Navigation
index
modules
|
Schrödinger Python API 2022-4 documentation
»
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
|
Z
_
__contains__() (schrodinger.application.bindingsite.cavutils.Cavity method)
(schrodinger.application.canvas.topo_descriptors.Descriptor method)
(schrodinger.application.dendrogram.core_class.GetPartitions.NameList method)
(schrodinger.application.dendrogram.core_class.RingSysInfo method)
(schrodinger.application.desmond.arkdb.ForEachDo method)
(schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.desmond.fep_edge_data.ResData method)
(schrodinger.application.desmond.packages.msys.Atom method)
(schrodinger.application.desmond.packages.msys.Bond method)
(schrodinger.application.desmond.packages.timer.Timer.Args method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.basis.BasisSet method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.jaguar.utils.ChgAt method)
(schrodinger.application.jaguar.utils.FreeEnergy method)
(schrodinger.application.jaguar.utils.LewisStructure method)
(schrodinger.application.licensing.licadmin.stat_info method)
(schrodinger.application.licensing.lmgrd_log_parser.event method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.livedesign.login.Version method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.CacheInfo method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.codeutils.ModuleInfo method)
(schrodinger.application.matsci.nano.space_groups.SpaceGroup method)
(schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo method)
(schrodinger.application.scaffold_enumeration.cxsmiles.MCG method)
(schrodinger.application.scaffold_enumeration.cxsmiles.SRU method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup method)
(schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup method)
(schrodinger.forcefield.ffld_options.ForceFieldOptions method)
(schrodinger.forcefield.ffld_options.MinimizationOptions method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.infra.mmlist.mmlist method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.job.server.ServerInfo method)
(schrodinger.livedesign.preprocessor.PreprocessorOptions method)
(schrodinger.math.multi_parameter_optimization.Transition method)
(schrodinger.models.diffy.DictDiff method)
(schrodinger.models.diffy.ListDiff method)
(schrodinger.models.diffy.SetDiff method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.models.jsonable.JsonableTuple method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.protein.tasks.structure_alignment.StructAlignResult method)
(schrodinger.rdkit.substructure.QueryOptions method)
(schrodinger.structure._StructureProperty method)
(schrodinger.structutils.markush_enumerate.PlaceHolder method)
(schrodinger.structutils.rgroup_enumerate.RGroup method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.cgxutils.FragmentLibrary method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.scollections.IdItemsView method)
(schrodinger.utils.scollections.IdSet method)
(schrodinger.utils.sea.sea.Key method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
__init__() (schrodinger.adapter.InconsistentStructureError method)
(schrodinger.adapter.UnsupportedStructureError 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.epitope.psc_workflow.psc_workflow method)
(schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method)
(schrodinger.application.bioluminate.patch_utils.settings.PatchType method)
(schrodinger.application.bioluminate.patch_utils.settings.PatchTypeSettings method)
(schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method)
(schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method)
(schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI 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.TopoError method)
(schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method)
(schrodinger.application.canvas.utils.chm_bluebird method)
(schrodinger.application.canvas.utils.chm_excel method)
(schrodinger.application.canvas.utils.ChmCSVTools 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_screen.combinatorial_screener.CombinatorialScreener method)
(schrodinger.application.dendrogram.core_class.Deepest0 method)
(schrodinger.application.dendrogram.core_class.Deepest1 method)
(schrodinger.application.dendrogram.core_class.Deepest2 method)
(schrodinger.application.dendrogram.core_class.Deepest3a method)
(schrodinger.application.dendrogram.core_class.Deepest3b method)
(schrodinger.application.dendrogram.core_class.Deepest4 method)
(schrodinger.application.dendrogram.core_class.Deepest5 method)
(schrodinger.application.dendrogram.core_class.Deepest6 method)
(schrodinger.application.dendrogram.core_class.GetPartitions method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.dfa.DFA method)
(schrodinger.application.desmond.antlr3.exceptions.BacktrackingFailed method)
(schrodinger.application.desmond.antlr3.exceptions.EarlyExitException method)
(schrodinger.application.desmond.antlr3.exceptions.FailedPredicateException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedNotSetException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedRangeException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedSetException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTokenException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTreeNodeException method)
(schrodinger.application.desmond.antlr3.exceptions.MissingTokenException method)
(schrodinger.application.desmond.antlr3.exceptions.NoViableAltException method)
(schrodinger.application.desmond.antlr3.exceptions.RecognitionException method)
(schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method)
(schrodinger.application.desmond.antlr3.recognizers.RecognizerSharedState method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.DeleteOp method)
(schrodinger.application.desmond.antlr3.streams.InsertBeforeOp method)
(schrodinger.application.desmond.antlr3.streams.ReplaceOp method)
(schrodinger.application.desmond.antlr3.streams.RewriteOperation method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteCardinalityException method)
(schrodinger.application.desmond.antlr3.tree.RewriteEarlyExitException method)
(schrodinger.application.desmond.antlr3.tree.RewriteEmptyStreamException method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method)
(schrodinger.application.desmond.antlr3.tree.TreeVisitor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method)
(schrodinger.application.desmond.antlr3.treewizard.TreeWizard method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
(schrodinger.application.desmond.arkdb.ArkDb method)
(schrodinger.application.desmond.arkdb.ArkDbDelError method)
(schrodinger.application.desmond.arkdb.ArkDbGetError method)
(schrodinger.application.desmond.arkdb.ArkDbPutError method)
(schrodinger.application.desmond.arkdb.CompositeKeySyntaxError 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.DictRestrainGroup method)
(schrodinger.application.desmond.cms.FBHWPosRestrainArray method)
(schrodinger.application.desmond.cms.ModelRestrainList 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.constants.MaePropertyName method)
(schrodinger.application.desmond.correlation_tau.ConfidenceInterval method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.ArraySyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.BinaryThreadSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.MetaSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.RMSDSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.SimpleSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.ThreadSyntax method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.atom_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.bind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.block_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.comp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_meta_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_output_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expr_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.exprOrBind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.factor_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.fcnCall_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.header_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.if__return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.iter_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.meta_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.output_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.prog_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.series_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.signedExpComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.static_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.varWithType_return method)
(schrodinger.application.desmond.enhsamp.ASLObject method)
(schrodinger.application.desmond.enhsamp.Bind method)
(schrodinger.application.desmond.enhsamp.binding method)
(schrodinger.application.desmond.enhsamp.Env method)
(schrodinger.application.desmond.enhsamp.FcnCall method)
(schrodinger.application.desmond.enhsamp.If method)
(schrodinger.application.desmond.enhsamp.Iter method)
(schrodinger.application.desmond.enhsamp.Let method)
(schrodinger.application.desmond.enhsamp.Lit method)
(schrodinger.application.desmond.enhsamp.Meta method)
(schrodinger.application.desmond.enhsamp.Node method)
(schrodinger.application.desmond.enhsamp.Series method)
(schrodinger.application.desmond.enhsamp.String method)
(schrodinger.application.desmond.enhsamp.Var method)
(schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPTorsions method)
(schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
(schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
(schrodinger.application.desmond.fep_schedule.FepSchedule method)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical method)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge method)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault method)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding method)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault method)
(schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
(schrodinger.application.desmond.ffiostructure.CMSReader method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.application.desmond.gaussian_filter.GaussianFilter method)
(schrodinger.application.desmond.measurement.Measurement method)
(schrodinger.application.desmond.memory.MemoryGauger method)
(schrodinger.application.desmond.multisim.parser.Msj 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.CatPiFinder 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.DipoleDirector method)
(schrodinger.application.desmond.packages.analysis.Distance 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.MassAvgVel 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.MoleculeWiseCom method)
(schrodinger.application.desmond.packages.analysis.MomentOfInertia method)
(schrodinger.application.desmond.packages.analysis.MomentOfInertiaDirector method)
(schrodinger.application.desmond.packages.analysis.OrderParameter method)
(schrodinger.application.desmond.packages.analysis.Pbc method)
(schrodinger.application.desmond.packages.analysis.PiPiFinder 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.ProteinRMSF 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.SystemDipoleDirector 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.msys.AnnotatedSystem method)
(schrodinger.application.desmond.packages.msys.Atom method)
(schrodinger.application.desmond.packages.msys.atomsel.Atomsel method)
(schrodinger.application.desmond.packages.msys.Bond method)
(schrodinger.application.desmond.packages.msys.Chain method)
(schrodinger.application.desmond.packages.msys.Ct method)
(schrodinger.application.desmond.packages.msys.Graph method)
(schrodinger.application.desmond.packages.msys.Handle method)
(schrodinger.application.desmond.packages.msys.HydrogenBondFinder method)
(schrodinger.application.desmond.packages.msys.InChI method)
(schrodinger.application.desmond.packages.msys.IndexedFileLoader method)
(schrodinger.application.desmond.packages.msys.molfile.FrameIter method)
(schrodinger.application.desmond.packages.msys.molfile.Grid method)
(schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method)
(schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method)
(schrodinger.application.desmond.packages.msys.Param method)
(schrodinger.application.desmond.packages.msys.ParamTable method)
(schrodinger.application.desmond.packages.msys.PropertyMap method)
(schrodinger.application.desmond.packages.msys.Residue method)
(schrodinger.application.desmond.packages.msys.SmartsPattern method)
(schrodinger.application.desmond.packages.msys.SpatialHash method)
(schrodinger.application.desmond.packages.msys.System method)
(schrodinger.application.desmond.packages.msys.Term method)
(schrodinger.application.desmond.packages.msys.TermTable method)
(schrodinger.application.desmond.packages.pfx.Frame method)
(schrodinger.application.desmond.packages.restraint.builder.AtomID method)
(schrodinger.application.desmond.packages.restraint.builder.RestraintBuilder method)
(schrodinger.application.desmond.packages.restraint.builder.Restraints method)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraint method)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintCentroid method)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintInteraction method)
(schrodinger.application.desmond.packages.restraint.cross_link.FragmentLinkingRestraint method)
(schrodinger.application.desmond.packages.restraint.utils.CentroidData method)
(schrodinger.application.desmond.packages.restraint.utils.CrossLinkGenerationError method)
(schrodinger.application.desmond.packages.restraint.utils.PLInteractionAids method)
(schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis method)
(schrodinger.application.desmond.packages.staf.CompositeAnalyzer method)
(schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer 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.MaestroAnalysis method)
(schrodinger.application.desmond.packages.staf.Positer method)
(schrodinger.application.desmond.packages.staf.UpdatedCmsFsysCtAnalysis method)
(schrodinger.application.desmond.packages.timer.Timer method)
(schrodinger.application.desmond.packages.topo.DuckFrame method)
(schrodinger.application.desmond.packages.traj.DtrSource method)
(schrodinger.application.desmond.packages.traj.Frame method)
(schrodinger.application.desmond.packages.traj.MaeFrameReader method)
(schrodinger.application.desmond.packages.traj.MaeSource method)
(schrodinger.application.desmond.packages.traj.Source method)
(schrodinger.application.desmond.packages.traj.XtcSource method)
(schrodinger.application.desmond.packages.traj_util.TrajectoryUnreadableError method)
(schrodinger.application.desmond.picklejar.CustomUnpickler method)
(schrodinger.application.desmond.picklejar.PicklableMetaClass method)
(schrodinger.application.desmond.replica_dE.replica_container method)
(schrodinger.application.desmond.replica_dE.replica_energy method)
(schrodinger.application.desmond.replica_dE.replicas_monitor method)
(schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.application.desmond.simulation_block_data.Array_Prop method)
(schrodinger.application.desmond.simulation_block_test.Block method)
(schrodinger.application.desmond.simulation_block_test.BoxSize method)
(schrodinger.application.desmond.simulation_block_test.E_f method)
(schrodinger.application.desmond.simulation_block_test.E_k method)
(schrodinger.application.desmond.simulation_block_test.E_x method)
(schrodinger.application.desmond.simulation_block_test.Energy method)
(schrodinger.application.desmond.simulation_block_test.Job_Details method)
(schrodinger.application.desmond.simulation_block_test.PotentialEnergy method)
(schrodinger.application.desmond.simulation_block_test.Pressure method)
(schrodinger.application.desmond.simulation_block_test.T_0 method)
(schrodinger.application.desmond.simulation_block_test.Temperature method)
(schrodinger.application.desmond.simulation_block_test.Test method)
(schrodinger.application.desmond.simulation_block_test.V method)
(schrodinger.application.desmond.starter.starter.Starter method)
(schrodinger.application.desmond.task.Option method)
(schrodinger.application.desmond.task.ParchTrajectoryForAbsoluteFep method)
(schrodinger.application.desmond.task.ParchTrajectoryForFep method)
(schrodinger.application.desmond.task.ParchTrajectoryForFepLambda method)
(schrodinger.application.desmond.task.ParchTrajectoryForSolubilityFep method)
(schrodinger.application.desmond.task.Premise method)
(schrodinger.application.desmond.task.SubtaskExecutionError method)
(schrodinger.application.desmond.task.Task method)
(schrodinger.application.desmond.task.TrajectoryForSolubilityFep method)
(schrodinger.application.desmond.torsion_related.BondRotator method)
(schrodinger.application.desmond.torsion_related.IncompleteFragmentError method)
(schrodinger.application.desmond.torsion_related.TorsionPotential method)
(schrodinger.application.desmond.util.Counter method)
(schrodinger.application.desmond.util.TestSuite method)
(schrodinger.application.fpsim.FPsimSearcher method)
(schrodinger.application.fpsim.QueryError method)
(schrodinger.application.fpsim.SearchError method)
(schrodinger.application.fpsim.ServerError method)
(schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method)
(schrodinger.application.glide.poseviewconvert.Complex method)
(schrodinger.application.glide.xpdes.XpPVParser method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.exceptions.JaguarIOError method)
(schrodinger.application.jaguar.exceptions.JaguarRuntimeError method)
(schrodinger.application.jaguar.exceptions.JaguarUnsupportedBasisSet method)
(schrodinger.application.jaguar.exceptions.JaguarUserFacingException method)
(schrodinger.application.jaguar.exceptions.QRNNSupportError method)
(schrodinger.application.jaguar.exceptions.xTBFailure method)
(schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method)
(schrodinger.application.jaguar.keywordDB.Keyword method)
(schrodinger.application.jaguar.keywordDB.Setting method)
(schrodinger.application.jaguar.mmjag.MmJag method)
(schrodinger.application.jaguar.mmjag.MMJagManager method)
(schrodinger.application.jaguar.neural_network_optimizer.AniServerError method)
(schrodinger.application.jaguar.neural_network_optimizer.OptimizationFailure method)
(schrodinger.application.jaguar.neural_network_optimizer.UnsupportedElementError method)
(schrodinger.application.jaguar.results.BondCharge method)
(schrodinger.application.jaguar.results.ConvCriteria method)
(schrodinger.application.jaguar.results.DerivedAttrs method)
(schrodinger.application.jaguar.results.Dipole method)
(schrodinger.application.jaguar.results.FukuiIndices method)
(schrodinger.application.jaguar.results.IncompleteOutput method)
(schrodinger.application.jaguar.results.JaguarAtomicResults method)
(schrodinger.application.jaguar.results.JaguarOptions method)
(schrodinger.application.jaguar.results.JaguarResults method)
(schrodinger.application.jaguar.results.NormalMode method)
(schrodinger.application.jaguar.results.Orbital method)
(schrodinger.application.jaguar.results.ScfIteration method)
(schrodinger.application.jaguar.results.SpinSpinCoupling method)
(schrodinger.application.jaguar.results.ThermoCollection method)
(schrodinger.application.jaguar.results.ThermoProp method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.jaguar.scan.Scan method)
(schrodinger.application.jaguar.user_config.JaguarConfigError method)
(schrodinger.application.jaguar.workflow_validation.ConstraintFormatError method)
(schrodinger.application.jaguar.workflow_validation.JaguarKeywordConflict method)
(schrodinger.application.jaguar.workflow_validation.WorkflowConservationError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordConflictError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordFormatError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordValueError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordValueTypeError method)
(schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.IncompatibleLicenseError method)
(schrodinger.application.licensing.flexlm.License method)
(schrodinger.application.licensing.flexlm.LicenseLine method)
(schrodinger.application.licensing.flexlm.LicfileError method)
(schrodinger.application.licensing.flexlm.Package method)
(schrodinger.application.licensing.flexlm.Server method)
(schrodinger.application.licensing.flexlm.UseServer method)
(schrodinger.application.licensing.flexlm.Vendor method)
(schrodinger.application.licensing.licadmin.LicenseFeature method)
(schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
(schrodinger.application.licensing.licadmin.MissingExecutableError method)
(schrodinger.application.licensing.licadmin.MissingLicenseFile method)
(schrodinger.application.licensing.licadmin.NetsuiteError method)
(schrodinger.application.licensing.licadmin.ServerInfo method)
(schrodinger.application.licensing.licadmin.Status method)
(schrodinger.application.licensing.licadmin.UsageError method)
(schrodinger.application.licensing.licerror.LicenseError method)
(schrodinger.application.licensing.licerror.LicenseException method)
(schrodinger.application.licensing.lmgrd_log_parser.UsageError method)
(schrodinger.application.ligprep.ionizer.Fragment method)
(schrodinger.application.ligprep.ionizer.Ionizer method)
(schrodinger.application.ligprep.ionizer.Spec method)
(schrodinger.application.ligprep.ionizer.TolerableError method)
(schrodinger.application.ligprep.ionizer.TooManyGroupsError method)
(schrodinger.application.livedesign.data_classes.LDData method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandGroup method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandPair method)
(schrodinger.application.livedesign.entry_types.BaseEntryData method)
(schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
(schrodinger.application.livedesign.ld_folder_tree.LDFolderTree method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.frozenset_cached_property method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.cache.readonly_cached_property method)
(schrodinger.application.matsci.cctbx.rot_mx.parse_string method)
(schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method)
(schrodinger.application.matsci.cctbx.rot_mx.rt_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
(schrodinger.application.matsci.cctbx.rot_mx.translation_part_info method)
(schrodinger.application.matsci.graph.NetworkLoopError 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)
(schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
(schrodinger.application.matsci.mlearn.descriptor.Featurize method)
(schrodinger.application.matsci.mlearn.descriptor.FeaturizeError method)
(schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
(schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptorError method)
(schrodinger.application.matsci.mlearn.sklearn_json.ModellNotSupported method)
(schrodinger.application.matsci.msconst.DIMENSIONALITY method)
(schrodinger.application.matsci.msprops.PropertyNameError method)
(schrodinger.application.matsci.nano.space_groups.CrystalSystems.Cubic method)
(schrodinger.application.matsci.nano.space_groups.CrystalSystems.Hexagonal method)
(schrodinger.application.matsci.nano.space_groups.CrystalSystems.Monoclinic method)
(schrodinger.application.matsci.nano.space_groups.CrystalSystems.Orthorhombic method)
(schrodinger.application.matsci.nano.space_groups.CrystalSystems.Tetragonal method)
(schrodinger.application.matsci.nano.space_groups.CrystalSystems.Triclinic method)
(schrodinger.application.matsci.nano.space_groups.CrystalSystems.Trigonal method)
(schrodinger.application.matsci.nano.space_groups.SpaceGroups method)
(schrodinger.application.matsci.qb_sdk.client.QubecClient method)
(schrodinger.application.matsci.qb_sdk.client.QubecTokenData method)
(schrodinger.application.matsci.qb_sdk.job.QubecJob method)
(schrodinger.application.matsci.qb_sdk.parameters.QubecChemistryProblem method)
(schrodinger.application.matsci.qb_sdk.parameters.QubecSdkError method)
(schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qeschema.qeschema.exceptions.QESchemaError method)
(schrodinger.application.matsci.qeschema.qeschema.exceptions.XmlDocumentError method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.exceptions.ConfigError method)
(schrodinger.application.matsci.qexsd.qespresso.exceptions.QEspressoError method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.FileFormatError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLDecodeError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLEncodeError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLSchemaValidationError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLValueError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDComplexType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method)
(schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.application.matsci.uq_utils.BilinearHistogramData method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData method)
(schrodinger.application.matsci.xrd.XRDCalculator method)
(schrodinger.application.mopac.exceptions.MopacIOError method)
(schrodinger.application.mopac.exceptions.MopacRuntimeError method)
(schrodinger.application.mopac.exceptions.MopacUserFacingException method)
(schrodinger.application.mopac.results_main.MopacBasisError1 method)
(schrodinger.application.mopac.results_main.MopacBasisError2 method)
(schrodinger.application.mopac.results_main.MopacBasisError3 method)
(schrodinger.application.mopac.results_main.MopacBasisError4 method)
(schrodinger.application.mopac.results_main.MopacBasisError5 method)
(schrodinger.application.mopac.results_main.MopacGradientParserError method)
(schrodinger.application.mopac.results_main.MopacMainTextParser method)
(schrodinger.application.mopac.results_main.MopacNumericalError method)
(schrodinger.application.mopac.results_main.MopacPropertyError method)
(schrodinger.application.mopac.results_main.MopacResultsMain method)
(schrodinger.application.mopac.structure_launchers.StructureLauncher method)
(schrodinger.application.mopac.structure_launchers.StructureLauncherError method)
(schrodinger.application.msv.gui.color_ramp.NamedColorRamp method)
(schrodinger.application.msv.gui.color_ramp.NamedRainbowColorRamp method)
(schrodinger.application.pathfinder.aligner.AlignedMolStructureGenerator method)
(schrodinger.application.pathfinder.reaction.Reaction method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.pathfinder.reaction.ReagentClass method)
(schrodinger.application.pathfinder.render.RouteRenderer method)
(schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.phase.packages.ligand_aligner.LigandAligner method)
(schrodinger.application.phase.packages.ligand_aligner.LigandAlignerOptions method)
(schrodinger.application.phase.packages.mmp2d.MMPDatabaseConnection method)
(schrodinger.application.phase.packages.mmp3dscreener.MMP3DScreener method)
(schrodinger.application.phase.packages.shape_binary_utils.ShapeFileReader method)
(schrodinger.application.phase.packages.shape_binary_utils.ShapeFileWriter method)
(schrodinger.application.phase.packages.shape_binary_utils.SingularShapeFileReader method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.primefix.FixForPrime method)
(schrodinger.application.prime.residue_interaction.InteractionReader method)
(schrodinger.application.prime.wrapper.BasePrimeAlignment method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.application.prime.wrapper.PrimeTemplate method)
(schrodinger.application.qsite.input.Cut method)
(schrodinger.application.qsite.input.HydrogenCap method)
(schrodinger.application.qsite.input.QMRegion method)
(schrodinger.application.qsite.input.QSiteInput method)
(schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method)
(schrodinger.application.scaffold_enumeration.mdl.MdlFileReader method)
(schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method)
(schrodinger.application.scaffold_enumeration.rdcml.CmlFileReader method)
(schrodinger.application.vss.config.Config method)
(schrodinger.application.vss.database.Database method)
(schrodinger.forcefield.common.AtomTypingFailure method)
(schrodinger.forcefield.minimizer.Constraint method)
(schrodinger.forcefield.minimizer.Restraint method)
(schrodinger.infra.canvas.ChmException method)
(schrodinger.infra.canvas.CtAssertion method)
(schrodinger.infra.canvas.CtException method)
(schrodinger.infra.canvas.CtMsgException method)
(schrodinger.infra.canvas.CtRdrException method)
(schrodinger.infra.fast3d.f3d_Exception method)
(schrodinger.infra.growthspace.GrowthSpaceGenerator method)
(schrodinger.infra.mmbitset.Bitset method)
(schrodinger.infra.mmcheck.MmException method)
(schrodinger.infra.mmcheck.ReturnCode method)
(schrodinger.infra.mmerr.Capture method)
(schrodinger.infra.mmerr.disable_mmerr method)
(schrodinger.infra.mmerr.Level method)
(schrodinger.infra.mmim.MMIMArgList method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.infra.mminit.Initializer method)
(schrodinger.infra.mmkv.MMKVArgList method)
(schrodinger.infra.mmlist.mmlist method)
(schrodinger.infra.mmobject.MmObject method)
(schrodinger.infra.phase.PhpException method)
(schrodinger.infra.structure.MmctSerializerException method)
(schrodinger.infra.structure.PyStructureReaderException 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.util.CreateWhenNeeded method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.job.host_check.Error method)
(schrodinger.job.launchparams.ArgumentParserError method)
(schrodinger.job.launchparams.LaunchParameters method)
(schrodinger.job.remote_command.CommandError method)
(schrodinger.job.resource.ComputeRequirement method)
(schrodinger.livedesign.preprocessor.BlindedCompoundError method)
(schrodinger.livedesign.rgfile_parse.ForwardRGMolSupplier method)
(schrodinger.MaestroNotAvailableError method)
(schrodinger.math.mathutils.Interpolate1D method)
(schrodinger.math.mathutils.Interpolate2D method)
(schrodinger.math.multi_parameter_optimization.DoubleSigmoid method)
(schrodinger.math.multi_parameter_optimization.Sigmoid method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.json.JSONEncodeError method)
(schrodinger.models.jsonable.AbstractJsonSerializer method)
(schrodinger.models.jsonable.JsonableEnum method)
(schrodinger.models.jsonable.JsonableIntEnum method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.models.jsonable.MolSerializer method)
(schrodinger.models.jsonable.SetSerializer method)
(schrodinger.models.jsonable.StructureSerializer method)
(schrodinger.models.jsonable.TupleSerializer 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.pipeutils.BackwardsReader method)
(schrodinger.pipeline.pipeutils.DotPrinter method)
(schrodinger.project.surface.ProjectSurface method)
(schrodinger.project.surface.ProjectSurface.Color method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.protein.analysis.Report method)
(schrodinger.protein.analysis.Report.backbone_dihedral_data_set method)
(schrodinger.protein.analysis.Report.backbone_dihedral_data_set.data_point method)
(schrodinger.protein.analysis.Report.Bfactor_data_set method)
(schrodinger.protein.analysis.Report.Bfactor_data_set.data_point method)
(schrodinger.protein.analysis.Report.bond_angle_data_set method)
(schrodinger.protein.analysis.Report.bond_angle_data_set.data_point method)
(schrodinger.protein.analysis.Report.bond_length_data_set method)
(schrodinger.protein.analysis.Report.bond_length_data_set.data_point method)
(schrodinger.protein.analysis.Report.chirality_data_set method)
(schrodinger.protein.analysis.Report.chirality_data_set.data_point method)
(schrodinger.protein.analysis.Report.data_set method)
(schrodinger.protein.analysis.Report.data_set.data_point method)
(schrodinger.protein.analysis.Report.gamma_Bfactor_data_set method)
(schrodinger.protein.analysis.Report.gamma_Bfactor_data_set.data_point method)
(schrodinger.protein.analysis.Report.Gfactor_summary_data_set method)
(schrodinger.protein.analysis.Report.Gfactor_summary_data_set.data_point method)
(schrodinger.protein.analysis.Report.improper_torsion_data_set method)
(schrodinger.protein.analysis.Report.improper_torsion_data_set.data_point method)
(schrodinger.protein.analysis.Report.local_atom method)
(schrodinger.protein.analysis.Report.local_protein method)
(schrodinger.protein.analysis.Report.local_residue method)
(schrodinger.protein.analysis.Report.missing_atoms_data_set method)
(schrodinger.protein.analysis.Report.missing_atoms_data_set.data_point method)
(schrodinger.protein.analysis.Report.peptide_planarity_data_set method)
(schrodinger.protein.analysis.Report.peptide_planarity_data_set.data_point method)
(schrodinger.protein.analysis.Report.primex_steric_clash_data_set method)
(schrodinger.protein.analysis.Report.primex_steric_clash_data_set.data_point method)
(schrodinger.protein.analysis.Report.sidechain_dihedral_data_set method)
(schrodinger.protein.analysis.Report.sidechain_dihedral_data_set.data_point method)
(schrodinger.protein.analysis.Report.sidechain_planarity_data_set method)
(schrodinger.protein.analysis.Report.sidechain_planarity_data_set.data_point method)
(schrodinger.protein.analysis.Report.steric_clash_data_set method)
(schrodinger.protein.analysis.Report.steric_clash_data_set.data_point method)
(schrodinger.protein.biounit.BiounitOverrunError method)
(schrodinger.protein.helm.Monomer method)
(schrodinger.protein.rotamers.Rotamers method)
(schrodinger.Qt.PyQt6.QtCore.QSignalBlocker method)
(schrodinger.rdkit.filtering.ComparableMol method)
(schrodinger.rdkit.filtering.JSONFilterAdapter method)
(schrodinger.rdkit.molio.BaseCsvMolReader method)
(schrodinger.rdkit.molio.BasePfxMolReader method)
(schrodinger.rdkit.molio.CsvMergeHandler method)
(schrodinger.rdkit.molio.CsvMolIterator method)
(schrodinger.rdkit.molio.CsvMolReader method)
(schrodinger.rdkit.molio.CsvMolWriter method)
(schrodinger.rdkit.molio.GzippedSDMolSupplier method)
(schrodinger.rdkit.molio.MolWriter method)
(schrodinger.rdkit.molio.NoneSkipper method)
(schrodinger.rdkit.molio.PfxMolIterator method)
(schrodinger.rdkit.molio.PfxMolReader method)
(schrodinger.rdkit.molio.PfxMolWriter method)
(schrodinger.rdkit.molio.RdkitMergeHandler method)
(schrodinger.rdkit.molio.RdkitMolWriter method)
(schrodinger.rdkit.molio.StructureMergeHandler method)
(schrodinger.rdkit.molio.StructureReaderAdapter method)
(schrodinger.rdkit.rdkit_adapter.InconsistentStructureError method)
(schrodinger.rdkit.rdkit_adapter.UnsupportedStructureError method)
(schrodinger.rdkit.sorted_molwriter.SortedMolWriter method)
(schrodinger.structure._AtomBondContainer method)
(schrodinger.structure._AtomCollection method)
(schrodinger.structure._Chain method)
(schrodinger.structure._Molecule method)
(schrodinger.structure._Residue method)
(schrodinger.structure._Ring method)
(schrodinger.structure._StructureAtom method)
(schrodinger.structure._StructureBond method)
(schrodinger.structure._StructureProperty method)
(schrodinger.structure.AtomsInRingError method)
(schrodinger.structure.MaestroReader method)
(schrodinger.structure.MaestroTextReader method)
(schrodinger.structure.MaestroWriter method)
(schrodinger.structure.MultiFileStructureReader method)
(schrodinger.structure.MultiFileStructureWriter method)
(schrodinger.structure.PDBReader method)
(schrodinger.structure.PDBWriter method)
(schrodinger.structure.PropertyName method)
(schrodinger.structure.SDReader 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.StructureReader method)
(schrodinger.structure.StructureWriter method)
(schrodinger.structure.TextualStructure method)
(schrodinger.structure.UndefinedStereochemistry 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.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.PropFilter method)
(schrodinger.structutils.filter.SinglePropFilter method)
(schrodinger.structutils.filter.SingleSmartsFilter method)
(schrodinger.structutils.filter.SmartsFilter 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.markush_enumerate.FragmentReader method)
(schrodinger.structutils.markush_enumerate.FragmentsIterator method)
(schrodinger.structutils.markush_enumerate.Scaffold method)
(schrodinger.structutils.markush_enumerate.VirtualLibrary method)
(schrodinger.structutils.measure.DistanceCellIterator method)
(schrodinger.structutils.measure.LinearError method)
(schrodinger.structutils.minimize.Minimizer method)
(schrodinger.structutils.rgroup_enumerate.BondOrderMismatch method)
(schrodinger.structutils.rgroup_enumerate.Concentration method)
(schrodinger.structutils.rgroup_enumerate.RGroupEnumerator method)
(schrodinger.structutils.rgroup_enumerate.RGroupError method)
(schrodinger.structutils.rgroup_enumerate.RGroupSource method)
(schrodinger.structutils.rmsd.ConformerRmsd method)
(schrodinger.structutils.rmsd.ConformerRmsdX method)
(schrodinger.structutils.rmsd.DisabledSymmetryWarning method)
(schrodinger.structutils.shuffle.ShuffleException method)
(schrodinger.structutils.sitealign.BindingSiteAligner method)
(schrodinger.structutils.sitealign.SiteMatchLookup method)
(schrodinger.structutils.smiles.SmilesGenerator method)
(schrodinger.structutils.structalign.StructAlign method)
(schrodinger.surface.Surface method)
(schrodinger.surface.Surface.Color method)
(schrodinger.test.cluster_info.GPUCardInfo method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
(schrodinger.test.darwinconsole.UnsupportedPlatformException method)
(schrodinger.test.darwinconsole.Utmpx method)
(schrodinger.test.decorate_fflag.disable_feature_flag method)
(schrodinger.test.decorate_fflag.enable_feature_flag method)
(schrodinger.test.fixtures.safe_patch_os_environ method)
(schrodinger.test.ioredirect.FullIORedirect method)
(schrodinger.test.ioredirect.IOCapture method)
(schrodinger.test.ioredirect.IORedirect method)
(schrodinger.test.ioredirect.IOSilence method)
(schrodinger.test.memtest.Leak method)
(schrodinger.test.memtest.Suppression method)
(schrodinger.test.memtest.ValgrindWarning method)
(schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.performance.exceptions.BadResponse method)
(schrodinger.test.project_mock.MockProjectRow method)
(schrodinger.test.project_mock.MockProjectTable method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableFile.CollectError method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.Makefile.CollectError method)
(schrodinger.test.pytest.exetest.MakefileTest method)
(schrodinger.test.pytest.exetest.ProcessDied method)
(schrodinger.test.pytest.exetest.ProcessKilled method)
(schrodinger.test.structurecheck.ProteinReportCheck method)
(schrodinger.test.stu.common.FileInfo method)
(schrodinger.test.stu.common.ZipError method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System 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.EDA method)
(schrodinger.trajectory.prody.pca.PCA 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.playback_settings_data.PlaybackSettingsData method)
(schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences method)
(schrodinger.ui.dendrogram.DendrogramNode method)
(schrodinger.ui.dendrogram.DendrogramNodeBFIterator method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramTreeBuilder method)
(schrodinger.ui.dendrogram.DendrogramView method)
(schrodinger.ui.dendrogram.TestStdException method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict 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.validation.ValidationResult method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.ui.qt.appframework2.validators.BaseTextValidator method)
(schrodinger.ui.qt.appframework2.validators.FileExists method)
(schrodinger.ui.qt.appframework2.validators.IsInteger method)
(schrodinger.ui.qt.appframework2.validators.JobName method)
(schrodinger.ui.qt.appframework2.validators.PathExists method)
(schrodinger.ui.qt.appframework2.validators.Validator method)
(schrodinger.ui.qt.filter_dialog_dir.filter_core.Criterion method)
(schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method)
(schrodinger.ui.qt.label_cursor.LabelCursor method)
(schrodinger.ui.qt.label_cursor.LabelCursorAxes method)
(schrodinger.ui.qt.label_cursor.MultiAxesLabelCursor method)
(schrodinger.utils.cgxutils.FragmentLibrary method)
(schrodinger.utils.cgxutils.SerializationError method)
(schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.deprecation.DeprecationError method)
(schrodinger.utils.env.EnvironmentContext method)
(schrodinger.utils.env.MultiEnvironmentContext method)
(schrodinger.utils.fileutils.chdir method)
(schrodinger.utils.fileutils.SharingViolationError method)
(schrodinger.utils.funcchains.FuncChainMarker method)
(schrodinger.utils.funcchains.FuncChainMixin method)
(schrodinger.utils.funcgroups.FuncData method)
(schrodinger.utils.funcgroups.FuncGroupMarker method)
(schrodinger.utils.funcgroups.FuncGroupMixin method)
(schrodinger.utils.license.License method)
(schrodinger.utils.license.LicenseStatus method)
(schrodinger.utils.ligfilter.AslCriterion method)
(schrodinger.utils.ligfilter.Criterion method)
(schrodinger.utils.ligfilter.CriterionParser method)
(schrodinger.utils.ligfilter.Definition method)
(schrodinger.utils.ligfilter.DefinitionParser method)
(schrodinger.utils.ligfilter.PredefinedCriterion method)
(schrodinger.utils.ligfilter.PropertyCriterion method)
(schrodinger.utils.ligfilter.SmartsCriterion method)
(schrodinger.utils.moduleproxy.ModuleProxy method)
(schrodinger.utils.multifpfile.MultiFPFile method)
(schrodinger.utils.multifpfile.MultiFPFileWriter method)
(schrodinger.utils.preferences.Preferences method)
(schrodinger.utils.profiling.Profiler method)
(schrodinger.utils.profiling.RecordingTimer method)
(schrodinger.utils.profiling.Timer method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultFactoryDictMixin method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.scollections.IdItemsView method)
(schrodinger.utils.scollections.IdSet method)
(schrodinger.utils.sea.evalor.Evalor method)
(schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.Key method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
(schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
(schrodinger.utils.singledashoptionparser.SingleDashOption method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
(schrodinger.utils.timeit.TimeIt method)
__len__() (schrodinger.application.canvas.topo_descriptors.Descriptor method)
(schrodinger.application.dendrogram.core_class.GetPartitions.NameList method)
(schrodinger.application.dendrogram.core_class.RingSysInfo method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
(schrodinger.application.desmond.arkdb.ForEachDo method)
(schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.FBHWPosRestrainArray method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.cms.PosRestrainArray method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.desmond.fep_edge_data.ResData method)
(schrodinger.application.desmond.packages.msys.atomsel.Atomsel method)
(schrodinger.application.desmond.packages.msys.IndexedFileLoader method)
(schrodinger.application.desmond.packages.timer.Timer.Args method)
(schrodinger.application.desmond.packages.traj.MaeFrameReader method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.basis.BasisSet method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.jaguar.utils.ChgAt method)
(schrodinger.application.jaguar.utils.FreeEnergy method)
(schrodinger.application.jaguar.utils.LewisStructure method)
(schrodinger.application.licensing.licadmin.stat_info method)
(schrodinger.application.licensing.lmgrd_log_parser.event method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.livedesign.login.Version method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.CacheInfo method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.codeutils.ModuleInfo method)
(schrodinger.application.matsci.nano.space_groups.SpaceGroup method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.application.qsite.input.QMRegion method)
(schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo method)
(schrodinger.application.scaffold_enumeration.cxsmiles.MCG method)
(schrodinger.application.scaffold_enumeration.cxsmiles.SRU method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup method)
(schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup method)
(schrodinger.forcefield.ffld_options.ForceFieldOptions method)
(schrodinger.forcefield.ffld_options.MinimizationOptions method)
(schrodinger.infra.mmbitset.Bitset method)
(schrodinger.infra.mmim.MMIMArgList method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.infra.mmkv.MMKVArgList method)
(schrodinger.infra.mmlist.mmlist method)
(schrodinger.infra.table.Table method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.job.server.ServerInfo method)
(schrodinger.livedesign.preprocessor.PreprocessorOptions method)
(schrodinger.math.multi_parameter_optimization.Transition method)
(schrodinger.models.diffy.DictDiff method)
(schrodinger.models.diffy.ListDiff method)
(schrodinger.models.diffy.SetDiff method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.models.jsonable.JsonableTuple method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.protein.tasks.structure_alignment.StructAlignResult method)
(schrodinger.rdkit.molio.CsvMolReader method)
(schrodinger.rdkit.molio.NoneSkipper method)
(schrodinger.rdkit.molio.PfxMolReader method)
(schrodinger.rdkit.substructure.QueryOptions method)
(schrodinger.structure._AtomBondContainer method)
(schrodinger.structure._AtomCollection method)
(schrodinger.structure._Chain method)
(schrodinger.structure._Molecule method)
(schrodinger.structure._Residue method)
(schrodinger.structure._Ring method)
(schrodinger.structure._StructureProperty method)
(schrodinger.structutils.color.ColorScheme method)
(schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
(schrodinger.structutils.markush_enumerate.PlaceHolder method)
(schrodinger.structutils.rgroup_enumerate.RGroup method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System 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.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.cgxutils.FragmentLibrary method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.scollections.IdItemsView method)
(schrodinger.utils.scollections.IdSet method)
(schrodinger.utils.sea.sea.Key method)
(schrodinger.utils.sea.sea.List method)
_AtomBondContainer (class in schrodinger.structure)
_AtomCollection (class in schrodinger.structure)
_Chain (class in schrodinger.structure)
_Molecule (class in schrodinger.structure)
_Residue (class in schrodinger.structure)
_Ring (class in schrodinger.structure)
_StructureAtom (class in schrodinger.structure)
_StructureBond (class in schrodinger.structure)
_StructureProperty (class in schrodinger.structure)
A
A2cell() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
A2Gmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
A2invcell() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
abeles() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
AbFEPEdgeData (class in schrodinger.application.desmond.fep_edge_data)
aboutToUpdatePositions (schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
abs_schrodinger_path() (in module schrodinger.utils.subprocess)
ABSOLUTE_BINDING (schrodinger.application.desmond.constants.FEP_TYPES attribute)
absolutePosition() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
Absorb() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
AbsorbDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
AbstractAdapter (class in schrodinger.models.adapters.abstractadapter)
AbstractDebugViewer (class in schrodinger.ui.qt.appframework2.debugcore)
AbstractJsonSerializer (class in schrodinger.models.jsonable)
ACC_LEVEL (class in schrodinger.application.jaguar.csrch_input_constants)
accept() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method)
accept_reject_parse() (in module schrodinger.application.desmond.replica_exchange_review)
accept_test() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method)
(schrodinger.application.matsci.gsas.GSASIImath.fast_sa method)
(schrodinger.application.matsci.gsas.GSASIImath.log_sa method)
ACCEPTABLE (schrodinger.application.msv.gui.homology_modeling.constants.AlignmentQuality attribute)
acceptDrops() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
acceptedMouseButtons() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
acceptHoverEvents() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
ACCEPTOR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
acceptTouchEvents() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
accessibleDescription() (schrodinger.ui.dendrogram.DendrogramView method)
accessibleName() (schrodinger.ui.dendrogram.DendrogramView method)
accumulate() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
ack() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
acosd() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIImath)
(in module schrodinger.application.matsci.gsas.GSASIIpwd)
acquire() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.infra.mmerr.Capture method)
(schrodinger.infra.structure.TextBlockReader method)
(schrodinger.infra.structure.TextBlockWriter method)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter method)
(schrodinger.structutils.color.ColorScheme method)
acroForm (schrodinger.application.desmond.rl_helper.NumberedCanvas property)
action_names (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
actionEvent() (schrodinger.ui.dendrogram.DendrogramView method)
ACTIONS (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
actions() (schrodinger.ui.dendrogram.DendrogramView method)
activateWindow() (schrodinger.ui.dendrogram.DendrogramView method)
active_total (schrodinger.application.desmond.cms.Cms property)
active_total_from_nactive_gids() (schrodinger.application.desmond.cms.Cms method)
activePanel() (schrodinger.ui.dendrogram.DendrogramScene method)
activeWindow() (schrodinger.ui.dendrogram.DendrogramScene method)
adapter() (in module schrodinger.models.json)
adaptor (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser property)
add() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
(schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.rdkit.sorted_molwriter.SortedMolWriter method)
(schrodinger.structutils.color.ColorScheme method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.scollections.IdSet method)
ADD_ALL (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute)
add_amide_constraints() (in module schrodinger.structutils.rgroup_enumerate)
add_and_parse_SMILES() (in module schrodinger.application.desmond.rl_helper)
add_argument() (schrodinger.utils.compare.DiffCompareArgumentParser method)
add_argument_group() (schrodinger.utils.compare.DiffCompareArgumentParser method)
add_build_tools_to_path() (in module schrodinger.test)
add_chiral_hs() (in module schrodinger.livedesign.preprocessor)
add_code() (schrodinger.infra.mmcheck.ReturnCode method)
add_cuda_stubs_for_tensorflow() (in module schrodinger.utils.env)
add_descriptors() (in module schrodinger.rdkit.filtering)
(in module schrodinger.structutils.rgroup_enumerate)
add_descriptors_gen() (in module schrodinger.rdkit.filtering)
add_error() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
(schrodinger.application.licensing.licadmin.ServerInfo method)
add_explicit_hydrogens() (in module schrodinger.livedesign.preprocessor)
add_filters() (in module schrodinger.rdkit.filtering)
add_hs_to_aromatic_nitrogen() (in module schrodinger.livedesign.convert)
add_hydrogens() (in module schrodinger.structutils.build)
(schrodinger.application.desmond.fep_struc.SchrodStruc method)
add_inactive_solvent() (in module schrodinger.application.desmond.gcmc_utils)
add_inactive_solvent_file() (in module schrodinger.application.desmond.gcmc_utils)
add_kwarg() (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter method)
add_marker() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
add_mutually_exclusive_group() (schrodinger.utils.compare.DiffCompareArgumentParser method)
add_nondist_to_path() (in module schrodinger.test)
add_option() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
add_option_group() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
add_options() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
add_output() (schrodinger.application.desmond.enhsamp.Env method)
(schrodinger.application.licensing.licerror.LicenseError method)
add_override() (in module schrodinger.application.desmond.packages.msys.vdw)
add_package_dir_to_path() (in module schrodinger.application.utils)
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.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)
add_report_section() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.MakefileTest method)
add_rl_pair_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
add_rl_pairs (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
add_signature() (schrodinger.application.licensing.flexlm.Feature method)
add_signatures() (schrodinger.application.licensing.flexlm.License method)
add_spacer() (in module schrodinger.application.desmond.rl_helper)
add_static() (schrodinger.application.desmond.enhsamp.Env method)
add_subparsers() (schrodinger.utils.compare.DiffCompareArgumentParser method)
add_table() (in module schrodinger.application.desmond.rl_helper)
add_tag() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
add_validator() (in module schrodinger.ui.qt.appframework2.validation)
add_var() (schrodinger.application.desmond.enhsamp.binding method)
add_vtable() (in module schrodinger.application.desmond.rl_helper)
add_water_constraints() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
ADD_WEIGHTS (schrodinger.livedesign.molhash.EnhancedStereoUpdateMode attribute)
add_xsd_types_to_dict() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
addAction() (schrodinger.ui.dendrogram.DendrogramView method)
addActions() (schrodinger.ui.dendrogram.DendrogramView method)
addAnalyzer() (schrodinger.application.desmond.packages.staf.GeomCalc method)
addAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method)
addAngleRestraint() (schrodinger.structutils.minimize.Minimizer method)
addAtom() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.application.desmond.packages.msys.Residue method)
(schrodinger.application.desmond.packages.msys.System method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
addAtomProp() (schrodinger.application.desmond.packages.msys.System method)
addAtoms() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
addAttr() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addAuxTable() (schrodinger.application.desmond.packages.msys.System method)
addBond() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.application.desmond.packages.msys.Atom method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure._StructureAtom method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
addBondProp() (schrodinger.application.desmond.packages.msys.System method)
addBonds() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
addChain() (schrodinger.application.desmond.packages.msys.Ct method)
(schrodinger.application.desmond.packages.msys.System method)
addChild() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
(schrodinger.ui.dendrogram.DendrogramNode method)
addChildren() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
addClassCleanup() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase class method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase class method)
addCleanup() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
addCnst() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addConcentrationProperty() (schrodinger.structutils.rgroup_enumerate.Concentration method)
addCostProperties() (schrodinger.application.ligprep.ionizer.Ionizer method)
addCt() (schrodinger.application.desmond.packages.msys.System method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addCustom() (schrodinger.application.desmond.packages.staf.GeomCalc method)
addDefaultColorRule() (schrodinger.structutils.color.ColorScheme method)
addDistance() (schrodinger.application.desmond.packages.staf.GeomCalc method)
addDistanceRestraint() (schrodinger.structutils.minimize.Minimizer method)
added (schrodinger.models.diffy.DictDiff attribute)
(schrodinger.models.diffy.ListDiff attribute)
(schrodinger.models.diffy.SetDiff attribute)
ADDED_NOTHING (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
ADDED_PARENT (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
ADDED_PARENT_NAME (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
ADDED_RING_SYS (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
addEigenpair() (schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
addEllipse() (schrodinger.ui.dendrogram.DendrogramScene method)
addext() (in module schrodinger.trajectory.prody.writenmd)
addFeatureTypeEquivalencies() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addfinalizer() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
addFromFile() (schrodinger.project.surface.SurfaceDict method)
addFuncToGroup() (schrodinger.utils.funcchains.FuncChainMixin method)
(schrodinger.utils.funcgroups.FuncGroupMixin method)
addHydrogenCap() (schrodinger.application.qsite.input.QSiteInput method)
AddHydrogens() (in module schrodinger.application.matsci.gsas.GSASIImath)
addIonProperties() (schrodinger.application.ligprep.ionizer.Ionizer method)
addItem() (schrodinger.ui.dendrogram.DendrogramScene method)
addIvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addKey() (schrodinger.utils.ligfilter.Definition method)
addLine() (schrodinger.ui.dendrogram.DendrogramScene method)
addLiteral() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
addMask() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addMessagesAsDetails() (schrodinger.infra.mmerr.Capture method)
addNavigationNode() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
addNonbondedFromSchema() (schrodinger.application.desmond.packages.msys.System method)
addOptions() (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
addOutlineEntry() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
addPageLabel() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
addParam() (schrodinger.application.desmond.packages.msys.ParamTable method)
addParent() (schrodinger.application.dendrogram.core_class.RingSysStorage class method)
addPath() (schrodinger.ui.dendrogram.DendrogramScene method)
addPixmap() (schrodinger.ui.dendrogram.DendrogramScene method)
addPlanarAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method)
addPolygon() (schrodinger.ui.dendrogram.DendrogramScene method)
addPosFrozen() (schrodinger.structutils.minimize.Minimizer method)
addPosition() (schrodinger.application.desmond.packages.staf.GeomCalc method)
addPosRestraint() (schrodinger.structutils.minimize.Minimizer method)
addPostScriptCommand() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
addProp() (schrodinger.application.desmond.packages.msys.ParamTable method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addQMCut() (schrodinger.application.qsite.input.QSiteInput method)
addQMMolecule() (schrodinger.application.qsite.input.QSiteInput method)
addQsar() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addRad() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addRect() (schrodinger.ui.dendrogram.DendrogramScene method)
addReferenceSeries() (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method)
(schrodinger.analysis.enrichment.plotter.Plotter method)
addResidue() (schrodinger.application.desmond.packages.msys.Chain method)
(schrodinger.application.desmond.packages.msys.System method)
addResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method)
addRestraints() (schrodinger.application.desmond.packages.restraint.builder.RestraintBuilder method)
addRingSys() (schrodinger.application.dendrogram.core_class.RingSysStorage class method)
addRule() (schrodinger.structutils.color.ColorScheme method)
addRules() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addScrollBarWidget() (schrodinger.ui.dendrogram.DendrogramView method)
addSeries() (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method)
(schrodinger.analysis.enrichment.plotter.Plotter method)
addSimpleText() (schrodinger.ui.dendrogram.DendrogramScene method)
addSite() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addSource() (schrodinger.application.fpsim.FPsimSearcher method)
addStage() (schrodinger.pipeline.input.LinearWriter method)
(schrodinger.pipeline.input.Writer method)
addSurfaceToProject() (schrodinger.project.surface.ProjectSurface class method)
addTable() (schrodinger.application.desmond.packages.msys.System method)
addTableFromSchema() (schrodinger.application.desmond.packages.msys.System method)
addTerm() (schrodinger.application.desmond.packages.msys.TermTable method)
(schrodinger.application.desmond.packages.restraint.builder.Restraints method)
addTermProp() (schrodinger.application.desmond.packages.msys.TermTable method)
addText() (schrodinger.ui.dendrogram.DendrogramScene method)
ADDTOENTRY (schrodinger.job.launchparams.ProjectDisposition attribute)
addToGroup() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
addTol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addTolByType() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
addTorsion() (schrodinger.application.desmond.packages.staf.GeomCalc method)
addTorsionRestraint() (schrodinger.structutils.minimize.Minimizer method)
addTypeEqualityFunc() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
addVar() (schrodinger.pipeline.input.LinearWriter method)
(schrodinger.pipeline.input.Writer method)
addVector() (schrodinger.application.desmond.packages.staf.GeomCalc method)
addWidget() (schrodinger.ui.dendrogram.DendrogramScene method)
addXvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
adjHKLmax() (in module schrodinger.application.matsci.gsas.GSASIImath)
adjust() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
adjust_conjugated_five_rings (schrodinger.rdkit.substructure.QueryOptions attribute)
adjust_single_bonds_between_aromatic_atoms (schrodinger.rdkit.substructure.QueryOptions attribute)
adjust_single_bonds_to_degree_one_neighbors (schrodinger.rdkit.substructure.QueryOptions attribute)
AdjustIgnored (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.SizeAdjustPolicy attribute)
adjustImproperDihedral() (in module schrodinger.structutils.build)
adjustName() (schrodinger.application.dendrogram.core_class.Utilities static method)
adjustSize() (schrodinger.ui.dendrogram.DendrogramView method)
AdjustToContents (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.SizeAdjustPolicy attribute)
AdjustToContentsOnFirstShow (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.SizeAdjustPolicy attribute)
advance() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
advice (schrodinger.application.licensing.licerror.LicenseError property)
aid_match() (in module schrodinger.application.desmond.packages.topo)
aids (schrodinger.application.desmond.packages.restraint.utils.CentroidData attribute)
aids2gids() (in module schrodinger.application.desmond.packages.topo)
AIDX_TYPE (schrodinger.application.desmond.cms.FBHWPosRestrainArray attribute)
(schrodinger.application.desmond.cms.PosRestrainArray attribute)
ALCHEMICAL (schrodinger.application.desmond.constants.SystemType attribute)
ALGORITHM_TYPE (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData attribute)
alie_analysis_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
alie_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute)
align() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method)
(schrodinger.structutils.structalign.StructAlign method)
align_horizontally() (in module schrodinger.rdkit.alignment)
align_pos() (in module schrodinger.application.desmond.packages.analysis)
ALIGN_SEQUENCES (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
ALIGN_STRUCTURES (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
alignCoordinates() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method)
aligned_rmsd() (in module schrodinger.application.desmond.packages.msys.pfx)
AlignedMolStructureGenerator (class in schrodinger.application.pathfinder.aligner)
alignedRMSD() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method)
alignment() (schrodinger.ui.dendrogram.DendrogramView method)
AlignmentQuality (class in schrodinger.application.msv.gui.homology_modeling.constants)
AlignMethod (class in schrodinger.application.phase.packages.ligand_aligner)
alignSites() (schrodinger.structutils.sitealign.BindingSiteAligner method)
alignStructure() (schrodinger.structutils.structalign.StructAlign method)
ALL (schrodinger.application.desmond.constants.REST_REGION_RULE attribute)
all() (schrodinger.infra.mmbitset.Bitset method)
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_LAYERS (schrodinger.livedesign.molhash.HashScheme attribute)
all_multicomb() (in module schrodinger.application.desmond.autopartition)
all_rows (schrodinger.test.project_mock.MockProjectTable property)
all_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property)
allaid_gids (schrodinger.application.desmond.cms.Cms property)
allDescriptorFullLabels() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method)
AllLayers (schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramScene.SceneLayer attribute)
AllOps() (in module schrodinger.application.matsci.gsas.GSASIIspc)
allow_memtest() (in module schrodinger.test.pytest.fixture)
AlogP() (in module schrodinger.rdkit.filtering)
alpa_homo_lumo_energy() (in module schrodinger.application.mopac.results_main)
alpha_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
alpha_somo_lumo_energy() (in module schrodinger.application.mopac.results_main)
AlphaHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
alreadyParsedRule() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
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)
altSettingOrtho (in module schrodinger.application.matsci.gsas.GSASIIspc)
ALWAYS_TYPED_ACTIONS (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
AmorphousCrystalInter (class in schrodinger.application.desmond.packages.analysis)
AMU_TO_GRAM (schrodinger.application.desmond.packages.analysis.MembraneDensityProfile attribute)
analyze() (in module schrodinger.application.desmond.packages.analysis)
(schrodinger.application.desmond.packages.msys.System 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_pair() (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method)
(schrodinger.protein.analysis.Report.steric_clash_data_set method)
AnchorUnderMouse (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.ViewportAnchor attribute)
AnchorViewCenter (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.ViewportAnchor attribute)
Angle (class in schrodinger.application.desmond.packages.analysis)
angle (schrodinger.structutils.interactions.pi.CationPiInteraction property)
(schrodinger.structutils.interactions.pi.PiPiInteraction property)
ANGLE_FBHW (schrodinger.application.desmond.constants.RestrainTypes attribute)
angle_iterator() (in module schrodinger.structutils.analyze)
AngleDistortion (class in schrodinger.structutils.check)
ANI_1CCX (schrodinger.energy.ANIModel attribute)
ANIModel (class in schrodinger.energy)
AnionCation (schrodinger.structutils.interactions.salt_bridge.OrderBy attribute)
ANIPrecision (class in schrodinger.energy)
AniServerError
ANISOTROPIC (schrodinger.application.desmond.constants.IsotropyPolicy attribute)
ANN (schrodinger.forcefield.constants.GeometryOptMethod attribute)
anneal() (in module schrodinger.application.matsci.gsas.GSASIImath)
annealtests() (in module schrodinger.application.matsci.gsas.GSASIImath)
AnnotatedSystem (class in schrodinger.application.desmond.packages.msys)
ANNOTATION_PROP (in module schrodinger.rdkit.rdkit_adapter)
ANTIBODY (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute)
ANTIBODY_MODEL (schrodinger.infra.structure.WorkflowType attribute)
ANTIGEN (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute)
AntiparallelPleatedSheet (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
antlr_version (schrodinger.application.desmond.antlr3.debug.DebugParser attribute)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Lexer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Parser attribute)
(schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
antlr_version_str (schrodinger.application.desmond.antlr3.debug.DebugParser attribute)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Lexer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Parser attribute)
(schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
ANTLRFileStream (class in schrodinger.application.desmond.antlr3.streams)
ANTLRInputStream (class in schrodinger.application.desmond.antlr3.streams)
ANTLRStringStream (class in schrodinger.application.desmond.antlr3.streams)
any_atom_in_distance_cell() (in module schrodinger.structutils.measure)
ANY_CONTACT (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
ANY_VALUE (schrodinger.application.desmond.arkdb.DSC attribute)
ao_index() (in module schrodinger.application.mopac.results_main)
ao_zeta() (in module schrodinger.application.mopac.results_main)
api_token (schrodinger.application.matsci.qb_sdk.client.QubecTokenData attribute)
APIVersion (schrodinger.job.server.ServerInfo attribute)
APPEND (schrodinger.job.launchparams.ProjectDisposition attribute)
append() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.application.desmond.packages.msys.Ct method)
(schrodinger.application.desmond.packages.msys.System method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.application.phase.packages.shape_binary_utils.ShapeFileWriter method)
(schrodinger.application.qsite.input.QMRegion method)
(schrodinger.infra.mmerr.Capture method)
(schrodinger.infra.mmim.MMIMArgList method)
(schrodinger.infra.mmkv.MMKVArgList method)
(schrodinger.infra.structure.TextBlockReader method)
(schrodinger.infra.structure.TextBlockWriter method)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableStructure 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.SDWriter 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.color.ColorScheme method)
(schrodinger.structutils.filter.Filter method)
(schrodinger.structutils.filter.PropFilter method)
(schrodinger.structutils.filter.SmartsFilter method)
(schrodinger.structutils.io.MultiFileWriter method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.multifpfile.MultiFPFileWriter method)
(schrodinger.utils.sea.sea.List method)
append_comment() (in module schrodinger.application.desmond.util)
APPEND_FIT (schrodinger.job.launchparams.ProjectDisposition attribute)
append_outfiles_to_recover_file() (in module schrodinger.application.jaguar.utils)
append_path() (in module schrodinger.utils.env)
append_row_to_data() (in module schrodinger.structutils.block_data)
APPENDINPLACE (schrodinger.job.launchparams.ProjectDisposition attribute)
APPENDINPLACE_FIT (schrodinger.job.launchparams.ProjectDisposition attribute)
appendLigand() (schrodinger.application.glide.poseviewconvert.Complex method)
appendReceptor() (schrodinger.application.glide.poseviewconvert.Complex method)
appendSource() (schrodinger.structutils.rgroup_enumerate.Concentration method)
APPENDUNGROUPED (schrodinger.job.launchparams.ProjectDisposition attribute)
apply() (in module schrodinger.application.desmond.packages.msys.posre)
(schrodinger.application.desmond.gaussian_filter.GaussianFilter method)
(schrodinger.application.pathfinder.reaction.Reaction method)
(schrodinger.structutils.color.ColorScheme method)
(schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
apply_biounit() (in module schrodinger.protein.biounit)
apply_color_scheme() (in module schrodinger.structutils.color)
apply_exclusion() (in module schrodinger.application.desmond.r_group_asl)
apply_lewis() (in module schrodinger.application.jaguar.utils)
apply_override() (in module schrodinger.application.desmond.packages.msys.vdw)
apply_random_color() (in module schrodinger.application.livedesign.io_utils)
apply_substructure_coordinates() (in module schrodinger.rdkit.substructure)
apply_substructure_coordinates_from_mapping() (in module schrodinger.rdkit.substructure)
apply_transform() (in module schrodinger.analysis.transformations)
apply_transformations() (in module schrodinger.livedesign.preprocessor)
apply_transforms() (in module schrodinger.analysis.transformations)
ApplyBNSlatt() (in module schrodinger.application.matsci.gsas.GSASIIspc)
applyCPKStyle() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
ApplyDihedralGeometry() (in module schrodinger.application.desmond.packages.msys)
applyEnergyFilter() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
applyGoldsteinSingles() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
ApplyModulation() (in module schrodinger.application.matsci.gsas.GSASIImath)
applyScheme() (schrodinger.structutils.color.ColorScheme method)
ApplySeqData() (in module schrodinger.application.matsci.gsas.GSASIImath)
applyShowHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
ApplyStringOps() (in module schrodinger.application.matsci.gsas.GSASIIspc)
ApplyStringOpsMom() (in module schrodinger.application.matsci.gsas.GSASIIspc)
applyStyle() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure._Chain method)
(schrodinger.structure._Molecule method)
(schrodinger.structure._Residue method)
(schrodinger.structure._Ring method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
applyTubeStyle() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
applyVisibilityAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
applyWireStyle() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
arc() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
architecture() (schrodinger.test.cluster_info.GPUCardInfo method)
archive_path (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute)
archive_wm() (in module schrodinger.application.watermap.utils)
are_sts_the_same() (in module schrodinger.structutils.createfragments)
AreaPerLipid (class in schrodinger.application.desmond.packages.analysis)
areBound() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
args (schrodinger.adapter.InconsistentStructureError attribute)
(schrodinger.adapter.UnsupportedStructureError attribute)
(schrodinger.analysis.visanalysis.vdexception.VDException attribute)
(schrodinger.application.canvas.similarity.CanvasSimilarityNotImplemented attribute)
(schrodinger.application.canvas.topo_descriptors.TopoError attribute)
(schrodinger.application.desmond.antlr3.exceptions.BacktrackingFailed attribute)
(schrodinger.application.desmond.antlr3.exceptions.EarlyExitException attribute)
(schrodinger.application.desmond.antlr3.exceptions.FailedPredicateException attribute)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedNotSetException attribute)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedRangeException attribute)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedSetException attribute)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTokenException attribute)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTreeNodeException attribute)
(schrodinger.application.desmond.antlr3.exceptions.MissingTokenException attribute)
(schrodinger.application.desmond.antlr3.exceptions.NoViableAltException attribute)
(schrodinger.application.desmond.antlr3.exceptions.RecognitionException attribute)
(schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException attribute)
(schrodinger.application.desmond.antlr3.tree.RewriteCardinalityException attribute)
(schrodinger.application.desmond.antlr3.tree.RewriteEarlyExitException attribute)
(schrodinger.application.desmond.antlr3.tree.RewriteEmptyStreamException attribute)
(schrodinger.application.desmond.arkdb.ArkDbDelError attribute)
(schrodinger.application.desmond.arkdb.ArkDbGetError attribute)
(schrodinger.application.desmond.arkdb.ArkDbPutError attribute)
(schrodinger.application.desmond.arkdb.CompositeKeySyntaxError attribute)
(schrodinger.application.desmond.packages.restraint.utils.CrossLinkGenerationError attribute)
(schrodinger.application.desmond.packages.traj_util.TrajectoryUnreadableError attribute)
(schrodinger.application.desmond.task.SubtaskExecutionError attribute)
(schrodinger.application.desmond.torsion_related.IncompleteFragmentError attribute)
(schrodinger.application.fpsim.QueryError attribute)
(schrodinger.application.fpsim.SearchError attribute)
(schrodinger.application.fpsim.ServerError attribute)
(schrodinger.application.jaguar.exceptions.JaguarIOError attribute)
(schrodinger.application.jaguar.exceptions.JaguarRuntimeError attribute)
(schrodinger.application.jaguar.exceptions.JaguarUnsupportedBasisSet attribute)
(schrodinger.application.jaguar.exceptions.JaguarUserFacingException attribute)
(schrodinger.application.jaguar.exceptions.QRNNSupportError attribute)
(schrodinger.application.jaguar.exceptions.xTBFailure attribute)
(schrodinger.application.jaguar.neural_network_optimizer.AniServerError attribute)
(schrodinger.application.jaguar.neural_network_optimizer.OptimizationFailure attribute)
(schrodinger.application.jaguar.neural_network_optimizer.UnsupportedElementError attribute)
(schrodinger.application.jaguar.results.IncompleteOutput attribute)
(schrodinger.application.jaguar.user_config.JaguarConfigError attribute)
(schrodinger.application.jaguar.workflow_validation.ConstraintFormatError attribute)
(schrodinger.application.jaguar.workflow_validation.JaguarKeywordConflict attribute)
(schrodinger.application.jaguar.workflow_validation.WorkflowConservationError attribute)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordConflictError attribute)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordError attribute)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException attribute)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordFormatError attribute)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordValueError attribute)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordValueTypeError attribute)
(schrodinger.application.licensing.flexlm.IncompatibleLicenseError attribute)
(schrodinger.application.licensing.flexlm.LicfileError attribute)
(schrodinger.application.licensing.licadmin.MissingExecutableError attribute)
(schrodinger.application.licensing.licadmin.MissingLicenseFile attribute)
(schrodinger.application.licensing.licadmin.NetsuiteError attribute)
(schrodinger.application.licensing.licadmin.UsageError attribute)
(schrodinger.application.licensing.licerror.LicenseException attribute)
(schrodinger.application.licensing.lmgrd_log_parser.UsageError attribute)
(schrodinger.application.ligprep.ionizer.TolerableError attribute)
(schrodinger.application.ligprep.ionizer.TooManyGroupsError attribute)
(schrodinger.application.matsci.graph.NetworkLoopError attribute)
(schrodinger.application.matsci.mlearn.descriptor.FeaturizeError attribute)
(schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptorError attribute)
(schrodinger.application.matsci.mlearn.sklearn_json.ModellNotSupported attribute)
(schrodinger.application.matsci.msprops.PropertyNameError attribute)
(schrodinger.application.matsci.qb_sdk.parameters.QubecSdkError attribute)
(schrodinger.application.matsci.qeschema.qeschema.exceptions.QESchemaError attribute)
(schrodinger.application.matsci.qeschema.qeschema.exceptions.XmlDocumentError attribute)
(schrodinger.application.matsci.qexsd.qespresso.exceptions.ConfigError attribute)
(schrodinger.application.matsci.qexsd.qespresso.exceptions.QEspressoError attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.FileFormatError attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLDecodeError attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLEncodeError attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLSchemaValidationError attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLValueError attribute)
(schrodinger.application.mopac.exceptions.MopacIOError attribute)
(schrodinger.application.mopac.exceptions.MopacRuntimeError attribute)
(schrodinger.application.mopac.exceptions.MopacUserFacingException attribute)
(schrodinger.application.mopac.results_main.MopacBasisError1 attribute)
(schrodinger.application.mopac.results_main.MopacBasisError2 attribute)
(schrodinger.application.mopac.results_main.MopacBasisError3 attribute)
(schrodinger.application.mopac.results_main.MopacBasisError4 attribute)
(schrodinger.application.mopac.results_main.MopacBasisError5 attribute)
(schrodinger.application.mopac.results_main.MopacGradientParserError attribute)
(schrodinger.application.mopac.results_main.MopacNumericalError attribute)
(schrodinger.application.mopac.results_main.MopacPropertyError attribute)
(schrodinger.application.mopac.structure_launchers.StructureLauncherError attribute)
(schrodinger.forcefield.common.AtomTypingFailure attribute)
(schrodinger.infra.canvas.ChmException attribute)
(schrodinger.infra.canvas.CtAssertion attribute)
(schrodinger.infra.canvas.CtException attribute)
(schrodinger.infra.canvas.CtMsgException attribute)
(schrodinger.infra.canvas.CtRdrException attribute)
(schrodinger.infra.fast3d.f3d_Exception attribute)
(schrodinger.infra.mmcheck.MmException attribute)
(schrodinger.infra.phase.PhpException attribute)
(schrodinger.infra.structure.MmctSerializerException attribute)
(schrodinger.infra.structure.PyStructureReaderException attribute)
(schrodinger.job.launchparams.ArgumentParserError attribute)
(schrodinger.job.remote_command.CommandError attribute)
(schrodinger.livedesign.preprocessor.BlindedCompoundError attribute)
(schrodinger.MaestroNotAvailableError attribute)
(schrodinger.models.json.JSONEncodeError attribute)
(schrodinger.protein.biounit.BiounitOverrunError attribute)
(schrodinger.rdkit.rdkit_adapter.InconsistentStructureError attribute)
(schrodinger.rdkit.rdkit_adapter.UnsupportedStructureError attribute)
(schrodinger.structure.AtomsInRingError attribute)
(schrodinger.structure.UndefinedStereochemistry attribute)
(schrodinger.structutils.measure.LinearError attribute)
(schrodinger.structutils.rgroup_enumerate.BondOrderMismatch attribute)
(schrodinger.structutils.rgroup_enumerate.RGroupError attribute)
(schrodinger.structutils.rmsd.DisabledSymmetryWarning attribute)
(schrodinger.structutils.shuffle.ShuffleException attribute)
(schrodinger.test.darwinconsole.UnsupportedPlatformException attribute)
(schrodinger.test.performance.exceptions.BadResponse attribute)
(schrodinger.test.pytest.exetest.ExecutableFile.CollectError attribute)
(schrodinger.test.pytest.exetest.Makefile.CollectError attribute)
(schrodinger.test.pytest.exetest.ProcessDied attribute)
(schrodinger.test.pytest.exetest.ProcessKilled attribute)
(schrodinger.test.stu.common.ZipError attribute)
(schrodinger.utils.cgxutils.SerializationError attribute)
(schrodinger.utils.deprecation.DeprecationError attribute)
(schrodinger.utils.fileutils.SharingViolationError attribute)
ArgumentParserError
ArkDb (class in schrodinger.application.desmond.arkdb)
ArkDbDelError
ArkDbGetError
ArkDbPutError
aromatic (schrodinger.application.desmond.packages.msys.Atom property)
aromatic() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method)
AROMATIC_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
AROMATIC_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
AROMATIC_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
Array_Prop (class in schrodinger.application.desmond.simulation_block_data)
ArrayCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
ArraySyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
as_bool() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
as_double() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
as_float() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
AS_INPUT (schrodinger.adapter.Hydrogens attribute)
as_int() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
AS_IS (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute)
as_list() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
asDict() (schrodinger.application.pathfinder.reaction.Reaction method)
(schrodinger.application.pathfinder.reaction.ReagentClass method)
asind() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIImath)
asl2gids() (in module schrodinger.application.desmond.packages.topo)
AslCriterion (class in schrodinger.utils.ligfilter)
AslLigandSearcher (class in schrodinger.structutils.analyze)
ASLObject (class in schrodinger.application.desmond.enhsamp)
aslselect_atom() (in module schrodinger.application.desmond.cms)
asMsjSetting() (schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraint method)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintCentroid method)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintInteraction method)
(schrodinger.application.desmond.packages.restraint.cross_link.FragmentLinkingRestraint method)
asNamedTuple() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
aspectScale() (in module schrodinger.application.desmond.rl_helper)
assert_() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assert_approx() (in module schrodinger.application.phase.packages.mmp_compare_utils)
assert_build_id_matches() (in module schrodinger.test.stu.common)
assert_no_major_problems() (in module schrodinger.test.structurecheck)
assert_no_x() (in module schrodinger.test.stu.common)
assert_not_blinded() (in module schrodinger.livedesign.preprocessor)
assert_not_query() (in module schrodinger.livedesign.preprocessor)
assert_properties_match() (in module schrodinger.test.custom_assertions)
assert_raises_in_slot_or_event() (in module schrodinger.test.custom_assertions)
assert_structures_identical() (in module schrodinger.test)
assert_valid_scaffold() (in module schrodinger.livedesign.rgroup_decomposition)
assertAlmostEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertAlmostEquals() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertAtomMapsEqual() (in module schrodinger.test.canvas_utils)
assertConformersAlmostEqual() (in module schrodinger.test.custom_assertions)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertCountEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertCSVFilesMatch() (in module schrodinger.test.canvas_utils)
assertDictContainsSubset() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertDictEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertEqual() (in module schrodinger.test.canvas_utils)
(schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertEqualCommandArgs() (in module schrodinger.test.custom_assertions)
assertEqualCommandFiles() (in module schrodinger.test.custom_assertions)
assertEqualDicts() (in module schrodinger.test.custom_assertions)
assertEquals() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertEqualShFiles() (in module schrodinger.test.custom_assertions)
assertFalse() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertGreater() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertGreaterEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertIn() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertIs() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertIsInstance() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertIsNone() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertIsNot() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertIsNotNone() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertLess() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertLessEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertListEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertLogs() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertMultiLineEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertNotAlmostEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertNotAlmostEquals() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertNotEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertNotEquals() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertNotIn() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertNotIsInstance() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertNotRegex() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertNotRegexpMatches() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertProteinHealth() (schrodinger.test.structurecheck.ProteinReportCheck method)
assertRaises() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertRaisesRegex() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertRaisesRegexp() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertRegex() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertRegexpMatches() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertSameNumberOfAtoms() (in module schrodinger.test.custom_assertions)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertSameStructure() (in module schrodinger.test.custom_assertions)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertSequenceEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertSetEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertTrue() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertTupleEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertWarns() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
assertWarnsRegex() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
ASSIGN (schrodinger.application.desmond.constants.CUSTOM_CHARGE_MODE attribute)
assign() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util)
(in module schrodinger.Qt.PyQt6.sip)
(schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method)
assign_bonded_params() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util)
assign_force_field() (in module schrodinger.forcefield.common)
assign_phased() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util)
assign_setup() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util)
assign_stereochemistry() (in module schrodinger.livedesign.preprocessor)
assign_zero_coords_chirality() (in module schrodinger.livedesign.preprocessor)
AssignBondOrderAndFormalCharge() (in module schrodinger.application.desmond.packages.msys)
assignColorsWithThreshold() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
assume_3d (schrodinger.structure.SDWriter.Options attribute)
ASU_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup 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)
(schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method)
(schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method)
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)
atEnd() (schrodinger.rdkit.molio.GzippedSDMolSupplier method)
Atom (class in schrodinger.application.desmond.packages.msys)
(class in schrodinger.application.desmond.packages.viparr1.viparr.viparr)
(class in schrodinger.utils.sea.sea)
atom (schrodinger.application.desmond.cms.Cms attribute)
(schrodinger.application.desmond.ffiostructure.FFIOStructure attribute)
(schrodinger.application.desmond.packages.restraint.builder.AtomID attribute)
(schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo attribute)
(schrodinger.models.jsonable.JsonableStructure attribute)
(schrodinger.structure._AtomCollection property)
(schrodinger.structure._Chain property)
(schrodinger.structure._Molecule property)
(schrodinger.structure._Residue property)
(schrodinger.structure._Ring property)
(schrodinger.structure._StructureBond property)
(schrodinger.structure.Structure attribute)
(schrodinger.structure.TextualStructure property)
(schrodinger.structutils.markush_enumerate.PlaceHolder attribute)
atom() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
(schrodinger.application.desmond.packages.msys.System method)
atom_charges() (in module schrodinger.application.mopac.results_main)
atom_color (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
atom_el() (in module schrodinger.application.mopac.results_main)
atom_has_attachment_point() (in module schrodinger.livedesign.convert)
atom_index (schrodinger.structutils.rgroup_enumerate.RGroup attribute)
atom_indexes (schrodinger.structutils.analyze.Ligand property)
atom_mapping (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
atom_name (schrodinger.structure._StructureAtom property)
atom_objects (schrodinger.structutils.analyze.Ligand property)
atom_pqn() (in module schrodinger.application.mopac.results_main)
atom_props (schrodinger.application.desmond.packages.msys.System property)
atom_style (schrodinger.structure._StructureAtom property)
atom_symtype() (in module schrodinger.application.mopac.results_main)
atom_total (schrodinger.application.desmond.cms.Cms property)
ATOM_TOTAL (schrodinger.application.desmond.constants.IdConversion attribute)
atom_total (schrodinger.application.desmond.ffiostructure.FFIOStructure property)
(schrodinger.application.jaguar.results.JaguarResults property)
(schrodinger.models.jsonable.JsonableStructure property)
(schrodinger.structure.Structure property)
(schrodinger.structure.TextualStructure property)
atom_type (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.structure._StructureAtom property)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
atom_type_name (schrodinger.structure._StructureAtom property)
atom_typeMM (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
ATOM_TYPING_SCHEMES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI attribute)
atom_x_angstroms() (in module schrodinger.application.mopac.results_main)
atom_x_opt() (in module schrodinger.application.mopac.results_main)
AtomGroup (class in schrodinger.application.desmond.cms)
ATOMGROUP_PREFIX (schrodinger.application.desmond.cms.Cms attribute)
atomic_number (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.structure._StructureAtom property)
ATOMIC_SYMBOLS (in module schrodinger.application.matsci.atomicsymbols)
atomic_weight (schrodinger.structure._StructureAtom property)
AtomicPosition (class in schrodinger.application.desmond.packages.analysis)
AtomID (class in schrodinger.application.desmond.packages.restraint.builder)
AtomListEnumerable (class in schrodinger.application.scaffold_enumeration.atomlist)
AtomListInfo (class in schrodinger.application.scaffold_enumeration.atomlist)
atomPropType() (schrodinger.application.desmond.packages.msys.System method)
atoms
properties
atoms (schrodinger.application.desmond.packages.msys.Bond property)
(schrodinger.application.desmond.packages.msys.Ct property)
(schrodinger.application.desmond.packages.msys.Residue property)
(schrodinger.application.desmond.packages.msys.System property)
(schrodinger.application.desmond.packages.msys.Term property)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraint property)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintCentroid property)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintInteraction property)
(schrodinger.application.scaffold_enumeration.cxsmiles.MCG attribute)
(schrodinger.application.scaffold_enumeration.cxsmiles.SRU attribute)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup attribute)
(schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup attribute)
atoms() (schrodinger.application.desmond.packages.msys.Graph method)
Atomsel (class in schrodinger.application.desmond.packages.msys.atomsel)
atomsel() (schrodinger.application.desmond.enhsamp.ASLObject method)
(schrodinger.application.desmond.packages.msys.System method)
atomsGroupedBy() (schrodinger.application.desmond.packages.msys.System method)
AtomsInRingError (class in schrodinger.structure)
AtomTLS2UIJ() (in module schrodinger.application.matsci.gsas.GSASIImath)
AtomTyper (class in schrodinger.application.bindingsite.atomtyping)
AtomTypingFailure
attach_fragment() (in module schrodinger.structutils.build)
attach_structure() (in module schrodinger.structutils.build)
AttachmentPoint (class in schrodinger.application.combiglide.corehop)
attachSidechains() (schrodinger.structutils.rgroup_enumerate.RGroupEnumerator method)
ATTRACTION (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute)
attrib (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup attribute)
AttributableType (class in schrodinger.models.json)
attribute_groups (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
attributes (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
ATTRS (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
AU_TO_KG (schrodinger.application.desmond.constants.Conversion attribute)
audit_changes() (in module schrodinger.livedesign.preprocessor)
authSocketPath (schrodinger.job.server.ServerInfo attribute)
AUTO (schrodinger.application.desmond.packages.traj.Fmt attribute)
AUTO_DETECT (schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
auto_partition() (in module schrodinger.application.desmond.autopartition)
autoFillBackground() (schrodinger.ui.dendrogram.DendrogramView method)
AUTOTS_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
auxinfo (schrodinger.application.desmond.packages.msys.InChI property)
auxtable() (schrodinger.application.desmond.packages.msys.System method)
auxtable_names (schrodinger.application.desmond.packages.msys.System property)
auxtables (schrodinger.application.desmond.packages.msys.System property)
AV2Q() (in module schrodinger.application.matsci.gsas.GSASIImath)
available_color_schemes() (in module schrodinger.structutils.color)
AVAILABLE_RADIATION (schrodinger.application.matsci.xrd.XRDCalculator attribute)
available_tokens() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
AVdeg2Q() (in module schrodinger.application.matsci.gsas.GSASIImath)
