatplotlibCanvas method) drawChmmol() (schrodinger.ui.qt.structure2d.StructurePicture method) drawDataIntoRect() (schrodinger.ui.qt.table.StructureDataViewerDelegate method) drawFixedContents() (schrodinger.application.matsci.reportutils.CanvasWithHeaderAndFooter method) drawPlot() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) drawRDMol() (schrodinger.ui.qt.structure2d.StructurePicture method) drawStructure() (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.ui.qt.structure2d.StructurePicture method) drawTicks() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) driv() (schrodinger.application.macromodel.utils.ComUtil method) DRIVER (schrodinger.application.matsci.jwsteps.BaseNoJobStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.FreeVolumeStep attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.RDFStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) (schrodinger.application.matsci.jwsteps.VoidStep attribute) driver (schrodinger.application.matsci.multiapp.CMD_DRIVER_DATA attribute) DRIVER_HOST (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog attribute) driver_host_settings (schrodinger.application.livedesign.tasks.AbHumanizationTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MultisimTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) driver_host_settingsChanged (schrodinger.application.livedesign.tasks.AbHumanizationTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MultisimTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) driver_host_settingsReplaced (schrodinger.application.livedesign.tasks.AbHumanizationTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MultisimTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) driver_logging() (in module schrodinger.application.matsci.textlogger) driver_main() (in module schrodinger.application.matsci.jobutils) DRIVER_PATH (schrodinger.application.matsci.jwsteps.BaseNoJobStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.CombinerStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionGKStep attribute) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.EvaporationStep attribute) (schrodinger.application.matsci.jwsteps.ExtractClustersStep attribute) (schrodinger.application.matsci.jwsteps.FreeVolumeStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep attribute) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.RDFStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StressStrainStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.ViscosityStep attribute) (schrodinger.application.matsci.jwsteps.VoidStep attribute) (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) (schrodinger.application.matsci.permittivity.AveCellAnalysis attribute) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) (schrodinger.application.matsci.permittivity.CMSParser attribute) (schrodinger.application.matsci.permittivity.DensityAnalysis attribute) (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) (schrodinger.application.matsci.permittivity.JaguarMerge attribute) (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) (schrodinger.application.matsci.permittivity.StaticPermittivity attribute) (schrodinger.application.matsci.permittivity.StepBase attribute) DRIVERHOST (schrodinger.utils.cmdline.Options attribute) DriverParser (class in schrodinger.application.matsci.parserutils) driverReservesCores() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) DROPDOWN_BUTTON (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) DROPDOWN_LINK (schrodinger.ui.qt.standard.design_tokens.ButtonTypes attribute) dropEvent() (schrodinger.ui.two_d_viewer.TwoDTableView method) dropped_file (schrodinger.application.livedesign.tasks.AbHumanizationTask.Output attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) dropped_fileChanged (schrodinger.application.livedesign.tasks.AbHumanizationTask.Output attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) dropped_fileReplaced (schrodinger.application.livedesign.tasks.AbHumanizationTask.Output attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) DRUG_DISCOVERY (schrodinger.application.livedesign.ldclient_proxy.LDMode attribute) DrugLikeSplitStage (class in schrodinger.pipeline.stages.filtering) DRX (schrodinger.application.matsci.kmc.PairsMixin attribute) DRY (schrodinger.application.matsci.kmc.PairsMixin attribute) DRZ (schrodinger.application.matsci.kmc.PairsMixin attribute) DS_DNA (schrodinger.livedesign.entity_type.EntityClass attribute) DS_RNA (schrodinger.livedesign.entity_type.EntityClass attribute) DSB_DRIVER (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) DSC (class in schrodinger.application.desmond.arkdb) DSC_ACCEP (schrodinger.glide.Ptype attribute) DSC_DEFAULT (schrodinger.glide.Ptype attribute) DSC_DONOR (schrodinger.glide.Ptype attribute) DSC_HALO_ACCEP (schrodinger.glide.Ptype attribute) DSC_HALO_DONOR (schrodinger.glide.Ptype attribute) DSC_MAX_BASE (schrodinger.glide.Ptype attribute) DSC_METAL (schrodinger.glide.Ptype attribute) DSC_PHOBHVY (schrodinger.glide.Ptype attribute) DSC_PHOBHYD (schrodinger.glide.Ptype attribute) DSC_POLAR (schrodinger.glide.Ptype attribute) Dsp2pos() (in module schrodinger.application.matsci.gsas.GSASIIlattice) dsq (schrodinger.application.matsci.clusterstruct.Neighbor attribute) dt_au (schrodinger.application.matsci.espresso.qeinput.MdType property) DTDTreeBuilder (class in schrodinger.application.jaguar.keywordDB) DTR (schrodinger.application.desmond.packages.traj.Fmt attribute) DtrSource (class in schrodinger.application.desmond.packages.traj) DTYPE (schrodinger.application.desmond.cms.FBHWPosRestrainArray attribute) (schrodinger.application.desmond.cms.PosRestrainArray attribute) DU_BUTTON_ID (schrodinger.ui.qt.periodictable.PeriodicTableDialog attribute) DU_ELEMENT (schrodinger.ui.qt.periodictable.PeriodicTableDialog attribute) DU_SYMBOL (schrodinger.ui.qt.periodictable.PeriodicTableDialog attribute) DuckFrame (class in schrodinger.application.desmond.packages.topo) DummiesToHydrogens (class in schrodinger.application.matsci.buildcomplex2d) DUMMY (schrodinger.energy.MonoMetalComplexType attribute) DUMMY_ATOMIC_NUMBER (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae attribute) DUMMY_ELEMENT (schrodinger.application.matsci.cg_mapping.CoarseGrainBond attribute) DUMMY_FIELDS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) DummyCalculateScoreNode (class in schrodinger.active_learning.fake_nodes) DummyComplex (class in schrodinger.energy) DummyComplex_create() (in module schrodinger.energy) DummyGpuHost (class in schrodinger.ui.qt.config_dialog) DummyMaestroModule (class in schrodinger.infra.unusable_module_importer) DummyMaker (class in schrodinger.application.matsci.etatoggle) DummyModule (class in schrodinger.infra.unusable_module_importer) DummyPilotScoreNode (class in schrodinger.active_learning.fake_nodes) DummyRescoreNode (class in schrodinger.active_learning.fake_nodes) dump() (in module schrodinger.models.json) (schrodinger.job.queue.JobDJ method) (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.stage.Stage method) (schrodinger.utils.preferences.PreferenceFile method) (schrodinger.utils.sea.sea.Sea method) dump_output_csv_file() (in module schrodinger.application.jaguar.macro_pka_utils) dump_yaml_file() (in module schrodinger.application.matsci.yamlutils) dumps() (in module schrodinger.models.json) dumpSavedItems() (schrodinger.ui.qt.swidgets.ItemsManagerMixin method) Duplicate (class in schrodinger.application.bioluminate.pml_menus) DUPLICATE (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) duplicate_and_enumerate_replicate() (in module schrodinger.application.peptide_workflow.beam_adapter) DuplicateColumnError duplicateRelaxStage() (schrodinger.application.matsci.permittivity.MdStageModifier method) duplicateRings() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) duration (schrodinger.application.jaguar.output.JaguarOutput property) (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) (schrodinger.seam.runners.events.PipelineFinished attribute) (schrodinger.seam.viz.inspect.PipelineDisplayInfo attribute) durationChanged (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) (schrodinger.seam.runners.events.PipelineFinished attribute) durationEdited() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) durationOptionChanged() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) durationReplaced (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) (schrodinger.seam.runners.events.PipelineFinished attribute) DurationType (class in schrodinger.trajectory.trajectory_gui_dir.export_movie) dval (schrodinger.utils.sea.sea.Atom property) (schrodinger.utils.sea.sea.List property) (schrodinger.utils.sea.sea.Map property) DVDSequenceIndexer (class in schrodinger.application.bioluminate.antibody.sequence_indexer) DYNAMIC_SORT_FILTER (schrodinger.ui.qt.table_helper.PythonSortProxyModel attribute) DynamicAslAnalyzer (class in schrodinger.application.desmond.packages.staf) DynamicPositerAnalyzer (class in schrodinger.application.desmond.packages.staf) dynamics (schrodinger.application.matsci.espresso.qeinput.IonControlType property) DynamicTypeDelegate (class in schrodinger.ui.qt.mapperwidgets.param_editor) DynamXColumns (class in schrodinger.application.bioluminate.pose_filtering.hdx_io)

E

e (schrodinger.comparison.dedup_utils.CrystalData attribute) (schrodinger.comparison.results.OptResult attribute) (schrodinger.comparison.results.SyncedOptResult attribute) E_ANNIHILIATIONS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) E_INJECTIONS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) e_xvol (schrodinger.glide.EnergyComponents attribute) EA2DEBYE (schrodinger.application.desmond.packages.analysis.Dipole attribute) EA_LABEL() (in module schrodinger.application.matsci.cgforcefieldgui) eaf_file (schrodinger.application.livedesign.tasks.EventAnalysisTask.Input attribute) eaf_fileChanged (schrodinger.application.livedesign.tasks.EventAnalysisTask.Input attribute) eaf_fileReplaced (schrodinger.application.livedesign.tasks.EventAnalysisTask.Input attribute) EANION (schrodinger.application.matsci.kmc.SegmentsTable attribute) early_stop() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) ECATION (schrodinger.application.matsci.kmc.SegmentsTable attribute) ECD_Spectrum (class in schrodinger.application.matsci.spectra) ECDSAWithSHA256 (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) ECDSAWithSHA384 (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) ECDSAWithSHA512 (schrodinger.application.licensing.licserver.client.SignatureAlgorithm attribute) ECL (schrodinger.protein.annotation.GPCRSegmentLabel attribute) ecoul (schrodinger.glide.ScoreTerms attribute) ecutrho (schrodinger.application.matsci.espresso.utils.PPSpecies attribute) (schrodinger.application.matsci.espresso.utils.PseudoData attribute) ecutwfc (schrodinger.application.matsci.espresso.utils.PPSpecies attribute) (schrodinger.application.matsci.espresso.utils.PseudoData attribute) EDA (class in schrodinger.trajectory.prody.pca) Edge (class in schrodinger.application.matsci.shapes) (class in schrodinger.ui.qt.network_visualizer) edge (schrodinger.structure._Ring property) EDGE_TO_FACE (schrodinger.infra.structure.PiPiInteraction attribute) edgeCount() (schrodinger.ui.qt.network_visualizer.Graph method) edgeHovered() (schrodinger.ui.qt.network_views.NetworkViewer method) edgeMenu() (schrodinger.ui.qt.network_views.NetworkViewer method) EDGES (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) (schrodinger.ui.qt.schart.BinsDialog attribute) edges() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) EDGES_ADDED (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) EDGES_DELETED (schrodinger.ui.qt.network_visualizer.SyncLevels attribute) edgesChanged (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) EDGETYPE1 (schrodinger.application.matsci.nano.constants.Constants attribute) EDGETYPE2 (schrodinger.application.matsci.nano.constants.Constants attribute) EDGETYPES (schrodinger.application.matsci.nano.constants.Constants attribute) edgeUnhovered() (schrodinger.ui.qt.network_views.NetworkViewer method) EDIT (schrodinger.application.livedesign.mapping_widgets.MappingMode attribute) EDIT_DLG_CLASS (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) EDIT_ICON (schrodinger.application.livedesign.panel_components.AbstractSelectionPopUpDelegate attribute) (schrodinger.ui.qt.delegates.AbstractDelegateWithEditIcon attribute) (schrodinger.ui.qt.delegates.ComboBoxDelegate attribute) edit_parameters() (schrodinger.ui.qt.navtoolbar.NavToolbar method) EDITABLE_COLS (schrodinger.ui.qt.table_helper.RowBasedModelMixin attribute) EDITABLE_ITEM (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) EditButton (class in schrodinger.ui.qt.swidgets) EditDialog (class in schrodinger.application.jaguar.gui.edit_dialog) editFigureOptions() (schrodinger.ui.qt.navtoolbar.NavToolbar method) editingFinished (schrodinger.application.phase.phase_markers.PhaseMarkers attribute) editInput() (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) editorEvent() (schrodinger.application.job_monitor.job_monitor_table.JobDetailsArrowDelegate method) (schrodinger.ui.qt.delegates.CheckboxDelegate method) (schrodinger.ui.qt.delegates.PushButtonDelegate method) (schrodinger.ui.qt.delegates.ToolTipIconDelegate method) (schrodinger.ui.qt.delegates.WorkspaceInclusionDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) EditWithFocusOutEvent (class in schrodinger.ui.qt.swidgets) EDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) EELS (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) ef_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) EFERMI_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) eff_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) effectiveRadius() (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) efield (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) efp_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) efs_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) eigenvalues (schrodinger.energy.LfmmOutput attribute) (schrodinger.energy.MetalComplexOutput attribute) eigenvalues() (in module schrodinger.application.mopac.results_main) eigenvectors() (in module schrodinger.application.mopac.results_main) einsum_sequence() (schrodinger.application.matsci.elasticity.tensors.Tensor method) Eint (schrodinger.application.glide.utils.ResidueInteraction attribute) El2EstVol() (in module schrodinger.application.matsci.gsas.GSASIImath) El2Mass() (in module schrodinger.application.matsci.gsas.GSASIImath) elapsed (schrodinger.utils.profiling.Timer property) elapsed_timer() (in module schrodinger.application.matsci.permittivity) ElapsedFormatter (class in schrodinger.stepper.stepper) ElasticConstantsStep (class in schrodinger.application.matsci.jwsteps) ElasticConstantsStressStep (class in schrodinger.application.matsci.jwsteps) ElasticControlType (class in schrodinger.application.matsci.espresso.qeinput) ElasticTensor (class in schrodinger.application.matsci.elasticity.elastic) ElasticType (class in schrodinger.application.matsci.espresso.qeinput) ele_smoothing() (in module schrodinger.application.bioluminate.patch_utils.msurfext) elec (schrodinger.application.jaguar.results.ThermoComponents attribute) ELECTRIC_POLARIZABILITY (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_FREQ_PROP (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_INTERCEPT (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_INTERCEPT_FREQ (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_PROP (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_SLOPE (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ELECTRIC_POLARIZABILITY_SLOPE_FREQ (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) ElectricPolarizability (class in schrodinger.application.matsci.permittivity) electron_transfer() (in module schrodinger.application.jaguar.textparser) ElectronControlType (class in schrodinger.application.matsci.espresso.qeinput) electronic (schrodinger.application.jaguar.results.SolvThermoProp attribute) (schrodinger.application.jaguar.results.ThermoProp attribute) electronic_e() (in module schrodinger.application.jaguar.textparser) electrostatic14_energy() (in module schrodinger.application.qsite.output) electrostatic_energy() (in module schrodinger.application.qsite.output) electrostatic_reward (schrodinger.glide.ScoreDescriptors attribute) (schrodinger.glide.ScoreTerms attribute) Electrostatics (schrodinger.energy.MlffFixedInteractionType attribute) element (schrodinger.application.matsci.espresso.utils.PseudoData attribute) ELEMENT (schrodinger.application.matsci.kmc.AtomsTable attribute) element (schrodinger.application.matsci.sculptcomplex.SiteAtom attribute) (schrodinger.structure.StructureAtom property) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSpec attribute) ELEMENT1 (schrodinger.application.matsci.nano.constants.Constants attribute) ELEMENT2 (schrodinger.application.matsci.nano.constants.Constants attribute) elemental_generator() (in module schrodinger.application.matsci.mlearn.features) elemental_mutator() (in module schrodinger.application.matsci.genetic_optimization) ElementAlchemist (class in schrodinger.application.matsci.enumeration) ElementalProperties (class in schrodinger.application.matsci.elementalprops) ElementButton (class in schrodinger.ui.qt.periodictable) elementChanged (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) ElementClass (schrodinger.protein.sequence.AbstractSequence attribute) (schrodinger.protein.sequence.CombinedChainProteinSequence attribute) (schrodinger.protein.sequence.NucleicAcidSequence attribute) (schrodinger.protein.sequence.ProteinSequence attribute) ElementEdit (class in schrodinger.application.matsci.atomicsymbolsgui) ElementListEdit (class in schrodinger.application.matsci.atomicsymbolsgui) ElementListValidator (class in schrodinger.application.matsci.atomicsymbolsgui) elementReplaced (schrodinger.ui.qt.atom_weights_table_widget.AtomWeight attribute) ELEMENTS (schrodinger.application.jaguar.xray.constants.KEYWORDS attribute) elements (schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo attribute) ELEMENTS (schrodinger.ui.qt.periodictable.PeriodicTableDialog attribute) elementSelected (schrodinger.ui.qt.periodictable.PeriodicTableDialogSingleClick attribute) elementsToContiguousColumns() (schrodinger.protein.alignment.BaseAlignment method) elementsToken (schrodinger.infra.canvas.MCSsettings attribute) ElementType (class in schrodinger.protein.residue) ElementValidator (class in schrodinger.application.matsci.atomicsymbolsgui) ElemPosition() (in module schrodinger.application.matsci.gsas.GSASIIspc) elide_rich_text() (in module schrodinger.ui.qt.swidgets) ElidedLabel (class in schrodinger.ui.qt.swidgets) ElidedLineEdit (class in schrodinger.ui.qt.swidgets) ElidedTextHTMLParser (class in schrodinger.ui.qt.swidgets) ElidedTextHTMLParser.HTMLType (class in schrodinger.ui.qt.swidgets) elideRichText() (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) eliminatePairs() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) eliminateSingles() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) ellipseSize() (in module schrodinger.application.matsci.gsas.GSASIIpwd) ellipseSizeDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd) elmnt_mult_dict() (in module schrodinger.application.jaguar.utils) ElongatedMicelleInputFile (class in schrodinger.application.matsci.packmol) elst() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.ComUtilAppSci method) email (schrodinger.tasks.test.cli.customized_param_cli.User attribute) emailChanged (schrodinger.tasks.test.cli.customized_param_cli.User attribute) emailReplaced (schrodinger.tasks.test.cli.customized_param_cli.User attribute) EmbeddedSolventWidget (class in schrodinger.application.matsci.jagwidgets) embl (schrodinger.utils.fileutils.SeqFormat attribute) EmbraceConfSearch (class in schrodinger.application.macromodel.input) EmbraceMinimization (class in schrodinger.application.macromodel.input) emit() (schrodinger.utils.qt_utils.SignalAndSlot method) emitAddMarker() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) emitAnnTitleChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitCountChanged() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) emitElementSelected() (schrodinger.ui.qt.periodictable.PeriodicTableDialogSingleClick method) emitRemoveMarker() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) emitSeqNameChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitSeqResChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitSetMarkerHighlighting() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) EmittingScrollBar (class in schrodinger.ui.qt.table) emitValueChanged() (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.application.matsci.mswidgets.PopupMenu method) emodel (schrodinger.glide.RefinedPose attribute) emodel_coeff (schrodinger.application.glide.sort_utils.CustomScoringFunction attribute) EMPHASIZED_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) emphasized_widget_style() (in module schrodinger.application.matsci.stylemanager) empirical_pka_predictor() (schrodinger.protein.assignment.ProtAssign method) EMPTY (schrodinger.infra.structure.TextBlockReader attribute) empty() (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.matsci.wfmanagement.WorkflowMetadata method) (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.canvas.ChmPattern method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.OPLSArchive method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.structure.MoleculeGraph method) (schrodinger.infra.structure.StructureCoordinates method) EMPTY_MCS (schrodinger.glide.SkipReason attribute) EMPTY_PATH_TUPLE (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) EMPTY_PLP (schrodinger.ui.qt.mapperwidgets.plptarget.PLPTargetMixin attribute) EmptyInputError EmptyIterator (class in schrodinger.project.project) emptyMethod() (schrodinger.ui.qt.appframework2.appmethods.MethodsDict method) EN_ANALYSIS (schrodinger.application.matsci.desconfig.MSJStringer attribute) Enable (schrodinger.adapter.Canonicalize attribute) (schrodinger.adapter.Generate2DCoordinates attribute) (schrodinger.adapter.LabelAtoms attribute) (schrodinger.adapter.Sanitize attribute) (schrodinger.adapter.UniqueFilter attribute) enable() (schrodinger.project.project.Project method) enable_auto_scaling (schrodinger.livedesign.draw.ImageGenOptions attribute) enable_debugging() (schrodinger.application.livedesign.ldclient_proxy.LDClientLogger method) enable_deprecated() (in module schrodinger.utils.deprecation) enable_dummy_maestro_imports() (in module schrodinger.infra.unusable_module_importer) enable_dummy_missing_product_imports() (in module schrodinger.infra.unusable_module_importer) enable_dummy_non_post_test_imports() (in module schrodinger.infra.unusable_module_importer) ENABLE_ITEM (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) enable_lasso (schrodinger.ui.picking.PickMixedToggle property) enable_maestro_features (schrodinger.ui.two_d_viewer.TwoDViewer attribute) ENABLE_WHEN_NO_STRUC (schrodinger.application.jaguar.gui.basis_selector.BasisSelector attribute) enableActiveChkIfConstraintsAdded() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ActiveOptimizationTab method) enableAllFeatures() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) enableAllItems() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) (schrodinger.ui.qt.swidgets.SComboBox method) enableBaseEnergies() (schrodinger.energy.MlffFixedInteractions method) enableButtonViaCheckBox() (schrodinger.ui.qt.swidgets.ColorWidget method) enableCapture() (schrodinger.glide.LoggerConfig method) enabled (schrodinger.maestro_utils.surface_manager.menus.MenuActionData attribute) (schrodinger.rdkit.rdkit_adapter.RdkitLoggerstate attribute) ENABLED_STYLE (schrodinger.ui.qt.delegates.LinkDelegate attribute) enableExcitedState() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) enableExcitedStatesType() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) enableItems() (schrodinger.ui.qt.swidgets.SComboBox method) enableMaestroSync() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) enableOK() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) enableRows() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) enableSaveButton() (schrodinger.ui.qt.rename_favorite_dialog.RenameFavoriteDialog method) enableSelectedCoordinates() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) enableSidechainPacking() (schrodinger.protein.reliability.ProteinCheckParameters method) enableStructureCombos() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) enableTestingMode() (schrodinger.infra.structure.MmpdbxReader method) enableWithCBox() (schrodinger.application.matsci.chargegui.FFInfo method) encode() (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer class method) (schrodinger.seam.coders.MolCoder method) (schrodinger.seam.coders.MolToSmilesCoder method) (schrodinger.seam.coders.RouteNodeCoder method) (schrodinger.seam.coders.StructureCoder method) (schrodinger.seam.transforms.window.StringIDWindowCoder method) encode_acc() (in module schrodinger.protein.predictors) encode_char() (schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer class method) encode_seqs() (in module schrodinger.application.bioluminate.peptide_sar.encode) encode_ssa() (in module schrodinger.protein.predictors) encode_str() (in module schrodinger.application.desmond.cms) encode_string_into_structure_property() (in module schrodinger.application.desmond.struc) encodeForPatternSearch() (schrodinger.protein.sequence.NucleicAcidSequence method) (schrodinger.protein.sequence.ProteinSequence method) ENCODING_KEY (schrodinger.models.jsonable.JsonableSet attribute) (schrodinger.models.jsonable.JsonableTuple attribute) encrypt_cms() (in module schrodinger.application.matsci.enc) END (schrodinger.application.bioluminate.pose_filtering.hdx_io.DynamXColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.HDExaminerColumns attribute) (schrodinger.application.bioluminate.pose_filtering.hdx_io.StandardColumns attribute) (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) (schrodinger.application.matsci.packmol.PackmolKw attribute) end (schrodinger.protein.annotation.AntibodyCDR attribute) (schrodinger.protein.annotation.Region attribute) (schrodinger.protein.helm.helm_renderer.HelmConnector attribute) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) end() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.structure.StructureCoordinates method) (schrodinger.infra.structure.StructureReader method) end_atom0 (schrodinger.infra.mm.UTTParameter attribute) end_atom3 (schrodinger.infra.mm.UTTParameter attribute) end_atoms1 (schrodinger.infra.mm.UTT attribute) end_atoms2 (schrodinger.infra.mm.UTT attribute) end_color (schrodinger.application.matsci.stylemanager.GradientDefinition attribute) end_date (schrodinger.application.licensing.licserver.entitlement_status.ActiveEntitlementFeature attribute) (schrodinger.application.licensing.licserver.entitlement_status.NonActiveEntitlementFeature attribute) end_geometry() (in module schrodinger.application.jaguar.textparser) end_index (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainNumbering attribute) end_node() (schrodinger.application.glide_ws.nodes.CrossNode method) (schrodinger.application.glide_ws.nodes.DecoysNode method) (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) (schrodinger.application.glide_ws.nodes.MMGBSAModelBaseNode method) (schrodinger.application.glide_ws.nodes.MMGBSAReceptorBaseNode method) (schrodinger.application.glide_ws.nodes.MMGBSATestsetNode method) (schrodinger.application.glide_ws.nodes.ModelNode method) (schrodinger.application.glide_ws.nodes.NativeNode method) (schrodinger.application.glide_ws.nodes.Node method) (schrodinger.application.glide_ws.nodes.OptimizeNode method) (schrodinger.application.glide_ws.nodes.SPDecoysNode method) (schrodinger.application.glide_ws.nodes.TestSetNode method) end_node_models() (schrodinger.application.glide_ws.nodes.MMGBSAModelBaseNode method) end_node_per_complex() (schrodinger.application.glide_ws.nodes.Node method) end_node_per_model() (schrodinger.application.glide_ws.nodes.MMGBSAModelBaseNode method) (schrodinger.application.glide_ws.nodes.MMGBSANode method) (schrodinger.application.glide_ws.nodes.MMGBSATestsetNode method) END_OF_DEF_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) end_progress() (in module schrodinger.application.bioluminate.pml_menus) end_residue (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) end_scan() (in module schrodinger.application.jaguar.textparser) END_TAG (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser.HTMLType attribute) end_time (schrodinger.seam.viz.inspect.PipelineDisplayInfo attribute) end_time() (in module schrodinger.application.jaguar.textparser) endChanged() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) endDate (schrodinger.application.licensing.licserver.client.LocalEntitlement attribute) endFilter() (schrodinger.ui.qt.swidgets.SFilteredListWidget method) endGeopt() (schrodinger.application.jaguar.textparser.TextParser method) endGroup() (schrodinger.infra.mm.MMPREF method) (schrodinger.utils.preferences.Preferences method) endIRC() (schrodinger.application.jaguar.textparser.TextParser method) endOsAttribute() (schrodinger.infra.mm.MMPREF method) Endpoint (class in schrodinger.maestro_utils.composer_agent.request_manager.urls) (schrodinger.application.livedesign.panel_components.ExportTableColumns attribute) endpoint() (in module schrodinger.seam.viz.watcher) EndpointInfo (class in schrodinger.seam.viz.watcher) EndpointSelectionLineEdit (class in schrodinger.application.livedesign.panel_components) EndpointSelectionModel (class in schrodinger.application.livedesign.panel_components) EndpointSelectionPopUp (class in schrodinger.application.livedesign.panel_components) EndpointSelectionPopUpDelegate (class in schrodinger.application.livedesign.panel_components) endRangeModified() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) endScan() (schrodinger.application.jaguar.textparser.TextParser method) ENE_INTERVAL (schrodinger.application.matsci.desconfig.MSJStringer attribute) eneg (schrodinger.application.matsci.elementalprops.ElementalProperties property) enegrp (schrodinger.application.matsci.deswidgets.DesmondMDWidgets.NUM_FRMS_TYPE attribute) ENEGRP_NFRM_LABEL (schrodinger.application.matsci.deswidgets.DesmondMDWidgets attribute) EnergeticSpan (class in schrodinger.application.matsci.reaction_workflow_utils) EnergeticSpanException energy (schrodinger.application.jaguar.input.GuessOrbital attribute) (schrodinger.application.jaguar.results.JaguarResults property) (schrodinger.application.jaguar.results.NofailResult attribute) (schrodinger.application.jaguar.thermochemical_properties.InputParams attribute) (schrodinger.application.jaguar.thermochemical_properties.ThermoProps attribute) ENERGY (schrodinger.application.transforms.prime.RefineType attribute) energy (schrodinger.energy.AniEnergyOutput attribute) (schrodinger.energy.FlucCTOutput attribute) (schrodinger.energy.QRNNEnergyOutput attribute) (schrodinger.energy.XTBEnergyOutput attribute) (schrodinger.glide.MinimizerResult attribute) (schrodinger.glide.Minimum attribute) (schrodinger.infra.mm.WaterMapAtom attribute) energy() (in module schrodinger.application.xtb.textparser) Energy_Barrier_kcal_per_mol (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) energy_components (schrodinger.glide.ScoreDescriptors attribute) energy_convergence (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) energy_criterion (schrodinger.structutils.minimize.Minimizer property) energy_info (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) ENERGY_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) energy_key (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) ENERGY_KEY (schrodinger.application.matsci.reaction_workflow_utils.JMSWFConformerSelection attribute) (schrodinger.application.matsci.reaction_workflow_utils.MopacConformerSelection attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) energy_lj_repulsive_only (schrodinger.structutils.minimize.Minimizer property) energy_no_electrostatics (schrodinger.structutils.minimize.Minimizer property) energy_prec (schrodinger.application.jaguar.results.ConvCriteria attribute) energy_precision (schrodinger.application.jaguar.results.JaguarResults attribute) (schrodinger.application.qsite.output.QSiteResults attribute) energy_precision_hartree (schrodinger.application.jaguar.results.DerivedAttrs attribute) Energy_Property (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) (schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns attribute) energy_scaling (schrodinger.energy.MlffPostProcessSteps attribute) ENERGY_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) ENERGY_UNIT_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) energy_units (schrodinger.application.jaguar.results.ThermoProp attribute) EnergyAnalysisProperty (class in schrodinger.application.matsci.reaction_workflow_utils) EnergyAndGradients (class in schrodinger.application.matsci.mecp_mod) EnergyComponents (class in schrodinger.glide) EnergyDiagramPlotter (class in schrodinger.application.matsci.reaction_workflow_utils) EnergyListing (class in schrodinger.application.macromodel.input) EnergyOptions (class in schrodinger.glide) EnergySurface (class in schrodinger.application.matsci.amorphous) eneseq (schrodinger.application.matsci.deswidgets.DesmondMDWidgets.NUM_FRMS_TYPE attribute) ENESEQ_NFRM_LABEL (schrodinger.application.matsci.deswidgets.DesmondMDWidgets attribute) ENEUTRAL (schrodinger.application.matsci.kmc.SegmentsTable attribute) enforceBasis() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) enforceOneChecked() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) enforceScrollBarPolicies() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) EnforcingValidatorMixin (class in schrodinger.ui.qt.swidgets) Engine (class in schrodinger.infra.fast3d) engine (schrodinger.application.matsci.espresso.qeinput.DataType attribute) Engine_dataDir() (in module schrodinger.infra.fast3d) Engine_defaultCustomRepository() (in module schrodinger.infra.fast3d) Engine_defaultRepositories() (in module schrodinger.infra.fast3d) Engine_FROZEN_ATOMS_PROPERTY_NAME_get() (in module schrodinger.infra.fast3d) Engine_isFragmentLibraryFile() (in module schrodinger.infra.fast3d) Engine_SCHRODINGER_CONFGENX_CSP_MODE_get() (in module schrodinger.infra.fast3d) Engine_SCHRODINGER_CONFGENX_FEPGPGPU_MODE_get() (in module schrodinger.infra.fast3d) Engine_SCHRODINGER_CONFGENX_IFDMD_MODE_get() (in module schrodinger.infra.fast3d) Engine_SCHRODINGER_CONFGENX_PHASE_MODE_get() (in module schrodinger.infra.fast3d) enhance_cms() (in module schrodinger.application.desmond.packages.topo) EnhancedComboBox (class in schrodinger.application.jaguar.gui.utils) Enrichment (class in schrodinger.application.glide_ws.model) enrichment_report() (schrodinger.application.glide_ws.model.Model method) Ensemble (class in schrodinger.trajectory.prody.ensemble) ensemble (schrodinger.application.glide_ws.optimizer.ScoredEnsembleTuple attribute) ENSEMBLE (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.SimulationParams attribute) (schrodinger.application.matsci.permittivity.MultiStageMd attribute) ensemble (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) ENSEMBLE_CLASS (schrodinger.application.matsci.desconfig.MSJStringer attribute) ensemble_data_file (schrodinger.application.glide_ws.nodes.OptimizeNode property) ENSEMBLE_METHOD (schrodinger.application.matsci.desconfig.MSJStringer attribute) Ensemble_Priority_Queue (class in schrodinger.application.glide.ensemble_selection) EnsembleLigand (class in schrodinger.application.glide_ws.model) ensembles (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue property) EnsembleScore (class in schrodinger.application.glide_ws.entropy_score) ensure_decoys() (in module schrodinger.application.vss.tasks) ensure_file_exists() (in module schrodinger.application.desmond.util) ensure_localhost_server_running() (in module schrodinger.job.server) ensure_logfile() (in module schrodinger.utils.installation_check) ensure_logger() (in module schrodinger.application.bindingsite.common) ensure_no_domains_reused() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) ensure_project_entry() (in module schrodinger.application.matsci.maestrocmds) ensure_proper_extension() (in module schrodinger.application.bioluminate.pml_menus) ensure_user_is_logged_in() (in module schrodinger.application.livedesign.ld_maestro_actions) ensure_value_in_range() (in module schrodinger.application.bioluminate.protein_interaction.tasks) ensureValidity() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) enter_timing_context() (in module schrodinger.application.glide.runner) enterDisplaySnapshotMode() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) enterEvent() (schrodinger.application.bioluminate.pml_menus.ColorLabel method) (schrodinger.ui.qt.swidgets.HelpButton method) enterZoomView() (schrodinger.ui.two_d_viewer.TwoDViewer method) enthalpy (schrodinger.application.jaguar.thermochemical_properties.ThermoProps attribute) EntitlementStatus (class in schrodinger.application.licensing.licserver.entitlement_status) ENTITY (schrodinger.application.livedesign.models2.datamodels.definition.InputType attribute) entity_class (schrodinger.livedesign.registration.RegistrationData attribute) entity_id (schrodinger.application.livedesign.ld_tasks.StructureInfo attribute) entity_image_path() (in module schrodinger.livedesign.entity_type) entity_registration() (in module schrodinger.livedesign.cmdline) entity_registration_status (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entity_registration_statusChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entity_registration_statusReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) ENTITY_TYPE (schrodinger.livedesign.custom_entity.registration.EntityComponent attribute) EntityClass (class in schrodinger.livedesign.entity_type) EntityComponent (class in schrodinger.livedesign.custom_entity.registration) EntityRegistrationStatus (class in schrodinger.application.livedesign.export_models) ENTRIES (schrodinger.infra.structure.SuperImposeBy attribute) entries_excluded() (in module schrodinger.ui.qt.appframework2.maestro_callback) entries_included() (in module schrodinger.ui.qt.appframework2.maestro_callback) entriesInfoChanged (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync attribute) entropy (schrodinger.application.jaguar.thermochemical_properties.ThermoProps attribute) (schrodinger.infra.mm.WaterMapAtom attribute) entropy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) ENTROPY_PROP (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) ENTROPY_STARTER (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) ENTRY (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) entry (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) entry_data (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entry_dataChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entry_dataReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) entry_excluded() (in module schrodinger.project.utils) entry_id (schrodinger.application.glide.gui.GridSite attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTupleMacroPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) (schrodinger.application.matsci.sculptcomplex.SiteAtom attribute) (schrodinger.maestro_utils.surface_manager.surface_info.SurfaceInfo attribute) (schrodinger.project.project.ProjectRow property) (schrodinger.protein.residue.ResidueKey attribute) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) (schrodinger.structure.StructureAtom property) entry_idChanged (schrodinger.application.glide.gui.GridSite attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) entry_idReplaced (schrodinger.application.glide.gui.GridSite attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask.Input attribute) entry_index (schrodinger.application.matsci.sculptcomplex.SiteAtom attribute) entry_is_included() (in module schrodinger.project.utils) entry_is_locked() (in module schrodinger.project.utils) entry_is_marked() (in module schrodinger.project.utils) entry_is_pinned() (in module schrodinger.project.utils) entry_is_selected() (in module schrodinger.project.utils) entry_name (schrodinger.protein.sequence.CombinedChainProteinSequence property) ENTRY_NAME_KEY (schrodinger.application.matsci.nano.xtal.CheckInput attribute) (schrodinger.application.matsci.rxn_channel.CheckInput attribute) ENTRY_NODE (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceNodeType attribute) entry_singular (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData attribute) entry_type (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_description (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_descriptionChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_descriptionReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_name (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_nameChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_type_nameReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ENTRY_TYPE_NAMES (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) entry_typeChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) entry_typeReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) entryByName() (schrodinger.utils.installation_check.TestJobDJ method) EntryContextMenu (class in schrodinger.maestro_utils.surface_manager.menus) EntryGroup (class in schrodinger.project.project) EntryGroupManager (class in schrodinger.project.manager) entryIds() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) ENTRYKEY (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) EntryMode (class in schrodinger.application.pymol.pymol4maestro) ENTRYNAMEKEY (schrodinger.application.matsci.rxn_path.CheckInput attribute) EntryNodeItem (class in schrodinger.maestro_utils.surface_manager.surface_item) ENTRYPOINT (schrodinger.tasks.tasks.AbstractComboTask attribute) entrySelectionChanged (schrodinger.application.livedesign.maestro_sync.EntrySelectionMaestroSync attribute) EntrySelectionMaestroSync (class in schrodinger.application.livedesign.maestro_sync) EntrySubMenu (class in schrodinger.application.bioluminate.pml_menus) EntrySurface (class in schrodinger.project.project) EntryTimingTable (class in schrodinger.application.jaguar.gui.timing) entryTitles() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) enum_speedup() (in module schrodinger.infra.util) EnumerableMixin (class in schrodinger.application.scaffold_enumeration.common) ENUMERATE (schrodinger.application.transforms.autosar.config.Command attribute) enumerate_acceptor_acceptor_states() (schrodinger.protein.protassign.changeables.WaterStateEnumerator method) enumerate_acceptor_states() (schrodinger.protein.protassign.changeables.WaterStateEnumerator method) enumerate_changeable_states() (schrodinger.protein.assignment.ProtAssign method) enumerate_donor_donor_states() (schrodinger.protein.protassign.changeables.WaterStateEnumerator method) enumerate_donor_states() (schrodinger.protein.protassign.changeables.WaterStateEnumerator method) enumerate_rgroups() (in module schrodinger.application.scaffold_enumeration.layered) enumerate_states() (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) enumerate_stereoisomers() (in module schrodinger.livedesign.bbchem_endpoints) enumerate_swap() (in module schrodinger.application.matsci.reaction_workflow_utils) enumerateChannels() (schrodinger.application.matsci.rxn_channel.Channels method) EnumerateCombination (class in schrodinger.application.transforms.autosar.transforms) EnumerateReactionWorkflow (class in schrodinger.application.matsci.reaction_workflow_enum_utils) EnumerateRoutes (class in schrodinger.application.transforms.enumerators.synthesize) EnumerateSwap (class in schrodinger.application.matsci.reaction_workflow_utils) EnumerateSwapMixin (class in schrodinger.application.matsci.reaction_workflow_enum_utils) EnumMetaWithContains (class in schrodinger.application.matsci.msutils) EnumParam (class in schrodinger.models.parameters) ENV (schrodinger.application.licensing.licserver.client.ServerIdentifierSourceType attribute) env_update_and_run() (in module schrodinger.utils.installation_check) env_var_feature_flag_is_set() (in module schrodinger.utils.featureflags.featureflags) EnvAction (class in schrodinger.application.glide.utils) environment (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) environment variable PATH, [1] PYTHONPATH, [1], [2], [3], [4], [5], [6] SCHRODINGER SCHRODINGER_PYTHONPATH, [1] SCHRODINGER_SCRIPTS, [1], [2] EnvironmentContext (class in schrodinger.utils.env) Envs (schrodinger.job.jobcontrol.Job property) EnvVar (class in schrodinger.utils.openmpi) eof() (schrodinger.infra.structure.StructureReader method) (schrodinger.infra.structure.TextBlockReader method) EP (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings attribute) epik_args (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) epik_argsChanged (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) epik_argsReplaced (schrodinger.application.livedesign.tasks.EpikTask.Input attribute) epik_classic_args (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_argsChanged (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_argsReplaced (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_infile (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_infileChanged (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_classic_infileReplaced (schrodinger.application.livedesign.tasks.EpikClassicTask.Input attribute) epik_pH (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHt (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHtChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) epik_pHtReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesInput attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings attribute) EpikClassicProtonateLigands (class in schrodinger.seam.yaml.transforms) EpikClassicTask (class in schrodinger.application.livedesign.tasks) EpikClassicTask.Input (class in schrodinger.application.livedesign.tasks) EpikClassicTask.JobConfig (class in schrodinger.application.livedesign.tasks) EpikClassicTask.Output (class in schrodinger.application.livedesign.tasks) EpikProtonateLigands (class in schrodinger.seam.yaml.transforms) EpikTask (class in schrodinger.application.livedesign.tasks) EpikTask.Input (class in schrodinger.application.livedesign.tasks) EpikTask.JobConfig (class in schrodinger.application.livedesign.tasks) EpikTask.Output (class in schrodinger.application.livedesign.tasks) epn() (in module schrodinger.application.jaguar.textparser) epn_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) eps_alpha_cav (schrodinger.application.jaguar.garza.SolvEntropyProps attribute) EPS_METAL_ERR (schrodinger.application.matsci.espresso.qeoutput.Output attribute) EPSILON_ALPHA_KEY (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) epsilon_cav (schrodinger.application.jaguar.garza.SolvEntropyProps attribute) EPSILON_KEY (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) EpsilonType (class in schrodinger.application.matsci.espresso.qeinput) EPV_RECEP (schrodinger.application.glide.sort_utils.StructureType attribute) EpvReader (class in schrodinger.application.glide.utils) eq_re (schrodinger.application.jaguar.utils.GenOptions attribute) equal_rotations() (in module schrodinger.application.matsci.nano.space_groups) EQUALS (schrodinger.application.matsci.genetic_optimization.Property attribute) equals() (schrodinger.application.matsci.wfmanagement.WorkflowMetadata method) equilibrium() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) equilibrium_constant() (in module schrodinger.application.jaguar.kinetics) EquilibriumMdBase (class in schrodinger.application.matsci.equilibrium_md) equivalentBead() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMapper method) erase() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method)

erf_then_divide() (in module schrodinger.application.bioluminate.patch_utils.msurfext) err (schrodinger.application.licensing.licserver.client.LocalEntitlement attribute) (schrodinger.application.licensing.licserver.client.ServerIdentifier attribute) (schrodinger.utils.sea.evalor.Evalor property) ERR_MSG (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter attribute) err_no() (schrodinger.infra.structure.IOException method) Error (class in schrodinger.job.host_check) error (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) ERROR (schrodinger.application.jaguar.utils.GenOptions attribute) (schrodinger.maestro_utils.composer_agent.message_handler.MessageState attribute) (schrodinger.maestro_utils.composer_agent.request_manager.urls.ResponseStatus attribute) (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.MessageType attribute) error() (in module schrodinger.application.matsci.gutils) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) (schrodinger.application.matsci.espresso.utils.ArgumentParserNoExit method) (schrodinger.application.matsci.parserutils.DriverParser method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.swidgets.SDialog method) (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) (schrodinger.utils.ligfilter.CriterionParser method) (schrodinger.utils.ligfilter.DefinitionParser method) ERROR_BACKGROUND_BRUSH (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) error_code (schrodinger.utils.license.LicenseStatus property) error_message (schrodinger.seam.runners.events.StageFailed attribute) error_message() (in module schrodinger.application.xtb.textparser) error_messageChanged (schrodinger.seam.runners.events.StageFailed attribute) error_messageReplaced (schrodinger.seam.runners.events.StageFailed attribute) error_msg (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) (schrodinger.glide.ScoreInfo attribute) error_msgChanged (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) error_msgReplaced (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask.Output attribute) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel attribute) error_pattern (schrodinger.infra.mmcheck.ReturnCode attribute) ERROR_POST (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) ERROR_PRE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) ERROR_TEXT (schrodinger.application.matsci.stylemanager.SolidColors attribute) (schrodinger.ui.qt.standard.colors.LightModeColors attribute) error_text_style() (in module schrodinger.application.matsci.stylemanager) error_threshold (schrodinger.stepper.stepper.BatchSettings attribute) error_thresholdChanged (schrodinger.stepper.stepper.BatchSettings attribute) error_thresholdReplaced (schrodinger.stepper.stepper.BatchSettings attribute) ErrorForDialog errorOccurred (schrodinger.application.glide.http_client.NonBlockingGlideServerManager attribute) (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) (schrodinger.application.glide.http_client.NonBlockingHTTPClient attribute) Errors (schrodinger.job.jobcontrol.Job property) errors() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) ES_EXCLUDE_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) esm (schrodinger.application.matsci.espresso.qeinput.BoundaryType property) ESM_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) EsmType (class in schrodinger.application.matsci.espresso.qeinput) (class in schrodinger.application.matsci.espresso.qeoutput) EsolInput (class in schrodinger.application.jaguar.esol_input) esp_analysis() (in module schrodinger.application.jaguar.textparser) esp_analysis_precision (schrodinger.application.jaguar.results.JaguarResults attribute) ESP_ATOMS (schrodinger.application.jaguar.results.JaguarOptions attribute) ESP_ATOMS_AND_BOND_MIDPOINTS (schrodinger.application.jaguar.results.JaguarOptions attribute) esp_charge() (in module schrodinger.application.mopac.results_main) esp_charges() (in module schrodinger.application.jaguar.textparser) esp_fit_atoms() (in module schrodinger.application.jaguar.textparser) esp_fit_atoms_and_bonds() (in module schrodinger.application.jaguar.textparser) ESP_FOR_MD (schrodinger.application.matsci.jaguar_multistage_workflow_utils.QMMoleculeKeywords attribute) esp_gradients (schrodinger.energy.OnsiteEspData attribute) ESP_NONE (schrodinger.application.jaguar.results.JaguarOptions attribute) esp_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) esps (schrodinger.energy.OnsiteEspData attribute) ESPSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) estate_is_physical() (in module schrodinger.application.jaguar.workflow_validation) estimate_size() (in module schrodinger.comparison.struc) (schrodinger.seam.coders.MaybeCompressedCoder method) (schrodinger.seam.coders.MolCoder method) estimate_time_cost() (in module schrodinger.active_learning.al_node) estimateMaxHeight() (schrodinger.ui.qt.pop_up_widgets.PopUp method) estimateMaxWidth() (schrodinger.ui.qt.pop_up_widgets.PopUp method) estimateRadius() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) estimateRecordCount() (schrodinger.infra.canvas.ChmMmctAdaptor static method) (schrodinger.infra.canvas.ChmSDReader static method) estimateResolution() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) EtaFFAssignmentError EtaFindingMixin (class in schrodinger.application.matsci.buildcomplex) EtaRotamersException eth0_is_missing() (in module schrodinger.application.licensing.licadmin) ETHANOL (schrodinger.energy.Solvent attribute) ETHR_FLAG (schrodinger.application.matsci.crest.CrestCSearch attribute) ETHYLACETATE (schrodinger.energy.Solvent attribute) etot() (in module schrodinger.application.jaguar.textparser) euler_angles (schrodinger.glide.RefinedPose attribute) ev() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method) ev_to_hartree() (in module schrodinger.application.matsci.mecp_mod) evalColMetadataDicts() (in module schrodinger.application.matsci.gsas.GSASIIfiles) evalDJ() (schrodinger.active_learning.al_node.LigandMLEvalNode method) evalMQ() (schrodinger.active_learning.al_node.LigandMLEvalNode method) Evalor (class in schrodinger.utils.sea.evalor) evaluate() (schrodinger.application.jaguar.discretized_1d_function.DiscretelySampledFunction method) (schrodinger.application.matsci.genetic_optimization.StructureGenome method) (schrodinger.energy.FlucCTCalculator method) (schrodinger.energy.FlucCTSystem method) evaluate_asl() (in module schrodinger.structutils.analyze) evaluate_f() (in module schrodinger.application.matsci.anharmonic) (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) evaluate_multiple_smarts() (in module schrodinger.application.matsci.deprecated_pattern) evaluate_smarts() (in module schrodinger.adapter) (in module schrodinger.application.matsci.deprecated_pattern) (in module schrodinger.application.matsci.rdpattern) evaluate_smarts_by_molecule() (in module schrodinger.application.matsci.rdpattern) evaluate_smarts_canvas() (in module schrodinger.application.matsci.deprecated_pattern) evaluate_smarts_ex() (in module schrodinger.application.canvas.r_group) evaluateAsl() (schrodinger.structutils.rmsd.ConformerRmsd method) evaluateASLs() (schrodinger.protein.align.CustomASLStructureAligner method) evaluateFlucCT() (schrodinger.energy.ConcreteMetalSystem method) (schrodinger.energy.MetalSystem method) evaluateFlucCTLocal() (schrodinger.energy.MetalSystem method) evaluateLfmm() (schrodinger.energy.ConcreteMetalSystem method) (schrodinger.energy.MetalSystem method) evaluateLiveReportText() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) evaluateMultipleSmarts() (schrodinger.application.matsci.rdpattern.EvaluateSMARTS method) EvaluateRoutes (class in schrodinger.application.transforms.enumerators.synthesize) EvaluateSMARTS (class in schrodinger.application.matsci.rdpattern) evaluateSmarts() (schrodinger.application.matsci.rdpattern.CanvasPattern method) (schrodinger.application.matsci.rdpattern.Pattern method) (schrodinger.application.matsci.rdpattern_gui.GuiPattern method) evaluateSmiles() (schrodinger.application.matsci.rdpattern.Pattern method) evaluateSpeciesCriterion() (schrodinger.application.matsci.clusterstruct.Dimer method) evaluator (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) evalue (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) evalue_threshold (schrodinger.protein.tasks.blast.BlastSettings attribute) evalue_thresholdChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) evalue_thresholdReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) EvaporationStep (class in schrodinger.application.matsci.jwsteps) evdw (schrodinger.application.glide_ws.entropy_score.GreasyScore attribute) (schrodinger.application.glide_ws.optimizer.WScoreOptimizerPose attribute) (schrodinger.glide.ScoreTerms attribute) EVEN_ROW_STYLE (schrodinger.application.matsci.stage_widgets.RowFrame attribute) even_row_style() (in module schrodinger.application.matsci.stylemanager) event (class in schrodinger.application.licensing.lmgrd_log_parser) event() (schrodinger.application.matsci.builderwidgets.StructureLabel method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin method) (schrodinger.ui.residueselector.ResidueToolTipMixin method) EventAnalysisTask (class in schrodinger.application.livedesign.tasks) EventAnalysisTask.Input (class in schrodinger.application.livedesign.tasks) EventAnalysisTask.Output (class in schrodinger.application.livedesign.tasks) eventFilter() (schrodinger.application.jaguar.gui.input_tab_widgets.CommitMultipleDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.livedesign.live_report_widget.SwallowEnterFilter method) (schrodinger.application.matsci.gutils.WheelEventFilterer method) (schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackWidgetMixin method) (schrodinger.ui.qt.delegates.LinkDelegate method) (schrodinger.ui.qt.delegates.MouseTrackingDelegateMixin method) (schrodinger.ui.qt.delegates.PushButtonDelegate method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.pop_up_widgets.PopUpDelegate method) (schrodinger.ui.qt.smatplotlib.SmatplotlibCanvas method) (schrodinger.ui.qt.swidgets.PersistentMenu method) (schrodinger.ui.qt.swidgets.SLineEdit method) (schrodinger.ui.qt.swidgets.SRetainableMenu method) (schrodinger.ui.qt.table.ToolTipFilter method) (schrodinger.ui.two_d_viewer.TwoDViewer method) EventLoop (class in schrodinger.utils.qt_utils) evolution() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) EWIN_FLAG (schrodinger.application.matsci.crest.CrestCSearch attribute) examine_constraints() (in module schrodinger.application.jaguar.autots_bonding) example_ligands (schrodinger.active_learning.scaffold_methods.ScaffoldData attribute) example_name (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_nameChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_nameReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_prop_string (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_prop_stringChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) example_prop_stringReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) ExampleStage (class in schrodinger.pipeline.stages.example) exc_energy_precision_ev (schrodinger.application.jaguar.results.DerivedAttrs attribute) exc_energy_precision_nm (schrodinger.application.jaguar.results.DerivedAttrs attribute) exc_precision (schrodinger.application.jaguar.results.JaguarResults attribute) EXCEPTION (schrodinger.application.steps.licensing.LicenseMixin attribute) Exception (schrodinger.glide.MinimizerStatus attribute) EXCEPTION (schrodinger.glide.SkipReason attribute) exception (schrodinger.seam.testing.failures.FailingTransformSettings attribute) exception_class_name (schrodinger.tasks.tasks.FailureInfo attribute) exception_class_nameChanged (schrodinger.tasks.tasks.FailureInfo attribute) exception_class_nameReplaced (schrodinger.tasks.tasks.FailureInfo attribute) ExceptionDialog (class in schrodinger.infra.exception_handler_dir.exception_dialog) ExceptionRecorder (class in schrodinger.infra.exception_handler) exchange_acceptance_ratio() (schrodinger.application.desmond.bennett.CalcBAR method) excited_state (schrodinger.application.jaguar.gui.tabs.theory_tab.ExcitedStateInfo attribute) EXCITED_STATE_CB_TEXT (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabOptimization attribute) excited_state_changed (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget attribute) EXCITED_STATE_KEYWORDS (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) excited_state_mode (schrodinger.application.jaguar.gui.tabs.theory_tab.ExcitedStateInfo attribute) EXCITED_STATE_TEXT (schrodinger.application.jaguar.gui.theory_tab_widgets.HFExcitedStateWidget attribute) EXCITED_STATE_TYPES (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabOptimization attribute) ExcitedStateInfo (class in schrodinger.application.jaguar.gui.tabs.theory_tab) ExcitedStateValidatorMixin (class in schrodinger.application.jaguar.gui.base_panel) ExcitedStateWidget (class in schrodinger.application.jaguar.gui.theory_tab_widgets) exclude() (schrodinger.application.transforms.filters.ProductFilter method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) exclude_amino_acids (schrodinger.structutils.analyze.AslLigandSearcher property) exclude_ions (schrodinger.structutils.analyze.AslLigandSearcher property) EXCLUDE_RESTRAINTS_KEY (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) excludeCommandParser() (schrodinger.application.ligprep.ionizer.Ionizer method) excluded_residue_names (schrodinger.infra.mm.LigandParameters attribute) excluded_residues (schrodinger.structutils.analyze.AslLigandSearcher property) excludedGroups() (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints method) ExcludedVolumeGenerator (class in schrodinger.application.phase.create_xvol) excludeEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) ExcludeFromSelection (class in schrodinger.application.bioluminate.pml_menus) ExcludeInorganicFromSelection (class in schrodinger.application.bioluminate.pml_menus) excludeNext() (schrodinger.infra.canvas.ChmRangeFilter method) ExcludeOrganicFromSelection (class in schrodinger.application.bioluminate.pml_menus) excludeOtherEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) ExcludePolymerFromSelection (class in schrodinger.application.bioluminate.pml_menus) excludes() (schrodinger.utils.ligfilter.Definition method) ExcludeSolventFromSelection (class in schrodinger.application.bioluminate.pml_menus) ExcludeSubMenu (class in schrodinger.application.bioluminate.pml_menus) ExcludeVisibleFromSelection (class in schrodinger.application.bioluminate.pml_menus) EXCLUSION_BIG_RING_SIZE (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner attribute) exclusive (schrodinger.infra.canvas.MCSsettings attribute) ExclVols (schrodinger.application.phase.phase_widgets.HypothesisColumns attribute) EXE (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) EXEC (schrodinger.job.util.DirectoryType attribute) exec() (schrodinger.application.jaguar.update_pka_settings.UpdatePKASettingsDlg method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.filedialog.FileDialog method) (schrodinger.ui.qt.forcefield.ffprojectsettingsdlg.FFProjectSettingsDlg method) (schrodinger.ui.qt.messagebox.MessageBox method) (schrodinger.ui.qt.pdb_dialog.PDBDialog method) (schrodinger.utils.qt_utils.EventLoop method) exec_module() (schrodinger.infra.unusable_module_importer.UnusableModuleLoader static method) execRemoteQueryDialog() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) ExecStagesWithSlowCoder (class in schrodinger.seam.testing.benchmarks) execText() (schrodinger.ui.qt.appframework2.debugwidgets.ExecWidget method) execute_cmd() (in module schrodinger.application.matsci.maestrocmds) execute_lictest() (in module schrodinger.application.licensing.licadmin) execute_lictool() (in module schrodinger.application.licensing.licserver.client) execute_lmutil() (in module schrodinger.application.licensing.licadmin) EXECUTING (schrodinger.maestro_utils.composer_agent.message_handler.MessageState attribute) execution (schrodinger.energy.MlffDeviceConfig attribute) execution_cputime_seconds (schrodinger.seam.metric.ExecutionMetrics attribute) EXECUTION_ERROR (schrodinger.maestro_utils.composer_agent.message_handler.MessageState attribute) execution_mode (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.tasks.MultisimTask.Input attribute) execution_modeChanged (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.tasks.MultisimTask.Input attribute) execution_modeReplaced (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.tasks.MultisimTask.Input attribute) EXECUTION_STATUS (schrodinger.maestro_utils.composer_agent.request_manager.urls.PostExecutionFeedbackPayloadKey attribute) ExecutionContext (class in schrodinger.application.livedesign.models2.execution.context) ExecutionFeedbackQuery (class in schrodinger.maestro_utils.composer_agent.request_manager.network_manager) ExecutionMetrics (class in schrodinger.seam.metric) ExecutionMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) ExecutionMode (class in schrodinger.application.livedesign.models2.datamodels.definition) ExecutionModes (class in schrodinger.application.livedesign.tasks) ExecWidget (class in schrodinger.ui.qt.appframework2.debugwidgets) EXEUCTION_FEEDBACK (schrodinger.maestro_utils.composer_agent.request_manager.urls.Endpoint attribute) existingDatabaseJobFilename() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) exists() (schrodinger.seam.io.jobfilesystem.JobFileSystem method) exit (schrodinger.seam.testing.failures.FailingTransformSettings attribute) exit() (schrodinger.pipeline.stage.Stage method) (schrodinger.utils.compare.DiffCompareArgumentParser method) exit_code (schrodinger.tasks.tasks.SubprocessMixin attribute) exit_event_loop_on_exception() (in module schrodinger.utils.qt_utils) exit_if_incompatible_with_desmond() (in module schrodinger.application.matsci.desmondutils) ExitCode (schrodinger.job.jobcontrol.Job property) exitDisplaySnapshotMode() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) ExitStatus (schrodinger.job.jobcontrol.Job property) exitZoomView() (schrodinger.ui.two_d_viewer.TwoDViewer method) Expand (class in schrodinger.application.bioluminate.pml_menus) expand() (schrodinger.application.peptide_workflow.beam_adapter.CreateReplicates method) (schrodinger.application.peptide_workflow.beam_adapter.PeptideWorkflowMonteCarlo method) (schrodinger.application.peptide_workflow.beam_adapter.PostProcessPeptides method) (schrodinger.application.peptide_workflow.beam_adapter.RunMonte method) (schrodinger.application.transforms.autosar.transforms.ComputeNormalizedProperties method) (schrodinger.application.transforms.autosar.transforms.EnumerateCombination method) (schrodinger.application.transforms.autosar.transforms.ExpandCombination method) (schrodinger.application.transforms.autosar.transforms.FilterCombination method) (schrodinger.application.transforms.chem.Desalt method) (schrodinger.application.transforms.chem.Standardize method) (schrodinger.application.transforms.chem.Uncharge method) (schrodinger.application.transforms.dockers.multi_receptor_dock.MultiReceptorDock method) (schrodinger.application.transforms.dockers.redock.ExtractLigand method) (schrodinger.application.transforms.dockers.redock.ReDock method) (schrodinger.application.transforms.enumerators.decorate.Decorate method) (schrodinger.application.transforms.enumerators.fragment.Fragment method) (schrodinger.application.transforms.enumerators.substitute.Substitute method) (schrodinger.application.transforms.enumerators.substitute.SubstructureSubstitute method) (schrodinger.application.transforms.enumerators.synthesize.DeduplicateRoutes method) (schrodinger.application.transforms.enumerators.synthesize.EnumerateRoutes method) (schrodinger.application.transforms.enumerators.synthesize.EvaluateRoutes method) (schrodinger.application.transforms.enumerators.synthesize.Synthesize method) (schrodinger.application.transforms.enumerators.synthesize.SystematicSynthesize method) (schrodinger.application.transforms.filters.ChargedNHpKaFilter method) (schrodinger.application.transforms.filters.DistinctStructures method) (schrodinger.application.transforms.filters.FepAmenable method) (schrodinger.application.transforms.filters.ProductFilter method) (schrodinger.application.transforms.filters.StructurePropertyFilter method) (schrodinger.application.transforms.filters.TanimotoFilter method) (schrodinger.application.transforms.ligprep.LigandPrep method) (schrodinger.application.transforms.prepwizard.ProteinPrep method) (schrodinger.application.transforms.template.starter.CarbonCount method) (schrodinger.application.transforms.template.starter.CarbonCountingWorkflow method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.seam.debug.ReadElementsFromBeamEncodedBytes method) (schrodinger.seam.debug.WriteElementsAsBeamEncodedBytes method) (schrodinger.seam.examples.active_learning_weigher.ActiveLearning method) (schrodinger.seam.examples.active_learning_weigher.CalculateMolWt method) (schrodinger.seam.examples.active_learning_weigher.Iteration method) (schrodinger.seam.examples.active_learning_weigher.PickRandomly method) (schrodinger.seam.examples.active_learning_weigher.PickTopScoring method) (schrodinger.seam.examples.lipinski.DownloadRandomSmiles method) (schrodinger.seam.testing.failures.FailingTransform method) (schrodinger.seam.testing.test_pipelines.BenchFlow method) (schrodinger.seam.testing.test_pipelines.CPUTransform method) (schrodinger.seam.testing.test_pipelines.GPUExampleWorkflow method) (schrodinger.seam.testing.test_pipelines.GPUTransform method) (schrodinger.seam.transforms.core.GroupIntoBatches method) (schrodinger.seam.transforms.core.TeeIf method) (schrodinger.seam.transforms.grouping.AssignNearestBinKey method) (schrodinger.seam.transforms.grouping.GroupIntoBins method) (schrodinger.seam.transforms.grouping.UnbinAndPartitionBoundaryValues method) (schrodinger.seam.yaml.schemad.SchemadParDo method) (schrodinger.seam.yaml.transforms.CreateMols method) (schrodinger.seam.yaml.transforms.CreateStructures method) (schrodinger.seam.yaml.transforms.GlideDock method) (schrodinger.seam.yaml.transforms.LigPrep method) (schrodinger.seam.yaml.transforms.MolToSmiles method) (schrodinger.seam.yaml.transforms.MolToStructure method) (schrodinger.seam.yaml.transforms.PrettyPrintJson method) (schrodinger.seam.yaml.transforms.QikProp method) (schrodinger.seam.yaml.transforms.ReadFromPDB method) (schrodinger.seam.yaml.transforms.ReadMolsFromFile method) (schrodinger.seam.yaml.transforms.ReadStructuresFromFile method) (schrodinger.seam.yaml.transforms.SmilesToMol method) (schrodinger.seam.yaml.transforms.SmilesToStructure method) (schrodinger.seam.yaml.transforms.StructureToMol method) (schrodinger.seam.yaml.transforms.WriteMolsToFile method) (schrodinger.seam.yaml.transforms.WriteStructuresToFile method) (schrodinger.stepper.shims.ShimMapStep method) (schrodinger.stepper.shims.ShimReduceStep method) (schrodinger.utils.ligfilter.Definition method) (schrodinger.utils.ligfilter.SmartsCriterion method) expand_concatenated_stages() (in module schrodinger.application.matsci.desconfig) expand_macro() (in module schrodinger.application.desmond.util) (in module schrodinger.utils.sea.sea) expand_macros() (in module schrodinger.application.glide.utils) expand_query() (in module schrodinger.rdkit.substructure) expand_settings_from_group() (in module schrodinger.ui.qt.appframework2.af2) expand_solutions() (schrodinger.protein.protassign.hbond_cluster.hbond_cluster method) expandAll() (schrodinger.application.matsci.mswidgets.MultiStageArea method) ExpandCell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) ExpandCombination (class in schrodinger.application.transforms.autosar.transforms) ExpandCombination.Algorithm (class in schrodinger.application.transforms.autosar.transforms) expandFamily() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) expandMapping() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMapper method) expandNodeClusters() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) expandResidualMapping() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) expandToNodes() (schrodinger.ui.qt.network_views.NetworkViewer method) expansion_coeff (schrodinger.application.jaguar.garza.SolventParams attribute) (schrodinger.application.jaguar.utils.JagSolventParams attribute) expect_single_datum() (in module schrodinger.application.desmond.arkdb) expected_text_width() (in module schrodinger.application.matsci.gutils) ExperimentalPersistentWorkerOptions (class in schrodinger.seam.options.pipeline_options) expiration_str() (schrodinger.application.licensing.flexlm.Feature method) expired_entitlements (schrodinger.application.licensing.licserver.entitlement_status.EntitlementStatus attribute) EXPLICIT (schrodinger.adapter.Hydrogens attribute) EXPLICIT_HYDROGENS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) ExplicitHydrogens (class in schrodinger.livedesign.preprocessor) (schrodinger.infra.mm.UnpairedElectronsReplacementMode attribute) explore_solutions() (schrodinger.protein.protassign.network_solver.NetworkSolver method) exploreEdge() (schrodinger.ui.qt.network_views.NetworkViewer method) EXPONENTIAL_REP_DAT (schrodinger.infra.mm.OPLSDatafileType attribute) export() (schrodinger.application.pymol.export_handler.ExportToPyMolMediator method) Export2DTask (class in schrodinger.application.livedesign.export_tasks) Export3DTask (class in schrodinger.application.livedesign.export_tasks) export_3d (schrodinger.application.livedesign.export_models.TaskInput attribute) export_3dChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) export_3dReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) EXPORT_ALL_DATA (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) export_asl (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) export_file_path (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) export_frame_option (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) export_generic_entities (schrodinger.application.livedesign.export_models.TaskInput attribute) export_generic_entitiesChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) export_generic_entitiesReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) export_hits_or_hypo() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) export_job_poses() (in module schrodinger.application.glide_ws.db_queries) export_ligand_poses() (in module schrodinger.application.glide_ws.db_queries) export_mode (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) export_modeChanged (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) export_modeReplaced (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) (schrodinger.application.pymol.gui_models.MovieSettingsModel attribute) export_plp_to_csv() (in module schrodinger.ui.qt.mapperwidgets.plptable) export_poses() (in module schrodinger.application.glide_ws.db_queries) export_poses_to_file() (in module schrodinger.application.glide_ws.db_queries) EXPORT_ROW_CLASS (schrodinger.application.livedesign.export_map_manager.ExportMap attribute) export_specs (schrodinger.application.livedesign.export_models.SummaryModel attribute) export_specsChanged (schrodinger.application.livedesign.export_models.SummaryModel attribute) export_specsReplaced (schrodinger.application.livedesign.export_models.SummaryModel attribute) export_table_model (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) export_table_modelChanged (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) export_table_modelReplaced (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel attribute) export_task (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_taskChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_taskReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) EXPORT_TEXT (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) export_text (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_textChanged (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_textReplaced (schrodinger.application.livedesign.ld_export.ExportModel attribute) export_to_bucket() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) export_to_csv() (in module schrodinger.ui.qt.table) export_to_csv_with_dialog() (in module schrodinger.ui.qt.table) export_to_ld() (in module schrodinger.application.livedesign.export_tasks) export_to_option (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) EXPORT_TRJ_FILE_PREF (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter attribute) EXPORT_VOLUME_TO_MAP (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) ExportableProxyModel (class in schrodinger.ui.qt.table) exportAllTables() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) exportBuriedVolumeContour() (schrodinger.application.matsci.mlearn.features.Complex method) exportButtonClicked (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures attribute) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures attribute) exportClicked() (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) exportCoordinatesFromMinimizer() (schrodinger.infra.canvas.Chm2DCoordGen static method) exportCurrentTable() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) exportData() (schrodinger.application.matsci.density_analysis_widget.MeasurementTableFrame method) exportDatabase() (schrodinger.protein.nonstandard_residues.ResidueDatabase static method) exportEnergyDiagrams() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter static method) (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) exportFailed (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) ExportFrameOption (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums) exportGrid() (schrodinger.ui.two_d_viewer.TwoDViewer method) exportImage() (schrodinger.ui.qt.schart.SChart method) exportImages() (schrodinger.ui.two_d_viewer.TwoDViewer method) ExportMainPanel (class in schrodinger.application.livedesign.ld_export_gui) ExportMap (class in schrodinger.application.livedesign.export_map_manager) ExportMapManager (class in schrodinger.application.livedesign.export_map_manager) ExportMode (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums) ExportModel (class in schrodinger.application.livedesign.ld_export) ExportMovieDialog (class in schrodinger.trajectory.trajectory_gui_dir.export_movie) ExportPanelWizard (class in schrodinger.application.livedesign.ld_export_gui) exportPresets() (schrodinger.models.presets.PresetManager method) ExportRow (class in schrodinger.application.livedesign.panel_components) exportScaffolds() (schrodinger.infra.canvas.ChmScaffoldFinder method) exportSelectedEntries() (schrodinger.project.project.Project method) ExportSetupPanel (class in schrodinger.application.livedesign.ld_export_gui) ExportStructures (class in schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures) (class in schrodinger.trajectory.trajectory_gui_dir.export_structures) exportStructures() (schrodinger.ui.two_d_viewer.TwoDViewer method) exportStructuresForDebugging() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) ExportTableColumns (class in schrodinger.application.livedesign.panel_components) ExportTableDataColumnDelegate (class in schrodinger.application.livedesign.panel_components) ExportTableModel (class in schrodinger.application.livedesign.panel_components) exportTables() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) ExportTableView (class in schrodinger.application.livedesign.panel_components) ExportTask87 (class in schrodinger.application.livedesign.export_tasks) exportTo2dSdFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) exportTo3dSdWithSmilesFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) exportToCsv() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.table.ExportableProxyModel method) exportToImageFiles() (schrodinger.ui.two_d_viewer.TwoDViewer method) ExportToOption (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums) exportToPngGridFile() (schrodinger.ui.two_d_viewer.TwoDViewer method) ExportToPyMolMediator (class in schrodinger.application.pymol.export_handler) ExportToPyMolPanel (class in schrodinger.application.pymol.export_to_pymol_gui) ExportToPymolSettings (class in schrodinger.application.pymol.gui_models) exportTrace() (schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis method) exportTrajectory() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) ExportType (class in schrodinger.application.livedesign.export_tasks) EXPOSED (schrodinger.protein.predictors.SolventAccessibility attribute) Exposure (schrodinger.application.glide.xpdes.TermKeywords attribute) exposure_tendency (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) expression_error() (schrodinger.utils.ligfilter.CriterionParser method) expval (schrodinger.application.matsci.espresso.qeinput.FreePositionsType.PWallType attribute) ext (schrodinger.application.glide.utils.OutfileNameAttributes attribute) EXT (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.genetic_optimization.DeepChem attribute) ext_gcd() (in module schrodinger.application.matsci.nano.plane) EXT_OPEN_VALUES (schrodinger.protein.tasks.blast.BlastSettings attribute) Extend (class in schrodinger.application.bioluminate.pml_menus) extend() (schrodinger.application.glide.csv_utils.RawCsvWriter method) (schrodinger.application.glide.phase_subset.PhaseSubsetWriter method) (schrodinger.application.glide.utils.PoseWriter method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.structure.Structure method) (schrodinger.structure.StructureWriter method) (schrodinger.utils.sea.sea.List method) (schrodinger.utils.typing.Extendable method) extend_comp() (in module schrodinger.application.matsci.desmondutils) extend_connection_colors() (in module schrodinger.application.combiglide.connection_storage) extend_targeted_to_hyds() (schrodinger.protein.assignment.ProtAssign method) Extendable (class in schrodinger.utils.typing) extendBrokenAnnotations() (schrodinger.protein.gpcr.tasks.GPCRTask method) EXTENDED (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants attribute) (schrodinger.application.transforms.prime.RefineType attribute) Extended (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute) extended (schrodinger.surface.MolSurfType attribute) EXTENDED_SMARTS (schrodinger.rdkit_extensions.Format attribute) EXTENDED_SMILES (schrodinger.rdkit_extensions.Format attribute) EXTENDED_TIP (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants attribute) extended_windows_path() (in module schrodinger.utils.fileutils) extendedType() (schrodinger.infra.canvas.ChmAtomTyper method) extendedTypeAvg (schrodinger.infra.canvas.ChmAtomTyper attribute) extendedTypeLast (schrodinger.infra.canvas.ChmAtomTyper attribute) extendedTypeSum (schrodinger.infra.canvas.ChmAtomTyper attribute) extendedValueTypeMean() (schrodinger.infra.canvas.ChmAtomTyper method) extendedValueTypeSum() (schrodinger.infra.canvas.ChmAtomTyper method) ExtendSubMenu (class in schrodinger.application.bioluminate.pml_menus) extendWithSpectator() (schrodinger.application.matsci.rxn_channel.Products method) EXTERNAL_FILE (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportToOption attribute) external_program_energy() (in module schrodinger.application.jaguar.textparser) external_program_nn_energy_stddev() (in module schrodinger.application.jaguar.textparser) ExternalMethod (class in schrodinger.application.jaguar.rotation_barriers_keywords) EXTRA_COLS (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) EXTRA_INPUT_FILES_DICT (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) extra_keywords (schrodinger.application.mopac.mopac_launchers.MopacLauncherMain property) extra_keywords_args() (in module schrodinger.application.glide.utils) EXTRA_NROOT (schrodinger.application.matsci.mecp_mod.JaguarJobs attribute) EXTRA_SITES_RESTRAINTS_KEY (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) extract() (in module schrodinger.infra.structure) (schrodinger.application.phase.subset_screening.SubsetExtractor method) (schrodinger.structure.Structure method) extract_active_titles_from_csv() (in module schrodinger.analysis.enrichment.enrichment_input) extract_active_titles_from_list() (in module schrodinger.analysis.enrichment.enrichment_input) extract_active_titles_from_mae() (in module schrodinger.analysis.enrichment.enrichment_input) extract_active_titles_from_txt() (in module schrodinger.analysis.enrichment.enrichment_input) extract_and_contract() (in module schrodinger.application.matsci.cg_mapping) extract_archive() (in module schrodinger.application.combinatorial_screen.driver_utils) extract_asl (schrodinger.application.livedesign.tasks.Trj2maeTask.Input attribute) extract_aslChanged (schrodinger.application.livedesign.tasks.Trj2maeTask.Input attribute) extract_aslReplaced (schrodinger.application.livedesign.tasks.Trj2maeTask.Input attribute) extract_binding_sites() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) extract_biopolymer_graph() (in module schrodinger.livedesign.biologics.registration) extract_chain() (in module schrodinger.ui.qt.pdb_dialog) extract_chiral_center_data() (in module schrodinger.protein.process_enamine_db) extract_chorus_lattice_vector() (in module schrodinger.application.matsci.nano.xtal) extract_compressed_files() (in module schrodinger.active_learning.al_utils) extract_dict() (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) extract_file_ext_from_tgz() (in module schrodinger.utils.fileutils) extract_file_from_grid() (in module schrodinger.application.glide.grid) extract_files() (schrodinger.application.glide_ws.driver.GlideWSJob method) extract_grid_and_radius() (in module schrodinger.application.matsci.freevolume) extract_gridfile() (in module schrodinger.application.glide_ws.utils) extract_gridfiles() (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) extract_het_from_complex() (in module schrodinger.application.prepwizard) extract_hets_from_complex() (in module schrodinger.application.prepwizard) extract_hypotheses() (in module schrodinger.application.phase.hypothesis) extract_hypothesis() (in module schrodinger.application.phase.subset_screening) extract_input_st_filenames() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) extract_job_data() (in module schrodinger.application.matsci.jobutils) extract_model_file() (in module schrodinger.application.glide_ws.model) extract_Phob_pack_ligand_indices() (in module schrodinger.application.glide.xpdes) extract_port() (in module schrodinger.autoinstall.misc) extract_properties() (in module schrodinger.application.transforms.autosar.transforms) (in module schrodinger.pipeline.stages.phase) extract_ranks_from_csv() (in module schrodinger.analysis.enrichment.enrichment_input) extract_ranks_from_list() (in module schrodinger.analysis.enrichment.enrichment_input) extract_ranks_from_mae() (in module schrodinger.analysis.enrichment.enrichment_input) extract_ranks_from_structures() (in module schrodinger.analysis.enrichment.enrichment_input) extract_registration_data() (in module schrodinger.livedesign.biologics.registration) (in module schrodinger.livedesign.custom_entity.registration) extract_release() (in module schrodinger.autoinstall.suite_install) extract_route_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) extract_smiles_and_cids() (in module schrodinger.application.vss.pilot) extract_state_charges_and_orders() (in module schrodinger.application.prepwizard) extract_structure() (in module schrodinger.structutils.build) extract_structures() (in module schrodinger.application.phase.hypothesis) (in module schrodinger.rdkit.molio) extract_subjob_chunks() (in module schrodinger.application.combinatorial_diversity.driver_utils) extract_subsystem() (in module schrodinger.application.desmond.packages.topo) (in module schrodinger.application.desmond.packages.traj) extract_supercell() (in module schrodinger.comparison.struc) extract_titration_states() (schrodinger.application.desmond.cms.Cms method) extract_with_asl() (schrodinger.application.desmond.cms.Cms method) extract_with_comp_selection() (schrodinger.application.desmond.cms.Cms method) extract_wmap_files() (schrodinger.application.glide_ws.model.Complex method) extract_zprime2_asus() (in module schrodinger.comparison.struc) extractBarriers() (schrodinger.application.matsci.desconfig.BarrierHeader static method) ExtractClustersStep (class in schrodinger.application.matsci.jwsteps) extractData() (schrodinger.application.matsci.cgforcefield.FFIOAngle method) (schrodinger.application.matsci.cgforcefield.FFIOBond method) (schrodinger.application.matsci.cgforcefield.FFIODihedral method) (schrodinger.application.matsci.cgforcefield.FFIOImproper method) (schrodinger.application.matsci.cgforcefield.FFIOParam method) (schrodinger.application.matsci.cgforcefield.FFIOSite method) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) ExtractLigand (class in schrodinger.application.transforms.dockers.redock) extractMoieties() (schrodinger.application.matsci.amorphous.PolymerFragments method) extractOPLS2005Files() (schrodinger.infra.mm.OPLSArchive method) extractStateChargesAndOrders() (schrodinger.application.prepwizard.HetState method) extractStructure() (schrodinger.structure._AtomCollection method) extractWithMap() (schrodinger.application.matsci.amorphous.PolymerFragments method) ExtraSectionData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) ExtraWidthHelpFormatter (class in schrodinger.tasks.cmdline)

