Index

A

A (rdkit.Chem.QED.ADSparameter attribute) AAtomQueryAtom() (in module rdkit.Chem.rdqueries) abbreviation (rdkit.Chem.rdDeprotect.DeprotectData property) AbbreviationDefinition (class in rdkit.Chem.rdAbbreviations) acceptFailure (rdkit.Chem.rdDepictor.ConstrainedDepictionParams property) AccumulateVotes() (rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRanker method) acidbaseFile (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) actCol (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) Add() (rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition method) add_new_match() (rdkit.Chem.fmcs.fmcs.SingleBestAtoms method) (rdkit.Chem.fmcs.fmcs.SingleBestAtomsCompleteRingsOnly method) (rdkit.Chem.fmcs.fmcs.SingleBestBonds method) (rdkit.Chem.fmcs.fmcs.SingleBestBondsCompleteRingsOnly method) ADD_WEIGHTS (rdkit.Chem.RegistrationHash.EnhancedStereoUpdateMode attribute) AddAgentTemplate() (rdkit.Chem.rdChemReactions.ChemicalReaction method) AddAtom() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) addAtomIndices (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) AddAtomWithBookmark() (rdkit.Chem.rdchem.SubstanceGroup method) AddAtomWithIdx() (rdkit.Chem.rdchem.SubstanceGroup method) AddAttachPoint() (rdkit.Chem.rdchem.SubstanceGroup method) AddBinary() (rdkit.Chem.rdSubstructLibrary.CachedMolHolder method) AddBit() (rdkit.DataStructs.BitEnsemble.BitEnsemble method) AddBond() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) addBondIndices (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) AddBondWithBookmark() (rdkit.Chem.rdchem.SubstanceGroup method) AddBondWithIdx() (rdkit.Chem.rdchem.SubstanceGroup method) AddBracket() (rdkit.Chem.rdchem.SubstanceGroup method) AddCatalog() (rdkit.Chem.rdfiltercatalog.FilterCatalogParams method) AddChild() (rdkit.Chem.rdfiltercatalog.FilterHierarchyMatcher method) (rdkit.ML.Cluster.Clusters.Cluster method) (rdkit.VLib.Node.VLibNode method) AddChildren() (rdkit.ML.Cluster.Clusters.Cluster method) AddColumn() (rdkit.Dbase.DbConnection.DbConnect method) AddConformer() (rdkit.Chem.rdchem.Mol method) AddConformersToMol() (rdkit.Chem.rdtrajectory.Trajectory method) AddCoords() (in module rdkit.Chem.rdCoordGen) AddCState() (rdkit.Chem.rdchem.SubstanceGroup method) AddDistanceConstraint() (rdkit.ForceField.rdForceField.ForceField method) AddEdge() (rdkit.Chem.rdMolCatalog.MolCatalog method) AddEntry() (rdkit.Chem.rdfiltercatalog.FilterCatalog method) (rdkit.Chem.rdMolCatalog.MolCatalog method) AddExcludedVolumes() (in module rdkit.Chem.Pharm3D.EmbedLib) AddExclusion() (rdkit.Chem.FragmentMatcher.FragmentMatcher method) AddExtraPoint() (rdkit.ForceField.rdForceField.ForceField method) AddFeatPoint() (rdkit.Chem.FeatMaps.FeatMaps.FeatMap method) AddFeature() (rdkit.Chem.FeatMaps.FeatMaps.FeatMap method) AddFingerprint() (rdkit.Chem.rdSubstructLibrary.FPHolderBase method) AddFixedPoint() (rdkit.ForceField.rdForceField.ForceField method) AddFragsFromMol() (rdkit.Chem.rdfragcatalog.FragCatGenerator method) AddHs() (in module rdkit.Chem.rdmolops) additionalAtomLabelPadding (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) AdditionalOutput (class in rdkit.Chem.rdFingerprintGenerator) AddKey() (rdkit.Chem.rdSubstructLibrary.KeyHolderBase method) AddMetadataToPNGFile() (in module rdkit.Chem.rdmolfiles) AddMetadataToPNGString() (in module rdkit.Chem.rdmolfiles) AddMol() (rdkit.Chem.Draw.MolDrawing.MolDrawing method) (rdkit.Chem.rdchem.MolBundle method) (rdkit.Chem.rdSubstructLibrary.FPHolderBase method) (rdkit.Chem.rdSubstructLibrary.KeyHolderBase method) (rdkit.Chem.rdSubstructLibrary.MolHolderBase method) (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) AddMoleculeColumnToFrame() (in module rdkit.Chem.PandasTools) AddMoleculeMetadata() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG method) AddMolSubstanceGroup() (in module rdkit.Chem.rdchem) addMolToView() (in module rdkit.Chem.Draw.IPythonConsole) AddMurckoToFrame() (in module rdkit.Chem.PandasTools) AddParent() (rdkit.VLib.Node.VLibNode method) (rdkit.VLib.Supply.SupplyNode method) AddParentAtomWithBookmark() (rdkit.Chem.rdchem.SubstanceGroup method) AddParentAtomWithIdx() (rdkit.Chem.rdchem.SubstanceGroup method) AddPattern() (rdkit.Chem.rdfiltercatalog.ExclusionList method) AddPatterns() (in module rdkit.Chem.rdSubstructLibrary) AddPharmacophore() (rdkit.Chem.PyMol.MolViewer method) AddPoint() (rdkit.ML.Data.MLData.MLDataSet method) AddPoints() (rdkit.ML.Data.MLData.MLDataSet method) AddProductTemplate() (rdkit.Chem.rdChemReactions.ChemicalReaction method) AddReactantTemplate() (rdkit.Chem.rdChemReactions.ChemicalReaction method) AddReader() (rdkit.DataStructs.cDataStructs.MultiFPBReader method) AddRecursiveQueriesToReaction() (rdkit.Chem.rdChemReactions.ChemicalReaction method) AddRecursiveQuery() (in module rdkit.Chem.rdmolops) AddRing() (rdkit.Chem.rdchem.RingInfo method) AddRingSystemTemplates() (in module rdkit.Chem.rdDepictor) AddSmiles() (rdkit.Chem.rdSubstructLibrary.CachedSmilesMolHolder method) (rdkit.Chem.rdSubstructLibrary.CachedTrustedSmilesMolHolder method) AddSnapshot() (rdkit.Chem.rdtrajectory.Trajectory method) addStereoAnnotation (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) AddStereoAnnotations() (in module rdkit.Chem.rdmolops) AddTable() (rdkit.Dbase.DbConnection.DbConnect method) AddVect() (rdkit.DataStructs.VectCollection.VectCollection method) AddWavyBondsForStereoAny() (in module rdkit.Chem.rdmolops) ADJUST_IGNOREALL (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) ADJUST_IGNORECHAINS (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) ADJUST_IGNOREDUMMIES (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) ADJUST_IGNOREMAPPED (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) ADJUST_IGNORENONDUMMIES (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) ADJUST_IGNORENONE (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) ADJUST_IGNORERINGS (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) adjustCharges (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnectorOptions property) adjustConjugatedFiveRings (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustDegree (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustDegreeFlags (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustHeavyDegree (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustHeavyDegreeFlags (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustMolBlockWedging (rdkit.Chem.rdDepictor.ConstrainedDepictionParams property) AdjustQueryParameters (class in rdkit.Chem.rdmolops) AdjustQueryProperties() (in module rdkit.Chem.rdmolops) AdjustQueryPropertiesWithGenericGroups() (in module rdkit.Chem.rdmolops) AdjustQueryWhichFlags (class in rdkit.Chem.rdmolops) adjustRingChain (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustRingChainFlags (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustRingCount (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustRingCountFlags (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustSingleBondsBetweenAromaticAtoms (rdkit.Chem.rdmolops.AdjustQueryParameters property) adjustSingleBondsToDegreeOneNeighbors (rdkit.Chem.rdmolops.AdjustQueryParameters property) ads() (in module rdkit.Chem.QED) ADSparameter (class in rdkit.Chem.QED) agentWeight (rdkit.Chem.rdChemReactions.ReactionFingerprintParams property) AHAtomQueryAtom() (in module rdkit.Chem.rdqueries) aIdx (rdkit.Chem.rdchem.SubstanceGroupAttach property) ALERTS (rdkit.Chem.QED.QEDproperties attribute) algorithm (rdkit.Chem.rdFreeSASA.SASAOpts property) alias_conversion_failed (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) Align() (rdkit.Chem.rdMolAlign.O3A method) AlignDepict() (in module rdkit.Chem.ChemUtils.AlignDepict) alignedConfId (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment attribute) alignment (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) AlignMol() (in module rdkit.Chem.PandasTools) (in module rdkit.Chem.rdMolAlign) AlignMolConformers() (in module rdkit.Chem.rdMolAlign) AlignMolToTemplate2D() (in module rdkit.Chem.TemplateAlign) alignOnly (rdkit.Chem.rdDepictor.ConstrainedDepictionParams property) AlignToScaffold() (in module rdkit.Chem.PandasTools) All (rdkit.Chem.FeatMaps.FeatMaps.FeatMapScoreMode attribute) ALL (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) ALL_LAYERS (rdkit.Chem.RegistrationHash.HashScheme attribute) all_subgraph_extensions() (in module rdkit.Chem.fmcs.fmcs) AllBitSimilarity() (in module rdkit.DataStructs.cDataStructs) allBondsExplicit (rdkit.Chem.rdmolfiles.SmilesWriteParams property) allHsExplicit (rdkit.Chem.rdmolfiles.SmilesWriteParams property) AllocateAtomCounts() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) AllocateAtomToBits() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) AllocateBitInfoMap() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) AllocateBitPaths() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) ALLOW_CHARGE_SEPARATION (rdkit.Chem.rdchem.ResonanceFlags attribute) ALLOW_INCOMPLETE_OCTETS (rdkit.Chem.rdchem.ResonanceFlags attribute) allowAromaticBondType (rdkit.Chem.MolStandardize.rdMolStandardize.FeaturesValidation property) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) allowAtomAliases (rdkit.Chem.MolStandardize.rdMolStandardize.FeaturesValidation property) allowAtomBondClashExemption (rdkit.Chem.MolStandardize.rdMolStandardize.Layout2DValidation property) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property)