AVPAslOption (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data)
axis (schrodinger.application.desmond.packages.msys.molfile.Grid property)
AxisDirector (class in schrodinger.application.desmond.packages.analysis)
B
b64_decode() (in module schrodinger.application.desmond.packages.restraint.utils)
b64_encode() (in module schrodinger.application.desmond.packages.restraint.utils)
back_substitution_int() (in module schrodinger.application.matsci.cctbx.rot_mx)
back_transparency (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
BACKBONE (schrodinger.application.desmond.constants.ConfRestraintType attribute)
backbone_dihedrals (in module schrodinger.protein.analysis_params)
BACKBONE_INTERACTION (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
BACKBONE_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
backboneAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
backgroundBrush() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
BackgroundLayer (schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramScene.SceneLayer attribute)
backgroundRole() (schrodinger.ui.dendrogram.DendrogramView method)
backtrack() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method)
BacktrackingFailed
backup (schrodinger.application.jaguar.basis.BasisSet attribute)
backupFile() (in module schrodinger.trajectory.prody.writenmd)
BACKWARD (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Direction attribute)
BackwardsReader (class in schrodinger.pipeline.pipeutils)
BAD (schrodinger.application.desmond.fep_edge_data_classifier.Rating attribute)
BAD_INTERNALS (schrodinger.application.jaguar.constants.FatalErrors attribute)
BadResponse
balance_alie_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
balance_esp_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
base_functional() (in module schrodinger.application.jaguar.utils)
base_schedule (class in schrodinger.application.matsci.gsas.GSASIImath)
BASE_URL (in module schrodinger.test.stu.common)
BaseCacheData (class in schrodinger.application.matsci.cache)
BaseCsvMolReader (class in schrodinger.rdkit.molio)
BaseEntryData (class in schrodinger.application.livedesign.entry_types)
BaseFeaturizer (class in schrodinger.application.matsci.mlearn.base)
BaseMergeHandler (class in schrodinger.rdkit.molio)
basename() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDComplexType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method)
basename_no_ext() (in module schrodinger.application.prime.wrapper)
BasePfxMolReader (class in schrodinger.rdkit.molio)
BasePrimeAlignment (class in schrodinger.application.prime.wrapper)
BaseRecognizer (class in schrodinger.application.desmond.antlr3.recognizers)
baseSize() (schrodinger.ui.dendrogram.DendrogramView method)
BaseTextValidator (class in schrodinger.ui.qt.appframework2.validators)
BaseTree (class in schrodinger.application.desmond.antlr3.tree)
BaseTreeAdaptor (class in schrodinger.application.desmond.antlr3.tree)
basic_windows_path() (in module schrodinger.application.jaguar.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.matsci.qb_sdk.parameters.QubecChemistryProblem attribute)
basis_set_is_valid() (in module schrodinger.application.jaguar.workflow_validation)
BasisSet (class in schrodinger.application.jaguar.basis)
becomeRoot() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
beginBacktrack() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
beginForm() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
beginGroup() (schrodinger.utils.preferences.Preferences method)
beginPath() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
beginResync() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
beginText() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
bend_conj_amines (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute)
bennett() (schrodinger.application.desmond.bennett.CalcBAR method)
BessIn() (in module schrodinger.application.matsci.gsas.GSASIImath)
BessJn() (in module schrodinger.application.matsci.gsas.GSASIImath)
best_scoring_element() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method)
beta_au() (in module schrodinger.application.jaguar.utils)
beta_homo_lumo_energy() (in module schrodinger.application.mopac.results_main)
beta_kcalmol() (in module schrodinger.application.jaguar.utils)
beta_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
beta_somo_lumo_energy() (in module schrodinger.application.mopac.results_main)
betaij2Uij() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
bezier() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
BilinearHistogramData (class in schrodinger.application.matsci.uq_utils)
BinaryThreadSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
Bind (class in schrodinger.application.desmond.enhsamp)
bind() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
binding (class in schrodinger.application.desmond.enhsamp)
BINDING (schrodinger.application.desmond.constants.SystemType attribute)
BindingSiteAligner (class in schrodinger.structutils.sitealign)
bins() (schrodinger.application.desmond.packages.analysis.Rdf method)
BiounitOverrunError
biounits_from_structure() (in module schrodinger.protein.biounit)
Bitset (class in schrodinger.infra.mmbitset)
bitset_to_list() (in module schrodinger.utils.multifpfile)
BiunivocalMap (class in schrodinger.application.matsci.qeschema.qeschema.utils)
(class in schrodinger.application.matsci.qexsd.qespresso.utils.mapping)
BLACK (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
(schrodinger.ui.qt.standard.colors.NativeColors attribute)
BlankDebugEventListener (class in schrodinger.application.desmond.antlr3.debug)
BlenResCW() (in module schrodinger.application.matsci.gsas.GSASIIElem)
BlenResTOF() (in module schrodinger.application.matsci.gsas.GSASIIElem)
BlindedCompoundError
BLKSIZE (schrodinger.pipeline.pipeutils.BackwardsReader attribute)
Block (class in schrodinger.application.desmond.simulation_block_test)
block() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
BLOCK_NAME (schrodinger.application.prime.residue_interaction.InteractionReader attribute)
blockSignals() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
bodyToNode() (in module schrodinger.application.desmond.enhsamp)
boltzmann_probability() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
Bond (class in schrodinger.application.desmond.packages.msys)
bond (schrodinger.application.desmond.cms.Cms attribute)
(schrodinger.application.desmond.ffiostructure.FFIOStructure attribute)
(schrodinger.models.jsonable.JsonableStructure attribute)
(schrodinger.structure._StructureAtom property)
(schrodinger.structure.Structure attribute)
(schrodinger.structure.TextualStructure attribute)
bond() (schrodinger.application.desmond.packages.msys.System method)
bond_iterator() (in module schrodinger.structutils.analyze)
bond_order (schrodinger.structutils.rgroup_enumerate.RGroup attribute)
bond_props (schrodinger.application.desmond.packages.msys.System property)
bond_total (schrodinger.structure._StructureAtom property)
BondCharge (class in schrodinger.application.jaguar.results)
BondDistortion (class in schrodinger.structutils.check)
bonded_atoms (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.structure._StructureAtom property)
bonded_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
bonded_div (schrodinger.application.desmond.fep_schedule.FepSchedule attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault attribute)
(schrodinger.application.desmond.fep_schedule.FepSchemeChargeMixIn attribute)
(schrodinger.application.desmond.fep_schedule.FepSchemeMixIn attribute)
(schrodinger.application.desmond.fep_schedule.FepSchemeQuickchargeMixIn attribute)
(schrodinger.application.desmond.fep_schedule.FepSchemeSuperquickchargeMixIn attribute)
bondedA (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault property)
bondedB (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault property)
BondOrderMismatch
bondPropType() (schrodinger.application.desmond.packages.msys.System method)
BondRotator (class in schrodinger.application.desmond.torsion_related)
bonds
properties
bonds (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.application.desmond.packages.msys.Ct property)
(schrodinger.application.desmond.packages.msys.System property)
(schrodinger.application.jaguar.utils.LewisStructure attribute)
(schrodinger.structutils.markush_enumerate.PlaceHolder attribute)
BondType (class in schrodinger.structure)
bookmarkHorizontal() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
bookmarkHorizontalAbsolute() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
bookmarkPage() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
boolean() (in module schrodinger.utils.sea.common)
bootstrap() (in module schrodinger.application.desmond.bennett)
BootstrapNoiseHistogramData (class in schrodinger.application.matsci.uq_utils)
bootstrapped_solvation_free_energy() (in module schrodinger.application.desmond.solubility_utils)
BORESCH_RESTRAINT (schrodinger.application.desmond.constants.CorrectionTerm attribute)
boundingRect() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
BoundingRectViewportUpdate (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.ViewportUpdateMode attribute)
boundingRegion() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
boundingRegionGranularity() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
box (schrodinger.application.desmond.packages.analysis.Pbc property)
(schrodinger.application.desmond.packages.pfx.Frame attribute)
(schrodinger.application.desmond.packages.topo.DuckFrame property)
(schrodinger.application.desmond.packages.traj.Frame property)
Box (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shape attribute)
BoxSize (class in schrodinger.application.desmond.simulation_block_test)
break_infinite_segment() (in module schrodinger.application.matsci.graph)
bspTreeDepth() (schrodinger.ui.dendrogram.DendrogramScene method)
BspTreeIndex (schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramScene.ItemIndexMethod attribute)
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_GEOMETRY (class in schrodinger.application.desmond.constants)
BUILD_ID_RE (in module schrodinger.test.stu.common)
build_peptide() (in module schrodinger.protein.buildpeptide)
build_protein_helix() (in module schrodinger.test.build_test_structures)
buildAllAttr() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
buildCovariance() (schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
buildDerivedAttrs() (schrodinger.application.jaguar.results.DerivedAttrs method)
buildTree() (schrodinger.ui.dendrogram.DendrogramTreeBuilder method)
BULK (schrodinger.application.matsci.msconst.DIMENSIONALITY attribute)
bval (schrodinger.utils.sea.sea.Atom property)
(schrodinger.utils.sea.sea.Hydrogen property)
(schrodinger.utils.sea.sea.List property)
(schrodinger.utils.sea.sea.Map property)
C
c6() (schrodinger.application.desmond.cms.Vdw method)
cache_hostname_plink() (in module schrodinger.utils.sshconfig)
CACHE_LIMIT_BYTES (schrodinger.application.desmond.packages.traj.DtrSource attribute)
(schrodinger.application.desmond.packages.traj.MaeSource attribute)
(schrodinger.application.desmond.packages.traj.Source attribute)
(schrodinger.application.desmond.packages.traj.XtcSource attribute)
CacheBackground (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.CacheModeFlag attribute)
cached_topo_descriptor() (in module schrodinger.application.canvas.topo_descriptors)
CacheInfo (class in schrodinger.application.matsci.cache)
cacheMode() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
CacheNone (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.CacheModeFlag attribute)
CAL_CM_TO_MPA (schrodinger.application.desmond.constants.Conversion attribute)
calc_ActivesInN() (in module schrodinger.analysis.enrichment.metrics)
calc_ActivesInNStar() (in module schrodinger.analysis.enrichment.metrics)
calc_AUAC() (in module schrodinger.analysis.enrichment.metrics)
calc_AveNumberOutrankingDecoys() (in module schrodinger.analysis.enrichment.metrics)
calc_average_vdw_coeff() (in module schrodinger.application.desmond.cms)
calc_BEDROC() (in module schrodinger.analysis.enrichment.metrics)
calc_block_average() (in module schrodinger.application.desmond.simulation_block_data)
calc_buried_sasa_by_residue() (in module schrodinger.structutils.analyze)
calc_complementarity_by_atom() (in module schrodinger.application.bioluminate.surfcomp)
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_EF() (in module schrodinger.analysis.enrichment.metrics)
calc_EFF() (in module schrodinger.analysis.enrichment.metrics)
calc_EFP() (in module schrodinger.analysis.enrichment.metrics)
calc_EFStar() (in module schrodinger.analysis.enrichment.metrics)
calc_FOD() (in module schrodinger.analysis.enrichment.metrics)
calc_prob_profile() (in module schrodinger.application.desmond.ana)
calc_property() (in module schrodinger.application.matsci.uq_utils)
calc_rDsq() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_rDsq2() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_rDsqSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_rDsqT() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_rDsqTSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_rDsqZ() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_rDsqZSS() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_RIE() (in module schrodinger.analysis.enrichment.metrics)
calc_ROC() (in module schrodinger.analysis.enrichment.metrics)
calc_rV() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_rVsq() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_sensitivity_with_rank() (in module schrodinger.analysis.enrichment.plotter)
calc_specificity_with_rank() (in module schrodinger.analysis.enrichment.plotter)
calc_time_series() (in module schrodinger.application.desmond.ana)
calc_total_complementarity() (in module schrodinger.application.bioluminate.surfcomp)
calc_V() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
calc_volume() (in module schrodinger.application.desmond.fep_net_charge)
calcActivesInN() (schrodinger.analysis.enrichment.calculator.Calculator method)
calcActivesInNStar() (schrodinger.analysis.enrichment.calculator.Calculator method)
CalcAngle() (in module schrodinger.application.desmond.packages.msys)
(in module schrodinger.application.matsci.gsas.GSASIImath)
calcAngle() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method)
CalcAngleDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath)
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)
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() (in module schrodinger.application.desmond.packages.msys)
calcDihedral() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method)
CalcDist() (in module schrodinger.application.matsci.gsas.GSASIImath)
CalcDistance() (in module schrodinger.application.desmond.packages.msys)
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)
calcFOD() (schrodinger.analysis.enrichment.calculator.Calculator method)
calcIncident() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
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.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
CalcPDF() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
calcPlanarAngle() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method)
CalcPlanarity() (in module schrodinger.application.desmond.packages.msys)
calcRamaEnergy() (in module schrodinger.application.matsci.gsas.GSASIImath)
calcRIE() (schrodinger.analysis.enrichment.calculator.Calculator method)
calcROC() (schrodinger.analysis.enrichment.calculator.Calculator method)
CalcStackingPWDR() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
CalcStackingSADP() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
calcTorsionEnergy() (in module schrodinger.application.matsci.gsas.GSASIImath)
calculate() (schrodinger.structutils.rmsd.ConformerRmsd method)
(schrodinger.structutils.rmsd.ConformerRmsdX method)
calculate_binding_modes() (in module schrodinger.application.phase.hypothesis_binding_modes)
calculate_ciexy() (in module schrodinger.application.matsci.colorutils)
calculate_cri() (in module schrodinger.application.matsci.colorutils)
calculate_enhanced_stereo() (in module schrodinger.livedesign.preprocessor)
calculate_in_place_rmsd() (in module schrodinger.structutils.rmsd)
calculate_nits() (in module schrodinger.application.matsci.colorutils)
calculate_principal_moments() (in module schrodinger.structutils.analyze)
calculate_report_rmse() (in module schrodinger.application.desmond.solubility_utils)
calculate_RIP() (in module schrodinger.application.desmond.fep_net_charge)
calculate_sasa() (in module schrodinger.structutils.analyze)
calculate_sasa_by_atom() (in module schrodinger.structutils.analyze)
calculate_sasa_by_residue() (in module schrodinger.structutils.analyze)
calculate_solubility_free_energy() (in module schrodinger.application.desmond.solubility_utils)
calculate_total_usage() (in module schrodinger.application.licensing.lmgrd_log_parser)
CalculateContainingVolume() (in module schrodinger.analysis.visanalysis.volumedatautils)
calculateEnergy() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
calculateEnergyDifference() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
calculateMatrix() (schrodinger.structutils.sitealign.BindingSiteAligner method)
calculateSimilarity() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
calculateSpecificity() (schrodinger.analysis.enrichment.calculator.Calculator method)
calculateTopologicalDescriptors() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method)
Calculator (class in schrodinger.analysis.enrichment.calculator)
call() (in module schrodinger.utils.subprocess)
call_in_loop() (in module schrodinger.test.performance.general)
callback() (in module schrodinger.application.mopac.results_main)
(schrodinger.utils.env.MultiEnvironmentContext method)
callback_minimal (schrodinger.application.mopac.results_main.MopacMainTextParser attribute)
callback_minimal() (in module schrodinger.application.mopac.results_main)
callbacks (schrodinger.application.mopac.results_main.MopacMainTextParser attribute)
CALPHA_RUNG (schrodinger.application.desmond.constants.ConfRestraintType attribute)
can_atom_hydrogen_bond() (in module schrodinger.structutils.analyze)
can_skip_line() (in module schrodinger.utils.compare)
can_write_file() (in module schrodinger.application.licensing.licadmin)
cancel() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
(schrodinger.application.matsci.qb_sdk.job.QubecJob method)
cancel_job() (schrodinger.application.matsci.qb_sdk.client.QubecClient method)
canonical_filename() (schrodinger.application.licensing.flexlm.License method)
(schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
CANONICAL_SMILES (schrodinger.livedesign.molhash.HashLayer attribute)
Canonicalize (class in schrodinger.adapter)
canonicalize() (schrodinger.structutils.smiles.SmilesGenerator method)
canonicalize_cop_sgroup() (in module schrodinger.livedesign.molhash)
canonicalize_data_sgroup() (in module schrodinger.livedesign.molhash)
canonicalize_R_labels() (in module schrodinger.application.scaffold_enumeration.markush)
canonicalize_sgroups() (in module schrodinger.livedesign.molhash)
canonicalize_sru_sgroup() (in module schrodinger.livedesign.molhash)
canonicalize_stereo_groups() (in module schrodinger.livedesign.molhash)
canvas (schrodinger.application.matsci.msconst.SMARTS_METHOD attribute)
CanvasFingerprintCluster (class in schrodinger.application.canvas.cluster)
CanvasFingerprintClusterCLI (class in schrodinger.application.canvas.cluster)
CanvasFingerprintGenerator (class in schrodinger.application.canvas.fingerprint)
CanvasFingerprintGeneratorCLI (class in schrodinger.application.canvas.fingerprint)
CanvasFingerprintSimilarity (class in schrodinger.application.canvas.similarity)
CanvasFingerprintSimilarityCLI (class in schrodinger.application.canvas.similarity)
CanvasSimilarityNotImplemented
capitalize() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
capped_smi (schrodinger.application.dendrogram.core_class.RingSysInfo attribute)
capped_st (schrodinger.application.dendrogram.core_class.RingSysInfo attribute)
capToStar() (schrodinger.application.dendrogram.core_class.Utilities static method)
Capture (class in schrodinger.infra.mmerr)
casefold() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
CaseInsensitiveString (class in schrodinger.application.jaguar.jaguar_diff)
cast() (in module schrodinger.Qt.PyQt6.sip)
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)
catch_subprocess_errors() (in module schrodinger.utils.sysinfo)
category (schrodinger.application.desmond.packages.msys.TermTable property)
cation_centroid (schrodinger.structutils.interactions.pi.CationPiInteraction attribute)
cation_structure (schrodinger.structutils.interactions.pi.CationPiInteraction attribute)
CationPiInteraction (class in schrodinger.structutils.interactions.pi)
catOpText() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
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)
Cavity (class in schrodinger.application.bindingsite.cavutils)
cavity_depth (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
cdf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
cell (schrodinger.application.desmond.packages.msys.System 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)
CellAbsorption() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
CellBlock() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
cellClearData() (schrodinger.infra.table.Table method)
cellDijFill() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
cellHasData() (schrodinger.infra.table.Table method)
CentCheck() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
center (schrodinger.application.desmond.packages.msys.Residue property)
(schrodinger.application.desmond.packages.msys.System property)
(schrodinger.application.scaffold_enumeration.cxsmiles.MCG attribute)
(schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup attribute)
(schrodinger.math.multi_parameter_optimization.Transition attribute)
center() (in module schrodinger.application.desmond.packages.pfx)
(in module schrodinger.application.desmond.packages.topo)
(schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
center_cms() (in module schrodinger.application.desmond.packages.pfx)
(in module schrodinger.application.desmond.packages.topo)
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.structutils.analyze)
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)
CenterOf (class in schrodinger.application.desmond.packages.analysis)
CenterOfMotion (in module schrodinger.application.desmond.packages.analysis)
centerOn() (schrodinger.ui.dendrogram.DendrogramView method)
Centroid (class in schrodinger.application.desmond.packages.analysis)
(class in schrodinger.structutils.interactions.pi)
centroid (schrodinger.application.desmond.packages.restraint.utils.CentroidData attribute)
(schrodinger.structutils.analyze.Ligand property)
CentroidData (class in schrodinger.application.desmond.packages.restraint.utils)
Chain (class in schrodinger.application.desmond.packages.msys)
chain (schrodinger.application.desmond.cms.Cms attribute)
(schrodinger.application.desmond.fep_edge_data.ResData attribute)
(schrodinger.application.desmond.ffiostructure.FFIOStructure attribute)
(schrodinger.application.desmond.packages.msys.Residue property)
(schrodinger.application.qsite.input.Cut property)
(schrodinger.models.jsonable.JsonableStructure attribute)
(schrodinger.structure._Residue property)
(schrodinger.structure._StructureAtom property)
(schrodinger.structure.Structure attribute)
(schrodinger.structure.TextualStructure property)
chain() (schrodinger.application.desmond.packages.msys.System method)
chain_name (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.structure._StructureAtom property)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
chains (schrodinger.application.desmond.packages.msys.Ct property)
(schrodinger.application.desmond.packages.msys.System property)
change_to_rgroup() (in module schrodinger.rdkit.rgroup)
change_working_directory() (in module schrodinger.utils.fileutils)
changed (schrodinger.ui.dendrogram.DendrogramScene attribute)
changeEvent() (schrodinger.ui.dendrogram.DendrogramView method)
changeGroup() (schrodinger.utils.preferences.Preferences method)
characters_written (schrodinger.utils.fileutils.SharingViolationError attribute)
CHARGE (schrodinger.application.desmond.constants.Schedule attribute)
charge (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.application.jaguar.utils.ChgAt attribute)
(schrodinger.application.matsci.qb_sdk.parameters.QubecChemistryProblem attribute)
CHARGE (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute)
charge_div (schrodinger.application.desmond.fep_schedule.FepSchedule attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault attribute)
(schrodinger.application.desmond.fep_schedule.FepSchemeChargeMixIn attribute)
(schrodinger.application.desmond.fep_schedule.FepSchemeMixIn attribute)
(schrodinger.application.desmond.fep_schedule.FepSchemeQuickchargeMixIn attribute)
(schrodinger.application.desmond.fep_schedule.FepSchemeSuperquickchargeMixIn attribute)
charge_is_consistent() (in module schrodinger.application.jaguar.workflow_validation)
charge_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute)
chargeA (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault property)
chargeB (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault property)
CHARGED (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute)
CHARGED_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
CHARGED_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
CHARGED_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
ChargeFlip() (in module schrodinger.application.matsci.gsas.GSASIImath)
charges (schrodinger.application.jaguar.utils.LewisStructure attribute)
charges_from_ct (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute)
(schrodinger.structutils.minimize.Minimizer property)
charPositionInLine (schrodinger.application.desmond.antlr3.tree.CommonErrorNode property)
(schrodinger.application.desmond.antlr3.tree.CommonTree property)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern property)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern property)
CharStream (class in schrodinger.application.desmond.antlr3.streams)
CHCL3 (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute)
chdir (class in schrodinger.utils.fileutils)
chdir() (in module schrodinger.application.desmond.util)
check() (schrodinger.application.desmond.enhanced_sampling.FcnTypes.ArraySyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.BinaryThreadSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.MetaSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.RMSDSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.SimpleSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.Syntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.ThreadSyntax method)
(schrodinger.pipeline.pipeio.Grid method)
(schrodinger.pipeline.pipeio.PhaseDB method)
(schrodinger.pipeline.pipeio.PipeIO method)
(schrodinger.pipeline.pipeio.Structures method)
(schrodinger.pipeline.pipeio.Text method)
check1_subst_code() (in module schrodinger.application.desmond.fep_util)
check_atom_clashes() (in module schrodinger.test.stu.outcomes.confgen_workups)
check_attachment_point() (in module schrodinger.structutils.rgroup_enumerate)
check_attachment_points_changed() (in module schrodinger.livedesign.preprocessor)
check_call() (in module schrodinger.utils.subprocess)
check_canvas_license() (in module schrodinger.application.canvas.topo_descriptors)
check_command() (in module schrodinger.application.desmond.util)
check_conflicts() (in module schrodinger.application.jaguar.hydrokinetic_validation)
(in module schrodinger.application.jaguar.solvation_validation)
check_consistency() (in module schrodinger.application.desmond.packages.topo)
check_cstate_changed() (in module schrodinger.livedesign.preprocessor)
check_disk_usage() (in module schrodinger.test.stu.common)
check_hbond() (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method)
(schrodinger.protein.analysis.Report.steric_clash_data_set method)
check_kekulization() (in module schrodinger.livedesign.preprocessor)
check_key_pair() (in module schrodinger.utils.sshconfig)
check_map() (in module schrodinger.utils.sea.evalor)
check_memory_use() (in module schrodinger.application.mopac.results_main)
CHECK_METHODS (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
check_module() (in module schrodinger.application.bioluminate.validate_imported_modules)
check_moved_variables() (in module schrodinger.application.matsci.codeutils)
check_output() (in module schrodinger.utils.subprocess)
check_property_sign() (in module schrodinger.application.matsci.uq_utils)
check_required_gridfiles() (in module schrodinger.application.glide.utils)
check_sanity() (in module schrodinger.application.desmond.cms)
CHECK_SOLVENT_OVERLAP (schrodinger.application.desmond.constants.SYSTEM_BUILDER_INP attribute)
check_subst_code() (in module schrodinger.application.desmond.fep_util)
check_value() (schrodinger.utils.singledashoptionparser.SingleDashOption method)
check_values() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
checkArgs() (schrodinger.structutils.createfragments.FragmentCreator method)
CheckElement() (in module schrodinger.application.matsci.gsas.GSASIIElem)
checkHKLextc() (in module schrodinger.application.matsci.gsas.GSASIIspc)
checkin() (schrodinger.utils.license.License method)
checkLigands() (schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
checkMagextc() (in module schrodinger.application.matsci.gsas.GSASIIspc)
checkNumAtoms() (schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
checkNumEntries() (schrodinger.application.livedesign.entry_types.BaseEntryData method)
(schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
checkNumNodes() (schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
checkout() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
checkpoint() (schrodinger.utils.profiling.RecordingTimer method)
(schrodinger.utils.profiling.Timer method)
(schrodinger.utils.timeit.TimeIt method)
checkResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method)
checkRunning() (schrodinger.application.licensing.licadmin.LocalServerProcess method)
checkSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix 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)
checkStructure() (schrodinger.structutils.filter.Filter method)
(schrodinger.structutils.filter.PropFilter method)
(schrodinger.structutils.filter.SingleFilter method)
(schrodinger.structutils.filter.SinglePropFilter method)
(schrodinger.structutils.filter.SingleSmartsFilter method)
(schrodinger.structutils.filter.SmartsFilter method)
checkTargets() (schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
checkWeights() (in module schrodinger.trajectory.prody.ensemble)
ChgAt (class in schrodinger.application.jaguar.utils)
childAt() (schrodinger.ui.dendrogram.DendrogramView method)
childEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
childItems() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
children() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
childrenBoundingRect() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
childrenRect() (schrodinger.ui.dendrogram.DendrogramView method)
childrenRegion() (schrodinger.ui.dendrogram.DendrogramView method)
CHIMERA (schrodinger.application.msv.gui.homology_modeling.constants.HeteromultimerMode attribute)
(schrodinger.application.msv.gui.homology_modeling.constants.Mode attribute)
chiral_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
CHIRAL_FLAG_0_MEANING (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
ChiralFlag0Meaning (class in schrodinger.livedesign.preprocessor)
chirality (schrodinger.structure._StructureAtom property)
chm_bluebird (class in schrodinger.application.canvas.utils)
chm_excel (class in schrodinger.application.canvas.utils)
chm_sparse_bitset_from_string() (in module schrodinger.structutils.interactionfp)
ChmCSVTools (class in schrodinger.application.canvas.utils)
ChmException
CHOOSE_CANONICAL_TAUTOMER (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
CHOOSE_LIGANDS (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
chop() (in module schrodinger.utils.cgxutils)
ciexy_to_cie1960uv() (in module schrodinger.application.matsci.colorutils)
ciexy_to_upvp() (in module schrodinger.application.matsci.colorutils)
CIF (schrodinger.infra.structure.FileFormat attribute)
circle() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
clash_iterator() (in module schrodinger.structutils.interactions.steric_clash)
clash_volume() (in module schrodinger.structutils.interactions.steric_clash)
ClassicToken (class in schrodinger.application.desmond.antlr3.tokens)
clean() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
clean_ct_properties() (schrodinger.application.desmond.cms.Cms static method)
clean_hypo() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils)
clean_up_polymer_brackets() (in module schrodinger.livedesign.convert)
cleanup() (in module schrodinger.application.desmond.fep_net_charge)
(schrodinger.application.licensing.flexlm.License method)
cleanup_external() (in module schrodinger.application.mopac.utils)
cleanup_resources() (schrodinger.structutils.minimize.Minimizer method)
CLEAR (schrodinger.application.desmond.constants.CUSTOM_CHARGE_MODE attribute)
clear() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.desmond.task.ParchTrajectoryForAbsoluteFep method)
(schrodinger.application.desmond.task.ParchTrajectoryForFep method)
(schrodinger.application.desmond.task.ParchTrajectoryForFepLambda method)
(schrodinger.application.desmond.task.ParchTrajectoryForSolubilityFep method)
(schrodinger.application.desmond.task.Task method)
(schrodinger.application.desmond.task.TrajectoryForSolubilityFep method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.preferences.Preferences method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.scollections.IdSet method)
(schrodinger.utils.sea.sea.List method)
clear_all_tag() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
clear_cache() (schrodinger.application.desmond.packages.traj.DtrSource method)
(schrodinger.application.desmond.packages.traj.MaeSource method)
(schrodinger.application.desmond.packages.traj.Source method)
(schrodinger.application.desmond.packages.traj.XtcSource method)
clear_encoded_restraints() (in module schrodinger.application.desmond.packages.restraint.utils)
clear_input() (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter method)
CLEAR_INVALID_WEDGE_BONDS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
clear_ld_library_path() (in module schrodinger.application.livedesign.pse_helpers)
clear_restrain() (schrodinger.application.desmond.cms.Cms method)
clear_wedge_bonds_from_achiral_centers() (in module schrodinger.livedesign.preprocessor)
clearData() (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method)
clearDataFrame() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
clearFocus() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
clearMask() (schrodinger.ui.dendrogram.DendrogramView method)
clearResources() (schrodinger.application.licensing.licadmin.LocalServerProcess method)
ClearResults() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method)
clearRules() (schrodinger.structutils.color.ColorScheme method)
clearSelection() (schrodinger.ui.dendrogram.DendrogramScene method)
click_to_run (schrodinger.application.livedesign.upload_utils.CommandType attribute)
clipPath() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
clone() (schrodinger.application.desmond.packages.msys.System method)
(schrodinger.application.qsite.input.Cut method)
(schrodinger.application.qsite.input.HydrogenCap method)
(schrodinger.utils.sea.sea.Map method)
CloneSystem() (in module schrodinger.application.desmond.packages.msys)
close() (in module schrodinger.ui.qt.appframework2.appmethods)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
(schrodinger.application.desmond.ffiostructure.CMSReader method)
(schrodinger.application.desmond.packages.traj.DtrSource method)
(schrodinger.application.desmond.packages.traj.MaeSource method)
(schrodinger.application.desmond.packages.traj.Source method)
(schrodinger.application.desmond.packages.traj.XtcSource method)
(schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method)
(schrodinger.infra.structure.TextBlockReader method)
(schrodinger.infra.structure.TextBlockWriter method)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter method)
(schrodinger.rdkit.molio.BaseCsvMolReader method)
(schrodinger.rdkit.molio.BasePfxMolReader method)
(schrodinger.rdkit.molio.CsvMolIterator method)
(schrodinger.rdkit.molio.CsvMolReader method)
(schrodinger.rdkit.molio.CsvMolWriter method)
(schrodinger.rdkit.molio.MolWriter method)
(schrodinger.rdkit.molio.PfxMolIterator method)
(schrodinger.rdkit.molio.PfxMolReader method)
(schrodinger.rdkit.molio.PfxMolWriter method)
(schrodinger.rdkit.molio.RdkitMolWriter method)
(schrodinger.structure.MaestroReader method)
(schrodinger.structure.MaestroTextReader method)
(schrodinger.structure.MaestroWriter method)
(schrodinger.structure.MultiFileStructureWriter method)
(schrodinger.structure.PDBReader method)
(schrodinger.structure.PDBWriter method)
(schrodinger.structure.SDReader method)
(schrodinger.structure.SDWriter method)
(schrodinger.structure.SmilesCsvReader method)
(schrodinger.structure.SmilesCsvWriter method)
(schrodinger.structure.SmilesWriter method)
(schrodinger.structure.StructureReader method)
(schrodinger.structure.StructureWriter method)
(schrodinger.structutils.io.MultiFileWriter method)
(schrodinger.ui.dendrogram.DendrogramView method)
(schrodinger.utils.cgxutils.FragmentLibrary method)
(schrodinger.utils.env.MultiEnvironmentContext method)
(schrodinger.utils.multifpfile.MultiFPFile method)
(schrodinger.utils.multifpfile.MultiFPFileWriter method)
close_output() (schrodinger.application.desmond.bennett.CalcBAR method)
closeBlockIfNecessary() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
closeEvent() (schrodinger.ui.dendrogram.DendrogramView method)
clustal (schrodinger.utils.fileutils.SeqFormat attribute)
cluster() (in module schrodinger.application.desmond.packages.analysis)
clusterDM() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
clusterFP() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
clustering (schrodinger.application.livedesign.upload_utils.CommandType attribute)
cmd (schrodinger.application.licensing.licerror.LicenseError property)
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_atom() (in module schrodinger.application.desmond.packages.topo)
cms_atom_index() (in module schrodinger.application.desmond.packages.topo)
CMSReader (class in schrodinger.application.desmond.ffiostructure)
coalesce() (schrodinger.application.desmond.packages.msys.TermTable method)
coalesceTables() (schrodinger.application.desmond.packages.msys.System method)
Coc (class in schrodinger.application.desmond.packages.analysis)
code (schrodinger.application.licensing.licerror.LicenseError property)
CollagenHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
collect() (schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.Makefile method)
collect_logs() (in module schrodinger.application.desmond.task)
collection() (in module schrodinger.application.scaffold_enumeration.layered)
collectIonCandidates() (schrodinger.application.ligprep.ionizer.Ionizer method)
collidesWithItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
collidesWithPath() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
collidingItems() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
Color (class in schrodinger.structutils.color)
color (schrodinger.project.surface.ProjectSurface property)
(schrodinger.structure._StructureAtom property)
(schrodinger.surface.Surface property)
color() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method)
color_distance() (in module schrodinger.application.matsci.colorutils)
color_scheme (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
color_source (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
color_temperature() (in module schrodinger.application.matsci.colorutils)
ColorBy (class in schrodinger.surface)
colorByRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method)
colorCount() (schrodinger.ui.dendrogram.DendrogramView method)
ColorFrom (class in schrodinger.surface)
coloring() (schrodinger.project.surface.ProjectSurface method)
(schrodinger.surface.Surface method)
ColorRamp (class in schrodinger.structutils.color)
COLORS (schrodinger.application.msv.gui.color_ramp.NamedRainbowColorRamp attribute)
(schrodinger.structutils.color.RainbowColorRamp attribute)
ColorScheme (class in schrodinger.structutils.color)
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)
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)
Com (class in schrodinger.application.desmond.packages.analysis)
combinations() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(schrodinger.structutils.rgroup_enumerate.RGroupEnumerator method)
CombinatorialScreener (class in schrodinger.application.combinatorial_screen.combinatorial_screener)
combine_arithmetic_geometric() (in module schrodinger.application.desmond.packages.msys.vdw)
combine_fingerprints() (in module schrodinger.application.combinatorial_screen.fingerprint_utils)
combine_geometric() (in module schrodinger.application.desmond.packages.msys.vdw)
combine_output_files() (in module schrodinger.rdkit.molio)
combine_rings() (in module schrodinger.application.desmond.r_group_asl)
combine_vdw() (in module schrodinger.application.desmond.cms)
combineFollows() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
combobox_selections() (in module schrodinger.test.hypothesis.strategies.ui)
CommandError
commandify() (in module schrodinger.application.desmond.util)
CommandType (class in schrodinger.application.livedesign.upload_utils)
commence() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
comment() (schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method)
commonAncestorItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
CommonErrorNode (class in schrodinger.application.desmond.antlr3.tree)
CommonToken (class in schrodinger.application.desmond.antlr3.tokens)
CommonTokenStream (class in schrodinger.application.desmond.antlr3.streams)
CommonTree (class in schrodinger.application.desmond.antlr3.tree)
CommonTreeAdaptor (class in schrodinger.application.desmond.antlr3.tree)
CommonTreeNodeStream (class in schrodinger.application.desmond.antlr3.tree)
comp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
comp_atom_total (schrodinger.application.desmond.cms.Cms property)
comp_atoms() (in module schrodinger.application.desmond.packages.topo)
COMPACT (schrodinger.application.phase.packages.conformer_storage.Format attribute)
ComparableMol (class in schrodinger.rdkit.filtering)
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_csv() (in module schrodinger.test.stu.outcomes.compare_csv)
compare_dfs() (in module schrodinger.test.stu.outcomes.compare_csv)
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_lists() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
compare_mmp_transformations() (in module schrodinger.application.phase.packages.mmp_compare_utils)
compare_sites() (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)
compareDesmondSystems() (in module schrodinger.test.stu.outcomes.compareDesmondSystems)
compile_xy() (in module schrodinger.application.desmond.gchart)
Complex (class in schrodinger.application.glide.poseviewconvert)
COMPLEX (schrodinger.application.desmond.constants.FepLegTypes attribute)
(schrodinger.application.desmond.constants.REST_COMPONENT attribute)
COMPLEX_HOTREGION (schrodinger.application.desmond.constants.REST_PROPERTIES attribute)
Complexes (class in schrodinger.application.livedesign.entry_types)
COMPONENT_TO_COMBINED (schrodinger.application.desmond.constants.IdConversion attribute)
CompositeAnalyzer (class in schrodinger.application.desmond.packages.staf)
CompositeDynamicAslAnalyzer (class in schrodinger.application.desmond.packages.staf)
CompositeKeySyntaxError
compress_residue_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
ComptonFac() (in module schrodinger.application.matsci.gsas.GSASIIElem)
compute() (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.DiversityFingerprinter method)
compute_alogp() (in module schrodinger.application.medchem.property)
compute_energy() (in module schrodinger.structutils.minimize)
compute_factor_scores() (in module schrodinger.application.combinatorial_diversity.splitter_utils)
compute_filter_score() (in module schrodinger.application.combinatorial_diversity.diversity_selector)
compute_medchem_properties() (in module schrodinger.application.medchem.property)
compute_mw() (in module schrodinger.application.medchem.property)
compute_net_charge_correction() (in module schrodinger.application.desmond.fep_net_charge)
compute_net_charge_corrections() (in module schrodinger.application.desmond.fep_net_charge)
compute_num_hbond_acceptors() (in module schrodinger.application.medchem.property)
compute_num_hbond_donors() (in module schrodinger.application.medchem.property)
compute_num_rot_bonds() (in module schrodinger.application.medchem.property)
compute_polar_surf_area() (in module schrodinger.application.medchem.property)
compute_rip_correction() (in module schrodinger.application.desmond.fep_net_charge)
compute_rmse() (in module schrodinger.application.desmond.correlation_tau)
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_title() (in module schrodinger.application.medchem.property)
computeContextSensitiveRuleFOLLOW() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
computeErrorRecoverySet() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
ComputeGradients (class in schrodinger.energy)
ComputeRequirement (class in schrodinger.job.resource)
computeTokenTypes() (in module schrodinger.application.desmond.antlr3.treewizard)
ComputeTopologicalIds() (in module schrodinger.application.desmond.packages.msys)
ComputeType (class in schrodinger.job.resource)
concat() (in module schrodinger.application.desmond.packages.traj)
Concentration (class in schrodinger.structutils.rgroup_enumerate)
cond_1d_dist_mat() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
(schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
CONFGEN (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute)
ConfidenceInterval (class in schrodinger.application.desmond.correlation_tau)
Config (class in schrodinger.application.vss.config)
config (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableFile attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.Makefile attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
ConfigError
configure_local_ssh_setup() (in module schrodinger.utils.sshconfig)
ConformerRmsd (class in schrodinger.structutils.rmsd)
ConformerRmsdX (class in schrodinger.structutils.rmsd)
ConfRestraintType (class in schrodinger.application.desmond.constants)
connect (schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup attribute)
connect() (in module schrodinger.structutils.build)
connect_variable_attachment_points() (in module schrodinger.livedesign.preprocessor)
CONNECTED (schrodinger.application.desmond.packages.restraint.builder.GeneratorType attribute)
ConnectedMoleculeChain (class in schrodinger.analysis.substructure)
connectNotify() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
CONSENSUS (schrodinger.application.msv.gui.homology_modeling.constants.Mode attribute)
ConsensusConfig (class in schrodinger.application.prime.wrapper)
CONST (class in schrodinger.application.desmond.envir)
CONST_ACTIONS (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
CONSTANT_AXIS_A (schrodinger.application.desmond.constants.IsotropyPolicy attribute)
CONSTANT_AXIS_B (schrodinger.application.desmond.constants.IsotropyPolicy attribute)
CONSTANT_AXIS_C (schrodinger.application.desmond.constants.IsotropyPolicy attribute)
constant_fold() (schrodinger.application.desmond.enhsamp.Bind method)
(schrodinger.application.desmond.enhsamp.FcnCall method)
(schrodinger.application.desmond.enhsamp.If method)
(schrodinger.application.desmond.enhsamp.Iter method)
(schrodinger.application.desmond.enhsamp.Let method)
(schrodinger.application.desmond.enhsamp.Lit method)
(schrodinger.application.desmond.enhsamp.Node method)
(schrodinger.application.desmond.enhsamp.Series method)
(schrodinger.application.desmond.enhsamp.String method)
(schrodinger.application.desmond.enhsamp.Var method)
CONSTANT_PH (schrodinger.application.desmond.constants.PRODUCT attribute)
Constants (class in schrodinger.application.desmond.constants)
Constraint (class in schrodinger.application.desmond.cms)
(class in schrodinger.forcefield.minimizer)
ConstraintFormatError
constraints (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
construct_lists() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
constructHostArg() (schrodinger.job.launchparams.LaunchParameters method)
consume() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer method)
consumeCommandLine() (schrodinger.job.launchparams.LaunchParameters method)
consumeHiddenToken() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
consumeInitialHiddenTokens() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
consumeNode() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
consumeToken() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
consumeUntil() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
CONTACT_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
contains() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.utils.preferences.Preferences method)
contentsMargins() (schrodinger.ui.dendrogram.DendrogramView method)
contentsRect() (schrodinger.ui.dendrogram.DendrogramView method)
contextMenuEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
contextMenuPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
ConvCriteria (class in schrodinger.application.jaguar.results)
Conversion (class in schrodinger.application.desmond.constants)
conversion_maps_builder() (in module schrodinger.application.matsci.qeschema.qeschema.converters)
(in module schrodinger.application.matsci.qexsd.qespresso.converters)
convert() (in module schrodinger.livedesign.convert)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.models.adapters.abstractadapter.AbstractAdapter class method)
(schrodinger.models.adapters.inputconfig.ParamToConfigObj class method)
(schrodinger.models.adapters.inputconfig.ParamToInputConfig class method)
convert_arg_line_to_args() (schrodinger.utils.compare.DiffCompareArgumentParser method)
convert_attachment_point() (in module schrodinger.structutils.rgroup_enumerate)
convert_diff_token_to_float() (in module schrodinger.utils.compare)
convert_file() (in module schrodinger.infra.epydoc_to_sphinx)
convert_fragment_from_v3000() (in module schrodinger.structutils.markush_enumerate)
convert_gaps_to_dots() (in module schrodinger.application.prime.wrapper)
convert_gaps_to_tildes() (in module schrodinger.application.prime.wrapper)
convert_gibbs_energy_to_std_conc() (in module schrodinger.application.jaguar.utils)
convert_heavy_hydrogens() (in module schrodinger.livedesign.preprocessor)
convert_helm1_to_helm2() (in module schrodinger.protein.helm)
convert_log_to_exception() (in module schrodinger.rdkit.rdkit_adapter)
convert_scaffold_from_v3000() (in module schrodinger.structutils.markush_enumerate)
convert_sparse_dict_to_list() (in module schrodinger.application.mopac.utils)
convert_string() (in module schrodinger.infra.mmim)
convert_to_gids() (schrodinger.application.desmond.cms.Cms method)
convert_to_local_timezone() (in module schrodinger.application.job_monitor.util)
convert_to_molblock() (in module schrodinger.livedesign.preprocessor)
convert_value() (schrodinger.utils.singledashoptionparser.SingleDashOption method)
convertSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
convertToEnv() (schrodinger.job.launchparams.LaunchParameters method)
convertToJLaunchOptions() (schrodinger.job.launchparams.LaunchParameters method)
ConvertToRdkit() (in module schrodinger.application.desmond.packages.msys)
convertToStatic() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
CoordinateFrame (schrodinger.analysis.visanalysis.volumedata.VolumeData property)
Coordinates (class in schrodinger.adapter)
Coordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
coords_all_zero() (in module schrodinger.livedesign.preprocessor)
Copy (schrodinger.adapter.Coordinates attribute)
(schrodinger.adapter.Properties attribute)
(schrodinger.adapter.StereoChemistry attribute)
copy() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.application.desmond.packages.traj.Frame method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmbitset.Bitset method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.project.surface.ProjectSurface method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
(schrodinger.structutils.color.ColorScheme method)
(schrodinger.surface.Surface method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.scollections.IdSet method)
(schrodinger.utils.sea.sea.List method)
copy_and_compress_files() (in module schrodinger.application.desmond.util)
copy_csv_file() (in module schrodinger.rdkit.molio)
copy_custom_config_file() (in module schrodinger.utils.postinstall)
copy_customized_files() (in module schrodinger.utils.postinstall)
copy_from() (schrodinger.utils.sea.evalor.Evalor method)
copy_lewis_structure_and_hydrogens() (in module schrodinger.livedesign.preprocessor)
copy_structure_bonding() (in module schrodinger.application.jaguar.utils)
copyReagentFile() (schrodinger.application.pathfinder.reaction.ReagentClass method)
copySchemeColors() (schrodinger.structutils.color.ColorScheme method)
copySelectionFrom() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
COREHOPPING (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute)
cornerWidget() (schrodinger.ui.dendrogram.DendrogramView method)
CORR_ENERGY (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute)
correct_sgroup_coordinates() (in module schrodinger.livedesign.preprocessor)
CorrectionTerm (class in schrodinger.application.desmond.constants)
correlate_to_reference_file_workup() (in module schrodinger.test.stu.outcomes.correlate_to_reference_file)
correlate_workup() (in module schrodinger.test.stu.outcomes.correlate_workup)
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)
CosSinAngle() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
coulomb (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault property)
count (schrodinger.application.licensing.licerror.LicenseError property)
count() (in module schrodinger.application.macromodel.tools)
(schrodinger.application.canvas.topo_descriptors.Descriptor method)
(schrodinger.application.dendrogram.core_class.GetPartitions.NameList method)
(schrodinger.application.dendrogram.core_class.RingSysInfo method)
(schrodinger.application.desmond.arkdb.ForEachDo method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.desmond.fep_edge_data.ResData method)
(schrodinger.application.desmond.packages.timer.Timer.Args method)
(schrodinger.application.jaguar.basis.BasisSet method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.application.jaguar.utils.ChgAt method)
(schrodinger.application.jaguar.utils.FreeEnergy method)
(schrodinger.application.jaguar.utils.LewisStructure method)
(schrodinger.application.licensing.licadmin.stat_info method)
(schrodinger.application.licensing.lmgrd_log_parser.event method)
(schrodinger.application.livedesign.login.Version method)
(schrodinger.application.matsci.cache.CacheInfo method)
(schrodinger.application.matsci.codeutils.ModuleInfo method)
(schrodinger.application.matsci.nano.space_groups.SpaceGroup method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo method)
(schrodinger.application.scaffold_enumeration.cxsmiles.MCG method)
(schrodinger.application.scaffold_enumeration.cxsmiles.SRU method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup method)
(schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup method)
(schrodinger.forcefield.ffld_options.ForceFieldOptions method)
(schrodinger.forcefield.ffld_options.MinimizationOptions method)
(schrodinger.infra.mmbitset.Bitset method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.job.server.ServerInfo method)
(schrodinger.livedesign.preprocessor.PreprocessorOptions method)
(schrodinger.math.multi_parameter_optimization.Transition method)
(schrodinger.models.diffy.DictDiff method)
(schrodinger.models.diffy.ListDiff method)
(schrodinger.models.diffy.SetDiff method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableTuple method)
(schrodinger.pipeline.pipeio.Structures method)
(schrodinger.protein.tasks.structure_alignment.StructAlignResult method)
(schrodinger.rdkit.substructure.QueryOptions method)
(schrodinger.structutils.markush_enumerate.PlaceHolder method)
(schrodinger.structutils.rgroup_enumerate.RGroup method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
(schrodinger.utils.sea.sea.List method)
count_atoms_in_smarts() (in module schrodinger.structutils.analyze)
count_heavy_atoms() (in module schrodinger.application.desmond.r_group_asl)
count_lines() (in module schrodinger.utils.fileutils)
count_overrides() (in module schrodinger.application.desmond.packages.msys.vdw)
count_structures() (in module schrodinger.structure)
(schrodinger.application.vss.database.Database method)
Counter (class in schrodinger.application.desmond.util)
countHeavyAtoms() (in module schrodinger.application.desmond.r_group_asl)
countRoots() (in module schrodinger.pipeline.pipeutils)
countTestCases() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
COVALENT_LIGAND (schrodinger.application.desmond.constants.FEP_TYPES attribute)
CovalentDockingComplexes (class in schrodinger.application.livedesign.entry_types)
CovalentFEPEdgeData (class in schrodinger.application.desmond.fep_edge_data)
CPU (schrodinger.job.resource.ComputeType attribute)
cpx_charge (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_forward (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_forward_dg (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_end_time_ns (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_ensemble (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_ff (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_rest_exchanges (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_result (schrodinger.application.desmond.fep_edge_data.FEPTorsions property)
cpx_salt_info (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_salt_molecules (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_sid_lp_results (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_sid_pl_results (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_sid_protein_residues (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_sid_snapshot_times_ps (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_sim_time (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_start_time_ns (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_temperature (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_timestep_interval (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_timestep_list (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_total_atoms (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_total_replicas (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
cpx_total_waters (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
create() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreeWizard method)
(schrodinger.ui.dendrogram.DendrogramView method)
create_archive_file() (in module schrodinger.application.licensing.licadmin)
create_argparse_namespace() (in module schrodinger.application.phase.packages.phase_option_utils)
create_blast_db() (in module schrodinger.protein.gpcr.update_gpcr_db)
create_chmmol_from_structure() (in module schrodinger.structutils.analyze)
create_cms_from_mae() (in module schrodinger.application.desmond.repair_cms)
create_config_dir() (in module schrodinger.utils.postinstall)
create_conn() (in module schrodinger.protein.gpcr.sql)
create_csv() (in module schrodinger.application.livedesign.io_utils)
create_distance_cell() (in module schrodinger.structutils.measure)
create_entry_database() (in module schrodinger.protein.gpcr.update_gpcr_db)
create_fragment() (in module schrodinger.test.build_test_structures)
create_fragment_structure() (in module schrodinger.structutils.rgroup_enumerate)
create_full_system_from_comp() (in module schrodinger.application.desmond.repair_cms)
create_hard_link() (in module schrodinger.utils.fileutils)
create_header() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils)
create_hypo (schrodinger.application.phase.input.InputSpecs attribute)
create_isosurface_from_grid_data() (in module schrodinger.surface)
create_new_structure() (in module schrodinger.structure)
create_nx_graph() (in module schrodinger.structutils.analyze)
create_oligomer() (in module schrodinger.application.matsci.mlearn.descriptor)
create_reactant_fp_file() (in module schrodinger.application.combinatorial_screen.fingerprint_utils)
create_sim_cormat() (in module schrodinger.application.combinatorial_diversity.splitter_utils)
create_stub_license() (in module schrodinger.application.licensing.licadmin)
create_surface() (in module schrodinger.application.bioluminate.surfcomp)
create_xvol (schrodinger.application.phase.input.InputSpecs attribute)
createExcludedVolumeClash() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method)
createExcludedVolumeReceptor() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method)
createExcludedVolumeShell() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method)
createFromToken() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
createFromType() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
createItemGroup() (schrodinger.ui.dendrogram.DendrogramScene method)
CreateLike() (in module schrodinger.analysis.visanalysis.volumedatautils)
createMatMinerDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
createMols() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
createMorganDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
createNode() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
CreateParamTable() (in module schrodinger.application.desmond.packages.msys)
createPolymerDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
createRdkitDescriptors() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
CreateSystem() (in module schrodinger.application.desmond.packages.msys)
createToken() (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
CreateWhenNeeded (class in schrodinger.infra.util)
createWindowContainer() (schrodinger.ui.dendrogram.DendrogramView method)
createWithPayload() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
Criterion (class in schrodinger.ui.qt.filter_dialog_dir.filter_core)
(class in schrodinger.utils.ligfilter)
CriterionParser (class in schrodinger.utils.ligfilter)
criticalEllipse() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
cross() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
CROSS_ENERGY_ONLY (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute)
CrossLinkGenerationError
CrossLinkRestraint (class in schrodinger.application.desmond.packages.restraint.cross_link)
CrossLinkRestraintCentroid (class in schrodinger.application.desmond.packages.restraint.cross_link)
CrossLinkRestraintInteraction (class in schrodinger.application.desmond.packages.restraint.cross_link)
crossprod() (in module schrodinger.application.desmond.cms)
CrsAng() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
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)
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)
CS_METHOD (class in schrodinger.application.jaguar.csrch_input_constants)
csv (schrodinger.utils.fileutils.SeqFormat attribute)
csv_mol_reader_class (schrodinger.rdkit.molio.PfxMolIterator attribute)
(schrodinger.rdkit.molio.PfxMolReader attribute)
CsvMergeHandler (class in schrodinger.rdkit.molio)
CsvMolIterator (class in schrodinger.rdkit.molio)
CsvMolReader (class in schrodinger.rdkit.molio)
CsvMolWriter (class in schrodinger.rdkit.molio)
Ct (class in schrodinger.application.desmond.packages.msys)
ct (schrodinger.application.desmond.packages.msys.Chain property)
(schrodinger.application.desmond.packages.restraint.builder.AtomID attribute)
ct() (schrodinger.application.desmond.packages.msys.System method)
CtAssertion
CtAtoms() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util)
CtBonds() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util)
CtException
CtMsgException
CtRdrException
cts (schrodinger.application.desmond.packages.msys.System property)
CUBIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute)
CURRENT (schrodinger.trajectory.trajectory_gui_dir.display_settings_data.DisplayOnly attribute)
current_filename (schrodinger.structure.MultiFileStructureReader attribute)
CURRENT_FRAME_WITH_COMPONENT_CTS (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute)
current_user() (schrodinger.application.matsci.qb_sdk.client.QubecClient method)
currentRMSD() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method)
currsize (schrodinger.application.matsci.cache.CacheInfo attribute)
cursor() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
curvatures() (schrodinger.project.surface.ProjectSurface method)
(schrodinger.surface.Surface method)
CUSTOM (schrodinger.job.launchparams.ProjectDisposition attribute)
Custom (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
custom() (in module schrodinger.ui.qt.appframework2.appmethods)
CUSTOM_CHARGE_MODE (class in schrodinger.application.desmond.constants)
custom_config_file_exists() (in module schrodinger.utils.postinstall)
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_SELECTION (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute)
CustomAngles (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
CustomConfigFiles (class in schrodinger.utils.postinstall)
customContextMenuRequested (schrodinger.ui.dendrogram.DendrogramView attribute)
customEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
customizeFuncResult() (schrodinger.utils.funcchains.FuncChainMarker method)
CustomMaestroAnalysis (class in schrodinger.application.desmond.packages.staf)
CustomUnpickler (class in schrodinger.application.desmond.picklejar)
Cut (class in schrodinger.application.qsite.input)
cutoffLength (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute)
CXSMILES (schrodinger.livedesign.convert.Format attribute)
D
D (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
D1d (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
darken_colors_by_cavity_depth (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
DarkModeColors (class in schrodinger.ui.qt.standard.colors)
data (schrodinger.application.desmond.packages.msys.molfile.Grid property)
DATA (schrodinger.job.util.DirectoryType attribute)
data() (schrodinger.application.desmond.packages.msys.Atom method)
(schrodinger.application.desmond.packages.msys.Bond method)
(schrodinger.application.desmond.packages.msys.Chain method)
(schrodinger.application.desmond.packages.msys.Ct method)
(schrodinger.application.desmond.packages.msys.Residue method)
(schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
data_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
data_name (schrodinger.application.livedesign.data_classes.LDData property)
Database (class in schrodinger.application.vss.database)
DATABASES (schrodinger.infra.licensing.SimilarityEndpoint attribute)
databaseType (schrodinger.job.server.ServerInfo attribute)
dataName() (schrodinger.structure.PropertyName method)
DataPointLocator (class in schrodinger.analysis.visanalysis.volumedatautils)
DATE_RE (in module schrodinger.test.stu.common)
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)
dbg (schrodinger.application.desmond.antlr3.debug.DebugParser property)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream property)
dbscan_cluster() (in module schrodinger.math.mathutils)
ddg_corrections_map (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ddg_corrections_sum (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
debug() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
(schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
debug_func() (in module schrodinger.ui.qt.appframework2.debugcore)
debug_func_args() (in module schrodinger.ui.qt.appframework2.debugcore)
debug_mols() (in module schrodinger.application.pathfinder.reaction)
debug_outfile (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
debug_print() (in module schrodinger.utils.sea.common)
DebugEventListener (class in schrodinger.application.desmond.antlr3.debug)
DebugEventSocketProxy (class in schrodinger.application.desmond.antlr3.debug)
DebugParser (class in schrodinger.application.desmond.antlr3.debug)
debugPrint() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method)
debugReactants() (schrodinger.application.pathfinder.reaction.Reaction method)
DebugStderr (class in schrodinger.ui.qt.appframework2.debugcore)
DebugStdout (class in schrodinger.ui.qt.appframework2.debugcore)
DebugTokenStream (class in schrodinger.application.desmond.antlr3.debug)
DebugTreeAdaptor (class in schrodinger.application.desmond.antlr3.debug)
decl() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
decl_meta() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
decl_output() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
decode() (in module schrodinger.models.json)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDComplexType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method)
decode_atom_ids() (in module schrodinger.application.desmond.packages.restraint.builder)
decode_to_server_info() (in module schrodinger.job.server)
decomp_rawfep_structure() (in module schrodinger.application.desmond.cms)
decompose_to_comp_ct() (in module schrodinger.application.desmond.repair_cms)
decrypt_cms() (in module schrodinger.application.matsci.enc)
dedent() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
deduplicate_xy_data() (in module schrodinger.math.mathutils)
DEE_Backtracking (class in schrodinger.application.canvas.r_group_dee)
DEE_EnergyMatrix (class in schrodinger.application.canvas.r_group_dee)
Deepest0 (class in schrodinger.application.dendrogram.core_class)
Deepest1 (class in schrodinger.application.dendrogram.core_class)
Deepest2 (class in schrodinger.application.dendrogram.core_class)
Deepest3a (class in schrodinger.application.dendrogram.core_class)
Deepest3b (class in schrodinger.application.dendrogram.core_class)
Deepest4 (class in schrodinger.application.dendrogram.core_class)
Deepest5 (class in schrodinger.application.dendrogram.core_class)
Deepest6 (class in schrodinger.application.dendrogram.core_class)
DEFAULT (schrodinger.application.desmond.constants.REST_REGION_RULE attribute)
(schrodinger.application.desmond.constants.Schedule attribute)
(schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute)
default (schrodinger.application.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.forcefield.constants.GeometryOptMethod attribute)
default_accounter() (in module schrodinger.application.desmond.starter.starter)
DEFAULT_ATOM_TYPING_SCHEMES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI attribute)
default_custom_fraglib() (in module schrodinger.utils.cgxutils)
DEFAULT_DEBUGGER_PORT (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy attribute)
default_factory (schrodinger.application.desmond.cms.RestrainGroupContainer attribute)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute)
DEFAULT_INPUT_BUILDER (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument attribute)
default_logging_config() (in module schrodinger.utils.log)
DEFAULT_PROGRAM_NAME (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream attribute)
DEFAULT_SCHEMA (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument attribute)
DEFAULT_START_FRAME (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
DEFAULT_TOKEN_CHANNEL (schrodinger.application.desmond.antlr3.debug.DebugParser attribute)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Lexer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Parser attribute)
(schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DEFAULT_TOLERANCE (in module schrodinger.test.stu.outcomes.compare_csv)
DEFAULT_TRANSPARENCY (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings attribute)
DefaultFactoryDict (class in schrodinger.utils.scollections)
DefaultFactoryDictMixin (class in schrodinger.utils.scollections)
DefaultIdDict (class in schrodinger.utils.scollections)
defaultTestResult() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
Definition (class in schrodinger.utils.ligfilter)
DEFINITION_ID (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
definition_id (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
DefinitionParser (class in schrodinger.utils.ligfilter)
degree() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method)
del_from() (schrodinger.application.desmond.arkdb.Datum method)
(schrodinger.application.desmond.task.Option method)
(schrodinger.application.desmond.task.Premise method)
del_key() (schrodinger.utils.sea.sea.Map method)
delAtomProp() (schrodinger.application.desmond.packages.msys.System method)
delAtoms() (schrodinger.application.desmond.packages.msys.System method)
delAuxTable() (schrodinger.application.desmond.packages.msys.System method)
delBondProp() (schrodinger.application.desmond.packages.msys.System method)
delBonds() (schrodinger.application.desmond.packages.msys.System method)
delCatalogEntry() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
delChains() (schrodinger.application.desmond.packages.msys.System method)
DelegatingIndentedHelpFormatter (class in schrodinger.utils.singledashoptionparser)
delete() (in module schrodinger.Qt.PyQt6.sip)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.arkdb.ArkDb method)
(schrodinger.application.desmond.multisim.parser.Msj method)
(schrodinger.project.surface.ProjectSurface method)
(schrodinger.structure._StructureBond method)
(schrodinger.surface.Surface method)
delete_all_atom_group() (schrodinger.application.desmond.cms.Cms method)
delete_atom() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
delete_atom_group() (schrodinger.application.desmond.cms.Cms method)
delete_bonds() (in module schrodinger.structutils.build)
delete_bonds_to_atoms() (in module schrodinger.structutils.build)
delete_fepio() (in module schrodinger.application.desmond.cms)
delete_hydrogens() (in module schrodinger.structutils.build)
delete_zobs() (in module schrodinger.structutils.build)
deleteAllRestraints() (schrodinger.structutils.minimize.Minimizer method)
deleteAllRows() (schrodinger.infra.table.Table method)
deleteAtoms() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
deleteAttr() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
deleteBond() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure._StructureAtom method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
deleteChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
deleteColumn() (schrodinger.infra.table.Table method)
deleteDefaultColorRule() (schrodinger.structutils.color.ColorScheme method)
deleteFile() (schrodinger.structutils.color.ColorScheme method)
deleteLater() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
DeleteOp (class in schrodinger.application.desmond.antlr3.streams)
deleteProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
deleteProp() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
deletePropertyFromAllAtoms() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
deleteRow() (schrodinger.infra.table.Table method)
deleteSite() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
deleteSiteFast() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
deletion_penalty (schrodinger.structutils.structalign.StructAlign property)
delimiter (schrodinger.application.canvas.utils.chm_bluebird attribute)
(schrodinger.application.canvas.utils.chm_excel attribute)
delKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method)
delProp() (schrodinger.application.desmond.packages.msys.ParamTable method)
delResidues() (schrodinger.application.desmond.packages.msys.System method)
delta (schrodinger.application.bindingsite.cavutils.Grid property)
DELTA_2022_1 (schrodinger.energy.QRNNModel attribute)
delta_delta_g (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
DELTA_TRANSFER_2022_1 (schrodinger.energy.QRNNModel attribute)
delTermProp() (schrodinger.application.desmond.packages.msys.TermTable method)
delTermsWithAtom() (schrodinger.application.desmond.packages.msys.TermTable method)
delViewerPreference() (schrodinger.application.desmond.rl_helper.NumberedCanvas 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)
DendrogramGraphicNode (class in schrodinger.ui.dendrogram)
DendrogramGraphicNode.CacheMode (class in schrodinger.ui.dendrogram)
DendrogramGraphicNode.GraphicsItemChange (class in schrodinger.ui.dendrogram)
DendrogramGraphicNode.GraphicsItemFlag (class in schrodinger.ui.dendrogram)
DendrogramGraphicNode.PanelModality (class in schrodinger.ui.dendrogram)
DendrogramGraphicNodeLabel (class in schrodinger.ui.dendrogram)
DendrogramGraphicNodeLabel.CacheMode (class in schrodinger.ui.dendrogram)
DendrogramGraphicNodeLabel.GraphicsItemChange (class in schrodinger.ui.dendrogram)
DendrogramGraphicNodeLabel.GraphicsItemFlag (class in schrodinger.ui.dendrogram)
DendrogramGraphicNodeLabel.PanelModality (class in schrodinger.ui.dendrogram)
DendrogramGraphicTree (class in schrodinger.ui.dendrogram)
DendrogramGraphicTree.CacheMode (class in schrodinger.ui.dendrogram)
DendrogramGraphicTree.GraphicsItemChange (class in schrodinger.ui.dendrogram)
DendrogramGraphicTree.GraphicsItemFlag (class in schrodinger.ui.dendrogram)
DendrogramGraphicTree.PanelModality (class in schrodinger.ui.dendrogram)
DendrogramGraphicTreeCoordinatesPreferences (class in schrodinger.ui.dendrogram)
DendrogramNode (class in schrodinger.ui.dendrogram)
DendrogramNodeBFIterator (class in schrodinger.ui.dendrogram)
DendrogramScene (class in schrodinger.ui.dendrogram)
DendrogramScene.ItemIndexMethod (class in schrodinger.ui.dendrogram)
DendrogramScene.SceneLayer (class in schrodinger.ui.dendrogram)
DendrogramTreeBuilder (class in schrodinger.ui.dendrogram)
DendrogramView (class in schrodinger.ui.dendrogram)
DendrogramView.CacheModeFlag (class in schrodinger.ui.dendrogram)
DendrogramView.DragMode (class in schrodinger.ui.dendrogram)
DendrogramView.OptimizationFlag (class in schrodinger.ui.dendrogram)
DendrogramView.PaintDeviceMetric (class in schrodinger.ui.dendrogram)
DendrogramView.RenderFlag (class in schrodinger.ui.dendrogram)
DendrogramView.Shadow (class in schrodinger.ui.dendrogram)
DendrogramView.Shape (class in schrodinger.ui.dendrogram)
DendrogramView.SizeAdjustPolicy (class in schrodinger.ui.dendrogram)
DendrogramView.StyleMask (class in schrodinger.ui.dendrogram)
DendrogramView.ViewportAnchor (class in schrodinger.ui.dendrogram)
DendrogramView.ViewportUpdateMode (class in schrodinger.ui.dendrogram)
deprecate() (in module schrodinger.application.matsci.codeutils)
deprecate_module() (in module schrodinger.utils.deprecation)
deprecated() (in module schrodinger.utils.deprecation)
DeprecationError
depth() (schrodinger.ui.dendrogram.DendrogramView method)
DerivedAttrs (class in schrodinger.application.jaguar.results)
desalt_structure() (in module schrodinger.structutils.build)
description (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.IndividualStructureBase attribute)
(schrodinger.application.livedesign.entry_types.Ligands attribute)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute)
(schrodinger.application.livedesign.entry_types.TargetlessBase attribute)
Descriptor (class in schrodinger.application.canvas.topo_descriptors)
DESCRIPTORS (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor attribute)
deserialize() (schrodinger.application.desmond.picklejar.PickleJar static method)
deserialize_bernoulli_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_compact() (in module schrodinger.application.phase.packages.conformer_storage)
deserialize_complement_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_conformations() (in module schrodinger.utils.cgxutils)
deserialize_csr_matrix() (in module schrodinger.application.matsci.mlearn.sklearn_json.csr)
deserialize_decision_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_decision_tree_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
deserialize_gaussian_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_gradient_boosting() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_gradient_boosting_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
deserialize_label_binarizer() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_lasso_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
deserialize_lda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_linear_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
deserialize_logistic_regression() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_lossless() (in module schrodinger.application.phase.packages.conformer_storage)
deserialize_mlp() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_mlp_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
deserialize_model() (in module schrodinger.application.matsci.mlearn.sklearn_json)
deserialize_multinomial_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_params_random_state() (in module schrodinger.application.matsci.mlearn.sklearn_json.common)
deserialize_pca() (in module schrodinger.application.matsci.mlearn.sklearn_json.decomposition)
deserialize_perceptron() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_qda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_random_forest() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_random_forest_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
deserialize_ridge_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
deserialize_svm() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
deserialize_svr() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
deserialize_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
(in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
Desmond
DESMOND (schrodinger.energy.ANIModel attribute)
desmond_build_version() (in module schrodinger.application.desmond.bld_ver)
DESMOND_DATA_DIR (schrodinger.application.desmond.envir.CONST attribute)
DESMOND_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute)
DESMOND_LIB_DIR (schrodinger.application.desmond.envir.CONST attribute)
DESMOND_VERSION (schrodinger.application.desmond.envir.CONST attribute)
destroy() (schrodinger.ui.dendrogram.DendrogramView method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
destroyed (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramView attribute)
destroyItemGroup() (schrodinger.ui.dendrogram.DendrogramScene method)
determinant() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
determine_jobtype() (in module schrodinger.application.inputconfig)
DeviceCoordinateCache (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.CacheMode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.CacheMode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.CacheMode attribute)
devicePixelRatio() (schrodinger.ui.dendrogram.DendrogramView method)
devicePixelRatioF() (schrodinger.ui.dendrogram.DendrogramView method)
devicePixelRatioFScale() (schrodinger.ui.dendrogram.DendrogramView method)
deviceTransform() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
devType() (schrodinger.ui.dendrogram.DendrogramView method)
DFA (class in schrodinger.application.desmond.antlr3.dfa)
DFA12_accept (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
DFA12_eof (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
DFA12_eot (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
DFA12_max (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
DFA12_min (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
DFA12_special (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
DFA12_transition (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
DFA15_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA15_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA15_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA15_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA15_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA15_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA15_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA17_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA17_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA17_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA17_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA17_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA17_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA17_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA18_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA18_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA18_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA18_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA18_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA18_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA18_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA19_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA19_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA19_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA19_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA19_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA19_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA19_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA1_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA1_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA1_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA1_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA1_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA1_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA1_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA20_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA20_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA20_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA20_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA20_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA20_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA20_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA21_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA21_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA21_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA21_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA21_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA21_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA21_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA22_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA22_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA22_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA22_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA22_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA22_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA22_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA24_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA24_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA24_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA24_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA24_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA24_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA24_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA25_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA25_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA25_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA25_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA25_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA25_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
DFA25_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
dfs() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
DFT (schrodinger.forcefield.constants.GeometryOptMethod attribute)
diagonalize_symmat() (in module schrodinger.application.combinatorial_diversity.splitter_utils)
dict() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
Dict2Values() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
dict_to_xml() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree)
DictDiff (class in schrodinger.models.diffy)
dictKeys() (schrodinger.application.canvas.utils.ChmCSVTools method)
DictRestrainGroup (class in schrodinger.application.desmond.cms)
dictValues() (schrodinger.application.canvas.utils.ChmCSVTools method)
dielectric_constant (schrodinger.structutils.minimize.Minimizer property)
diff (schrodinger.application.desmond.packages.restraint.utils.CentroidData attribute)
diff() (in module schrodinger.utils.sea.sea)
(schrodinger.application.jaguar.results.DerivedAttrs method)
(schrodinger.application.jaguar.results.JaguarAtomicResults method)
(schrodinger.application.jaguar.results.JaguarResults method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
DiffCompareArgumentParser (class in schrodinger.utils.compare)
difference() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
difference_update() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
dih (schrodinger.application.desmond.torsion_related.TorsionPotential attribute)
DIMENSIONALITY (class in schrodinger.application.matsci.msconst)
DIPEPTIDE_SASA (schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceAreaByResidue attribute)
Dipole (class in schrodinger.application.desmond.packages.analysis)
(class in schrodinger.application.jaguar.results)
dipole() (in module schrodinger.application.mopac.results_main)
dipole_esp() (in module schrodinger.application.mopac.results_main)
dipole_strength_precision (schrodinger.application.jaguar.results.NormalMode attribute)
dipole_xyz() (in module schrodinger.application.mopac.results_main)
DipoleDirector (class in schrodinger.application.desmond.packages.analysis)
DIRECT_2022_1 (schrodinger.energy.QRNNModel attribute)
DIRECT_TRANSFER_2022_3 (schrodinger.energy.QRNNModel attribute)
Direction (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data)
DirectoryType (class in schrodinger.job.util)
dis_solvent_correction() (in module schrodinger.application.desmond.fep_net_charge)
Disable (schrodinger.adapter.Canonicalize attribute)
(schrodinger.adapter.Generate2DCoordinates attribute)
(schrodinger.adapter.LabelAtoms attribute)
(schrodinger.adapter.Sanitize attribute)
(schrodinger.adapter.UniqueFilter attribute)
(schrodinger.energy.ComputeGradients attribute)
disable_feature_flag (class in schrodinger.test.decorate_fflag)
disable_interspersed_args() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
disable_mmerr (class in schrodinger.infra.mmerr)
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)
DisabledSymmetryWarning
disableDyncalc() (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.CatPiFinder 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.DipoleDirector method)
(schrodinger.application.desmond.packages.analysis.Distance 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.MassAvgVel 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.MoleculeWiseCom method)
(schrodinger.application.desmond.packages.analysis.MomentOfInertia method)
(schrodinger.application.desmond.packages.analysis.MomentOfInertiaDirector method)
(schrodinger.application.desmond.packages.analysis.OrderParameter method)
(schrodinger.application.desmond.packages.analysis.PiPiFinder 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.ProteinRMSF 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.SystemDipoleDirector 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.CompositeAnalyzer method)
(schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer 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.MaestroAnalysis method)
(schrodinger.application.desmond.packages.staf.UpdatedCmsFsysCtAnalysis method)
discard() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
discardTokenType() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
disconnect() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
disconnectNotify() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
discover_leaks() (in module schrodinger.test.memtest)
disown() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.infra.mmerr.Capture method)
(schrodinger.infra.structure.TextBlockReader method)
(schrodinger.infra.structure.TextBlockWriter method)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter method)
(schrodinger.structutils.color.ColorScheme method)
displacement_prec (schrodinger.application.jaguar.results.ConvCriteria attribute)
displayLabels() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
DisplayOnly (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_data)
displayRecognitionError() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
DisplaySettingsData (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_data)
DisplaySettingsManager (class in schrodinger.trajectory.trajectory_gui_dir.display_settings_manager)
dist3() (in module schrodinger.application.bindingsite.cavutils)
dist_cell_iterator() (in module schrodinger.structutils.measure)
Distance (class in schrodinger.application.desmond.packages.analysis)
DISTANCE (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute)
distance (schrodinger.application.qsite.input.HydrogenCap property)
(schrodinger.structutils.interactions.pi.CationPiInteraction property)
(schrodinger.structutils.interactions.pi.PiPiInteraction property)
distance_from_planckian() (in module schrodinger.application.matsci.colorutils)
DistanceCellIterator (class in schrodinger.structutils.measure)
Distortion (class in schrodinger.structutils.check)
DiversityFingerprinter (class in schrodinger.application.combinatorial_diversity.diversity_fingerprinter)
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)
DoCalibInst() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
DockedPoses (class in schrodinger.application.livedesign.entry_types)
doClassCleanups() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase class method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase class method)
doCleanups() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
doctype() (schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method)
doForm() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
DONOR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
DontAdjustForAntialiasing (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.OptimizationFlag attribute)
DontSavePainterState (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.OptimizationFlag attribute)
DoPeakFit() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
doPropsMatch() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method)
dot (schrodinger.project.surface.ProjectSurface.Style attribute)
(schrodinger.surface.Style attribute)
(schrodinger.surface.Surface.Style attribute)
dot() (schrodinger.pipeline.pipeutils.DotPrinter method)
dotdot (schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
dotdotPattern (schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
DotPrinter (class in schrodinger.pipeline.pipeutils)
dotprod() (in module schrodinger.application.desmond.cms)
DOUBLE (schrodinger.energy.ANIPrecision attribute)
Double (schrodinger.structure.BondType attribute)
doubleEtc (schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
doubleEtcPattern (schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
doublequote (schrodinger.application.canvas.utils.chm_bluebird attribute)
(schrodinger.application.canvas.utils.chm_excel attribute)
doubleRingAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
DoubleSigmoid (class in schrodinger.math.multi_parameter_optimization)
download_all_entry_data() (in module schrodinger.protein.gpcr.gpcrdb)
download_cif() (in module schrodinger.protein.getpdb)
download_em_map() (in module schrodinger.protein.getpdb)
download_ent() (in module schrodinger.protein.getpdb)
download_fasta() (in module schrodinger.protein.getpdb)
download_file() (in module schrodinger.protein.getpdb)
download_ld_client() (in module schrodinger.application.livedesign.login)
download_nodelocked_license() (in module schrodinger.application.licensing.licadmin)
download_pdb() (in module schrodinger.protein.getpdb)
download_reflection_data() (in module schrodinger.protein.getpdb)
download_server_license() (in module schrodinger.application.licensing.licadmin)
download_sf() (in module schrodinger.protein.getpdb)
dpi (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
dragEnterEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
dragLeaveEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
dragMode() (schrodinger.ui.dendrogram.DendrogramView method)
dragMoveEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
drawAlignedString() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
drawBackground() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
drawBoundary (schrodinger.application.desmond.rl_helper.NumberedCanvas property)