F

F14 (schrodinger.infra.mm.OPLSVersion attribute) F16 (schrodinger.infra.mm.OPLSVersion attribute) F17 (schrodinger.infra.mm.OPLSVersion attribute) f3d_Exception FAB (schrodinger.application.bioluminate.antibody.assembly_yaml.AntibodyFormat attribute) (schrodinger.livedesign.entity_type.EntityClass attribute) FAB2 (schrodinger.livedesign.entity_type.EntityClass attribute) fab_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) Face (class in schrodinger.application.matsci.shapes) FACE_TO_FACE (schrodinger.infra.structure.PiPiInteraction attribute) FACIAL (in module schrodinger.application.matsci.buildcomplex) factorize() (in module schrodinger.application.matsci.gsas.GSASIIpwd) Factory (class in schrodinger.application.bioluminate.actions.factory) FAILED (schrodinger.job.jobcontrol.DisplayStatus attribute) (schrodinger.job.queue.CancelSubmittedStatus attribute) (schrodinger.job.queue.JobState attribute) (schrodinger.seam.viz.inspect.PipelineStatus attribute) (schrodinger.seam.viz.inspect.TransformStatus attribute) (schrodinger.tasks.slurmtasks.JobState attribute) (schrodinger.tasks.taskmanager.TaskManager attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.Status attribute) FAILED_ALL (schrodinger.tasks.queue.AutoFileMode attribute) failed_files (schrodinger.structure.MultiFileStructureReader attribute) failed_jobs (schrodinger.job.queue.JobDJ property) FAILED_LOG (schrodinger.tasks.queue.AutoFileMode attribute) FAILED_MESSAGE (schrodinger.application.glide.ligand_designer.GridgenTask attribute) FAILED_RETRYABLE (schrodinger.job.queue.JobState attribute) failed_tasks (schrodinger.tasks.queue.QueueResults attribute) failed_tasksChanged (schrodinger.tasks.queue.QueueResults attribute) failed_tasksReplaced (schrodinger.tasks.queue.QueueResults attribute) FAILED_TO_ACQUIRE_LICENSE (schrodinger.job.queue.CancelSubmittedStatus attribute) FAILED_TO_LAUNCH (schrodinger.job.queue.PrintableStatus attribute) FailedTrigger (class in schrodinger.application.glide_ws.trigger) FailingTransform (class in schrodinger.seam.testing.failures) FailingTransformSettings (class in schrodinger.seam.testing.failures) failure_info (schrodinger.tasks.tasks.AbstractTask attribute) failure_infoChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.ld_tasks.StructureInfoTask attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask attribute) (schrodinger.application.livedesign.tasks.AbModelingTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.EventAnalysisTask attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MultisimTask attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.Trj2maeTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.BuildMissingLoopsTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.beamtasks.BeamTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.maptasks.MapTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.slurmtasks.ComboSlurmTask attribute) (schrodinger.tasks.slurmtasks.FooTask attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask attribute) (schrodinger.tasks.test.cli.preprocessor_cli.FooJobTask attribute) (schrodinger.ui.qt.pdb_dialog.Sf2MapConversionTask attribute) failure_infoReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.ld_tasks.StructureInfoTask attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask attribute) (schrodinger.application.livedesign.tasks.AbModelingTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.EventAnalysisTask attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MultisimTask attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.Trj2maeTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.BuildMissingLoopsTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.beamtasks.BeamTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.maptasks.MapTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.slurmtasks.ComboSlurmTask attribute) (schrodinger.tasks.slurmtasks.FooTask attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask attribute) (schrodinger.tasks.test.cli.preprocessor_cli.FooJobTask attribute) (schrodinger.ui.qt.pdb_dialog.Sf2MapConversionTask attribute) failure_infos (schrodinger.tasks.queue.QueueReport attribute) failure_infosChanged (schrodinger.tasks.queue.QueueReport attribute) failure_infosReplaced (schrodinger.tasks.queue.QueueReport attribute) FailureInfo (class in schrodinger.tasks.tasks) FakeMaestro (class in schrodinger.application.bioluminate.protein_structure_quality) FALLBACK_BASE_NAME (schrodinger.application.matsci.jaguarworkflows.WorkFlow attribute) FALSE (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolOperator attribute) family (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) family_name (schrodinger.application.livedesign.data_classes.LDData property) FamilyPairwiseAligner (class in schrodinger.protein.align) FarContact (schrodinger.protein.annotation.BINDING_SITE attribute) fast (schrodinger.ui.qt.appframework2.debug_gui.DebugViewer attribute) (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute) fast_sa (class in schrodinger.application.matsci.gsas.GSASIImath) FASTA (schrodinger.infra.structure.FileFormat attribute) (schrodinger.rdkit_extensions.Format attribute) fasta (schrodinger.utils.fileutils.SeqFormat attribute) FASTA_DNA (schrodinger.rdkit_extensions.Format attribute) FASTA_PEPTIDE (schrodinger.rdkit_extensions.Format attribute) FASTA_RNA (schrodinger.rdkit_extensions.Format attribute) fasta_single_entity_mapping (schrodinger.livedesign.registration.RegistrationOptions attribute) FastaHeader (class in schrodinger.livedesign.biologics.fasta) fastas_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) FastDecorator (class in schrodinger.application.steps.enumerators) FastFragmenter (class in schrodinger.application.steps.enumerators) FastFragmenter.Settings (class in schrodinger.application.steps.enumerators) fastItem() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.infra.canvas.ChmSymmetricMatrixUnsignedInt method) fastReadItem() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.infra.canvas.ChmSymmetricMatrixUnsignedInt method) FASTSIM (schrodinger.infra.licensing.SimilarityEndpoint attribute) fatal() (in module schrodinger.application.desmond.util) fatal_error() (in module schrodinger.application.jaguar.textparser) FatalCoordinateError FatalErrors (class in schrodinger.application.jaguar.constants) faux_epi_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) favicon_endpoints() (schrodinger.seam.viz.watcher.WatcherWebServer method) FAVORABLE_COLOR (schrodinger.ui.qt.rama.RamaContourMixin attribute) FAVORED (schrodinger.ui.qt.rama.RamaClassification attribute) favorite_categories (schrodinger.tasks.test.cli.customized_param_cli.Preferences attribute) favorite_categoriesChanged (schrodinger.tasks.test.cli.customized_param_cli.Preferences attribute) favorite_categoriesReplaced (schrodinger.tasks.test.cli.customized_param_cli.Preferences attribute) FBHWPosRestrainArray (class in schrodinger.application.desmond.cms) FC_KEY (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) FC_LABEL() (in module schrodinger.application.matsci.cgforcefieldgui) fcc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) fcjde_gen (class in schrodinger.application.matsci.gsas.GSASIIpwd) fcp (schrodinger.application.matsci.espresso.qeinput.BoundaryType property) FDPOL_FREQ1 (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) FDPOLAR_ALPHA1 (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) FDPOLAR_FREQ1 (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) Feature (class in schrodinger.application.glide.constraints) (class in schrodinger.application.licensing.flexlm) feature (schrodinger.application.glide_ws.model.Constraint attribute) (schrodinger.application.licensing.lmgrd_log_parser.event attribute) feature_coordinates (schrodinger.application.phase.phase_markers.PhaseFeatureMarker property) feature_counter (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) FEATURE_DEFINITION_PRESETS (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo attribute) FEATURE_EQUIV_PRESETS (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo attribute) feature_expiring() (in module schrodinger.application.licensing.licadmin) FEATURE_FLAGS (schrodinger.utils.postinstall.CustomConfigFiles attribute) feature_name (schrodinger.application.phase.phase_markers.PhaseFeatureMarker property) FEATURE_QCOLORS() (in module schrodinger.application.phase.constants) FEATURE_TYPE (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) feature_type (schrodinger.application.phase.phase_markers.PhaseFeatureMarker property) FeatureColumns (class in schrodinger.application.phase.featureselector) featureExists() (schrodinger.application.phase.phase_markers.PhaseMarkers method) FeatureMatchCombo (class in schrodinger.application.phase.phase_widgets) FeatureModel (class in schrodinger.application.phase.featureselector) FeatureName (schrodinger.application.phase.featureselector.FeatureColumns attribute) FeatureOptionsCombo (class in schrodinger.application.phase.phase_widgets) FeaturePattern (class in schrodinger.application.glide.constraints) FeatureRow (class in schrodinger.application.phase.featureselector) FEATURES (schrodinger.application.matsci.mlearn.features.LatticeFeatures attribute) features (schrodinger.application.phase.shape_screen_reporter.option_utils.ClusterBy attribute) FeatureSelector (class in schrodinger.application.phase.featureselector) featureToggled (schrodinger.application.phase.featureselector.FeatureModel attribute) Featurize (class in schrodinger.application.matsci.mlearn.descriptor) featurize() (schrodinger.application.matsci.mlearn.features.CrystalNNFeatures method) FeaturizeError fedit() (in module schrodinger.ui.qt.formlayout) FEDORA (schrodinger.autoinstall.misc.OperatingSystem attribute) feedback (schrodinger.maestro_utils.composer_agent.request_manager.network_manager.ExecutionFeedbackQuery attribute) (schrodinger.maestro_utils.composer_agent.request_manager.network_manager.UserFeedbackQuery attribute) FEEDBACK (schrodinger.maestro_utils.composer_agent.request_manager.urls.PostUserFeedbackPayloadKey attribute) FeedbackSubplotToolQt (class in schrodinger.ui.qt.navtoolbar) fep() (schrodinger.application.macromodel.utils.ComUtil method) fep_mut (schrodinger.application.desmond.struc.CompStruc attribute) fep_ref (schrodinger.application.desmond.struc.CompStruc attribute) fep_references_file (schrodinger.application.steps.filters.FepFilter.Settings attribute) fep_references_fileChanged (schrodinger.application.steps.filters.FepFilter.Settings attribute) fep_references_fileReplaced (schrodinger.application.steps.filters.FepFilter.Settings attribute) FepAmenable (class in schrodinger.application.transforms.filters) FepFilter (class in schrodinger.application.steps.filters) FepFilter.Settings (class in schrodinger.application.steps.filters) fepNone (schrodinger.infra.canvas.ChmMCSRecord attribute) fepNoRingBreak (schrodinger.infra.canvas.ChmMCSRecord attribute) fepRingBreak (schrodinger.infra.canvas.ChmMCSRecord attribute) fetch_iupac_from_smiles() (in module schrodinger.application.matsci.rdpattern) fetchPPDB() (schrodinger.application.matsci.espresso.qeinput.StructureType method) ff_changed (schrodinger.application.matsci.chargegui.ForceFieldDialog attribute) ff_clash_tolerance (schrodinger.application.peptide_workflow.beam_adapter.SuperimposeSettings attribute) ff_dielectric_constant (schrodinger.application.peptide_workflow.beam_adapter.SuperimposeSettings attribute) FFBuilderTask (class in schrodinger.application.livedesign.tasks) FFBuilderTask.Input (class in schrodinger.application.livedesign.tasks) FFBuilderTask.JobConfig (class in schrodinger.application.livedesign.tasks) FFBuilderTask.Output (class in schrodinger.application.livedesign.tasks) FFBundleVersionData (class in schrodinger.infra.mm) ffc_export_specs (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ffc_export_specsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ffc_export_specsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) FFCExportSpec (class in schrodinger.application.livedesign.export_models) ffComboBox (class in schrodinger.ui.qt.forcefield.ffselector) FFCustomOPLSSettingMixin (class in schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget) FFCustomOPLSSettingWidget (class in schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget) FFGlobalPreferenceWidget (class in schrodinger.ui.qt.forcefield.ffglobalpreferencewidget) FFInfo (class in schrodinger.application.matsci.chargegui) FFIO_ATOM_VEL() (in module schrodinger.application.matsci.msprops) ffio_refresh() (schrodinger.application.desmond.cms.Cms method) FFIOAngle (class in schrodinger.application.matsci.cgforcefield) FFIOBond (class in schrodinger.application.matsci.cgforcefield) FFIODihedral (class in schrodinger.application.matsci.cgforcefield) FFIOExclusion (class in schrodinger.application.matsci.cgforcefield) FFIOImproper (class in schrodinger.application.matsci.cgforcefield) FFIOParam (class in schrodinger.application.matsci.cgforcefield) FFIOSite (class in schrodinger.application.matsci.cgforcefield) FFIOVdwType (class in schrodinger.application.matsci.cgforcefield) FFIOVdwTypesCombined (class in schrodinger.application.matsci.cgforcefield) ffld() (in module schrodinger.application.qsite.output) ffld_main_licenses_exist() (in module schrodinger.infra.mm) ffld_project_incompatible() (in module schrodinger.forcefield.test.fixtures) ffld_project_ring() (in module schrodinger.forcefield.test.fixtures) ffld_project_skipped() (in module schrodinger.forcefield.test.fixtures) ffld_spec_to_string() (in module schrodinger.infra.mm) ffld_use_db_v2() (in module schrodinger.forcefield.test.fixtures) FfldSpec (class in schrodinger.infra.mm) ffldVersion() (schrodinger.infra.fast3d.Volumizer method) FFProjectSettingsDlg (class in schrodinger.ui.qt.forcefield.ffprojectsettingsdlg) FFSettingsButton (class in schrodinger.ui.qt.forcefield.ffsettingsbutton) FFVersionData (class in schrodinger.infra.mm) Field (class in schrodinger.application.bindingsite.intfield) field (schrodinger.application.jaguar.nmr_utils.NMRData attribute) field_str (schrodinger.application.matsci.kmc.MSDInfo attribute) FieldColumn (class in schrodinger.ui.qt.mapperwidgets.plptable) FIELDX (schrodinger.application.matsci.kmc.SchrodingerTable attribute) FIELDY (schrodinger.application.matsci.kmc.SchrodingerTable attribute) FIELDZ (schrodinger.application.matsci.kmc.SchrodingerTable attribute) FIFOCacheData (class in schrodinger.application.matsci.cache) figure_edit() (in module schrodinger.ui.qt.figureoptions) FILE (schrodinger.application.livedesign.models2.datamodels.definition.InputType attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputType attribute) (schrodinger.application.matsci.genetic_optimization.GlassTransitionTemperature attribute) (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) (schrodinger.application.matsci.mswidgets.StructureLoader attribute) (schrodinger.ui.qt.input_selector.InputSelector attribute) File (schrodinger.ui.qt.structure_selector.InputSource attribute) file_arguments_for_launch_command() (in module schrodinger.job.jobcontrol) file_batches (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) file_batchesChanged (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) file_batchesReplaced (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) file_config() (in module schrodinger.utils.log) file_dirname() (in module schrodinger.application.licensing.licadmin) FILE_EXT (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) file_format (schrodinger.application.livedesign.export_models.GETaskInput attribute) file_formatChanged (schrodinger.application.livedesign.export_models.GETaskInput attribute) file_formatReplaced (schrodinger.application.livedesign.export_models.GETaskInput attribute) FILE_IMPORT_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) file_is_empty() (in module schrodinger.utils.compare) file_name (schrodinger.application.prime.wrapper.PrimeTemplate property) FILE_NAME_COL (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame attribute) file_path (schrodinger.application.livedesign.export_models.AttachmentItem attribute) (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_pathChanged (schrodinger.application.livedesign.export_models.AttachmentItem attribute) (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_pathReplaced (schrodinger.application.livedesign.export_models.AttachmentItem attribute) (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_paths (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_pathsChanged (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) file_pathsReplaced (schrodinger.ui.qt.structure_selector.StructureSelectorModel attribute) FILE_PICK_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) file_remover() (in module schrodinger.utils.fileutils) FILE_SELECTOR_CLASS (schrodinger.ui.qt.structure_selector.SlimStructureSelector attribute) (schrodinger.ui.qt.structure_selector.StructureSelector attribute) file_to_tmp_fn() (in module schrodinger.application.matsci.msutils) file_type (schrodinger.application.livedesign.export_models.AttachmentItem attribute) FILE_TYPE (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) file_typeChanged (schrodinger.application.livedesign.export_models.AttachmentItem attribute) FILE_TYPEChanged (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) file_typeReplaced (schrodinger.application.livedesign.export_models.AttachmentItem attribute) FILE_TYPEReplaced (schrodinger.application.livedesign.export_models.FFCExportSpec attribute) FileBaseNameValidator (class in schrodinger.ui.qt.swidgets) FileBatch (class in schrodinger.application.livedesign.export_models) FileDebugViewer (class in schrodinger.ui.qt.appframework2.debugcore) FileDialog (class in schrodinger.ui.qt.filedialog) FileDialogWithExtraCombo (class in schrodinger.application.jaguar.gui.filedialog) FileDownloader (class in schrodinger.application.matsci.jobutils) FileDownloadError FileExists (class in schrodinger.ui.qt.appframework2.validators) fileExplorerError (schrodinger.application.job_monitor.buttons.FileExplorerMenuButton attribute) FileExplorerMenuButton (class in schrodinger.application.job_monitor.buttons) FileFormat (class in schrodinger.application.livedesign.export_tasks) (class in schrodinger.infra.structure) FileInMixin (class in schrodinger.application.steps.dataclasses) FileLayout (class in schrodinger.ui.qt.formlayout) FileLogger (class in schrodinger.application.jaguar.file_logger) FileLoggerError FileMolWorkflow (class in schrodinger.application.steps.basesteps) filename (schrodinger.application.glide_ws.utils.LignumReader property) (schrodinger.application.jaguar.input.JaguarInput property) (schrodinger.application.jaguar.nmr_utils.NMRData attribute) (schrodinger.application.steps.converters.MaeFileWriter.Settings attribute) filenameChanged (schrodinger.application.steps.converters.MaeFileWriter.Settings attribute) filenameReplaced (schrodinger.application.steps.converters.MaeFileWriter.Settings attribute) filepath (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filepathChanged (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filepathReplaced (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) FILES (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) files (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.structure.MultiFileStructureReader attribute) files_are_equal() (in module schrodinger.glide) filesChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame attribute) fileSelectionChanged (schrodinger.ui.qt.file_selector.FileSelector attribute) FileSelector (class in schrodinger.ui.qt.file_selector) filesReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) FILETYPE (schrodinger.application.matsci.packmol.PackmolKw attribute) fill() (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.structure.StructureCoordinates method) fill_table_with_data_frame() (in module schrodinger.application.matsci.gutils) fillAdsCache() (schrodinger.application.matsci.rxn_channel.CacheInfo method) FillAtomLookUp() (in module schrodinger.application.matsci.gsas.GSASIImath) fillAtoms() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillBranchPoints() (schrodinger.application.matsci.amorphous.Initiator method) fillFolderTree() (schrodinger.application.livedesign.ld_folder_tree.LDFolderTree method) fillFragments() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillFrames() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillgmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice) fillloops (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillloopsChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillloopsReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillMolecules() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillPairs() (schrodinger.application.matsci.kmc.BaseDatabaseManager method) fillSchrodinger() (schrodinger.application.matsci.kmc.BaseDatabaseManager method) fillSegments() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillSegmentTypes() (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) fillsidechains (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillsidechainsChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillsidechainsReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) fillSites() (schrodinger.application.matsci.kmc.MatSciDatabaseManager method) fillStatusLabel() (schrodinger.application.matsci.builderwidgets.RowTemplateMixin method) FillUnitCell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) fillWeightedDiffList() (schrodinger.infra.mm.MMFfldEsp method) fillWithResults() (schrodinger.application.jaguar.gui.timing.TimerInfoDialog method) Filter (class in schrodinger.structutils.filter) (class in schrodinger.ui.qt.filter_dialog_dir.filter_core) filter() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) (schrodinger.infra.canvas.ChmMatches method) (schrodinger.infra.canvas.ChmMatchesEx method) (schrodinger.math.sampling.SystematicSampler class method) (schrodinger.rdkit.filtering.JSONFilterAdapter method) (schrodinger.structutils.filter.Filter method) filter_by_core_RMSD() (in module schrodinger.application.glide.runner_utils) filter_csv() (in module schrodinger.application.bioluminate.pose_filtering.csv_filter) filter_data() (schrodinger.application.desmond.bennett.CalcBAR method) filter_entry_node_indices() (in module schrodinger.maestro_utils.surface_manager.utils) filter_file (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.steps.filters.PropertyFilter.Settings attribute) filter_fileChanged (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.steps.filters.PropertyFilter.Settings attribute) filter_fileReplaced (schrodinger.application.livedesign.tasks.LigFilterTask.Input attribute) (schrodinger.application.steps.filters.PropertyFilter.Settings attribute) filter_glide_results() (in module schrodinger.application.livedesign.ld_glide_utils) filter_hits() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) filter_hydrogen_from_list() (in module schrodinger.application.jaguar.gui.input_tab_widgets_pka) filter_missing_entry() (in module schrodinger.application.livedesign.panel_components) filter_monatomic_mols() (in module schrodinger.application.desmond.struc) filter_nonshared_rotatables() (in module schrodinger.protein.protassign.changeables) filter_qt_msg() (in module schrodinger.infra.qt_message_handler) filter_query (schrodinger.protein.tasks.blast.BlastSettings attribute) filter_queryChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) filter_queryReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) filter_reactions() (in module schrodinger.application.pathfinder.analysis) filter_res_datas() (schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter method) (schrodinger.application.bioluminate.pose_filtering.residue_filter.ResidueFilter method) (schrodinger.application.bioluminate.pose_filtering.residue_filter.SasaResidueFilter method) filter_residues_mutating_to_custom() (in module schrodinger.protein.nonstandard_residues) filter_routes() (in module schrodinger.application.combinatorial_explorer.driver_utils) filter_string_from_extensions() (in module schrodinger.ui.qt.filedialog) filter_string_from_formats() (in module schrodinger.ui.qt.filedialog) filter_string_from_supported() (in module schrodinger.ui.qt.appframework) filter_structure_chains() (in module schrodinger.application.bioluminate.tcr.annotate) filter_structures() (in module schrodinger.application.bioluminate.pose_filtering.csv_filter) filter_terms (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filter_termsChanged (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filter_termsReplaced (schrodinger.ui.qt.standard.icons.icons.IconMetadata attribute) filter_undesired_states() (in module schrodinger.application.prepwizard) filterAcceptsColumn() (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesProxyModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel method) filterAcceptsIndex() (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterAcceptsParent() (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterAcceptsRow() (schrodinger.application.bioluminate.protein_report_widget.ProxyModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) (schrodinger.application.livedesign.panel_components.ColumnSelectionProxyModel method) (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterAction() (schrodinger.maestro_utils.surface_manager.menus.BaseMenu method) filterAll() (schrodinger.seam.testing.stateful.StatefulBeamPipelineMachine method) FilterBasisSelectorReadOnlyLineEdit (class in schrodinger.application.jaguar.gui.basis_selector) filterByCoreRmsd() (schrodinger.glide.RefinedPoseEnsemble method) FilterCheckBox (class in schrodinger.ui.qt.filter_list) FilterCombination (class in schrodinger.application.transforms.autosar.transforms) FilterCriteria (class in schrodinger.application.bioluminate.pose_filtering.residue_filter) FilterDBTask (class in schrodinger.application.phase.shape_screen_reporter.tasks) FilterDBTask.Input (class in schrodinger.application.phase.shape_screen_reporter.tasks) FilterDBTask.Output (class in schrodinger.application.phase.shape_screen_reporter.tasks) FilterDialog (class in schrodinger.ui.qt.filter_dialog) filtered_combinations() (in module schrodinger.structutils.rgroup_enumerate) filtered_combinations_for_selection() (in module schrodinger.structutils.rgroup_enumerate) filtered_filename() (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) filtered_row_nums (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Output attribute) filtered_row_numsChanged (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Output attribute) filtered_row_numsReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask.Output attribute) FilteredComplexTemplateSketcher (class in schrodinger.application.matsci.builderwidgets) FilteredSketcherBox (class in schrodinger.application.matsci.builderwidgets) FilteredTemplateSelector (class in schrodinger.application.matsci.builderwidgets) filterEntities() (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask method) filterFile() (schrodinger.pipeline.stages.filtering.SubSetStage method) filteringChanged() (schrodinger.ui.qt.propertyselector.PropertySelector method) filterList() (schrodinger.application.bioluminate.propfilter.SelectingFilteredListWidget method) (schrodinger.application.matsci.wfmanagement.WorkflowFilterWidget method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) (schrodinger.ui.qt.swidgets.SFilteredListWidget method) FilterListPopUp (class in schrodinger.ui.qt.filter_list) FilterParameters (class in schrodinger.application.bioluminate.pose_filtering.csv_filter) filterProperties() (schrodinger.ui.qt.propertyselector.PropertySelector method) FilterReporter (class in schrodinger.structutils.smilesfilter) filterRowsByExcitedState() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) filters (schrodinger.application.bioluminate.pose_filtering.residue_filter.FilterCriteria attribute) filters_unsanitizable() (in module schrodinger.application.transforms.chem) filtersChanged (schrodinger.application.jaguar.gui.basis_selector.FilterBasisSelectorReadOnlyLineEdit attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetDelegate attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.MethodDelegate attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog attribute) (schrodinger.application.jaguar.gui.theory_selector.FilterTheorySelectorReadOnlyLineEdit attribute) (schrodinger.ui.qt.filter_list.FilterListPopUp attribute) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp attribute) filterSelectionChanged() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) filtersInvalidated (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) filterSmilesFile() (schrodinger.pipeline.stages.filtering.SubSetStage method) filterTemplates() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) FilterTheorySelectorReadOnlyLineEdit (class in schrodinger.application.jaguar.gui.theory_selector) FilterUndockable (class in schrodinger.application.transforms.dock) FilterWidget (class in schrodinger.ui.qt.filter_dialog_dir.filter_widgets) filterWorkflows() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) final (schrodinger.application.jaguar.scan.Scan property) (schrodinger.application.jaguar.utils.ScanCoord attribute) FINAL_VAL (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) finalize() (schrodinger.application.xtb.textparser.TextParser static method) (schrodinger.job.queue.BaseJob method) finalize_csv() (in module schrodinger.application.glide.csv_utils) finalize_smap() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) finalize_solvation_entropy_params() (in module schrodinger.application.jaguar.thermochemical_properties) finalize_subjob() (in module schrodinger.application.matsci.jobutils) finalizeJMSWFOutput() (schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin method) finalizeSideGroup() (schrodinger.application.matsci.amorphous.BaseMoiety method) finalizeStep() (schrodinger.application.matsci.permittivity.AnalyzeSimulation static method) (schrodinger.application.matsci.permittivity.AveCellAnalysis static method) (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis static method) (schrodinger.application.matsci.permittivity.ComplexPermittivity static method) (schrodinger.application.matsci.permittivity.DensityAnalysis static method) (schrodinger.application.matsci.permittivity.ElectricPolarizability static method) (schrodinger.application.matsci.permittivity.JaguarCalculation static method) (schrodinger.application.matsci.permittivity.JaguarMerge static method) (schrodinger.application.matsci.permittivity.RefractiveIndex static method) (schrodinger.application.matsci.permittivity.StaticPermittivity static method) (schrodinger.application.matsci.permittivity.StepBase static method) (schrodinger.application.matsci.permittivity.SusceptibilityMerge static method) FinalTSFailure find() (schrodinger.application.desmond.arkdb.ArkDb method) find_ab_chain() (in module schrodinger.livedesign.biologics.registration) find_abs_by_connectivity() (in module schrodinger.livedesign.biologics.registration) find_all_entries() (in module schrodinger.application.bioluminate.pml_menus) find_all_rings() (in module schrodinger.infra.structure) (in module schrodinger.structutils.rings) find_all_table_entry_objects() (in module schrodinger.application.bioluminate.pml_menus) find_antibodies() (in module schrodinger.livedesign.biologics.registration) find_atom() (in module schrodinger.protein.nonstandard_residues) find_atom_with_pdb_name() (in module schrodinger.ui.residueselector) find_atoms_closest_to_atoms() (in module schrodinger.application.matsci.clusterstruct) find_atoms_near_point() (in module schrodinger.application.matsci.reorder) find_atoms_to_remove() (in module schrodinger.application.matsci.buildcomplex) find_attached_atom_index() (in module schrodinger.application.matsci.amorphous) find_backbone() (in module schrodinger.application.matsci.graph) find_best_core_match() (in module schrodinger.application.canvas.r_group) find_best_match_with_director() (in module schrodinger.application.matsci.rxn_channel) find_box() (in module schrodinger.application.desmond.struc) find_buddies_on_other_surf() (in module schrodinger.application.bioluminate.surfcomp) find_center_of_atoms() (in module schrodinger.application.bioluminate.pml_menus) find_closest_point() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) (schrodinger.ui.qt.rama.Rama method) find_closest_xval() (in module schrodinger.application.matsci.spectra) find_common (schrodinger.application.phase.input.InputSpecs attribute) find_common_properties() (in module schrodinger.structutils.analyze) find_common_substructure() (in module schrodinger.structutils.analyze) find_data_file() (in module schrodinger.glide) find_decorated_methods() (in module schrodinger.infra.util) find_distortions() (in module schrodinger.structutils.check) find_disulfide_atoms() (in module schrodinger.structutils.analyze) find_duplicate_titles() (in module schrodinger.application.desmond.struc) find_eq_stress() (in module schrodinger.application.matsci.elasticity.elastic) find_equivalent_atoms() (in module schrodinger.application.glide.gui) (in module schrodinger.structutils.analyze) find_equivalent_st() (in module schrodinger.application.desmond.system_builder_util) find_failed_logfiles() (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) find_families() (in module schrodinger.protein.gpcr.gpcrdb) find_filename_in_model() (in module schrodinger.application.matsci.ml_formulations_utils) find_first_normal() (in module schrodinger.application.jaguar.utils) find_forcefield_invalid_structures() (in module schrodinger.application.matsci.desmondutils) find_full_product_version() (in module schrodinger.application.utils) find_furthest_atom_along_vector() (in module schrodinger.application.matsci.nano.xtal) find_generalized_pattern() (in module schrodinger.protein.sequence) find_good_bond_vector() (in module schrodinger.application.matsci.rxn_channel) find_grd_file() (in module schrodinger.application.glide.grid) find_group_data() (in module schrodinger.application.matsci.smartsutils) find_hbond_hydrogen() (schrodinger.protein.analysis.Report.steric_clash_data_set method) find_head_tail() (in module schrodinger.application.matsci.graph) find_het_atoms() (in module schrodinger.application.prepwizard) find_hets() (in module schrodinger.protein.findhets) find_isolated_water_molecules() (in module schrodinger.protein.reliability) find_key_for_value() (in module schrodinger.application.jaguar.gui.utils) find_key_pair() (in module schrodinger.utils.sshconfig) find_knime_java_path() (in module schrodinger.utils.env) find_license_file() (in module schrodinger.application.licensing.flexlm) find_license_files() (in module schrodinger.application.licensing.licserver.client) find_license_resources() (in module schrodinger.application.licensing.licadmin) find_ligand_atoms() (in module schrodinger.infra.mm) find_ligand_molecules() (in module schrodinger.infra.mm) find_ligands() (in module schrodinger.structutils.analyze) FIND_LIGANDS_KWARGS (schrodinger.application.prime.wrapper.PrimeTemplate attribute) find_local_pdb() (in module schrodinger.protein.getpdb) find_local_repository() (in module schrodinger.protein.getpdb) find_lone_hydrogen() (in module schrodinger.application.matsci.buildcomplex) find_marked_backbone_path() (in module schrodinger.application.matsci.geometry) find_metal() (in module schrodinger.application.matsci.etarotamers) find_metals_in_structure() (in module schrodinger.application.prepwizard) find_missing_coupling_data() (in module schrodinger.application.matsci.kmc) find_missing_lambda_data() (in module schrodinger.application.matsci.kmc) find_missing_loops() (in module schrodinger.application.prepwizard) find_missing_peptide_bonds() (in module schrodinger.application.prepwizard2.tasks) find_missing_res_atoms() (in module schrodinger.application.prepwizard) find_missing_site_energies() (in module schrodinger.application.matsci.kmc) find_mol_species_from_rdmol() (in module schrodinger.application.matsci.clusterstruct) find_molecule_fragments() (in module schrodinger.application.matsci.clusterstruct) find_molecules_closest_to_atoms() (in module schrodinger.application.matsci.clusterstruct) find_n1_atom() (in module schrodinger.protein.pdbname) find_na_entities() (in module schrodinger.livedesign.biologics.registration) find_new_group_id() (in module schrodinger.application.matsci.automated_cg_mapping) find_next_residue() (in module schrodinger.application.desmond.cms) find_origin_on_structure_exterior() (in module schrodinger.application.matsci.nano.xtal) find_overlapping_atoms() (in module schrodinger.structutils.analyze) find_oxt_atom() (in module schrodinger.protein.pdbname) find_param() (in module schrodinger.ui.qt.mapperwidgets.plptarget) find_pattern() (in module schrodinger.protein.sequence) find_pi_cation_interactions() (in module schrodinger.structutils.interactions.pi) find_pi_pi_interactions() (in module schrodinger.structutils.interactions.pi) find_polar_contacts() (in module schrodinger.application.bioluminate.pml_menus) find_polygon_vertices() (in module schrodinger.application.matsci.nano.tools) find_polymer_species() (in module schrodinger.application.matsci.polymer) find_ppw_atom() (in module schrodinger.application.prepwizard) find_prev_residue() (in module schrodinger.application.desmond.cms) find_product_package_dir() (in module schrodinger.application.utils) find_protonation_state_changes() (schrodinger.protein.assignment.ProtAssign method) find_reactions() (in module schrodinger.application.combinatorial_screen.driver_utils) find_recap_bonds() (in module schrodinger.structutils.createfragments) find_res_species() (in module schrodinger.application.matsci.clusterstruct) find_residue_atom() (in module schrodinger.application.bioluminate.protein.utils) find_residues_with_multiple_occupancies() (in module schrodinger.application.prepwizard2.diagnostics) find_rgroup_from_smarts() (in module schrodinger.structutils.rgroup_enumerate) find_ring_atoms() (in module schrodinger.infra.structure) (in module schrodinger.structutils.rings) find_ring_bonds() (in module schrodinger.infra.structure) (in module schrodinger.structutils.rings) find_ring_systems() (in module schrodinger.infra.structure) (in module schrodinger.structutils.rings) find_rings() (in module schrodinger.structutils.rings) (schrodinger.structure.Structure method) find_scaffolds() (in module schrodinger.application.bioluminate.antibody.scaffold_search) find_segments() (in module schrodinger.application.matsci.graph) find_shortest_bond_path() (in module schrodinger.structutils.analyze) find_signals() (in module schrodinger.ui.qt.appframework2.debugwidgets) find_spec() (schrodinger.infra.unusable_module_importer.AbstractUnusableModuleFinder method) (schrodinger.infra.unusable_module_importer.NonPostTestUnusableModuleFinder method) find_species() (in module schrodinger.application.matsci.clusterstruct) find_staying_atom() (in module schrodinger.structutils.rgroup_enumerate) find_test_file() (in module schrodinger.glide) FIND_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) find_traj_path() (in module schrodinger.application.desmond.packages.topo) find_traj_path_from_cms_path() (in module schrodinger.application.desmond.packages.topo) find_user_libstdcpp() (in module schrodinger.utils.installation_check) find_validators() (in module schrodinger.ui.qt.appframework2.validation) FINDALL (schrodinger.application.jaguar.utils.LewisModes attribute) FindAllNeighbors() (in module schrodinger.application.matsci.gsas.GSASIImath) findAnchoredPath() (schrodinger.application.matsci.custom_lipid_prep.FindHeadTail method) findAnchorHierarchy() (schrodinger.application.matsci.custom_lipid_prep.FindHeadTail method) findAntibodyRegions() (schrodinger.application.bioluminate.pml_menus.AntibodyPreset method) FindAtomIndexByIDs() (in module schrodinger.application.matsci.gsas.GSASIImath) findAttachedAtomIndex() (schrodinger.application.matsci.amorphous.BaseMoiety method) findAttachmentMarkers() (schrodinger.application.matsci.builderwidgets.MinimizeMixin method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) findBackbone() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Monomer method) findBackbone2BranchingPoint() (schrodinger.application.matsci.amorphous.BaseMoiety method) findBackboneAngles() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) findBackboneAtomsIds() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner static method) findBackboneChains() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder static method) findBindingAtoms() (schrodinger.application.matsci.buildcomplex.ComplexSplitter method) findBondGroups() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) findBondsToBreak() (schrodinger.application.matsci.amorphous.Monomer method) findCapNeighbors() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder method) findChiAtoms() (schrodinger.protein.rotamers.Rotamers method) findCommonDatanames() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) findCoordinate() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) findCTerminae() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder method) findData() (schrodinger.ui.qt.swidgets.SComboBox method) findDataPy() (schrodinger.ui.qt.swidgets.SComboBox method) finder (schrodinger.application.matsci.species.SC_TYPE_DATA attribute) findEtaGroups() (schrodinger.application.matsci.buildcomplex.EtaFindingMixin method) findExclusiveAtoms() (schrodinger.application.matsci.automated_cg_mapping.StructData method) findFirstDisorderedMolecule() (schrodinger.application.matsci.montecarlo.Metropolizer method) findFragments() (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule method) findFreeVolume() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) findFuncGroupsFromMolecule() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) findGenerations() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) findGroupsFromMolecule() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) findGroupsInSet() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) findGroupsMapping() (schrodinger.application.matsci.automated_cg_mapping.StructData method) findHead() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Terminator method) FindHeadTail (class in schrodinger.application.matsci.custom_lipid_prep) findHeadTail() (schrodinger.application.matsci.amorphous.PolymerFragments static method) findHeadTailBranch() (schrodinger.application.matsci.amorphous.Monomer method) findHetAtoms() (schrodinger.application.prepwizard.HetState method) findHydrophilicAtoms() (schrodinger.application.matsci.custom_lipid_prep.LipidEndProcessor method) findHydrophobicAtoms() (schrodinger.application.matsci.custom_lipid_prep.LipidEndProcessor method) findHydrophobicCenter() (schrodinger.protein.membrane.Membrane_Model method) findInStructure() (schrodinger.ui.picking.ResidueRow method) findInvalidAtomsAndBonds() (schrodinger.infra.canvas.ChmMCSRecord method) findInvalidFFStructures() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) (schrodinger.application.matsci.chargegui.MLFFDialog method) findItem() (schrodinger.application.livedesign.panel_components.LDSelectionModel method) findLargestTranslat() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) findLigandAtoms() (schrodinger.application.glide.gui.GridSite method) findLinearAtoms() (schrodinger.application.matsci.vsepr.VSEPRFinder method)

findLocally() (schrodinger.protein.getpdb_utility.Code method) findManageOutfiles() (schrodinger.pipeline.stages.phase.DBExportStage method) findMarkHeadTailMarkers() (schrodinger.application.matsci.amorphous.Moieties method) findMatchingGroup() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) findMinVolume() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) FindMolecule() (in module schrodinger.application.matsci.gsas.GSASIImath) findNativeLigand() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) findNearbyImages() (schrodinger.infra.structure.PBC method) findNeighborFrags() (schrodinger.application.matsci.amorphous.PolymerFragments method) findNeighboringCells() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) FindNeighbors() (in module schrodinger.application.matsci.gsas.GSASIImath) findNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) findNonlinearAngle() (schrodinger.application.matsci.zmutils.ZMatrix method) FindNonstandard() (in module schrodinger.application.matsci.gsas.GSASIIlattice) findNTerminae() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder method) findNTerminiAtomIds() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner static method) findOffset() (in module schrodinger.application.matsci.gsas.GSASIImath) findOrCreateDBEntry() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) findOxygenToReplace() (schrodinger.protein.captermini.CapTermini method) findPath() (schrodinger.application.livedesign.panel_components.PathTreeDict method) findPattern() (schrodinger.protein.alignment.ProteinAlignment method) FindPCSubMenu (class in schrodinger.application.bioluminate.pml_menus) findPoint() (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin method) findReagentFile() (schrodinger.application.pathfinder.reaction.ReagentClass method) (schrodinger.application.pathfinder.route.ReagentNode method) findResidue() (schrodinger.structure.Structure method) findResidues() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) findRingCenterAndNormal() (in module schrodinger.application.jaguar.utils) findRings() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) (schrodinger.application.matsci.montecarlo.ClashChecker method) findRingSideGroup() (schrodinger.application.matsci.amorphous.Monomer method) findRingSpears() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) findRingSystems() (schrodinger.infra.structure.MoleculeGraph method) findRotatableBonds() (schrodinger.application.matsci.amorphous.BaseMoiety method) findRowsMatching() (schrodinger.project.project.Project method) findSameGenerationIndices() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) findSampleNodes() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMapper method) findSideGroup() (schrodinger.application.matsci.amorphous.BaseMoiety method) findSimpleHeadTailMarkers() (schrodinger.application.matsci.amorphous.Moieties method) findSmallestAngleAtom() (schrodinger.application.matsci.vsepr.VSEPRFinder method) findSMARTSError() (schrodinger.ui.qt.swidgets.SMARTSEdit method) findSMARTSMatchingIndexes() (schrodinger.application.matsci.automated_cg_mapping.StructData method) findSpears() (schrodinger.structutils.ringspear.SpearRing method) findSpecies() (schrodinger.application.matsci.speciesgui.GroupingMethodSelector method) findSpeciesInStruct() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) findSpiroSystems() (schrodinger.infra.structure.MoleculeGraph method) findSSOffset() (in module schrodinger.application.matsci.gsas.GSASIImath) findStructAromaticBonds() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) findTextChanged() (schrodinger.application.bioluminate.ssv.toolbars.FindToolBar method) FindToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) (class in schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) FindToolBarSketcherDialog (class in schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) findTotalEnergyProp() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) findXvolSphereIndex() (schrodinger.application.phase.phase_markers.PhaseMarkers method) FINGERPRINT_TYPES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) fingerprintChanged (schrodinger.ui.qt.fp_selector_widget.FingerprintsPopUp attribute) FingerprintComponent (class in schrodinger.analysis.enrichment.enrichment_input) FingerprintsModel (class in schrodinger.ui.qt.fp_selector_widget) FingerprintsPopUp (class in schrodinger.ui.qt.fp_selector_widget) FingerprintsSelectorWidget (class in schrodinger.ui.qt.fp_selector_widget) FingerprintUse (class in schrodinger.livedesign.search) finish() (schrodinger.application.bioluminate.pml_menus.PresetAction method) (schrodinger.application.glide.http_server.GlideHTTPHandler method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.RDFStep method) (schrodinger.pipeline.pipeline.StageJob method) (schrodinger.ui.qt.structure2d.StructureToolTip method) FINISH_ALL (schrodinger.active_learning.al_driver.StopAfterPattern attribute) finish_bundle() (schrodinger.seam.examples.haystack.Bale method) (schrodinger.seam.yaml.schemad.SchemadDoFn method) finish_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) FINISHED (schrodinger.application.fragment_virtual_screening.frag_vs_utils.StageStatus attribute) finished (schrodinger.maestro_utils.composer_agent.request_manager.network_manager.NetworkManager attribute) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel attribute) (schrodinger.ui.qt.appframework2.wizards.MultiPanelWizard attribute) finished_nodes (schrodinger.active_learning.al_driver.StopAfterValidator property) finishGuess() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) finishPolymerFrags() (schrodinger.application.matsci.amorphous.PolymerFragments method) finishPrevStep() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) finishProcessingJobControlJob() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.SubdirectoryStepMixin method) finishWord() (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator method) (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator64 method) FIRST (schrodinger.application.matsci.permittivity.MdStageModifier attribute) first() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) FIRST_CELL (schrodinger.application.matsci.nano.xtal.PBCBonds attribute) first_line_re (schrodinger.application.jaguar.textparser.TextParser attribute) first_property() (in module schrodinger.application.matsci.genetic_optimization) FIRST_SEP (schrodinger.application.matsci.rxn_channel.ChannelDefinition attribute) firstNeighbor() (schrodinger.infra.canvas.ChmAtom method) firstNode() (schrodinger.ui.qt.network_visualizer.ConnectionValidator method) fit() (schrodinger.application.matsci.mlearn.base.BaseFeaturizer method) fit_bin_f (schrodinger.application.matsci.kmc.MSDInfo attribute) fit_bin_i (schrodinger.application.matsci.kmc.MSDInfo attribute) FIT_ESP_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab attribute) fit_plane_to_points() (in module schrodinger.structutils.measure) fit_plane_to_points_as_list() (in module schrodinger.structutils.measure) fit_points_to_circle() (in module schrodinger.application.matsci.geometry) fit_sd_by_t (schrodinger.application.matsci.kmc.MSDInfo attribute) FIT_SELECTED_ATOMS (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin attribute) fit_structure_to_ellipsoid() (in module schrodinger.application.matsci.geometry) fit_to_structure() (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) fit_type (schrodinger.application.matsci.kmc.MSDInfo attribute) fitCellsToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fitColumnsToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fitColumnToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) FitError fitLine() (schrodinger.ui.qt.schart.SeriesData static method) fitMsd() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase static method) fitMSD() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) fitness (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) FitParamInfo (class in schrodinger.infra.mm) fitRowsToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fitRowToData() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) FittedPlanarAngle (class in schrodinger.application.desmond.packages.analysis) FitTexture() (in module schrodinger.application.matsci.gsas.GSASIImath) fitToColumns() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fitToRows() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fix_all_metal_bond_orders() (in module schrodinger.application.matsci.buildcomplex) fix_and_validate_res_structure() (in module schrodinger.protein.nonstandard_residues) fix_cmd() (in module schrodinger.job.jobcontrol) fix_common_structure_mistakes() (in module schrodinger.application.prepwizard) fix_elements() (schrodinger.protein.assignment.ProtAssign method) fix_filenames() (schrodinger.application.desmond.cms.Cms method) fix_for_prime() (in module schrodinger.application.prime.primefix) fix_formal_charge() (in module schrodinger.application.prime.primefix) fix_free_volume_coordinates() (in module schrodinger.application.matsci.freevolume) fix_idx_traj_path() (in module schrodinger.application.desmond.cms) fix_jaguar_file_links() (in module schrodinger.application.matsci.jaguarworkflows) fix_linear_angles() (in module schrodinger.application.matsci.coarsegrain) fix_metal_bond_orders() (in module schrodinger.application.matsci.buildcomplex) fix_metal_bonding() (in module schrodinger.application.matsci.nano.xtal) fix_particle_parent_indices() (in module schrodinger.application.matsci.cg_mapping) FIX_SITE_KEYWORDS (schrodinger.application.matsci.kmc.SchrodingerTable attribute) fix_splitter() (in module schrodinger.ui.qt.filedialog) fix_sulfur_charges() (in module schrodinger.application.prepwizard) fixAll() (schrodinger.application.prime.primefix.FixForPrime method) fixButton() (schrodinger.ui.qt.appframework2.af2.KBotResponseWidget method) fixDiameter() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) fixDisconnectedDonors() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) fixDNACaps() (schrodinger.application.prime.primefix.FixForPrime method) FIXED (schrodinger.application.livedesign.models2.datamodels.instance.ChildInheritanceMode attribute) (schrodinger.application.matsci.packmol.PackmolKw attribute) fixed (schrodinger.infra.canvas.AtomData attribute) fixed_bundle_size_999() (in module schrodinger.seam.testing.fixtures) fixed_size_list() (in module schrodinger.application.glide_ws.scoring_report) FIXED_VALUE (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) FixedSample (class in schrodinger.seam.transforms.partitioners) FixedSizeRDMolImageLabel (class in schrodinger.ui.qt.rdmol_views) FixForPrime (class in schrodinger.application.prime.primefix) fixheavy (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) fixheavyChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) fixheavyReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) fixHets() (schrodinger.application.prime.primefix.FixForPrime method) fixHydrogens() (schrodinger.application.matsci.enumeration.ElementAlchemist method) fixInvalidAtomsAndBonds() (schrodinger.infra.canvas.ChmMCSRecord method) fixLegend() (schrodinger.ui.qt.schart.SHistogramBarSet method) fixLocations() (schrodinger.application.matsci.sculptcomplex.Sculptor method) fixMetals() (schrodinger.application.prime.primefix.FixForPrime method) fixMono() (in module schrodinger.application.matsci.gsas.GSASIIspc) fixPdbresAndPdbnames() (schrodinger.application.prime.primefix.FixForPrime method) fixRibbons() (schrodinger.application.bioluminate.pml_menus.ColorRibbonMixin method) fixRingSpears() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) fixSize() (schrodinger.ui.qt.appframework2.af2.KBotResponseWidget method) (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) fixSpecialResidues() (schrodinger.application.prime.primefix.FixForPrime method) fixup() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.FrameIntValidator method) fixup_duplicate_properties() (in module schrodinger.application.desmond.struc) FixValence() (in module schrodinger.application.matsci.gsas.GSASIIElem) flag (schrodinger.application.matsci.mlearn.features.MomentData attribute) FLAG_ABBE_NUMBER_WAVELENGTH (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) FLAG_COMPOSITION (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) flag_context_manager() (in module schrodinger.infra.util) FLAG_DATA_LAST_FRAC (schrodinger.application.matsci.permittivity.DipoleAnalysis attribute) FLAG_DENSITY (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) FLAG_ELEC_POLARIZABILITY (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) FLAG_ELECTRIC_POLAR (schrodinger.application.matsci.permittivity.CMSParser attribute) FLAG_JAGUAR_FINER_OPTIONS (schrodinger.application.matsci.permittivity.JaguarFinerCalculation attribute) FLAG_JAGUAR_OPTIONS (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) FLAG_MOLECULES (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) FLAG_MONOMER_CHARGE (schrodinger.application.matsci.permittivity.DisorderSystemBuilder attribute) FLAG_NORMALIZATION (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) FLAG_NUM_CRU (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) FLAG_PARALLEL (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) FLAG_POLYMER_CRU_NUM (schrodinger.application.matsci.permittivity.PolymerBuilder attribute) FLAG_REFRACTIVE_INDEX_WAVELENGTH (schrodinger.application.matsci.permittivity.RefractiveIndex attribute) FLAG_SLICE_INTVL (schrodinger.application.matsci.permittivity.BaseDipoleAnalysis attribute) FLAG_TO_KEY (schrodinger.application.matsci.permittivity.MultiStageMd attribute) FlagCacheProxyMixin (class in schrodinger.ui.qt.table_speed_up) FLAGS (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep attribute) (schrodinger.application.matsci.jwsteps.PrepForMDStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) (schrodinger.application.matsci.jwsteps.VoidStep attribute) flags() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.livedesign.panel_components.EndpointSelectionModel method) (schrodinger.application.livedesign.panel_components.ExportTableModel method) (schrodinger.application.livedesign.panel_components.LDSelectionModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.recent_completer.SeparatorStringModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) (schrodinger.ui.qt.table_speed_up.FlagCacheProxyMixin method) (schrodinger.ui.two_d_viewer.TwoDTableModel method) FLAGS_ADD_DOUBLE_DASH (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.BDEStep attribute) FLAGS_ADD_INPUT_NAME (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) FLAGS_ADD_JOB_NAME (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.HOFStep attribute) (schrodinger.application.matsci.jwsteps.JaguarStep attribute) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep attribute) FLAGS_ADD_TPP (schrodinger.application.matsci.jwsteps.BaseMetaJaguarWorkflowStep attribute) (schrodinger.application.matsci.jwsteps.BaseStep attribute) FLAGS_INPUT_NAME_FLAG (schrodinger.application.matsci.jwsteps.BaseStep attribute) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep attribute) (schrodinger.application.matsci.jwsteps.ElasticConstantsStressStep attribute) (schrodinger.application.matsci.jwsteps.PolymerCrosslinkStep attribute) (schrodinger.application.matsci.jwsteps.SimulationProfileStep attribute) (schrodinger.application.matsci.jwsteps.StructureFactorStep attribute) (schrodinger.application.matsci.jwsteps.TgStep attribute) flat_enumerator() (in module schrodinger.application.scaffold_enumeration.layered) flat_list_enumerator() (in module schrodinger.application.scaffold_enumeration.layered) FlatButton (class in schrodinger.ui.qt.standard_widgets.buttons) flatten() (in module schrodinger.application.matsci.msutils) (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis class method) flatten_list() (in module schrodinger.application.bioluminate.surfcomp) flatten_sibling_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) FlattenBenchmark (class in schrodinger.seam.testing.benchmarks) flattenChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions static method) flattenParamArgs() (schrodinger.tasks.param_cli.ParamCLI method) flattenWithoutDict() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) FlattenWithSlowCoder (class in schrodinger.seam.testing.benchmarks) flex_align_args (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) flex_align_argsChanged (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) flex_align_argsReplaced (schrodinger.application.livedesign.tasks.FlexAlignTask.Input attribute) FlexAlignLigands (class in schrodinger.seam.yaml.transforms) FlexAlignTask (class in schrodinger.application.livedesign.tasks) FlexAlignTask.Input (class in schrodinger.application.livedesign.tasks) FlexAlignTask.Output (class in schrodinger.application.livedesign.tasks) flexdist (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) flexdistChanged (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) flexdistReplaced (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Input attribute) FlexibleBetaLinkage (schrodinger.infra.canvas.ChmHierarchicalClustering attribute) flip() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) flip_isomer() (in module schrodinger.protein.nonstandard_residues) flip_ring_conformation() (in module schrodinger.application.jaguar.utils) flipAndRotateMol() (schrodinger.ui.two_d_viewer.Cell method) flipBondDirectionHint() (schrodinger.infra.canvas.ChmBond method) flipChirality() (schrodinger.infra.canvas.ChmAtom method) flipDirection() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) flipHorizontal() (schrodinger.infra.canvas.Chm2DCoordGen static method) (schrodinger.ui.two_d_viewer.TwoDViewer method) flipTailFirst() (schrodinger.application.matsci.amorphous.Monomer method) flipVertical() (schrodinger.infra.canvas.Chm2DCoordGen static method) (schrodinger.ui.two_d_viewer.TwoDViewer method) Flnh() (in module schrodinger.application.matsci.gsas.GSASIIlattice) FLOAT (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute) (schrodinger.application.livedesign.models2.datamodels.definition.InputType attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputType attribute) float() (schrodinger.ui.qt.swidgets.SLineEdit method) FLOAT_BASE (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor attribute) FLOAT_FIELDS (schrodinger.application.matsci.permittivity.MultiStageMd attribute) FLOAT_PROP_PREFIX (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) float_valid() (schrodinger.ui.qt.formlayout.FormDialog method) FLOATABLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) floatChange() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) floatValue() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) (schrodinger.ui.qt.swidgets.SLabeledSlider method) FlorySchulzDistribution (class in schrodinger.application.matsci.amorphous) fluc_ct (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute) fluc_ct_energy (schrodinger.energy.MetalForceFieldEnergy attribute) FLUC_CT_LIGAND (schrodinger.energy.MetalParameterType attribute) FLUC_CT_METAL (schrodinger.energy.MetalParameterType attribute) FLUC_CT_METAL_SIGMOID (schrodinger.energy.MetalParameterType attribute) FlucCTCalculator (class in schrodinger.energy) flucCTEnabled() (schrodinger.energy.MetalSystem method) FlucCTIntermediateOutput (class in schrodinger.energy) FlucCTOutput (class in schrodinger.energy) FlucCTParameter (class in schrodinger.energy) FlucCTParamKeys (class in schrodinger.energy) FlucCTSigmoid (class in schrodinger.energy) FlucCTSystem (class in schrodinger.energy) flush() (schrodinger.ui.qt.appframework2.debugcore.DebugStderr class method) (schrodinger.ui.qt.appframework2.debugcore.DebugStdout class method) FMP (schrodinger.rdkit_extensions.Format attribute) Fmt (class in schrodinger.application.desmond.packages.traj) fmt_bedroc() (in module schrodinger.application.glide_ws.optimizer) fmt_decoys_in_top_n() (in module schrodinger.application.glide_ws.optimizer) fmt_ensemble() (in module schrodinger.application.glide_ws.optimizer) fmt_gbshifts() (in module schrodinger.application.glide_ws.optimizer) fmt_offsets() (in module schrodinger.application.glide_ws.optimizer) fmt_score() (in module schrodinger.application.glide_ws.optimizer) fname() (schrodinger.application.glide_ws.driver.State static method) focusFinder() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) focusInEvent() (schrodinger.application.livedesign.panel_components.AddNewLineEdit method) (schrodinger.ui.qt.pop_up_widgets.LineEditWithPopUp method) (schrodinger.ui.qt.swidgets.ElidedLineEdit method) focusOnStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) focusOutEvent() (schrodinger.application.matsci.mswidgets.PopupMenu method) (schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets.PlotTitleLineEdit method) (schrodinger.ui.qt.swidgets.EditWithFocusOutEvent method) (schrodinger.ui.qt.swidgets.ElidedLineEdit method) fod_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) folder (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfo attribute) Folder (schrodinger.application.livedesign.panel_components.LRSort attribute) folderChanged (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfo attribute) folderReplaced (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfo attribute) foldXOR() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) FONT (schrodinger.ui.qt.delegates.DefaultMessageDelegate attribute) font_is_installed() (in module schrodinger.ui.qt.formlayout) font_role() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) FontLayout (class in schrodinger.ui.qt.formlayout) FontSizes (class in schrodinger.ui.qt.standard.design_tokens) FontStyles (class in schrodinger.application.phase.phase_markers) FontWeights (class in schrodinger.ui.qt.standard.design_tokens) foo() (schrodinger.tasks.test.cli.preprocessor_cli.PreprocessorCLI method) foo_host (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) foo_hostChanged (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) foo_hostReplaced (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) FooComboJobTask (class in schrodinger.tasks.test.cli.customized_cli) FooComboJobTask.Input (class in schrodinger.tasks.test.cli.customized_cli) FooJobTask (class in schrodinger.tasks.test.cli.preprocessor_cli) FooJobTask.Input (class in schrodinger.tasks.test.cli.preprocessor_cli) FooTask (class in schrodinger.tasks.slurmtasks) FooTask.Input (class in schrodinger.tasks.slurmtasks) FooTask.Output (class in schrodinger.tasks.slurmtasks) Footer (class in schrodinger.application.matsci.reportutils) FOOTERS (schrodinger.application.matsci.reportutils.CanvasWithHeaderAndFooter attribute) FORBIDDEN_TO_MATCH (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) force_constant_precision (schrodinger.application.jaguar.results.NormalMode attribute) force_copy2() (in module schrodinger.utils.fileutils) force_dummy_missing_product_imports() (in module schrodinger.infra.unusable_module_importer) force_field (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) FORCE_FIELD (schrodinger.glide.SkipReason attribute) force_field_name_to_file_name() (in module schrodinger.application.matsci.cgforcefield) force_fieldChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) force_fieldReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.CleanupInput attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementInput attribute) force_list (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) force_listChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) force_listReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) force_remove() (in module schrodinger.utils.fileutils) force_rename() (in module schrodinger.utils.fileutils) force_rmtree() (in module schrodinger.utils.fileutils) force_rmtree_resist_nfs() (in module schrodinger.application.matsci.msutils) FORCED_ACCEPTOR_PKA_SHIFT (schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor attribute) forceDetail (schrodinger.infra.canvas.MCSsettings attribute) ForceField (class in schrodinger.application.matsci.cgforcefield) Forcefield (class in schrodinger.application.matsci.msutils) FORCEFIELD (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox attribute) ForceField() (schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.MockOpenMM.App method) forceFieldChanged (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector attribute) forceFieldChanged() (schrodinger.application.matsci.chargegui.FFInfo method) ForceFieldDialog (class in schrodinger.application.matsci.chargegui) forcefieldOptionChanged (schrodinger.ui.qt.forcefield.ffselector.MaestroForceFieldSelector attribute) ForceFieldOptions (class in schrodinger.forcefield.ffld_options) ForceFieldSelector (class in schrodinger.ui.qt.forcefield.ffselector) ForceFieldSelectorUi (class in schrodinger.ui.qt.forcefield.ffselector) forceIndexReassignment() (schrodinger.protein.annotation.AbstractRegionFinder method) forces (schrodinger.application.jaguar.results.JaguarResults property) forces() (in module schrodinger.application.jaguar.textparser) FORCES_KEY (schrodinger.application.matsci.espresso.qeinput.ControlType attribute) forces_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) forceSetChecked() (schrodinger.ui.qt.swidgets.SCheckBox method) forceSetText() (schrodinger.ui.qt.swidgets.LineEditWithDisabledText method) ForEachDo (class in schrodinger.application.desmond.arkdb) FOREGROUND (schrodinger.ui.qt.delegates.DefaultMessageDelegate attribute) foreground_role() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) forgetMessageBoxResponse() (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) forgetResponse() (schrodinger.ui.qt.messagebox.MessageBox method) ForkStep (class in schrodinger.stepper.sideinputs) form_inscode_asl() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) form_jaguar_cpu_flags() (in module schrodinger.ui.qt.config_dialog) form_range_asl() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) form_resid_defaultdict() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) form_set_val_string() (in module schrodinger.application.matsci.kmc) formal_charge (schrodinger.structure.Structure property) (schrodinger.structure.StructureAtom property) formASL() (schrodinger.application.bioluminate.pml_menus.RegionInfo method) Format (class in schrodinger.livedesign.draw) (class in schrodinger.rdkit_extensions) format() (in module schrodinger.application.jaguar.check_headers) (schrodinger.analysis.enrichment.calculator.Calculator static method) (schrodinger.application.hitexpander.LogFormatter method) (schrodinger.application.matsci.textlogger.GetLogger.MyFormatter method) (schrodinger.stepper.stepper.ElapsedFormatter method) format_alignment_ids() (in module schrodinger.application.matsci.nano.particle) format_as() (in module schrodinger.infra.structure) format_charge() (in module schrodinger.application.ligprep.ionizer) format_description() (in module schrodinger.application.licensing.licserver.main) FORMAT_END (schrodinger.application.matsci.cg_mapping.CoarseGrainBond attribute) format_host() (in module schrodinger.application.livedesign.login) format_human_time() (in module schrodinger.application.glide.utils) format_ijob() (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) format_info() (in module schrodinger.application.matsci.typography) format_isotope_latex() (in module schrodinger.application.jaguar.simple_spec) format_json() (in module schrodinger.utils.featureflags.write) format_json_output() (in module schrodinger.autoinstall.misc) format_list_to_filter_string() (in module schrodinger.ui.qt.input_selector) format_numbered_message() (in module schrodinger.application.livedesign.entry_types) format_option_strings() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method) format_pressure() (in module schrodinger.application.matsci.jaguarworkflows) format_row() (in module schrodinger.application.glide.csv_utils) format_species_display_name() (in module schrodinger.application.matsci.species) FORMAT_START (schrodinger.application.matsci.cg_mapping.CoarseGrainBond attribute) format_temperature() (in module schrodinger.application.matsci.jaguarworkflows) format_time() (in module schrodinger.application.jaguar.utils) format_tooltip() (in module schrodinger.application.matsci.gutils) format_usage_row() (in module schrodinger.application.licensing.lmgrd_log_parser) format_value() (in module schrodinger.application.glide_ws.scoring_report) formatBinary (schrodinger.infra.canvas.ChmPairwiseFPOut attribute) formatCSV (schrodinger.infra.canvas.ChmPairwiseFPOut attribute) formatFloat() (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) FormatInpFile() (schrodinger.application.livedesign.tasks.GlideTask method) (schrodinger.application.livedesign.tasks.MCSDockingTask method) formatLong (schrodinger.infra.canvas.ChmPairwiseFPOut attribute) formatParticleLabel() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond static method) FORMATS (schrodinger.application.matsci.textlogger.GetLogger.MyFormatter attribute) formatTime() (schrodinger.application.jaguar.gui.timing.TimingResults method) formatWide (schrodinger.infra.canvas.ChmPairwiseFPOut attribute) FormComboWidget (class in schrodinger.ui.qt.formlayout) formCommand() (schrodinger.utils.installation_check.TestJob method) FormDialog (class in schrodinger.ui.qt.formlayout) FormHashes (class in schrodinger.application.desmond.struc) formJaguarCPUFlags() (schrodinger.ui.qt.config_dialog.StartDialogParams method) formLine() (schrodinger.application.matsci.desconfig.ConcatMSJStringer method) (schrodinger.application.matsci.desconfig.MSJStringer method) FormMols (class in schrodinger.application.desmond.struc) FormTabWidget (class in schrodinger.ui.qt.formlayout) formula (schrodinger.application.matsci.buildcomplex.LigandInfo attribute) (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) formula_res (schrodinger.application.matsci.species.SpeciesCollectionTypes attribute) FORMULAE (class in schrodinger.application.jaguar.ames.ames_constants) FORMULATION (schrodinger.livedesign.entity_type.EntityClass attribute) FormulationDriverMixin (class in schrodinger.application.matsci.ml_formulations_utils) FormWidget (class in schrodinger.ui.qt.formlayout) fortfloat() (in module schrodinger.application.mopac.results_main) FORWARD (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Direction attribute) ForwardAnalyzer (class in schrodinger.application.pathfinder.analysis) ForwardRGMolSupplier (class in schrodinger.livedesign.rgfile_parse) Fourier4DMap() (in module schrodinger.application.matsci.gsas.GSASIImath) FourierMap() (in module schrodinger.application.matsci.gsas.GSASIImath) FP_CLASSES (schrodinger.application.matsci.cgforcefield.ForceField attribute) FP_EXT (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) FP_TEXT_FILE (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) fp_type (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) fp_typeChanged (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) fp_typeReplaced (schrodinger.ui.qt.fp_selector_widget.FingerprintsModel attribute) fp_types() (in module schrodinger.application.hitexpander) FPcalc() (in module schrodinger.application.matsci.gsas.GSASIIElem) FPhononControlType (class in schrodinger.application.matsci.espresso.qeinput) FPsimSearcher (class in schrodinger.application.fpsim) FPTypeCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) fracCrenel() (in module schrodinger.application.matsci.gsas.GSASIImath) fracFourier() (in module schrodinger.application.matsci.gsas.GSASIImath) FractionAromatic() (in module schrodinger.rdkit.filtering) FRAG (schrodinger.application.matsci.kmc.AtomsTable attribute) frag_handle (schrodinger.application.combiglide.corehop.SubstCoreDatabase attribute) FRAG_ID (schrodinger.application.bioluminate.pose_filtering.hdx_calc.AnalysisColumns attribute) frag_is_smaller() (in module schrodinger.livedesign.preprocessor) Fragment (class in schrodinger.application.ligprep.ionizer) (class in schrodinger.application.matsci.fragments) (class in schrodinger.application.transforms.enumerators.fragment) fragment_mutator() (in module schrodinger.application.matsci.genetic_optimization) FRAGMENT_NAME (schrodinger.application.matsci.nano.constants.Constants attribute) fragment_to_molecule() (in module schrodinger.application.steps.utils) FragmentCreator (class in schrodinger.structutils.createfragments) FragmentLibrary (class in schrodinger.utils.cgxutils) FragmentReactor (class in schrodinger.application.matsci.fragments) fragments() (schrodinger.application.matsci.amorphous.PolymerFragment method) FragmentsTable (class in schrodinger.application.matsci.kmc) fragmentStructure() (schrodinger.structutils.createfragments.FragmentCreator method) fragmentStructureForEA() (schrodinger.structutils.createfragments.FragmentCreator method) FragmentVSStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) Frame (class in schrodinger.application.desmond.packages.traj) FRAME (schrodinger.application.matsci.kmc.Table attribute) frame_count (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures property) FRAME_DURATION_STEP (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) frame_number (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameListItem property) FRAME_SETTINGS_DICT (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute) frame_style() (in module schrodinger.application.matsci.stylemanager) FrameAttributeLambdaType (schrodinger.application.desmond.packages.traj.Frame attribute) FrameAttributeType (schrodinger.application.desmond.packages.traj.Frame attribute) frameDurationChanged (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) FrameIntValidator (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings) FrameListItem (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_panel) FrameLoader (class in schrodinger.application.desmond.packages.topo) frameOptionChanged() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) FrameRangeValidator (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_panel) frames_list (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures property) FrameSpinBox (class in schrodinger.application.matsci.deswidgets) FramesTable (class in schrodinger.application.matsci.kmc) FrameStructureExporter (class in schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter) FrameworkModel (class in schrodinger.application.bioluminate.antibody.search_results_table) FrameworkTemplate (class in schrodinger.application.bioluminate.antibody.utils) free_energy (schrodinger.infra.mm.WaterMapAtom attribute) free_energy() (in module schrodinger.application.xtb.textparser) free_energy_costs() (in module schrodinger.application.ligprep.ionizer) FREE_ENERGY_PROP (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) (schrodinger.application.matsci.thermo_correction_utils.ThermoCorrection attribute) FREE_ENERGY_STARTER (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) (schrodinger.application.matsci.thermo_correction_utils.ThermoCorrection attribute) freeAll() (schrodinger.application.matsci.zmutils.ZAtom method) FreeAtom (schrodinger.glide.Hybridization attribute) freeAtom() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomAngle() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomBond() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomDihedral() (schrodinger.application.matsci.zmutils.ZMatrix method) freeCachedEntries() (schrodinger.project.project.Project method) freeCoord() (schrodinger.application.matsci.zmutils.ZAtom method) FreeEnergy (class in schrodinger.application.jaguar.utils) FreePositionsType (class in schrodinger.application.matsci.espresso.qeinput) FreePositionsType.PWallType (class in schrodinger.application.matsci.espresso.qeinput) FreeVolumeDriver (class in schrodinger.application.matsci.freevolume) FreeVolumeException FreeVolumeStep (class in schrodinger.application.matsci.jwsteps) freeze_atom() (in module schrodinger.application.desmond.remd) (schrodinger.forcefield.minimizer.Restraint class method) freeze_existing_hydrogens() (schrodinger.protein.assignment.ProtAssign method) FREQ_KEY (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) freq_off (schrodinger.application.jaguar.thermochemical_properties.LowModeParams attribute) FREQ_TITLE (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) freq_to_angular_freq() (in module schrodinger.application.matsci.anharmonic) frequencies (schrodinger.application.jaguar.thermochemical_properties.InputParams attribute) frequencies() (in module schrodinger.application.jaguar.textparser) frequencies_old() (in module schrodinger.application.jaguar.textparser) frequency (schrodinger.application.matsci.bandshape_utils.NormalMode attribute) frequency_precision (schrodinger.application.jaguar.results.NormalMode attribute) from_anarci_resinfo() (schrodinger.application.bioluminate.classify.NumberedResidue class method) from_anarci_tuple() (schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo static method) from_atom_indices() (schrodinger.forcefield.minimizer.Restraint class method) from_CA_index() (schrodinger.ui.qt.rama.BackboneDihedral class method) from_deformation() (schrodinger.application.matsci.elasticity.strain.Strain class method) from_dict() (in module schrodinger.application.matsci.mlearn.sklearn_json) (schrodinger.application.matsci.wfmanagement.WorkflowMetadata class method) (schrodinger.job.server.ServerInfo class method) from_domain_result() (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult class method) from_end (schrodinger.protein.sequence.GapRegion attribute) from_idx (schrodinger.application.matsci.reaction_workflow_enum_utils.Site attribute) from_independent_strains() (schrodinger.application.matsci.elasticity.elastic.ElasticTensor class method) from_index_amount() (schrodinger.application.matsci.elasticity.strain.Deformation class method) (schrodinger.application.matsci.elasticity.strain.Strain class method) from_initial_population() (in module schrodinger.application.matsci.genetic_optimization) from_json() (in module schrodinger.application.matsci.mlearn.sklearn_json) from_list() (schrodinger.infra.mmbitset.Bitset class method) from_maestro() (in module schrodinger.protein.getpdb_utility) from_module_spec() (in module schrodinger.utils.imputils) from_pymatgen_structure() (in module schrodinger.application.matsci.pmgutils) from_rdkit() (in module schrodinger.rdkit.rdkit_adapter) from_res_3l (schrodinger.application.bioluminate.mutation.Mutation attribute) from_residue() (schrodinger.ui.qt.rama.BackboneDihedral class method) (schrodinger.ui.qt.rama.RamaResidueType class method) from_runner_api_parameter() (schrodinger.seam.coders.MaybeCompressedCoder static method) (schrodinger.seam.transforms.window.StringIDWindowCoder static method) from_start (schrodinger.protein.sequence.GapRegion attribute) from_string() (schrodinger.application.desmond.measurement.Measurement class method) (schrodinger.autoinstall.misc.OperatingSystem class method) from_style (schrodinger.structure.StructureBond property) FROM_TORS_ATOMS_ONLY (schrodinger.infra.mm.UTTPolicy attribute) from_values_indices() (schrodinger.application.matsci.elasticity.tensors.Tensor class method) from_voigt() (schrodinger.application.matsci.elasticity.tensors.Tensor class method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection class method) from_yaml() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) fromAnarciChainResultAndSeq() (schrodinger.application.bioluminate.classify.ProteinClass class method) fromAnarciDomainResult() (schrodinger.application.bioluminate.classify.ProteinClass class method) fromArgs() (schrodinger.application.glide.sort_utils.GlideSortUtility class method) (schrodinger.application.peptide_workflow.beam_adapter.GlideSettings class method) (schrodinger.application.peptide_workflow.beam_adapter.PrimeSettings class method) (schrodinger.application.peptide_workflow.beam_adapter.SuperimposeSettings class method) (schrodinger.application.peptide_workflow.monte.MonteOptions class method) fromArgv() (in module schrodinger.infra.ark) fromAtom() (schrodinger.application.matsci.espresso.qeoutput.MagresAtom class method) fromBinary() (schrodinger.infra.canvas.ChmBitset static method) (schrodinger.infra.canvas.ChmBitset64 static method) (schrodinger.infra.canvas.ChmSearchKey static method) fromBlob() (schrodinger.infra.canvas.ChmBitset static method) (schrodinger.infra.canvas.ChmBitset64 static method) (schrodinger.infra.canvas.ChmRangeUIDFilter static method) (schrodinger.infra.canvas.ChmSparseBitset static method) (schrodinger.infra.canvas.ChmSparseBitset64 static method) fromCanvasGUI (schrodinger.infra.canvas.MCSsettings attribute) fromClustalFile() (schrodinger.protein.alignment.ProteinAlignment class method) fromConfig() (schrodinger.livedesign.bbchem_configuration.BBChemConfiguration static method) (schrodinger.livedesign.preprocessor.PreprocessorOptions static method) fromConformer() (schrodinger.glide.RefinedPose static method) fromConformerEnsemble() (schrodinger.glide.RefinedPoseEnsemble static method) fromCurrentException() (schrodinger.tasks.tasks.FailureInfo class method) fromData() (schrodinger.application.matsci.nano.space_groups.SpaceGroup class method) fromDict() (schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction class method) fromDirectory() (schrodinger.seam.viz.watcherd.Watcher class method) fromEtotString() (schrodinger.application.jaguar.results.ScfIteration static method) fromException() (schrodinger.tasks.tasks.FailureInfo class method) fromFastaFile() (schrodinger.protein.alignment.ProteinAlignment class method) fromFastaString() (schrodinger.protein.alignment.ProteinAlignment class method) fromFastaStringList() (schrodinger.protein.alignment.ProteinAlignment class method) fromFile() (schrodinger.application.matsci.espresso.qeoutput.Magres class method) (schrodinger.application.matsci.espresso.qeoutput.PhDOSTensors class method) FromFile() (schrodinger.application.transforms.ligprep.LigandPrep class method) fromFile() (schrodinger.infra.canvas.ChmColumnUIDFilter static method) (schrodinger.infra.canvas.ChmFPTypeInfo static method) (schrodinger.infra.canvas.ChmRangeUIDFilter static method) (schrodinger.infra.canvas.ChmRowUIDFilter static method) (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter class method) (schrodinger.utils.pythonpatch.ModulePatch class method) FromFilterFile() (schrodinger.application.transforms.filters.ProductFilter class method) fromFragment() (schrodinger.application.matsci.fragments.Fragment class method) fromHex() (schrodinger.infra.canvas.ChmBitset64 static method) (schrodinger.infra.canvas.ChmSearchKey static method) fromIterable() (schrodinger.utils.scollections.DefaultIdDict class method) (schrodinger.utils.scollections.IdDict class method) (schrodinger.utils.scollections.IdSet class method) fromJagin() (schrodinger.application.matsci.zmutils.ZAtom class method) fromJobControlHost() (schrodinger.tasks.hosts.Host class method) fromJobObject() (schrodinger.application.job_monitor.job_monitor_models.JobModel static method) fromJson() (schrodinger.application.glide.http_client.GlideResult class method) fromJSON() (schrodinger.glide.SkipLigand class method) (schrodinger.job.launchapi.JobSpecification static method) (schrodinger.job.launchapi.TaskSpecification static method) fromJson() (schrodinger.models.json.JsonableClassMixin class method) fromJSON() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter class method) fromJsonData() (schrodinger.application.matsci.freevolume.JsonObject class method) fromJsonFilename() (schrodinger.tasks.tasks.AbstractTask class method) fromJsonImplementation() (schrodinger.application.bioluminate.pose_filtering.residue_filter.BaseResidueFilter class method) (schrodinger.application.livedesign.data_classes.LDData class method) (schrodinger.application.livedesign.export_models.JsonablePropertyName class method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel class method) (schrodinger.application.livedesign.panel_components.BaseLDTreeItemWrapper class method) (schrodinger.application.livedesign.panel_components.ExportRow class method) (schrodinger.application.livedesign.panel_components.ExportTableModel class method) (schrodinger.application.prepwizard.JsonableHetStates class method) (schrodinger.models.json.JsonableClassMixin class method) (schrodinger.models.jsonable.JsonableBytes class method) (schrodinger.models.jsonable.JsonableEnum class method) (schrodinger.models.jsonable.JsonableIntEnum class method) (schrodinger.models.jsonable.JsonableSet class method) (schrodinger.models.jsonable.JsonableStructure class method) (schrodinger.models.jsonable.JsonableTuple class method) (schrodinger.models.parameters.CompoundParam class method) (schrodinger.protein.alignment.ProteinAlignment class method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES class method) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES class method) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES class method) (schrodinger.protein.residue.Gap class method) (schrodinger.protein.residue.Residue class method) (schrodinger.protein.sequence.ProteinSequence class method) (schrodinger.protein.tasks.blast.BlastSettings class method) (schrodinger.protein.tasks.blast.BlastTask.Input class method) (schrodinger.seam.metric.ExecutionMetrics class method) (schrodinger.seam.metric.UserMetrics class method) (schrodinger.seam.metric.WorkerMetrics class method) (schrodinger.seam.metric.WorkerPeakMemUsageDistributionInMB class method) (schrodinger.seam.runners.events.SeamEvent class method) (schrodinger.tasks.hosts.Gpu class method) (schrodinger.tasks.hosts.Host class method) fromList() (schrodinger.application.matsci.espresso.qeoutput.MagresAtom class method) fromMAE() (schrodinger.infra.canvas.ChmMol static method) fromMDL() (schrodinger.infra.canvas.ChmMol static method) (schrodinger.infra.canvas.ChmQuery static method) fromMDLFile() (schrodinger.infra.canvas.ChmQuery static method) fromModule() (schrodinger.utils.pythonpatch.ModulePatch class method) fromPHDOS() (schrodinger.application.matsci.espresso.qeoutput.PhDOS class method) fromProteinSequence() (schrodinger.livedesign.biologics.sequence.AlignedSequence static method) fromRdkitStatus() (schrodinger.rdkit.rdkit_adapter.RdkitLoggerstate class method) FromRGroupFile() (schrodinger.application.transforms.enumerators.decorate.Decorate class method) fromRoughPose() (schrodinger.glide.RefinedPose static method) fromScaffoldMatch() (schrodinger.application.bioluminate.antibody.grafting.GraftingInput class method) fromSeed() (schrodinger.infra.canvas.ChmRandom static method) fromSeqDict() (schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput class method) fromSequence() (schrodinger.application.bioluminate.classify.ProteinClass class method) fromSMARTS() (schrodinger.infra.canvas.ChmQuery static method) fromSmartsError() (schrodinger.application.canvas.r_group.RGroupException class method) fromSmiles() (schrodinger.application.matsci.custom_lipid_prep.SetStereochemistry method) (schrodinger.glide.Ligand static method) fromSMILES() (schrodinger.infra.canvas.ChmMol static method) fromSPM() (schrodinger.application.matsci.espresso.qeoutput.PhDOS class method) fromStream() (schrodinger.infra.canvas.ChmQuery static method) fromString() (in module schrodinger.infra.ark) (schrodinger.application.jaguar.utils.GenOptions static method) (schrodinger.application.steps.dataclasses.MolToSmilesSerializer method) (schrodinger.application.steps.dataclasses.ScoredMolSerializer method) (schrodinger.application.steps.enumerators.RouteSerializer method) (schrodinger.infra.canvas.ChmCompressedBitset static method) (schrodinger.infra.canvas.ChmCompressedBitset64 static method) (schrodinger.infra.canvas.ChmSparseBitset static method) (schrodinger.infra.canvas.ChmSparseBitset64 static method) (schrodinger.infra.structure.MaeReader static method) (schrodinger.infra.structure.MmpdbxReader static method) (schrodinger.stepper.stepper.Serializer method) (schrodinger.structure.StructureReader static method) fromStructure() (schrodinger.application.matsci.espresso.qeoutput.Magres class method) (schrodinger.application.matsci.espresso.utils.MagSpecies method) (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.glide.Ligand static method) (schrodinger.glide.Receptor static method) (schrodinger.protein.alignment.ProteinAlignment class method) fromSubFormat() (schrodinger.infra.canvas.ChmRangeFilter static method) fromText() (schrodinger.application.jaguar.gui.input_tab_widgets.Basis class method) fromVIB() (schrodinger.application.matsci.espresso.qeoutput.PhDOS class method) fromYamlFile() (schrodinger.models.parameters.CompoundParam class method) fromYamlString() (schrodinger.models.parameters.CompoundParam class method) front() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.structure.StructureCoordinates method) front_transparency (schrodinger.surface.Surface property) FROZEN_ATOMS_PROPERTY_NAME (schrodinger.infra.fast3d.Engine attribute) FROZEN_PHONON_CORR (schrodinger.application.matsci.desconfig.MSJStringer attribute) FrozenPhononStringer (class in schrodinger.application.matsci.desconfig) frozenset_cached_property (class in schrodinger.application.matsci.cache) FrozenStep (class in schrodinger.application.matsci.jaguarworkflows) fruchterman_reingold_layout() (in module schrodinger.ui.qt.network_visualizer) FSCALE (schrodinger.application.matsci.packmol.PackmolKw attribute) FSStructureReader (class in schrodinger.seam.io.filesystems) FSStructureWriter (class in schrodinger.seam.io.filesystems) fukui_indices() (in module schrodinger.application.jaguar.textparser) FukuiIndices (class in schrodinger.application.jaguar.results) FULL (schrodinger.infra.mm.MetadataCompatibility attribute) (schrodinger.livedesign.preprocessor.GenerateCoordinates attribute) (schrodinger.rdkit_extensions.Sanitization attribute) FULL_ALIGNED (schrodinger.livedesign.preprocessor.GenerateCoordinates attribute) FULL_HERMANN_MAUGUIN_SYMBOL (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) FULL_MOVIE (schrodinger.trajectory.trajectory_gui_dir.export_movie.DurationType attribute) FULL_MOVIE_MAX_VALUE (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) FULL_MOVIE_MIN_VALUE (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog attribute) full_name (schrodinger.protein.annotation.ImmuneReceptorDisplayNames attribute) FULL_NAME_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) full_summary_string() (schrodinger.application.jaguar.simple_spec.Peak method) FullColumns (class in schrodinger.application.bioluminate.antibody.search_results_table) FullFunnelDockingMethod (class in schrodinger.application.glide.runner) FullMinimizer (class in schrodinger.glide) fullname (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo property) (schrodinger.project.project.Project property) (schrodinger.protein.sequence.AbstractSingleChainSequence property) (schrodinger.protein.sequence.CombinedChainProteinSequence property) (schrodinger.utils.pythonpatch.ModulePatch attribute) FullProxyModel (class in schrodinger.application.bioluminate.antibody.search_results_table) FullTable (class in schrodinger.application.bioluminate.antibody.search_results_table) FULLY_ANALYTIC_ACCURACY (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) fully_conserved (schrodinger.protein.annotation.Consensus attribute) FULLY_REL (schrodinger.application.matsci.espresso.utils.UPFParser attribute) func (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) func() (in module schrodinger.application.mopac.results_main) funcbottom() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) FuncChainMarker (class in schrodinger.utils.funcchains) FuncChainMixin (class in schrodinger.utils.funcchains) FuncData (class in schrodinger.utils.funcgroups) FuncGroupMarker (class in schrodinger.utils.funcgroups) FuncGroupMixin (class in schrodinger.utils.funcgroups) funchspace() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) funcleft() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) funcright() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) FUNCTION (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwType attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) function (schrodinger.application.matsci.kmcgui.PlotInfo attribute) functional() (in module schrodinger.application.jaguar.textparser) functop() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) funcwspace() (schrodinger.ui.qt.navtoolbar.FeedbackSubplotToolQt method) further_annotate_ligand_atoms() (in module schrodinger.protein.protassign.changeables) fused_ring_nonbond_iterator() (in module schrodinger.application.matsci.coarsegrain) FusedRing (class in schrodinger.application.matsci.coarsegrain) fuseIonFragment() (schrodinger.application.ligprep.ionizer.Ionizer method) fuseRings() (schrodinger.infra.canvas.ChmPathTools static method) future_entitlements (schrodinger.application.licensing.licserver.entitlement_status.EntitlementStatus attribute) fuzzy_aromatic_matching (schrodinger.rdkit.substructure.QueryOptions attribute) FV (schrodinger.application.bioluminate.antibody.assembly_yaml.AntibodyFormat attribute) (schrodinger.livedesign.entity_type.EntityClass attribute) FVAL_DICT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVAL_KEYS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVAL_VALUES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVALINCREMENT (schrodinger.application.matsci.rxn_path.ReactionPath attribute)