allowCXSMILES (rdkit.Chem.rdmolfiles.SmartsParserParams property) (rdkit.Chem.rdmolfiles.SmilesParserParams property) allowDativeBondType (rdkit.Chem.MolStandardize.rdMolStandardize.FeaturesValidation property) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) allowDummies (rdkit.Chem.MolStandardize.rdMolStandardize.FeaturesValidation property) AllowedAtomsValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) allowEmptyMolecules (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) (rdkit.Chem.MolStandardize.rdMolStandardize.RDKitValidation property) allowEnhancedStereo (rdkit.Chem.MolStandardize.rdMolStandardize.FeaturesValidation property) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) allowLongBondsInRings (rdkit.Chem.MolStandardize.rdMolStandardize.Layout2DValidation property) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) allowMultipleRGroupsOnUnlabelled (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) allowNonTerminalRGroups (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) allowQueries (rdkit.Chem.MolStandardize.rdMolStandardize.FeaturesValidation property) allowRGroups (rdkit.Chem.rdDepictor.ConstrainedDepictionParams property) AllProbeBitsMatch() (in module rdkit.DataStructs.cDataStructs) AllProps (rdkit.Chem.rdchem.PropertyPickleOptions attribute) ALOGP (rdkit.Chem.QED.QEDproperties attribute) AnalyzeSparseVects() (in module rdkit.ML.InfoTheory.BitRank) AngleTo() (rdkit.Geometry.rdGeometry.Point2D method) (rdkit.Geometry.rdGeometry.Point3D method) (rdkit.Geometry.rdGeometry.PointND method) AnnotateProperties() (rdkit.Chem.rdMolDescriptors.Properties method) annotationFontScale (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) AnonymousGraph (rdkit.Chem.rdMolHash.HashFunction attribute) APolar (rdkit.Chem.rdFreeSASA.SASAClass attribute) append() (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineLog method) (rdkit.Chem.rdchem.StereoGroup_vect method) (rdkit.Chem.rdchem.SubstanceGroup_VECT method) (rdkit.Chem.rdChemReactions.MOL_SPTR_VECT method) (rdkit.Chem.rdChemReactions.VectMolVect method) (rdkit.Chem.rdDeprotect.DeprotectDataVect method) (rdkit.Chem.rdfiltercatalog.FilterCatalogEntryList method) (rdkit.Chem.rdfiltercatalog.FilterCatalogListOfEntryList method) (rdkit.Chem.rdfiltercatalog.MolList method) (rdkit.Chem.rdfiltercatalog.VectFilterMatch method) (rdkit.Chem.Scaffolds.rdScaffoldNetwork.NetworkEdge_VECT method) (rdkit.rdBase.MatchTypeVect method) (rdkit.rdBase.UnsignedLong_Vect method) (rdkit.rdBase.VectorOfStringVectors method) AppendSkeletonPoints() (in module rdkit.Chem.Subshape.BuilderUtils) ArbAxisRotation() (in module rdkit.Chem.Features.FeatDirUtilsRD) AreAtomsInSameRing() (rdkit.Chem.rdchem.RingInfo method) AreAtomsInSameRingOfSize() (rdkit.Chem.rdchem.RingInfo method) AreBondsInSameRing() (rdkit.Chem.rdchem.RingInfo method) AreBondsInSameRingOfSize() (rdkit.Chem.rdchem.RingInfo method) AreRingFamiliesInitialized() (rdkit.Chem.rdchem.RingInfo method) AreRingsFused() (rdkit.Chem.rdchem.RingInfo method) AROM (rdkit.Chem.QED.QEDproperties attribute) AROMATIC (rdkit.Chem.rdchem.BondType attribute) AROMATICITY_CUSTOM (rdkit.Chem.rdmolops.AromaticityModel attribute) AROMATICITY_DEFAULT (rdkit.Chem.rdmolops.AromaticityModel attribute) AROMATICITY_MDL (rdkit.Chem.rdmolops.AromaticityModel attribute) AROMATICITY_MMFF94 (rdkit.Chem.rdmolops.AromaticityModel attribute) AROMATICITY_RDKIT (rdkit.Chem.rdmolops.AromaticityModel attribute) AROMATICITY_SIMPLE (rdkit.Chem.rdmolops.AromaticityModel attribute) AromaticityModel (class in rdkit.Chem.rdmolops) aromaticMatchesConjugated (rdkit.Chem.rdchem.SubstructMatchParameters property) aromatizeIfPossible (rdkit.Chem.rdmolops.AdjustQueryParameters property) ArthorSubstructureOrder (rdkit.Chem.rdMolHash.HashFunction attribute) Asphericity() (in module rdkit.Chem.Descriptors3D) assign_isotopes_from_class_tag() (in module rdkit.Chem.fmcs.fmcs) AssignAtomChiralTagsFromMolParity() (in module rdkit.Chem.rdmolops) AssignAtomChiralTagsFromStructure() (in module rdkit.Chem.rdmolops) AssignBondOrdersFromTemplate() (in module rdkit.Chem.AllChem) AssignChiralTypesFromBondDirs() (in module rdkit.Chem.rdmolops) AssignCIPLabels() (in module rdkit.Chem.rdCIPLabeler) AssignMolFeatsToPoints() (in module rdkit.Chem.Subshape.BuilderUtils) AssignPattyTypes() (in module rdkit.Chem.AtomPairs.Sheridan) AssignRadicals() (in module rdkit.Chem.rdmolops) AssignStereochemistry() (in module rdkit.Chem.rdmolops) AssignStereochemistryFrom3D() (in module rdkit.Chem.rdmolops) AsymmetricSimilarity() (in module rdkit.DataStructs.cDataStructs) AsymmetricSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) AsymmetricSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) atEnd() (rdkit.Chem.rdchem.ResonanceMolSupplier method) (rdkit.Chem.rdmolfiles.ForwardSDMolSupplier method) (rdkit.Chem.rdmolfiles.MaeMolSupplier method) (rdkit.Chem.rdmolfiles.MultithreadedSDMolSupplier method) (rdkit.Chem.rdmolfiles.MultithreadedSmilesMolSupplier method) (rdkit.Chem.rdmolfiles.SDMolSupplier method) Atom (class in rdkit.Chem.fmcs.fmcs) (class in rdkit.Chem.rdchem) atom_check_failed (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) atom_clash (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) atom_indices (rdkit.Chem.fmcs.fmcs.Bond attribute) (rdkit.Chem.fmcs.fmcs.Subgraph attribute) Atom_Octahedral (rdkit.Chem.rdchem.StereoType attribute) atom_smarts (rdkit.Chem.fmcs.fmcs.Atom attribute) (rdkit.Chem.fmcs.fmcs.CangenNode attribute) Atom_SquarePlanar (rdkit.Chem.rdchem.StereoType attribute) Atom_Tetrahedral (rdkit.Chem.rdchem.StereoType attribute) Atom_TrigonalBipyramidal (rdkit.Chem.rdchem.StereoType attribute) atom_typer_any() (in module rdkit.Chem.fmcs.fmcs) atom_typer_elements() (in module rdkit.Chem.fmcs.fmcs) atom_typer_isotopes() (in module rdkit.Chem.fmcs.fmcs) AtomBondCounts (rdkit.Chem.rdMolHash.HashFunction attribute) atomClashLimit (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) atomColors (rdkit.Chem.Draw.FingerprintEnv attribute) AtomCompare (class in rdkit.Chem.rdFMCS) atomCompare (rdkit.Chem.fmcs.fmcs.Default attribute) AtomCompareParameters (rdkit.Chem.rdFMCS.MCSParameters property) atomContrib() (in module rdkit.Chem.Fraggle.FraggleSim) AtomFromSmarts() (in module rdkit.Chem.rdmolfiles) AtomFromSmiles() (in module rdkit.Chem.rdmolfiles) AtomHasConjugatedBond() (in module rdkit.Chem.rdmolops) atomHighlightsAreCircles (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) AtomIndexLabels (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) AtomInvariantsGenerator (class in rdkit.Chem.rdFingerprintGenerator) AtomKekulizeException atomLabelDeuteriumTritium (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) atomLabelFontFace (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) atomLabelFontSize (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) atomLabelMinFontSize (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) atomLabels (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) AtomMap (rdkit.Chem.rdRGroupDecomposition.RGroupLabelling attribute) AtomMapLabels (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) AtomMapNumber (rdkit.Chem.rdmolops.MolzipLabel attribute) AtomMembers() (rdkit.Chem.rdchem.RingInfo method) AtomMonomerInfo (class in rdkit.Chem.rdchem) AtomMonomerType (class in rdkit.Chem.rdchem) atomNumberOffset (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) AtomNumEqualsQueryAtom() (in module rdkit.Chem.rdqueries) AtomNumGreaterQueryAtom() (in module rdkit.Chem.rdqueries) AtomNumLessQueryAtom() (in module rdkit.Chem.rdqueries) AtomPairFingerprintOptions (class in rdkit.Chem.rdFingerprintGenerator) AtomPairFP (rdkit.Chem.rdChemReactions.FingerprintType attribute) (rdkit.Chem.rdFingerprintGenerator.FPType attribute) atomPairs (rdkit.Chem.rdfiltercatalog.FilterMatch property) AtomPairsParameters (class in rdkit.Chem.rdMolDescriptors) AtomPDBResidueInfo (class in rdkit.Chem.rdchem) atomProperties (rdkit.Chem.rdchem.SubstructMatchParameters property) AtomProps (rdkit.Chem.rdchem.PropertyPickleOptions attribute) atomRegions (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) AtomRingFamilies() (rdkit.Chem.rdchem.RingInfo method) AtomRings() (rdkit.Chem.rdchem.RingInfo method) AtomRingSizes() (rdkit.Chem.rdchem.RingInfo method) AtomSanitizeException AtomSmartsNoAromaticity (class in rdkit.Chem.fmcs.fmcs) AtomType (rdkit.Chem.rdmolops.MolzipLabel attribute) AtomTyper (rdkit.Chem.rdFMCS.MCSParameters property) atomTypes (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) AtomValenceException AttachFileToLog() (in module rdkit.rdBase) AutoDetect (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) Average (rdkit.Chem.FeatMaps.FeatMapUtils.MergeMethod attribute) AVG() (in module rdkit.ML.Descriptors.Parser) AvgIpc() (in module rdkit.Chem.GraphDescriptors)

B

B (rdkit.Chem.QED.ADSparameter attribute) BAD_DOUBLE_BOND_STEREO (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) bad_molecule (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) bad_set (rdkit.Avalon.pyAvalonTools.StruChkResult attribute) BadMoleculeException BalabanJ() (in module rdkit.Chem.GraphDescriptors) baseFontSize (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) BASIC_VALIDATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) BCUT2D() (in module rdkit.Chem.rdMolDescriptors) BeginBatchEdit() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) BEGINDASH (rdkit.Chem.rdchem.BondDir attribute) beginIdx (rdkit.Chem.Scaffolds.rdScaffoldNetwork.NetworkEdge property) BEGINWEDGE (rdkit.Chem.rdchem.BondDir attribute) BertzCT() (in module rdkit.Chem.GraphDescriptors) Best (rdkit.Chem.FeatMaps.FeatMaps.FeatMapScoreMode attribute) bgColor (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) BIASCHISQUARE (rdkit.ML.InfoTheory.rdInfoTheory.InfoType attribute) BIASENTROPY (rdkit.ML.InfoTheory.rdInfoTheory.InfoType attribute) biasList (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) BinsTriangleInequality() (in module rdkit.Chem.Pharm2D.Utils) BitClusterer (class in rdkit.ML.InfoTheory.BitClusterer) BitCorrMatGenerator (class in rdkit.ML.InfoTheory.rdInfoTheory) BitEnsemble (class in rdkit.DataStructs.BitEnsemble) BitGainsInfo (class in rdkit.Chem.FragmentCatalog) bitRatioAgents (rdkit.Chem.rdChemReactions.ReactionFingerprintParams property) BitsInCommon() (in module rdkit.Chem.AtomPairs.Utils) BitVectToBinaryText() (in module rdkit.DataStructs.cDataStructs) BitVectToFPSText() (in module rdkit.DataStructs.cDataStructs) BitVectToText() (in module rdkit.DataStructs.cDataStructs) BlockLogs (class in rdkit.rdBase) Bond (class in rdkit.Chem.fmcs.fmcs) (class in rdkit.Chem.rdchem) Bond_Atropisomer (rdkit.Chem.rdchem.StereoType attribute) Bond_Cis (rdkit.Chem.rdchem.StereoDescriptor attribute) Bond_Cumulene_Even (rdkit.Chem.rdchem.StereoType attribute) Bond_Double (rdkit.Chem.rdchem.StereoType attribute) bond_index (rdkit.Chem.fmcs.fmcs.DirectedEdge attribute) (rdkit.Chem.fmcs.fmcs.OutgoingEdge attribute) bond_indices (rdkit.Chem.fmcs.fmcs.Atom attribute) (rdkit.Chem.fmcs.fmcs.Subgraph attribute) bond_smarts (rdkit.Chem.fmcs.fmcs.Bond attribute) (rdkit.Chem.fmcs.fmcs.OutgoingEdge attribute) Bond_Trans (rdkit.Chem.rdchem.StereoDescriptor attribute) bond_typer_any() (in module rdkit.Chem.fmcs.fmcs) bond_typer_bondtypes() (in module rdkit.Chem.fmcs.fmcs) bondColors (rdkit.Chem.Draw.FingerprintEnv attribute) BondCompare (class in rdkit.Chem.rdFMCS) bondCompare (rdkit.Chem.fmcs.fmcs.Default attribute) BondCompareParameters (rdkit.Chem.rdFMCS.MCSParameters property) BondDir (class in rdkit.Chem.rdchem) BondFromSmarts() (in module rdkit.Chem.rdmolfiles) BondFromSmiles() (in module rdkit.Chem.rdmolfiles) bondIdx (rdkit.Chem.rdchem.SubstanceGroupCState property) BondInvariantsGenerator (class in rdkit.Chem.rdFingerprintGenerator) bondLengthLimit (rdkit.Chem.MolStandardize.rdMolStandardize.Layout2DValidation property) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property)