drawCentredString() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
DrawChildren (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.RenderFlag attribute)
drawFixedContents() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
drawForeground() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
drawFrame() (schrodinger.ui.dendrogram.DendrogramView method)
drawImage() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
drawInlineImage() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
drawPath() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
drawRightString() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
drawString() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
drawText() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
drawTree() (schrodinger.ui.dendrogram.DendrogramScene method)
DrawWindowBackground (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.RenderFlag attribute)
dropEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
DRUG_DISCOVERY (schrodinger.application.livedesign.login.LDMode attribute)
DSC (class in schrodinger.application.desmond.arkdb)
Dsp2pos() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
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)
DuckFrame (class in schrodinger.application.desmond.packages.topo)
dummy() (in module schrodinger.application.desmond.starter.starter)
dump() (in module schrodinger.models.json)
(in module schrodinger.Qt.PyQt6.sip)
(schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
dumpObjectInfo() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
dumpObjectTree() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
dumps() (in module schrodinger.models.json)
dup() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
duplicate() (schrodinger.application.desmond.packages.msys.Param method)
duplicate_overrides() (in module schrodinger.application.desmond.packages.msys.vdw)
dupNode() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
dupTree() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
dval (schrodinger.utils.sea.sea.Atom property)
(schrodinger.utils.sea.sea.Hydrogen property)
(schrodinger.utils.sea.sea.List property)
(schrodinger.utils.sea.sea.Map property)
DynamicAslAnalyzer (class in schrodinger.application.desmond.packages.staf)
DynamicPositerAnalyzer (class in schrodinger.application.desmond.packages.staf)
dynamicPropertyNames() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
E
E_f (class in schrodinger.application.desmond.simulation_block_test)
E_k (class in schrodinger.application.desmond.simulation_block_test)
E_x (class in schrodinger.application.desmond.simulation_block_test)
EA2DEBYE (schrodinger.application.desmond.packages.analysis.Dipole attribute)
EarlyExitException
EDA (class in schrodinger.trajectory.prody.pca)
edge (schrodinger.structure._Ring property)
ef_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute)
eff_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute)
effectiveOpacity() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
effectiveWinId() (schrodinger.ui.dendrogram.DendrogramView method)
efp_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute)
efs_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute)
eigenvalues() (in module schrodinger.application.mopac.results_main)
eigenvectors() (in module schrodinger.application.mopac.results_main)
El2EstVol() (in module schrodinger.application.matsci.gsas.GSASIImath)
El2Mass() (in module schrodinger.application.matsci.gsas.GSASIImath)
elapsed (schrodinger.utils.profiling.RecordingTimer property)
(schrodinger.utils.profiling.Timer property)
(schrodinger.utils.timeit.TimeIt property)
element (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.structure._StructureAtom property)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
elements (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
(schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo attribute)
ElemPosition() (in module schrodinger.application.matsci.gsas.GSASIIspc)
eliminatePairs() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
eliminateSingles() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
ellipse() (schrodinger.application.desmond.rl_helper.NumberedCanvas 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)
Email (schrodinger.test.perceptualdiff.Notify attribute)
email_failure_summary() (in module schrodinger.test.perceptualdiff)
embl (schrodinger.utils.fileutils.SeqFormat attribute)
emit() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
emitErrorMessage() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
EMPHASIZED_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
EMPTY (schrodinger.infra.structure.TextBlockReader attribute)
empty() (schrodinger.application.licensing.flexlm.License method)
emptyMethod() (schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
Enable (schrodinger.adapter.Canonicalize attribute)
(schrodinger.adapter.Generate2DCoordinates attribute)
(schrodinger.adapter.LabelAtoms attribute)
(schrodinger.adapter.Sanitize attribute)
(schrodinger.adapter.UniqueFilter attribute)
(schrodinger.energy.ComputeGradients attribute)
enable_account() (in module schrodinger.application.matsci.qb_sdk.api)
enable_deprecated() (in module schrodinger.utils.deprecation)
enable_feature_flag (class in schrodinger.test.decorate_fflag)
enable_interspersed_args() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
enableautoconversion() (in module schrodinger.Qt.PyQt6.sip)
enabledChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
encode() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDComplexType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
encode_extended() (in module schrodinger.application.desmond.gchart)
encode_geometry_xyz() (in module schrodinger.application.matsci.qb_sdk.tools)
encode_simple() (in module schrodinger.application.desmond.gchart)
ENCODING_KEY (schrodinger.models.jsonable.JsonableSet attribute)
(schrodinger.models.jsonable.JsonableTuple attribute)
encrypt_cms() (in module schrodinger.application.matsci.enc)
end() (schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method)
END_OF_DEF_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
end_time (schrodinger.utils.timeit.TimeIt attribute)
endBacktrack() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
endForm() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
endGroup() (schrodinger.utils.preferences.Preferences method)
endResync() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
endswith() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
Energy (class in schrodinger.application.desmond.simulation_block_test)
energy (schrodinger.application.jaguar.results.JaguarResults property)
ENERGY (schrodinger.application.msv.gui.homology_modeling.constants.PrimeMethod attribute)
energy_convergence (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
energy_criterion (schrodinger.structutils.minimize.Minimizer property)
ENERGY_GROUPS (class in schrodinger.application.desmond.constants)
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)
energy_precision_hartree (schrodinger.application.jaguar.results.DerivedAttrs attribute)
EnhancedStereoUpdateMode (class in schrodinger.livedesign.molhash)
Ensemble (class in schrodinger.trajectory.prody.ensemble)
Ensemble_Priority_Queue (class in schrodinger.application.glide.ensemble_selection)
Ensembles (class in schrodinger.application.desmond.constants)
ensembles (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue property)
ensure_file_exists() (in module schrodinger.application.desmond.util)
ensure_localhost_server_running() (in module schrodinger.job.server)
ensure_logger() (in module schrodinger.application.bindingsite.common)
ensurePolished() (schrodinger.ui.dendrogram.DendrogramView method)
ensureVisible() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
enter_context() (schrodinger.utils.env.MultiEnvironmentContext method)
enter_scope() (schrodinger.application.desmond.enhsamp.binding method)
enterAlt() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
enterDecision() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
enterEvent() (schrodinger.ui.dendrogram.DendrogramView method)
enterRule() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
enterSubRule() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
entropy() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
entry (schrodinger.project.surface.ProjectSurface.ColorFrom attribute)
(schrodinger.surface.ColorFrom attribute)
(schrodinger.surface.Surface.ColorFrom attribute)
entry_id (schrodinger.structure._StructureAtom property)
entry_singular (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.IndividualStructureBase attribute)
(schrodinger.application.livedesign.entry_types.Ligands attribute)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute)
(schrodinger.application.livedesign.entry_types.TargetlessBase attribute)
enum_speedup() (in module schrodinger.infra.util)
EnumerableMixin (class in schrodinger.application.scaffold_enumeration.common)
enumerate_rgroups() (in module schrodinger.application.scaffold_enumeration.layered)
Env (class in schrodinger.application.desmond.enhsamp)
env_var_feature_flag_is_set() (in module schrodinger.utils.featureflags.featureflags)
ENVIRONMENT (schrodinger.application.desmond.constants.REST_COMPONENT 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)
EnvVar (class in schrodinger.utils.openmpi)
EOF (schrodinger.application.desmond.antlr3.streams.ANTLRFileStream attribute)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream attribute)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream attribute)
(schrodinger.application.desmond.antlr3.streams.CharStream attribute)
eof() (schrodinger.infra.structure.TextBlockReader method)
EP (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings attribute)
epn_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute)
equal_rotations() (in module schrodinger.application.matsci.nano.space_groups)
equalize_number_waters() (in module schrodinger.application.desmond.gcmc_utils)
equals() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method)
err (schrodinger.utils.sea.evalor.Evalor property)
errno (schrodinger.utils.fileutils.SharingViolationError attribute)
Error (class in schrodinger.job.host_check)
error() (schrodinger.application.desmond.antlr3.dfa.DFA method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25 method)
(schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.ligfilter.CriterionParser method)
(schrodinger.utils.ligfilter.DefinitionParser method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
error_code (schrodinger.utils.license.LicenseStatus property)
error_pattern (schrodinger.infra.mmcheck.ReturnCode attribute)
ERROR_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
errorNode() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
errors (schrodinger.application.desmond.packages.msys.AnnotatedSystem property)
errors() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
ESCAPE (schrodinger.livedesign.molhash.HashLayer attribute)
escapechar (schrodinger.application.canvas.utils.chm_bluebird attribute)
(schrodinger.application.canvas.utils.chm_excel attribute)
escapeNewlines() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
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_NONE (schrodinger.application.jaguar.results.JaguarOptions attribute)
esp_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute)
estate_is_physical() (in module schrodinger.application.jaguar.workflow_validation)
estimate_memory() (in module schrodinger.application.desmond.memory)
eth0_is_missing() (in module schrodinger.application.licensing.licadmin)
etree_iter_path() (in module schrodinger.application.matsci.qeschema.qeschema.utils)
(in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree)
etree_node_to_dict() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree)
etree_to_dict() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree)
ev() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method)
evalColMetadataDicts() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
Evalor (class in schrodinger.utils.sea.evalor)
evaluate_asl() (in module schrodinger.structutils.analyze)
evaluate_matched_list() (in module schrodinger.application.desmond.smarts)
evaluate_multiple_smarts() (in module schrodinger.structutils.analyze)
evaluate_net_smarts() (in module schrodinger.application.desmond.smarts)
evaluate_smarts() (in module schrodinger.structutils.analyze)
evaluate_smarts_by_molecule() (in module schrodinger.structutils.analyze)
evaluate_smarts_canvas() (in module schrodinger.structutils.analyze)
evaluate_substructure() (in module schrodinger.structutils.analyze)
evaluateAsl() (schrodinger.structutils.rmsd.ConformerRmsd method)
(schrodinger.structutils.rmsd.ConformerRmsdX method)
event (class in schrodinger.application.licensing.lmgrd_log_parser)
event() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
eventFilter() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
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)
exchange_acceptance_ratio() (schrodinger.application.desmond.bennett.CalcBAR method)
exclude_amino_acids (schrodinger.structutils.analyze.AslLigandSearcher property)
exclude_ions (schrodinger.structutils.analyze.AslLigandSearcher property)
excludeCommandParser() (schrodinger.application.ligprep.ionizer.Ionizer method)
excluded_residues (schrodinger.structutils.analyze.AslLigandSearcher property)
ExcludedVolumeGenerator (class in schrodinger.application.phase.create_xvol)
excludes() (schrodinger.utils.ligfilter.Definition method)
EXEC (schrodinger.job.util.DirectoryType attribute)
ExecutableFile (class in schrodinger.test.pytest.exetest)
ExecutableFile.CollectError
ExecutableTest (class in schrodinger.test.pytest.exetest)
execute() (in module schrodinger.application.desmond.task)
(in module schrodinger.application.matsci.qb_sdk.api)
(schrodinger.application.desmond.antlr3.streams.DeleteOp method)
(schrodinger.application.desmond.antlr3.streams.InsertBeforeOp method)
(schrodinger.application.desmond.antlr3.streams.ReplaceOp method)
(schrodinger.application.desmond.antlr3.streams.RewriteOperation method)
(schrodinger.application.desmond.task.ParchTrajectoryForAbsoluteFep method)
(schrodinger.application.desmond.task.ParchTrajectoryForFep method)
(schrodinger.application.desmond.task.ParchTrajectoryForFepLambda method)
(schrodinger.application.desmond.task.ParchTrajectoryForSolubilityFep method)
(schrodinger.application.desmond.task.Task method)
(schrodinger.application.desmond.task.TrajectoryForSolubilityFep method)
execute_lictest() (in module schrodinger.application.licensing.licadmin)
execute_lmutil() (in module schrodinger.application.licensing.licadmin)
EXISTING_RESTRAINT (class in schrodinger.application.desmond.constants)
exit() (schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
exitDecision() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
exitRule() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
exitSubRule() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
expand() (schrodinger.utils.ligfilter.Definition method)
(schrodinger.utils.ligfilter.SmartsCriterion method)
expand_default() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
expand_macro() (in module schrodinger.application.desmond.util)
(in module schrodinger.utils.sea.sea)
expand_prog_name() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
expand_query() (in module schrodinger.rdkit.substructure)
ExpandCell() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
expandtabs() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
expComp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
expect() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
expect_single_datum() (in module schrodinger.application.desmond.arkdb)
expecter() (schrodinger.application.desmond.enhanced_sampling.FcnTypes.BinaryThreadSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.MetaSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.RMSDSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.SimpleSyntax method)
(schrodinger.application.desmond.enhanced_sampling.FcnTypes.ThreadSyntax method)
expiration_str() (schrodinger.application.licensing.flexlm.Feature method)
EXPLICIT (schrodinger.adapter.Hydrogens attribute)
EXPLICIT_HYDROGENS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
ExplicitHydrogens (class in schrodinger.livedesign.preprocessor)
export() (schrodinger.application.desmond.replica_dE.replica_container method)
(schrodinger.application.desmond.replica_dE.replicas_monitor method)
export_dE_data() (schrodinger.application.desmond.replica_dE.replica_container method)
ExportFrameOption (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums)
ExportMode (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums)
ExportToOption (class in schrodinger.trajectory.trajectory_gui_dir.export_structure_enums)
Exposure (schrodinger.application.glide.xpdes.TermKeywords attribute)
expr() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
expression_error() (schrodinger.utils.ligfilter.CriterionParser method)
exprOrBind() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
EXTEND (schrodinger.application.desmond.constants.UiMode attribute)
extend() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.rdkit.molio.MolWriter method)
(schrodinger.structure.Structure method)
(schrodinger.structure.StructureWriter method)
(schrodinger.structure.TextualStructure method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.sea.sea.List method)
extend_hotregion() (in module schrodinger.application.desmond.r_group_asl)
Extended (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
extended (schrodinger.surface.MolSurfType attribute)
EXTENDED_SMILES (schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
extended_windows_path() (in module schrodinger.utils.fileutils)
EXTERNAL_FILE (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportToOption attribute)
extra_keyword_matches (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableFile attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.Makefile attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
extra_validations() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
extract() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure 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_atoms() (in module schrodinger.application.desmond.packages.traj_util)
extract_binding_sites() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
extract_file_from_grid() (in module schrodinger.application.glide.utils)
extract_hypotheses() (in module schrodinger.application.phase.hypothesis)
extract_most_exposed_solute_molecules() (in module schrodinger.application.desmond.solubility_utils)
extract_Phob_pack_ligand_indices() (in module schrodinger.application.glide.xpdes)
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_solute_ct() (in module schrodinger.application.desmond.solubility_utils)
extract_structure() (in module schrodinger.structutils.build)
extract_structures() (in module schrodinger.application.phase.hypothesis)
(in module schrodinger.rdkit.molio)
extract_subsystem() (in module schrodinger.application.desmond.packages.topo)
(in module schrodinger.application.desmond.packages.traj)
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)
extractInformationFromTreeNodeStream() (schrodinger.application.desmond.antlr3.exceptions.EarlyExitException method)
(schrodinger.application.desmond.antlr3.exceptions.FailedPredicateException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedNotSetException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedRangeException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedSetException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTokenException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTreeNodeException method)
(schrodinger.application.desmond.antlr3.exceptions.MissingTokenException method)
(schrodinger.application.desmond.antlr3.exceptions.NoViableAltException method)
(schrodinger.application.desmond.antlr3.exceptions.RecognitionException method)
(schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException method)
extractStructure() (schrodinger.structure._AtomCollection method)
(schrodinger.structure._Chain method)
(schrodinger.structure._Molecule method)
(schrodinger.structure._Residue method)
(schrodinger.structure._Ring method)
F
f3d_Exception
fab_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
factor() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
factorize() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
fail() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
failed() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
failed_files (schrodinger.structure.MultiFileStructureReader attribute)
FailedPredicateException
failIf() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
failIfAlmostEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
failIfEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
failUnless() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
failUnlessAlmostEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
failUnlessEqual() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
failUnlessRaises() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
failureException (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase attribute)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase attribute)
FAIR (schrodinger.application.desmond.fep_edge_data_classifier.Rating attribute)
family_name (schrodinger.application.livedesign.data_classes.LDData property)
fast (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer attribute)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer attribute)
fast_jobdj() (in module schrodinger.test.pytest.fixture)
fast_sa (class in schrodinger.application.matsci.gsas.GSASIImath)
fasta (schrodinger.utils.fileutils.SeqFormat attribute)
fastas_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
FASTSIM (schrodinger.infra.licensing.SimilarityEndpoint attribute)
fatal() (in module schrodinger.application.desmond.util)
FatalErrors (class in schrodinger.application.jaguar.constants)
faux_epi_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
FBHWPosRestrainArray (class in schrodinger.application.desmond.cms)
fcjde_gen (class in schrodinger.application.matsci.gsas.GSASIIpwd)
FcnCall (class in schrodinger.application.desmond.enhsamp)
fcnCall() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
Feature (class in schrodinger.application.licensing.flexlm)
feature (schrodinger.application.licensing.lmgrd_log_parser.event attribute)
feature_expiring() (in module schrodinger.application.licensing.licadmin)
FEATURE_FLAGS (schrodinger.utils.postinstall.CustomConfigFiles attribute)
FEATURE_QCOLORS() (in module schrodinger.application.phase.constants)
Featurize (class in schrodinger.application.matsci.mlearn.descriptor)
FeaturizeError
FEP (schrodinger.application.desmond.constants.PRODUCT attribute)
fep_simulation_details (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
FEP_STATE_KEYS (class in schrodinger.application.desmond.constants)
FEP_TYPES (class in schrodinger.application.desmond.constants)
FEPEdgeData (class in schrodinger.application.desmond.fep_edge_data)
fepio (schrodinger.application.desmond.ffiostructure.FFIOStructure attribute)
FepLegTypes (class in schrodinger.application.desmond.constants)
FepSchedule (class in schrodinger.application.desmond.fep_schedule)
FepScheduleAlchemical (class in schrodinger.application.desmond.fep_schedule)
FepScheduleAlchemicalCharge (class in schrodinger.application.desmond.fep_schedule)
FepScheduleAlchemicalDefault (class in schrodinger.application.desmond.fep_schedule)
FepScheduleBinding (class in schrodinger.application.desmond.fep_schedule)
FepScheduleBindingDefault (class in schrodinger.application.desmond.fep_schedule)
FepSchemeChargeMixIn (class in schrodinger.application.desmond.fep_schedule)
FepSchemeMixIn (class in schrodinger.application.desmond.fep_schedule)
FepSchemeQuickchargeMixIn (class in schrodinger.application.desmond.fep_schedule)
FepSchemeSuperquickchargeMixIn (class in schrodinger.application.desmond.fep_schedule)
FEPTorsions (class in schrodinger.application.desmond.fep_edge_data)
FEPTorsionsContainer (class in schrodinger.application.desmond.fep_edge_data)
fetch_schema() (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument class method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument class method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument class method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument class method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument class method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument class method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument class method)
ffio (schrodinger.application.desmond.ffiostructure.FFIOStructure attribute)
ffio_add_atoms_block() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util)
ffio_add_block() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util)
ffio_add_header() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util)
ffio_add_pseudo_block() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util)
FFIO_ATOM_VEL() (in module schrodinger.application.matsci.msprops)
ffio_delete_atoms() (in module schrodinger.application.desmond.gcmc_utils)
ffio_extend_ct() (in module schrodinger.application.desmond.gcmc_utils)
ffio_refresh() (schrodinger.application.desmond.cms.Cms method)
FFIOStructure (class in schrodinger.application.desmond.ffiostructure)
Field (class in schrodinger.application.bindingsite.intfield)
FIFOCacheData (class in schrodinger.application.matsci.cache)
file_config() (in module schrodinger.utils.log)
file_dirname() (in module schrodinger.application.licensing.licadmin)
file_name (schrodinger.application.prime.wrapper.PrimeTemplate property)
FileDebugViewer (class in schrodinger.ui.qt.appframework2.debugcore)
FileExists (class in schrodinger.ui.qt.appframework2.validators)
FileFormat (class in schrodinger.infra.structure)
FileFormatError
FileInfo (class in schrodinger.test.stu.common)
filename (schrodinger.application.desmond.arkdb.CompositeKeySyntaxError attribute)
(schrodinger.utils.fileutils.SharingViolationError attribute)
filename2 (schrodinger.utils.fileutils.SharingViolationError attribute)
filename_extensions (schrodinger.application.desmond.packages.msys.molfile.SeqFile attribute)
(schrodinger.application.desmond.packages.msys.molfile.StkFile attribute)
files (schrodinger.structure.MultiFileStructureReader attribute)
FileSize (schrodinger.infra.structure.FileSplitStrategy attribute)
FileSplitStrategy (class in schrodinger.infra.structure)
FileStream (in module schrodinger.application.desmond.antlr3.streams)
fill() (schrodinger.infra.mmbitset.Bitset method)
FillAtomLookUp() (in module schrodinger.application.matsci.gsas.GSASIImath)
fillBuffer() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
fillFolderTree() (schrodinger.application.livedesign.ld_folder_tree.LDFolderTree method)
fillgmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
FillUnitCell() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
Filter (class in schrodinger.structutils.filter)
(class in schrodinger.ui.qt.filter_dialog_dir.filter_core)
filter() (schrodinger.rdkit.filtering.JSONFilterAdapter method)
(schrodinger.structutils.filter.Filter method)
(schrodinger.structutils.filter.PropFilter method)
(schrodinger.structutils.filter.SmartsFilter method)
filter_data() (schrodinger.application.desmond.bennett.CalcBAR method)
filtered_combinations() (in module schrodinger.structutils.rgroup_enumerate)
filtered_combinations_for_selection() (in module schrodinger.structutils.rgroup_enumerate)
filtersChildEvents() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
final (schrodinger.application.jaguar.scan.Scan property)
find() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method)
(schrodinger.application.desmond.arkdb.ArkDb method)
(schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.desmond.multisim.parser.Msj method)
(schrodinger.application.desmond.packages.msys.HydrogenBondFinder method)
(schrodinger.application.desmond.packages.msys.ParamTable method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
(schrodinger.ui.dendrogram.DendrogramView method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
find_all_rings() (in module schrodinger.structutils.rings)
find_backbone() (in module schrodinger.application.matsci.graph)
find_block() (schrodinger.application.desmond.simulation_block_test.Block method)
find_buddies_on_other_surf() (in module schrodinger.application.bioluminate.surfcomp)
find_class() (schrodinger.application.desmond.picklejar.CustomUnpickler method)
find_closest_rotbond() (in module schrodinger.application.desmond.r_group_asl)
find_common (schrodinger.application.phase.input.InputSpecs attribute)
find_common_properties() (in module schrodinger.structutils.analyze)
find_common_substructure() (in module schrodinger.structutils.analyze)
find_component_cts() (in module schrodinger.application.desmond.fep_net_charge)
find_decorated_methods() (in module schrodinger.infra.util)
find_distortions() (in module schrodinger.structutils.check)
find_equivalent_atoms() (in module schrodinger.structutils.analyze)
find_families() (in module schrodinger.protein.gpcr.gpcrdb)
find_frag_from_closest_rotbond() (in module schrodinger.application.desmond.r_group_asl)
find_full_product_version() (in module schrodinger.application.utils)
find_hbond_hydrogen() (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method)
(schrodinger.protein.analysis.Report.steric_clash_data_set method)
find_hets() (in module schrodinger.protein.findhets)
FIND_HOMOLOGS (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
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_resources() (in module schrodinger.application.licensing.licadmin)
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_next_residue() (in module schrodinger.application.desmond.cms)
find_overlapping_atoms() (in module schrodinger.structutils.analyze)
find_pi_cation_interactions() (in module schrodinger.structutils.interactions.pi)
find_pi_pi_interactions() (in module schrodinger.structutils.interactions.pi)
find_prev_residue() (in module schrodinger.application.desmond.cms)
find_product_package_dir() (in module schrodinger.application.utils)
find_recap_bonds() (in module schrodinger.structutils.createfragments)
find_rgroup_from_smarts() (in module schrodinger.structutils.rgroup_enumerate)
find_ring_atoms() (in module schrodinger.structutils.rings)
find_ring_bonds() (in module schrodinger.structutils.rings)
find_ring_systems() (in module schrodinger.structutils.rings)
find_rings() (in module schrodinger.structutils.rings)
(schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
find_segments() (in module schrodinger.application.matsci.graph)
find_shortest_bond_path() (in module schrodinger.structutils.analyze)
find_stages() (schrodinger.application.desmond.multisim.parser.Msj method)
find_staying_atom() (in module schrodinger.structutils.rgroup_enumerate)
find_traj_path() (in module schrodinger.application.desmond.packages.topo)
find_traj_path_from_cms_path() (in module schrodinger.application.desmond.packages.topo)
find_trajectories() (in module schrodinger.application.desmond.packages.traj_util)
find_validators() (in module schrodinger.ui.qt.appframework2.validation)
findall() (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
FindAllNeighbors() (in module schrodinger.application.matsci.gsas.GSASIImath)
FindAtomIndexByIDs() (in module schrodinger.application.matsci.gsas.GSASIImath)
findBest() (schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraint static method)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintCentroid static method)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintInteraction static method)
findBond() (schrodinger.application.desmond.packages.msys.Atom method)
(schrodinger.application.desmond.packages.msys.System method)
findBondGroups() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
findChiAtoms() (schrodinger.protein.rotamers.Rotamers method)
findChild() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
findChildren() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
findContactIds() (schrodinger.application.desmond.packages.msys.System method)
findContacts() (schrodinger.application.desmond.packages.msys.SpatialHash method)
FindDistinctFragments() (in module schrodinger.application.desmond.packages.msys)
findExact() (schrodinger.application.desmond.packages.msys.TermTable method)
findMatches() (schrodinger.application.desmond.packages.msys.SmartsPattern method)
FindMolecule() (in module schrodinger.application.matsci.gsas.GSASIImath)
findNearest() (schrodinger.application.desmond.packages.msys.SpatialHash method)
FindNeighbors() (in module schrodinger.application.matsci.gsas.GSASIImath)
FindNonstandard() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
findOffset() (in module schrodinger.application.matsci.gsas.GSASIImath)
findReagentFile() (schrodinger.application.pathfinder.reaction.ReagentClass method)
findResidue() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
findRestraint() (schrodinger.application.desmond.packages.restraint.cross_link.FragmentLinkingRestraint class method)
findSSOffset() (in module schrodinger.application.matsci.gsas.GSASIImath)
findValgrindSuppressionsFiles() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.MakefileTest method)
findWithAll() (schrodinger.application.desmond.packages.msys.TermTable method)
findWithAny() (schrodinger.application.desmond.packages.msys.TermTable method)
findWithin() (schrodinger.application.desmond.packages.msys.SpatialHash method)
findWithOnly() (schrodinger.application.desmond.packages.msys.TermTable method)
FINGERPRINT_TYPES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI attribute)
FingerprintComponent (class in schrodinger.analysis.enrichment.enrichment_input)
first (schrodinger.application.desmond.packages.msys.Bond property)
first() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method)
fit() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
(schrodinger.application.matsci.mlearn.base.BaseFeaturizer method)
fit_loc_scale() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
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_structure_to_ellipsoid() (in module schrodinger.application.matsci.geometry)
fit_transform() (schrodinger.application.matsci.mlearn.base.BaseFeaturizer method)
fitInView() (schrodinger.ui.dendrogram.DendrogramView method)
FitTexture() (in module schrodinger.application.matsci.gsas.GSASIImath)
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_idx_traj_path() (in module schrodinger.application.desmond.cms)
fixAll() (schrodinger.application.prime.primefix.FixForPrime method)
fixDNACaps() (schrodinger.application.prime.primefix.FixForPrime method)
FixForPrime (class in schrodinger.application.prime.primefix)
fixHets() (schrodinger.application.prime.primefix.FixForPrime method)
fixMetals() (schrodinger.application.prime.primefix.FixForPrime method)
fixMono() (in module schrodinger.application.matsci.gsas.GSASIIspc)
fixPdbresAndPdbnames() (schrodinger.application.prime.primefix.FixForPrime method)
fixSpecialResidues() (schrodinger.application.prime.primefix.FixForPrime method)
FixValence() (in module schrodinger.application.matsci.gsas.GSASIIElem)
flag_context_manager() (in module schrodinger.infra.util)
flags() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
flat_enumerator() (in module schrodinger.application.scaffold_enumeration.layered)
flat_list_enumerator() (in module schrodinger.application.scaffold_enumeration.layered)
flatten_list() (in module schrodinger.application.bioluminate.surfcomp)
FLEXIBLE (schrodinger.application.desmond.constants.IsotropyPolicy attribute)
(schrodinger.application.desmond.constants.Schedule attribute)
Flnh() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
FLOAT (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute)
FLOAT_BASE (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor attribute)
flush() (schrodinger.ui.qt.appframework2.debugcore.DebugStderr class method)
(schrodinger.ui.qt.appframework2.debugcore.DebugStdout class method)
Fmt (class in schrodinger.application.desmond.packages.traj)
fmt (schrodinger.application.desmond.packages.timer.Timer.Args attribute)
focusInEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
focusItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
focusItemChanged (schrodinger.ui.dendrogram.DendrogramScene attribute)
focusNextChild() (schrodinger.ui.dendrogram.DendrogramView method)
focusNextPrevChild() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
focusOnTouch() (schrodinger.ui.dendrogram.DendrogramScene method)
focusOutEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
focusPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
focusPreviousChild() (schrodinger.ui.dendrogram.DendrogramView method)
focusProxy() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
focusWidget() (schrodinger.ui.dendrogram.DendrogramView method)
fod_precision (schrodinger.analysis.enrichment.calculator.Calculator attribute)
FOLLOW_45_in_static244 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_46_in_decl_output296 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_47_in_decl_meta349 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_48_in_meta_term592 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_48_in_output_term404 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_49_in_meta_term664 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_49_in_output_term476 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_50_in_meta_term681 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_50_in_meta_term745 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_50_in_meta_term809 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_50_in_output_term493 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_50_in_output_term557 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_51_in_meta_term724 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_51_in_output_term536 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_52_in_meta_term786 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_53_in_meta_term852 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_54_in_meta_term922 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_55_in_series1392 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_56_in_if_1436 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_57_in_if_1442 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_58_in_if_1448 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_ADDOP_in_signedExpComp1111 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_atom_in_comp1149 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_BCLOSE_in_comp1158 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_bind_in_exprOrBind1017 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_block_in_atom1379 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_block_in_prog160 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_BOPEN_in_comp1152 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_CCLOSE_in_atom1381 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_COLON_in_iter1484 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_COMMA_in_decl_meta358 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_COMMA_in_decl_output305 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_COMMA_in_fcnCall1192 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_COMMA_in_series1401 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_COMMA_in_static251 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_comp_in_expComp1129 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_COPEN_in_atom1376 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_decl_in_header191 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_decl_meta_in_decl222 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_decl_output_in_decl226 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EOF_in_prog162 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_bind1029 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_iter1478 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_meta_term600 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_meta_term671 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_meta_term728 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_meta_term792 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_meta_term855 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_meta_term927 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_output_term412 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_output_term483 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EQ_in_output_term540 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_EXP_in_expComp1132 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expComp_in_signedExpComp1121 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_atom1354 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_bind1033 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_comp1156 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_exprOrBind1013 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_fcnCall1189 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_fcnCall1195 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_if_1440 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_if_1446 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_if_1452 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_iter1482 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_iter1488 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_expr_in_series1413 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_exprOrBind_in_block980 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_exprOrBind_in_block987 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_factor_in_expr1057 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_factor_in_expr1070 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_fcnCall_in_atom1267 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_header_in_prog158 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_IDENT_in_atom1304 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_IDENT_in_bind1027 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_IDENT_in_fcnCall1182 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_IDENT_in_iter1476 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_IDENT_in_varWithType272 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_if__in_atom1248 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_iter_in_series1398 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_iter_in_series1405 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_LIT_in_atom1332 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_LIT_in_meta_term687 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_LIT_in_meta_term751 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_LIT_in_meta_term815 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_LIT_in_meta_term869 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_LIT_in_output_term499 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_LIT_in_output_term563 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_LIT_in_varWithType276 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_meta_term_in_decl_meta355 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_meta_term_in_decl_meta362 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_output_term_in_decl_output302 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_output_term_in_decl_output309 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_PCLOSE_in_atom1356 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_PCLOSE_in_decl_meta366 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_PCLOSE_in_decl_output313 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_PCLOSE_in_fcnCall1201 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_PCLOSE_in_series1409 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_PCLOSE_in_varWithType278 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_POPEN_in_atom1351 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_POPEN_in_decl_meta351 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_POPEN_in_decl_output298 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_POPEN_in_fcnCall1185 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_POPEN_in_series1394 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_POPEN_in_varWithType274 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_SEMI_in_block983 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_SEMI_in_block991 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_SEMI_in_header193 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_series_in_atom1229 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_set_in_expr1061 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_set_in_factor1086 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_signedExpComp_in_expComp1135 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_signedExpComp_in_factor1081 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_signedExpComp_in_factor1096 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_static_in_decl230 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_STRING_in_atom1286 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_STRING_in_meta_term614 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_STRING_in_meta_term941 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_STRING_in_output_term426 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_SUBTROP_in_meta_term675 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_SUBTROP_in_output_term487 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_SUBTROP_in_signedExpComp1116 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_varWithType_in_static248 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
FOLLOW_varWithType_in_static255 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
font() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
fontInfo() (schrodinger.ui.dendrogram.DendrogramView method)
fontMetrics() (schrodinger.ui.dendrogram.DendrogramView method)
force_constant_precision (schrodinger.application.jaguar.results.NormalMode attribute)
force_copy2() (in module schrodinger.utils.fileutils)
force_remove() (in module schrodinger.utils.fileutils)
force_rename() (in module schrodinger.utils.fileutils)
force_rmtree() (in module schrodinger.utils.fileutils)
ForceFieldOptions (class in schrodinger.forcefield.ffld_options)
forces (schrodinger.application.jaguar.results.JaguarResults property)
forces_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute)
ForEachDo (class in schrodinger.application.desmond.arkdb)
foregroundBrush() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
ForegroundLayer (schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramScene.SceneLayer attribute)
foregroundRole() (schrodinger.ui.dendrogram.DendrogramView method)
formal_charge (schrodinger.application.desmond.cms.Cms property)
(schrodinger.application.desmond.ffiostructure.FFIOStructure property)
(schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.models.jsonable.JsonableStructure property)
(schrodinger.structure._StructureAtom property)
(schrodinger.structure.Structure property)
(schrodinger.structure.TextualStructure property)
FORMALCHARGED (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute)
Format (class in schrodinger.application.phase.packages.conformer_storage)
(class in schrodinger.livedesign.convert)
(class in schrodinger.rdkit_extensions)
format() (in module schrodinger.application.jaguar.check_headers)
(schrodinger.analysis.enrichment.calculator.Calculator static method)
(schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
format_charge() (in module schrodinger.application.ligprep.ionizer)
format_description() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
format_epilog() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
format_heading() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
format_help() (schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
format_host() (in module schrodinger.application.livedesign.login)
format_json() (in module schrodinger.utils.featureflags.write)
format_map() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
format_numbered_message() (in module schrodinger.application.livedesign.entry_types)
format_option() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
format_option_help() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
format_option_strings() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
format_process_status() (in module schrodinger.test.stu.process_management)
format_process_tree() (in module schrodinger.test.stu.process_management)
format_usage() (schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
format_usage_row() (in module schrodinger.application.licensing.lmgrd_log_parser)
FormatSDF() (in module schrodinger.application.desmond.packages.msys)
formatSummaryMessage() (schrodinger.application.livedesign.entry_types.BaseEntryData method)
(schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
FORMULA (schrodinger.livedesign.molhash.HashLayer attribute)
fortfloat() (in module schrodinger.application.mopac.results_main)
FORWARD (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Direction attribute)
ForwardRGMolSupplier (class in schrodinger.livedesign.rgfile_parse)
Fourier4DMap() (in module schrodinger.application.matsci.gsas.GSASIImath)
FourierMap() (in module schrodinger.application.matsci.gsas.GSASIImath)
FPcalc() (in module schrodinger.application.matsci.gsas.GSASIIElem)
FPsimSearcher (class in schrodinger.application.fpsim)
fracCrenel() (in module schrodinger.application.matsci.gsas.GSASIImath)
fracFourier() (in module schrodinger.application.matsci.gsas.GSASIImath)
FractionAromatic() (in module schrodinger.rdkit.filtering)
frag_handle (schrodinger.application.combiglide.corehop.SubstCoreDatabase attribute)
frag_is_smaller() (in module schrodinger.livedesign.preprocessor)
fragid (schrodinger.application.desmond.packages.msys.Atom property)
Fragment (class in schrodinger.application.ligprep.ionizer)
FRAGMENT (schrodinger.application.desmond.constants.FepLegTypes attribute)
FRAGMENT_HYDRATION (schrodinger.application.desmond.constants.FepLegTypes attribute)
FRAGMENT_LINKING (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute)
FRAGMENT_SOLVATION (schrodinger.application.desmond.constants.CorrectionTerm attribute)
FragmentCreator (class in schrodinger.structutils.createfragments)
fragmentIDs (schrodinger.structutils.markush_enumerate.Scaffold property)
FragmentLibrary (class in schrodinger.utils.cgxutils)
FragmentLinkingRestraint (class in schrodinger.application.desmond.packages.restraint.cross_link)
FragmentReader (class in schrodinger.structutils.markush_enumerate)
FragmentsIterator (class in schrodinger.structutils.markush_enumerate)
fragmentStructure() (schrodinger.structutils.createfragments.FragmentCreator method)
fragmentStructureForEA() (schrodinger.structutils.createfragments.FragmentCreator method)
Frame (class in schrodinger.application.desmond.packages.pfx)
(class in schrodinger.application.desmond.packages.traj)
frame() (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method)
(schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method)
FRAME_SETTINGS_DICT (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
frameGeometry() (schrodinger.ui.dendrogram.DendrogramView method)
FrameIter (class in schrodinger.application.desmond.packages.msys.molfile)
frameRect() (schrodinger.ui.dendrogram.DendrogramView method)
frames() (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method)
(schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method)
frameShadow() (schrodinger.ui.dendrogram.DendrogramView method)
frameShape() (schrodinger.ui.dendrogram.DendrogramView method)
frameSize() (schrodinger.ui.dendrogram.DendrogramView method)
frameStyle() (schrodinger.ui.dendrogram.DendrogramView method)
frameWidth() (schrodinger.ui.dendrogram.DendrogramView method)
free_energy_costs() (in module schrodinger.application.ligprep.ionizer)
FreeEnergy (class in schrodinger.application.jaguar.utils)
freeTextAnnotation() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
freeze() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
freeze_atom() (in module schrodinger.application.desmond.remd)
frequency_precision (schrodinger.application.jaguar.results.NormalMode attribute)
freshenParentAndChildIndexes() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
from_atom_indices() (schrodinger.forcefield.minimizer.Restraint class method)
from_dict() (in module schrodinger.application.matsci.mlearn.sklearn_json)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.job.server.ServerInfo class method)
from_id() (schrodinger.application.matsci.qb_sdk.job.QubecJob static method)
from_json() (in module schrodinger.application.matsci.mlearn.sklearn_json)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
from_list() (schrodinger.infra.mmbitset.Bitset class method)
from_parent() (schrodinger.test.perceptualdiff.PerceptualDiffTest class method)
(schrodinger.test.pytest.exetest.ExecutableFile class method)
(schrodinger.test.pytest.exetest.ExecutableTest class method)
(schrodinger.test.pytest.exetest.Makefile class method)
(schrodinger.test.pytest.exetest.MakefileTest class method)
from_rdkit() (in module schrodinger.rdkit.rdkit_adapter)
from_string() (schrodinger.application.desmond.measurement.Measurement class method)
from_style (schrodinger.structure._StructureBond property)
from_xml() (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
from_yaml() (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
fromArgv() (in module schrodinger.infra.ark)
fromConfig() (schrodinger.livedesign.preprocessor.PreprocessorOptions static method)
fromData() (schrodinger.application.matsci.nano.space_groups.SpaceGroup class method)
fromEtotString() (schrodinger.application.jaguar.results.ScfIteration static method)
fromFile() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter class method)
fromIterable() (schrodinger.utils.scollections.DefaultIdDict class method)
(schrodinger.utils.scollections.IdDict class method)
(schrodinger.utils.scollections.IdSet class method)
fromJson() (schrodinger.models.json.JsonableClassMixin class method)
(schrodinger.models.jsonable.JsonableNamedTuple class method)
(schrodinger.models.jsonable.JsonableSet class method)
(schrodinger.models.jsonable.JsonableStructure class method)
(schrodinger.models.jsonable.JsonableTuple class method)
fromJSON() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter class method)
fromJsonImplementation() (schrodinger.models.json.JsonableClassMixin class method)
(schrodinger.models.jsonable.JsonableEnum class method)
(schrodinger.models.jsonable.JsonableIntEnum class method)
(schrodinger.models.jsonable.JsonableNamedTuple class method)
(schrodinger.models.jsonable.JsonableSet class method)
(schrodinger.models.jsonable.JsonableStructure class method)
(schrodinger.models.jsonable.JsonableTuple class method)
fromkeys() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap class method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
FromSmilesString() (in module schrodinger.application.desmond.packages.msys)
fromString() (in module schrodinger.infra.ark)
(schrodinger.structure.StructureReader static method)
front_transparency (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
frozenset_cached_property (class in schrodinger.application.matsci.cache)
fspath (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableFile attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.Makefile attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
FukuiIndices (class in schrodinger.application.jaguar.results)
FULL (schrodinger.livedesign.preprocessor.GenerateCoordinates attribute)
FULL_ALIGNED (schrodinger.livedesign.preprocessor.GenerateCoordinates attribute)
FULL_HERMANN_MAUGUIN_SYMBOL (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
FULL_NAME_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
FullIORedirect (class in schrodinger.test.ioredirect)
fullname (schrodinger.application.desmond.packages.msys.Atom property)
fullName() (schrodinger.application.desmond.fep_edge_data.ResData method)
fullsystem_ct (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
FullViewportUpdate (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.ViewportUpdateMode attribute)
func (schrodinger.application.canvas.topo_descriptors.Descriptor attribute)
func() (in module schrodinger.application.mopac.results_main)
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)
fuseIonFragment() (schrodinger.application.ligprep.ionizer.Ionizer method)
fuzzy_aromatic_matching (schrodinger.rdkit.substructure.QueryOptions attribute)
G
G2Print() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
G2printLevel (in module schrodinger.application.matsci.gsas.GSASIIfiles)
G2SetPrintLevel() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
gamma_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
gap_penalty (schrodinger.structutils.structalign.StructAlign property)
gather_rings() (in module schrodinger.structutils.interactions.pi)
gaulegf() (in module schrodinger.application.matsci.gsas.GSASIImath)
GaussianFilter (class in schrodinger.application.desmond.gaussian_filter)
gcg (schrodinger.utils.fileutils.SeqFormat attribute)
GCMC_INFO (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute)
gen (schrodinger.application.qsite.input.QSiteInput property)
gen_alpha_helix_restraint() (in module schrodinger.application.desmond.cms)
gen_cross_link_restraint() (in module schrodinger.application.desmond.packages.restraint.cross_link)
gen_cross_link_restraint_centroid() (in module schrodinger.application.desmond.packages.restraint.cross_link)
gen_cross_link_restraint_interaction() (in module schrodinger.application.desmond.packages.restraint.cross_link)
gen_dE_files() (in module schrodinger.application.desmond.deltaE)
gen_fastas() (in module schrodinger.application.bioluminate.epitope.psc_workflow)
gen_faux_epitopes() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
(schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
gen_file_list() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
(schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
gen_jobname() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
gen_mifs() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
gen_names() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
(schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
gen_sim_mat() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
(schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
gen_test() (in module schrodinger.application.desmond.simulation_block_test)
GenAtom() (in module schrodinger.application.matsci.gsas.GSASIIspc)
generate() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
Generate2DCoordinates (class in schrodinger.adapter)
generate3dConformation() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
generate_asl() (in module schrodinger.structutils.analyze)
generate_canonical_tautomer() (in module schrodinger.livedesign.preprocessor)
generate_conf_pose_restraints() (in module schrodinger.application.desmond.packages.restraint.builder)
GENERATE_COORDINATES (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
generate_coordinates() (in module schrodinger.livedesign.preprocessor)
generate_criterion() (in module schrodinger.utils.ligfilter)
generate_crystal_mates() (in module schrodinger.structutils.analyze)
generate_dendrogram() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
generate_hierarchial_key() (in module schrodinger.application.matsci.hdfutils)
generate_lid() (in module schrodinger.application.livedesign.lid)
generate_molecular_formula() (in module schrodinger.structutils.analyze)
generate_partial_charges() (in module schrodinger.forcefield.common)
generate_residue_asl() (in module schrodinger.structutils.analyze)
generate_return_code_dict() (in module schrodinger.infra.mmcheck)
generate_smarts() (in module schrodinger.structutils.analyze)
generate_smarts_canvas() (in module schrodinger.structutils.analyze)
generate_smiles() (in module schrodinger.structutils.analyze)
generate_tautomer_code() (in module schrodinger.structutils.analyze)
generate_watermap_pse() (in module schrodinger.application.livedesign.pse_helpers)
generateAlignedStructure() (schrodinger.application.pathfinder.aligner.AlignedMolStructureGenerator method)
GenerateCoordinates (class in schrodinger.livedesign.preprocessor)
generateDM() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
generateFingerprint() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
generateSpecs() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
generateStateCT() (schrodinger.application.ligprep.ionizer.Ionizer method)
GeneratorType (class in schrodinger.application.desmond.packages.restraint.builder)
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)
GenPfHKLs() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
GenSHCoeff() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
GenSSHLaue() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
gensym() (schrodinger.application.desmond.enhsamp.Env method)
GEO_MAX_ITERS (schrodinger.application.jaguar.constants.FatalErrors attribute)
GeomAnalyzerBase (class in schrodinger.application.desmond.packages.staf)
GeomCalc (class in schrodinger.application.desmond.packages.staf)
geometry (schrodinger.application.matsci.qb_sdk.parameters.QubecChemistryProblem attribute)
geometry() (schrodinger.ui.dendrogram.DendrogramView method)
GeometryOptMethod (class in schrodinger.forcefield.constants)
get() (in module schrodinger.application.desmond.envir)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.arkdb.ArkDb method)
(schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.desmond.multisim.parser.Msj method)
(schrodinger.application.desmond.packages.msys.Ct method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmbitset.Bitset method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.utils.preferences.Preferences method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
get14EleEnergy() (schrodinger.structutils.minimize.Minimizer method)
get14LJEnergy() (schrodinger.structutils.minimize.Minimizer method)
get2dStructure() (schrodinger.structure.SmilesStructure method)
get3dStructure() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.SmilesStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
get_absolute_binding_num_lambda_windows() (in module schrodinger.application.desmond.fep_schedule)
get_active_fsys_ct_from_frame() (in module schrodinger.application.desmond.packages.topo)
get_active_sample_size() (in module schrodinger.analysis.enrichment.metrics)
get_active_sample_size_star() (in module schrodinger.analysis.enrichment.metrics)
get_activity_cliffs() (in module schrodinger.application.phase.packages.mmp2d)
get_added() (in module schrodinger.models.diffy)
get_added_dict() (in module schrodinger.models.diffy)
get_added_list() (in module schrodinger.models.diffy)
get_added_set() (in module schrodinger.models.diffy)
get_aids_with_virtuals() (in module schrodinger.application.desmond.packages.topo)
get_aligned_coordinates() (in module schrodinger.application.desmond.frag_snap)
get_aligned_coordinates_from_fragments() (in module schrodinger.application.desmond.frag_snap)
get_aligned_fragment_coords() (in module schrodinger.application.desmond.frag_snap)
get_alignment_matrix() (in module schrodinger.structutils.transform)
get_all_orthant_strings() (in module schrodinger.application.combinatorial_diversity.splitter_utils)
get_angle_between_vectors() (in module schrodinger.structutils.transform)
get_angle_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
get_angles() (schrodinger.application.desmond.torsion_related.TorsionPotential method)
get_api() (in module schrodinger.application.phase.packages.conformer_storage)
get_api_key() (in module schrodinger.test.stu.common)
get_appdata_dir() (in module schrodinger.utils.fileutils)
get_approximate_atomic_sasa() (in module schrodinger.structutils.analyze)
get_approximate_sasa() (in module schrodinger.structutils.analyze)
get_arg_parser() (in module schrodinger.utils.compare)
get_aromatic_hydrogen_bonds() (in module schrodinger.structutils.interactions.hbond)
get_atom_elements() (in module schrodinger.application.scaffold_enumeration.atomlist)
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_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
get_atom_positions() (in module schrodinger.application.bindingsite.cavutils)
get_atomic_constraints_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_atomic_element_symbols() (in module schrodinger.application.matsci.nano.util)
get_atomic_forces_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_atomic_positions() (schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
get_atomic_positions_cell_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_atomic_species_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
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_mapping() (in module schrodinger.livedesign.preprocessor)
get_attachment_bonds() (in module schrodinger.application.desmond.r_group_asl)
get_attachment_point() (in module schrodinger.structutils.rgroup_enumerate)
get_attachment_points() (in module schrodinger.structutils.markush_enumerate)
get_attribute_default() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
get_attribute_type() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
get_attributes() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
get_average_structure() (in module schrodinger.structutils.analyze)
get_b64decoded_str() (in module schrodinger.application.desmond.cmdline)
get_b64encoded_str() (in module schrodinger.application.desmond.cmdline)
get_backbone_atoms() (in module schrodinger.application.matsci.geometry)
get_backbone_indices() (schrodinger.protein.analysis.Report.local_residue method)
get_basename() (in module schrodinger.utils.fileutils)
get_bases() (in module schrodinger.application.jaguar.basis)
get_big_fused_rings() (in module schrodinger.application.desmond.r_group_asl)
get_bilinear_fit_property() (in module schrodinger.application.matsci.uq_utils)
get_bilinear_prop() (in module schrodinger.application.matsci.uq_utils)
get_bilinear_prop_from_points() (in module schrodinger.application.matsci.uq_utils)
get_bilinear_regions() (in module schrodinger.application.matsci.uq_utils)
get_bilinear_regression() (in module schrodinger.application.matsci.uq_utils)
get_block_summary() (in module schrodinger.application.desmond.simulation_block_data)
get_blocks() (in module schrodinger.structutils.block_data)
get_bond_id() (in module schrodinger.application.scaffold_enumeration.common)
get_bond_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
get_bonded_hydrogens() (in module schrodinger.application.ligprep.ionizer)
get_bonded_term_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
get_bonds() (in module schrodinger.application.jaguar.utils)
get_bonds_mapping() (in module schrodinger.livedesign.preprocessor)
get_bound_cache() (in module schrodinger.application.matsci.cache)
get_box() (in module schrodinger.application.desmond.cms)
get_boxsize() (in module schrodinger.application.desmond.cms)
get_boxvolume() (in module schrodinger.application.desmond.cms)
get_buildtime_file() (in module schrodinger.utils.machid)
get_canonical_atom_ranks_and_bonds() (in module schrodinger.livedesign.molhash)
get_canonical_smiles() (in module schrodinger.livedesign.molhash)
get_cell_dofree() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_cell_parameters() (schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
get_cell_parameters_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_center() (in module schrodinger.math.multi_parameter_optimization)
get_centroid() (in module schrodinger.structutils.transform)
get_charge() (in module schrodinger.application.bioluminate.propka_parse)
(schrodinger.application.desmond.cms.Cms method)
get_charge_r() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.charge)
get_charges() (in module schrodinger.application.jaguar.utils)
get_chiral_atoms() (in module schrodinger.structutils.analyze)
get_chiralities() (in module schrodinger.structutils.analyze)
get_client() (in module schrodinger.application.matsci.qb_sdk.client)
get_climbing_images() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_close_atoms() (in module schrodinger.structutils.measure)
get_close_coordinates() (in module schrodinger.structutils.measure)
get_closest_marker() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
get_color() (schrodinger.application.desmond.torsion_related.TorsionPotential method)
get_color_scheme() (in module schrodinger.structutils.color)
get_com_and_axes() (in module schrodinger.application.bindingsite.cavutils)
get_complete_spectrum() (in module schrodinger.application.matsci.colorutils)
get_compound_smiles() (in module schrodinger.application.phase.packages.mmp2d)
get_config_filename() (in module schrodinger.application.jaguar.user_config)
get_constraint() (schrodinger.application.desmond.cms.Cms method)
get_contrast() (in module schrodinger.ui.qt.standard.colors)
get_contrasting_color() (in module schrodinger.ui.qt.standard.colors)
get_control_gdir() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_coords_array_from_list() (in module schrodinger.structutils.transform)
get_cpu() (in module schrodinger.utils.sysinfo)
get_credentials() (in module schrodinger.application.livedesign.login)
get_csv_file_column_count() (in module schrodinger.utils.fileutils)
get_cts() (schrodinger.application.desmond.cms.Cms method)
get_current_utc_timestamp() (in module schrodinger.application.job_monitor.util)
get_custom_reagent_classes() (in module schrodinger.application.pathfinder.reaction)
get_db_filename() (in module schrodinger.protein.gpcr.sql)
get_decoy_sample_size() (in module schrodinger.analysis.enrichment.metrics)
get_default() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method)
(schrodinger.utils.compare.DiffCompareArgumentParser method)
get_default_criterion_parser() (in module schrodinger.utils.ligfilter)
get_default_params() (in module schrodinger.structutils.interactions.hbond)
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_values() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
get_degrees_of_freedom() (in module schrodinger.application.desmond.remd)
(schrodinger.application.desmond.cms.Cms method)
get_delta_property_values() (in module schrodinger.application.bioluminate.residue_scanning.properties)
get_denovo_parameters() (in module schrodinger.application.phase.utils)
get_description() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
get_desktop_dir() (in module schrodinger.utils.fileutils)
get_detailed() (in module schrodinger.application.bioluminate.propka_parse)
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_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_distance() (in module schrodinger.application.matsci.colorutils)
get_disulfide_bonds() (in module schrodinger.structutils.interactions.ssbond)
get_docs_dir() (in module schrodinger.utils.fileutils)
get_donor_acceptor_bonds() (in module schrodinger.structutils.interactions.hbond)
get_double_sigmoid() (in module schrodinger.math.multi_parameter_optimization)
get_dummy_filter() (in module schrodinger.structutils.rgroup_enumerate)
get_electric_potential_related() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_electrons_efield() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_element() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
get_element_default() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
get_element_tag() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
get_element_type() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
get_encoded_restraints() (in module schrodinger.application.desmond.packages.restraint.utils)
get_encryption_key() (in module schrodinger.application.matsci.enc)
get_ensemble_from_cfg() (in module schrodinger.application.desmond.simulation_block_data)
get_ent() (in module schrodinger.protein.getpdb)
get_env_var_warning() (in module schrodinger.utils.featureflags.featureflags)
get_environ_log_level() (in module schrodinger.utils.log)
get_error() (schrodinger.application.matsci.qb_sdk.job.QubecJob method)
get_existing_faulthandler_timeout() (in module schrodinger.test.pytest.faulthandler_setup)
get_existing_filepath() (in module schrodinger.utils.fileutils)
get_existing_files() (in module schrodinger.application.bioluminate.drivers.io)
get_families() (in module schrodinger.protein.gpcr.annotate)
get_faulthandler_timeout() (in module schrodinger.test.pytest.faulthandler_setup)
get_feature_text() (in module schrodinger.application.phase.constants)
get_features() (in module schrodinger.utils.featureflags.featureflags)
get_fep_cts() (in module schrodinger.application.desmond.r_group_asl)
(schrodinger.application.desmond.cms.Cms method)
get_fep_schedule() (in module schrodinger.application.desmond.fep_schedule)
get_fep_schedule_class() (in module schrodinger.application.desmond.fep_schedule)
get_fep_simulation_details() (in module schrodinger.application.desmond.fep_edge_data)
get_fepio_sub_block_std_prop_getter() (in module schrodinger.application.desmond.ffiostructure)
get_fepio_sub_block_std_prop_setter() (in module schrodinger.application.desmond.ffiostructure)
get_fepio_sub_block_std_prop_short_name() (in module schrodinger.application.desmond.ffiostructure)
get_ff() (schrodinger.application.desmond.cms.Cms method)
get_ffdir() (in module schrodinger.application.desmond.packages.viparr1)
get_ffio_sub_block_std_prop_getter() (in module schrodinger.application.desmond.ffiostructure)
get_ffio_sub_block_std_prop_setter() (in module schrodinger.application.desmond.ffiostructure)
get_ffio_sub_block_std_prop_short_name() (in module schrodinger.application.desmond.ffiostructure)
get_fieldnames() (in module schrodinger.rdkit.molio)
get_file() (in module schrodinger.job.files)
get_file_extension() (in module schrodinger.utils.fileutils)
get_file_format() (in module schrodinger.utils.fileutils)
get_filename() (in module schrodinger.application.matsci.hdfutils)
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_fingerprint() (in module schrodinger.rdkit.filtering)
get_fingerprint_components() (in module schrodinger.analysis.enrichment.enrichment_input)
get_fingerprint_types() (in module schrodinger.utils.multifpfile)
get_fingerprints() (schrodinger.utils.multifpfile.MultiFPFile method)
get_first_hostid() (in module schrodinger.application.licensing.licadmin)
get_flexlm_search_path() (in module schrodinger.application.licensing.licadmin)
get_fmt() (in module schrodinger.application.desmond.packages.traj)
get_forces() (schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
get_format_handler() (in module schrodinger.rdkit.molio)
get_formula_dict() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
get_fortran_input() (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
get_fp_domain() (in module schrodinger.application.combinatorial_diversity.diversity_selector)
get_fragment() (in module schrodinger.application.desmond.r_group_asl)
get_fragment_structure() (in module schrodinger.protein.buildpeptide)
get_fragments_from_att_points() (in module schrodinger.application.desmond.r_group_asl)
get_fragname() (schrodinger.application.desmond.cms.Cms method)
get_free_energy() (in module schrodinger.application.bioluminate.propka_parse)
get_from() (schrodinger.application.desmond.arkdb.Datum method)
(schrodinger.application.desmond.task.Option method)
(schrodinger.application.desmond.task.Premise method)
get_fullsys_ct_atom_index_range() (schrodinger.application.desmond.cms.Cms method)
get_fused_cycles() (in module schrodinger.application.matsci.graph)
get_gamut_area() (in module schrodinger.application.matsci.colorutils)
get_glibc_version() (in module schrodinger.utils.sysinfo)
get_gluepoints() (in module schrodinger.application.desmond.cms)
get_gpcrdb_url() (in module schrodinger.protein.gpcr.annotate)
get_grid_parameters() (in module schrodinger.application.bindingsite.cavutils)
get_halogen_bonds() (in module schrodinger.structutils.interactions.hbond)
get_handlers_for_key() (in module schrodinger.infra.mmkv)
get_hbond_direction() (in module schrodinger.application.bindingsite.intfield)
get_hbond_params() (in module schrodinger.structutils.interactions.hbond)
get_hdf_io() (in module schrodinger.application.matsci.hdfutils)
get_hdf_keys() (in module schrodinger.application.matsci.hdfutils)
get_header() (in module schrodinger.application.desmond.solubility_utils)
get_header_solvation() (in module schrodinger.application.desmond.solubility_utils)
get_heavy_atoms() (in module schrodinger.application.desmond.r_group_asl)
get_height() (in module schrodinger.rdkit.alignment)
get_hill_order() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
get_histogram() (schrodinger.application.desmond.replica_dE.replicas_monitor method)
get_home_dir() (in module schrodinger.utils.fileutils)
get_host() (in module schrodinger.application.livedesign.login)
get_hostid() (in module schrodinger.application.licensing.licadmin)
(in module schrodinger.utils.sysinfo)
get_hostname() (in module schrodinger.utils.sysinfo)
get_hubbard_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
get_hydrogen_bonds() (in module schrodinger.structutils.interactions.hbond)
get_hyperbola_fit_property() (in module schrodinger.application.matsci.uq_utils)
get_hyperbola_prop_from_points() (in module schrodinger.application.matsci.uq_utils)
get_hyperbola_regression() (in module schrodinger.application.matsci.uq_utils)
get_ids_from_pairs() (in module schrodinger.application.phase.packages.mmp2d)
get_image() (in module schrodinger.application.desmond.rl_helper)
get_imports() (in module schrodinger.application.matsci.codeutils)
get_input_path() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
get_interaction_sites() (in module schrodinger.application.bindingsite.intfield)
get_interface_atoms() (in module schrodinger.structutils.interactions.protein_protein_interactions)
get_intersection() (in module schrodinger.math.multi_parameter_optimization)
get_inversion_index() (in module schrodinger.application.matsci.nano.util)
get_job() (in module schrodinger.application.matsci.qb_sdk.api)
get_job_command_in_startup() (in module schrodinger.application.desmond.cmdline)
get_job_details() (in module schrodinger.application.desmond.simulation_block_test)
get_jobname() (in module schrodinger.application.jaguar.utils)
(in module schrodinger.utils.fileutils)
get_jobtype_name() (in module schrodinger.application.licensing.licadmin)
get_json_version_from_file() (in module schrodinger.models.json)
get_json_version_from_string() (in module schrodinger.models.json)
get_k_points() (schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
get_k_points_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_kernel_version() (in module schrodinger.utils.sysinfo)
get_key_name() (in module schrodinger.application.licensing.licadmin)
get_knime_workflows_url() (in module schrodinger.utils.config)
get_ks_eigenvalues() (schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
get_lambda() (schrodinger.application.desmond.fep_schedule.FepSchedule method)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical method)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge method)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault method)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding method)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault method)
get_lambda_atom_indices() (schrodinger.application.desmond.cms.Cms method)
get_largest_moment_normalized_vector() (in module schrodinger.structutils.analyze)
get_last_20_lines() (in module schrodinger.pipeline.pipeutils)
get_last_EZ_property_index() (in module schrodinger.structutils.rgroup_enumerate)
get_ld_client_and_models() (in module schrodinger.application.livedesign.login)
get_ld_library_path_for_system_ssh() (in module schrodinger.utils.env)
get_LD_mode() (in module schrodinger.application.livedesign.login)
get_LD_version() (in module schrodinger.application.livedesign.login)
get_leg_name_from_jobname() (in module schrodinger.application.desmond.util)
get_leg_type_from_jobname() (in module schrodinger.application.desmond.util)
get_lengths() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDComplexType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method)
get_lib_dir() (in module schrodinger.utils.postinstall)
get_libpath() (in module schrodinger.application.pathfinder.reaction)
get_license() (in module schrodinger.application.canvas.utils)
get_license_request_info() (in module schrodinger.application.licensing.netsuiteapi)
get_ligand1_atom_dict() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
get_ligand2_atom_dict() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
get_ligand_asl() (in module schrodinger.structutils.sitealign)
get_ligand_fragments() (in module schrodinger.application.desmond.packages.analysis)
get_ligands() (in module schrodinger.application.livedesign.entry_types)
get_linked_path() (in module schrodinger.application.licensing.flexlm)
get_listof_props_ene() (in module schrodinger.application.desmond.simulation_block_data)
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_log_props() (in module schrodinger.application.desmond.simulation_block_data)
get_logger() (in module schrodinger.application.matsci.qb_sdk.tools)
(in module schrodinger.utils.log)
get_long_family_name() (in module schrodinger.application.livedesign.data_classes)
get_low_energy_reps() (in module schrodinger.structutils.analyze)
get_luma() (in module schrodinger.ui.qt.standard.colors)
get_machid_output() (in module schrodinger.application.licensing.licadmin)
get_macro() (in module schrodinger.application.jaguar.user_config)
(schrodinger.application.jaguar.keywordDB.Keyword method)
(schrodinger.application.jaguar.keywordDB.Setting method)
get_macro_dict() (in module schrodinger.utils.sea.sea)
get_maestro() (in module schrodinger)
get_maestro_params() (in module schrodinger.structutils.interactions.hbond)
get_maestro_scripts_path() (in module schrodinger.utils.maestro_scripts_path)
get_map() (in module schrodinger.test.canvas_utils)
get_map_rdk_to_sdgr() (in module schrodinger.rdkit.rdkit_adapter)
get_map_sdgr_to_rdk() (in module schrodinger.rdkit.rdkit_adapter)
get_marked_func_order() (in module schrodinger.utils.funcgroups)
get_mass() (schrodinger.application.desmond.cms.Cms method)
get_match_options() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils)
get_matsci_module_graph() (in module schrodinger.application.matsci.codeutils)
get_matsci_module_paths() (in module schrodinger.application.matsci.codeutils)
get_max_occurs() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
get_membrane_cts() (schrodinger.application.desmond.cms.Cms method)
get_metals_and_neighbors() (in module schrodinger.structutils.rgroup_enumerate)
get_min_max_avg() (in module schrodinger.application.matsci.uq_utils)
get_min_occurs() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
get_minus_indexes() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.charge)
get_mmshare_common_dir() (in module schrodinger.utils.fileutils)
get_mmshare_data_dir() (in module schrodinger.utils.fileutils)
get_mmshare_dir() (in module schrodinger.utils.fileutils)
get_mmshare_listing() (in module schrodinger.application.licensing.licadmin)
get_mmshare_reagent_data_dir() (in module schrodinger.application.pathfinder.reaction)
get_mmshare_scripts_dir() (in module schrodinger.utils.fileutils)
get_mmshare_version() (in module schrodinger)
get_model_by_name() (in module schrodinger.application.livedesign.upload_utils)
get_model_system_type() (in module schrodinger.application.desmond.cms)
get_module_docstring() (in module schrodinger.utils.install_scripts)
get_module_from_path() (in module schrodinger.utils.imputils)
get_mol() (in module schrodinger.rdkit.molio)
get_mol_ids() (schrodinger.utils.multifpfile.MultiFPFile method)
get_mol_layers() (in module schrodinger.livedesign.molhash)
get_mol_reader() (in module schrodinger.rdkit.molio)
get_mol_writer() (in module schrodinger.rdkit.molio)
get_molecule_exposures() (in module schrodinger.application.desmond.solubility_utils)
get_molhash() (in module schrodinger.livedesign.molhash)
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_mpl_backend_name() (in module schrodinger)
get_msj_filename() (in module schrodinger.application.desmond.util)
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_filter() (in module schrodinger.utils.fileutils)
get_nat_todo_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
get_natoms_in_term() (in module schrodinger.application.desmond.packages.restraint.builder)
get_neb_atomic_forces_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_neb_cell_parameters_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_neb_images_positions_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_neighbor_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
get_netsuite_license() (in module schrodinger.application.licensing.licadmin)
get_network_info() (in module schrodinger.application.licensing.licadmin)
get_next_filename() (in module schrodinger.utils.fileutils)
get_next_filename_prefix() (in module schrodinger.utils.fileutils)
get_next_partition() (in module schrodinger.application.desmond.autopartition)
get_next_partition_array() (in module schrodinger.application.dendrogram.core_class)
get_no_stereo_layers() (in module schrodinger.livedesign.molhash)
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_normalized_vector() (in module schrodinger.structutils.transform)
get_notification_method() (in module schrodinger.test.perceptualdiff)
get_nrep() (schrodinger.application.desmond.replica_dE.replica_container method)
(schrodinger.application.desmond.replica_dE.replicas_monitor method)
get_num_constraint() (in module schrodinger.application.desmond.remd)
(schrodinger.application.desmond.cms.Cms method)
get_num_nonwateratom() (in module schrodinger.application.desmond.remd)
get_num_rotatable_bonds() (in module schrodinger.structutils.analyze)
get_num_wateratom() (in module schrodinger.application.desmond.remd)
get_number_electrons() (in module schrodinger.application.jaguar.utils)
get_numeric_property_range() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils)
get_old2new() (in module schrodinger.application.desmond.torsion_related)
get_opengl_version_string() (in module schrodinger.test.perceptualdiff)
get_openmpi_env() (in module schrodinger.utils.openmpi)
get_openmpi_prefix() (in module schrodinger.utils.openmpi)
get_opt_string() (schrodinger.utils.singledashoptionparser.SingleDashOption method)
get_optimal_atom_mapping() (in module schrodinger.structutils.rmsd)
get_option() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
get_option_group() (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_seq_name() (in module schrodinger.protein.tasks.structure_alignment)
get_orthant_strings() (in module schrodinger.application.combinatorial_diversity.splitter_utils)
get_osname() (in module schrodinger.utils.sysinfo)
get_output_logger() (in module schrodinger.utils.log)
get_output_logger_handler() (in module schrodinger.utils.log)
get_pair_rule_env_ids() (in module schrodinger.application.phase.packages.mmp2d)
get_params() (schrodinger.application.matsci.mlearn.base.BaseFeaturizer method)
get_pargph() (in module schrodinger.application.desmond.rl_helper)
get_path_from_module() (in module schrodinger.utils.imputils)
get_pattern() (schrodinger.application.matsci.xrd.XRDCalculator method)
get_pbc() (in module schrodinger.structutils.pbc_tools)
get_pdb() (in module schrodinger.protein.getpdb)
(in module schrodinger.test.stu.get_pdbs)
get_pdb_list() (in module schrodinger.test.stu.get_pdbs)
get_pdb_protein_bfactor() (in module schrodinger.application.desmond.packages.analysis)
get_pdir() (in module schrodinger.application.desmond.packages.viparr1)
get_percent_screen_curve_points() (in module schrodinger.analysis.enrichment.plotter)
get_pfx_size() (in module schrodinger.rdkit.molio)
get_placeholders() (in module schrodinger.structutils.markush_enumerate)
get_plot() (schrodinger.application.matsci.xrd.XRDCalculator method)
get_plot_data() (in module schrodinger.analysis.enrichment.plotter)
get_points_in_region() (in module schrodinger.application.matsci.uq_utils)
get_pos_vel() (schrodinger.application.desmond.cms.Cms method)
get_positions_units() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
get_potential() (schrodinger.application.desmond.torsion_related.TorsionPotential method)
get_preference() (in module schrodinger.utils.preferences)
get_prime_factors() (in module schrodinger.application.desmond.autopartition)
get_print_simbox_data() (in module schrodinger.application.desmond.simulation_block_data)
get_prob_from_temp_ladder() (in module schrodinger.application.desmond.remd)
get_process_name() (in module schrodinger.test.performance.general)
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_prog_name() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
get_prop() (in module schrodinger.application.glide.xpdes)
(schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method)
(schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method)
get_prop_idx() (in module schrodinger.application.glide.xpdes)
get_prop_value() (schrodinger.application.desmond.simulation_block_data.Array_Prop method)
get_proper_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
get_property_name() (in module schrodinger.structutils.smiles)
get_property_names() (in module schrodinger.application.phase.packages.mmp2d)
get_property_values() (in module schrodinger.application.phase.packages.mmp2d)
get_protein_families() (in module schrodinger.protein.gpcr.gpcrdb)
get_protein_residues_sequence_tags() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
get_pseudo_terms() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
get_public_databases() (in module schrodinger.application.fpsim)
get_public_ids() (in module schrodinger.application.phase.packages.mmp2d)
get_pyatom_from_cppatom() (in module schrodinger.structure)
get_pymol_cmd() (in module schrodinger.utils.fileutils)
get_python_versions() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
get_qe_input() (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
get_qpoints_card() (in module schrodinger.application.matsci.qeschema.qeschema.cards)
(in module schrodinger.application.matsci.qexsd.qespresso.cards)
get_rank() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDComplexType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method)
get_rate() (in module schrodinger.math.multi_parameter_optimization)
get_rb_potential() (in module schrodinger.application.desmond.torsion_related)
get_rb_torsions_potential() (in module schrodinger.application.desmond.torsion_related)
get_reactant_combo_sim() (in module schrodinger.application.combinatorial_screen.fingerprint_utils)
get_reactions() (in module schrodinger.application.pathfinder.reaction)
get_reader() (in module schrodinger.pipeline.pipeutils)
get_recep_structure_from_grid() (in module schrodinger.application.glide.utils)
get_reflection_matrix() (in module schrodinger.structutils.transform)
get_regex_patterns_of_lines_to_skip() (in module schrodinger.utils.compare)
get_release_name() (in module schrodinger)
get_remote_gpgpus() (in module schrodinger.infra.gpgpu_utils)
get_remote_path() (in module schrodinger.job.remote_command)
get_removed() (in module schrodinger.models.diffy)
get_removed_dict() (in module schrodinger.models.diffy)
get_removed_list() (in module schrodinger.models.diffy)
get_removed_set() (in module schrodinger.models.diffy)
get_report() (in module schrodinger.application.desmond.solubility_utils)
get_residue_annotations() (in module schrodinger.protein.gpcr.annotate)
get_residue_asl() (in module schrodinger.structutils.sitealign)
get_residue_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
get_residue_name() (schrodinger.protein.analysis.Report method)
get_residues_between() (in module schrodinger.structutils.residue)
get_residues_by_connectivity() (in module schrodinger.structure)
get_residues_for_asl() (in module schrodinger.application.bioluminate.protein_protein_docking_shared)
get_residues_unsorted() (in module schrodinger.structure)
get_rest_params() (in module schrodinger.application.desmond.remd)
get_restrain() (schrodinger.application.desmond.cms.Cms method)
get_result() (schrodinger.application.matsci.qb_sdk.job.QubecJob method)
get_rgb_from_color_index() (in module schrodinger.structutils.color)
get_rgroup_decomp() (in module schrodinger.livedesign.rgroup_decomposition)
get_rlabels_map() (in module schrodinger.application.scaffold_enumeration.markush)
get_rlabels_set() (in module schrodinger.application.scaffold_enumeration.markush)
get_roc_curve_points() (in module schrodinger.analysis.enrichment.plotter)
get_rotable_bonds() (in module schrodinger.application.desmond.r_group_asl)
get_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_rsh_exec() (in module schrodinger.job.remote_command)
get_rule_env_rule_id() (in module schrodinger.application.phase.packages.mmp2d)
get_rule_env_stats() (in module schrodinger.application.phase.packages.mmp2d)
get_rule_id_rule_smiles() (in module schrodinger.application.phase.packages.mmp2d)
get_safe_package() (in module schrodinger.application.matsci.codeutils)
get_salt_bridge_params() (in module schrodinger.structutils.interactions.salt_bridge)
get_salt_bridges() (in module schrodinger.structutils.interactions.salt_bridge)
get_sbt_tests() (in module schrodinger.application.desmond.simulation_block_test)
get_scaff_without_non_graph_hydrogen_rgroups() (in module schrodinger.livedesign.rgroup_decomposition)
get_schrodinger_temp_dir() (in module schrodinger.utils.fileutils)
get_scores() (in module schrodinger.application.jaguar.utils)
get_sd_reader() (in module schrodinger.livedesign.convert)
get_seqres() (in module schrodinger.protein.seqres)
get_sequence() (in module schrodinger.protein.gpcr.annotate)
get_sequence_file_format() (in module schrodinger.utils.fileutils)
get_server_info() (in module schrodinger.job.server)
get_server_processes() (in module schrodinger.application.licensing.licadmin)
get_set() (schrodinger.protein.analysis.Report method)
get_sgroups() (in module schrodinger.application.scaffold_enumeration.common)
get_shape_data() (schrodinger.application.vss.config.Config method)
(schrodinger.application.vss.database.Database method)
get_shared_file_listing() (in module schrodinger.application.licensing.licadmin)
get_shortest_distance() (in module schrodinger.structutils.measure)
get_sidechain_indices() (schrodinger.protein.analysis.Report.local_residue method)
get_sigmoid() (in module schrodinger.math.multi_parameter_optimization)
get_significant_figures() (in module schrodinger.math.mathutils)
get_site_mask_summary() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils)
get_site_masks() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils)
get_site_nondefaults() (in module schrodinger.utils.featureflags.featureflags)
get_site_tol() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils)
get_site_tol_probes() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils)
get_site_tol_summary() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils)
get_ska_transformation_matrix() (in module schrodinger.application.ska)
get_smiles() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData static method)
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_solvent_cts() (schrodinger.application.desmond.cms.Cms method)
get_sorted_shortest_path() (in module schrodinger.application.matsci.graph)
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_specie_related_values() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_starting_magnetization() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_state_string() (in module schrodinger.utils.featureflags.featureflags)
get_status() (schrodinger.application.matsci.qb_sdk.job.QubecJob method)
get_stereo_tautomer_hash() (in module schrodinger.livedesign.molhash)
get_steric_clashes() (in module schrodinger.structutils.interactions.steric_clash)
get_stoichiometry_string() (in module schrodinger.application.jaguar.utils)
get_stream_handler() (in module schrodinger.utils.log)
get_stress() (schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
get_structure_file_format() (in module schrodinger.utils.fileutils)
get_structure_ids() (in module schrodinger.application.livedesign.io_utils)
get_sub_graphs() (in module schrodinger.application.matsci.graph)
get_subgraphs() (in module schrodinger.thirdparty.networkx_algos)
get_subst_from_mapping() (in module schrodinger.application.desmond.fep_mapping)
get_subst_score() (schrodinger.application.combiglide.corehop.SubstCoreDatabase method)
get_subtrees() (in module schrodinger.thirdparty.networkx_algos)
get_summary() (in module schrodinger.application.bioluminate.propka_parse)