G

G (schrodinger.application.jaguar.results.ThermoCollection attribute) G2Print() (in module schrodinger.application.matsci.gsas.GSASIIfiles) G2printLevel (in module schrodinger.application.matsci.gsas.GSASIIfiles) G2SetPrintLevel() (in module schrodinger.application.matsci.gsas.GSASIIfiles) G_IDXS_TO_STARTERS (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) g_reuss (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) G_TOTAL_EPSILON_ALPHA_START (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) G_TOTAL_EPSILON_START (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) G_TOTAL_KEY (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) G_TOTAL_OMEGA_START (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties attribute) g_voigt (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) g_vrh (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) GAMMA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) GAMMA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) GAMMA_ONLY_KEY (schrodinger.application.matsci.espresso.qeinput.BasisType attribute) GAMMA_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) gamma_polar() (in module schrodinger.application.jaguar.textparser) gamma_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute) Gap (class in schrodinger.protein.residue) gap_char (schrodinger.protein.sequence.AbstractSequence property) gap_extend_cost (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_extend_costChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_extend_costReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_open_cost (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_open_costChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_open_costReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) gap_penalty (schrodinger.structutils.structalign.StructAlign property) gapless_idx_in_seq (schrodinger.protein.residue.AbstractSequenceElement property) GapRegion (class in schrodinger.protein.sequence) gas_phase() (in module schrodinger.application.jaguar.textparser) GATE_KEEPER (schrodinger.protein.annotation.KinaseFeatureLabel attribute) gather_rings() (in module schrodinger.structutils.interactions.pi) gatherAlnSets() (schrodinger.protein.alignment.BaseAlignment method) gauges (schrodinger.seam.metric.UserMetrics attribute) gaulegf() (in module schrodinger.application.matsci.gsas.GSASIImath) gaussian_delta() (in module schrodinger.application.matsci.espresso.qeoutput) gbk_executor (schrodinger.seam.testing.benchmarks.GroupByKey property) GBSA (schrodinger.energy.SolventModel attribute) gbsa_score (schrodinger.application.glide_ws.optimizer.WScoreOptimizerPose attribute) gbshift (schrodinger.application.glide_ws.optimizer.WScoreOptimizerReceptor attribute) gbshift() (schrodinger.application.glide_ws.model.Model method) gbshifts (schrodinger.application.glide_ws.optimizer.WScoreOptimizerEnsemble property) gcg (schrodinger.utils.fileutils.SeqFormat attribute) gcmc_solvent (schrodinger.application.desmond.struc.CompStruc attribute) gdata() (schrodinger.ui.qt.network_visualizer.Node method) ge_export_items (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ge_export_itemsChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ge_export_itemsReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.GETaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) ge_file_format (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ge_file_formatChanged (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ge_file_formatReplaced (schrodinger.application.livedesign.export_models.AttachmentTaskInput attribute) (schrodinger.application.livedesign.export_models.TaskInput attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) ge_file_type (schrodinger.application.livedesign.ld_tasks.StructureInfo attribute) ge_task (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) gedge (schrodinger.ui.qt.network_visualizer.Edge property) GEExportItem (class in schrodinger.application.livedesign.export_models) gen (schrodinger.application.qsite.input.QSiteInput property) gen_alpha_helix_restraint() (in module schrodinger.application.desmond.cms) gen_charges_spins() (in module schrodinger.application.jaguar.textparser) gen_fastas() (in module schrodinger.application.bioluminate.epitope.psc_workflow) gen_faux_epitopes() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_file_list() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_jobname() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_mifs() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_names() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_random_color() (in module schrodinger.application.combiglide.connection_storage) gen_resnums_and_inscodes() (in module schrodinger.protein.sequence) gen_sim_mat() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils) (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) gen_xvals() (in module schrodinger.application.matsci.spectra) genAllJobs() (schrodinger.job.queue.BaseJob method) genAllPrereqs() (schrodinger.job.queue.BaseJob method) GenAtom() (in module schrodinger.application.matsci.gsas.GSASIIspc) genCoords() (schrodinger.infra.canvas.ChmMol method) genDistHeadTail() (schrodinger.application.matsci.custom_lipid_prep.StretchMol method) genDistTails() (schrodinger.application.matsci.custom_lipid_prep.StretchMol method) Gene (class in schrodinger.application.bioluminate.update_germline_db.translate_db) GENERAL (schrodinger.ui.qt.rama.RamaResidueType attribute) GENERAL_VEC_1 (schrodinger.application.matsci.nano.xtal.Crystal attribute) GENERAL_VEC_2 (schrodinger.application.matsci.nano.xtal.Crystal attribute) GENERAL_VEC_3 (schrodinger.application.matsci.nano.xtal.Crystal attribute) GeneralContextSubMenu (class in schrodinger.application.bioluminate.pml_menus) GeneralIcons (class in schrodinger.ui.qt.standard.design_tokens) GeneralInfo (class in schrodinger.application.licensing.licserver.client) generalize() (schrodinger.infra.fast3d.Generalizer method) Generalizer (class in schrodinger.infra.fast3d) GENERATE (schrodinger.application.transforms.autosar.config.Command attribute) generate() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.infra.canvas.ChmCombinationOut32 method) (schrodinger.infra.canvas.ChmCombinationOut64 method) (schrodinger.infra.canvas.ChmDendriticOut32 method) (schrodinger.infra.canvas.ChmDendriticOut64 method) (schrodinger.infra.canvas.ChmFPOut32 method) (schrodinger.infra.canvas.ChmFPOut64 method) (schrodinger.infra.canvas.ChmLinearOut32 method) (schrodinger.infra.canvas.ChmLinearOut64 method) (schrodinger.infra.canvas.ChmMaccsOut32 method) (schrodinger.infra.canvas.ChmMaccsOut64 method) (schrodinger.infra.canvas.ChmMolprint2D32 method) (schrodinger.infra.canvas.ChmMolprint2D64 method) (schrodinger.infra.canvas.ChmPairwiseOut32 method) (schrodinger.infra.canvas.ChmPairwiseOut64 method) (schrodinger.infra.canvas.ChmQuartetOut32 method) (schrodinger.infra.canvas.ChmQuartetOut64 method) (schrodinger.infra.canvas.ChmRadialOut32 method) (schrodinger.infra.canvas.ChmRadialOut64 method) (schrodinger.infra.canvas.ChmSMARTSOut32 method) (schrodinger.infra.canvas.ChmSMARTSOut64 method) (schrodinger.infra.canvas.ChmTopologicalTorsionOut32 method) (schrodinger.infra.canvas.ChmTopologicalTorsionOut64 method) (schrodinger.infra.canvas.ChmTripletOut32 method) (schrodinger.infra.canvas.ChmTripletOut64 method) Generate2DCoordinates (class in schrodinger.adapter) generate3dConformation() (schrodinger.structure.Structure method) generate_1M_random_string() (schrodinger.seam.testing.benchmarks.GroupByKeyDiskSpaceWithLargeValues static method) (schrodinger.seam.testing.benchmarks.GroupByKeyLargeValues_runtime static method) generate_2d_coords() (in module schrodinger.ui.two_d_viewer) generate_3d_structure() (in module schrodinger.protein.process_enamine_db) generate_all_keywords() (in module schrodinger.application.jaguar.ames.ames_keywords) (in module schrodinger.application.jaguar.autots_keywords) (in module schrodinger.application.jaguar.distributed_frequencies.keywords) (in module schrodinger.application.jaguar.esol_keywords) (in module schrodinger.application.jaguar.hydrokinetic_keywords) (in module schrodinger.application.jaguar.macro_pka_keywords) (in module schrodinger.application.jaguar.mlff.keywords) (in module schrodinger.application.jaguar.nics_predictor.keywords) (in module schrodinger.application.jaguar.rotation_barriers_keywords) (in module schrodinger.application.jaguar.solvation_keywords) (in module schrodinger.application.jaguar.xray.keywords) (in module schrodinger.application.xtb.keywords) generate_allowed_hex_codes() (in module schrodinger.protein.mafft_utils) generate_annotated_ct() (in module schrodinger.protein.protassign.utils) generate_annotation() (in module schrodinger.application.prepwizard2.tasks) generate_asl() (in module schrodinger.structutils.analyze) generate_asl_for_atom_by_mode() (in module schrodinger.ui.qt.atomselector) generate_atom_groups() (in module schrodinger.application.desmond.struc) generate_attributes() (schrodinger.application.jaguar.results.RoutineTimes method) generate_canonical_tautomer() (in module schrodinger.livedesign.preprocessor) generate_cms_file_from_entry() (in module schrodinger.trajectory.utils) generate_coordinates (schrodinger.application.steps.converters.MolToStructureConverter.Settings attribute) GENERATE_COORDINATES (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) generate_coordinates() (in module schrodinger.livedesign.preprocessor) generate_coordinatesChanged (schrodinger.application.steps.converters.MolToStructureConverter.Settings attribute) generate_coordinatesReplaced (schrodinger.application.steps.converters.MolToStructureConverter.Settings attribute) generate_criterion() (in module schrodinger.utils.ligfilter) generate_crystal_mates() (in module schrodinger.structutils.analyze) generate_curve() (in module schrodinger.application.matsci.spectra) generate_custom_res_names() (in module schrodinger.protein.nonstandard_residues) generate_dendrogram() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method) generate_description() (in module schrodinger.application.jaguar.gui.basis_selector) generate_epik_states() (in module schrodinger.protein.assignment) generate_execution_feedback() (in module schrodinger.maestro_utils.composer_agent.query_generator) generate_fingerprints() (in module schrodinger.application.combinatorial_diversity.driver_utils) generate_fingerprints_from_csv() (in module schrodinger.application.combinatorial_diversity.driver_utils) generate_fingerprints_from_smi() (in module schrodinger.application.combinatorial_diversity.driver_utils) generate_hierarchial_key() (in module schrodinger.application.matsci.hdfutils) generate_image() (in module schrodinger.livedesign.bbchem_endpoints) generate_iter_values() (in module schrodinger.active_learning.al_utils) generate_job_id() (in module schrodinger.job.jobcontrol) generate_job_name() (in module schrodinger.application.jaguar.gui.utils) generate_json_header() (in module schrodinger.application.glide_ws.model) generate_keywords() (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput static method) (schrodinger.application.jaguar.workflow_input.WorkflowInput class method) (schrodinger.application.xtb.input.XTBInput class method) generate_lid() (in module schrodinger.application.livedesign.lid) generate_lid_as_html() (in module schrodinger.application.glide.visualization) generate_loop_ranges() (in module schrodinger.application.bioluminate.anarci.loop_ranges) generate_mae_file_with_unique_title() (in module schrodinger.active_learning.al_utils) generate_mates() (in module schrodinger.protein.protassign.utils) generate_metal_and_ion_states() (in module schrodinger.application.prepwizard) generate_method() (in module schrodinger.models.parameters) generate_molecular_formula() (in module schrodinger.structutils.analyze) generate_mols() (in module schrodinger.application.pathfinder.multiroute) (schrodinger.application.pathfinder.multiroute.MultiRouteEnumerator method) generate_mutant_combinations() (in module schrodinger.application.bioluminate.mutation) generate_partial_charges() (in module schrodinger.forcefield.common) generate_pic_with_text() (in module schrodinger.ui.two_d_viewer) generate_picture() (schrodinger.ui.qt.structure2d.structure_item method) generate_postmortem() (in module schrodinger.application.job_monitor.job_monitor_diagnostics_dialog) generate_preference_key() (in module schrodinger.ui.qt.appframework2.settings) generate_property_hist() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) generate_pw() (in module schrodinger.autoinstall.misc) generate_qimage_from_chmmol() (in module schrodinger.ui.qt.structure2d) generate_qimage_from_structure() (in module schrodinger.ui.qt.structure2d) generate_query() (in module schrodinger.maestro_utils.composer_agent.query_generator) generate_query_with_session() (in module schrodinger.maestro_utils.composer_agent.query_generator) generate_random_strings() (schrodinger.seam.testing.test_pipelines.BenchFlow static method) generate_records() (in module schrodinger.application.bioluminate.update_germline_db.translate_db) generate_residue_asl() (in module schrodinger.structutils.analyze) generate_residue_number_asl() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) generate_return_code_dict() (in module schrodinger.infra.mmcheck) generate_sar_analysis_image() (in module schrodinger.livedesign.bbchem_endpoints) generate_score_hist() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) generate_sh() (in module schrodinger.livedesign.sh_utils) generate_smarts() (in module schrodinger.application.matsci.deprecated_pattern) generate_smarts_canvas() (in module schrodinger.application.matsci.deprecated_pattern) generate_smiles() (in module schrodinger.application.matsci.deprecated_pattern) (in module schrodinger.application.matsci.msutils) generate_states_settings (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) generate_states_settingsChanged (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) generate_states_settingsReplaced (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) generate_summary_rows_for_ligands() (in module schrodinger.application.glide_ws.db_queries) generate_tautomer_hash() (in module schrodinger.structutils.analyze) generate_templates() (in module schrodinger.glide) generate_term_summary_string() (in module schrodinger.application.glide_ws.db_queries) generate_unique_group_name() (in module schrodinger.project.utils) generate_unique_smarts_pattern() (in module schrodinger.application.matsci.automated_cg_mapping) generate_user_feedback() (in module schrodinger.maestro_utils.composer_agent.query_generator) generate_votca_database() (in module schrodinger.application.matsci.kmc) generate_watermap_pse() (in module schrodinger.application.livedesign.pse_helpers) generateAlignedStructure() (schrodinger.application.pathfinder.aligner.AlignedMolStructureGenerator method) generateAlignmentFile() (schrodinger.protein.predictors.AbstractPredictor method) generateAndApply() (schrodinger.infra.canvas.Chm2DCoordGen static method) generateBaseName() (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) generateBestEnsembles() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) generateBoundingRect() (schrodinger.ui.qt.schart.Callout method) generateCellForEntry() (schrodinger.ui.two_d_viewer.TwoDViewer method) generateConformers() (schrodinger.application.matsci.custom_lipid_prep.StretchMol method) GenerateCoordinates (class in schrodinger.livedesign.preprocessor) generateCoordinates() (schrodinger.infra.canvas.Chm2DCoordGen static method) generateCsvFile() (schrodinger.pipeline.stages.glide.DockingStage method) generateCSVTable() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) generateDM() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) generateExportFiles() (schrodinger.application.livedesign.export_tasks.Export2DTask method) (schrodinger.application.livedesign.export_tasks.Export3DTask method) (schrodinger.application.livedesign.export_tasks.ExportTask87 method) generateExtraInput() (schrodinger.application.matsci.genetic_optimization.AutoQSAR method) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) generateFingerprint() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) generateFromTemplateAndApply() (schrodinger.infra.canvas.Chm2DCoordGen static method) generateFromTemplateAndApply2() (schrodinger.infra.canvas.Chm2DCoordGen static method) generateHtml() (schrodinger.application.report2d.Report2D method) (schrodinger.ui.two_d_viewer.TwoDViewer method) generateIdentitySubMatrix() (schrodinger.protein.align.BiopythonPairwiseAligner method) generateInputFile() (schrodinger.protein.predictors.AbstractPredictor method) (schrodinger.protein.predictors.AccproPredictor method) (schrodinger.protein.predictors.BetaproPredictor method) (schrodinger.protein.predictors.DiproPredictor method) (schrodinger.protein.predictors.DisproPredictor method) (schrodinger.protein.predictors.DomproPredictor method) (schrodinger.protein.predictors.SsproPredictor method) GenerateInterfaceSelection (class in schrodinger.application.bioluminate.pml_menus) generateJaguarInputForTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) generateJaguarStatus() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.StandardStatusMixin method) (schrodinger.application.jaguar.gui.base_panel.TaskStatusMixin method) GenerateLigandSelection (class in schrodinger.application.bioluminate.pml_menus) generateMap() (schrodinger.infra.canvas.ChmCombinationOut32 method) (schrodinger.infra.canvas.ChmCombinationOut64 method) (schrodinger.infra.canvas.ChmDendriticOut32 method) (schrodinger.infra.canvas.ChmDendriticOut64 method) (schrodinger.infra.canvas.ChmFPOut32 method) (schrodinger.infra.canvas.ChmFPOut64 method) (schrodinger.infra.canvas.ChmLinearOut32 method) (schrodinger.infra.canvas.ChmLinearOut64 method) (schrodinger.infra.canvas.ChmMaccsOut32 method) (schrodinger.infra.canvas.ChmMaccsOut64 method) (schrodinger.infra.canvas.ChmMolprint2D32 method) (schrodinger.infra.canvas.ChmMolprint2D64 method) (schrodinger.infra.canvas.ChmPairwiseOut32 method) (schrodinger.infra.canvas.ChmPairwiseOut64 method) (schrodinger.infra.canvas.ChmQuartetOut32 method) (schrodinger.infra.canvas.ChmQuartetOut64 method) (schrodinger.infra.canvas.ChmRadialOut32 method) (schrodinger.infra.canvas.ChmRadialOut64 method) (schrodinger.infra.canvas.ChmSMARTSOut32 method) (schrodinger.infra.canvas.ChmSMARTSOut64 method) (schrodinger.infra.canvas.ChmTopologicalTorsionOut32 method) (schrodinger.infra.canvas.ChmTopologicalTorsionOut64 method) (schrodinger.infra.canvas.ChmTripletOut32 method) (schrodinger.infra.canvas.ChmTripletOut64 method) generateModelFile() (schrodinger.protein.predictors.AbstractPredictor method) generateNeutralizedStates() (schrodinger.ui.two_d_viewer.TwoDViewer method) generateNeutralStateIfNeeded() (schrodinger.ui.two_d_viewer.Cell method) generatePCAFig() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) generatePdf() (schrodinger.application.report2d.Report2D method) (schrodinger.ui.two_d_viewer.TwoDViewer method) generatePicFromCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) generatePicture() (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.ui.qt.structtable.StructureReaderDelegate method) (schrodinger.ui.qt.structtable.StructureViewerDelegate method) (schrodinger.ui.qt.table.StructureDataViewerDelegate method) generatePlotData() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) GeneratePropsStage (class in schrodinger.pipeline.stages.filtering) generateReport() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) generateResidueMap() (schrodinger.protein.sequence.AbstractSingleChainSequence method) GenerateSelection (class in schrodinger.application.bioluminate.pml_menus) generateSeqProjectRows() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) generateSeqStructures() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) generateSipForPose() (schrodinger.application.glide_ws.scoring_report.WScoreSipReport method) generateSpecs() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) generateStateCT() (schrodinger.application.ligprep.ionizer.Ionizer method) GenerateStatesInput (class in schrodinger.application.prepwizard2.tasks) GenerateStatesSettings (class in schrodinger.application.prepwizard2.tasks) GenerateStatesTask (class in schrodinger.application.prepwizard2.tasks) generateStatus() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.ui.qt.appframework2.af2.JobApp method) generateSubMatrix() (schrodinger.protein.align.BiopythonPairwiseAligner method) (schrodinger.protein.align.FamilyPairwiseAligner method) GenerateSubMenu (class in schrodinger.application.bioluminate.pml_menus) generateSummaryLine() (schrodinger.application.glide_ws.scoring_report.WScoreSipPose method) GenerateSurfResSelection (class in schrodinger.application.bioluminate.pml_menus) generateSymmetryEquiv() (schrodinger.application.matsci.nano.sheet.SymmetryEquiv method) GenerateSymmetryMates (class in schrodinger.application.bioluminate.pml_menus) generateXls() (schrodinger.application.report2d.Report2D method) GenericAngle (class in schrodinger.application.jaguar.hess_guess) GenericEntities (class in schrodinger.application.livedesign.entry_types) GenericEntityExportTask (class in schrodinger.application.livedesign.export_tasks) GenericType (class in schrodinger.application.matsci.espresso.qeinput) GenericViewerDelegate (class in schrodinger.ui.qt.table) genEtaRotamers() (schrodinger.application.matsci.reaction_workflow_utils.ConformationalSearchMixin static method) GeneticOptimization (class in schrodinger.application.matsci.genetic_optimization) genFileName() (schrodinger.pipeline.stage.Stage method) GenHBravais() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GenHKL() (in module schrodinger.application.matsci.gsas.GSASIIspc) GenHKLf() (in module schrodinger.application.matsci.gsas.GSASIIspc) GenHLaue() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GenMagOps() (in module schrodinger.application.matsci.gsas.GSASIIspc) genomes (schrodinger.protein.tasks.blast.BlastTask.Input attribute) genomesChanged (schrodinger.protein.tasks.blast.BlastTask.Input attribute) genomesReplaced (schrodinger.protein.tasks.blast.BlastTask.Input attribute) GenOptions (class in schrodinger.application.jaguar.utils) genOutputFileName() (schrodinger.pipeline.stage.Stage method) GenPfHKLs() (in module schrodinger.application.matsci.gsas.GSASIIlattice) gensec() (in module schrodinger.application.jaguar.textparser) GenSelectionSubMenu (class in schrodinger.application.bioluminate.pml_menus) GenSHCoeff() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GenSSHLaue() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GenSymMatesSubMenu (class in schrodinger.application.bioluminate.pml_menus) GEO_MAX_ITERS (schrodinger.application.jaguar.constants.FatalErrors attribute) geom() (schrodinger.application.macromodel.utils.ComUtil method) GEOM_AND_SETTINGS (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) GEOM_ONLY (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) GeomAnalyzerBase (class in schrodinger.application.desmond.packages.staf) GeomCalc (class in schrodinger.application.desmond.packages.staf) GeomConstraint (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) geometry_read() (in module schrodinger.application.jaguar.textparser) geometry_scan_step() (in module schrodinger.application.jaguar.textparser) geometry_score (schrodinger.glide.HBond attribute) GEOMETRY_TO_CMDLINE (in module schrodinger.application.matsci.buildcomplex) GEOPT_CONV_CRITERIA (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog attribute) geopt_convcrit() (in module schrodinger.application.jaguar.textparser) geopt_geometry() (in module schrodinger.application.jaguar.textparser) geopt_nops_on() (in module schrodinger.application.jaguar.textparser) geopt_step_number() (in module schrodinger.application.jaguar.textparser) geopt_stuck1() (in module schrodinger.application.jaguar.textparser) geopt_stuck2() (in module schrodinger.application.jaguar.textparser) ger_parser() (in module schrodinger.seam.testing.failures) GermlineEntry (class in schrodinger.application.bioluminate.update_germline_db.translate_db) get() (schrodinger.application.desmond.arkdb.ArkDb method) (schrodinger.application.glide.job.GlideJob method) (schrodinger.application.glide_ws.props.LegacyDict method) (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) (schrodinger.glide.Config method) (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.mm.MMPREF method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.job.jobcontrol.Job method) (schrodinger.structure._StructureAtomProperty method) (schrodinger.ui.qt.formlayout.FormComboWidget method) (schrodinger.ui.qt.formlayout.FormDialog method) (schrodinger.ui.qt.formlayout.FormTabWidget method) (schrodinger.ui.qt.formlayout.FormWidget method) (schrodinger.utils.preferences.PreferenceFile method) (schrodinger.utils.preferences.Preferences method) get14EleEnergy() (schrodinger.structutils.minimize.Minimizer method) get14LJEnergy() (schrodinger.structutils.minimize.Minimizer method) get2dStructure() (schrodinger.structure.SmilesStructure method) get3DExportItems() (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask method) get3DExportSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) get3DIsomers() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) get3dStructure() (schrodinger.structure.SmilesStructure method) (schrodinger.structure.Structure method) get_2Dimage() (in module schrodinger.application.jaguar.macro_pka_utils) get_3_letter_mutation() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator static method) get_3_letter_mutation_list() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator class method) get_3d_isomers() (in module schrodinger.application.matsci.buildcomplex2d) get_3D_pymol_image() (in module schrodinger.livedesign.pymol_image) get_3point_normal() (in module schrodinger.application.jaguar.utils) get_ab_annotations() (in module schrodinger.livedesign.biologics.sequence) get_absolute_enthalpy_entropy_ratio() (in module schrodinger.application.watermap.shapes) get_absolute_free_ratio() (in module schrodinger.application.watermap.shapes) get_acentric_args() (schrodinger.application.jaguar.garza.SolvEntropyParams method) get_acs_name() (schrodinger.application.jaguar.simple_spec.Peak method) get_action_obj_name() (in module schrodinger.application.bioluminate.actions.factory) get_activated_module_names() (in module schrodinger.tasks.remote_modules) get_active_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_active_fsys_ct_from_frame() (in module schrodinger.application.desmond.packages.topo) get_active_patch() (in module schrodinger.utils.pythonpatch) get_active_sample_size() (in module schrodinger.analysis.enrichment.metrics) get_active_sample_size_star() (in module schrodinger.analysis.enrichment.metrics) get_added() (in module schrodinger.models.diffy) get_added_dict() (in module schrodinger.models.diffy) get_added_list() (in module schrodinger.models.diffy) get_added_set() (in module schrodinger.models.diffy) get_additional_and_stacked_features() (in module schrodinger.application.matsci.ml_formulations_utils) get_adjustable_atoms() (schrodinger.protein.protassign.changeables.amide_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) get_aids_with_pseudos() (in module schrodinger.application.desmond.packages.topo) get_al_script_name() (in module schrodinger.active_learning.al_utils) get_align_asl() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_align_ct() (in module schrodinger.application.bioluminate.antibody.utils) get_align_data() (in module schrodinger.application.bioluminate.antibody.utils) get_align_seq_data() (in module schrodinger.application.bioluminate.antibody.utils) get_aligned_mols() (in module schrodinger.application.jaguar.macro_pka_utils) get_aligned_residues() (in module schrodinger.protein.sequence) get_aligned_structure_residues() (in module schrodinger.protein.sequence) get_aligned_vectors_angle() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_alignment_matrix() (in module schrodinger.structutils.transform) get_all_atomic_subparams() (in module schrodinger.models.parameters) get_all_atoms_marked_as_neighbors() (in module schrodinger.application.matsci.clusterstruct) get_all_compound_subparams() (in module schrodinger.models.parameters) get_all_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_all_domain_structure_files() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_all_eta_atom_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_all_force_field_paths() (in module schrodinger.application.matsci.cgforcefield) get_all_loggerstates() (in module schrodinger.rdkit.rdkit_adapter) get_all_orthant_strings() (in module schrodinger.application.combinatorial_diversity.splitter_utils) get_all_refined_structures_filename() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_all_replaced_signals() (in module schrodinger.models.parameters) get_all_residues() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_all_steps_and_chains() (in module schrodinger.stepper.stepper) get_all_subjobs() (in module schrodinger.application.matsci.jobutils) get_allocator() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) get_allowed_ncpu() (in module schrodinger.active_learning.al_utils) get_analyzer() (in module schrodinger.application.bioluminate.methionine_oxidation) get_anarci_alignment_best_match() (in module schrodinger.application.bioluminate.tcr.annotate) get_anarci_chain_result() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_anarci_results() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_anarci_results_from_fasta() (in module schrodinger.application.bioluminate.anarci.annotate) get_angle() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_angle_between_two_vectors() (in module schrodinger.infra.mm) get_angle_between_vectors() (in module schrodinger.structutils.transform) get_angle_in_degrees() (in module schrodinger.application.matsci.mecp_mod) get_angle_potential_type() (in module schrodinger.application.matsci.coarsegrain) get_angles() (schrodinger.application.desmond.torsion_related.TorsionPotential method) get_anion() (in module schrodinger.application.matsci.mlearn.features) get_annotated_atom() (in module schrodinger.protein.protassign.pka_prediction) get_annotated_atom_property() (in module schrodinger.protein.protassign.pka_prediction) get_annotated_user_labels() (in module schrodinger.seam.viz.inspect) get_annotation_position() (in module schrodinger.ui.qt.smatplotlib) get_annotation_strings() (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult method) get_annotation_strings_with_gaps() (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult method) get_annotations() (in module schrodinger.application.bioluminate.anarci.annotate) get_annotations_for_helm_model() (in module schrodinger.livedesign.biologics.sequence) get_annotations_from_results() (in module schrodinger.application.bioluminate.anarci.annotate) get_antibody_heavy_domains() (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment method) get_antibody_light_domains() (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment method) get_antibody_scheme() (in module schrodinger.application.bioluminate.antibody.utils) get_antibody_type_char() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_APBS_potential_grid() (in module schrodinger.application.bioluminate.escomp) get_appdata_dir() (in module schrodinger.utils.fileutils) get_application() (in module schrodinger.utils.qapplication) get_approximate_atomic_sasa() (in module schrodinger.structutils.analyze) get_approximate_sasa() (in module schrodinger.structutils.analyze) get_archive_path() (in module schrodinger.infra.mm) get_arg_parser() (in module schrodinger.utils.compare) get_arm_index() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_arm_indices() (in module schrodinger.livedesign.biologics.sequence) get_arms() (in module schrodinger.livedesign.biologics.registration) get_arms_by_annotation() (in module schrodinger.livedesign.biologics.registration) get_arms_by_connectivity() (in module schrodinger.livedesign.biologics.registration) get_aromatic_hydrogen_bonds() (in module schrodinger.structutils.interactions.hbond) get_ase_atoms() (in module schrodinger.application.matsci.aseutils) get_asl_chain_name() (in module schrodinger.application.bioluminate.pml_menus) get_asl_for_ppw_atoms() (in module schrodinger.application.prepwizard) get_asl_for_search_option() (in module schrodinger.maestro_utils.find_tool_bar.constants) get_asl_from_meta_asl() (in module schrodinger.application.desmond.cms) get_asl_from_selection_picking_dialog() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_ASP_curve() (schrodinger.application.jaguar.pk50_report.Pk50Factory method) get_assembled_structure() (in module schrodinger.application.matsci.swap_fragments_utils) get_assembler_type() (in module schrodinger.livedesign.biologics.fasta) get_assignments() (schrodinger.application.jaguar.pk50_report.Pk50Factory method) get_asu_component_ids() (in module schrodinger.comparison.struc) get_asu_component_name() (in module schrodinger.comparison.struc) get_asu_id_array() (in module schrodinger.comparison.struc) get_ASU_RMSD() (in module schrodinger.comparison.struc) get_asu_volume() (in module schrodinger.comparison.struc) get_atom() (in module schrodinger.application.bioluminate.antibody.assembly) get_atom_chirality() (in module schrodinger.application.canvas.r_group) get_atom_elements() (in module schrodinger.application.scaffold_enumeration.atomlist) get_atom_ffio_velocity() (in module schrodinger.application.matsci.desmondutils) get_atom_group() (schrodinger.application.desmond.cms.Cms method) get_atom_id() (in module schrodinger.application.scaffold_enumeration.common) get_atom_id_map() (in module schrodinger.application.scaffold_enumeration.common) get_atom_indices() (schrodinger.protein.analysis.Report.local_residue method) get_atom_info() (in module schrodinger.application.jaguar.gui.utils) get_atom_label_font() (in module schrodinger.application.phase.phase_markers) get_atom_layers() (in module schrodinger.application.matsci.freevolume) get_atom_list() (in module schrodinger.application.phase.subset_screening) get_atom_name_formula() (in module schrodinger.application.matsci.coarsegrain) get_atom_numbering_chirality() (in module schrodinger.comparison.chirality) get_atom_positions() (in module schrodinger.application.bindingsite.cavutils) get_atom_radii_lines() (in module schrodinger.application.matsci.packmol) get_atom_reference_coordinates() (in module schrodinger.application.desmond.struc) get_atom_shell() (in module schrodinger.application.phase.subset_screening) get_atom_string() (in module schrodinger.protein.protassign.utils) get_atom_type() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) get_atom_type_dict() (in module schrodinger.application.matsci.rxn_channel) get_atomic_element() (in module schrodinger.application.matsci.msutils) get_atomic_element_symbols() (in module schrodinger.application.matsci.nano.util) get_atoms_asl() (in module schrodinger.application.matsci.maestrocmds) get_atoms_bitset() (in module schrodinger.infra.structure) get_atoms_by_orig_anum() (in module schrodinger.application.prepwizard) get_atoms_close_to_point() (in module schrodinger.structutils.measure) get_atoms_close_to_structure() (in module schrodinger.structutils.measure) get_atoms_close_to_subset() (in module schrodinger.structutils.measure) get_atoms_from_asl() (in module schrodinger.structutils.analyze) get_atoms_from_smarts_or_mcs() (in module schrodinger.structutils.clash_resolution) get_atoms_mapping() (in module schrodinger.livedesign.preprocessor) get_atoms_with_improper_atom_types() (in module schrodinger.application.prepwizard2.diagnostics) get_attach() (schrodinger.application.canvas.r_group.TempAtom method) get_attachment() (in module schrodinger.application.glide.http_server) get_attachment_point() (in module schrodinger.structutils.rgroup_enumerate) get_attachment_points() (schrodinger.application.canvas.r_group.Data method) get_available_devices() (in module schrodinger.gpgpu) get_available_properties() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_average_structure() (in module schrodinger.structutils.analyze) get_averaged_properties() (in module schrodinger.application.matsci.boltzmann_avg_props) get_avg() (in module schrodinger.application.matsci.desmondutils) get_axis_of_rotation() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_backbone_atoms() (in module schrodinger.application.matsci.geometry) get_backbone_indices() (schrodinger.protein.analysis.Report.local_residue method) get_backend() (in module schrodinger.job.jobcontrol) get_backend_args() (in module schrodinger.active_learning.mq_worker) get_backend_first_host() (in module schrodinger.application.matsci.jobutils) get_backend_host_list() (in module schrodinger.job.jobcontrol) get_backend_hosts_str() (in module schrodinger.application.matsci.jobutils) get_base64_str_from_structure() (in module schrodinger.application.matsci.coarsegrain) get_base_entry_group() (in module schrodinger.project.utils) get_base_esp_jobname() (in module schrodinger.application.matsci.clusterstruct) get_base_names() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_basename() (in module schrodinger.utils.fileutils) get_basename_if_relative_path() (in module schrodinger.application.desmond.util) get_bases() (in module schrodinger.application.jaguar.basis) get_basis() (in module schrodinger.application.mopac.mopac_surfaces) get_basis_display_name() (in module schrodinger.application.jaguar.gui.basis_selector) get_basis_set_list_items() (in module schrodinger.application.jaguar.gui.basis_selector) get_bbox_vectors() (in module schrodinger.comparison.struc) get_bead_count() (in module schrodinger.application.matsci.coarsegrain) get_benchmarks() (in module schrodinger.seam.testing.benchmarks) get_best_domain_result() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_best_image_scale() (in module schrodinger.ui.sketcher_image) get_best_pose() (in module schrodinger.application.glide_ws.entropy_score) (schrodinger.application.glide_ws.entropy_score.EnsembleScore method) (schrodinger.application.glide_ws.entropy_score.MMGBSAEntropyScore method) get_bfnorm() (in module schrodinger.application.mopac.mopac_surfaces) get_bilinear_fit_property() (in module schrodinger.application.matsci.uq_utils) get_bilinear_prop() (in module schrodinger.application.matsci.uq_utils) get_bilinear_prop_from_points() (in module schrodinger.application.matsci.uq_utils) get_bilinear_regions() (in module schrodinger.application.matsci.uq_utils) get_bilinear_regression() (in module schrodinger.application.matsci.uq_utils) get_bin() (in module schrodinger.application.glide_ws.ml_featurizer) get_bio_database() (in module schrodinger.application.bioluminate.antibody.utils) get_bispecific_model_job() (in module schrodinger.livedesign.biologics.modeling) get_blocks() (in module schrodinger.structutils.block_data) get_bond_asl() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_bond_id() (in module schrodinger.application.scaffold_enumeration.common) get_bond_labels() (in module schrodinger.application.pathfinder.synthesis) get_bond_residue() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_bond_type_dict() (in module schrodinger.application.matsci.rxn_channel) get_bonded_hydrogens() (in module schrodinger.application.ligprep.ionizer) get_bonds() (in module schrodinger.application.jaguar.utils) get_bonds_in_molecule() (in module schrodinger.application.matsci.rxn_channel) get_bonds_in_rings() (schrodinger.application.canvas.r_group.Data method) get_bonds_mapping() (in module schrodinger.livedesign.preprocessor) get_bound_cache() (in module schrodinger.application.matsci.cache) get_box() (in module schrodinger.application.desmond.cms) (schrodinger.application.glide_ws.nodes.GridGenNode method) get_boxsize() (in module schrodinger.application.desmond.cms) get_boxvolume() (in module schrodinger.application.desmond.cms) get_bridging_waters() (in module schrodinger.application.prepwizard) get_bs_base_name() (in module schrodinger.application.matsci.bandshape_utils) get_bs_ext() (in module schrodinger.application.matsci.bandshape_utils) get_bs_spectrum_file_temps_keys() (in module schrodinger.application.matsci.bandshape_utils) get_build_id() (in module schrodinger.application.glide_ws.version) get_buildtime_file() (in module schrodinger.utils.machid) get_built_in_aa_names() (in module schrodinger.protein.process_enamine_db) get_built_in_residues() (schrodinger.protein.nonstandard_residues.ResidueDatabase class method) get_builtin_directory() (in module schrodinger.application.matsci.builderwidgets) get_builtin_template_items() (in module schrodinger.application.matsci.builderwidgets) get_bulk_solvent_accessible_atoms() (in module schrodinger.protein.protassign.unsatisfied_donors) get_bumped_release_version() (in module schrodinger) get_bundled_libstdcpp() (in module schrodinger.utils.installation_check) get_CA_atom_props() (in module schrodinger.protein.properties) get_ca_positions() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_canonical_entity() (in module schrodinger.livedesign.custom_entity.registration) get_canvas_program() (in module schrodinger.protein.natural_analog) get_carb_atom_identifier_map() (in module schrodinger.application.matsci.polymer) get_carboxyl_atoms() (in module schrodinger.protein.protassign.pka_prediction) get_carts_from_anchor_string() (in module schrodinger.application.matsci.nano.xtal) get_carts_from_center_string() (in module schrodinger.application.matsci.nano.xtal) get_cell() (in module schrodinger.application.matsci.nano.xtal) get_cell_fast() (in module schrodinger.application.matsci.nano.xtal) (in module schrodinger.comparison.struc) get_cell_pairs() (in module schrodinger.application.matsci.nano.xtal) get_cells() (in module schrodinger.application.matsci.packmol) get_center() (in module schrodinger.application.matsci.geometry) (in module schrodinger.math.multi_parameter_optimization) get_center_gridlen() (in module schrodinger.application.bioluminate.escomp) get_center_of_mass_weight() (in module schrodinger.application.matsci.cg_mapping) get_centroid() (in module schrodinger.application.matsci.shapes) (in module schrodinger.structutils.transform) get_centroid_from_residues() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_centroid_radial_distance_vector() (in module schrodinger.comparison.struc) get_centroid_RMSDn() (in module schrodinger.comparison.neighbors) get_cert() (in module schrodinger.job.cert) get_cert_with_ldap() (in module schrodinger.job.cert) get_cert_with_socket_auth() (in module schrodinger.job.cert) get_cfg_names_from_msj_data() (in module schrodinger.application.matsci.desconfig) get_cfg_names_from_msj_file() (in module schrodinger.application.matsci.desconfig) get_cg_cutoff_data() (in module schrodinger.application.matsci.coarsegrain) get_cg_molecule_hash() (in module schrodinger.application.matsci.coarsegrain) get_cg_particle_indices() (in module schrodinger.application.matsci.cg_mapping) get_cg_particle_parent_indices() (in module schrodinger.application.matsci.cg_mapping) get_cg_radii_lines() (in module schrodinger.application.matsci.packmol) get_cg_structure() (in module schrodinger.ui.sketcher_extensions) get_cgparticle_to_element_mapper() (in module schrodinger.rdkit.coarsegrain) get_chain_atoms() (in module schrodinger.livedesign.biologics.rdmol_hierarchy) get_chain_fasta_sequence() (in module schrodinger.protein.sequence) get_chain_pairs() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_chain_sequence() (in module schrodinger.application.bioluminate.antibody.annotate) get_chain_sequences() (in module schrodinger.application.prepwizard2.tasks) get_chain_structures_from_model() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) get_chain_termini() (in module schrodinger.infra.structure) get_charge() (in module schrodinger.application.bioluminate.propka_parse) (schrodinger.application.desmond.cms.Cms method) get_charged_prop_value() (in module schrodinger.application.matsci.kmcgui) get_charges() (in module schrodinger.application.jaguar.utils) get_check_also_reg_bond() (in module schrodinger.application.matsci.nano.xtal) get_check_item_index() (in module schrodinger.maestro_utils.surface_manager.utils) get_check_min_jaguar_keywords() (in module schrodinger.application.matsci.reaction_workflow_utils) get_checksum() (in module schrodinger.application.matsci.espresso.ppdb) get_chemical_model() (in module schrodinger.livedesign.custom_entity.registration) get_child_like_parent() (in module schrodinger.application.matsci.genetic_optimization) get_chiral_atoms() (in module schrodinger.structutils.analyze) get_chiral_centers() (in module schrodinger.comparison.chirality) get_chiral_hash() (in module schrodinger.application.matsci.cg_mapping) get_chiral_pair() (in module schrodinger.application.matsci.cg_mapping) get_chiralities() (in module schrodinger.structutils.analyze) get_chirality() (in module schrodinger.comparison.chirality) get_chmmol_bonds_from_atoms() (in module schrodinger.ui.qt.structure2d) get_chorus_from_params() (in module schrodinger.application.matsci.nano.xtal) get_chorus_properties() (in module schrodinger.application.matsci.nano.xtal) get_chunk_file_name() (in module schrodinger.application.bb_database.bb_task_utils) get_chunk_info() (in module schrodinger.application.bb_database.bb_task_utils) get_chunk_row() (in module schrodinger.application.bb_database.bb_task_utils) get_chunk_rows() (in module schrodinger.application.bb_database.bb_task_utils) get_circular_delta() (in module schrodinger.ui.qt.dialbox) get_class_map() (in module schrodinger.application.matsci.packmol) get_cli_geom_str() (in module schrodinger.application.matsci.buildcomplex) get_clib_dir() (in module schrodinger.application.combinatorial_screen.driver_utils) get_close_atoms() (in module schrodinger.structutils.measure) get_close_coordinates() (in module schrodinger.structutils.measure) get_close_interactors() (schrodinger.protein.protassign.changeables.changeable method) get_close_list() (in module schrodinger.application.glide_ws.entropy_score) get_close_residues_asl() (in module schrodinger.structutils.interactions.protein_protein_interactions) get_closest_atom() (in module schrodinger.application.matsci.swap_fragments_utils) get_clustal_path() (in module schrodinger.protein.tasks.clustal) get_cluster_atom_ids() (in module schrodinger.application.matsci.clusterstruct) get_cms_and_trj_path() (in module schrodinger.application.matsci.deswidgets) get_cms_and_trj_path_from_st() (in module schrodinger.application.matsci.desmondutils) get_cms_file_path() (in module schrodinger.trajectory.utils) get_cms_path_from_proj_table() (in module schrodinger.application.matsci.deswidgets) get_coarse_grain_msj_family_header() (in module schrodinger.application.matsci.coarsegrain) get_coarse_grain_msj_header() (in module schrodinger.application.matsci.coarsegrain) get_coarsegrain_smiles() (in module schrodinger.rdkit.coarsegrain) get_code() (schrodinger.infra.unusable_module_importer.UnusableModuleLoader class method) get_collapsed_index() (in module schrodinger.application.matsci.nano.xtal) get_color() (in module schrodinger.application.bioluminate.pml_menus) (in module schrodinger.application.matsci.amorphous) (schrodinger.application.desmond.torsion_related.TorsionPotential method) (schrodinger.ui.qt.formlayout.ColorButton method) get_color_by_entry() (in module schrodinger.application.watermap.shapes) get_color_list() (in module schrodinger.application.combiglide.connection_storage) get_color_scheme() (in module schrodinger.structutils.color) get_colors() (in module schrodinger.application.matsci.maestrocmds) get_com_and_axes() (in module schrodinger.application.bindingsite.cavutils) get_combinatorial_synthesis_command() (in module schrodinger.application.combinatorial_screen.driver_utils) get_combined_exclusion_str() (in module schrodinger.application.matsci.coarsegrain) get_combined_reader() (in module schrodinger.application.glide_ws.merge) get_command() (in module schrodinger.job.queue) get_command_line_host_list() (in module schrodinger.job.jobcontrol) get_command_option_for_search_option() (in module schrodinger.maestro_utils.find_tool_bar.constants) get_common_atom_property_names() (in module schrodinger.application.matsci.msutils) get_common_float_atom_property_names() (in module schrodinger.application.matsci.msutils) get_common_float_property_names() (in module schrodinger.application.matsci.msutils) get_compatible_archive_path() (in module schrodinger.infra.mm) get_compatible_sequences_dict() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_compatible_sequences_from_fasta() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_complete_spectrum() (in module schrodinger.application.matsci.colorutils) get_complex_by_name() (schrodinger.application.glide_ws.driver.GlideWSJob method) get_component_id() (in module schrodinger.comparison.struc) get_compressive_relaxation_stringers() (in module schrodinger.application.matsci.desconfig) get_conclusion_string() (in module schrodinger.active_learning.al_report) get_confidence_interval_error() (in module schrodinger.application.matsci.mlearn.descriptor) get_config() (in module schrodinger.application.matsci.permittivity) get_config_as_json() (in module schrodinger.application.glide.http_server) get_config_filename() (in module schrodinger.application.jaguar.user_config) get_config_from_options() (in module schrodinger.application.matsci.permittivity) get_config_key_value_dict() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_conformer_dict() (in module schrodinger.application.matsci.boltzmann_avg_props) get_conformer_radial_distance_vector() (in module schrodinger.comparison.struc) get_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) get_connected_components() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) get_connected_ring_bonds() (in module schrodinger.application.canvas.r_group) get_connection_color() (in module schrodinger.application.combiglide.connection_storage) get_connection_status() (in module schrodinger.application.livedesign.maestro_ld_connection) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_const_ref_filename() (in module schrodinger.application.bioluminate.anarci.annotate) get_constant_domain_bounds() (in module schrodinger.application.bioluminate.anarci.annotate) get_constraint() (schrodinger.application.desmond.cms.Cms method) get_constraint_groups_from_dict() (in module schrodinger.application.glide_ws.model) get_consuming_transforms() (in module schrodinger.seam.viz.inspect) get_contacts() (in module schrodinger.infra.structure) get_contiguous_groups() (in module schrodinger.protein.alignment) get_contrast() (in module schrodinger.ui.qt.standard.colors) get_contrasting_color() (in module schrodinger.ui.qt.standard.colors) get_control_from_dict() (in module schrodinger.application.vss.control) get_control_from_file() (in module schrodinger.application.vss.control) get_conv_from_vecs() (in module schrodinger.application.matsci.nano.xtal) get_conventional_unit_cell() (in module schrodinger.comparison.struc) get_coords_array_from_list() (in module schrodinger.structutils.transform) get_core_bonds() (schrodinger.application.canvas.r_group.Data method) get_core_idcs() (in module schrodinger.glide) get_core_idxs() (in module schrodinger.application.matsci.reaction_workflow_enum_utils) get_core_num() (in module schrodinger.application.matsci.equilibrium_md) get_core_smarts_idcs() (in module schrodinger.glide) get_cores() (schrodinger.application.canvas.r_group.Data method) get_corrected_energy() (in module schrodinger.glide) get_corresponding_header() (schrodinger.livedesign.biologics.fasta.PolymerAssembler class method) get_cov_parameter() (in module schrodinger.application.matsci.nano.xtal) get_cov_radii() (in module schrodinger.application.matsci.nano.xtal) get_cov_radius() (in module schrodinger.application.matsci.nano.xtal) get_cpu() (in module schrodinger.utils.sysinfo) get_cpu_and_gpu_hosts() (in module schrodinger.application.matsci.parserutils) get_cpu_cores() (in module schrodinger.autoinstall.infra) get_crest_auto_restrain_atom_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_critical_reliability_issues() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_cross() (in module schrodinger.graphics3d.common) get_css_for_button_with_icon() (in module schrodinger.ui.two_d_viewer) get_csv_file_column_count() (in module schrodinger.utils.fileutils) get_csv_filenames() (in module schrodinger.application.glide.utils) get_csv_header() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.glide.csv_utils) get_csv_name() (in module schrodinger.application.bioluminate.methionine_oxidation) get_CSV_path() (in module schrodinger.application.matsci.stress_strain) get_csv_props() (in module schrodinger.application.glide.csv_utils) get_csvwriter() (in module schrodinger.application.glide_ws.nodes) get_ct_atoms_count() (in module schrodinger.application.matsci.msutils) get_ct_offsets() (schrodinger.application.canvas.r_group.Data method) get_ct_property() (in module schrodinger.application.glide.sort_utils) get_cts() (schrodinger.application.desmond.cms.Cms method) get_cuboid_vol() (in module schrodinger.application.matsci.packmol) get_current_context() (in module schrodinger.application.livedesign.models2.execution.context) get_current_OPLS_data_filename() (in module schrodinger.infra.mm) get_current_OPLS_data_subdirectory() (in module schrodinger.infra.mm) get_current_project_name() (in module schrodinger.ui.qt.forcefield.ffprojectsettingsdlg) get_current_time() (in module schrodinger.active_learning.al_utils) (in module schrodinger.job.queue) get_current_utc_timestamp() (in module schrodinger.application.job_monitor.util) get_custom_keq_rates() (in module schrodinger.application.matsci.reaction_workflow_utils) get_custom_opls_dir() (in module schrodinger.ui.qt.forcefield.forcefield) get_custom_rate() (in module schrodinger.application.matsci.reaction_workflow_utils) get_custom_reagent_classes() (in module schrodinger.application.pathfinder.reaction) get_cut_bonds() (in module schrodinger.application.matsci.swap_fragments_utils) get_cutoff() (in module schrodinger.application.matsci.desmondutils) get_cutoff_from_reduced_density() (in module schrodinger.application.matsci.cgforcefield) get_cutoff_server_config() (schrodinger.application.glide_ws.nodes.ModelNode method) get_data_file() (in module schrodinger.application.glide.utils) (in module schrodinger.application.glide_ws.utils) get_data_frame_from_project() (in module schrodinger.project.pandasutils) get_database_manager_class() (in module schrodinger.application.matsci.kmc) get_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_db_amino_acids() (in module schrodinger.protein.nonstandard_residues) get_db_filename() (in module schrodinger.protein.gpcr.sql) get_db_residues() (in module schrodinger.protein.nonstandard_residues) get_db_structure_path() (in module schrodinger.application.matsci.kmc) get_db_table_length() (in module schrodinger.application.matsci.kmc) get_debug_level() (in module schrodinger.stepper.stepper) get_decoy_sample_size() (in module schrodinger.analysis.enrichment.metrics) get_deduped_monomers() (in module schrodinger.application.matsci.rxn_channel) get_deduplication_hash() (in module schrodinger.livedesign.biologics.registration) (in module schrodinger.livedesign.custom_entity.registration) get_default_box_size() (in module schrodinger.application.glide.grid) get_default_criterion_parser() (in module schrodinger.utils.ligfilter) get_default_docking_keyword_value() (in module schrodinger.application.glide.job) get_default_far_timestep() (in module schrodinger.application.matsci.desmondutils) get_default_forcefield() (in module schrodinger.application.matsci.msutils) get_default_launch_timeout() (in module schrodinger.job.queue) get_default_licserver_user() (in module schrodinger.application.licensing.licserver.main) get_default_log_filename() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_default_minimal_caps_filename() (in module schrodinger.application.pathfinder.reaction) get_default_near_timestep() (in module schrodinger.application.matsci.desmondutils) get_default_opls_version() (in module schrodinger.ui.qt.forcefield.forcefield) get_default_params() (in module schrodinger.structutils.interactions.hbond) get_default_pymol_location() (in module schrodinger.application.pymol.utils) get_default_reactions_filename() (in module schrodinger.application.pathfinder.reaction) get_default_reagent_classes_filename() (in module schrodinger.application.pathfinder.reaction) get_default_serializer() (in module schrodinger.models.jsonable) get_default_user_dbfile() (in module schrodinger.protein.nonstandard_residues) get_default_weights_dir() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_degrees_of_freedom() (in module schrodinger.application.desmond.remd) (schrodinger.application.desmond.cms.Cms method) get_delta_energy() (in module schrodinger.application.matsci.jaguarworkflows) get_delta_property_values() (in module schrodinger.application.bioluminate.residue_scanning.properties) get_denovo_parameters() (in module schrodinger.application.phase.utils) get_density() (in module schrodinger.application.matsci.amorphous) get_density_from_scale_factor() (in module schrodinger.application.matsci.cgforcefield) get_depth() (schrodinger.application.jaguar.simple_spec.Peak method) get_depth_limits() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_description() (in module schrodinger.tasks.param_cli) get_descriptive_angles() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_descriptors_from_file() (in module schrodinger.application.matsci.order_parameter_mod) get_desktop_dir() (in module schrodinger.utils.fileutils) get_desmond_frames_from_options() (in module schrodinger.application.matsci.desmondutils) get_desmond_frames_in_range() (in module schrodinger.application.matsci.desmondutils) get_desmond_system_type() (in module schrodinger.application.matsci.desconfig) get_desmond_trj_frames() (in module schrodinger.application.matsci.desmondutils) get_detailed() (in module schrodinger.application.bioluminate.propka_parse) get_device_info() (schrodinger.gpgpu.CudaDevice method) get_device_uuid() (in module schrodinger.gpgpu) get_dialog() (schrodinger.ui.qt.formlayout.FormWidget method) get_dict_reader() (schrodinger.application.vss.csvsmiles.CsvSmilesFile method) get_dict_writer() (schrodinger.application.vss.csvsmiles.CsvSmilesFile method) get_diff() (in module schrodinger.models.diffy) get_diff_chunks() (in module schrodinger.utils.compare) get_diff_dict() (in module schrodinger.models.diffy) get_diff_list() (in module schrodinger.models.diffy) get_diff_output_with_numerical_tolerance() (in module schrodinger.utils.compare) get_diff_set() (in module schrodinger.models.diffy) get_diff_tokens_in_line() (in module schrodinger.utils.compare) get_dihedral() (in module schrodinger.infra.mm) get_dihedral_atoms() (in module schrodinger.protein.protassign.changeables) get_dimensionality_from_st() (in module schrodinger.application.matsci.pbcutils) get_dimer_com_sep() (in module schrodinger.application.matsci.kmc) get_dimers_in_structure() (in module schrodinger.application.matsci.clusterstruct) get_dimers_with_molecule() (in module schrodinger.application.matsci.clusterstruct) get_directory() (in module schrodinger.utils.fileutils) get_directory_path() (in module schrodinger.utils.fileutils) get_directory_size() (in module schrodinger.utils.fileutils) get_disabled_lib_dir() (in module schrodinger.utils.postinstall) get_dise() (in module schrodinger.application.vss.dise) get_disorder_groups() (in module schrodinger.application.matsci.pbcutils) get_display_string() (in module schrodinger.livedesign.biologics.registration) (in module schrodinger.livedesign.custom_entity.registration) get_distance() (in module schrodinger.application.matsci.colorutils) get_distance_cell() (in module schrodinger.application.matsci.mlearn.features) get_distributed_fp_commands() (in module schrodinger.application.combinatorial_screen.driver_utils) get_distributed_fp_generation_commands() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_distributed_screen_commands() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_distributed_selection_commands() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_distro_package() (in module schrodinger.utils.installation_check) get_disulfide_bonds() (in module schrodinger.structutils.interactions.ssbond) get_disulfide_center_point() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_docking_funnel() (in module schrodinger.application.glide.runner) get_docs_dir() (in module schrodinger.utils.documentation) (in module schrodinger.utils.fileutils) get_domain_bond() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_domain_key_pair() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_domain_structure_files() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_domain_type_shorthand() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_donor_acceptor_bonds() (in module schrodinger.structutils.interactions.hbond) get_double_sigmoid() (in module schrodinger.math.multi_parameter_optimization) get_dpd_scale_factor_from_FF() (in module schrodinger.application.matsci.cgforcefield) get_driver_parser() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_dummy_atoms() (in module schrodinger.application.matsci.etatoggle) (in module schrodinger.application.matsci.msutils) get_dummy_filter() (in module schrodinger.structutils.rgroup_enumerate) get_duplicate_atoms() (in module schrodinger.application.matsci.nano.xtal) get_e_pair_rates_from_database() (in module schrodinger.application.matsci.kmc) get_eigenvectors() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_element() (in module schrodinger.application.matsci.espresso.utils) get_element_counts() (in module schrodinger.application.matsci.atomicsymbols) get_element_histogram() (in module schrodinger.application.matsci.genetic_optimization) get_element_mutator_dict() (in module schrodinger.application.matsci.genetic_optimization) get_element_priority() (in module schrodinger.application.matsci.nano.xtal) get_enabled_flags() (in module schrodinger.seam.debug) get_enamine_dbfile() (in module schrodinger.protein.nonstandard_residues) get_enc_module() (in module schrodinger.application.matsci.codeutils) get_encrypted_text() (in module schrodinger.application.matsci.enc) get_encryption_key() (in module schrodinger.application.matsci.enc) get_energy() (in module schrodinger.application.macromodel.apps) get_energy_charge_correction() (in module schrodinger.glide) get_energy_db_term() (in module schrodinger.application.matsci.reaction_workflow_utils) get_energy_for_strain_corrections() (in module schrodinger.glide) get_enrichment_calculator() (in module schrodinger.application.glide.glideanalysis) get_enthalpy_info() (in module schrodinger.application.matsci.anharmonic) get_enthalpy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_entitlement_status() (in module schrodinger.application.licensing.licserver.entitlement_status) get_entity_class() (in module schrodinger.livedesign.biologics.registration) (in module schrodinger.livedesign.custom_entity.registration) get_entries() (in module schrodinger.application.matsci.reaction_workflow_gui_utils) (in module schrodinger.ui.qt.entryselector) get_entropy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_entry() (in module schrodinger.ui.qt.entryselector) get_entry_bitset() (in module schrodinger.infra.structure) get_entry_group() (in module schrodinger.project.utils) get_enum_member() (in module schrodinger.application.matsci.msutils) get_env_var_warning() (in module schrodinger.utils.featureflags.featureflags) get_environ_log_level() (in module schrodinger.utils.log) get_epik_info() (in module schrodinger.application.livedesign.ld_alogD_utils) get_error_icon() (in module schrodinger.ui.qt.tasks.taskwidgets) get_error_tagged_structure() (in module schrodinger.application.glide.utils) get_eta_marker_indexes() (in module schrodinger.application.matsci.buildcomplex) get_example_mol_tag() (in module schrodinger.application.matsci.clusterstruct) get_exception_handler() (in module schrodinger.infra.exception_handler) get_existing_directory() (in module schrodinger.ui.qt.filedialog) get_existing_filepath() (in module schrodinger.utils.fileutils) get_existing_files() (in module schrodinger.application.bioluminate.drivers.io) (in module schrodinger.application.matsci.jaguar_restart) get_existing_fp_file() (in module schrodinger.application.combinatorial_screen.driver_utils) get_existing_fp_files() (in module schrodinger.application.combinatorial_screen.driver_utils) get_existing_phase_database() (in module schrodinger.ui.qt.filedialog) get_existing_project_name() (in module schrodinger.ui.qt.filedialog) get_explicit_waters() (schrodinger.application.glide_ws.nodes.GridGenNode method) get_extra_features() (in module schrodinger.active_learning.al_utils) get_extracted_and_maps() (in module schrodinger.application.matsci.swap_fragments_utils) get_extracted_atom_index() (in module schrodinger.application.matsci.clusterstruct) get_failed_triggers_from_ct() (in module schrodinger.application.glide_ws.trigger) get_families() (in module schrodinger.protein.gpcr.annotate) get_family_data_dict_from_st() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_family_region_bounds() (in module schrodinger.application.bioluminate.anarci.annotate) get_family_region_bounds_from_chain_result() (in module schrodinger.application.bioluminate.anarci.annotate) get_family_region_bounds_from_domain_result() (in module schrodinger.application.bioluminate.anarci.annotate) get_fasta_helm_models() (in module schrodinger.livedesign.biologics.fasta) get_fasta_monomers() (in module schrodinger.livedesign.biologics.sequence) get_fasta_sequences() (in module schrodinger.protein.sequence) get_feature_overlap_mappings() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) get_feature_text() (in module schrodinger.application.phase.constants) get_features() (in module schrodinger.utils.featureflags.featureflags) get_features_from_dict() (in module schrodinger.application.glide_ws.model) get_fep_cts() (schrodinger.application.desmond.cms.Cms method) get_fep_structures() (in module schrodinger.application.desmond.struc) get_ff() (schrodinger.application.desmond.cms.Cms method) get_ffio_cache() (in module schrodinger.application.matsci.desmondutils) get_fflags_env_to_export() (in module schrodinger.utils.featureflags.featureflags) get_ffld_spec() (in module schrodinger.infra.mm) get_field_strength_string() (in module schrodinger.application.matsci.kmcgui) get_fieldnames() (in module schrodinger.rdkit.molio) get_file() (in module schrodinger.job.files) (schrodinger.application.matsci.permittivity.Config static method) get_file_data() (in module schrodinger.application.matsci.freevolume) (in module schrodinger.application.matsci.spectra) get_file_ext() (in module schrodinger.active_learning.al_utils) get_file_extension() (in module schrodinger.utils.fileutils) get_file_format() (in module schrodinger.utils.fileutils) get_file_from_options() (schrodinger.application.matsci.permittivity.Config class method) get_file_names_of_duplicates() (in module schrodinger.application.matsci.reaction_workflow_utils) get_file_path() (in module schrodinger.application.matsci.jobutils) get_file_path_errors() (in module schrodinger.application.desmond.util) get_file_url() (in module schrodinger.job.launchapi) get_filename() (in module schrodinger.application.matsci.hdfutils) get_files() (in module schrodinger.application.matsci.equilibrium_md) get_files_from_folder() (in module schrodinger.utils.fileutils) get_filter() (in module schrodinger.rdkit.filtering) get_filter_columns() (in module schrodinger.application.combinatorial_diversity.diversity_selector) get_filter_path() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) get_filter_properties() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_final_state() (in module schrodinger.application.matsci.mecp_mod) get_find_toolbar() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_fingerprint() (in module schrodinger.rdkit.filtering) (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) get_fingerprint_components() (in module schrodinger.analysis.enrichment.enrichment_input) get_fingerprint_types() (in module schrodinger.utils.multifpfile) get_fingerprints() (schrodinger.utils.multifpfile.MultiFPFile method) get_first_hostid() (in module schrodinger.application.licensing.licadmin) get_first_hostname() (in module schrodinger.ui.qt.appframework2.jobs) get_flags_from_solvent_params() (in module schrodinger.application.matsci.solvation_entropy_utils) get_flat_color_list() (in module schrodinger.application.combiglide.connection_storage) get_flexlm_search_path() (in module schrodinger.application.licensing.licadmin) get_float_value_from_column() (in module schrodinger.application.livedesign.io_utils) get_fmt() (in module schrodinger.application.desmond.packages.traj) get_font() (schrodinger.ui.qt.formlayout.FontLayout method) get_font_id() (in module schrodinger.utils.pymol) get_force_field_file_path() (in module schrodinger.application.matsci.cgforcefield) get_force_field_name() (in module schrodinger.application.matsci.cgforcefield) get_forcefield_typer() (in module schrodinger.application.matsci.parserutils) get_form_hashes() (in module schrodinger.application.desmond.struc) get_form_mols() (in module schrodinger.application.desmond.struc) get_format_arguments() (in module schrodinger.livedesign.biologics.modeling) get_format_from_extension() (in module schrodinger.infra.structure) get_format_handler() (in module schrodinger.rdkit.molio) get_formatted_bytesize() (in module schrodinger.utils.fileutils) get_formatted_residue() (in module schrodinger.protein.residue) get_formatted_residue_range() (in module schrodinger.protein.residue) get_formulas_basename() (in module schrodinger.application.matsci.nano.interface_mod) get_fp_basename() (in module schrodinger.application.pathfinder.multiroute) get_fp_domain() (in module schrodinger.application.combinatorial_diversity.diversity_selector) get_fp_file() (in module schrodinger.application.pathfinder.multiroute) get_fp_files() (in module schrodinger.application.combinatorial_screen.driver_utils) get_fp_matrix() (in module schrodinger.protein.natural_analog) get_frag_structure() (in module schrodinger.structutils.build) get_fragment_smiles() (in module schrodinger.application.matsci.rxn_channel) get_fragment_structure() (in module schrodinger.protein.buildpeptide) get_fragname() (schrodinger.application.desmond.cms.Cms method) get_frags_from_mol() (schrodinger.active_learning.substruct_enrichment.SubstructEnrichCalculator static method) get_free_energy() (in module schrodinger.application.bioluminate.propka_parse) get_free_energy_info() (in module schrodinger.application.matsci.anharmonic) get_free_energy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_free_volume_structure() (in module schrodinger.application.matsci.freevolume) get_freezer_structure() (in module schrodinger.application.matsci.genetic_optimization) get_from() (schrodinger.application.desmond.arkdb.Datum method) get_frozen_atoms() (in module schrodinger.application.pathfinder.analysis) get_fullsys_ct_atom_index_range() (schrodinger.application.desmond.cms.Cms method) get_functional_rings() (schrodinger.application.canvas.r_group.Data method) get_fused_cycles() (in module schrodinger.application.matsci.graph) get_gamut_area() (in module schrodinger.application.matsci.colorutils) get_gas_phase_zpe_key() (in module schrodinger.application.matsci.jaguarworkflows) get_gbrv_internal_folder() (in module schrodinger.application.matsci.espresso.utils) get_gbshift_for_complex_list() (in module schrodinger.application.glide_ws.merge) get_gcd_list_ints() (in module schrodinger.application.matsci.nano.xtal) get_generated_fingerprint_filename() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_generation_log_file_name() (in module schrodinger.application.matsci.genetic_optimization) get_generic_end_structure() (in module schrodinger.application.matsci.amorphous) get_gibbs_free_energy() (in module schrodinger.application.matsci.solvation_entropy_utils) get_git_hashes() (in module schrodinger.application.glide.utils) get_glibc_version() (in module schrodinger.utils.sysinfo) get_glide_job() (in module schrodinger.application.glide.job) get_global_logger() (in module schrodinger.application.matsci.textlogger) get_gluepoints() (in module schrodinger.application.desmond.cms) get_gpcrdb_url() (in module schrodinger.protein.gpcr.annotate) get_gpgpu_params() (in module schrodinger.job.jobcontrol) get_GPGPUs() (in module schrodinger.tasks.hosts) get_gpu_device_node_files() (in module schrodinger.autoinstall.infra) get_gpu_info() (in module schrodinger.autoinstall.infra) get_gpu_qarg() (in module schrodinger.application.matsci.espresso.utils) get_gradient() (in module schrodinger.application.matsci.stylemanager) get_greasy_scores() (in module schrodinger.application.glide_ws.entropy_score) get_grid_data() (schrodinger.application.desmond.cns_io.CNSData method) get_grid_parameters() (in module schrodinger.application.bindingsite.cavutils) get_grid_radius_property_values() (in module schrodinger.application.matsci.freevolume) get_group_atom_indices() (in module schrodinger.application.matsci.smartsutils) get_group_names() (in module schrodinger.application.matsci.smartsutils) get_group_numbers() (in module schrodinger.application.matsci.smartsutils) get_grow_idxs() (in module schrodinger.application.matsci.rxn_channel) get_guess() (in module schrodinger.application.matsci.mecp_mod) get_guide_atoms() (in module schrodinger.structutils.structalign2) get_h_pair_rates_from_database() (in module schrodinger.application.matsci.kmc) get_halogen_bonds() (in module schrodinger.structutils.interactions.hbond) get_handle_for_block() (in module schrodinger.structutils.block_data) get_handlers_for_key() (in module schrodinger.infra.mmkv) get_hashes() (schrodinger.active_learning.bloom_filter_methods.BuiltInBloomFilter method) get_hbond_direction() (in module schrodinger.application.bindingsite.intfield) get_hbond_params() (in module schrodinger.structutils.interactions.hbond) get_hbonds() (in module schrodinger.glide) get_hdf_io() (in module schrodinger.application.matsci.hdfutils) get_hdf_keys() (in module schrodinger.application.matsci.hdfutils) get_hdx_adapter() (in module schrodinger.application.bioluminate.pose_filtering.hdx_io) get_hdx_ms_properties() (in module schrodinger.application.bioluminate.pose_filtering.hdx_io) get_hdx_test_file() (in module schrodinger.application.bioluminate.pose_filtering.test) get_heavies() (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.histidine_changeable method) (schrodinger.protein.protassign.changeables.ligand_changeable method) (schrodinger.protein.protassign.changeables.rotatable_changeable method) (schrodinger.protein.protassign.changeables.water_changeable method) get_heavy_fv_name() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) get_heavy_light_chains() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_heavy_neighbors() (in module schrodinger.protein.assignment) (in module schrodinger.protein.protassign.changeables) get_height() (in module schrodinger.rdkit.alignment) get_helm_model_from_fasta_seq() (in module schrodinger.protein.helm) get_het_atom_numbers() (in module schrodinger.application.prepwizard) get_het_from_state() (schrodinger.protein.protassign.changeables.ligand_changeable method) get_het_name() (in module schrodinger.application.prepwizard) get_hidden_cms_file_path() (in module schrodinger.trajectory.utils) get_hkl() (in module schrodinger.application.matsci.nano.slab) get_hkl_indices() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_hmmerpath() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_home_dir() (in module schrodinger.utils.fileutils) get_host() (in module schrodinger.job.jobcontrol) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_host_by_name() (in module schrodinger.tasks.hosts) get_host_entries() (in module schrodinger.autoinstall.misc) (in module schrodinger.utils.installation_check) get_host_from_hostname() (in module schrodinger.ui.qt.config_dialog) get_host_list() (in module schrodinger.job.jobcontrol) get_host_ncpu() (in module schrodinger.active_learning.al_utils) (in module schrodinger.application.glide.utils) get_hostfile() (in module schrodinger.job.jobcontrol) get_hostid() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.utils.sysinfo) get_hostname() (in module schrodinger.autoinstall.infra) (in module schrodinger.utils.sysinfo) get_hostnames() (in module schrodinger.utils.net) get_hosts() (in module schrodinger.job.jobcontrol) (in module schrodinger.tasks.hosts) (in module schrodinger.ui.qt.config_dialog) get_hostsChanged_signal() (in module schrodinger.tasks.hosts) get_huang_rhys_fs() (in module schrodinger.application.matsci.bandshape_utils) get_hydrogen_bond_type() (in module schrodinger.application.bioluminate.protein_interaction.calculate) get_hydrogen_bonds() (in module schrodinger.infra.structure) (in module schrodinger.structutils.interactions.hbond) get_hyperbola_fit_property() (in module schrodinger.application.matsci.uq_utils) get_hyperbola_prop_from_points() (in module schrodinger.application.matsci.uq_utils) get_hyperbola_regression() (in module schrodinger.application.matsci.uq_utils) get_hypo_monitor() (in module schrodinger.application.phase.pt_hypothesis) get_hypothesis_entry_ids() (in module schrodinger.application.phase.pt_hypothesis) get_hypothesis_from_project() (in module schrodinger.application.phase.pt_hypothesis) get_icon() (in module schrodinger.ui.qt.figureoptions) (in module schrodinger.ui.qt.icons) (in module schrodinger.ui.two_d_viewer) get_icon_metadata_from_csv() (in module schrodinger.ui.qt.standard.icons.icons) get_icon_path_for_status() (in module schrodinger.application.job_monitor.job_monitor_table) get_idx_groups() (in module schrodinger.application.matsci.reaction_workflow_utils) (in module schrodinger.application.matsci.swap_fragments_utils) get_idx_groups_str() (in module schrodinger.application.matsci.swap_fragments_utils) get_idxs() (in module schrodinger.application.matsci.packmol) (in module schrodinger.application.matsci.swap_fragments_utils) get_idxs_marked_atoms() (in module schrodinger.application.matsci.swap_fragments_utils) get_idxs_str() (in module schrodinger.application.matsci.swap_fragments_utils) get_image() (in module schrodinger.active_learning.al_report) get_image_bytes() (in module schrodinger.protein.helm.image_generation) (in module schrodinger.ui.sketcher_image) get_imports() (in module schrodinger.application.matsci.codeutils) get_included_entry_ids() (in module schrodinger.project.utils) get_included_force_field_paths() (in module schrodinger.application.matsci.cgforcefield) get_included_hypotheses_ids() (in module schrodinger.application.phase.phase_markers) get_included_structures() (in module schrodinger.project.utils) get_index() (in module schrodinger.infra.structure) (schrodinger.application.canvas.r_group.TempAtom method) get_index_clusters() (in module schrodinger.protein.protassign.utils) get_index_from_default_name() (in module schrodinger.application.matsci.msutils) get_inferred_statuses() (in module schrodinger.seam.viz.inspect) get_infile_type() (in module schrodinger.application.combinatorial_diversity.driver_utils) get_input_files() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) get_input_group() (in module schrodinger.tasks.param_cli) get_input_paths() (in module schrodinger.application.transforms.autosar.config) get_inscribe_extents() (in module schrodinger.comparison.struc) get_installation_check_commands() (in module schrodinger.utils.installation_check) get_installed_hostfiles() (in module schrodinger.job.jobcontrol) get_instructions_from_yaml() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_int_tuples_from_str_property() (in module schrodinger.application.matsci.reaction_workflow_utils) get_interaction_data() (in module schrodinger.utils.pymol) get_interaction_label() (in module schrodinger.protein.protassign.pka_prediction) get_interaction_sites() (in module schrodinger.application.bindingsite.intfield) get_interface_atoms() (in module schrodinger.structutils.interactions.protein_protein_interactions) get_interface_crankshaft_backbone_atoms() (in module schrodinger.application.peptide_workflow.minimize) get_interface_kwargs() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_interface_normal() (in module schrodinger.application.matsci.msutils) get_intermediate_args() (schrodinger.application.jaguar.garza.SolvEntropyParams method) get_intermolecular_energy_and_forces() (in module schrodinger.glide) get_internal_coordinates() (schrodinger.application.jaguar.hess_guess.CoordinateManager method) get_internal_energy_info() (in module schrodinger.application.matsci.anharmonic) get_internal_energy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_internal_info() (in module schrodinger.application.matsci.coarsegrain) get_intersection() (in module schrodinger.math.multi_parameter_optimization) get_intramolecular_energy() (in module schrodinger.glide) get_inverse_reactions_by_reagent() (in module schrodinger.application.pathfinder.reaction) get_inversion_index() (in module schrodinger.application.matsci.nano.util) get_isoelectronic_mutator_indicies() (in module schrodinger.application.matsci.genetic_optimization) get_iterator() (in module schrodinger.application.matsci.msutils) get_iupacs_from_structures() (in module schrodinger.application.matsci.rdpattern) get_j_label() (schrodinger.application.jaguar.simple_spec.Peak method) get_j_summary() (schrodinger.application.jaguar.simple_spec.Peak method) get_jaguar_keywords_list() (in module schrodinger.application.matsci.reaction_workflow_utils) get_jaguar_max_atoms() (in module schrodinger.application.matsci.jaguarworkflows) get_jaguar_out_mae() (in module schrodinger.application.matsci.jaguarworkflows) get_jaguar_output() (in module schrodinger.application.matsci.jaguarworkflows) get_jaguar_solvents() (in module schrodinger.application.matsci.solvation_entropy_utils) get_jaguar_solvents_csv() (in module schrodinger.application.matsci.solvation_entropy_utils) get_jaguar_solvents_xml() (in module schrodinger.application.matsci.solvation_entropy_utils) get_job_dj() (in module schrodinger.application.glide.utils) get_job_from_hub() (in module schrodinger.application.matsci.jobutils) get_job_launch_commmand() (in module schrodinger.application.glide_ws.db) get_job_output_filenames() (in module schrodinger.application.glide.utils) get_job_spec_builder_from_args() (schrodinger.stepper.app.StepperApplication class method) get_job_spec_from_args() (in module schrodinger.active_learning.mq_driver) (in module schrodinger.active_learning.mq_worker) (in module schrodinger.application.bioluminate.antibody.assembly_yaml) (in module schrodinger.application.bioluminate.methionine_oxidation) (in module schrodinger.application.bioluminate.patch_utils.pre_analyze) (in module schrodinger.application.matsci.packmol) (schrodinger.stepper.app.StepperApplication class method) get_jobdj() (in module schrodinger.active_learning.al_node) get_jobhost() (in module schrodinger.application.matsci.jobutils) get_jobhost_name() (in module schrodinger.application.matsci.jobutils) get_jobhosts() (in module schrodinger.application.matsci.jobutils) get_jobname() (in module schrodinger.application.bb_database.bb_job_utils) (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) (in module schrodinger.application.bioluminate.methionine_oxidation) (in module schrodinger.application.combinatorial_diversity.driver_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) (in module schrodinger.application.combinatorial_screen.driver_utils) (in module schrodinger.application.glide.utils) (in module schrodinger.application.jaguar.utils) (in module schrodinger.application.matsci.jobutils) (in module schrodinger.application.matsci.parserutils) (in module schrodinger.application.phase.shape_screen_reporter.task_utils) (in module schrodinger.application.vss.tasks) (in module schrodinger.job.jobcontrol) (in module schrodinger.utils.fileutils) get_jobtype_name() (in module schrodinger.application.licensing.licadmin) get_json_formatted_structure_hierarchy() (in module schrodinger.livedesign.bbchem_endpoints) (in module schrodinger.livedesign.sh_utils) get_json_from_map_file() (in module schrodinger.utils.documentation) get_json_version_from_file() (in module schrodinger.models.json) get_json_version_from_string() (in module schrodinger.models.json) get_keep_idxs() (in module schrodinger.application.matsci.swap_fragments_utils) get_kekule_smiles() (in module schrodinger.application.pathfinder.route) get_keq() (in module schrodinger.application.matsci.reaction_workflow_utils) get_kernel_version() (in module schrodinger.utils.sysinfo) get_key_files() (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.bb_database.bb_job_utils) get_key_limits() (in module schrodinger.application.bb_database.bb_task_utils) get_key_name() (in module schrodinger.application.licensing.licadmin) get_keyword() (in module schrodinger.application.glide.specs) get_keywords_dicts() (in module schrodinger.application.glide.specs) get_keywords_set() (in module schrodinger.application.glide.specs) get_label() (in module schrodinger.application.bioluminate.peptide_sar.label) get_labeled_scores() (in module schrodinger.application.bioluminate.peptide_sar.sar) get_ladder_polymer_relaxation_stringers() (in module schrodinger.application.matsci.desconfig) get_lambda_atom_indices() (schrodinger.application.desmond.cms.Cms method) get_largest_moment_normalized_vector() (in module schrodinger.structutils.analyze) get_last_20_lines() (in module schrodinger.pipeline.pipeutils) get_last_exception() (in module schrodinger.utils.qt_utils) get_last_selected_directory() (in module schrodinger.ui.qt.filedialog) get_lattice_param_properties() (in module schrodinger.application.matsci.nano.xtal) get_lattice_properties() (in module schrodinger.application.matsci.nano.particle) get_lattice_vectors() (in module schrodinger.application.matsci.nano.sheet) (in module schrodinger.application.matsci.nano.xtal) get_launch_command_from_args() (in module schrodinger.job.jobcontrol) get_launch_command_without_toplevel() (in module schrodinger.job.jobcontrol) get_launch_path() (in module schrodinger.utils.fileutils) get_ld_client() (in module schrodinger.application.livedesign.login) get_ld_library_path_for_system_ssh() (in module schrodinger.utils.env) get_LD_mode() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_LD_similarity_score() (in module schrodinger.livedesign.cmdline) get_LD_version() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_ldclient_download_dir() (in module schrodinger.application.livedesign.login) get_ldclient_enums() (in module schrodinger.application.livedesign.login) get_ldclient_models() (in module schrodinger.application.livedesign.login) get_ldclient_requests() (in module schrodinger.application.livedesign.login) get_ldclient_responses() (in module schrodinger.application.livedesign.login) get_lead_confs() (in module schrodinger.application.macromodel.apps) get_leaf_transforms() (in module schrodinger.seam.viz.inspect) get_leg_name_from_jobname() (in module schrodinger.application.desmond.util) get_leg_type_from_jobname() (in module schrodinger.application.desmond.util) get_legal_name() (schrodinger.utils.pymol.PymolInstance method) get_lib_dir() (in module schrodinger.utils.postinstall) get_libpath() (in module schrodinger.application.pathfinder.reaction) get_libstdcpp_version() (in module schrodinger.utils.installation_check) get_license() (in module schrodinger.application.canvas.utils) get_license_request_info() (in module schrodinger.application.licensing.netsuiteapi) get_license_sources() (in module schrodinger.application.licensing.licserver.client) get_licenses() (in module schrodinger.seam.viz.inspect) get_licserverd_from_slm_installation() (in module schrodinger.application.licensing.licserver.quick_slm_setup) get_lictool_from_slm_installation() (in module schrodinger.application.licensing.licserver.quick_slm_setup) get_ligand() (in module schrodinger.ui.qt.structure2d) get_ligand_atom_indices() (in module schrodinger.protein.protassign.changeables) get_ligand_fragments() (in module schrodinger.application.desmond.packages.analysis) get_ligand_interactors() (in module schrodinger.protein.protassign.changeables) get_ligand_ml_metric() (in module schrodinger.active_learning.al_report) get_ligand_name() (in module schrodinger.application.matsci.buildcomplex) get_ligand_parameters() (in module schrodinger.infra.mm) get_ligand_rmsd() (in module schrodinger.application.desmond.util) get_ligand_summary_rows() (in module schrodinger.application.glide_ws.db_queries) get_ligandfiles_reader() (in module schrodinger.application.glide.utils) get_ligands() (in module schrodinger.application.livedesign.entry_types) get_ligands_info() (in module schrodinger.application.matsci.buildcomplex) get_ligfile_fields() (in module schrodinger.application.glide.csv_utils) get_light_fv_name() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) get_lignum_ranges() (in module schrodinger.application.glide.runner) get_ligprep_command() (in module schrodinger.application.vss.tasks) get_ligprep_files() (in module schrodinger.application.glide.utils) get_ligprep_parser() (in module schrodinger.application.glide.utils) get_limit_for_export_mode() (in module schrodinger.application.pymol.export_handler) get_limited_sanitized_mol() (in module schrodinger.livedesign.preprocessor) get_linked_path() (in module schrodinger.application.licensing.flexlm) get_lnq_key() (in module schrodinger.application.matsci.jaguarworkflows) get_lnQtot() (in module schrodinger.application.matsci.solvation_entropy_utils) get_lnQtot_info() (in module schrodinger.application.matsci.anharmonic) get_lnQvib_info() (in module schrodinger.application.matsci.anharmonic) get_local_appdata_dir() (in module schrodinger.utils.fileutils) get_local_gpgpus() (in module schrodinger.infra.gpgpu_utils) get_local_server() (in module schrodinger.application.licensing.licadmin) get_localhost_temp_dir() (in module schrodinger.infra.mm) get_lock() (in module schrodinger.application.pathfinder.multiroute) get_log_filename() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_logd_from_epik() (in module schrodinger.application.livedesign.ld_alogD_utils) get_loggable_float() (in module schrodinger.application.matsci.genetic_optimization) get_logger() (in module schrodinger.application.peptide_workflow.log) (in module schrodinger.autoinstall.misc) (in module schrodinger.utils.log) get_loggerstates() (in module schrodinger.rdkit.rdkit_adapter) get_logging_tag() (in module schrodinger.application.matsci.jobutils) get_long_family_name() (in module schrodinger.application.livedesign.data_classes) get_loop_instructions() (schrodinger.application.bioluminate.antibody.grafting.GraftingInput method) get_loop_ranges() (in module schrodinger.application.bioluminate.anarci.loop_ranges) get_low_energy_conformers() (in module schrodinger.application.matsci.genetic_optimization) get_low_energy_reps() (in module schrodinger.structutils.analyze) get_lscore() (in module schrodinger.application.glide_ws.entropy_score) get_luma() (in module schrodinger.ui.qt.standard.colors) get_machid_output() (in module schrodinger.application.licensing.licadmin) get_macro() (in module schrodinger.application.jaguar.user_config) (schrodinger.application.jaguar.keywordDB.Keyword method) (schrodinger.application.jaguar.keywordDB.Setting method) get_macro_dict() (in module schrodinger.utils.sea.sea) get_maestro() (in module schrodinger) get_maestro_find_toolbar_layout() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_maestro_forcefield_selector() (in module schrodinger.ui.qt.forcefield.ffselector) get_maestro_params() (in module schrodinger.structutils.interactions.hbond) get_maestro_scripts_path() (in module schrodinger.utils.maestro_scripts_path) get_maestro_view_settings() (in module schrodinger.application.pymol.mae_sync) get_maestrox_colors() (in module schrodinger.ui.qt.standard.colors) get_mag_hubbu() (in module schrodinger.application.matsci.espresso.utils) get_major_cuda_version() (in module schrodinger.autoinstall.infra) get_map_model_to_template() (in module schrodinger.application.bioluminate.antibody.assembly) get_map_rdk_to_sdgr() (in module schrodinger.rdkit.rdkit_adapter) get_map_sdgr_to_rdk() (in module schrodinger.rdkit.rdkit_adapter) get_mappings() (in module schrodinger.comparison.struc) get_marked_func_order() (in module schrodinger.utils.funcgroups) get_marker_atom_indexes_from_structure() (in module schrodinger.application.matsci.buildcomplex) get_marker_color() (schrodinger.ui.qt.rama.RamaScatterMixin method) get_martini_antifreeze_type_from_type() (in module schrodinger.application.matsci.coarsegrain) get_martini_bond_force_constant() (in module schrodinger.application.matsci.coarsegrain) get_martini_epsilon() (in module schrodinger.application.matsci.coarsegrain) get_martini_eq_length() (in module schrodinger.application.matsci.coarsegrain) get_martini_ring_type_from_type() (in module schrodinger.application.matsci.coarsegrain) get_martini_sigma() (in module schrodinger.application.matsci.coarsegrain) get_martini_subtypes() (in module schrodinger.application.matsci.coarsegrain) get_martini_tiny_type_from_type() (in module schrodinger.application.matsci.coarsegrain) get_martini_type_from_super_type() (in module schrodinger.application.matsci.coarsegrain) get_mask_name() (in module schrodinger.application.phase.phase_markers) get_mass() (in module schrodinger.application.matsci.coarsegrain) (schrodinger.application.desmond.cms.Cms method) get_matching_arm() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_matching_chains() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_matching_domain() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_matching_ws_atoms() (in module schrodinger.application.bioluminate.pml_menus) get_matching_ws_entries() (in module schrodinger.application.bioluminate.pml_menus) get_materials_relaxation_stringers() (in module schrodinger.application.matsci.desconfig) get_matplotlib_toolbar_message() (in module schrodinger.application.matsci.gutils) get_matrix_value() (in module schrodinger.protein.residue) get_matsci_module_graph() (in module schrodinger.application.matsci.codeutils) get_matsci_module_paths() (in module schrodinger.application.matsci.codeutils) get_matsci_user_data_dir() (in module schrodinger.application.matsci.msutils) get_max_and_rms_and_len() (in module schrodinger.application.matsci.mecp_mod) get_max_batch_size() (in module schrodinger.application.glide.sort_utils) get_max_chem_valencies() (in module schrodinger.application.matsci.elementalprops) get_max_chem_valencies_with_exceptions() (in module schrodinger.application.matsci.elementalprops) get_max_cov_radius() (in module schrodinger.application.matsci.nano.xtal) get_max_cuda_cores() (in module schrodinger.autoinstall.misc) get_max_distance_btw_groups() (in module schrodinger.application.matsci.packmol) get_max_height() (schrodinger.application.jaguar.simple_spec.Peak method) get_max_layer_index() (in module schrodinger.application.matsci.device_formulations) get_max_open_files() (in module schrodinger.active_learning.al_utils) get_max_ppm() (schrodinger.application.jaguar.simple_spec.Peak method) get_max_torsion_deviation() (in module schrodinger.comparison.struc) get_max_valencies() (in module schrodinger.application.matsci.elementalprops) get_maximum_vdw_radius() (in module schrodinger.application.matsci.amorphous) get_mcs_atoms() (in module schrodinger.ui.two_d_viewer) get_md5_coord_hash_for_structure() (in module schrodinger.application.glide_ws.db) get_md5_sum() (in module schrodinger.application.glide_ws.db) get_md_results() (in module schrodinger.application.matsci.equilibrium_md) get_measurement_items() (in module schrodinger.utils.pymol) get_MEL_class() (in module schrodinger.application.pathfinder.reaction) get_membrane_cts() (schrodinger.application.desmond.cms.Cms method) get_metals_and_neighbors() (in module schrodinger.structutils.rgroup_enumerate) get_methionines() (in module schrodinger.application.bioluminate.methionine_oxidation) get_metrics_from_events() (in module schrodinger.seam.viz.inspect) get_mhc_class() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_mhc_vectors() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_mig_info() (schrodinger.gpgpu.CudaDevice method) get_min_max_avg() (in module schrodinger.application.matsci.uq_utils) get_min_ppm() (schrodinger.application.jaguar.simple_spec.Peak method) get_minimum_nvml_driver() (in module schrodinger.gpgpu) get_missed_atom_id_groups() (in module schrodinger.application.matsci.amorphous) get_missing_columns() (in module schrodinger.application.bioluminate.pose_filtering.hdx_io) get_ml_features() (in module schrodinger.application.glide_ws.ml_featurizer) get_mlff_defaults() (in module schrodinger.application.matsci.parserutils) get_mlff_support() (in module schrodinger.application.jaguar.workflow_validation) get_mmct_max_valencies() (in module schrodinger.application.matsci.elementalprops) get_mmgbsa_corrected_wscore() (in module schrodinger.application.glide_ws.entropy_score) get_mmgbsa_parent_obj() (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) get_mmlewis_bonding() (in module schrodinger.application.jaguar.autots_bonding) get_mmod_energy_key() (in module schrodinger.application.matsci.reaction_workflow_utils) get_mmod_energy_keys() (in module schrodinger.application.matsci.reaction_workflow_utils) get_mmod_rel_energy_key() (in module schrodinger.application.matsci.reaction_workflow_utils) get_mmshare_common_dir() (in module schrodinger.utils.fileutils) get_mmshare_data_dir() (in module schrodinger.utils.fileutils) get_mmshare_data_directory() (in module schrodinger.infra.mm) get_mmshare_dir() (in module schrodinger.utils.fileutils) get_mmshare_listing() (in module schrodinger.application.licensing.licadmin) get_mmshare_reagent_data_dir() (in module schrodinger.application.pathfinder.reaction) get_mmshare_scripts_dir() (in module schrodinger.utils.fileutils) get_mmshare_version() (in module schrodinger) get_mode_for_search_option() (in module schrodinger.maestro_utils.find_tool_bar.constants) get_model() (in module schrodinger.application.matsci.equilibrium_md) get_model_by_name() (in module schrodinger.application.livedesign.upload_utils) get_model_ff_name() (in module schrodinger.application.matsci.desmondutils) get_model_output_file() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) get_model_system_type() (in module schrodinger.application.desmond.cms) get_models_from_optimizer_output() (in module schrodinger.application.glide_ws.model) get_module_docstring() (in module schrodinger.utils.install_scripts) get_module_from_path() (in module schrodinger.utils.imputils) get_mol() (in module schrodinger.rdkit.molio) get_mol_ids() (in module schrodinger.application.glide.utils) (schrodinger.utils.multifpfile.MultiFPFile method) get_mol_layers() (in module schrodinger.rdkit_extensions) get_mol_reader() (in module schrodinger.rdkit.molio) get_mol_writer() (in module schrodinger.rdkit.molio) get_molecular_formula() (in module schrodinger.application.matsci.species) get_molecular_weight() (in module schrodinger.application.matsci.msutils) (in module schrodinger.application.matsci.reaction_workflow_utils) get_molecule_color() (in module schrodinger.application.matsci.cg_mapping) get_molecules_pseudos() (in module schrodinger.application.matsci.desmondutils) get_monomer_data() (in module schrodinger.livedesign.biologics.sequence) get_mopfile_text() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) get_moved() (in module schrodinger.models.diffy) get_moved_list() (in module schrodinger.models.diffy) get_mpircores() (in module schrodinger.application.matsci.espresso.utils) get_mpl_backend_name() (in module schrodinger) get_msd_infos() (in module schrodinger.application.matsci.kmc) get_msg() (in module schrodinger.application.matsci.reaction_workflow_enum_utils) get_msj_filename() (in module schrodinger.application.desmond.util) get_multiplicity() (in module schrodinger.application.jaguar.utils) get_multisim_command() (in module schrodinger.application.matsci.desmondutils) get_muscle_path() (in module schrodinger.protein.tasks.muscle) get_mutate_to_filename() (in module schrodinger.protein.nonstandard_residues) get_mutation_encoding() (in module schrodinger.application.bioluminate.peptide_sar.encode) get_mwc_to_nm_transform() (in module schrodinger.application.matsci.bandshape_utils) get_mydocuments_dir() (in module schrodinger.utils.fileutils) get_mynetworkplaces_dir() (in module schrodinger.utils.fileutils) get_name() (schrodinger.infra.mmcheck.ReturnCode method) get_name_element_mapper_cg() (in module schrodinger.application.matsci.rdpattern) get_name_file() (in module schrodinger.application.jaguar.input) get_name_filter() (in module schrodinger.utils.fileutils) get_name_w_mol_n() (in module schrodinger.application.matsci.order_parameter_mod) get_name_wo_mol_n() (in module schrodinger.application.matsci.order_parameter_mod) get_names() (in module schrodinger.application.matsci.coarsegrain) get_natom_btw_two_cells() (in module schrodinger.application.matsci.nano.xtal) get_natural_analog() (in