bondLineWidth (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) BondMembers() (rdkit.Chem.rdchem.RingInfo method) bondProperties (rdkit.Chem.rdchem.SubstructMatchParameters property) BondProps (rdkit.Chem.rdchem.PropertyPickleOptions attribute) BondRingFamilies() (rdkit.Chem.rdchem.RingInfo method) BondRings() (rdkit.Chem.rdchem.RingInfo method) BondRingSizes() (rdkit.Chem.rdchem.RingInfo method) BondStereo (class in rdkit.Chem.rdchem) BondType (class in rdkit.Chem.rdchem) BondTyper (rdkit.Chem.rdFMCS.MCSParameters property) BondWedgingParameters (class in rdkit.Chem.rdmolops) boundsMatForceScaling (rdkit.Chem.rdDistGeom.EmbedParameters property) Box (rdkit.Chem.FeatMaps.FeatMaps.FeatMapParams.FeatProfile attribute) boxSizeMult (rdkit.Chem.rdDistGeom.EmbedParameters property) branchedPaths (rdkit.Chem.rdFingerprintGenerator.RDKitFingerprintOptions property) BraunBlanquetSimilarity() (in module rdkit.DataStructs.cDataStructs) BraunBlanquetSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) BraunBlanquetSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) BreakBRICSBonds() (in module rdkit.Chem.BRICS) BRENK (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) BRICSBuild() (in module rdkit.Chem.BRICS) BRICSDecompose() (in module rdkit.Chem.BRICS) BRICSScaffoldParams() (in module rdkit.Chem.Scaffolds.rdScaffoldNetwork) BuildAdjacencyList() (in module rdkit.Chem.FragmentCatalog) BuildAtomDict() (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) BuildAtomPairFP() (in module rdkit.Chem.MolDb.FingerprintUtils) BuildAvalonFP() (in module rdkit.Chem.MolDb.FingerprintUtils) BuildCatalog() (in module rdkit.Chem.BuildFragmentCatalog) BuildDataSet() (in module rdkit.ML.Data.DataUtils) BuildFeatureFactory() (in module rdkit.Chem.rdMolChemicalFeatures) BuildFeatureFactoryFromString() (in module rdkit.Chem.rdMolChemicalFeatures) BuildFuncGroupHierarchy() (in module rdkit.Chem.FunctionalGroups) BuildMorganFP() (in module rdkit.Chem.MolDb.FingerprintUtils) BuildPatts() (in module rdkit.Chem.EState.AtomTypes) BuildPharm2DFP() (in module rdkit.Chem.MolDb.FingerprintUtils) BuildQuantDataSet() (in module rdkit.ML.Data.DataUtils) BuildRDKitFP() (in module rdkit.Chem.MolDb.FingerprintUtils) BuildSigFactory() (in module rdkit.Chem.MolDb.FingerprintUtils) BuildTorsionsFP() (in module rdkit.Chem.MolDb.FingerprintUtils) BuildVoteImage() (in module rdkit.ML.MLUtils.VoteImg) BulkAllBitSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkAsymmetricSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkBraunBlanquetSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkCosineSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkDiceSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkKulczynskiSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkMcConnaugheySimilarity() (in module rdkit.DataStructs.cDataStructs) BulkOnBitSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkRogotGoldbergSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkRusselSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkSokalSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkTanimotoSimilarity() (in module rdkit.DataStructs.cDataStructs) BulkTverskySimilarity() (in module rdkit.DataStructs.cDataStructs) BurgesRiskBound() (in module rdkit.ML.SLT.Risk)