get_super_transformation_matrix() (in module schrodinger.structutils.rmsd)
get_surfnet_gaps() (in module schrodinger.application.bindingsite.cavutils)
get_symmops_from_spglib() (in module schrodinger.application.matsci.nano.space_groups)
get_system_eamp() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_system_edir() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_system_nspin() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
get_table_schema() (in module schrodinger.application.desmond.packages.restraint.builder)
get_template_vars() (in module schrodinger.application.livedesign.upload_utils)
get_test_owners() (in module schrodinger.test.pytest)
get_tg_props() (in module schrodinger.application.matsci.msprops)
get_ticks() (in module schrodinger.application.desmond.fep_edge_data)
get_title() (in module schrodinger.application.pathfinder.reaction)
get_titration_ct() (schrodinger.application.desmond.cms.Cms method)
get_top_level_props() (in module schrodinger.application.desmond.simulation_block_data)
get_total_charge() (in module schrodinger.application.jaguar.utils)
get_total_energy() (schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
get_traj_filename() (in module schrodinger.application.desmond.util)
get_trajectory_extname() (in module schrodinger.application.desmond.packages.traj)
get_transfer_free_energy() (in module schrodinger.application.desmond.solubility_utils)
get_transformations() (in module schrodinger.application.phase.packages.mmp2d)
get_translation_matrix() (in module schrodinger.structutils.transform)
get_type() (schrodinger.application.desmond.enhsamp.Bind method)
(schrodinger.application.desmond.enhsamp.FcnCall method)
(schrodinger.application.desmond.enhsamp.If method)
(schrodinger.application.desmond.enhsamp.Iter method)
(schrodinger.application.desmond.enhsamp.Let method)
(schrodinger.application.desmond.enhsamp.Lit method)
(schrodinger.application.desmond.enhsamp.Node method)
(schrodinger.application.desmond.enhsamp.Series method)
(schrodinger.application.desmond.enhsamp.String method)
(schrodinger.application.desmond.enhsamp.Var method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method)
get_typenames() (schrodinger.utils.multifpfile.MultiFPFile method)
get_umbrella_mode_command_line() (in module schrodinger.application.desmond.fep_util)
get_uname() (in module schrodinger.utils.sysinfo)
get_unencrypted_text() (in module schrodinger.application.matsci.enc)
get_unique_seq_names() (in module schrodinger.protein.tasks.structure_alignment)
get_updated() (in module schrodinger.models.diffy)
get_updated_dict() (in module schrodinger.models.diffy)
get_uploaded_model_url() (in module schrodinger.application.livedesign.upload_utils)
get_url() (in module schrodinger.protein.gpcr.gpcrdb)
get_usage() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
get_user_feature_env() (in module schrodinger.utils.featureflags.featureflags)
get_user_name() (in module schrodinger.application.matsci.msprops)
get_userdata_dir() (in module schrodinger.utils.fileutils)
get_username() (in module schrodinger.application.livedesign.login)
get_val() (in module schrodinger.utils.sea.sea)
get_value() (schrodinger.utils.sea.sea.Map method)
get_vdw() (schrodinger.application.desmond.cms.Cms method)
get_vdw_radius() (schrodinger.protein.analysis.Report method)
get_vector_magnitude() (in module schrodinger.structutils.transform)
get_version() (schrodinger.models.json.JsonableClassMixin method)
(schrodinger.models.jsonable.JsonableNamedTuple method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.models.jsonable.JsonableTuple method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
get_wavefunctions() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils)
get_weighted_score() (in module schrodinger.math.multi_parameter_optimization)
get_wf_attributes() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils)
get_wfc_miller_indices() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils)
get_working_resources() (in module schrodinger.application.licensing.licadmin)
get_xy_url() (in module schrodinger.application.desmond.gchart)
getActiveRankCsvRows() (schrodinger.analysis.enrichment.calculator.Calculator method)
getAddCtCount() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getAddCts() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getAddedFuncs() (schrodinger.utils.funcchains.FuncChainMixin method)
(schrodinger.utils.funcgroups.FuncGroupMixin method)
getAlignedMobileStructures() (schrodinger.structutils.sitealign.BindingSiteAligner method)
getAllArrayCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
getAllPreferences() (schrodinger.utils.preferences.Preferences method)
getAllSpaceGroups() (schrodinger.application.matsci.nano.space_groups.SpaceGroups method)
getAllVisibleLeaves() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
getAllWorldCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
getAlnFilename() (schrodinger.application.prime.wrapper.BasePrimeAlignment method)
getAlpha() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
getAlphaCarbon() (schrodinger.structure._Residue method)
getAncestor() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getAncestors() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method)
getAngleDerv() (in module schrodinger.application.matsci.gsas.GSASIImath)
GetAngleSig() (in module schrodinger.application.matsci.gsas.GSASIImath)
getAngSig() (in module schrodinger.application.matsci.gsas.GSASIImath)
getAromaticRingAtoms() (schrodinger.application.dendrogram.core_class.Utilities static method)
getArray() (schrodinger.trajectory.prody.mode.Mode method)
(schrodinger.trajectory.prody.mode.Vector method)
(schrodinger.trajectory.prody.mode.VectorBase method)
(schrodinger.trajectory.prody.modeset.ModeSet method)
(schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
getArrayNx3() (schrodinger.trajectory.prody.mode.Mode method)
(schrodinger.trajectory.prody.mode.Vector method)
(schrodinger.trajectory.prody.mode.VectorBase method)
GetAsfMean() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getAsl() (schrodinger.structure._Residue method)
getAtArrayCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
getAtArrayCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
getAtomBondTypingSchemeDescription() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
getAtomByPdbName() (schrodinger.structure._Residue method)
GetAtomCoordsByID() (in module schrodinger.application.matsci.gsas.GSASIImath)
GetAtomFracByID() (in module schrodinger.application.matsci.gsas.GSASIImath)
getAtomIndices() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure._AtomCollection method)
(schrodinger.structure._Chain method)
(schrodinger.structure._Molecule method)
(schrodinger.structure._Residue method)
(schrodinger.structure._Ring method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
GetAtomInfo() (in module schrodinger.application.matsci.gsas.GSASIIElem)
GetAtomItemsById() (in module schrodinger.application.matsci.gsas.GSASIImath)
getAtomList() (schrodinger.structure._AtomCollection method)
(schrodinger.structure._Chain method)
(schrodinger.structure._Molecule method)
(schrodinger.structure._Residue method)
(schrodinger.structure._Ring method)
getAtomPropertyNames() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
GetAtomsById() (in module schrodinger.application.matsci.gsas.GSASIImath)
getAtomTotal() (schrodinger.application.jaguar.results.JaguarResults method)
getAtomXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath)
getAtWorldCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
getAtWorldCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
getAutoCallerString() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method)
getAutoIndent() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method)
getAvailableFonts() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
getAverageDistanceFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getBackboneNitrogen() (schrodinger.structure._Residue method)
getBackboneOxygen() (schrodinger.structure._Residue method)
getBackground() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getBackgroundDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getBacktrackingLevel() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getBending() (schrodinger.structutils.minimize.Minimizer method)
getBendingEnergy() (schrodinger.structutils.minimize.Minimizer method)
getBestMatch() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method)
(schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
getBestNumberOfClusters() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getBeta() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
getBetaCarbon() (schrodinger.structure._Residue method)
getBindingSiteTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getBlock() (schrodinger.application.phase.packages.shape_binary_utils.ShapeFileReader method)
(schrodinger.application.phase.packages.shape_binary_utils.SingularShapeFileReader method)
GetBLtable() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getBLvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getBond() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
getBondedEnergies() (schrodinger.structutils.minimize.Minimizer method)
getBondedEnergyComponents() (schrodinger.structutils.minimize.Minimizer method)
getBondedInteractionEnergy() (schrodinger.structutils.minimize.Minimizer method)
getBranchColor() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
GetBraviasNum() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
getCanonicalBondRep() (in module schrodinger.livedesign.molhash)
getCarbonylCarbon() (schrodinger.structure._Residue method)
getCatalogEntry() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
getCell() (schrodinger.application.desmond.packages.msys.System method)
getChain() (schrodinger.structure._StructureAtom method)
getChainAtoms() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
getChannel() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
getCharErrorDisplay() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
getCharIndex() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
getCharPositionInLine() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
getChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getChildCount() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getChildIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getChildren() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
getChoiceSpectrum() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing static method)
getClusterContents() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getClusteringMap() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getClusterOrderMap() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getClusterTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getClusterVariance() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getCnst() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getCode() (schrodinger.structure._Residue method)
getColorSchemesDirPath() (schrodinger.structutils.color.ColorScheme method)
getColumnIndex() (schrodinger.infra.table.Table method)
GetColumnMetadata() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
getColumnNames() (schrodinger.infra.table.Table method)
getColumnTotal() (schrodinger.infra.table.Table method)
getCommand() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.MakefileTest 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)
getConnectivityChain() (schrodinger.analysis.substructure.ConnectedMoleculeChain method)
getCoordinates() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
getCoords() (schrodinger.trajectory.prody.ensemble.Ensemble method)
getCount() (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)
getCovariance() (schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA 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)
getCsvRows() (schrodinger.analysis.enrichment.calculator.Calculator method)
GetCSxinel() (in module schrodinger.application.matsci.gsas.GSASIIspc)
getCurrentAtomBondTyping() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
getCurrentInputSymbol() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getCurrentLinkage() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getCurrentPageContent() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
getCurrentSymbol() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
getCurrentType() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
getCustom() (schrodinger.application.desmond.packages.staf.GeomCalc 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)
getData() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
GetDATSig() (in module schrodinger.application.matsci.gsas.GSASIImath)
getDebugLevel() (schrodinger.job.launchparams.LaunchParameters method)
getDebugListener() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
getDefaultAtomTypingScheme() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
getDendrogramData() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getDensity() (in module schrodinger.application.matsci.gsas.GSASIImath)
getdEpsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getDescription() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
(schrodinger.application.desmond.antlr3.dfa.DFA method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25 method)
(schrodinger.structutils.color.ColorScheme method)
getDeviations() (schrodinger.trajectory.prody.ensemble.Ensemble method)
getdFCJVoigt3() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getDict() (schrodinger.application.matsci.msconst.DIMENSIONALITY class method)
getDihedralAtoms() (schrodinger.structure._Residue method)
getDisplayAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getDisplaySmarts() (schrodinger.application.pathfinder.reaction.Reaction method)
getDistance() (schrodinger.application.desmond.packages.staf.GeomCalc method)
(schrodinger.ui.dendrogram.DendrogramNode method)
getDistanceMatrixFile() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getDistanceToCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getDistDerv() (in module schrodinger.application.matsci.gsas.GSASIImath)
GetDistSig() (in module schrodinger.application.matsci.gsas.GSASIImath)
getDoubleAndTripleRingAtoms() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
getdPsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getEigval() (schrodinger.trajectory.prody.mode.Mode method)
getEigvals() (schrodinger.trajectory.prody.modeset.ModeSet method)
(schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
getEigvec() (schrodinger.trajectory.prody.mode.Mode method)
getEigvecs() (schrodinger.trajectory.prody.modeset.ModeSet method)
(schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
getEleEnergy() (schrodinger.structutils.minimize.Minimizer method)
GetElInfo() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getElSym() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getEncoded() (schrodinger.application.desmond.packages.restraint.builder.RestraintBuilder method)
getEnergy() (schrodinger.application.prime.residue_interaction.InteractionReader method)
(schrodinger.structutils.minimize.Minimizer method)
getEntries() (schrodinger.analysis.transformations.TransformsRepository method)
GetEOFHitOnRead() (schrodinger.rdkit.molio.GzippedSDMolSupplier method)
getEpsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getErrorHandler() (schrodinger.structure.MaestroReader method)
(schrodinger.structure.PDBReader method)
(schrodinger.structure.SDReader method)
getErrorHeader() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getErrorMessage() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getExcludedAtomList() (schrodinger.structutils.minimize.Minimizer method)
getExpandedRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method)
getExtendedRingAtomToRings() (schrodinger.application.dendrogram.core_class.Utilities static method)
getExtents() (schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method)
(schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method)
getFCJVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getFCJVoigt3() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getFcnSigs() (in module schrodinger.application.desmond.enhanced_sampling.FcnTypes)
getFd() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getFeatures() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
(schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
GetFFC5() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getFFIOblock() (schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
GetFFtable() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getFFvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getFHistogram() (schrodinger.application.desmond.replica_dE.replica_energy method)
getFilename() (schrodinger.infra.structure.WorkflowMenuMaestroWriter method)
getFileName() (schrodinger.structutils.color.ColorScheme 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.structutils.io.MultiFileWriter method)
getFingerprintDescription() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
getFingerprintString() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getFirstChildWithType() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getFirstNode() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
getFirstSelectedRow() (schrodinger.infra.table.Table method)
getFMax() (schrodinger.application.desmond.replica_dE.replica_energy method)
getFMean() (schrodinger.application.desmond.replica_dE.replica_energy method)
getFMin() (schrodinger.application.desmond.replica_dE.replica_energy method)
getFormat() (schrodinger.infra.structure.TextBlockReader method)
(schrodinger.infra.structure.TextBlockWriter method)
getFormattedNames() (schrodinger.application.dendrogram.core_class.GetPartitions method)
GetFormFactorCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getFuncGroup() (schrodinger.utils.funcchains.FuncChainMixin method)
(schrodinger.utils.funcgroups.FuncGroupMixin method)
getFWHM() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getgamFW() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
GetGenSym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
getGrammarFileName() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getGridSize() (schrodinger.infra.growthspace.GrowthSpaceGenerator method)
getGroup() (schrodinger.utils.preferences.Preferences method)
getGroupTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getHeader() (schrodinger.application.canvas.utils.ChmCSVTools method)
(schrodinger.rdkit.molio.CsvMergeHandler method)
getHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getHideAtomsBeyondBindingSiteASL() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getHideAtomsNonpolarHydrogensASL() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getHistogramData() (schrodinger.application.matsci.uq_utils.BilinearHistogramData method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData 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)
gethookproxy() (schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.Makefile method)
getHostname() (schrodinger.job.launchparams.LaunchParameters method)
getHoveredNode() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
getHypoCt() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getHypoID() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getHypoSites() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getImportantRotatableBonds() (in module schrodinger.application.desmond.r_group_asl)
getImpTorsion() (schrodinger.structutils.minimize.Minimizer method)
getImpTorsionEnergy() (schrodinger.structutils.minimize.Minimizer method)
getIndex() (schrodinger.trajectory.prody.mode.Mode method)
getIndices() (schrodinger.trajectory.prody.modeset.ModeSet method)
getInPlaceRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method)
getInputStream() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
getInteractionEnergy() (schrodinger.structutils.minimize.Minimizer method)
getInteractionMatrix() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getIsFarthestFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getIsNearestToCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getIter() (schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method)
(schrodinger.application.scaffold_enumeration.common.EnumerableMixin method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method)
(schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method)
getIvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getJobname() (schrodinger.job.launchparams.LaunchParameters method)
getJson() (schrodinger.application.desmond.packages.restraint.builder.RestraintBuilder method)
GetKcl() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
GetKclKsl() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
getKelleyPenaltyList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getkey() (schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
getKeys() (schrodinger.application.matsci.hdfutils.HDFIO method)
(schrodinger.application.matsci.hdfutils.HDFProxyPickleIO method)
getKeyType() (schrodinger.utils.preferences.Preferences method)
getKindOfOps() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
GetKNsym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
GetKsl() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
getLabel() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramNode method)
getLabels() (schrodinger.ui.dendrogram.DendrogramTreeBuilder method)
getLastRewriteTokenIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
getlattSym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
getLaunchDirectory() (schrodinger.job.launchparams.LaunchParameters method)
getLeafIndices() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
getLicenseFileList() (in module schrodinger.application.licensing.licadmin)
getLicenseRequirements() (schrodinger.application.steps.licensing.LicenseMixin method)
getLigandID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getLigandTitle() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getLine() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
getLinkageDescription() (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
GetLittleGrpOps() (in module schrodinger.application.matsci.gsas.GSASIIspc)
getLJEnergy() (schrodinger.structutils.minimize.Minimizer method)
getLogger() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method)
getlogin() (in module schrodinger.application.desmond.util)
getLongName() (schrodinger.structutils.color.ColorScheme method)
getMaestroProjectDisposition() (schrodinger.job.launchparams.LaunchParameters method)
getMaestroProjectDispositionString() (schrodinger.job.launchparams.LaunchParameters method)
getMaestroProjectName() (schrodinger.job.launchparams.LaunchParameters method)
getMaestroViewname() (schrodinger.job.launchparams.LaunchParameters method)
GetMagFormFacCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getMask() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getMass() (in module schrodinger.application.matsci.gsas.GSASIImath)
getMatches() (schrodinger.application.ligprep.ionizer.Spec method)
getMatchingAtomMap() (schrodinger.structutils.sitealign.SiteMatchLookup method)
getMatchingAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getMatrixTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getMaxDistanceFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getMaxRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method)
getMaxRes() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getMaxStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method)
getMeanWave() (in module schrodinger.application.matsci.gsas.GSASIImath)
getMergeDistanceList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getMessage() (schrodinger.application.desmond.antlr3.tree.RewriteCardinalityException method)
(schrodinger.application.desmond.antlr3.tree.RewriteEarlyExitException method)
(schrodinger.application.desmond.antlr3.tree.RewriteEmptyStreamException method)
getMessages() (schrodinger.infra.mmerr.Capture method)
getMessagesOrDefault() (schrodinger.infra.mmerr.Capture method)
getMetric() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
getMetricStyle() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
GetMFtable() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getMFvalues() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getMinRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method)
getMinRes() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getMissingSymbol() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getMissingType() (schrodinger.application.desmond.antlr3.exceptions.MissingTokenException method)
getMobileStRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method)
getModel() (schrodinger.trajectory.prody.mode.Mode method)
(schrodinger.trajectory.prody.modeset.ModeSet method)
(schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
getMolecule() (schrodinger.structure._StructureAtom method)
getMoleculeAtoms() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
getMorganCount() (schrodinger.application.matsci.mlearn.descriptor.Featurize method)
getMovingAtoms() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
getNB14Pairs() (schrodinger.structutils.minimize.Minimizer method)
getNBEnergyForTwoAtomLists() (schrodinger.structutils.minimize.Minimizer method)
getNewSolution() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
getNextFormattedNameArray() (schrodinger.application.dendrogram.core_class.GetPartitions method)
getNode() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
getNodeIndex() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
getNonBondedEnergies() (schrodinger.structutils.minimize.Minimizer method)
getNonpolarHydrogensTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getNormalParameters() (schrodinger.application.matsci.uq_utils.BilinearHistogramData static method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData static method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData static method)
getNormed() (schrodinger.trajectory.prody.mode.Vector method)
getNumber() (schrodinger.application.desmond.replica_dE.replica_energy method)
getNumberOfClustersList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getNumberOfProcessorsManyNodes() (schrodinger.job.launchparams.LaunchParameters method)
getNumberOfProcessorsOneNode() (schrodinger.job.launchparams.LaunchParameters method)
getNumberOfQueueSlots() (schrodinger.job.launchparams.LaunchParameters method)
getNumberOfSubjobs() (schrodinger.job.launchparams.LaunchParameters method)
getNumberOfSyntaxErrors() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
GetNumDensity() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getNumLigands() (schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
getNumNodes() (schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
getNumStructures() (schrodinger.structure.MultiFileStructureWriter method)
(schrodinger.structutils.io.MultiFileWriter method)
getNumTargets() (schrodinger.application.livedesign.entry_types.BaseEntryData method)
(schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
GetNXUPQsym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
GetOpNum() (in module schrodinger.application.matsci.gsas.GSASIIspc)
GetOprName() (in module schrodinger.application.matsci.gsas.GSASIIspc)
GetOprNames() (in module schrodinger.application.matsci.gsas.GSASIIspc)
GetOprPtrName() (in module schrodinger.application.matsci.gsas.GSASIIspc)
GetOprPtrNumber() (in module schrodinger.application.matsci.gsas.GSASIIspc)
getOptionDesc() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
getOptions() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method)
(schrodinger.structutils.minimize.Minimizer method)
getOrAddColumn() (schrodinger.infra.table.Table method)
getOriginalName() (schrodinger.structutils.color.ColorScheme 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)
getOutputPaths() (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)
getOverride() (schrodinger.application.desmond.packages.msys.TermTable method)
getPageNumber() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
getParent() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getparent() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
GetPartitions (class in schrodinger.application.dendrogram.core_class)
GetPartitions.NameList (class in schrodinger.application.dendrogram.core_class)
getPatchColorRamp() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method)
getPath() (schrodinger.pipeline.pipeio.Grid method)
(schrodinger.pipeline.pipeio.PhaseDB method)
getPatternString() (schrodinger.structutils.createfragments.FragmentCreator method)
getpdfdata() (schrodinger.application.desmond.rl_helper.NumberedCanvas 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)
getPercentScreenCurvePoints() (schrodinger.analysis.enrichment.calculator.Calculator method)
getPiperDict() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method)
(schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method)
getPlanarAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method)
getPlotFigure() (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method)
(schrodinger.analysis.enrichment.plotter.Plotter method)
getPointsFromCalc() (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method)
(schrodinger.analysis.enrichment.plotter.Plotter method)
getPositions() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method)
(schrodinger.application.desmond.packages.msys.System method)
getPrecision() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
GetProcessPropertyLists() (schrodinger.rdkit.molio.GzippedSDMolSupplier 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)
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)
getProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
getprop() (in module schrodinger.livedesign.preprocessor)
getProp() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getPropertyNames() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.rdkit.filtering.JSONFilterAdapter method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
(schrodinger.structutils.filter.PropFilter method)
(schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getProteinTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getPsVoigt() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getQsar() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getRad() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getRamaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath)
getRandomRealization() (schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method)
(schrodinger.application.scaffold_enumeration.common.EnumerableMixin method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method)
(schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method)
getRBTransMat() (in module schrodinger.application.matsci.gsas.GSASIImath)
getRealization() (schrodinger.application.scaffold_enumeration.atomlist.AtomListEnumerable method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeEnumerable method)
(schrodinger.application.scaffold_enumeration.posvarbond.PosVarBondEnumerable method)
getReceptorID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getRefCt() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getRefSites() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getReplica() (schrodinger.application.desmond.replica_dE.replica_container method)
getResidue() (schrodinger.structure._StructureAtom method)
getResidueAtoms() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
getResidueID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getResidueType() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
getRestAngle() (in module schrodinger.application.matsci.gsas.GSASIImath)
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)
getRestRama() (in module schrodinger.application.matsci.gsas.GSASIImath)
getRestTorsion() (in module schrodinger.application.matsci.gsas.GSASIImath)
getRGB() (schrodinger.application.msv.gui.color_ramp.NamedColorRamp method)
(schrodinger.application.msv.gui.color_ramp.NamedRainbowColorRamp method)
(schrodinger.structutils.color.ColorRamp method)
(schrodinger.structutils.color.RainbowColorRamp method)
getRHistogram() (schrodinger.application.desmond.replica_dE.replica_energy method)
getRho() (in module schrodinger.application.matsci.gsas.GSASIImath)
getRhos() (in module schrodinger.application.matsci.gsas.GSASIImath)
getRingAtomToRings() (schrodinger.application.dendrogram.core_class.Utilities static method)
getRingDataStructures() (schrodinger.application.dendrogram.core_class.Utilities static method)
getRingSysInfo() (schrodinger.application.dendrogram.core_class.Deepest0 method)
(schrodinger.application.dendrogram.core_class.Deepest1 method)
(schrodinger.application.dendrogram.core_class.Deepest2 method)
(schrodinger.application.dendrogram.core_class.Deepest3a method)
(schrodinger.application.dendrogram.core_class.Deepest3b method)
(schrodinger.application.dendrogram.core_class.Deepest4 method)
(schrodinger.application.dendrogram.core_class.Deepest5 method)
(schrodinger.application.dendrogram.core_class.Deepest6 method)
getRingSysSt() (schrodinger.application.dendrogram.core_class.Utilities static method)
GetRingSystems() (in module schrodinger.application.desmond.packages.msys)
getRLMap() (schrodinger.application.livedesign.entry_types.BaseEntryData method)
(schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
getRMax() (schrodinger.application.desmond.replica_dE.replica_energy method)
getRMean() (schrodinger.application.desmond.replica_dE.replica_energy method)
getRMin() (schrodinger.application.desmond.replica_dE.replica_energy method)
getRMSD() (in module schrodinger.trajectory.prody.ensemble)
getRmsdDataname() (schrodinger.structutils.rmsd.ConformerRmsd method)
(schrodinger.structutils.rmsd.ConformerRmsdX method)
getroot() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
getRotEnergy() (schrodinger.application.desmond.torsion_related.BondRotator method)
getRow() (schrodinger.test.project_mock.MockProjectTable method)
getRSquaredList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getRuleInvocationStack() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getRuleMemoization() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getRules() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.structutils.color.ColorScheme 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)
getScene() (schrodinger.ui.dendrogram.DendrogramView method)
getSelectedNodes() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
getSelectedRows() (schrodinger.infra.table.Table method)
getSelectedRowTotal() (schrodinger.infra.table.Table method)
getSelfEnergy() (schrodinger.structutils.minimize.Minimizer method)
getSemiPartialRSquaredList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
getSeparationRatioList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
GetSGSpin() (in module schrodinger.application.matsci.gsas.GSASIIspc)
GetSHCoeff() (in module schrodinger.application.matsci.gsas.GSASIImath)
getShortName() (schrodinger.structutils.color.ColorScheme method)
getSimilarityMetricDescription() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
getSite() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getSiteByDisplayName() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getSiteCount() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getSiteIndexFromDisplayName() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getSiteNumber() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getSiteTypes() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getSmarts() (schrodinger.analysis.transformations.TransformsRepository method)
getSmiles() (schrodinger.structutils.smiles.SmilesGenerator method)
getSmilesAndMap() (schrodinger.structutils.smiles.SmilesGenerator method)
getSolventsTooltip() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
getSourceName() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getSources() (schrodinger.application.fpsim.FPsimSearcher method)
getSpecsString() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
getSpgObjByName() (schrodinger.application.matsci.nano.space_groups.SpaceGroups method)
getSSA() (schrodinger.application.prime.wrapper.BasePrimeAlignment method)
GetSSfxuinel() (in module schrodinger.application.matsci.gsas.GSASIIspc)
GetSSSR() (in module schrodinger.application.desmond.packages.msys)
GetStackParms() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getStandardizedSmiles() (schrodinger.structutils.smiles.SmilesGenerator method)
getStart() (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method)
(schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method)
(schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.atom_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.bind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.block_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.comp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_meta_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_output_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expr_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.exprOrBind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.factor_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.fcnCall_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.header_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.if__return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.iter_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.meta_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.output_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.prog_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.series_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.signedExpComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.static_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.varWithType_return method)
getstart_temp() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method)
(schrodinger.application.matsci.gsas.GSASIImath.fast_sa method)
(schrodinger.application.matsci.gsas.GSASIImath.log_sa method)
getStop() (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method)
(schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method)
(schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.atom_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.bind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.block_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.comp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_meta_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_output_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expr_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.exprOrBind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.factor_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.fcnCall_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.header_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.if__return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.iter_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.meta_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.output_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.prog_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.series_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.signedExpComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.static_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.varWithType_return method)
getStretch() (schrodinger.structutils.minimize.Minimizer method)
getStretchEnergy() (schrodinger.structutils.minimize.Minimizer method)
getString() (schrodinger.application.desmond.packages.restraint.builder.RestraintBuilder method)
getStructure() (schrodinger.application.jaguar.results.JaguarResults method)
(schrodinger.structure.TextualStructure method)
(schrodinger.structutils.minimize.Minimizer method)
(schrodinger.test.project_mock.MockProjectRow method)
getStructureFile() (schrodinger.application.qsite.input.QSiteInput method)
getSubHostName() (schrodinger.job.launchparams.LaunchParameters method)
getSummary() (schrodinger.application.livedesign.entry_types.BaseEntryData method)
(schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getSuperimposedRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method)
getSyXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTable() (schrodinger.application.desmond.packages.msys.System method)
(schrodinger.application.desmond.packages.restraint.builder.Restraints method)
getTauT() (in module schrodinger.application.matsci.gsas.GSASIIspc)
getTemplate() (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method)
(schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method)
(schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.atom_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.bind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.block_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.comp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_meta_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_output_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expr_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.exprOrBind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.factor_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.fcnCall_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.header_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.if__return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.iter_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.meta_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.output_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.prog_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.series_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.signedExpComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.static_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.varWithType_return method)
getText() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
getTitle() (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.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
getTOFalpha() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTOFalphaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTOFbeta() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTOFbetaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTOFgamma() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTOFgammaDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTOFsig() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTOFsigDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath)
getToken() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getTokenErrorDisplay() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getTokenIndex() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
getTokens() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
getTokenSource() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
getTokenStartIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getTokenStopIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getTokenStream() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getTokenType() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method)
getTol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getTorsion() (schrodinger.application.desmond.packages.staf.GeomCalc method)
(schrodinger.structutils.minimize.Minimizer method)
getTorsionDeriv() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTorsionEnergy() (schrodinger.structutils.minimize.Minimizer method)
GetTorsionSig() (in module schrodinger.application.matsci.gsas.GSASIImath)
getTotal14Pair() (schrodinger.structutils.minimize.Minimizer method)
getTotalAtom() (schrodinger.structutils.minimize.Minimizer method)
getTotalBending() (schrodinger.structutils.minimize.Minimizer method)
getTotalEnergy() (schrodinger.structutils.minimize.Minimizer method)
getTotalImpTorsion() (schrodinger.structutils.minimize.Minimizer method)
getTotalStretch() (schrodinger.structutils.minimize.Minimizer method)
getTotalTorsion() (schrodinger.structutils.minimize.Minimizer method)
getTPP() (schrodinger.job.launchparams.LaunchParameters method)
getTrace() (schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
getTree() (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method)
(schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method)
(schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.atom_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.bind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.block_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.comp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_meta_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_output_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.decl_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.expr_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.exprOrBind_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.factor_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.fcnCall_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.header_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.if__return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.iter_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.meta_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.output_term_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.prog_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.series_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.signedExpComp_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.static_return method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.varWithType_return method)
getTreeAdaptor() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
getTreeNodeStream() (schrodinger.application.desmond.antlr3.tree.TreeParser method)
getTreeSource() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
getType() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
getUnexpectedToken() (schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException method)
getUnexpectedType() (schrodinger.application.desmond.antlr3.exceptions.EarlyExitException method)
(schrodinger.application.desmond.antlr3.exceptions.FailedPredicateException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedNotSetException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedRangeException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedSetException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTokenException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTreeNodeException method)
(schrodinger.application.desmond.antlr3.exceptions.MissingTokenException method)
(schrodinger.application.desmond.antlr3.exceptions.NoViableAltException method)
(schrodinger.application.desmond.antlr3.exceptions.RecognitionException method)
(schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException method)
GetUnique() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
getUniqueID() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
getUniqueOrder() (schrodinger.structutils.smiles.SmilesGenerator method)
getValue() (schrodinger.application.mopac.structure_launchers.StructureLauncher 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)
getVariance() (schrodinger.trajectory.prody.mode.Mode method)
getVariances() (schrodinger.trajectory.prody.modeset.ModeSet method)
(schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
getVCov() (in module schrodinger.application.matsci.gsas.GSASIImath)
getVector() (schrodinger.application.desmond.packages.staf.GeomCalc method)
getVelocities() (schrodinger.application.desmond.packages.msys.System method)
getViewerPreference() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
getVisibleColumnIndex() (schrodinger.infra.table.Table method)
getVisibleColumnTotal() (schrodinger.infra.table.Table method)
getVisibleRowIndex() (schrodinger.infra.table.Table method)
getVisibleRowTotal() (schrodinger.infra.table.Table method)
getWave() (in module schrodinger.application.matsci.gsas.GSASIImath)
getWeights() (schrodinger.trajectory.prody.ensemble.Ensemble method)
getWidthsCW() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getWidthsTOF() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
getWriter() (schrodinger.infra.structure.WorkflowMenuMaestroWriter static method)
GetXsectionCoeff() (in module schrodinger.application.matsci.gsas.GSASIIElem)
getXvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
getXYZ() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
GetXYZDist() (in module schrodinger.application.matsci.gsas.GSASIImath)
gibbs (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)
git_summary() (in module schrodinger.test.perceptualdiff)
Glide
Glnh() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
glue() (in module schrodinger.application.desmond.packages.pfx)
(in module schrodinger.application.desmond.packages.topo)
(schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.packages.msys.System method)
glue_cms() (in module schrodinger.application.desmond.packages.pfx)
(in module schrodinger.application.desmond.packages.topo)
glued_topology (schrodinger.application.desmond.cms.Cms property)
(schrodinger.application.desmond.packages.msys.System property)
Gmat2A() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
Gmat2AB() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
Gmat2cell() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
GOOD (schrodinger.application.desmond.fep_edge_data_classifier.Rating attribute)
GOOD_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
GPU (schrodinger.job.resource.ComputeType attribute)
GPUCardInfo (class in schrodinger.test.cluster_info)
grab() (schrodinger.ui.dendrogram.DendrogramView method)
grabGesture() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramView method)
grabKeyboard() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
grabMouse() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
grabShortcut() (schrodinger.ui.dendrogram.DendrogramView method)
grad_prec (schrodinger.application.jaguar.results.ConvCriteria attribute)
gradient_convergence (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
gradient_criterion (schrodinger.structutils.minimize.Minimizer property)
grammarFileName (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
Graph (class in schrodinger.application.desmond.packages.msys)
graphicsEffect() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
graphicsProxyWidget() (schrodinger.ui.dendrogram.DendrogramView method)
GRAY (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
(schrodinger.ui.qt.standard.colors.NativeColors attribute)
Grease() (in module schrodinger.application.desmond.packages.msys.grease)
GREEN (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
(schrodinger.ui.qt.standard.colors.NativeColors attribute)
greyColorMap() (in module schrodinger.application.matsci.plotwidgets)
Grid (class in schrodinger.application.bindingsite.cavutils)
(class in schrodinger.application.desmond.packages.msys.molfile)
(class in schrodinger.pipeline.pipeio)
grid() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
grid_property (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
group() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
group_by_connectivity() (in module schrodinger.structutils.analyze)
group_id (schrodinger.structutils.markush_enumerate.PlaceHolder attribute)
group_items() (in module schrodinger.application.jaguar.utils)
groups (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
grow_fragment() (in module schrodinger.protein.buildpeptide)
grow_mult() (in module schrodinger.structutils.build)
growname (schrodinger.structure._StructureAtom property)
GrowthSpaceGenerator (class in schrodinger.infra.growthspace)
guess_filetype() (in module schrodinger.application.desmond.packages.msys.molfile)
guess_value_type() (schrodinger.utils.sea.sea.Atom static method)
(schrodinger.utils.sea.sea.Hydrogen static method)
guessBonds() (schrodinger.application.desmond.packages.msys.System method)
Gyradius (class in schrodinger.application.desmond.packages.analysis)
gz_fname_if_exists() (in module schrodinger.application.desmond.util)
gzip_open() (in module schrodinger.trajectory.prody.writenmd)
GzippedSDMolSupplier (class in schrodinger.rdkit.molio)
H
H2O (schrodinger.energy.Solvent attribute)
H_bonds (schrodinger.application.glide.xpdes.TermKeywords attribute)
ha2ry() (in module schrodinger.application.matsci.qeschema.qeschema.options)
Ha2Ry() (in module schrodinger.application.matsci.qexsd.qespresso.options)
HalogenBondFinder (class in schrodinger.application.desmond.packages.analysis)
Handle (class in schrodinger.application.desmond.packages.msys)
handle_check_action() (in module schrodinger.application.licensing.licadmin)
handle_diag_action() (in module schrodinger.application.licensing.licadmin)
handle_generic_action() (in module schrodinger.application.licensing.licadmin)
handle_info_action() (in module schrodinger.application.licensing.licadmin)
handle_install_action() (in module schrodinger.application.licensing.licadmin)
handle_list_action() (in module schrodinger.application.licensing.licadmin)
handle_start_action() (in module schrodinger.application.licensing.licadmin)
handle_stat_action() (in module schrodinger.application.licensing.licadmin)
handle_stop_action() (in module schrodinger.application.licensing.licadmin)
handle_ver_action() (in module schrodinger.application.licensing.licadmin)
handle_verify_action() (in module schrodinger.application.licensing.licadmin)
handshake() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
has3dCoords() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
has_authenticator() (schrodinger.job.server.ServerInfo method)
has_cloud_services() (in module schrodinger.application.steps.env_keys)
has_fepio() (in module schrodinger.application.desmond.cms)
has_ffio() (in module schrodinger.application.desmond.cms)
has_key() (schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.sea.sea.Map method)
has_license_file_suffix() (in module schrodinger.application.licensing.licadmin)
has_option() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
has_persistent (schrodinger.application.desmond.packages.restraint.builder.Restraints property)
has_plink_ssh_host_key() (in module schrodinger.utils.sshconfig)
has_positional (schrodinger.application.desmond.packages.restraint.builder.Restraints property)
has_positional_restraints() (in module schrodinger.application.desmond.packages.restraint.builder)
has_seqres() (in module schrodinger.protein.seqres)
has_tag() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
has_undefined_stereo() (in module schrodinger.utils.cgxutils)
has_valid_lewis_structure() (in module schrodinger.structutils.analyze)
has_velocities (schrodinger.application.desmond.cms.Cms property)
has_vertex_colors (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
hasAddCts() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasAncestor() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
hasCnst() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasCursor() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
hasData() (schrodinger.application.prime.residue_interaction.InteractionReader class method)
hasFepio() (schrodinger.application.desmond.ffiostructure.FFIOStructure method)
hasFfio() (schrodinger.application.desmond.ffiostructure.FFIOStructure method)
hasFocus() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
hasForm() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
hash() (schrodinger.application.desmond.packages.msys.Graph method)
hash_for_file() (in module schrodinger.utils.fileutils)
hasHeightForWidth() (schrodinger.ui.dendrogram.DendrogramView method)
HashLayer (class in schrodinger.livedesign.molhash)
HashScheme (class in schrodinger.livedesign.molhash)
hasIvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method)
hasLicenseChecking (schrodinger.job.server.ServerInfo attribute)
hasMask() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasMissingAtoms() (schrodinger.structure._Residue method)
hasMouseTracking() (schrodinger.ui.dendrogram.DendrogramView method)
hasNext() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
hasProp() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasQsar() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasRad() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasRefCt() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasRules() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasServerAuth (schrodinger.job.server.ServerInfo attribute)
hasSocketAuth (schrodinger.job.server.ServerInfo attribute)
hasTabletTracking() (schrodinger.ui.dendrogram.DendrogramView method)
hasTerm() (schrodinger.application.desmond.packages.msys.TermTable method)
hasTol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hasUniqueNavigationNodes() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
hasXvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
hbond_iterator() (in module schrodinger.structutils.analyze)
hcount() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method)
HDFIO (class in schrodinger.application.matsci.hdfutils)
HDFProxyPickleIO (class in schrodinger.application.matsci.hdfutils)
HDFStore() (in module schrodinger.application.matsci.hdfutils)
header (schrodinger.application.jaguar.results.ScfIteration attribute)
header() (in module schrodinger.application.desmond.rl_helper)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
(schrodinger.application.qsite.input.Cut method)
(schrodinger.application.qsite.input.HydrogenCap method)
HEADER_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
headerToEnv() (in module schrodinger.application.desmond.enhsamp)
health() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
healthier() (in module schrodinger.application.licensing.licadmin)
heat_of_formation() (in module schrodinger.application.mopac.results_main)
heavy_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
HEAVY_HYDROGEN_DT (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
height() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
heightForWidth() (schrodinger.ui.dendrogram.DendrogramView method)
heightMM() (schrodinger.ui.dendrogram.DendrogramView method)
HELIX (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute)
help() (in module schrodinger.test.stu.outcomes.compare_csv)
helpEvent() (schrodinger.ui.dendrogram.DendrogramScene method)
HessianLSQ() (in module schrodinger.application.matsci.gsas.GSASIImath)
HessianSVD() (in module schrodinger.application.matsci.gsas.GSASIImath)
HETEROMULTIMER (schrodinger.application.msv.gui.homology_modeling.constants.Mode attribute)
HeteromultimerMode (class in schrodinger.application.msv.gui.homology_modeling.constants)
Hex_pairs (schrodinger.application.glide.xpdes.TermKeywords attribute)
Hex_sp (schrodinger.application.glide.xpdes.TermKeywords attribute)
hex_string (schrodinger.project.surface.ProjectSurface.Color property)
(schrodinger.structutils.color.Color property)
(schrodinger.surface.Surface.Color property)
HEXAGONAL_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute)
HIDDEN (schrodinger.application.desmond.antlr3.debug.DebugParser attribute)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Lexer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Parser attribute)
(schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
hide() (schrodinger.project.surface.ProjectSurface method)
(schrodinger.surface.Surface method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
hideEvent() (schrodinger.ui.dendrogram.DendrogramView method)
HIGH (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute)
highlightAnnotation() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
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)
hijackPos() (schrodinger.application.desmond.packages.traj.Frame method)
hit (schrodinger.application.matsci.cache.CacheInfo attribute)
HKL2SpAng() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
HLine (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shape attribute)
HOME (schrodinger.application.desmond.envir.CONST attribute)
homo_lumo_energy() (in module schrodinger.application.mopac.results_main)
homog_rank_2() (in module schrodinger.application.matsci.cctbx.rot_mx)
HOMOMULTIMER (schrodinger.application.msv.gui.homology_modeling.constants.Mode attribute)
honorHideAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
honorMatchingAtomsAsl() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
horizontalScrollBar() (schrodinger.ui.dendrogram.DendrogramView method)
horizontalScrollBarPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
host (schrodinger.application.licensing.lmgrd_log_parser.event attribute)
host_check() (in module schrodinger.job.host_check)
hostid_is_local() (in module schrodinger.application.licensing.licadmin)
hostid_order() (in module schrodinger.application.licensing.flexlm)
hostname (schrodinger.job.server.ServerInfo attribute)
hostname() (schrodinger.application.licensing.flexlm.Server method)
hostname_in_registry() (in module schrodinger.utils.sshconfig)
hostname_is_local() (in module schrodinger.application.licensing.licadmin)
hostport() (schrodinger.application.licensing.flexlm.Server method)
hoverEnter (schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
hoverEnterEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
hoverLeave (schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
hoverLeaveEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
hoverMoveEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
HStrainNames() (in module schrodinger.application.matsci.gsas.GSASIIspc)
HStrainVals() (in module schrodinger.application.matsci.gsas.GSASIIspc)
html_embed_image() (in module schrodinger.application.desmond.util)
hunt() (in module schrodinger.job.util)
Hx2Rh() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
HYBRID (schrodinger.forcefield.constants.GeometryOptMethod attribute)
hybridization() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method)
hyd_charge (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_forward (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_end_time_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_ensemble (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_ff (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_mol_number (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_rest_exchanges (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_sid_molsa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
hyd_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_sid_psa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
hyd_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
hyd_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
hyd_sid_sasa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
hyd_sid_snapshot_times_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_sim_time (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_start_time_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_temperature (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_total_atoms (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_total_replicas (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
hyd_total_waters (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
HYDRATION (schrodinger.application.desmond.constants.FepLegTypes attribute)
Hydrogen (class in schrodinger.utils.sea.sea)
HYDROGEN_BOND_ACCEPTOR (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
HYDROGEN_BOND_DONOR (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
HydrogenBondFinder (class in schrodinger.application.desmond.packages.analysis)
(class in schrodinger.application.desmond.packages.msys)
HydrogenCap (class in schrodinger.application.qsite.input)
Hydrogens (class in schrodinger.adapter)
hydrogens_present() (in module schrodinger.structutils.analyze)
HYDROKINETIC_RATING (schrodinger.infra.structure.WorkflowType attribute)
HYDROPHOB_ASL (schrodinger.application.desmond.packages.analysis.HydrophobicInterFinder attribute)
hydrophobic (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute)
HYDROPHOBIC_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
HYDROPHOBIC_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
HYDROPHOBIC_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
HydrophobicInter (class in schrodinger.application.desmond.packages.analysis)
HydrophobicInterFinder (class in schrodinger.application.desmond.packages.analysis)
HyperbolaHistogramData (class in schrodinger.application.matsci.uq_utils)
I
ichoice (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
id (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.application.desmond.packages.msys.Bond property)
(schrodinger.application.desmond.packages.msys.Chain property)
(schrodinger.application.desmond.packages.msys.Ct property)
(schrodinger.application.desmond.packages.msys.Handle property)
(schrodinger.application.desmond.packages.msys.Param property)
(schrodinger.application.desmond.packages.msys.Residue property)
(schrodinger.application.desmond.packages.msys.Term property)
id() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
(schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
ID_fab (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
ID_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
IdConversion (class in schrodinger.application.desmond.constants)
IdDict (class in schrodinger.utils.scollections)
ident() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
IdItemsView (class in schrodinger.utils.scollections)
ids (schrodinger.application.desmond.packages.msys.atomsel.Atomsel property)
IdSet (class in schrodinger.utils.scollections)
If (class in schrodinger.application.desmond.enhsamp)
if_() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
IFD_MD (schrodinger.application.desmond.constants.PRODUCT attribute)
Ignore (schrodinger.adapter.Coordinates attribute)
(schrodinger.adapter.Properties attribute)
(schrodinger.adapter.StereoChemistry attribute)
IGNORE (schrodinger.application.desmond.constants.EXISTING_RESTRAINT attribute)
(schrodinger.job.launchparams.ProjectDisposition attribute)
IGNORE_POSRE (schrodinger.application.desmond.constants.EXISTING_RESTRAINT attribute)
IgnoreMask (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.RenderFlag attribute)
ihook (schrodinger.test.perceptualdiff.PerceptualDiffTest property)
(schrodinger.test.pytest.exetest.ExecutableFile property)
(schrodinger.test.pytest.exetest.ExecutableTest property)
(schrodinger.test.pytest.exetest.Makefile property)
(schrodinger.test.pytest.exetest.MakefileTest property)
IMPLICIT (schrodinger.adapter.Hydrogens attribute)
import_from_file() (in module schrodinger.utils.imputils)
IMPORT_HOMOLOGS (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
import_module_from_file() (in module schrodinger.utils.imputils)
import_script() (in module schrodinger.utils.imputils)
IMPORT_SEQUENCE (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
IMPORT_SEQUENCES (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
importLA() (in module schrodinger.trajectory.prody.ensemble)
importStructure() (schrodinger.test.project_mock.MockProjectTable method)
importStructureFile() (schrodinger.test.project_mock.MockProjectTable method)
improper_dihedral_iterator() (in module schrodinger.structutils.analyze)
IMPROPER_FBHW (schrodinger.application.desmond.constants.RestrainTypes attribute)
in_temporary_directory() (in module schrodinger.utils.fileutils)
in_tmp_dir() (in module schrodinger.test.fixtures)
in_xy_plane() (in module schrodinger.livedesign.preprocessor)
InBounds() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
InChI (class in schrodinger.application.desmond.packages.msys)
INCHI (schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
INCHI_KEY (schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
included_rows (schrodinger.test.project_mock.MockProjectTable property)
includeOnly() (schrodinger.test.project_mock.MockProjectRow method)
includeRows() (schrodinger.test.project_mock.MockProjectTable method)
includes() (schrodinger.utils.ligfilter.Definition method)
IncompatibleLicenseError
IncompleteFragmentError
IncompleteOutput
InconsistentStructureError
,
[1]
inContext() (schrodinger.application.desmond.antlr3.tree.TreeParser method)
indent() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
index (schrodinger.application.jaguar.utils.ChgAt attribute)
(schrodinger.structure._StructureAtom property)
index() (schrodinger.application.canvas.topo_descriptors.Descriptor method)
(schrodinger.application.dendrogram.core_class.GetPartitions.NameList method)
(schrodinger.application.dendrogram.core_class.RingSysInfo method)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.antlr3.treewizard.TreeWizard method)
(schrodinger.application.desmond.arkdb.ForEachDo method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.desmond.fep_edge_data.ResData method)
(schrodinger.application.desmond.packages.timer.Timer.Args method)
(schrodinger.application.jaguar.basis.BasisSet method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.application.jaguar.utils.FreeEnergy method)
(schrodinger.application.jaguar.utils.LewisStructure method)
(schrodinger.application.licensing.licadmin.stat_info method)
(schrodinger.application.licensing.lmgrd_log_parser.event method)
(schrodinger.application.livedesign.login.Version method)
(schrodinger.application.matsci.cache.CacheInfo method)
(schrodinger.application.matsci.codeutils.ModuleInfo method)
(schrodinger.application.matsci.nano.space_groups.SpaceGroup method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.scaffold_enumeration.atomlist.AtomListInfo method)
(schrodinger.application.scaffold_enumeration.cxsmiles.MCG method)
(schrodinger.application.scaffold_enumeration.cxsmiles.SRU method)
(schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup method)
(schrodinger.application.scaffold_enumeration.posvarbond.MulticenterSgroup method)
(schrodinger.forcefield.ffld_options.ForceFieldOptions method)
(schrodinger.forcefield.ffld_options.MinimizationOptions method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.job.server.ServerInfo method)
(schrodinger.livedesign.preprocessor.PreprocessorOptions method)
(schrodinger.math.multi_parameter_optimization.Transition method)
(schrodinger.models.diffy.DictDiff method)
(schrodinger.models.diffy.ListDiff method)
(schrodinger.models.diffy.SetDiff method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableTuple method)
(schrodinger.protein.tasks.structure_alignment.StructAlignResult method)
(schrodinger.rdkit.substructure.QueryOptions method)
(schrodinger.structutils.markush_enumerate.PlaceHolder method)
(schrodinger.structutils.rgroup_enumerate.RGroup method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
(schrodinger.utils.sea.sea.List method)
index_in_current_file (schrodinger.structure.MultiFileStructureReader attribute)
index_lists() (in module schrodinger.test.hypothesis.strategies.indices)
INDEX_PATTERN (schrodinger.utils.sea.sea.Map attribute)
INDEX_PATTERN2 (schrodinger.utils.sea.sea.Map attribute)
IndexedFileLoader (class in schrodinger.application.desmond.packages.msys)
indices() (in module schrodinger.test.hypothesis.strategies.indices)
indicesToPositions() (schrodinger.application.bindingsite.cavutils.Grid method)
IndividualStructureBase (class in schrodinger.application.livedesign.entry_types)
info (schrodinger.application.matsci.cache.BaseCacheData property)
(schrodinger.application.matsci.cache.FIFOCacheData property)
(schrodinger.application.matsci.cache.LRUCacheData property)
info() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
INFORMATIONAL_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
inherits() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
init() (in module schrodinger.protein.remediate)
(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_ff() (schrodinger.application.desmond.torsion_related.TorsionPotential method)
init_graphics_state() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
initial (schrodinger.application.jaguar.scan.Scan property)
initial_tokens() (in module schrodinger.application.licensing.lmgrd_log_parser)
initialize() (schrodinger.application.jaguar.mmjag.MmJag static method)
(schrodinger.infra.mminit.Initializer method)
(schrodinger.infra.mmlist.mmlist static method)
(schrodinger.infra.table.Table static method)
initialize_audit_log() (in module schrodinger.livedesign.preprocessor)
initializeCoordinates() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
initializeMmlibs() (schrodinger.application.ligprep.ionizer.Ionizer method)
initializeProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
Initializer (class in schrodinger.infra.mminit)
initializeWithSize() (schrodinger.ui.dendrogram.DendrogramTreeBuilder method)
initialSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
initPainter() (schrodinger.ui.dendrogram.DendrogramView method)
initStyleOption() (schrodinger.ui.dendrogram.DendrogramView method)
inkAnnotation() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
inkAnnotation0() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
INPLACE_PROPERTY (schrodinger.structutils.sitealign.SiteMatchLookup attribute)
input_namelists (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter attribute)
input_path (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument property)
InputConfig (class in schrodinger.application.inputconfig)
inputconfig_subset() (in module schrodinger.application.phase.input)
InputConversionTestCase (class in schrodinger.application.matsci.qexsd.tests.test_converters)
inputMethodEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
inputMethodHints() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
inputMethodQuery() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
InputOrder (schrodinger.structutils.interactions.salt_bridge.OrderBy attribute)
InputSpecs (class in schrodinger.application.phase.input)
InputStream (in module schrodinger.application.desmond.antlr3.streams)
inscode (schrodinger.application.qsite.input.Cut property)
(schrodinger.structure._Residue property)
(schrodinger.structure._StructureAtom property)
insert() (schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.sea.sea.List method)
insertActions() (schrodinger.ui.dendrogram.DendrogramView method)
insertAfter() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
insertBefore() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
InsertBeforeOp (class in schrodinger.application.desmond.antlr3.streams)
insertColumn() (schrodinger.infra.table.Table method)
insertion (schrodinger.application.desmond.packages.msys.Residue property)
insertRow() (schrodinger.infra.table.Table method)
install_license() (in module schrodinger.application.licensing.licadmin)
install_license_text() (in module schrodinger.application.licensing.licadmin)
install_netsuite_license() (in module schrodinger.application.licensing.licadmin)
install_remote_pubkey() (in module schrodinger.utils.sshconfig)
install_remote_server_license() (in module schrodinger.application.licensing.licadmin)
install_schrod_plist() (in module schrodinger.application.licensing.licadmin)
installed_pathname() (in module schrodinger.application.licensing.licadmin)
installEventFilter() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
installing modules
installSceneEventFilter() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
INT (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute)
INTERACTION_NAMES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
InteractionReader (class in schrodinger.application.prime.residue_interaction)
interactive prompt
internal (schrodinger.application.matsci.msconst.SMARTS_METHOD attribute)
Interpolate1D (class in schrodinger.math.mathutils)
Interpolate2D (class in schrodinger.math.mathutils)
INTERSECT_KEYS (schrodinger.application.desmond.cms.FBHWPosRestrainArray attribute)
(schrodinger.application.desmond.cms.PosRestrainArray attribute)
intersection() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
intersection_update() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
intersects() (schrodinger.application.bindingsite.cavutils.Cavity method)
interval() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
intrinsic_part() (schrodinger.application.matsci.cctbx.rot_mx.translation_part_info method)
IntStream (class in schrodinger.application.desmond.antlr3.streams)
inv_box (schrodinger.application.desmond.packages.analysis.Pbc property)
INVALID_STATE_BORDER (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
invalidate() (schrodinger.ui.dendrogram.DendrogramScene method)
invalidateScene() (schrodinger.ui.dendrogram.DendrogramView method)
invariant_map (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter attribute)
invcell2Gmat() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
inverse() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.pathfinder.reaction.Reaction method)
inverse_cancel() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
invert() (schrodinger.infra.mmbitset.Bitset method)
invert_reaction_smarts() (in module schrodinger.application.pathfinder.reaction)
invpolfcal() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
invQ() (in module schrodinger.application.matsci.gsas.GSASIImath)
IO
IOCapture (class in schrodinger.test.ioredirect)
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)
IORedirect (class in schrodinger.test.ioredirect)
IOSilence (class in schrodinger.test.ioredirect)
ip_default (schrodinger.application.jaguar.results.JaguarOptions attribute)
ir_intensity_precision (schrodinger.application.jaguar.results.NormalMode attribute)
IRC_IS_NOT_TS (schrodinger.application.jaguar.constants.FatalErrors attribute)
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)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
is_aacg_cms_file() (in module schrodinger.application.aacg.utils)
is_aacg_ffio_struct() (in module schrodinger.application.aacg.utils)
is_another_best_config() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
is_atom_list() (in module schrodinger.utils.sea.sea)
is_aws_service_available() (in module schrodinger.application.steps.env_keys)
is_bond_rotatable() (in module schrodinger.structutils.analyze)
is_branch (schrodinger.protein.helm.Monomer attribute)
is_builtin_fragment() (in module schrodinger.utils.cgxutils)
is_chiral_atom() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
is_cms_file() (in module schrodinger.utils.fileutils)
is_color_dark() (in module schrodinger.ui.qt.standard.colors)
is_console_user() (in module schrodinger.test.darwinconsole)
is_counted() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.License method)
is_covalently_bound (schrodinger.structutils.analyze.Ligand property)
is_csv_file() (in module schrodinger.utils.fileutils)
is_csvgz() (in module schrodinger.rdkit.molio)
is_current_mac_builder() (in module schrodinger.test.test_markers)
is_datetime() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
is_display_present() (in module schrodinger.utils.sysinfo)
is_dummy_structure() (in module schrodinger.application.desmond.util)
is_dynamic_asl() (in module schrodinger.application.desmond.packages.topo)
is_ecp (schrodinger.application.jaguar.basis.BasisSet attribute)
is_empty_trajectory() (in module schrodinger.application.desmond.packages.traj)
is_equal() (in module schrodinger.utils.sea.common)
is_expired() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.LicenseLine method)
(schrodinger.application.licensing.flexlm.Package method)
(schrodinger.application.licensing.flexlm.Server method)
(schrodinger.application.licensing.flexlm.UseServer method)
(schrodinger.application.licensing.flexlm.Vendor method)
is_for_gcmc (schrodinger.application.desmond.cms.Cms property)
is_future_license_error() (in module schrodinger.application.licensing.licadmin)
is_gcmc (schrodinger.application.desmond.packages.traj.Frame property)
is_grid_good_for_ligand() (in module schrodinger.application.glide.utils)
is_gzipped_structure_file() (in module schrodinger.utils.fileutils)
is_halogen (schrodinger.structure._StructureAtom property)
is_hypothesis_file() (in module schrodinger.utils.fileutils)
is_ipv4_addr() (in module schrodinger.application.licensing.licadmin)
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_list() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDComplexType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method)
is_local_server() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
is_localhost_platform_compatible() (in module schrodinger.utils.platform)
is_maestro_file() (in module schrodinger.utils.fileutils)
is_matsci() (in module schrodinger.utils.license)
is_metal() (in module schrodinger.application.prime.primefix)
is_mopac_file() (in module schrodinger.application.mopac.utils)
is_nodelocked() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.Server method)
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_optional() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method)
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_polymer() (in module schrodinger.livedesign.convert)
is_poseviewer_file() (in module schrodinger.utils.fileutils)
is_powerof2() (in module schrodinger.utils.sea.evalor)
is_ps (schrodinger.application.jaguar.basis.BasisSet attribute)
is_pv_file() (in module schrodinger.application.glide.poseviewconvert)
is_python_file() (in module schrodinger.application.matsci.codeutils)
is_queryatom_exception() (in module schrodinger.livedesign.preprocessor)
is_reagent_file() (in module schrodinger.application.pathfinder.reaction)
is_reagent_filename() (in module schrodinger.application.pathfinder.reaction)
is_ring_atom() (in module schrodinger.application.desmond.r_group_asl)
is_rotabond() (in module schrodinger.application.desmond.r_group_asl)
is_same_day() (in module schrodinger.application.job_monitor.util)
is_sd_file() (in module schrodinger.utils.fileutils)
is_server() (in module schrodinger.application.licensing.flexlm)
(schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
is_signed() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.Package method)
is_small_struc() (in module schrodinger.application.desmond.packages.analysis)
is_smiles_file() (in module schrodinger.utils.fileutils)
is_soluble() (in module schrodinger.application.desmond.solubility_utils)
is_structure_soluble() (in module schrodinger.application.desmond.solubility_utils)
is_stub() (schrodinger.application.licensing.flexlm.License method)
(schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
is_subdir() (in module schrodinger.application.desmond.util)
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_jobname() (in module schrodinger.utils.fileutils)
is_valid_property_name() (in module schrodinger.application.matsci.msprops)
is_valid_pv_file() (in module schrodinger.application.glide.utils)
is_water() (in module schrodinger.application.desmond.remd)
is_wildcard() (in module schrodinger.livedesign.preprocessor)
is_within_directory() (in module schrodinger.utils.fileutils)
is_zero() (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
isActive() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
isActiveWindow() (schrodinger.ui.dendrogram.DendrogramView method)
isalnum() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isalpha() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isAncestorOf() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
isAromatic() (schrodinger.structure._Ring method)
isascii() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isBlockedByModalPanel() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
isChecked() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method)
isClipped() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
IsCompatible() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
isConnectedToResidue() (schrodinger.structure._Residue method)
isdecimal() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isdeleted() (in module schrodinger.Qt.PyQt6.sip)
isdigit() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isdisjoint() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdItemsView method)
(schrodinger.utils.scollections.IdSet method)
isDistance() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method)
isDynamic() (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.CatPiFinder 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.DipoleDirector method)
(schrodinger.application.desmond.packages.analysis.Distance 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.MassAvgVel 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.MoleculeWiseCom method)
(schrodinger.application.desmond.packages.analysis.MomentOfInertia method)
(schrodinger.application.desmond.packages.analysis.MomentOfInertiaDirector method)
(schrodinger.application.desmond.packages.analysis.OrderParameter method)
(schrodinger.application.desmond.packages.analysis.PiPiFinder 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.ProteinRMSF 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.SystemDipoleDirector 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.CompositeAnalyzer method)
(schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer 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.MaestroAnalysis method)
(schrodinger.application.desmond.packages.staf.UpdatedCmsFsysCtAnalysis method)
iselement() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
isEnabled() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
isEnabledTo() (schrodinger.ui.dendrogram.DendrogramView method)
isEnergy() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method)
isEOF() (schrodinger.infra.structure.PyStructureReaderException method)
isEquivalent() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
isf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen 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)
isFullScreen() (schrodinger.ui.dendrogram.DendrogramView method)
isHeteroaromatic() (schrodinger.structure._Ring method)
isHidden() (schrodinger.ui.dendrogram.DendrogramView method)
isidentifier() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isinitpath() (schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.Makefile method)
IsInteger (class in schrodinger.ui.qt.appframework2.validators)
isInteractive() (schrodinger.ui.dendrogram.DendrogramView method)
isLeaf() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
isLeftToRight() (schrodinger.ui.dendrogram.DendrogramView method)
islower() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isMaximized() (schrodinger.ui.dendrogram.DendrogramView method)
isMinimized() (schrodinger.ui.dendrogram.DendrogramView method)
isModal() (schrodinger.ui.dendrogram.DendrogramView method)
isNil() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
isnumeric() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isObscured() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
isObscuredBy() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
isomorph() (in module schrodinger.application.desmond.packages.viparr1.viparr.isomorph)
isotope (schrodinger.structure._StructureAtom property)
ISOTROPIC (schrodinger.application.desmond.constants.IsotropyPolicy attribute)
IsotropyPolicy (class in schrodinger.application.desmond.constants)
isovalue (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
isPanel() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
isprintable() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
ispycreated() (in module schrodinger.Qt.PyQt6.sip)
ispyowned() (in module schrodinger.Qt.PyQt6.sip)
isRightToLeft() (schrodinger.ui.dendrogram.DendrogramView method)
isRowSelected() (schrodinger.infra.table.Table method)
isRunning() (schrodinger.application.licensing.licadmin.LocalServerProcess method)
isSelected() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
isSignalConnected() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
isSohnckeGroup() (schrodinger.application.matsci.nano.space_groups.SpaceGroup method)
isspace() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isStandardResidue() (schrodinger.structure._Residue method)
isStatic() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
issubset() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
issued_str() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.Package method)
issuperset() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
istitle() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isTransformed() (schrodinger.ui.dendrogram.DendrogramView method)
isUnderMouse() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
isupper() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
isValid() (schrodinger.utils.license.License method)
isValidStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method)
isVisible() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
isVisibleTo() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
isWidget() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
isWidgetType() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
isWindow() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
isWindowModified() (schrodinger.ui.dendrogram.DendrogramView method)
isWindowType() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
isWithinCutoff() (schrodinger.application.desmond.packages.analysis.Pbc method)
ItemAcceptsInputMethod (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
itemAt() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
itemChange() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
ItemChildAddedChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemChildRemovedChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemClipsChildrenToShape (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemClipsToShape (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemContainsChildrenInShape (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemCoordinateCache (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.CacheMode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.CacheMode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.CacheMode attribute)
ItemCursorChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemCursorHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemDoesntPropagateOpacityToChildren (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemEnabledChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemEnabledHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemFlagsChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemFlagsHaveChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemHasNoContents (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemIgnoresParentOpacity (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemIgnoresTransformations (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
itemIndexMethod() (schrodinger.ui.dendrogram.DendrogramScene method)
ItemIsFocusable (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemIsMovable (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemIsPanel (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemIsSelectable (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemLayer (schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramScene.SceneLayer attribute)
ItemNegativeZStacksBehindParent (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemOpacityChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemOpacityHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemParentChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemParentHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemPositionChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemPositionHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemRotationChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemRotationHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
items() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
itemsBoundingRect() (schrodinger.ui.dendrogram.DendrogramScene method)
ItemScaleChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemScaleHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemSceneChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemSceneHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemScenePositionHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemSelectedChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemSelectedHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemSendsGeometryChanges (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemSendsScenePositionChanges (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemStacksBehindParent (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemToolTipChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemToolTipHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
itemTransform() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
ItemTransformChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemTransformHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemTransformOriginPointChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemTransformOriginPointHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemUsesExtendedStyleOption (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemFlag attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemFlag attribute)
ItemVisibleChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemVisibleHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemZValueChange (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
ItemZValueHasChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.GraphicsItemChange attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.GraphicsItemChange attribute)
Iter (class in schrodinger.application.desmond.enhsamp)
iter() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
iter_fingerprints() (schrodinger.utils.multifpfile.MultiFPFile method)
iter_markers() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
iter_markers_with_node() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
iterate_minimize_structure() (in module schrodinger.forcefield.minimizer)
iterateNeighboringAtoms() (schrodinger.structutils.measure.DistanceCellIterator method)
iteritems() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.utils.cgxutils.FragmentLibrary method)
iterkeys() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
iterpose() (schrodinger.trajectory.prody.ensemble.Ensemble method)
itervalues() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
J
JAG_GEOPT (schrodinger.infra.structure.WorkflowType attribute)
JAG_MACRO_PKA_RESULTS (schrodinger.infra.structure.WorkflowType attribute)
JAG_SCAN (schrodinger.infra.structure.WorkflowType attribute)
Jaguar
JaguarAtomicResults (class in schrodinger.application.jaguar.results)
JaguarConfigError
JaguarIOError
JaguarKeywordConflict
JaguarOptions (class in schrodinger.application.jaguar.results)
JaguarResults (class in schrodinger.application.jaguar.results)
JaguarRuntimeError
JaguarUnsupportedBasisSet
JaguarUserFacingException
jar (schrodinger.application.desmond.picklejar.PickleJar attribute)
job_capacity() (in module schrodinger.application.licensing.licadmin)
job_capacity_by_product() (in module schrodinger.application.licensing.licadmin)
Job_Details (class in schrodinger.application.desmond.simulation_block_test)
job_product_names() (in module schrodinger.application.licensing.licadmin)
JobName (class in schrodinger.ui.qt.appframework2.validators)
jobname (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
(schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
(schrodinger.application.qsite.input.QSiteInput property)
jobs() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
join() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
join_cont_lines() (in module schrodinger.application.licensing.licadmin)
jsc() (in module schrodinger.job.server)
json_version() (in module schrodinger.test.pytest.fixture)
JsonableClass (schrodinger.models.jsonable.AbstractJsonSerializer 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.MolSerializer class method)
(schrodinger.models.jsonable.SetSerializer class method)
(schrodinger.models.jsonable.StructureSerializer class method)
(schrodinger.models.jsonable.TupleSerializer class method)
JsonableIntEnum (class in schrodinger.models.jsonable)
JsonableNamedTuple (class in schrodinger.models.jsonable)
JsonableSet (class in schrodinger.models.jsonable)
JsonableStructure (class in schrodinger.models.jsonable)
JsonableTuple (class in schrodinger.models.jsonable)
JSONEncodeError
JSONFilterAdapter (class in schrodinger.rdkit.filtering)
K
kcal_prop_to_ev_prop() (in module schrodinger.application.matsci.msprops)
KCAL_TO_JOUL (schrodinger.application.desmond.constants.Conversion attribute)
KEEP (schrodinger.application.desmond.constants.CUSTOM_CHARGE_MODE attribute)
KEEP_ONLY_LARGEST_STRUCTURE (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
keep_top_n() (in module schrodinger.rdkit.filtering)
KEEP_WEDGED (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute)
Key (class in schrodinger.utils.sea.sea)
key (schrodinger.application.canvas.topo_descriptors.Descriptor attribute)
(schrodinger.application.desmond.arkdb.Datum property)
(schrodinger.application.desmond.packages.msys.InChI property)
(schrodinger.application.desmond.task.Option property)