module schrodinger.protein.helm.helm_renderer) get_natural_analog_map() (in module schrodinger.protein.process_enamine_db) get_nearest_image() (in module schrodinger.application.matsci.pbcutils) get_neighboring_atom_distances() (in module schrodinger.application.bioluminate.protein_interaction.calculate) get_netsuite_license() (in module schrodinger.application.licensing.licadmin) get_network_info() (in module schrodinger.application.licensing.licadmin) get_neutralization_patterns() (in module schrodinger.application.pathfinder.synthesis) get_new_filename() (in module schrodinger.application.vss.tasks) get_new_index() (schrodinger.protein.protassign.changeables.changeable method) get_next_filename() (in module schrodinger.utils.fileutils) get_next_filename_prefix() (in module schrodinger.utils.fileutils) get_next_jobname() (in module schrodinger.ui.qt.appframework) (in module schrodinger.ui.qt.appframework2.jobnames) get_next_name() (in module schrodinger.application.matsci.msutils) get_next_unused_arm_index() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_niggli_params() (in module schrodinger.comparison.struc) get_nmr() (in module schrodinger.application.jaguar.textparser) get_nmr_shifts() (in module schrodinger.application.jaguar.textparser) get_nonbond_potential_type() (in module schrodinger.application.matsci.coarsegrain) get_noncovalent_ligands() (in module schrodinger.protein.assignment) get_nondefault_features() (in module schrodinger.utils.featureflags.featureflags) get_nonduplicated_atom() (in module schrodinger.application.desmond.remd) get_nonzero_data() (in module schrodinger.application.matsci.uq_utils) get_normal_modes() (in module schrodinger.application.matsci.anharmonic) get_normal_surf() (in module schrodinger.application.matsci.nano.xtal) get_normal_surf_from_HKL() (in module schrodinger.application.matsci.nano.xtal) get_normal_vector_to_three_points() (in module schrodinger.infra.mm) get_normalized() (in module schrodinger.graphics3d.common) get_normalized_spanning_vectors() (in module schrodinger.application.matsci.nano.xtal) get_normalized_vector() (in module schrodinger.structutils.transform) get_npseudos_per_molecule() (in module schrodinger.application.matsci.desmondutils) get_nucleotide_dihedrals() (in module schrodinger.trajectory.trajectory_gui_dir.custom_analyzers) get_null_job() (in module schrodinger.application.job_monitor.job_monitor_models) get_null_mag_element() (in module schrodinger.application.matsci.espresso.utils) get_num_aromatic_rings() (schrodinger.infra.canvas.ChmProfiler static method) get_num_clashes_with_metals() (in module schrodinger.application.prepwizard) get_num_constraint() (in module schrodinger.application.desmond.remd) (schrodinger.application.desmond.cms.Cms method) get_num_license_tokens() (in module schrodinger.application.combinatorial_screen.driver_utils) get_num_missing_data() (in module schrodinger.application.matsci.kmc) get_num_nonwateratom() (in module schrodinger.application.desmond.remd) get_num_nprocs() (in module schrodinger.ui.qt.config_dialog) get_num_rotatable_bonds() (in module schrodinger.structutils.analyze) (schrodinger.infra.canvas.ChmProfiler static method) get_num_simple_bonds() (in module schrodinger.application.matsci.genetic_optimization) get_num_wateratom() (in module schrodinger.application.desmond.remd) get_number_electrons() (in module schrodinger.application.jaguar.utils) get_numbering_scheme_args() (in module schrodinger.application.bioluminate.anarci.annotate) get_numbering_scheme_from_arg_str() (in module schrodinger.application.bioluminate.anarci.annotate) get_numbers_by_region_name() (in module schrodinger.application.bioluminate.anarci.annotate) get_numeric_operator() (in module schrodinger.application.bioluminate.pose_filtering.operators) get_numeric_operators_by_name() (in module schrodinger.application.bioluminate.pose_filtering.operators) get_numeric_property_range() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) get_obj_value() (in module schrodinger.ui.qt.appframework2.settings) get_old2new() (in module schrodinger.application.desmond.torsion_related) get_oled_layer_color() (in module schrodinger.application.matsci.device_formulations) get_one_step_route() (in module schrodinger.application.pathfinder.synthesis) get_op_trans_idx() (in module schrodinger.comparison.struc) get_open_file_name() (in module schrodinger.ui.qt.filedialog) (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog static method) get_open_file_names() (in module schrodinger.ui.qt.filedialog) (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog static method) get_open_wm_file_name() (in module schrodinger.ui.qt.filedialog) get_openmpi_env() (in module schrodinger.utils.openmpi) get_openmpi_prefix() (in module schrodinger.utils.openmpi) get_OPLS_data_filename() (in module schrodinger.infra.mm) get_OPLS_data_subdirectory() (in module schrodinger.infra.mm) get_opls_dir() (in module schrodinger.utils.cmdline) get_opls_metadata_compatibility() (in module schrodinger.infra.mm) get_opls_version_display_name() (in module schrodinger.ui.qt.forcefield.forcefield) get_optimal_atom_mapping() (in module schrodinger.structutils.rmsd) get_option() (in module schrodinger.application.matsci.jobutils) (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method) get_ordered_backbone_atoms() (in module schrodinger.application.matsci.geometry) get_ordered_polymer_backbone() (in module schrodinger.application.matsci.geometry) get_orig_atom_idx() (in module schrodinger.application.matsci.amorphous) get_orig_seq_name() (in module schrodinger.protein.tasks.structure_alignment) get_orig_title() (in module schrodinger.application.matsci.reaction_workflow_utils) get_orthant_strings() (in module schrodinger.application.combinatorial_diversity.splitter_utils) get_os_info() (in module schrodinger.autoinstall.infra) get_osname() (in module schrodinger.utils.sysinfo) get_other_item() (in module schrodinger.application.matsci.amorphous) get_other_reactive_indexes() (in module schrodinger.application.matsci.msprops) get_out_file_paths() (in module schrodinger.application.matsci.bandshape_utils) get_out_filename() (in module schrodinger.application.bioluminate.anarci.annotate) get_out_mae_path() (in module schrodinger.application.matsci.jaguarworkflows) get_out_rep() (in module schrodinger.application.matsci.reaction_workflow_utils) get_outer_box_length() (in module schrodinger.application.transforms.dockers.box) get_outfile_name() (in module schrodinger.livedesign.biologics.modeling) get_output_file_name() (in module schrodinger.application.glide.utils) (in module schrodinger.application.matsci.genetic_optimization) get_output_filename() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_output_files() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_output_logger() (in module schrodinger.utils.log) get_output_logger_handler() (in module schrodinger.utils.log) get_output_paths() (in module schrodinger.application.transforms.autosar.config) get_output_writer() (in module schrodinger.application.pathfinder.multiroute) get_overlap_dim() (in module schrodinger.application.jaguar.output) get_overlapping_atoms() (in module schrodinger.application.prepwizard2.diagnostics) get_pair_info() (in module schrodinger.application.matsci.kmc) get_pair_rates_from_database() (in module schrodinger.application.matsci.kmc) get_pairs_from_database() (in module schrodinger.application.matsci.kmc) get_pairs_table() (in module schrodinger.application.matsci.kmc) get_pairwise_sequence_similarity() (in module schrodinger.protein.sequence) get_parallelepiped_vertices() (in module schrodinger.application.matsci.shapes) get_param_string() (in module schrodinger.application.matsci.textlogger) get_params_from_chorus() (in module schrodinger.application.matsci.nano.xtal) get_params_from_vectors() (in module schrodinger.application.matsci.nano.xtal) get_parser() (in module schrodinger.active_learning.mq_driver) (in module schrodinger.application.bb_database.bb_arg_utils) (in module schrodinger.application.combinatorial_diversity.driver_utils) (in module schrodinger.application.combinatorial_explorer.driver_utils) (in module schrodinger.application.combinatorial_screen.driver_utils) (in module schrodinger.application.licensing.licserver.main) (in module schrodinger.application.matsci.packmol) (in module schrodinger.application.matsci.vsepr) (in module schrodinger.application.phase.shape_screen_reporter.option_utils) (in module schrodinger.seam.testing.preemption) (in module schrodinger.seam.viz.watcher) (in module schrodinger.seam.viz.watcherd) get_partial_parser() (in module schrodinger.application.peptide_workflow.driver_utils) get_password() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_patch_info() (in module schrodinger.tasks.remote_modules) get_path_from_module() (in module schrodinger.utils.imputils) get_pattern() (in module schrodinger.application.matsci.rdpattern) (schrodinger.application.matsci.xrd.XRDCalculator method) get_pbc() (in module schrodinger.structutils.pbc_tools) (schrodinger.infra.structure.PBC static method) get_pbc_bonded_atom_pairs() (in module schrodinger.application.matsci.nano.xtal) get_pbc_bonds_dict() (in module schrodinger.application.matsci.nano.xtal) get_pbc_origin() (in module schrodinger.application.matsci.nano.xtal) get_pcoll_type() (in module schrodinger.seam.viz.inspect) get_pdb() (in module schrodinger.protein.getpdb) get_pdb_data() (in module schrodinger.application.matsci.packmol) get_pdb_id() (in module schrodinger.application.prepwizard) get_pdb_protein_bfactor() (in module schrodinger.application.desmond.packages.analysis) get_penalty() (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) get_percent_screen_curve_points() (in module schrodinger.analysis.enrichment.plotter) get_persistent_value() (in module schrodinger.ui.qt.appframework2.settings) get_perspective() (in module schrodinger.application.pymol.mae_sync) get_perturbed_indices() (schrodinger.application.matsci.elasticity.strain.Deformation method) get_pfx_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_pfx_size() (in module schrodinger.rdkit.molio) get_pH_population_factors() (schrodinger.application.jaguar.macro_pka_utils.PhPopulations method) get_phase_markers() (in module schrodinger.application.phase.phase_markers) get_physical_properties() (in module schrodinger.application.matsci.nano.xtal) get_pi_cation_interactions() (in module schrodinger.infra.structure) get_pi_pi_interactions() (in module schrodinger.infra.structure) get_picked() (schrodinger.ui.qt.rama.Rama method) get_picture_as_text() (in module schrodinger.ui.qt.swidgets) get_pipeline_info() (in module schrodinger.seam.viz.inspect) get_pipeline_start_time() (in module schrodinger.seam.viz.inspect) get_pka() (in module schrodinger.protein.protassign.pka_prediction) get_pkeywords() (in module schrodinger.application.matsci.espresso.utils) get_plane_alignment_angle() (in module schrodinger.application.jaguar.utils) get_plane_trans_cart_to_frac() (in module schrodinger.application.matsci.desconfig) get_platform_incompatibility_message() (in module schrodinger.utils.platform) get_player_toolbar() (in module schrodinger.trajectory.trajectoryviewer) get_plot_data() (in module schrodinger.analysis.enrichment.plotter) get_plottable_table_data() (in module schrodinger.application.matsci.kmcgui) get_pointgroup_symmetry_ops() (in module schrodinger.comparison.struc) get_points_in_region() (in module schrodinger.application.matsci.uq_utils) get_polygon_area() (in module schrodinger.application.matsci.shapes) get_polymer_annotations() (in module schrodinger.livedesign.biologics.sequence) get_populations_at_pH() (schrodinger.application.jaguar.macro_pka_utils.PhPopulations method) get_portnum() (in module schrodinger.tasks.taskszmq) get_pos_vel() (schrodinger.application.desmond.cms.Cms method) get_pose_data() (in module schrodinger.application.glide_ws.ml_featurizer) get_postmortem_command() (in module schrodinger.utils.installation_check) get_potential() (schrodinger.application.desmond.torsion_related.TorsionPotential method) get_potential_alignment() (in module schrodinger.comparison.struc) get_powder_diffraction_pattern() (in module schrodinger.application.matsci.spectra) get_ppdb() (in module schrodinger.application.matsci.espresso.ppdb) get_preference() (in module schrodinger.utils.preferences) get_preference_custom_opls_path() (in module schrodinger.infra.mm) get_preference_handler() (in module schrodinger.ui.qt.appframework2.settings) get_preference_most_recent_custom_opls_paths() (in module schrodinger.infra.mm) get_preference_opls_version() (in module schrodinger.infra.mm) get_preference_use_custom_opls() (in module schrodinger.infra.mm) get_pressure() (in module schrodinger.application.matsci.jaguarworkflows) get_pressure_str() (in module schrodinger.application.matsci.jaguarworkflows) get_pretty_geom_str() (in module schrodinger.application.matsci.buildcomplex) get_prevent_chirality_flip_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_primitive_cell() (in module schrodinger.application.matsci.nano.xtal) get_prob_from_temp_ladder() (in module schrodinger.application.desmond.remd) get_problems() (in module schrodinger.application.prepwizard2.diagnostics) get_procs() (in module schrodinger.application.matsci.jobutils) get_producing_transform() (in module schrodinger.seam.viz.inspect) get_product() (in module schrodinger.application.licensing.licadmin) get_product_description() (in module schrodinger.utils.machid) get_product_git_hashes() (in module schrodinger.utils.machid) get_product_info() (in module schrodinger.application.desmond.util) get_product_name() (in module schrodinger.application.glide.utils) get_profile_name_key() (in module schrodinger.utils.documentation) get_project_group_hierarchy() (in module schrodinger.application.matsci.msutils) get_project_preference_custom_opls_path() (in module schrodinger.ui.qt.forcefield.forcefield) get_prop() (in module schrodinger.application.glide.csv_utils) (in module schrodinger.application.glide.xpdes) (in module schrodinger.application.glide_ws.entropy_score) get_prop_from_datablock() (in module schrodinger.application.glide_ws.entropy_score) get_prop_idx() (in module schrodinger.application.glide.xpdes) get_prop_list() (schrodinger.application.canvas.r_group.Data method) get_prop_name_to_display_name_map() (in module schrodinger.protein.properties) get_prop_type() (in module schrodinger.application.glide_ws.scoring_report) get_prop_values() (schrodinger.application.canvas.r_group.Data method) get_properties() (in module schrodinger.application.livedesign.ld_utils) get_properties_datanames_from_entry_data() (in module schrodinger.application.livedesign.ld_utils) get_properties_from_inputfiles() (in module schrodinger.application.matsci.permittivity) get_properties_with_negative_values() (in module schrodinger.application.transforms.autosar.util) get_property() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport static method) get_property_dataframe() (in module schrodinger.application.glide.visualization) get_property_info() (in module schrodinger.application.matsci.genetic_optimization) get_property_keys_from_keywords() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) get_property_strings() (in module schrodinger.ui.two_d_viewer) get_property_type() (in module schrodinger.application.combinatorial_diversity.driver_utils) (in module schrodinger.infra.structure) get_property_value() (in module schrodinger.application.livedesign.ld_utils) get_props() (in module schrodinger.application.glide.csv_utils) (in module schrodinger.application.glide_ws.entropy_score) get_props_from_datablock() (in module schrodinger.application.glide_ws.entropy_score) get_protein_alphabet() (in module schrodinger.protein.residue) get_protein_families() (in module schrodinger.protein.gpcr.gpcrdb) get_protein_family() (in module schrodinger.application.bioluminate.classify) get_protein_family_data() (in module schrodinger.application.bioluminate.classify) get_providers() (in module schrodinger.seam.yaml.generate_yaml_docs) (in module schrodinger.seam.yaml.providers) get_proxy_periodic_table() (in module schrodinger.rdkit.coarsegrain) get_pseudochirality() (in module schrodinger.comparison.chirality) get_PT() (in module schrodinger.project.utils) get_ptensor_from_plugin() (in module schrodinger.application.matsci.desmondutils) get_ptensor_from_trj() (in module schrodinger.application.matsci.desmondutils) get_public_class_tokens_by_name() (in module schrodinger.ui.qt.standard.design_tokens) get_public_databases() (in module schrodinger.application.fpsim) get_pv_file_merged_structures() (in module schrodinger.application.glide.poseviewconvert) get_pyatom_from_cppatom() (in module schrodinger.structure) get_pymatgen_mol() (in module schrodinger.comparison.struc) get_pymatgen_structure() (in module schrodinger.application.matsci.pmgutils) get_pymol_cmd() (in module schrodinger.livedesign.pymol_image) (in module schrodinger.utils.fileutils) get_pymol_location_preference() (in module schrodinger.application.pymol.utils) get_pymol_scripts_dir() (in module schrodinger.application.pymol.utils) get_python_versions() (in module schrodinger.application.matsci.gsas.GSASIIfiles) get_qimage() (in module schrodinger.ui.sketcher_image) get_qpicture() (in module schrodinger.ui.sketcher_image) get_qpicture_highlight() (in module schrodinger.ui.qt.structure2d) get_qpicture_protected() (in module schrodinger.ui.qt.structure2d) get_qrnn_mlff_support() (in module schrodinger.application.jaguar.workflow_validation) get_qrnn_support() (in module schrodinger.application.jaguar.workflow_validation) get_query_job_config() (in module schrodinger.application.fragment_virtual_screening.bq_query_task) get_query_url() (in module schrodinger.maestro_utils.composer_agent.request_manager.urls) get_r_group_for_atom() (schrodinger.application.canvas.r_group.Data method) get_r_groups() (schrodinger.application.canvas.r_group.Data method) get_r_groups_per_atom() (schrodinger.application.canvas.r_group.Data method) get_radial_count() (in module schrodinger.comparison.struc) get_random_csearch_seed() (in module schrodinger.application.matsci.genetic_optimization) get_random_nonzero_to_one() (in module schrodinger.application.matsci.amorphous) get_random_structure() (in module schrodinger.application.matsci.genetic_optimization) get_ranged_float_typer() (in module schrodinger.application.matsci.parserutils) get_ranged_int_typer() (in module schrodinger.application.matsci.parserutils) get_rate() (in module schrodinger.math.multi_parameter_optimization) get_raw_csv_filenames() (in module schrodinger.application.glide.utils) get_raw_file_name() (in module schrodinger.application.glide.utils) get_raw_user_labels() (in module schrodinger.seam.viz.inspect) get_raw_wscores() (in module schrodinger.application.glide_ws.entropy_score) get_rb_potential() (in module schrodinger.application.desmond.torsion_related) get_rb_torsions_potential() (in module schrodinger.application.desmond.torsion_related) get_rdkit_atoms() (in module schrodinger.application.matsci.smartsutils) get_rdkit_mol() (in module schrodinger.active_learning.scaffold_methods) get_rdmol() (in module schrodinger.livedesign.custom_entity.registration) get_rdmol_for_labels() (in module schrodinger.ui.two_d_viewer) get_reactant_classes_from_routes() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_reactant_combo_sim() (in module schrodinger.application.combinatorial_screen.fingerprint_utils) get_reactant_files() (in module schrodinger.application.combinatorial_screen.driver_utils) get_reactions() (in module schrodinger.application.pathfinder.reaction) get_reactions_data() (in module schrodinger.application.matsci.reaction_workflow_utils) get_readable_cmd_list() (in module schrodinger.ui.qt.appframework2.af2) get_reader() (in module schrodinger.application.bioluminate.antibody.io.csv_reader) (in module schrodinger.application.glide_ws.merge) (in module schrodinger.pipeline.pipeutils) (schrodinger.application.glide_ws.nodes.SPDecoysNode method) get_reagent_sources() (in module schrodinger.application.pathfinder.synthesis) get_recep_structure_from_grid() (in module schrodinger.application.glide.grid) get_receptor_centroid() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_receptor_disulfide_axis() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_receptor_info() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_receptor_interdomain_axis() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_reciprocal_lattice_vectors() (in module schrodinger.application.matsci.nano.xtal) get_reduced_density_from_cutoff() (in module schrodinger.application.matsci.cgforcefield) get_reduced_smiles() (in module schrodinger.application.desmond.struc) get_ref_mhc_file_path() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_ref_nov_close_pairs() (in module schrodinger.application.matsci.swap_fragments_utils) get_reference_ct() (in module schrodinger.application.desmond.struc) get_reference_data() (in module schrodinger.application.matsci.shapes) get_refined_filename() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_reflection_matrix() (in module schrodinger.structutils.transform) get_reflig() (in module schrodinger.application.glide.http_server) (schrodinger.application.glide.client_module.GlideClientModule method) get_regex_patterns_of_lines_to_skip() (in module schrodinger.utils.compare) get_region_bounds() (in module schrodinger.application.bioluminate.anarci.annotate) get_region_lengths() (in module schrodinger.application.bioluminate.anarci.annotate) get_region_to_replace() (in module schrodinger.application.bioluminate.antibody.assembly) get_registration_data() (in module schrodinger.livedesign.biologics.registration) (in module schrodinger.livedesign.custom_entity.registration) (in module schrodinger.livedesign.md.registration) (in module schrodinger.livedesign.registration) get_release_name() (in module schrodinger) get_remote_gpgpus() (in module schrodinger.infra.gpgpu_utils) get_remote_path() (in module schrodinger.job.remote_command) get_remote_registered_jobservers() (in module schrodinger.application.jobserver_cert_gui_dir.utils) get_removed() (in module schrodinger.models.diffy) get_removed_dict() (in module schrodinger.models.diffy) get_removed_list() (in module schrodinger.models.diffy) get_removed_set() (in module schrodinger.models.diffy) get_rep_confs() (in module schrodinger.application.macromodel.apps) get_rep_stage_idx() (in module schrodinger.application.matsci.reaction_workflow_utils) get_replica_exchange_stage_number() (in module schrodinger.application.desmond.util) get_report_maker() (in module schrodinger.active_learning.al_report) get_representatives() (in module schrodinger.application.matsci.boltzmann_avg_props) get_requested_seqs_by_chain_type() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) get_requirements_url() (in module schrodinger.utils.installation_check) get_res_ct_and_atom_idx() (in module schrodinger.application.desmond.struc) get_res_data_from_res_id() (in module schrodinger.application.bioluminate.pose_filtering.residue_filter) get_res_type() (in module schrodinger.livedesign.biologics.sequence) get_res_zones_by_res_type() (in module schrodinger.application.bioluminate.antibody.annotate) get_reserved_aa_names() (in module schrodinger.protein.process_enamine_db) get_reserves_cores_state() (in module schrodinger.application.matsci.equilibrium_md) get_residue_annotations() (in module schrodinger.protein.gpcr.annotate) get_residue_asl() (in module schrodinger.application.bioluminate.protein.protein) (in module schrodinger.structutils.sitealign) get_residue_atoms() (in module schrodinger.infra.structure) get_residue_database() (in module schrodinger.protein.nonstandard_residues) get_residue_flip_state() (in module schrodinger.protein.assignment) get_residue_from_ccd() (in module schrodinger.infra.structure) get_residue_from_changeable() (in module schrodinger.protein.protassign.changeables) get_residue_interactions() (in module schrodinger.application.glide.utils) get_residue_key() (in module schrodinger.protein.residue) get_residue_label() (schrodinger.ui.qt.rama.Rama method) get_residue_name() (in module schrodinger.protein.helix) (schrodinger.protein.analysis.Report method) get_residue_neighborhoods() (in module schrodinger.protein.protassign.pka_prediction) get_residue_representation() (in module schrodinger.application.bioluminate.protein_interaction.utils) get_residue_sitename() (in module schrodinger.application.desmond.struc) get_residue_sorting_key() (in module schrodinger.application.bioluminate.protein_interaction.utils) get_residue_string() (in module schrodinger.protein.protassign.utils) get_residues() (in module schrodinger.application.glide.utils) get_residues_asl() (in module schrodinger.application.bioluminate.protein.protein) get_residues_between() (in module schrodinger.structutils.residue) get_residues_by_connectivity() (in module schrodinger.structure) get_residues_containing_atoms() (in module schrodinger.structutils.residue) get_residues_for_asl() (in module schrodinger.application.bioluminate.protein_protein_docking_shared) get_residues_unsorted() (in module schrodinger.structure) get_residues_within() (in module schrodinger.application.bioluminate.protein.protein) get_residues_within_bounds() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_response_status_from_reply() (in module schrodinger.maestro_utils.composer_agent.request_manager.urls) get_rest_params() (in module schrodinger.application.desmond.remd) get_restart_files() (schrodinger.application.glide_ws.driver.GlideWSJob method) get_restart_id_filename() (in module schrodinger.application.matsci.jobutils) get_restart_options() (in module schrodinger.application.matsci.jobutils) get_restart_zip_files() (in module schrodinger.application.matsci.jaguar_restart) get_restrain() (schrodinger.application.desmond.cms.Cms method) get_restrain_angle_idxs() (in module schrodinger.application.matsci.thermo_correction_utils) get_restrain_atom_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_restrain_dihedral_idxs() (in module schrodinger.application.matsci.thermo_correction_utils) get_restrain_distance_idxs() (in module schrodinger.application.matsci.thermo_correction_utils) get_rev_dict() (in module schrodinger.application.matsci.cgforcefield) get_RGB_enthalpy_entropy() (in module schrodinger.application.watermap.shapes) get_RGB_free() (in module schrodinger.application.watermap.shapes) get_rgb_from_color_index() (in module schrodinger.structutils.color) get_rge_sources() (in module schrodinger.application.matsci.reaction_workflow_enum_utils) get_rgroup_decomp() (in module schrodinger.livedesign.rgroup_decomposition) get_rgroup_DEE() (in module schrodinger.application.canvas.r_group) get_rgroup_labels() (in module schrodinger.livedesign.bbchem_endpoints) get_rgroup_MCS() (in module schrodinger.application.canvas.r_group) get_rgroup_SMARTS() (in module schrodinger.application.canvas.r_group) get_rgroup_smiles() (in module schrodinger.application.transforms.autosar.transforms) get_rgroup_sts_by_n_site() (in module schrodinger.application.matsci.reaction_workflow_enum_utils) get_ring_spears() (in module schrodinger.infra.structure) get_rings() (schrodinger.application.canvas.r_group.Data method) get_rlabels_map() (in module schrodinger.application.scaffold_enumeration.markush) get_rlabels_set() (in module schrodinger.application.scaffold_enumeration.markush) get_RMSDn() (in module schrodinger.comparison.struc) get_roc_curve_points() (in module schrodinger.analysis.enrichment.plotter) get_rotamers() (in module schrodinger.application.matsci.etarotamers) get_rotatable_bonds_in_smarts() (in module schrodinger.application.glide.utils) get_rotatable_haptic_ligands() (in module schrodinger.application.matsci.etarotamers) get_rotatable_id_to_atom() (schrodinger.protein.protassign.changeables.ligand_changeable method) get_rotated_rotamers() (in module schrodinger.glide) get_rotated_vector() (in module schrodinger.application.matsci.nano.util) get_rotation_matrix() (in module schrodinger.structutils.transform) get_rotation_matrix_from_eulers() (in module schrodinger.structutils.transform) get_rotational_args() (schrodinger.application.jaguar.thermochemical_properties.InputParams method) get_round_trip_hash() (in module schrodinger.application.livedesign.ld_utils) get_route_files_from_zip() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_route_input_files() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_route_source_type() (in module schrodinger.application.combinatorial_explorer.driver_utils) get_row() (in module schrodinger.project.utils) get_row_data() (in module schrodinger.ui.qt.table) get_row_from_proj_table() (in module schrodinger.application.matsci.deswidgets) get_row_from_pt() (in module schrodinger.application.matsci.gutils) get_rows() (in module schrodinger.project.utils) get_rsh_exec() (in module schrodinger.job.remote_command) get_runner_io() (in module schrodinger.application.glide.runner_utils) get_runtime_path() (in module schrodinger.application.glide.utils) (in module schrodinger.job.jobcontrol) get_runtime_relpath() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) get_rxnwf_graph() (in module schrodinger.application.matsci.reaction_workflow_utils) get_rxnwf_structures() (in module schrodinger.application.matsci.boltzmann_avg_props) get_s3() (in module schrodinger.application.glide_ws.entropy_score) get_s_inv12() (in module schrodinger.application.mopac.mopac_surfaces) get_safe_package() (in module schrodinger.application.matsci.codeutils) get_safe_yaml_with_tuples() (in module schrodinger.application.matsci.yamlutils) get_salt_bridge_params() (in module schrodinger.structutils.interactions.salt_bridge) get_salt_bridges() (in module schrodinger.infra.structure) (in module schrodinger.structutils.interactions.salt_bridge) get_sample_property_value() (in module schrodinger.application.livedesign.ld_utils) get_save_file_name() (in module schrodinger.ui.qt.filedialog) get_saved_db_file() (in module schrodinger.protein.nonstandard_residues) get_sca_by_res() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) get_scaff_without_non_graph_hydrogen_rgroups() (in module schrodinger.livedesign.rgroup_decomposition) get_scaffold_dictionary() (in module schrodinger.active_learning.scaffold_methods) get_scaffold_from_smiles() (in module schrodinger.active_learning.scaffold_methods) get_scaffold_mol_from_smiles() (in module schrodinger.active_learning.scaffold_methods) get_scale_factor_from_density() (in module schrodinger.application.matsci.cgforcefield) get_scaled() (schrodinger.application.matsci.elasticity.tensors.SquareTensor method) get_scaled_token_count() (in module schrodinger.gpgpu) get_scaled_volume() (in module schrodinger.application.matsci.cgforcefield) get_scheme_for_arg() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_scheme_region_prop() (in module schrodinger.application.bioluminate.tcr.annotate) get_schrodinger_db_value() (in module schrodinger.application.matsci.kmc) get_schrodinger_package_dirs() (in module schrodinger.infra.unusable_module_importer) get_schrodinger_run() (in module schrodinger.tasks.tasks) get_schrodinger_temp_dir() (in module schrodinger.infra.mm) (in module schrodinger.utils.fileutils) get_score_pred_as_array() (in module schrodinger.active_learning.al_report) get_scored_seqs() (in module schrodinger.application.bioluminate.peptide_sar.io) get_scored_wt() (in module schrodinger.application.bioluminate.peptide_sar.io) get_scores() (in module schrodinger.application.jaguar.utils) get_scratch_entry_name() (in module schrodinger.infra.structure) get_script_property_info_dict() (in module schrodinger.application.matsci.genetic_optimization) get_sd_property() (in module schrodinger.application.glide.sort_utils) get_sd_reader() (in module schrodinger.livedesign.convert) get_sdgr_atom_index() (in module schrodinger.application.matsci.rdpattern) get_sds_by_t() (in module schrodinger.application.matsci.kmc) get_section() (in module schrodinger.application.jaguar.output) get_segment_indices() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_selected_entry_ids() (in module schrodinger.project.utils) get_selected_structures() (in module schrodinger.project.utils) get_semicrystalline_relaxation1_stringers() (in module schrodinger.application.matsci.desconfig) get_semicrystalline_relaxation2_stringers() (in module schrodinger.application.matsci.desconfig) get_sentinel_sites() (in module schrodinger.application.matsci.buildcomplex) get_seq_data() (in module schrodinger.application.matsci.anharmonic) get_seq_labels() (in module schrodinger.application.bioluminate.peptide_sar.label) get_seqres() (in module schrodinger.protein.seqres) get_seqres_fasta() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) get_seqs_from_fasta_file() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_sequence() (in module schrodinger.protein.gpcr.annotate) get_sequence_chain_mapping() (in module schrodinger.livedesign.sh_utils) get_sequence_dict() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) get_sequence_file_format() (in module schrodinger.utils.fileutils) get_sequence_filter_chain_name() (in module schrodinger.livedesign.biologics.sequence) get_sequence_indexer() (in module schrodinger.application.bioluminate.antibody.sequence_indexer) get_sequence_numbering() (in module schrodinger.application.bioluminate.classify) get_sequence_to_structure_mapping() (in module schrodinger.livedesign.bbchem_endpoints) get_sequence_viewer_data() (in module schrodinger.livedesign.biologics.sequence) get_server_info() (in module schrodinger.job.server) get_server_processes() (in module schrodinger.application.licensing.licadmin) get_server_tls_names() (in module schrodinger.application.licensing.licserver.server) get_set() (schrodinger.protein.analysis.Report method) get_settings() (in module schrodinger.application.bb_database.bb_task_utils) (in module schrodinger.ui.qt.appframework2.settings) get_sgroups() (in module schrodinger.application.scaffold_enumeration.common) get_sha1() (in module schrodinger.application.livedesign.ld_utils) (in module schrodinger.application.pathfinder.multiroute) get_shape_data() (schrodinger.application.vss.config.Config method) (schrodinger.application.vss.database.Database method) get_shape_object_by_name() (in module schrodinger.application.matsci.shapes) get_shape_query() (in module schrodinger.application.vss.tasks) get_shared_file_listing() (in module schrodinger.application.licensing.licadmin) get_shell_runner() (in module schrodinger.application.matsci.espresso.utils) get_shifts() (schrodinger.application.jaguar.simple_spec.Peak method) get_shortest_distance() (in module schrodinger.structutils.measure) get_sibling_ownership_information() (in module schrodinger.application.matsci.reaction_workflow_utils) get_sidechain_att_atom() (in module schrodinger.application.desmond.struc) get_sidechain_indices() (schrodinger.protein.analysis.Report.local_residue method) get_sigmoid() (in module schrodinger.math.multi_parameter_optimization) get_signal() (schrodinger.application.jaguar.simple_spec.Peak method) get_signals() (in module schrodinger.utils.qt_utils) get_signed_angles_for_ring_flip_torsions() (in module schrodinger.application.jaguar.utils) get_significant_figures() (in module schrodinger.math.mathutils) get_simple_model_job() (in module schrodinger.livedesign.biologics.modeling) get_simple_supercell() (in module schrodinger.application.matsci.nano.xtal) get_simple_supercell_matrix() (in module schrodinger.application.matsci.nano.xtal) get_single_letter_code() (in module schrodinger.protein.sequence) get_site_nondefaults() (in module schrodinger.utils.featureflags.featureflags) get_sites() (in module schrodinger.application.matsci.reaction_workflow_utils) get_sites_from_structure() (in module schrodinger.application.matsci.buildcomplex) get_sites_table() (in module schrodinger.application.matsci.kmc) get_size_of() (in module schrodinger.application.matsci.jobutils) get_ska_transformation_matrix() (in module schrodinger.application.ska) get_skipped_file_name() (in module schrodinger.application.glide.utils) get_slice_limits() (in module schrodinger.application.bb_database.bb_arg_utils) get_smallest_metal_penalty() (in module schrodinger.application.prepwizard) get_smart_distribution_from_environ() (in module schrodinger.application.matsci.jobutils) get_smarts_from_sketcher() (in module schrodinger.ui.sketcher_smarts_dialog) get_smarts_from_ws() (in module schrodinger.application.matsci.smartsutilsgui) get_smarts_from_ws_selection() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_smi_from_csv() (in module schrodinger.active_learning.al_utils) get_smi_header() (in module schrodinger.active_learning.al_utils) get_smiles() (in module schrodinger.application.matsci.reaction_workflow_enum_utils) get_smiles_and_map() (in module schrodinger.application.matsci.rdpattern) get_smiles_column() (in module schrodinger.application.combinatorial_diversity.diversity_selector) get_smiles_csv() (schrodinger.application.vss.config.Config method) (schrodinger.application.vss.database.Database method) get_smiles_from_al_csv_or_smi_line() (in module schrodinger.active_learning.al_utils) get_smiles_without_wildcard() (in module schrodinger.application.matsci.rdpattern) get_smiles_wrapped_process() (in module schrodinger.application.transforms.test) get_snapshot_panel() (in module schrodinger.trajectory.trajectoryviewer) get_solvent_cts() (schrodinger.application.desmond.cms.Cms method) get_solvent_infos() (in module schrodinger.application.matsci.packmol) get_solvent_parameters() (in module schrodinger.application.jaguar.utils) get_solvent_params() (in module schrodinger.application.matsci.solvation_entropy_utils) get_solvent_params_by_t_and_p() (in module schrodinger.application.matsci.solvation_entropy_utils) get_solvent_params_solventropy() (in module schrodinger.application.jaguar.garza) get_sorption_free_energy_props() (in module schrodinger.application.matsci.msprops) get_sort_filters_from_config() (in module schrodinger.application.glide.utils) get_sorted_atomic_smarts() (in module schrodinger.application.matsci.rxn_channel) get_sorted_shortest_path() (in module schrodinger.application.matsci.graph) get_source_file_path() (in module schrodinger.application.livedesign.ld_utils) get_source_path() (in module schrodinger.application.matsci.jobutils) get_sources_from_r_labels() (in module schrodinger.structutils.rgroup_enumerate) get_spacegroups() (in module schrodinger.application.matsci.nano.space_groups) get_spec_dict() (in module schrodinger.application.combiglide.utils) get_species_display_names() (in module schrodinger.application.matsci.clusterstruct) get_species_display_names_from_cms() (in module schrodinger.application.matsci.clusterstructgui) get_species_from_mol() (in module schrodinger.application.matsci.clusterstruct) get_species_masses() (in module schrodinger.application.matsci.clusterstruct) get_spectral_params() (in module schrodinger.application.jaguar.nmr_utils) get_spectrum() (in module schrodinger.application.jaguar.simple_spec) get_spectrum_type() (in module schrodinger.application.matsci.bandshape_utils) get_spglib_symmops() (in module schrodinger.application.matsci.elasticity.tensors) get_spherical_cluster_RMSDn() (in module schrodinger.comparison.neighbors) get_spin_icons() (in module schrodinger.ui.qt.tasks.taskwidgets) get_splitting_pattern() (in module schrodinger.application.jaguar.simple_spec) get_splittings() (schrodinger.application.jaguar.simple_spec.Peak method) get_spt_args() (schrodinger.application.jaguar.garza.SolvEntropyParams method) get_sql_output_name() (in module schrodinger.application.matsci.kmc) get_sssr() (in module schrodinger.infra.structure) get_st_entity_id_map() (in module schrodinger.application.livedesign.import_utils) get_st_jaguar_output() (in module schrodinger.application.matsci.anharmonic) get_stage_idx() (in module schrodinger.application.matsci.thermo_correction_utils) get_standard_cell() (in module schrodinger.comparison.struc) get_standard_icon_pixmap() (in module schrodinger.ui.qt.icons) get_standardized_aa_structure() (in module schrodinger.protein.process_enamine_db) get_start_index_for_entries() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_start_range_end_lists() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_starting_sasas() (in module schrodinger.application.bioluminate.methionine_oxidation) get_state_penalties() (in module schrodinger.application.prepwizard) get_state_sites() (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.histidine_changeable method) (schrodinger.protein.protassign.changeables.ligand_changeable method) (schrodinger.protein.protassign.changeables.rotatable_changeable method) (schrodinger.protein.protassign.changeables.water_changeable method) get_state_string() (in module schrodinger.utils.featureflags.featureflags) get_static_constraints() (in module schrodinger.application.jaguar.autots_bonding) get_std_cell_from_spglib_dataset() (in module schrodinger.application.matsci.nano.xtal) get_steric_clashes() (in module schrodinger.structutils.interactions.steric_clash) get_stoich_charge() (in module schrodinger.application.jaguar.autots_validation) get_stoichiometry_string() (in module schrodinger.application.jaguar.utils) get_strain_state_dict() (in module schrodinger.application.matsci.elasticity.elastic) get_strained_cell() (in module schrodinger.application.matsci.nano.xtal) get_stream_handler() (in module schrodinger.utils.log) get_string_from_flag() (in module schrodinger.application.matsci.jobutils) get_stripped_defaults() (in module schrodinger.application.matsci.parserutils) get_struct_from_CIF() (in module schrodinger.application.matsci.nano.xtal) get_structure() (in module schrodinger.application.matsci.aseutils) (in module schrodinger.project.utils) (in module schrodinger.ui.sketcher_extensions) (schrodinger.infra.structure.Structure static method) get_structure_charge() (in module schrodinger.energy) get_structure_digest() (in module schrodinger.application.glide.ligand_designer) get_structure_file_format() (in module schrodinger.utils.fileutils) get_structure_from_base64_str() (in module schrodinger.application.matsci.coarsegrain) get_structure_ids() (in module schrodinger.application.livedesign.io_utils) get_structure_index() (in module schrodinger.application.bioluminate.protein_interaction.tasks) get_structure_info_via_structure_group_search() (in module schrodinger.application.livedesign.ld_tasks) get_structure_multiplicity() (in module schrodinger.energy) get_structure_output_file() (in module schrodinger.application.glide.utils) get_structure_record_class() (in module schrodinger.application.glide.sort_utils) get_structure_residue() (in module schrodinger.application.bioluminate.protein_interaction.utils) get_structure_residue_chain_key() (in module schrodinger.protein.residue) get_structure_residue_key() (in module schrodinger.protein.residue) get_structure_score() (in module schrodinger.application.matsci.genetic_optimization) get_structure_sequences() (in module schrodinger.protein.sequence) get_structure_UTTs() (in module schrodinger.infra.mm) get_structure_with_contiguous_molecules() (in module schrodinger.application.matsci.rxn_channel) get_structures() (in module schrodinger.application.phase.shape_screen_reporter.task_utils) get_structures_for_entry_ids() (in module schrodinger.project.utils) get_structures_from_bytes() (in module schrodinger.structure) get_structures_subset() (in module schrodinger.driver.structsubset) get_style_sheet_text() (in module schrodinger.ui.qt.style) get_sub_graphs() (in module schrodinger.application.matsci.graph) get_sub_host_str() (in module schrodinger.application.matsci.reaction_workflow_utils) get_subgraphs() (in module schrodinger.thirdparty.networkx_algos) get_subhosts() (schrodinger.job.jobcontrol.Host method) get_subjob_configuration() (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) get_subparam_type_hints() (in module schrodinger.models.paramtools) get_subst_score() (schrodinger.application.combiglide.corehop.SubstCoreDatabase method) get_subtrees() (in module schrodinger.thirdparty.networkx_algos) get_summary() (in module schrodinger.application.bioluminate.propka_parse) get_super_transformation_matrix() (in module schrodinger.structutils.rmsd) get_superposition_idxs() (in module schrodinger.application.matsci.swap_fragments_utils) get_surf_surf() (in module schrodinger.sitemap) get_surface_contour() (in module schrodinger.protein.getpdb) get_surface_kwargs() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_surface_manager_hub() (in module schrodinger.maestro_utils.surface_manager.surface_manager_panel) get_surfaces() (in module schrodinger.application.bioluminate.pml_menus) get_surfactant_infos() (in module schrodinger.application.matsci.packmol) get_surfnet_gaps() (in module schrodinger.application.bindingsite.cavutils) get_symmetric() (in module schrodinger.application.matsci.elasticity.tensors) get_symmops_from_spglib() (in module schrodinger.application.matsci.nano.space_groups) get_tcr_bounds() (in module schrodinger.application.bioluminate.tcr.annotate) get_tcr_type_name() (in module schrodinger.application.bioluminate.tcr.annotate) get_tcr_variable_domain_details() (in module schrodinger.application.bioluminate.tcr.annotate) get_temp_from_bs_spectrum_file_key() (in module schrodinger.application.matsci.bandshape_utils) get_temp_press_key_ext() (in module schrodinger.application.matsci.jaguarworkflows) get_temperature() (in module schrodinger.application.matsci.jaguarworkflows) get_temperature_str() (in module schrodinger.application.matsci.jaguarworkflows) get_template_domain() (in module schrodinger.application.bioluminate.antibody.assembly_yaml) get_template_vars() (in module schrodinger.application.livedesign.upload_utils) get_text_item() (in module schrodinger.maestro_utils.surface_manager.utils) get_tg_props() (in module schrodinger.application.matsci.msprops) get_thread_id() (in module schrodinger.utils.thread_utils) get_thread_name() (in module schrodinger.utils.thread_utils) get_time() (in module schrodinger.pipeline.stage) get_time_cost() (in module schrodinger.active_learning.al_report) get_title() (in module schrodinger.application.pathfinder.reaction) get_titles_by_failure() (in module schrodinger.protein.process_enamine_db) get_titles_of_duplicates() (in module schrodinger.application.matsci.reaction_workflow_utils) get_titration_ct() (schrodinger.application.desmond.cms.Cms method) get_titration_ct_index() (schrodinger.application.desmond.cms.Cms method) get_titration_ct_with_index() (schrodinger.application.desmond.cms.Cms method) get_titration_sites() (in module schrodinger.application.desmond.cms) get_titration_states() (in module schrodinger.application.desmond.cms) get_tkd_value() (in module schrodinger.application.matsci.elasticity.tensors) get_token() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_tokens_by_name() (in module schrodinger.ui.qt.standard.design_tokens) get_tooltip_for_search_option() (in module schrodinger.maestro_utils.find_tool_bar.constants) get_top_entry() (in module schrodinger.project.utils) get_top_ligands_from_csv_list() (in module schrodinger.active_learning.al_node) get_top_poses_from_sorted_ligands() (in module schrodinger.application.fragment_virtual_screening.frag_vs_utils) get_topic_dict() (in module schrodinger.utils.documentation) get_topic_fragment() (in module schrodinger.utils.documentation) get_torsion_atoms() (in module schrodinger.comparison.struc) get_torsion_fit_info() (in module schrodinger.infra.mm) get_torsions() (in module schrodinger.comparison.struc) get_total_charge() (in module schrodinger.application.jaguar.utils) get_total_energy() (in module schrodinger.glide) get_traj_filename() (in module schrodinger.application.desmond.util) get_trajectory_extname() (in module schrodinger.application.desmond.packages.traj) get_trajectory_frames() (schrodinger.application.desmond.packages.topo.FrameLoader method) get_trajectory_path() (in module schrodinger.application.livedesign.ld_utils) (in module schrodinger.project.utils) (in module schrodinger.trajectory.utils) get_transform_info() (in module schrodinger.seam.viz.inspect) get_transform_info_from_pipeline() (in module schrodinger.seam.viz.inspect) get_transformation_matrix() (in module schrodinger.application.matsci.nano.xtal) get_transformed_vectors() (in module schrodinger.application.matsci.nano.xtal) get_transition_type() (in module schrodinger.application.matsci.bandshape_utils) get_transitions() (in module schrodinger.application.matsci.bandshape_utils) get_translated_xyz_vec() (in module schrodinger.application.matsci.bandshape_utils) get_translation_matrix() (in module schrodinger.structutils.transform) get_translational_args() (schrodinger.application.jaguar.thermochemical_properties.InputParams method) get_trigger_config() (schrodinger.application.glide_ws.driver.GlideWSJob method) get_trj_dir_name() (in module schrodinger.application.matsci.parserutils) get_trj_from_cms_file() (in module schrodinger.application.matsci.order_parameter_mod) get_tube_dimensions() (in module schrodinger.application.matsci.nano.tube) get_tube_unit_cell() (in module schrodinger.application.matsci.nano.tube) get_tube_vectors() (in module schrodinger.application.matsci.nano.tube) get_type() (schrodinger.application.canvas.r_group.TempAtom method) get_type_dict_from_ff_file() (in module schrodinger.application.matsci.cgforcefield) get_type_dict_from_st() (in module schrodinger.application.matsci.coarsegrain) get_type_name() (in module schrodinger.application.matsci.cgforcefield) get_typenames() (schrodinger.utils.multifpfile.MultiFPFile method) get_uname() (in module schrodinger.utils.sysinfo) get_uncorrected_energy() (in module schrodinger.glide) get_unencrypted_text() (in module schrodinger.application.matsci.enc) get_unicode_file_handle() (in module schrodinger.utils.csv_unicode) get_unique_aa_names() (in module schrodinger.protein.process_enamine_db) get_unique_bonds() (in module schrodinger.application.matsci.coarsegrain) get_unique_cms_file_name() (in module schrodinger.trajectory.utils) get_unique_geom_title() (in module schrodinger.application.matsci.reaction_workflow_utils) get_unique_matches() (in module schrodinger.application.matsci.deprecated_pattern) get_unique_molecule_nums() (in module schrodinger.application.matsci.species) get_unique_molecule_struct() (in module schrodinger.application.matsci.species) get_unique_name() (in module schrodinger.application.matsci.msutils) get_unique_ordered_list() (in module schrodinger.application.matsci.msutils) get_unique_res_name() (in module schrodinger.protein.nonstandard_residues) get_unique_seq_names() (in module schrodinger.protein.tasks.structure_alignment) get_unique_session_id() (in module schrodinger.application.livedesign.ldclient_proxy) get_unique_titles() (in module schrodinger.application.matsci.mlearn.features) get_unit_cell_formula() (in module schrodinger.application.matsci.nano.xtal) get_unit_lattice_vector_info() (in module schrodinger.application.matsci.nano.xtal) get_unit_vector() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_units() (in module schrodinger.application.matsci.thermo_correction_utils) get_unmodified_trajectory_entry_ct() (in module schrodinger.trajectory.trajectoryviewer) get_unrefined_filename() (in module schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) get_unsatisfied_donors() (in module schrodinger.protein.protassign.unsatisfied_donors) get_unsupported_atoms() (in module schrodinger.application.jaguar.basis) get_unsupported_features() (in module schrodinger.glide) get_unsupported_graphics_card() (in module schrodinger.infra.gpgpu_utils) get_unused_name() (schrodinger.utils.pymol.PymolInstance method) get_update_delay() (in module schrodinger.job.queue) get_updated() (in module schrodinger.models.diffy) get_updated_dict() (in module schrodinger.models.diffy) get_updated_sites_dict() (in module schrodinger.application.matsci.reaction_workflow_enum_utils) get_updated_time_display() (in module schrodinger.application.job_monitor.job_monitor_table) get_updated_time_tooltip() (in module schrodinger.application.job_monitor.job_monitor_table) get_uploaded_model_url() (in module schrodinger.application.livedesign.upload_utils) get_url() (in module schrodinger.protein.gpcr.gpcrdb) get_usable_port() (in module schrodinger.application.licensing.licserver.main) get_user_feature_env() (in module schrodinger.utils.featureflags.featureflags) get_user_label_to_stage_mapping() (in module schrodinger.seam.viz.inspect) get_user_name() (in module schrodinger.application.matsci.msprops) get_userdata_dir() (in module schrodinger.utils.fileutils) get_username() (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy method) get_uvec() (in module schrodinger.application.matsci.elasticity.tensors) get_val() (in module schrodinger.utils.sea.sea) get_val_from_cmdline() (in module schrodinger.application.matsci.msutils) get_valid_header_groups_string() (in module schrodinger.application.bioluminate.antibody.io.csv_reader) get_validated_settings_kwargs() (in module schrodinger.application.transforms.dockers.validation) get_validation_pixmaps() (in module schrodinger.ui.qt.icons) get_value() (schrodinger.utils.sea.sea.Map method) get_variable_region_names() (in module schrodinger.application.bioluminate.anarci.annotate) get_vdw() (schrodinger.application.desmond.cms.Cms method) get_vdw_radius() (schrodinger.protein.analysis.Report method) get_vdw_type_name() (in module schrodinger.application.matsci.cgforcefield) get_vector_atoms_from_internal_coords() (schrodinger.protein.membrane.Membrane_Model method) get_vector_magnitude() (in module schrodinger.structutils.transform) get_vectors_from_chorus() (in module schrodinger.application.matsci.nano.xtal) get_vectors_from_residues() (in module schrodinger.application.bioluminate.mhc.docking_angles) get_version() (schrodinger.models.json.JsonableClassMixin method) get_vetted_vec_index() (in module schrodinger.application.jaguar.textparser) get_view_atoms() (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) get_view_item_options() (in module schrodinger.ui.qt.utils) get_visible_ws_asl() (in module schrodinger.application.bioluminate.pml_menus) get_visible_ws_atoms() (in module schrodinger.application.bioluminate.pml_menus) get_voids_data() (in module schrodinger.application.matsci.freevolume) get_voigt_dict() (schrodinger.application.matsci.elasticity.tensors.Tensor static method) get_volume_and_density() (in module schrodinger.comparison.struc) get_volume_data() (in module schrodinger.application.matsci.freevolume) get_volume_from_params() (in module schrodinger.application.matsci.nano.xtal) get_volume_from_vecs() (in module schrodinger.application.matsci.nano.xtal) get_weighted_score() (in module schrodinger.math.multi_parameter_optimization) get_widgets() (in module schrodinger.ui.qt.layout) (schrodinger.ui.qt.formlayout.FormComboWidget method) (schrodinger.ui.qt.formlayout.FormTabWidget method) (schrodinger.ui.qt.formlayout.FormWidget method) get_widgets_in_layout() (in module schrodinger.ui.qt.utils) get_wildcard_energy_key() (in module schrodinger.application.matsci.jaguarworkflows) get_window_coder() (schrodinger.seam.transforms.window.BatchWindows method) (schrodinger.seam.transforms.window.StringIDWindows method) get_windows_drive_sidebar_links() (in module schrodinger.ui.qt.filedialog) get_workflow_action_menu() (in module schrodinger.infra.structure) get_workflow_node_names() (in module schrodinger.active_learning.al_driver) get_workflow_settings() (in module schrodinger.application.peptide_workflow.beam_adapter) get_working_resources() (in module schrodinger.application.licensing.licadmin) get_workspace_structure() (in module schrodinger.ui.qt.input_selector) get_workspacehub_connection_requests() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) get_writer() (in module schrodinger.application.matsci.packmol) (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) get_ws_grid_wmap_files() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage method) get_ws_sip_docking_config() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage method) get_x() (schrodinger.application.canvas.r_group.TempAtom method) get_xlink_type_atoms() (in module schrodinger.application.matsci.freevolume) get_xyz_matches() (in module schrodinger.comparison.struc) get_xyz_RMSDn() (in module schrodinger.comparison.struc) get_y() (schrodinger.application.canvas.r_group.TempAtom method) get_z() (schrodinger.application.canvas.r_group.TempAtom method) get_zip_contents() (in module schrodinger.active_learning.al_utils) get_zpe_info() (in module schrodinger.application.matsci.anharmonic) getAbbeNum() (schrodinger.application.matsci.permittivity.RefractiveIndex class method) getAbbeWavelengths() (schrodinger.application.matsci.permittivity.ElectricPolarizability static method) getABInfo() (schrodinger.infra.canvas.ChmQuery method) getAbstractColumns() (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) getAbstractParam() (schrodinger.models.parameters.CompoundParam method) getAcceptor() (schrodinger.infra.structure.InteractionAtomPair method) getAcceptorAtomicNumbers() (schrodinger.infra.structure.AtomQueryParams method) getAccuracyAndInitialGuessKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getAction() (schrodinger.application.bioluminate.actions.factory.Factory method) getActiveCompPair() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis static method) getActiveCoordItem() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab method) getActiveHost() (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel method) getActivePairFromModel() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis static method) getActiveProcCounts() (schrodinger.job.queue.JobDJ method) getActiveProcsOnHost() (schrodinger.job.queue.JobDJ method) getActiveRankCsvRows() (schrodinger.analysis.enrichment.calculator.Calculator method) getAcuteAngle() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getAcyclicBonds() (schrodinger.infra.canvas.ChmMmctAdaptor method) getAddedFuncs() (schrodinger.utils.funcgroups.FuncGroupMixin method) getAdditionalDataDir() (schrodinger.project.project.Project method) getAdjustedDisplacement() (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis method) getAdjustedNJobs() (schrodinger.pipeline.stage.Stage method) getAdjustedYValues() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) getAdvancedSettingString() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getAliasedSettings() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) getAliasedValue() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) getAlignedMobileStructures() (schrodinger.structutils.sitealign.BindingSiteAligner method) getAlignmentMinimizedWithSpaces() (schrodinger.protein.alignment.BaseAlignment method) getAlignmentScore() (schrodinger.protein.align.BiopythonPairwiseAligner method) (schrodinger.protein.align.SchrodingerPairwiseAligner method) getAlignmentVector() (schrodinger.application.matsci.nano.particle.Nanoparticle method) getAlignmentVectors() (schrodinger.application.matsci.mlearn.features.Complex method) getAllAngles() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllArrayCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAllAtomicBases() (schrodinger.application.jaguar.input.JaguarInput method) getAllAtomIds() (schrodinger.application.matsci.clusterstruct.SpeciesData method) (schrodinger.application.matsci.species.SpeciesData method) getAllAtomPairs() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllCells() (schrodinger.ui.two_d_viewer.TwoDViewer method) getAllChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getAllColNames() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getAllComponents() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getAllData() (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) getAllEstates() (schrodinger.infra.canvas.ChmEstateDescriptors method) getAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getAllHypoIDs() (schrodinger.application.phase.phase_widgets.HypothesisModel method) getAllHypotheses() (schrodinger.application.phase.phase_widgets.HypothesisModel method) getAllJaguarMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) getAllJobs() (schrodinger.application.matsci.jobdirdlg.JobManager method) getAllKeys() (schrodinger.infra.canvas.ChmEstateDescriptors method) getAllKeysSortedByValue() (schrodinger.infra.canvas.ChmEstateDescriptors method) getAllLigandIndices() (schrodinger.energy.MonoMetalComplex method) getAllMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) getAllModelFiles() (schrodinger.application.matsci.genetic_optimization.ChemInformatics static method) getAllMoietyNames() (schrodinger.application.matsci.amorphous.Moieties method) getAllowedProcessors() (schrodinger.job.queue.ResourceHost method) getAllowedRange() (schrodinger.application.glide.job.GlideJob method) getAllowedRows() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) getAllowRelativeStereoMatches() (schrodinger.infra.canvas.ChmQueryMatcher method) getAllParentIndices() (schrodinger.application.matsci.cg_mapping.CoarseGrainBond method) getAllPossibleAssignments() (schrodinger.infra.canvas.ChmAtomTyper method) getAllPotentialAtomChargeProperties() (schrodinger.application.matsci.chargegui.ChargePropertySelector static method) getAllPreferences() (schrodinger.utils.preferences.Preferences method) getAllProperties() (schrodinger.ui.qt.propertyselector.PropertySelectorList method) getAllResidueStrings() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput method) getAllSegmentTypes() (schrodinger.application.matsci.kmc.Table static method) getAllSpaceGroups() (schrodinger.application.matsci.nano.space_groups.SpaceGroups method) getAllStages() (schrodinger.application.matsci.permittivity.MultiStageMd class method) getAllStandardItems() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) getAllTableModels() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) getAllTopLevelJobs() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) getAllTorsions() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllUniqueTrackers() (schrodinger.application.matsci.fragments.FragmentReactor method) getAllUsedTheoryLevels() (schrodinger.application.jaguar.gui.tabs.base_tab.LoadsTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getAllVibData() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getAllWorldCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAlnFilename() (schrodinger.application.prime.wrapper.BasePrimeAlignment method) getAlnSet() (schrodinger.protein.alignment.BaseAlignment method) getAlpha() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getAlphaCarbon() (schrodinger.structure.Residue method) getAlphaParameter() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getAltXYZ() (schrodinger.infra.structure.Structure method) getAminoAcid() (schrodinger.protein.nonstandard_residues.ResidueDatabase method) getAnalysis() (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) getAnchoredResidues() (schrodinger.protein.alignment.BaseAlignment method) getAnchoredResiduesWithRef() (schrodinger.protein.alignment.BaseAlignment method) getAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method) (schrodinger.infra.structure.PBC method) getAngleDerv() (in module schrodinger.application.matsci.gsas.GSASIImath) GetAngleSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getAngleType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getAngSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getAnharmonicVibPartitionFunctions() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getAnion() (schrodinger.infra.structure.SaltBridge method) getAnnotation() (schrodinger.protein.sequence.AbstractSequence method) getAnnotationValueForComparison() (schrodinger.protein.sequence.AbstractSequence method) getAntibodyCDR() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAntibodyCDRs() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAntibodyRegion() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAntibodyRegions() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.AntibodyRegionsFinder method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAomParameters() (schrodinger.energy.MetalForceFieldManager method) getApp() (schrodinger.ui.qt.appframework.AppFramework method) getApplicationHeaderFields() (schrodinger.job.jobcontrol.Job method) getApplicationHeaderString() (schrodinger.job.jobcontrol.Job method) getApplyGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getArcCenter() (schrodinger.application.matsci.atom_group.HelixArc method) getArginineType() (schrodinger.ui.residueselector.ResidueGroups method) getArgList() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) getArgName() (schrodinger.tasks.ldi.InputColumn method) (schrodinger.tasks.ldi.PoseColumn method) getAromaticityInfo() (schrodinger.infra.canvas.ChmMmctAdaptor method) getArray() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getArrayNx3() (schrodinger.trajectory.prody.mode.VectorBase method) getArrowheadPos() (schrodinger.protein.helm.helm_renderer.ArrowheadConnectorMixin method) GetAsfMean() (in module schrodinger.application.matsci.gsas.GSASIIpwd) GETaskInput (class in schrodinger.application.livedesign.export_models) GETaskOutput (class in schrodinger.application.livedesign.export_models) getAsl() (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo method) (schrodinger.application.bioluminate.patch_utils.patch_finder.ResPatchData method) getASL() (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) getAsl() (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.structure.Residue method) (schrodinger.ui.qt.atomselector.AtomSelector method) getASLName() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) getAspartateType() (schrodinger.ui.residueselector.ResidueGroups method) getAssayFolderPath() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) getAssignedAndUnassigned() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getAssociationChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getAsymmetricUnit() (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) getAtArrayCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtArrayCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtom() (schrodinger.glide.Pose method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.ui.qt.structure2d.RedSquareAnnotator method) getAtom1() (schrodinger.infra.structure.AtomPairWithValue method) getAtom2() (schrodinger.infra.structure.AtomPairWithValue method) getAtomAndBondCount() (schrodinger.infra.canvas.ChmFPMapItem32 method) (schrodinger.infra.canvas.ChmFPMapItem64 method) getAtomBondTypingSchemeDescription() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getAtomByPdbName() (schrodinger.structure.Residue method) getAtomColorList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getAtomConeAngle() (schrodinger.application.matsci.mlearn.features.Ligand method) GetAtomCoordsByID() (in module schrodinger.application.matsci.gsas.GSASIImath) getAtomCount() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.infra.canvas.ChmFPMapItem32 method) (schrodinger.infra.canvas.ChmFPMapItem64 method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmQuery method) (schrodinger.infra.canvas.ChmScaffold method) getAtomDefinitions() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) GetAtomFracByID() (in module schrodinger.application.matsci.gsas.GSASIImath) getAtomGroupKeyName() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) getAtomGroups() (schrodinger.application.matsci.species.SpeciesData method) getAtomHighlights() (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) getAtomicBasis() (schrodinger.application.jaguar.input.JaguarInput method) getAtomicCharge() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.infra.canvas.AtomicInvariant method) getAtomicChargeAttr() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getAtomicEnergy() (schrodinger.energy.MlffOutput method) getAtomicMass() (schrodinger.infra.canvas.AtomicInvariant method) getAtomicMultiplicity() (schrodinger.application.jaguar.input.JaguarInput method) getAtomicNonPolarSASAGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getAtomicNumAttr() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getAtomicNumber() (schrodinger.glide.Pose method) (schrodinger.infra.canvas.AtomicInvariant method) (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.structure.StructureAtom method) getAtomicPolarizabilities() (schrodinger.infra.canvas.ChmAtomTyperPolarMiller method) getAtomicPolarSASAGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getAtomicSpecies() (schrodinger.application.matsci.espresso.qeinput.StructureType method) getAtomicSpeciesIn() (schrodinger.application.matsci.espresso.qeinput.StructureType static method) getAtomicStructure() (schrodinger.application.matsci.espresso.qeinput.StructureType method) getAtomicStructureIn() (schrodinger.application.matsci.espresso.qeinput.StructureType method) getAtomicWeight() (schrodinger.infra.structure.StructureAtom method) getAtomIndices() (schrodinger.application.matsci.coarsegrain.FusedRing method) (schrodinger.structure._AtomCollection method) (schrodinger.structure.Structure method) GetAtomInfo() (in module schrodinger.application.matsci.gsas.GSASIIElem) GetAtomItemsById() (in module schrodinger.application.matsci.gsas.GSASIImath) getAtomList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.structure._AtomCollection method) getAtomName() (schrodinger.application.matsci.zmutils.ZAtom method) (schrodinger.infra.structure.StructureAtom method) getAtomNums() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) getAtomNumsForEntry() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateBasisSetSubTab method) getAtomPolymerNames() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getAtomPropertyNames() (schrodinger.infra.structure.Structure method) (schrodinger.structure.Structure method) getAtomResidueNames() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getAtoms() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) (schrodinger.glide.Pose method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.structure.StructureRing method) getAtomsAndWeight() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) GetAtomsById() (in module schrodinger.application.matsci.gsas.GSASIImath) getAtomsByMask() (schrodinger.infra.canvas.ChmMol method) getAtomsMaskForCode() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getAtomsToTerminate() (schrodinger.application.matsci.nano.sheet.Grow method) getAtomText() (schrodinger.application.matsci.reordergui.ComparisonListWidget method) (schrodinger.application.matsci.reordergui.ReferenceListWidget method) getAtomTotal() (schrodinger.application.jaguar.results.JaguarResults method) getAtomType() (schrodinger.infra.structure.StructureAtom method) getAtomTypeName() (schrodinger.infra.structure.StructureAtom method) getAtomTypes() (schrodinger.infra.canvas.ChmGasteigerCharge method) getAtomXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath) getAttachedHydrogens() (schrodinger.infra.canvas.ChmAtom method) getAttachmentData() (schrodinger.application.livedesign.export_models.FFCExportSpec method) getAtWorldCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtWorldCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAUC() (schrodinger.infra.canvas.ChmKPLSParser method) getAugmentedStructGraph() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getAutoCallerString() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) getAutoIndent() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method) getAutoscaleFactor() (in module schrodinger.infra.canvas) getAutoScaleInfo() (schrodinger.infra.canvas.ChmColumnUIDFilter method) getAuxListboxSelection() (schrodinger.ui.qt.propertyselector.PropertySelector method) getAvailableGeometries() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) getAvailableMappings() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) getAvailableMappingsByRecency() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) getAvailablePresets() (schrodinger.models.presets.PresetManager method) getAverage() (schrodinger.infra.canvas.ChmEstateDescriptors method) getAverageDistanceFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getAvgVibData() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getAVPAsl() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) getAxisDataRange() (schrodinger.ui.qt.schart.SChart static method) getAxisExtreme() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) getAxisNum() (schrodinger.application.matsci.sliceplot.SlicePlot method) getBackboneIdxs() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getBackboneNitrogen() (schrodinger.structure.Residue method) getBackboneOxygen() (schrodinger.structure.Residue method) getBackground() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getBackgroundDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getBandGap() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) getBarrierInfo() (schrodinger.application.matsci.desconfig.BarrierHeader static method) getBarriersAsEncodedProperty() (schrodinger.application.matsci.desconfig.BarrierHeader static method) getBarrierTermMSJ() (schrodinger.application.matsci.desconfig.BarrierHeader method) getBasename() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getBaseName() (schrodinger.application.matsci.genetic_optimization.ClassEvaluator method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getBasis() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterListToolButton method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) getBasisForEid() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) getBasisSetSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getBatch() (schrodinger.application.matsci.stylemanager.ColorCycle method) getBeadSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getBeadsType() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getBending() (schrodinger.structutils.minimize.Minimizer method) getBendingEnergy() (schrodinger.structutils.minimize.Minimizer method) getBestAlignment() (schrodinger.protein.gpcr.tasks.GPCRTask method) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask method) getBestClashResolutionResult() (schrodinger.structutils.clash_resolution.ReceptorLigandClashResolver method) getBestMatch() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) getBestMatchAndRmsd() (schrodinger.glide.CoreDefinition method) getBestNumberOfClusters() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getBestResults() (schrodinger.active_learning.al_node.LigandMLEvalNode method) getBestRingSpearResolutionResult() (schrodinger.structutils.clash_resolution.ReceptorLigandClashResolver method) getBestRMS() (schrodinger.application.matsci.vsepr.VSEPRFinder method) getBestSpanningVector() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getBeta() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction static method) getBetaCarbon() (schrodinger.structure.Residue method) getBFGSObject() (schrodinger.application.matsci.mecp_mod.MECP method) getBinarySimilarity() (schrodinger.protein.residue.Residue method) getBindingSiteTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) getBinIndices() (schrodinger.ui.qt.schart.SHistogramBarSeries method) getBinnedSites() (schrodinger.application.matsci.reaction_workflow_enum_utils.Sites static method) getBiteAngle() (schrodinger.application.matsci.mlearn.features.Ligand method) getBitMask() (schrodinger.infra.canvas.ChmPatterns method) getBlastAlignment() (schrodinger.protein.tasks.blast.BlastTask method) getBlastSettings() (schrodinger.protein.tasks.blast.BlastSettings method) GetBLtable() (in module schrodinger.application.matsci.gsas.GSASIIElem) getBLvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem) getBond() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.structure.Structure method) getBondAngle() (schrodinger.application.matsci.mlearn.features.Complex method) getBondAtLocation() (schrodinger.ui.qt.structure2d.structure_item method) getBondColorList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondCount() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmFPMapItem32 method) (schrodinger.infra.canvas.ChmFPMapItem64 method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmQuery method) getBondDirectionHint() (schrodinger.infra.canvas.ChmBond method) getBondedEnergies() (schrodinger.structutils.minimize.Minimizer method) getBondedEnergyComponents() (schrodinger.structutils.minimize.Minimizer method) getBondedSideChainAtom() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) getBondedSideChainAtoms() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getBondingInfo() (schrodinger.application.matsci.nano.sheet.Grow method) getBondLength() (schrodinger.application.matsci.amorphous.BaseMoiety method) (schrodinger.application.matsci.mlearn.features.Ligand method) (schrodinger.infra.canvas.ChmBond method) getBondList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondListWithIgnored() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondMaskForAtomMask() (schrodinger.infra.canvas.ChmMol method) getBonds() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmMol method) getBondsForAtomMask() (schrodinger.infra.canvas.ChmMol method) getBondsMaskForCode() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getBondsOrderAttr() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getBondsToNonHydrogen() (schrodinger.infra.canvas.AtomicInvariant method) getBondTo() (schrodinger.infra.canvas.ChmAtom method) getBondType() (schrodinger.infra.structure.Structure method) getBool() (schrodinger.glide.Config method) (schrodinger.infra.canvas.ChmFPTypeInfo method) (schrodinger.infra.mm.MMPREF method) getBoolArray() (schrodinger.glide.Config method) getBoolList() (schrodinger.infra.mm.MMPREF method) getBounds() (schrodinger.infra.canvas.Chm2DCoordGen static method) getBoxAngles() (schrodinger.infra.structure.PBC method) getBoxLengths() (schrodinger.infra.structure.PBC method) getBoxSizes() (schrodinger.application.glide.gui.GridSite method) getBoxSliceVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getBoxVectors() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) (schrodinger.infra.structure.PBC method) getBranchConvergentNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getBranchDivergentNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) GetBraviasNum() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getBuffer() (schrodinger.application.matsci.mswidgets.PlaneSelectorMixin method) getBuildingBlocks() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getBuriedNode() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getBuriedSASALimits() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput method) getBuriedVDWVolumePct() (schrodinger.application.matsci.mlearn.features.Complex method) getBuriedVolumeStructure() (schrodinger.application.matsci.mlearn.features.Complex method) getBuriedXYZ() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getButtonByText() (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) getButtonId() (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) getButtons() (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getButtonWithIcon() (schrodinger.application.job_monitor.job_monitor_widgets.JobBar method) getCalculatedData() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) getCalculationDict() (schrodinger.application.matsci.crest.CrestTOML method) getCalculationGUI() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) getCallResult() (schrodinger.application.matsci.mstest.MSTestCase method) getCanvasDescriptorsSwitch() (schrodinger.infra.canvas.ChmDescriptorMarshaler method) getCanvasSizeInPixels() (schrodinger.ui.two_d_viewer.SaveImagesDialogModel method) getCapperTerminator() (schrodinger.application.matsci.amorphous.PolymerFragments method) getCarbonylCarbon() (schrodinger.structure.Residue method) getCartesianCoords() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getCascadeGenerations() (schrodinger.application.matsci.amorphous.Moieties method) getCategory() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) getCation() (schrodinger.infra.structure.PiCationInteraction method) (schrodinger.infra.structure.SaltBridge method) getCbmVbm() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getCDRResidueList() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getCellFromI() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getCellSize() (schrodinger.infra.structure.DistanceCell method) getCellValue() (schrodinger.ui.qt.table.StructureDataViewerModel method) getCenter() (schrodinger.infra.structure.StructureRing method) getCenterIdx() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) getCenterOfMass() (schrodinger.application.matsci.atom_group.MSAtomGroup method) getCenterOrientationOfAtoms() (schrodinger.protein.membrane.Membrane_Model method) getCenterRotation() (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync method) getCenterX() (schrodinger.infra.structure.StructureRing method) getCenterY() (schrodinger.infra.structure.StructureRing method) getCenterZ() (schrodinger.infra.structure.StructureRing method) getCentralAtoms() (schrodinger.glide.ConformerTemplate method) getCentralInteractingAtomIndices() (schrodinger.glide.ConformerTemplate method) getCentroid() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.atom_group.MSAtomGroup method) (schrodinger.application.matsci.mlearn.features.Ligand method) getCGGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getChain() (schrodinger.structure.StructureAtom method) getChainAtoms() (schrodinger.structure.Structure method) getChainKey() (schrodinger.protein.residue.Residue method) getChainSV() (schrodinger.infra.structure.StructureAtom method) getCharactersForLongPDBName() (schrodinger.application.matsci.amorphous.Monomer static method) getCharge() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) (schrodinger.energy.MlffOutput method) getChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) getChargeConstraintSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getCharges() (schrodinger.infra.canvas.ChmGasteigerCharge method) getChartImage() (schrodinger.ui.qt.schart.SChart method) getCheckedColumns() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) getCheckedData() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) getCheckedDataCount() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) getCheckedResidues() (schrodinger.ui.residueselector.MutationSelectorMixin method) getCheckedRowNumbers() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) getChildItems() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) getChildWidgets() (schrodinger.ui.residueselector.GridContainer method) getChiralAngle() (schrodinger.application.matsci.nano.tube.NanoTube method) getChiralCenters() (schrodinger.infra.canvas.ChmAtom method) getChiralDeterminant() (schrodinger.infra.canvas.ChmAtom method) getChiralityInfo() (schrodinger.infra.canvas.ChmAtom method) getChiralityType() (schrodinger.infra.canvas.ChmAtom method) getChmDescriptorInfo() (schrodinger.infra.canvas.ChmModelTypeInfo method) getChoiceSpectrum() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing static method) getChorusPBC() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) (schrodinger.application.matsci.nano.tube.NanoTube method) getCircumRadius() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Tetrahedron method) getCis() (schrodinger.infra.canvas.ChmBond method) getCISDAll() (schrodinger.infra.canvas.ChmKPLSParser method) getCISDs() (schrodinger.infra.canvas.ChmKPLSParser method) getClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) getClashPenalty() (schrodinger.application.matsci.montecarlo.Metropolizer method) getClashResult() (schrodinger.structutils.clash_resolution.ReceptorLigandClashResolver method) getClassicalParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getCleanupRequested() (schrodinger.pipeline.stage.Stage method) getCLI() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) getClosest() (schrodinger.application.bioluminate.protein.protein.Consensus method) getClosestApproach() (schrodinger.application.matsci.montecarlo.Metropolizer method) getClusterContents() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getClusteringMap() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusteringStatistics() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterOrderMap() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterSize() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getClusterStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getClusterTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterVariance() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getCmd() (schrodinger.application.matsci.crest.Crest method) (schrodinger.application.matsci.crest.CrestCSearch method) (schrodinger.application.matsci.genetic_optimization.AutoQSAR method) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) (schrodinger.application.matsci.genetic_optimization.DeepChem method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Jaguar method) (schrodinger.application.matsci.reaction_workflow_gui_utils.QMPreOptimization method) (schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame method) (schrodinger.application.matsci.solvation_entropy_utils.TempPressData method) getCmdFromFlagBlock() (schrodinger.application.matsci.permittivity.TaskProtocol method) getCmdListArgValue() (schrodinger.ui.qt.appframework2.af2.JobApp method) getCMDValue() (schrodinger.application.matsci.builderwidgets.CleanOptionsCheckbox method) getCode() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) (schrodinger.structure.Residue method) getCodeCount() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getCodeForAtom() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getColMask() (schrodinger.infra.canvas.ChmPatterns method) getColor() (schrodinger.infra.structure.StructureAtom method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) getColoredMapping() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getColorFromWidget() (schrodinger.ui.qt.schart.SeriesParams method) getColors() (schrodinger.application.matsci.stylemanager.ColorProvider method) (schrodinger.application.matsci.stylemanager.GradientDefinition method) (schrodinger.application.matsci.stylemanager.ShadeDefinition method) getColorsForPatchVertices() (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) getColumn() (schrodinger.infra.canvas.ChmPairwiseFPIn method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) getColumnIndex() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) (schrodinger.ui.qt.swidgets.STableWidget method) getColumnLabels() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis static method) getColumnMeans() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) getColumnMeansAndDeviations() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) GetColumnMetadata() (in module schrodinger.application.matsci.gsas.GSASIIfiles) getColumnName() (schrodinger.infra.canvas.ChmPairwiseFPIn method) (schrodinger.infra.canvas.ChmPatterns method) getColumnNames() (schrodinger.infra.canvas.ChmPairwiseFPIn method) (schrodinger.infra.table.Table method) getColumns() (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) getColumnTotal() (schrodinger.infra.table.Table method) getCommand() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.queue.BaseJob method) getCommandArgs() (schrodinger.job.launcher.Launcher method) getCommandDir() (schrodinger.job.queue.BaseJob method) getCommandLineArgs() (schrodinger.application.matsci.mswidgets.SaveDesmondFilesWidget method) getCommandLineFlag() (schrodinger.application.matsci.mswidgets.RandomSeedWidget method) getCommandLineFlags() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) getCommandTemplate() (schrodinger.job.launchapi.TaskSpecification method) getCommonBasis() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getCommonBasisForRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) getCommonFunctional() (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) getCommonMethod() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getCommonTheoryForRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) getCommonTheoryLevel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getCommonValueProp() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder method) getComName() (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) getCompareKey() (schrodinger.rdkit.molio.BaseMergeHandler method) (schrodinger.rdkit.molio.CsvMergeHandler method) (schrodinger.rdkit.molio.RdkitMergeHandler method) (schrodinger.rdkit.molio.SmiMergeHandler method) (schrodinger.rdkit.molio.StructureMergeHandler method) getCompCtName() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis static method) getComplement() (schrodinger.protein.sequence.NASequence method) (schrodinger.protein.sequence.NucleicAcidSequence method) getCompleteBondList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getCompleteEnsemble() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getComplexDescriptors() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getComponentCount() (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmPathTools static method) getComponents() (schrodinger.infra.canvas.ChmMmctAdaptor static method) (schrodinger.infra.canvas.ChmPathTools static method) getComponentsMappings() (schrodinger.infra.canvas.ChmPathTools static method) getCompressionRatio() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) getCompressionWithHeader() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) getComUtil() (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) getConeAngle() (schrodinger.application.matsci.mlearn.features.Ligand method) getConfAvgRelEnergies() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) getConfidenceIntervals() (schrodinger.infra.canvas.ChmKPLSParser method) getConfig() (schrodinger.glide.JobConstraintData method) (schrodinger.glide.LigandConstraintData method) (schrodinger.glide.LoggerManager method) getConfigDialog() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.timing.TimerMixin method) (schrodinger.ui.qt.appframework2.af2.JobApp method) (schrodinger.ui.qt.appframework2.af2_template.AppTemplate method) getConformation() (schrodinger.infra.canvas.ChmMol method) getConformationCount() (schrodinger.infra.canvas.ChmMol method) getConformer() (schrodinger.glide.Pose method) getConformerList() (schrodinger.application.matsci.crest.CrestCSearch method) getConformers() (schrodinger.application.matsci.crest.CrestCSearch method) (schrodinger.glide.ConformerEnsemble method) getConformerStructures() (schrodinger.glide.ConformerEnsemble method) getConnectedComponents() (schrodinger.ui.qt.network_visualizer.Graph method) getConnectedTransitionStateTriples() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getConnectionColor() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionFile() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionInfos() (schrodinger.application.matsci.amorphous.PolymerFragments method) getConnectionMaxLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionMinLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionName() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionOrder() (schrodinger.infra.canvas.connectInfo method) getConnectionSize() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionTable() (schrodinger.infra.canvas.ChmMol method) getConnectionTableWithBondOrders() (schrodinger.infra.canvas.ChmMol method) getConnectivityChain() (schrodinger.analysis.substructure.ConnectedMoleculeChain method) getConnectorData() (schrodinger.protein.helm.helm_renderer.HelmScene method) getConservation() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) getConsiderHydrogens() (schrodinger.infra.canvas.ChmRadialOut32 method) (schrodinger.infra.canvas.ChmRadialOut64 method) getConsiderStereoEZ() (schrodinger.infra.canvas.ChmRadialOut32 method) (schrodinger.infra.canvas.ChmRadialOut64 method) getConsiderStereoRS() (schrodinger.infra.canvas.ChmRadialOut32 method) (schrodinger.infra.canvas.ChmRadialOut64 method) getConstraint() (schrodinger.application.jaguar.input.JaguarInput method) getConstraintDict() (schrodinger.application.glide_ws.model.ConstraintGroup method) (schrodinger.application.matsci.crest.CrestTOML method) getConstraintIndicesByType() (schrodinger.application.jaguar.input.JaguarInput method) getConstraints() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getConstraintsForModelComplexes() (schrodinger.application.glide_ws.driver.GlideWSJob method) getConstraintsRefXYZFileName() (schrodinger.application.matsci.crest.Crest method) getConstraintType() (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile method) getContentRect() (schrodinger.ui.qt.delegates.PictureDelegate method) getContractedGraphAndMapping() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getContractedMapping() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getConvergenceCriteriaKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getConvergenceKeywords() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getConvergenceMethodsKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getConvTempPress() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getCoordinates() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) (schrodinger.infra.canvas.ChmMol method) getCoordinationVec() (schrodinger.application.matsci.mlearn.features.Ligand method) getCoordName() (schrodinger.application.matsci.zmutils.ZAtom method) getCoords() (schrodinger.application.matsci.espresso.qeoutput.KPoint method) (schrodinger.glide.RotamerGroup method) (schrodinger.glide.WaterMap method) (schrodinger.glide.WmapWater method) (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.structure.CellMatchAtom method) (schrodinger.trajectory.prody.ensemble.Ensemble method) getCoordsStr() (schrodinger.application.matsci.espresso.qeoutput.KPoint method) getCordsIterator() (schrodinger.application.matsci.atom_group.MSAtomGroupsBase method) getCoreAtoms() (schrodinger.glide.CoreDefinition method) (schrodinger.glide.JobConstraintData method) (schrodinger.infra.canvas.ChmPathTools static method) getCoreDefinition() (schrodinger.glide.LigandConstraintData method) getCoreIndices() (schrodinger.glide.CoreDefinition method) getCoreRestraintIndex() (schrodinger.glide.ConformerTemplate method) (schrodinger.glide.CoreDefinition method) getCoreRotbondIndices() (schrodinger.glide.ConformerTemplate method) getCoreSmarts() (schrodinger.glide.CoreDefinition method) getCorrectionParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getCount() (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) getCounts() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getCouplerAndGrower() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getCouplerAtom() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getCovariance() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.trajectory.prody.nma.NMA method) getCovarianceofTranspose() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getCrashLog() (schrodinger.active_learning.mq_worker.LigandMLBackend method) getCriteria() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.FilterWidget method) getCriterion() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) getCrystalSystem() (schrodinger.application.matsci.nano.space_groups.CrystalSystems method) GetCSpqinel() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetCSuinel() (in module schrodinger.application.matsci.gsas.GSASIIspc) getCsvData() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getCSVEncoding() (schrodinger.application.matsci.ml_formulations_utils.BaseCSVReader static method) getCsvFilePath() (schrodinger.application.matsci.reportutils.ReportInfo method) getCsvRows() (schrodinger.analysis.enrichment.calculator.Calculator method) GetCSxinel() (in module schrodinger.application.matsci.gsas.GSASIIspc) getCt() (schrodinger.infra.structure.DistanceCell method) getCumulativeMatches() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) getCurrentASLData() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getCurrentAtomBondTyping() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getCurrentAxis() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getCurrentButton() (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getCurrentConfig() (schrodinger.glide.LoggerConfig static method) getCurrentFile() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) getCurrentHost() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getCurrentInfoAndProp() (schrodinger.application.matsci.kmcgui.PropertyCombo method) getCurrentInfoPropAndValues() (schrodinger.application.matsci.kmcgui.PropertyCombo method) getCurrentJobDir() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) getCurrentLinkage() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getCurrentRowCount() (schrodinger.infra.canvas.ChmDenseFPOut method) (schrodinger.infra.canvas.ChmFPOut32 method) (schrodinger.infra.canvas.ChmFPOut64 method) getCurrentSelection() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) (schrodinger.ui.qt.datamapper.MappableButtonGroup method) getCurrentSet() (schrodinger.ui.qt.protein_health_viewer.ProteinHealthViewer method) getCurrentSetting() (schrodinger.application.matsci.qualityslider.QualitySlider method) getCurrentTableModel() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) getCurrentType() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getCurrentValue() (schrodinger.application.matsci.mswidgets.AtomNameWidgetItem method) getCurrServerAddress() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) getCustom() (schrodinger.application.desmond.packages.staf.GeomCalc method) getCustomChargeInfo() (schrodinger.application.matsci.chargegui.ChargeDialog method) getCustomInfo() (schrodinger.application.matsci.genetic_optimization.Property static method) getCustomOPLSDir() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) getCustomOPLSDIR() (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) getCustomPresetsNames() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) getCustomStructToSave() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getCutBonds() (schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder static method) getCutoff() (schrodinger.infra.structure.ContactParams method) getCWgam() (in module schrodinger.application.matsci.gsas.GSASIImath) getCWgamDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getCWsig() (in module schrodinger.application.matsci.gsas.GSASIImath) getCWsigDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getCycleNeighbors() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) getCylinderSliceVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getDalkeHeader() (schrodinger.infra.canvas.ChmFPTypeInfo method) getData() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) (schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType method) (schrodinger.application.matsci.mswidgets.Stepper method) (schrodinger.application.matsci.spectra.PowderDiffractionFile static method) (schrodinger.application.matsci.spectra.SpectrumFile static method) (schrodinger.infra.canvas.ChmPairwiseFPIn method) (schrodinger.ui.qt.network_visualizer.Edge method) (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.network_visualizer.Node method) getDatabaseData() (schrodinger.application.matsci.cgforcefield.ForceField method) getDatabasePath() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) getDataModelClass() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) GetDATSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getDBFile() (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask method) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask method) getDebugLevel() (schrodinger.job.launchparams.LaunchParameters method) getDebugString() (schrodinger.tasks.tasks.AbstractTask method) getDecoyScore() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getDefault() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getDefaultAtomTypingScheme() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getDefaultCustomTemplateDir() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getDefaultKeywords() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) (schrodinger.application.matsci.jagwidgets.PresetsDialog method) getDefaultPreset() (schrodinger.models.presets.PresetManager method) getDefaultPresetName() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) getDefaultSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getDefaultStderr() (schrodinger.job.launchapi.JobSpecification method) getDefaultStdout() (schrodinger.job.launchapi.JobSpecification method) getDefinedData() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getDefinition() (schrodinger.ui.ligfilter.AddDefinitionDialog method) getDefinitionDict() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getDefinitionString() (schrodinger.infra.mm.UTT method) getDelimiter() (schrodinger.infra.canvas.ChmDelimitedPatterns static method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getDelimiterAndQualifier() (schrodinger.infra.canvas.ChmDelimitedPatterns static method) getDelNextResnumByAtomID() (schrodinger.application.matsci.amorphous.PolymerFragments method) getDelNextResnumByResnum() (schrodinger.application.matsci.amorphous.PolymerFragments method) getDeltaE() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getDeltaERxn() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getDendrogramData() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)