C

C (rdkit.Chem.QED.ADSparameter attribute) CachedMolHolder (class in rdkit.Chem.rdSubstructLibrary) CachedSmilesMolHolder (class in rdkit.Chem.rdSubstructLibrary) CachedTrustedSmilesMolHolder (class in rdkit.Chem.rdSubstructLibrary) CachingTargetsMatcher (class in rdkit.Chem.fmcs.fmcs) CalcAsphericity() (in module rdkit.Chem.rdMolDescriptors) calcAtomGaussians() (in module rdkit.Chem.Draw) CalcAUC() (in module rdkit.ML.Scoring.Scoring) CalcAUTOCORR2D() (in module rdkit.Chem.rdMolDescriptors) CalcAUTOCORR3D() (in module rdkit.Chem.rdMolDescriptors) CalcBEDROC() (in module rdkit.ML.Scoring.Scoring) CalcChi0n() (in module rdkit.Chem.rdMolDescriptors) CalcChi0v() (in module rdkit.Chem.rdMolDescriptors) CalcChi1n() (in module rdkit.Chem.rdMolDescriptors) CalcChi1v() (in module rdkit.Chem.rdMolDescriptors) CalcChi2n() (in module rdkit.Chem.rdMolDescriptors) CalcChi2v() (in module rdkit.Chem.rdMolDescriptors) CalcChi3n() (in module rdkit.Chem.rdMolDescriptors) CalcChi3v() (in module rdkit.Chem.rdMolDescriptors) CalcChi4n() (in module rdkit.Chem.rdMolDescriptors) CalcChi4v() (in module rdkit.Chem.rdMolDescriptors) CalcChiNn() (in module rdkit.Chem.rdMolDescriptors) CalcChiNv() (in module rdkit.Chem.rdMolDescriptors) CalcCompoundDescriptorsForComposition() (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) CalcCoulombMat() (in module rdkit.Chem.rdMolDescriptors) CalcCrippenDescriptors() (in module rdkit.Chem.rdMolDescriptors) CalcDescriptors() (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) (rdkit.ML.Descriptors.Descriptors.DescriptorCalculator method) (rdkit.ML.Descriptors.MoleculeDescriptors.MolecularDescriptorCalculator method) CalcDescriptorsForComposition() (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) CalcEccentricity() (in module rdkit.Chem.rdMolDescriptors) CalcEEMcharges() (in module rdkit.Chem.rdMolDescriptors) CalcEnergy() (rdkit.ForceField.rdForceField.ForceField method) CalcEnrichment() (in module rdkit.ML.Scoring.Scoring) CalcExactMolWt() (in module rdkit.Chem.rdMolDescriptors) CalcFractionCSP3() (in module rdkit.Chem.rdMolDescriptors) CalcGains() (in module rdkit.Chem.BuildFragmentCatalog) CalcGainsFromFps() (in module rdkit.Chem.BuildFragmentCatalog) CalcGETAWAY() (in module rdkit.Chem.rdMolDescriptors) CalcGrad() (rdkit.ForceField.rdForceField.ForceField method) CalcHallKierAlpha() (in module rdkit.Chem.rdMolDescriptors) CalcInertialShapeFactor() (in module rdkit.Chem.rdMolDescriptors) CalcInfoGains() (in module rdkit.ML.InfoTheory.BitRank) CalcKappa1() (in module rdkit.Chem.rdMolDescriptors) CalcKappa2() (in module rdkit.Chem.rdMolDescriptors) CalcKappa3() (in module rdkit.Chem.rdMolDescriptors) CalcLabuteASA() (in module rdkit.Chem.rdMolDescriptors) CalcMetricMatrix() (in module rdkit.ML.Cluster.Resemblance) CalcMolDescriptors() (in module rdkit.Chem.Descriptors) CalcMolDescriptors3D() (in module rdkit.Chem.Descriptors3D) CalcMolFormula() (in module rdkit.Chem.rdMolDescriptors) CalcMORSE() (in module rdkit.Chem.rdMolDescriptors) CalcMultipleCompoundsDescriptor() (in module rdkit.ML.Descriptors.Parser) CalcNPossibleUsingMap() (in module rdkit.ML.Data.DataUtils) CalcNPR1() (in module rdkit.Chem.rdMolDescriptors) CalcNPR2() (in module rdkit.Chem.rdMolDescriptors) CalcNumAliphaticCarbocycles() (in module rdkit.Chem.rdMolDescriptors) CalcNumAliphaticHeterocycles() (in module rdkit.Chem.rdMolDescriptors) CalcNumAliphaticRings() (in module rdkit.Chem.rdMolDescriptors) CalcNumAmideBonds() (in module rdkit.Chem.rdMolDescriptors) CalcNumAromaticCarbocycles() (in module rdkit.Chem.rdMolDescriptors) CalcNumAromaticHeterocycles() (in module rdkit.Chem.rdMolDescriptors) CalcNumAromaticRings() (in module rdkit.Chem.rdMolDescriptors) CalcNumAtoms() (in module rdkit.Chem.rdMolDescriptors) CalcNumAtomStereoCenters() (in module rdkit.Chem.rdMolDescriptors) CalcNumBridgeheadAtoms() (in module rdkit.Chem.rdMolDescriptors) CalcNumHBA() (in module rdkit.Chem.rdMolDescriptors) CalcNumHBD() (in module rdkit.Chem.rdMolDescriptors) CalcNumHeavyAtoms() (in module rdkit.Chem.rdMolDescriptors) CalcNumHeteroatoms() (in module rdkit.Chem.rdMolDescriptors) CalcNumHeterocycles() (in module rdkit.Chem.rdMolDescriptors) CalcNumLipinskiHBA() (in module rdkit.Chem.rdMolDescriptors) CalcNumLipinskiHBD() (in module rdkit.Chem.rdMolDescriptors) CalcNumRings() (in module rdkit.Chem.rdMolDescriptors) CalcNumRotatableBonds() (in module rdkit.Chem.rdMolDescriptors) CalcNumSaturatedCarbocycles() (in module rdkit.Chem.rdMolDescriptors) CalcNumSaturatedHeterocycles() (in module rdkit.Chem.rdMolDescriptors) CalcNumSaturatedRings() (in module rdkit.Chem.rdMolDescriptors) CalcNumSpiroAtoms() (in module rdkit.Chem.rdMolDescriptors) CalcNumUnspecifiedAtomStereoCenters() (in module rdkit.Chem.rdMolDescriptors) CalcOxidationNumbers() (in module rdkit.Chem.rdMolDescriptors) CalcPBF() (in module rdkit.Chem.rdMolDescriptors) CalcPhi() (in module rdkit.Chem.rdMolDescriptors) CalcPMI1() (in module rdkit.Chem.rdMolDescriptors) CalcPMI2() (in module rdkit.Chem.rdMolDescriptors) CalcPMI3() (in module rdkit.Chem.rdMolDescriptors) CalcRadiusOfGyration() (in module rdkit.Chem.rdMolDescriptors) CalcRDF() (in module rdkit.Chem.rdMolDescriptors) CalcRIE() (in module rdkit.ML.Scoring.Scoring) CalcRMS() (in module rdkit.Chem.rdMolAlign) CalcROC() (in module rdkit.ML.Scoring.Scoring) CalcSASA() (in module rdkit.Chem.rdFreeSASA) CalcSimpleDescriptorsForComposition() (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) CalcSingleCompoundDescriptor() (in module rdkit.ML.Descriptors.Parser) CalcSpherocityIndex() (in module rdkit.Chem.rdMolDescriptors) CalcTPSA() (in module rdkit.Chem.rdMolDescriptors) CalculateDirectionsAtPoint() (in module rdkit.Chem.Subshape.BuilderUtils) CalculateTFD() (in module rdkit.Chem.TorsionFingerprints) CalculateTorsionAngles() (in module rdkit.Chem.TorsionFingerprints) CalculateTorsionLists() (in module rdkit.Chem.TorsionFingerprints) CalculateTorsionWeights() (in module rdkit.Chem.TorsionFingerprints) CalcWHIM() (in module rdkit.Chem.rdMolDescriptors) call_desc() (rdkit.Chem.ChemUtils.DescriptorUtilities.VectorDescriptorWrapper method) Canceled (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorStatus attribute) canceled (rdkit.Chem.rdFMCS.MCSResult property) CangenNode (class in rdkit.Chem.fmcs.fmcs) canon() (in module rdkit.Chem.fmcs.fmcs) canonical (rdkit.Chem.rdmolfiles.SmilesWriteParams property) canonical_bondtype (rdkit.Chem.fmcs.fmcs.Bond attribute) CANONICAL_SMILES (rdkit.Chem.RegistrationHash.HashLayer attribute) Canonicalize() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) CanonicalizeConformer() (in module rdkit.Chem.rdMolTransforms) CanonicalizeEnhancedStereo() (in module rdkit.Chem.rdmolfiles) CanonicalizeMol() (in module rdkit.Chem.rdMolTransforms) CanonicalRankAtoms() (in module rdkit.Chem.rdmolfiles) CanonicalRankAtomsInFragment() (in module rdkit.Chem.rdmolfiles) CanonicalSmiles (rdkit.Chem.rdMolHash.HashFunction attribute) CanonicalTautomer() (in module rdkit.Chem.MolStandardize.rdMolStandardize) CanonSmiles() (in module rdkit.Chem) CartesianProductStrategy (class in rdkit.Chem.rdChemReactions) catalogName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) centeredOn (rdkit.Chem.rdchem.StereoInfo property) centreMoleculesBeforeDrawing (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) CENTROID (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute) ChangeMoleculeRendering() (in module rdkit.Chem.PandasTools) CharacteristicPolynomial() (in module rdkit.Chem.Graphs) Charge (rdkit.Chem.MolStandardize.rdMolStandardize.ChargeCorrection property) CHARGE_CORRECTIONS() (in module rdkit.Chem.MolStandardize.rdMolStandardize) CHARGE_STANDARDIZATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) ChargeCorrection (class in rdkit.Chem.MolStandardize.rdMolStandardize) ChargeParent() (in module rdkit.Chem.MolStandardize.rdMolStandardize) ChargeParentInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) Check2DBounds() (in module rdkit.Chem.Pharm3D.EmbedLib) CHECK_CHIRAL_CENTERS (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) CHECK_CHIRAL_CENTERS2 (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) check_completeRingsOnly() (in module rdkit.Chem.fmcs.fmcs) CHECK_TETRAHEDRAL_CENTERS (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) CheckAtomCharge() (rdkit.Chem.rdFMCS.MCSAtomCompare method) CheckAtomChirality() (rdkit.Chem.rdFMCS.MCSAtomCompare method) CheckAtomRingMatch() (rdkit.Chem.rdFMCS.MCSAtomCompare method) CheckBondRingMatch() (rdkit.Chem.rdFMCS.MCSBondCompare method) CheckBondStereo() (rdkit.Chem.rdFMCS.MCSBondCompare method) CheckCTAB() (in module rdkit.Chem.MolKey.MolKey) CheckMolecule() (in module rdkit.Avalon.pyAvalonTools) CheckMoleculeString() (in module rdkit.Avalon.pyAvalonTools) CHEMBL (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) CHEMBL_BMS (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) CHEMBL_Dundee (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) CHEMBL_Glaxo (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) CHEMBL_Inpharmatica (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) CHEMBL_LINT (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) CHEMBL_MLSMR (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) CHEMBL_SureChEMBL (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) ChemicalReaction (class in rdkit.Chem.rdChemReactions) CherkasskyRiskBound() (in module rdkit.ML.SLT.Risk) Chi0() (in module rdkit.Chem.GraphDescriptors) Chi0n() (in module rdkit.Chem.GraphDescriptors) Chi0v() (in module rdkit.Chem.GraphDescriptors) Chi1() (in module rdkit.Chem.GraphDescriptors) Chi1n() (in module rdkit.Chem.GraphDescriptors) Chi1v() (in module rdkit.Chem.GraphDescriptors) Chi2n() (in module rdkit.Chem.GraphDescriptors) Chi2v() (in module rdkit.Chem.GraphDescriptors) Chi3n() (in module rdkit.Chem.GraphDescriptors) Chi3v() (in module rdkit.Chem.GraphDescriptors) Chi4n() (in module rdkit.Chem.GraphDescriptors) Chi4v() (in module rdkit.Chem.GraphDescriptors) CHI_ALLENE (rdkit.Chem.rdchem.ChiralType attribute) CHI_OCTAHEDRAL (rdkit.Chem.rdchem.ChiralType attribute) CHI_OTHER (rdkit.Chem.rdchem.ChiralType attribute) CHI_SQUAREPLANAR (rdkit.Chem.rdchem.ChiralType attribute) CHI_TETRAHEDRAL (rdkit.Chem.rdchem.ChiralType attribute) CHI_TETRAHEDRAL_CCW (rdkit.Chem.rdchem.ChiralType attribute) CHI_TETRAHEDRAL_CW (rdkit.Chem.rdchem.ChiralType attribute) CHI_TRIGONALBIPYRAMIDAL (rdkit.Chem.rdchem.ChiralType attribute) CHI_UNSPECIFIED (rdkit.Chem.rdchem.ChiralType attribute) children (rdkit.Chem.FunctionalGroups.FGHierarchyNode attribute) (rdkit.Chem.Recap.RecapHierarchyNode attribute) ChiNn_() (in module rdkit.Chem.GraphDescriptors) ChiNv_() (in module rdkit.Chem.GraphDescriptors) CHIRAL_ATOM (rdkit.Chem.rdmolops.StereoBondThresholds attribute) ChiralType (class in rdkit.Chem.rdchem) CHISQUARE (rdkit.ML.InfoTheory.rdInfoTheory.InfoType attribute) ChiSquare() (in module rdkit.ML.InfoTheory.rdInfoTheory) choose() (rdkit.Chem.MolStandardize.rdMolStandardize.LargestFragmentChooser method) chooseInPlace() (rdkit.Chem.MolStandardize.rdMolStandardize.LargestFragmentChooser method) chunkSize (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) CircleAndLine (rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle attribute) circleAtoms (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) clashLimit (rdkit.Chem.MolStandardize.rdMolStandardize.Layout2DValidation property) classifier (rdkit.Chem.rdFreeSASA.SASAOpts property) classifyAtoms() (in module rdkit.Chem.rdFreeSASA) Cleanup() (in module rdkit.Chem.MolStandardize.rdMolStandardize) (in module rdkit.Chem.rdmolops)