(schrodinger.application.desmond.task.Premise property)
key_value() (schrodinger.utils.sea.sea.Map method)
keyboardGrabber() (schrodinger.ui.dendrogram.DendrogramView method)
keyPressEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
keyReleaseEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
keys() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.desmond.packages.msys.Ct method)
(schrodinger.application.desmond.packages.msys.Param method)
(schrodinger.application.desmond.packages.msys.PropertyMap method)
(schrodinger.application.desmond.packages.msys.Term method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.infra.table.Table method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.sea.sea.Map method)
Keyword (class in schrodinger.application.jaguar.keywordDB)
keywords (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableFile attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.Makefile attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
kill_launched_jobcontrol_jobs() (in module schrodinger.test.stu.process_management)
kill_process() (in module schrodinger.utils.subprocess)
kill_process_children() (in module schrodinger.test.stu.process_management)
killTimer() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
KNOWLEDGE (schrodinger.application.msv.gui.homology_modeling.constants.PrimeMethod attribute)
known_hostname() (in module schrodinger.utils.sshconfig)
kT (in module schrodinger.protein.analysis)
L
L (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
LA() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
label (schrodinger.application.canvas.topo_descriptors.Descriptor attribute)
label_color (schrodinger.structure._StructureAtom property)
label_format (schrodinger.structure._StructureAtom property)
label_user_text (schrodinger.structure._StructureAtom property)
LabelAtoms (class in schrodinger.adapter)
LabelCursor (class in schrodinger.ui.qt.label_cursor)
LabelCursorAxes (class in schrodinger.ui.qt.label_cursor)
labelDrawn() (schrodinger.ui.qt.label_cursor.LabelCursorAxes method)
LARGE_DENSITY_CHANGE (schrodinger.application.jaguar.constants.FatalErrors attribute)
LARGE_DIIS_ERROR (schrodinger.application.jaguar.constants.FatalErrors attribute)
LargestRingAtomCount() (in module schrodinger.rdkit.filtering)
last_issued() (schrodinger.application.licensing.flexlm.License method)
last_update (schrodinger.application.matsci.qb_sdk.client.QubecTokenData attribute)
LATEST (schrodinger.utils.openmpi.OpenMPIVersion attribute)
Latt2text() (in module schrodinger.application.matsci.gsas.GSASIIspc)
LaueUnique() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
LaueUnique2() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
LaunchParameters (class in schrodinger.job.launchparams)
layout() (schrodinger.ui.dendrogram.DendrogramView method)
layoutDirection() (schrodinger.ui.dendrogram.DendrogramView method)
lazy_canvas_import() (in module schrodinger.structutils.analyze)
lazy_import() (in module schrodinger.utils.imputils)
LB() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
LD_LIBRARY_PATH (schrodinger.utils.openmpi.EnvVar attribute)
LDData (class in schrodinger.application.livedesign.data_classes)
LDFolderTree (class in schrodinger.application.livedesign.ld_folder_tree)
LDMode (class in schrodinger.application.livedesign.login)
Leak (class in schrodinger.test.memtest)
LEAK_VERSIONS (schrodinger.application.licensing.licadmin.LicenseResource attribute)
(schrodinger.application.licensing.licadmin.LocalServerProcess attribute)
least_squares (schrodinger.application.phase.packages.ligand_aligner.AlignMethod attribute)
leave_scope() (schrodinger.application.desmond.enhsamp.binding method)
leaveEvent() (schrodinger.ui.dendrogram.DendrogramView method)
leaving_atoms (schrodinger.structutils.rgroup_enumerate.RGroup attribute)
LeftHandedAlphaHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
leg1_name (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
(schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
leg2_name (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
(schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
leg2_names (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
leg2_names_short (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
length (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue property)
(schrodinger.structure._StructureBond property)
Let (class in schrodinger.application.desmond.enhsamp)
Level (class in schrodinger.infra.mmerr)
level (schrodinger.application.licensing.licerror.LicenseError property)
LewisStructure (class in schrodinger.application.jaguar.utils)
Lexer (class in schrodinger.application.desmond.antlr3.recognizers)
LIB (schrodinger.job.util.DirectoryType attribute)
License (class in schrodinger.application.licensing.flexlm)
(class in schrodinger.utils.license)
LICENSE_CHECK_FILE (in module schrodinger.test.stu.constants)
license_class() (schrodinger.application.licensing.flexlm.License method)
license_description() (schrodinger.application.licensing.flexlm.License method)
license_directory() (in module schrodinger.application.licensing.licadmin)
LICENSE_KEY (schrodinger.application.steps.licensing.LicenseMixin attribute)
LicenseError (class in schrodinger.application.licensing.licerror)
LicenseException
LicenseFeature (class in schrodinger.application.licensing.licadmin)
LicenseLine (class in schrodinger.application.licensing.flexlm)
LicenseMixin (class in schrodinger.application.steps.licensing)
LicenseResource (class in schrodinger.application.licensing.licadmin)
LicenseStatus (class in schrodinger.utils.license)
LicfileError
Ligand (class in schrodinger.structutils.analyze)
LIGAND (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute)
(schrodinger.application.desmond.constants.REST_COMPONENT attribute)
(schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute)
ligand1_alchemical_atom_total (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_alchemical_mols (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_atomic_mass (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_charge (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_cpx_asl (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_cpx_sid_lighb() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_cpx_sid_molsa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_cpx_sid_psa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_cpx_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_cpx_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_cpx_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_cpx_sid_sasa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_cpx_sid_waters() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_cpx_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
ligand1_fragments() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_hash (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_mol_formula (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_name (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_pdb_name (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_rot_bonds (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_smiles (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_sol_asl (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_sol_sid_lighb() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_sol_sid_molsa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_sol_sid_psa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_sol_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_sol_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_sol_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_sol_sid_sasa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand1_st (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_total_atoms (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_total_fragments (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_total_heavy (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand1_total_hot (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_alchemical_atom_total (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_alchemical_mols (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_atomic_mass (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_charge (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_cpx_asl (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_cpx_sid_lighb() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_cpx_sid_molsa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_cpx_sid_psa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_cpx_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_cpx_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_cpx_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_cpx_sid_sasa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_cpx_sid_waters() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_cpx_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
ligand2_fragments() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_hash (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_mol_formula (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_name (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_pdb_name (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_rot_bonds (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_smiles (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_sol_asl (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_sol_sid_lighb() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_sol_sid_molsa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_sol_sid_psa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_sol_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_sol_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_sol_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_sol_sid_sasa() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
ligand2_st (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_total_atoms (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_total_fragments (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_total_heavy (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand2_total_hot (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand_aid (schrodinger.application.desmond.packages.restraint.utils.PLInteractionAids attribute)
ligand_asl (schrodinger.structutils.analyze.Ligand property)
ligand_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
ligand_name() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData static method)
LIGAND_PLUS_BINDING_SITE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute)
LIGAND_SELECTIVITY (schrodinger.application.desmond.constants.FEP_TYPES attribute)
ligand_st_mol_formula (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ligand_torsions (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
LigandAligner (class in schrodinger.application.phase.packages.ligand_aligner)
LigandAlignerOptions (class in schrodinger.application.phase.packages.ligand_aligner)
LigandRMSD (class in schrodinger.application.desmond.packages.analysis)
Ligands (class in schrodinger.application.livedesign.entry_types)
ligands (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
(schrodinger.application.prime.wrapper.PrimeTemplate property)
LightModeColors (class in schrodinger.ui.qt.standard.colors)
lignum_reader() (in module schrodinger.application.glide.ensemble_selection)
line (schrodinger.application.desmond.antlr3.tree.CommonErrorNode property)
(schrodinger.application.desmond.antlr3.tree.CommonTree property)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern property)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern property)
line() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
line_match_final_log() (in module schrodinger.application.desmond.replica_exchange_review)
line_search_method (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
LinearError
linearGradient() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
LinearWriter (class in schrodinger.pipeline.input)
LineIntersectsTriangle() (in module schrodinger.application.desmond.packages.msys)
lineno (schrodinger.application.desmond.arkdb.CompositeKeySyntaxError attribute)
lines() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
lineterminator (schrodinger.application.canvas.utils.chm_bluebird attribute)
(schrodinger.application.canvas.utils.chm_excel attribute)
lineWidth() (schrodinger.ui.dendrogram.DendrogramView method)
LINK (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
LINK_DISABLED (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
LINK_HOVERED (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
LINK_PRESSED (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
linkAbsolute() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
LINKAGE_TYPES (schrodinger.application.canvas.cluster.CanvasFingerprintCluster attribute)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI attribute)
LinknodeEnumerable (class in schrodinger.application.scaffold_enumeration.linknode)
LinknodeSgroup (class in schrodinger.application.scaffold_enumeration.linknode)
linkRect() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
linkURL() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
LipidDirector (class in schrodinger.application.desmond.packages.analysis)
List (class in schrodinger.utils.sea.sea)
list_features() (in module schrodinger.utils.featureflags.featureflags)
list_to_csv() (in module schrodinger.structutils.rgroup_enumerate)
listAllNodes() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
listchain() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
ListDiff (class in schrodinger.models.diffy)
listextrakeywords() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
listLoadedFonts0() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
listnames() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
Lit (class in schrodinger.application.desmond.enhsamp)
ljust() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
lmdiag() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
lmgrd_lines() (in module schrodinger.application.licensing.licadmin)
lmstat() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
Lnorm() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
lo_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
Load() (in module schrodinger.application.desmond.packages.msys)
load() (in module schrodinger.models.json)
(schrodinger.analysis.transformations.TransformsRepository method)
(schrodinger.application.desmond.picklejar.CustomUnpickler method)
load_data() (schrodinger.application.desmond.bennett.CalcBAR method)
load_fortran_input() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
load_job_products() (in module schrodinger.application.licensing.licadmin)
load_job_reqs() (in module schrodinger.application.licensing.licadmin)
load_keywords() (in module schrodinger.application.jaguar.keywordDB)
load_shared_library() (in module schrodinger.application.desmond.packages.msys.molfile)
LoadCNSFile() (in module schrodinger.analysis.visanalysis.volumedataio)
LoadControls() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
LoadDMS() (in module schrodinger.application.desmond.packages.msys)
LoadExportRoutines() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
loadFile() (schrodinger.analysis.transformations.TransformsRepository method)
(schrodinger.ui.dendrogram.DendrogramTreeBuilder method)
LoadImportRoutines() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
LoadMAE() (in module schrodinger.application.desmond.packages.msys)
LoadMany() (in module schrodinger.application.desmond.packages.msys)
LoadMol2() (in module schrodinger.application.desmond.packages.msys)
LoadPDB() (in module schrodinger.application.desmond.packages.msys)
LoadPrmTop() (in module schrodinger.application.desmond.packages.msys)
loads() (in module schrodinger.models.json)
(schrodinger.analysis.transformations.TransformsRepository method)
LoadVisFile() (in module schrodinger.analysis.visanalysis.volumedataio)
LoadXYZ() (in module schrodinger.application.desmond.packages.msys)
local_server_files() (in module schrodinger.application.licensing.licadmin)
local_server_resource() (in module schrodinger.application.licensing.licadmin)
local_server_resources() (in module schrodinger.application.licensing.licadmin)
locale() (schrodinger.ui.dendrogram.DendrogramView method)
LocalServerProcess (class in schrodinger.application.licensing.licadmin)
locate_darwin_pymol() (in module schrodinger.utils.fileutils)
locate_pymol() (in module schrodinger.utils.fileutils)
location (schrodinger.test.perceptualdiff.PerceptualDiffTest property)
(schrodinger.test.pytest.exetest.ExecutableTest property)
(schrodinger.test.pytest.exetest.MakefileTest property)
location() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
location_part() (schrodinger.application.matsci.cctbx.rot_mx.translation_part_info method)
log() (in module schrodinger.ui.qt.appframework2.debugcore)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method)
log_deleted_lines() (schrodinger.application.licensing.flexlm.License method)
log_sa (class in schrodinger.application.matsci.gsas.GSASIImath)
log_to_stdout() (in module schrodinger.test.pytest.fixture)
logcdf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
LogEntry (class in schrodinger.ui.qt.appframework2.debugcore)
logfile() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
logger (in module schrodinger.structutils.rgroup_enumerate)
(schrodinger.application.desmond.packages.timer.Timer.Args attribute)
logging_config() (in module schrodinger.utils.log)
logicalDpiX() (schrodinger.ui.dendrogram.DendrogramView method)
logicalDpiY() (schrodinger.ui.dendrogram.DendrogramView method)
login() (schrodinger.application.matsci.qb_sdk.client.QubecClient method)
logistic() (in module schrodinger.application.desmond.bennett)
logistic_full() (in module schrodinger.application.desmond.bennett)
logistic_function() (in module schrodinger.application.desmond.bennett)
logistic_function_full() (in module schrodinger.application.desmond.bennett)
logout() (schrodinger.application.matsci.qb_sdk.client.QubecClient method)
logpdf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
logS() (in module schrodinger.rdkit.filtering)
logScale (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute)
logsf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
logString() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method)
loneelectrons() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method)
LONG_ERROR_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
LongestConsecutiveRBCount() (in module schrodinger.rdkit.filtering)
longMessage (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase attribute)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase attribute)
Loop (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data)
LOOP (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute)
LorchWeight() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
LOSSLESS (schrodinger.application.phase.packages.conformer_storage.Format attribute)
LOW (schrodinger.application.msv.gui.homology_modeling.constants.AlignmentQuality attribute)
lower() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.ui.dendrogram.DendrogramView method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
lower_bound (schrodinger.application.desmond.correlation_tau.ConfidenceInterval attribute)
LOWMODE (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute)
LRUCacheData (class in schrodinger.application.matsci.cache)
ls (in module schrodinger.application.desmond.packages.msys.molfile)
lstrip() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
LT() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
LT_token() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
LT_tree() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
luminance_level() (in module schrodinger.application.matsci.colorutils)
M
m2ioPropertyName() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method)
m_glide_XPviz_exposure() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_hbonds() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_hexpairs() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_hexsp() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_penal_blkpchg() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_penal_charge() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_penal_ddpen() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_penal_polar() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_penal_twistam() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_penalties() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_phobcon_hb() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_phobpack() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_picat() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_rotbonds() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_stacking() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_water_ligand() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_water_protein() (in module schrodinger.application.glide.xpdes)
m_glide_XPviz_watmol() (in module schrodinger.application.glide.xpdes)
m_hideAfterAnimation (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
MACROCYCLE_COREHOPPING (schrodinger.application.desmond.constants.SIMULATION_PROTOCOL attribute)
MacroModel
mADDOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
MaeFrameReader (class in schrodinger.application.desmond.packages.traj)
MaePropertyName (class in schrodinger.application.desmond.constants)
MaeSource (class in schrodinger.application.desmond.packages.traj)
Maestro
callbacks
commands
project table
,
[1]
running scripts
script installation
workspace
,
[1]
MAESTRO (schrodinger.infra.structure.FileFormat attribute)
MaestroAnalysis (class in schrodinger.application.desmond.packages.staf)
MaestroNotAvailableError
MaestroReader (class in schrodinger.structure)
MaestroTextReader (class in schrodinger.structure)
MaestroWriter (class in schrodinger.structure)
MagFF (in module schrodinger.application.matsci.gsas.atmdata)
MagMod() (in module schrodinger.application.matsci.gsas.GSASIImath)
MagScatFac() (in module schrodinger.application.matsci.gsas.GSASIIElem)
MagSGSym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
MagSSText2MTS() (in module schrodinger.application.matsci.gsas.GSASIIspc)
MagSytSym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
MagText2MTS() (in module schrodinger.application.matsci.gsas.GSASIIspc)
main() (in module schrodinger.application.canvas.r_group_dee)
(in module schrodinger.application.dendrogram.core_class)
(in module schrodinger.application.desmond.bennett)
(in module schrodinger.application.desmond.enhanced_sampling.mexpLexer)
(in module schrodinger.application.desmond.enhanced_sampling.mexpParser)
(in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
(in module schrodinger.application.jaguar.check_headers)
(in module schrodinger.application.licensing.licadmin)
(in module schrodinger.application.licensing.lmgrd_log_parser)
(in module schrodinger.infra.epydoc_to_sphinx)
(in module schrodinger.protein.gpcr.update_gpcr_db)
(in module schrodinger.test.log_parser)
(in module schrodinger.utils.compare)
(in module schrodinger.utils.featureflags.featureflags)
(in module schrodinger.utils.featureflags.write)
(in module schrodinger.utils.machid)
(in module schrodinger.utils.postinstall)
maintain_planarity (schrodinger.structutils.minimize.Minimizer property)
major (schrodinger.application.livedesign.login.Version attribute)
make() (schrodinger.application.desmond.packages.restraint.builder.AtomID static method)
make_fp_generator() (in module schrodinger.utils.multifpfile)
make_glued_topology() (in module schrodinger.application.desmond.packages.topo)
make_local_protein() (schrodinger.protein.analysis.Report method)
make_property() (in module schrodinger.application.desmond.ffiostructure)
make_property_fepio() (in module schrodinger.application.desmond.ffiostructure)
make_scratch_dir() (in module schrodinger.application.mopac.utils)
make_structure_dummy() (in module schrodinger.application.desmond.util)
make_test_function() (in module schrodinger.application.matsci.qexsd.tests.test_converters)
make_whole() (in module schrodinger.application.desmond.packages.pfx)
(in module schrodinger.application.desmond.packages.topo)
make_whole_cms() (in module schrodinger.application.desmond.packages.pfx)
(in module schrodinger.application.desmond.packages.topo)
makeBilbaoPhase() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
MakeConsistent() (in module schrodinger.analysis.visanalysis.volumedatautils)
makeFFTsizeList() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
Makefile (class in schrodinger.test.pytest.exetest)
Makefile.CollectError
MakefileTest (class in schrodinger.test.pytest.exetest)
makeInstDict() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
makeIter() (schrodinger.structutils.rgroup_enumerate.RGroupSource method)
makeLogEntry() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method)
makeMEMfile() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
makeNestedRowVisible() (schrodinger.infra.table.Table method)
makePRFfile() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
makeQuat() (in module schrodinger.application.matsci.gsas.GSASIImath)
MakeRDF() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
makeRefdFFT() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
makeRowObject() (schrodinger.application.combiglide.corehop.AttachmentPoint method)
makeSLDprofile() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
maketrans() (schrodinger.application.desmond.constants.MaePropertyName static method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString static method)
(schrodinger.utils.fileutils.tempfilename static method)
(schrodinger.utils.fileutils.TempStructureFile static method)
(schrodinger.utils.sea.sea.Key static method)
makeTsched() (in module schrodinger.application.matsci.gsas.GSASIImath)
makeWaves() (in module schrodinger.application.matsci.gsas.GSASIImath)
makeWavesDerv() (in module schrodinger.application.matsci.gsas.GSASIImath)
mALPHA() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
manageXvolIsOpen() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
MANY_ONE (schrodinger.application.msv.gui.homology_modeling.constants.Mode attribute)
Map (class in schrodinger.utils.sea.sea)
mapFrom() (schrodinger.ui.dendrogram.DendrogramView method)
mapFromGlobal() (schrodinger.ui.dendrogram.DendrogramView method)
mapFromItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
mapFromParent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
mapFromScene() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
mapRectFromItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
mapRectFromParent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
mapRectFromScene() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
mapRectToItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
mapRectToParent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
mapRectToScene() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
mapTo() (schrodinger.ui.dendrogram.DendrogramView method)
mapToGlobal() (schrodinger.ui.dendrogram.DendrogramView method)
mapToItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
mapToParent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
mapToScene() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
mark() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
mark_fullsystem_ct() (in module schrodinger.application.desmond.cms)
mark_warnings_as_errors() (in module schrodinger.test.pytest.warnings)
markup (schrodinger.application.matsci.typography.TYPO_TYPE attribute)
mask() (schrodinger.ui.dendrogram.DendrogramView method)
mass (schrodinger.application.desmond.packages.msys.Atom property)
MassAvgVel (class in schrodinger.application.desmond.packages.analysis)
match() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
(schrodinger.application.desmond.packages.msys.Graph method)
(schrodinger.application.desmond.packages.msys.SmartsPattern method)
match_compstr() (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)
match_hbond() (in module schrodinger.structutils.interactions.hbond)
matchAll() (schrodinger.application.desmond.packages.msys.Graph method)
matchAny() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
matched_gids() (in module schrodinger.application.desmond.packages.topo)
matched_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property)
matched_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property)
matches() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.utils.ligfilter.AslCriterion method)
(schrodinger.utils.ligfilter.Criterion method)
(schrodinger.utils.ligfilter.PredefinedCriterion method)
(schrodinger.utils.ligfilter.PropertyCriterion method)
(schrodinger.utils.ligfilter.SmartsCriterion method)
matches_canonical_filename() (in module schrodinger.application.licensing.flexlm)
MATCHING (schrodinger.trajectory.trajectory_gui_dir.display_settings_data.DisplayOnly attribute)
matchRange() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
MATERIALS_SCIENCE (schrodinger.application.livedesign.login.LDMode attribute)
matrix_cofactor() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
matrix_matches (schrodinger.structutils.sitealign.BindingSiteAligner attribute)
matrix_reciprocal() (in module schrodinger.application.canvas.topo_descriptors)
matsci (schrodinger.application.matsci.msprops.PROP_FAMILY attribute)
max_atom_count (schrodinger.structutils.analyze.AslLigandSearcher property)
MAX_FRAME_DURATION (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
max_num_atoms (schrodinger.application.livedesign.entry_types.Ligands attribute)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute)
(schrodinger.application.livedesign.entry_types.TargetlessBase attribute)
MAX_NUM_ATOMS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
MAX_PEPTIDE_BOND_LENGTH (schrodinger.protein.analysis.Report.peptide_planarity_data_set attribute)
max_potential_energy (schrodinger.application.desmond.fep_edge_data.FEPTorsions property)
MAX_REPLICATE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
max_step (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
max_steps (schrodinger.structutils.minimize.Minimizer property)
max_with_none() (in module schrodinger.utils.withnone)
maxDiff (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase attribute)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase attribute)
maximum_usage() (in module schrodinger.application.licensing.lmgrd_log_parser)
maximumHeight() (schrodinger.ui.dendrogram.DendrogramView method)
maximumSize() (schrodinger.ui.dendrogram.DendrogramView method)
maximumViewportSize() (schrodinger.ui.dendrogram.DendrogramView method)
maximumWidth() (schrodinger.ui.dendrogram.DendrogramView method)
MaxIndex() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
maxsize (schrodinger.application.matsci.cache.CacheInfo attribute)
mBCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mBOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mCCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
MCG (class in schrodinger.application.scaffold_enumeration.cxsmiles)
MCMM (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute)
mCOLON() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mCOMMA() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mCOMMENT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mCOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mcsaSearch() (in module schrodinger.application.matsci.gsas.GSASIImath)
MD (schrodinger.application.desmond.constants.FepLegTypes attribute)
mDIGIT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mDIVOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
MDL_MOLV2000 (schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
MDL_MOLV3000 (schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
MdlFileReader (class in schrodinger.application.scaffold_enumeration.mdl)
mean() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
MeanConsecutiveRBCount() (in module schrodinger.rdkit.filtering)
measure() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
measure_angle_between_rings() (in module schrodinger.structutils.measure)
measure_bond_angle() (in module schrodinger.structutils.measure)
measure_dihedral_angle() (in module schrodinger.structutils.measure)
measure_distance() (in module schrodinger.structutils.measure)
measure_plane_angle() (in module schrodinger.structutils.measure)
Measurement (class in schrodinger.application.desmond.measurement)
median() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
median_sublimation_free_energy() (in module schrodinger.application.desmond.solubility_utils)
mem_usage() (schrodinger.application.desmond.memory.MemoryGauger method)
MEMBRANE (schrodinger.application.desmond.constants.REST_COMPONENT attribute)
MembraneDensityProfile (class in schrodinger.application.desmond.packages.analysis)
MembraneThickness (class in schrodinger.application.desmond.packages.analysis)
memo (schrodinger.application.desmond.picklejar.CustomUnpickler attribute)
MEMO_RULE_FAILED (schrodinger.application.desmond.antlr3.debug.DebugParser attribute)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Lexer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Parser attribute)
(schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
MEMO_RULE_UNKNOWN (schrodinger.application.desmond.antlr3.debug.DebugParser attribute)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Lexer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Parser attribute)
(schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
memoize() (in module schrodinger.application.matsci.qb_sdk.client)
(schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
memoized_method() (in module schrodinger.application.matsci.cache)
memory_leak_server() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
MemoryGauger (class in schrodinger.application.desmond.memory)
MEMupdateReflData() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
mEQ() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
merge() (in module schrodinger.application.desmond.packages.traj)
(in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
(in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge)
(schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.licensing.flexlm.License method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
merge_atom_group() (schrodinger.application.desmond.cms.Cms method)
merge_atom_group_from_asl() (schrodinger.application.desmond.cms.Cms method)
merge_blocks() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
merge_blocks2() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
merge_csv_files() (in module schrodinger.application.bioluminate.drivers.io)
merge_ct() (in module schrodinger.application.desmond.ffiostructure)
merge_files_as_streams() (in module schrodinger.rdkit.molio)
merge_files_in_memory() (in module schrodinger.rdkit.molio)
merge_group() (schrodinger.application.desmond.cms.RestrainGroupContainer method)
merge_lists() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge)
merge_rules() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge)
merge_single() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.FBHWPosRestrainArray method)
(schrodinger.application.desmond.cms.PosRestrainArray method)
(schrodinger.application.desmond.cms.RestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
merge_subunit_sts() (in module schrodinger.structutils.build)
merge_with() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.FBHWPosRestrainArray method)
(schrodinger.application.desmond.cms.PosRestrainArray method)
(schrodinger.application.desmond.cms.Restrain method)
(schrodinger.application.desmond.cms.RestrainGroup method)
mergeByIndex() (schrodinger.application.canvas.utils.ChmCSVTools method)
mergeByName() (schrodinger.application.canvas.utils.ChmCSVTools method)
mesh (schrodinger.project.surface.ProjectSurface.Style attribute)
(schrodinger.surface.Style attribute)
(schrodinger.surface.Surface.Style attribute)
message (schrodinger.application.desmond.packages.msys.InChI property)
(schrodinger.application.desmond.packages.timer.Timer.Args attribute)
(schrodinger.application.licensing.licerror.LicenseError property)
messages (schrodinger.infra.mmerr.Capture property)
Meta (class in schrodinger.application.desmond.enhsamp)
META_ASL (schrodinger.application.desmond.cms.Cms attribute)
meta_term() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
metadata (schrodinger.application.phase.packages.shape_binary_utils.ShapeFileReader property)
(schrodinger.application.phase.packages.shape_binary_utils.SingularShapeFileReader property)
MetalInter (class in schrodinger.application.desmond.packages.analysis)
MetalL (schrodinger.application.desmond.packages.analysis.MetalInter attribute)
METALLOPROTEIN (schrodinger.application.desmond.constants.FEP_TYPES attribute)
MetalloproteinEdgeData (class in schrodinger.application.desmond.fep_edge_data)
MetalP (schrodinger.application.desmond.packages.analysis.MetalInter attribute)
metaObject() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
MetaSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
method (schrodinger.application.mopac.results_main.MopacResultsMain property)
method() (in module schrodinger.application.mopac.results_main)
MethodsDict (class in schrodinger.ui.qt.appframework2.appmethods)
metric() (schrodinger.ui.dendrogram.DendrogramView method)
mEXP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mexpLexer (class in schrodinger.application.desmond.enhanced_sampling.mexpLexer)
mexpLexer.DFA12 (class in schrodinger.application.desmond.enhanced_sampling.mexpLexer)
mexpParser (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.atom_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.bind_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.block_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.comp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.decl_meta_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.decl_output_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.decl_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA1 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA15 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA17 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA18 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA19 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA20 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA21 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA22 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA24 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.DFA25 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.expComp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.expr_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.exprOrBind_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.factor_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.fcnCall_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.header_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.if__return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.iter_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.meta_term_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.output_term_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.prog_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.series_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.signedExpComp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.static_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mexpParser.varWithType_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser)
mIDENT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
midLineWidth() (schrodinger.ui.dendrogram.DendrogramView method)
mif_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
min_atom_count (schrodinger.structutils.analyze.AslLigandSearcher property)
MIN_FRAME_DURATION (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
min_func() (in module schrodinger.application.desmond.bennett)
min_method (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
(schrodinger.structutils.minimize.Minimizer property)
min_nodes (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.IndividualStructureBase attribute)
(schrodinger.application.livedesign.entry_types.Ligands attribute)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute)
(schrodinger.application.livedesign.entry_types.TargetlessBase attribute)
MIN_REF_FRAME (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
MIN_REPLICATE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
MIN_STEP (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
min_structures (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.IndividualStructureBase attribute)
(schrodinger.application.livedesign.entry_types.Ligands attribute)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute)
(schrodinger.application.livedesign.entry_types.TargetlessBase attribute)
MIN_TOKEN_INDEX (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream attribute)
min_with_none() (in module schrodinger.utils.withnone)
MinimalViewportUpdate (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.ViewportUpdateMode attribute)
minimization
MinimizationOptions (class in schrodinger.forcefield.ffld_options)
minimize() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method)
(schrodinger.structutils.minimize.Minimizer method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
minimize_ligands() (in module schrodinger.forcefield.minimizer)
minimize_structure() (in module schrodinger.forcefield.minimizer)
(in module schrodinger.structutils.minimize)
minimize_substructure() (in module schrodinger.forcefield.minimizer)
Minimizer (class in schrodinger.structutils.minimize)
minimizer_context() (in module schrodinger.structutils.minimize)
minimum_length (schrodinger.structutils.structalign.StructAlign property)
minimum_similarity (schrodinger.structutils.structalign.StructAlign property)
minimumHeight() (schrodinger.ui.dendrogram.DendrogramView method)
minimumLength (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute)
minimumRenderSize() (schrodinger.ui.dendrogram.DendrogramScene method)
minimumSize() (schrodinger.ui.dendrogram.DendrogramView method)
minimumSizeHint() (schrodinger.ui.dendrogram.DendrogramView method)
minimumWidth() (schrodinger.ui.dendrogram.DendrogramView method)
minor (schrodinger.application.livedesign.login.Version attribute)
minus() (schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
minus_unit_mx() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
mismatch() (schrodinger.application.desmond.antlr3.tree.TreeParser method)
MismatchedNotSetException
MismatchedRangeException
MismatchedSetException
MismatchedTokenException
MismatchedTreeNodeException
mismatchIsMissingToken() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
mismatchIsUnwantedToken() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
miss (schrodinger.application.matsci.cache.CacheInfo attribute)
MISSING (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute)
MissingExecutableError
MissingLicenseFile
MissingLoopFinder (class in schrodinger.structutils.analyze)
MissingModule (class in schrodinger.application.matsci.codeutils)
MissingTokenException
MIXED (schrodinger.application.jaguar.csrch_input_constants.CS_METHOD attribute)
mkdir_p() (in module schrodinger.utils.fileutils)
mktemp() (in module schrodinger.application.canvas.cluster)
mLIT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mm (schrodinger.application.qsite.input.HydrogenCap property)
mmatom (schrodinger.application.qsite.input.Cut property)
mmct() (in module schrodinger.infra.mminit)
MmctSerializerException
MmException
mmffld_environment() (in module schrodinger.forcefield.common)
mmfile_path() (in module schrodinger.utils.fileutils)
mmfrag() (in module schrodinger.infra.mminit)
MMIMArgList (class in schrodinger.infra.mmim)
MMIMDict (class in schrodinger.infra.mmim)
MmJag (class in schrodinger.application.jaguar.mmjag)
mmjag_function() (in module schrodinger.application.jaguar.mmjag)
mmjag_reset_connectivity() (in module schrodinger.application.jaguar.utils)
mmjag_update_lewis() (in module schrodinger.application.jaguar.utils)
MMJagManager (class in schrodinger.application.jaguar.mmjag)
mmkey (schrodinger.application.qsite.input.QSiteInput property)
MMKVArgList (class in schrodinger.infra.mmkv)
MMLib() (in module schrodinger.infra.mminit)
mmlist (class in schrodinger.infra.mmlist)
MmObject (class in schrodinger.infra.mmobject)
MMOK (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute)
MMP3DScreener (class in schrodinger.application.phase.packages.mmp3dscreener)
MMPDatabaseConnection (class in schrodinger.application.phase.packages.mmp2d)
MMSHARE_DATA_DESMOND_DIR (schrodinger.application.desmond.envir.CONST attribute)
MMSHARE_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute)
mmshare_nondist_dir() (in module schrodinger.test)
mmshare_source_dir() (in module schrodinger.test)
MMSHARE_SYSTEM_BUILDER_DATA_DIR (schrodinger.application.desmond.envir.CONST attribute)
MMSHARE_VERSION (schrodinger.application.desmond.envir.CONST attribute)
mmsmiles_initialized (schrodinger.structure.SmilesStructure attribute)
mMULTOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mNEWLINE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mo_occupancies() (in module schrodinger.application.mopac.results_main)
mob_keys (schrodinger.structutils.sitealign.SiteMatchLookup property)
mock_gpgpu_hosts_env() (in module schrodinger.test.pytest.fixture)
mock_task_helper() (in module schrodinger.test.pytest.fixture)
MockProjectRow (class in schrodinger.test.project_mock)
MockProjectTable (class in schrodinger.test.project_mock)
Mode (class in schrodinger.application.msv.gui.homology_modeling.constants)
(class in schrodinger.trajectory.prody.mode)
MODEL_SYSTEM_TYPE (schrodinger.application.desmond.cms.Cms attribute)
model_system_type() (schrodinger.application.desmond.cms.Cms method)
ModellNotSupported
ModelRestrainList (class in schrodinger.application.desmond.cms)
ModeSet (class in schrodinger.trajectory.prody.modeset)
modify() (schrodinger.application.qsite.input.QMRegion method)
modify_enum_access() (in module schrodinger.infra.fix_sip6_enum_access)
Modulation() (in module schrodinger.application.matsci.gsas.GSASIImath)
ModulationDerv() (in module schrodinger.application.matsci.gsas.GSASIImath)
ModulationTw() (in module schrodinger.application.matsci.gsas.GSASIImath)
module
schrodinger
schrodinger.adapter
schrodinger.analysis
schrodinger.analysis.enrichment
schrodinger.analysis.enrichment.calculator
schrodinger.analysis.enrichment.enrichment_input
schrodinger.analysis.enrichment.metrics
schrodinger.analysis.enrichment.plotter
schrodinger.analysis.substructure
schrodinger.analysis.transformations
schrodinger.analysis.visanalysis
schrodinger.analysis.visanalysis.vdaxis
schrodinger.analysis.visanalysis.vdcoordinateframe
schrodinger.analysis.visanalysis.vdexception
schrodinger.analysis.visanalysis.volumedata
schrodinger.analysis.visanalysis.volumedataio
schrodinger.analysis.visanalysis.volumedatastructureutils
schrodinger.analysis.visanalysis.volumedatautils
schrodinger.application
schrodinger.application.aacg
schrodinger.application.aacg.utils
schrodinger.application.bindingsite
schrodinger.application.bindingsite.atomtyping
schrodinger.application.bindingsite.cavutils
schrodinger.application.bindingsite.common
schrodinger.application.bindingsite.intfield
schrodinger.application.bindingsite.schema
schrodinger.application.bioluminate
schrodinger.application.bioluminate.actions
schrodinger.application.bioluminate.antibody
schrodinger.application.bioluminate.drivers
schrodinger.application.bioluminate.drivers.io
schrodinger.application.bioluminate.epitope.psc_workflow
schrodinger.application.bioluminate.epitope.utils.esc_utils
schrodinger.application.bioluminate.patch_utils
schrodinger.application.bioluminate.patch_utils.settings
schrodinger.application.bioluminate.propfilter_ui
schrodinger.application.bioluminate.propka_parse
schrodinger.application.bioluminate.protein_interaction
schrodinger.application.bioluminate.protein_protein_docking_shared
schrodinger.application.bioluminate.protein_structure_quality_ui
schrodinger.application.bioluminate.residue_scanning
schrodinger.application.bioluminate.residue_scanning.properties
schrodinger.application.bioluminate.run_propka
schrodinger.application.bioluminate.surfcomp
schrodinger.application.bioluminate.validate_imported_modules
schrodinger.application.canvas
schrodinger.application.canvas.base
schrodinger.application.canvas.cluster
schrodinger.application.canvas.fingerprint
schrodinger.application.canvas.r_group_dee
schrodinger.application.canvas.similarity
schrodinger.application.canvas.topo_descriptors
schrodinger.application.canvas.utils
schrodinger.application.combiglide
schrodinger.application.combiglide.corehop
schrodinger.application.combiglide.packages
schrodinger.application.combiglide.utils
schrodinger.application.combinatorial_diversity
schrodinger.application.combinatorial_diversity.diversity_fingerprinter
schrodinger.application.combinatorial_diversity.diversity_selector
schrodinger.application.combinatorial_diversity.diversity_splitter
schrodinger.application.combinatorial_diversity.splitter_utils
schrodinger.application.combinatorial_explorer
schrodinger.application.combinatorial_screen
schrodinger.application.combinatorial_screen.combinatorial_screener
schrodinger.application.combinatorial_screen.fingerprint_utils
schrodinger.application.dendrogram.core_class
schrodinger.application.dendrogram.randTestSet
schrodinger.application.desmond
schrodinger.application.desmond.ana
schrodinger.application.desmond.antlr3
schrodinger.application.desmond.antlr3.compat
schrodinger.application.desmond.antlr3.constants
schrodinger.application.desmond.antlr3.debug
schrodinger.application.desmond.antlr3.dfa
schrodinger.application.desmond.antlr3.exceptions
schrodinger.application.desmond.antlr3.recognizers
schrodinger.application.desmond.antlr3.streams
schrodinger.application.desmond.antlr3.tokens
schrodinger.application.desmond.antlr3.tree
schrodinger.application.desmond.antlr3.treewizard
schrodinger.application.desmond.arkdb
schrodinger.application.desmond.autopartition
schrodinger.application.desmond.bennett
schrodinger.application.desmond.bld_def
schrodinger.application.desmond.bld_ver
schrodinger.application.desmond.cmdline
schrodinger.application.desmond.cms
schrodinger.application.desmond.constants
schrodinger.application.desmond.correlation_tau
schrodinger.application.desmond.deltaE
schrodinger.application.desmond.desmond_advanced_tab_ui
schrodinger.application.desmond.enhanced_sampling
schrodinger.application.desmond.enhanced_sampling.FcnTypes
schrodinger.application.desmond.enhanced_sampling.mexpLexer
schrodinger.application.desmond.enhanced_sampling.mexpParser
schrodinger.application.desmond.enhsamp
schrodinger.application.desmond.envir
schrodinger.application.desmond.event_analysis
schrodinger.application.desmond.fep_edge_data
schrodinger.application.desmond.fep_edge_data_classifier
schrodinger.application.desmond.fep_mapping
schrodinger.application.desmond.fep_net_charge
schrodinger.application.desmond.fep_schedule
schrodinger.application.desmond.fep_scholar_rules
schrodinger.application.desmond.fep_struc
schrodinger.application.desmond.fep_util
schrodinger.application.desmond.ffiostructure
schrodinger.application.desmond.frag_snap
schrodinger.application.desmond.gaussian_filter
schrodinger.application.desmond.gchart
schrodinger.application.desmond.gcmc_utils
schrodinger.application.desmond.input_group_ui
schrodinger.application.desmond.measurement
schrodinger.application.desmond.memory
schrodinger.application.desmond.move_alchem_ions
schrodinger.application.desmond.multisim
schrodinger.application.desmond.multisim.parser
schrodinger.application.desmond.packages
schrodinger.application.desmond.packages.analysis
schrodinger.application.desmond.packages.destro
schrodinger.application.desmond.packages.msys
schrodinger.application.desmond.packages.msys.atomsel
schrodinger.application.desmond.packages.msys.grease
schrodinger.application.desmond.packages.msys.molfile
schrodinger.application.desmond.packages.msys.molfile.findframe
schrodinger.application.desmond.packages.msys.pfx
schrodinger.application.desmond.packages.msys.posre
schrodinger.application.desmond.packages.msys.vdw
schrodinger.application.desmond.packages.pfx
schrodinger.application.desmond.packages.restraint
schrodinger.application.desmond.packages.restraint.builder
schrodinger.application.desmond.packages.restraint.cross_link
schrodinger.application.desmond.packages.restraint.utils
schrodinger.application.desmond.packages.staf
schrodinger.application.desmond.packages.test
schrodinger.application.desmond.packages.test.DESMOND_11543
schrodinger.application.desmond.packages.timer
schrodinger.application.desmond.packages.topo
schrodinger.application.desmond.packages.traj
schrodinger.application.desmond.packages.traj_util
schrodinger.application.desmond.packages.viparr
schrodinger.application.desmond.packages.viparr1
schrodinger.application.desmond.packages.viparr1.plugins
schrodinger.application.desmond.packages.viparr1.systest
schrodinger.application.desmond.packages.viparr1.systest.systest
schrodinger.application.desmond.packages.viparr1.viparr
schrodinger.application.desmond.packages.viparr1.viparr.elements
schrodinger.application.desmond.packages.viparr1.viparr.isomorph
schrodinger.application.desmond.packages.viparr1.viparr.version
schrodinger.application.desmond.packages.viparr1.viparr.viparr
schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge
schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util
schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue
schrodinger.application.desmond.packages.viparr1.viparr.viparr_util
schrodinger.application.desmond.picklejar
schrodinger.application.desmond.platforms
schrodinger.application.desmond.r_group_asl
schrodinger.application.desmond.remd
schrodinger.application.desmond.repair_cms
schrodinger.application.desmond.replica_dE
schrodinger.application.desmond.replica_exchange_review
schrodinger.application.desmond.rest_tab_ui
schrodinger.application.desmond.rl_helper
schrodinger.application.desmond.simulation_block_data
schrodinger.application.desmond.simulation_block_test
schrodinger.application.desmond.smarts
schrodinger.application.desmond.solubility_utils
schrodinger.application.desmond.starter
schrodinger.application.desmond.starter.starter
schrodinger.application.desmond.task
schrodinger.application.desmond.test_utils
schrodinger.application.desmond.torsion_related
schrodinger.application.desmond.util
schrodinger.application.epik
schrodinger.application.fpsim
schrodinger.application.glide
schrodinger.application.glide.ensemble_selection
schrodinger.application.glide.packages
schrodinger.application.glide.poseviewconvert
schrodinger.application.glide.utils
schrodinger.application.glide.xpdes
schrodinger.application.inputconfig
schrodinger.application.jaguar
schrodinger.application.jaguar.autots_constants
schrodinger.application.jaguar.autots_input_constants
schrodinger.application.jaguar.basis
schrodinger.application.jaguar.boltzmann_prop_defaults
schrodinger.application.jaguar.check_headers
schrodinger.application.jaguar.constants
schrodinger.application.jaguar.csrch_input_constants
schrodinger.application.jaguar.exceptions
schrodinger.application.jaguar.global_macros
schrodinger.application.jaguar.gui
schrodinger.application.jaguar.hydrokinetic_constants
schrodinger.application.jaguar.hydrokinetic_input_constants
schrodinger.application.jaguar.hydrokinetic_validation
schrodinger.application.jaguar.jaguar_diff
schrodinger.application.jaguar.keywordDB
schrodinger.application.jaguar.macro_pka_constants
schrodinger.application.jaguar.mmjag
schrodinger.application.jaguar.neural_network_optimizer
schrodinger.application.jaguar.results
schrodinger.application.jaguar.scan
schrodinger.application.jaguar.solvation_validation
schrodinger.application.jaguar.update_pka_settings_ui
schrodinger.application.jaguar.user_config
schrodinger.application.jaguar.utils
schrodinger.application.jaguar.workflow_validation
schrodinger.application.job_monitor
schrodinger.application.job_monitor.diagnostics_dialog_ui
schrodinger.application.job_monitor.file_browser_ui
schrodinger.application.job_monitor.util
schrodinger.application.licensing
schrodinger.application.licensing.flexlm
schrodinger.application.licensing.licadmin
schrodinger.application.licensing.licerror
schrodinger.application.licensing.lmgrd_log_parser
schrodinger.application.licensing.netsuiteapi
schrodinger.application.ligprep
schrodinger.application.ligprep.ionizer
schrodinger.application.livedesign
schrodinger.application.livedesign.data_classes
schrodinger.application.livedesign.entry_types
schrodinger.application.livedesign.io_utils
schrodinger.application.livedesign.ld_folder_tree
schrodinger.application.livedesign.lid
schrodinger.application.livedesign.login
schrodinger.application.livedesign.login2_ui
schrodinger.application.livedesign.login_ui
schrodinger.application.livedesign.pose_name_panel_ui
schrodinger.application.livedesign.pse_helpers
schrodinger.application.livedesign.save_mapping_dialog_ui
schrodinger.application.livedesign.selection_pop_up_ui
schrodinger.application.livedesign.upload_utils
schrodinger.application.macromodel
schrodinger.application.macromodel.packages
schrodinger.application.macromodel.tools
schrodinger.application.matsci
schrodinger.application.matsci.atomicsymbols
schrodinger.application.matsci.basiselements
schrodinger.application.matsci.cache
schrodinger.application.matsci.cctbx
schrodinger.application.matsci.cctbx.rot_mx
schrodinger.application.matsci.codeutils
schrodinger.application.matsci.colorutils
schrodinger.application.matsci.elasticity
schrodinger.application.matsci.enc
schrodinger.application.matsci.espresso
schrodinger.application.matsci.geometry
schrodinger.application.matsci.graph
schrodinger.application.matsci.gsas
schrodinger.application.matsci.gsas.atmdata
schrodinger.application.matsci.gsas.ElementTable
schrodinger.application.matsci.gsas.GSASIIElem
schrodinger.application.matsci.gsas.GSASIIfiles
schrodinger.application.matsci.gsas.GSASIIlattice
schrodinger.application.matsci.gsas.GSASIImath
schrodinger.application.matsci.gsas.GSASIIpwd
schrodinger.application.matsci.gsas.GSASIIspc
schrodinger.application.matsci.hdfutils
schrodinger.application.matsci.mlearn
schrodinger.application.matsci.mlearn.base
schrodinger.application.matsci.mlearn.descriptor
schrodinger.application.matsci.mlearn.sklearn_json
schrodinger.application.matsci.mlearn.sklearn_json.classification
schrodinger.application.matsci.mlearn.sklearn_json.common
schrodinger.application.matsci.mlearn.sklearn_json.csr
schrodinger.application.matsci.mlearn.sklearn_json.decomposition
schrodinger.application.matsci.mlearn.sklearn_json.regression
schrodinger.application.matsci.msconst
schrodinger.application.matsci.msprops
schrodinger.application.matsci.nano
schrodinger.application.matsci.nano.space_groups
schrodinger.application.matsci.nano.util
schrodinger.application.matsci.optoelectronics
schrodinger.application.matsci.plotwidgets
schrodinger.application.matsci.property_names
schrodinger.application.matsci.qb_sdk
schrodinger.application.matsci.qb_sdk.api
schrodinger.application.matsci.qb_sdk.client
schrodinger.application.matsci.qb_sdk.job
schrodinger.application.matsci.qb_sdk.parameters
schrodinger.application.matsci.qb_sdk.tools
schrodinger.application.matsci.qeschema
schrodinger.application.matsci.qeschema.qeschema
schrodinger.application.matsci.qeschema.qeschema.cards
schrodinger.application.matsci.qeschema.qeschema.converters
schrodinger.application.matsci.qeschema.qeschema.documents
schrodinger.application.matsci.qeschema.qeschema.exceptions
schrodinger.application.matsci.qeschema.qeschema.hdf5
schrodinger.application.matsci.qeschema.qeschema.hdf5.charge
schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils
schrodinger.application.matsci.qeschema.qeschema.namespaces
schrodinger.application.matsci.qeschema.qeschema.options
schrodinger.application.matsci.qeschema.qeschema.utils
schrodinger.application.matsci.qeschema.scripts.xml2qeinput
schrodinger.application.matsci.qeschema.scripts.yaml2qeinput
schrodinger.application.matsci.qeschema.tests
schrodinger.application.matsci.qeschema.utils
schrodinger.application.matsci.qexsd
schrodinger.application.matsci.qexsd.qespresso
schrodinger.application.matsci.qexsd.qespresso.cards
schrodinger.application.matsci.qexsd.qespresso.converters
schrodinger.application.matsci.qexsd.qespresso.documents
schrodinger.application.matsci.qexsd.qespresso.exceptions
schrodinger.application.matsci.qexsd.qespresso.options
schrodinger.application.matsci.qexsd.qespresso.utils
schrodinger.application.matsci.qexsd.qespresso.utils.logger
schrodinger.application.matsci.qexsd.qespresso.utils.mapping
schrodinger.application.matsci.qexsd.qespresso.utils.xml2nebinput
schrodinger.application.matsci.qexsd.qespresso.utils.xml2qeinput
schrodinger.application.matsci.qexsd.qespresso.xsdtypes
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes
schrodinger.application.matsci.qexsd.tests.test_converters
schrodinger.application.matsci.qexsd.utils
schrodinger.application.matsci.siteselector
schrodinger.application.matsci.typography
schrodinger.application.matsci.uq_utils
schrodinger.application.matsci.xrd
schrodinger.application.medchem
schrodinger.application.medchem.property
schrodinger.application.mopac
schrodinger.application.mopac.exceptions
schrodinger.application.mopac.results_main
schrodinger.application.mopac.structure_launchers
schrodinger.application.mopac.utils
schrodinger.application.msv
schrodinger.application.msv.gui
schrodinger.application.msv.gui.binding_site_aln_dialog_ui
schrodinger.application.msv.gui.color_ramp
schrodinger.application.msv.gui.homology_modeling.constants
schrodinger.application.msv.gui.homology_modeling.homology_modeling_step_ui
schrodinger.application.msv.gui.multiple_seq_aln_dialog_ui
schrodinger.application.msv.gui.pairwise_seq_aln_dialog_ui
schrodinger.application.msv.gui.toolbar_ui
schrodinger.application.pathfinder
schrodinger.application.pathfinder.aligner
schrodinger.application.pathfinder.reaction
schrodinger.application.pathfinder.render
schrodinger.application.phase
schrodinger.application.phase.compare_utils
schrodinger.application.phase.constants
schrodinger.application.phase.create_xvol
schrodinger.application.phase.hypothesis
schrodinger.application.phase.hypothesis_binding_modes
schrodinger.application.phase.input
schrodinger.application.phase.packages
schrodinger.application.phase.packages.conformer_storage
schrodinger.application.phase.packages.hypo_refine.hypo_utils
schrodinger.application.phase.packages.ligand_aligner
schrodinger.application.phase.packages.mmp2d
schrodinger.application.phase.packages.mmp3dscreener
schrodinger.application.phase.packages.mmp_compare_utils
schrodinger.application.phase.packages.phase_option_utils
schrodinger.application.phase.packages.shape_binary_utils
schrodinger.application.phase.packages.test
schrodinger.application.phase.shape_screen_reporter
schrodinger.application.phase.shape_screen_reporter.prop_utils
schrodinger.application.phase.utils
schrodinger.application.prepwizard2
schrodinger.application.prime
schrodinger.application.prime.gui
schrodinger.application.prime.gui.ui
schrodinger.application.prime.gui.ui.environment_options_ui
schrodinger.application.prime.input
schrodinger.application.prime.primefix
schrodinger.application.prime.residue_interaction
schrodinger.application.prime.wrapper
schrodinger.application.qsite
schrodinger.application.qsite.input
schrodinger.application.scaffold_enumeration
schrodinger.application.scaffold_enumeration.atomlist
schrodinger.application.scaffold_enumeration.common
schrodinger.application.scaffold_enumeration.cxsmiles
schrodinger.application.scaffold_enumeration.layered
schrodinger.application.scaffold_enumeration.linknode
schrodinger.application.scaffold_enumeration.markush
schrodinger.application.scaffold_enumeration.mdl
schrodinger.application.scaffold_enumeration.posvarbond
schrodinger.application.scaffold_enumeration.rdcml
schrodinger.application.scisol
schrodinger.application.scisol.packages
schrodinger.application.ska
schrodinger.application.steps
schrodinger.application.steps.env_keys
schrodinger.application.steps.licensing
schrodinger.application.utils
schrodinger.application.vss
schrodinger.application.vss.config
schrodinger.application.vss.database
schrodinger.application.vss.dise
schrodinger.application.watermap
schrodinger.application.watermap.utils
schrodinger.energy
schrodinger.forcefield
schrodinger.forcefield.common
schrodinger.forcefield.constants
schrodinger.forcefield.ffld_options
schrodinger.forcefield.minimizer
schrodinger.forcefield.packages
schrodinger.genericfp
schrodinger.geometry
schrodinger.gpgpu
schrodinger.graphics3d
schrodinger.infra
schrodinger.infra.ark
schrodinger.infra.canvas
schrodinger.infra.canvas2d
schrodinger.infra.color
schrodinger.infra.epydoc_to_sphinx
schrodinger.infra.exception_handler_dir
schrodinger.infra.exception_handler_dir.exception_dialog_ui
schrodinger.infra.fast3d
schrodinger.infra.fix_sip6_enum_access
schrodinger.infra.gpgpu_utils
schrodinger.infra.growthspace
schrodinger.infra.jobhub
schrodinger.infra.licensing
schrodinger.infra.mm
schrodinger.infra.mmbitset
schrodinger.infra.mmcheck
schrodinger.infra.mmerr
schrodinger.infra.mmim
schrodinger.infra.mminit
schrodinger.infra.mmjob
schrodinger.infra.mmkv
schrodinger.infra.mmlist
schrodinger.infra.mmobject
schrodinger.infra.mmproj
schrodinger.infra.mmreflect
schrodinger.infra.mmsurf
schrodinger.infra.mopac
schrodinger.infra.phase
schrodinger.infra.projectmodel
schrodinger.infra.structure
schrodinger.infra.table
schrodinger.infra.test
schrodinger.infra.util
schrodinger.job
schrodinger.job.files
schrodinger.job.host_check
schrodinger.job.jobwriter
schrodinger.job.launchparams
schrodinger.job.remote_command
schrodinger.job.resource
schrodinger.job.server
schrodinger.job.util
schrodinger.livedesign.convert
schrodinger.livedesign.molhash
schrodinger.livedesign.preprocessor
schrodinger.livedesign.rgfile_parse
schrodinger.livedesign.rgroup_decomposition
schrodinger.math.mathutils
schrodinger.math.multi_parameter_optimization
schrodinger.models
schrodinger.models.adapters
schrodinger.models.adapters.abstractadapter
schrodinger.models.adapters.inputconfig
schrodinger.models.diffy
schrodinger.models.json
schrodinger.models.jsonable
schrodinger.pipeline
schrodinger.pipeline.compiled_functions
schrodinger.pipeline.input
schrodinger.pipeline.pipeio
schrodinger.pipeline.pipeutils
schrodinger.pipeline.stages
schrodinger.project.surface
schrodinger.protein
schrodinger.protein.analysis
schrodinger.protein.analysis_params
schrodinger.protein.biounit
schrodinger.protein.buildpeptide
schrodinger.protein.constants
schrodinger.protein.findhets
schrodinger.protein.getpdb
schrodinger.protein.gpcr
schrodinger.protein.gpcr.annotate
schrodinger.protein.gpcr.gpcrdb
schrodinger.protein.gpcr.sql
schrodinger.protein.gpcr.update_gpcr_db
schrodinger.protein.helix
schrodinger.protein.helm
schrodinger.protein.remediate
schrodinger.protein.renumber_residues
schrodinger.protein.rotamers
schrodinger.protein.seqres
schrodinger.protein.tasks.mock_blast_output
schrodinger.protein.tasks.structure_alignment
schrodinger.Qt
schrodinger.Qt.PyQt6
schrodinger.Qt.PyQt6.QtCharts
schrodinger.Qt.PyQt6.QtCore
schrodinger.Qt.PyQt6.QtGui
schrodinger.Qt.PyQt6.QtNetwork
schrodinger.Qt.PyQt6.QtOpenGL
schrodinger.Qt.PyQt6.QtOpenGLWidgets
schrodinger.Qt.PyQt6.QtPrintSupport
schrodinger.Qt.PyQt6.QtStateMachine
schrodinger.Qt.PyQt6.QtSvg
schrodinger.Qt.PyQt6.QtWidgets
schrodinger.Qt.PyQt6.sip
schrodinger.rdkit.alignment
schrodinger.rdkit.filtering
schrodinger.rdkit.molio
schrodinger.rdkit.rdkit_adapter
schrodinger.rdkit.rgroup
schrodinger.rdkit.sorted_molwriter
schrodinger.rdkit.substructure
schrodinger.rdkit_extensions
schrodinger.shape
schrodinger.sitemap
schrodinger.structure
schrodinger.structure.structure
schrodinger.structure.workflow_action_menu
schrodinger.structutils
schrodinger.structutils.analyze
schrodinger.structutils.block_data
schrodinger.structutils.build
schrodinger.structutils.check
schrodinger.structutils.color
schrodinger.structutils.createfragments
schrodinger.structutils.filter
schrodinger.structutils.interactionfp
schrodinger.structutils.interactions
schrodinger.structutils.interactions.hbond
schrodinger.structutils.interactions.pi
schrodinger.structutils.interactions.protein_protein_interactions
schrodinger.structutils.interactions.salt_bridge
schrodinger.structutils.interactions.ssbond
schrodinger.structutils.interactions.steric_clash
schrodinger.structutils.io
schrodinger.structutils.markush_enumerate
schrodinger.structutils.measure
schrodinger.structutils.minimize
schrodinger.structutils.pbc_tools
schrodinger.structutils.properties
schrodinger.structutils.residue
schrodinger.structutils.rgroup_enumerate
schrodinger.structutils.rings
schrodinger.structutils.rmsd
schrodinger.structutils.shuffle
schrodinger.structutils.sitealign
schrodinger.structutils.smiles
schrodinger.structutils.standard_nuclear_orientation
schrodinger.structutils.structalign
schrodinger.structutils.transform
schrodinger.surface
schrodinger.tasks
schrodinger.test
schrodinger.test.build_test_structures
schrodinger.test.canvas_utils
schrodinger.test.cluster_info
schrodinger.test.custom_assertions
schrodinger.test.darwinconsole
schrodinger.test.decorate_fflag
schrodinger.test.fixtures
schrodinger.test.hypothesis.hypothesis_profiles
schrodinger.test.hypothesis.strategies.indices
schrodinger.test.hypothesis.strategies.structures
schrodinger.test.hypothesis.strategies.ui
schrodinger.test.hypothesis.utils
schrodinger.test.ioredirect
schrodinger.test.log_parser
schrodinger.test.memtest
schrodinger.test.perceptualdiff
schrodinger.test.performance
schrodinger.test.performance.exceptions
schrodinger.test.performance.general
schrodinger.test.project_mock
schrodinger.test.pytest
schrodinger.test.pytest.exetest
schrodinger.test.pytest.faulthandler_setup
schrodinger.test.pytest.fixture
schrodinger.test.pytest.warnings
schrodinger.test.squish
schrodinger.test.squish.general
schrodinger.test.squish.maestro
schrodinger.test.squish.matsci
schrodinger.test.structurecheck
schrodinger.test.stu
schrodinger.test.stu.common
schrodinger.test.stu.constants
schrodinger.test.stu.get_pdbs
schrodinger.test.stu.outcomes.compare_csv
schrodinger.test.stu.outcomes.compareDesmondSystems
schrodinger.test.stu.outcomes.confgen_workups
schrodinger.test.stu.outcomes.correlate_to_reference_file
schrodinger.test.stu.outcomes.correlate_workup
schrodinger.test.stu.process_management
schrodinger.test.stu.workups
schrodinger.test.stu.workups.workup_tools
schrodinger.test.test_markers
schrodinger.test.warning_messages
schrodinger.thirdparty.networkx_algos
schrodinger.trajectory
schrodinger.trajectory.pbc_manager
schrodinger.trajectory.prody
schrodinger.trajectory.prody.crosscorrelation
schrodinger.trajectory.prody.ensemble
schrodinger.trajectory.prody.mode
schrodinger.trajectory.prody.modeset
schrodinger.trajectory.prody.nma
schrodinger.trajectory.prody.pca
schrodinger.trajectory.prody.writenmd
schrodinger.trajectory.traj_dialog_ui
schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui
schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui
schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui
schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui
schrodinger.trajectory.trajectory_gui_dir.display_settings_data
schrodinger.trajectory.trajectory_gui_dir.display_settings_manager
schrodinger.trajectory.trajectory_gui_dir.export_movie_ui
schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui
schrodinger.trajectory.trajectory_gui_dir.export_structure_enums
schrodinger.trajectory.trajectory_gui_dir.export_structures_ui
schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui
schrodinger.trajectory.trajectory_gui_dir.playback_settings_data
schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui
schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui
schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui
schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data
schrodinger.trajectory.trajectory_gui_dir.shortcut_ui
schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui
schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui
schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui
schrodinger.ui
schrodinger.ui.dendrogram
schrodinger.ui.ligfilter_definition_dialog_ui
schrodinger.ui.ligfilter_ui
schrodinger.ui.maestro_ui
schrodinger.ui.picking_dir
schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui
schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui
schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui
schrodinger.ui.qt
schrodinger.ui.qt.appframework2
schrodinger.ui.qt.appframework2.appmethods
schrodinger.ui.qt.appframework2.debug_gui_ui
schrodinger.ui.qt.appframework2.debugcore
schrodinger.ui.qt.appframework2.validation
schrodinger.ui.qt.appframework2.validators
schrodinger.ui.qt.borderless_popup_ui
schrodinger.ui.qt.config_dialog_open_mp_ui
schrodinger.ui.qt.config_dialog_queue_ui
schrodinger.ui.qt.dialbox_dir
schrodinger.ui.qt.entryselector_ui
schrodinger.ui.qt.filter_dialog_dir
schrodinger.ui.qt.filter_dialog_dir.filter_core
schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui
schrodinger.ui.qt.filter_dialog_ui
schrodinger.ui.qt.label_cursor
schrodinger.ui.qt.pdb_dialog_ui
schrodinger.ui.qt.presets.manage_presets_dialog_ui
schrodinger.ui.qt.presets.save_presets_dialog_ui
schrodinger.ui.qt.protein_health_viewer_ui
schrodinger.ui.qt.rename_favorite_dialog_ui
schrodinger.ui.qt.schrodingerstyle
schrodinger.ui.qt.select_residues_dialog_ui
schrodinger.ui.qt.standard
schrodinger.ui.qt.standard.colors
schrodinger.ui.qt.standard.constants
schrodinger.ui.qt.standard.icons
schrodinger.ui.qt.tasks
schrodinger.ui.qt.tasks.config_dialog_ui
schrodinger.ui.qt.tasks.config_info_ui
schrodinger.ui.sketcher
schrodinger.utils
schrodinger.utils.cgxutils
schrodinger.utils.colorscheme
schrodinger.utils.compare
schrodinger.utils.config
schrodinger.utils.csv_unicode
schrodinger.utils.deprecation
schrodinger.utils.env
schrodinger.utils.featureflags
schrodinger.utils.featureflags.featureflags
schrodinger.utils.featureflags.write
schrodinger.utils.fileutils
schrodinger.utils.funcchains
schrodinger.utils.funcgroups
schrodinger.utils.imputils
schrodinger.utils.install_scripts
schrodinger.utils.license
schrodinger.utils.ligfilter
schrodinger.utils.log
schrodinger.utils.machid
schrodinger.utils.maestro_scripts_path
schrodinger.utils.mmutil
schrodinger.utils.moduleproxy
schrodinger.utils.multifpfile
schrodinger.utils.openmpi
schrodinger.utils.platform
schrodinger.utils.postinstall
schrodinger.utils.preferences
schrodinger.utils.profiling
schrodinger.utils.scollections
schrodinger.utils.sea
schrodinger.utils.sea.common
schrodinger.utils.sea.evalor
schrodinger.utils.sea.sea
schrodinger.utils.singledashoptionparser
schrodinger.utils.sshconfig
schrodinger.utils.subproc
schrodinger.utils.subprocess
schrodinger.utils.sysinfo
schrodinger.utils.timeit
schrodinger.utils.units
schrodinger.utils.withnone
ModuleInfo (class in schrodinger.application.matsci.codeutils)
ModuleProxy (class in schrodinger.utils.moduleproxy)
modules
accessing your own
installing
MOL2 (schrodinger.infra.structure.FileFormat attribute)
mol_atomic_mass (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_charge (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_formula (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_from_cxsmiles() (in module schrodinger.application.scaffold_enumeration.cxsmiles)
mol_hash (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_name (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_num (schrodinger.structutils.analyze.Ligand property)
mol_number (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
mol_number_carbon (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
mol_pdb_name (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_smiles (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_st (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_to_qpicture() (in module schrodinger.application.pathfinder.render)
mol_torsions (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_total (schrodinger.application.desmond.cms.Cms property)
(schrodinger.application.desmond.ffiostructure.FFIOStructure property)
(schrodinger.models.jsonable.JsonableStructure property)
(schrodinger.structure.Structure property)
(schrodinger.structure.TextualStructure property)
mol_total_atoms (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_total_fragments (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_total_heavy (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
mol_total_rot_bonds (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
molecular (schrodinger.surface.MolSurfType attribute)
Molecular_formula() (in module schrodinger.utils.ligfilter)
Molecular_weight() (in module schrodinger.utils.ligfilter)
MolecularSurfaceArea (class in schrodinger.application.desmond.packages.analysis)
molecule (schrodinger.application.desmond.cms.Cms attribute)
(schrodinger.application.desmond.ffiostructure.FFIOStructure attribute)
Molecule (schrodinger.application.glide.xpdes.TermKeywords attribute)
molecule (schrodinger.models.jsonable.JsonableStructure attribute)
(schrodinger.structure.Structure attribute)
(schrodinger.structure.TextualStructure property)
MOLECULE_1 (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute)
molecule_number (schrodinger.structure._Residue property)
(schrodinger.structure._StructureAtom property)
molecule_number_by_entry (schrodinger.structure._Residue property)
(schrodinger.structure._StructureAtom property)
molecules() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
MoleculeWiseCom (class in schrodinger.application.desmond.packages.analysis)
molHasRing() (schrodinger.application.dendrogram.core_class.Utilities static method)
molid (schrodinger.application.qsite.input.Cut property)
molnum (schrodinger.application.desmond.fep_edge_data.ResData attribute)
MolSerializer (class in schrodinger.models.jsonable)
MolSurfType (class in schrodinger.surface)
MolWriter (class in schrodinger.rdkit.molio)
moment() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
MomentOfInertia (class in schrodinger.application.desmond.packages.analysis)
MomentOfInertiaDirector (class in schrodinger.application.desmond.packages.analysis)
MonitorAtomNumbering() (in module schrodinger.structutils.build)
MONOCLINIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute)
Monomer (class in schrodinger.protein.helm)
mopac (schrodinger.application.qsite.input.QSiteInput property)
MopacBasisError1
MopacBasisError2
MopacBasisError3
MopacBasisError4
MopacBasisError5
MopacGradientParserError
MopacIOError
MopacMainTextParser (class in schrodinger.application.mopac.results_main)
MopacNumericalError
MopacPropertyError
MopacResultsMain (class in schrodinger.application.mopac.results_main)
MopacRuntimeError
MopacUserFacingException
mouseDoubleClickEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
mouseGrabber() (schrodinger.ui.dendrogram.DendrogramView method)
mouseGrabberItem() (schrodinger.ui.dendrogram.DendrogramScene method)
mouseMoveEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
mousePressEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
mouseReleaseEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
move() (schrodinger.ui.dendrogram.DendrogramView method)
move_alchemical_ions() (in module schrodinger.application.desmond.move_alchem_ions)
move_ions_in_file() (in module schrodinger.application.desmond.move_alchem_ions)
move_ions_to_ligands() (in module schrodinger.application.desmond.move_alchem_ions)
move_solvent_cts_back() (schrodinger.application.desmond.cms.Cms method)
move_to_end() (schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
moveby() (schrodinger.application.desmond.packages.traj.Frame method)
moveColumn() (schrodinger.infra.table.Table method)
moved (schrodinger.models.diffy.ListDiff attribute)
moveEvent() (schrodinger.ui.dendrogram.DendrogramView method)
moveRows() (schrodinger.infra.table.Table method)
moveToThread() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
MoveToUnitCell() (in module schrodinger.application.matsci.gsas.GSASIIspc)
mPCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
MPmcsaSearch() (in module schrodinger.application.matsci.gsas.GSASIImath)
mPOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mro() (schrodinger.application.desmond.picklejar.PicklableMetaClass method)
MS_ADSORPTION_ENERGY (schrodinger.infra.structure.WorkflowType attribute)
MS_AMORPHOUS_DIELECTRIC (schrodinger.infra.structure.WorkflowType attribute)
MS_BAND_STRUCTURE (schrodinger.infra.structure.WorkflowType attribute)
MS_BANDSHAPE (schrodinger.infra.structure.WorkflowType attribute)
MS_BOND_DISSOCIATION (schrodinger.infra.structure.WorkflowType attribute)
MS_CG_FF_ASSIGNMENT (schrodinger.infra.structure.WorkflowType attribute)
MS_CG_FF_BUILDER (schrodinger.infra.structure.WorkflowType attribute)
MS_CLUSTER_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
MS_CONVERGENCE_TESTS (schrodinger.infra.structure.WorkflowType attribute)
MS_DENSITY_OF_STATES (schrodinger.infra.structure.WorkflowType attribute)
MS_DIELECTRIC_FUNCTION (schrodinger.infra.structure.WorkflowType attribute)
MS_DIFFUSION_COEFFICIENT (schrodinger.infra.structure.WorkflowType attribute)
MS_DISORDERED_NO_SYSTEM (schrodinger.infra.structure.WorkflowType attribute)
MS_DISORDERED_SYSTEM (schrodinger.infra.structure.WorkflowType attribute)
MS_DROPLET_CONTACT (schrodinger.infra.structure.WorkflowType attribute)
MS_ELASTIC_CONSTANTS (schrodinger.infra.structure.WorkflowType attribute)
MS_ELECTROLYTE_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
MS_EQUATION_OF_STATE (schrodinger.infra.structure.WorkflowType attribute)
MS_ESM_DENSITY_POTENTIAL (schrodinger.infra.structure.WorkflowType attribute)
MS_EVAPORATION_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
MS_EXCITED_STATE_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
MS_FREE_VOLUME (schrodinger.infra.structure.WorkflowType attribute)
MS_GENETIC_OPTIMIZATION (schrodinger.infra.structure.WorkflowType attribute)
MS_KMC_CHARGE_HOPPING (schrodinger.infra.structure.WorkflowType attribute)
MS_KMC_CHARGE_MOBILITY (schrodinger.infra.structure.WorkflowType attribute)
MS_MD_BUILDERS_CMS (schrodinger.infra.structure.WorkflowType attribute)
MS_MD_BUILDERS_MAE (schrodinger.infra.structure.WorkflowType attribute)
MS_MD_TRAJ_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
MS_MORPHOLOGY (schrodinger.infra.structure.WorkflowType attribute)
MS_OPTOELECTRONICS (schrodinger.infra.structure.WorkflowType attribute)
MS_ORDER_PARAMETER (schrodinger.infra.structure.WorkflowType attribute)
MS_PENETRANT_LOADING (schrodinger.infra.structure.WorkflowType attribute)
MS_PHONON_DENSITY_OF_STATES (schrodinger.infra.structure.WorkflowType attribute)
MS_PHONON_DISPERSION (schrodinger.infra.structure.WorkflowType attribute)
MS_POLYMER_BUILDER (schrodinger.infra.structure.WorkflowType attribute)
MS_POLYMER_CHAIN_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
MS_POLYMER_CROSSLINK (schrodinger.infra.structure.WorkflowType attribute)
MS_POWDER_DIFFRACTION_PATTERN (schrodinger.infra.structure.WorkflowType attribute)
MS_PREPARE_FOR_MD (schrodinger.infra.structure.WorkflowType attribute)
MS_PROJECTED_DENSITY_OF_STATES (schrodinger.infra.structure.WorkflowType attribute)
MS_SIMULATION_PROFILE (schrodinger.infra.structure.WorkflowType attribute)
MS_STRESS_STRAIN (schrodinger.infra.structure.WorkflowType attribute)
MS_STRUCTURE_FACTOR (schrodinger.infra.structure.WorkflowType attribute)
MS_SURFACE_TENSION (schrodinger.infra.structure.WorkflowType attribute)
MS_SURFACES_INTERFACES (schrodinger.infra.structure.WorkflowType attribute)
MS_SURFACTANT_TILT (schrodinger.infra.structure.WorkflowType attribute)
MS_TG (schrodinger.infra.structure.WorkflowType attribute)
MS_TORSION_PROFILE_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
MS_TRAJECTORY_ESP_ANALYSIS (schrodinger.infra.structure.WorkflowType attribute)
MS_UNCERTIANTY_QUANTIFICATION (schrodinger.infra.structure.WorkflowType attribute)
MS_VISCOSITY (schrodinger.infra.structure.WorkflowType attribute)
MS_VISCOSITY_DIFFUSION (schrodinger.infra.structure.WorkflowType attribute)
mSEMI() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
msg (schrodinger.application.desmond.arkdb.CompositeKeySyntaxError attribute)
(schrodinger.MaestroNotAvailableError attribute)
Msj (class in schrodinger.application.desmond.multisim.parser)
mSTRING() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mSUBTROP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
MT2text() (in module schrodinger.application.matsci.gsas.GSASIIspc)
mT__45() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__46() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__47() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__48() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__49() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__50() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__51() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__52() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__53() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__54() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__55() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__56() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__57() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mT__58() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mTokens() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
Muiso2Shkl() (in module schrodinger.application.matsci.gsas.GSASIIspc)
mulliken_charge() (in module schrodinger.application.mopac.results_main)
mulliken_electronegativity() (in module schrodinger.application.mopac.results_main)
multi_validator() (in module schrodinger.ui.qt.appframework2.validation)
MultiAxesLabelCursor (class in schrodinger.ui.qt.label_cursor)
MulticenterSgroup (class in schrodinger.application.scaffold_enumeration.posvarbond)
MultiEnvironmentContext (class in schrodinger.utils.env)
MultiFileStructureReader (class in schrodinger.structure)
MultiFileStructureWriter (class in schrodinger.structure)
MultiFileWriter (class in schrodinger.structutils.io)
MultiFPFile (class in schrodinger.utils.multifpfile)
MultiFPFileWriter (class in schrodinger.utils.multifpfile)
multiple_align_ct() (in module schrodinger.application.ska)
multiplicity (schrodinger.application.matsci.qb_sdk.parameters.QubecChemistryProblem attribute)
multiply() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
MULTISIM_EXEC (schrodinger.application.desmond.envir.CONST attribute)
MuShklMean() (in module schrodinger.application.matsci.gsas.GSASIIspc)
MustrainCoeff() (in module schrodinger.application.matsci.gsas.GSASIIspc)
MustrainNames() (in module schrodinger.application.matsci.gsas.GSASIIspc)
MUT (schrodinger.application.desmond.constants.FEP_STATE_KEYS attribute)
mut_frag_st (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
mut_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
mut_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
mut_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
mut_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
mutate() (in module schrodinger.structutils.build)
MUVT (schrodinger.application.desmond.constants.Ensembles attribute)
MVCorrMW() (in module schrodinger.rdkit.filtering)
mWS() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
mysplit() (in module schrodinger.utils.ligfilter)
N
N_fab (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
n_win (schrodinger.application.desmond.fep_schedule.FepSchedule attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding attribute)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault attribute)
NA (schrodinger.application.desmond.fep_edge_data_classifier.Rating attribute)
nactive (schrodinger.application.desmond.packages.msys.System property)
(schrodinger.application.desmond.packages.pfx.Frame attribute)
(schrodinger.application.desmond.packages.topo.DuckFrame property)
(schrodinger.application.desmond.packages.traj.Frame property)
nactive_gids (schrodinger.application.desmond.cms.Cms property)
name (schrodinger.application.dendrogram.core_class.RingSysInfo attribute)
NAME (schrodinger.application.desmond.constants.BUILD_GEOMETRY attribute)
name (schrodinger.application.desmond.fep_edge_data.ResData attribute)
(schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.application.desmond.packages.msys.Chain property)
(schrodinger.application.desmond.packages.msys.Ct property)
(schrodinger.application.desmond.packages.msys.molfile.Grid property)
(schrodinger.application.desmond.packages.msys.molfile.SeqFile attribute)
(schrodinger.application.desmond.packages.msys.molfile.StkFile attribute)
(schrodinger.application.desmond.packages.msys.Residue property)
(schrodinger.application.desmond.packages.msys.System property)
(schrodinger.application.desmond.packages.msys.TermTable property)
(schrodinger.application.desmond.packages.traj.DtrSource property)
(schrodinger.application.desmond.packages.traj.MaeSource property)
(schrodinger.application.desmond.packages.traj.Source property)
(schrodinger.application.desmond.packages.traj.XtcSource property)
NAME (schrodinger.application.desmond.simulation_block_test.BoxSize attribute)
(schrodinger.application.desmond.simulation_block_test.E_f attribute)
(schrodinger.application.desmond.simulation_block_test.E_k attribute)
(schrodinger.application.desmond.simulation_block_test.E_x attribute)
(schrodinger.application.desmond.simulation_block_test.Energy attribute)
(schrodinger.application.desmond.simulation_block_test.Job_Details attribute)
(schrodinger.application.desmond.simulation_block_test.PotentialEnergy attribute)
(schrodinger.application.desmond.simulation_block_test.Pressure attribute)
(schrodinger.application.desmond.simulation_block_test.T_0 attribute)
(schrodinger.application.desmond.simulation_block_test.Temperature attribute)
(schrodinger.application.desmond.simulation_block_test.V attribute)
name (schrodinger.application.jaguar.basis.BasisSet attribute)
(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.IndividualStructureBase attribute)
(schrodinger.application.livedesign.entry_types.Ligands attribute)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute)
(schrodinger.application.livedesign.entry_types.TargetlessBase attribute)
(schrodinger.application.matsci.codeutils.ModuleInfo attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement attribute)
(schrodinger.application.mopac.results_main.MopacResultsMain property)
(schrodinger.application.msv.gui.color_ramp.NamedColorRamp property)
(schrodinger.application.msv.gui.color_ramp.NamedRainbowColorRamp property)
(schrodinger.application.prime.wrapper.BasePrimeAlignment property)
(schrodinger.MaestroNotAvailableError attribute)
(schrodinger.project.surface.ProjectSurface property)
(schrodinger.protein.helm.Monomer attribute)
(schrodinger.structure._Chain property)
(schrodinger.structure._StructureAtom property)
(schrodinger.surface.Surface property)
(schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableFile attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.Makefile attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
name0 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute)
name1 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute)
name2 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute)
name3a (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute)
name3b (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute)
name4 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute)
name5 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute)
name6 (schrodinger.application.dendrogram.core_class.GetPartitions.NameList attribute)
NamedColorRamp (class in schrodinger.application.msv.gui.color_ramp)
NamedRainbowColorRamp (class in schrodinger.application.msv.gui.color_ramp)
nameNum() (schrodinger.application.desmond.fep_edge_data.ResData method)
namespaces (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument property)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
NativeColors (class in schrodinger.ui.qt.standard.colors)
nativeEvent() (schrodinger.ui.dendrogram.DendrogramView method)
nativeParentWidget() (schrodinger.ui.dendrogram.DendrogramView method)
natoms (schrodinger.application.desmond.packages.msys.Ct property)
(schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader property)
(schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader property)
(schrodinger.application.desmond.packages.msys.Residue property)
(schrodinger.application.desmond.packages.msys.SmartsPattern property)
(schrodinger.application.desmond.packages.msys.System property)
(schrodinger.application.desmond.packages.msys.TermTable property)
(schrodinger.application.desmond.packages.pfx.Frame attribute)
(schrodinger.application.desmond.packages.topo.DuckFrame property)
(schrodinger.application.desmond.packages.traj.Frame property)
nbonds (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.application.desmond.packages.msys.System property)
nchains (schrodinger.application.desmond.packages.msys.Ct property)
(schrodinger.application.desmond.packages.msys.System property)
NCScattDen() (in module schrodinger.application.matsci.gsas.GSASIImath)
ncts (schrodinger.application.desmond.packages.msys.System property)
nearest_asl_atom (schrodinger.project.surface.ProjectSurface.ColorFrom attribute)
(schrodinger.surface.ColorFrom attribute)
(schrodinger.surface.Surface.ColorFrom attribute)
nearest_atom_distance() (schrodinger.application.bindingsite.intfield.Field method)
nearest_atom_indices (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
NEB_NAMESPACE (in module schrodinger.application.matsci.qeschema.qeschema.namespaces)
neb_set_system_nat() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
NEB_TEMPLATE_MAP (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter attribute)
NebDocument (class in schrodinger.application.matsci.qeschema.qeschema.documents)
(class in schrodinger.application.matsci.qexsd.qespresso.documents)
NebInputConverter (class in schrodinger.application.matsci.qeschema.qeschema.converters)
(class in schrodinger.application.matsci.qexsd.qespresso.converters)
need_msys (schrodinger.application.desmond.cms.Cms property)
need_server() (schrodinger.application.licensing.flexlm.License method)
needVisibilityUpdate() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
negative (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute)
neighbor() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
NetsuiteError
NetworkLoopError
NEUTRALIZE (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
neutralize() (in module schrodinger.livedesign.preprocessor)
neutralize_structure() (in module schrodinger.structutils.build)
NEW (schrodinger.application.desmond.constants.UiMode attribute)
new_best() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
new_default_session() (in module schrodinger.application.matsci.qb_sdk.api)
new_denominator() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
new_page() (in module schrodinger.application.desmond.rl_helper)
new_temperature() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
newMolecularSurface() (schrodinger.project.surface.ProjectSurface class method)
(schrodinger.surface.Surface class method)
next() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.infra.mmerr.Capture method)
(schrodinger.infra.structure.TextBlockReader method)
(schrodinger.infra.structure.TextBlockWriter method)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter method)
(schrodinger.structutils.color.ColorScheme method)
(schrodinger.ui.dendrogram.DendrogramNodeBFIterator method)
next_prime() (in module schrodinger.application.desmond.autopartition)
nextInFocusChain() (schrodinger.ui.dendrogram.DendrogramView method)
nextitem (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
nextNode() (schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
nextToken() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.TokenSource method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
nextTree() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
nframes (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader property)
(schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader property)
nframes() (schrodinger.application.desmond.packages.traj.DtrSource method)
(schrodinger.application.desmond.packages.traj.MaeSource method)
(schrodinger.application.desmond.packages.traj.Source method)
(schrodinger.application.desmond.packages.traj.XtcSource method)
nhydrogens (schrodinger.application.desmond.packages.msys.Atom property)
nil() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
nilNode() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
NMA (class in schrodinger.trajectory.prody.nma)