getDensities() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getDensity() (in module schrodinger.application.matsci.gsas.GSASIImath) getDenticity() (schrodinger.application.matsci.mlearn.features.Ligand method) getdEpsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getDescription() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getDescriptor() (schrodinger.application.matsci.order_parameter_mod.Descriptor method) getDescriptorKeys() (schrodinger.protein.residue.Residue method) getDescriptors() (schrodinger.application.matsci.mlearn.features.Complex method) (schrodinger.application.matsci.mlearn.features.Ligand method) getDescriptorUtilityJob() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getDescriptorValue() (schrodinger.protein.residue.Residue method) getDesiredVolume() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getDesolvationPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getDetailedAtomSmarts() (schrodinger.application.matsci.rdpattern.Pattern method) getDetailedAtomsSmarts() (schrodinger.application.matsci.rdpattern.Pattern method) getDeterminingStates() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getDeterminingStatesTOF() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getDeviations() (schrodinger.trajectory.prody.ensemble.Ensemble method) getdFCJVoigt3() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getDg() (schrodinger.glide.WaterMap method) (schrodinger.glide.WmapWater method) getdGLigandAtom() (schrodinger.infra.mm.LigandScoreStructure method) getdGSite() (schrodinger.infra.mm.LigandScoreStructure method) getdHLigandAtom() (schrodinger.infra.mm.LigandScoreStructure method) getdHSite() (schrodinger.infra.mm.LigandScoreStructure method) getDiagonalFinalPoint() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getDiameterAtomIndices() (schrodinger.glide.Conformer method) getDict() (schrodinger.application.matsci.msconst.DIMENSIONALITY class method) getDifference() (schrodinger.application.jaguar.autots_bonding.Coordinate method) getDihedral() (schrodinger.infra.structure.PBC method) getDihedralAtoms() (schrodinger.structure.Residue method) getDihedralType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getDiheValues() (schrodinger.application.matsci.amorphous.PolymerFragment method) getDirections() (schrodinger.glide.DataFiles method) getDirective() (schrodinger.application.jaguar.input.JaguarInput method) getDirectives() (schrodinger.application.jaguar.input.JaguarInput method) getDirector() (schrodinger.application.matsci.order_parameter_mod.OrderParameter static method) getDirectoryPath() (schrodinger.ui.qt.directory_selector.DirectorySelector method) getDiscontinuousSubalignment() (schrodinger.protein.alignment.BaseAlignment method) getDisplacementFromConstTranslation() (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis method) getDisplayAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getDisplayInfo() (schrodinger.infra.canvas.ChmFPTypeInfo method) getDisplayInfoEx() (schrodinger.infra.canvas.ChmFPTypeInfo method) getDisplayName() (schrodinger.application.matsci.builderwidgets.FilteredSketcherBox method) (schrodinger.application.matsci.builderwidgets.SketcherBox static method) getDisplaySmarts() (schrodinger.application.pathfinder.reaction.Reaction method) getDisplayTime() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getDisplayTypeInfo() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getDissociationChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getDistance() (schrodinger.application.desmond.packages.staf.GeomCalc method) (schrodinger.infra.structure.PBC method) getDistanceCell() (schrodinger.glide.Receptor method) getDistanceCellDistance() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) getDistanceConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) getDistanceMatrix() (schrodinger.infra.canvas.ChmMol method) getDistanceMatrix3D() (schrodinger.infra.canvas.ChmMol method) getDistanceMatrixFile() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getDistanceSquared() (schrodinger.infra.structure.CellMatchAtom method) getDistancesToCentroid() (schrodinger.infra.canvas.ChmPathTools static method) getDistanceToCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getDistDerv() (in module schrodinger.application.matsci.gsas.GSASIImath) GetDistSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getDM() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) getDmatrix() (schrodinger.application.matsci.rxn_path.InternalCoords method) getDockingOutputFiles() (schrodinger.application.glide.runner.CombinedRunner method) getDonor() (schrodinger.infra.structure.InteractionAtomPair method) getDonorAlphaAtomicNumbers() (schrodinger.infra.structure.AtomQueryParams method) getDonorAtomicNumbers() (schrodinger.infra.structure.AtomQueryParams method) getDOrbitalOccupancies() (schrodinger.energy.MetalForceFieldManager method) getDOrbitalOccupancy() (schrodinger.energy.AomComplex method) (schrodinger.energy.LfmmComplex method) getDOS() (schrodinger.application.matsci.espresso.qeoutput.DOS method) (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) getDot() (schrodinger.seam.viz.watcher.WatcherDirReader method) getDotFromEventsFile() (schrodinger.seam.viz.watcher.WatcherDirReader method) getDouble() (schrodinger.glide.Config method) (schrodinger.infra.canvas.ChmPattern method) (schrodinger.infra.mm.MMPREF method) getDoubleAndTripleRingAtoms() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) getDoubleArray() (schrodinger.glide.Config method) getDoubleDisplacementChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getDoubleList() (schrodinger.infra.mm.MMPREF method) getDownStreamPolymerJob() (schrodinger.application.matsci.permittivity.StepBase method) getDpdBeadSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getdPsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getDriver() (schrodinger.infra.canvas.ChmDescriptorInfo method) getDriverPath() (schrodinger.application.matsci.permittivity.TaskProtocol method) getDualGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getDuration() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getEdge() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) getEdgeApproval() (schrodinger.ui.qt.network_visualizer.Graph method) getEdgeLength() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Tetrahedron method) getEdgeList() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getEdges() (schrodinger.application.matsci.shapes.Face method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.schart.SHistogramBarSeries method) getEdgeToFaceMaximumDistance() (schrodinger.infra.structure.PiPiParams method) getEdgeToFaceMinimumAngle() (schrodinger.infra.structure.PiPiParams method) getEids() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) GetEigenVectorAndValues() (in module schrodinger.infra.canvas) getEigv() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) getEigval() (schrodinger.trajectory.prody.mode.Mode method) getEigvals() (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getEigvec() (schrodinger.trajectory.prody.mode.Mode method) getEigvecs() (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getElapsedTime() (schrodinger.infra.canvas.MCSsettings method) getEleEnergy() (schrodinger.structutils.minimize.Minimizer method) getElement() (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) getElementalInfo() (schrodinger.infra.canvas.ChmAtom method) getElementRestrictions() (schrodinger.infra.structure.AtomQueryParams method) getElidedTitle() (schrodinger.application.matsci.appbase.StructureLoadButton method) GetElInfo() (in module schrodinger.application.matsci.gsas.GSASIIElem) getEllipsoidSliceVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getElSym() (in module schrodinger.application.matsci.gsas.GSASIIElem) getEndFrameValue() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getEndPos() (schrodinger.protein.helm.helm_renderer.AABranchingConnectorItem method) (schrodinger.protein.helm.helm_renderer.DisulfideConnectorMixin method) (schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin method) getEnergeticSpans() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getEnergies() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) (schrodinger.application.matsci.fragments.BondEnergies method) (schrodinger.application.matsci.fragments.UniqueTracker method) (schrodinger.glide.ConformerTemplate method) getEnergy() (schrodinger.application.matsci.fragments.BondEnergies method) (schrodinger.application.matsci.montecarlo.Metropolizer method) (schrodinger.application.prime.residue_interaction.InteractionReader method) (schrodinger.glide.Conformer method) (schrodinger.structutils.minimize.Minimizer method) getEnergyAndGradients() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) getEnergyAndGradientsObject() (schrodinger.application.matsci.mecp_mod.MECP method) getEnergyOutput() (schrodinger.energy.AniPredictor method) (schrodinger.energy.QRNNPredictor method) getEnergyPropertyValues() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getEnrichmentCalculator() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getEnsemblePoses() (schrodinger.application.glide_ws.optimizer.WScoreOptimizerLigand method) getEnsembleSizeRange() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getEnthalpy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getEntries() (schrodinger.analysis.transformations.TransformsRepository method) getEntropy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getEntropyInfos() (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties static method) getEntryAtoms() (schrodinger.infra.structure.Structure method) getEntryID() (schrodinger.infra.structure.StructureAtom method) (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceItem method) getEntryIds() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput method) getEntryIDs() (schrodinger.infra.structure.Structure method) getEntryIds() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getEntryName() (schrodinger.infra.structure.StructureAtom method) getEntryNameSV() (schrodinger.infra.structure.StructureAtom method) getEnumeratedRXNWFSts() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) getEpsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getError() (schrodinger.infra.canvas.ChmSDReader method) (schrodinger.infra.canvas.ChmSmilesFileReader method) getErrorHandler() (schrodinger.structure.MaestroReader method) getEventsFileFromPipelineID() (schrodinger.seam.viz.watcher.WatcherDirReader method) getEwaldRealSpaceFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getExampleAtomGroup() (schrodinger.application.matsci.species.SpeciesData method) getExampleMemberTag() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) getExampleTag() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) (schrodinger.application.matsci.species.ResidueSpeciesFinder method) getExcitedState() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) getExcludedAtomList() (schrodinger.structutils.minimize.Minimizer method) getExcludedVolume() (schrodinger.application.matsci.amorphous.Scaffold method) getExistingDirectory() (schrodinger.ui.qt.filedialog.FileDialog static method) getExistingFragmentTracker() (schrodinger.application.matsci.fragments.FragmentReactor method) getExocyc() (schrodinger.infra.canvas.ChmScaffoldFinder method) getExolink() (schrodinger.infra.canvas.ChmScaffoldFinder method) getExpandedRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) getExpectedRuntime() (schrodinger.protein.tasks.blast.BlastTask method) getExportSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getExtendedFactors() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getExtension() (schrodinger.application.matsci.equilibrium_md.Model method) getExtents() (schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method) (schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method) (schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method) getExtentsAndStrainedLength() (schrodinger.application.matsci.nano.interface_mod.Interface method) getExtraColumnNames() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getExtraInputFiles() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) getExtraMolecularDescriptorsProps() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getFaces() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) getFaceToFaceMaximumAngle() (schrodinger.infra.structure.PiPiParams method) getFaceToFaceMaximumDistance() (schrodinger.infra.structure.PiPiParams method) getFactors() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials static method) getFailureCount() (schrodinger.infra.canvas.ChmSmilesFileReader method) getFallOffPower() (schrodinger.infra.canvas.ChmAtomTyperEstate method) getFCJVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getFCJVoigt3() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeatureCheckbox() (schrodinger.application.phase.featureselector.FeatureSelector method) getFeatureFromId() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeatureNames() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeaturePaths() (schrodinger.infra.canvas.ChmPathTools static method) getFeatures() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method) (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) GetFFC5() (in module schrodinger.application.matsci.gsas.GSASIIElem) getFFCExportSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getFFIOParam() (schrodinger.application.matsci.cgforcefield.ForceField method) GetFFtable() (in module schrodinger.application.matsci.gsas.GSASIIElem) getFFvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem) getFieldNames() (schrodinger.application.matsci.atom_group.HelixData method) getfile() (schrodinger.ui.qt.formlayout.FileLayout method) getFile() (schrodinger.ui.qt.input_selector.InputSelector method) getFileInputInfo() (schrodinger.ui.qt.input_selector.InputSelector method) getFilename() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) getFileName() (schrodinger.application.matsci.order_parameter_mod.Descriptor method) getFilename() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmFPOut32 method) (schrodinger.infra.canvas.ChmFPOut64 method) (schrodinger.infra.mm.OPLSArchive method) (schrodinger.infra.structure.StructureReader method) (schrodinger.infra.structure.StructureWriter method) (schrodinger.ui.qt.filedialog.OpenDirAsFileDialog method) getFileNameFromDisplayName() (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem static method) getFileNames() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) getFilePath() (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.structure_selector.MultiStructureLoadButton method) (schrodinger.ui.qt.structure_selector.StructureSelector method) getFilePaths() (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.structure_selector.StructureSelector method) getFiles() (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) (schrodinger.structure.MultiFileStructureWriter method) (schrodinger.ui.qt.input_selector.InputSelector method) getFileSize() (schrodinger.infra.structure.StructureReader method) getFilterName() (schrodinger.ui.qt.filter_dialog.FilterDialog method) getFilterText() (schrodinger.ui.ligfilter.LigfilterFrame method) getFinalForcesHartreePerAngstrom() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFinalPoint() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getFinalStructure() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFinalThermoProps() (schrodinger.application.matsci.thermo_correction_utils.ThermoCorrection method) getFinalTotalEnergy() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFingerprint() (schrodinger.ui.qt.fp_selector_widget.FingerprintsPopUp method) getFingerprintCopy() (schrodinger.infra.canvas.ChmProfiler method) getFingerprintDescription() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getFingerprintRef() (schrodinger.infra.canvas.ChmProfiler method) getFingerprintString() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getFirstCellPositions() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) getFirstFragmentStruct() (schrodinger.application.matsci.fragments.BreakingBond method) getFirstHost() (schrodinger.job.queue.JobDJ method) getFirstImplicitHydrogenIndex() (schrodinger.infra.canvas.ChmMol method) getFirstItem() (schrodinger.infra.canvas.ChmRangeUIDFilter method) getFirstLevelParentNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) getFirstLevelTasknames() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getFirstMatchedfilename() (schrodinger.application.matsci.permittivity.StepBase method) getFirstObsColumnAsDoubles() (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getFirstOutputStructure() (schrodinger.application.matsci.jwsteps.BaseStep method) getFirstSelectedRow() (schrodinger.infra.table.Table method) getFirstTmpResname() (schrodinger.application.matsci.amorphous.Monomer method) getFitBinIF() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getFitRect() (schrodinger.ui.qt.network_views.NetworkViewer method) getFittedPlanarAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method) getFixedColumnsCount() (schrodinger.project.project.Project method) getFixedInteractions() (schrodinger.energy.IterativeMlffModel method) (schrodinger.energy.MlffModel method) getFlagBlock() (schrodinger.application.matsci.permittivity.TaskProtocol method) getFlags() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) (schrodinger.application.matsci.chargegui.MLFFDialog method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) (schrodinger.application.matsci.kmcgui.NeighborsTab method) (schrodinger.application.matsci.kmcgui.Tab method) (schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants method) (schrodinger.application.matsci.speciesgui.GroupingMethodSelector method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) getFlattening() (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) getFlippableIdxs() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) getFloat() (schrodinger.infra.canvas.ChmFPTypeInfo method) getFlowChartData() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) getFlucCTLigandParameters() (schrodinger.energy.MetalForceFieldManager method) getFlucCTMetalParameters() (schrodinger.energy.MetalForceFieldManager method) getFlucCTSigmoidParameters() (schrodinger.energy.MetalForceFieldManager method) getFlucCTSystem() (schrodinger.energy.ConcreteMetalSystem method) getForce() (schrodinger.energy.MlffOutput method) getForceConstant() (schrodinger.application.matsci.deswidgets.SubstrateRestraintGroupBox method) getForceFieldFlag() (schrodinger.application.matsci.permittivity.DisorderSystemBuilder class method) (schrodinger.application.matsci.permittivity.PolymerBuilder class method) (schrodinger.application.matsci.permittivity.StepBase class method) getForceFieldMenuItem() (schrodinger.application.matsci.chargegui.ForceFieldDialog method) getForceFieldOptions() (schrodinger.ui.qt.forcefield.ffselector.MaestroForceFieldSelector method) getFormalCharge() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.structure.StructureAtom method) getFormat() (schrodinger.infra.structure.TextBlockReader method) (schrodinger.infra.structure.TextBlockWriter method) getFormattedSummaryLine() (schrodinger.application.matsci.mecp_mod.MECPStep method) GetFormFactorCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem) getFormulationsFromCSV() (schrodinger.application.matsci.ml_formulations_utils.BaseCSVReader method) getFP() (schrodinger.infra.canvas.ChmModelTypeInfo method) getFPInfo() (in module schrodinger.infra.canvas) getFpOptions() (schrodinger.application.matsci.genetic_optimization.CanvasKPLS static method) getFPPrecision() (in module schrodinger.infra.canvas) getFPTypeInfo() (schrodinger.infra.canvas.ChmKPLSParser method) getFragCentroid() (schrodinger.application.matsci.amorphous.PolymerFragments method) getFragmentCount() (schrodinger.infra.canvas.ChmQuery method) getFragments() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) (schrodinger.application.matsci.fragments.BreakingBond method) getFragmentTags() (schrodinger.application.matsci.fragments.FragmentReactor method) getFragmentTracker() (schrodinger.application.matsci.fragments.FragmentReactor method) getFragRingMapping() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) getFrames() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) getFrameTotal() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getFreeEnergyInfos() (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties static method) getFreePositions() (schrodinger.application.matsci.espresso.qeoutput.Output static method) getFreeVolumeData() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getFreqFromPropkey() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getFrequencies() (schrodinger.protein.alignment.BaseAlignment method) getFrequencyHash() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getFromRestartFile() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getFromSelection() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage method) getFromSpacing() (schrodinger.application.matsci.espresso.qeinput.KpointsType method) getFromString() (schrodinger.infra.structure.StructureReader static method) getFrozenAtoms() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getFuncGroup() (schrodinger.utils.funcgroups.FuncGroupMixin method) getFunctional() (schrodinger.application.jaguar.gui.tabs.base_tab.LoadsTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) getFurthestPair() (schrodinger.application.matsci.custom_lipid_prep.LipidEndProcessor method) getFusedRings() (schrodinger.application.matsci.coarsegrain.FusedRing static method) getFuzzyMatches() (schrodinger.infra.canvas.ChmScaffoldMatcher method) getFuzzyScaffold() (schrodinger.infra.canvas.ChmScaffold method) getFWHM() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getgamFW() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getGap() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getGapCount() (schrodinger.protein.sequence.AbstractSequence method) getGaplessLength() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) getGapOnlyColumns() (schrodinger.protein.alignment.BaseAlignment method) getGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.tasks.sta.STATask method) getGEdge() (schrodinger.ui.qt.network_visualizer.Graph method) GetGenSym() (in module schrodinger.application.matsci.gsas.GSASIIspc) getGibbsFreeEnergy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getGlobalAnnotationData() (schrodinger.protein.alignment.BaseAlignment method) getGlutamateType() (schrodinger.ui.residueselector.ResidueGroups method) getGoodFFTDim() (schrodinger.application.matsci.espresso.utils.MemoryEstimator method) getGPCRAnnotationMap() (schrodinger.protein.gpcr.tasks.GPCRTask method) getGPCRs() (schrodinger.protein.annotation.GPCRSegmentFinder method) getGPCRSegment() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getGPCRSegments() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getGradient() (schrodinger.infra.mm.LigandScoreStructure method) getGravityEnergy() (schrodinger.application.matsci.montecarlo.Metropolizer method) getGrids() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getGridSize() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) getGroundStateEnergy() (schrodinger.glide.ConformerTemplate method) getGroup() (schrodinger.infra.mm.MMPREF method) (schrodinger.utils.preferences.Preferences method) getGroupTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getGroupXYZ() (schrodinger.application.matsci.atom_group.MSAtomGroup method) getGrowName() (schrodinger.infra.structure.StructureAtom method) getGrowParams() (schrodinger.application.matsci.nano.tube.NanoSheet method) getGrowVectors() (schrodinger.application.matsci.nano.sheet.Grow method) getGuessGeometry() (schrodinger.application.matsci.mecp_mod.MECP method) getGUI() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) getHalfShortBoxLength() (schrodinger.infra.structure.PBC method) getHalfShortOrthogonalBoxLength() (schrodinger.infra.structure.PBC method) getHalfStep() (schrodinger.infra.canvas.ChmLinearOut32 method) (schrodinger.infra.canvas.ChmLinearOut64 method) getHamiltonian() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) getHandle() (schrodinger.infra.mm.MMFfldHandle method) (schrodinger.infra.mm.MMFragHandle method) (schrodinger.infra.structure.MM_Bitset method) (schrodinger.infra.structure.Structure method) getHapticCharacter() (schrodinger.application.matsci.mlearn.features.Ligand method) getHapticity() (schrodinger.application.matsci.mlearn.features.Ligand method) getHarmonicVibPartitionFunctions() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getHash() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.infra.canvas.ChmUniqueSmilesGenerator method) getHash64() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.infra.canvas.ChmUniqueSmilesGenerator method) getHashCode() (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) getHashCode64() (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) getHBondEquivalentAtoms() (schrodinger.glide.ReceptorAtom method) getHeader() (schrodinger.application.matsci.atom_group.HelixData method) (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) (schrodinger.application.matsci.stage_widgets.BaseTableWidgetDefinition method) (schrodinger.maestro_utils.surface_manager.secondary_pane.SecondaryPane method) (schrodinger.rdkit.molio.CsvMergeHandler method) getHeaderLine() (schrodinger.infra.canvas.ChmDelimitedPatterns method) getHeadTailCOM() (schrodinger.application.matsci.custom_lipid_prep.StretchMol method) getHeatCapacity() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getHeavyAtomCount() (schrodinger.infra.canvas.ChmMol method) getHeavyAtoms() (schrodinger.infra.canvas.ChmMol method) getHeavyBondCount() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmMol method) getHeavyBonds() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmMol method) getHeavyNeighbors() (schrodinger.infra.canvas.ChmAtom method) getHeavyStructGraph() (schrodinger.application.matsci.custom_lipid_prep.LipidEndProcessor static method) getHeight() (schrodinger.ui.qt.tablewidget.Row method) getHelixData() (schrodinger.application.matsci.atom_group.HelixGroups method) getHelixDataIterator() (schrodinger.application.matsci.atom_group.HelixGroups method) getHelp() (schrodinger.ui.qt.pdb_dialog.PDBDialog method) getHessian() (schrodinger.application.jaguar.input.JaguarInput method) getHetTypesToProcess() (schrodinger.application.prepwizard2.tasks.GenerateStatesSettings method) getHiddenColCount() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) getHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getHideAtomsBeyondBindingSiteASL() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getHideAtomsNonpolarHydrogensASL() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getHistidineType() (schrodinger.ui.residueselector.ResidueGroups method) getHistogramData() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method) getHits() (schrodinger.protein.gpcr.tasks.GPCRTask method) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask method) (schrodinger.protein.tasks.hit_align.CustomFamilyTask method) getHitsFile() (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask method) getHKLIndices() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getHKLmax() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getHKLMpeak() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getHKLpeak() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getHost() (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.job.jobcontrol.Host method) (schrodinger.job.launchapi.JobSpecification method) getHostCombo() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getHostList() (schrodinger.pipeline.stage.Stage method) getHostname() (schrodinger.job.launchparams.LaunchParameters method) getHostPlaceholderArg() (schrodinger.tasks.jobtasks.HostSettings method) getHostPref() (schrodinger.ui.qt.config_dialog.ConfigDialog method) getHosts() (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.config_dialog.GPUConfigDialog method) getHostStr() (schrodinger.application.matsci.genetic_optimization.ClassEvaluator static method) (schrodinger.pipeline.stage.Stage method) getHostType() (schrodinger.ui.qt.config_dialog.ConfigDialog method) getHSliderMax() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getHSliderMin() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getHtml() (schrodinger.stepper.viz.AbstractPlot method) (schrodinger.stepper.viz.OutputsPlot method) (schrodinger.stepper.viz.TimelinePlot method) (schrodinger.stepper.viz.TopologyChart method) getHumanReadable() (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) getHybridization() (schrodinger.infra.canvas.ChmAtom method) getHydrogenCount() (schrodinger.infra.canvas.ChmAtom method) getHydrogensInterchangeable() (schrodinger.infra.canvas.ChmQueryMatcher method) getHydropathyGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getHydrophilicAndHydrophobic() (schrodinger.application.matsci.custom_lipid_prep.LipidEndProcessor method) getHypoID() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) getHypotheses() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) getId() (schrodinger.glide.Conformer method) (schrodinger.glide.ConformerTemplate method) getID() (schrodinger.infra.canvas.ChmPattern method) getIdentity() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) getIdentityStrict() (schrodinger.protein.residue.Residue method) getIdStr() (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo method) (schrodinger.application.bioluminate.patch_utils.patch_finder.ResPatchData method) getIdx() (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis method) getIdxPairs() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getIFromCell() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getIgnoredSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getImageFromPic() (schrodinger.ui.two_d_viewer.TwoDViewer method) getImagesDirPath() (schrodinger.application.matsci.reportutils.ReportInfo method) getImplicitHydrogenCount() (schrodinger.infra.canvas.ChmAtom method) getImplicitHydrogensIgnored() (schrodinger.infra.canvas.ChmQueryMatcher method) getImplicitNeighbors() (schrodinger.infra.canvas.ChmAtom method) getImpTorsion() (schrodinger.structutils.minimize.Minimizer method) getImpTorsionEnergy() (schrodinger.structutils.minimize.Minimizer method) getIncludedColIndexes() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getIncludedColNames() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getIncludedCols() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getIncludedEntry() (schrodinger.application.matsci.appbase.BaseAnalysisGui method) getIncludedState() (schrodinger.ui.two_d_viewer.Cell method) getIncludedStructures() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) getIncludedXvarNames() (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getIncludeToggleOffset() (schrodinger.ui.two_d_viewer.TwoDViewer method) getIndex() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.structure.CellMatchAtom method) (schrodinger.infra.structure.StructureAtom method) (schrodinger.trajectory.prody.mode.Mode method) getIndexFromI() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getIndexResOrder() (schrodinger.glide.ReceptorAtom method) getIndexWithinSelection() (schrodinger.infra.canvas.ChmDelimitedPatterns method) getIndices() (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) (schrodinger.graphics3d.polyhedron.MaestroCube method) (schrodinger.graphics3d.polyhedron.MaestroDodecahedron method) (schrodinger.graphics3d.polyhedron.MaestroIcosahedron method) (schrodinger.graphics3d.polyhedron.MaestroOctahedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) (schrodinger.graphics3d.polyhedron.MaestroTetrahedron method) (schrodinger.trajectory.prody.modeset.ModeSet method) getInfo() (schrodinger.application.matsci.genetic_optimization.ChemInformatics class method) (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) (schrodinger.application.matsci.genetic_optimization.GlassTransitionTemperature static method) (schrodinger.application.matsci.genetic_optimization.RefractiveIndex static method) (schrodinger.application.matsci.genetic_optimization.StructureEvaluator static method) (schrodinger.glide.GridArchive method) (schrodinger.infra.canvas.ChmDescriptorSourceMapper static method) getInfoAll() (schrodinger.infra.canvas.ChmDescriptorSourceMapper static method) getInfraStructure() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) getIniDiameter() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getInitialGbshift() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getInitialGuess() (schrodinger.application.matsci.rxn_path.ReactionPath method) getInitialInputs() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getInitialInvHessian() (schrodinger.application.matsci.mecp_mod.BFGS method) getInitialMapping() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getInitialOffset() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getInitiatorSubBackbone() (schrodinger.application.matsci.amorphous.PolymerFragments method) getInnerRadius() (schrodinger.application.matsci.packmol.LiposomeInputFile method) getInPlaceRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getInput() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.pipeline.stage.Stage method) getInputDef() (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition method) getInputFile() (schrodinger.ui.qt.appframework.AppFramework method) getInputFileName() (schrodinger.infra.canvas.ChmFPSplitter method) getInputFiles() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.launchapi.JobSpecification method) getInputKeys() (schrodinger.job.launchapi.TaskSpecification method) getInputMolecule() (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput method) (schrodinger.application.jaguar.macro_pka_input.MacroKaInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getInputMolecules() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getInputName() (schrodinger.application.matsci.jwsteps.BaseDesmondStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.HOFStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep method) getInputNames() (schrodinger.pipeline.stage.Stage method) getInputPath() (schrodinger.application.matsci.jwsteps.BaseStep method) getInputs() (schrodinger.active_learning.mq_worker.Worker method) (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) getInputsForTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) getInputSource() (schrodinger.ui.qt.appframework.AppFramework method) getInputText() (schrodinger.application.jaguar.input.JaguarInput method) getInputTopic() (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) getInstance() (schrodinger.application.livedesign.ld_import_utils.LDImportTaskManager static method) (schrodinger.application.livedesign.ldclient_proxy.LDClientLogger class method) (schrodinger.application.livedesign.ldclient_proxy.LDClientProxy class method) (schrodinger.tasks.param_cli.ParamCLI class method) (schrodinger.ui.qt.forcefield.ffglobalpreferencewidget.FFGlobalPreferenceWidget static method) getInt() (schrodinger.glide.Config method) (schrodinger.infra.canvas.ChmFPTypeInfo method) (schrodinger.infra.mm.MMPREF method) getIntArray() (schrodinger.glide.Config method) getInTemplate() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getInteractionEnergy() (schrodinger.structutils.minimize.Minimizer method) getInteractionEnergyGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getInteractionMatrix() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getInteractionPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getInterChainAnchors() (schrodinger.protein.alignment.CombinedChainProteinAlignment method) getInterface() (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) getInterfaceASL() (schrodinger.application.bioluminate.pml_menus.InterfaceMixin method) getInterfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) getIntermediateNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getInternalEnergy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) (schrodinger.glide.Pose method) (schrodinger.glide.RefinedPose method) getInternalEnergyGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getInterpFlagBlock() (schrodinger.application.matsci.permittivity.TaskProtocol method) getInterPlanarSeparation() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getInterpolatedStructure() (schrodinger.application.matsci.rxn_path.ReactionPath method) getIntList() (schrodinger.infra.mm.MMPREF method) getInvariant() (schrodinger.infra.canvas.ChmAtom method) getInvariantBits() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getIonicRadii() (schrodinger.glide.JobConstraintData method) (schrodinger.glide.LigandConstraintData method) getIsFarthestFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getIsNearestToCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getIsolates() (schrodinger.ui.qt.network_visualizer.Graph method) getIsomorphicFragments() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getIsotope() (schrodinger.infra.canvas.ChmAtom method) getItem() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) (schrodinger.infra.canvas.ChmSymmetricMatrixUnsignedInt method) getItemByIndex() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getItemCount() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) (schrodinger.infra.canvas.ChmFPMapItem32 method) (schrodinger.infra.canvas.ChmFPMapItem64 method) getItemFromInt() (schrodinger.application.livedesign.login_gui2.AuthenticationMode class method) getItemsForAtom() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getItemsToSelect() (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceItem method) getItemTooltip() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) getItemType() (schrodinger.maestro_utils.surface_manager.surface_item.EntryNodeItem method) (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceNodeItem method) getIter() (schrodinger.application.scaffold_enumeration.common.EnumerableMixin method) getIterations() (schrodinger.infra.canvas.ChmRadialOut32 method) (schrodinger.infra.canvas.ChmRadialOut64 method) getJagOutFileName() (schrodinger.application.matsci.thermo_correction_utils.ThermoCorrection method) getJaguarDescriptors() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getJaguarFlags() (schrodinger.application.matsci.reaction_workflow_utils.DescriptorsMixin method) getJaguarInputFromFile() (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) getJaguarJob() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getJaguarKeywords() (schrodinger.application.matsci.solvation_entropy_utils.TempPressData method) getJaguarMarker() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) getJaguarNonDefault() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getJaguarRestartFileName() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) getJaguarValue() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) getJob() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.job.queue.JobControlJob method) getJobCmd() (schrodinger.application.matsci.multiapp.MultiCmdJobApp method) getJobConstraintData() (schrodinger.glide.LigandConstraintData method) getJobCount() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) (schrodinger.application.matsci.multiapp.MultiJobApp method) getJobDJ() (schrodinger.job.queue.BaseJob method) (schrodinger.pipeline.stage.Stage method) getJobFSFileMap() (schrodinger.seam.io.jobfilesystem.JobFileSystem class method) getJobname() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchparams.LaunchParameters method) getJobnameSource() (schrodinger.job.launchapi.TaskSpecification method) getJobSpec() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.JobSpecificationBuilder method) (schrodinger.ui.qt.appframework2.af2.JobApp method) getJobSpecFromArgs() (schrodinger.tasks.cli.TaskCLI method) getJoiningGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getJsonBlacklist() (schrodinger.application.livedesign.export_models.PoseNameEditModel class method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel class method) (schrodinger.models.parameters.CompoundParam class method) (schrodinger.protein.tasks.blast.BlastTask.Input class method) getJSScript() (schrodinger.stepper.viz.AbstractPlot method) (schrodinger.stepper.viz.OutputsPlot method) (schrodinger.stepper.viz.TimelinePlot method) (schrodinger.stepper.viz.TopologyChart method) getKcalPerMolConversion() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) GetKcl() (in module schrodinger.application.matsci.gsas.GSASIIlattice) GetKclKsl() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getKelleyPenaltyList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getKey() (schrodinger.infra.canvas.ChmValueAssignment method) (schrodinger.protein.residue.Residue method) getKeyBool() (schrodinger.infra.canvas.ChmEstateDescriptors method) getKeyCount() (schrodinger.infra.canvas.ChmEstateDescriptors method) getKeyData() (schrodinger.application.matsci.cgforcefield.ForceField method) getKeyName() (schrodinger.application.matsci.species.BaseSignature method) (schrodinger.application.matsci.species.MolecularFormulaSignature method) (schrodinger.application.matsci.species.PolymerSmilesSignature method) (schrodinger.application.matsci.species.SmilesSignature method) getKeyNamePrefix() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) (schrodinger.application.matsci.species.ResidueSpeciesFinder method) getKeys() (schrodinger.application.matsci.hdfutils.HDFIO method) (schrodinger.application.matsci.hdfutils.HDFProxyPickleIO method) getKeySource() (schrodinger.infra.mm.MMPREF method) getKeystring() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) getKeyType() (schrodinger.utils.preferences.Preferences method) getKeywordDict() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.KeywordEdit method) (schrodinger.application.matsci.qualityslider.QualitySlider method) getKeywords() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParameterLine method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) getKeywordString() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) (schrodinger.application.matsci.jagwidgets.KeywordEdit method) (schrodinger.application.matsci.qualityslider.QualitySlider method) getKinaseFeatures() (schrodinger.protein.tasks.kinase.KinaseFeatureTask method) GetKNsym() (in module schrodinger.application.matsci.gsas.GSASIIspc) getKplsData() (schrodinger.ui.two_d_viewer.TwoDViewer method) getKptFromCfg() (schrodinger.application.matsci.espresso.qeoutput.KPoint static method) GetKsl() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getKwargs() (schrodinger.application.matsci.genetic_optimization.Property static method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getLabel() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getLabeledMols() (schrodinger.application.pathfinder.route.ReagentNode method) getLabelText() (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getLaplacian() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) getLargestSpan() (schrodinger.application.matsci.amorphous.Box method) getLargestVoid() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getLast() (schrodinger.infra.canvas.ChmRangeFilter method) getLastCustomFeatureNum() (schrodinger.application.phase.featureselector.FeatureModel method) getLastLine() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getLastName() (schrodinger.infra.canvas.ChmSmilesFileReader method) getLastRecordInfo() (schrodinger.infra.canvas.ChmSDReader method) (schrodinger.infra.canvas.ChmSmilesFileReader method) getLastSMILES() (schrodinger.infra.canvas.ChmSmilesFileReader method) getLatticeParameters() (schrodinger.application.matsci.nano.xtal.Crystal method) getLatticeProperties() (schrodinger.application.matsci.nano.slab.Surface method) getlattSym() (in module schrodinger.application.matsci.gsas.GSASIIspc) getLaunchCommand() (schrodinger.application.macromodel.utils.ComUtil method) getLaunchDirectory() (schrodinger.job.launchparams.LaunchParameters method) getLaunchSubDir() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) getLayerVolume() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getLDDataTreePopUp() (schrodinger.application.livedesign.panel_components.LDDataTreePopUpButton method) getLeafTaskNodes() (schrodinger.application.matsci.permittivity.WorkflowParser method) getLeafTransforms() (schrodinger.seam.viz.watcher.WatcherDirReader method) getLeftAngles() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getLength() (schrodinger.application.matsci.shapes.Edge method) getLevelDicts() (schrodinger.application.matsci.crest.CrestTOML method) getLfmmParameters() (schrodinger.energy.MetalForceFieldManager method) getLicenseFileList() (in module schrodinger.application.licensing.licadmin) getLicenseRequirements() (schrodinger.application.steps.licensing.LicenseMixin method) (schrodinger.application.steps.ligprep.LigPrepStep method) (schrodinger.stepper.stepper.Chain method) getLicenses() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) getLicHost() (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog method) getLigand() (schrodinger.glide.Conformer method) (schrodinger.glide.ConformerEnsemble method) (schrodinger.glide.ConformerTemplate method) (schrodinger.glide.LigandConstraintData method) (schrodinger.glide.Pose method) (schrodinger.glide.RefinedPose method) getLigandCenterAndSize() (schrodinger.application.glide_ws.model.Complex method) getLigandCompoundID() (schrodinger.application.livedesign.export_models.ThreeDExportItem method) getLigandCorpID() (schrodinger.application.livedesign.export_models.ThreeDExportItem method) getLigandID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getLigandIndices() (schrodinger.energy.ConcreteMetalSystem method) (schrodinger.energy.FlucCTSystem method) (schrodinger.energy.MetalSystem method) getLigandStructure() (schrodinger.application.matsci.sculptcomplex.Sculptor method) getLigandTitle() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getLigandTypes() (schrodinger.energy.FlucCTSystem method) (schrodinger.energy.MetalSystem method) getLigandWScore() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getLigDonorOrAcceptor() (schrodinger.glide.HBond method) getLimits() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BoolCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericCriterion method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.StringCriterion method) getLinDepPlaneVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getLineData() (schrodinger.application.matsci.espresso.qeoutput.Magres static method) getLinkageDescription() (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method) getLinkageGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getLinkerAtoms() (schrodinger.infra.canvas.ChmScaffold method) getLinkerCount() (schrodinger.infra.canvas.ChmScaffold method) getLipidStructure() (schrodinger.application.matsci.custom_lipid_prep.CustomLipidPrep static method) getListboxSelection() (schrodinger.ui.qt.propertyselector.PropertySelector method) GetLittleGrpOps() (in module schrodinger.application.matsci.gsas.GSASIIspc) getLiveReportID() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) getLJEnergy() (schrodinger.structutils.minimize.Minimizer method) getlnQInfos() (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties static method) getLoading() (schrodinger.infra.canvas.ChmPLSParser method) getLocalArgs() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getLocalInputFiles() (schrodinger.stepper.app.StepperApplication class method) getLocalInputFolders() (schrodinger.stepper.app.StepperApplication class method) getLocalPath() (schrodinger.seam.io.jobfilesystem.JobFileSystem method) getLocationItems() (schrodinger.ui.qt.forcefield.pathselectorwidget.PathSelectorWidget method) getLogAsString() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.slurmtasks.ComboSlurmTask method) (schrodinger.tasks.tasks.SubprocessMixin method) getLogFilename() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.slurmtasks.ComboSlurmTask method) (schrodinger.tasks.tasks.SubprocessMixin method) GetLogger (class in schrodinger.application.matsci.textlogger) GetLogger.MyFormatter (class in schrodinger.application.matsci.textlogger) getlogin() (in module schrodinger.application.desmond.util) getLogPath() (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask method) getLogs() (schrodinger.seam.viz.watcher.WatcherDirReader method) getLonePairCount() (schrodinger.infra.canvas.ChmAtom method) getLongPDBResname() (schrodinger.application.matsci.amorphous.Monomer static method) getLongSaltBridge() (schrodinger.glide.ReceptorAtom method) getLoopMutation() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) getLowerBound() (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) getLRDependentColumns() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getLysineType() (schrodinger.ui.residueselector.ResidueGroups method) getMacromodelResidue() (schrodinger.infra.structure.StructureAtom method) getMaefilename() (schrodinger.application.jaguar.input.JaguarInput method) getMaeOrder() (schrodinger.infra.canvas.ChmBond method) getMaestroProjectDisposition() (schrodinger.job.launchparams.LaunchParameters method) getMaestroProjectDispositionString() (schrodinger.job.launchparams.LaunchParameters method) getMaestroProjectName() (schrodinger.job.launchparams.LaunchParameters method) getMaestroPropertiesPopUp() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) getMaestroSettings() (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync method) getMaestroViewname() (schrodinger.job.launchparams.LaunchParameters method) getMaeStructure() (schrodinger.application.matsci.espresso.qeoutput.Output method) (schrodinger.application.matsci.jaguarworkflows.Results method) getMag() (schrodinger.application.matsci.espresso.utils.MagSpecies method) GetMagFormFacCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem) getMahalanobisDM() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) getMajorRadius() (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) getManagedResource() (schrodinger.job.queue.ResourceHost method) getManager() (schrodinger.application.matsci.jobdirdlg.JobManager static method) getMapFilePath() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) getMappableRows() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getMappedBeadInfo() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) getMappedParticles() (schrodinger.application.matsci.cg_mapping.CGMapper method) getMapping() (in module schrodinger.infra.canvas) (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getMappingFromOrder() (schrodinger.application.matsci.automated_cg_mapping.MartiniMapper method) getMappingModel() (schrodinger.application.livedesign.export_map_manager.ExportMap class method) getMappingOrderPermulations() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) getMarkedAtoms() (schrodinger.application.matsci.reordergui.StructureListWidget method) getMarkerAtoms() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) getMartiniBeadSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getMartiniEdgesInMapping() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) getMaskTarget() (schrodinger.application.matsci.jwsteps.BaseStep method) getMass() (in module schrodinger.application.matsci.gsas.GSASIImath) getMatchCount() (schrodinger.infra.canvas.ChmFPMapItem32 method) (schrodinger.infra.canvas.ChmFPMapItem64 method) getMatchCountLimit() (schrodinger.infra.canvas.ChmQueryMatcher method) getMatchedAtomIndices() (schrodinger.infra.canvas.ChmMatchEx method) getMatchedAtoms() (schrodinger.infra.canvas.ChmMatch method) (schrodinger.infra.canvas.ChmMatchEx method) getMatchedAtomsInfo() (schrodinger.infra.canvas.ChmMatch method) (schrodinger.infra.canvas.ChmMatchEx method) getMatchedBondIndices() (schrodinger.infra.canvas.ChmMatchEx method) getMatchedBonds() (schrodinger.infra.canvas.ChmMatchEx method) getMatches() (schrodinger.application.ligprep.ionizer.Spec method) (schrodinger.glide.CoreDefinition method) (schrodinger.infra.canvas.ChmScaffoldMatcher method) getMatchingAtomMap() (schrodinger.structutils.sitealign.SiteMatchLookup method) getMatchingAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) getMatrix() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getMatrixTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMaxBits() (schrodinger.infra.canvas.ChmFPTypeInfo method) getMaxDistanceFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMaxDists() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getMaxFactor() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getMaxFpFilesOpen() (schrodinger.infra.canvas.ChmFPSplitter method) getMaxFreq() (schrodinger.infra.canvas.ChmFPTypeInfo method) getMaximumAcceptorAngle() (schrodinger.infra.structure.AtomQueryParams method) getMaximumAngle() (schrodinger.infra.structure.PiCationParams method) getMaximumDistance() (schrodinger.infra.structure.AtomQueryParams method) (schrodinger.infra.structure.PiCationParams method) getMaximumDonorAngle() (schrodinger.infra.structure.AtomQueryParams method) getMaximumViolations() (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) getMaxPath() (schrodinger.infra.canvas.ChmAtomTyperEstate method) (schrodinger.infra.canvas.ChmDendriticOut32 method) (schrodinger.infra.canvas.ChmDendriticOut64 method) (schrodinger.infra.canvas.ChmLinearOut32 method) (schrodinger.infra.canvas.ChmLinearOut64 method) getMaxRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method) getMaxRes() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getMaxRetries() (schrodinger.pipeline.stage.Stage method) getMaxRingPath() (schrodinger.infra.canvas.ChmLinearOut32 method) (schrodinger.infra.canvas.ChmLinearOut64 method) getMaxSpan() (schrodinger.infra.canvas.ChmDendriticOut32 method) (schrodinger.infra.canvas.ChmDendriticOut64 method) getMaxStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) getMaxVibData() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getMaxWorkers() (schrodinger.seam.options.pipeline_options.SeamOptions method) getMaxXY() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) getMCSMatches() (in module schrodinger.application.canvas.r_group) getMDLParity() (schrodinger.infra.canvas.ChmAtom method) getMDStepStruct() (schrodinger.application.matsci.espresso.qeoutput.Output method) getMeanWave() (in module schrodinger.application.matsci.gsas.GSASIImath) getMenu() (schrodinger.application.bioluminate.actions.factory.Factory method) getMenuAction() (schrodinger.application.matsci.speciesgui.GroupingMethodSelector method) getMenuActions() (schrodinger.maestro_utils.surface_manager.menus.BaseMenu method) (schrodinger.maestro_utils.surface_manager.menus.BaseSurfaceActionsMenu method) (schrodinger.maestro_utils.surface_manager.menus.EntryContextMenu method) (schrodinger.maestro_utils.surface_manager.menus.GlobalActionsMenu method) getMenuBar() (schrodinger.application.bioluminate.actions.factory.Factory method) getMenuIndicatorRect() (schrodinger.ui.qt.utils.HeaderViewWithMenuIndicator method) getMergeDistanceList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMeshShift() (schrodinger.application.matsci.espresso.qeinput.KpointsType static method) getMessages() (schrodinger.glide.LoggerConfig method) getMetadata() (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) getMetal() (schrodinger.infra.structure.MetalInteraction method) getMetalIndex() (schrodinger.energy.MonoMetalComplex method) getMetalIndices() (schrodinger.energy.FlucCTSystem method) (schrodinger.energy.MetalSystem method) getMetalType() (schrodinger.energy.MonoMetalComplex method) getMetalTypes() (schrodinger.energy.FlucCTSystem method) (schrodinger.energy.MetalSystem method) getMethod() (schrodinger.application.jaguar.gui.tabs.base_tab.LoadsTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListPopUp method) (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListToolButton method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) getMethodForEid() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getMetric() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) getMetricKey() (schrodinger.seam.metric.UserMetrics static method) getMetricString() (in module schrodinger.infra.canvas) getMetricStyle() (in module schrodinger.infra.canvas) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) GetMFtable() (in module schrodinger.application.matsci.gsas.GSASIIElem) getMFvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem) getMinCellLengths() (schrodinger.application.matsci.packmol.BilayerInputFile method) (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile method) getMinDistance() (schrodinger.application.matsci.density_analysis_widget.MeasurementLine method) getMinEnergy() (schrodinger.glide.RefinedPoseEnsemble method) getMinFactor() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getMinFreq() (schrodinger.infra.canvas.ChmFPTypeInfo method) getMinima() (schrodinger.glide.ConformerTemplate method) getMinimumAcceptorAngle() (schrodinger.infra.structure.AtomQueryParams method) getMinimumDonorAngle() (schrodinger.infra.structure.AtomQueryParams method) getMinMax() (schrodinger.application.matsci.amorphous.Box method) getMinPath() (schrodinger.infra.canvas.ChmDendriticOut32 method) (schrodinger.infra.canvas.ChmDendriticOut64 method) (schrodinger.infra.canvas.ChmLinearOut32 method) (schrodinger.infra.canvas.ChmLinearOut64 method) getMinRadius() (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.infra.growthspace.GrowthSpaceGenerator method) getMinRes() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getMinSize() (schrodinger.infra.canvas.ChmRadialOut32 method) (schrodinger.infra.canvas.ChmRadialOut64 method) getMinXY() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) getMLFFName() (schrodinger.application.matsci.chargegui.MLFFDialog method) (schrodinger.application.matsci.mswidgets.OPLS5ForceFieldSelector method) getMList() (schrodinger.application.matsci.density_analysis_widget.ImagePlotFrame method) (schrodinger.application.matsci.density_analysis_widget.LinePlotFrame method) getMmJagKeywords() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MossbauerSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MullikenSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MultipoleSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.RamanSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) getmmsymLikeGroup() (schrodinger.infra.canvas.ChmPathTools static method) getMmVsQmRmse() (schrodinger.infra.mm.MMFfldEsp method) getMobileStRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getMode() (schrodinger.application.livedesign.login.LoginManager method) getModel() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getModelDirectory() (schrodinger.energy.MlffModelType method) getModelEdges() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) getModelFile() (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) getModelFiles() (schrodinger.application.matsci.genetic_optimization.ChemInformatics class method) getModelName() (schrodinger.application.matsci.jagwidgets.MLFFSelector method) getModelNodes() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) getModels() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelectorButton method) getModelType() (schrodinger.infra.canvas.ChmModelTypeInfo method) getModelTypeStr() (schrodinger.energy.MlffModelType method) getModule() (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator static method) getMoiety() (schrodinger.application.matsci.amorphous.Moieties method) getMol() (schrodinger.infra.canvas.ChmAtom method) getMoldesFlags() (schrodinger.application.matsci.reaction_workflow_utils.DescriptorsMixin method) getMolecularDescriptorsJob() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getMolecularFormula() (schrodinger.application.matsci.builderwidgets.RowTemplateMixin method) getMolecularWeight() (schrodinger.application.matsci.mswidgets.StructureLoader method) (schrodinger.infra.structure.Structure method) getMolecule() (schrodinger.structure.StructureAtom method) getMoleculeAtoms() (schrodinger.structure.Structure method) getMoleculeGraph() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getMoleculeInfo() (schrodinger.application.matsci.kmc.Table method) getMoleculeNumber() (schrodinger.infra.structure.StructureAtom method) getMoleculeSmarts() (schrodinger.application.matsci.rdpattern.Pattern method) getMoleculeSmiles() (schrodinger.application.matsci.rdpattern.Pattern method) getMoleculeType() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) getMolIndex() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) getMolInfo() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) getMolSize() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) getMonomer() (schrodinger.application.matsci.amorphous.Moieties method) getMonomerData() (schrodinger.protein.helm.helm_renderer.HelmScene method) getMonomerResizingProposal() (schrodinger.protein.helm.helm_renderer.BBPhosphateMonomerBase method) (schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin method) (schrodinger.protein.helm.helm_renderer.NABaseMonomerBase method) getMonomers() (schrodinger.protein.helm.helm_renderer.HelmConnector method) getMonomerTypes() (schrodinger.protein.helm.helm_renderer.HelmConnector method) getMonoMetalComplexes() (schrodinger.energy.ConcreteMetalSystem method) getMonoMetalComplexType() (schrodinger.energy.MonoMetalComplex method) getMonosaccharideType() (schrodinger.application.matsci.amorphous.Monomer method) getMorganCount() (schrodinger.application.matsci.mlearn.descriptor.Featurize method) getMorseParameters() (schrodinger.energy.MetalForceFieldManager method) getMovieData() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getMovingAtoms() (schrodinger.structure.Structure method) getMSCoeffcientMS1() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis method) getMSCoeffcientMS2() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis method) getMSCoefficientMS3() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis method) getMsdHeader() (schrodinger.application.matsci.equilibrium_md.MsdTrajBase method) getMSDRelatedFiles() (schrodinger.application.matsci.equilibrium_md.MultiToOneConverter method) getMSJName() (schrodinger.application.matsci.jwsteps.MDCustomMSJStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) getMultisliderASLData() (schrodinger.application.matsci.density_analysis_widget.LinePlotFrame method) getMungedPdbName() (schrodinger.glide.ReceptorAtom method) getMungedResidueName() (schrodinger.glide.ReceptorAtom method) getMutationFromChanges() (schrodinger.application.bioluminate.protein.mutator.ProteinMutator method) getMW() (schrodinger.infra.canvas.ChmAtoms method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmScaffold method) getName() (schrodinger.active_learning.al_node.ActiveLearningNode class method) (schrodinger.application.livedesign.export_models.PropertyExportSpec method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.jagwidgets.NewPresetDialog class method) (schrodinger.application.matsci.wfmanagement.WorkflowMetadataFrame method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmValueAssignment method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.qt.ligand_list.Ligand method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) (schrodinger.ui.qt.swidgets.NewNameDialog method) getNameAndSave() (schrodinger.ui.qt.swidgets.ItemsManagerMixin method) getNameField() (schrodinger.infra.canvas.ChmSDReader method) getNameFromFlag() (schrodinger.application.matsci.parserutils.SubscriptableNameSpace method) getNamesAll() (schrodinger.infra.canvas.ChmKPLSParser method) getNanoSheet() (schrodinger.application.matsci.nano.tube.NanoSheet method) getNativePose() (schrodinger.application.glide_ws.optimizer.WScoreOptimizerLigand method) getNB14Pairs() (schrodinger.structutils.minimize.Minimizer method) getNBEnergyForTwoAtomLists() (schrodinger.structutils.minimize.Minimizer method) getNbnd() (schrodinger.application.matsci.espresso.qeinput.BandsType method) getNCombinations() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) getNCpus() (schrodinger.pipeline.stage.Stage method) getNearestImage() (schrodinger.infra.structure.PBC method) getNearestImages() (schrodinger.infra.structure.PBC method) getNeighborCoordVal() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) getNeighborCount() (schrodinger.infra.structure.StructureAtom method) getNeighborPBCBond() (schrodinger.application.matsci.nano.xtal.PBCBond method) getNeighbors() (schrodinger.glide.PoseAtom method) (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.structure.StructureAtom method) (schrodinger.ui.qt.network_visualizer.Graph method) getNeighborsByAtomicNumber() (schrodinger.infra.canvas.ChmAtom method) getNeighborsMasked() (schrodinger.infra.canvas.ChmAtom method) getNeighborTypes() (schrodinger.application.matsci.nano.sheet.Grow method) getNetCharge() (schrodinger.infra.canvas.ChmMol method) getNewAngles() (schrodinger.application.matsci.coarsegrain.Internals method) getNewAssay() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) getNewCell() (schrodinger.application.matsci.amorphous.Scaffold method) getNewCellStructure() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getNewDihedrals() (schrodinger.application.matsci.coarsegrain.Internals method) getNewImpropers() (schrodinger.application.matsci.coarsegrain.Internals method) getNewResidueName() (schrodinger.application.matsci.amorphous.Monomer method) getNewSolution() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) getNextColor() (schrodinger.ui.qt.schart.SChart method) getNextDirname() (schrodinger.application.matsci.permittivity.chdir method) getNextResidue() (schrodinger.protein.sequence.AbstractSequence method) getNextStructure() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getNJobs() (schrodinger.pipeline.stage.Stage method) getNKpts() (schrodinger.application.matsci.espresso.qeinput.KpointsType method) getNLags() (schrodinger.application.matsci.kmc.MSDVariableTimeStep static method) getNode() (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.network_visualizer.Graph method) getNodeCentralityType() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getNodeClasses() (schrodinger.active_learning.al_driver.ActiveLearningJob static method) getNodeClusterSets() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getNodeConfigReport() (schrodinger.active_learning.al_node.LigandMLTrainNode method) (schrodinger.active_learning.al_node.PrepareSmilesNode method) getNodeConnectedComponent() (schrodinger.ui.qt.network_visualizer.Graph method) getNodes() (schrodinger.ui.qt.network_visualizer.Graph method) getNodesByCondition() (schrodinger.application.matsci.custom_lipid_prep.LipidEndProcessor method) getNodesToRun() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getNodeXYZ() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) (schrodinger.application.matsci.freevolume.VoidInfo method) getNonBondedEnergies() (schrodinger.structutils.minimize.Minimizer method) getNonBondType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getNonDefault() (schrodinger.application.jaguar.input.JaguarInput method) getNonDefaultKeys() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.xtb.input.XTBInput method) getNonPeriodicPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getNonpolarHydrogensTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) getNonRingContToSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getNormal() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getNormalisedValue() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) getNormalOrdering() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getNormalParameters() (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData static method) getNormalsAndRadius() (schrodinger.structutils.ringspear.SpearRing method) getNormed() (schrodinger.trajectory.prody.mode.Vector method) getNotes() (schrodinger.application.jaguar.input.JaguarInput method) getNPairs() (schrodinger.application.matsci.kmc.MSDVariableTimeStep static method) getNPairsMax() (schrodinger.application.matsci.kmc.MSDVariableTimeStep static method) getNSitesByHashIdx() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) getNSpin() (schrodinger.application.matsci.espresso.qeinput.SpinType method) getNumAnnValues() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.sequence.AbstractSequence method) getNumAtoms() (schrodinger.glide.Pose method) (schrodinger.infra.structure.Structure method) getNumber() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getNumberOfClustersList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getNumberOfProcessorsManyNodes() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfProcessorsOneNode() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfQueueSlots() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfSubjobs() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfType() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) getNumberOfUniqueValues() (in module schrodinger.infra.canvas) getNumberRXNWFFiles() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) getNumBrokenRings() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) getNumCells() (schrodinger.ui.two_d_viewer.TwoDViewer method) getNumClashes() (schrodinger.application.matsci.montecarlo.Metropolizer method) getNumColumns() (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) getNumCoreRotbonds() (schrodinger.glide.Ligand method) getNumCores() (schrodinger.glide.CoreDefinition method) getNumCpusToValidate() (schrodinger.application.jaguar.gui.base_panel.JaguarConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) GetNumDensity() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getNumDirections() (schrodinger.glide.GridArchive method) getNumericalColNames() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getNumGPUS() (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog method) getNumIncludedEntries() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) getNumLigandAtom() (schrodinger.infra.mm.LigandScoreStructure method) getNumMarkers() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) getNumMols() (schrodinger.infra.structure.Structure method) getNumNodes() (schrodinger.application.livedesign.entry_types.Complexes method) getNumObsInTrainingTestTotal() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getNumOfXvarsWithLoading() (schrodinger.infra.canvas.ChmPLSParser method) getNumParticles() (schrodinger.energy.MlffInput method) getNumPeripheralRotbonds() (schrodinger.glide.ConformerTemplate method) getNumPlanes() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getNumResidues() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) getNumRotbondsBetween() (schrodinger.glide.Ligand method) getNumSelected() (schrodinger.application.prepwizard2.tasks.PreprocessInput method) getNumSelectedEntries() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) getNumSite() (schrodinger.infra.mm.LigandScoreStructure method) getNumSplits() (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.ExtractClustersStep method) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getNumStructures() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.InputTabJobMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.structure.MultiFileStructureWriter method) getNumSubjobsSpinbox() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getNumTargets() (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData method) getNumUnitCells() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getNumUsedCoordSites() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) GetNXUPQsym() (in module schrodinger.application.matsci.gsas.GSASIIspc) getObject() (schrodinger.application.matsci.cgforcefield.FFIOAngle method) (schrodinger.application.matsci.cgforcefield.FFIOBond method) (schrodinger.application.matsci.cgforcefield.FFIODihedral method) (schrodinger.application.matsci.cgforcefield.FFIOExclusion method) (schrodinger.application.matsci.cgforcefield.FFIOParam method) (schrodinger.application.matsci.cgforcefield.FFIOSite method) (schrodinger.application.matsci.cgforcefield.FFIOVdwType method) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getObjValue() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) getObsAll() (schrodinger.infra.canvas.ChmKPLSParser method) getObsColumnAsDoubles() (schrodinger.infra.canvas.ChmDelimitedPatterns method) getObservationIncludedIndex() (schrodinger.infra.canvas.ChmDelimitedPatterns method) getObservationIncludedIndexes() (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getObservationIndex() (schrodinger.infra.canvas.ChmDelimitedPatterns method) getObservationIndexes() (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getObservationName() (schrodinger.infra.canvas.ChmDelimitedPatterns method) getObservationNames() (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getOccupancy() (schrodinger.infra.structure.StructureAtom method) getOfficialMlffType() (schrodinger.energy.MlffModelType method) getOfficialModelTypes() (schrodinger.energy.MlffModelType static method) getOffsetPBCBonds() (schrodinger.application.matsci.nano.xtal.PBCBonds method) getOnBits() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getOnBitsCopy() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getOnBitsCount() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getOneLetterCodes() (schrodinger.application.matsci.amorphous.Moieties method) getOneLineRepresentation() (schrodinger.application.pathfinder.route.RouteNode method) getOpcdArgs() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.SbcUtil method) getOpenFileName() (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.filedialog.FileDialog static method) getOpenFileNames() (schrodinger.ui.qt.filedialog.FileDialog static method) getOpenMPSettings() (schrodinger.application.jaguar.gui.base_panel.JaguarConfigDialog method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) GetOpNum() (in module schrodinger.application.matsci.gsas.GSASIIspc) getOpposite() (schrodinger.infra.canvas.ChmRangeFilter method) GetOprName() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetOprNames() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetOprPtrName() (in module schrodinger.application.matsci.gsas.GSASIIspc) GetOprPtrNumber() (in module schrodinger.application.matsci.gsas.GSASIIspc) getOptimizationCmd() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) getOptionDesc() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getOptions() (schrodinger.structutils.minimize.Minimizer method) getoptionsGUI() (schrodinger.ui.qt.dendrogram.Dendrogram method) getOptKwargs() (schrodinger.application.matsci.mecp_mod.MECP method) getOrAddColumn() (schrodinger.infra.table.Table method) getOrbitalsKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getOrder() (schrodinger.infra.canvas.ChmBond method) (schrodinger.infra.canvas.ChmRangeFilter method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) getOrderedBackbone() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getOrderedIntersections() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getOrderedNodeNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getOrderedTaskSubjobDirs() (schrodinger.application.matsci.permittivity.WorkflowParser method) getOrigin() (schrodinger.application.matsci.nano.interface_mod.Interface method) getOrthantPairs() (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method) getOrthantPopulations() (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method) getOrthantRows() (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method) getOtherNode() (schrodinger.ui.qt.network_views.NetworkEdge method) getOutboundNodes() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) getOutboundSideChain() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) getOuterChiralIndicies() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getOuterTubeVectors() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getOutfileName() (schrodinger.application.matsci.desmondutils.AnalysisDriverMixin method) getOutMaeFileName() (schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties method) getOutput() (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.CombinerStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.energy.AomComplex method) (schrodinger.energy.DummyComplex method) (schrodinger.energy.LfmmComplex method) (schrodinger.energy.MonoMetalComplex method) (schrodinger.energy.MorseComplex method) (schrodinger.pipeline.stage.Stage method) getOutputEnding() (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep method) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep method) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getOutputFile() (schrodinger.job.launchapi.JobSpecification method) getOutputFileNamePattern() (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getOutputFileNames() (schrodinger.infra.canvas.ChmFPSplitter method) getOutputFiles() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.launchapi.JobSpecification method) getOutputKeys() (schrodinger.job.launchapi.TaskSpecification method) getOutputName() (schrodinger.application.matsci.jwsteps.BaseDesmondStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.ClusterAnalysisStep method) (schrodinger.application.matsci.jwsteps.CustomCmsToMaeStep method) (schrodinger.application.matsci.jwsteps.DisorderedSystemBuilderStep method) (schrodinger.application.matsci.jwsteps.ElasticConstantsStep method) (schrodinger.application.matsci.jwsteps.EvaporationStep method) (schrodinger.application.matsci.jwsteps.ExtractClustersStep method) (schrodinger.application.matsci.jwsteps.FreeVolumeStep method) (schrodinger.application.matsci.jwsteps.HOFStep method) (schrodinger.application.matsci.jwsteps.JaguarStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep method) (schrodinger.application.matsci.jwsteps.PolymerBuilderStep method) (schrodinger.application.matsci.jwsteps.PolymerChainAnalysisStep method) (schrodinger.application.matsci.jwsteps.PrepForMDStep method) (schrodinger.application.matsci.jwsteps.RDFStep method) (schrodinger.application.matsci.jwsteps.VoidStep method) (schrodinger.pipeline.stage.Stage method) getOutputNames() (schrodinger.pipeline.stage.Stage method) getOutputOPLSArchive() (schrodinger.application.livedesign.tasks.FFBuilderTask method) getOutputPaths() (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) getOutputs() (in module schrodinger.application.steps.test) getOutputsFromSmiles() (in module schrodinger.application.steps.test) getOutputTopic() (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) getOutputType() (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) getOutsideCylinderVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getOutsideEllipsoidVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getOutsideSphereVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getOutsideVol() (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile method) getOverlapSite() (schrodinger.infra.mm.LigandScoreStructure method) getPairedSurface() (schrodinger.project.surface.ProjectSurface method) getPairFromRow() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getPairInfo() (schrodinger.application.matsci.kmcgui.NeighborsTab method) getPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getPanelInstance() (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin class method) getPanelState() (schrodinger.ui.qt.appframework2.settings.SettingsPanelMixin method) getParallelepipedLineSegments() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getParallelepipedVertices() (schrodinger.application.matsci.shapes.Parallelepiped method) getParameters() (schrodinger.energy.FlucCTSystem method) (schrodinger.energy.MetalForceFieldManager method) (schrodinger.energy.MetalSystem method) (schrodinger.energy.MonoMetalComplex method) getParamRows() (schrodinger.ui.qt.schart.SeriesParams static method) getParams() (schrodinger.application.matsci.qubec_utils.Qubec method) getParamSignal() (schrodinger.models.parameters.Param class method) getParamSlot() (schrodinger.models.mappers.TargetParamMapper method) getParamValue() (schrodinger.models.parameters.Param class method) getParentalInformation() (schrodinger.application.matsci.jwsteps.BaseStep method) getParentBonds() (schrodinger.application.matsci.cg_mapping.Particle static method) getParentCutBonds() (schrodinger.application.matsci.cg_mapping.Particle static method) getParentGroup() (schrodinger.project.project.EntryGroup method) getParentIndices() (schrodinger.application.matsci.cg_mapping.Particle static method) getParentJob() (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel method) getParentTasknameByIndexFromDict() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getParentTasknames() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getParserDescription() (schrodinger.tasks.cli.TaskCLI method) (schrodinger.tasks.param_cli.ParamCLI method) getPartialCharge() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.structure.StructureAtom method) getParticipants() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) getParticleDensity() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction method) getParticles() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) getPassword() (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel method) getPatchColorRamp() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) getPatchDetails() (schrodinger.utils.pythonpatch.ModulePatch method) (schrodinger.utils.pythonpatch.Patch method) getPath() (schrodinger.application.matsci.kmcgui.DatabaseInfo method) (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) getPathLabelText() (schrodinger.application.matsci.kmcgui.DatabaseInfo method) getPathLength() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getPattern() (schrodinger.application.matsci.rdpattern.Pattern method) getPatternString() (schrodinger.structutils.createfragments.FragmentCreator method) getPBC() (schrodinger.infra.structure.DistanceCell method) getPBCMinMaxes() (schrodinger.application.matsci.amorphous.Scaffold method) getPBCSide() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getPDBAtomName() (schrodinger.glide.ReceptorAtom method) (schrodinger.infra.structure.StructureAtom method) getPdbDialog() (in module schrodinger.ui.qt.pdb_dialog) getPDBName() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Initiator method) (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getPDBNames() (schrodinger.application.matsci.custom_lipid_prep.RenumberLipid method) getPDBResidue() (schrodinger.infra.structure.StructureAtom method) getPDFPath() (schrodinger.application.matsci.reportutils.ReportInfo method) getPDOS() (schrodinger.application.matsci.espresso.qeoutput.PDOS method) getPeakPos() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getPeakProfile() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getPeakProfileDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getPearsonR() (schrodinger.infra.canvas.ChmPLSParser method) getPercentOfPosesWithInteractions() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) getPercentScreenCurvePoints() (schrodinger.analysis.enrichment.calculator.Calculator method) getPeriodicPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getPerMolFileName() (schrodinger.application.matsci.order_parameter_mod.Descriptor method) getPermutationIdxDict() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) getPersistenceKey() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) getPerWindowCoefficients() (schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis method) getPickingMode() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) getPicture() (schrodinger.ui.qt.delegates.PictureDelegate method) getPictureForCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) getPilotScoreFile() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getPipeFilename() (schrodinger.stepper.sideinputs.ForkStep method) getPiperDict() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method) getPkaAtom() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getPkaAtomObjs() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getPkaAtoms() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getPlaceholderText() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getPlanarAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method) getPlaneBoxIntersections() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getPLP() (schrodinger.maestro_utils.maestro_sync.PLPTarget method) getPointInBox() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) (schrodinger.application.matsci.amorphous.Scaffold method) getPointsFromCalc() (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method) (schrodinger.analysis.enrichment.plotter.Plotter method) getPolygonVertices() (schrodinger.protein.helm.helm_renderer.NABaseMonomerBase method) getPolymerFragments() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getPos() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getPose() (schrodinger.glide.PoseAtom method) getPoseIds() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) getPoses() (schrodinger.glide.RefinedPoseEnsemble method) (schrodinger.glide.RoughPoseEnsemble method) getPosition() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) (schrodinger.application.matsci.desconfig.BarrierInfo static method) getPositionedRGroups() (schrodinger.application.matsci.reaction_workflow_enum_utils.SculptMultiRGroup method) getPositions() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getPositionsByBitCount() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getPostProcessSteps() (schrodinger.energy.IterativeMlffModel method) (schrodinger.energy.MlffModel method) getPotentialEnergyGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getPotentialType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getPotentialWallConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) getPrecision() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.infra.canvas.ChmFPSplitter method) getPredAll() (schrodinger.infra.canvas.ChmKPLSParser method) getPrereqs() (schrodinger.job.queue.BaseJob method) getPreScript() (schrodinger.application.matsci.permittivity.TaskProtocol method) getPressure() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getPressuresTemperatures() (schrodinger.application.matsci.solvation_entropy_utils.TempPressData method) getPreviousResidue() (schrodinger.protein.sequence.AbstractSequence method) getPrimaryLigandIndices() (schrodinger.energy.MonoMetalComplex method) getPrimaryLigandTypes() (schrodinger.energy.MonoMetalComplex method) getPrimarySubAtomMap() (schrodinger.energy.MonoMetalComplex method) getPrimarySubAtomMaps() (schrodinger.energy.MetalSystem method) getPrimeEnergyByResidues() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getProductAppender() (schrodinger.rdkit.molio.BaseMergeHandler method) (schrodinger.rdkit.molio.CsvMergeHandler method) (schrodinger.rdkit.molio.RdkitMergeHandler method) (schrodinger.rdkit.molio.SmiMergeHandler method) (schrodinger.rdkit.molio.StructureMergeHandler method) getProductComplex() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getProductNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getProductReader() (schrodinger.rdkit.molio.BaseMergeHandler method) (schrodinger.rdkit.molio.CsvMergeHandler method) (schrodinger.rdkit.molio.RdkitMergeHandler method) (schrodinger.rdkit.molio.SmiMergeHandler method) (schrodinger.rdkit.molio.StructureMergeHandler method) getProducts() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getProgramName() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) getProgressAsPercentage() (schrodinger.job.jobcontrol.Job method) getProgressAsSteps() (schrodinger.job.jobcontrol.Job method) getProgressAsString() (schrodinger.job.jobcontrol.Job method) getProjectedBonds() (schrodinger.application.matsci.mlearn.features.Complex method) getProjectID() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) getProjectName() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) getProjectRow() (schrodinger.ui.two_d_viewer.Cell method) getProjectStructure() (schrodinger.application.matsci.reaction_workflow_gui_utils.WorkspaceSuperpositionFrame static method) getProp() (schrodinger.infra.canvas.ChmFPTypeInfo method) getPropAndValues() (schrodinger.application.matsci.kmcgui.PropertyCombo method) getProperties() (schrodinger.application.livedesign.entry_types.BaseEntryData method) (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData method) (schrodinger.application.livedesign.entry_types.GenericEntities method) (schrodinger.application.matsci.espresso.qeoutput.Output class method) (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) (schrodinger.infra.canvas.ChmMol method) getPropertiesBegin() (schrodinger.infra.canvas.ChmMol method) getPropertiesEnd() (schrodinger.infra.canvas.ChmMol method) getPropertiesFor() (schrodinger.infra.canvas.ChmMol method) getPropertiesToShow() (schrodinger.ui.two_d_viewer.TwoDViewer method) getProperty() (schrodinger.application.bioluminate.pml_menus.LabelAtomByEntryIndex method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByMolIndex method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByNumType method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByOccupancy method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByProp method) (schrodinger.application.bioluminate.pml_menus.LabelAtomByVDW method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.structure.Structure method) (schrodinger.infra.structure.StructureAtom method) (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.ui.qt.dendrogram.Dendrogram method) getPropertyBool() (schrodinger.infra.structure.Structure method) getPropertyCount() (schrodinger.infra.canvas.ChmMol method) getPropertyEnsemble() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) getPropertyExportSpecMap() (schrodinger.application.livedesign.panel_components.ExportTableModel method) getPropertyForAtom() (schrodinger.infra.canvas.ChmMol method) getPropertyForBond() (schrodinger.infra.canvas.ChmMol method) getPropertyInt() (schrodinger.infra.structure.Structure method) getPropertyKeys() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) getPropertyMinMax() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) getPropertyNames() (schrodinger.infra.structure.Structure method) (schrodinger.infra.structure.StructureAtom method) (schrodinger.project.project.Project method) (schrodinger.rdkit.filtering.JSONFilterAdapter