CleanupAtropisomers() (in module rdkit.Chem.rdmolops) CleanupChirality() (in module rdkit.Chem.rdmolops) CleanupInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) CleanupOrganometallics() (in module rdkit.Chem.rdmolops) CleanupParameters (class in rdkit.Chem.MolStandardize.rdMolStandardize) Clear() (rdkit.Chem.rdtrajectory.Trajectory method) ClearAttachPoints() (rdkit.Chem.rdchem.SubstanceGroup method) clearBackground (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) ClearBrackets() (rdkit.Chem.rdchem.SubstanceGroup method) ClearCache() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) ClearComputedProps() (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) clearConfs (rdkit.Chem.rdDistGeom.EmbedParameters property) ClearCStates() (rdkit.Chem.rdchem.SubstanceGroup method) ClearDrawing() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) ClearMolSubstanceGroups() (in module rdkit.Chem.rdchem) ClearProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) CLINK (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute) close() (rdkit.Chem.rdmolfiles.MaeWriter method) (rdkit.Chem.rdmolfiles.PDBWriter method) (rdkit.Chem.rdmolfiles.SDWriter method) (rdkit.Chem.rdmolfiles.SmilesWriter method) (rdkit.Chem.rdmolfiles.TDTWriter method) CloseCheckMolFiles() (in module rdkit.Avalon.pyAvalonTools) Closest (rdkit.Chem.FeatMaps.FeatMaps.FeatMapScoreMode attribute) Cluster (class in rdkit.ML.Cluster.Clusters) Cluster() (rdkit.SimDivFilters.rdSimDivPickers.HierarchicalClusterPicker method) ClusterAlignments() (in module rdkit.Chem.Subshape.SubshapeAligner) ClusterBits() (rdkit.ML.InfoTheory.BitClusterer.BitClusterer method) ClusterData() (in module rdkit.ML.Cluster.Butina) (in module rdkit.ML.Cluster.Murtagh) ClusterFromDetails() (in module rdkit.Chem.Fingerprints.ClusterMols) ClusterMethod (class in rdkit.SimDivFilters.rdSimDivPickers) ClusterPoints() (in module rdkit.Chem.Fingerprints.ClusterMols) ClusterRenderer (class in rdkit.ML.Cluster.ClusterVis) ClusterTerminalPts() (in module rdkit.Chem.Subshape.BuilderUtils) ClusterToImg() (in module rdkit.ML.Cluster.ClusterVis) ClusterToPDF() (in module rdkit.ML.Cluster.ClusterVis) ClusterToSVG() (in module rdkit.ML.Cluster.ClusterVis) cmp() (in module rdkit.Chem.Draw.MolDrawing) (in module rdkit.ML.Cluster.Clusters) coarseGridToleranceMult (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner attribute) CoarseScreenPharmacophore() (in module rdkit.Chem.Pharm3D.EmbedLib) codeSize (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) CollapseAttachmentPoints() (in module rdkit.Chem.rdmolops) CollectAtomCounts() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) CollectAtomToBits() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) CollectBitInfoMap() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) CollectBitPaths() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) collectMolCounts (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) CollectVotes() (in module rdkit.ML.MLUtils.VoteImg) (rdkit.ML.InfoTheory.rdInfoTheory.BitCorrMatGenerator method) colorBonds (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) CombiEnum() (in module rdkit.Chem.Pharm3D.EmbedLib) CombineFeatMaps() (in module rdkit.Chem.FeatMaps.FeatMapUtils) CombineMols() (in module rdkit.Chem.rdmolops) CombineSubshapes() (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder method) comicMode (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) Commit() (rdkit.Dbase.DbConnection.DbConnect method) CommitBatchEdit() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) CompactListRepr() (in module rdkit.utils.listutils) Compare() (rdkit.ML.Cluster.Clusters.Cluster method) CompareAny (rdkit.Chem.rdFMCS.AtomCompare attribute) (rdkit.Chem.rdFMCS.BondCompare attribute) CompareAnyHeavyAtom (rdkit.Chem.rdFMCS.AtomCompare attribute) CompareElements (rdkit.Chem.rdFMCS.AtomCompare attribute) CompareIsotopes (rdkit.Chem.rdFMCS.AtomCompare attribute) CompareOrder (rdkit.Chem.rdFMCS.BondCompare attribute) CompareOrderExact (rdkit.Chem.rdFMCS.BondCompare attribute) CompareParams() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) COMPLETED (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) Completed (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorStatus attribute) completeRingsOnly (rdkit.Chem.fmcs.fmcs.Default attribute) CompleteRingsOnly (rdkit.Chem.rdFMCS.MCSAtomCompareParameters property) (rdkit.Chem.rdFMCS.MCSBondCompareParameters property) COMPOSITE_AND (rdkit.Chem.rdchem.CompositeQueryType attribute) COMPOSITE_OR (rdkit.Chem.rdchem.CompositeQueryType attribute) COMPOSITE_XOR (rdkit.Chem.rdchem.CompositeQueryType attribute) CompositeQueryType (class in rdkit.Chem.rdchem) Compound (class in rdkit.Chem.MolDb.Loader_sa) CompoundDescriptorCalculator (class in rdkit.ML.Descriptors.CompoundDescriptors) Compute2DCoords() (in module rdkit.Chem.rdDepictor) (rdkit.Chem.rdchem.Mol method) Compute2DCoordsForReaction() (in module rdkit.Chem.rdChemReactions) Compute2DCoordsMimicDistmat() (in module rdkit.Chem.rdDepictor) compute_fraggle_similarity_for_subs() (in module rdkit.Chem.Fraggle.FraggleSim) compute_mcs() (in module rdkit.Chem.fmcs.fmcs) ComputeCanonicalTransform() (in module rdkit.Chem.rdMolTransforms) ComputeCentroid() (in module rdkit.Chem.rdMolTransforms) ComputeChiralVolume() (in module rdkit.Chem.Pharm3D.EmbedLib) ComputeConfBox() (in module rdkit.Chem.rdShapeHelpers) ComputeConfDimsAndOffset() (in module rdkit.Chem.rdShapeHelpers) ComputeDihedralAngle() (in module rdkit.Geometry.rdGeometry) ComputedProps (rdkit.Chem.rdchem.PropertyPickleOptions attribute) ComputeGasteigerCharges() (in module rdkit.Chem.rdPartialCharges) (rdkit.Chem.rdchem.Mol method) ComputeGridCentroid() (in module rdkit.Geometry.rdGeometry) ComputeGridIndices() (in module rdkit.Chem.Subshape.BuilderUtils) ComputeL1Norm() (in module rdkit.DataStructs.cDataStructs) ComputeMolShape() (in module rdkit.Chem.AllChem) ComputeMolVolume() (in module rdkit.Chem.AllChem) ComputePrincipalAxesAndMoments() (in module rdkit.Chem.rdMolTransforms) ComputePrincipalAxesAndMomentsFromGyrationMatrix() (in module rdkit.Chem.rdMolTransforms) ComputeProperties() (rdkit.Chem.rdMolDescriptors.Properties method) ComputeShapeGridCentroid() (in module rdkit.Chem.Subshape.BuilderUtils) ComputeSignedDihedralAngle() (in module rdkit.Geometry.rdGeometry) ComputeUnionBox() (in module rdkit.Chem.rdShapeHelpers) CondenseAbbreviationSubstanceGroups() (in module rdkit.Chem.rdAbbreviations) CondenseMolAbbreviations() (in module rdkit.Chem.rdAbbreviations) ConfigToNumElectrons() (in module rdkit.utils.chemutils) Conformer (class in rdkit.Chem.rdchem) connect() (in module rdkit.Dbase.DbModule) ConnectToSchema() (in module rdkit.Chem.MolDb.Loader_sa) ConstrainedDepictionParams (class in rdkit.Chem.rdDepictor) ConstrainedEmbed() (in module rdkit.Chem.AllChem) ConstrainedEnum() (in module rdkit.Chem.Pharm3D.EmbedLib) ConstructEnsembleBV() (in module rdkit.DataStructs.BitUtils) ConstructSidechains() (in module rdkit.Chem.ChemUtils.TemplateExpand) continuousHighlight (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) ContourAndDrawGaussians() (in module rdkit.Chem.Draw.rdMolDraw2D) ContourAndDrawGrid() (in module rdkit.Chem.Draw.rdMolDraw2D) ContourParams (class in rdkit.Chem.Draw.rdMolDraw2D) contourWidth (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property) controllingAtoms (rdkit.Chem.rdchem.StereoInfo property) Convert() (in module rdkit.Chem.ChemUtils.SDFToCSV) convert_input_to_typed_molecules() (in module rdkit.Chem.fmcs.fmcs) ConvertGenericQueriesToSubstanceGroups() (in module rdkit.Chem.rdmolops) ConvertRows() (in module rdkit.Chem.MolDb.Loader_orig) ConvertToExplicit() (in module rdkit.DataStructs.cDataStructs) ConvertToNumpyArray() (in module rdkit.DataStructs.cDataStructs) CoordGenParams (class in rdkit.Chem.rdCoordGen) coordgenScaling (rdkit.Chem.rdCoordGen.CoordGenParams property) CoordsAsDouble (rdkit.Chem.rdchem.PropertyPickleOptions attribute) coordScale (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) coordScaleForQuantization (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property) CosineSimilarity() (in module rdkit.Chem.AtomPairs.Utils) (in module rdkit.DataStructs.cDataStructs) CosineSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) CosineSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) CountAtomElec() (in module rdkit.Chem.rdmolops) CountMatches() (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) CountResults() (in module rdkit.ML.Data.DataUtils) counts (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetwork property) countSimulation (rdkit.Chem.rdFingerprintGenerator.FingerprintOptions property) CountUpTo() (in module rdkit.Chem.Pharm2D.Utils) CreateAtomBoolPropertyList() (in module rdkit.Chem.rdmolfiles) CreateAtomDoublePropertyList() (in module rdkit.Chem.rdmolfiles) CreateAtomIntPropertyList() (in module rdkit.Chem.rdmolfiles) CreateAtomStringPropertyList() (in module rdkit.Chem.rdmolfiles) CreateDifferenceFingerprintForReaction() (in module rdkit.Chem.rdChemReactions) CreateEmptyForceFieldForMol() (in module rdkit.Chem.rdForceFieldHelpers) CreateFromBinaryText() (in module rdkit.DataStructs.cDataStructs) CreateFromBitString() (in module rdkit.DataStructs.cDataStructs) CreateFromFPSText() (in module rdkit.DataStructs.cDataStructs) CreateMolCatalog() (in module rdkit.Chem.rdMolCatalog) CreateMolDataSubstanceGroup() (in module rdkit.Chem.rdchem) CreateMolFingerprint() (in module rdkit.Chem.FunctionalGroups) CreateMolSubstanceGroup() (in module rdkit.Chem.rdchem) CreateScaffoldNetwork() (in module rdkit.Chem.Scaffolds.rdScaffoldNetwork) CreateShinglingFromMol() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) CreateShinglingFromSmiles() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) CreateStereoGroup() (in module rdkit.Chem.rdchem) CreateStructuralFingerprintForReaction() (in module rdkit.Chem.rdChemReactions) CristianiRiskBound() (in module rdkit.ML.SLT.Risk) critical() (rdkit.RDLogger.logger method) cross() (in module rdkit.Chem.Features.FeatDirUtilsRD) CrossProduct() (rdkit.Geometry.rdGeometry.Point3D method) CustomProp_VSA_() (in module rdkit.Chem.rdMolDescriptors) CX_ALL (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_ALL_BUT_COORDS (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_ATOM_LABELS (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_ATOM_PROPS (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_BOND_ATROPISOMER (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_BOND_CFG (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_COORDINATE_BONDS (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_COORDS (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_ENHANCEDSTEREO (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_LINKNODES (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_MOLFILE_VALUES (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_NONE (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_POLYMER (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_RADICALS (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CX_SGROUPS (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) CXSmilesFields (class in rdkit.Chem.rdmolfiles)