nmodels (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
nmr_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute)
nn_optimize() (in module schrodinger.application.jaguar.neural_network_optimizer)
nnlf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
No (schrodinger.test.perceptualdiff.Notify attribute)
no_cm1a_bcc (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute)
NO_DEFAULT_VALUE (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter attribute)
NO_MORE_LICENSES (schrodinger.application.steps.licensing.LicenseMixin attribute)
no_pandastools_side_effects() (in module schrodinger.test.pytest.fixture)
no_restrain_zob (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute)
no_stack() (in module schrodinger.application.jaguar)
(in module schrodinger.application.mopac)
NO_STEREO_SMILES (schrodinger.livedesign.molhash.HashLayer attribute)
NO_STEREO_TAUTOMER_HASH (schrodinger.livedesign.molhash.HashLayer attribute)
NO_VALUE (schrodinger.application.desmond.arkdb.DSC attribute)
no_zob_restrain (schrodinger.structutils.minimize.Minimizer property)
NoAnchor (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.ViewportAnchor attribute)
NoCache (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.CacheMode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.CacheMode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.CacheMode attribute)
Node (class in schrodinger.application.desmond.enhsamp)
node() (schrodinger.ui.dendrogram.DendrogramNodeBFIterator method)
node_str (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.IndividualStructureBase attribute)
(schrodinger.application.livedesign.entry_types.Ligands attribute)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute)
(schrodinger.application.livedesign.entry_types.TargetlessBase attribute)
nodeid (schrodinger.test.perceptualdiff.PerceptualDiffTest property)
(schrodinger.test.pytest.exetest.ExecutableFile property)
(schrodinger.test.pytest.exetest.ExecutableTest property)
(schrodinger.test.pytest.exetest.Makefile property)
(schrodinger.test.pytest.exetest.MakefileTest property)
NoDrag (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.DragMode attribute)
NoFrame (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shape attribute)
NoIndex (schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramScene.ItemIndexMethod attribute)
NOMM (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute)
nonbond_cutoff (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute)
nonbonded_cutoff (schrodinger.structutils.minimize.Minimizer property)
nonbonded_info (schrodinger.application.desmond.packages.msys.System property)
NonbondedSchemas() (in module schrodinger.application.desmond.packages.msys)
NONE (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute)
(schrodinger.energy.Solvent attribute)
(schrodinger.infra.structure.WorkflowType attribute)
(schrodinger.job.launchparams.ProjectDisposition attribute)
(schrodinger.livedesign.preprocessor.GenerateCoordinates attribute)
(schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Loop attribute)
NoneSkipper (class in schrodinger.rdkit.molio)
NonModal (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.PanelModality attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.PanelModality attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.PanelModality attribute)
norm() (in module schrodinger.application.desmond.cms)
norm_gen (class in schrodinger.application.matsci.gsas.GSASIIpwd)
normal (schrodinger.application.livedesign.upload_utils.CommandType attribute)
normalGeometry() (schrodinger.ui.dendrogram.DendrogramView method)
NormalMode (class in schrodinger.application.jaguar.results)
normQ() (in module schrodinger.application.matsci.gsas.GSASIImath)
Notify (class in schrodinger.test.perceptualdiff)
noverrides (schrodinger.application.desmond.packages.msys.TermTable property)
noViableAlt() (schrodinger.application.desmond.antlr3.dfa.DFA method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25 method)
NoViableAltException
NoViewportUpdate (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.ViewportUpdateMode attribute)
npacosd() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
nparams (schrodinger.application.desmond.packages.msys.ParamTable property)
nparent (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
npasind() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
npatan2d() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
npatand() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
npcosd() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
(in module schrodinger.application.matsci.gsas.GSASIIspc)
nplus (schrodinger.application.jaguar.basis.BasisSet attribute)
nprops (schrodinger.application.desmond.packages.msys.ParamTable property)
npsind() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
(in module schrodinger.application.matsci.gsas.GSASIIspc)
NPT (schrodinger.application.desmond.constants.Ensembles attribute)
npT2q() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
npT2stl() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
nptand() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
nresidues (schrodinger.application.desmond.packages.msys.Chain property)
(schrodinger.application.desmond.packages.msys.System property)
nring_sys (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
nstar (schrodinger.application.jaguar.basis.BasisSet attribute)
nterms (schrodinger.application.desmond.packages.msys.TermTable property)
nuclear_magnetic_dipole_moment_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute)
nuclear_spin_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute)
nucrep_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
NULL_Y_LIM (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute)
num() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
Num_aliphatic_rings() (in module schrodinger.utils.ligfilter)
Num_aromatic_rings() (in module schrodinger.utils.ligfilter)
Num_atoms() (in module schrodinger.utils.ligfilter)
NUM_BITS_PER_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
NUM_CENTERING_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
num_centering_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
Num_chiral_centers() (in module schrodinger.utils.ligfilter)
num_choices (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
NUM_CONSTRAINT (schrodinger.application.desmond.cms.Constraint attribute)
num_constraint() (schrodinger.application.desmond.cms.Constraint method)
num_electrons() (in module schrodinger.application.mopac.results_main)
Num_heavy_atoms() (in module schrodinger.utils.ligfilter)
Num_heteroaromatic_rings() (in module schrodinger.utils.ligfilter)
Num_molecules() (in module schrodinger.utils.ligfilter)
Num_negative_atoms() (in module schrodinger.utils.ligfilter)
Num_positive_atoms() (in module schrodinger.utils.ligfilter)
NUM_PRIMARY_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
num_primary_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
Num_residues() (in module schrodinger.utils.ligfilter)
Num_rings() (in module schrodinger.utils.ligfilter)
num_rl_groups (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
Num_rotatable_bonds() (in module schrodinger.utils.ligfilter)
NUM_SPACE_GROUPS (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute)
NUM_SYMMETRY_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
num_symmetry_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
num_wildcard() (schrodinger.utils.sea.sea.Atom static method)
(schrodinger.utils.sea.sea.Hydrogen static method)
NumAlkyne() (in module schrodinger.rdkit.filtering)
numAtoms() (schrodinger.trajectory.prody.ensemble.Ensemble method)
(schrodinger.trajectory.prody.mode.Mode method)
(schrodinger.trajectory.prody.mode.Vector method)
(schrodinger.trajectory.prody.mode.VectorBase method)
(schrodinger.trajectory.prody.modeset.ModeSet method)
(schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
number (schrodinger.application.desmond.fep_edge_data.ResData attribute)
(schrodinger.structure._Molecule property)
number_by_entry (schrodinger.structure._Molecule property)
(schrodinger.structure._StructureAtom property)
number_by_molecule (schrodinger.structure._StructureAtom property)
NumberedCanvas (class in schrodinger.application.desmond.rl_helper)
numbering_scheme (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
NumChiralCenters() (in module schrodinger.rdkit.filtering)
numChoices() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
numConfs() (schrodinger.trajectory.prody.ensemble.Ensemble method)
numd (schrodinger.application.jaguar.basis.BasisSet attribute)
numDOF() (schrodinger.trajectory.prody.mode.Mode method)
(schrodinger.trajectory.prody.mode.Vector method)
(schrodinger.trajectory.prody.modeset.ModeSet method)
(schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
numerical_diff_is_acceptable() (in module schrodinger.utils.compare)
numf (schrodinger.application.jaguar.basis.BasisSet attribute)
NumFiveFiveRings() (in module schrodinger.rdkit.filtering)
numModes() (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)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
NumNonSpiroCR4() (in module schrodinger.rdkit.filtering)
numPos() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method)
(schrodinger.application.desmond.packages.staf.Positer method)
numResources() (schrodinger.application.licensing.licadmin.LocalServerProcess method)
NumSAtoms() (in module schrodinger.rdkit.filtering)
numSelected() (schrodinger.trajectory.prody.ensemble.Ensemble method)
NVT (schrodinger.application.desmond.constants.Ensembles attribute)
O
ObjectClass (schrodinger.models.jsonable.AbstractJsonSerializer attribute)
(schrodinger.models.jsonable.MolSerializer attribute)
(schrodinger.models.jsonable.SetSerializer attribute)
(schrodinger.models.jsonable.StructureSerializer attribute)
(schrodinger.models.jsonable.TupleSerializer attribute)
objectFromJson() (schrodinger.models.jsonable.AbstractJsonSerializer 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)
objectFromJsonable() (schrodinger.models.jsonable.AbstractJsonSerializer 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)
objectName() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
objectNameChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramView attribute)
Oblique() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
OCTANOL (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute)
OdfChk() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
offset (schrodinger.application.desmond.arkdb.CompositeKeySyntaxError attribute)
OFFSET (schrodinger.ui.qt.label_cursor.LabelCursorAxes attribute)
ok (schrodinger.application.desmond.packages.msys.InChI property)
ok_pattern (schrodinger.infra.mmcheck.ReturnCode attribute)
OmitMap() (in module schrodinger.application.matsci.gsas.GSASIImath)
on (schrodinger.test.decorate_fflag.disable_feature_flag attribute)
(schrodinger.test.decorate_fflag.enable_feature_flag attribute)
ON_HETERO_AND_KEEP_WEDGED (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute)
on_same_drive_letter() (in module schrodinger.utils.fileutils)
onDraw() (schrodinger.ui.qt.label_cursor.LabelCursor method)
(schrodinger.ui.qt.label_cursor.MultiAxesLabelCursor method)
ONE_ONE (schrodinger.application.msv.gui.homology_modeling.constants.HeteromultimerMode attribute)
(schrodinger.application.msv.gui.homology_modeling.constants.Mode attribute)
ONE_PER_STEP_IN_RANGE (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute)
OneIndexedList (class in schrodinger.infra.util)
ONLY_CURRENT_FRAME (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute)
onMove() (schrodinger.ui.qt.label_cursor.LabelCursor method)
(schrodinger.ui.qt.label_cursor.MultiAxesLabelCursor method)
opacity() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
opacityChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
OPAL_PREFIX (schrodinger.utils.openmpi.EnvVar attribute)
opaqueArea() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
opdiv() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
open() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
open_database() (in module schrodinger.protein.gpcr.sql)
open_file() (in module schrodinger.application.mopac.utils)
open_filename() (in module schrodinger.protein.getpdb)
open_maybe_compressed() (in module schrodinger.utils.fileutils)
openFile() (in module schrodinger.trajectory.prody.writenmd)
OpenMPIVersion (class in schrodinger.utils.openmpi)
oper_multiply() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
opls_force_field() (in module schrodinger.forcefield.common)
Opposite() (in module schrodinger.application.matsci.gsas.GSASIIspc)
OpsfromStringOps() (in module schrodinger.application.matsci.gsas.GSASIIspc)
OPT_STUCK (schrodinger.application.jaguar.constants.FatalErrors attribute)
OptimizationFailure
optimizationFlags() (schrodinger.ui.dendrogram.DendrogramView method)
OptimizePDF() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
Option (class in schrodinger.application.desmond.task)
optionfile() (schrodinger.application.licensing.flexlm.Vendor method)
options (schrodinger.application.desmond.task.ParchTrajectoryForAbsoluteFep property)
(schrodinger.application.desmond.task.ParchTrajectoryForFep property)
(schrodinger.application.desmond.task.ParchTrajectoryForFepLambda property)
(schrodinger.application.desmond.task.ParchTrajectoryForSolubilityFep property)
(schrodinger.application.desmond.task.Task property)
(schrodinger.application.desmond.task.TrajectoryForSolubilityFep property)
options_file() (in module schrodinger.application.licensing.licadmin)
ORANGE (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
(schrodinger.ui.qt.standard.colors.NativeColors attribute)
orbe_precision (schrodinger.application.jaguar.results.DerivedAttrs attribute)
Orbital (class in schrodinger.application.jaguar.results)
order (schrodinger.application.desmond.packages.msys.Bond property)
(schrodinger.structure._StructureBond property)
order() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
OrderBy (class in schrodinger.structutils.interactions.salt_bridge)
OrderedEnum (class in schrodinger.application.msv.gui.homology_modeling.constants)
OrderParameter (class in schrodinger.application.desmond.packages.analysis)
OrganometallicCompounds (class in schrodinger.application.livedesign.entry_types)
orig_idx_to_cur_idx() (in module schrodinger.trajectory.prody.writenmd)
orig_index (schrodinger.application.desmond.packages.traj.Frame property)
orig_index_prop (schrodinger.structutils.rmsd.ConformerRmsd attribute)
(schrodinger.structutils.rmsd.ConformerRmsdX attribute)
orig_key() (schrodinger.utils.sea.sea.Key method)
origin (schrodinger.application.desmond.packages.msys.molfile.Grid property)
origin_shift() (schrodinger.application.matsci.cctbx.rot_mx.translation_part_info method)
ORTHORHOMBIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute)
osc_precision (schrodinger.application.jaguar.results.DerivedAttrs attribute)
(schrodinger.application.jaguar.results.JaguarResults attribute)
OSCILLATE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Loop attribute)
OTHER (schrodinger.application.desmond.constants.SystemType attribute)
other() (schrodinger.application.desmond.packages.msys.Bond method)
other_sse (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute)
other_string (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute)
otherAtom() (schrodinger.structure._StructureBond method)
outdated_server() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
output (schrodinger.application.licensing.licerror.LicenseError property)
output() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method)
output_file (schrodinger.application.mopac.results_main.MopacResultsMain property)
output_path (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument property)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument property)
output_term() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
overlap_matrix() (in module schrodinger.application.mopac.results_main)
Override() (in module schrodinger.application.desmond.packages.msys.vdw)
override_params (schrodinger.application.desmond.packages.msys.TermTable property)
overrides() (schrodinger.application.desmond.packages.msys.TermTable method)
overrideWindowFlags() (schrodinger.ui.dendrogram.DendrogramView method)
overrideWindowState() (schrodinger.ui.dendrogram.DendrogramView method)
overwrite_data (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
own() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.infra.mmerr.Capture method)
(schrodinger.infra.structure.TextBlockReader method)
(schrodinger.infra.structure.TextBlockWriter method)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter method)
(schrodinger.structutils.color.ColorScheme method)
own_markers (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableFile attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.Makefile attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
P
Package (class in schrodinger.application.licensing.flexlm)
PackRot() (in module schrodinger.application.matsci.gsas.GSASIIspc)
pageHasData() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
paint() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
paintEngine() (schrodinger.ui.dendrogram.DendrogramView method)
paintEvent() (schrodinger.ui.dendrogram.DendrogramView method)
paintingActive() (schrodinger.ui.dendrogram.DendrogramView method)
pairwise_align_ct() (in module schrodinger.application.ska)
palette() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
Panel (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shape attribute)
panel() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
PanelModal (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.PanelModality attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.PanelModality attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.PanelModality attribute)
panelModality() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
ParallelPleatedSheet (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
Param (class in schrodinger.application.desmond.packages.msys)
param (schrodinger.application.desmond.packages.msys.Term property)
param() (schrodinger.application.desmond.packages.msys.ParamTable method)
paramid (schrodinger.application.desmond.packages.msys.Term property)
params (schrodinger.application.desmond.packages.msys.ParamTable property)
(schrodinger.application.desmond.packages.msys.TermTable property)
ParamTable (class in schrodinger.application.desmond.packages.msys)
ParamToConfigObj (class in schrodinger.models.adapters.inputconfig)
ParamToInputConfig (class in schrodinger.models.adapters.inputconfig)
ParchTrajectoryForAbsoluteFep (class in schrodinger.application.desmond.task)
ParchTrajectoryForFep (class in schrodinger.application.desmond.task)
ParchTrajectoryForFepLambda (class in schrodinger.application.desmond.task)
ParchTrajectoryForSolubilityFep (class in schrodinger.application.desmond.task)
parent (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableFile attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.Makefile attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
parent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
(schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
PARENT2PSEUDO (schrodinger.application.desmond.constants.IdConversion attribute)
parent_d (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
parent_dir() (in module schrodinger.application.desmond.util)
parentChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
parentItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
parentObject() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
parents (schrodinger.application.matsci.codeutils.ModuleInfo attribute)
parentWidget() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
pargph() (in module schrodinger.application.desmond.rl_helper)
parr_and_pople() (in module schrodinger.application.mopac.results_main)
parse() (in module schrodinger.application.desmond.multisim.parser)
(schrodinger.application.desmond.antlr3.treewizard.TreeWizard method)
(schrodinger.application.jaguar.scan.Scan static method)
(schrodinger.application.mopac.results_main.MopacMainTextParser method)
(schrodinger.utils.ligfilter.CriterionParser method)
(schrodinger.utils.ligfilter.DefinitionParser method)
parse_and_drop_xmlns() (in module schrodinger.application.scaffold_enumeration.rdcml)
parse_args() (in module schrodinger.application.licensing.licadmin)
(in module schrodinger.application.licensing.lmgrd_log_parser)
(in module schrodinger.application.matsci.qeschema.scripts.xml2qeinput)
(in module schrodinger.application.matsci.qeschema.scripts.yaml2qeinput)
(in module schrodinger.application.matsci.qexsd.qespresso.utils.xml2nebinput)
(in module schrodinger.application.matsci.qexsd.qespresso.utils.xml2qeinput)
(in module schrodinger.utils.featureflags.featureflags)
(in module schrodinger.utils.postinstall)
(schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
parse_basis() (in module schrodinger.application.jaguar.basis)
parse_components() (in module schrodinger.application.licensing.flexlm)
parse_cx_extensions() (in module schrodinger.application.scaffold_enumeration.cxsmiles)
parse_date() (in module schrodinger.application.licensing.flexlm)
parse_datetime() (in module schrodinger.application.licensing.lmgrd_log_parser)
parse_edge_file() (in module schrodinger.application.desmond.util)
parse_events() (in module schrodinger.application.licensing.lmgrd_log_parser)
parse_expiration() (in module schrodinger.application.licensing.flexlm)
parse_filter_expression() (in module schrodinger.structutils.filter)
parse_gibbs_energies() (in module schrodinger.application.jaguar.utils)
parse_indices() (in module schrodinger.application.desmond.enhsamp)
parse_intermixed_args() (schrodinger.utils.compare.DiffCompareArgumentParser method)
parse_inverse_tags() (in module schrodinger.application.pathfinder.reaction)
parse_json() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
parse_known_args() (schrodinger.utils.compare.DiffCompareArgumentParser method)
parse_known_intermixed_args() (schrodinger.utils.compare.DiffCompareArgumentParser method)
parse_lewis_data() (in module schrodinger.application.jaguar.utils)
parse_ligand_file() (in module schrodinger.application.desmond.util)
parse_line() (in module schrodinger.application.licensing.flexlm)
parse_lmdiag_entry() (in module schrodinger.application.licensing.licadmin)
parse_lmdiag_output() (in module schrodinger.application.licensing.licadmin)
parse_lmgrd_event() (in module schrodinger.application.licensing.licadmin)
parse_lmgrd_lines() (in module schrodinger.application.licensing.licadmin)
parse_lmgrd_log() (in module schrodinger.application.licensing.licadmin)
parse_lmhostid_output() (in module schrodinger.application.licensing.licadmin)
parse_lmstat_output() (in module schrodinger.application.licensing.licadmin)
parse_log() (in module schrodinger.test.log_parser)
parse_logfile() (in module schrodinger.application.licensing.lmgrd_log_parser)
parse_logs() (in module schrodinger.test.log_parser)
parse_mcg() (in module schrodinger.application.scaffold_enumeration.cxsmiles)
parse_mexpr() (in module schrodinger.application.desmond.enhsamp)
parse_multiple_jobs() (schrodinger.application.mopac.results_main.MopacMainTextParser method)
parse_output_structure_properties() (in module schrodinger.application.desmond.solubility_utils)
parse_pathfinder_data() (in module schrodinger.application.pathfinder.reaction)
parse_reaction_data() (in module schrodinger.application.pathfinder.reaction)
parse_reagent_classes_data() (in module schrodinger.application.pathfinder.reaction)
parse_report() (in module schrodinger.application.desmond.solubility_utils)
parse_res() (in module schrodinger.application.desmond.util)
parse_rgmol() (in module schrodinger.livedesign.rgfile_parse)
parse_sba() (in module schrodinger.application.desmond.simulation_block_data)
parse_sbt() (in module schrodinger.application.desmond.simulation_block_test)
parse_sea() (in module schrodinger.application.desmond.fep_edge_data)
parse_shape_screen_options() (in module schrodinger.application.phase.packages.phase_option_utils)
parse_sid() (in module schrodinger.application.desmond.fep_edge_data)
parse_sru() (in module schrodinger.application.scaffold_enumeration.cxsmiles)
parse_string (class in schrodinger.application.matsci.cctbx.rot_mx)
parse_symm_op() (schrodinger.application.matsci.cctbx.rot_mx.parse_string method)
parse_timedelta() (in module schrodinger.application.licensing.lmgrd_log_parser)
parse_tokens() (in module schrodinger.application.licensing.flexlm)
parse_xml() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
parse_xvol_file() (in module schrodinger.application.glide.utils)
parse_yaml() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
parseBlock_F() (schrodinger.application.glide.xpdes.XpPVParser method)
parseBlock_SL() (schrodinger.application.glide.xpdes.XpPVParser method)
parseLine() (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)
parseNode() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method)
parseOptions() (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
Parser (class in schrodinger.application.desmond.antlr3.recognizers)
ParserRuleReturnScope (class in schrodinger.application.desmond.antlr3.recognizers)
ParseSDF() (in module schrodinger.application.desmond.packages.msys)
parseStr() (in module schrodinger.application.desmond.enhsamp)
parseTree() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method)
partial_charge (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.structure._StructureAtom property)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
particle_total (schrodinger.application.desmond.cms.Cms property)
partition() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
partition_scores() (in module schrodinger.application.combinatorial_diversity.splitter_utils)
pass_errors (schrodinger.structure.MultiFileStructureReader attribute)
password (schrodinger.application.matsci.qb_sdk.client.QubecTokenData attribute)
patch_count (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
patch_vertices (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
PatchSettings (class in schrodinger.application.bioluminate.patch_utils.settings)
PatchType (class in schrodinger.application.bioluminate.patch_utils.settings)
PatchTypeSettings (class in schrodinger.application.bioluminate.patch_utils.settings)
PATH
,
[1]
path (schrodinger.application.desmond.packages.msys.IndexedFileLoader property)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement attribute)
(schrodinger.MaestroNotAvailableError attribute)
(schrodinger.test.stu.common.FileInfo attribute)
PATH (schrodinger.utils.openmpi.EnvVar attribute)
PathExists (class in schrodinger.ui.qt.appframework2.validators)
pathname() (schrodinger.application.licensing.flexlm.Vendor method)
(schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
pattern (schrodinger.application.desmond.packages.msys.SmartsPattern property)
pattern() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method)
Pbc (class in schrodinger.application.desmond.packages.analysis)
pbc (schrodinger.application.desmond.cms.Cms property)
(schrodinger.application.desmond.ffiostructure.FFIOStructure property)
(schrodinger.models.jsonable.JsonableStructure property)
(schrodinger.structure.Structure property)
(schrodinger.structure.TextualStructure property)
PBCMeasureMananger (class in schrodinger.trajectory.pbc_manager)
PCA (class in schrodinger.trajectory.prody.pca)
PDB (schrodinger.infra.structure.FileFormat attribute)
(schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
pdbcode (schrodinger.structure._StructureAtom property)
pdbname (schrodinger.structure._StructureAtom property)
PDBReader (class in schrodinger.structure)
pdbres (schrodinger.structure._Residue property)
(schrodinger.structure._StructureAtom property)
(schrodinger.structutils.analyze.Ligand property)
PDBWriter (class in schrodinger.structure)
pdf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
PDFPeakFit() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
PDFWrite() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
PdmDepth (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmDevicePixelRatio (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmDevicePixelRatioScaled (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmDpiX (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmDpiY (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmHeight (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmHeightMM (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmNumColors (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmPhysicalDpiX (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmPhysicalDpiY (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmWidth (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PdmWidthMM (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.PaintDeviceMetric attribute)
PeaksEquiv() (in module schrodinger.application.matsci.gsas.GSASIImath)
PeaksUnique() (in module schrodinger.application.matsci.gsas.GSASIImath)
Penalties (schrodinger.application.glide.xpdes.TermKeywords attribute)
peptide_name() (schrodinger.application.desmond.fep_edge_data.PRMEdgeData static method)
PER_STRUCTURE (schrodinger.infra.structure.WorkflowType attribute)
Percent_helix() (in module schrodinger.utils.ligfilter)
Percent_loop() (in module schrodinger.utils.ligfilter)
Percent_strand() (in module schrodinger.utils.ligfilter)
PercentScreenPlotter (class in schrodinger.analysis.enrichment.plotter)
PerceptualDiffTest (class in schrodinger.test.perceptualdiff)
performSVD() (schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
period_start() (in module schrodinger.application.licensing.lmgrd_log_parser)
permutations() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
persistent_load (schrodinger.application.desmond.picklejar.CustomUnpickler attribute)
perturb (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
PfxMolIterator (class in schrodinger.rdkit.molio)
PfxMolReader (class in schrodinger.rdkit.molio)
PfxMolWriter (class in schrodinger.rdkit.molio)
pharma_testfile() (in module schrodinger.application.phase.packages.test)
PHASE_COMMON_PH4 (schrodinger.infra.structure.WorkflowType attribute)
PhaseDB (class in schrodinger.pipeline.pipeio)
PhaseHypothesis (class in schrodinger.application.phase.hypothesis)
PhaseHypothesisFromLigand (class in schrodinger.application.phase.hypothesis)
PhaseHypothesisHybrid (class in schrodinger.application.phase.hypothesis)
PhaseHypothesisInputConfig (class in schrodinger.application.phase.input)
PhaseHypothesisStandard (class in schrodinger.application.phase.hypothesis)
PhaseHypothesisStatic (class in schrodinger.application.phase.hypothesis)
PhaseWtSum() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
Phob_pack (schrodinger.application.glide.xpdes.TermKeywords attribute)
Phobcon_HB (schrodinger.application.glide.xpdes.TermKeywords attribute)
PHONON_NAMESPACE (in module schrodinger.application.matsci.qeschema.qeschema.namespaces)
PHONON_TEMPLATE_MAP (schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter attribute)
PhononDocument (class in schrodinger.application.matsci.qeschema.qeschema.documents)
(class in schrodinger.application.matsci.qexsd.qespresso.documents)
PhononInputConverter (class in schrodinger.application.matsci.qeschema.qeschema.converters)
(class in schrodinger.application.matsci.qexsd.qespresso.converters)
PhpException
physicalDpiX() (schrodinger.ui.dendrogram.DendrogramView method)
physicalDpiY() (schrodinger.ui.dendrogram.DendrogramView method)
pi() (schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method)
pi_centroid (schrodinger.structutils.interactions.pi.CationPiInteraction attribute)
pi_structure (schrodinger.structutils.interactions.pi.CationPiInteraction attribute)
Picat (schrodinger.application.glide.xpdes.TermKeywords attribute)
PICK (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
PICK_CATEGORY() (in module schrodinger.application.phase.constants)
Picklable (class in schrodinger.application.desmond.picklejar)
PicklableMetaClass (class in schrodinger.application.desmond.picklejar)
PickleJar (class in schrodinger.application.desmond.picklejar)
PickleState (class in schrodinger.application.desmond.picklejar)
PiHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
pinv() (in module schrodinger.application.matsci.gsas.GSASIImath)
PipeIO (class in schrodinger.pipeline.pipeio)
pipeline_init_wrapper() (in module schrodinger.pipeline.compiled_functions)
PIPERConstraint (class in schrodinger.application.bioluminate.protein_protein_docking_shared)
PIPERDistanceConstraintPair (class in schrodinger.application.bioluminate.protein_protein_docking_shared)
PiPiFinder (class in schrodinger.application.desmond.packages.analysis)
PiPiInteraction (class in schrodinger.structutils.interactions.pi)
(in module schrodinger.application.desmond.packages.analysis)
pir (schrodinger.utils.fileutils.SeqFormat attribute)
PKA (schrodinger.application.desmond.constants.CorrectionTerm attribute)
pl_contact_data0 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
pl_contact_data1 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
pl_interaction_similarity_matrix0 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
pl_interaction_similarity_matrix1 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
place_rgroups() (in module schrodinger.application.scaffold_enumeration.layered)
(in module schrodinger.application.scaffold_enumeration.markush)
PlaceHolder (class in schrodinger.structutils.markush_enumerate)
Plain (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shadow attribute)
PlanarAngle (class in schrodinger.application.desmond.packages.analysis)
planckian_locus() (in module schrodinger.application.matsci.colorutils)
planckian_radiator() (in module schrodinger.application.matsci.colorutils)
PlaneIntercepts() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
PlaybackSettingsData (class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_data)
PLInteractionAids (class in schrodinger.application.desmond.packages.restraint.utils)
plot() (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method)
(schrodinger.analysis.enrichment.plotter.Plotter method)
(schrodinger.application.desmond.fep_edge_data.FEPTorsions method)
plot_height (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
plot_mat() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
plot_sim_mat() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
plot_structures() (schrodinger.application.matsci.xrd.XRDCalculator method)
plot_width (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
Plotter (class in schrodinger.analysis.enrichment.plotter)
pmode() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
POINT_GROUP_NAME (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
point_group_name (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
POINT_GROUP_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
POLAR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
POLAR_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
POLAR_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
Polarization() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
PolarSurfaceArea (class in schrodinger.application.desmond.packages.analysis)
polfcal() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
polyfit() (in module schrodinger.math.mathutils)
PolymerDescriptor (class in schrodinger.application.matsci.mlearn.descriptor)
PolymerDescriptorError
pop() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.scollections.IdSet method)
(schrodinger.utils.sea.sea.List method)
pop_all() (schrodinger.utils.env.MultiEnvironmentContext method)
pop_level() (in module schrodinger.infra.mmerr)
pop_state_stack() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
Popen() (in module schrodinger.utils.subprocess)
popitem() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
populate() (schrodinger.structutils.markush_enumerate.Scaffold method)
POPULATION (schrodinger.application.desmond.constants.CorrectionTerm attribute)
port() (schrodinger.application.licensing.flexlm.Vendor method)
POS (schrodinger.application.desmond.constants.RestrainTypes attribute)
pos (schrodinger.application.desmond.packages.msys.Atom property)
pos() (schrodinger.application.desmond.packages.pfx.Frame method)
(schrodinger.application.desmond.packages.topo.DuckFrame method)
(schrodinger.application.desmond.packages.traj.Frame method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
Pos2dsp() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
POS_FBHW (schrodinger.application.desmond.constants.RestrainTypes attribute)
PosAlign (class in schrodinger.application.desmond.packages.analysis)
posBlock() (in module schrodinger.application.matsci.gsas.GSASIImath)
POSE_VIEWER (schrodinger.infra.structure.WorkflowType attribute)
posFourier() (in module schrodinger.application.matsci.gsas.GSASIImath)
Positer (class in schrodinger.application.desmond.packages.staf)
Position (in module schrodinger.application.desmond.packages.analysis)
position_in_polymer (schrodinger.protein.helm.Monomer attribute)
position_in_token (schrodinger.protein.helm.Monomer attribute)
positions (schrodinger.application.desmond.packages.msys.System property)
positive (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute)
PosRestrainArray (class in schrodinger.application.desmond.cms)
PosTrack (class in schrodinger.application.desmond.packages.analysis)
PosVarBondEnumerable (class in schrodinger.application.scaffold_enumeration.posvarbond)
posZigZag() (in module schrodinger.application.matsci.gsas.GSASIImath)
POT_NTICKS (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute)
potential() (schrodinger.application.desmond.torsion_related.BondRotator method)
potential_energy (schrodinger.application.desmond.fep_edge_data.FEPTorsions property)
PotentialEnergy (class in schrodinger.application.desmond.simulation_block_test)
ppf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
PRECISION (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI attribute)
precision (schrodinger.application.jaguar.results.BondCharge attribute)
(schrodinger.application.jaguar.results.Dipole attribute)
(schrodinger.application.jaguar.results.FukuiIndices attribute)
(schrodinger.application.jaguar.results.Orbital attribute)
(schrodinger.application.jaguar.results.ThermoCollection attribute)
(schrodinger.application.jaguar.results.ThermoProp attribute)
(schrodinger.application.jaguar.results.ZVariables attribute)
(schrodinger.application.jaguar.scan.Scan attribute)
PRECISION (schrodinger.utils.profiling.RecordingTimer attribute)
(schrodinger.utils.profiling.Timer attribute)
PredefinedCriterion (class in schrodinger.utils.ligfilter)
predict() (schrodinger.application.desmond.antlr3.dfa.DFA method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25 method)
predict_correlation() (in module schrodinger.application.desmond.correlation_tau)
predict_expected_slope() (in module schrodinger.application.desmond.correlation_tau)
predict_kendall_tau() (in module schrodinger.application.desmond.correlation_tau)
predict_memory_utilization() (in module schrodinger.application.desmond.util)
predict_temperature_ladder() (in module schrodinger.application.desmond.remd)
predict_with_nreplica_and_exch() (in module schrodinger.application.desmond.remd)
predict_with_temp_and_exch() (in module schrodinger.application.desmond.remd)
predict_with_temp_and_nreplica() (in module schrodinger.application.desmond.remd)
Preferences (class in schrodinger.utils.preferences)
PREFERENCES (schrodinger.utils.postinstall.CustomConfigFiles attribute)
Premise (class in schrodinger.application.desmond.task)
premises (schrodinger.application.desmond.task.ParchTrajectoryForAbsoluteFep property)
(schrodinger.application.desmond.task.ParchTrajectoryForFep property)
(schrodinger.application.desmond.task.ParchTrajectoryForFepLambda property)
(schrodinger.application.desmond.task.ParchTrajectoryForSolubilityFep property)
(schrodinger.application.desmond.task.Task property)
(schrodinger.application.desmond.task.TrajectoryForSolubilityFep property)
prepare_ions() (in module schrodinger.application.desmond.move_alchem_ions)
prepareGeometryChange() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
prepend_mmfile_path() (in module schrodinger.application.ligprep.ionizer)
prepend_path() (in module schrodinger.utils.env)
prepend_sys_path() (in module schrodinger.utils.env)
prependWorkingDirectory() (schrodinger.application.prime.wrapper.BasePrimeAlignment method)
(schrodinger.application.prime.wrapper.PrimeTemplate method)
preprocess() (in module schrodinger.livedesign.preprocessor)
preprocess_infile() (in module schrodinger.application.jaguar.user_config)
preprocess_molblock() (in module schrodinger.livedesign.preprocessor)
PreprocessorOptions (class in schrodinger.livedesign.preprocessor)
PRESSED_BUTTON_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
Pressure (class in schrodinger.application.desmond.simulation_block_test)
PRESSURE_TENSOR (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute)
prestart() (in module schrodinger.ui.qt.appframework2.appmethods)
pretty_filesize() (in module schrodinger.application.desmond.packages.traj_util)
previousInFocusChain() (schrodinger.ui.dendrogram.DendrogramView method)
prewrite() (in module schrodinger.ui.qt.appframework2.appmethods)
PRIMARY (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute)
PRIMARY_OPERATIONS_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
PRIMARY_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
primary_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
primary_opers_strs (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
Prime (class in schrodinger.application.prime.input)
PRIME_HOMOLOGY (schrodinger.infra.structure.WorkflowType attribute)
PrimeConfig (class in schrodinger.application.prime.wrapper)
PrimeMethod (class in schrodinger.application.msv.gui.homology_modeling.constants)
PrimeTemplate (class in schrodinger.application.prime.wrapper)
print_fields() (in module schrodinger.utils.machid)
(schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.LicenseLine method)
(schrodinger.application.licensing.flexlm.Package method)
(schrodinger.application.licensing.flexlm.Server method)
(schrodinger.application.licensing.flexlm.UseServer method)
(schrodinger.application.licensing.flexlm.Vendor method)
print_file_and_line (schrodinger.application.desmond.arkdb.CompositeKeySyntaxError attribute)
print_help() (schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
print_product_versions() (in module schrodinger.utils.machid)
print_usage() (in module schrodinger.application.desmond.simulation_block_data)
(in module schrodinger.application.desmond.simulation_block_test)
(schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
print_val() (schrodinger.application.desmond.simulation_block_test.BoxSize method)
(schrodinger.application.desmond.simulation_block_test.E_f method)
(schrodinger.application.desmond.simulation_block_test.E_k method)
(schrodinger.application.desmond.simulation_block_test.E_x method)
(schrodinger.application.desmond.simulation_block_test.Energy method)
(schrodinger.application.desmond.simulation_block_test.Job_Details method)
(schrodinger.application.desmond.simulation_block_test.PotentialEnergy method)
(schrodinger.application.desmond.simulation_block_test.Pressure method)
(schrodinger.application.desmond.simulation_block_test.T_0 method)
(schrodinger.application.desmond.simulation_block_test.Temperature method)
(schrodinger.application.desmond.simulation_block_test.Test method)
(schrodinger.application.desmond.simulation_block_test.V method)
print_version() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
printAllSpgInfo() (schrodinger.application.matsci.nano.space_groups.SpaceGroups method)
printDatabaseEntry() (schrodinger.application.matsci.nano.space_groups.SpaceGroup method)
printInfo() (schrodinger.application.desmond.replica_dE.replica_container method)
printout() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
printParameters() (schrodinger.structutils.minimize.Minimizer method)
printRho() (in module schrodinger.application.matsci.gsas.GSASIImath)
printSymmetryOpers() (schrodinger.application.matsci.nano.space_groups.SpaceGroup method)
priority() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
PRM_LIGAND_BINDING (schrodinger.application.desmond.constants.FEP_TYPES attribute)
prm_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
PRM_PROTEIN_BINDING (schrodinger.application.desmond.constants.FEP_TYPES attribute)
PRMEdgeData (class in schrodinger.application.desmond.fep_edge_data)
process() (schrodinger.utils.singledashoptionparser.SingleDashOption method)
process_attributes() (in module schrodinger.application.licensing.licadmin)
process_bennett_log() (schrodinger.application.desmond.replica_dE.replica_container method)
process_chunks() (in module schrodinger.application.desmond.simulation_block_test)
process_docstring() (in module schrodinger.infra.epydoc_to_sphinx)
process_nonchange_diffs() (in module schrodinger.utils.compare)
process_option_strings() (schrodinger.utils.singledashoptionparser.SingleDashOption method)
process_sequence() (in module schrodinger.protein.helix)
process_status() (in module schrodinger.test.stu.process_management)
process_tree_lines() (in module schrodinger.test.stu.process_management)
ProcessDied
processFuncChain() (schrodinger.utils.funcchains.FuncChainMixin method)
ProcessKilled
procText() (in module schrodinger.application.desmond.enhsamp)
prodMGMT() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
prodQQ() (in module schrodinger.application.matsci.gsas.GSASIImath)
prodQVQ() (in module schrodinger.application.matsci.gsas.GSASIImath)
PRODUCT (class in schrodinger.application.desmond.constants)
(schrodinger.application.desmond.packages.restraint.builder.GeneratorType attribute)
product_of_ranges() (in module schrodinger.application.scaffold_enumeration.common)
profile_call() (in module schrodinger.utils.profiling)
Profiler (class in schrodinger.utils.profiling)
prog() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
progress_job() (schrodinger.application.matsci.qb_sdk.client.QubecClient method)
progress_report_frame_number() (in module schrodinger.application.desmond.packages.analysis)
project table
Maestro
,
[1]
project_name (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
PROJECT_TABLE (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportToOption attribute)
ProjectDisposition (class in schrodinger.job.launchparams)
ProjectSurface (class in schrodinger.project.surface)
ProjectSurface.Color (class in schrodinger.project.surface)
ProjectSurface.ColorBy (class in schrodinger.project.surface)
ProjectSurface.ColorFrom (class in schrodinger.project.surface)
ProjectSurface.Style (class in schrodinger.project.surface)
PROP_CMS (schrodinger.application.desmond.cms.Cms attribute)
PROP_FAMILY (class in schrodinger.application.matsci.msprops)
PROP_TRJ (schrodinger.application.desmond.cms.Cms attribute)
prop_value (schrodinger.application.desmond.simulation_block_data.Array_Prop attribute)
Properties (class in schrodinger.adapter)
properties (schrodinger.application.matsci.qb_sdk.parameters.QubecChemistryProblem attribute)
property (schrodinger.application.desmond.cms.Cms property)
(schrodinger.application.desmond.ffiostructure.FFIOStructure property)
(schrodinger.application.phase.hypothesis.PhaseHypothesis property)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand property)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid property)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard property)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic property)
(schrodinger.models.jsonable.JsonableStructure property)
(schrodinger.structure._StructureAtom property)
(schrodinger.structure._StructureBond property)
(schrodinger.structure.Structure property)
(schrodinger.structure.TextualStructure property)
property() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
property_key (schrodinger.application.jaguar.utils.FreeEnergy attribute)
PropertyCriterion (class in schrodinger.utils.ligfilter)
PropertyFilter (class in schrodinger.application.combinatorial_diversity.diversity_selector)
PropertyMap (class in schrodinger.application.desmond.packages.msys)
PropertyName (class in schrodinger.structure)
PropertyNameError
PropertyType (class in schrodinger.application.combinatorial_diversity.diversity_fingerprinter)
PropFilter (class in schrodinger.structutils.filter)
props (schrodinger.application.desmond.packages.msys.ParamTable property)
(schrodinger.application.desmond.packages.msys.TermTable property)
propType() (schrodinger.application.desmond.packages.msys.ParamTable method)
PROTEIN (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.AVPAslOption attribute)
PROTEIN_DOCKING_POSE (schrodinger.infra.structure.WorkflowType attribute)
protein_residue() (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData static method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData static method)
PROTEIN_SELECTIVITY (schrodinger.application.desmond.constants.FEP_TYPES attribute)
PROTEIN_STABILITY (schrodinger.application.desmond.constants.FEP_TYPES attribute)
ProteinReportCheck (class in schrodinger.test.structurecheck)
ProteinRMSF (class in schrodinger.application.desmond.packages.analysis)
ProteinSF (class in schrodinger.application.desmond.packages.analysis)
ProtLigInter (class in schrodinger.application.desmond.packages.analysis)
ProtLigPolarInter (class in schrodinger.application.desmond.packages.analysis)
PROTOCOL_VERSION (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener attribute)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener attribute)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy attribute)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener attribute)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener attribute)
ProtProtHbondInter (class in schrodinger.application.desmond.packages.analysis)
ProtProtInter (class in schrodinger.application.desmond.packages.analysis)
ProtProtPiInter (class in schrodinger.application.desmond.packages.analysis)
provenance (schrodinger.application.desmond.packages.msys.System property)
prune_largest_files() (in module schrodinger.test.stu.common)
psc_workflow (class in schrodinger.application.bioluminate.epitope.psc_workflow)
psd (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute)
Pseudo (class in schrodinger.application.desmond.cms)
PSEUDO2PARENT (schrodinger.application.desmond.constants.IdConversion attribute)
PSEUDO_END (schrodinger.application.desmond.constants.IdConversion attribute)
pseudoatom_match() (in module schrodinger.application.desmond.packages.topo)
push() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.utils.env.MultiEnvironmentContext method)
push_level() (in module schrodinger.infra.mmerr)
push_state_stack() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
pushpop() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method)
put() (schrodinger.application.desmond.arkdb.ArkDb method)
(schrodinger.application.desmond.multisim.parser.Msj method)
put_to() (schrodinger.application.desmond.arkdb.Datum method)
(schrodinger.application.desmond.task.Option method)
(schrodinger.application.desmond.task.Premise method)
putToM2ioFile() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
PW_NAMESPACE (in module schrodinger.application.matsci.qeschema.qeschema.namespaces)
PW_TEMPLATE_MAP (schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter attribute)
PwDocument (class in schrodinger.application.matsci.qeschema.qeschema.documents)
(class in schrodinger.application.matsci.qexsd.qespresso.documents)
PwInputConverter (class in schrodinger.application.matsci.qeschema.qeschema.converters)
(class in schrodinger.application.matsci.qexsd.qespresso.converters)
pyqtConfigure() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
PyStructureReaderException
PYTHON_EXE (in module schrodinger.utils.sysinfo)
PYTHONPATH
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
Q
Q2AV() (in module schrodinger.application.matsci.gsas.GSASIImath)
Q2AVdeg() (in module schrodinger.application.matsci.gsas.GSASIImath)
Q2Mat() (in module schrodinger.application.matsci.gsas.GSASIImath)
QeDocument (class in schrodinger.application.matsci.qeschema.qeschema.documents)
(class in schrodinger.application.matsci.qexsd.qespresso.documents)
QESchemaError
QEspressoError
qm (schrodinger.application.qsite.input.HydrogenCap property)
qmatom (schrodinger.application.qsite.input.Cut property)
QMRegion (class in schrodinger.application.qsite.input)
qmregion (schrodinger.application.qsite.input.QSiteInput property)
qpe_re (schrodinger.application.matsci.qb_sdk.parameters.QubecAlgorithm attribute)
QRNNModel (class in schrodinger.energy)
QRNNSupportError
QSignalBlocker (class in schrodinger.Qt.PyQt6.QtCore)
QSiteInput (class in schrodinger.application.qsite.input)
QubecAlgorithm (class in schrodinger.application.matsci.qb_sdk.parameters)
QubecChemistryProblem (class in schrodinger.application.matsci.qb_sdk.parameters)
QubecClient (class in schrodinger.application.matsci.qb_sdk.client)
QubecJob (class in schrodinger.application.matsci.qb_sdk.job)
QubecSdkError
QubecTokenData (class in schrodinger.application.matsci.qb_sdk.client)
query() (in module schrodinger.application.fpsim)
(schrodinger.application.fpsim.FPsimSearcher method)
query_registry() (in module schrodinger.utils.sysinfo)
query_sequence (schrodinger.application.prime.wrapper.BasePrimeAlignment property)
QueryError
QueryOptions (class in schrodinger.rdkit.substructure)
QUICK (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute)
quick_append() (schrodinger.utils.sea.sea.List method)
quotechar (schrodinger.application.canvas.utils.chm_bluebird attribute)
(schrodinger.application.canvas.utils.chm_excel attribute)
quoting (schrodinger.application.canvas.utils.chm_bluebird attribute)
(schrodinger.application.canvas.utils.chm_excel attribute)
R
r() (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method)
radialGradient() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
radius (schrodinger.structure._StructureAtom property)
radius_of_gyration() (in module schrodinger.application.matsci.geometry)
(in module schrodinger.structutils.analyze)
RadiusOfGyration (in module schrodinger.application.desmond.packages.analysis)
RainbowColorRamp (class in schrodinger.structutils.color)
raise_() (schrodinger.ui.dendrogram.DendrogramView method)
raise_deprecation_error() (in module schrodinger.utils.deprecation)
raise_voluptuous_exception() (in module schrodinger.application.jaguar.workflow_validation)
Raised (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shadow attribute)
Ramachandran (class in schrodinger.application.desmond.packages.analysis)
raman_activity_precision (schrodinger.application.jaguar.results.NormalMode attribute)
raman_intensity_precision (schrodinger.application.jaguar.results.NormalMode attribute)
random_state (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen property)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen property)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen property)
random_string() (in module schrodinger.application.desmond.util)
randomAVdeg() (in module schrodinger.application.matsci.gsas.GSASIImath)
randomQ() (in module schrodinger.application.matsci.gsas.GSASIImath)
range() (schrodinger.infra.mmbitset.Bitset method)
rank_reactants() (in module schrodinger.application.combinatorial_screen.fingerprint_utils)
rate (schrodinger.math.multi_parameter_optimization.Transition attribute)
rate() (in module schrodinger.application.desmond.fep_edge_data_classifier)
(schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData method)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData method)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData method)
Rating (class in schrodinger.application.desmond.fep_edge_data_classifier)
raw_alignment() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method)
raw_val (schrodinger.utils.sea.sea.Atom property)
(schrodinger.utils.sea.sea.Hydrogen property)
(schrodinger.utils.sea.sea.List property)
(schrodinger.utils.sea.sea.Map property)
RawInputConverter (class in schrodinger.application.matsci.qeschema.qeschema.converters)
(class in schrodinger.application.matsci.qexsd.qespresso.converters)
rb_potential_from_struct() (in module schrodinger.application.desmond.torsion_related)
Rdf (class in schrodinger.application.desmond.packages.analysis)
rdk_mol_from_cml_element() (in module schrodinger.application.scaffold_enumeration.rdcml)
rdkit (schrodinger.application.matsci.msconst.SMARTS_METHOD attribute)
rdkit_reaction_from_smarts() (in module schrodinger.analysis.transformations)
rdkit_to_cxsmiles() (in module schrodinger.livedesign.convert)
rdkit_to_sdf() (in module schrodinger.livedesign.convert)
RdkitMergeHandler (class in schrodinger.rdkit.molio)
RdkitMolWriter (class in schrodinger.rdkit.molio)
rdsq2d() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIIpwd)
Reaction (class in schrodinger.application.pathfinder.reaction)
ReactionDict (class in schrodinger.application.pathfinder.reaction)
read() (in module schrodinger.ui.qt.appframework2.appmethods)
(schrodinger.application.desmond.cms.Cms static method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure static method)
(schrodinger.application.desmond.packages.msys.molfile.SeqFile class method)
(schrodinger.application.desmond.packages.msys.molfile.StkFile class method)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.models.jsonable.JsonableStructure static method)
(schrodinger.project.surface.ProjectSurface class method)
(schrodinger.structure.MaestroReader method)
(schrodinger.structure.Structure static method)
(schrodinger.structure.StructureReader static method)
(schrodinger.structure.TextualStructure static method)
(schrodinger.surface.Surface class method)
(schrodinger.test.memtest.Leak class method)
(schrodinger.test.memtest.Suppression class method)
read_and_uniquify() (in module schrodinger.test.memtest)
read_build_time() (in module schrodinger.utils.machid)
read_charge_file_hdf5() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.charge)
read_cms() (in module schrodinger.application.desmond.packages.topo)
read_cms_and_traj() (in module schrodinger.application.desmond.packages.traj_util)
read_constraints_file() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint static method)
read_csv() (in module schrodinger.test.canvas_utils)
read_data_from_log_file() (in module schrodinger.application.desmond.replica_exchange_review)
read_dE_Replicas() (schrodinger.application.desmond.replica_dE.replica_container method)
read_etotv() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils)
read_git_hash() (in module schrodinger.utils.machid)
read_hdf() (in module schrodinger.application.matsci.hdfutils)
read_json_data() (in module schrodinger.utils.featureflags.write)
read_keys() (in module schrodinger.utils.ligfilter)
read_license_file() (in module schrodinger.application.licensing.flexlm)
read_mode (schrodinger.application.desmond.ffiostructure.CMSReader attribute)
(schrodinger.structure.MaestroReader attribute)
(schrodinger.structure.MaestroTextReader attribute)
read_postqe_output_file() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils)
read_prop_by_title() (in module schrodinger.test.stu.outcomes.correlate_to_reference_file)
read_property_filters() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils)
read_property_filters_from_iterable() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils)
read_pseudo_file() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils)
read_pw() (in module schrodinger.test.canvas_utils)
read_qe_input() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
read_reactant_fps() (in module schrodinger.application.combinatorial_screen.fingerprint_utils)
read_reactions_file() (in module schrodinger.application.pathfinder.reaction)
read_reagent_classes_file() (in module schrodinger.application.pathfinder.reaction)
read_restraints() (in module schrodinger.forcefield.minimizer)
read_rxn_file() (in module schrodinger.application.pathfinder.reaction)
read_scaffold() (in module schrodinger.structutils.markush_enumerate)
read_seqres_from_ct() (in module schrodinger.structutils.analyze)
read_string() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
read_structures_as_conformations() (in module schrodinger.utils.cgxutils)
read_table() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util)
read_traj() (in module schrodinger.application.desmond.packages.traj)
(in module schrodinger.application.desmond.packages.traj_util)
read_unique_field() (in module schrodinger.pipeline.pipeutils)
read_valgrind_log() (in module schrodinger.test.memtest)
readColMetadata() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
readColMetadataLabels() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
ReadCrdCoordinates() (in module schrodinger.application.desmond.packages.msys)
reader (schrodinger.structure.MultiFileStructureReader attribute)
reader_class (schrodinger.structure.MultiFileStructureReader attribute)
reader_open() (in module schrodinger.utils.csv_unicode)
readFile() (schrodinger.structutils.filter.Filter method)
(schrodinger.structutils.filter.PropFilter method)
(schrodinger.structutils.filter.SmartsFilter method)
readFileName() (schrodinger.structutils.filter.Filter method)
(schrodinger.structutils.filter.PropFilter method)
(schrodinger.structutils.filter.SmartsFilter method)
readFragmentLibrary() (schrodinger.application.ligprep.ionizer.Ionizer method)
readFrameSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method)
readHDF() (schrodinger.application.matsci.hdfutils.HDFIO method)
(schrodinger.application.matsci.hdfutils.HDFProxyPickleIO method)
readMasks() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
readonly_cached_property (class in schrodinger.application.matsci.cache)
ReadPDBCoordinates() (in module schrodinger.application.desmond.packages.msys)
ReadPowderInstprm() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
readRulesFromFile() (schrodinger.structutils.color.ColorScheme method)
readSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method)
readSpecFile() (schrodinger.application.ligprep.ionizer.Ionizer method)
ReagentClass (class in schrodinger.application.pathfinder.reaction)
realtime (schrodinger.application.livedesign.upload_utils.CommandType attribute)
reassignHets() (schrodinger.application.prime.primefix.FixForPrime method)
reassignResNums() (schrodinger.application.prime.primefix.FixForPrime method)
reblock() (schrodinger.Qt.PyQt6.QtCore.QSignalBlocker method)
receivers() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
recentered() (schrodinger.ui.dendrogram.DendrogramNode method)
RECEPTOR (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute)
(schrodinger.application.desmond.constants.REST_COMPONENT attribute)
receptor_aids (schrodinger.application.desmond.packages.restraint.utils.PLInteractionAids property)
receptor_b_factor (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_c_aid (schrodinger.application.desmond.packages.restraint.utils.PLInteractionAids attribute)
receptor_ca_aid (schrodinger.application.desmond.packages.restraint.utils.PLInteractionAids attribute)
receptor_chain_names (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_charge (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
receptor_n_aid (schrodinger.application.desmond.packages.restraint.utils.PLInteractionAids attribute)
receptor_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_residues_interaction_ligand1 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_residues_interaction_ligand2 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_sid_rmsd_backbone_lambda0 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_sid_rmsd_backbone_lambda1 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_sid_rmsd_ligand_lambda0 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_sid_rmsd_ligand_lambda1 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_sid_rmsf_backbone_lambda0 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_sid_rmsf_backbone_lambda1 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_st (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_title (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_total_atom (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_total_heavy (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_total_residues (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
receptor_total_residues_in_chains (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
ReceptorLigandGroup (class in schrodinger.application.livedesign.data_classes)
ReceptorLigandMap (class in schrodinger.application.livedesign.data_classes)
ReceptorLigandPair (class in schrodinger.application.livedesign.data_classes)
receptors (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
RecognitionException
recognitionException() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
RecognizerSharedState (class in schrodinger.application.desmond.antlr3.recognizers)
recompute_stereo() (in module schrodinger.utils.cgxutils)
record (schrodinger.application.desmond.packages.timer.Timer.Args attribute)
record() (schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
record_error() (schrodinger.utils.sea.evalor.Evalor method)
record_failures() (in module schrodinger.application.livedesign.io_utils)
RecordDebugEventListener (class in schrodinger.application.desmond.antlr3.debug)
RecordingTimer (class in schrodinger.utils.profiling)
recover() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
recoverFromMismatchedSet() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
recoverFromMismatchedToken() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
rect() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.ui.dendrogram.DendrogramView method)
rectangular (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute)
recur_caller (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer attribute)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer attribute)
RED (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
(schrodinger.ui.qt.standard.colors.NativeColors attribute)
redirect (schrodinger.ui.qt.appframework2.debugcore.DebugStderr attribute)
(schrodinger.ui.qt.appframework2.debugcore.DebugStdout attribute)
reduce() (schrodinger.application.desmond.packages.analysis.AmorphousCrystalInter method)
(schrodinger.application.desmond.packages.analysis.MembraneDensityProfile method)
(schrodinger.application.desmond.packages.analysis.ProteinRMSF method)
(schrodinger.application.desmond.packages.analysis.ProteinSF method)
(schrodinger.application.desmond.packages.analysis.ProtProtInter method)
(schrodinger.application.desmond.packages.analysis.Ramachandran method)
(schrodinger.application.desmond.packages.analysis.Rdf method)
(schrodinger.application.desmond.packages.analysis.RMSF method)
(schrodinger.application.desmond.packages.analysis.SecondaryStructure method)
(schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceAreaByResidue method)
(schrodinger.application.desmond.packages.analysis.VolumeMapper method)
(schrodinger.application.desmond.packages.traj.Frame method)
reduce_lipid_vec_list() (in module schrodinger.application.desmond.packages.analysis)
reduce_vec() (in module schrodinger.application.desmond.packages.analysis)
(schrodinger.application.desmond.packages.analysis.SmartsDirector method)
reduce_vec_list() (in module schrodinger.application.desmond.packages.analysis)
reduced_mass_precision (schrodinger.application.jaguar.results.NormalMode attribute)
reduceFunction() (schrodinger.application.steps.licensing.LicenseMixin method)
reduceToSingleOperationPerIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
redundant_server() (schrodinger.application.licensing.flexlm.License method)
ref (schrodinger.application.desmond.cms.Restrain property)
ref_keys (schrodinger.structutils.sitealign.SiteMatchLookup property)
REF_LICENSE_CHECK_FILE (in module schrodinger.test.stu.constants)
ref_sse (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute)
ref_string (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute)
REFDModelFxn() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
REFDRefine() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
refresh() (in module schrodinger.application.licensing.licadmin)
(schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
refresh_session() (schrodinger.application.matsci.qb_sdk.client.QubecClient method)
reg_xcheck() (in module schrodinger.utils.sea.evalor)
register() (schrodinger.utils.compare.DiffCompareArgumentParser method)
register_plugin() (in module schrodinger.application.desmond.packages.msys.molfile)
register_profiles() (in module schrodinger.test.hypothesis.hypothesis_profiles)
reject() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method)
release() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
releaseKeyboard() (schrodinger.ui.dendrogram.DendrogramView method)
releaseMouse() (schrodinger.ui.dendrogram.DendrogramView method)
releaseShortcut() (schrodinger.ui.dendrogram.DendrogramView method)
reload() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
relpath() (in module schrodinger.application.desmond.util)
relpath_from_testdir() (in module schrodinger.test)
remediate_ct() (in module schrodinger.protein.remediate)
remote_command() (in module schrodinger.job.remote_command)
remove() (schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.desmond.packages.msys.Atom method)
(schrodinger.application.desmond.packages.msys.Bond method)
(schrodinger.application.desmond.packages.msys.Chain method)
(schrodinger.application.desmond.packages.msys.Ct method)
(schrodinger.application.desmond.packages.msys.Residue method)
(schrodinger.application.desmond.packages.msys.Term method)
(schrodinger.application.desmond.packages.msys.TermTable method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.preferences.Preferences method)
(schrodinger.utils.scollections.IdSet method)
(schrodinger.utils.sea.sea.List method)
REMOVE_ALL (schrodinger.livedesign.preprocessor.ExplicitHydrogens attribute)
remove_alternate_positions() (in module schrodinger.structutils.build)
remove_atom_alternate_positions() (in module schrodinger.structutils.build)
remove_cts_property() (schrodinger.application.desmond.cms.Cms method)
remove_explicit_hydrogens() (in module schrodinger.livedesign.preprocessor)
remove_extra_rotable_atoms() (in module schrodinger.application.desmond.r_group_asl)
remove_file() (in module schrodinger.application.desmond.util)
remove_fragments() (in module schrodinger.livedesign.preprocessor)
remove_gibbs_energies() (in module schrodinger.application.jaguar.utils)
remove_handlers() (in module schrodinger.utils.log)
remove_inactive_solvent() (in module schrodinger.application.desmond.gcmc_utils)
remove_inactive_solvent_file() (in module schrodinger.application.desmond.gcmc_utils)
remove_invalid_config_options() (in module schrodinger.livedesign.preprocessor)
remove_option() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
REMOVE_OVERLAPPED_SOLVENT (schrodinger.application.desmond.constants.BUILD_GEOMETRY attribute)
remove_previous_existing_files() (in module schrodinger.application.livedesign.login)
REMOVE_PROPERTIES (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
remove_properties() (in module schrodinger.livedesign.preprocessor)
remove_react_atom_props() (in module schrodinger.rdkit.molio)
remove_ssl_ld_library_path() (in module schrodinger.utils.env)
remove_stereo_annotation() (in module schrodinger.structutils.smiles)
remove_tag() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
remove_validator() (in module schrodinger.ui.qt.appframework2.validation)
REMOVE_WEIGHTS (schrodinger.livedesign.molhash.EnhancedStereoUpdateMode attribute)
remove_wiggly_bonds_around_double_bonds() (in module schrodinger.livedesign.preprocessor)
removeAction() (schrodinger.ui.dendrogram.DendrogramView method)
removed (schrodinger.models.diffy.DictDiff attribute)
(schrodinger.models.diffy.ListDiff attribute)
(schrodinger.models.diffy.SetDiff attribute)
removeEventFilter() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
removeFromGroup() (schrodinger.ui.dendrogram.DendrogramGraphicTree method)
removeItem() (schrodinger.ui.dendrogram.DendrogramScene method)
removeKey() (schrodinger.utils.ligfilter.Definition method)
removeprefix() (in module schrodinger.application.matsci.qeschema.qeschema.documents)
removeSceneEventFilter() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
rename() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.project.surface.ProjectSurface method)
(schrodinger.surface.Surface method)
render() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
renderHints() (schrodinger.ui.dendrogram.DendrogramView method)
renderToFile() (schrodinger.application.pathfinder.render.RouteRenderer method)
renumber_conformer() (in module schrodinger.structutils.rmsd)
renumberByMolecule() (schrodinger.application.prime.primefix.FixForPrime method)
renumberBySymmetry() (schrodinger.structutils.rmsd.ConformerRmsd method)
(schrodinger.structutils.rmsd.ConformerRmsdX method)
renumberWorkingStructures() (schrodinger.structutils.rmsd.ConformerRmsd method)
(schrodinger.structutils.rmsd.ConformerRmsdX method)
reorder_atoms() (in module schrodinger.structutils.build)
reorder_protein_atoms_by_sequence() (in module schrodinger.structutils.build)
reorder_water() (in module schrodinger.structutils.build)
rep (schrodinger.application.dendrogram.core_class.RingSysInfo attribute)
repaint() (schrodinger.ui.dendrogram.DendrogramView method)
repair_box_vector() (in module schrodinger.application.desmond.repair_cms)
repeats (schrodinger.application.scaffold_enumeration.linknode.LinknodeSgroup attribute)
REPLACE (schrodinger.job.launchparams.ProjectDisposition attribute)
replace() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
REPLACE_FIT (schrodinger.job.launchparams.ProjectDisposition attribute)
replace_generic_h_queries() (in module schrodinger.rdkit.substructure)
replace_output_logger_stream() (in module schrodinger.test.ioredirect)
replace_rgroups_with_dummy_atoms() (in module schrodinger.livedesign.rgroup_decomposition)
replaceChildren() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
ReplaceOp (class in schrodinger.application.desmond.antlr3.streams)
replica_container (class in schrodinger.application.desmond.replica_dE)
replica_energy (class in schrodinger.application.desmond.replica_dE)
replicas_monitor (class in schrodinger.application.desmond.replica_dE)
Report (class in schrodinger.protein.analysis)
report() (schrodinger.analysis.enrichment.calculator.Calculator 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)
Report.backbone_dihedral_data_set (class in schrodinger.protein.analysis)
Report.backbone_dihedral_data_set.data_point (class in schrodinger.protein.analysis)
Report.Bfactor_data_set (class in schrodinger.protein.analysis)
Report.Bfactor_data_set.data_point (class in schrodinger.protein.analysis)
Report.bond_angle_data_set (class in schrodinger.protein.analysis)
Report.bond_angle_data_set.data_point (class in schrodinger.protein.analysis)
Report.bond_length_data_set (class in schrodinger.protein.analysis)
Report.bond_length_data_set.data_point (class in schrodinger.protein.analysis)
Report.chirality_data_set (class in schrodinger.protein.analysis)
Report.chirality_data_set.data_point (class in schrodinger.protein.analysis)
Report.data_set (class in schrodinger.protein.analysis)
Report.data_set.data_point (class in schrodinger.protein.analysis)
Report.gamma_Bfactor_data_set (class in schrodinger.protein.analysis)
Report.gamma_Bfactor_data_set.data_point (class in schrodinger.protein.analysis)
Report.Gfactor_summary_data_set (class in schrodinger.protein.analysis)
Report.Gfactor_summary_data_set.data_point (class in schrodinger.protein.analysis)
Report.improper_torsion_data_set (class in schrodinger.protein.analysis)
Report.improper_torsion_data_set.data_point (class in schrodinger.protein.analysis)
Report.local_atom (class in schrodinger.protein.analysis)
Report.local_protein (class in schrodinger.protein.analysis)
Report.local_residue (class in schrodinger.protein.analysis)
Report.missing_atoms_data_set (class in schrodinger.protein.analysis)
Report.missing_atoms_data_set.data_point (class in schrodinger.protein.analysis)
Report.peptide_planarity_data_set (class in schrodinger.protein.analysis)
Report.peptide_planarity_data_set.data_point (class in schrodinger.protein.analysis)
Report.primex_steric_clash_data_set (class in schrodinger.protein.analysis)
Report.primex_steric_clash_data_set.data_point (class in schrodinger.protein.analysis)
Report.sidechain_dihedral_data_set (class in schrodinger.protein.analysis)
Report.sidechain_dihedral_data_set.data_point (class in schrodinger.protein.analysis)
Report.sidechain_planarity_data_set (class in schrodinger.protein.analysis)
Report.sidechain_planarity_data_set.data_point (class in schrodinger.protein.analysis)
Report.steric_clash_data_set (class in schrodinger.protein.analysis)
Report.steric_clash_data_set.data_point (class in schrodinger.protein.analysis)
report_add_logo() (in module schrodinger.application.desmond.rl_helper)
report_add_ms_logo() (in module schrodinger.application.desmond.rl_helper)
report_data_points() (schrodinger.protein.analysis.Report.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)
report_t() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
report_total_usage() (in module schrodinger.application.licensing.lmgrd_log_parser)
report_usage() (in module schrodinger.application.licensing.lmgrd_log_parser)
reportError() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
reportinfo() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.MakefileTest method)
reportSet() (schrodinger.test.structurecheck.ProteinReportCheck method)
reportValidation() (schrodinger.application.livedesign.entry_types.BaseEntryData method)
(schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
(schrodinger.ui.qt.appframework2.validation.ValidationMixin method)
repr_failure() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
REPULSION (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute)
requests_retry_session() (in module schrodinger.protein.getpdb)
require_local_pdb() (in module schrodinger.test.stu.get_pdbs)
require_product() (in module schrodinger.test.test_markers)
required_login_info_set() (in module schrodinger.application.livedesign.login)
requires_3d (schrodinger.application.livedesign.data_classes.LDData property)
requires_ffc (schrodinger.application.livedesign.data_classes.LDData property)
requires_xml_data() (in module schrodinger.application.matsci.qeschema.qeschema.documents)
RereadImageData() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
res_add_externals() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
rescale_ff() (in module schrodinger.application.desmond.remd)
rescale_ff_solute_tempering() (in module schrodinger.application.desmond.remd)
ResData (class in schrodinger.application.desmond.fep_edge_data)
reset() (in module schrodinger.ui.qt.appframework2.appmethods)
(schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
(schrodinger.application.desmond.util.Counter method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
reset_tag() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
resetCachedContent() (schrodinger.ui.dendrogram.DendrogramView method)
resetGroup() (schrodinger.utils.preferences.Preferences method)
resetSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method)
resetTransform() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
resetTransforms() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
resid (schrodinger.application.desmond.packages.msys.Residue property)
Residue (class in schrodinger.application.desmond.packages.msys)
residue (schrodinger.application.desmond.cms.Cms property)
(schrodinger.application.desmond.ffiostructure.FFIOStructure property)
(schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.models.jsonable.JsonableStructure property)
(schrodinger.structure._Chain property)
(schrodinger.structure._Molecule property)
(schrodinger.structure.Structure property)
(schrodinger.structure.TextualStructure property)
residue() (schrodinger.application.desmond.packages.msys.System method)
residue_charge (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
residue_formula() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
residue_hydrophobicity (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
residue_position (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
RESIDUE_SCANNING (schrodinger.infra.structure.WorkflowType attribute)
residue_structure_mae() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
residue_structure_template() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
residue_type (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
residues (schrodinger.application.desmond.packages.msys.Chain property)
(schrodinger.application.desmond.packages.msys.System property)
Resize() (in module schrodinger.analysis.visanalysis.volumedatautils)
resize() (schrodinger.infra.mmbitset.Bitset method)
(schrodinger.ui.dendrogram.DendrogramView method)
resizeAnchor() (schrodinger.ui.dendrogram.DendrogramView method)
resizeEvent() (schrodinger.ui.dendrogram.DendrogramView method)
resKey() (schrodinger.application.prime.residue_interaction.InteractionReader static method)
resnum (schrodinger.application.qsite.input.Cut property)
(schrodinger.structure._Residue property)
(schrodinger.structure._StructureAtom property)
RESOLVE_AMBIGUOUS_TAUTOMERS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
resolve_atomsel() (in module schrodinger.application.desmond.enhsamp)
(schrodinger.application.desmond.enhsamp.Bind method)
(schrodinger.application.desmond.enhsamp.FcnCall method)
(schrodinger.application.desmond.enhsamp.If method)
(schrodinger.application.desmond.enhsamp.Iter method)
(schrodinger.application.desmond.enhsamp.Let method)
(schrodinger.application.desmond.enhsamp.Lit method)
(schrodinger.application.desmond.enhsamp.Node method)
(schrodinger.application.desmond.enhsamp.Series method)
(schrodinger.application.desmond.enhsamp.String method)
(schrodinger.application.desmond.enhsamp.Var method)
resource_summary() (in module schrodinger.application.licensing.licadmin)
resources() (in module schrodinger.application.licensing.licadmin)
resources_from_list() (in module schrodinger.application.licensing.licadmin)
resources_from_path() (in module schrodinger.application.licensing.licadmin)
REST_COMPONENT (class in schrodinger.application.desmond.constants)
REST_PROPERTIES (class in schrodinger.application.desmond.constants)
REST_REGION_RULE (class in schrodinger.application.desmond.constants)
RESTART (schrodinger.application.desmond.constants.UiMode attribute)
restart_name() (in module schrodinger.application.jaguar.utils)
restore() (schrodinger.infra.mmerr.Capture method)
(schrodinger.protein.rotamers.Rotamers method)
restore_default() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
restore_defaults() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
restoreDefaultVisibility() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
restoreGeometry() (schrodinger.ui.dendrogram.DendrogramView method)
restoreIonCenterProps() (schrodinger.application.ligprep.ionizer.Ionizer method)
restoreState() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
Restrain (class in schrodinger.application.desmond.cms)
RESTRAINED_FRAGMENT_HYDRATION (schrodinger.application.desmond.constants.FepLegTypes attribute)
RestrainGroup (class in schrodinger.application.desmond.cms)
RestrainGroupContainer (class in schrodinger.application.desmond.cms)
Restraint (class in schrodinger.forcefield.minimizer)
RestraintBuilder (class in schrodinger.application.desmond.packages.restraint.builder)
Restraints (class in schrodinger.application.desmond.packages.restraint.builder)
restraints (schrodinger.forcefield.ffld_options.MinimizationOptions attribute)
RestrainTypes (class in schrodinger.application.desmond.constants)
RESULT_NAMES (schrodinger.application.desmond.packages.analysis.AmorphousCrystalInter attribute)
Results (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator property)
RETAIN (schrodinger.application.desmond.constants.EXISTING_RESTRAINT attribute)
retain_ref_single() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.FBHWPosRestrainArray method)
(schrodinger.application.desmond.cms.PosRestrainArray method)
(schrodinger.application.desmond.cms.RestrainGroup method)
retain_refs() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.FBHWPosRestrainArray method)
(schrodinger.application.desmond.cms.PosRestrainArray method)
(schrodinger.application.desmond.cms.RestrainGroup method)
retranslateUi() (schrodinger.application.bioluminate.propfilter_ui.Ui_Form method)
(schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form method)
(schrodinger.application.desmond.desmond_advanced_tab_ui.Ui_Dialog method)
(schrodinger.application.desmond.input_group_ui.Ui_Form method)
(schrodinger.application.desmond.rest_tab_ui.Ui_Form method)
(schrodinger.application.jaguar.update_pka_settings_ui.Ui_UpdatePKASettingsDlg method)
(schrodinger.application.job_monitor.diagnostics_dialog_ui.Ui_Form method)
(schrodinger.application.job_monitor.file_browser_ui.Ui_Form method)
(schrodinger.application.livedesign.login2_ui.Ui_Form method)
(schrodinger.application.livedesign.login_ui.Ui_Dialog method)
(schrodinger.application.livedesign.pose_name_panel_ui.Ui_Form method)
(schrodinger.application.livedesign.save_mapping_dialog_ui.Ui_Form method)
(schrodinger.application.livedesign.selection_pop_up_ui.Ui_Form method)
(schrodinger.application.msv.gui.binding_site_aln_dialog_ui.Ui_Form method)
(schrodinger.application.msv.gui.homology_modeling.homology_modeling_step_ui.Ui_Form method)
(schrodinger.application.msv.gui.multiple_seq_aln_dialog_ui.Ui_Form method)
(schrodinger.application.msv.gui.pairwise_seq_aln_dialog_ui.Ui_Form method)
(schrodinger.application.msv.gui.toolbar_ui.Ui_Form method)
(schrodinger.application.prime.gui.ui.environment_options_ui.Ui_Form method)
(schrodinger.infra.exception_handler_dir.exception_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.traj_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.export_movie_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.export_structures_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.shortcut_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui.Ui_snapshot_panel method)
(schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui.Ui_trajectory_form method)
(schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog method)
(schrodinger.ui.ligfilter_ui.Ui_Form method)
(schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui.Ui_Dialog method)
(schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui.Ui_Dialog method)
(schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui.Ui_Dialog method)
(schrodinger.ui.qt.appframework2.debug_gui_ui.Ui_Form method)
(schrodinger.ui.qt.borderless_popup_ui.Ui_Frame method)
(schrodinger.ui.qt.config_dialog_open_mp_ui.Ui_Form method)
(schrodinger.ui.qt.config_dialog_queue_ui.Ui_Form method)
(schrodinger.ui.qt.entryselector_ui.Ui_Dialog method)
(schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui.Ui_Form method)
(schrodinger.ui.qt.filter_dialog_ui.Ui_Dialog method)
(schrodinger.ui.qt.pdb_dialog_ui.Ui_PdbDialog method)
(schrodinger.ui.qt.presets.manage_presets_dialog_ui.Ui_Form method)
(schrodinger.ui.qt.presets.save_presets_dialog_ui.Ui_Form method)
(schrodinger.ui.qt.protein_health_viewer_ui.Ui_Form method)
(schrodinger.ui.qt.rename_favorite_dialog_ui.Ui_Dialog method)
(schrodinger.ui.qt.select_residues_dialog_ui.Ui_Dialog method)
(schrodinger.ui.qt.tasks.config_dialog_ui.Ui_Form method)
(schrodinger.ui.qt.tasks.config_info_ui.Ui_Form method)
retrieve_ent() (in module schrodinger.protein.getpdb)
retrieve_frame() (schrodinger.application.desmond.packages.traj.DtrSource method)
(schrodinger.application.desmond.packages.traj.MaeSource method)
(schrodinger.application.desmond.packages.traj.Source method)
(schrodinger.application.desmond.packages.traj.XtcSource method)
retrieve_license_file() (in module schrodinger.application.licensing.netsuiteapi)
retrieve_pdb() (in module schrodinger.protein.getpdb)
ReturnCode (class in schrodinger.infra.mmcheck)
retype() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure._StructureAtom method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
reverse() (schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.sea.sea.List method)
reviseIonizedGroup() (schrodinger.application.ligprep.ionizer.Ionizer method)
rewind() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
rewrite() (schrodinger.application.canvas.utils.ChmCSVTools method)
rewriteByIndex() (schrodinger.application.canvas.utils.ChmCSVTools method)
RewriteCardinalityException
RewriteEarlyExitException
RewriteEmptyStreamException
RewriteOperation (class in schrodinger.application.desmond.antlr3.streams)
RewriteRuleElementStream (class in schrodinger.application.desmond.antlr3.tree)
RewriteRuleNodeStream (class in schrodinger.application.desmond.antlr3.tree)
RewriteRuleSubtreeStream (class in schrodinger.application.desmond.antlr3.tree)
RewriteRuleTokenStream (class in schrodinger.application.desmond.antlr3.tree)
rfind() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
rgb_float (schrodinger.project.surface.ProjectSurface.Color property)
(schrodinger.structutils.color.Color property)
(schrodinger.surface.Surface.Color property)
RGroup (class in schrodinger.structutils.rgroup_enumerate)
RGroupEnumerator (class in schrodinger.structutils.rgroup_enumerate)
RgroupEnumerator (in module schrodinger.structutils.rgroup_enumerate)
RGroupError
RgroupError (in module schrodinger.structutils.rgroup_enumerate)
RGroupSource (class in schrodinger.structutils.rgroup_enumerate)
Rh2Hx() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
rindex() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
ring (schrodinger.application.desmond.cms.Cms attribute)
(schrodinger.application.desmond.ffiostructure.FFIOStructure attribute)
(schrodinger.models.jsonable.JsonableStructure attribute)
(schrodinger.structure.Structure attribute)
(schrodinger.structure.TextualStructure property)
ring_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
ring_sys_d (schrodinger.application.dendrogram.core_class.RingSysStorage attribute)
ringAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
ringbondcount() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method)
RingSysInfo (class in schrodinger.application.dendrogram.core_class)
RingSysStorage (class in schrodinger.application.dendrogram.core_class)
rjust() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
rl_group_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
rl_groups (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
RMSD (class in schrodinger.application.desmond.packages.analysis)
rmsd (schrodinger.protein.tasks.structure_alignment.StructAlignResult attribute)
rmsd_matrix() (in module schrodinger.application.desmond.packages.analysis)
RMSDSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
RMSF (class in schrodinger.application.desmond.packages.analysis)
rollback() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
Rot_bonds (schrodinger.application.glide.xpdes.TermKeywords attribute)
rot_mx (class in schrodinger.application.matsci.cctbx.rot_mx)
rot_mx_info (class in schrodinger.application.matsci.cctbx.rot_mx)
Rotamers (class in schrodinger.protein.rotamers)
rotamers (schrodinger.protein.rotamers.Rotamers property)
rotatable_bonds_iterator() (in module schrodinger.structutils.analyze)
rotatableBondsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
rotate() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.ui.dendrogram.DendrogramView method)
rotate_2D() (in module schrodinger.rdkit.alignment)
rotate_structure() (in module schrodinger.structutils.transform)
RotateRBXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath)
rotation() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
rotational_strength_precision (schrodinger.application.jaguar.results.NormalMode attribute)
rotationChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
rotdMat() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
rotdMat4() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
round_value() (in module schrodinger.math.mathutils)
roundRect() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
roundup() (in module schrodinger.math.mathutils)
RouteRenderer (class in schrodinger.application.pathfinder.render)
rowGetExpanded() (schrodinger.infra.table.Table method)
rowGetVisible() (schrodinger.infra.table.Table method)
rowSetExpanded() (schrodinger.infra.table.Table method)
rowSetVisible() (schrodinger.infra.table.Table method)
rpartition() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
rsh_put_cmd() (in module schrodinger.job.remote_command)
rsh_test() (in module schrodinger.job.remote_command)
rsplit() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
rstrip() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
rt_mx (class in schrodinger.application.matsci.cctbx.rot_mx)
rubberBandChanged (schrodinger.ui.dendrogram.DendrogramView attribute)
RubberBandDrag (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.DragMode attribute)
rubberBandRect() (schrodinger.ui.dendrogram.DendrogramView method)
rubberBandSelectionMode() (schrodinger.ui.dendrogram.DendrogramView method)
Ruland() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
rulePostProcessing() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
RuleReturnScope (class in schrodinger.application.desmond.antlr3.recognizers)
run() (in module schrodinger.application.licensing.licadmin)
(schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method)
(schrodinger.application.desmond.starter.starter.Starter method)
(schrodinger.application.desmond.util.TestSuite method)
(schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
(schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.application.mopac.structure_launchers.StructureLauncher method)
(schrodinger.structutils.analyze.MissingLoopFinder method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
run_align() (in module schrodinger.application.ska)
RUN_ALIGNMENT (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
run_analysis() (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method)
(schrodinger.protein.analysis.Report.steric_clash_data_set method)
run_apbs() (in module schrodinger.application.desmond.fep_net_charge)
run_cleanup() (in module schrodinger.application.mopac.utils)
run_full_workflow() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
run_lmdiag() (in module schrodinger.application.licensing.licadmin)
run_lmstat() (in module schrodinger.application.licensing.licadmin)
run_mcs() (in module schrodinger.test.canvas_utils)
run_mcs_pw() (in module schrodinger.test.canvas_utils)
run_propka() (in module schrodinger.application.bioluminate.run_propka)
run_subprocess_test() (in module schrodinger.test.pytest.exetest)
running_message (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer attribute)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer attribute)
runStructureAlignment() (in module schrodinger.protein.tasks.structure_alignment)
runtest() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.MakefileTest method)
runValidation() (schrodinger.application.livedesign.entry_types.BaseEntryData method)
(schrodinger.application.livedesign.entry_types.Complexes method)
(schrodinger.application.livedesign.entry_types.CovalentDockingComplexes method)
(schrodinger.application.livedesign.entry_types.DockedPoses method)
(schrodinger.application.livedesign.entry_types.IndividualStructureBase method)
(schrodinger.application.livedesign.entry_types.Ligands method)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds method)
(schrodinger.application.livedesign.entry_types.TargetlessBase method)
(schrodinger.ui.qt.appframework2.validation.ValidationMixin method)
rvs() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
rxn_coord_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
S
S (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
safe_extractall_tar() (in module schrodinger.utils.fileutils)
safe_extractall_zip() (in module schrodinger.utils.fileutils)
safe_mkdir() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
(schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
safe_patch_os_environ (class in schrodinger.test.fixtures)
SaltBridgeFinder (class in schrodinger.application.desmond.packages.analysis)
SamAng() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
sameSizeAndThreshold() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method)
sample_pdbs() (in module schrodinger.test.stu.get_pdbs)
SAMPLE_SIZE (schrodinger.application.matsci.uq_utils.BilinearHistogramData attribute)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData attribute)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData attribute)
Sanitize (class in schrodinger.adapter)