method) (schrodinger.structure.Structure method) (schrodinger.structutils.filter.PropFilter method) (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getPropertyNamesForSelectedRows() (schrodinger.project.project.Project method) getPropertyPairs() (schrodinger.infra.canvas.ChmProfiler method) getPropertyPrecision() (schrodinger.project.project.Project method) getPropertyReal() (schrodinger.infra.structure.Structure method) getPropertyString() (schrodinger.infra.structure.Structure method) getPropertyStrings() (schrodinger.application.matsci.genetic_optimization.Property static method) getPropertyValue() (schrodinger.application.matsci.genetic_optimization.CanvasKPLS method) (schrodinger.application.matsci.genetic_optimization.ChemInformatics method) getPropName() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getProps() (schrodinger.infra.canvas.ChmFPTypeInfo method) getPropsToShowForCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) getProteinTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) getPseudo() (schrodinger.application.matsci.espresso.utils.UPFParser method) getPsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getQProp() (schrodinger.application.matsci.chargegui.NeighborTreatment method) getQsqr() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getQueryName() (schrodinger.protein.tasks.blast.BlastTask method) (schrodinger.protein.tasks.blast.BlastTask.Input method) getQueue() (schrodinger.application.matsci.genetic_optimization.ClassEvaluator method) (schrodinger.application.matsci.genetic_optimization.RefractiveIndex method) getRadius() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.infra.structure.StructureAtom method) getRamaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getRandGridXYZ() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getRandomLigandsPCA() (schrodinger.active_learning.al_report.ActiveLearningHtmlReport method) getRandomRealization() (schrodinger.application.scaffold_enumeration.common.EnumerableMixin method) getRandXYZ() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getRange() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorFrame method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) getRangeLabel() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) getRangeLimit() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) getRBoxVectors() (schrodinger.infra.structure.PBC method) getRBTransMat() (in module schrodinger.application.matsci.gsas.GSASIImath) getRDMol() (schrodinger.ui.qt.rdmol_views.RDMolStructureItem method) getReactantComplex() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getReactantNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getReactants() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getReactantsConformersDict() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowFile method) getReactantTrackers() (schrodinger.application.matsci.fragments.FragmentReactor method) getReactionAtomIndex() (schrodinger.infra.canvas.ChmAtom method) getReactionIndices() (schrodinger.infra.canvas.ChmMatch method) (schrodinger.infra.canvas.ChmMatchEx method) getReactionInternals() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getReactionSet() (schrodinger.application.pathfinder.route.Node method) getReactionSmarts() (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) getReactionSmiles() (schrodinger.application.pathfinder.route.RouteNode method) getReactiveAtoms() (schrodinger.application.matsci.rxn_path.ReactionPath method) getReader() (schrodinger.infra.structure.StructureReader static method) getReagentMol() (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) getReagentSmarts() (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) getReagentSource() (schrodinger.application.pathfinder.route.ReagentNode method) getRealization() (schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method) (schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method) (schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method) getRecentTemplatePath() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getRecentTemplatesList() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getRecepDonorOrAcceptor() (schrodinger.glide.HBond method) getReceptor() (schrodinger.glide.GridArchive method) getReceptorID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getReciprocals() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getReciprocalVal() (schrodinger.application.matsci.desconfig.BarrierHeader static method) getReducedMass() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getReducedMass1() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getReducedMass2() (schrodinger.application.matsci.anharmonic.AnharmonicPotentials method) getRedundantAtoms() (schrodinger.application.matsci.nano.sheet.Grow method) getRefCoords() (schrodinger.glide.CoreDefinition method) getReferenceEdges() (schrodinger.application.matsci.shapes.Face method) getReferenceEntryId() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) getReferenceFaces() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) getReferenceIndex() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getReferenceLigand() (schrodinger.glide.JobConstraintData method) getReferenceMenuItemNames() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getReferenceSeq() (schrodinger.protein.alignment.BaseAlignment method) getReferenceStructure() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) getRefinedPose() (schrodinger.glide.Pose method) getRefinedStructures() (schrodinger.glide.RefinedPoseEnsemble method) getRefractiveIndex() (schrodinger.application.matsci.permittivity.RefractiveIndex static method) getRegF() (schrodinger.infra.canvas.ChmPLSParser method) getRegP() (schrodinger.infra.canvas.ChmPLSParser method) getRelatedFile() (schrodinger.application.matsci.permittivity.MdPostAnalysis static method) getRelatedJobFile() (schrodinger.application.matsci.permittivity.MdPostAnalysis static method) getRelaxationProtocolFile() (schrodinger.application.matsci.permittivity.MultiStageMd class method) getRelaxationStages() (schrodinger.application.matsci.permittivity.MultiStageMd static method) getRelEnergy() (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection method) getRelicaNodeIndexes() (schrodinger.application.matsci.permittivity.WorkflowParser method) getRelPath() (schrodinger.application.matsci.genetic_optimization.Property static method) getRemoteModulesDir() (schrodinger.tasks.tasks.AbstractComboTask method) getReorderedStructure() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) getRepeatLength() (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator method) (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator64 method) getReplicaKeywords() (schrodinger.application.matsci.permittivity.TaskProtocol method) getReplicaType() (schrodinger.application.matsci.permittivity.WorkflowParser method) getReportData() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) getRepresentativeEntries() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getRepresentatives() (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae method) getRepresentativeStructure() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) getRequestedProperties() (schrodinger.infra.canvas.ChmProfiler method) getRequired() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getResByKey() (schrodinger.protein.sequence.AbstractSingleChainSequence method) getResID() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) getResidualPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidualPotentialByAtom() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidualPotentialByResidue() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidue() (schrodinger.structure.StructureAtom method) getResidueAtomicNonPolarSASA() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueAtomicPolarSASA() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueAtoms() (schrodinger.structure.Structure method) getResidueGroups() (schrodinger.ui.residueselector.MutationSelectorMixin method) getResidueHydropathy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueId() (schrodinger.infra.structure.StructureAtom method) getResidueID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getResidueIndices() (schrodinger.protein.alignment.BaseAlignment method) getResidueInteractionEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueInternalEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueNum() (schrodinger.glide.ReceptorAtom method) getResiduepKa() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResiduePotentialEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidueRotatableBonds() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResidues() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getResidueSASA() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResiduesCenter() (schrodinger.ui.picking.PickResiduesChangedMixin method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) getResiduesData() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getResidueSeqProps() (schrodinger.protein.alignment.BaseAlignment method) getResidueSimilarity() (schrodinger.protein.alignment.BaseAlignment method) getResiduesList() (schrodinger.ui.picking.PickResiduesChangedMixin method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) getResidueSurfComp() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getResiduesWithStructure() (schrodinger.protein.alignment.BaseAlignment method) getResidueToggle() (schrodinger.ui.residueselector.MutationSelectorMixin method) getResidueType() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getResistance() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getResolution() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getResources() (schrodinger.stepper.stepper.UnbatchedChain method) getResponse() (schrodinger.ui.qt.forcefield.forcefield.ValidateOplsDirMessageBox method) (schrodinger.ui.qt.messagebox.MessageBox method) (schrodinger.ui.qt.messagebox.QuestionMessageBox method) getRestAngle() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestartNode() (schrodinger.active_learning.al_driver.ActiveLearningJob method) getRestChiral() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestDist() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestPlane() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestPolefig() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestPolefigDerv() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestraint() (schrodinger.energy.MetalForceFieldManager method) getRestRama() (in module schrodinger.application.matsci.gsas.GSASIImath) getRestTorsion() (in module schrodinger.application.matsci.gsas.GSASIImath) getResultSeqs() (schrodinger.protein.align.AbstractStructureAligner method) getResultsGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getResultsParser() (schrodinger.infra.canvas.ChmModelParser static method) getResultWithThisEnergy() (schrodinger.application.matsci.jaguarworkflows.Results method) getReverse() (schrodinger.protein.sequence.NucleicAcidSequence method) getReverseComplement() (schrodinger.protein.sequence.NASequence method) (schrodinger.protein.sequence.NucleicAcidSequence method) getRGACodes() (schrodinger.infra.canvas.ChmFingerprints static method) getRGB() (schrodinger.structutils.color.ColorRamp method) getRGroup() (schrodinger.infra.canvas.ChmAtom method) getRGroups() (schrodinger.application.steps.enumerators.BaseDecorator.Settings method) getRGroupSitesDict() (schrodinger.application.matsci.reaction_workflow_enum_utils.SculptMultiRGroup method) getRho() (in module schrodinger.application.matsci.gsas.GSASIImath) getRhos() (in module schrodinger.application.matsci.gsas.GSASIImath) getRightShift() (schrodinger.infra.canvas.ChmFPTypeInfo method) getRing() (schrodinger.glide.LigandAtom method) (schrodinger.infra.structure.PiCationInteraction method) getRing1() (schrodinger.infra.structure.PiPiInteraction method) getRing2() (schrodinger.infra.structure.PiPiInteraction method) getRingBondCount() (schrodinger.infra.canvas.ChmAtom method) getRingBonds() (schrodinger.infra.canvas.ChmMmctAdaptor method) getRingCentroid() (schrodinger.structutils.ringspear.SpearRing method) getRingCount() (schrodinger.infra.canvas.ChmMol method) getRingDecorations() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getRingNodeContToSize() (schrodinger.application.matsci.automated_cg_mapping.StructData method) getRingOrderPermutations() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) getRingPath() (schrodinger.infra.canvas.ChmScaffold method) getRingSize() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) getRingSystemAtoms() (schrodinger.infra.canvas.ChmScaffold method) getRingSystemCount() (schrodinger.infra.canvas.ChmScaffold method) getRingSystemIndex() (schrodinger.glide.LigandAtom method) getRingSystemSize() (schrodinger.infra.canvas.ChmScaffold method) getRLMap() (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData method) getRMSD() (in module schrodinger.trajectory.prody.ensemble) (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) getRmsdDataname() (schrodinger.structutils.rmsd.ConformerRmsd method) getRole() (schrodinger.infra.canvas.ChmDescriptorInfo method) getRotamerAngles() (schrodinger.glide.Conformer method) getRotamerGroupIndices() (schrodinger.glide.ConformerTemplate method) getRotamers() (schrodinger.application.matsci.etarotamers.HapticLigand method) (schrodinger.glide.Conformer method) getRotamerStructures() (schrodinger.glide.Conformer method) (schrodinger.glide.ConformerEnsemble method) getRotatableBonds() (schrodinger.glide.ConformerTemplate method) (schrodinger.glide.Ligand method) (schrodinger.infra.canvas.ChmMol method) getRotatableBondsGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getRotatedComplex() (schrodinger.application.matsci.mlearn.features.Complex method) getRotationToZ() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getRotEnergy() (schrodinger.application.desmond.torsion_related.BondRotator method) getRoughStructures() (schrodinger.glide.RoughPoseEnsemble method) getRoutes() (schrodinger.application.pathfinder.route.RetroSynthesisNode method) getRow() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.infra.canvas.ChmPairwiseFPIn method) (schrodinger.project.project.Project method) getRowColumnFromI() (schrodinger.ui.two_d_viewer.TwoDTableModel method) getRowCount() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmFPSplitter method) getRowCriteria() (schrodinger.ui.ligfilter.CriteriaListModel method) getRowData() (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.table.ExportableProxyModel method) getRowIndex() (schrodinger.application.matsci.stage_widgets.MultiRowArea method) getRowMask() (schrodinger.infra.canvas.ChmPatterns method) getRowName() (schrodinger.infra.canvas.ChmPairwiseFPIn method) getRowNames() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getRows() (schrodinger.ui.qt.swidgets.STableWidget method) getRowText() (schrodinger.ui.ligfilter.PatternModel method) getRsqr() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getRsqrCv() (schrodinger.infra.canvas.ChmPLSParser method) getRSquaredList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getRun() (schrodinger.protein.sequence.AbstractSequence method) getRunningJobIDs() (schrodinger.application.matsci.jobdirdlg.JobManager method) getRuntimePath() (schrodinger.pipeline.stage.Stage method) getRxAtoms() (schrodinger.application.matsci.builderwidgets.SketcherStructureMixin method) getRXNWFInputFiles() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateSwapMixin method) getSaccharideConnectivityPatterns() (schrodinger.application.matsci.automated_cg_mapping.PolysaccharideDetector class method) getSampleAtomAndStructTag() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) getSampleAtomId() (schrodinger.application.matsci.species.SpeciesData method) getSampleHistogram() (schrodinger.application.matsci.uq_utils.BilinearHistogramData static method) (schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData static method) (schrodinger.application.matsci.uq_utils.HyperbolaHistogramData static method) getSampleIndices() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) getSampleMolNumber() (schrodinger.application.matsci.clusterstruct.SpeciesData method) (schrodinger.application.matsci.clusterstructgui.SpeciesCombo method) getSamplePoints() (schrodinger.application.matsci.rxn_path.ReactionPath method) getSamplePropertyValue() (schrodinger.application.livedesign.entry_types.BaseEntryData method) (schrodinger.application.livedesign.entry_types.BaseReceptorLigandData method) (schrodinger.application.livedesign.entry_types.GenericEntities method) getSampleResidues() (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) getSampleStructure() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) getSASAGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getSASANonPolarGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getSASAPolarGenerator() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getSavedItems() (schrodinger.ui.qt.swidgets.ItemsManagerMixin method) getSaveFileAndDefinition() (schrodinger.trajectory.trajectory_gui_dir.trajectory_messages.SaveDefinitionsDialog method) getSaveFileName() (schrodinger.ui.qt.filedialog.FileDialog static method) getSaveOptions() (schrodinger.application.matsci.mswidgets.SaveDesmondFilesWidget method) getScaffold() (schrodinger.infra.canvas.ChmScaffoldFinder method) getScaffoldCount() (schrodinger.infra.canvas.ChmScaffoldFinder method) getScaffoldMol() (schrodinger.infra.canvas.ChmScaffold method) getScaffolds() (schrodinger.infra.canvas.ChmScaffoldFinder method) getScaffoldSMARTS() (schrodinger.infra.canvas.ChmScaffold method) getScaffoldSMILES() (schrodinger.infra.canvas.ChmScaffold method) getScaffoldSources() (schrodinger.infra.canvas.ChmScaffoldFinder method) getScaffoldSourcesCount() (schrodinger.infra.canvas.ChmScaffoldFinder method) getScale() (schrodinger.infra.canvas.Chm2DCoordGen static method) getScaledCovariance() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) getScaledCovarianceofTranspose() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getScaledEwaldConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getScaledMahalanobisDM() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) getScaleFactor() (schrodinger.protein.helm.helm_renderer.HelmWidget method) getScaleType() (schrodinger.infra.canvas.ChmFPTypeInfo method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) getScanCoordinate() (schrodinger.application.jaguar.input.JaguarInput method) getScenesData() (schrodinger.application.pymol.mae_sync.PyMOLMaestroSync method) getScore() (schrodinger.glide.Conformer method) (schrodinger.infra.mm.LigandScoreStructure method) getScoredStructure() (schrodinger.glide.Pose method) getSD() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getSearchKey() (schrodinger.infra.canvas.ChmQuery method) getSecondaryStructure() (schrodinger.infra.structure.StructureAtom method) getSectionText() (schrodinger.application.jaguar.input.JaguarInput method) getSectorAnnotation() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) getSectorAnnotationLoc() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) getSeed() (schrodinger.application.matsci.mswidgets.RandomSeedWidget method) (schrodinger.application.matsci.permittivity.TaskProtocol method) getSeedFlag() (schrodinger.application.matsci.permittivity.DisorderSystemBuilder class method) (schrodinger.application.matsci.permittivity.StepBase class method) getSegmentPDBNames() (schrodinger.application.matsci.custom_lipid_prep.RenumberLipid method) getSegmentPlaneIntersections() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) getSegmentType() (schrodinger.application.matsci.kmc.Table static method) getSelected() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.ui.qt.propertyselector.PropertySelector method) (schrodinger.ui.qt.propertyselector.PropertySelectorList method) (schrodinger.ui.qt.propertyselector.PropertySelectorMenu method) getSelectedAslNames() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) getSelectedCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) getSelectedDataTitles() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) getSelectedElements() (schrodinger.ui.qt.periodictable.PeriodicTableDialogMultipleClick method) getSelectedEntryIds() (schrodinger.ui.two_d_viewer.TwoDViewer method) getSelectedEntryInfo() (schrodinger.ui.qt.input_selector.InputSelector method) getSelectedExcludedVolumes() (schrodinger.application.phase.featureselector.FeatureModel method) getSelectedFeatureEquivalencies() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) getSelectedFeatures() (schrodinger.application.phase.featureselector.FeatureModel method) (schrodinger.application.phase.featureselector.FeatureSelector method) getSelectedFileName() (schrodinger.application.matsci.builderwidgets.FilteredTemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListToolButton method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateToolButton method) getSelectedIndexes() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) getSelectedItem() (schrodinger.application.matsci.builderwidgets.TemplateSelectorPopUp method) getSelectedItems() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) getSelectedLigand() (schrodinger.ui.chooseligand.ChooseLigandDialog method) getSelectedLocationType() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedMutations() (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) getSelectedName() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedPath() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedPatternName() (schrodinger.ui.ligfilter.LigfilterFrame method) getSelectedPreset() (schrodinger.application.matsci.jagwidgets.PresetsDialog method) getSelectedProp() (schrodinger.application.matsci.chargegui.ChargePropertySelector method) getSelectedResult() (schrodinger.application.bioluminate.antibody.search_results_table.FullTable method) (schrodinger.application.bioluminate.antibody.search_results_table.TableView method) getSelectedResults() (schrodinger.application.bioluminate.antibody.search_results_table.SplitTable method) getSelectedRowAtoms() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) getSelectedRowIndexes() (schrodinger.ui.qt.swidgets.STableWidget method) getSelectedRows() (schrodinger.infra.table.Table method) getSelectedRowTotal() (schrodinger.infra.table.Table method) (schrodinger.project.project.Project method) getSelectedStandardItems() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) getSelectedStructure() (schrodinger.application.matsci.builderwidgets.FilteredTemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateToolButton method) getSelectedStructures() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) getSelectedSurfaceInfos() (schrodinger.maestro_utils.surface_manager.surface_table.SurfaceTable method) getSelectedTemplateName() (schrodinger.application.matsci.builderwidgets.FilteredTemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateToolButton method) getSelectedText() (schrodinger.ui.qt.appframework2.debugwidgets.BaseTable method) getSelectedX() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getSelectedXY() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getSelection() (schrodinger.application.matsci.builderwidgets.TemplateSelector method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListPopUp method) (schrodinger.application.matsci.builderwidgets.TemplateSelectorFilterListToolButton method) (schrodinger.application.matsci.mswidgets.ConvenientSelectorWithPopUp method) (schrodinger.ui.qt.swidgets.SelectorWithPopUp method) getSelectionForceField() (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) getSelectionForceFieldInt() (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) getSelfEnergy() (schrodinger.structutils.minimize.Minimizer method) getSemiPartialRSquaredList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getSeparationRatioList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getSeqsDescriptors() (schrodinger.protein.alignment.BaseAlignment method) getSeqsMatchingRefType() (schrodinger.protein.alignment.BaseAlignment method) getSeqStructure() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) getSeriesXVals() (schrodinger.ui.qt.schart.SChart static method) getSeriesYVals() (schrodinger.ui.qt.schart.SChart static method) getSessionId() (schrodinger.maestro_utils.composer_agent.session_handler.ChatSessionHandler method) getSettings() (schrodinger.ui.qt.appframework2.settings.SettingsMixin method) (schrodinger.ui.qt.config_dialog.ConfigDialog method) (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp method) getSettingsAffectedBySpinTreatment() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) getSettingsFile() (schrodinger.infra.mm.MMPREF method) getSettingsMenuActions() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) GetSGSpin() (in module schrodinger.application.matsci.gsas.GSASIIspc) getShapeReferenceLigand() (schrodinger.glide.JobConstraintData method) GetSHCoeff() (in module schrodinger.application.matsci.gsas.GSASIImath) getShiftedCoulombFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getShiftedLennardJonesFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getShiftVectorByRecenterMass() (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis method) getShortestPathsBetweenAtoms() (schrodinger.infra.canvas.ChmPathTools static method) getShortestPathsBetweenAtomsWithSideChains() (schrodinger.infra.canvas.ChmPathTools static method) getShortestVector() (schrodinger.infra.structure.PBC method) getShortSaltBridge() (schrodinger.glide.ReceptorAtom method) getShow1_4() (schrodinger.infra.structure.ContactParams method) getSibling() (schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter method) getSideAxis() (schrodinger.ui.qt.schart.SChart method) getSigma() (schrodinger.infra.canvas.ChmKPLSParser method) getSigmaScaled() (schrodinger.glide.LigandAtom method) getSigmoidParameters() (schrodinger.energy.FlucCTSystem method) (schrodinger.energy.MetalSystem method) getSignalsAndSlots() (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.ServerRegistrationMixin method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.models.mappers.TargetParamMapper method) (schrodinger.ui.qt.atom_weights_table_widget.WeightSphereManager method) (schrodinger.ui.qt.network_views.NetworkViewer method) (schrodinger.ui.qt.network_visualizer.AbstractNetworkView method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.structure_selector.ImportButtonMixin method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskbarwidgets.NameLineEdit method) getSimilarity() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.AbstractSequence method) getSimilarityMetricDescription() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method) getSimilarityScore() (schrodinger.protein.sequence.AbstractSequence method) getSimpleSlabVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSimplified() (schrodinger.application.matsci.bandshape_utils.Transition static method) getSimplifiedTreeData() (schrodinger.application.pathfinder.route.RouteNode method) getSimulationParam() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getSingleDisplacementChannels() (schrodinger.application.matsci.rxn_channel.ChannelDefinitions method) getSipTermTable() (schrodinger.application.glide_ws.scoring_report.WScoreSipReport method) getSiteNumber() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) getSites() (schrodinger.application.matsci.reaction_workflow_enum_utils.Sites static method) (schrodinger.application.phase.phase_markers.PhaseMarkers method) getSiteType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getSize() (in module schrodinger.infra.canvas) (schrodinger.glide.WaterMap method) (schrodinger.ui.qt.schart.BarSeriesParams method) (schrodinger.ui.qt.schart.SeriesParams method) getSketcherStructure() (schrodinger.application.matsci.builderwidgets.SketcherStructureMixin method) getSkipEtaRotamers() (schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch method) getSlabVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSliceToFit() (schrodinger.application.matsci.kmc.MSDFit method) getSlots() (schrodinger.application.matsci.siteselector.siteselector.Ligand method) (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getSmarts() (schrodinger.analysis.transformations.TransformsRepository method) getSMARTS() (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) (schrodinger.infra.canvas.ChmMol method) (schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog method) getSmartsDictData() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) getSMARTSFromSelection() (schrodinger.ui.ligfilter.AddDefinitionDialog method) getSMARTSPatterns() (schrodinger.ui.qt.swidgets.SMARTSEdit method) getSmiles() (schrodinger.application.matsci.deprecated_pattern.SmilesGenerator method) (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) (schrodinger.infra.canvas.ChmSmilesGenerator method) (schrodinger.infra.canvas.ChmUniqueSmilesGenerator method) getSmilesAndMap() (schrodinger.application.matsci.deprecated_pattern.SmilesGenerator method) (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) (schrodinger.infra.canvas.ChmSmilesGenerator method) (schrodinger.infra.canvas.ChmUniqueSmilesGenerator method) getSmilesChirality() (schrodinger.infra.canvas.ChmAtom method) getSMILESForFrag() (schrodinger.application.matsci.fragments.Fragment method) getSmilesWrappedOutputs() (in module schrodinger.application.steps.test) getSolvationCharge() (schrodinger.infra.structure.StructureAtom method) getSolvent() (schrodinger.application.jaguar.gui.solvent_selector.SolventSelectorFilterListPopUp method) (schrodinger.application.jaguar.gui.solvent_selector.SolventSelectorFilterListToolButton method) getSolventConstraints() (schrodinger.application.matsci.packmol.LiposomeInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) getSolventLayers() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getSolventName() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) getSolventsTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) getSOSTOF() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getSource() (schrodinger.infra.canvas.ChmModelTypeInfo method) (schrodinger.infra.canvas.ChmQuery method) getSourceRowPoint() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) getSources() (schrodinger.application.fpsim.FPsimSearcher method) getSourceType() (schrodinger.infra.canvas.ChmQuery method) getSpanningVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSparseRescodes() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getSpecialProperties() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) getSpecies() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) getSpeciesCount() (schrodinger.application.matsci.species.SpeciesCollection method) getSpeciesFromAtomIndex() (schrodinger.application.matsci.species.SpeciesCollection method) getSpeciesMolNum() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) getSpecificInteractionSummary() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions method) getSpecsString() (schrodinger.application.inputconfig.InputConfig method) getSpectators() (schrodinger.application.jaguar.autots_input.AutoTSInput method) getSpgObjByName() (schrodinger.application.matsci.nano.space_groups.SpaceGroups method) getSpgSymbol() (schrodinger.application.matsci.espresso.qeinput.KpointsType static method) getSphereSliceVol() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getSpinTreatment() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) getSqDispByTime() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getSqDispHistograms() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getSquareVertices() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSSA() (schrodinger.application.prime.wrapper.BasePrimeAlignment method) getSSBondPartner() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) GetSSfxuinel() (in module schrodinger.application.matsci.gsas.GSASIIspc) getSSSR() (schrodinger.infra.canvas.ChmPathTools static method) getSSSRAndAcyclicAtoms() (schrodinger.infra.canvas.ChmPathTools static method) getStability() (schrodinger.infra.canvas.ChmPLSParser method) GetStackParms() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getStageByJobid() (schrodinger.pipeline.pipeline.Pipeline method) getStageDirectory() (schrodinger.pipeline.stage.Stage method) getStageIndex() (schrodinger.application.matsci.mswidgets.MultiStageArea method) getStageIndicesByMarker() (schrodinger.application.matsci.permittivity.MdStageModifier static method) getStages() (schrodinger.application.matsci.permittivity.MultiStageMd method) getStandardOrientation() (schrodinger.glide.Conformer method) getstart_temp() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) getStartFrameValue() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getStartingMagDotIn() (schrodinger.application.matsci.espresso.qeinput.StructureType method) getStartingNodes() (schrodinger.application.pathfinder.route.RouteNode method) getStartPos() (schrodinger.protein.helm.helm_renderer.AABranchingConnectorItem method) (schrodinger.protein.helm.helm_renderer.DisulfideConnectorMixin method) (schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin method) getState() (schrodinger.ui.qt.network_visualizer.Graph method) (schrodinger.ui.qt.swidgets.SValidIndicator method) getStateChargeAndMultiplicity() (schrodinger.application.matsci.fragments.FragmentReactor method) getStateModifier() (schrodinger.application.matsci.fragments.FragmentReactor method) getStatus() (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq method) (schrodinger.application.glide.http_client.ZmqClient method) (schrodinger.infra.canvas.ChmModelReporter method) getStatusStrings() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) getStderr() (schrodinger.job.launchapi.JobSpecification method) getStdout() (schrodinger.job.launchapi.JobSpecification method) getStep() (schrodinger.application.matsci.deswidgets.TrajRangeSelectorDialog method) getStepAtomicCharge() (schrodinger.infra.canvas.ChmGasteigerCharge method) getStepAtomicEneg() (schrodinger.infra.canvas.ChmGasteigerCharge method) getStepClass() (schrodinger.stepper.stepper.StepTaskMixin method) getSteps() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSWorkFlow method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.jwsteps.BaseWorkflow method) getStereo() (schrodinger.infra.canvas.ChmBond method) getStereoDeterminant() (schrodinger.infra.canvas.ChmBond method) getStoichiometry() (schrodinger.application.matsci.mlearn.features.Ligand method) getStorage() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) getstr() (in module schrodinger.application.matsci.msutils) getStrainedAdsorptionLayer() (schrodinger.application.matsci.nano.interface_mod.Interface method) getStrainedAngle() (schrodinger.application.matsci.nano.interface_mod.Interface method) getStretch() (schrodinger.application.matsci.stage_widgets.BaseTableWidgetDefinition method) (schrodinger.structutils.minimize.Minimizer method) getStretchEnergy() (schrodinger.structutils.minimize.Minimizer method) getString() (schrodinger.glide.Config method) (schrodinger.infra.canvas.ChmPattern method) (schrodinger.infra.mm.MMPREF method) (schrodinger.ui.qt.swidgets.SLineEdit method) getStringArray() (schrodinger.glide.Config method) getStringers() (schrodinger.application.matsci.jwsteps.BaseRelaxationStep method) (schrodinger.application.matsci.jwsteps.CompressiveRelaxationStep method) (schrodinger.application.matsci.jwsteps.MatSciMDRelaxationStep method) (schrodinger.application.matsci.jwsteps.MolecularDynamicsStep method) (schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation1Step method) (schrodinger.application.matsci.jwsteps.SemiCrystalRelaxation2Step method) (schrodinger.application.matsci.jwsteps.SingleMDStep method) getStringList() (schrodinger.infra.mm.MMPREF method) getStrucChargeAndSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getStrucEid() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryMacroPkaByPka method) getStruct() (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem method) (schrodinger.application.matsci.equilibrium_md.CmsModel method) (schrodinger.application.matsci.equilibrium_md.Model method) (schrodinger.ui.qt.table.ViewerModel method) getStructEidMap() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) getStructForChild() (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.CombinerStep method) (schrodinger.application.matsci.jwsteps.ExtractClustersStep method) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getStructFromPtEntry() (schrodinger.application.matsci.multiapp.MultiDesmondJobApp method) getStructsForWriting() (schrodinger.application.matsci.jwsteps.BaseDesmondStep method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.jwsteps.BDEStep method) (schrodinger.application.matsci.jwsteps.ExtractClustersStep method) (schrodinger.application.matsci.jwsteps.MacromodelConfSearchStep method) (schrodinger.application.matsci.jwsteps.MultipleStructSplitterStep method) (schrodinger.application.matsci.jwsteps.ReplicateMakerMixin method) getStructsOfType() (schrodinger.application.matsci.jwsteps.BDEStep method) getStructToRender() (schrodinger.ui.two_d_viewer.TwoDViewer method) getStructure() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.jaguar.results.JaguarResults method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.builderwidgets.LigandSketcherStructGetter method) (schrodinger.application.matsci.builderwidgets.RowTemplateMixin method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Results method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jwsteps.BaseStep method) (schrodinger.application.matsci.mswidgets.LipidImporter method) (schrodinger.application.matsci.mswidgets.StructureLoader static method) (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.glide.Conformer method) (schrodinger.glide.ConformerTemplate method) (schrodinger.glide.GridArchive method) (schrodinger.glide.Pose method) (schrodinger.glide.RefinedPose method) (schrodinger.glide.RoughPose method) (schrodinger.infra.mm.MMFragHandle method) (schrodinger.infra.structure.DistanceCell method) (schrodinger.infra.structure.StructureAtom method) (schrodinger.project.project.ProjectRow method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.structure.TextualStructure method) (schrodinger.structutils.minimize.Minimizer method) getStructureFile() (schrodinger.application.qsite.input.QSiteInput method) getStructureForCoupling() (schrodinger.application.matsci.amorphous.BaseMoiety method) getStructureHandle() (schrodinger.infra.structure.StructureAtom method) getStructureOutput() (schrodinger.pipeline.pipeline.Pipeline method) getStructureResForRes() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) getStructureResProperties() (schrodinger.protein.residue.Residue method) getStructures() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.livedesign.entry_types.GenericEntities method) (schrodinger.application.matsci.chargegui.ForceFieldDialog method) (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) (schrodinger.application.matsci.species.SpeciesData method) getStructureSize() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) getStructureTitleForJobname() (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) getStructureWithJagNames() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getStructureWithoutProps() (schrodinger.application.matsci.fragments.UniqueTracker method) getStructureWithProps() (schrodinger.application.matsci.fragments.UniqueTracker method) getStsInfo() (schrodinger.application.livedesign.panel_components.StructSelectionModel method) getSubalignment() (schrodinger.protein.alignment.BaseAlignment method) getSubgroups() (schrodinger.infra.mm.MMPREF method) getSubHostName() (schrodinger.job.launchparams.LaunchParameters method) getSubjobname() (schrodinger.application.matsci.permittivity.WorkflowParser method) getSubjobsLabel() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getSubjobsUnitLabel() (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) getSubParam() (schrodinger.models.parameters.CompoundParam class method) getSubParams() (schrodinger.models.parameters.CompoundParam class method) getSubplotDialog() (schrodinger.ui.qt.navtoolbar.AtomInfoToolbar method) (schrodinger.ui.qt.navtoolbar.NavToolbar method) getSubScaffolds() (schrodinger.infra.canvas.ChmScaffold method) (schrodinger.infra.canvas.ChmScaffoldFinder method) getSubScaffoldsCount() (schrodinger.infra.canvas.ChmScaffoldFinder method) getSubsequence() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) getSubsetSMARTS() (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) getSubsidiaryAtoms() (schrodinger.energy.MetalForceFieldManager method) getSubStAndAids() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) getSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getSuccessCount() (schrodinger.infra.canvas.ChmSmilesFileReader method) getSugarRingPatterns() (schrodinger.application.matsci.automated_cg_mapping.PolysaccharideDetector class method) getSum() (schrodinger.infra.canvas.ChmEstateDescriptors method) getSummary() (schrodinger.application.livedesign.entry_types.BaseEntryData method) getSummaryData() (schrodinger.application.bioluminate.protein_structure_quality.MultiReportWithChart method) getSumX() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) getSuperimposedRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getSuperScaffolds() (schrodinger.infra.canvas.ChmScaffoldFinder method) getSuperScaffoldsCount() (schrodinger.infra.canvas.ChmScaffoldFinder method) getSupportedAtNums() (schrodinger.energy.QRNNPredictor method) getSurface() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getSurfaceArea() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.application.matsci.shapes.Cylinder method) (schrodinger.application.matsci.shapes.Sphere method) getSurfaceComplementarityLimits() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput method) getSurfaceInfo() (schrodinger.maestro_utils.surface_manager.surface_info.SurfaceInfo class method) getSurfaceNodes() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) (schrodinger.application.matsci.freevolume.Void method) getSurfaceNodesFromEntryNode() (schrodinger.maestro_utils.surface_manager.surface_model.SurfaceModel method) getSurfaceNodesFromIndices() (schrodinger.maestro_utils.surface_manager.surface_model.SurfaceModel method) getSurfaceObject() (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceNodeItem method) getSurfacePotential() (schrodinger.application.bioluminate.escomp.PotGrid method) getSurfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getSurfactantConstraints() (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) getSurfactantLayers() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getSwappingGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getSwaps() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) (schrodinger.application.matsci.automated_cg_mapping.DpdMapper method) (schrodinger.application.matsci.automated_cg_mapping.MartiniMapper method) getSymbol() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.ui.qt.periodictable.PeriodicTableDialog method) getSymbolForSMARTS() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) getSymbolicLine() (schrodinger.application.matsci.zmutils.ZAtom method) getSymmetrizedCell() (schrodinger.application.matsci.espresso.qeinput.StructureType static method) getSymmetryGroups() (schrodinger.infra.canvas.ChmPathTools static method) getSyXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath) getTab() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) getTabByLabel() (schrodinger.ui.qt.swidgets.STabWidget method) getTableStyle() (schrodinger.application.matsci.reportutils.PDFBuilder method) getTabParentAndLayout() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) getTargetIndexMap() (schrodinger.application.pathfinder.route.ReagentNode method) getTargetMolecule() (schrodinger.application.matsci.montecarlo.Metropolizer method) getTargetSlot() (schrodinger.models.mappers.TargetParamMapper method) getTask() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) getTaskBar() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) getTaskDir() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.jobtasks.ComboJobTask method) (schrodinger.tasks.slurmtasks.ComboSlurmTask method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.tasks.tasks.ComboSubprocessTask method) getTaskFilename() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.tasks.AbstractTask method) getTaskManager() (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) getTaskName() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getTaskNames() (schrodinger.application.matsci.permittivity.Config method) (schrodinger.application.matsci.permittivity.WorkflowProtocol method) getTaskProtocol() (schrodinger.application.matsci.permittivity.Config method) getTasks() (schrodinger.tasks.queue.TaskQueue method) getTaskSpec() (schrodinger.job.launchapi.TaskSpecificationBuilder method) getTaskSubClass() (schrodinger.application.matsci.permittivity.WorkflowParser class method) getTauT() (in module schrodinger.application.matsci.gsas.GSASIIspc) getTautomerCode() (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) (schrodinger.infra.canvas.ChmMol method) getTautomerCode64() (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) (schrodinger.infra.canvas.ChmMol method) getTCRRegion() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getTCRRegions() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) (schrodinger.protein.annotation.TCRRegionFinder method) getTdSLigandAtom() (schrodinger.infra.mm.LigandScoreStructure method) getTdSSite() (schrodinger.infra.mm.LigandScoreStructure method) getTemperature() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getTempFilename() (schrodinger.application.matsci.density_analysis.DensityAnalysisMixin method) getTempImageFilename() (schrodinger.application.matsci.reportutils.PDFBuilder method) getTemplate() (schrodinger.glide.Conformer method) getTemplateID() (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) getTemplates() (schrodinger.application.matsci.builderwidgets.SketcherBox method) (schrodinger.application.matsci.permittivity.PolymerBuilder static method) (schrodinger.glide.ConformerEnsemble method) getTemplateStructures() (schrodinger.glide.ConformerEnsemble method) getTempPressDataFromJaguarKeywords() (schrodinger.application.matsci.solvation_entropy_utils.TempPressData static method) getTempPressDataFromOptions() (schrodinger.application.matsci.solvation_entropy_utils.TempPressData static method) getTerminalGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) getTerminatingAtoms() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) getTerminatingIdxs() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getTerminiIdxs() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) getTermList() (schrodinger.application.glide_ws.scoring_report.WScoreSipPose method) getTermsFromPose() (schrodinger.application.glide_ws.entropy_score.GreasyScore method) getTestSetNames() (schrodinger.infra.canvas.ChmModelParser method) getTestSetObs() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getTestSetPred() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getTestSetRMSE() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getText() (schrodinger.ui.qt.tablewidget.Cell method) getTextStruct() (schrodinger.application.matsci.builderwidgets.TemplateListWidgetItem method) getTextSummary() (schrodinger.protein.reliability.Results method) getTFactor() (schrodinger.infra.structure.StructureAtom method) getTheoryAndSpinData() (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) getTheoryLevel() (schrodinger.application.jaguar.gui.tabs.base_tab.LoadsTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) getTheoryLevelForEid() (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesTheoryMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTab method) getThermoExts() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) getThermoKeys() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AnalyzeStageData method) getThreadId() (schrodinger.utils.thread_utils.ThreadTool method) getThreadName() (schrodinger.utils.thread_utils.ThreadTool method) getThreeLetterResidueCode() (schrodinger.ui.residueselector.ResidueGroups method) getTime() (schrodinger.application.matsci.jobdirdlg.JobManager method) getTimeBinIdx() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getTimeBinWidth() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getTimeHistograms() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getTimePS() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getTimeSqDispPairs() (schrodinger.application.matsci.kmc.MSDVariableTimeStep method) getTimeStepFromModel() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets class method) getTimestepPS() (schrodinger.application.matsci.deswidgets.DesmondMDWidgets method) getTitle() (schrodinger.application.matsci.desconfig.AveCellMSJStringer method) (schrodinger.application.matsci.desconfig.BrownieMSJStringer method) (schrodinger.application.matsci.desconfig.MDMSJStringer method) (schrodinger.application.matsci.desconfig.MSAnalysisMSJStringer method) (schrodinger.application.matsci.desconfig.MSJStringer method) (schrodinger.infra.canvas.ChmMmctAdaptor method) (schrodinger.infra.structure.Structure 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) getTodoAtoms() (schrodinger.application.matsci.espresso.qeinput.PHControlType static method) getTOFalpha() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFalphaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFbeta() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFbetaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFgamma() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFgammaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFsig() (in module schrodinger.application.matsci.gsas.GSASIImath) getTOFsigDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getToken() (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel method) getTokens() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) getTolerance() (schrodinger.glide.CoreDefinition method) getToolBar() (schrodinger.application.bioluminate.actions.factory.Factory method) getTopLocationItem() (schrodinger.ui.qt.forcefield.pathselectorwidget.PathSelectorWidget method) getTorsion() (schrodinger.application.desmond.packages.staf.GeomCalc method) (schrodinger.structutils.minimize.Minimizer method) getTorsionalConstraints() (schrodinger.glide.LigandConstraintData method) getTorsionConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) getTorsionDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath) getTorsionEnergy() (schrodinger.structutils.minimize.Minimizer method) getTorsions() (schrodinger.glide.Conformer method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.AbstractTorsionAnalyzer method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.NucleotideTorsions method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.ResiduesTorsions method) (schrodinger.trajectory.trajectory_gui_dir.custom_analyzers.SmallMoleculeTorsions method) GetTorsionSig() (in module schrodinger.application.matsci.gsas.GSASIImath) getTorsionValueInRange() (schrodinger.application.matsci.amorphous.TorsionAngler method) getTotal14Pair() (schrodinger.structutils.minimize.Minimizer method) getTotalAggregation() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalAtom() (schrodinger.structutils.minimize.Minimizer method) getTotalBending() (schrodinger.structutils.minimize.Minimizer method) getTotalCharge() (schrodinger.application.matsci.mswidgets.SystemInformationFrame method) (schrodinger.infra.structure.Structure method) getTotalCIonThickness() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getTotalCols() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getTotalComplementarity() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalEnergy() (schrodinger.energy.MlffOutput method) (schrodinger.structutils.minimize.Minimizer method) getTotalHydrogenBondCount() (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions method) getTotalHydrogens() (schrodinger.infra.canvas.AtomicInvariant method) getTotalHydropathy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalImpTorsion() (schrodinger.structutils.minimize.Minimizer method) getTotalInteractionCount() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions method) getTotalInteractionCountLimits() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput method) getTotalIteration() (schrodinger.infra.canvas.ChmGasteigerCharge method) getTotalMovieFrames() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) getTotalNCombinations() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) getTotalNonSurfactantThickness() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getTotalOpenMPCPUs() (schrodinger.ui.qt.config_dialog.ConfigDialog method) getTotalpKa() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalPotentialEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalPrimeEnergy() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalProcessors() (schrodinger.job.queue.ResourceHost method) getTotalRotatableBonds() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalSASA() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalSASANonPolar() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalSASAPolar() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalSolubility() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalStretch() (schrodinger.structutils.minimize.Minimizer method) getTotalSurfactantThickness() (schrodinger.application.matsci.packmol.StructuredLiquidInputFile method) getTotalSurfComp() (schrodinger.application.bioluminate.protein.protein.PropertyCalculator method) getTotalTime() (schrodinger.application.jaguar.gui.timing.TimingResults method) getTotalTorsion() (schrodinger.structutils.minimize.Minimizer method) getTotalTypes() (schrodinger.graphics3d.common.Group method) getTotalValence() (schrodinger.infra.canvas.AtomicInvariant method) (schrodinger.infra.canvas.ChmAtom method) getTPP() (schrodinger.job.launchparams.LaunchParameters method) getTrace() (schrodinger.trajectory.prody.nma.NMA method) getTrainingSetNames() (schrodinger.infra.canvas.ChmModelParser method) getTrainingSetObs() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getTrainingSetPred() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getTrajectoryFromCms() (schrodinger.application.matsci.permittivity.MdPostTrajectoryAnalysis static method) getTrajectoryName() (schrodinger.application.matsci.jwsteps.BaseDesmondStep method) (schrodinger.application.matsci.jwsteps.DiffusionGKStep method) (schrodinger.application.matsci.jwsteps.DiffusionMSDStep method) (schrodinger.application.matsci.jwsteps.PenetrantLoadingStep method) (schrodinger.application.matsci.jwsteps.SurfaceTensionStep method) getTrajFlags() (schrodinger.application.matsci.deswidgets.TrajAnalysisGuiMixin method) getTrans() (schrodinger.infra.canvas.ChmBond method) getTransitionStateNames() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) getTranslation() (schrodinger.protein.sequence.NASequence method) (schrodinger.protein.sequence.NucleicAcidSequence method) getTranslationToBox() (schrodinger.application.matsci.amorphous.Box method) getTree() (schrodinger.application.matsci.espresso.qeoutput.Output method) getTreeData() (schrodinger.application.pathfinder.route.RouteNode method) getTreePath() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) getTrialScales() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) getTrimmedTable() (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile static method) getTrueValues() (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) getTubeSpacings() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getType() (schrodinger.glide.Config method) (schrodinger.infra.canvas.ChmBitComparable32 method) (schrodinger.infra.canvas.ChmBitComparable64 method) (schrodinger.infra.canvas.ChmLicenseAutoQsar method) (schrodinger.infra.canvas.ChmLicenseElements method) (schrodinger.infra.canvas.ChmLicenseFull method) (schrodinger.infra.canvas.ChmLicenseMain method) (schrodinger.infra.canvas.ChmLicenseMatSci method) (schrodinger.infra.canvas.ChmLicenseShared method) (schrodinger.infra.canvas.ChmLicenseXCluster method) (schrodinger.infra.mm.MMPREF method) getTypeHint() (schrodinger.models.parameters.DictParam method) (schrodinger.models.parameters.ListParam method) (schrodinger.models.parameters.Param method) (schrodinger.models.parameters.SetParam method) getTypeInfo() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmFPOut32 method) (schrodinger.infra.canvas.ChmFPOut64 method) getTypeInfoEx() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getTyper() (schrodinger.energy.MetalForceFieldManager method) getUID() (schrodinger.infra.canvas.ChmFPTypeInfo method) (schrodinger.infra.canvas.ChmObjChmAtomImpl method) (schrodinger.infra.canvas.ChmObjChmAtomTyperImpl method) (schrodinger.infra.canvas.ChmObjChmMatcherImpl method) (schrodinger.infra.canvas.ChmObjChmQueryImpl method) (schrodinger.infra.canvas.ChmSDReaderImpl method) getUncompressedStorage() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) getUnionCount() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) getUnionOfDataFields() (schrodinger.infra.canvas.ChmSDReader method) GetUnique() (in module schrodinger.application.matsci.gsas.GSASIIlattice) getUniqueDefNames() (schrodinger.application.matsci.cg_mapping.CGMapperMixin static method) getUniqueFilter() (schrodinger.infra.canvas.ChmQueryMatcher method) getUniqueItems() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) getUniqueLigands() (schrodinger.application.matsci.buildcomplex.ComplexSplitter static method) getUniqueMolNums() (schrodinger.application.matsci.rdpattern.Pattern method) getUniqueProductTrackers() (schrodinger.application.matsci.fragments.FragmentReactor method) getUniqueSmiles() (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) getUniqueSmilesAndMap() (schrodinger.infra.canvas.ChmMmctSmilesGenerator method) getUniqueSpecies() (schrodinger.application.matsci.automated_cg_mapping.StructureAnalyzer method) getUnitNormalToDeltaForces() (schrodinger.application.matsci.mecp_mod.MECPStep method) getUnits() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis static method) getUnitsData() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis method) getUnknownKeywords() (schrodinger.application.jaguar.input.JaguarInput method) getUnpairedElectronCount() (schrodinger.infra.canvas.ChmAtom method) getUnusedHostList() (schrodinger.pipeline.pipeline.StageJob method) getUpdated() (schrodinger.glide.Config method) getUpdatedCMSModelCopy() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) getUpdatedCParams() (schrodinger.application.matsci.nano.interface_mod.Interface method) getUpdatedFrameStructure() (schrodinger.trajectory.trajectory_gui_dir.frame_structure_exporter.FrameStructureExporter method) getUpperBound() (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) getUseCustomOPLS() (schrodinger.ui.qt.forcefield.ffsettingsbutton.FFSettingsButton method) getUsedHosts() (schrodinger.pipeline.pipeline.Pipeline method) getUserData() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) (schrodinger.infra.canvas.ChmMol method) getUserDefinedASLSets() (schrodinger.project.project.Project method) getUserLabelFormat() (schrodinger.infra.structure.StructureAtom method) getUserLabelText() (schrodinger.infra.structure.StructureAtom method) getUsername() (schrodinger.application.livedesign.login.LoginManager method) (schrodinger.application.livedesign.login_gui2.LDLoginPanelModel method) getUserOutputFiles() (schrodinger.pipeline.pipeline.Pipeline method) getUserOutputs() (schrodinger.pipeline.pipeline.Pipeline method) getUserTemplateList() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getUserText() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) getUserWavelengths() (schrodinger.application.matsci.permittivity.ElectricPolarizability static method) getUtilityDescriptors() (schrodinger.application.matsci.mlearn.features.ComplexFeatures method) getUUID() (schrodinger.infra.structure.Structure method) getValidatedOPLSDir() (schrodinger.application.matsci.multiapp.MultiJobApp method) getValidator() (schrodinger.application.matsci.deswidgets.DesmondMDWEdit method) getValue() (schrodinger.application.jaguar.autots_bonding.Coordinate method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.mopac.structure_launchers.StructureLauncher method) (schrodinger.application.xtb.input.XTBInput method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.infra.canvas.ChmValueAssignment method) (schrodinger.infra.structure.AtomPairWithValue method) (schrodinger.models.mappers.AttrTargetSpec method) (schrodinger.models.mappers.ParamTargetSpec method) (schrodinger.models.mappers.TargetSpec method) (schrodinger.ui.qt.swidgets.STableWidgetItem method) getvalue() (schrodinger.utils.ligfilter.AslCriterion method) (schrodinger.utils.ligfilter.Criterion method) (schrodinger.utils.ligfilter.PredefinedCriterion method) (schrodinger.utils.ligfilter.PropertyCriterion method) (schrodinger.utils.ligfilter.SmartsCriterion method) getValueFromItem() (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) getValues() (schrodinger.application.matsci.atom_group.HelixData method) (schrodinger.application.matsci.mswidgets.MultiSlider method) (schrodinger.application.matsci.reaction_workflow_gui_utils.UniformSequence method) (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) (schrodinger.ui.qt.swidgets.SpinBoxDoubleSlider method) getValuesFromFile() (schrodinger.application.matsci.kmcgui.PropertyCombo method) getValuesFromStr() (schrodinger.ui.qt.swidgets.SCheckBoxEdit static method) getValuesOfColumn() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) getVariableLines() (schrodinger.application.matsci.zmutils.ZAtom method) getVariableNames() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getVariance() (schrodinger.trajectory.prody.mode.Mode method) getVariances() (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getVbmCbm() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) getVCov() (in module schrodinger.application.matsci.gsas.GSASIImath) getVDWSurfaceArea() (schrodinger.application.matsci.mlearn.features.Complex method) getVDWVolume() (schrodinger.application.matsci.mlearn.features.Complex method) getVec() (schrodinger.application.matsci.mlearn.features.Ligand method) getVector() (schrodinger.application.desmond.packages.staf.GeomCalc method) getVectorizedDescriptors() (schrodinger.application.matsci.mlearn.features.Complex method) getVerbosity() (schrodinger.pipeline.stage.Stage method) getVertices() (schrodinger.application.matsci.nano.plane.CrystalPlane method) (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.graphics3d.polyhedron.MaestroCube method) (schrodinger.graphics3d.polyhedron.MaestroDodecahedron method) (schrodinger.graphics3d.polyhedron.MaestroIcosahedron method) (schrodinger.graphics3d.polyhedron.MaestroOctahedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) (schrodinger.graphics3d.polyhedron.MaestroTetrahedron method) getVerticesOfAllPlanes() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getVibPartitionFunction() (schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction static method) getVibrationalTemperature() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getVibStates() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getVibStateWeight() (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis method) getVirial() (schrodinger.energy.MlffOutput method) getVisibleColCount() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) getVisibleColumnIndex() (schrodinger.infra.table.Table method) getVisibleColumnTotal() (schrodinger.infra.table.Table method) getVisibleHydrogenCount() (schrodinger.infra.canvas.ChmAtom method) getVisiblePropertyNames() (schrodinger.project.project.Project method) getVisibleRowIndex() (schrodinger.infra.table.Table method) getVisibleRowTotal() (schrodinger.infra.table.Table method) getVoidData() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getVoidVolumes() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getVol() (schrodinger.application.matsci.packmol.ElongatedMicelleInputFile method) (schrodinger.application.matsci.packmol.MicelleInputFile method) (schrodinger.application.matsci.packmol.MonolayerInputFile method) (schrodinger.application.matsci.packmol.WormlikeMicelleInputFile method) getVoltage() (schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan method) getVolume() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Cylinder method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Parallelepiped method) (schrodinger.application.matsci.shapes.Sphere method) (schrodinger.application.matsci.shapes.Tetrahedron method) (schrodinger.infra.structure.PBC method) getVolumeName() (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceNodeItem method) getVolumeVisibility() (schrodinger.project.surface.ProjectSurface method) getVolumeVisibilty() (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceNodeItem method) getVSliderIndexes() (schrodinger.application.matsci.plotwidgets.SliderchartVLPlot method) getVSliderMax() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getVSliderMin() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getWaterModelDict() (schrodinger.application.matsci.mswidgets.WaterTypesComboBox method) getWaterStructure() (schrodinger.glide.GridArchive method) getWavAndPolar() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWavAndPolars() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWavAndProp() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWavAndProps() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWave() (in module schrodinger.application.matsci.gsas.GSASIImath) getWavelengths() (schrodinger.application.matsci.permittivity.ElectricPolarizability class method) getWeakestBonds() (schrodinger.application.matsci.fragments.UniqueTracker method) getWeightedRingGraph() (schrodinger.application.matsci.automated_cg_mapping.CGGraphHelper static method) getWeights() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector.ChargeSelectorLineEdit method) (schrodinger.infra.canvas.ChmAtomTyperEstate method) (schrodinger.trajectory.prody.ensemble.Ensemble method) getWidget() (schrodinger.application.matsci.stage_widgets.BaseTableWidgetDefinition method) getWidth() (schrodinger.ui.qt.tablewidget.Column method) getWidthParameter() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getWidthsCW() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getWidthsTOF() (in module schrodinger.application.matsci.gsas.GSASIIpwd) getWmapWater() (schrodinger.glide.WaterMap method) getWord() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) getWorkerTimeoutInSeconds() (schrodinger.seam.options.pipeline_options.SeamOptions method) getWorkflowPaths() (schrodinger.application.matsci.wfmanagement.WorkflowFinder method) getWorkflowType() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) getWorkspaceCounts() (schrodinger.protein.alignment.BaseAlignment method) getWorkspaceStructure() (schrodinger.ui.qt.appframework2.af2.App method) getWriter() (schrodinger.infra.structure.StructureWriter static method) getX() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmModelTypeInfo method) getX2() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) GetXsectionCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem) getXtalCell() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getXTBEnergyOutput() (in module schrodinger.energy) getXtbParams() (schrodinger.energy.MlffFixedInteractions method) getXY() (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) getXYZ() (schrodinger.application.matsci.atom_group.MSAtom method) (schrodinger.glide.ConformerTemplate method) (schrodinger.infra.structure.StructureAtom method) (schrodinger.structure.Structure method) GetXYZDist() (in module schrodinger.application.matsci.gsas.GSASIImath) getXyzRef() (schrodinger.glide.Pose method) (schrodinger.glide.PoseAtom method) getY() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmModelTypeInfo method) getYvar() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) getZ() (schrodinger.infra.canvas.ChmAtom method) getZeroOrderBonds() (schrodinger.infra.canvas.ChmMol method) getZeroPointEnergy() (schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties method) getZmatrix() (schrodinger.application.matsci.rxn_path.InternalCoords method) getZmatText() (schrodinger.application.jaguar.input.JaguarInput method) getZoomCell() (schrodinger.ui.two_d_viewer.TwoDViewer method) gg_task (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) ggraph (schrodinger.ui.qt.network_visualizer.Graph property) GhostAtomIndexError gibbs (schrodinger.application.jaguar.thermochemical_properties.ThermoProps attribute) (schrodinger.application.jaguar.utils.FreeEnergy attribute) gibbs_energy_property_string() (in module schrodinger.application.jaguar.utils) gid() (schrodinger.application.desmond.cms.Cms method) gid_refresh() (schrodinger.application.desmond.cms.Cms method) gids() (schrodinger.application.desmond.packages.staf.Positer method) GIF_FNAME (schrodinger.ui.qt.swidgets.SpinnerIcon attribute) GIPAWType (class in schrodinger.application.matsci.espresso.qeinput) giveHelp() (schrodinger.ui.qt.swidgets.SDialog method) GlassTransitionTemperature (class in schrodinger.application.matsci.genetic_optimization) glibc() (in module schrodinger.application.jaguar.textparser) Glide glide_data (schrodinger.application.glide.http_server.GlideHTTPHandler attribute) glide_finish() (schrodinger.application.glide.http_server.GlideHTTPHandler method) glide_grid_file (schrodinger.application.steps.docking.GlideSettings attribute) glide_grid_fileChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_grid_fileReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_http_handler (schrodinger.application.glide.http_server.GlideHTTPServer attribute) glide_in_file (schrodinger.application.steps.docking.GlideSettings attribute) glide_in_fileChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_in_fileReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_infile (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) glide_infileChanged (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) glide_infileReplaced (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) glide_input_overrides (schrodinger.application.steps.docking.GlideSettings attribute) glide_input_overridesChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_input_overridesReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_merge() (in module schrodinger.application.glide_ws.utils) glide_minimizer_options (schrodinger.application.peptide_workflow.beam_adapter.GlideSettings attribute) glide_name (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode attribute) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode attribute) (schrodinger.application.glide_ws.nodes.MMGBSACrossNode attribute) (schrodinger.application.glide_ws.nodes.MMGBSADecoysNode attribute) (schrodinger.application.glide_ws.nodes.MMGBSANode attribute) (schrodinger.application.glide_ws.nodes.MMGBSATestsetNode attribute) glide_node (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode property) glide_raw_filename() (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) glide_ref_ligand_file (schrodinger.application.steps.docking.GlideSettings attribute) glide_ref_ligand_fileChanged (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_ref_ligand_fileReplaced (schrodinger.application.steps.docking.GlideDocker.Settings attribute) (schrodinger.application.steps.docking.GlideSettings attribute) (schrodinger.application.steps.docking.MaeGlideDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDocker.Settings attribute) (schrodinger.application.steps.docking.SmilesDockerSettings attribute) glide_request (schrodinger.application.glide.http_server.GlideHTTPServer attribute) glide_send_response() (schrodinger.application.glide.http_server.GlideHTTPHandler method) glide_server_log_level() (in module schrodinger.application.steps.docking) GLIDE_SERVER_START_TASK_CLASS (schrodinger.application.steps.docking.GlideDocker attribute) (schrodinger.application.steps.docking.MaeGlideDocker attribute) (schrodinger.application.steps.docking.SmilesDocker attribute) glide_shutdown_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) glide_stop (schrodinger.application.glide.http_server.GlideHTTPHandler attribute) glide_timeout (schrodinger.application.glide.http_server.GlideHTTPServer attribute) glide_ws_license_exists() (in module schrodinger.glide) GlideALControl (class in schrodinger.application.vss.control) GlideBaseNode (class in schrodinger.application.glide_ws.nodes) GlideClientModule (class in schrodinger.application.glide.client_module) GlideClientModuleAdapter (class in schrodinger.application.glide.client_module) GlideControl (class in schrodinger.application.vss.control) GlideDock (class in schrodinger.seam.yaml.transforms) GlideDocker (class in schrodinger.application.steps.docking) GlideDocker.Settings (class in schrodinger.application.steps.docking) GlideDockingResult (class in schrodinger.application.glide.runner) GlideError GlideHTTPHandler (class in schrodinger.application.glide.http_server) GlideHTTPServer (class in schrodinger.application.glide.http_server) GlideJob (class in schrodinger.application.glide.job) GlideLicenseRequirements (class in schrodinger.application.glide.license_requirements) GlideResult (class in schrodinger.application.glide.http_client) GlideResultIterator (class in schrodinger.application.glide.http_client) GlideRunnerState (class in schrodinger.application.glide.runner) GlideServerManager (class in schrodinger.application.glide.http_client) GlideSettings (class in schrodinger.application.peptide_workflow.beam_adapter) (class in schrodinger.application.steps.docking) GlideSortStage (class in schrodinger.pipeline.stages.glide) GlideSortUtility (class in schrodinger.application.glide.sort_utils) GlideStage (class in schrodinger.application.fragment_virtual_screening.frag_vs_stages) GlideTask (class in schrodinger.application.livedesign.tasks) GlideTask.Input (class in schrodinger.application.livedesign.tasks) GlideTask.JobConfig (class in schrodinger.application.livedesign.tasks) GlideTask.Output (class in schrodinger.application.livedesign.tasks) GlideWorkspaceMarkers (class in schrodinger.application.glide.gui) GlideWSError GlideWSJob (class in schrodinger.application.glide_ws.driver) Glnh() (in module schrodinger.application.matsci.gsas.GSASIIlattice) global_annotations (schrodinger.protein.alignment.BaseAlignment property) global_st_file (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) global_st_fileChanged (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) global_st_fileReplaced (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) GlobalActionsMenu (class in schrodinger.maestro_utils.surface_manager.menus) GLOW_COLOR (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) glue() (in module schrodinger.application.desmond.packages.topo) (schrodinger.application.desmond.cms.Cms method) glue_cms() (in module schrodinger.application.desmond.packages.topo) glued_topology (schrodinger.application.desmond.cms.Cms property) GlutamicAcidpKaPredictor (class in schrodinger.protein.protassign.pka_prediction) GLY (schrodinger.ui.qt.rama.RamaResidueType attribute) GLYCINE_RICH_LOOP (schrodinger.protein.annotation.KinaseFeatureLabel attribute) Gmat2A() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Gmat2AB() (in module schrodinger.application.matsci.gsas.GSASIIlattice) Gmat2cell() (in module schrodinger.application.matsci.gsas.GSASIIlattice) gnode (schrodinger.ui.qt.network_visualizer.Node property) GOOD_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) gotStatus (schrodinger.application.glide.http_client.NonBlockingGlideServerManagerZmq attribute) (schrodinger.application.glide.http_client.ZmqClient attribute) gpcr_anno (schrodinger.protein.gpcr.tasks.GPCRTask.Output attribute) gpcr_generic_number (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) gpcr_segment (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Nucleotide attribute) (schrodinger.protein.residue.Residue attribute) GPCRSegmentFinder (class in schrodinger.protein.annotation) GPCRSegmentLabel (class in schrodinger.protein.annotation) GPCRTask (class in schrodinger.protein.gpcr.tasks) GPCRTask.Input (class in schrodinger.protein.gpcr.tasks) GPCRTask.Output (class in schrodinger.protein.gpcr.tasks) Gpu (class in schrodinger.tasks.hosts) GPU (schrodinger.job.resource.ComputeType attribute) gpu() (schrodinger.energy.AniPredictor method) gpu_count (schrodinger.gpgpu.MIGInfo attribute) gpu_hosts_available() (in module schrodinger.ui.qt.config_dialog) GPU_ONLY (schrodinger.tasks.jobtasks.AllowedHostTypes attribute) GPU_PLACEHOLDER_ARG (schrodinger.tasks.jobtasks.HostSettings attribute) GPU_SUBHOST (schrodinger.application.matsci.configdlgs.DesmondSubhostConfigDialog attribute) GPU_UNIT_LABEL (schrodinger.application.matsci.configdlgs.PerStrucConfigDialog attribute) (schrodinger.application.matsci.configdlgs.PerStrucSingleGpuConfigDialog attribute) (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) GPUConfigDialog (class in schrodinger.ui.qt.config_dialog) GPUExampleWorkflow (class in schrodinger.seam.testing.test_pipelines) GpuHostProductMode (class in schrodinger.ui.qt.config_dialog) GPUTransform (class in schrodinger.seam.testing.test_pipelines) GPUTYPE (schrodinger.tasks.hosts.Host attribute) grad_prec (schrodinger.application.jaguar.results.ConvCriteria attribute) gradient (schrodinger.energy.AniEnergyOutput attribute) (schrodinger.energy.QRNNEnergyOutput attribute) (schrodinger.energy.XTBEnergyOutput attribute) gradient_convergence (schrodinger.forcefield.ffld_options.MinimizationOptions attribute) gradient_criterion (schrodinger.structutils.minimize.Minimizer property) GradientDefinition (class in schrodinger.application.matsci.stylemanager) Gradients (class in schrodinger.application.matsci.stylemanager) gradients (schrodinger.energy.MetalComplexOutput attribute) graft() (in module schrodinger.application.bioluminate.antibody.grafting) graft_constant_domain() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) graft_constant_domains() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) graft_residues (schrodinger.application.livedesign.tasks.AbHumanizationTask.Input attribute) graft_residuesChanged (schrodinger.application.livedesign.tasks.AbHumanizationTask.Input attribute) graft_residuesReplaced (schrodinger.application.livedesign.tasks.AbHumanizationTask.Input attribute) graft_structures() (in module schrodinger.application.bioluminate.antibody.antibody_modeling_yaml) grafted_sts (schrodinger.application.bioluminate.antibody.grafting.GraftingOutput attribute) GraftingInput (class in schrodinger.application.bioluminate.antibody.grafting) GraftingOutput (class in schrodinger.application.bioluminate.antibody.grafting) Graph (class in schrodinger.ui.qt.network_visualizer) graph (schrodinger.application.jaguar.hess_guess.CoordinateManager attribute) (schrodinger.ui.qt.network_visualizer.Edge property) graph_ASP_curves() (in module schrodinger.application.jaguar.pk50_report) graphChanged (schrodinger.ui.qt.network_visualizer.GraphSignals attribute) GraphData (class in schrodinger.application.jaguar.macro_pka_utils) GraphSignals (class in schrodinger.ui.qt.network_visualizer) GRAY (schrodinger.application.matsci.stylemanager.Shades attribute) (schrodinger.ui.qt.standard.colors.NativeColors attribute) Gray3 (schrodinger.protein.helm.helm_renderer.HexColor attribute) Gray4 (schrodinger.protein.helm.helm_renderer.HexColor attribute) Gray6 (schrodinger.protein.helm.helm_renderer.HexColor attribute) GRAY_05 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_10 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_20 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_30 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_40 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GRAY_90 (schrodinger.ui.qt.standard.design_tokens.GrayColors attribute) GrayColors (class in schrodinger.ui.qt.standard.design_tokens) GreasyScore (class in schrodinger.application.glide_ws.entropy_score) GREATER (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.NumericOperator attribute) GREATER_THAN (schrodinger.application.matsci.genetic_optimization.Property attribute) GREEDY (schrodinger.active_learning.al_utils.SelectionRule attribute) greedySelect() (schrodinger.active_learning.al_node.PrepareSmilesNode method) GREEN (schrodinger.application.matsci.stylemanager.Shades attribute) (schrodinger.application.matsci.stylemanager.SolidColors attribute) (schrodinger.ui.qt.standard.colors.NativeColors attribute) GREEN() (in module schrodinger.utils.color) green_lagrange_strain (schrodinger.application.matsci.elasticity.strain.Deformation property) greyColorMap() (in module schrodinger.application.matsci.plotwidgets) Grid (class in schrodinger.application.bindingsite.cavutils) (class in schrodinger.application.glide.grid) (class in schrodinger.pipeline.pipeio) grid (schrodinger.application.matsci.freevolume.GridRadius attribute) (schrodinger.application.peptide_workflow.beam_adapter.GlideSettings attribute) (schrodinger.infra.mm.MMFfldEspData attribute) grid() (in module schrodinger.ui.qt.layout) GRID_CENTER (schrodinger.application.transforms.dockers.box.BoxSettings attribute) GRID_DENSITY (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) GRID_DENSITY_REV (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) grid_file (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.Input attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask.Input attribute) grid_fileChanged (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.Input attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask.Input attribute) grid_fileReplaced (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Input attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.Input attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask.Input attribute) grid_gen_params (schrodinger.application.transforms.dockers.multi_receptor_dock.MultiReceptorDockSettings attribute) (schrodinger.application.transforms.dockers.redock.ReDockSettings attribute) grid_property (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) GridArchive (class in schrodinger.glide) GridBox (class in schrodinger.graphics3d.gridbox) GridCenter (class in schrodinger.application.glide.gui) GridContainer (class in schrodinger.ui.residueselector) gridContextMenuRequested() (schrodinger.ui.two_d_viewer.TwoDViewer method) gridfile (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.glide_ws.model.Complex property) gridfileChanged (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) gridfileReplaced (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) Gridgen (class in schrodinger.application.glide.job) gridgen_job() (schrodinger.application.glide_ws.model.Complex method) gridgen_sif() (schrodinger.application.glide_ws.model.Complex method) GridgenLicense() (in module schrodinger.glide) GridgenLicenseRequirements (class in schrodinger.application.glide.license_requirements) GridGenNode (class in schrodinger.application.glide_ws.nodes) GridgenRunningException GridgenStage (class in schrodinger.pipeline.stages.glide) GridgenTask (class in schrodinger.application.glide.ligand_designer) GridgenTask.Input (class in schrodinger.application.glide.ligand_designer) GridgenTask.Output (class in schrodinger.application.glide.ligand_designer) gridJobStarted (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) GridLayoutPopUp (class in schrodinger.ui.residueselector) gridname (schrodinger.application.glide_ws.model.Complex property) gridNeighbors() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) GridRadius (class in schrodinger.application.matsci.freevolume) GridSaveImagesDialogModel (class in schrodinger.ui.two_d_viewer) GridSite (class in schrodinger.application.glide.gui) GROOVE_THICKNESS (schrodinger.application.matsci.mswidgets.MultiSlider attribute) ground_multipole_qm() (in module schrodinger.application.jaguar.textparser) Group (class in schrodinger.graphics3d.common) group (schrodinger.project.manager.EntryGroupManager property) (schrodinger.project.project.ProjectRow property) group() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) (schrodinger.infra.canvas.ChmClusterGrouper method) group_by_connectivity() (in module schrodinger.structutils.analyze) group_infos_by_layer() (in module schrodinger.application.matsci.packmol) GROUP_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) group_ligand_het_states() (in module schrodinger.protein.protassign.changeables) GROUP_MEMBERS_KEY (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints attribute) group_objects_by_hash() (in module schrodinger.application.matsci.species) group_score (schrodinger.glide.GroupPhobscorePacking attribute) group_subtuples_by_key_and_value() (in module schrodinger.application.matsci.nano.particle) group_with_comparison() (in module schrodinger.application.jaguar.utils) groupAtoms() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) (schrodinger.application.matsci.atom_group.MSAtomGroup method) (schrodinger.application.matsci.atom_group.MSRingAtomGroup method) GroupAverageLinkage (schrodinger.infra.canvas.ChmHierarchicalClustering attribute) groupby_stoichiometry() (in module schrodinger.application.jaguar.utils) GroupByKey (class in schrodinger.seam.testing.benchmarks) GroupByKeyDiskSpaceWithLargeValues (class in schrodinger.seam.testing.benchmarks) GroupByKeyLargeElements_memory (class in schrodinger.seam.testing.benchmarks) GroupByKeyLargeValues_runtime (class in schrodinger.seam.testing.benchmarks) GroupByKeyWithManyDataChunkFiles (class in schrodinger.seam.testing.benchmarks) GroupByKeyWithSlowCoder (class in schrodinger.seam.testing.benchmarks) groupFragments() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) groupFragmentsByPattern() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) groupHidden() (schrodinger.graphics3d.common.Primitive method) groupIdx() (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis class method) GroupingMethodSelector (class in schrodinger.application.matsci.speciesgui) GroupIntoBatches (class in schrodinger.seam.transforms.core) GroupIntoBins (class in schrodinger.seam.transforms.grouping) groupName() (schrodinger.maestro_utils.maestro_sync.ProjectEntryMaestroSync method) GroupPhobscorePacking (class in schrodinger.glide) groups (schrodinger.glide.PhobscoreData attribute) (schrodinger.project.project.Project property) groupShown() (schrodinger.graphics3d.common.Primitive method) groupSymmetricBeads() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) groupTitleChanged (schrodinger.project.manager.EntryGroupManager attribute) GroupType (class in schrodinger.application.desmond.packages.analysis) Grow (class in schrodinger.application.matsci.nano.sheet) grow_fragment() (in module schrodinger.protein.buildpeptide) grow_marker (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) grow_mult() (in module schrodinger.structutils.build) grow_peptide() (in module schrodinger.infra.structure) growEnsemble() (schrodinger.application.glide_ws.optimizer.WScoreOptimizer method) grower (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) growFragmentCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) GROWINDICIES (schrodinger.application.matsci.nano.sheet.Grow attribute) growname (schrodinger.structure.StructureAtom property) growNodeCluster() (schrodinger.application.matsci.automated_cg_mapping.ResidueData method) GrowthSpaceGenerator (class in schrodinger.infra.growthspace) gscore (schrodinger.glide.ScoreInfo attribute) gscore_coeff (schrodinger.application.glide.sort_utils.CustomScoringFunction attribute) GTot_S_epsilon (schrodinger.application.jaguar.results.ThermoCollection attribute) (schrodinger.application.jaguar.textparser.ThermoTotalEnergies attribute) GTot_S_epsilon_alpha (schrodinger.application.jaguar.results.ThermoCollection attribute) (schrodinger.application.jaguar.textparser.ThermoTotalEnergies attribute) GTot_S_omega (schrodinger.application.jaguar.results.ThermoCollection attribute) (schrodinger.application.jaguar.textparser.ThermoTotalEnergies attribute) GTotal (schrodinger.application.jaguar.results.ThermoCollection attribute) (schrodinger.application.jaguar.textparser.ThermoTotalEnergies attribute) Guanine (schrodinger.protein.helm.helm_renderer.HexColor attribute) guard() (schrodinger.tasks.tasks.AbstractTask method) guard_method() (schrodinger.tasks.tasks.SignalTask static method) guess_seq_type() (in module schrodinger.protein.sequence) guess_value_type() (schrodinger.utils.sea.sea.Atom static method) guessAccepted() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) GUESSCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) guessMode() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) GuessOrbital (class in schrodinger.application.jaguar.input) guessOrder() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) guessRejected() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) GUI (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.CallingContext attribute) gui_closed (schrodinger.ui.qt.appframework2.baseapp.BasePanel attribute) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin attribute) gui_validate_local_gpus() (in module schrodinger.ui.qt.config_dialog) GuiPanel (class in schrodinger.ui.qt.dendrogram) GuiPattern (class in schrodinger.application.matsci.rdpattern_gui) GVB (schrodinger.application.jaguar.constants.CalcType attribute) GVBLMP2 (schrodinger.application.jaguar.constants.CalcType attribute) gvblmp2() (in module schrodinger.application.jaguar.textparser) GVBRCI (schrodinger.application.jaguar.constants.CalcType attribute) GXG_DATA (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) GXG_DATA_PRIME (schrodinger.application.bioluminate.protein.mutator.ProteinMutator attribute) Gyradius (class in schrodinger.application.desmond.packages.analysis) gz_fname_if_exists() (in module schrodinger.application.desmond.util) GZIP (schrodinger.rdkit_extensions.CompressionType attribute) gzip_file() (in module schrodinger.utils.fileutils) gzip_open() (in module schrodinger.trajectory.prody.writenmd) GzippedSDMolSupplier (class in schrodinger.rdkit.molio)