D

D (rdkit.Chem.QED.ADSparameter attribute) dash (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) dashNegative (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property) data (rdkit.Chem.FeatMaps.FeatMapParser.FeatMapParser attribute) data() (rdkit.Chem.Draw.rdMolDraw2D.map_indexing_suite_IntStringMap_entry method) (rdkit.Chem.MolStandardize.rdMolStandardize.map_indexing_suite_SmilesTautomerMap_entry method) DatabaseToDatabase() (in module rdkit.Dbase.DbUtils) DatabaseToText() (in module rdkit.Dbase.DbUtils) DATIVE (rdkit.Chem.rdchem.BondType attribute) DativeBondsToHaptic() (in module rdkit.Chem.rdmolops) DATIVEL (rdkit.Chem.rdchem.BondType attribute) DATIVEONE (rdkit.Chem.rdchem.BondType attribute) DATIVER (rdkit.Chem.rdchem.BondType attribute) DbConnect (class in rdkit.Dbase.DbConnection) DbError DbFpSupplier (class in rdkit.Chem.Fingerprints.DbFpSupplier) dbg_useConstrained (rdkit.Chem.rdCoordGen.CoordGenParams property) dbg_useFixed (rdkit.Chem.rdCoordGen.CoordGenParams property) DBL_BOND_NO_STEREO (rdkit.Chem.rdmolops.StereoBondThresholds attribute) DBL_BOND_SPECIFIED_STEREO (rdkit.Chem.rdmolops.StereoBondThresholds attribute) dblBondLengthFrac (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) dblBondOffset (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) DbMolSupplier (class in rdkit.Chem.Suppliers.DbMolSupplier) DbMolSupplyNode (class in rdkit.VLib.NodeLib.DbMolSupply) dbName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) DbPickleSupplyNode (class in rdkit.VLib.NodeLib.DbPickleSupplier) DbResultBase (class in rdkit.Dbase.DbResultSet) DbResultSet (class in rdkit.Dbase.DbResultSet) DBToData() (in module rdkit.ML.Data.DataUtils) Debug() (rdkit.Chem.rdchem.Mol method) debug() (rdkit.RDLogger.logger method) DebugDraw() (in module rdkit.Chem.Draw) debugParse (rdkit.Chem.rdmolfiles.SmartsParserParams property) (rdkit.Chem.rdmolfiles.SmilesParserParams property) Default (class in rdkit.Chem.fmcs.fmcs) (rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions attribute) default() (in module rdkit.Chem.QED) default_atom_typer() (in module rdkit.Chem.fmcs.fmcs) default_bond_typer() (in module rdkit.Chem.fmcs.fmcs) defaultColor (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) DefaultSigFactory() (in module rdkit.Chem.Pharm2D) defnFilename (rdkit.Chem.SaltRemover.SaltRemover attribute) degenerateSmartsQueryMolDict (rdkit.Chem.rdFMCS.MCSResult property) DegreeVector (rdkit.Chem.rdMolHash.HashFunction attribute) delete_bonds() (in module rdkit.Chem.Fraggle.FraggleSim) DeleteAll() (rdkit.Chem.PyMol.MolViewer method) DeleteAllExcept() (rdkit.Chem.PyMol.MolViewer method) DeleteSubstructs() (in module rdkit.Chem.rdmolops) delim (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) DepickleFP() (in module rdkit.Chem.MolDb.FingerprintUtils) Deprotect() (in module rdkit.Chem.rdDeprotect) DeprotectData (class in rdkit.Chem.rdDeprotect) DeprotectDataVect (class in rdkit.Chem.rdDeprotect) DeprotectInPlace() (in module rdkit.Chem.rdDeprotect) deprotection_class (rdkit.Chem.rdDeprotect.DeprotectData property) DescribeQuery() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) description (rdkit.Chem.FragmentCatalog.BitGainsInfo attribute) descriptor (rdkit.Chem.rdchem.StereoInfo property) DescriptorCalculator (class in rdkit.ML.Descriptors.Descriptors) Destroy() (rdkit.VLib.Node.VLibNode method) DetachVectsMatchingBit() (rdkit.DataStructs.VectCollection.VectCollection method) DetachVectsNotMatchingBit() (rdkit.DataStructs.VectCollection.VectCollection method) detail (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineLogEntry property) detailsName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) DetectBondStereoChemistry() (in module rdkit.Chem.rdmolops) DetectBondStereochemistry() (in module rdkit.Chem.rdmolops) DetectChemistryProblems() (in module rdkit.Chem.rdmolops) DetermineBondOrders() (in module rdkit.Chem.rdDetermineBonds) DetermineBonds() (in module rdkit.Chem.rdDetermineBonds) DetermineConnectivity() (in module rdkit.Chem.rdDetermineBonds) DEV() (in module rdkit.ML.Descriptors.Parser) (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) DiceSimilarity() (in module rdkit.Chem.AtomPairs.Utils) (in module rdkit.DataStructs.cDataStructs) DiceSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) DiceSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) Dimension() (rdkit.Chem.rdtrajectory.Trajectory method) (rdkit.ForceField.rdForceField.ForceField method) DirectedEdge (class in rdkit.Chem.fmcs.fmcs) DIRECTION_SET (rdkit.Chem.rdmolops.StereoBondThresholds attribute) DirectionVector() (rdkit.Geometry.rdGeometry.Point2D method) (rdkit.Geometry.rdGeometry.Point3D method) (rdkit.Geometry.rdGeometry.PointND method) dirMatch (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment attribute) DirMergeMode (class in rdkit.Chem.FeatMaps.FeatMapUtils) dirScoreMode (rdkit.Chem.FeatMaps.FeatMaps.FeatMap attribute) dirThresh (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner attribute)

DisableLog() (in module rdkit.rdBase) DisableSubstructMatchRendering() (in module rdkit.Chem.Draw.IPythonConsole) DisallowedAtomsValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) DisallowedRadicalValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) Disconnect() (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnector method) DisconnectInPlace() (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnector method) DisconnectOrganometallics() (in module rdkit.Chem.MolStandardize.rdMolStandardize) DisconnectOrganometallicsInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) DiscreteValueType (class in rdkit.DataStructs.cDataStructs) DiscreteValueVect (class in rdkit.DataStructs.cDataStructs) display_pil_image() (in module rdkit.Chem.Draw.IPythonConsole) DisplayCollisions() (rdkit.Chem.PyMol.MolViewer method) DisplayHBonds() (rdkit.Chem.PyMol.MolViewer method) displayLabel (rdkit.Chem.rdAbbreviations.AbbreviationDefinition property) displayLabelW (rdkit.Chem.rdAbbreviations.AbbreviationDefinition property) DisplayObject() (rdkit.Chem.PyMol.MolViewer method) DisplaySubshape() (in module rdkit.Chem.Subshape.SubshapeObjects) DisplaySubshapeSkeleton() (in module rdkit.Chem.Subshape.SubshapeObjects) Distance (rdkit.Chem.FeatMaps.FeatMapUtils.MergeMetric attribute) Distance() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder static method) (rdkit.Geometry.rdGeometry.Point3D method) (rdkit.Geometry.rdGeometry.PointND method) distMetric (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner attribute) DMAX (rdkit.Chem.QED.ADSparameter attribute) doBuild (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) doCanonical (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) doDetails (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) doEnumeration (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) doGains (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) doIsomericSmiles (rdkit.Chem.rdmolfiles.SmilesWriteParams property) doKekule (rdkit.Chem.rdmolfiles.SmilesWriteParams property) doRandom (rdkit.Chem.rdMolEnumerator.MolEnumeratorParams property) (rdkit.Chem.rdmolfiles.SmilesWriteParams property) doScore (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) doSigs (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) Dot() (in module rdkit.Chem.AtomPairs.Utils) doTautomers (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) DotFullRange (rdkit.Chem.FeatMaps.FeatMaps.FeatDirScoreMode attribute) DotPosRange (rdkit.Chem.FeatMaps.FeatMaps.FeatDirScoreMode attribute) DotProduct() (rdkit.Geometry.rdGeometry.Point2D method) (rdkit.Geometry.rdGeometry.Point3D method) (rdkit.Geometry.rdGeometry.PointND method) DoTriangleSmoothing() (in module rdkit.DistanceGeometry.DistGeom) dotsPerAngstrom (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) DOUBLE (rdkit.Chem.rdchem.BondType attribute) DoubleCubicLatticeVolume (class in rdkit.Chem.rdMolDescriptors) DownsampleBoundsMatrix() (in module rdkit.Chem.Pharm3D.EmbedLib) DrawArc() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawArrow() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) drawAsLines (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property) DrawAttachmentLine() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawClusterTree() (in module rdkit.ML.Cluster.ClusterVis) DrawEllipse() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawingOptions (class in rdkit.Chem.Draw.MolDrawing) DrawLine() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) drawMol3D() (in module rdkit.Chem.Draw.IPythonConsole) DrawMolecule() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawMoleculeACS1996() (in module rdkit.Chem.Draw.rdMolDraw2D) DrawMolecules() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawMoleculeWithHighlights() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) drawMolsSameScale (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) DrawMorganBit() (in module rdkit.Chem.Draw) (in module rdkit.Chem.Draw.IPythonConsole) DrawMorganBits() (in module rdkit.Chem.Draw) (in module rdkit.Chem.Draw.IPythonConsole) DrawMorganEnv() (in module rdkit.Chem.Draw) DrawMorganEnvs() (in module rdkit.Chem.Draw) drawOptions() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawPolygon() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawRDKitBit() (in module rdkit.Chem.Draw) (in module rdkit.Chem.Draw.IPythonConsole) DrawRDKitBits() (in module rdkit.Chem.Draw) (in module rdkit.Chem.Draw.IPythonConsole) DrawRDKitEnv() (in module rdkit.Chem.Draw) DrawRDKitEnvs() (in module rdkit.Chem.Draw) DrawReaction() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawRect() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawSpiral() (in module rdkit.utils.spiral) DrawString() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawTree() (rdkit.ML.Cluster.ClusterVis.ClusterRenderer method) DrawTriangle() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DrawWavyLine() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) DropFeature() (rdkit.Chem.FeatMaps.FeatMaps.FeatMap method) dubious_stereo_removed (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) dummiesAreAttachments (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) DummyAtomLabels (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) dummyIsotopeLabels (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) DupeFilter (class in rdkit.VLib.NodeLib.SmilesDupeFilter)

E

E (rdkit.Chem.QED.ADSparameter attribute) Eccentricity() (in module rdkit.Chem.Descriptors3D) edges (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetwork property) edgeTol (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner attribute) EdgeType (class in rdkit.Chem.Scaffolds.rdScaffoldNetwork) EditableMol (class in rdkit.Chem.rdchem) EHTResults (class in rdkit.Chem.rdEHTTools) EIGHTBITVALUE (rdkit.DataStructs.cDataStructs.DiscreteValueType attribute) either_warning (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) EITHERDOUBLE (rdkit.Chem.rdchem.BondDir attribute) elemDict (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) ElementGraph (rdkit.Chem.rdMolHash.HashFunction attribute) EmbedBoundsMatrix() (in module rdkit.DistanceGeometry.DistGeom) EmbedFailureCauses (class in rdkit.Chem.rdDistGeom) embedFragmentsSeparately (rdkit.Chem.rdDistGeom.EmbedParameters property) EmbedMol() (in module rdkit.Chem.Pharm3D.EmbedLib) EmbedMolecule() (in module rdkit.Chem.rdDistGeom) EmbedMultipleConfs() (in module rdkit.Chem.rdDistGeom) EmbedOne() (in module rdkit.Chem.Pharm3D.EmbedLib) EmbedParameters (class in rdkit.Chem.rdDistGeom) EmbedPharmacophore() (in module rdkit.Chem.Pharm3D.EmbedLib) EnableLog() (in module rdkit.rdBase) enableSequentialRandomSeeds (rdkit.Chem.rdDistGeom.EmbedParameters property) EnableSubstructMatchRendering() (in module rdkit.Chem.Draw.IPythonConsole) EncodeMol() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) EncodeMolsBulk() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) EncodeSECFPMol() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) EncodeSECFPMolsBulk() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) EncodeSECFPSmiles() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) EncodeSECFPSmilesBulk() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) EncodeShape() (in module rdkit.Chem.rdShapeHelpers) EncodeSmiles() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) EncodeSmilesBulk() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) end_atom_index (rdkit.Chem.fmcs.fmcs.DirectedEdge attribute) ENDDOWNRIGHT (rdkit.Chem.rdchem.BondDir attribute) endIdx (rdkit.Chem.Scaffolds.rdScaffoldNetwork.NetworkEdge property) ENDUPRIGHT (rdkit.Chem.rdchem.BondDir attribute) enforceChirality (rdkit.Chem.rdDistGeom.EmbedParameters property) enforceValenceRules (rdkit.Chem.rdmolops.MolzipParams property) EnhancedStereoUpdateMode (class in rdkit.Chem.RegistrationHash) ENTROPY (rdkit.ML.InfoTheory.rdInfoTheory.InfoType attribute) Enumerate() (in module rdkit.Chem.rdMolEnumerator) (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) (rdkit.Chem.rdchem.ResonanceMolSupplier method) enumerate_subgraphs() (in module rdkit.Chem.fmcs.fmcs) EnumerateHeterocycles() (in module rdkit.Chem.EnumerateHeterocycles) EnumerateLibrary (class in rdkit.Chem.rdChemReactions) EnumerateLibraryBase (class in rdkit.Chem.rdChemReactions) EnumerateLibraryCanSerialize() (in module rdkit.Chem.rdChemReactions) EnumerateLibraryFromReaction() (in module rdkit.Chem.AllChem) EnumerateReaction() (in module rdkit.Chem.SimpleEnum.Enumerator) EnumerateStereoisomers() (in module rdkit.Chem.EnumerateStereoisomers) EnumerationMolecule (in module rdkit.Chem.fmcs.fmcs) EnumerationParams (class in rdkit.Chem.rdChemReactions) EnumerationStrategyBase (class in rdkit.Chem.rdChemReactions) EnumeratorType (class in rdkit.Chem.rdMolEnumerator) error (rdkit.Chem.MolKey.MolKey.InchiResult attribute) (rdkit.Chem.MolKey.MolKey.MolKeyResult attribute) error() (in module rdkit.Chem.Fingerprints.FingerprintMols) (rdkit.RDLogger.logger method) ErrorBitsToText() (in module rdkit.Chem.MolKey.MolKey) ESCAPE (rdkit.Chem.RegistrationHash.HashLayer attribute)