sanitize_for_viparr() (schrodinger.application.desmond.cms.Cms method)
sanityCheckParentAndChildIndexes() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
Save() (in module schrodinger.application.desmond.packages.msys)
save() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
save_hypo_with_score() (in module schrodinger.application.phase.packages.hypo_refine.hypo_utils)
save_mat_csv() (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
save_mkdir() (in module schrodinger.application.bioluminate.epitope.psc_workflow)
save_plot() (in module schrodinger.analysis.enrichment.plotter)
save_sym_mat_csv() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
SaveDMS() (in module schrodinger.application.desmond.packages.msys)
saveGeometry() (schrodinger.ui.dendrogram.DendrogramView method)
saveIonCenterProps() (schrodinger.application.ligprep.ionizer.Ionizer method)
SaveMAE() (in module schrodinger.application.desmond.packages.msys)
SaveMol2() (in module schrodinger.application.desmond.packages.msys)
SavePDB() (in module schrodinger.application.desmond.packages.msys)
savePlot() (schrodinger.analysis.enrichment.calculator.Calculator method)
(schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method)
(schrodinger.analysis.enrichment.plotter.Plotter method)
saveState() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
SaveVisFile() (in module schrodinger.analysis.visanalysis.volumedataio)
Scaffold (class in schrodinger.structutils.markush_enumerate)
Scale() (in module schrodinger.application.desmond.packages.msys.vdw)
scale() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.tr_vec method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
scaleChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
SCALED_INTENSITY_TOL (schrodinger.application.matsci.xrd.XRDCalculator attribute)
scaleFactor (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute)
Scan (class in schrodinger.application.jaguar.scan)
ScatFac() (in module schrodinger.application.matsci.gsas.GSASIIElem)
scene() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
sceneBoundingRect() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
sceneEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
sceneEventFilter() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
SceneModal (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNode.PanelModality attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel.PanelModality attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree.PanelModality attribute)
scenePos() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
sceneRect() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
sceneRectChanged (schrodinger.ui.dendrogram.DendrogramScene attribute)
sceneTransform() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
SCF_MAX_ITERS (schrodinger.application.jaguar.constants.FatalErrors attribute)
ScfIteration (class in schrodinger.application.jaguar.results)
Schedule (class in schrodinger.application.desmond.constants)
schrod_port() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
SCHRODINGER
schrodinger
(schrodinger.application.desmond.envir.CONST attribute)
(schrodinger.energy.ANIModel attribute)
module
schrodinger.adapter
module
schrodinger.analysis
module
schrodinger.analysis.enrichment
module
schrodinger.analysis.enrichment.calculator
module
schrodinger.analysis.enrichment.enrichment_input
module
schrodinger.analysis.enrichment.metrics
module
schrodinger.analysis.enrichment.plotter
module
schrodinger.analysis.substructure
module
schrodinger.analysis.transformations
module
schrodinger.analysis.visanalysis
module
schrodinger.analysis.visanalysis.vdaxis
module
schrodinger.analysis.visanalysis.vdcoordinateframe
module
schrodinger.analysis.visanalysis.vdexception
module
schrodinger.analysis.visanalysis.volumedata
module
schrodinger.analysis.visanalysis.volumedataio
module
schrodinger.analysis.visanalysis.volumedatastructureutils
module
schrodinger.analysis.visanalysis.volumedatautils
module
schrodinger.application
module
schrodinger.application.aacg
module
schrodinger.application.aacg.utils
module
schrodinger.application.bindingsite
module
schrodinger.application.bindingsite.atomtyping
module
schrodinger.application.bindingsite.cavutils
module
schrodinger.application.bindingsite.common
module
schrodinger.application.bindingsite.intfield
module
schrodinger.application.bindingsite.schema
module
schrodinger.application.bioluminate
module
schrodinger.application.bioluminate.actions
module
schrodinger.application.bioluminate.antibody
module
schrodinger.application.bioluminate.drivers
module
schrodinger.application.bioluminate.drivers.io
module
schrodinger.application.bioluminate.epitope.psc_workflow
module
schrodinger.application.bioluminate.epitope.utils.esc_utils
module
schrodinger.application.bioluminate.patch_utils
module
schrodinger.application.bioluminate.patch_utils.settings
module
schrodinger.application.bioluminate.propfilter_ui
module
schrodinger.application.bioluminate.propka_parse
module
schrodinger.application.bioluminate.protein_interaction
module
schrodinger.application.bioluminate.protein_protein_docking_shared
module
schrodinger.application.bioluminate.protein_structure_quality_ui
module
schrodinger.application.bioluminate.residue_scanning
module
schrodinger.application.bioluminate.residue_scanning.properties
module
schrodinger.application.bioluminate.run_propka
module
schrodinger.application.bioluminate.surfcomp
module
schrodinger.application.bioluminate.validate_imported_modules
module
schrodinger.application.canvas
module
schrodinger.application.canvas.base
module
schrodinger.application.canvas.cluster
module
schrodinger.application.canvas.fingerprint
module
schrodinger.application.canvas.r_group_dee
module
schrodinger.application.canvas.similarity
module
schrodinger.application.canvas.topo_descriptors
module
schrodinger.application.canvas.utils
module
schrodinger.application.combiglide
module
schrodinger.application.combiglide.corehop
module
schrodinger.application.combiglide.packages
module
schrodinger.application.combiglide.utils
module
schrodinger.application.combinatorial_diversity
module
schrodinger.application.combinatorial_diversity.diversity_fingerprinter
module
schrodinger.application.combinatorial_diversity.diversity_selector
module
schrodinger.application.combinatorial_diversity.diversity_splitter
module
schrodinger.application.combinatorial_diversity.splitter_utils
module
schrodinger.application.combinatorial_explorer
module
schrodinger.application.combinatorial_screen
module
schrodinger.application.combinatorial_screen.combinatorial_screener
module
schrodinger.application.combinatorial_screen.fingerprint_utils
module
schrodinger.application.dendrogram.core_class
module
schrodinger.application.dendrogram.randTestSet
module
schrodinger.application.desmond
module
schrodinger.application.desmond.ana
module
schrodinger.application.desmond.antlr3
module
schrodinger.application.desmond.antlr3.compat
module
schrodinger.application.desmond.antlr3.constants
module
schrodinger.application.desmond.antlr3.debug
module
schrodinger.application.desmond.antlr3.dfa
module
schrodinger.application.desmond.antlr3.exceptions
module
schrodinger.application.desmond.antlr3.recognizers
module
schrodinger.application.desmond.antlr3.streams
module
schrodinger.application.desmond.antlr3.tokens
module
schrodinger.application.desmond.antlr3.tree
module
schrodinger.application.desmond.antlr3.treewizard
module
schrodinger.application.desmond.arkdb
module
schrodinger.application.desmond.autopartition
module
schrodinger.application.desmond.bennett
module
schrodinger.application.desmond.bld_def
module
schrodinger.application.desmond.bld_ver
module
schrodinger.application.desmond.cmdline
module
schrodinger.application.desmond.cms
module
schrodinger.application.desmond.constants
module
schrodinger.application.desmond.correlation_tau
module
schrodinger.application.desmond.deltaE
module
schrodinger.application.desmond.desmond_advanced_tab_ui
module
schrodinger.application.desmond.enhanced_sampling
module
schrodinger.application.desmond.enhanced_sampling.FcnTypes
module
schrodinger.application.desmond.enhanced_sampling.mexpLexer
module
schrodinger.application.desmond.enhanced_sampling.mexpParser
module
schrodinger.application.desmond.enhsamp
module
schrodinger.application.desmond.envir
module
schrodinger.application.desmond.event_analysis
module
schrodinger.application.desmond.fep_edge_data
module
schrodinger.application.desmond.fep_edge_data_classifier
module
schrodinger.application.desmond.fep_mapping
module
schrodinger.application.desmond.fep_net_charge
module
schrodinger.application.desmond.fep_schedule
module
schrodinger.application.desmond.fep_scholar_rules
module
schrodinger.application.desmond.fep_struc
module
schrodinger.application.desmond.fep_util
module
schrodinger.application.desmond.ffiostructure
module
schrodinger.application.desmond.frag_snap
module
schrodinger.application.desmond.gaussian_filter
module
schrodinger.application.desmond.gchart
module
schrodinger.application.desmond.gcmc_utils
module
schrodinger.application.desmond.input_group_ui
module
schrodinger.application.desmond.measurement
module
schrodinger.application.desmond.memory
module
schrodinger.application.desmond.move_alchem_ions
module
schrodinger.application.desmond.multisim
module
schrodinger.application.desmond.multisim.parser
module
schrodinger.application.desmond.packages
module
schrodinger.application.desmond.packages.analysis
module
schrodinger.application.desmond.packages.destro
module
schrodinger.application.desmond.packages.msys
module
schrodinger.application.desmond.packages.msys.atomsel
module
schrodinger.application.desmond.packages.msys.grease
module
schrodinger.application.desmond.packages.msys.molfile
module
schrodinger.application.desmond.packages.msys.molfile.findframe
module
schrodinger.application.desmond.packages.msys.pfx
module
schrodinger.application.desmond.packages.msys.posre
module
schrodinger.application.desmond.packages.msys.vdw
module
schrodinger.application.desmond.packages.pfx
module
schrodinger.application.desmond.packages.restraint
module
schrodinger.application.desmond.packages.restraint.builder
module
schrodinger.application.desmond.packages.restraint.cross_link
module
schrodinger.application.desmond.packages.restraint.utils
module
schrodinger.application.desmond.packages.staf
module
schrodinger.application.desmond.packages.test
module
schrodinger.application.desmond.packages.test.DESMOND_11543
module
schrodinger.application.desmond.packages.timer
module
schrodinger.application.desmond.packages.topo
module
schrodinger.application.desmond.packages.traj
module
schrodinger.application.desmond.packages.traj_util
module
schrodinger.application.desmond.packages.viparr
module
schrodinger.application.desmond.packages.viparr1
module
schrodinger.application.desmond.packages.viparr1.plugins
module
schrodinger.application.desmond.packages.viparr1.systest
module
schrodinger.application.desmond.packages.viparr1.systest.systest
module
schrodinger.application.desmond.packages.viparr1.viparr
module
schrodinger.application.desmond.packages.viparr1.viparr.elements
module
schrodinger.application.desmond.packages.viparr1.viparr.isomorph
module
schrodinger.application.desmond.packages.viparr1.viparr.version
module
schrodinger.application.desmond.packages.viparr1.viparr.viparr
module
schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge
module
schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util
module
schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue
module
schrodinger.application.desmond.packages.viparr1.viparr.viparr_util
module
schrodinger.application.desmond.picklejar
module
schrodinger.application.desmond.platforms
module
schrodinger.application.desmond.r_group_asl
module
schrodinger.application.desmond.remd
module
schrodinger.application.desmond.repair_cms
module
schrodinger.application.desmond.replica_dE
module
schrodinger.application.desmond.replica_exchange_review
module
schrodinger.application.desmond.rest_tab_ui
module
schrodinger.application.desmond.rl_helper
module
schrodinger.application.desmond.simulation_block_data
module
schrodinger.application.desmond.simulation_block_test
module
schrodinger.application.desmond.smarts
module
schrodinger.application.desmond.solubility_utils
module
schrodinger.application.desmond.starter
module
schrodinger.application.desmond.starter.starter
module
schrodinger.application.desmond.task
module
schrodinger.application.desmond.test_utils
module
schrodinger.application.desmond.torsion_related
module
schrodinger.application.desmond.util
module
schrodinger.application.epik
module
schrodinger.application.fpsim
module
schrodinger.application.glide
module
schrodinger.application.glide.ensemble_selection
module
schrodinger.application.glide.packages
module
schrodinger.application.glide.poseviewconvert
module
schrodinger.application.glide.utils
module
schrodinger.application.glide.xpdes
module
schrodinger.application.inputconfig
module
schrodinger.application.jaguar
module
schrodinger.application.jaguar.autots_constants
module
schrodinger.application.jaguar.autots_input_constants
module
schrodinger.application.jaguar.basis
module
schrodinger.application.jaguar.boltzmann_prop_defaults
module
schrodinger.application.jaguar.check_headers
module
schrodinger.application.jaguar.constants
module
schrodinger.application.jaguar.csrch_input_constants
module
schrodinger.application.jaguar.exceptions
module
schrodinger.application.jaguar.global_macros
module
schrodinger.application.jaguar.gui
module
schrodinger.application.jaguar.hydrokinetic_constants
module
schrodinger.application.jaguar.hydrokinetic_input_constants
module
schrodinger.application.jaguar.hydrokinetic_validation
module
schrodinger.application.jaguar.jaguar_diff
module
schrodinger.application.jaguar.keywordDB
module
schrodinger.application.jaguar.macro_pka_constants
module
schrodinger.application.jaguar.mmjag
module
schrodinger.application.jaguar.neural_network_optimizer
module
schrodinger.application.jaguar.results
module
schrodinger.application.jaguar.scan
module
schrodinger.application.jaguar.solvation_validation
module
schrodinger.application.jaguar.update_pka_settings_ui
module
schrodinger.application.jaguar.user_config
module
schrodinger.application.jaguar.utils
module
schrodinger.application.jaguar.workflow_validation
module
schrodinger.application.job_monitor
module
schrodinger.application.job_monitor.diagnostics_dialog_ui
module
schrodinger.application.job_monitor.file_browser_ui
module
schrodinger.application.job_monitor.util
module
schrodinger.application.licensing
module
schrodinger.application.licensing.flexlm
module
schrodinger.application.licensing.licadmin
module
schrodinger.application.licensing.licerror
module
schrodinger.application.licensing.lmgrd_log_parser
module
schrodinger.application.licensing.netsuiteapi
module
schrodinger.application.ligprep
module
schrodinger.application.ligprep.ionizer
module
schrodinger.application.livedesign
module
schrodinger.application.livedesign.data_classes
module
schrodinger.application.livedesign.entry_types
module
schrodinger.application.livedesign.io_utils
module
schrodinger.application.livedesign.ld_folder_tree
module
schrodinger.application.livedesign.lid
module
schrodinger.application.livedesign.login
module
schrodinger.application.livedesign.login2_ui
module
schrodinger.application.livedesign.login_ui
module
schrodinger.application.livedesign.pose_name_panel_ui
module
schrodinger.application.livedesign.pse_helpers
module
schrodinger.application.livedesign.save_mapping_dialog_ui
module
schrodinger.application.livedesign.selection_pop_up_ui
module
schrodinger.application.livedesign.upload_utils
module
schrodinger.application.macromodel
module
schrodinger.application.macromodel.packages
module
schrodinger.application.macromodel.tools
module
schrodinger.application.matsci
module
schrodinger.application.matsci.atomicsymbols
module
schrodinger.application.matsci.basiselements
module
schrodinger.application.matsci.cache
module
schrodinger.application.matsci.cctbx
module
schrodinger.application.matsci.cctbx.rot_mx
module
schrodinger.application.matsci.codeutils
module
schrodinger.application.matsci.colorutils
module
schrodinger.application.matsci.elasticity
module
schrodinger.application.matsci.enc
module
schrodinger.application.matsci.espresso
module
schrodinger.application.matsci.geometry
module
schrodinger.application.matsci.graph
module
schrodinger.application.matsci.gsas
module
schrodinger.application.matsci.gsas.atmdata
module
schrodinger.application.matsci.gsas.ElementTable
module
schrodinger.application.matsci.gsas.GSASIIElem
module
schrodinger.application.matsci.gsas.GSASIIfiles
module
schrodinger.application.matsci.gsas.GSASIIlattice
module
schrodinger.application.matsci.gsas.GSASIImath
module
schrodinger.application.matsci.gsas.GSASIIpwd
module
schrodinger.application.matsci.gsas.GSASIIspc
module
schrodinger.application.matsci.hdfutils
module
schrodinger.application.matsci.mlearn
module
schrodinger.application.matsci.mlearn.base
module
schrodinger.application.matsci.mlearn.descriptor
module
schrodinger.application.matsci.mlearn.sklearn_json
module
schrodinger.application.matsci.mlearn.sklearn_json.classification
module
schrodinger.application.matsci.mlearn.sklearn_json.common
module
schrodinger.application.matsci.mlearn.sklearn_json.csr
module
schrodinger.application.matsci.mlearn.sklearn_json.decomposition
module
schrodinger.application.matsci.mlearn.sklearn_json.regression
module
schrodinger.application.matsci.msconst
module
schrodinger.application.matsci.msprops
module
schrodinger.application.matsci.nano
module
schrodinger.application.matsci.nano.space_groups
module
schrodinger.application.matsci.nano.util
module
schrodinger.application.matsci.optoelectronics
module
schrodinger.application.matsci.plotwidgets
module
schrodinger.application.matsci.property_names
module
schrodinger.application.matsci.qb_sdk
module
schrodinger.application.matsci.qb_sdk.api
module
schrodinger.application.matsci.qb_sdk.client
module
schrodinger.application.matsci.qb_sdk.job
module
schrodinger.application.matsci.qb_sdk.parameters
module
schrodinger.application.matsci.qb_sdk.tools
module
schrodinger.application.matsci.qeschema
module
schrodinger.application.matsci.qeschema.qeschema
module
schrodinger.application.matsci.qeschema.qeschema.cards
module
schrodinger.application.matsci.qeschema.qeschema.converters
module
schrodinger.application.matsci.qeschema.qeschema.documents
module
schrodinger.application.matsci.qeschema.qeschema.exceptions
module
schrodinger.application.matsci.qeschema.qeschema.hdf5
module
schrodinger.application.matsci.qeschema.qeschema.hdf5.charge
module
schrodinger.application.matsci.qeschema.qeschema.hdf5.readutils
module
schrodinger.application.matsci.qeschema.qeschema.namespaces
module
schrodinger.application.matsci.qeschema.qeschema.options
module
schrodinger.application.matsci.qeschema.qeschema.utils
module
schrodinger.application.matsci.qeschema.scripts.xml2qeinput
module
schrodinger.application.matsci.qeschema.scripts.yaml2qeinput
module
schrodinger.application.matsci.qeschema.tests
module
schrodinger.application.matsci.qeschema.utils
module
schrodinger.application.matsci.qexsd
module
schrodinger.application.matsci.qexsd.qespresso
module
schrodinger.application.matsci.qexsd.qespresso.cards
module
schrodinger.application.matsci.qexsd.qespresso.converters
module
schrodinger.application.matsci.qexsd.qespresso.documents
module
schrodinger.application.matsci.qexsd.qespresso.exceptions
module
schrodinger.application.matsci.qexsd.qespresso.options
module
schrodinger.application.matsci.qexsd.qespresso.utils
module
schrodinger.application.matsci.qexsd.qespresso.utils.logger
module
schrodinger.application.matsci.qexsd.qespresso.utils.mapping
module
schrodinger.application.matsci.qexsd.qespresso.utils.xml2nebinput
module
schrodinger.application.matsci.qexsd.qespresso.utils.xml2qeinput
module
schrodinger.application.matsci.qexsd.qespresso.xsdtypes
module
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree
module
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions
module
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument
module
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema
module
schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes
module
schrodinger.application.matsci.qexsd.tests.test_converters
module
schrodinger.application.matsci.qexsd.utils
module
schrodinger.application.matsci.siteselector
module
schrodinger.application.matsci.typography
module
schrodinger.application.matsci.uq_utils
module
schrodinger.application.matsci.xrd
module
schrodinger.application.medchem
module
schrodinger.application.medchem.property
module
schrodinger.application.mopac
module
schrodinger.application.mopac.exceptions
module
schrodinger.application.mopac.results_main
module
schrodinger.application.mopac.structure_launchers
module
schrodinger.application.mopac.utils
module
schrodinger.application.msv
module
schrodinger.application.msv.gui
module
schrodinger.application.msv.gui.binding_site_aln_dialog_ui
module
schrodinger.application.msv.gui.color_ramp
module
schrodinger.application.msv.gui.homology_modeling.constants
module
schrodinger.application.msv.gui.homology_modeling.homology_modeling_step_ui
module
schrodinger.application.msv.gui.multiple_seq_aln_dialog_ui
module
schrodinger.application.msv.gui.pairwise_seq_aln_dialog_ui
module
schrodinger.application.msv.gui.toolbar_ui
module
schrodinger.application.pathfinder
module
schrodinger.application.pathfinder.aligner
module
schrodinger.application.pathfinder.reaction
module
schrodinger.application.pathfinder.render
module
schrodinger.application.phase
module
schrodinger.application.phase.compare_utils
module
schrodinger.application.phase.constants
module
schrodinger.application.phase.create_xvol
module
schrodinger.application.phase.hypothesis
module
schrodinger.application.phase.hypothesis_binding_modes
module
schrodinger.application.phase.input
module
schrodinger.application.phase.packages
module
schrodinger.application.phase.packages.conformer_storage
module
schrodinger.application.phase.packages.hypo_refine.hypo_utils
module
schrodinger.application.phase.packages.ligand_aligner
module
schrodinger.application.phase.packages.mmp2d
module
schrodinger.application.phase.packages.mmp3dscreener
module
schrodinger.application.phase.packages.mmp_compare_utils
module
schrodinger.application.phase.packages.phase_option_utils
module
schrodinger.application.phase.packages.shape_binary_utils
module
schrodinger.application.phase.packages.test
module
schrodinger.application.phase.shape_screen_reporter
module
schrodinger.application.phase.shape_screen_reporter.prop_utils
module
schrodinger.application.phase.utils
module
schrodinger.application.prepwizard2
module
schrodinger.application.prime
module
schrodinger.application.prime.gui
module
schrodinger.application.prime.gui.ui
module
schrodinger.application.prime.gui.ui.environment_options_ui
module
schrodinger.application.prime.input
module
schrodinger.application.prime.primefix
module
schrodinger.application.prime.residue_interaction
module
schrodinger.application.prime.wrapper
module
schrodinger.application.qsite
module
schrodinger.application.qsite.input
module
schrodinger.application.scaffold_enumeration
module
schrodinger.application.scaffold_enumeration.atomlist
module
schrodinger.application.scaffold_enumeration.common
module
schrodinger.application.scaffold_enumeration.cxsmiles
module
schrodinger.application.scaffold_enumeration.layered
module
schrodinger.application.scaffold_enumeration.linknode
module
schrodinger.application.scaffold_enumeration.markush
module
schrodinger.application.scaffold_enumeration.mdl
module
schrodinger.application.scaffold_enumeration.posvarbond
module
schrodinger.application.scaffold_enumeration.rdcml
module
schrodinger.application.scisol
module
schrodinger.application.scisol.packages
module
schrodinger.application.ska
module
schrodinger.application.steps
module
schrodinger.application.steps.env_keys
module
schrodinger.application.steps.licensing
module
schrodinger.application.utils
module
schrodinger.application.vss
module
schrodinger.application.vss.config
module
schrodinger.application.vss.database
module
schrodinger.application.vss.dise
module
schrodinger.application.watermap
module
schrodinger.application.watermap.utils
module
schrodinger.energy
module
schrodinger.forcefield
module
schrodinger.forcefield.common
module
schrodinger.forcefield.constants
module
schrodinger.forcefield.ffld_options
module
schrodinger.forcefield.minimizer
module
schrodinger.forcefield.packages
module
schrodinger.genericfp
module
schrodinger.geometry
module
schrodinger.gpgpu
module
schrodinger.graphics3d
module
schrodinger.infra
module
schrodinger.infra.ark
module
schrodinger.infra.canvas
module
schrodinger.infra.canvas2d
module
schrodinger.infra.color
module
schrodinger.infra.epydoc_to_sphinx
module
schrodinger.infra.exception_handler_dir
module
schrodinger.infra.exception_handler_dir.exception_dialog_ui
module
schrodinger.infra.fast3d
module
schrodinger.infra.fix_sip6_enum_access
module
schrodinger.infra.gpgpu_utils
module
schrodinger.infra.growthspace
module
schrodinger.infra.jobhub
module
schrodinger.infra.licensing
module
schrodinger.infra.mm
module
schrodinger.infra.mmbitset
module
schrodinger.infra.mmcheck
module
schrodinger.infra.mmerr
module
schrodinger.infra.mmim
module
schrodinger.infra.mminit
module
schrodinger.infra.mmjob
module
schrodinger.infra.mmkv
module
schrodinger.infra.mmlist
module
schrodinger.infra.mmobject
module
schrodinger.infra.mmproj
module
schrodinger.infra.mmreflect
module
schrodinger.infra.mmsurf
module
schrodinger.infra.mopac
module
schrodinger.infra.phase
module
schrodinger.infra.projectmodel
module
schrodinger.infra.structure
module
schrodinger.infra.table
module
schrodinger.infra.test
module
schrodinger.infra.util
module
schrodinger.job
module
schrodinger.job.files
module
schrodinger.job.host_check
module
schrodinger.job.jobwriter
module
schrodinger.job.launchparams
module
schrodinger.job.remote_command
module
schrodinger.job.resource
module
schrodinger.job.server
module
schrodinger.job.util
module
schrodinger.livedesign.convert
module
schrodinger.livedesign.molhash
module
schrodinger.livedesign.preprocessor
module
schrodinger.livedesign.rgfile_parse
module
schrodinger.livedesign.rgroup_decomposition
module
schrodinger.math.mathutils
module
schrodinger.math.multi_parameter_optimization
module
schrodinger.models
module
schrodinger.models.adapters
module
schrodinger.models.adapters.abstractadapter
module
schrodinger.models.adapters.inputconfig
module
schrodinger.models.diffy
module
schrodinger.models.json
module
schrodinger.models.jsonable
module
schrodinger.pipeline
module
schrodinger.pipeline.compiled_functions
module
schrodinger.pipeline.input
module
schrodinger.pipeline.pipeio
module
schrodinger.pipeline.pipeutils
module
schrodinger.pipeline.stages
module
schrodinger.project.surface
module
schrodinger.protein
module
schrodinger.protein.analysis
module
schrodinger.protein.analysis_params
module
schrodinger.protein.biounit
module
schrodinger.protein.buildpeptide
module
schrodinger.protein.constants
module
schrodinger.protein.findhets
module
schrodinger.protein.getpdb
module
schrodinger.protein.gpcr
module
schrodinger.protein.gpcr.annotate
module
schrodinger.protein.gpcr.gpcrdb
module
schrodinger.protein.gpcr.sql
module
schrodinger.protein.gpcr.update_gpcr_db
module
schrodinger.protein.helix
module
schrodinger.protein.helm
module
schrodinger.protein.remediate
module
schrodinger.protein.renumber_residues
module
schrodinger.protein.rotamers
module
schrodinger.protein.seqres
module
schrodinger.protein.tasks.mock_blast_output
module
schrodinger.protein.tasks.structure_alignment
module
schrodinger.Qt
module
schrodinger.Qt.PyQt6
module
schrodinger.Qt.PyQt6.QtCharts
module
schrodinger.Qt.PyQt6.QtCore
module
schrodinger.Qt.PyQt6.QtGui
module
schrodinger.Qt.PyQt6.QtNetwork
module
schrodinger.Qt.PyQt6.QtOpenGL
module
schrodinger.Qt.PyQt6.QtOpenGLWidgets
module
schrodinger.Qt.PyQt6.QtPrintSupport
module
schrodinger.Qt.PyQt6.QtStateMachine
module
schrodinger.Qt.PyQt6.QtSvg
module
schrodinger.Qt.PyQt6.QtWidgets
module
schrodinger.Qt.PyQt6.sip
module
schrodinger.rdkit.alignment
module
schrodinger.rdkit.filtering
module
schrodinger.rdkit.molio
module
schrodinger.rdkit.rdkit_adapter
module
schrodinger.rdkit.rgroup
module
schrodinger.rdkit.sorted_molwriter
module
schrodinger.rdkit.substructure
module
schrodinger.rdkit_extensions
module
schrodinger.shape
module
schrodinger.sitemap
module
schrodinger.structure
module
schrodinger.structure.structure
module
schrodinger.structure.workflow_action_menu
module
schrodinger.structutils
module
schrodinger.structutils.analyze
module
schrodinger.structutils.block_data
module
schrodinger.structutils.build
module
schrodinger.structutils.check
module
schrodinger.structutils.color
module
schrodinger.structutils.createfragments
module
schrodinger.structutils.filter
module
schrodinger.structutils.interactionfp
module
schrodinger.structutils.interactions
module
schrodinger.structutils.interactions.hbond
module
schrodinger.structutils.interactions.pi
module
schrodinger.structutils.interactions.protein_protein_interactions
module
schrodinger.structutils.interactions.salt_bridge
module
schrodinger.structutils.interactions.ssbond
module
schrodinger.structutils.interactions.steric_clash
module
schrodinger.structutils.io
module
schrodinger.structutils.markush_enumerate
module
schrodinger.structutils.measure
module
schrodinger.structutils.minimize
module
schrodinger.structutils.pbc_tools
module
schrodinger.structutils.properties
module
schrodinger.structutils.residue
module
schrodinger.structutils.rgroup_enumerate
module
schrodinger.structutils.rings
module
schrodinger.structutils.rmsd
module
schrodinger.structutils.shuffle
module
schrodinger.structutils.sitealign
module
schrodinger.structutils.smiles
module
schrodinger.structutils.standard_nuclear_orientation
module
schrodinger.structutils.structalign
module
schrodinger.structutils.transform
module
schrodinger.surface
module
schrodinger.tasks
module
schrodinger.test
module
schrodinger.test.build_test_structures
module
schrodinger.test.canvas_utils
module
schrodinger.test.cluster_info
module
schrodinger.test.custom_assertions
module
schrodinger.test.darwinconsole
module
schrodinger.test.decorate_fflag
module
schrodinger.test.fixtures
module
schrodinger.test.hypothesis.hypothesis_profiles
module
schrodinger.test.hypothesis.strategies.indices
module
schrodinger.test.hypothesis.strategies.structures
module
schrodinger.test.hypothesis.strategies.ui
module
schrodinger.test.hypothesis.utils
module
schrodinger.test.ioredirect
module
schrodinger.test.log_parser
module
schrodinger.test.memtest
module
schrodinger.test.perceptualdiff
module
schrodinger.test.performance
module
schrodinger.test.performance.exceptions
module
schrodinger.test.performance.general
module
schrodinger.test.project_mock
module
schrodinger.test.pytest
module
schrodinger.test.pytest.exetest
module
schrodinger.test.pytest.faulthandler_setup
module
schrodinger.test.pytest.fixture
module
schrodinger.test.pytest.warnings
module
schrodinger.test.squish
module
schrodinger.test.squish.general
module
schrodinger.test.squish.maestro
module
schrodinger.test.squish.matsci
module
schrodinger.test.structurecheck
module
schrodinger.test.stu
module
schrodinger.test.stu.common
module
schrodinger.test.stu.constants
module
schrodinger.test.stu.get_pdbs
module
schrodinger.test.stu.outcomes.compare_csv
module
schrodinger.test.stu.outcomes.compareDesmondSystems
module
schrodinger.test.stu.outcomes.confgen_workups
module
schrodinger.test.stu.outcomes.correlate_to_reference_file
module
schrodinger.test.stu.outcomes.correlate_workup
module
schrodinger.test.stu.process_management
module
schrodinger.test.stu.workups
module
schrodinger.test.stu.workups.workup_tools
module
schrodinger.test.test_markers
module
schrodinger.test.warning_messages
module
schrodinger.thirdparty.networkx_algos
module
schrodinger.trajectory
module
schrodinger.trajectory.pbc_manager
module
schrodinger.trajectory.prody
module
schrodinger.trajectory.prody.crosscorrelation
module
schrodinger.trajectory.prody.ensemble
module
schrodinger.trajectory.prody.mode
module
schrodinger.trajectory.prody.modeset
module
schrodinger.trajectory.prody.nma
module
schrodinger.trajectory.prody.pca
module
schrodinger.trajectory.prody.writenmd
module
schrodinger.trajectory.traj_dialog_ui
module
schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui
module
schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui
module
schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui
module
schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui
module
schrodinger.trajectory.trajectory_gui_dir.display_settings_data
module
schrodinger.trajectory.trajectory_gui_dir.display_settings_manager
module
schrodinger.trajectory.trajectory_gui_dir.export_movie_ui
module
schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui
module
schrodinger.trajectory.trajectory_gui_dir.export_structure_enums
module
schrodinger.trajectory.trajectory_gui_dir.export_structures_ui
module
schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui
module
schrodinger.trajectory.trajectory_gui_dir.playback_settings_data
module
schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui
module
schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui
module
schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui
module
schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data
module
schrodinger.trajectory.trajectory_gui_dir.shortcut_ui
module
schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui
module
schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui
module
schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui
module
schrodinger.ui
module
schrodinger.ui.dendrogram
module
schrodinger.ui.ligfilter_definition_dialog_ui
module
schrodinger.ui.ligfilter_ui
module
schrodinger.ui.maestro_ui
module
schrodinger.ui.picking_dir
module
schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui
module
schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui
module
schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui
module
schrodinger.ui.qt
module
schrodinger.ui.qt.appframework2
module
schrodinger.ui.qt.appframework2.appmethods
module
schrodinger.ui.qt.appframework2.debug_gui_ui
module
schrodinger.ui.qt.appframework2.debugcore
module
schrodinger.ui.qt.appframework2.validation
module
schrodinger.ui.qt.appframework2.validators
module
schrodinger.ui.qt.borderless_popup_ui
module
schrodinger.ui.qt.config_dialog_open_mp_ui
module
schrodinger.ui.qt.config_dialog_queue_ui
module
schrodinger.ui.qt.dialbox_dir
module
schrodinger.ui.qt.entryselector_ui
module
schrodinger.ui.qt.filter_dialog_dir
module
schrodinger.ui.qt.filter_dialog_dir.filter_core
module
schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui
module
schrodinger.ui.qt.filter_dialog_ui
module
schrodinger.ui.qt.label_cursor
module
schrodinger.ui.qt.pdb_dialog_ui
module
schrodinger.ui.qt.presets.manage_presets_dialog_ui
module
schrodinger.ui.qt.presets.save_presets_dialog_ui
module
schrodinger.ui.qt.protein_health_viewer_ui
module
schrodinger.ui.qt.rename_favorite_dialog_ui
module
schrodinger.ui.qt.schrodingerstyle
module
schrodinger.ui.qt.select_residues_dialog_ui
module
schrodinger.ui.qt.standard
module
schrodinger.ui.qt.standard.colors
module
schrodinger.ui.qt.standard.constants
module
schrodinger.ui.qt.standard.icons
module
schrodinger.ui.qt.tasks
module
schrodinger.ui.qt.tasks.config_dialog_ui
module
schrodinger.ui.qt.tasks.config_info_ui
module
schrodinger.ui.sketcher
module
schrodinger.utils
module
schrodinger.utils.cgxutils
module
schrodinger.utils.colorscheme
module
schrodinger.utils.compare
module
schrodinger.utils.config
module
schrodinger.utils.csv_unicode
module
schrodinger.utils.deprecation
module
schrodinger.utils.env
module
schrodinger.utils.featureflags
module
schrodinger.utils.featureflags.featureflags
module
schrodinger.utils.featureflags.write
module
schrodinger.utils.fileutils
module
schrodinger.utils.funcchains
module
schrodinger.utils.funcgroups
module
schrodinger.utils.imputils
module
schrodinger.utils.install_scripts
module
schrodinger.utils.license
module
schrodinger.utils.ligfilter
module
schrodinger.utils.log
module
schrodinger.utils.machid
module
schrodinger.utils.maestro_scripts_path
module
schrodinger.utils.mmutil
module
schrodinger.utils.moduleproxy
module
schrodinger.utils.multifpfile
module
schrodinger.utils.openmpi
module
schrodinger.utils.platform
module
schrodinger.utils.postinstall
module
schrodinger.utils.preferences
module
schrodinger.utils.profiling
module
schrodinger.utils.scollections
module
schrodinger.utils.sea
module
schrodinger.utils.sea.common
module
schrodinger.utils.sea.evalor
module
schrodinger.utils.sea.sea
module
schrodinger.utils.singledashoptionparser
module
schrodinger.utils.sshconfig
module
schrodinger.utils.subproc
module
schrodinger.utils.subprocess
module
schrodinger.utils.sysinfo
module
schrodinger.utils.timeit
module
schrodinger.utils.units
module
schrodinger.utils.withnone
module
SCHRODINGER_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute)
SCHRODINGER_OPENMPI (schrodinger.utils.openmpi.EnvVar attribute)
SCHRODINGER_PYTHONPATH
,
[1]
SCHRODINGER_SCRIPTS
,
[1]
,
[2]
SCHRODINGER_UTILITIES (schrodinger.application.desmond.envir.CONST attribute)
schrodingerInstallation (schrodinger.job.server.ServerInfo attribute)
SchrodStruc (class in schrodinger.application.desmond.fep_struc)
score (schrodinger.application.jaguar.utils.LewisStructure attribute)
screen() (schrodinger.application.combinatorial_screen.combinatorial_screener.CombinatorialScreener method)
(schrodinger.application.phase.packages.mmp3dscreener.MMP3DScreener method)
(schrodinger.ui.dendrogram.DendrogramView method)
script_dir() (in module schrodinger.application.jaguar)
scrollBarWidgets() (schrodinger.ui.dendrogram.DendrogramView method)
ScrollHandDrag (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.DragMode attribute)
SD (schrodinger.infra.structure.FileFormat attribute)
SDF (schrodinger.livedesign.convert.Format attribute)
sdf_to_rdkit() (in module schrodinger.livedesign.convert)
SDReader (class in schrodinger.structure)
SDWriter (class in schrodinger.structure)
SDWriter.Options (class in schrodinger.structure)
Sea (class in schrodinger.utils.sea.sea)
sea_filter() (in module schrodinger.utils.sea.sea)
search() (schrodinger.structutils.analyze.AslLigandSearcher method)
search_and_scan() (schrodinger.application.desmond.torsion_related.BondRotator method)
SEARCH_PATHS (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument attribute)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument attribute)
SearchError
SearchForDataPointsWithin() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method)
SearchMap() (in module schrodinger.application.matsci.gsas.GSASIImath)
sec2HMS() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
second (schrodinger.application.desmond.packages.msys.Bond property)
SECONDARY_STRUCTURE (class in schrodinger.protein.buildpeptide)
secondary_structure (schrodinger.structure._Residue property)
(schrodinger.structure._StructureAtom property)
SecondaryStructure (class in schrodinger.application.desmond.packages.analysis)
SecondaryStructureData (class in schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data)
seedRandom() (schrodinger.application.matsci.uq_utils.BilinearHistogramData method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData method)
seek() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.structure.MaestroReader method)
segid (schrodinger.application.desmond.packages.msys.Chain property)
select() (schrodinger.application.combinatorial_diversity.diversity_selector.DiversitySelector method)
(schrodinger.application.desmond.packages.msys.System method)
select_atom() (schrodinger.application.desmond.cms.Cms method)
select_atom_comp() (schrodinger.application.desmond.cms.Cms method)
select_data() (in module schrodinger.application.desmond.arkdb)
select_dictionary() (in module schrodinger.application.phase.packages.mmp2d)
select_probes() (in module schrodinger.application.combinatorial_diversity.splitter_utils)
selectAddRows() (schrodinger.infra.table.Table method)
selectArr() (schrodinger.application.desmond.packages.msys.System method)
selectAtom() (schrodinger.application.desmond.packages.msys.Residue method)
selectChain() (schrodinger.application.desmond.packages.msys.System method)
selectCt() (schrodinger.application.desmond.packages.msys.System method)
selected_rows (schrodinger.test.project_mock.MockProjectTable property)
selected_st (schrodinger.trajectory.prody.ensemble.Ensemble property)
selectedItems() (schrodinger.ui.dendrogram.DendrogramScene method)
selectIds() (schrodinger.application.desmond.packages.msys.System method)
selectionArea() (schrodinger.ui.dendrogram.DendrogramScene method)
selectionChanged (schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramScene attribute)
selections() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
selectResidue() (schrodinger.application.desmond.packages.msys.Chain method)
selectRows() (schrodinger.infra.table.Table method)
SELF_ENERGY_ONLY (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute)
self_polarizability() (in module schrodinger.application.mopac.results_main)
selfReorganize (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute)
selftestlist (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIIspc)
semanticPredicate() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
SEMI_ISOTROPIC (schrodinger.application.desmond.constants.IsotropyPolicy attribute)
sender() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
senderSignalIndex() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
sendEvent() (schrodinger.ui.dendrogram.DendrogramScene method)
sense() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method)
sense_of_rotation() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method)
separate_complex() (in module schrodinger.application.livedesign.entry_types)
seq (in module schrodinger.application.desmond.packages.msys.molfile)
seq_align_match() (in module schrodinger.structutils.analyze)
SeqFile (class in schrodinger.application.desmond.packages.msys.molfile)
SeqFile.Reader (class in schrodinger.application.desmond.packages.msys.molfile)
SeqFormat (class in schrodinger.utils.fileutils)
serial_split() (in module schrodinger.application.macromodel.tools)
SerializationError
serialize() (schrodinger.application.desmond.picklejar.PickleJar static method)
(schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method)
serialize_bernoulli_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_compact() (in module schrodinger.application.phase.packages.conformer_storage)
serialize_complement_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_conformations() (in module schrodinger.utils.cgxutils)
serialize_csr_matrix() (in module schrodinger.application.matsci.mlearn.sklearn_json.csr)
serialize_decision_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_decision_tree_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_dummy_classifier() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_dummy_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_gaussian_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_gradient_boosting() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_gradient_boosting_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_label_binarizer() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_lasso_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_lda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_linear_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_logistic_regression() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_lossless() (in module schrodinger.application.phase.packages.conformer_storage)
serialize_mlp() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_mlp_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_model() (in module schrodinger.application.matsci.mlearn.sklearn_json)
serialize_multinomial_nb() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_params_random_state() (in module schrodinger.application.matsci.mlearn.sklearn_json.common)
serialize_pca() (in module schrodinger.application.matsci.mlearn.sklearn_json.decomposition)
serialize_perceptron() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_qda() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_random_forest() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_random_forest_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_ridge_regressor() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_svm() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
serialize_svr() (in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
serialize_tree() (in module schrodinger.application.matsci.mlearn.sklearn_json.classification)
(in module schrodinger.application.matsci.mlearn.sklearn_json.regression)
SerializeMAE() (in module schrodinger.application.desmond.packages.msys)
serializeNode() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
serializer (in module schrodinger.models.jsonable)
serializeToken() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
Series (class in schrodinger.application.desmond.enhsamp)
series() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
Server (class in schrodinger.application.licensing.flexlm)
SERVER (schrodinger.utils.postinstall.CustomConfigFiles attribute)
server_host() (schrodinger.application.licensing.flexlm.License method)
server_host_and_port() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
server_hostid() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
server_hostids() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
server_hostnames() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
server_hostport() (schrodinger.application.licensing.flexlm.License method)
server_log() (in module schrodinger.application.licensing.licadmin)
server_pathname() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
server_version() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
ServerError
ServerInfo (class in schrodinger.application.licensing.licadmin)
(class in schrodinger.job.server)
session (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableFile attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.Makefile attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
set() (schrodinger.infra.mmbitset.Bitset method)
(schrodinger.utils.preferences.Preferences method)
set_alpha() (schrodinger.ui.qt.label_cursor.LabelCursorAxes method)
SET_AS_REFERENCE (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
set_atom_elements() (in module schrodinger.application.scaffold_enumeration.atomlist)
set_atom_group() (schrodinger.application.desmond.cms.Cms method)
set_atom_group_from_asl() (schrodinger.application.desmond.cms.Cms method)
set_atom_velocity() (in module schrodinger.application.desmond.packages.topo)
set_boolean_flag() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
set_color() (schrodinger.application.desmond.torsion_related.TorsionPotential method)
set_conflict_handler() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
set_cts_property() (schrodinger.application.desmond.cms.Cms method)
set_default() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
set_defaults() (schrodinger.utils.compare.DiffCompareArgumentParser method)
(schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
set_description() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
set_dummy_atoms_as_attachment_points() (in module schrodinger.rdkit.rgroup)
set_encoded_restraints() (in module schrodinger.application.desmond.packages.restraint.utils)
set_expires() (schrodinger.application.licensing.licadmin.LicenseFeature method)
set_features() (in module schrodinger.utils.featureflags.featureflags)
set_file_logger() (in module schrodinger.application.licensing.flexlm)
set_freezing_atommass() (in module schrodinger.application.desmond.remd)
set_globals() (in module schrodinger.infra.mm)
set_hostid() (schrodinger.application.licensing.licadmin.LicenseFeature method)
set_hotregion() (in module schrodinger.application.desmond.r_group_asl)
set_ibrav_to_zero() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
set_id() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
set_lda_plus_u_flag() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
set_ligand_from() (schrodinger.application.desmond.torsion_related.TorsionPotential method)
set_ligand_to() (schrodinger.application.desmond.torsion_related.TorsionPotential method)
set_logger() (in module schrodinger.application.licensing.flexlm)
(in module schrodinger.application.matsci.qeschema.qeschema.utils)
(in module schrodinger.application.matsci.qexsd.qespresso.utils.logger)
set_long_opt_delimiter() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
set_macro_dict() (in module schrodinger.utils.sea.sea)
set_mmffld_option() (in module schrodinger.forcefield.common)
set_nactive_gids() (schrodinger.application.desmond.cms.Cms method)
set_nresamples() (schrodinger.application.desmond.bennett.CalcBAR method)
set_one_amass_line() (in module schrodinger.application.matsci.qeschema.qeschema.options)
set_original_index_property() (in module schrodinger.application.desmond.packages.topo)
set_output() (schrodinger.application.desmond.bennett.CalcBAR method)
set_parameter() (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter method)
set_params() (schrodinger.application.matsci.mlearn.base.BaseFeaturizer method)
set_parent() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
set_parser() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
set_path() (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter method)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter method)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter method)
set_pmode() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
set_preference() (in module schrodinger.utils.preferences)
set_process_default_values() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
set_range() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method)
(schrodinger.application.matsci.gsas.GSASIImath.fast_sa method)
(schrodinger.application.matsci.gsas.GSASIImath.log_sa method)
set_rbpotential() (schrodinger.application.desmond.torsion_related.TorsionPotential method)
set_restrain() (schrodinger.application.desmond.cms.Cms method)
set_seed() (schrodinger.application.desmond.bennett.CalcBAR method)
set_seqres() (in module schrodinger.protein.seqres)
set_server_refresh() (in module schrodinger.application.licensing.licadmin)
set_sgroups() (in module schrodinger.application.scaffold_enumeration.common)
set_sh_file_flags() (in module schrodinger.job.jobwriter)
set_short_opt_delimiter() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
set_significant_figures() (in module schrodinger.math.mathutils)
set_sort_index() (schrodinger.application.licensing.flexlm.Feature method)
set_starts() (schrodinger.application.licensing.licadmin.LicenseFeature method)
set_structure_soluble() (in module schrodinger.application.desmond.solubility_utils)
set_timeout() (in module schrodinger.test.pytest.faulthandler_setup)
set_title() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
set_tokens() (schrodinger.application.licensing.licadmin.LicenseFeature method)
set_usage() (schrodinger.utils.singledashoptionparser.SingleDashOptionParser method)
set_val() (schrodinger.application.desmond.simulation_block_test.BoxSize method)
(schrodinger.application.desmond.simulation_block_test.E_f method)
(schrodinger.application.desmond.simulation_block_test.E_k method)
(schrodinger.application.desmond.simulation_block_test.E_x method)
(schrodinger.application.desmond.simulation_block_test.Energy method)
(schrodinger.application.desmond.simulation_block_test.Job_Details method)
(schrodinger.application.desmond.simulation_block_test.PotentialEnergy method)
(schrodinger.application.desmond.simulation_block_test.Pressure method)
(schrodinger.application.desmond.simulation_block_test.T_0 method)
(schrodinger.application.desmond.simulation_block_test.Temperature method)
(schrodinger.application.desmond.simulation_block_test.Test method)
(schrodinger.application.desmond.simulation_block_test.V method)
set_value() (schrodinger.utils.sea.sea.Map method)
set_value_fast() (schrodinger.utils.sea.sea.Map method)
set_visible() (schrodinger.ui.qt.label_cursor.LabelCursor method)
(schrodinger.ui.qt.label_cursor.LabelCursorAxes method)
(schrodinger.ui.qt.label_cursor.MultiAxesLabelCursor method)
set_what_td_calculation() (in module schrodinger.application.matsci.qeschema.qeschema.options)
(in module schrodinger.application.matsci.qexsd.qespresso.options)
setAcceptDrops() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setAcceptedMouseButtons() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setAcceptHoverEvents() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setAcceptTouchEvents() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setAccessibleDescription() (schrodinger.ui.dendrogram.DendrogramView method)
setAccessibleName() (schrodinger.ui.dendrogram.DendrogramView method)
setActive() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setActivePanel() (schrodinger.ui.dendrogram.DendrogramScene method)
setActiveWindow() (schrodinger.ui.dendrogram.DendrogramScene method)
setAlignment() (schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.ui.dendrogram.DendrogramView method)
setAlpha() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
setArtBox() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setAtomBondTyping() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
setAttribute() (schrodinger.ui.dendrogram.DendrogramView method)
setAuthor() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setAutoFillBackground() (schrodinger.ui.dendrogram.DendrogramView method)
setBackgroundBrush() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
SetBackgroundParms() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
setBackgroundRole() (schrodinger.ui.dendrogram.DendrogramView method)
setBacktrackingLevel() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
setBaseSize() (schrodinger.ui.dendrogram.DendrogramView method)
setBeta() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
setBindingSiteAtoms() (schrodinger.structutils.sitealign.BindingSiteAligner method)
setBleedBox() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setBlendMode() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setBoundingRegionGranularity() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setBranchColor() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
setBranchWidth() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
setBspTreeDepth() (schrodinger.ui.dendrogram.DendrogramScene method)
setButtonMethods() (schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
setCacheMode() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setCatalogEntry() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setCell() (schrodinger.application.desmond.packages.msys.System method)
SetCellAtoms() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
setChannel() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
setCharPositionInLine() (schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
setCharStream() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
setChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
setChildIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
setColoring() (schrodinger.project.surface.ProjectSurface method)
(schrodinger.surface.Surface method)
setColorRGB() (schrodinger.structure._StructureAtom method)
setCompStr() (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)
setConfs() (schrodinger.trajectory.prody.ensemble.Ensemble method)
setContentsMargins() (schrodinger.ui.dendrogram.DendrogramView method)
setContextMenuPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
setCoordinates() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
setCoords() (schrodinger.trajectory.prody.ensemble.Ensemble method)
setCornerWidget() (schrodinger.ui.dendrogram.DendrogramView method)
setCovariance() (schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
setCreator() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setCropBox() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setCursor() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setDash() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setData() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
(schrodinger.application.matsci.hdfutils.HDFIO method)
(schrodinger.application.matsci.hdfutils.HDFProxyPickleIO method)
(schrodinger.livedesign.rgfile_parse.ForwardRGMolSupplier method)
(schrodinger.pipeline.pipeio.Grid method)
(schrodinger.pipeline.pipeio.PhaseDB method)
(schrodinger.pipeline.pipeio.Structures method)
(schrodinger.pipeline.pipeio.Text method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setDateFormatter() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setDebug() (schrodinger.infra.table.Table static method)
setDebugLevel() (schrodinger.job.launchparams.LaunchParameters method)
setDebugListener() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
setdefault() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
setDeleteAfterIncorporation() (schrodinger.job.launchparams.LaunchParameters method)
setdeleted() (in module schrodinger.Qt.PyQt6.sip)
setDescription() (schrodinger.structutils.color.ColorScheme method)
SetDiff (class in schrodinger.models.diffy)
setDisabled() (schrodinger.ui.dendrogram.DendrogramView method)
setDisplayAtomsASL() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
setDistance() (schrodinger.ui.dendrogram.DendrogramNode method)
setDragMode() (schrodinger.ui.dendrogram.DendrogramView method)
setEigens() (schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
setEnabled() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setEncrypt() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setExpandedRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method)
setFileName() (schrodinger.structutils.color.ColorScheme method)
setFillAlpha() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setFillColor() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setFillColorCMYK() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setFillColorRGB() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setFillGray() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setFillOverprint() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setFiltersChildEvents() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setFitFunction() (schrodinger.application.matsci.uq_utils.BilinearHistogramData method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData method)
setFixedHeight() (schrodinger.ui.dendrogram.DendrogramView method)
setFixedSize() (schrodinger.ui.dendrogram.DendrogramView method)
setFixedWidth() (schrodinger.ui.dendrogram.DendrogramView method)
setFlag() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setFlags() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setFocus() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
setFocusItem() (schrodinger.ui.dendrogram.DendrogramScene method)
setFocusOnTouch() (schrodinger.ui.dendrogram.DendrogramScene method)
setFocusPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
setFocusProxy() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setFont() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
setFontSize() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setForegroundBrush() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
setForegroundRole() (schrodinger.ui.dendrogram.DendrogramView method)
setFrameRect() (schrodinger.ui.dendrogram.DendrogramView method)
setFrameShadow() (schrodinger.ui.dendrogram.DendrogramView method)
setFrameShape() (schrodinger.ui.dendrogram.DendrogramView method)
setFrameSSData() (schrodinger.trajectory.trajectory_gui_dir.secondary_structure_data.SecondaryStructureData method)
setFrameStyle() (schrodinger.ui.dendrogram.DendrogramView method)
setGeometry() (schrodinger.ui.dendrogram.DendrogramView method)
setGidOffset() (schrodinger.application.desmond.packages.staf.Positer method)
setglobalprecision() (in module schrodinger.application.desmond.packages.destro)
setGraphicsEffect() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setGridSize() (schrodinger.infra.growthspace.GrowthSpaceGenerator method)
setGroup() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setHbondParameters() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setHidden() (schrodinger.ui.dendrogram.DendrogramView method)
setHorizontalScrollBar() (schrodinger.ui.dendrogram.DendrogramView method)
setHorizontalScrollBarPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
setHostname() (schrodinger.job.launchparams.LaunchParameters method)
setHypoID() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
setImage() (schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
setIncludeAcceptor() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIncludeAromatic() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIncludeBackbone() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIncludeCharged() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIncludeContact() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIncludeDonor() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIncludeHydrophobic() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIncludePolar() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIncludeSidechain() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setIndex() (schrodinger.structure.StructureReader method)
setInput() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
setInputMethodHints() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setInputStream() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
setInteractionCutoff() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setInteractive() (schrodinger.ui.dendrogram.DendrogramView method)
setItemIndexMethod() (schrodinger.ui.dendrogram.DendrogramScene method)
setJobname() (schrodinger.job.launchparams.LaunchParameters method)
setKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method)
setKeywords() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setLabel() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramNode method)
setLastRewriteTokenIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
setLaunchDirectory() (schrodinger.job.launchparams.LaunchParameters method)
setLayout() (schrodinger.ui.dendrogram.DendrogramView method)
setLayoutDirection() (schrodinger.ui.dendrogram.DendrogramView method)
setLeaf() (schrodinger.ui.dendrogram.DendrogramNode method)
setLigandCleanupOptions() (schrodinger.structutils.minimize.Minimizer method)
setLine() (schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
setLineCap() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setLineJoin() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setLineWidth() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.ui.dendrogram.DendrogramView method)
setLinkage() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method)
(schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method)
setLocale() (schrodinger.ui.dendrogram.DendrogramView method)
setLogger() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method)
setLongName() (schrodinger.structutils.color.ColorScheme method)
setMaestroProjectDisposition() (schrodinger.job.launchparams.LaunchParameters method)
setMaestroProjectName() (schrodinger.job.launchparams.LaunchParameters method)
setMaestroViewname() (schrodinger.job.launchparams.LaunchParameters method)
SetMagnetic() (in module schrodinger.application.matsci.gsas.GSASIIspc)
setMask() (schrodinger.ui.dendrogram.DendrogramView method)
setMaximumHeight() (schrodinger.ui.dendrogram.DendrogramView method)
setMaximumSize() (schrodinger.ui.dendrogram.DendrogramView method)
setMaximumWidth() (schrodinger.ui.dendrogram.DendrogramView method)
setMaxRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method)
setMetric() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
setMidLineWidth() (schrodinger.ui.dendrogram.DendrogramView method)
setMinimumHeight() (schrodinger.ui.dendrogram.DendrogramView method)
setMinimumRenderSize() (schrodinger.ui.dendrogram.DendrogramScene method)
setMinimumSize() (schrodinger.ui.dendrogram.DendrogramView method)
setMinimumWidth() (schrodinger.ui.dendrogram.DendrogramView method)
setMinRadius() (schrodinger.infra.growthspace.GrowthSpaceGenerator method)
setMiterLimit() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
SetMolCent() (in module schrodinger.application.matsci.gsas.GSASIImath)
setMouseTracking() (schrodinger.ui.dendrogram.DendrogramView method)
setNumberOfProcessorsManyNodes() (schrodinger.job.launchparams.LaunchParameters method)
setNumberOfProcessorsOneNode() (schrodinger.job.launchparams.LaunchParameters method)
setNumberOfSubjobs() (schrodinger.job.launchparams.LaunchParameters method)
setObjectName() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
setOneAmassLine() (in module schrodinger.application.matsci.qexsd.qespresso.options)
setOpacity() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setOPLSDir() (schrodinger.job.launchparams.LaunchParameters method)
setOptimizationFlag() (schrodinger.ui.dendrogram.DendrogramView method)
setOptimizationFlags() (schrodinger.ui.dendrogram.DendrogramView method)
setOption() (schrodinger.rdkit.molio.MolWriter method)
(schrodinger.structure.MaestroWriter method)
(schrodinger.structure.PDBWriter method)
(schrodinger.structure.SDWriter method)
(schrodinger.structure.SmilesCsvWriter method)
(schrodinger.structure.SmilesWriter method)
(schrodinger.structure.StructureWriter method)
setOptions() (schrodinger.application.phase.packages.ligand_aligner.LigandAligner method)
(schrodinger.structutils.minimize.Minimizer method)
setOriginalData() (schrodinger.application.matsci.uq_utils.BilinearHistogramData method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData method)
setOriginalName() (schrodinger.structutils.color.ColorScheme method)
setOutlineNames0() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setOverprintMask() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setOverride() (schrodinger.application.desmond.packages.msys.TermTable method)
setPageCallBack() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setPageCompression() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setPageDuration() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setPageRotation() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setPageSize() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setPageTransition() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setPalette() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
setPanelModality() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setParent() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
setParentItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setPeakparms() (in module schrodinger.application.matsci.gsas.GSASIImath)
setPicture() (schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
setPos() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setPositions() (schrodinger.application.desmond.packages.msys.System method)
SetPowderInstParms() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
setPrecision() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
SetProcessPropertyLists() (schrodinger.rdkit.molio.GzippedSDMolSupplier method)
setProducer() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setProperty() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
SetPWDRscan() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
setReceptorStructure() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
setRefCtTitle() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
setRenderHint() (schrodinger.ui.dendrogram.DendrogramView method)
setRenderHints() (schrodinger.ui.dendrogram.DendrogramView method)
setResidues() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method)
(schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method)
setResizeAnchor() (schrodinger.ui.dendrogram.DendrogramView method)
setRotation() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setRubberBandSelectionMode() (schrodinger.ui.dendrogram.DendrogramView method)
setRules() (schrodinger.structutils.color.ColorScheme method)
setSampleSize() (schrodinger.application.matsci.uq_utils.BilinearHistogramData method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData method)
setSaveAllJobOutput() (schrodinger.job.launchparams.LaunchParameters method)
setSaveAllSubJobOutput() (schrodinger.job.launchparams.LaunchParameters method)
setScale() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setScene() (schrodinger.ui.dendrogram.DendrogramView method)
setSceneRect() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
setScreen() (schrodinger.ui.dendrogram.DendrogramView method)
setSelected() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setSelectionArea() (schrodinger.ui.dendrogram.DendrogramScene method)
setSelfMethods() (schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
SetSerializer (class in schrodinger.models.jsonable)
setShortcutAutoRepeat() (schrodinger.ui.dendrogram.DendrogramView method)
setShortcutEnabled() (schrodinger.ui.dendrogram.DendrogramView method)
setShortName() (schrodinger.structutils.color.ColorScheme method)
setSiteMatches() (schrodinger.structutils.sitealign.BindingSiteAligner method)
setSize() (schrodinger.infra.mmim.MMIMArgList method)
(schrodinger.infra.mmkv.MMKVArgList method)
setSizeAdjustPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
setSizeIncrement() (schrodinger.ui.dendrogram.DendrogramView method)
setSizePolicy() (schrodinger.ui.dendrogram.DendrogramView method)
setSoluteCoords() (schrodinger.trajectory.prody.ensemble.Ensemble method)
SetStackingClay() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
SetStackingSF() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
SetStackingTrans() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
setStatusTip() (schrodinger.ui.dendrogram.DendrogramView method)
setStickyFocus() (schrodinger.ui.dendrogram.DendrogramScene method)
setStrokeAlpha() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setStrokeColor() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setStrokeColorCMYK() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setStrokeColorRGB() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setStrokeGray() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setStrokeOverprint() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setStructure() (schrodinger.structutils.minimize.Minimizer method)
(schrodinger.test.project_mock.MockProjectRow method)
setStructureFile() (schrodinger.application.qsite.input.QSiteInput method)
setStructureOutput() (schrodinger.pipeline.input.LinearWriter method)
(schrodinger.pipeline.input.Writer method)
setStyle() (schrodinger.structure._StructureBond method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
setStyleSheet() (schrodinger.ui.dendrogram.DendrogramView method)
setSubject() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setTabletTracking() (schrodinger.ui.dendrogram.DendrogramView method)
setTargetFunction() (schrodinger.application.matsci.uq_utils.BilinearHistogramData method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData method)
setTemplate() (schrodinger.application.prime.wrapper.BasePrimeAlignment method)
setTemplateResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method)
setText() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
Setting (class in schrodinger.application.jaguar.keywordDB)
SETTING_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
SETTINGS_DICT (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData attribute)
setTitle() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.trajectory.prody.mode.Vector method)
(schrodinger.trajectory.prody.nma.NMA method)
(schrodinger.trajectory.prody.pca.EDA method)
(schrodinger.trajectory.prody.pca.PCA method)
setTokenBoundaries() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
setTokenIndex() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
setTokenSource() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
setTokenStartIndex() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
setTokenStopIndex() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
setTokenStream() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
setTokenTypeChannel() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
setToMinStep() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method)
setToolTip() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setToolTipDuration() (schrodinger.ui.dendrogram.DendrogramView method)
setTPP() (schrodinger.job.launchparams.LaunchParameters method)
settracemask() (in module schrodinger.Qt.PyQt6.sip)
setTransform() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setTransformationAnchor() (schrodinger.ui.dendrogram.DendrogramView method)
setTransformations() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setTransformOriginPoint() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setTransparency() (schrodinger.project.surface.ProjectSurface method)
(schrodinger.surface.Surface method)
setTreeAdaptor() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
setTreeNodeStream() (schrodinger.application.desmond.antlr3.tree.TreeParser method)
setTrimBox() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setType() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
(schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tokens.CommonToken method)
(schrodinger.application.desmond.antlr3.tokens.Token method)
(schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method)
(schrodinger.application.desmond.antlr3.tree.TreeAdaptor method)
(schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method)
setUniqueNavigationNodes() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
setUnknownTokenBoundaries() (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
setup() (in module schrodinger.infra.epydoc_to_sphinx)
setUp() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
setup() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
setup_atom() (in module schrodinger.trajectory.prody.writenmd)
setup_mol() (in module schrodinger.livedesign.preprocessor)
setup_protein() (schrodinger.protein.analysis.Report method)
setUpClass() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase class method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase class method)
setUpdatesEnabled() (schrodinger.ui.dendrogram.DendrogramView method)
SetupPDFEval() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
setupUi() (schrodinger.application.bioluminate.propfilter_ui.Ui_Form method)
(schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form method)
(schrodinger.application.desmond.desmond_advanced_tab_ui.Ui_Dialog method)
(schrodinger.application.desmond.input_group_ui.Ui_Form method)
(schrodinger.application.desmond.rest_tab_ui.Ui_Form method)
(schrodinger.application.jaguar.update_pka_settings_ui.Ui_UpdatePKASettingsDlg method)
(schrodinger.application.job_monitor.diagnostics_dialog_ui.Ui_Form method)
(schrodinger.application.job_monitor.file_browser_ui.Ui_Form method)
(schrodinger.application.livedesign.login2_ui.Ui_Form method)
(schrodinger.application.livedesign.login_ui.Ui_Dialog method)
(schrodinger.application.livedesign.pose_name_panel_ui.Ui_Form method)
(schrodinger.application.livedesign.save_mapping_dialog_ui.Ui_Form method)
(schrodinger.application.livedesign.selection_pop_up_ui.Ui_Form method)
(schrodinger.application.msv.gui.binding_site_aln_dialog_ui.Ui_Form method)
(schrodinger.application.msv.gui.homology_modeling.homology_modeling_step_ui.Ui_Form method)
(schrodinger.application.msv.gui.multiple_seq_aln_dialog_ui.Ui_Form method)
(schrodinger.application.msv.gui.pairwise_seq_aln_dialog_ui.Ui_Form method)
(schrodinger.application.msv.gui.toolbar_ui.Ui_Form method)
(schrodinger.application.prime.gui.ui.environment_options_ui.Ui_Form method)
(schrodinger.infra.exception_handler_dir.exception_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.traj_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.export_movie_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.export_structures_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.shortcut_ui.Ui_Form method)
(schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui.Ui_Dialog method)
(schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui.Ui_snapshot_panel method)
(schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui.Ui_trajectory_form method)
(schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog method)
(schrodinger.ui.ligfilter_ui.Ui_Form method)
(schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui.Ui_Dialog method)
(schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui.Ui_Dialog method)
(schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui.Ui_Dialog method)
(schrodinger.ui.qt.appframework2.debug_gui_ui.Ui_Form method)
(schrodinger.ui.qt.borderless_popup_ui.Ui_Frame method)
(schrodinger.ui.qt.config_dialog_open_mp_ui.Ui_Form method)
(schrodinger.ui.qt.config_dialog_queue_ui.Ui_Form method)
(schrodinger.ui.qt.entryselector_ui.Ui_Dialog method)
(schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui.Ui_Form method)
(schrodinger.ui.qt.filter_dialog_ui.Ui_Dialog method)
(schrodinger.ui.qt.pdb_dialog_ui.Ui_PdbDialog method)
(schrodinger.ui.qt.presets.manage_presets_dialog_ui.Ui_Form method)
(schrodinger.ui.qt.presets.save_presets_dialog_ui.Ui_Form method)
(schrodinger.ui.qt.protein_health_viewer_ui.Ui_Form method)
(schrodinger.ui.qt.rename_favorite_dialog_ui.Ui_Dialog method)
(schrodinger.ui.qt.select_residues_dialog_ui.Ui_Dialog method)
(schrodinger.ui.qt.tasks.config_dialog_ui.Ui_Form method)
(schrodinger.ui.qt.tasks.config_info_ui.Ui_Form method)
setupViewport() (schrodinger.ui.dendrogram.DendrogramView method)
setVelocities() (schrodinger.application.desmond.packages.msys.System method)
setVerticalScrollBar() (schrodinger.ui.dendrogram.DendrogramView method)
setVerticalScrollBarPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
setViewerPreference() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
setViewport() (schrodinger.ui.dendrogram.DendrogramView method)
setViewportMargins() (schrodinger.ui.dendrogram.DendrogramView method)
setViewportUpdateMode() (schrodinger.ui.dendrogram.DendrogramView method)
setVisible() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
setWeight() (schrodinger.trajectory.prody.ensemble.Ensemble method)
setWhatsThis() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowFilePath() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowFlag() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowFlags() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowIcon() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowIconText() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowModality() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowModified() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowOpacity() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowRole() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowState() (schrodinger.ui.dendrogram.DendrogramView method)
setWindowTitle() (schrodinger.ui.dendrogram.DendrogramView method)
setWorkingDirectory() (schrodinger.application.prime.wrapper.BasePrimeAlignment method)
(schrodinger.application.prime.wrapper.PrimeTemplate method)
setX() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setXBiasFunction() (schrodinger.application.matsci.uq_utils.BilinearHistogramData method)
(schrodinger.application.matsci.uq_utils.BootstrapNoiseHistogramData method)
(schrodinger.application.matsci.uq_utils.HyperbolaHistogramData method)
setXYZ() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
setY() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
setZValue() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
sf() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
sfloat() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
sg_t_den (schrodinger.application.matsci.cctbx.rot_mx.tr_vec attribute)
sgequiv_2002_orthorhombic (in module schrodinger.application.matsci.gsas.GSASIIspc)
SGErrors() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SGpolar() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SGPrint() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SGProd() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SGPtGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SGROUP_DATA (schrodinger.livedesign.molhash.HashLayer attribute)
shade() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
Shadow_Mask (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.StyleMask attribute)
shape() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
shape_based (schrodinger.application.phase.packages.ligand_aligner.AlignMethod attribute)
Shape_Mask (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.StyleMask attribute)
ShapeFileReader (class in schrodinger.application.phase.packages.shape_binary_utils)
ShapeFileWriter (class in schrodinger.application.phase.packages.shape_binary_utils)
shared_tags (schrodinger.analysis.transformations.TransformsRepository property)
sharedPainter() (schrodinger.ui.dendrogram.DendrogramView method)
SharingViolationError
shell() (in module schrodinger.job.remote_command)
short() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.LicenseLine method)
(schrodinger.application.licensing.flexlm.Package method)
(schrodinger.application.licensing.flexlm.Server method)
(schrodinger.application.licensing.flexlm.UseServer method)
(schrodinger.application.licensing.flexlm.Vendor method)
SHORT_FINGERPRINT_TYPES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI attribute)
short_hash (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
(schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
SHORT_HERMANN_MAUGUIN_SYMBOL (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
SHORT_NAME_TAG (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
shortDescription() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
shorten_name() (in module schrodinger.application.desmond.fep_edge_data)
shorthost() (in module schrodinger.application.licensing.flexlm)
(in module schrodinger.application.licensing.licadmin)
shouldRestoreVisibility() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
shouldUpdateVisibility() (schrodinger.trajectory.trajectory_gui_dir.display_settings_manager.DisplaySettingsManager method)
show() (in module schrodinger.ui.qt.appframework2.appmethods)
(schrodinger.project.surface.ProjectSurface method)
(schrodinger.surface.Surface method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
show_plot() (schrodinger.application.matsci.xrd.XRDCalculator method)
showEvent() (schrodinger.ui.dendrogram.DendrogramView method)
showFullScreen() (schrodinger.ui.dendrogram.DendrogramView method)
showFullScreen0() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
showMaximized() (schrodinger.ui.dendrogram.DendrogramView method)
showMinimized() (schrodinger.ui.dendrogram.DendrogramView method)
showNormal() (schrodinger.ui.dendrogram.DendrogramView method)
showOutline() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
showPage() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
showPlotWindow() (schrodinger.analysis.enrichment.plotter.PercentScreenPlotter method)
(schrodinger.analysis.enrichment.plotter.Plotter method)
showtype() (in module schrodinger.application.desmond.enhanced_sampling.FcnTypes)
(in module schrodinger.application.desmond.enhsamp)
shuffle_ct_atoms() (in module schrodinger.test.build_test_structures)
shuffle_merge() (in module schrodinger.structutils.shuffle)
shuffle_structs() (in module schrodinger.structutils.shuffle)
ShuffleException
SIDECHAIN (schrodinger.application.desmond.constants.ConfRestraintType attribute)
sidechain_dihedral_atomnames (in module schrodinger.protein.analysis_params)
sidechain_dihedrals (in module schrodinger.protein.analysis_params)
SIDECHAIN_INTERACTION (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
SIDECHAIN_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute)
sig_fig_round() (in module schrodinger.math.mathutils)
Sigmoid (class in schrodinger.math.multi_parameter_optimization)
signalsBlocked() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
signature() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.Package method)
signedExpComp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
sim2dist() (in module schrodinger.application.bioluminate.epitope.utils.esc_utils)
(schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow method)
simBuser() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simCosine() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simDice() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simDixon() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simEuclidean() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simHamann() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simHamming() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
SIMILARITY_METRICS (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity attribute)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI attribute)
SimilarityEndpoint (class in schrodinger.infra.licensing)
simKulczynski() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simMatching() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simMcConnaughey() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simMinMax() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simModifiedTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simPatternDifference() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simPearson() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simPetke() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
SimpleSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
simplify() (in module schrodinger.test.memtest)
simRogersTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simShape() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simSimpson() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simSize() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simSoergel() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simTversky() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
SimulatedAnnealing (class in schrodinger.application.canvas.r_group_dee)
simulateTreeConstruction() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method)
SIMULATION_BOX (schrodinger.application.desmond.constants.ENERGY_GROUPS attribute)
SIMULATION_PROTOCOL (class in schrodinger.application.desmond.constants)
simVariance() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
simYule() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method)
(schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method)
sind() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIImath)
SINGLE (schrodinger.energy.ANIPrecision attribute)
Single (schrodinger.structure.BondType attribute)
SINGLE (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.Loop attribute)
SingleDashOption (class in schrodinger.utils.singledashoptionparser)
SingleDashOptionParser (class in schrodinger.utils.singledashoptionparser)
SingleFilter (class in schrodinger.structutils.filter)
SinglePropFilter (class in schrodinger.structutils.filter)
SingleSmartsFilter (class in schrodinger.structutils.filter)
SingularShapeFileReader (class in schrodinger.application.phase.packages.shape_binary_utils)
Site (class in schrodinger.application.desmond.cms)
site() (schrodinger.application.desmond.cms.Cms method)
site_matches (schrodinger.structutils.sitealign.BindingSiteAligner attribute)
SiteMatchLookup (class in schrodinger.structutils.sitealign)
size (schrodinger.test.stu.common.FileInfo attribute)
size() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.IntStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.packages.msys.Graph method)
(schrodinger.application.pathfinder.reaction.ReagentClass method)
(schrodinger.infra.mmbitset.Bitset method)
(schrodinger.ui.dendrogram.DendrogramView method)
sizeAdjustPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
sizeHint() (schrodinger.ui.dendrogram.DendrogramView method)
sizeIncrement() (schrodinger.ui.dendrogram.DendrogramView method)
sizePolicy() (schrodinger.ui.dendrogram.DendrogramView method)
skew() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
skip() (schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.packages.msys.molfile.FrameIter method)
skip_funcnames (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer attribute)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer attribute)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer attribute)
skip_if() (in module schrodinger.infra.util)
SKIP_LICENSE_TAG (in module schrodinger.test.stu.constants)
skip_m1() (in module schrodinger.test.test_markers)
skip_rule() (in module schrodinger.test.hypothesis.utils)
skipinitialspace (schrodinger.application.canvas.utils.chm_bluebird attribute)
(schrodinger.application.canvas.utils.chm_excel attribute)
skipOffTokenChannels() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
skipOffTokenChannelsReverse() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
skipTest() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
SLAB_XY (schrodinger.application.matsci.msconst.DIMENSIONALITY attribute)
slice_pairs() (in module schrodinger.test.hypothesis.strategies.indices)
slugify() (in module schrodinger.utils.fileutils)
SMALL_MOLECULE (schrodinger.application.desmond.constants.FEP_TYPES attribute)
SMARTS (schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
smarts() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
SMARTS_METHOD (class in schrodinger.application.matsci.msconst)
SmartsCriterion (class in schrodinger.utils.ligfilter)
SmartsDirector (class in schrodinger.application.desmond.packages.analysis)
SmartsFilter (class in schrodinger.structutils.filter)
SmartsPattern (class in schrodinger.application.desmond.packages.msys)
SmartViewportUpdate (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.ViewportUpdateMode attribute)
SmearAbeles() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
SMILES (schrodinger.livedesign.convert.Format attribute)
(schrodinger.rdkit_extensions.Format attribute)
smiles() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
smiles_to_fingerprint() (in module schrodinger.application.combinatorial_screen.fingerprint_utils)
smiles_to_fingerprints() (in module schrodinger.application.combinatorial_screen.fingerprint_utils)
SmilesCsvReader (class in schrodinger.structure)
SmilesCsvWriter (class in schrodinger.structure)
SmilesGenerator (class in schrodinger.structutils.smiles)
SmilesReader (class in schrodinger.structure)
SmilesStructure (class in schrodinger.structure)
SmilesWriter (class in schrodinger.structure)
SmiMergeHandler (class in schrodinger.rdkit.molio)
smoothColors() (schrodinger.project.surface.ProjectSurface method)
(schrodinger.surface.Surface method)
snap_core (schrodinger.application.phase.packages.ligand_aligner.AlignMethod attribute)
SNAPSHOT_FRAMES (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportFrameOption attribute)
SNAPSHOT_VIEWER (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportMode attribute)
sol_charge (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_forward (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_forward_dg (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_end_time_ns (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_ensemble (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_ff (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_rest_exchanges (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_result (schrodinger.application.desmond.fep_edge_data.FEPTorsions property)
sol_salt_info (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_salt_molecules (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_sid_snapshot_times_ps (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_sim_time (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_start_time_ns (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_temperature (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_timestep_interval (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_timestep_list (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_total_atoms (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_total_replicas (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sol_total_waters (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
solid (schrodinger.project.surface.ProjectSurface.Style attribute)
(schrodinger.surface.Style attribute)
(schrodinger.surface.Surface.Style attribute)
SOLUBILITY (schrodinger.application.desmond.constants.FEP_TYPES attribute)
solubility_dg (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
SolubilityFEPEdgeData (class in schrodinger.application.desmond.fep_edge_data)
solute_st (schrodinger.trajectory.prody.ensemble.Ensemble property)
SOLVATION (schrodinger.application.desmond.constants.FepLegTypes attribute)
solvation_charge (schrodinger.structure._StructureAtom property)
SOLVENT (class in schrodinger.application.jaguar.csrch_input_constants)
Solvent (class in schrodinger.energy)
SOLVENT (schrodinger.application.desmond.constants.FepLegTypes attribute)
solvent_fullsystem_ct (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
SOLVENT_HOTREGION (schrodinger.application.desmond.constants.REST_PROPERTIES attribute)
SolventAccessibleSurfaceArea (class in schrodinger.application.desmond.packages.analysis)
SolventAccessibleSurfaceAreaByResidue (class in schrodinger.application.desmond.packages.analysis)
sort() (schrodinger.application.desmond.cms.ModelRestrainList method)
(schrodinger.application.licensing.flexlm.License method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method)
(schrodinger.infra.util.OneIndexedList method)
(schrodinger.models.json.AttributableType method)
(schrodinger.ui.qt.appframework2.validation.ValidationResults method)
(schrodinger.utils.sea.sea.List method)
sort_index() (schrodinger.application.licensing.flexlm.Feature method)
sort_key() (schrodinger.structutils.analyze.Ligand method)
sort_order() (in module schrodinger.ui.qt.appframework2.appmethods)
sort_with_none() (in module schrodinger.utils.withnone)
sortArray() (in module schrodinger.application.matsci.gsas.GSASIImath)
sorted() (schrodinger.application.desmond.packages.msys.System method)
sorted_hypo_structures() (in module schrodinger.application.phase.hypothesis)
sorted_with_none() (in module schrodinger.utils.withnone)
SortedMolWriter (class in schrodinger.rdkit.sorted_molwriter)
sortHKLd() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
sortRows() (schrodinger.infra.table.Table method)
Source (class in schrodinger.application.desmond.packages.traj)
source() (schrodinger.application.desmond.packages.traj.Frame method)
source_color (schrodinger.project.surface.ProjectSurface.ColorBy attribute)
(schrodinger.surface.ColorBy attribute)
(schrodinger.surface.Surface.ColorBy attribute)
source_index (schrodinger.structutils.rgroup_enumerate.RGroup attribute)
sp3AtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
space_group_full_name (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
SPACE_GROUP_ID (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
space_group_id (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
SPACE_GROUP_SETTING (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
space_group_short_name (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
SpaceGroup (class in schrodinger.application.matsci.nano.space_groups)
SpaceGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SpaceGroupNumber() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SpaceGroups (class in schrodinger.application.matsci.nano.space_groups)
SpatialHash (class in schrodinger.application.desmond.packages.msys)
SPC (schrodinger.application.desmond.constants.WATER_MODELS attribute)
SPCE (schrodinger.application.desmond.constants.WATER_MODELS attribute)
SpcGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc)
Spec (class in schrodinger.application.ligprep.ionizer)
SPEC_TEMPLACE_MAP (schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter attribute)
SPEC_TEMPLATE_MAP (schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter attribute)
specialStateTransition() (schrodinger.application.desmond.antlr3.dfa.DFA method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24 method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25 method)
specs (schrodinger.application.prime.wrapper.ConsensusConfig attribute)
(schrodinger.application.prime.wrapper.PrimeConfig attribute)
SpectrumDocument (class in schrodinger.application.matsci.qexsd.qespresso.documents)
spg2origins (in module schrodinger.application.matsci.gsas.GSASIIspc)
spg_setting (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
spgbyNum (in module schrodinger.application.matsci.gsas.GSASIIspc)
spglist (in module schrodinger.application.matsci.gsas.GSASIIspc)