H

H (schrodinger.application.jaguar.results.ThermoCollection attribute) h (schrodinger.application.matsci.espresso.qeoutput.PhDOS.Thermo attribute) H (schrodinger.protein.annotation.AntibodyRegionLabel attribute) H1 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H2 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H2O (schrodinger.energy.Solvent attribute) H3 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H8 (schrodinger.protein.annotation.GPCRSegmentLabel attribute) H_All (schrodinger.infra.canvas.ChmAtomOption attribute) (schrodinger.infra.canvas.optionMDL attribute) H_Always (schrodinger.infra.canvas.optionSMARTS attribute) H_ANNIHILIATIONS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) H_AsIs (schrodinger.infra.canvas.ChmAtomOption attribute) H_AsWritten (schrodinger.infra.canvas.optionMDL attribute) H_BOND (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) H_bonds (schrodinger.application.glide.xpdes.TermKeywords attribute) H_Chiral (schrodinger.infra.canvas.ChmAtomOption attribute) (schrodinger.infra.canvas.optionMDL attribute) H_Default (schrodinger.infra.canvas.ChmAtomOption attribute) (schrodinger.infra.canvas.optionMDL attribute) (schrodinger.infra.canvas.optionSMARTS attribute) H_ExplicitChiral (schrodinger.infra.canvas.ChmAtomOption attribute) H_ExplicitOnly (schrodinger.infra.canvas.ChmAtomOption attribute) H_ExplicitPolar (schrodinger.infra.canvas.ChmAtomOption attribute) H_ExplicitPolarAndChiral (schrodinger.infra.canvas.ChmAtomOption attribute) H_INJECTIONS (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) h_l_code (schrodinger.protein.annotation.AntibodyDisplayNames attribute) H_Never (schrodinger.infra.canvas.ChmAtomOption attribute) (schrodinger.infra.canvas.optionMDL attribute) (schrodinger.infra.canvas.optionSMARTS attribute) H_Polar (schrodinger.infra.canvas.ChmAtomOption attribute) (schrodinger.infra.canvas.optionMDL attribute) H_SMILES_behavior (schrodinger.infra.canvas.optionSMARTS attribute) h_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) H_Visible (schrodinger.infra.canvas.optionMDL attribute) half_life() (in module schrodinger.application.jaguar.kinetics) HALFREVOLUTION (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) HALO (schrodinger.livedesign.draw.ColoringStyle attribute) HalogenBondFinder (class in schrodinger.application.desmond.packages.analysis) halogenicity (schrodinger.application.jaguar.utils.JagSolventParams attribute) HAMILTONIAN (schrodinger.application.jaguar.gui.tabs.theory_tab.ProvidesTheoryTheoryTabNoSoZora attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabNoSoZora attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabWithSoZora attribute) hamiltonianChanged (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) handle_check_action() (in module schrodinger.application.licensing.licadmin) handle_data() (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) handle_debug_sources() (in module schrodinger.application.licensing.licserver.main) handle_diag_action() (in module schrodinger.application.licensing.licadmin) HANDLE_DISABLED (schrodinger.ui.qt.standard.design_tokens.QSliderIcons attribute) HANDLE_ENABLED (schrodinger.ui.qt.standard.design_tokens.QSliderIcons attribute) handle_endtag() (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) handle_generic_action() (in module schrodinger.application.licensing.licadmin) HANDLE_HOVER (schrodinger.ui.qt.standard.design_tokens.QSliderIcons attribute) handle_info_action() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.licserver.main) handle_install() (in module schrodinger.application.licensing.licserver.main) handle_install_action() (in module schrodinger.application.licensing.licadmin) handle_list_action() (in module schrodinger.application.licensing.licadmin) handle_live_design_request() (in module schrodinger.application.livedesign.ld_maestro_actions) handle_machineid() (in module schrodinger.application.licensing.licserver.main) HANDLE_PRESSED (schrodinger.ui.qt.standard.design_tokens.QSliderIcons attribute) handle_quick_slm_setup() (in module schrodinger.application.licensing.licserver.main) handle_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) handle_start_action() (in module schrodinger.application.licensing.licadmin) handle_starttag() (schrodinger.application.matsci.espresso.utils.PPHeaderHTMLParser method) (schrodinger.ui.qt.swidgets.ElidedTextHTMLParser method) handle_stat_action() (in module schrodinger.application.licensing.licadmin) handle_stop_action() (in module schrodinger.application.licensing.licadmin) handle_timeout() (schrodinger.application.glide.http_server.GlideHTTPServer method) handle_ver_action() (in module schrodinger.application.licensing.licadmin) handle_verify_action() (in module schrodinger.application.licensing.licadmin) handleCSV() (schrodinger.active_learning.mq_worker.Worker method) HandledError handleDONE() (schrodinger.active_learning.mq_worker.Worker method) handleException() (schrodinger.utils.qt_utils.EventLoop method) handleFileLinkProperties() (schrodinger.application.matsci.jaguarworkflows.Step method) handleFinalGeometry() (schrodinger.application.matsci.mecp_mod.MECPStep method) handleFiniteDifferences() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) handleGET() (schrodinger.active_learning.mq_worker.Worker method) handleInclusonToggled() (schrodinger.ui.two_d_viewer.TwoDTableModel method) handleLDExceptions() (schrodinger.application.livedesign.export_tasks.LDExportTaskMixin method) handleManyToOne() (schrodinger.application.matsci.nano.particle.Nanoparticle method) handleMetalBonding() (schrodinger.application.matsci.rxn_channel.Products method) handleNewDatabaseSource() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) handleObsolete() (schrodinger.protein.getpdb_utility.Code method) handleOneToMany() (schrodinger.application.matsci.nano.particle.Nanoparticle method) handlePING() (schrodinger.active_learning.mq_worker.Worker method) handlePONG() (schrodinger.active_learning.mq_worker.Worker method) handleProps() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) (schrodinger.application.matsci.nano.tube.NanoTube method) handleRangeChange() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) handleREADY() (schrodinger.active_learning.mq_worker.Worker method) handleRingExclusions() (schrodinger.application.matsci.coarsegrain.Internals method) handleSettings() (schrodinger.application.matsci.nano.xtal.Crystal method) handleShiftClick() (schrodinger.ui.two_d_viewer.TwoDTableModel method) handleSimpleInput() (schrodinger.application.matsci.amorphous.Moieties method) handleStageMessages() (schrodinger.pipeline.pipeline.Pipeline method) handleSTOP() (schrodinger.active_learning.mq_worker.Worker method) handleStructure() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) HAPTIC_ATOM_PROP (schrodinger.application.matsci.buildcomplex2d.ComplexSdfToMae attribute) HapticLigand (class in schrodinger.application.matsci.etarotamers) hard (schrodinger.glide.EnergyOptions attribute) HARDNESS (schrodinger.energy.FlucCTParamKeys attribute) Hartree (schrodinger.application.jaguar.constants.Unit attribute) (schrodinger.energy.MlffEnergyUnit attribute) hartree_to_kcal_per_mol() (in module schrodinger.application.matsci.mecp_mod) HartreePerBohr (schrodinger.application.jaguar.constants.Unit attribute) has2DCoords() (schrodinger.infra.canvas.ChmMol method) has3DCoords() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmMol method) has3dCoords() (schrodinger.structure.Structure method) has_antibody_heavy (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult property) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults property) (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment property) has_antibody_light (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult property) (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults property) (schrodinger.application.bioluminate.anarci.anarci_adapter.ChainAlignment property) has_at_least_n_structures() (in module schrodinger.application.peptide_workflow.driver_utils) has_atom_vel() (in module schrodinger.application.matsci.desmondutils) has_authenticator() (schrodinger.job.server.ServerInfo method) has_bad_contacts_for_sampling() (in module schrodinger.glide) has_bad_contacts_for_scoring() (in module schrodinger.glide) has_bad_contacts_for_scoring_relaxed() (in module schrodinger.glide) has_block() (in module schrodinger.structutils.block_data) has_branch (schrodinger.protein.helm.helm_renderer.HelmConnector property) has_cert_for_server() (in module schrodinger.job.cert) has_chorus_box_props() (in module schrodinger.application.matsci.desmondutils) has_clash() (in module schrodinger.comparison.struc) has_cloud_services() (in module schrodinger.application.steps.env_keys) has_concatenated_stage() (in module schrodinger.application.matsci.desconfig) has_densities (schrodinger.application.matsci.espresso.qeoutput.PhDOS property) has_desmond_trajectory() (in module schrodinger.project.utils) has_dirs() (schrodinger.seam.io.jobfilesystem.JobFileSystem method) HAS_E (schrodinger.application.matsci.kmc.PairsTable attribute) (schrodinger.application.matsci.kmc.SitesMixin attribute) has_eigv (schrodinger.application.matsci.espresso.qeoutput.PhDOS property) has_fepio() (in module schrodinger.application.desmond.cms) has_ffio() (in module schrodinger.application.desmond.cms) has_fused_rings() (in module schrodinger.application.glide_ws.entropy_score) has_gipaw (schrodinger.application.matsci.espresso.utils.PseudoData attribute) HAS_H (schrodinger.application.matsci.kmc.PairsTable attribute) (schrodinger.application.matsci.kmc.SitesMixin attribute) has_head_tail_roles_marked() (in module schrodinger.application.matsci.amorphous) has_hubbard() (in module schrodinger.application.matsci.espresso.utils) has_imperfect_packing() (in module schrodinger.application.matsci.packmol) has_interaction_label() (in module schrodinger.protein.protassign.pka_prediction) has_keep_and_superpose_atoms() (in module schrodinger.application.matsci.reaction_workflow_utils) has_key() (schrodinger.utils.scollections.IdDict method) (schrodinger.utils.sea.sea.Map method) has_LD_filter_match() (in module schrodinger.livedesign.cmdline) has_LD_substructure_fp_match() (in module schrodinger.livedesign.cmdline) has_LD_substructure_match() (in module schrodinger.livedesign.cmdline) has_license_file_suffix() (in module schrodinger.application.licensing.licadmin) has_low_energy() (schrodinger.application.glide_ws.entropy_score.MMGBSAEntropyScore static method) has_materials_trajectory() (in module schrodinger.project.utils) has_option() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method) has_orthorhombic_pbc() (in module schrodinger.application.matsci.desmondutils) has_pair_data() (in module schrodinger.application.matsci.kmc) has_pbc() (in module schrodinger.application.matsci.nano.xtal) has_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) has_player_toolbar() (in module schrodinger.trajectory.trajectoryviewer) has_plink_ssh_host_key() (in module schrodinger.utils.sshconfig) has_query_stereo() (in module schrodinger.application.matsci.rdpattern) has_seqres() (in module schrodinger.protein.seqres) has_snapshot_panel() (in module schrodinger.trajectory.trajectoryviewer) has_space_group_pbc_props() (in module schrodinger.application.matsci.desmondutils) has_stage_separator() (in module schrodinger.application.matsci.thermo_correction_utils) has_stereo_smarts() (in module schrodinger.application.matsci.rdpattern) has_substructure_match() (in module schrodinger.livedesign.bbchem_endpoints) has_tag() (schrodinger.utils.sea.sea.Sea method) has_trajectory() (in module schrodinger.project.utils) has_transition_state() (in module schrodinger.application.matsci.thermo_correction_utils) has_undefined_stereo() (in module schrodinger.utils.cgxutils) has_valid_custom_OPLS_preference() (in module schrodinger.ui.qt.forcefield.forcefield) has_valid_lewis_structure() (in module schrodinger.structutils.analyze) has_valid_opls_dir (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector property) has_valid_wscore_block() (in module schrodinger.project.utils) has_variable_reactants() (in module schrodinger.application.pathfinder.multiroute) has_velocities (schrodinger.application.desmond.cms.Cms property) has_vertex_colors (schrodinger.surface.Surface property) has_view_asl (schrodinger.maestro_utils.surface_manager.surface_info.SurfaceInfo attribute) has_watermap() (in module schrodinger.project.utils) hasAcceptableInput() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterListToolButton method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) hasActiveFilters() (schrodinger.ui.qt.filter_list.PredefinedFiltersPopUp method) hasAllHydrogens() (schrodinger.infra.canvas.ChmMol method) hasAlnSets() (schrodinger.protein.alignment.BaseAlignment method) hasAtomProperty() (schrodinger.structure.Structure method) hasAutoScaleInfo() (schrodinger.infra.canvas.ChmColumnUIDFilter method) hasBondDirectionHint() (schrodinger.infra.canvas.ChmBond method) (schrodinger.infra.canvas.ChmMol method) hasBrancher() (schrodinger.application.matsci.amorphous.Moieties method) hasCascader() (schrodinger.application.matsci.amorphous.Moieties method) hasChain() (schrodinger.protein.sequence.CombinedChainProteinSequence method) hasChanged() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) hasChirality() (schrodinger.application.matsci.amorphous.Monomer method) hasClashes() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) hasCode() (schrodinger.infra.canvas.ChmFPMap32 method) (schrodinger.infra.canvas.ChmFPMap64 method) hasCompleted() (schrodinger.pipeline.stage.Stage method) hasConstraints() (schrodinger.glide.GridArchive method) hasCoords (schrodinger.infra.canvas.AtomData attribute) hasCoords() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmMol method) hasCore() (schrodinger.glide.LigandConstraintData method) hasCorrectScale() (schrodinger.infra.canvas.Chm2DCoordGen static method) hasData() (schrodinger.application.prime.residue_interaction.InteractionReader class method) hasDescriptors() (schrodinger.protein.sequence.AbstractSequence method) hasDifference() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) hasDisabledText() (schrodinger.ui.qt.swidgets.LineEditWithDisabledText method) hasDisorderedRegionsPredictions() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasDistinctCoords() (schrodinger.infra.canvas.ChmMol method) hasDisulfideBondPredictions() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasDocking() (schrodinger.glide.LicenseManager method) hasDomainArrangementPredictions() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasEdge() (schrodinger.ui.qt.network_visualizer.Graph method) hasEdges() (schrodinger.ui.qt.schart.SHistogramBarSeries method) hasElectrostatics() (schrodinger.energy.MlffFixedInteractions method) hasError() (schrodinger.infra.canvas.ChmSDReader method) (schrodinger.infra.canvas.ChmSmilesFileReader method) hasExactMatch() (schrodinger.infra.canvas.ChmQueryMatcher method) hasExited() (schrodinger.job.queue.BaseJob method) hasFitden() (schrodinger.glide.LicenseManager method) hasFreeEnergy() (schrodinger.application.matsci.fragments.BondEnergies method) hasGridgen() (schrodinger.glide.LicenseManager method) hash() (schrodinger.infra.canvas.ChmSearchKey method) hash64() (schrodinger.infra.canvas.ChmSearchKey method) hash_for_file() (in module schrodinger.utils.fileutils) hash_idx (schrodinger.application.matsci.reaction_workflow_enum_utils.PositionedRGroup attribute) (schrodinger.application.matsci.reaction_workflow_enum_utils.Site attribute) hash_scheme (schrodinger.livedesign.registration.RegistrationOptions attribute) hash_title() (in module schrodinger.application.desmond.struc) HashableRdMol (class in schrodinger.ui.qt.delegates) hasHandle() (schrodinger.infra.structure.Structure method) hasHeader() (schrodinger.infra.canvas.ChmDelimitedPatterns method) (schrodinger.infra.canvas.ChmMultiYDelimitedPatterns method) hasImplicitHydrogens() (schrodinger.infra.canvas.ChmMol method) hasInteractions() (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions method) hasIsotope() (schrodinger.infra.canvas.ChmMol method) hasKey() (schrodinger.infra.mm.MMPREF method) (schrodinger.infra.mm.Preferences method) hasKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) hasLadder() (schrodinger.application.matsci.amorphous.Moieties method) hasLicenseChecking (schrodinger.job.server.ServerInfo attribute) hasLigandDensity() (schrodinger.glide.LigandConstraintData method) hasLigandsInBox() (schrodinger.application.glide.gui.GridSite method) hasLoading() (schrodinger.infra.canvas.ChmPLSParser method) hasLowerBound() (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) hasMatch() (schrodinger.glide.CoreDefinition method) (schrodinger.infra.canvas.ChmQueryMatcher method) hasMatchStartingWith() (schrodinger.infra.canvas.ChmQueryMatcher method) hasMetallicNeighbor() (schrodinger.infra.canvas.ChmAtom method) hasMissingAtoms() (schrodinger.structure.Residue method) hasNearerImage() (schrodinger.infra.structure.PBC method) hasNeighborOfElementType() (schrodinger.infra.canvas.ChmAtom method) hasNext() (schrodinger.infra.canvas.ChmAssignments method) (schrodinger.infra.canvas.ChmAtomIterator method) (schrodinger.infra.canvas.ChmBitsetIterator method) (schrodinger.infra.canvas.ChmBondIterator method) (schrodinger.infra.canvas.ChmCompressedBitsetIterator method) (schrodinger.infra.canvas.ChmCompressedBitsetIterator64 method) (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator method) (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator64 method) (schrodinger.infra.canvas.ChmFPIn32 method) (schrodinger.infra.canvas.ChmFPIn64 method) (schrodinger.infra.canvas.ChmMatchExIterator method) (schrodinger.infra.canvas.ChmMatchIterator method) (schrodinger.infra.canvas.ChmPatterns method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) (schrodinger.infra.canvas.ChmSDReader method) (schrodinger.infra.canvas.ChmValueAssignmentIterator method) hasNextMol() (schrodinger.infra.canvas.ChmSmilesFileReader method) hasOnlyWedge() (schrodinger.infra.canvas.ChmAtom method) hasPBC() (schrodinger.infra.structure.DistanceCell method) hasPfam() (schrodinger.protein.sequence.AbstractSequence method) hasPolarNeighbor() (schrodinger.infra.canvas.ChmAtom method) hasPositions() (schrodinger.ui.qt.network_visualizer.Graph method) hasPrev() (schrodinger.infra.canvas.ChmAssignments method) (schrodinger.infra.canvas.ChmAtomIterator method) (schrodinger.infra.canvas.ChmBitsetIterator method) (schrodinger.infra.canvas.ChmBondIterator method) (schrodinger.infra.canvas.ChmMatchExIterator method) (schrodinger.infra.canvas.ChmMatchIterator method) (schrodinger.infra.canvas.ChmValueAssignmentIterator method) hasProp() (schrodinger.infra.canvas.ChmFPTypeInfo method) hasProperty() (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.structure.Structure method) (schrodinger.infra.structure.StructureAtom method) hasReceptorBasedConstraints() (schrodinger.glide.LigandConstraintData method) hasReceptorBasedFiltersAndRestraints() (schrodinger.glide.LigandConstraintData method) hasRefCtMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hasReferenceShape() (schrodinger.glide.LigandConstraintData method) hasRibbonColor() (schrodinger.infra.structure.StructureAtom method) hasRingNeighbor() (schrodinger.infra.canvas.ChmAtom method) hasRings() (schrodinger.application.matsci.amorphous.Moieties method) hasServerAuth (schrodinger.job.server.ServerInfo attribute) hasSetResNum() (schrodinger.protein.residue.Residue method) hasShapeConstraints() (schrodinger.glide.LigandConstraintData method) hasSocketAuth (schrodinger.job.server.ServerInfo attribute) hasSolventAccessibility() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.speciesgui.SpeciesSelector method) hasSpecifiedIsotope() (schrodinger.infra.canvas.ChmAtom method) hasSSAPredictions() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) hasStarted() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobDJ method) (schrodinger.pipeline.stage.Stage method) hasStructure() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.protein.residue.AbstractSequenceElement method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) hasStructuredResidues() (schrodinger.protein.sequence.AbstractSequence method) hasTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hasTorsionalConstraints() (schrodinger.glide.LigandConstraintData method) hasUpperBound() (schrodinger.infra.canvas.ChmPairwiseFPOut method) (schrodinger.infra.canvas.ChmPairwiseFPOut32 method) (schrodinger.infra.canvas.ChmPairwiseFPOut64 method) hasValidBasis() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.PerAtomBasisRow method) hasValues() (schrodinger.infra.canvas.ChmFPTypeInfo method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) hasWedge() (schrodinger.infra.canvas.ChmAtom method) hasXtbContribution() (schrodinger.energy.MlffFixedInteractions method) hasXvolGrids() (schrodinger.glide.GridArchive method) hasXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) have_constraints() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) have_frozen_atoms() (schrodinger.application.jaguar.workflow_input.WorkflowInput method) haveConfidenceInterval() (schrodinger.infra.canvas.ChmKPLSParser method) haveTestSet() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) haveTrainingSet() (schrodinger.infra.canvas.ChmKPLSParser method) (schrodinger.infra.canvas.ChmPLSParser method) hb_bb (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bbChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bbReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bs (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bsChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_bsReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_sb (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_sbChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_sbReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_ss (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_ssChanged (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) hb_ssReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.SingleProteinInteractions attribute) HBond (class in schrodinger.glide) hbond (schrodinger.application.glide.utils.ResidueInteraction attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) hbond_charged_charged (schrodinger.glide.ScoreTerms attribute) hbond_cluster (class in schrodinger.protein.protassign.hbond_cluster) hbond_energy() (in module schrodinger.application.qsite.output) hbond_heavy_max_angle (schrodinger.protein.protassign.changeables.changeable attribute) hbond_heavy_min_angle (schrodinger.protein.protassign.changeables.changeable attribute) hbond_iterator() (in module schrodinger.structutils.analyze) hbond_max_dist (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_max_distChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_max_distReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_acceptor_angle (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_acceptor_angleChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_acceptor_angleReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_angle (schrodinger.protein.protassign.changeables.changeable attribute) hbond_min_donor_angle (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_donor_angleChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) hbond_min_donor_angleReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) HBOND_TYPE (class in schrodinger.application.bioluminate.protein_interaction.calculate) hbondChanged (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) HBondData (class in schrodinger.glide) hbondReplaced (schrodinger.application.prepwizard2.tasks.PPWorkflowInput attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowSettings attribute) HBonds (class in schrodinger.glide) hbonds (schrodinger.glide.HBonds attribute) (schrodinger.glide.ScoreDescriptors attribute) hbonds_data (schrodinger.glide.VisualizationData attribute) HBondType (class in schrodinger.glide) HbondWScoreSipTerm (class in schrodinger.application.glide_ws.scoring_report) hbox() (in module schrodinger.ui.qt.layout) HC (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) HC1 (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) HC2 (schrodinger.application.bioluminate.antibody.io.csv_reader.Headers attribute) HC_SEQ (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) HCENTER (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) HDExaminerColumns (class in schrodinger.application.bioluminate.pose_filtering.hdx_io) HDFIO (class in schrodinger.application.matsci.hdfutils) HDFProxyPickleIO (class in schrodinger.application.matsci.hdfutils) HDFStore() (in module schrodinger.application.matsci.hdfutils) HdxMsProperties (class in schrodinger.application.bioluminate.pose_filtering.hdx_io) header (schrodinger.application.jaguar.results.ScfIteration attribute) (schrodinger.application.matsci.mlearn.features.MomentData attribute) header() (schrodinger.application.qsite.input.Cut method) (schrodinger.application.qsite.input.HydrogenCap method) HEADER_BY_SUBTYPE (schrodinger.livedesign.biologics.fasta.AntibodyAssembler attribute) (schrodinger.livedesign.biologics.fasta.NucleicAcidAssembler attribute) (schrodinger.livedesign.biologics.fasta.PolymerAssembler attribute) HEADER_CPUS (schrodinger.application.jaguar.gui.timing.EntryTimingTable attribute) HEADER_STYLE (schrodinger.application.matsci.stage_widgets.BaseTableWidgetDefinition attribute) HEADER_SUBJOB (schrodinger.application.jaguar.gui.timing.EntryTimingTable attribute) HEADER_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HEADER_TIME (schrodinger.application.jaguar.gui.timing.EntryTimingTable attribute) HEADER_TITLE (schrodinger.application.jaguar.gui.timing.EntryTimingTable attribute) header_titles (schrodinger.ui.qt.appframework2.debugwidgets.LogTable attribute) (schrodinger.ui.qt.appframework2.debugwidgets.LogTagTable attribute) (schrodinger.ui.qt.appframework2.debugwidgets.SignalTable attribute) headerClicked() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VStackedDataViewerTable method) headerData() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.bioluminate.protein_structure_quality.DataModelWithChart method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelMacroPkaByPka method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.job_monitor.job_monitor_table.TableProxy method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.PatternModel method) (schrodinger.ui.qt.mapperwidgets.plptable.ColumnSeries method) (schrodinger.ui.qt.mapperwidgets.plptable.TableSpec method) (schrodinger.ui.qt.select_residues_dialog.ResiduesModel method) (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table_helper.RowBasedListModel method) (schrodinger.ui.qt.table_helper.RowBasedModelMixin method) headerDataChanged (schrodinger.ui.qt.table.StructureDataViewerModel attribute) HeaderLabel (class in schrodinger.ui.qt.standard_widgets.labels) Headers (class in schrodinger.application.bioluminate.antibody.io.csv_reader) HEADERS (schrodinger.application.bioluminate.antibody.io.csv_reader.DataViolation attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByCharge attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.SpectrumFile attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) (schrodinger.application.matsci.spectra.VCD_Spectrum attribute) (schrodinger.application.matsci.stage_widgets.BaseTableWidgetDefinition attribute) headers() (schrodinger.application.glide_ws.entropy_score.MMGBSAEntropyScore static method)

HeaderViewWithMenuIndicator (class in schrodinger.ui.qt.utils) health() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) healthier() (in module schrodinger.application.licensing.licadmin) heat_capacity (schrodinger.application.jaguar.thermochemical_properties.ThermoProps attribute) heat_of_formation() (in module schrodinger.application.mopac.results_main) HEAVY (schrodinger.application.bioluminate.antibody.grafting.ChainTypes attribute) (schrodinger.application.bioluminate.antibody.models.VariableDomainType attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) (schrodinger.application.matsci.kmcgui.NeighborsTab attribute) HEAVY_FR_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) HEAVY_FR_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) HEAVY_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) HEAVY_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) height (schrodinger.application.matsci.reportutils.Footer attribute) (schrodinger.livedesign.draw.ImageGenOptions attribute) height_inches (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) height_inchesChanged (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) height_inchesReplaced (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) height_pixels (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) height_pixelsChanged (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) height_pixelsReplaced (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel attribute) (schrodinger.ui.two_d_viewer.SaveImagesDialogModel attribute) heightForWidth() (schrodinger.ui.qt.dialbox.Dial method) HELIX (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute) HELIX_BLD (schrodinger.application.transforms.prime.RefineType attribute) HELIX_PROPENSITY (class in schrodinger.protein.residue) helix_propensity (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) HELIX_TERMINATION_TENDENCY (class in schrodinger.protein.residue) helix_termination_tendency (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) HelixArc (class in schrodinger.application.matsci.atom_group) HelixArcAtomGroup (class in schrodinger.application.matsci.atom_group) HelixBreaking (schrodinger.protein.residue.HELIX_PROPENSITY attribute) HelixData (class in schrodinger.application.matsci.atom_group) HelixEnding (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) HelixGroups (class in schrodinger.application.matsci.atom_group) helixGroupToData() (schrodinger.application.matsci.atom_group.HelixArcAtomGroup method) HelixStarting (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) HELM (schrodinger.rdkit_extensions.Format attribute) helm_mol_to_binary() (in module schrodinger.livedesign.biologics.registration) HelmConnector (class in schrodinger.protein.helm.helm_renderer) HelmConnectorItemMixin (class in schrodinger.protein.helm.helm_renderer) helmholtz_free_energy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) HelmMonomer (class in schrodinger.protein.helm.helm_renderer) HelmMonomerItemMixin (class in schrodinger.protein.helm.helm_renderer) HelmMonomerTextLabel (class in schrodinger.protein.helm.helm_renderer) HelmScene (class in schrodinger.protein.helm.helm_renderer) HelmWidget (class in schrodinger.protein.helm.helm_renderer) HELP (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) help (schrodinger.tasks.cmdline.ArgSpec attribute) HELP (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) Help (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin.StdBtn attribute) help() (schrodinger.application.bioluminate.protein_structure_quality.ProteinStructureQualityViewer method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.matsci.jagwidgets.SolventDialog method) (schrodinger.application.pymol.pymol4maestro.panel method) (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.settings.BaseOptionsPanel method) HELP_BUTTON_STYLESHEET (schrodinger.ui.qt.swidgets.HelpButton attribute) HELP_TOPIC (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) HelpButton (class in schrodinger.ui.qt.swidgets) helpEvent() (schrodinger.ui.qt.delegates.MatplotlibDelegate method) (schrodinger.ui.qt.mapperwidgets.param_editor.DynamicTypeDelegate method) helpPressed() (schrodinger.ui.ligfilter.AddDefinitionDialog method) hess_array_from_section() (in module schrodinger.application.jaguar.input) hess_section_from_array() (in module schrodinger.application.jaguar.input) HessianLSQ() (in module schrodinger.application.matsci.gsas.GSASIImath) HessianSVD() (in module schrodinger.application.matsci.gsas.GSASIImath) HetState (class in schrodinger.application.prepwizard) HetType (class in schrodinger.application.prepwizard) hex() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) Hex_pairs (schrodinger.application.glide.xpdes.TermKeywords attribute) Hex_sp (schrodinger.application.glide.xpdes.TermKeywords attribute) hex_string (schrodinger.structutils.color.Color property) (schrodinger.surface.Surface.Color property) hex_to_rgb() (in module schrodinger.application.matsci.stylemanager) HEXADECANE (schrodinger.energy.Solvent attribute) HEXAGONAL_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute) HEXANE (schrodinger.energy.Solvent attribute) HexColor (class in schrodinger.protein.helm.helm_renderer) HF (schrodinger.application.jaguar.constants.CalcType attribute) HFExcitedStateWidget (class in schrodinger.application.jaguar.gui.theory_tab_widgets) HFR (schrodinger.protein.annotation.AntibodyRegionLabel attribute) HIDDEN (schrodinger.application.livedesign.models2.datamodels.instance.ChildInheritanceMode attribute) hidden (schrodinger.infra.canvas.AtomData attribute) (schrodinger.ui.qt.atomselector.ASLPopupMenu attribute) (schrodinger.ui.qt.table.EmittingScrollBar attribute) hide() (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.gridbox.GridBox method) (schrodinger.protein.membrane.Membrane_Model method) (schrodinger.surface.Surface method) (schrodinger.ui.qt.forcefield.ffselector.ForceFieldSelector method) (schrodinger.ui.qt.tablewidget.Row method) HIDE_ALL (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) HIDE_ATOM_WIDGETS (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings attribute) hide_atoms() (in module schrodinger.application.bioluminate.pml_menus) HIDE_BOUNDING_BOX (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) hide_everything() (in module schrodinger.application.bioluminate.pml_menus) hide_labels() (in module schrodinger.application.bioluminate.pml_menus) hide_layout_elements() (in module schrodinger.ui.qt.utils) hide_non_polar_hydrogens() (in module schrodinger.application.prepwizard2.tasks) hide_phase_hover_markers() (in module schrodinger.application.phase.phase_markers) HIDE_POSE_PAGE (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget attribute) hide_ribbons() (in module schrodinger.application.bioluminate.pml_menus) HIDE_SURFACE (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) hide_surface() (in module schrodinger.application.bioluminate.pml_menus) hide_workspace_phase_markers() (in module schrodinger.application.phase.phase_markers) hideAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hideAllFeaturesForEntry() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hideAllJaguarMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) hideAllMarkers() (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.select_residues_dialog.SelectResiduesDialog method) HideAllOthers (class in schrodinger.application.bioluminate.pml_menus) HideAtoms (class in schrodinger.application.bioluminate.pml_menus) hideDefineButton() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) hideDoNotShowCheckbox() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) hideEvent() (schrodinger.application.matsci.sliceplot.SlicePlot method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) (schrodinger.ui.qt.appframework2.markers.MarkerMixin method) (schrodinger.ui.qt.atomselector.ASLPopupMenu method) (schrodinger.ui.qt.atomselector.AtomSelector method) (schrodinger.ui.qt.input_selector.InputSelector method) (schrodinger.ui.qt.pop_up_widgets.PopUp method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.swidgets.SEmittingScrollBar method) (schrodinger.ui.qt.table.EmittingScrollBar method) HideEverything (class in schrodinger.application.bioluminate.pml_menus) hideFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) HideHydrogens (class in schrodinger.application.bioluminate.pml_menus) HideHydrogenSubMenu (class in schrodinger.application.bioluminate.pml_menus) HideLabel (class in schrodinger.application.bioluminate.pml_menus) hideLabels() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) hideLayoutElements() (schrodinger.ui.qt.appframework2.af2.App method) HideMainChain (class in schrodinger.application.bioluminate.pml_menus) hideMatched() (schrodinger.infra.canvas.ChmQueryMatcher method) HideMenu (class in schrodinger.application.bioluminate.pml_menus) HideNonBonded (class in schrodinger.application.bioluminate.pml_menus) hideNonMatched() (schrodinger.infra.canvas.ChmQueryMatcher method) HidePolarHydrogens (class in schrodinger.application.bioluminate.pml_menus) hidePopup() (schrodinger.ui.qt.pop_up_widgets.ComboBoxWithPopUp method) hideProgress() (schrodinger.ui.qt.appframework2.af2.StatusBar method) HideRibbons (class in schrodinger.application.bioluminate.pml_menus) hideScheme() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) HideSideChain (class in schrodinger.application.bioluminate.pml_menus) hideSlab() (schrodinger.application.matsci.sliceplot.SlicePlot method) hideSphere() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) hideStructureTooltip() (schrodinger.ui.two_d_viewer.TwoDTableDelegate method) HideSurface (class in schrodinger.application.bioluminate.pml_menus) HideSymmetryMates (class in schrodinger.application.bioluminate.pml_menus) hideTolMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) (schrodinger.application.phase.phase_markers.PhaseTolMarkers method) hideToolbarStyle() (schrodinger.ui.qt.appframework2.af2.BottomBar method) hideToolTip() (schrodinger.ui.qt.matplot_widget.StructureTooltipMixin method) HideWaters (class in schrodinger.application.bioluminate.pml_menus) hideWidgets() (schrodinger.application.matsci.mswidgets.MultiComboWithCount method) HIGH (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute) High (schrodinger.protein.annotation.KinaseConservation attribute) HIGH (schrodinger.trajectory.trajectory_gui_dir.export_movie.Quality attribute) highlight_atom_colors (schrodinger.livedesign.draw.ImageGenOptions attribute) highlight_atoms (schrodinger.livedesign.draw.ImageGenOptions attribute) highlight_bond_colors (schrodinger.livedesign.draw.ImageGenOptions attribute) highlight_bonds (schrodinger.livedesign.draw.ImageGenOptions attribute) HIGHLIGHT_COLOR (schrodinger.application.matsci.mswidgets.MultiSlider attribute) highlight_rotatable_bonds() (in module schrodinger.application.glide.visualization) HIGHLIGHT_STYLE (schrodinger.application.matsci.stage_widgets.RowFrame attribute) highlight_style (schrodinger.livedesign.draw.ImageGenOptions attribute) highlight_style() (in module schrodinger.application.matsci.stylemanager) highlightAtom() (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.application.matsci.reordergui.StructurePic method) highlightCompAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) Highlighted (schrodinger.ui.qt.standard_widgets.buttons.StyledButton.Style attribute) HIGHLIGHTED_BUTTON_BACKGROUND (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HIGHLIGHTED_BUTTON_BORDER_DISABLED (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HIGHLIGHTED_BUTTON_BORDER_ENABLED (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HIGHLIGHTED_BUTTON_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HIGHLIGHTED_PRESSED_BUTTON_BACKGROUND_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute) HighlightedText (schrodinger.ui.qt.standard_widgets.buttons.StyledButton.Style attribute) highlightMapPair() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) highlightMolecule() (schrodinger.application.matsci.kmcgui.MinMaxNeighborWidgets method) highlightRefAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) highlightSuggestedAtom() (schrodinger.application.matsci.reordergui.StructurePic method) HIGHSCORE (schrodinger.protein.predictors.Disordered attribute) HighSymmetryKPath (class in schrodinger.application.matsci.espresso.utils) hijackPos() (schrodinger.application.desmond.packages.traj.Frame method) Hinge (schrodinger.protein.annotation.AntibodyRegionLabel attribute) HINGE (schrodinger.protein.annotation.KinaseFeatureLabel attribute) histidine_changeable (class in schrodinger.protein.protassign.changeables) HistidinepKaPredictor (class in schrodinger.protein.protassign.pka_prediction) HistogramComponent (class in schrodinger.application.glide.visualization) hit (schrodinger.application.matsci.cache.CacheInfo attribute) hit_tables (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults attribute) hits (schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciChainResult attribute) hits_file (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) hits_fileChanged (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) hits_fileReplaced (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask.Input attribute) HKL2SpAng() (in module schrodinger.application.matsci.gsas.GSASIIlattice) HKLS_KEY (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) HKLS_TITLE (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) HMC (schrodinger.application.bioluminate.methionine_oxidation.SamplingMode attribute) HmcAnalyzer (class in schrodinger.application.bioluminate.methionine_oxidation) HmcStats (class in schrodinger.application.bioluminate.methionine_oxidation) HmmerHit (class in schrodinger.application.bioluminate.anarci.anarci_adapter) HOF_PROP (schrodinger.application.matsci.jwsteps.HOFStep attribute) HOFMANN (schrodinger.application.matsci.permittivity.MultiStageMd attribute) HOFMANN_PROTOCOL (schrodinger.application.matsci.permittivity.MultiStageMd attribute) HOFStep (class in schrodinger.application.matsci.jwsteps) HOH_ANGLE (schrodinger.protein.protassign.changeables.WaterStateEnumerator attribute) home_atom (schrodinger.application.matsci.clusterstruct.Neighbor attribute) homo() (in module schrodinger.application.jaguar.textparser) homo_lumo_energy() (in module schrodinger.application.mopac.results_main) homog_rank_2() (in module schrodinger.application.matsci.cctbx.rot_mx) homogeneous_poisson (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) homogenizeBeadSizes() (schrodinger.application.matsci.automated_cg_mapping.BaseMapper method) homogenizeRingBeadSizes() (schrodinger.application.matsci.automated_cg_mapping.MartiniMapper method) HomologyRama (class in schrodinger.application.bioluminate.protein_structure_quality) HoneycombBilayers (class in schrodinger.application.matsci.nano.sheet) HoneycombCell (class in schrodinger.application.matsci.nano.sheet) HoneycombLattice (class in schrodinger.application.matsci.nano.sheet) HoneycombUnitCell (class in schrodinger.application.matsci.nano.sheet) honorHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) honorMatchingAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method) (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) hookUpPropTableTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) hookUpTiming() (schrodinger.application.jaguar.gui.timing.TimerMixin method) HORIZONTAL_ALIGNS (schrodinger.ui.qt.swidgets.STableWidgetItem attribute) HorizontalHeader (class in schrodinger.application.job_monitor.job_monitor_table) (class in schrodinger.ui.qt.tablewidget) Host (class in schrodinger.job.jobcontrol) (class in schrodinger.tasks.hosts) host (schrodinger.active_learning.mq_driver.Worker attribute) (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.licensing.lmgrd_log_parser.event attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) (schrodinger.job.jobcontrol.Host property) Host (schrodinger.job.jobcontrol.Job property) HOST (schrodinger.utils.cmdline.Options attribute) host_check() (in module schrodinger.job.host_check) host_combo (schrodinger.ui.qt.tasks.configwidgets.HostSelector property) HOST_LABEL_TEXT (schrodinger.ui.qt.config_dialog.ConfigDialog attribute) (schrodinger.ui.qt.config_dialog.GPUConfigDialog attribute) host_list_to_str() (in module schrodinger.job.jobcontrol) HOST_NOT_FOUND (schrodinger.maestro_utils.composer_agent.request_manager.urls.ResponseStatus attribute) HOST_NOT_FOUND_ERROR (schrodinger.maestro_utils.composer_agent.message_handler.MessageState attribute) HOST_PLACEHOLDER_ARGS (schrodinger.tasks.jobtasks.HostSettings attribute) host_settings (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) host_settingsChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MultisimTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) host_settingsReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.CovDockTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.EpikTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.GlideTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MemPermTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.MultisimTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.JobConfig attribute) (schrodinger.application.livedesign.tasks.QikPropTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.RBSSTask.JobConfig attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) HOST_STR (schrodinger.application.matsci.genetic_optimization.ClassEvaluator attribute) host_str_to_list() (in module schrodinger.job.jobcontrol) hostChanged (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) HostEntry (schrodinger.job.jobcontrol.Job property) hostfile_is_empty() (in module schrodinger.job.jobcontrol) hostfile_is_valid() (in module schrodinger.job.jobcontrol) hostid_is_local() (in module schrodinger.application.licensing.licadmin) hostid_order() (in module schrodinger.application.licensing.flexlm) HostLayoutWidget (class in schrodinger.ui.qt.tasks.configwidgets) HOSTLIST (schrodinger.utils.cmdline.Options attribute) hostname (schrodinger.application.licensing.licserver.client.GeneralInfo attribute) (schrodinger.application.licensing.licserver.entitlement_status.ClientUsage attribute) (schrodinger.job.server.ServerInfo attribute) (schrodinger.stepper.stepper.BatchSettings attribute) (schrodinger.tasks.remote_modules.PatchInfo attribute) (schrodinger.utils.pythonpatch.ModulePatch attribute) hostname() (schrodinger.application.licensing.flexlm.Server method) hostname_and_port() (in module schrodinger.utils.net) hostname_in_registry() (in module schrodinger.utils.sshconfig) hostname_is_local() (in module schrodinger.utils.net) hostnameChanged (schrodinger.stepper.stepper.BatchSettings attribute) hostnameReplaced (schrodinger.stepper.stepper.BatchSettings attribute) hostport() (schrodinger.application.licensing.flexlm.Server method) HostProduct (class in schrodinger.ui.qt.config_dialog) hostReplaced (schrodinger.application.job_monitor.job_monitor_models.JobModel attribute) (schrodinger.application.livedesign.export_models.LDDestination attribute) HostSelector (class in schrodinger.ui.qt.tasks.configwidgets) HostSettings (class in schrodinger.tasks.jobtasks) hostType() (schrodinger.tasks.hosts.Host method) HostTypeError HOSTWITHSUBJOBS (schrodinger.utils.cmdline.Options attribute) HOSTWITHTHREADS (schrodinger.utils.cmdline.Options attribute) HOVER (schrodinger.ui.qt.standard.design_tokens.BorderColors attribute) (schrodinger.ui.qt.standard.design_tokens.StateColors attribute) (schrodinger.ui.qt.standard.design_tokens.TextColors attribute) HOVER_HORIZONTAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) HOVER_LABEL_X_FORMAT (schrodinger.ui.qt.schart.SChartView attribute) HOVER_LABEL_Y_FORMAT (schrodinger.ui.qt.schart.SChartView attribute) HOVER_VERTICAL (schrodinger.ui.qt.standard.design_tokens.ColorGradients attribute) hoverEnterEvent() (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) hoverLeaveEvent() (schrodinger.ui.qt.network_views.NetworkEdge method) (schrodinger.ui.qt.network_views.NetworkNode method) (schrodinger.ui.qt.schart.SChart method) hoverMoveEvent() (schrodinger.application.matsci.reordergui.StructurePic method) (schrodinger.ui.qt.schart.SChart method) HPType (class in schrodinger.application.matsci.espresso.qeinput) hr_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute) HRD (schrodinger.protein.annotation.KinaseFeatureLabel attribute) hscore (schrodinger.glide.ScoreDescriptors attribute) (schrodinger.glide.ScoreTerms attribute) hso_singlet_triplet() (in module schrodinger.application.jaguar.textparser) HsoSingletTripletElement (class in schrodinger.application.jaguar.results) HStrainNames() (in module schrodinger.application.matsci.gsas.GSASIIspc) HStrainVals() (in module schrodinger.application.matsci.gsas.GSASIIspc) HTML (schrodinger.seam.viz.watcher.ResponseType attribute) html_embed_image() (in module schrodinger.application.desmond.util) HTotal (schrodinger.application.jaguar.results.ThermoCollection attribute) (schrodinger.application.jaguar.textparser.ThermoTotalEnergies attribute) HTTPClient (class in schrodinger.application.glide.http_client) https_session() (in module schrodinger.utils.installation_check) hubb_j0 (schrodinger.application.matsci.espresso.utils.MagElement attribute) hubb_u (schrodinger.application.matsci.espresso.utils.MagElement attribute) human2opspec() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) hunt() (in module schrodinger.job.hunt_stub) (in module schrodinger.job.util) Hx2Rh() (in module schrodinger.application.matsci.gsas.GSASIIlattice) hybrid (schrodinger.application.matsci.espresso.qeinput.DftType property) HYBRID (schrodinger.energy.AomParamKeys attribute) HYBRID_MPNICE (schrodinger.application.jaguar.rotation_barriers_keywords.ExternalMethod attribute) Hybridization (class in schrodinger.glide) HybridMethodsMixin (class in schrodinger.models.parameters) HybridType (class in schrodinger.application.matsci.espresso.qeinput) Hydrogen (class in schrodinger.utils.sea.sea) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomType attribute) HYDROGEN_BOND_ACCEPTOR (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROGEN_BOND_DONOR (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROGEN_BOND_ORDER (schrodinger.application.matsci.rxn_channel.ReactantMolecule attribute) hydrogen_neighbors() (in module schrodinger.application.prepwizard) HYDROGEN_SYM (schrodinger.application.matsci.rxn_channel.ReactantMolecule attribute) HydrogenBondFinder (class in schrodinger.application.desmond.packages.analysis) HydrogenCap (class in schrodinger.application.qsite.input) Hydrogens (class in schrodinger.adapter) hydrogens (schrodinger.adapter.RDKitOptions attribute) hydrogens_present() (in module schrodinger.structutils.analyze) hydrogensInterchangeable (schrodinger.infra.canvas.ChmMatcherData attribute) HydrogenSubMenu (class in schrodinger.application.bioluminate.pml_menus) HydrokineticInput (class in schrodinger.application.jaguar.hydrokinetic_input) Hydrophilic (schrodinger.protein.helm.helm_renderer.HexColor attribute) hydrophilic_idxs (schrodinger.application.matsci.packmol.SurfactantInfo attribute) hydrophilicity (schrodinger.protein.residue.Residue property) HYDROPHOB_ASL (schrodinger.application.desmond.packages.analysis.HydrophobicInterFinder attribute) hydrophobic (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute) hydrophobic_idxs (schrodinger.application.matsci.packmol.SurfactantInfo attribute) HYDROPHOBIC_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROPHOBIC_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROPHOBIC_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HydrophobicConstraint (class in schrodinger.application.glide.constraints) HydrophobicInter (class in schrodinger.application.desmond.packages.analysis) HydrophobicInterFinder (class in schrodinger.application.desmond.packages.analysis) hydrophobicity (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) hydrophobicity_window_padding (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) HydrophobicVectorizer (in module schrodinger.application.bioluminate.peptide_sar.encode) HYDROXYL (schrodinger.application.bioluminate.methionine_oxidation.NeighborAtom attribute) HyperbolaHistogramData (class in schrodinger.application.matsci.uq_utils) hypo_file (schrodinger.application.livedesign.tasks.PhaseScreenTask.Input attribute) hypo_fileChanged (schrodinger.application.livedesign.tasks.PhaseScreenTask.Input attribute) hypo_fileReplaced (schrodinger.application.livedesign.tasks.PhaseScreenTask.Input attribute) HypoName (schrodinger.application.phase.featureselector.FeatureColumns attribute) (schrodinger.application.phase.phase_widgets.HypothesisColumns attribute) HypothesesListWidget (class in schrodinger.application.phase.phase_widgets) hypothesisChanged (schrodinger.application.phase.pt_hypothesis.PhaseHypothesisMonitor attribute) HypothesisColumns (class in schrodinger.application.phase.phase_widgets) HypothesisModel (class in schrodinger.application.phase.phase_widgets) HypothesisRow (class in schrodinger.application.phase.phase_widgets) hz_to_ppm() (in module schrodinger.application.jaguar.nmr_utils)

I

i (schrodinger.application.bioluminate.mhc.docking_angles.MhcClass attribute) IACC_FDPOL (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) IACCG (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) ichoice (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) ichunked() (in module schrodinger.stepper.stepper) ICL (schrodinger.protein.annotation.GPCRSegmentLabel attribute) ICMS (schrodinger.application.matsci.permittivity.CMSParser attribute) icon (schrodinger.ui.qt.swidgets.ActionPushButton attribute) icon() (schrodinger.ui.qt.swidgets.LargeSpinner method) ICON_CLASS (schrodinger.ui.qt.swidgets.LargeSpinner attribute) (schrodinger.ui.qt.swidgets.ThreeDotsLoader attribute) ICON_SIZE (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider attribute) IconMetadata (class in schrodinger.ui.qt.standard.icons.icons) icons (schrodinger.application.matsci.mswidgets.StageFrame property) Icosahedron (class in schrodinger.application.matsci.shapes) icosahedron() (schrodinger.application.watermap.shapes.ShapeFactory method) id (schrodinger.application.bioluminate.anarci.anarci_adapter.DomainAlignment attribute) (schrodinger.application.bioluminate.anarci.anarci_adapter.HmmerHit attribute) (schrodinger.application.glide_ws.db_queries.Pose attribute) (schrodinger.application.glide_ws.db_queries.Property attribute) ID (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) id (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule.RingNodeInfo attribute) ID (schrodinger.livedesign.custom_entity.registration.InputPropertyDataComponent attribute) ID_fab (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute) id_key (schrodinger.application.transforms.autosar.transforms.ComputeNormalizedPropertiesSettings attribute) id_or_url (schrodinger.application.livedesign.live_report_widget.LRInputType attribute) ID_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute) IdDict (class in schrodinger.utils.scollections) idealize_hydrogen_temp_factor() (in module schrodinger.application.prepwizard) idealize_hydrogen_tf (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) idealize_hydrogen_tfChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) idealize_hydrogen_tfReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) (schrodinger.application.prepwizard2.tasks.PreprocessInput attribute) idealLength() (schrodinger.infra.canvas.ChmBond method) ident() (schrodinger.application.licensing.licadmin.LicenseResource method) ident_release_by_installpath() (in module schrodinger.autoinstall.misc) ident_release_by_installsource() (in module schrodinger.autoinstall.misc) Identical (schrodinger.protein.alignment.ResidueSimilarity attribute) identifier (schrodinger.protein.nonstandard_residues.AminoAcid property) identifiers (schrodinger.application.matsci.automated_cg_mapping.UNSUPPORTED_MOL_TYPE attribute) identify_all_hbonders() (in module schrodinger.protein.protassign.changeables) identify_changeables() (in module schrodinger.protein.protassign.changeables) identify_forced_amide_states() (schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor method) identify_ligand_changeables() (in module schrodinger.protein.protassign.changeables) identify_nonshared_rotatable() (in module schrodinger.protein.protassign.changeables) identify_species() (in module schrodinger.protein.protassign.changeables) identifyOutboundNodes() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) identity (schrodinger.livedesign.biologics.sequence.AlignedSequence attribute) IdItemsView (class in schrodinger.utils.scollections) IdSet (class in schrodinger.utils.scollections) idx (schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo attribute) (schrodinger.application.matsci.cg_mapping.ATOM_DEFINITION attribute) (schrodinger.ui.qt.standard.colors.MaestroXColor attribute) idx_in_seq (schrodinger.protein.residue.AbstractSequenceElement property) (schrodinger.protein.residue.CombinedChainResidueWrapper property) IFDMDCongenericTask (class in schrodinger.application.livedesign.tasks) IFDMDCongenericTask.Input (class in schrodinger.application.livedesign.tasks) IFDMDCongenericTask.JobConfig (class in schrodinger.application.livedesign.tasks) IFDMDCongenericTask.Output (class in schrodinger.application.livedesign.tasks) IFDPOL (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) ig_type_str (schrodinger.application.bioluminate.anarci.annotate.AnnotationResult property) IGEOPT (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) Ignore (schrodinger.adapter.Properties attribute) (schrodinger.adapter.StereoChemistry attribute) IGNORE (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.tasks.jobtasks.IncorporationMode attribute) ignore_backbone (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) ignore_backboneChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) ignore_backboneReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions attribute) IGNORE_DELAYED_CALLBACKS (schrodinger.ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin attribute) ignore_maestro_callbacks() (in module schrodinger.application.matsci.gutils) ignore_ssl_warnings() (in module schrodinger.application.matsci.msutils) ignoreCheckboxChanged() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) ignored (schrodinger.infra.canvas.AtomData attribute) ignoreImplicitHydrogens (schrodinger.infra.canvas.ChmMatcherData attribute) ignoreMaestroCallbacks() (schrodinger.ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin method) ii (schrodinger.application.bioluminate.mhc.docking_angles.MhcClass attribute) ijk (schrodinger.glide.Placement attribute) ILEVAL (schrodinger.ui.qt.rama.RamaResidueType attribute) IMAG_TOL (schrodinger.application.matsci.mecp_mod.BFGS attribute) IMAGE_FILE (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) image_options (schrodinger.livedesign.bbchem_configuration.BBChemConfiguration attribute) image_to_string() (in module schrodinger.ui.qt.utils) ImageGenOptions (class in schrodinger.livedesign.draw) ImageLabel (class in schrodinger.ui.qt.swidgets) ImagePlotFrame (class in schrodinger.application.matsci.density_analysis_widget) imagesRequested() (schrodinger.application.matsci.reportutils.ReportInfo method) img_format (schrodinger.livedesign.draw.ImageGenOptions attribute) ImgtLoopRange (class in schrodinger.application.bioluminate.anarci.loop_ranges) IminoAcid (schrodinger.protein.helm.helm_renderer.HexColor attribute) (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) ImmuneBuilderType (class in schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter) ImmuneReceptorDisplayNames (class in schrodinger.protein.annotation) IMPLICIT (schrodinger.adapter.Hydrogens attribute) Import3DGenericEntitiesTask (class in schrodinger.application.livedesign.ld_tasks) Import3DGenericEntitiesTask.Input (class in schrodinger.application.livedesign.ld_tasks) Import3DGenericEntitiesTask.Output (class in schrodinger.application.livedesign.ld_tasks) import_canvas() (in module schrodinger.application.canvas.r_group) import_driver() (in module schrodinger.application.matsci.jwsteps) IMPORT_FILE_COL (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame attribute) import_from_file() (in module schrodinger.utils.imputils) import_ge_task (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) import_module_from_file() (in module schrodinger.utils.imputils) import_script() (in module schrodinger.utils.imputils) import_structures_to_maestro() (in module schrodinger.application.livedesign.ld_import) import_sts_task (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) IMPORT_SURFACE_OR_VOLUME (schrodinger.maestro_utils.surface_manager.menus.MenuActions attribute) import_task (schrodinger.application.livedesign.ld_import_utils.LDImportTask attribute) IMPORT_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) ImportButtonMixin (class in schrodinger.ui.qt.structure_selector) imported_structures (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask.Output attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask.Output attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) imported_structuresChanged (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask.Output attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask.Output attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) imported_structuresReplaced (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask.Output attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask.Output attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask.Output attribute) ImportExportBasePanel (class in schrodinger.application.livedesign.ld_base_classes) importFile() (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) importFilterFile() (schrodinger.ui.ligfilter.LigfilterFrame method) importFromFile() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) (schrodinger.application.matsci.mswidgets.StructureLoader method) importFromFilePaths() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromMaestro() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromPDB() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromProjectTable() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromWorkspace() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) (schrodinger.application.matsci.mswidgets.StructureLoader method) ImportGenericEntity (schrodinger.application.livedesign.ld_maestro_actions_constants.RequestType attribute) importLA() (in module schrodinger.trajectory.prody.ensemble) importLipid() (schrodinger.application.matsci.mswidgets.LipidImporter method) importMapping() (schrodinger.application.livedesign.export_map_manager.ExportMapManager method) importName() (in module schrodinger.pipeline.pipeline) importPresets() (schrodinger.models.presets.PresetManager method) importRegion() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) importRequested (schrodinger.ui.qt.structure_selector.ImportButtonMixin attribute) ImportStructure (schrodinger.application.livedesign.ld_maestro_actions_constants.RequestType attribute) importStructure() (schrodinger.project.project.Project method) importStructureFile() (schrodinger.project.project.Project method) ImportStructuresTask (class in schrodinger.application.livedesign.ld_tasks) ImportStructuresTask.Output (class in schrodinger.application.livedesign.ld_tasks) ImportTask (class in schrodinger.application.livedesign.ld_tasks) ImportTask.Input (class in schrodinger.application.livedesign.ld_tasks) ImportTask.Output (class in schrodinger.application.livedesign.ld_tasks) ImportTaskInput (class in schrodinger.application.livedesign.ld_tasks) ImportToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) ImportWidget (class in schrodinger.application.bioluminate.bwidgets) importWorkspace() (schrodinger.application.matsci.builderwidgets.SketcherBox method) improper_dihedral_iterator() (in module schrodinger.structutils.analyze) IMPROPER_TORSIONS_DAT (schrodinger.infra.mm.OPLSDatafileType attribute) in_dev_env() (in module schrodinger.gpgpu) IN_EXT (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.Jaguar attribute) (schrodinger.application.matsci.packmol.PackmolInputFile attribute) (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) in_main_thread() (in module schrodinger.utils.thread_utils) IN_PROCESS (schrodinger.application.livedesign.models2.datamodels.definition.ExecutionMode attribute) in_same_residue() (in module schrodinger.infra.structure) in_same_structure() (in module schrodinger.infra.structure) in_temporary_directory() (in module schrodinger.utils.fileutils) in_workspace (schrodinger.project.project.ProjectRow property) in_xy_plane() (in module schrodinger.livedesign.preprocessor) InBounds() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) INC (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) Inches (schrodinger.ui.two_d_viewer.SizeUnits attribute) INCHI (schrodinger.rdkit_extensions.Format attribute) INCHI_KEY (schrodinger.rdkit_extensions.Format attribute) InchiKey() (in module schrodinger.rdkit.filtering) incident_angle (schrodinger.application.bioluminate.mhc.docking_angles.DescriptiveAngles attribute) incline_angle (schrodinger.application.bioluminate.mhc.docking_angles.DescriptiveAngles attribute) Include (class in schrodinger.ui.qt.table_helper) include() (schrodinger.ui.ligfilter.AddDefinitionDialog method) include_and_show_trajectory() (in module schrodinger.trajectory.trajectoryviewer) include_and_show_trajectory_snapshot() (in module schrodinger.trajectory.trajectoryviewer) include_entries() (in module schrodinger.project.utils) include_epik_states (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) include_epik_statesChanged (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) include_epik_statesReplaced (schrodinger.application.prepwizard.PrepWizardSettings attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondInput attribute) include_only_entry() (in module schrodinger.trajectory.trajectoryviewer) include_property (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) include_propertyChanged (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) include_propertyReplaced (schrodinger.application.livedesign.export_models.PoseNameEditModel attribute) include_traj (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) include_trajChanged (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) include_trajReplaced (schrodinger.application.pymol.gui_models.ExportToPymolSettings attribute) INCLUDE_USE_CONSISTENT_ORBITALS_CB (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals attribute) include_x_terms (schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty attribute) included (schrodinger.application.jaguar.gui.input_tab_widgets.UseFrom attribute) (schrodinger.project.project.EntrySurface property) (schrodinger.ui.qt.ligand_list.LigSource attribute) INCLUDED_ENTRIES (schrodinger.ui.qt.input_selector.InputSelector attribute) INCLUDED_ENTRY (schrodinger.ui.qt.input_selector.InputSelector attribute) included_residue_names (schrodinger.infra.mm.LigandParameters attribute) included_rows (schrodinger.project.project.EntryGroup property) (schrodinger.project.project.Project property) IncludedEntries (schrodinger.ui.qt.structure_selector.InputSource attribute) IncludedEntry (schrodinger.ui.qt.structure_selector.InputSource attribute) includeEntries() (schrodinger.ui.two_d_viewer.CellContextualMenu method) IncludeInSelection (class in schrodinger.application.bioluminate.pml_menus) includeNext() (schrodinger.infra.canvas.ChmRangeFilter method) includeOnly() (schrodinger.project.project.ProjectRow method) includeRows() (schrodinger.project.project.Project method) includes() (schrodinger.utils.ligfilter.Definition method) includeSelectedCellsEntries() (schrodinger.ui.two_d_viewer.TwoDViewer method) IncludeSubMenu (class in schrodinger.application.bioluminate.pml_menus) IncludeVisibleInSelection (class in schrodinger.application.bioluminate.pml_menus) INCLUSION (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsMacroPkaByPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) inclusion_threshold (schrodinger.protein.tasks.blast.BlastSettings attribute) inclusion_thresholdChanged (schrodinger.protein.tasks.blast.BlastSettings attribute) inclusion_thresholdReplaced (schrodinger.protein.tasks.blast.BlastSettings attribute) inclusionAndSelectionAreIdentical() (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync method) inclusionChanged (schrodinger.ui.qt.structure_selector.StructureSelectorMaestroSync attribute) inclusionStateChanged (schrodinger.ui.qt.appframework2.maestro_callback.InclusionStateMixin attribute) InclusionStateMixin (class in schrodinger.ui.qt.appframework2.maestro_callback) INCOMPATIBLE_PARAMS_MSG (schrodinger.ui.qt.forcefield.forcefield.OPLSValidator attribute) IncompatibleLicenseError IncompleteFragmentError IncompleteOutput InconsistentStructureError, [1] incorporation (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) incorporation_file (schrodinger.tasks.jobtasks.JobOutput attribute) incorporation_fileChanged (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask.Output attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.Output attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.MultisimTask.Output attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask.Output attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) (schrodinger.tasks.jobtasks.JobOutput attribute) incorporation_fileReplaced (schrodinger.application.glide.ligand_designer.GridgenTask.Output attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask.Output attribute) (schrodinger.application.livedesign.tasks.AbModelingTask.Output attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask.Output attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask.Output attribute) (schrodinger.application.livedesign.tasks.CovDockTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask.Output attribute) (schrodinger.application.livedesign.tasks.EpikTask.Output attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask.Output attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask.Output attribute) (schrodinger.application.livedesign.tasks.GlideTask.Output attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask.Output attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask.Output attribute) (schrodinger.application.livedesign.tasks.LigFilterTask.Output attribute) (schrodinger.application.livedesign.tasks.LigPrepTask.Output attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask.Output attribute) (schrodinger.application.livedesign.tasks.MemPermTask.Output attribute) (schrodinger.application.livedesign.tasks.MultisimTask.Output attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask.Output attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask.Output attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask.Output attribute) (schrodinger.application.livedesign.tasks.QikPropTask.Output attribute) (schrodinger.application.livedesign.tasks.RBSSTask.Output attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask.Output attribute) (schrodinger.application.livedesign.tasks.TugAlignTask.Output attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.Output attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask.Output attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask.Output attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask.Output attribute) (schrodinger.protein.tasks.pfam.PfamTask.Output attribute) (schrodinger.tasks.jobtasks.JobOutput attribute) incorporationChanged (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) IncorporationMode (class in schrodinger.tasks.jobtasks) IncorporationParam (class in schrodinger.tasks.jobtasks) incorporationReplaced (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask.JobConfig attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask.JobConfig attribute) IncorporationSelector (class in schrodinger.ui.qt.tasks.configwidgets) increaseSpeed() (schrodinger.trajectory.trajectory_gui_dir.playback_settings.PlaybackSettings method) increment_state_of_changeable() (schrodinger.protein.assignment.ProtAssign method) incrementNestingLevel() (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) incrementTorsionValue() (schrodinger.application.matsci.amorphous.TorsionAngler method) inCustomizeParamArgs() (schrodinger.tasks.param_cli.ParamCLI method) IND_DEFAULT (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) IND_DISABLED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) IND_HOVER (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) IND_PRESSED (schrodinger.ui.qt.standard.design_tokens.CheckboxIcons attribute) INDENT (schrodinger.application.matsci.desconfig.MSJStringer attribute) index (schrodinger.application.jaguar.input.OrbSpec attribute) (schrodinger.application.jaguar.utils.ChgAt attribute) (schrodinger.application.matsci.atom_group.MSAtom property) (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData.RING_NODE_TYPE attribute) (schrodinger.application.matsci.kmc.MoleculeData attribute) (schrodinger.project.project.ProjectRow property) (schrodinger.structure.StructureAtom property) index() (schrodinger.infra.util.OneIndexedList method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.ui.qt.table_helper.RowBasedListModel method) (schrodinger.utils.sea.sea.List method) INDEX_COLUMN_NAME (schrodinger.application.matsci.stage_widgets.BaseTableWidgetDefinition attribute) index_endpoint() (schrodinger.seam.viz.watcher.WatcherWebServer method) index_in_current_file (schrodinger.structure.MultiFileStructureReader attribute) index_of_flag_in_args() (in module schrodinger.application.mopac.mopac_parser) INDEX_PATTERN (schrodinger.utils.sea.sea.Map attribute) INDEX_PATTERN2 (schrodinger.utils.sea.sea.Map attribute) index_to_nodes (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule.CycleMappings attribute) indexChanged() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) indexChanges() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin static method) indexes (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) indexIsEnabled() (schrodinger.ui.qt.delegates.LinkDelegate method) IndexString (class in schrodinger.application.jaguar.autots_constants) indexToSeqAndIndex() (schrodinger.protein.sequence.CombinedChainProteinSequence method) indexUnbalancedWorkflow() (schrodinger.application.matsci.permittivity.WorkflowProtocol method) indicator (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec attribute) indicator_icon() (schrodinger.application.job_monitor.job_monitor_table.JobTableSpec method) INDICES (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) indices (schrodinger.application.jaguar.hess_guess.InternalCoordinate property) (schrodinger.application.matsci.coarsegrain.InternalInfo attribute) INDICES (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis attribute) (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) indices (schrodinger.protein.annotation.ProteinAlignmentAnnotations property) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) indices() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) indicesToPositions() (schrodinger.application.bindingsite.cavutils.Grid method) indicies_from_bonds_deep() (in module schrodinger.application.matsci.rxn_channel) INFERRED (schrodinger.seam.options.pipeline_options.SeamOptions attribute) infile (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.tasks.slurmtasks.FooTask.Input attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) infile_setup() (schrodinger.application.fragment_virtual_screening.frag_vs_stages.GlideStage method) (schrodinger.application.fragment_virtual_screening.frag_vs_stages.WScoreSIPStage method) infileChanged (schrodinger.tasks.slurmtasks.FooTask.Input attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) infileReplaced (schrodinger.tasks.slurmtasks.FooTask.Input attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask.Input attribute) INFILES (class in schrodinger.application.jaguar.ames.ames_constants) info (schrodinger.application.matsci.cache.BaseCacheData property) (schrodinger.infra.mm.UTT attribute) (schrodinger.infra.mm.UTTDefSpec attribute) info() (in module schrodinger.application.matsci.gutils) (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) (schrodinger.application.prepwizard2.tasks.LoggerMixin method) (schrodinger.pipeline.stage.Stage method) (schrodinger.ui.qt.appframework.AppFramework method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.swidgets.SDialog method) (schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin method) (schrodinger.ui.two_d_viewer.TwoDViewer method) INFO_BTN_STYLESHEET (schrodinger.ui.qt.pop_up_widgets.InfoButtonWithPopUp attribute) INFO_BUTTON_STYLESHEET (schrodinger.ui.qt.swidgets.InfoButton attribute) INFO_H_ICON (schrodinger.ui.qt.swidgets.InfoButton attribute) INFO_ICON (schrodinger.ui.qt.swidgets.InfoButton attribute) info_task (schrodinger.application.livedesign.ld_import_utils.LDImportTask attribute) info_text_style() (in module schrodinger.application.matsci.stylemanager) InfoButton (class in schrodinger.ui.qt.swidgets) InfoButtonWithPopUp (class in schrodinger.ui.qt.pop_up_widgets) INFORMATIONAL_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute) InfoTab (class in schrodinger.maestro_utils.surface_manager.info_tab) InfoTextLabel (class in schrodinger.ui.qt.standard_widgets.labels) InFrontMonomer (schrodinger.protein.helm.helm_renderer.ZOrder attribute) inheritProperties() (schrodinger.application.matsci.cg_mapping.CGMapperMixin method) Init (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom.NextGeomFrom attribute) init() (in module schrodinger.protein.remediate) (schrodinger.application.bioluminate.interaction_calculator.Interactions class method) (schrodinger.application.bioluminate.interaction_calculator.ResTuple class method) (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) (schrodinger.application.glide_ws.nodes.GridGenNode method) (schrodinger.application.glide_ws.nodes.Node method) (schrodinger.application.glide_ws.nodes.SPDecoysNode method) (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method) (schrodinger.application.matsci.gsas.GSASIImath.fast_sa method) (schrodinger.application.matsci.gsas.GSASIImath.log_sa method) init_complexes() (schrodinger.application.glide_ws.driver.GlideWSJob method) init_count (schrodinger.job.queue.BaseJob attribute) (schrodinger.job.queue.SubprocessJob attribute) init_ff() (schrodinger.application.desmond.torsion_related.TorsionPotential method) init_mmgbsa_job_obj_attributes() (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) init_model() (schrodinger.application.glide_ws.driver.GlideWSJob method) init_nodes() (schrodinger.application.glide_ws.driver.GlideWSJob method) init_random_seed() (in module schrodinger.application.matsci.rxn_channel) init_state() (schrodinger.application.glide_ws.driver.GlideWSJob method) initAbstract() (schrodinger.models.parameters.Param method) initActionStates() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) initConcrete() (schrodinger.application.glide.gui.GridSite method) (schrodinger.application.glide.ligand_designer.BuildServerTask method) (schrodinger.application.glide.ligand_designer.GridgenTask method) (schrodinger.application.livedesign.ld_export.ExportModel method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel method) (schrodinger.application.livedesign.models2.execution.context.ExecutionContext method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.protein.tasks.blast.BlastSettings method) (schrodinger.protein.tasks.blast.BlastTask.Input method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsSettings method) initCycleFragments() (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) initDlg() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) initFigure() (schrodinger.ui.qt.radial_plot.RadialRingHistogram method) initFinalize() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) initFromEpikOutput() (schrodinger.application.prepwizard.HetState class method) initial (schrodinger.application.jaguar.scan.Scan property) (schrodinger.application.jaguar.utils.ScanCoord attribute) INITIAL_GUESS_OPTS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) INITIAL_HESSIAN (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) initial_tokens() (in module schrodinger.application.licensing.lmgrd_log_parser) initializator (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) initialize() (schrodinger.application.jaguar.mmjag.MmJag static method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.permittivity.WorkflowParser method) (schrodinger.infra.mminit.Initializer method) (schrodinger.infra.mmlist.mmlist static method) (schrodinger.infra.table.Table static method) (schrodinger.project.project.Project static method) (schrodinger.seam.examples.active_learning_weigher.LinearRegressionModel class method) initialize_atom_types() (schrodinger.application.jaguar.autots_rmsd.AutoTSAtomMapper method) (schrodinger.application.jaguar.autots_rmsd.AutoTSTemplateAtomMapper method) (schrodinger.comparison.atom_mapper.BaseAtomMapper method) (schrodinger.comparison.atom_mapper.ConnectivityAtomMapper method) (schrodinger.comparison.atom_mapper.CSPAtomMapper method) (schrodinger.comparison.atom_mapper.LewisAtomMapper method) initialize_audit_log() (in module schrodinger.livedesign.preprocessor) initialize_disk_file() (schrodinger.active_learning.bloom_filter_methods.BuiltInBloomFilter method) initialize_map_data() (in module schrodinger.utils.documentation) initialize_map_numbers() (in module schrodinger.livedesign.check_reaction) initialize_property_table() (in module schrodinger.application.glide_ws.db) initialize_tddft() (in module schrodinger.application.jaguar.textparser) initializeDatabase() (schrodinger.application.matsci.kmc.BaseDatabaseManager method) (schrodinger.application.matsci.kmc.MatSciDatabaseManager method) (schrodinger.application.matsci.kmc.VotcaDatabaseManager method) initializeGA() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) initializeGenome() (schrodinger.application.matsci.genetic_optimization.GeneticOptimization method) initializeLeaves() (schrodinger.ui.qt.dendrogram.Dendrogram method) initializeMinimizerFromMolecule() (schrodinger.infra.canvas.Chm2DCoordGen static method) initializeMmlibs() (schrodinger.application.ligprep.ionizer.Ionizer method) Initializer (class in schrodinger.infra.mminit) initializeTopics() (schrodinger.stepper.stepper.PubsubEnabledStepMixin method) initializeValue() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOptions method) (schrodinger.application.glide.gui.GridSite method) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask method) (schrodinger.application.livedesign.ld_export.ExportModel method) (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask method) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask method) (schrodinger.application.livedesign.ld_tasks.ImportTask method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsModel method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel method) (schrodinger.application.pymol.gui_models.AdvancedSettingsModel method) (schrodinger.models.param_class_convertors.DCCompoundParam method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.protein.gpcr.tasks.GPCRTask method) (schrodinger.protein.tasks.blast.BlastSettings method) (schrodinger.stepper.stepper.BatchSettings method) (schrodinger.tasks.maptasks.MapTaskMixin method) (schrodinger.tasks.tasks.AbstractComboTask method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.ui.two_d_viewer.GridSaveImagesDialogModel method) initializeValueMatrix() (schrodinger.ui.qt.table.StructureDataViewerModel method) initialSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) InitialSuggestionLineEdit (class in schrodinger.application.livedesign.panel_components) initiateAndAddMdJobs() (schrodinger.application.matsci.equilibrium_md.MultiDriver method) initiateCellSizes() (schrodinger.ui.qt.table.DataViewerTable method) (schrodinger.ui.qt.table.VSubDataViewerTable method) initiateMultiMols() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) InitiationError Initiator (class in schrodinger.application.matsci.amorphous) initKnime() (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) initLayOut() (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog method) (schrodinger.application.jaguar.jaguar_config_dialog.JaguarHostSelector method) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.job_monitor.job_monitor_table.JobTableWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobBar method) (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) (schrodinger.application.job_monitor.job_monitor_widgets.SubJobBar method) (schrodinger.application.job_monitor.job_monitor_widgets.TopLevelJobBar method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget method) (schrodinger.ui.qt.directory_selector.DirectorySelector method) (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.file_selector.SlimFileSelector method) (schrodinger.ui.qt.mapperwidgets.param_editor.ParamEditor method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.structure_selector.ImportButtonMixin method) (schrodinger.ui.qt.structure_selector.MultiStructureLoadButton method) (schrodinger.ui.qt.structure_selector.SlimMultiStructureLoadButton method) (schrodinger.ui.qt.structure_selector.SlimStructureLoadButton method) (schrodinger.ui.qt.structure_selector.SlimStructureSelector method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.configwidgets.HostLayoutWidget method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.tasks.configwidgets.IncorporationSelector method) (schrodinger.ui.qt.tasks.configwidgets.JobnameWidget method) (schrodinger.ui.qt.tasks.taskwidgets.KillableProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.StatusBarMixin method) initMaestroWriter() (schrodinger.application.matsci.rxn_channel.Channels method) InitMixin (class in schrodinger.ui.qt.widgetmixins.basicmixins) initMixinOptions() (schrodinger.application.matsci.appbase.MatSciAppMixin method) initNonPersistent() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) initPositions() (schrodinger.application.matsci.mswidgets.MultiSlider method) initReport() (schrodinger.active_learning.al_report.ALReportMaker method) initServersCombo() (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) initSetDefaults() (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfoDialog method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.structure_selector.MultiStructureLoadButton method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) initSetOptions() (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfoDialog method) (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel method) (schrodinger.application.livedesign.widgets.InvalidGEIdWarningDialog method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.maestro_utils.composer_agent.composer_gui.ComposerAgentPanel method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.basewidgets.BaseDialog method) (schrodinger.ui.qt.basewidgets.BaseOptionsDialog method) (schrodinger.ui.qt.presets.save_presets_dialog.SavePresetsDialog method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.SchrodingerStyleMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.KnimeMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) (schrodinger.ui.two_d_viewer.AtomPropertyDialog method) (schrodinger.ui.two_d_viewer.CtPropsDialog method) (schrodinger.ui.two_d_viewer.SaveImagesDialog method) initSetUp() (schrodinger.application.jaguar.gui.input_tab_widgets.MultiBasisSelectorDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets.MultiTheorySelectorDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.PkaPage method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.SmartsSelector method) (schrodinger.application.jaguar.jaguar_config_dialog.JaguarHostSelector method) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsDialog method) (schrodinger.application.job_monitor.job_monitor_file_browser.JobMonitorFileBrowser method) (schrodinger.application.job_monitor.job_monitor_gui.JobMonitor method) (schrodinger.application.job_monitor.job_monitor_widgets.JobBar method) (schrodinger.application.job_monitor.job_monitor_widgets.JobDetailsPane method) (schrodinger.application.job_monitor.job_monitor_widgets.JobInfoWidget method) (schrodinger.application.job_monitor.job_monitor_widgets.JobsListPane method) (schrodinger.application.jobserver_cert_gui_dir.registration_dialogs.RegistrationPanel method) (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportMainPanel method) (schrodinger.application.livedesign.ld_export_gui.ExportSetupPanel method) (schrodinger.application.livedesign.ld_model_info_dialog.LDModelInfoDialog method) (schrodinger.application.livedesign.live_report_widget.LiveReportWidget method) (schrodinger.application.livedesign.login_gui.LiveDesignLoginDialog method) (schrodinger.application.livedesign.login_gui2.LDLoginPanel method) (schrodinger.application.livedesign.mapping_widgets.CreateOrEditMappingsDialog method) (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingWidget method) (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) (schrodinger.application.livedesign.pose_name_panel.PoseNameEditPanel method) (schrodinger.application.livedesign.summary.LiveDesignExportSummaryPanel method) (schrodinger.application.livedesign.widgets.InvalidGEIdWarningDialog method) (schrodinger.application.pymol.export_to_pymol_gui.AdvancedSettingsPopUp method) (schrodinger.application.pymol.export_to_pymol_gui.ExportToPyMolPanel method) (schrodinger.maestro_utils.composer_agent.composer_gui.ComposerAgentPanel method) (schrodinger.trajectory.trajectory_gui_dir.banners.CentroidBanner method) (schrodinger.trajectory.trajectory_gui_dir.banners.PlanarBanner method) (schrodinger.ui.qt.appframework2.wizards.BaseWizardPanel method) (schrodinger.ui.qt.atom_weights_table_widget.AtomWeightsWidget method) (schrodinger.ui.qt.basewidgets.BaseDialog method) (schrodinger.ui.qt.basewidgets.TaskPanel method) (schrodinger.ui.qt.directory_selector.DirectorySelector method) (schrodinger.ui.qt.file_selector.FileSelector method) (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin method) (schrodinger.ui.qt.fp_selector_widget.FingerprintsSelectorWidget method) (schrodinger.ui.qt.mapperwidgets.param_editor.ParamEditor method) (schrodinger.ui.qt.mapperwidgets.plptable.PLPTableWidget method) (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsDialog method) (schrodinger.ui.qt.presets.save_presets_dialog.SavePresetsDialog method) (schrodinger.ui.qt.standard_widgets.sketcher_text_widget.SketcherTextWidget method) (schrodinger.ui.qt.structure_selector.ImportButtonMixin method) (schrodinger.ui.qt.structure_selector.MultiStructureLoadButton method) (schrodinger.ui.qt.structure_selector.SlimStructureSelector method) (schrodinger.ui.qt.structure_selector.StructureLoadButton method) (schrodinger.ui.qt.structure_selector.StructureSelector method) (schrodinger.ui.qt.tasks.configwidgets.ConfigDialog method) (schrodinger.ui.qt.tasks.configwidgets.HostLayoutWidget method) (schrodinger.ui.qt.tasks.configwidgets.HostSelector method) (schrodinger.ui.qt.tasks.configwidgets.IncorporationSelector method) (schrodinger.ui.qt.tasks.configwidgets.JobnameWidget method) (schrodinger.ui.qt.tasks.taskbar2.TaskBar2 method) (schrodinger.ui.qt.tasks.taskwidgets.JobTaskBar method) (schrodinger.ui.qt.tasks.taskwidgets.KillableProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) (schrodinger.ui.qt.tasks.taskwidgets.TaskBar method) (schrodinger.ui.qt.widgetmixins.basicmixins.BottomButtonMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.InitMixin method) (schrodinger.ui.qt.widgetmixins.basicmixins.StatusBarMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.PanelMixin method) (schrodinger.ui.qt.widgetmixins.panelmixins.TaskPanelMixin method) (schrodinger.ui.two_d_viewer.SaveGridImagesDialog method) (schrodinger.ui.two_d_viewer.SaveImagesDialog method) (schrodinger.ui.two_d_viewer.SaveIndividualImagesDialog method) initSockets() (schrodinger.active_learning.mq_worker.Worker method) initStack() (schrodinger.application.peptide_workflow.minimize.AbstractMinimizer method) (schrodinger.application.peptide_workflow.minimize.OPLSMinimizer method) (schrodinger.application.peptide_workflow.minimize.PrimeMinimizer method) (schrodinger.application.peptide_workflow.minimize.SkateMinimizer method) initStyleOption() (schrodinger.ui.qt.table_speed_up.SpeedUpDelegate method) initTangledMethod() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) initVariables() (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider method) INJECTS_E (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) INJECTS_H (schrodinger.application.matsci.kmc.MatSciSitesTable attribute) InMemoryRandomSampleFilter (class in schrodinger.application.steps.filters) InMemoryRandomSampleFilter.Settings (class in schrodinger.application.steps.filters) InMemoryUniqueRandomSampleFilter (class in schrodinger.application.steps.filters) InMemoryUniqueRandomSampleFilter.Settings (class in schrodinger.application.steps.filters) InMemoryUniqueSmilesFilter (class in schrodinger.application.steps.filters) inner_box (schrodinger.application.glide.gui.GridSite attribute) inner_boxChanged (schrodinger.application.glide.gui.GridSite attribute) inner_boxReplaced (schrodinger.application.glide.gui.GridSite attribute) INNERBOX (schrodinger.application.transforms.dockers.box.BoxSettings attribute) INORGANIC_MPNICE (schrodinger.application.jaguar.rotation_barriers_keywords.ExternalMethod attribute) INPLACE_PROPERTY (schrodinger.structutils.sitealign.SiteMatchLookup attribute) InplaceDockingMethod (class in schrodinger.application.glide.runner) Input (class in schrodinger.application.livedesign.models2.execution.context) input (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.ld_tasks.StructureInfoTask attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask attribute) (schrodinger.application.livedesign.tasks.AbModelingTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.EventAnalysisTask attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MultisimTask attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.Trj2maeTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) INPUT (schrodinger.application.matsci.crest.CrestTOML attribute) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CustomScriptLine attribute) input (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.BuildMissingLoopsTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) Input (schrodinger.application.steps.converters.SmilesToMolConverter attribute) (schrodinger.application.steps.dataclasses.FileInMixin attribute) (schrodinger.application.steps.dataclasses.MaeInMixin attribute) (schrodinger.application.steps.dataclasses.MolInMixin attribute) (schrodinger.application.steps.dataclasses.ScoredMolInMixin attribute) (schrodinger.application.steps.dataclasses.ScorerMixin attribute) (schrodinger.application.steps.enumerators.RouteDeduplicator attribute) (schrodinger.application.steps.enumerators.RouteEvaluator attribute) (schrodinger.application.steps.enumerators.TransformApplyer attribute) (schrodinger.application.steps.filters.RangeFilter attribute) input (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) Input (schrodinger.stepper.core_steps.DedupeAndRandomSampleFilter attribute) (schrodinger.stepper.core_steps.DeduplicationStep attribute) (schrodinger.stepper.core_steps.RandomSampleFilter attribute) input (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.stepper.stepper.StepTaskMixin attribute) Input (schrodinger.stepper.stepper.UnbatchedChain property) input (schrodinger.tasks.beamtasks.BeamTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.maptasks.MapTask attribute) (schrodinger.tasks.slurmtasks.FooTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask attribute) (schrodinger.tasks.test.cli.preprocessor_cli.FooJobTask attribute) (schrodinger.ui.qt.pdb_dialog.Sf2MapConversionTask attribute) input() (schrodinger.energy.MlffSystemPredictor method) input_at_index_str (schrodinger.application.jaguar.autots_constants.IndexString attribute) input_changed (schrodinger.ui.qt.input_selector.InputSelector attribute) input_columns (schrodinger.application.livedesign.models2.datamodels.execution_record.ModelExecution attribute) input_columnsChanged (schrodinger.application.livedesign.models2.datamodels.execution_record.ModelExecution attribute) input_columnsReplaced (schrodinger.application.livedesign.models2.datamodels.execution_record.ModelExecution attribute) input_config (schrodinger.application.transforms.prime.PrimeSettings attribute) input_deviation (schrodinger.application.jaguar.results.NofailResult attribute) input_file (schrodinger.application.peptide_workflow.driver_utils.PeptideConfig attribute) (schrodinger.tasks.beamtasks.BeamTask.Input attribute) (schrodinger.tasks.maptasks.MapTask.Input attribute) input_file_arguments() (in module schrodinger.job.jobcontrol) input_file_keys (schrodinger.application.jaguar.ames.ames_input.AMESInput attribute) (schrodinger.application.jaguar.autots_input.AutoTSInput attribute) (schrodinger.application.jaguar.distributed_frequencies.input.DistributedFrequenciesInput attribute) (schrodinger.application.jaguar.esol_input.EsolInput attribute) (schrodinger.application.jaguar.hydrokinetic_input.HydrokineticInput attribute) (schrodinger.application.jaguar.macro_pka_input.MacroKaInput attribute) (schrodinger.application.jaguar.mlff.input.MLFFInput attribute) (schrodinger.application.jaguar.nics_predictor.input.NICSInput attribute) (schrodinger.application.jaguar.rotation_barriers_input.RotationBarriersInput attribute) (schrodinger.application.jaguar.solvation_input.SolvationInput attribute) (schrodinger.application.jaguar.workflow_input.WorkflowInput property) (schrodinger.application.jaguar.xray.input.XrayInput attribute) (schrodinger.application.xtb.input.XTBInput attribute) input_fileChanged (schrodinger.tasks.beamtasks.BeamTask.Input attribute) (schrodinger.tasks.maptasks.MapTask.Input attribute) input_filename() (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) (schrodinger.application.glide_ws.nodes.GlideBaseNode method) (schrodinger.application.glide_ws.nodes.MMGBSAReceptorBaseNode method) (schrodinger.application.glide_ws.nodes.Node method) input_fileReplaced (schrodinger.tasks.beamtasks.BeamTask.Input attribute) (schrodinger.tasks.maptasks.MapTask.Input attribute) input_files (schrodinger.application.vss.control.GlideALControl property) (schrodinger.application.vss.control.GlideControl property) (schrodinger.application.vss.control.LigandMLControl property) (schrodinger.application.vss.control.RunnerControl property) (schrodinger.application.vss.control.ShapeControl property) (schrodinger.application.vss.csvsmiles.CsvSmilesFile property) INPUT_FLAG (schrodinger.application.matsci.crest.Crest attribute) input_fname (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsproPredictor attribute) input_fnameChanged (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) input_fnameReplaced (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) input_is_lipid() (in module schrodinger.application.matsci.custom_lipid_prep) input_items (schrodinger.tasks.beamtasks.BeamTask.Input attribute) (schrodinger.tasks.maptasks.MapTask.Input attribute) input_itemsChanged (schrodinger.tasks.beamtasks.BeamTask.Input attribute) (schrodinger.tasks.maptasks.MapTask.Input attribute) input_itemsReplaced (schrodinger.tasks.beamtasks.BeamTask.Input attribute) (schrodinger.tasks.maptasks.MapTask.Input attribute) INPUT_MASK (schrodinger.application.matsci.jaguar_multistage_workflow_utils.CommandLine attribute) input_mol_index_str (schrodinger.application.jaguar.autots_constants.IndexString attribute) INPUT_MOLECULES (schrodinger.application.jaguar.xray.constants.KEYWORDS attribute) input_pcolls (schrodinger.seam.viz.inspect.TransformDisplayInfo attribute) INPUT_PROPERTY_DATA (schrodinger.livedesign.custom_entity.registration.EntityComponent attribute) input_property_data (schrodinger.livedesign.registration.RegistrationData attribute) INPUT_ST2 (schrodinger.application.matsci.permittivity.AnalyzeSimulation attribute) input_st_count (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) input_st_countChanged (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) input_st_countReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) input_string (schrodinger.livedesign.registration.RegistrationData attribute) input_string() (schrodinger.application.glide_ws.nodes.DecoysNode method) (schrodinger.application.glide_ws.nodes.DistributedGlideBaseNode method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) (schrodinger.application.glide_ws.nodes.GridGenNode method) (schrodinger.application.glide_ws.nodes.MMGBSAReceptorBaseNode method) (schrodinger.application.glide_ws.nodes.ModelNode method) (schrodinger.application.glide_ws.nodes.NativeNode method) (schrodinger.application.glide_ws.nodes.Node method) (schrodinger.application.glide_ws.nodes.SPDecoysNode method) (schrodinger.application.glide_ws.nodes.TestSetNode method) INPUT_SUB_TABS (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) input_summary (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) input_summaryChanged (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) input_summaryReplaced (schrodinger.application.livedesign.export_models.SummaryModel attribute) (schrodinger.application.livedesign.ld_export.ExportModel attribute) inputChanged (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.ld_tasks.StructureInfoTask attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask attribute) (schrodinger.application.livedesign.tasks.AbModelingTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.EventAnalysisTask attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MultisimTask attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.Trj2maeTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.BuildMissingLoopsTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.beamtasks.BeamTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.maptasks.MapTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.slurmtasks.ComboSlurmTask attribute) (schrodinger.tasks.slurmtasks.FooTask attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask attribute) (schrodinger.tasks.test.cli.preprocessor_cli.FooJobTask attribute) (schrodinger.ui.qt.pdb_dialog.Sf2MapConversionTask attribute) (schrodinger.ui.qt.structure_selector.StructureSelector attribute) InputColumn (class in schrodinger.tasks.ldi) InputConfig (class in schrodinger.application.inputconfig) inputconfig_subset() (in module schrodinger.application.phase.input) InputDef (class in schrodinger.application.livedesign.models2.datamodels.definition) InputDeviation (class in schrodinger.application.jaguar.results) InputEntriesColumns (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesColumnsHB (class in schrodinger.application.jaguar.gui.input_tab_widgets_hb) InputEntriesColumnsMacroPkaByCharge (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesColumnsMacroPkaByPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesColumnsPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesModel (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesModelHB (class in schrodinger.application.jaguar.gui.input_tab_widgets_hb) InputEntriesModelMacroPkaByCharge (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesModelMacroPkaByPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesModelPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesProxyModel (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesView (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesViewPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputError, [1] InputFiles (schrodinger.job.jobcontrol.Job property) InputInst (class in schrodinger.application.livedesign.models2.datamodels.instance) InputItem (schrodinger.tasks.maptasks.MapTaskMixin attribute) inputLoaded (schrodinger.ui.qt.structure_selector.MultiStructureLoadButton attribute) (schrodinger.ui.qt.structure_selector.SlimStructureSelector attribute) InputMultiplicityMixin (class in schrodinger.application.jaguar.gui.base_panel) InputOrder (schrodinger.structutils.interactions.salt_bridge.OrderBy attribute) InputParams (class in schrodinger.application.jaguar.thermochemical_properties) InputPropertyDataComponent (class in schrodinger.livedesign.custom_entity.registration) inputReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionSubTask attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionTask attribute) (schrodinger.application.glide.ligand_designer.BuildServerTask attribute) (schrodinger.application.glide.ligand_designer.GridgenTask attribute) (schrodinger.application.jaguar.jaguar_tasks.JaguarCmdJobTask attribute) (schrodinger.application.job_monitor.job_monitor_diagnostics_dialog.CollectJobDiagnosticsTask attribute) (schrodinger.application.livedesign.export_tasks.AttachmentExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask attribute) (schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86 attribute) (schrodinger.application.livedesign.export_tasks.Export2DTask attribute) (schrodinger.application.livedesign.export_tasks.Export3DTask attribute) (schrodinger.application.livedesign.export_tasks.ExportTask87 attribute) (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) (schrodinger.application.livedesign.export_tasks.MasterExportTask attribute) (schrodinger.application.livedesign.ld_tasks.Import3DGenericEntitiesTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportStructuresTask attribute) (schrodinger.application.livedesign.ld_tasks.ImportTask attribute) (schrodinger.application.livedesign.ld_tasks.StructureInfoTask attribute) (schrodinger.application.livedesign.tasks.AbHumanizationTask attribute) (schrodinger.application.livedesign.tasks.AbModelingTask attribute) (schrodinger.application.livedesign.tasks.AlignLigandsTask attribute) (schrodinger.application.livedesign.tasks.CanvasSearchTask attribute) (schrodinger.application.livedesign.tasks.CovDockTask attribute) (schrodinger.application.livedesign.tasks.EpikClassicTask attribute) (schrodinger.application.livedesign.tasks.EpikTask attribute) (schrodinger.application.livedesign.tasks.EventAnalysisTask attribute) (schrodinger.application.livedesign.tasks.FFBuilderTask attribute) (schrodinger.application.livedesign.tasks.FlexAlignTask attribute) (schrodinger.application.livedesign.tasks.GlideTask attribute) (schrodinger.application.livedesign.tasks.IFDMDCongenericTask attribute) (schrodinger.application.livedesign.tasks.LigandStrainTask attribute) (schrodinger.application.livedesign.tasks.LigFilterTask attribute) (schrodinger.application.livedesign.tasks.LigPrepTask attribute) (schrodinger.application.livedesign.tasks.MCSDockingTask attribute) (schrodinger.application.livedesign.tasks.MemPermTask attribute) (schrodinger.application.livedesign.tasks.MultisimTask attribute) (schrodinger.application.livedesign.tasks.PeptideDockingTask attribute) (schrodinger.application.livedesign.tasks.PhaseScreenTask attribute) (schrodinger.application.livedesign.tasks.PrimeMMGBSATask attribute) (schrodinger.application.livedesign.tasks.QikPropTask attribute) (schrodinger.application.livedesign.tasks.RBSSTask attribute) (schrodinger.application.livedesign.tasks.StrainRescoreTask attribute) (schrodinger.application.livedesign.tasks.Trj2maeTask attribute) (schrodinger.application.livedesign.tasks.TugAlignTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.CreateScreeningDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.FilterDBTask attribute) (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) (schrodinger.application.prepwizard2.tasks.BuildMissingLoopsTask attribute) (schrodinger.application.prepwizard2.tasks.CleanupTask attribute) (schrodinger.application.prepwizard2.tasks.DeleteWatersTask attribute) (schrodinger.application.prepwizard2.tasks.GenerateStatesTask attribute) (schrodinger.application.prepwizard2.tasks.OptimizeHBondTask attribute) (schrodinger.application.prepwizard2.tasks.PPBatchWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PPWorkflowTask attribute) (schrodinger.application.prepwizard2.tasks.PreprocessTask attribute) (schrodinger.application.prepwizard2.tasks.ProteinRefinementTask attribute) (schrodinger.protein.gpcr.tasks.GPCRTask attribute) (schrodinger.protein.predictors.AbstractPredictor attribute) (schrodinger.protein.predictors.AccproPredictor attribute) (schrodinger.protein.predictors.BetaproPredictor attribute) (schrodinger.protein.predictors.DiproPredictor attribute) (schrodinger.protein.predictors.DisproPredictor attribute) (schrodinger.protein.predictors.DomproPredictor attribute) (schrodinger.protein.predictors.PredictorWrapperTask attribute) (schrodinger.protein.predictors.SsAccDependentPredictors attribute) (schrodinger.protein.predictors.SsproPredictor attribute) (schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask attribute) (schrodinger.protein.tasks.blast.BlastTask attribute) (schrodinger.protein.tasks.descriptors.SequenceDescriptorsTask attribute) (schrodinger.protein.tasks.descriptors.StructureDescriptorsTask attribute) (schrodinger.protein.tasks.hit_align.BaseHitAlignTask attribute) (schrodinger.protein.tasks.hit_align.CustomFamilyTask attribute) (schrodinger.protein.tasks.kinase.KinaseConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureAndConservationTask attribute) (schrodinger.protein.tasks.kinase.KinaseFeatureTask attribute) (schrodinger.protein.tasks.optimize_alignment.OptimizeAlignmentTask attribute) (schrodinger.protein.tasks.pfam.PfamTask attribute) (schrodinger.protein.tasks.sta.STATask attribute) (schrodinger.seam.testing.fixtures.TaskWithLicenseManager attribute) (schrodinger.stepper.stepper.StepJobTask attribute) (schrodinger.stepper.stepper.StepSubprocessTask attribute) (schrodinger.tasks.beamtasks.BeamTask attribute) (schrodinger.tasks.drivers.BaseDriverTask attribute) (schrodinger.tasks.jobtasks.CmdJobTask attribute) (schrodinger.tasks.jobtasks.ComboJobTask attribute) (schrodinger.tasks.maptasks.MapTask attribute) (schrodinger.tasks.queue.TaskQueue attribute) (schrodinger.tasks.slurmtasks.ComboSlurmTask attribute) (schrodinger.tasks.slurmtasks.FooTask attribute) (schrodinger.tasks.tasks.AbstractCmdTask attribute) (schrodinger.tasks.tasks.AbstractComboTask attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks.BlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboBlockingFunctionTask attribute) (schrodinger.tasks.tasks.ComboSubprocessTask attribute) (schrodinger.tasks.tasks.SignalTask attribute) (schrodinger.tasks.tasks.SubprocessCmdTask attribute) (schrodinger.tasks.tasks.ThreadFunctionTask attribute) (schrodinger.tasks.test.cli.customized_cli.FooComboJobTask attribute) (schrodinger.tasks.test.cli.preprocessor_cli.FooJobTask attribute) (schrodinger.ui.qt.pdb_dialog.Sf2MapConversionTask attribute)