EState_VSA1() (in module rdkit.Chem.EState.EState_VSA) EState_VSA10() (in module rdkit.Chem.EState.EState_VSA) EState_VSA11() (in module rdkit.Chem.EState.EState_VSA) EState_VSA2() (in module rdkit.Chem.EState.EState_VSA) EState_VSA3() (in module rdkit.Chem.EState.EState_VSA) EState_VSA4() (in module rdkit.Chem.EState.EState_VSA) EState_VSA5() (in module rdkit.Chem.EState.EState_VSA) EState_VSA6() (in module rdkit.Chem.EState.EState_VSA) EState_VSA7() (in module rdkit.Chem.EState.EState_VSA) EState_VSA8() (in module rdkit.Chem.EState.EState_VSA) EState_VSA9() (in module rdkit.Chem.EState.EState_VSA) EState_VSA_() (in module rdkit.Chem.EState.EState_VSA) EStateIndices() (in module rdkit.Chem.EState.EState) ETDG() (in module rdkit.Chem.rdDistGeom) ETK_MINIMIZATION (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) ETKDG() (in module rdkit.Chem.rdDistGeom) ETKDGv2() (in module rdkit.Chem.rdDistGeom) ETKDGv3() (in module rdkit.Chem.rdDistGeom) ETversion (rdkit.Chem.rdDistGeom.EmbedParameters property) EuclideanDist() (in module rdkit.ML.Cluster.Butina) EuclideanDistance() (in module rdkit.ML.Cluster.Resemblance) EvenSamplePairsStrategy (class in rdkit.Chem.rdChemReactions) ExactMolWt() (in module rdkit.Chem.Descriptors) example (rdkit.Chem.rdDeprotect.DeprotectData property) ExcludedVolume (class in rdkit.Chem.Pharm3D.ExcludedVolume) ExclusionList (class in rdkit.Chem.rdfiltercatalog) Exhaustive (rdkit.Chem.rdRGroupDecomposition.RGroupMatching attribute) existingConfId (rdkit.Chem.rdDepictor.ConstrainedDepictionParams property) existingFile() (in module rdkit.Chem.ChemUtils.SDFToCSV) (in module rdkit.Chem.FeatFinderCLI) ExpandAttachmentPoints() (in module rdkit.Chem.rdmolops) ExpandQuery() (rdkit.Chem.rdchem.QueryAtom method) (rdkit.Chem.rdchem.QueryBond method) ExpandTerminalPts() (in module rdkit.Chem.Subshape.BuilderUtils) ExplainAtomCode() (in module rdkit.Chem.AtomPairs.Utils) ExplainPairScore() (in module rdkit.Chem.AtomPairs.Pairs) ExplainPathScore() (in module rdkit.Chem.AtomPairs.Torsions) ExplicitBitVect (class in rdkit.DataStructs.cDataStructs) ExplicitDegreeEqualsQueryAtom() (in module rdkit.Chem.rdqueries) ExplicitDegreeGreaterQueryAtom() (in module rdkit.Chem.rdqueries) ExplicitDegreeLessQueryAtom() (in module rdkit.Chem.rdqueries) explicitMethyl (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) ExplicitPharmacophore (class in rdkit.Chem.Pharm3D.Pharmacophore) ExplicitValenceEqualsQueryAtom() (in module rdkit.Chem.rdqueries) ExplicitValenceGreaterQueryAtom() (in module rdkit.Chem.rdqueries) ExplicitValenceLessQueryAtom() (in module rdkit.Chem.rdqueries) Explode() (in module rdkit.Chem.ChemUtils.TemplateExpand) extend() (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineLog method) (rdkit.Chem.rdchem.StereoGroup_vect method) (rdkit.Chem.rdchem.SubstanceGroup_VECT method) (rdkit.Chem.rdChemReactions.MOL_SPTR_VECT method) (rdkit.Chem.rdChemReactions.VectMolVect method) (rdkit.Chem.rdDeprotect.DeprotectDataVect method) (rdkit.Chem.rdfiltercatalog.FilterCatalogEntryList method) (rdkit.Chem.rdfiltercatalog.FilterCatalogListOfEntryList method) (rdkit.Chem.rdfiltercatalog.MolList method) (rdkit.Chem.rdfiltercatalog.VectFilterMatch method) (rdkit.Chem.Scaffolds.rdScaffoldNetwork.NetworkEdge_VECT method) (rdkit.rdBase.MatchTypeVect method) (rdkit.rdBase.UnsignedLong_Vect method) (rdkit.rdBase.VectorOfStringVectors method) ExtendedMurcko (rdkit.Chem.rdMolHash.HashFunction attribute) extraGridPadding (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property)

F

F (rdkit.Chem.QED.ADSparameter attribute) familiesMatch() (in module rdkit.Chem.FeatMaps.FeatMapUtils) FastFindRings() (in module rdkit.Chem.rdmolops) FastSDMolSupplier (class in rdkit.Chem.FastSDMolSupplier) featDirs (rdkit.Chem.FeatMaps.FeatMapPoint.FeatMapPoint attribute) FeatDirScoreMode (class in rdkit.Chem.FeatMaps.FeatMaps) featFactory (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder attribute) FeatMap (class in rdkit.Chem.FeatMaps.FeatMaps) featMap (rdkit.Chem.Subshape.SubshapeObjects.SubshapeShape attribute) featmapFeatures (rdkit.Chem.Subshape.SubshapeObjects.SkeletonPoint attribute) FeatMapParams (class in rdkit.Chem.FeatMaps.FeatMaps) FeatMapParams.FeatProfile (class in rdkit.Chem.FeatMaps.FeatMaps) FeatMapParseError FeatMapParser (class in rdkit.Chem.FeatMaps.FeatMapParser) FeatMapPoint (class in rdkit.Chem.FeatMaps.FeatMapPoint) FeatMapScoreMode (class in rdkit.Chem.FeatMaps.FeatMaps) featProfile (rdkit.Chem.FeatMaps.FeatMaps.FeatMapParams attribute) FEATURES_VALIDATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) FeaturesValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) feq() (in module rdkit.Chem.FeatMaps.FeatMapUtils) (in module rdkit.ML.Data.Quantize) fermiEnergy (rdkit.Chem.rdEHTTools.EHTResults property) FGHierarchyNode (class in rdkit.Chem.FunctionalGroups) fillGrid (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property) fillHighlights (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) FillPolys() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) filter() (rdkit.VLib.NodeLib.SmartsMolFilter.SmartsFilter method) (rdkit.VLib.NodeLib.SmilesDupeFilter.DupeFilter method) FilterCatalog (class in rdkit.Chem.rdfiltercatalog) FilterCatalogCanSerialize() (in module rdkit.Chem.rdfiltercatalog) FilterCatalogEntry (class in rdkit.Chem.rdfiltercatalog) FilterCatalogEntryList (class in rdkit.Chem.rdfiltercatalog) FilterCatalogListOfEntryList (class in rdkit.Chem.rdfiltercatalog) FilterCatalogParams (class in rdkit.Chem.rdfiltercatalog) FilterCatalogParams.FilterCatalogs (class in rdkit.Chem.rdfiltercatalog) FilterData() (in module rdkit.ML.Data.DataUtils) FilterHierarchyMatcher (class in rdkit.Chem.rdfiltercatalog) FilterMatch (class in rdkit.Chem.rdfiltercatalog) filterMatch (rdkit.Chem.rdfiltercatalog.FilterMatch property) FilterMatcher (class in rdkit.Chem.FilterCatalog) FilterMatcherBase (class in rdkit.Chem.rdfiltercatalog) FilterNode (class in rdkit.VLib.Filter) FINAL_CENTER_IN_VOLUME (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) FINAL_CHIRAL_BOUNDS (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) FinalMatchChecker (rdkit.Chem.rdFMCS.MCSParameters property) find_duplicates() (in module rdkit.Chem.fmcs.fmcs) find_extension_size() (in module rdkit.Chem.fmcs.fmcs) find_extensions() (in module rdkit.Chem.fmcs.fmcs) find_upper_fragment_size_limits() (in module rdkit.Chem.fmcs.fmcs) FindAllPathsOfLengthN() (in module rdkit.Chem.rdmolops) FindAllSubgraphsOfLengthMToN() (in module rdkit.Chem.rdmolops) FindAllSubgraphsOfLengthN() (in module rdkit.Chem.rdmolops) FindAtomEnvironmentOfRadiusN() (in module rdkit.Chem.rdmolops) FindBRICSBonds() (in module rdkit.Chem.BRICS) FindClusterCentroidFromDists() (in module rdkit.ML.Cluster.ClusterUtils) FindFarthestGridPoint() (in module rdkit.Chem.Subshape.BuilderUtils) FindGridPointBetweenPoints() (in module rdkit.Chem.Subshape.BuilderUtils) FindGridTerminalPoints() (in module rdkit.Geometry.rdGeometry) FindMCS() (in module rdkit.Chem.MCS) (in module rdkit.Chem.rdFMCS) FindMesoCenters() (in module rdkit.Chem.rdmolops) FindMinValInList() (in module rdkit.ML.Cluster.Resemblance) FindMolChiralCenters() (in module rdkit.Chem) findNeighbors() (in module rdkit.Chem.Features.FeatDirUtilsRD) FindPotentialStereo() (in module rdkit.Chem.rdmolops) FindPotentialStereoBonds() (in module rdkit.Chem.rdmolops) FindRingFamilies() (in module rdkit.Chem.rdmolops) FindSubtree() (rdkit.ML.Cluster.Clusters.Cluster method) FindTerminalPtsFromConformer() (in module rdkit.Chem.Subshape.BuilderUtils) FindTerminalPtsFromShape() (in module rdkit.Chem.Subshape.BuilderUtils) FindUniqueSubgraphsOfLengthN() (in module rdkit.Chem.rdmolops) FindVarMultQuantBounds() (in module rdkit.ML.Data.Quantize) FindVarQuantBound() (in module rdkit.ML.Data.Quantize) FingerprintEnv (class in rdkit.Chem.Draw) FingerprinterDetails (class in rdkit.Chem.Fingerprints.FingerprintMols) FingerprintGenerator32 (class in rdkit.Chem.rdFingerprintGenerator) FingerprintGenerator64 (class in rdkit.Chem.rdFingerprintGenerator) FingerprintMol() (in module rdkit.Chem.EState.Fingerprinter) (in module rdkit.Chem.Fingerprints.FingerprintMols) FingerprintOptions (class in rdkit.Chem.rdFingerprintGenerator) FingerprintsFromDetails() (in module rdkit.Chem.Fingerprints.FingerprintMols) FingerprintsFromMols() (in module rdkit.Chem.Fingerprints.FingerprintMols) FingerprintsFromPickles() (in module rdkit.Chem.Fingerprints.FingerprintMols) FingerprintsFromSmiles() (in module rdkit.Chem.Fingerprints.FingerprintMols) FingerprintSimilarity() (in module rdkit.DataStructs) FingerprintType (class in rdkit.Chem.rdChemReactions) FingerprintVariance (rdkit.Chem.rdRGroupDecomposition.RGroupScore attribute) FinishDrawing() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo method) (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG method) FIRST_MINIMIZATION (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) FIVEANDAHALF (rdkit.Chem.rdchem.BondType attribute) fixed_ctab (rdkit.Chem.MolKey.MolKey.InchiResult attribute) (rdkit.Chem.MolKey.MolKey.MolKeyResult attribute) fixedBondLength (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) fixedFontSize (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) FixedMolSizeMolBundle (class in rdkit.Chem.rdchem) fixedScale (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) flagCloseContactsDist (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) flattenChirality (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) flattenIsotopes (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) flattenKeepLargest (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) FlexiMode() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) flush() (rdkit.Chem.rdmolfiles.MaeWriter method) (rdkit.Chem.rdmolfiles.PDBWriter method) (rdkit.Chem.rdmolfiles.SDWriter method) (rdkit.Chem.rdmolfiles.SmilesWriter method) (rdkit.Chem.rdmolfiles.TDTWriter method) fmcs() (in module rdkit.Chem.fmcs.fmcs) FoldFingerprint() (in module rdkit.DataStructs.cDataStructs) FoldFingerprintToTargetDensity() (in module rdkit.Chem.Fingerprints.FingerprintMols) FoldToTargetDensity() (in module rdkit.DataStructs) Font (class in rdkit.Chem.Draw.MolDrawing) fontFile (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) FontSize() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) ForceField (class in rdkit.ForceField.rdForceField) forceRDKit (rdkit.Chem.rdDepictor.ConstrainedDepictionParams property) forceTransAmides (rdkit.Chem.rdDistGeom.EmbedParameters property) forceV3000 (rdkit.Chem.rdmolfiles.MolWriterParams property) FormalChargeEqualsQueryAtom() (in module rdkit.Chem.rdqueries) FormalChargeGreaterQueryAtom() (in module rdkit.Chem.rdqueries) FormalChargeLessQueryAtom() (in module rdkit.Chem.rdqueries) FormCorrelationMatrix() (in module rdkit.ML.Data.Stats) FormCounts() (in module rdkit.ML.InfoTheory.BitRank) FormCovarianceMatrix() (in module rdkit.ML.Data.Stats) FORMULA (rdkit.Chem.RegistrationHash.HashLayer attribute) ForwardDbFpSupplier (class in rdkit.Chem.Fingerprints.DbFpSupplier) ForwardDbMolSupplier (class in rdkit.Chem.Suppliers.DbMolSupplier) ForwardSDMolSupplier (class in rdkit.Chem.rdmolfiles) ForwardStereoGroupIds() (in module rdkit.Chem.rdchem) FOURANDAHALF (rdkit.Chem.rdchem.BondType attribute)