sphere_overlap_volume() (in module schrodinger.structutils.interactions.steric_clash)
spin_splitting_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
SpinSpinCoupling (class in schrodinger.application.jaguar.results)
split() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
split_and_shuffle() (in module schrodinger.structutils.shuffle)
split_ct() (in module schrodinger.application.desmond.remd)
split_list() (in module schrodinger.utils.scollections)
split_outfile() (in module schrodinger.application.mopac.results_main)
splitext() (in module schrodinger.utils.fileutils)
splitFingerprints() (schrodinger.application.combinatorial_diversity.diversity_splitter.DiversitySplitter method)
splitlines() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
splitSSsym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
squared_centroid_distance() (in module schrodinger.structutils.interactions.pi)
SRU (class in schrodinger.application.scaffold_enumeration.cxsmiles)
SSChargeFlip() (in module schrodinger.application.matsci.gsas.GSASIImath)
SSChoice() (in module schrodinger.application.matsci.gsas.GSASIIspc)
sse_limits_lambda0 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
sse_limits_lambda1 (schrodinger.application.desmond.fep_edge_data.AbFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.FEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
SSGModCheck() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SSGPrint() (in module schrodinger.application.matsci.gsas.GSASIIspc)
ssh_check() (in module schrodinger.job.host_check)
SSLatt2text() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SSMT2text() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SSpaceGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc)
SSpcGroup() (in module schrodinger.application.matsci.gsas.GSASIIspc)
st (schrodinger.application.prime.wrapper.PrimeTemplate property)
(schrodinger.structutils.analyze.Ligand property)
st_matches_criteria() (in module schrodinger.utils.ligfilter)
stackBefore() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
StackSim() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
stackUnder() (schrodinger.ui.dendrogram.DendrogramView method)
stage (schrodinger.application.desmond.multisim.parser.Msj property)
STANDARD_BACKGROUND (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
STANDARD_BORDER (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
STANDARD_BUTTON_BACKGROUND (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
STANDARD_BUTTON_BORDER_DISABLED (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
STANDARD_BUTTON_BORDER_ENABLED (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
STANDARD_BUTTON_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
standard_nuclear_orientation() (in module schrodinger.structutils.standard_nuclear_orientation)
standard_option_list (schrodinger.utils.singledashoptionparser.SingleDashOptionParser attribute)
STANDARD_PRESSED_BUTTON_BACKGROUND_COLOR (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
STANDARD_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
StandardizeSpcName() (in module schrodinger.application.matsci.gsas.GSASIIspc)
start() (in module schrodinger.ui.qt.appframework2.appmethods)
(in module schrodinger.ui.qt.appframework2.debugcore)
(schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
(schrodinger.test.decorate_fflag.disable_feature_flag method)
(schrodinger.test.decorate_fflag.enable_feature_flag method)
(schrodinger.test.fixtures.safe_patch_os_environ method)
start_str() (schrodinger.application.licensing.flexlm.Feature method)
start_time (schrodinger.utils.timeit.TimeIt attribute)
Starter (class in schrodinger.application.desmond.starter.starter)
starting_conformation (schrodinger.application.desmond.fep_edge_data.FEPTorsions property)
startswith() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
startTimer() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
stat_info (class in schrodinger.application.licensing.licadmin)
STATE_ATTRIBUTES (schrodinger.application.desmond.rl_helper.NumberedCanvas attribute)
STATE_PENALTY (schrodinger.application.desmond.constants.CorrectionTerm attribute)
STATE_RANGE (schrodinger.application.desmond.rl_helper.NumberedCanvas attribute)
static() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
staticMetaObject (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
(schrodinger.ui.dendrogram.DendrogramScene attribute)
(schrodinger.ui.dendrogram.DendrogramView attribute)
stats() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
Status (class in schrodinger.application.licensing.licadmin)
statusOk (schrodinger.application.mopac.results_main.MopacResultsMain property)
statusTip() (schrodinger.ui.dendrogram.DendrogramView method)
staying_atom (schrodinger.structutils.rgroup_enumerate.RGroup attribute)
STD (schrodinger.application.jaguar.csrch_input_constants.ACC_LEVEL attribute)
std() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
StdoutDebugViewer (class in schrodinger.ui.qt.appframework2.debugcore)
step_size (schrodinger.application.jaguar.scan.Scan property)
StepAction (class in schrodinger.application.msv.gui.homology_modeling.constants)
steps (schrodinger.application.jaguar.scan.Scan property)
StepState (in module schrodinger.application.msv.gui.homology_modeling.constants)
stereo (schrodinger.structure.SDWriter.Options attribute)
STEREO_INSENSITIVE_LAYERS (schrodinger.livedesign.molhash.HashScheme attribute)
StereoChemistry (class in schrodinger.adapter)
stereospecific (schrodinger.rdkit.substructure.QueryOptions attribute)
stickyFocus() (schrodinger.ui.dendrogram.DendrogramScene method)
StkFile (class in schrodinger.application.desmond.packages.msys.molfile)
StkFile.Reader (class in schrodinger.application.desmond.packages.msys.molfile)
stop() (in module schrodinger.ui.qt.appframework2.debugcore)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
(schrodinger.test.decorate_fflag.disable_feature_flag method)
(schrodinger.test.decorate_fflag.enable_feature_flag method)
(schrodinger.test.fixtures.safe_patch_os_environ method)
STOP_RXN_FAIL (schrodinger.application.jaguar.constants.FatalErrors attribute)
STORE_ACTIONS (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
store_option_strings() (schrodinger.utils.singledashoptionparser.DelegatingIndentedHelpFormatter method)
STR (schrodinger.application.combinatorial_diversity.diversity_fingerprinter.PropertyType attribute)
str2hexid() (in module schrodinger.application.desmond.util)
str2list() (in module schrodinger.test.stu.common)
str2strlist() (in module schrodinger.test.stu.common)
strain (schrodinger.application.desmond.fep_edge_data.FEPTorsions property)
STRAND (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute)
StrEnum (class in schrodinger.surface)
strerror (schrodinger.utils.fileutils.SharingViolationError attribute)
STRETCH_FBHW (schrodinger.application.desmond.constants.RestrainTypes attribute)
String (class in schrodinger.application.desmond.enhsamp)
string (schrodinger.application.desmond.packages.msys.InChI property)
string() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.LicenseLine method)
(schrodinger.application.licensing.flexlm.Package method)
(schrodinger.application.licensing.flexlm.Server method)
(schrodinger.application.licensing.flexlm.UseServer method)
(schrodinger.application.licensing.flexlm.Vendor method)
(schrodinger.application.matsci.cctbx.rot_mx.parse_string method)
string2measurement() (in module schrodinger.application.desmond.measurement)
stringio_handler() (in module schrodinger.test)
StringOpsProd() (in module schrodinger.application.matsci.gsas.GSASIIspc)
StringStream (in module schrodinger.application.desmond.antlr3.streams)
stringWidth() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
strip() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
STRIP_AND_GROUPS_ON_SINGLE_ATOM (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
strip_atom_map_labels() (in module schrodinger.livedesign.molhash)
strip_extension() (in module schrodinger.utils.fileutils)
strip_lines() (in module schrodinger.application.jaguar.check_headers)
strip_r() (in module schrodinger.application.canvas.utils)
STRIP_SALTS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
strip_salts() (in module schrodinger.livedesign.preprocessor)
STRIP_STEREO_ABSOLUTE_GROUP (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
strip_stereo_and() (in module schrodinger.livedesign.preprocessor)
stripBrackets() (schrodinger.application.dendrogram.core_class.Utilities static method)
Struc (class in schrodinger.application.desmond.fep_struc)
Struct (class in schrodinger.application.desmond.packages.viparr1.viparr.viparr)
StructAlign (class in schrodinger.structutils.structalign)
StructAlignResult (class in schrodinger.protein.tasks.structure_alignment)
StructuralInteractionFingerprintGenerator (class in schrodinger.structutils.interactionfp)
structure
adjustment
creation
i/o
measurement
minimization
properties
substructure searching
Structure (class in schrodinger.structure)
structure (schrodinger.application.mopac.results_main.MopacResultsMain property)
(schrodinger.structure._AtomCollection property)
(schrodinger.structure._Chain property)
(schrodinger.structure._Molecule property)
(schrodinger.structure._Residue property)
(schrodinger.structure._Ring property)
(schrodinger.structure._StructureAtom property)
structure_files() (in module schrodinger.test.hypothesis.strategies.structures)
structure_from_smiles() (in module schrodinger.test.build_test_structures)
structure_to_rdkit_smiles() (in module schrodinger.analysis.transformations)
StructureAssertionsTestCase (class in schrodinger.test.custom_assertions)
StructureCount (schrodinger.infra.structure.FileSplitStrategy attribute)
StructureLauncher (class in schrodinger.application.mopac.structure_launchers)
StructureLauncherError
StructureMergeHandler (class in schrodinger.rdkit.molio)
StructureReader (class in schrodinger.structure)
StructureReaderAdapter (class in schrodinger.rdkit.molio)
Structures (class in schrodinger.pipeline.pipeio)
structures (schrodinger.application.livedesign.data_classes.ReceptorLigandMap property)
structures() (in module schrodinger.test.hypothesis.strategies.structures)
StructureSerializer (class in schrodinger.models.jsonable)
StructureWriter (class in schrodinger.structure)
stub_license() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
Style (class in schrodinger.surface)
style (schrodinger.project.surface.ProjectSurface property)
(schrodinger.structure._StructureAtom property)
(schrodinger.structure._StructureBond property)
(schrodinger.surface.Surface property)
style() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
StyledPanel (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shape attribute)
styleSheet() (schrodinger.ui.dendrogram.DendrogramView method)
sub_charge (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_forward (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_end_time_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_ensemble (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_ff (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_interactions() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
sub_median_delta_g (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_mol_number (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_rest_exchanges (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_sid_molsa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
sub_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_sid_psa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
sub_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
sub_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
sub_sid_sasa() (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData method)
sub_sid_snapshot_times_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_sim_time (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_start_time_ns (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_temperature (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_total_atoms (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_total_replicas (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
sub_total_waters (schrodinger.application.desmond.fep_edge_data.SolubilityFEPEdgeData property)
SUBLIMATION (schrodinger.application.desmond.constants.FepLegTypes attribute)
sublists() (in module schrodinger.test.hypothesis.strategies.indices)
submit_job() (schrodinger.application.matsci.qb_sdk.client.QubecClient method)
subscript (schrodinger.application.scaffold_enumeration.cxsmiles.SRU attribute)
subscript_digits() (in module schrodinger.application.matsci.typography)
SubstCoreDatabase (class in schrodinger.application.combiglide.corehop)
substring() (schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRInputStream method)
(schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method)
(schrodinger.application.desmond.antlr3.streams.CharStream method)
substructure_matches() (in module schrodinger.rdkit.substructure)
SubtaskExecutionError
subTest() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
SUCCESS_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
suggestReagentClasses() (schrodinger.application.pathfinder.reaction.Reaction method)
summarize_properties() (in module schrodinger.application.phase.shape_screen_reporter.prop_utils)
summary() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
Sunken (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shadow attribute)
superimpose() (in module schrodinger.application.desmond.packages.pfx)
(in module schrodinger.application.desmond.packages.topo)
(in module schrodinger.structutils.rmsd)
superimpose_bond() (in module schrodinger.structutils.rmsd)
superimpose_cms() (in module schrodinger.application.desmond.packages.pfx)
(in module schrodinger.application.desmond.packages.topo)
superimpose_substructure_molecules() (in module schrodinger.structutils.rmsd)
SUPERIMPOSED_PROPERTY (schrodinger.structutils.sitealign.SiteMatchLookup attribute)
superimposition
superpose() (schrodinger.trajectory.prody.ensemble.Ensemble method)
superscript (schrodinger.application.scaffold_enumeration.cxsmiles.SRU attribute)
supersedes() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.Package method)
support() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
supported_output_format() (in module schrodinger.rdkit.molio)
suppress_rdkit_log() (in module schrodinger.rdkit.rdkit_adapter)
Suppression (class in schrodinger.test.memtest)
Surface (class in schrodinger.surface)
surface (schrodinger.project.surface.ProjectSurface.ColorFrom attribute)
(schrodinger.surface.ColorFrom attribute)
(schrodinger.surface.Surface.ColorFrom attribute)
Surface.Color (class in schrodinger.surface)
Surface.ColorBy (class in schrodinger.surface)
Surface.ColorFrom (class in schrodinger.surface)
Surface.Style (class in schrodinger.surface)
surface_area (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
surface_type (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
SURFACE_TYPE_NAME (schrodinger.project.surface.ProjectSurface attribute)
(schrodinger.surface.Surface attribute)
surface_volume (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
SurfaceDict (class in schrodinger.project.surface)
SurfaceRough() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
SurfaceRoughDerv() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
surfnet_gaps_supplier() (in module schrodinger.application.bindingsite.cavutils)
sval (schrodinger.utils.sea.sea.Atom property)
(schrodinger.utils.sea.sea.Hydrogen property)
(schrodinger.utils.sea.sea.List property)
(schrodinger.utils.sea.sea.Map property)
(schrodinger.utils.sea.sea.Sea property)
svd_3x3() (in module schrodinger.application.desmond.packages.msys.pfx)
swap_ld_library_path() (in module schrodinger.utils.env)
swapcase() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
SwapIndx() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
swissprot (schrodinger.utils.fileutils.SeqFormat attribute)
SYMBOL_START (in module schrodinger.application.matsci.atomicsymbols)
symlink() (in module schrodinger.application.desmond.util)
symmetric_difference() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
symmetric_difference_update() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
SYMMETRY (schrodinger.application.matsci.nano.space_groups.SpaceGroups attribute)
SYMMETRY_OPERS (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
symmetry_opers (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
symmetry_opers_strs (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
sync() (schrodinger.utils.preferences.Preferences method)
sync_dummy_atoms() (in module schrodinger.application.jaguar.utils)
synchronize_fsys_ct() (schrodinger.application.desmond.cms.Cms method)
Syntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
System (class in schrodinger.application.desmond.packages.msys)
(class in schrodinger.test.stu.outcomes.compareDesmondSystems)
system (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.application.desmond.packages.msys.atomsel.Atomsel property)
(schrodinger.application.desmond.packages.msys.Bond property)
(schrodinger.application.desmond.packages.msys.Chain property)
(schrodinger.application.desmond.packages.msys.Ct property)
(schrodinger.application.desmond.packages.msys.Handle property)
(schrodinger.application.desmond.packages.msys.Param property)
(schrodinger.application.desmond.packages.msys.Residue property)
(schrodinger.application.desmond.packages.msys.Term property)
(schrodinger.application.desmond.packages.msys.TermTable property)
SYSTEM_BUILDER_INP (class in schrodinger.application.desmond.constants)
system_file (schrodinger.analysis.transformations.TransformsRepository attribute)
system_hosts_file() (in module schrodinger.application.licensing.licadmin)
SystemDipoleDirector (class in schrodinger.application.desmond.packages.analysis)
SystemType (class in schrodinger.application.desmond.constants)
SytSym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
T
t() (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method)
T_0 (class in schrodinger.application.desmond.simulation_block_test)
t_intrinsic_part() (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method)
t_location_part() (schrodinger.application.matsci.cctbx.rot_mx.rt_mx method)
Table (class in schrodinger.infra.table)
table (schrodinger.application.desmond.packages.msys.Param property)
(schrodinger.application.desmond.packages.msys.Term property)
table() (schrodinger.application.desmond.packages.msys.System method)
table_exists() (in module schrodinger.application.phase.packages.mmp2d)
table_names (schrodinger.application.desmond.packages.msys.System property)
TableRow (class in schrodinger.infra.table)
tables (schrodinger.application.desmond.packages.msys.System property)
TableSchemas() (in module schrodinger.application.desmond.packages.msys)
tabletEvent() (schrodinger.ui.dendrogram.DendrogramView method)
tag (schrodinger.application.licensing.licerror.LicenseError property)
tag() (schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
(schrodinger.utils.sea.sea.Sea method)
tag_gcmc_ligand() (in module schrodinger.application.desmond.gcmc_utils)
tag_gcmc_ligand_file() (in module schrodinger.application.desmond.gcmc_utils)
tag_gcmc_near_ligand() (in module schrodinger.application.desmond.gcmc_utils)
tag_gcmc_near_ligand_file() (in module schrodinger.application.desmond.gcmc_utils)
tag_mol_indexes() (in module schrodinger.livedesign.preprocessor)
tag_protein() (in module schrodinger.application.desmond.fep_edge_data)
tags (schrodinger.analysis.transformations.TransformsRepository property)
take_action() (schrodinger.utils.singledashoptionparser.SingleDashOption method)
takes_value() (schrodinger.utils.singledashoptionparser.SingleDashOption method)
tand() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIImath)
(in module schrodinger.application.matsci.gsas.GSASIIpwd)
tar_files() (in module schrodinger.utils.fileutils)
target_namespace (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
target_pattern (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter attribute)
target_prefix (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
target_str (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.IndividualStructureBase attribute)
(schrodinger.application.livedesign.entry_types.Ligands attribute)
(schrodinger.application.livedesign.entry_types.OrganometallicCompounds attribute)
(schrodinger.application.livedesign.entry_types.TargetlessBase attribute)
target_validate() (schrodinger.ui.qt.appframework2.validators.BaseTextValidator method)
(schrodinger.ui.qt.appframework2.validators.FileExists method)
(schrodinger.ui.qt.appframework2.validators.IsInteger method)
(schrodinger.ui.qt.appframework2.validators.JobName method)
(schrodinger.ui.qt.appframework2.validators.PathExists method)
(schrodinger.ui.qt.appframework2.validators.Validator method)
TargetlessBase (class in schrodinger.application.livedesign.entry_types)
Task (class in schrodinger.application.desmond.task)
TAUTOMER_HASH (schrodinger.livedesign.molhash.HashLayer attribute)
tautomer_insensitive (schrodinger.rdkit.substructure.QueryOptions attribute)
TAUTOMER_INSENSITIVE_LAYERS (schrodinger.livedesign.molhash.HashScheme attribute)
TD_NAMESPACE (in module schrodinger.application.matsci.qeschema.qeschema.namespaces)
TD_spctInConverter (class in schrodinger.application.matsci.qexsd.qespresso.converters)
(in module schrodinger.application.matsci.qeschema.qeschema.converters)
TD_SPECTRUM_NAMESPACE (in module schrodinger.application.matsci.qeschema.qeschema.namespaces)
TD_TEMPLATE_MAP (schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter attribute)
TdDocument (class in schrodinger.application.matsci.qeschema.qeschema.documents)
(class in schrodinger.application.matsci.qexsd.qespresso.documents)
TdInputConverter (class in schrodinger.application.matsci.qeschema.qeschema.converters)
(class in schrodinger.application.matsci.qexsd.qespresso.converters)
tdm_precision (schrodinger.application.jaguar.results.Dipole attribute)
(schrodinger.application.jaguar.results.JaguarResults attribute)
TdSpectrumDocument (class in schrodinger.application.matsci.qeschema.qeschema.documents)
TdSpectrumInputConverter (class in schrodinger.application.matsci.qeschema.qeschema.converters)
tearDown() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase method)
teardown() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
tearDownClass() (schrodinger.application.matsci.qexsd.tests.test_converters.InputConversionTestCase class method)
(schrodinger.test.custom_assertions.StructureAssertionsTestCase class method)
temp (schrodinger.application.jaguar.utils.FreeEnergy attribute)
Temperature (class in schrodinger.application.desmond.simulation_block_test)
temperature_factor (schrodinger.structure._AtomCollection property)
(schrodinger.structure._Chain property)
(schrodinger.structure._Molecule property)
(schrodinger.structure._Residue property)
(schrodinger.structure._Ring property)
(schrodinger.structure._StructureAtom property)
tempfilename (class in schrodinger.utils.fileutils)
template (schrodinger.application.prime.wrapper.BasePrimeAlignment property)
template_sequence (schrodinger.application.prime.wrapper.BasePrimeAlignment property)
templates_convert() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
templates_reorder_atoms() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue)
temporary_directory() (in module schrodinger.application.licensing.licadmin)
TempStructureFile (class in schrodinger.utils.fileutils)
Term (class in schrodinger.application.desmond.packages.msys)
term() (schrodinger.application.desmond.packages.msys.TermTable method)
term_props (schrodinger.application.desmond.packages.msys.TermTable property)
Terminal (schrodinger.test.perceptualdiff.Notify attribute)
terminate() (schrodinger.application.desmond.antlr3.debug.BlankDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method)
(schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method)
(schrodinger.application.jaguar.mmjag.MmJag static method)
(schrodinger.infra.mminit.Initializer method)
(schrodinger.infra.mmlist.mmlist static method)
(schrodinger.infra.table.Table static method)
TermKeywords (class in schrodinger.application.glide.xpdes)
termPropType() (schrodinger.application.desmond.packages.msys.TermTable method)
terms (schrodinger.application.desmond.packages.msys.TermTable property)
TermTable (class in schrodinger.application.desmond.packages.msys)
Test (class in schrodinger.application.desmond.simulation_block_test)
test0() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIIpwd)
(in module schrodinger.application.matsci.gsas.GSASIIspc)
test1() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIIpwd)
(in module schrodinger.application.matsci.gsas.GSASIIspc)
test2() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIIpwd)
(in module schrodinger.application.matsci.gsas.GSASIIspc)
test3() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIIpwd)
(in module schrodinger.application.matsci.gsas.GSASIIspc)
test4() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
test5() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
test6() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
test7() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
test8() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
test9() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
testAttribute() (schrodinger.ui.dendrogram.DendrogramView method)
TestData() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
(in module schrodinger.application.matsci.gsas.GSASIIpwd)
TestStdException (class in schrodinger.ui.dendrogram)
TestSuite (class in schrodinger.application.desmond.util)
TETRAGONAL_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute)
Text (class in schrodinger.pipeline.pipeio)
text (schrodinger.application.desmond.antlr3.recognizers.Lexer property)
(schrodinger.application.desmond.antlr3.tokens.CommonToken property)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode property)
(schrodinger.application.desmond.antlr3.tree.CommonTree property)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern property)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern property)
(schrodinger.application.desmond.arkdb.CompositeKeySyntaxError attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer property)
Text2MT() (in module schrodinger.application.matsci.gsas.GSASIIspc)
textAnnotation() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
textAnnotation0() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
TextBlockReader (class in schrodinger.infra.structure)
TextBlockWriter (class in schrodinger.infra.structure)
TextGen() (in module schrodinger.application.matsci.gsas.GSASIIspc)
TextOps() (in module schrodinger.application.matsci.gsas.GSASIIspc)
TextualStructure (class in schrodinger.structure)
textureIndex() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
theory (schrodinger.application.qsite.input.Cut property)
(schrodinger.application.qsite.input.HydrogenCap property)
ThermoCollection (class in schrodinger.application.jaguar.results)
ThermoProp (class in schrodinger.application.jaguar.results)
this (schrodinger.application.phase.hypothesis.PhaseHypothesis attribute)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand attribute)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid attribute)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard attribute)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic attribute)
(schrodinger.infra.mmerr.Capture attribute)
(schrodinger.infra.structure.TextBlockReader attribute)
(schrodinger.infra.structure.TextBlockWriter attribute)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter attribute)
(schrodinger.structutils.color.ColorScheme attribute)
thisown (schrodinger.application.phase.hypothesis.PhaseHypothesis attribute)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand attribute)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid attribute)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard attribute)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic attribute)
(schrodinger.infra.mmerr.Capture attribute)
(schrodinger.infra.structure.TextBlockReader attribute)
(schrodinger.infra.structure.TextBlockWriter attribute)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter attribute)
(schrodinger.structutils.color.ColorScheme attribute)
thread() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
ThreadSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
ThreeTenHelix (schrodinger.protein.buildpeptide.SECONDARY_STRUCTURE attribute)
thresh_prec (schrodinger.application.jaguar.results.ConvCriteria attribute)
threshold (schrodinger.application.desmond.packages.timer.Timer.Args attribute)
throwBadAlloc() (schrodinger.ui.dendrogram.TestStdException method)
throwLogicError() (schrodinger.ui.dendrogram.TestStdException method)
throwOutOfRange() (schrodinger.ui.dendrogram.TestStdException method)
throwRuntimeError() (schrodinger.ui.dendrogram.TestStdException method)
time (schrodinger.application.desmond.packages.traj.Frame property)
(schrodinger.application.licensing.lmgrd_log_parser.event attribute)
time_duration() (in module schrodinger.application.desmond.util)
TIME_FORMAT (schrodinger.utils.profiling.RecordingTimer attribute)
(schrodinger.utils.profiling.Timer attribute)
(schrodinger.utils.timeit.TimeIt attribute)
time_weighted_usage() (in module schrodinger.application.licensing.lmgrd_log_parser)
TimeIt (class in schrodinger.utils.timeit)
Timer (class in schrodinger.application.desmond.packages.timer)
(class in schrodinger.utils.profiling)
Timer.Args (class in schrodinger.application.desmond.packages.timer)
timerEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
TIP3P (schrodinger.application.desmond.constants.WATER_MODELS attribute)
TIP3P_CHARMM (schrodinger.application.desmond.constants.WATER_MODELS attribute)
TIP4P (schrodinger.application.desmond.constants.WATER_MODELS attribute)
TIP4P2005 (schrodinger.application.desmond.constants.WATER_MODELS attribute)
TIP4PD (schrodinger.application.desmond.constants.WATER_MODELS attribute)
TIP4PEW (schrodinger.application.desmond.constants.WATER_MODELS attribute)
TIP5P (schrodinger.application.desmond.constants.WATER_MODELS attribute)
title (schrodinger.application.desmond.cms.Cms property)
(schrodinger.application.desmond.ffiostructure.FFIOStructure property)
(schrodinger.application.phase.hypothesis.PhaseHypothesis property)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand property)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid property)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard property)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic property)
(schrodinger.models.jsonable.JsonableStructure property)
(schrodinger.structure.SmilesStructure property)
(schrodinger.structure.Structure property)
(schrodinger.structure.TextualStructure property)
title() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
TLS2Uij() (in module schrodinger.application.matsci.gsas.GSASIImath)
TM_METAL_LIST (in module schrodinger.application.matsci.atomicsymbols)
TM_METAL_SET (in module schrodinger.application.matsci.atomicsymbols)
tmp_cwd() (in module schrodinger.test.pytest.fixture)
to_dict() (in module schrodinger.application.matsci.mlearn.sklearn_json)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
to_fortran() (in module schrodinger.application.matsci.qeschema.qeschema.utils)
(in module schrodinger.application.matsci.qexsd.qespresso.converters)
to_helm() (in module schrodinger.protein.helm)
to_json() (in module schrodinger.application.matsci.mlearn.sklearn_json)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
to_rdkit() (in module schrodinger.protein.helm)
(in module schrodinger.rdkit.rdkit_adapter)
to_string() (schrodinger.application.desmond.measurement.Measurement method)
to_style (schrodinger.structure._StructureBond property)
to_yaml() (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
ToArrayCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
ToArrayCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
toConfig() (schrodinger.livedesign.preprocessor.PreprocessorOptions method)
toDebugString() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
toDict() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method)
TOF2dsp() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
toFile() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter method)
toGraphicsObject() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
toJson() (schrodinger.application.desmond.packages.restraint.builder.Restraints method)
(schrodinger.models.json.JsonableClassMixin method)
(schrodinger.models.jsonable.JsonableNamedTuple method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.models.jsonable.JsonableTuple method)
toJsonImplementation() (schrodinger.models.json.JsonableClassMixin method)
(schrodinger.models.jsonable.JsonableEnum method)
(schrodinger.models.jsonable.JsonableIntEnum method)
(schrodinger.models.jsonable.JsonableNamedTuple method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.models.jsonable.JsonableTuple method)
Token (class in schrodinger.application.desmond.antlr3.tokens)
tokenNames (schrodinger.application.desmond.antlr3.debug.DebugParser attribute)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Lexer attribute)
(schrodinger.application.desmond.antlr3.recognizers.Parser attribute)
(schrodinger.application.desmond.antlr3.tree.TreeParser attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute)
TokenRewriteStream (class in schrodinger.application.desmond.antlr3.streams)
tokens (schrodinger.application.licensing.lmgrd_log_parser.event attribute)
tokens() (in module schrodinger.application.licensing.licadmin)
(schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
tokens_str() (schrodinger.application.licensing.flexlm.Feature method)
TokenSource (class in schrodinger.application.desmond.antlr3.recognizers)
tokenStartIndex (schrodinger.application.desmond.antlr3.tree.CommonErrorNode property)
(schrodinger.application.desmond.antlr3.tree.CommonTree property)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern property)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern property)
tokenStopIndex (schrodinger.application.desmond.antlr3.tree.CommonErrorNode property)
(schrodinger.application.desmond.antlr3.tree.CommonTree property)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern property)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern property)
TokenStream (class in schrodinger.application.desmond.antlr3.streams)
TolerableError
toolTip() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
toolTipDuration() (schrodinger.ui.dendrogram.DendrogramView method)
TooManyGroupsError
toOriginalString() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
topLevelItem() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
topLevelWidget() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
TopoError
TopologicalDescriptors (class in schrodinger.application.canvas.topo_descriptors)
TOPOLOGY (schrodinger.application.desmond.constants.IdConversion attribute)
topology (schrodinger.application.desmond.packages.msys.System property)
tors_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property)
Torsion (class in schrodinger.application.desmond.packages.analysis)
torsion_iterator() (in module schrodinger.structutils.analyze)
TorsionPotential (class in schrodinger.application.desmond.torsion_related)
toSmiles() (schrodinger.rdkit.molio.CsvMolWriter method)
toString() (in module schrodinger.infra.ark)
(schrodinger.application.desmond.antlr3.debug.DebugTokenStream method)
(schrodinger.application.desmond.antlr3.streams.CommonTokenStream method)
(schrodinger.application.desmond.antlr3.streams.DeleteOp method)
(schrodinger.application.desmond.antlr3.streams.InsertBeforeOp method)
(schrodinger.application.desmond.antlr3.streams.ReplaceOp method)
(schrodinger.application.desmond.antlr3.streams.RewriteOperation method)
(schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method)
(schrodinger.application.desmond.antlr3.streams.TokenStream method)
(schrodinger.application.desmond.antlr3.tokens.ClassicToken method)
(schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.tree.TreeNodeStream method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
(schrodinger.application.jaguar.results.ScfIteration method)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter static method)
toStrings() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
toStringTree() (schrodinger.application.desmond.antlr3.tree.BaseTree method)
(schrodinger.application.desmond.antlr3.tree.CommonErrorNode method)
(schrodinger.application.desmond.antlr3.tree.CommonTree method)
(schrodinger.application.desmond.antlr3.tree.Tree method)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern method)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern method)
total (schrodinger.application.licensing.licadmin.stat_info attribute)
total_charge() (in module schrodinger.application.desmond.fep_net_charge)
Total_charge() (in module schrodinger.utils.ligfilter)
total_charge() (schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
total_energy() (in module schrodinger.application.mopac.results_main)
total_nucleophilic_superdelocalizability() (in module schrodinger.application.mopac.results_main)
total_tokens() (schrodinger.application.licensing.licadmin.LicenseResource method)
(schrodinger.application.licensing.licadmin.LocalServerProcess method)
total_weight (schrodinger.application.desmond.cms.Cms property)
(schrodinger.application.desmond.ffiostructure.FFIOStructure property)
(schrodinger.models.jsonable.JsonableStructure property)
(schrodinger.structure.Structure property)
(schrodinger.structure.TextualStructure property)
totalAngle (schrodinger.ui.dendrogram.DendrogramGraphicTreeCoordinatesPreferences attribute)
toTree() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method)
(schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method)
ToWorldCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
ToWorldCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
TPSAIncludeSandP() (in module schrodinger.rdkit.filtering)
tr() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
tr_vec (class in schrodinger.application.matsci.cctbx.rot_mx)
TraceDebugEventListener (class in schrodinger.application.desmond.antlr3.debug)
traceIn() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
traceOut() (schrodinger.application.desmond.antlr3.debug.DebugParser method)
(schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method)
(schrodinger.application.desmond.antlr3.recognizers.Lexer method)
(schrodinger.application.desmond.antlr3.recognizers.Parser method)
(schrodinger.application.desmond.antlr3.tree.TreeParser method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
Trajectory
TRAJECTORY_VIEWER (schrodinger.trajectory.trajectory_gui_dir.export_structure_enums.ExportMode attribute)
TrajectoryForSolubilityFep (class in schrodinger.application.desmond.task)
TrajectoryUnreadableError
Trans2Text() (in module schrodinger.application.matsci.gsas.GSASIIspc)
transferback() (in module schrodinger.Qt.PyQt6.sip)
transferto() (in module schrodinger.Qt.PyQt6.sip)
transform() (in module schrodinger.livedesign.preprocessor)
(schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.application.matsci.mlearn.base.BaseFeaturizer method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
transform_atom_coordinates() (in module schrodinger.structutils.transform)
transform_conformer() (in module schrodinger.rdkit.alignment)
transform_structure() (in module schrodinger.application.ska)
(in module schrodinger.structutils.transform)
transformationAnchor() (schrodinger.ui.dendrogram.DendrogramView method)
TRANSFORMATIONS (schrodinger.livedesign.preprocessor.PreprocessorOptions attribute)
transformations() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
TransformCell() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
transformOriginPoint() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
TransformPhase() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
TransformsRepository (class in schrodinger.analysis.transformations)
TransformU6() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
TransformXYZ() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
Transition (class in schrodinger.math.multi_parameter_optimization)
translate() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.desmond.packages.msys.System method)
(schrodinger.application.desmond.rl_helper.NumberedCanvas method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
translate_atom_to_origin() (in module schrodinger.structutils.transform)
translate_center_to_origin() (in module schrodinger.structutils.transform)
translate_centroid_to_origin() (in module schrodinger.structutils.transform)
translate_mdl_enumerable_features() (in module schrodinger.application.scaffold_enumeration.mdl)
translate_nan_tokens_in_line() (in module schrodinger.utils.compare)
translate_rdkit_props_dict() (in module schrodinger.rdkit.rdkit_adapter)
translate_structure() (in module schrodinger.structutils.transform)
translate_to_origin() (in module schrodinger.structutils.transform)
translation_part_info (class in schrodinger.application.matsci.cctbx.rot_mx)
Transmission() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
transmit() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
transpose() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
transpose_box() (schrodinger.application.desmond.packages.traj.Frame method)
transposeHKLF() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
Tree (class in schrodinger.application.desmond.antlr3.tree)
TreeAdaptor (class in schrodinger.application.desmond.antlr3.tree)
TreeNodeStream (class in schrodinger.application.desmond.antlr3.tree)
TreeParser (class in schrodinger.application.desmond.antlr3.tree)
TreePattern (class in schrodinger.application.desmond.antlr3.treewizard)
TreePatternLexer (class in schrodinger.application.desmond.antlr3.treewizard)
TreePatternParser (class in schrodinger.application.desmond.antlr3.treewizard)
TreePatternTreeAdaptor (class in schrodinger.application.desmond.antlr3.treewizard)
TreeRuleReturnScope (class in schrodinger.application.desmond.antlr3.tree)
TreeVisitor (class in schrodinger.application.desmond.antlr3.tree)
TreeWizard (class in schrodinger.application.desmond.antlr3.treewizard)
TRICLINIC_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute)
TRIGONAL_NAME (schrodinger.application.matsci.nano.space_groups.CrystalSystems attribute)
Triple (schrodinger.structure.BondType attribute)
tripleRingAtomsFraction() (schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor method)
try_import() (in module schrodinger.utils.moduleproxy)
ts_component_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
TupleSerializer (class in schrodinger.models.jsonable)
TURN (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute)
tv_sec (schrodinger.test.darwinconsole.Utmpx attribute)
tv_usec (schrodinger.test.darwinconsole.Utmpx attribute)
TWO_THETA_TOL (schrodinger.application.matsci.xrd.XRDCalculator attribute)
type (schrodinger.application.desmond.antlr3.tree.CommonErrorNode property)
(schrodinger.application.desmond.antlr3.tree.CommonTree property)
(schrodinger.application.desmond.antlr3.treewizard.TreePattern property)
(schrodinger.application.desmond.antlr3.treewizard.WildcardTreePattern property)
(schrodinger.structure._StructureBond property)
Type (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
type() (schrodinger.application.matsci.cctbx.rot_mx.rot_mx method)
(schrodinger.application.matsci.cctbx.rot_mx.rot_mx_info method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
TYPE_CHECKER (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
TYPED_ACTIONS (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
types (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
TYPES (schrodinger.utils.singledashoptionparser.SingleDashOption attribute)
TYPO_TYPE (class in schrodinger.application.matsci.typography)
U
U2Uij() (in module schrodinger.application.matsci.gsas.GSASIIspc)
U6toUij() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
Ui_Dialog (class in schrodinger.application.desmond.desmond_advanced_tab_ui)
(class in schrodinger.application.livedesign.login_ui)
(class in schrodinger.infra.exception_handler_dir.exception_dialog_ui)
(class in schrodinger.trajectory.traj_dialog_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.advanced_settings_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.custom_asl_sets_dialog_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.custom_substructure_sets_dialog_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.export_movie_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.export_snapshot_structures_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.export_structures_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.rmsd_settings_dialog_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.snapshot_custom_display_settings_ui)
(class in schrodinger.ui.ligfilter_definition_dialog_ui)
(class in schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui)
(class in schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui)
(class in schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui)
(class in schrodinger.ui.qt.entryselector_ui)
(class in schrodinger.ui.qt.filter_dialog_ui)
(class in schrodinger.ui.qt.rename_favorite_dialog_ui)
(class in schrodinger.ui.qt.select_residues_dialog_ui)
Ui_Form (class in schrodinger.application.bioluminate.propfilter_ui)
(class in schrodinger.application.bioluminate.protein_structure_quality_ui)
(class in schrodinger.application.desmond.input_group_ui)
(class in schrodinger.application.desmond.rest_tab_ui)
(class in schrodinger.application.job_monitor.diagnostics_dialog_ui)
(class in schrodinger.application.job_monitor.file_browser_ui)
(class in schrodinger.application.livedesign.login2_ui)
(class in schrodinger.application.livedesign.pose_name_panel_ui)
(class in schrodinger.application.livedesign.save_mapping_dialog_ui)
(class in schrodinger.application.livedesign.selection_pop_up_ui)
(class in schrodinger.application.msv.gui.binding_site_aln_dialog_ui)
(class in schrodinger.application.msv.gui.homology_modeling.homology_modeling_step_ui)
(class in schrodinger.application.msv.gui.multiple_seq_aln_dialog_ui)
(class in schrodinger.application.msv.gui.pairwise_seq_aln_dialog_ui)
(class in schrodinger.application.msv.gui.toolbar_ui)
(class in schrodinger.application.prime.gui.ui.environment_options_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.centroid_banner_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.planar_banner_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.playback_settings_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.rama_plot_panel_ui)
(class in schrodinger.trajectory.trajectory_gui_dir.shortcut_ui)
(class in schrodinger.ui.ligfilter_ui)
(class in schrodinger.ui.qt.appframework2.debug_gui_ui)
(class in schrodinger.ui.qt.config_dialog_open_mp_ui)
(class in schrodinger.ui.qt.config_dialog_queue_ui)
(class in schrodinger.ui.qt.filter_dialog_dir.filter_widget_ui)
(class in schrodinger.ui.qt.presets.manage_presets_dialog_ui)
(class in schrodinger.ui.qt.presets.save_presets_dialog_ui)
(class in schrodinger.ui.qt.protein_health_viewer_ui)
(class in schrodinger.ui.qt.tasks.config_dialog_ui)
(class in schrodinger.ui.qt.tasks.config_info_ui)
Ui_Frame (class in schrodinger.ui.qt.borderless_popup_ui)
Ui_PdbDialog (class in schrodinger.ui.qt.pdb_dialog_ui)
Ui_snapshot_panel (class in schrodinger.trajectory.trajectory_gui_dir.snapshot_panel_ui)
Ui_trajectory_form (class in schrodinger.trajectory.trajectory_gui_dir.traj_plot_ui)
Ui_UpdatePKASettingsDlg (class in schrodinger.application.jaguar.update_pka_settings_ui)
Uij2betaij() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
Uij2U() (in module schrodinger.application.matsci.gsas.GSASIIspc)
Uij2Ueqv() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
UijtoU6() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
UiMode (class in schrodinger.application.desmond.constants)
unblock() (schrodinger.Qt.PyQt6.QtCore.QSignalBlocker method)
uncapped_smi (schrodinger.application.dendrogram.core_class.RingSysInfo attribute)
uncapped_st (schrodinger.application.dendrogram.core_class.RingSysInfo attribute)
unchecked_map (schrodinger.utils.sea.evalor.Evalor property)
UndefinedStereochemistry (class in schrodinger.structure)
underMouse() (schrodinger.ui.dendrogram.DendrogramView method)
unexpectedType (schrodinger.application.desmond.antlr3.exceptions.EarlyExitException property)
(schrodinger.application.desmond.antlr3.exceptions.FailedPredicateException property)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedNotSetException property)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedRangeException property)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedSetException property)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTokenException property)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTreeNodeException property)
(schrodinger.application.desmond.antlr3.exceptions.MissingTokenException property)
(schrodinger.application.desmond.antlr3.exceptions.NoViableAltException property)
(schrodinger.application.desmond.antlr3.exceptions.RecognitionException property)
(schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException property)
ungrabGesture() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramView method)
ungrabKeyboard() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
ungrabMouse() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
UNGROUPED_ARE_ABSOLUTE (schrodinger.livedesign.preprocessor.ChiralFlag0Meaning attribute)
UNGROUPED_ARE_RACEMIC (schrodinger.livedesign.preprocessor.ChiralFlag0Meaning attribute)
UNGROUPED_ARE_RELATIVE (schrodinger.livedesign.preprocessor.ChiralFlag0Meaning attribute)
unicode (schrodinger.application.matsci.typography.TYPO_TYPE attribute)
unicode_to_str() (in module schrodinger.livedesign.preprocessor)
union() (schrodinger.models.jsonable.JsonableSet method)
(schrodinger.utils.scollections.IdSet method)
unique() (in module schrodinger.application.desmond.util)
unique_smiles (schrodinger.structutils.analyze.Ligand property)
uniqueCombinations() (in module schrodinger.application.matsci.gsas.GSASIIlattice)
UniqueFilter (class in schrodinger.adapter)
uniquesmiler() (in module schrodinger.utils.cgxutils)
uniquify_leaks() (in module schrodinger.test.memtest)
uniquify_suppression_titles() (in module schrodinger.test.memtest)
UniquifyResults() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method)
unit_vector() (in module schrodinger.structutils.interactions.pi)
unit_vector_points() (in module schrodinger.structutils.interactions.pi)
unittest_preset_manager() (in module schrodinger.test.pytest.fixture)
UNKNOWN (schrodinger.application.desmond.constants.CorrectionTerm attribute)
unmatched_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property)
unmatched_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer property)
unpack() (schrodinger.application.desmond.antlr3.dfa.DFA class method)
(schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer.DFA12 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA1 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA15 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA17 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA18 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA19 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA20 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA21 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA22 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA24 class method)
(schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser.DFA25 class method)
unpaired (schrodinger.application.jaguar.utils.LewisStructure attribute)
unselectRows() (schrodinger.infra.table.Table method)
unset() (schrodinger.infra.mmbitset.Bitset method)
unsetCursor() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
unsetLayoutDirection() (schrodinger.ui.dendrogram.DendrogramView method)
unsetLocale() (schrodinger.ui.dendrogram.DendrogramView method)
unsign() (schrodinger.application.licensing.flexlm.Feature method)
(schrodinger.application.licensing.flexlm.License method)
(schrodinger.application.licensing.flexlm.LicenseLine method)
(schrodinger.application.licensing.flexlm.Package method)
(schrodinger.application.licensing.flexlm.Server method)
(schrodinger.application.licensing.flexlm.UseServer method)
(schrodinger.application.licensing.flexlm.Vendor method)
UnsupportedElementError
UnsupportedPlatformException
UnsupportedStructureError
,
[1]
unused (schrodinger.test.darwinconsole.Utmpx attribute)
UnwantedTokenException
unwrap_lines() (in module schrodinger.application.jaguar.check_headers)
unwrapinstance() (in module schrodinger.Qt.PyQt6.sip)
unzip_and_get_membrane_test_files() (in module schrodinger.application.desmond.test_utils)
update() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.models.jsonable.JsonableSet method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.scollections.IdSet method)
(schrodinger.utils.sea.sea.Atom method)
(schrodinger.utils.sea.sea.Hydrogen method)
(schrodinger.utils.sea.sea.List method)
(schrodinger.utils.sea.sea.Map method)
update_cms() (in module schrodinger.application.desmond.packages.topo)
update_cms_physical() (in module schrodinger.application.desmond.packages.topo)
update_ct() (in module schrodinger.application.desmond.packages.topo)
update_ct_box() (in module schrodinger.application.desmond.packages.topo)
update_enhanced_stereo_group_weights() (in module schrodinger.livedesign.molhash)
update_fsys_ct_from_frame() (in module schrodinger.application.desmond.packages.topo)
update_fsys_ct_from_frame_GF() (in module schrodinger.application.desmond.packages.topo)
update_guess() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method)
(schrodinger.application.matsci.gsas.GSASIImath.fast_sa method)
(schrodinger.application.matsci.gsas.GSASIImath.log_sa method)
update_macro_dict() (in module schrodinger.utils.sea.sea)
update_mol_groups() (in module schrodinger.livedesign.preprocessor)
update_msys() (in module schrodinger.application.desmond.packages.topo)
update_once() (in module schrodinger.structure)
update_pass_fail() (schrodinger.application.desmond.simulation_block_test.BoxSize method)
(schrodinger.application.desmond.simulation_block_test.E_f method)
(schrodinger.application.desmond.simulation_block_test.E_k method)
(schrodinger.application.desmond.simulation_block_test.E_x method)
(schrodinger.application.desmond.simulation_block_test.Energy method)
(schrodinger.application.desmond.simulation_block_test.Job_Details method)
(schrodinger.application.desmond.simulation_block_test.PotentialEnergy method)
(schrodinger.application.desmond.simulation_block_test.Pressure method)
(schrodinger.application.desmond.simulation_block_test.T_0 method)
(schrodinger.application.desmond.simulation_block_test.Temperature method)
(schrodinger.application.desmond.simulation_block_test.Test method)
(schrodinger.application.desmond.simulation_block_test.V method)
update_props() (in module schrodinger.application.mopac.results_main)
update_pseudo_residue_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr)
update_sgroup_indexes() (in module schrodinger.livedesign.preprocessor)
update_sgroups() (in module schrodinger.livedesign.preprocessor)
update_stereo_groups() (in module schrodinger.livedesign.preprocessor)
update_temp() (schrodinger.application.matsci.gsas.GSASIImath.base_schedule method)
(schrodinger.application.matsci.gsas.GSASIImath.fast_sa method)
(schrodinger.application.matsci.gsas.GSASIImath.log_sa method)
update_templates() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge)
update_templates_strict() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge)
update_with_frame() (schrodinger.application.desmond.cms.Cms method)
updateCoordinates() (schrodinger.structutils.minimize.Minimizer method)
updated (schrodinger.models.diffy.DictDiff attribute)
UpdatedCmsFsysCtAnalysis (class in schrodinger.application.desmond.packages.staf)
updateFragids() (schrodinger.application.desmond.packages.msys.System method)
updateFromIterable() (schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
updateGeometry() (schrodinger.ui.dendrogram.DendrogramView method)
updateLabel() (schrodinger.ui.qt.label_cursor.LabelCursorAxes method)
UpdateMCSAxyz() (in module schrodinger.application.matsci.gsas.GSASIImath)
updateMicroFocus() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
UpdateRBUIJ() (in module schrodinger.application.matsci.gsas.GSASIImath)
UpdateRBXYZ() (in module schrodinger.application.matsci.gsas.GSASIImath)
updateScene() (schrodinger.ui.dendrogram.DendrogramView method)
updateSceneRect() (schrodinger.ui.dendrogram.DendrogramView method)
updatesEnabled() (schrodinger.ui.dendrogram.DendrogramView method)
updateSite() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
UpdateSytSym() (in module schrodinger.application.matsci.gsas.GSASIIspc)
upload_ld_attachment() (in module schrodinger.application.livedesign.upload_utils)
upload_ld_model() (in module schrodinger.application.livedesign.upload_utils)
upper() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
upper_bound (schrodinger.application.desmond.correlation_tau.ConfidenceInterval attribute)
urlencode() (in module schrodinger.application.desmond.gchart)
UsageError
,
[1]
use_custom_oplsdir() (in module schrodinger.application.desmond.util)
use_gfactors (in module schrodinger.protein.analysis)
use_scanning_alignment (schrodinger.structutils.structalign.StructAlign property)
use_static_opls_directory() (in module schrodinger.test.fixtures)
use_titration (schrodinger.application.desmond.cms.Cms property)
used (schrodinger.application.licensing.licadmin.stat_info attribute)
used_space() (schrodinger.application.desmond.packages.traj.DtrSource method)
(schrodinger.application.desmond.packages.traj.MaeSource method)
(schrodinger.application.desmond.packages.traj.Source method)
(schrodinger.application.desmond.packages.traj.XtcSource method)
user (schrodinger.application.licensing.lmgrd_log_parser.event attribute)
(schrodinger.application.matsci.msprops.PROP_FAMILY attribute)
user_name (schrodinger.application.livedesign.data_classes.LDData property)
user_properties (schrodinger.test.perceptualdiff.PerceptualDiffTest attribute)
(schrodinger.test.pytest.exetest.ExecutableTest attribute)
(schrodinger.test.pytest.exetest.MakefileTest attribute)
username (schrodinger.application.matsci.qb_sdk.client.QubecTokenData attribute)
userName() (schrodinger.structure.PropertyName method)
userNameWithFamily() (schrodinger.structure.PropertyName method)
userOutput() (schrodinger.pipeline.input.LinearWriter method)
(schrodinger.pipeline.input.Writer method)
UserType (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel attribute)
(schrodinger.ui.dendrogram.DendrogramGraphicTree attribute)
UseServer (class in schrodinger.application.licensing.flexlm)
ut_host (schrodinger.test.darwinconsole.Utmpx attribute)
ut_id (schrodinger.test.darwinconsole.Utmpx attribute)
ut_line (schrodinger.test.darwinconsole.Utmpx attribute)
ut_pid (schrodinger.test.darwinconsole.Utmpx attribute)
ut_type (schrodinger.test.darwinconsole.Utmpx attribute)
ut_user (schrodinger.test.darwinconsole.Utmpx attribute)
util_scripts_dir (schrodinger.application.bioluminate.epitope.psc_workflow.psc_workflow attribute)
Utilities (class in schrodinger.application.dendrogram.core_class)
Utmpx (class in schrodinger.test.darwinconsole)
V
V (class in schrodinger.application.desmond.simulation_block_test)
va_ (schrodinger.application.desmond.util.Counter property)
VACUUM (schrodinger.application.desmond.constants.FepLegTypes attribute)
val (schrodinger.application.desmond.arkdb.ArkDb property)
(schrodinger.application.desmond.correlation_tau.ConfidenceInterval attribute)
(schrodinger.application.desmond.multisim.parser.Msj property)
(schrodinger.application.desmond.util.Counter property)
(schrodinger.utils.sea.sea.Atom property)
(schrodinger.utils.sea.sea.Hydrogen property)
(schrodinger.utils.sea.sea.List property)
(schrodinger.utils.sea.sea.Map property)
valence (schrodinger.application.desmond.packages.msys.Atom property)
valence() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method)
ValEsd() (in module schrodinger.application.matsci.gsas.GSASIImath)
ValgrindWarning (class in schrodinger.test.memtest)
validate (schrodinger.analysis.transformations.TransformsRepository attribute)
validate() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.licensing.flexlm.License method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDComplexType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.application.vss.database.Database method)
validate_asl() (in module schrodinger.structutils.analyze)
validate_connection() (in module schrodinger.application.licensing.licadmin)
validate_fragment() (in module schrodinger.structutils.markush_enumerate)
validate_host() (in module schrodinger.application.desmond.platforms)
validate_license_host_port() (in module schrodinger.application.licensing.licadmin)
validate_localhost_platform_compatibility() (in module schrodinger.utils.platform)
validate_obj() (in module schrodinger.ui.qt.appframework2.validation)
validate_scaffold() (in module schrodinger.structutils.markush_enumerate)
validate_smarts() (in module schrodinger.structutils.analyze)
validate_smarts_canvas() (in module schrodinger.structutils.analyze)
validate_stoichiometry() (in module schrodinger.application.jaguar.utils)
validate_structures() (in module schrodinger.application.jaguar.hydrokinetic_validation)
(in module schrodinger.application.jaguar.solvation_validation)
validateInput() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
validateKeywords() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
validateText() (schrodinger.ui.qt.appframework2.validators.BaseTextValidator method)
(schrodinger.ui.qt.appframework2.validators.FileExists method)
(schrodinger.ui.qt.appframework2.validators.IsInteger method)
(schrodinger.ui.qt.appframework2.validators.JobName method)
(schrodinger.ui.qt.appframework2.validators.PathExists method)
validateValues() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
validationEnabled() (schrodinger.ui.qt.appframework2.validators.BaseTextValidator method)
(schrodinger.ui.qt.appframework2.validators.FileExists method)
(schrodinger.ui.qt.appframework2.validators.IsInteger method)
(schrodinger.ui.qt.appframework2.validators.JobName method)
(schrodinger.ui.qt.appframework2.validators.PathExists method)
(schrodinger.ui.qt.appframework2.validators.Validator method)
ValidationMixin (class in schrodinger.ui.qt.appframework2.validation)
ValidationResult (class in schrodinger.ui.qt.appframework2.validation)
ValidationResults (class in schrodinger.ui.qt.appframework2.validation)
Validator (class in schrodinger.ui.qt.appframework2.validators)
validator() (in module schrodinger.ui.qt.appframework2.validation)
validProtein() (in module schrodinger.application.matsci.gsas.GSASIImath)
valueMatches() (schrodinger.ui.qt.filter_dialog_dir.filter_core.Criterion method)
values() (schrodinger.application.desmond.cms.DictRestrainGroup method)
(schrodinger.application.desmond.cms.FBHWPosRestrainArray method)
(schrodinger.application.desmond.cms.PosRestrainArray method)
(schrodinger.application.desmond.cms.RestrainGroup method)
(schrodinger.application.desmond.cms.RestrainGroupContainer method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.jaguar.results.ZVariables method)
(schrodinger.application.livedesign.data_classes.ReceptorLigandMap method)
(schrodinger.application.matsci.cache.BaseCacheData method)
(schrodinger.application.matsci.cache.FIFOCacheData method)
(schrodinger.application.matsci.cache.LRUCacheData method)
(schrodinger.application.matsci.qeschema.qeschema.utils.BiunivocalMap method)
(schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method)
(schrodinger.application.pathfinder.reaction.ReactionDict method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.infra.mmim.MMIMDict method)
(schrodinger.project.surface.SurfaceDict method)
(schrodinger.structure._StructureProperty method)
(schrodinger.test.stu.outcomes.compareDesmondSystems.System method)
(schrodinger.ui.qt.appframework2.appmethods.MethodsDict method)
(schrodinger.utils.scollections.DefaultFactoryDict method)
(schrodinger.utils.scollections.DefaultIdDict method)
(schrodinger.utils.scollections.IdDict method)
(schrodinger.utils.sea.sea.Map method)
Values2Dict() (in module schrodinger.application.matsci.gsas.GSASIIpwd)
Var (class in schrodinger.application.desmond.enhsamp)
var() (schrodinger.application.matsci.gsas.GSASIIpwd.cauchy_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.fcjde_gen method)
(schrodinger.application.matsci.gsas.GSASIIpwd.norm_gen method)
variance (schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraint property)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintCentroid property)
(schrodinger.application.desmond.packages.restraint.cross_link.CrossLinkRestraintInteraction property)
variant_map (schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.RawInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter attribute)
(schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter attribute)
(schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter attribute)
varWithType() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method)
VDException
Vdw (class in schrodinger.application.desmond.cms)
vdw (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault property)
(schrodinger.surface.MolSurfType attribute)
vdw_radius (schrodinger.structure._StructureAtom property)
vdwA (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault property)
vdwB (schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge property)
(schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBinding property)
(schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault property)
Vector (class in schrodinger.application.desmond.packages.analysis)
(class in schrodinger.trajectory.prody.mode)
VectorBase (class in schrodinger.trajectory.prody.mode)
vel (schrodinger.application.desmond.packages.msys.Atom property)
vel() (schrodinger.application.desmond.packages.pfx.Frame method)
(schrodinger.application.desmond.packages.topo.DuckFrame method)
(schrodinger.application.desmond.packages.traj.Frame method)
Vendor (class in schrodinger.application.licensing.flexlm)
vendor() (schrodinger.application.licensing.flexlm.Vendor method)
verbose (schrodinger.structutils.minimize.Minimizer property)
verify() (schrodinger.job.launchparams.LaunchParameters method)
verify_file_exists() (in module schrodinger.application.desmond.util)
verify_template_has_coordinates() (in module schrodinger.rdkit.substructure)
verify_traj_exists() (in module schrodinger.application.desmond.util)
verify_zip() (in module schrodinger.test.stu.common)
Version (class in schrodinger.application.livedesign.login)
version (schrodinger.forcefield.ffld_options.ForceFieldOptions attribute)
version() (in module schrodinger.application.matsci.qb_sdk.api)
VERSION_1_6_5 (schrodinger.utils.openmpi.OpenMPIVersion attribute)
version_at_least() (in module schrodinger)
version_at_most() (in module schrodinger)
version_compatible() (in module schrodinger)
version_str_to_tuple() (in module schrodinger.application.desmond.antlr3)
version_string() (in module schrodinger.utils.singledashoptionparser)
version_uptodate() (in module schrodinger.application.licensing.licadmin)
versionString (schrodinger.job.server.ServerInfo attribute)
vertex (schrodinger.project.surface.ProjectSurface.ColorFrom attribute)
(schrodinger.surface.ColorFrom attribute)
(schrodinger.surface.Surface.ColorFrom attribute)
vertex_colors (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
vertex_coords (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
vertex_count (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
vertex_normals (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
verticalScrollBar() (schrodinger.ui.dendrogram.DendrogramView method)
verticalScrollBarPolicy() (schrodinger.ui.dendrogram.DendrogramView method)
VIEW_SETTINGS (schrodinger.application.msv.gui.homology_modeling.constants.StepAction attribute)
viewer() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer class method)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer class method)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer class method)
viewport() (schrodinger.ui.dendrogram.DendrogramView method)
viewportEvent() (schrodinger.ui.dendrogram.DendrogramView method)
viewportMargins() (schrodinger.ui.dendrogram.DendrogramView method)
viewportSizeHint() (schrodinger.ui.dendrogram.DendrogramView method)
viewportTransform() (schrodinger.ui.dendrogram.DendrogramView method)
viewportUpdateMode() (schrodinger.ui.dendrogram.DendrogramView method)
views() (schrodinger.ui.dendrogram.DendrogramScene method)
virtualenv
VirtualLibrary (class in schrodinger.structutils.markush_enumerate)
visible (schrodinger.project.surface.ProjectSurface property)
(schrodinger.structure._StructureAtom property)
(schrodinger.surface.Surface property)
visibleChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
visibleFeatureLabels() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
visiblePropLabels() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
visibleRefCt() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
visibleRegion() (schrodinger.ui.dendrogram.DendrogramView method)
visibleTol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
visibleXvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
visit() (schrodinger.application.desmond.antlr3.tree.TreeVisitor method)
(schrodinger.application.desmond.antlr3.treewizard.TreeWizard method)
VLine (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shape attribute)
Vol2Den() (in module schrodinger.application.matsci.gsas.GSASIImath)
volume (schrodinger.application.desmond.packages.analysis.Pbc property)
(schrodinger.project.surface.ProjectSurface.ColorFrom attribute)
(schrodinger.surface.ColorFrom attribute)
(schrodinger.surface.Surface.ColorFrom attribute)
volume_name (schrodinger.project.surface.ProjectSurface property)
(schrodinger.surface.Surface property)
VolumeData (class in schrodinger.analysis.visanalysis.volumedata)
VolumeMapper (class in schrodinger.application.desmond.packages.analysis)
voxelize() (schrodinger.application.desmond.packages.msys.SpatialHash method)
vqa (schrodinger.application.matsci.qb_sdk.parameters.QubecAlgorithm attribute)
vx (schrodinger.application.desmond.packages.msys.Atom property)
vy (schrodinger.application.desmond.packages.msys.Atom property)
vz (schrodinger.application.desmond.packages.msys.Atom property)
W
wait_and_monitor_usage() (in module schrodinger.test.performance.general)
wait_completion() (schrodinger.application.matsci.qb_sdk.job.QubecJob method)
wait_for_successful_completion() (in module schrodinger.test.performance.general)
waitForSchrodDaemon() (schrodinger.application.licensing.licadmin.LocalServerProcess method)
walk() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
warn() (schrodinger.test.perceptualdiff.PerceptualDiffTest method)
(schrodinger.test.pytest.exetest.ExecutableFile method)
(schrodinger.test.pytest.exetest.ExecutableTest method)
(schrodinger.test.pytest.exetest.Makefile method)
(schrodinger.test.pytest.exetest.MakefileTest method)
WARNING_TEXT (schrodinger.ui.qt.standard.colors.LightModeColors attribute)
warnings (schrodinger.application.desmond.packages.msys.SmartsPattern property)
WATER (schrodinger.application.jaguar.csrch_input_constants.SOLVENT attribute)
WATER_MODELS (class in schrodinger.application.desmond.constants)
water_mol() (in module schrodinger.application.desmond.fep_edge_data)
WATER_NAMES (schrodinger.application.prime.wrapper.PrimeTemplate attribute)
WATERMAP_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute)
WATERMAP_VERSION (schrodinger.application.desmond.envir.CONST attribute)
waters (schrodinger.application.prime.wrapper.PrimeTemplate property)
WatLigFragDistance (class in schrodinger.application.desmond.packages.analysis)
wavekE() (in module schrodinger.application.matsci.gsas.GSASIImath)
WEAK (schrodinger.application.msv.gui.homology_modeling.constants.AlignmentQuality attribute)
WeakRefAttribute (class in schrodinger.infra.util)
web_cie_to_rgb() (in module schrodinger.application.matsci.colorutils)
webServerSecret (schrodinger.job.server.ServerInfo attribute)
wedge() (schrodinger.application.desmond.rl_helper.NumberedCanvas method)
wedge_clean() (in module schrodinger.livedesign.preprocessor)
whatsThis() (schrodinger.ui.dendrogram.DendrogramView method)
wheelEvent() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
which() (in module schrodinger.job.remote_command)
WHITE (schrodinger.ui.qt.standard.colors.DarkModeColors attribute)
(schrodinger.ui.qt.standard.colors.LightModeColors attribute)
(schrodinger.ui.qt.standard.colors.NativeColors attribute)
whole_ring_test() (in module schrodinger.application.desmond.r_group_asl)
width() (schrodinger.ui.dendrogram.DendrogramScene method)
(schrodinger.ui.dendrogram.DendrogramView method)
widthMM() (schrodinger.ui.dendrogram.DendrogramView method)
WILDCARD_PATTERN (schrodinger.utils.sea.sea.Atom attribute)
(schrodinger.utils.sea.sea.Hydrogen attribute)
WildcardTreePattern (class in schrodinger.application.desmond.antlr3.treewizard)
window() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
window_length (schrodinger.structutils.structalign.StructAlign property)
windowFilePath() (schrodinger.ui.dendrogram.DendrogramView method)
windowFlags() (schrodinger.ui.dendrogram.DendrogramView method)
windowHandle() (schrodinger.ui.dendrogram.DendrogramView method)
windowIcon() (schrodinger.ui.dendrogram.DendrogramView method)
windowIconChanged (schrodinger.ui.dendrogram.DendrogramView attribute)
windowIconText() (schrodinger.ui.dendrogram.DendrogramView method)
windowIconTextChanged (schrodinger.ui.dendrogram.DendrogramView attribute)
windowModality() (schrodinger.ui.dendrogram.DendrogramView method)
windowOpacity() (schrodinger.ui.dendrogram.DendrogramView method)
windowRole() (schrodinger.ui.dendrogram.DendrogramView method)
windowState() (schrodinger.ui.dendrogram.DendrogramView method)
windowTitle() (schrodinger.ui.dendrogram.DendrogramView method)
windowTitleChanged (schrodinger.ui.dendrogram.DendrogramView attribute)
windowType() (schrodinger.ui.dendrogram.DendrogramView method)
winId() (schrodinger.ui.dendrogram.DendrogramView method)
WinPanel (schrodinger.ui.dendrogram.DendrogramView attribute)
(schrodinger.ui.dendrogram.DendrogramView.Shape attribute)
with_traceback() (schrodinger.adapter.InconsistentStructureError method)
(schrodinger.adapter.UnsupportedStructureError method)
(schrodinger.analysis.visanalysis.vdexception.VDException method)
(schrodinger.application.canvas.similarity.CanvasSimilarityNotImplemented method)
(schrodinger.application.canvas.topo_descriptors.TopoError method)
(schrodinger.application.desmond.antlr3.exceptions.BacktrackingFailed method)
(schrodinger.application.desmond.antlr3.exceptions.EarlyExitException method)
(schrodinger.application.desmond.antlr3.exceptions.FailedPredicateException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedNotSetException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedRangeException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedSetException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTokenException method)
(schrodinger.application.desmond.antlr3.exceptions.MismatchedTreeNodeException method)
(schrodinger.application.desmond.antlr3.exceptions.MissingTokenException method)
(schrodinger.application.desmond.antlr3.exceptions.NoViableAltException method)
(schrodinger.application.desmond.antlr3.exceptions.RecognitionException method)
(schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException method)
(schrodinger.application.desmond.antlr3.tree.RewriteCardinalityException method)
(schrodinger.application.desmond.antlr3.tree.RewriteEarlyExitException method)
(schrodinger.application.desmond.antlr3.tree.RewriteEmptyStreamException method)
(schrodinger.application.desmond.arkdb.ArkDbDelError method)
(schrodinger.application.desmond.arkdb.ArkDbGetError method)
(schrodinger.application.desmond.arkdb.ArkDbPutError method)
(schrodinger.application.desmond.arkdb.CompositeKeySyntaxError method)
(schrodinger.application.desmond.packages.restraint.utils.CrossLinkGenerationError method)
(schrodinger.application.desmond.packages.traj_util.TrajectoryUnreadableError method)
(schrodinger.application.desmond.task.SubtaskExecutionError method)
(schrodinger.application.desmond.torsion_related.IncompleteFragmentError method)
(schrodinger.application.fpsim.QueryError method)
(schrodinger.application.fpsim.SearchError method)
(schrodinger.application.fpsim.ServerError method)
(schrodinger.application.jaguar.exceptions.JaguarIOError method)
(schrodinger.application.jaguar.exceptions.JaguarRuntimeError method)
(schrodinger.application.jaguar.exceptions.JaguarUnsupportedBasisSet method)
(schrodinger.application.jaguar.exceptions.JaguarUserFacingException method)
(schrodinger.application.jaguar.exceptions.QRNNSupportError method)
(schrodinger.application.jaguar.exceptions.xTBFailure method)
(schrodinger.application.jaguar.neural_network_optimizer.AniServerError method)
(schrodinger.application.jaguar.neural_network_optimizer.OptimizationFailure method)
(schrodinger.application.jaguar.neural_network_optimizer.UnsupportedElementError method)
(schrodinger.application.jaguar.results.IncompleteOutput method)
(schrodinger.application.jaguar.user_config.JaguarConfigError method)
(schrodinger.application.jaguar.workflow_validation.ConstraintFormatError method)
(schrodinger.application.jaguar.workflow_validation.JaguarKeywordConflict method)
(schrodinger.application.jaguar.workflow_validation.WorkflowConservationError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordConflictError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordException method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordFormatError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordValueError method)
(schrodinger.application.jaguar.workflow_validation.WorkflowKeywordValueTypeError method)
(schrodinger.application.licensing.flexlm.IncompatibleLicenseError method)
(schrodinger.application.licensing.flexlm.LicfileError method)
(schrodinger.application.licensing.licadmin.MissingExecutableError method)
(schrodinger.application.licensing.licadmin.MissingLicenseFile method)
(schrodinger.application.licensing.licadmin.NetsuiteError method)
(schrodinger.application.licensing.licadmin.UsageError method)
(schrodinger.application.licensing.licerror.LicenseException method)
(schrodinger.application.licensing.lmgrd_log_parser.UsageError method)
(schrodinger.application.ligprep.ionizer.TolerableError method)
(schrodinger.application.ligprep.ionizer.TooManyGroupsError method)
(schrodinger.application.matsci.graph.NetworkLoopError method)
(schrodinger.application.matsci.mlearn.descriptor.FeaturizeError method)
(schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptorError method)
(schrodinger.application.matsci.mlearn.sklearn_json.ModellNotSupported method)
(schrodinger.application.matsci.msprops.PropertyNameError method)
(schrodinger.application.matsci.qb_sdk.parameters.QubecSdkError method)
(schrodinger.application.matsci.qeschema.qeschema.exceptions.QESchemaError method)
(schrodinger.application.matsci.qeschema.qeschema.exceptions.XmlDocumentError method)
(schrodinger.application.matsci.qexsd.qespresso.exceptions.ConfigError method)
(schrodinger.application.matsci.qexsd.qespresso.exceptions.QEspressoError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.FileFormatError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLDecodeError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLEncodeError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLSchemaValidationError method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions.XMLValueError method)
(schrodinger.application.mopac.exceptions.MopacIOError method)
(schrodinger.application.mopac.exceptions.MopacRuntimeError method)
(schrodinger.application.mopac.exceptions.MopacUserFacingException method)
(schrodinger.application.mopac.results_main.MopacBasisError1 method)
(schrodinger.application.mopac.results_main.MopacBasisError2 method)
(schrodinger.application.mopac.results_main.MopacBasisError3 method)
(schrodinger.application.mopac.results_main.MopacBasisError4 method)
(schrodinger.application.mopac.results_main.MopacBasisError5 method)
(schrodinger.application.mopac.results_main.MopacGradientParserError method)
(schrodinger.application.mopac.results_main.MopacNumericalError method)
(schrodinger.application.mopac.results_main.MopacPropertyError method)
(schrodinger.application.mopac.structure_launchers.StructureLauncherError method)
(schrodinger.forcefield.common.AtomTypingFailure method)
(schrodinger.infra.canvas.ChmException method)
(schrodinger.infra.canvas.CtAssertion method)
(schrodinger.infra.canvas.CtException method)
(schrodinger.infra.canvas.CtMsgException method)
(schrodinger.infra.canvas.CtRdrException method)
(schrodinger.infra.fast3d.f3d_Exception method)
(schrodinger.infra.mmcheck.MmException method)
(schrodinger.infra.phase.PhpException method)
(schrodinger.infra.structure.MmctSerializerException method)
(schrodinger.infra.structure.PyStructureReaderException method)
(schrodinger.job.launchparams.ArgumentParserError method)
(schrodinger.job.remote_command.CommandError method)
(schrodinger.livedesign.preprocessor.BlindedCompoundError method)
(schrodinger.MaestroNotAvailableError method)
(schrodinger.models.json.JSONEncodeError method)
(schrodinger.protein.biounit.BiounitOverrunError method)
(schrodinger.rdkit.rdkit_adapter.InconsistentStructureError method)
(schrodinger.rdkit.rdkit_adapter.UnsupportedStructureError method)
(schrodinger.structure.AtomsInRingError method)
(schrodinger.structure.UndefinedStereochemistry method)
(schrodinger.structutils.measure.LinearError method)
(schrodinger.structutils.rgroup_enumerate.BondOrderMismatch method)
(schrodinger.structutils.rgroup_enumerate.RGroupError method)
(schrodinger.structutils.rmsd.DisabledSymmetryWarning method)
(schrodinger.structutils.shuffle.ShuffleException method)
(schrodinger.test.darwinconsole.UnsupportedPlatformException method)
(schrodinger.test.performance.exceptions.BadResponse method)
(schrodinger.test.pytest.exetest.ExecutableFile.CollectError method)
(schrodinger.test.pytest.exetest.Makefile.CollectError method)
(schrodinger.test.pytest.exetest.ProcessDied method)
(schrodinger.test.pytest.exetest.ProcessKilled method)
(schrodinger.test.stu.common.ZipError method)
(schrodinger.utils.cgxutils.SerializationError method)
(schrodinger.utils.deprecation.DeprecationError method)
(schrodinger.utils.fileutils.SharingViolationError method)
within_three_bonds() (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method)
(schrodinger.protein.analysis.Report.steric_clash_data_set method)
worker() (in module schrodinger.application.matsci.gsas.GSASIImath)
WorkflowConservationError
WorkflowKeywordConflictError
WorkflowKeywordError
WorkflowKeywordException
WorkflowKeywordFormatError
WorkflowKeywordValueError
WorkflowKeywordValueTypeError
WorkflowMenuMaestroWriter (class in schrodinger.infra.structure)
WorkflowType (class in schrodinger.infra.structure)
working_directory() (in module schrodinger.application.licensing.licadmin)
workspace
Maestro
WORKSPACE (schrodinger.job.launchparams.ProjectDisposition attribute)
workspace, Maestro
workup() (in module schrodinger.test.stu.workups.workup_tools)
WorldCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method)
worst_saved_score() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method)
wrap() (schrodinger.application.desmond.packages.analysis.Pbc method)
wrap_module() (in module schrodinger.infra.mmcheck)
wrapinstance() (in module schrodinger.Qt.PyQt6.sip)
writable_server_log() (in module schrodinger.application.licensing.licadmin)
write() (in module schrodinger.ui.qt.appframework2.appmethods)
(schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint static method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method)
(schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method)
(schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method)
(schrodinger.application.desmond.arkdb.ArkDb method)
(schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.fep_struc.SchrodStruc method)
(schrodinger.application.desmond.fep_struc.Struc method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.application.desmond.gaussian_filter.GaussianFilter method)
(schrodinger.application.desmond.multisim.parser.Msj method)
(schrodinger.application.desmond.packages.traj.Frame method)
(schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.licensing.flexlm.License method)
(schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method)
(schrodinger.application.mopac.structure_launchers.StructureLauncher method)
(schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
(schrodinger.application.qsite.input.QSiteInput method)
(schrodinger.infra.structure.WorkflowMenuMaestroWriter static method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.pipeline.input.LinearWriter method)
(schrodinger.pipeline.input.Writer method)
(schrodinger.project.surface.ProjectSurface method)
(schrodinger.rdkit.molio.MolWriter static method)
(schrodinger.structure.PDBWriter method)
(schrodinger.structure.SmilesStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.StructureWriter static method)
(schrodinger.structure.TextualStructure method)
(schrodinger.surface.Surface method)
(schrodinger.ui.qt.appframework2.debugcore.DebugStderr class method)
(schrodinger.ui.qt.appframework2.debugcore.DebugStdout class method)
write_apbs_input_with_ligand() (in module schrodinger.application.desmond.fep_net_charge)
write_apbs_input_with_protein() (in module schrodinger.application.desmond.fep_net_charge)
write_attachment_block() (in module schrodinger.application.combiglide.corehop)
write_blocks() (in module schrodinger.structutils.block_data)
write_charge() (in module schrodinger.application.matsci.qeschema.qeschema.hdf5.charge)
write_cms() (in module schrodinger.application.desmond.ffiostructure)
write_cms_to_string() (in module schrodinger.application.desmond.ffiostructure)
write_ct_to_string() (in module schrodinger.structure)
write_cts() (in module schrodinger.structure)
write_data() (schrodinger.application.desmond.bennett.CalcBAR method)
write_dE() (in module schrodinger.application.desmond.deltaE)
write_elec_block() (in module schrodinger.application.desmond.fep_net_charge)
write_encrypted_file() (in module schrodinger.application.matsci.enc)
write_encrypted_text() (in module schrodinger.application.matsci.enc)
write_events_csv() (in module schrodinger.application.licensing.lmgrd_log_parser)
write_features_json() (in module schrodinger.utils.featureflags.write)
write_ff_solute_tempering() (in module schrodinger.application.desmond.remd)
write_file() (in module schrodinger.application.licensing.licadmin)
write_fortran_input() (schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument method)
(schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument method)
write_job_cmd() (in module schrodinger.job.jobwriter)
write_ligand_file() (in module schrodinger.application.desmond.util)
write_n_ct() (in module schrodinger.application.desmond.util)
write_overall_usage_csv() (in module schrodinger.application.licensing.lmgrd_log_parser)
write_pdb_cache() (in module schrodinger.test.stu.get_pdbs)
write_pqr() (in module schrodinger.application.desmond.fep_net_charge)
write_pqrs() (in module schrodinger.application.desmond.fep_net_charge)
write_props_to_csv() (in module schrodinger.application.bioluminate.residue_scanning.properties)
write_qe_input() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method)
(schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method)
write_reactions_file() (in module schrodinger.application.pathfinder.reaction)
write_reagent_classes_file() (in module schrodinger.application.pathfinder.reaction)
write_restraints() (in module schrodinger.forcefield.minimizer)
write_results() (schrodinger.application.desmond.bennett.CalcBAR method)
write_sba_file() (in module schrodinger.application.desmond.simulation_block_data)
write_to_stdout() (schrodinger.protein.analysis.Report method)
write_to_string() (schrodinger.application.desmond.cms.Cms method)
write_traj() (in module schrodinger.application.desmond.packages.traj)
write_unencrypted_file() (in module schrodinger.application.matsci.enc)
write_usage_csv() (in module schrodinger.application.licensing.lmgrd_log_parser)
write_v3000 (schrodinger.structure.SDWriter.Options attribute)
write_vis_files() (schrodinger.application.mopac.results_main.MopacResultsMain method)
writeAlignData() (schrodinger.structutils.sitealign.BindingSiteAligner method)
writeCommand() (schrodinger.structutils.rmsd.ConformerRmsd method)
(schrodinger.structutils.rmsd.ConformerRmsdX method)
writeConfig() (schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
WriteControls() (in module schrodinger.application.matsci.gsas.GSASIIfiles)
writeCSVFile() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
writeFile() (schrodinger.structutils.color.ColorScheme method)
writeFPFile() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
writeInputFile() (schrodinger.application.inputconfig.InputConfig method)
(schrodinger.application.phase.input.PhaseHypothesisInputConfig method)
(schrodinger.application.prime.input.Prime method)
(schrodinger.application.prime.wrapper.ConsensusConfig method)
(schrodinger.application.prime.wrapper.PrimeConfig method)
writeInputForConsensus() (schrodinger.application.prime.wrapper.BasePrimeAlignment method)
writeInputForPrime() (schrodinger.application.prime.wrapper.BasePrimeAlignment method)
writeInteractionsFile() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method)
writeLigand() (schrodinger.application.glide.poseviewconvert.Complex method)
writeLogEntry() (schrodinger.ui.qt.appframework2.debugcore.AbstractDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.FileDebugViewer method)
(schrodinger.ui.qt.appframework2.debugcore.StdoutDebugViewer method)
writeMatrixData() (schrodinger.structutils.sitealign.BindingSiteAligner method)
WriteMode_APPEND (schrodinger.infra.structure.WorkflowMenuMaestroWriter attribute)
WriteMode_OVERWRITE (schrodinger.infra.structure.WorkflowMenuMaestroWriter attribute)
writeNMD() (in module schrodinger.trajectory.prody.writenmd)
writeNMDmae() (in module schrodinger.trajectory.prody.writenmd)
writePDB() (schrodinger.application.prime.wrapper.PrimeTemplate method)
writePv() (schrodinger.application.glide.poseviewconvert.Complex method)
Writer (class in schrodinger.pipeline.input)
writer_open() (in module schrodinger.utils.csv_unicode)
writeReceptor() (schrodinger.application.glide.poseviewconvert.Complex method)
writeSchemeFile() (schrodinger.structutils.color.ColorScheme method)
writeSettings() (schrodinger.trajectory.trajectory_gui_dir.playback_settings_data.PlaybackSettingsData method)
writeStructures() (schrodinger.structutils.rmsd.ConformerRmsd method)
(schrodinger.structutils.rmsd.ConformerRmsdX method)
(schrodinger.structutils.sitealign.BindingSiteAligner method)
writeSummary() (schrodinger.application.phase.hypothesis.PhaseHypothesis method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStandard method)
(schrodinger.application.phase.hypothesis.PhaseHypothesisStatic method)
writeToString() (schrodinger.application.desmond.cms.Cms method)
(schrodinger.application.desmond.ffiostructure.FFIOStructure method)
(schrodinger.models.jsonable.JsonableStructure method)
(schrodinger.structure.Structure method)
(schrodinger.structure.TextualStructure method)
written_count (schrodinger.rdkit.molio.PfxMolWriter property)
(schrodinger.rdkit.molio.RdkitMolWriter property)
WT (schrodinger.application.desmond.constants.FEP_STATE_KEYS attribute)
wt_frag_st (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
wt_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
wt_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
wt_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
wt_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData property)
(schrodinger.application.desmond.fep_edge_data.PRMEdgeData property)
X
x (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.structure._StructureAtom property)
x() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
X_BIAS_F() (in module schrodinger.application.matsci.uq_utils)
XAnomAbs() (in module schrodinger.application.matsci.gsas.GSASIImath)
xChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
xfail_m1() (in module schrodinger.test.test_markers)
xml2in() (in module schrodinger.application.matsci.qeschema.utils)
(in module schrodinger.application.matsci.qexsd.utils)
XML_NAMESPACE (in module schrodinger.application.matsci.qeschema.qeschema.namespaces)
XML_SCHEMA_NAMESPACES (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute)
xml_to_dict() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree)
XMLDecodeError
XmlDocument (class in schrodinger.application.matsci.qeschema.qeschema.documents)
(class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument)
XmlDocumentError
XMLEncodeError
XMLSchema (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema)
XMLSchemaValidationError
XMLValueError
XpPVParser (class in schrodinger.application.glide.xpdes)
XRDCalculator (class in schrodinger.application.matsci.xrd)
XScattDen() (in module schrodinger.application.matsci.gsas.GSASIImath)
xsd_attribute_type_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSD_BUILTIN_TYPES (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
xsd_builtin_types_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
xsd_complex_type_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
xsd_element_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
xsd_get_type() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
xsd_group_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSD_NAMESPACE (in module schrodinger.application.matsci.qeschema.qeschema.namespaces)
xsd_simple_type_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
xsd_type (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute attribute)
(schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement attribute)
XSDAttribute (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSDComplexType (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSDElement (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSDGroup (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSDSimpleType (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSDType (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSI_ATTRIBUTES (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes)
XSI_NAMESPACE (in module schrodinger.application.matsci.qeschema.qeschema.namespaces)
xTBFailure
XTC (schrodinger.application.desmond.packages.traj.Fmt attribute)
XtcSource (class in schrodinger.application.desmond.packages.traj)
XYZ (schrodinger.infra.structure.FileFormat attribute)
xyz (schrodinger.structure._StructureAtom property)
xyz_to_sdf() (in module schrodinger.utils.fileutils)
xyzasu (schrodinger.application.matsci.nano.space_groups.SpaceGroup attribute)
Y
y (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.structure._StructureAtom property)
y() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
(schrodinger.ui.dendrogram.DendrogramView method)
Y_AXIS_SCALE (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute)
yChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
yield_enum_and_typed_val() (in module schrodinger.forcefield.ffld_options)
Z
z (schrodinger.application.desmond.packages.msys.Atom property)
(schrodinger.structure._StructureAtom property)
Z_INDEX (schrodinger.ui.qt.label_cursor.LabelCursorAxes attribute)
zChanged (schrodinger.ui.dendrogram.DendrogramGraphicNode attribute)
Zero (schrodinger.structure.BondType attribute)
ZERO_NORM_TANGENT (schrodinger.application.jaguar.constants.FatalErrors attribute)
zfill() (schrodinger.application.desmond.constants.MaePropertyName method)
(schrodinger.application.jaguar.jaguar_diff.CaseInsensitiveString method)
(schrodinger.utils.fileutils.tempfilename method)
(schrodinger.utils.fileutils.TempStructureFile method)
(schrodinger.utils.sea.sea.Key method)
zip_directory() (in module schrodinger.test.stu.common)
zip_files() (in module schrodinger.test.stu.common)
(in module schrodinger.utils.fileutils)
ZipError
zpe_precision (schrodinger.application.jaguar.results.JaguarResults attribute)
zValue() (schrodinger.ui.dendrogram.DendrogramGraphicNode method)
(schrodinger.ui.dendrogram.DendrogramGraphicNodeLabel method)
(schrodinger.ui.dendrogram.DendrogramGraphicTree method)
ZVariables (class in schrodinger.application.jaguar.results)
Quick search
Navigation
index
modules
|
Schrödinger Python API 2022-4 documentation
»
Index