inputs (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) inputs() (schrodinger.application.glide_ws.nodes.CrossNode method) (schrodinger.application.glide_ws.nodes.DecoysNode method) (schrodinger.application.glide_ws.nodes.DistributedMMGBSABaseNode method) (schrodinger.application.glide_ws.nodes.GridGenNode method) (schrodinger.application.glide_ws.nodes.MMGBSANode method) (schrodinger.application.glide_ws.nodes.MMGBSAReceptorModelNode method) (schrodinger.application.glide_ws.nodes.MMGBSATestsetNode method) (schrodinger.application.glide_ws.nodes.ModelNode method) (schrodinger.application.glide_ws.nodes.NativeNode method) (schrodinger.application.glide_ws.nodes.Node method) (schrodinger.application.glide_ws.nodes.OptimizeNode method) (schrodinger.application.glide_ws.nodes.SPDecoysNode method) (schrodinger.application.glide_ws.nodes.TestSetNode method) (schrodinger.application.glide_ws.nodes.WmapGenNode method) inputsChanged (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) InputSelector (class in schrodinger.ui.qt.input_selector) InputSelectorWithDatabase (class in schrodinger.application.matsci.kmcgui) InputSequence (class in schrodinger.application.bioluminate.anarci.anarci_adapter) InputSerializer (schrodinger.application.steps.dataclasses.MolInMixin attribute) (schrodinger.application.steps.dataclasses.ScoredMolInMixin attribute) (schrodinger.application.steps.dataclasses.ScorerMixin attribute) (schrodinger.application.steps.enumerators.RouteDeduplicator attribute) (schrodinger.application.steps.enumerators.RouteEvaluator attribute) (schrodinger.application.steps.filters.RangeFilter attribute) (schrodinger.stepper.stepper.UnbatchedChain property) inputsForStagesDefined() (schrodinger.pipeline.pipeline.Pipeline method) InputSource (class in schrodinger.ui.qt.structure_selector) inputSource() (schrodinger.ui.qt.structure_selector.StructureSelector method) InputSpecs (class in schrodinger.application.phase.input) inputsReplaced (schrodinger.application.livedesign.models2.datamodels.definition.ModelDefinition attribute) (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) (schrodinger.application.livedesign.models2.execution.context.ExecutionContext attribute) inputState() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) (schrodinger.ui.qt.input_selector.InputSelector method) InputTab (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabBase (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabCoordinateScan (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabHB (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabJobMixin (class in schrodinger.application.jaguar.gui.base_panel) InputTabMixin (class in schrodinger.application.jaguar.gui.base_panel) InputTabPka (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabWithSubTabs (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputType (class in schrodinger.application.livedesign.models2.datamodels.definition) (class in schrodinger.application.matsci.espresso.qeinput) InputVerificationError ins_code (schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo attribute) inscode (schrodinger.application.bioluminate.mutation.Mutation attribute) (schrodinger.application.bioluminate.protein_interaction.utils.Residue attribute) (schrodinger.application.glide.utils.ResidueId attribute) (schrodinger.application.glide.utils.ResidueInteraction attribute) (schrodinger.application.qsite.input.Cut property) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) (schrodinger.protein.residue.Residue property) (schrodinger.protein.residue.ResidueChainKey attribute) (schrodinger.protein.residue.ResidueKey attribute) (schrodinger.structure.Residue property) (schrodinger.structure.StructureAtom property) (schrodinger.ui.qt.rama.BackboneDihedral attribute) insert() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.util.OneIndexedList method) (schrodinger.utils.sea.sea.List method) insert_node_to_run() (schrodinger.application.glide_ws.driver.GlideWSJob method) insert_raw() (schrodinger.comparison.results.OptResultSet method) insert_stage_hash() (in module schrodinger.application.matsci.thermo_correction_utils) insert_temp_press() (in module schrodinger.application.matsci.thermo_correction_utils) insert_units() (in module schrodinger.application.matsci.thermo_correction_utils) insertColumn() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.swidgets.STableWidget method) (schrodinger.ui.qt.table.StructureDataViewerModel method) insertColumns() (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) insertElementByChain() (schrodinger.protein.sequence.CombinedChainProteinSequence method) insertElements() (schrodinger.protein.sequence.AbstractSequence method) (schrodinger.protein.sequence.AbstractSingleChainSequence method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) insertion_code (schrodinger.application.bioluminate.classify.NumberedResidue attribute) (schrodinger.infra.structure.ResidueId attribute) InsertionError insertRow() (schrodinger.infra.table.Table method) (schrodinger.ui.qt.table.StructureDataViewerModel method) insertRows() (schrodinger.ui.qt.table.StructureDataViewerModel method) (schrodinger.ui.qt.table.ViewerModel method) insertSubalignment() (schrodinger.protein.alignment.BaseAlignment method) INSIDE (schrodinger.application.matsci.packmol.PackmolKw attribute) insideFace() (schrodinger.application.matsci.shapes.Face method) insideRectangle() (schrodinger.application.matsci.nano.tube.Rectangle method) INSIDETHRESH (schrodinger.application.matsci.nano.tube.Rectangle attribute) install_handler() (in module schrodinger.infra.qt_message_handler) install_license() (in module schrodinger.application.licensing.licadmin) install_license_text() (in module schrodinger.application.licensing.licadmin) install_local_entitlement() (in module schrodinger.application.licensing.licserver.install) install_local_entitlement_from_key() (in module schrodinger.application.licensing.licserver.install) install_netsuite_license() (in module schrodinger.application.licensing.licadmin) install_nvidia() (in module schrodinger.autoinstall.prepare_os) install_release() (in module schrodinger.autoinstall.suite_install) install_remote_pubkey() (in module schrodinger.utils.sshconfig) install_remote_server_license() (in module schrodinger.application.licensing.licadmin) install_req_packages() (in module schrodinger.autoinstall.prepare_os) install_schrod_plist() (in module schrodinger.application.licensing.licadmin) install_server_identifier() (in module schrodinger.application.licensing.licserver.install) install_signal_handler() (in module schrodinger.glide) installation_archive_path() (in module schrodinger.infra.mm) installation_path (schrodinger.infra.mm.FfldSpec attribute) installed_pathname() (in module schrodinger.application.licensing.licadmin) InstallError installing modules installPopUpEventFilter() (schrodinger.ui.qt.pop_up_widgets.PopUp method) instance (schrodinger.application.livedesign.ld_import_utils.LDImportTaskManager attribute) instance() (schrodinger.glide.LicenseManager static method) (schrodinger.glide.LoggerManager static method) instance_id (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) instance_idChanged (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) instance_idReplaced (schrodinger.application.livedesign.models2.datamodels.instance.ModelInstance attribute) InstanceAlreadyRunningError InstanceMetadata (class in schrodinger.application.livedesign.models2.datamodels.instance) InstantToolTipTableView (class in schrodinger.ui.qt.swidgets) instruction (schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput attribute) INT (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute) int() (schrodinger.ui.qt.swidgets.SLineEdit method) INT_KEYWORDS (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) INT_PROP_PREFIX (schrodinger.application.phase.shape_screen_reporter.tasks.StructurePropertyTask attribute) INT_SIZE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) int_to_opls_version() (in module schrodinger.infra.mm) INTEGER (schrodinger.application.livedesign.models2.datamodels.definition.InputType attribute) (schrodinger.application.livedesign.models2.datamodels.definition.OutputType attribute) INTENSITY_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) INTENSITY_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) (schrodinger.application.matsci.bandshape_utils.NormalModeAnalysis attribute) (schrodinger.application.matsci.spectra.ECD_Spectrum attribute) (schrodinger.application.matsci.spectra.IR_Spectrum attribute) (schrodinger.application.matsci.spectra.NMRSpectrum attribute) (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) (schrodinger.application.matsci.spectra.RamanSpectrum attribute) (schrodinger.application.matsci.spectra.UVVis_Spectrum attribute) INTER_CUTOFF (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) interacting_greedy_score (schrodinger.glide.RoughPose attribute) InteractingResidue (class in schrodinger.application.bioluminate.interaction_calculator) INTERACTION_NAMES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) InteractionAtomPair (class in schrodinger.infra.structure) InteractionCalculator (class in schrodinger.application.bioluminate.interaction_calculator) InteractionCalculatorError InteractionParams (class in schrodinger.application.bioluminate.interaction_calculator) InteractionReader (class in schrodinger.application.prime.residue_interaction) Interactions (class in schrodinger.application.bioluminate.interaction_calculator) (class in schrodinger.application.jaguar.nmr_interactions) interactions (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) interactionsChanged (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) interactionsReplaced (schrodinger.application.bioluminate.protein_interaction.tasks.MultipleProteinInteractions attribute) (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionOutput attribute) interactionSummary() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) interactive prompt InteractiveFileDownloader (class in schrodinger.application.matsci.jobdirdlg) Interactors (class in schrodinger.protein.protassign.utils) INTERBUTTON_SPACING (schrodinger.ui.qt.standard_widgets.buttons.SplitPushButton attribute) Interdomain (schrodinger.protein.predictors.DomainArrangement attribute) Interface (class in schrodinger.application.matsci.nano.interface_mod) INTERFACE (schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes attribute) INTERFACE_RES (schrodinger.application.bioluminate.antibody.annotate.Properties attribute) InterfaceMixin (class in schrodinger.application.bioluminate.pml_menus) InterfacePreset (class in schrodinger.application.bioluminate.pml_menus) InterfaceResidueFilter (class in schrodinger.application.bioluminate.pose_filtering.residue_filter) Interfaces (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) interior() (schrodinger.ui.qt.appframework.AppFramework method) IntermolecularAtomPair (class in schrodinger.glide) internal (schrodinger.application.matsci.msconst.SMARTS_METHOD attribute) INTERNAL (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) internal_coeff (schrodinger.application.glide.sort_utils.CustomScoringFunction attribute) internal_energy (schrodinger.glide.ScoreInfo attribute) internal_energy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) INTERNAL_PKA (schrodinger.protein.protassign.pka_prediction.AsparticAcidpKaPredictor attribute) (schrodinger.protein.protassign.pka_prediction.GlutamicAcidpKaPredictor attribute) (schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor attribute) InternalCoordinate (class in schrodinger.application.jaguar.hess_guess) InternalCoords (class in schrodinger.application.matsci.rxn_path) InternalInfo (class in schrodinger.application.matsci.coarsegrain) internalParams (schrodinger.application.matsci.genetic_optimization.StructureGenome attribute) Internals (class in schrodinger.application.matsci.coarsegrain) internals_iterator() (in module schrodinger.application.matsci.coarsegrain) INTERPLANAR_SPACING_KEY (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) INTERPLANAR_SPACING_TITLE (schrodinger.application.matsci.spectra.PowderDiffractionFile attribute) interpolate() (schrodinger.application.matsci.zmutils.ZMatrix method) Interpolate1D (class in schrodinger.math.mathutils) Interpolate2D (class in schrodinger.math.mathutils) interpolate_color() (in module schrodinger.application.matsci.stylemanager) interpolateReactionCoords() (schrodinger.application.matsci.rxn_path.ReactionPath method) INTERPOLATIONCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) interpretFlagBlock() (schrodinger.application.matsci.permittivity.TaskProtocol method) interpretJobServerError() (schrodinger.application.matsci.jobutils.FileDownloader static method) INTERRUPT_ENABLED (schrodinger.tasks.tasks.AbstractTask attribute) INTERSECT_KEYS (schrodinger.application.desmond.cms.FBHWPosRestrainArray attribute) (schrodinger.application.desmond.cms.PosRestrainArray attribute) intersect_line_and_rect() (in module schrodinger.ui.qt.network_views) intersection() (schrodinger.utils.scollections.IdSet method) intersection_update() (schrodinger.utils.scollections.IdSet method) intersects() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) intersectSegmentAndPlane() (schrodinger.application.matsci.shapes.Face method) INTERSMEAR_KEY (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) INTERVAL (schrodinger.application.matsci.desconfig.MSJStringer attribute) (schrodinger.application.matsci.deswidgets.TrajectoryTimeSlider attribute) intrahb_count (schrodinger.glide.ScoreDescriptors attribute) intrahb_reward (schrodinger.glide.ScoreTerms attribute) INTRASMEAR_KEY (schrodinger.application.matsci.espresso.qeinput.EpsilonType attribute) intrinsic_part() (schrodinger.application.matsci.cctbx.rot_mx.translation_part_info method) intvector (class in schrodinger.infra.fast3d) inv (schrodinger.application.matsci.elasticity.tensors.SquareTensor property) inv_box (schrodinger.application.desmond.packages.analysis.Pbc property) invalid (schrodinger.application.combinatorial_explorer.driver_utils.RouteSourceType attribute) invalid_code() (in module schrodinger.protein.getpdb_utility) invalid_ids (schrodinger.application.livedesign.export_tasks.GenericEntityExportTask attribute) invalid_ids_handling_option (schrodinger.application.livedesign.export_models.GETaskInput attribute) invalid_ids_handling_optionChanged (schrodinger.application.livedesign.export_models.GETaskInput attribute) invalid_ids_handling_optionReplaced (schrodinger.application.livedesign.export_models.GETaskInput attribute) INVALID_MAP_NAME_MSG (schrodinger.application.livedesign.export_map_manager.MappingManagerDialog attribute) invalid_smarts_changed (schrodinger.ui.qt.swidgets.SMARTSEdit attribute) INVALID_STATE_BORDER (schrodinger.ui.qt.standard.colors.LightModeColors attribute) invalid_types (schrodinger.application.prepwizard2.diagnostics.Problems attribute) invalid_typesChanged (schrodinger.application.prepwizard2.diagnostics.Problems attribute) invalid_typesReplaced (schrodinger.application.prepwizard2.diagnostics.Problems attribute) InvalidAntibodySequenceError invalidatedDomains (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin attribute) invalidatedLigandContacts (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) invalidatedMaxMinBFactor (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) invalidateMaxMinBFactor() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) invalidateWindowHydrophobicity() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) invalidateWindowIsoelectricPoint() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) InvalidCDFTError InvalidCLIInputTypeError InvalidCSVFormattingError InvalidCSVLengthError InvalidFileTypeError InvalidGEIdHandlingPolicy (class in schrodinger.application.livedesign.export_models) InvalidGEIdWarningDialog (class in schrodinger.application.livedesign.widgets) InvalidInput InvalidProjectException InvalidProjectVersion InvalidPropertyError InvalidProteinStateError InvalidQueryLengthError InvalidRequestError InvalidResponseError InvalidRowError InvalidStageFileError InvalidSubstructureTypeError InvalidTimeSliceError invariant() (schrodinger.infra.mm.UTTEndAtom method) invcell2Gmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice) inverse() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.pathfinder.reaction.Reaction method) inverse_cancel() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) InverseCentimeter (schrodinger.application.jaguar.constants.Unit attribute) invert() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.infra.mmbitset.Bitset method) invert_axis (schrodinger.application.jaguar.spin_simulator_v2.Parameters attribute) invert_chirality() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) invert_reaction_smarts() (in module schrodinger.application.pathfinder.reaction) InvertCompleteSelection (class in schrodinger.application.bioluminate.pml_menus) invertNitrogens() (schrodinger.infra.fast3d.Engine method) InvertSubMenu (class in schrodinger.application.bioluminate.pml_menus) involvesAromaticity() (schrodinger.infra.canvas.ChmQuery method) involvesCisTrans() (schrodinger.infra.canvas.ChmQuery method) involvesHybridization() (schrodinger.infra.canvas.ChmQuery method) invpolfcal() (in module schrodinger.application.matsci.gsas.GSASIIlattice) invQ() (in module schrodinger.application.matsci.gsas.GSASIImath) inWorkspace() (schrodinger.project.project.ProjectRow method) inZoomMode() (schrodinger.ui.two_d_viewer.TwoDViewer method) IO IODINE_DB (schrodinger.application.matsci.stylemanager.Gradients attribute) IOException (class in schrodinger.infra.structure) ion (schrodinger.application.desmond.struc.CompStruc attribute) ion_action (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar property) ION_DYNAMICS_KEY (schrodinger.application.matsci.espresso.qeinput.IonControlType attribute) IonControlType (class in schrodinger.application.matsci.espresso.qeinput) ionization_potential() (in module schrodinger.application.mopac.results_main) ionizeCommandParser() (schrodinger.application.ligprep.ionizer.Ionizer method) Ionizer (class in schrodinger.application.ligprep.ionizer) ionizeStructure() (schrodinger.application.ligprep.ionizer.Ionizer method) ip_default (schrodinger.application.jaguar.results.JaguarOptions attribute) IPOL (schrodinger.application.matsci.espresso.qeinput.TurboLanczosType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) IPOLAR (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) IPythonInspect (class in schrodinger.seam.debug) ir_intensity_precision (schrodinger.application.jaguar.results.NormalMode attribute) IR_Spectrum (class in schrodinger.application.matsci.spectra) iradius (schrodinger.application.matsci.elementalprops.ElementalProperties property) IRC_IS_NOT_TS (schrodinger.application.jaguar.constants.FatalErrors attribute) irc_point() (in module schrodinger.application.jaguar.textparser) irc_step (schrodinger.application.jaguar.output.JaguarOutput property) irc_summary() (in module schrodinger.application.jaguar.textparser) IRCEndpointError IRCFailure IrcTab (class in schrodinger.application.jaguar.gui.tabs.irc_tab) IRCVettingFailure irr_sph_ten() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) IRREP_DROP (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem attribute) is32Bit() (schrodinger.infra.canvas.ChmFPTypeInfo method) is3cTheory() (in module schrodinger.application.jaguar.gui.utils) is3d() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) is64Bit() (schrodinger.infra.canvas.ChmFPTypeInfo method) is_active (schrodinger.application.job_monitor.job_monitor_models.JobModel property) is_alpha (schrodinger.application.jaguar.input.OrbSpec attribute) is_another_best_config() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) is_antibody_heavy_type() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) is_antibody_light_type() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) is_antibody_subunit() (in module schrodinger.livedesign.biologics.registration) is_antibody_type() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) is_any_gpu_available() (in module schrodinger.gpgpu) is_any_struct_coarse_grain() (in module schrodinger.application.matsci.msutils) is_any_text_label_visible() (in module schrodinger.application.phase.phase_markers) is_archived (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) is_archivedChanged (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) is_archivedReplaced (schrodinger.application.livedesign.models2.datamodels.instance.InstanceMetadata attribute) is_atom_list() (in module schrodinger.utils.sea.sea) is_atom_supported() (in module schrodinger.application.jaguar.basis) is_auto_download_active() (in module schrodinger.job.jobhandler) is_aws_service_available() (in module schrodinger.application.steps.env_keys) is_better_match() (in module schrodinger.comparison.struc) is_binary_string() (in module schrodinger.ui.qt.formlayout) is_bond_rotatable() (in module schrodinger.structutils.analyze) is_bs_spectrum_file_key() (in module schrodinger.application.matsci.bandshape_utils) is_built_in (schrodinger.application.livedesign.models2.datamodels.definition.Logic attribute) is_built_inChanged (schrodinger.application.livedesign.models2.datamodels.definition.Logic attribute) is_built_inReplaced (schrodinger.application.livedesign.models2.datamodels.definition.Logic attribute) is_builtin_fragment() (in module schrodinger.utils.cgxutils) is_center_set (schrodinger.application.glide.gui.GridCenter attribute) is_center_setChanged (schrodinger.application.glide.gui.GridCenter attribute) is_center_setReplaced (schrodinger.application.glide.gui.GridCenter attribute) is_change() (in module schrodinger.application.bioluminate.peptide_sar.label) is_charged_or_formal_charged() (in module schrodinger.application.desmond.struc) is_chiral() (in module schrodinger.comparison.struc) is_close_packed() (in module schrodinger.comparison.struc) is_cms (schrodinger.application.matsci.freevolume.FreeVolumeDriver property) is_cms_file() (in module schrodinger.infra.structure) (in module schrodinger.utils.fileutils) is_coarse_grain() (in module schrodinger.application.matsci.msutils) is_coarse_grain_input() (in module schrodinger.application.matsci.coarsegrain) is_colinear() (in module schrodinger.structutils.measure) is_color_dark() (in module schrodinger.ui.qt.standard.colors) is_column (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) is_column_prediction() (in module schrodinger.application.matsci.ml_formulations_utils) is_columnChanged (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) is_columnReplaced (schrodinger.application.livedesign.models2.datamodels.definition.InputDef attribute) is_composite_row_structure (schrodinger.application.livedesign.ld_tasks.StructureInfo attribute) is_core() (in module schrodinger.application.pathfinder.multiroute) is_core_application() (in module schrodinger.utils.qapplication) is_core_sm() (in module schrodinger.application.pathfinder.multiroute) is_counted() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.License method) is_covalent_ligand() (in module schrodinger.protein.assignment) is_covalently_bound (schrodinger.structutils.analyze.Ligand property) is_csv_file() (in module schrodinger.utils.fileutils) is_csvgz() (in module schrodinger.rdkit.molio) is_curr_project_scratch (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) is_curr_project_scratchChanged (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) is_curr_project_scratchReplaced (schrodinger.application.job_monitor.job_monitor_models.JobMonitorPanelModel attribute) is_cyclic (schrodinger.protein.helm.helm_renderer.HelmConnector attribute) is_d_amino_acid (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_daemon_enabled() (in module schrodinger.seam.viz.watcherd) is_default (schrodinger.ui.qt.presets.manage_presets_dialog.ManagePresetsTableSpec attribute) (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) is_defaultChanged (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) is_defaultReplaced (schrodinger.ui.qt.presets.manage_presets_dialog.PresetRowModel attribute) is_deoxyribose() (in module schrodinger.livedesign.biologics.registration) is_desmond_product_installed() (in module schrodinger.trajectory.utils) is_deterministic() (schrodinger.seam.coders.MaybeCompressedCoder method) (schrodinger.seam.coders.MolCoder method) (schrodinger.seam.coders.RouteNodeCoder method) (schrodinger.seam.coders.StructureCoder method) (schrodinger.seam.transforms.window.StringIDWindowCoder method) is_dilute() (in module schrodinger.comparison.struc) is_display_present() (in module schrodinger.utils.sysinfo) is_display_snapshot_active (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel property) is_display_using_xvfb() (in module schrodinger.utils.sysinfo) is_disulfide_bridge (schrodinger.protein.helm.helm_renderer.HelmConnector property) is_dockable() (in module schrodinger.ui.qt.widgetmixins.basicmixins) is_docked() (in module schrodinger.ui.qt.widgetmixins.basicmixins) is_docking_job() (schrodinger.application.glide_ws.driver.GlideWSJob method) is_docking_keyword() (in module schrodinger.application.glide.specs) is_downloadable_job_server_job() (in module schrodinger.application.matsci.jobutils) is_downloaded (schrodinger.application.job_monitor.job_monitor_models.JobModel property) is_dpd() (in module schrodinger.application.matsci.cgforcefield) is_dummy_atom() (in module schrodinger.application.matsci.msutils) is_dummy_structure() (in module schrodinger.application.desmond.util) is_dynamic_asl() (in module schrodinger.application.desmond.packages.topo) is_editable() (schrodinger.protein.nonstandard_residues.AminoAcid method) is_empty_trajectory() (in module schrodinger.application.desmond.packages.traj) is_enabled() (in module schrodinger.seam.debug) is_entry_node_index() (in module schrodinger.maestro_utils.surface_manager.utils) is_epv_file() (in module schrodinger.utils.fileutils) is_equal() (in module schrodinger.utils.sea.common) is_equal_formula() (in module schrodinger.application.matsci.msutils) is_equivalent_to_mininplace() (in module schrodinger.application.glide.job) is_excluded_amino_acid() (in module schrodinger.protein.nonstandard_residues) is_expired() (schrodinger.application.licensing.flexlm.LicenseLine method) is_false() (in module schrodinger.application.glide.job) is_feature_label_checked() (in module schrodinger.application.phase.phase_markers) is_file_encrypted() (in module schrodinger.application.matsci.enc) is_file_extension_valid() (in module schrodinger.utils.fileutils) is_file_not_found_exception() (in module schrodinger.job.launchapi) is_file_property() (in module schrodinger.application.matsci.permittivity) is_file_supported_by_structure_writer() (in module schrodinger.infra.structure) is_find_toolbar_visible() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) is_fit_to_structure() (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) is_float_valid() (in module schrodinger.ui.qt.formlayout) is_for_gcmc (schrodinger.application.desmond.cms.Cms property) is_force_field_encrypted() (in module schrodinger.application.matsci.cgforcefield) is_from_atom() (schrodinger.application.canvas.r_group.TempAtom method) is_fully_rel (schrodinger.application.matsci.espresso.utils.PseudoData attribute) is_future_license_error() (in module schrodinger.application.licensing.licadmin) is_gap (schrodinger.protein.residue.Gap attribute) (schrodinger.protein.residue.Residue attribute) is_gcmc (schrodinger.application.desmond.packages.traj.Frame property) is_gcp_service_available() (in module schrodinger.application.steps.env_keys) is_glide_pose_viewer_file() (in module schrodinger.infra.structure) is_grid_good_for_ligand() (in module schrodinger.application.glide.grid) is_gridgen_job() (in module schrodinger.application.glide.job) is_gridgen_keyword() (in module schrodinger.application.glide.specs) is_gzipped_structure_file() (in module schrodinger.utils.fileutils) is_halogen (schrodinger.structure.StructureAtom property) is_haptic() (in module schrodinger.application.matsci.etatoggle) is_harmonic_angle() (in module schrodinger.application.matsci.coarsegrain) is_hexagonal() (in module schrodinger.application.matsci.pbcutils) is_hidden_feature() (in module schrodinger.application.matsci.ml_formulations_utils) is_homo (schrodinger.application.jaguar.input.OrbSpec attribute) is_host_platform_compatible() (in module schrodinger.utils.platform) is_hostname_known() (in module schrodinger.job.jobcontrol) is_hostname_valid() (in module schrodinger.active_learning.al_utils) is_hydrogen (schrodinger.infra.mm.ScoreAtom attribute) is_hypothesis_entry() (in module schrodinger.application.phase.pt_hypothesis) is_hypothesis_file() (in module schrodinger.utils.fileutils) is_imgt_ins_code() (in module schrodinger.application.bioluminate.anarci.loop_ranges) is_independent() (schrodinger.application.matsci.elasticity.strain.Deformation method) is_infinite() (in module schrodinger.application.matsci.desmondutils) (in module schrodinger.application.matsci.nano.xtal) is_infinite2() (in module schrodinger.application.matsci.nano.xtal) is_inter_sequence (schrodinger.protein.residue.CombinedChainDisulfideBond property) (schrodinger.protein.residue.DisulfideBond property) is_intra_sequence (schrodinger.protein.residue.CombinedChainDisulfideBond property) (schrodinger.protein.residue.DisulfideBond property) is_ipv4_addr() (in module schrodinger.utils.net) is_iterable() (in module schrodinger.application.matsci.msutils) is_iteration_pattern (schrodinger.active_learning.al_driver.StopAfterRequest property) is_jag_license_needed() (in module schrodinger.application.matsci.jaguarworkflows) is_jaguar_file_property() (in module schrodinger.application.matsci.jaguarworkflows) is_job_server_job() (in module schrodinger.application.matsci.jobutils) is_jobhost_gpu_available() (in module schrodinger.application.matsci.jobutils) is_jobtask() (in module schrodinger.tasks.jobtasks) is_kinase_annotated (schrodinger.protein.sequence.NucleicAcidSequence property) (schrodinger.protein.sequence.ProteinSequence property) is_kinase_cons_annotated (schrodinger.protein.sequence.NucleicAcidSequence property) (schrodinger.protein.sequence.ProteinSequence property) is_lambd_prm_fep_type() (in module schrodinger.application.desmond.util) is_layer_allowed() (in module schrodinger.application.matsci.device_formulations) is_lennard_jones() (in module schrodinger.application.matsci.coarsegrain) is_library() (schrodinger.application.licensing.flexlm.License method) is_license_available() (in module schrodinger.utils.license) is_ligand() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils) is_like_lennard_jones() (in module schrodinger.application.matsci.cgforcefield) is_local_server() (schrodinger.application.licensing.licadmin.LicenseResource method) is_local_topic() (in module schrodinger.utils.documentation) is_localhost_platform_compatible() (in module schrodinger.utils.platform) is_logged (schrodinger.application.matsci.solvation_entropy_utils.StructurePropertyInfo attribute) is_mae_or_sd() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) is_maestro_file() (in module schrodinger.utils.fileutils) is_mark_monomer_grow_atom() (in module schrodinger.application.matsci.rxn_channel) is_martini_antifreeze_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_charge_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_ring_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_tiny_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_useries() (in module schrodinger.application.matsci.coarsegrain) is_matsci() (in module schrodinger.utils.license) is_matsci_engine_db() (in module schrodinger.application.matsci.kmc) is_metal() (in module schrodinger.application.prime.primefix) is_missing_module() (in module schrodinger.application.matsci.codeutils) is_mlff_app_lic_required() (in module schrodinger.application.matsci.desconfig) is_mlff_cpcmx() (in module schrodinger.application.jaguar.esol_validation) is_mlff_type() (in module schrodinger.application.matsci.desconfig) is_mmct_property_name() (in module schrodinger.application.glide.sort_utils) is_mopac_file() (in module schrodinger.application.mopac.utils) is_multi_receptor (schrodinger.application.livedesign.tasks.MCSDockingTask.Input attribute) is_multi_receptorChanged (schrodinger.application.livedesign.tasks.MCSDockingTask.Input attribute) is_multi_receptorReplaced (schrodinger.application.livedesign.tasks.MCSDockingTask.Input attribute) is_negative_surface (schrodinger.project.surface.ProjectSurface property) is_no_table_error() (in module schrodinger.application.matsci.kmc) is_nodelocked() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Server method) is_normal_surface() (in module schrodinger.application.matsci.nano.xtal) is_nucleotide_backbone (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_nucleotide_phosphate (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_nucleotide_sugar (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_null() (in module schrodinger.application.pathfinder.synthesis) is_null_job (schrodinger.application.job_monitor.job_monitor_models.JobModel property) is_ok() (schrodinger.utils.sea.evalor.Evalor method) is_open() (schrodinger.application.licensing.flexlm.License method) is_opls2_available() (in module schrodinger.utils.license) is_opls5_type() (in module schrodinger.application.matsci.desconfig) is_outlier (schrodinger.ui.qt.rama.BackboneDihedral attribute) is_oxidation_prone() (in module schrodinger.application.bioluminate.methionine_oxidation) is_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) is_pbc_enabled() (in module schrodinger.application.xtb.utilities) is_pdb_file() (in module schrodinger.utils.fileutils) is_permanent() (schrodinger.application.licensing.flexlm.Feature method) is_permanent_counted() (schrodinger.application.licensing.flexlm.License method) is_permanent_library() (schrodinger.application.licensing.flexlm.License method) is_permanent_nodelocked() (schrodinger.application.licensing.flexlm.License method) is_pfx() (in module schrodinger.rdkit.molio) is_phdb_path() (in module schrodinger.application.hitexpander) is_pka_ordering_physical() (in module schrodinger.application.jaguar.macro_pka_utils) is_polymer() (in module schrodinger.livedesign.preprocessor) is_polymer_builder_grow_atom() (in module schrodinger.application.matsci.rxn_channel) is_poseviewer_file() (in module schrodinger.utils.fileutils) is_positive (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) is_positive_int() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) is_positive_numeric() (in module schrodinger.application.phase.shape_screen_reporter.option_utils) is_powerof2() (in module schrodinger.utils.sea.evalor) is_projected (schrodinger.application.phase.phase_markers.PhaseFeatureMarker property) is_property_label_checked() (in module schrodinger.application.phase.phase_markers) is_pv_file() (in module schrodinger.application.glide.poseviewconvert) is_python_file() (in module schrodinger.application.matsci.codeutils) is_python_pre311() (in module schrodinger.application.matsci.codeutils) is_qrnn_cpcmx() (in module schrodinger.application.jaguar.esol_validation) is_queryatom_exception() (in module schrodinger.livedesign.preprocessor) is_reagent_file() (in module schrodinger.application.pathfinder.reaction) is_reagent_filename() (in module schrodinger.application.pathfinder.reaction) is_real_display() (in module schrodinger.utils.sysinfo) is_receptor() (in module schrodinger.application.glide.utils) is_rectangular (schrodinger.protein.alignment.BaseAlignment property) is_repulsive_harmonic() (in module schrodinger.application.matsci.coarsegrain) is_required_valid() (in module schrodinger.ui.qt.formlayout) is_res (schrodinger.protein.residue.AbstractSequenceElement property) is_rotation() (schrodinger.application.matsci.elasticity.tensors.SquareTensor method) is_same_day() (in module schrodinger.application.job_monitor.util) is_same_user_connected() (in module schrodinger.application.livedesign.ld_maestro_actions) is_scfv() (schrodinger.application.bioluminate.classify.ProteinClass method) is_scratch_entry_name() (in module schrodinger.infra.structure) is_sd_dataname() (in module schrodinger.application.livedesign.ld_utils) is_sd_file() (in module schrodinger.utils.fileutils) is_sd_file_list() (in module schrodinger.application.glide.sort_utils) is_selected (schrodinger.project.project.ProjectRow property) is_server() (in module schrodinger.application.licensing.flexlm) (schrodinger.application.licensing.licadmin.LicenseResource method) is_shifted_lennard_jones() (in module schrodinger.application.matsci.coarsegrain) is_signed() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) is_site_grouped() (in module schrodinger.application.phase.phase_markers) is_small_struc() (in module schrodinger.application.desmond.packages.analysis) is_smarts_bonding_pair() (in module schrodinger.application.matsci.smartsutils) is_smiles_file() (in module schrodinger.utils.fileutils) is_special_residue() (in module schrodinger.application.bioluminate.antibody.annotate) is_spiro_junction() (in module schrodinger.application.jaguar.utils) is_standard (schrodinger.protein.helm.helm_renderer.HelmMonomer property) is_standard_ribose() (in module schrodinger.livedesign.biologics.registration) is_string() (in module schrodinger.ui.qt.formlayout) is_stub() (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.licensing.licadmin.LicenseResource method) is_subdir() (in module schrodinger.application.desmond.util) is_subpath() (in module schrodinger.utils.fileutils) is_supported (schrodinger.application.jaguar.workflow_validation.MLFFSupportSummary attribute) (schrodinger.infra.mm.MetalSupportStatus attribute) is_supported_ge (schrodinger.application.livedesign.ld_tasks.StructureInfo attribute) is_surface_node_index() (in module schrodinger.maestro_utils.surface_manager.utils) is_symmetric() (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) is_tcr_type() (in module schrodinger.application.bioluminate.anarci.anarci_adapter) is_terminal (schrodinger.glide.Ring attribute) is_text_string() (in module schrodinger.ui.qt.formlayout) is_top_level_job (schrodinger.application.job_monitor.job_monitor_models.JobModel property) is_torchff_lib_open() (in module schrodinger.energy) is_total_energy (schrodinger.application.matsci.solvation_entropy_utils.StructurePropertyInfo attribute) is_traj_gcmc() (in module schrodinger.application.matsci.desmondutils) is_transformation() (in module schrodinger.application.pathfinder.analysis) is_trigonometric_angle() (in module schrodinger.application.matsci.coarsegrain) is_type_name_encrypted() (in module schrodinger.application.matsci.cgforcefield) is_type_small_or_tiny() (in module schrodinger.application.matsci.coarsegrain) is_unit_mx() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method) is_unreachable_hostname() (in module schrodinger.application.licensing.licadmin) is_valid() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) is_valid_epv_file() (in module schrodinger.application.glide.utils) is_valid_hostname() (in module schrodinger.job.jobcontrol) is_valid_jobname() (in module schrodinger.utils.fileutils) is_valid_lower_triangle() (in module schrodinger.application.matsci.nano.xtal) is_valid_opls_directory() (in module schrodinger.infra.mm) is_valid_property_name() (in module schrodinger.application.matsci.msprops) is_valid_pv_file() (in module schrodinger.application.glide.utils) is_valid_rdkit_property_name() (in module schrodinger.application.transforms.validators) is_valid_smiles() (in module schrodinger.adapter) is_valid_str() (in module schrodinger.application.jaguar.jaguar_diff) is_varying_atoms_trajectory_loaded() (in module schrodinger.trajectory.trajectoryviewer) is_voigt_symmetric() (schrodinger.application.matsci.elasticity.tensors.Tensor method) (schrodinger.application.matsci.elasticity.tensors.TensorCollection method) is_votca_prop() (in module schrodinger.application.matsci.kmc) is_water() (in module schrodinger.application.desmond.remd) is_watermap_file() (in module schrodinger.infra.structure) is_wildcard() (in module schrodinger.livedesign.preprocessor) is_within_cutoffs() (in module schrodinger.application.transforms.autosar.transforms) is_within_directory() (in module schrodinger.utils.fileutils) is_workspace_non_empty() (in module schrodinger.maestro_utils.find_tool_bar.find_tool_bar_widget) is_wt_mut (schrodinger.application.bioluminate.mutation.Mutation attribute) is_xsignal() (in module schrodinger.ui.qt.xsignals) is_zero() (in module schrodinger.math.mathutils) (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method) isAbstract() (schrodinger.models.parameters.Param class method) isAcceptableEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) isAccepted() (schrodinger.application.matsci.montecarlo.Metropolizer method) isAcceptor() (schrodinger.infra.canvas.ChmHbond method) isAcid() (schrodinger.infra.canvas.ChmAtom method) isActive() (schrodinger.ui.qt.navtoolbar.AtomInfoToolbar method) isActivelyScrolling() (schrodinger.ui.qt.structtable.ViewerTable method) (schrodinger.ui.qt.table.DataViewerTable method) isAliphatic() (schrodinger.infra.canvas.ChmAtom method) isAlive() (schrodinger.application.pymol.pymol4maestro.panel method) isAllAtomPolymer() (schrodinger.application.matsci.amorphous.PolymerFragments method) isAlreadyMatched() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) isAntibodyChain() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations method) (schrodinger.protein.annotation.NucleicAcidSequenceAnnotations method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) isAntibodyHeavyChain() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) isAntibodyLightChain() (schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin method) (schrodinger.protein.annotation.ProteinSequenceAnnotations method) isAnyTextLabelVisible() (schrodinger.application.phase.phase_markers.PhaseMarkers method) isApplyTimeBasedGradient() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.SnapshotPanel method) isAromatic() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) (schrodinger.infra.structure.StructureRing method) (schrodinger.structure._Ring method) isAtomMember() (schrodinger.application.matsci.species.SpeciesData method) isAvailable() (schrodinger.infra.canvas.Chm2DCoordGen static method) isBackboneAtom() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin static method) (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner static method) isBackboneSidechain() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) isBackendMode() (schrodinger.tasks.jobtasks.ComboJobMixin method) (schrodinger.tasks.tasks.AbstractComboTask method) isBandshapeTable() (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile static method) isBinaryColumn() (schrodinger.infra.canvas.ChmDelimitedPatterns method) isBondedTo() (schrodinger.infra.canvas.ChmAtom method) isBrancher() (schrodinger.application.matsci.amorphous.Monomer method) isCanceled() (schrodinger.stepper.stepper.StepJobTask method) isCarbon() (schrodinger.infra.canvas.ChmAtom method) isCarbonyl() (schrodinger.infra.canvas.ChmAtom method) isCCBond() (schrodinger.application.matsci.custom_lipid_prep.SetStereochemistry method) isCgPolymer() (schrodinger.application.matsci.amorphous.PolymerFragments method) isChecked() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method) (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) isChiral() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) isChiralAttachment() (schrodinger.infra.canvas.ChmAtom method) isChiralCenter() (schrodinger.application.matsci.custom_lipid_prep.SetStereochemistry method) isColumnFixed() (schrodinger.project.project.Project method) isColumnGanged() (schrodinger.ui.qt.table.DataViewerTable method) IsCompatible() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) isCompatible() (schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow method) (schrodinger.energy.AniPredictor method) (schrodinger.energy.QRNNPredictor method) (schrodinger.infra.canvas.ChmFPTypeInfo method) (schrodinger.infra.mm.OPLSArchive static method) isComplete() (schrodinger.application.glide.http_client.SubprocessJobAdapter method) (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobDJ method) isConformationalSearchesChecked() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) isConjugated() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) isConnected() (schrodinger.infra.canvas.ChmPathTools static method) (schrodinger.ui.qt.network_visualizer.Graph method) isConnectedToResidue() (schrodinger.structure.Residue method) isConsistentWith() (schrodinger.infra.canvas.ChmFPTypeInfo method) isConstrained() (schrodinger.infra.canvas.ChmAtom method) isContainedBy() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) isCorrectPrecision() (schrodinger.infra.canvas.ChmFPIn32 static method) (schrodinger.infra.canvas.ChmFPIn64 static method) isCPUHost() (schrodinger.ui.qt.config_dialog.ConfigDialog method) isCurrentMaestroProject() (schrodinger.project.project.Project method) isCustom() (schrodinger.infra.canvas.ChmFPTypeInfo method) isCustomMaestroAssay() (schrodinger.application.livedesign.panel_components.ExportTableModel method) isCustomType() (schrodinger.infra.canvas.ChmFPTypeInfo method) isDatabaseSource() (schrodinger.application.matsci.kmcgui.InputSelectorWithDatabase method) isDebugEnabled() (schrodinger.tasks.tasks.AbstractTask method) isDefault() (schrodinger.application.prepwizard2.tasks.PreprocessInput method) (schrodinger.infra.canvas.ChmRangeFilter method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.seam.options.pipeline_options.SeamOptions method) isDefined() (schrodinger.application.glide.gui.GridSite method) (schrodinger.infra.canvas.XYZ method) (schrodinger.protein.membrane.Membrane_Model method) isDirty() (schrodinger.ui.qt.datamapper.TrackingDataWidgetMapper method) isdisjoint() (schrodinger.utils.scollections.IdSet method) isDisplayOnlyCurrentDisplayedAtoms() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) isDistance() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) isDistanceMatrix() (schrodinger.infra.canvas.ChmPairwiseFPIn method) isDockableInMaestro() (schrodinger.ui.qt.appframework.AppFramework method) isDonor() (schrodinger.infra.canvas.ChmHbond method) isDouble() (schrodinger.infra.canvas.ChmBond method) isDoubleBond() (schrodinger.application.matsci.custom_lipid_prep.SetStereochemistry method) isDown() (schrodinger.infra.canvas.ChmBond method) isDownloaded() (schrodinger.job.jobcontrol.Job method) isDummy() (schrodinger.infra.canvas.ChmAtom method) isDynamic() (schrodinger.application.desmond.packages.staf.GeomAnalyzerBase method) isEdgeToFace() (schrodinger.infra.structure.PiPiInteraction method) isEditEnabled() (schrodinger.application.matsci.jagwidgets.JaguarOptionsDialog method) isEmpty() (schrodinger.infra.canvas.ChmMol method) (schrodinger.infra.canvas.ChmSearchKey method) isEnabled() (schrodinger.ui.qt.filter_dialog_dir.filter_widgets.BaseCriterion method) isEnergy() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) isENotationProperty() (schrodinger.project.project.Project method) isEOF() (schrodinger.infra.canvas.ChmRangeFilter method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) (schrodinger.infra.structure.PyStructureReaderException method) (schrodinger.infra.structure.StructureReaderException method) isEqual() (schrodinger.glide.GridArchive method) (schrodinger.glide.Receptor method) isEquivalent() (schrodinger.application.jaguar.utils.GenOptions method) (schrodinger.structure.Structure method) isEquivalentInput() (schrodinger.application.jaguar.input.JaguarInput method) isEster() (schrodinger.infra.canvas.ChmAtom method) isEverything() (schrodinger.infra.canvas.ChmRangeFilter method) isEZAttachment() (schrodinger.infra.canvas.ChmAtom method) isEZAttachmentToN() (schrodinger.infra.canvas.ChmAtom method) isFaceToFace() (schrodinger.infra.structure.PiPiInteraction method) isFamily() (schrodinger.structure.PropertyName method) isFastMode() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) isFEPAtomtype() (schrodinger.infra.canvas.MCSsettings static method) isFileValid() (schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame method) isFill() (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator method) (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator64 method) isFilled() (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) isFiltered() (schrodinger.infra.canvas.ChmFPTypeInfo method) isFilteredOrReduced() (schrodinger.infra.canvas.ChmFPTypeInfo method) isFixed() (schrodinger.infra.canvas.ChmAtom method) isForward() (schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph method) isFragmentLibraryFile() (schrodinger.infra.fast3d.Engine static method) isFromPatch() (schrodinger.utils.pythonpatch.ModulePatch method) isFull() (schrodinger.infra.canvas.ChmSearchKey method) isFullRange() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) isGenericEntity() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel method) isGoodDim() (schrodinger.application.matsci.espresso.utils.MemoryEstimator method) isGPUHost() (schrodinger.ui.qt.config_dialog.ConfigDialog method) isGroupShown() (schrodinger.graphics3d.common.Primitive method) isHalogen() (schrodinger.infra.canvas.ChmAtom method) isHeavy() (schrodinger.infra.canvas.ChmAtom method) isHeavyChain() (schrodinger.protein.annotation.SeqTypeMixin method) isHetero() (schrodinger.infra.canvas.ChmAtom method) isHeteroaromatic() (schrodinger.structure._Ring method) isHidden() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) (schrodinger.ui.qt.swidgets.SRadioButtonGroup method) (schrodinger.ui.qt.tablewidget.Column method) (schrodinger.ui.qt.tablewidget.Row method) isHydrogen() (schrodinger.infra.canvas.ChmAtom method) isIgnored() (schrodinger.infra.canvas.ChmAtom method) isImplicit() (schrodinger.infra.canvas.ChmAtom method) isIncluded() (schrodinger.ui.two_d_viewer.Cell method) isIndefinite() (schrodinger.infra.canvas.ChmRangeFilter method) isIndexable() (schrodinger.infra.canvas.ChmQuery method) isIndexEnabled() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) isIndexSelected() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) isInDisplayedChain() (schrodinger.application.bioluminate.protein_structure_quality.HomologyRama method) isInExcludedGroups() (schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints method) isInGuessMode() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) isInMol() (schrodinger.infra.canvas.ChmAtom method) isInRing() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) isInside() (schrodinger.application.matsci.nano.particle.Nanoparticle method) IsInteger (class in schrodinger.ui.qt.appframework2.validators) isInterruptionRequested() (schrodinger.tasks.tasks.AbstractTask method) isIntraChainInteractions() (schrodinger.application.bioluminate.protein_interaction.tasks.ProteinInteractionInput method) isInvalid() (schrodinger.ui.qt.swidgets.SMARTSEdit method) isItemChecked() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) isItemEnabled() (schrodinger.application.livedesign.panel_components.LDDataTreePopUp method) isItemHidden() (schrodinger.application.jaguar.gui.theory_selector.TheorySelectorFilterListPopUp method) (schrodinger.ui.qt.filter_list.FilterListPopUp method) (schrodinger.ui.qt.filter_list.ToolButtonWithFilterListPopUp method) isIterable() (schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis static method) isKeepSideChainAtom() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin static method) isKekulized() (schrodinger.infra.canvas.ChmMol method) isKinaseChain() (schrodinger.protein.sequence.AbstractProteinSequenceMixin method) (schrodinger.protein.sequence.CombinedChainProteinSequence method) (schrodinger.protein.sequence.NucleicAcidSequence method) (schrodinger.protein.sequence.ProteinSequence method) isLadder() (schrodinger.application.matsci.amorphous.Monomer method) isLightChain() (schrodinger.protein.annotation.SeqTypeMixin method) isLogAxis() (schrodinger.ui.qt.schart.SChart static method) isLst() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) isMacroPka() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) isMaestroAssistantOptionShown() (schrodinger.ui.qt.swidgets.HelpButton method) isMember() (schrodinger.application.matsci.clusterstruct.AtomGroupData method) (schrodinger.application.matsci.clusterstruct.SpeciesData method) isMetal() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) (schrodinger.infra.canvas.ChmAtom method) isMethod() (schrodinger.application.matsci.msconst.SMARTS_METHOD method) isMetricADistance() (in module schrodinger.infra.canvas) isMetricASimilarity() (in module schrodinger.infra.canvas) isMLFFSelected() (schrodinger.application.matsci.chargegui.MLFFDialog method) (schrodinger.application.matsci.mswidgets.OPLS5ForceFieldSelector method) isMovable() (schrodinger.glide.ReceptorAtom method) isNewGenericEntity() (schrodinger.application.livedesign.mapping_widgets.MaestroLDMappingModel method) isNitrogen() (schrodinger.infra.canvas.ChmAtom method) isNodeElement() (schrodinger.application.matsci.custom_lipid_prep.LipidEndProcessor method) isNodeTerminal() (schrodinger.application.matsci.custom_lipid_prep.LipidEndProcessor method) isNonDefault() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.workflow_input.WorkflowInput method) (schrodinger.application.jaguar.workflow_keywords.WorkflowKeyword method) (schrodinger.application.xtb.input.XTBInput method) isNumericalCol() (schrodinger.infra.canvas.ChmPatterns method) iso (schrodinger.application.matsci.espresso.qeoutput.MagresAtom property) isoelectric_point (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue property) isoelectric_point_window_padding (schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations property) (schrodinger.protein.annotation.ProteinSequenceAnnotations property) isoelectronic_mutator() (in module schrodinger.application.matsci.genetic_optimization) ISOLATE_PRODUCTS (schrodinger.application.matsci.rxn_channel.Constants attribute) isolateProducts() (schrodinger.application.matsci.rxn_channel.Products method) IsomerError isomeric_atom_sets() (schrodinger.comparison.atom_mapper.BaseAtomMapper method) isOneFill() (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator method) (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator64 method) isOPLS5Selected() (schrodinger.application.matsci.chargegui.MLFFDialog method) (schrodinger.application.matsci.mswidgets.OPLS5ForceFieldSelector method) isOptional() (schrodinger.tasks.cmdline.ArgSpec method) isOrthorhombic() (schrodinger.infra.structure.DistanceCell method) (schrodinger.infra.structure.PBC method) isotope (schrodinger.application.jaguar.simple_spec.Peak attribute) (schrodinger.structure.StructureAtom property) IsotopeData (class in schrodinger.application.jaguar.nmr_utils) isotopes (schrodinger.application.jaguar.nmr_utils.NMRData attribute) isotopes_are_conserved() (in module schrodinger.application.jaguar.autots_validation) ISOTROPIC (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) ISOTROPIC_3D (schrodinger.application.matsci.equilibrium_md.MsdTrajBase attribute) isotropic_avg_tensor() (in module schrodinger.application.matsci.kmc) ISOTROPIC_POLARIZABILITY_KEY (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) ISOTROPY (schrodinger.application.matsci.desconfig.MSJStringer attribute) isovalue (schrodinger.maestro_utils.surface_manager.surface_info.SurfaceInfo attribute) (schrodinger.surface.Surface property) isovalue() (in module schrodinger.application.jaguar.textparser) isOverlapAllowedInMatch() (schrodinger.application.matsci.smartsutils.SMARTSGroup method) isOxygen() (schrodinger.infra.canvas.ChmAtom method) isPhosphorous() (schrodinger.infra.canvas.ChmAtom method) isPlaceholderItemSelected() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) isPointBeyondThreshold() (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.gamma_Bfactor_data_set method) (schrodinger.protein.analysis.Report.improper_torsion_data_set method) (schrodinger.protein.analysis.Report.peptide_planarity_data_set method) (schrodinger.protein.analysis.Report.sidechain_dihedral_data_set method) (schrodinger.protein.analysis.Report.sidechain_planarity_data_set method) isPointInBox() (schrodinger.application.glide.gui.GridSite method) (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isPointInHull() (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isPolar() (schrodinger.infra.canvas.ChmAtom method) isPolarHydrogen() (schrodinger.infra.canvas.ChmAtom method) isPolysaccharide() (schrodinger.application.matsci.automated_cg_mapping.PolysaccharideDetector static method) isPopulated() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) isPreempted() (in module schrodinger.job.jobcontrol) isProteinStructure() (schrodinger.application.matsci.cgforcefield.MartiniProteinFFCleaner method) isPW (schrodinger.infra.canvas.MCSsettings attribute) isPyroleN() (schrodinger.infra.canvas.ChmAtom method) isQueue() (schrodinger.job.jobcontrol.Host method) isQueued() (schrodinger.job.jobcontrol.Job method) isRangeModifiedByUser() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) isRangePka() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) isRangeToken() (schrodinger.trajectory.trajectory_gui_dir.snapshot_panel.FrameRangeValidator method) isReady() (schrodinger.application.glide.http_client.AbstractGlideServerManager method) isReduced() (schrodinger.infra.canvas.ChmFPTypeInfo method) isReferenceSeq() (schrodinger.protein.alignment.BaseAlignment method) isRingEligible() (schrodinger.application.matsci.automated_cg_mapping.DpdMolecule method) (schrodinger.application.matsci.automated_cg_mapping.MartiniMolecule method) (schrodinger.application.matsci.automated_cg_mapping.MoleculeData method) (schrodinger.application.matsci.automated_cg_mapping.SaccharideMolecule method) isRotatable() (schrodinger.infra.canvas.ChmBond method) isRowGanged() (schrodinger.ui.qt.table.DataViewerTable method) isRowSelected() (schrodinger.infra.table.Table method) isRunning() (schrodinger.active_learning.mq_worker.LigandMLBackend method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressBar method) (schrodinger.ui.qt.tasks.taskwidgets.ProgressDialog method) isScoreImproved() (schrodinger.application.matsci.automated_cg_mapping.MappingValidator method) isScriptProperty() (schrodinger.application.matsci.genetic_optimization.Property method) isScrolling() (schrodinger.ui.qt.structtable.ViewerTable method) (schrodinger.ui.qt.table.DataViewerTable method) isSelected() (schrodinger.ui.qt.tablewidget.Cell method) (schrodinger.ui.qt.tablewidget.Row method) isSeparator() (schrodinger.ui.qt.recent_completer.SeparatorStringModel method) isSharedNode() (schrodinger.application.matsci.automated_cg_mapping.SymmRingFragmentData method) isShiftPressed() (schrodinger.application.matsci.density_analysis_widget.BasePlotFrame method) isShown() (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.gridbox.GridBox method) isSideChainAtom() (schrodinger.application.matsci.cgforcefield.AngleAdaptationMixin method) isSimilarity() (schrodinger.infra.canvas.ChmCustomMetric method) isSimilarityMatrix() (schrodinger.infra.canvas.ChmPairwiseFPIn method) isSingle() (schrodinger.infra.canvas.ChmBond method) isSohnckeGroup() (schrodinger.application.matsci.nano.space_groups.SpaceGroup method) isSolventModelUsed() (schrodinger.application.matsci.jagwidgets.CompactSolventSelector method) isSorted() (schrodinger.infra.canvas.ChmRangeFilter method) (schrodinger.infra.canvas.ChmRangeUIDFilter method) isSP() (schrodinger.infra.canvas.ChmAtom method) isSP2() (schrodinger.infra.canvas.ChmAtom method) isSP3() (schrodinger.infra.canvas.ChmAtom method) isSpecialHydroxyl() (schrodinger.glide.PoseAtom method) isSphereInBox() (schrodinger.application.glide.gui.GridSite method) isSquare() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.infra.canvas.ChmPairwiseFPIn method) isStandardResidue() (schrodinger.structure.Residue method) isStartable() (schrodinger.tasks.taskmanager.TaskManager method) (schrodinger.tasks.tasks.AbstractTask method) isStartingMaterial() (schrodinger.application.pathfinder.route.RouteNode method) isStereo() (schrodinger.infra.canvas.ChmBond method) isStoppable() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) isStreamingRunning() (schrodinger.application.job_monitor.job_monitor_file_browser.SubprocessStdOutStreamer method) isStructure() (schrodinger.ui.qt.table.StructureDataViewerDelegate method) issubset() (schrodinger.utils.scollections.IdSet method) isSubsetOf() (schrodinger.infra.canvas.ChmBitset method) (schrodinger.infra.canvas.ChmBitset64 method) (schrodinger.infra.canvas.ChmSparseBitset method) (schrodinger.infra.canvas.ChmSparseBitset64 method) issued (schrodinger.application.licensing.licserver.entitlement_status.ActiveEntitlementFeature attribute) (schrodinger.application.licensing.licserver.entitlement_status.NonActiveEntitlementFeature attribute) issued_str() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) isSulfur() (schrodinger.infra.canvas.ChmAtom method) issuperset() (schrodinger.utils.scollections.IdSet method) isSupersetOf() (schrodinger.infra.canvas.ChmFPTypeInfo method) isSymmetric() (schrodinger.infra.canvas.ChmPairwiseFPIn method) ist_product_table() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) isTabVisibleByLabel() (schrodinger.ui.qt.swidgets.STabWidget method) isTerminal() (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) isTriple() (schrodinger.infra.canvas.ChmBond method) isUnfiltered() (schrodinger.infra.canvas.ChmFPCombiner method) (schrodinger.infra.canvas.ChmFPCombiner64 method) isUp() (schrodinger.infra.canvas.ChmBond method) isUseConsistentOrbitalsChecked() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals method) isUseCustomizedVersionChecked() (schrodinger.ui.qt.forcefield.ffcustomoplssettingwidget.FFCustomOPLSSettingMixin method) isUsingDefaultAcceptorFile() (schrodinger.infra.canvas.ChmHbond method) isUsingDefaultDonorFile() (schrodinger.infra.canvas.ChmHbond method) isV3000() (schrodinger.infra.canvas.ChmSDReader method) isValid() (schrodinger.application.glide.grid.Grid method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorFilterPopUp method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.rdpattern_gui.SMARTSFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame method) (schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor method) (schrodinger.application.matsci.reaction_workflow_gui_utils.WorkspaceSuperpositionFrame method) (schrodinger.glide.EnergyComponents method) (schrodinger.infra.canvas.ChmAssignments method) (schrodinger.infra.canvas.ChmAtomIterator method) (schrodinger.infra.canvas.ChmBitsetIterator method) (schrodinger.infra.canvas.ChmBondIterator method) (schrodinger.infra.canvas.ChmFPTypeInfo method) (schrodinger.infra.canvas.ChmLicenseAutoQsar static method) (schrodinger.infra.canvas.ChmLicenseElements static method) (schrodinger.infra.canvas.ChmLicenseElementsOrFull method) (schrodinger.infra.canvas.ChmLicenseFull static method) (schrodinger.infra.canvas.ChmLicenseFullOrMain method) (schrodinger.infra.canvas.ChmLicenseMain static method) (schrodinger.infra.canvas.ChmLicenseMatSci static method) (schrodinger.infra.canvas.ChmLicenseShared static method) (schrodinger.infra.canvas.ChmLicenseXCluster static method) (schrodinger.infra.canvas.ChmMatchExIterator method) (schrodinger.infra.canvas.ChmMatchIterator method) (schrodinger.infra.canvas.ChmObjChmAtomImpl method) (schrodinger.infra.canvas.ChmObjChmAtomTyperImpl method) (schrodinger.infra.canvas.ChmObjChmMatcherImpl method) (schrodinger.infra.canvas.ChmObjChmQueryImpl method) (schrodinger.infra.canvas.ChmPairwiseFPIn method) (schrodinger.infra.canvas.ChmSDReaderImpl method) (schrodinger.infra.canvas.ChmValueAssignmentIterator method) (schrodinger.infra.structure.MM_Bitset method) (schrodinger.infra.structure.Structure method) (schrodinger.infra.structure.StructureAtom method) (schrodinger.protein.residue.DisulfideBond method) (schrodinger.protein.sequence.AbstractSingleChainSequence class method) (schrodinger.protein.sequence.ProteinSequence class method) (schrodinger.ui.qt.swidgets.SMARTSEdit method) (schrodinger.utils.license.License method) isValidASL() (schrodinger.trajectory.trajectory_gui_dir.advanced_settings.AdvancedSettings method) (schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) (schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings.CustomDisplaySettings method) isValidAtomIndex() (schrodinger.application.matsci.reordergui.StructureFrame method) isValidConformer() (schrodinger.application.matsci.crest.CrestCSearch method) isValidEnd() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) isValidFrameRange() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) isValidPoint() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isValidSMARTS() (in module schrodinger.infra.canvas) isValidStart() (schrodinger.trajectory.trajectory_gui_dir.export_structures.ExportStructures method) isValidStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method) isValueAxis() (schrodinger.ui.qt.schart.SChart static method) isVisible() (schrodinger.application.matsci.chargegui.ChargePropertySelector method) (schrodinger.infra.canvas.ChmAtom method) (schrodinger.infra.canvas.ChmBond method) (schrodinger.ui.qt.dendrogram.Dendrogram method) isVolumeBased() (schrodinger.maestro_utils.surface_manager.surface_item.SurfaceNodeItem method) isWildcard() (schrodinger.infra.canvas.ChmAtom method) isWithinCutoff() (schrodinger.application.desmond.packages.analysis.Pbc method) isWordAligned() (schrodinger.infra.canvas.ChmCompressedBitset method) (schrodinger.infra.canvas.ChmCompressedBitset64 method) isWorkspaceResolution() (schrodinger.trajectory.trajectory_gui_dir.export_movie.ExportMovieDialog method) isZeroFill() (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator method) (schrodinger.infra.canvas.ChmCompressedBitsetWordIterator64 method) isZwitterionChecked() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) ITALIC (schrodinger.application.phase.phase_markers.FontStyles attribute) ItalicsPlaceholderComboBox (class in schrodinger.ui.qt.standard_widgets.combo_boxes) item() (schrodinger.infra.canvas.ChmMatrixUnsignedInt method) (schrodinger.ui.qt.tablewidget.Cell method) ITEM_KEY (schrodinger.ui.qt.swidgets.SavedSMARTSManager attribute) item_type (schrodinger.application.matsci.builderwidgets.TemplateFamily attribute) ITEM_TYPE_TEXT (schrodinger.application.matsci.mswidgets.MSAtomSelector attribute) (schrodinger.ui.qt.swidgets.ItemsManagerMixin attribute) (schrodinger.ui.qt.swidgets.SavedItemsManager attribute) (schrodinger.ui.qt.swidgets.SavedSMARTSManager attribute) ItemChanged (schrodinger.models.parameters.SignalType attribute) ItemClassMixin (class in schrodinger.models.parameters) itemClicked (schrodinger.application.matsci.mswidgets.SavedASLItem attribute) (schrodinger.ui.qt.atomselector.ASLItem attribute) (schrodinger.ui.qt.swidgets.SavedMenuItem attribute) (schrodinger.ui.qt.swidgets.StdMenuItem attribute) itemClicked() (schrodinger.ui.qt.swidgets.SavedItemsManager method) ItemRow (class in schrodinger.application.matsci.builderwidgets) ItemRowWithTemplates (class in schrodinger.application.matsci.builderwidgets) items() (schrodinger.ui.qt.multi_combo_box.MultiComboBox method) (schrodinger.ui.qt.swidgets.SComboBox method) (schrodinger.utils.scollections.IdDict method) itemSelected (schrodinger.application.livedesign.panel_components.LDSelectionTreeView attribute) (schrodinger.ui.qt.swidgets.ActionComboBox attribute) itemSelected() (schrodinger.application.matsci.reordergui.StructureListWidget method) ItemsManagerMixin (class in schrodinger.ui.qt.swidgets) iter_fingerprints() (schrodinger.utils.multifpfile.MultiFPFile method) ITERABLE_ARG_METHOD_NAMES (schrodinger.models.parameters.BaseMutableParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.SetParam attribute) iterate_minimize_structure() (in module schrodinger.forcefield.minimizer) iterate_to_convergence() (schrodinger.protein.protassign.hbond_cluster.hbond_cluster method) iterateNeighboringAtoms() (schrodinger.structutils.measure.DistanceCellIterator method) iterateOverSelectedCells() (schrodinger.ui.two_d_viewer.TwoDViewer method) iterateOverSelectedIs() (schrodinger.ui.two_d_viewer.TwoDViewer method) iterateResidues() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) Iteration (class in schrodinger.seam.examples.active_learning_weigher) iteration_number (schrodinger.active_learning.al_driver.StopAfterRequest property) IterationError IterativeMlffModel (class in schrodinger.energy) iterAtomCollections() (schrodinger.application.matsci.species.MoleculeSpeciesFinder method) (schrodinger.application.matsci.species.ResidueSpeciesFinder method) iterator() (schrodinger.energy.VecMetalSystem method) (schrodinger.infra.canvas.ChmBitsetVector method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mm.WaterMapAtomList method) (schrodinger.infra.structure.StructureCoordinates method) iterInputs() (schrodinger.pipeline.stage.Stage method) iteritems() (schrodinger.utils.cgxutils.FragmentLibrary method) ITERMAX (schrodinger.application.matsci.espresso.qeinput.TurboEelsType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboLanczosType attribute) (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) ITERMAX0 (schrodinger.application.matsci.espresso.qeinput.TurboSpectrumType attribute) iterNeighbors() (schrodinger.protein.sequence.AbstractSequence method) iterpose() (schrodinger.trajectory.prody.ensemble.Ensemble method) IUHF (schrodinger.application.matsci.permittivity.JaguarCalculation attribute) IUPAC (schrodinger.application.matsci.rdpattern.CactusIdentifiers attribute) iupac (schrodinger.application.matsci.rdpattern.CactusRes attribute) iupac_to_smiles() (in module schrodinger.protein.process_enamine_db) ix (schrodinger.comparison.neighbors.MoleculeNeighbor attribute) iy (schrodinger.comparison.neighbors.MoleculeNeighbor attribute) iz (schrodinger.comparison.neighbors.MoleculeNeighbor attribute)

J

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

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

K

k_reuss (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) K_STRETCH (schrodinger.application.jaguar.hess_guess.LindhConstants attribute) k_superop() (schrodinger.application.jaguar.spin_simulator_v2.SpinSystem method) k_voigt (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) k_vrh (schrodinger.application.matsci.elasticity.elastic.ElasticTensor property) KAPPA (schrodinger.application.bioluminate.update_germline_db.translate_db.Locus attribute) KBotFrame (class in schrodinger.ui.qt.appframework2.af2) KBotResponseWidget (class in schrodinger.ui.qt.appframework2.af2) kcal_prop_to_ev_prop() (in module schrodinger.application.matsci.msprops) KcalPerMol (schrodinger.application.jaguar.constants.Unit attribute) (schrodinger.energy.MlffEnergyUnit attribute) KEEP_ONLY_LARGEST_STRUCTURE (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute) keep_top_n() (in module schrodinger.rdkit.filtering) KEEP_WEDGED (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute) KEKULE (schrodinger.livedesign.draw.AromaticBondDisplay attribute) kekulize() (schrodinger.infra.canvas.ChmMmctAdaptor method) (schrodinger.infra.canvas.ChmMol method) Keq (schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns attribute) Key (class in schrodinger.utils.sea.sea) key (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) (schrodinger.application.desmond.arkdb.Datum property) (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) KEY (schrodinger.application.matsci.genetic_optimization.AutoQSAR attribute) (schrodinger.application.matsci.genetic_optimization.CanvasKPLS attribute) (schrodinger.application.matsci.genetic_optimization.CustomClassEvaluator attribute) (schrodinger.application.matsci.genetic_optimization.DeepChem attribute) (schrodinger.application.matsci.genetic_optimization.GlassTransitionTemperature attribute) key (schrodinger.application.matsci.genetic_optimization.PropertyInfo attribute) KEY (schrodinger.application.matsci.genetic_optimization.RefractiveIndex attribute) (schrodinger.application.matsci.permittivity.ElectricPolarizability attribute) key (schrodinger.application.matsci.solvation_entropy_utils.StructurePropertyInfo attribute) key_val_re (schrodinger.application.jaguar.utils.GenOptions attribute) key_value() (schrodinger.utils.sea.sea.Map method) keyChanged (schrodinger.application.livedesign.export_models.ThreeDExportItem attribute) KeyPairDict (class in schrodinger.application.matsci.parserutils) keyPressEvent() (schrodinger.trajectory.trajectory_gui_dir.traj_plot_widgets.PlotTitleLineEdit method) (schrodinger.ui.qt.appframework2.baseapp.BasePanel method) (schrodinger.ui.qt.appframework2.debugwidgets.BaseTable method) (schrodinger.ui.qt.appframework2.debugwidgets.ExecWidget method)