FOURBITVALUE (rdkit.DataStructs.cDataStructs.DiscreteValueType attribute) FPBReader (class in rdkit.DataStructs.cDataStructs) FpDensityMorgan1() (in module rdkit.Chem.Descriptors) FpDensityMorgan2() (in module rdkit.Chem.Descriptors) FpDensityMorgan3() (in module rdkit.Chem.Descriptors) FPHolderBase (class in rdkit.Chem.rdSubstructLibrary) fpName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) fpSize (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions attribute) (rdkit.Chem.rdChemReactions.ReactionFingerprintParams property) (rdkit.Chem.rdFingerprintGenerator.FingerprintOptions property) FPType (class in rdkit.Chem.rdFingerprintGenerator) fpType (rdkit.Chem.rdChemReactions.ReactionFingerprintParams property) fr_Al_COO() (in module rdkit.Chem.Fragments) fr_Al_OH() (in module rdkit.Chem.Fragments) fr_Al_OH_noTert() (in module rdkit.Chem.Fragments) fr_aldehyde() (in module rdkit.Chem.Fragments) fr_alkyl_carbamate() (in module rdkit.Chem.Fragments) fr_alkyl_halide() (in module rdkit.Chem.Fragments) fr_allylic_oxid() (in module rdkit.Chem.Fragments) fr_amide() (in module rdkit.Chem.Fragments) fr_amidine() (in module rdkit.Chem.Fragments) fr_aniline() (in module rdkit.Chem.Fragments) fr_Ar_COO() (in module rdkit.Chem.Fragments) fr_Ar_N() (in module rdkit.Chem.Fragments) fr_Ar_NH() (in module rdkit.Chem.Fragments) fr_Ar_OH() (in module rdkit.Chem.Fragments) fr_ArN() (in module rdkit.Chem.Fragments) fr_aryl_methyl() (in module rdkit.Chem.Fragments) fr_azide() (in module rdkit.Chem.Fragments) fr_azo() (in module rdkit.Chem.Fragments) fr_barbitur() (in module rdkit.Chem.Fragments) fr_benzene() (in module rdkit.Chem.Fragments) fr_benzodiazepine() (in module rdkit.Chem.Fragments) fr_bicyclic() (in module rdkit.Chem.Fragments) fr_C_O() (in module rdkit.Chem.Fragments) fr_C_O_noCOO() (in module rdkit.Chem.Fragments) fr_C_S() (in module rdkit.Chem.Fragments) fr_COO() (in module rdkit.Chem.Fragments) fr_COO2() (in module rdkit.Chem.Fragments) fr_diazo() (in module rdkit.Chem.Fragments) fr_dihydropyridine() (in module rdkit.Chem.Fragments) fr_epoxide() (in module rdkit.Chem.Fragments) fr_ester() (in module rdkit.Chem.Fragments) fr_ether() (in module rdkit.Chem.Fragments) fr_furan() (in module rdkit.Chem.Fragments) fr_guanido() (in module rdkit.Chem.Fragments) fr_halogen() (in module rdkit.Chem.Fragments) fr_hdrzine() (in module rdkit.Chem.Fragments) fr_hdrzone() (in module rdkit.Chem.Fragments) fr_HOCCN() (in module rdkit.Chem.Fragments) fr_imidazole() (in module rdkit.Chem.Fragments) fr_imide() (in module rdkit.Chem.Fragments) fr_Imine() (in module rdkit.Chem.Fragments) fr_isocyan() (in module rdkit.Chem.Fragments) fr_isothiocyan() (in module rdkit.Chem.Fragments) fr_ketone() (in module rdkit.Chem.Fragments) fr_ketone_Topliss() (in module rdkit.Chem.Fragments) fr_lactam() (in module rdkit.Chem.Fragments) fr_lactone() (in module rdkit.Chem.Fragments) fr_methoxy() (in module rdkit.Chem.Fragments) fr_morpholine() (in module rdkit.Chem.Fragments) fr_N_O() (in module rdkit.Chem.Fragments) fr_Ndealkylation1() (in module rdkit.Chem.Fragments) fr_Ndealkylation2() (in module rdkit.Chem.Fragments) fr_NH0() (in module rdkit.Chem.Fragments) fr_NH1() (in module rdkit.Chem.Fragments) fr_NH2() (in module rdkit.Chem.Fragments) fr_Nhpyrrole() (in module rdkit.Chem.Fragments) fr_nitrile() (in module rdkit.Chem.Fragments) fr_nitro() (in module rdkit.Chem.Fragments) fr_nitro_arom() (in module rdkit.Chem.Fragments) fr_nitro_arom_nonortho() (in module rdkit.Chem.Fragments) fr_nitroso() (in module rdkit.Chem.Fragments) fr_oxazole() (in module rdkit.Chem.Fragments) fr_oxime() (in module rdkit.Chem.Fragments) fr_para_hydroxylation() (in module rdkit.Chem.Fragments) fr_phenol() (in module rdkit.Chem.Fragments) fr_phenol_noOrthoHbond() (in module rdkit.Chem.Fragments) fr_phos_acid() (in module rdkit.Chem.Fragments) fr_phos_ester() (in module rdkit.Chem.Fragments) fr_piperdine() (in module rdkit.Chem.Fragments) fr_piperzine() (in module rdkit.Chem.Fragments) fr_priamide() (in module rdkit.Chem.Fragments) fr_prisulfonamd() (in module rdkit.Chem.Fragments) fr_pyridine() (in module rdkit.Chem.Fragments) fr_quatN() (in module rdkit.Chem.Fragments) fr_SH() (in module rdkit.Chem.Fragments) fr_sulfide() (in module rdkit.Chem.Fragments) fr_sulfonamd() (in module rdkit.Chem.Fragments) fr_sulfone() (in module rdkit.Chem.Fragments) fr_term_acetylene() (in module rdkit.Chem.Fragments) fr_tetrazole() (in module rdkit.Chem.Fragments) fr_thiazole() (in module rdkit.Chem.Fragments) fr_thiocyan() (in module rdkit.Chem.Fragments) fr_thiophene() (in module rdkit.Chem.Fragments) fr_unbrch_alkane() (in module rdkit.Chem.Fragments) fr_urea() (in module rdkit.Chem.Fragments) fraction (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder attribute) FractionCSP3() (in module rdkit.Chem.Lipinski) fracVol (rdkit.Chem.Subshape.SubshapeObjects.SkeletonPoint attribute) FragCatalog (class in rdkit.Chem.rdfragcatalog) FragCatGenerator (class in rdkit.Chem.rdfragcatalog) FragCatParams (class in rdkit.Chem.rdfragcatalog) FragFPGenerator (class in rdkit.Chem.rdfragcatalog) Fragment (rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType attribute) FRAGMENT_STANDARDIZATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) fragmented_mol_to_enumeration_mols() (in module rdkit.Chem.fmcs.fmcs) FragmentedTypedMolecule (class in rdkit.Chem.fmcs.fmcs) fragmentFile (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) FragmentMatcher (class in rdkit.Chem.FragmentMatcher) FragmentMol() (in module rdkit.Chem.rdMMPA) FragmentOnBonds (rdkit.Chem.rdmolops.MolzipLabel attribute) FragmentOnBonds() (in module rdkit.Chem.rdmolops) FragmentOnBRICSBonds() (in module rdkit.Chem.rdmolops) FragmentOnSomeBonds() (in module rdkit.Chem.rdmolops) FragmentParent() (in module rdkit.Chem.MolStandardize.rdMolStandardize) FragmentParentInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) FragmentRemover (class in rdkit.Chem.MolStandardize.rdMolStandardize) FragmentRemoverFromData() (in module rdkit.Chem.MolStandardize.rdMolStandardize) fragments_found (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) FRAGMENTS_REMOVED (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) FragmentValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) FrameToGridImage() (in module rdkit.Chem.PandasTools) FreeChemicalFeature (class in rdkit.Chem.rdChemicalFeatures) from_atom_index (rdkit.Chem.fmcs.fmcs.OutgoingEdge attribute) FromArray() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) FromBase64() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) FromStringArray() (rdkit.Chem.rdMHFPFingerprint.MHFPEncoder method) full_name (rdkit.Chem.rdDeprotect.DeprotectData property) FuncGroupFileParseError

G

GA (rdkit.Chem.rdRGroupDecomposition.RGroupMatching attribute) gain (rdkit.Chem.FragmentCatalog.BitGainsInfo attribute) gainsName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) gaMaximumOperations (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) gaNumberOperationsWithoutImprovement (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) gaNumberRuns (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) gaParallelRuns (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) gaPopulationSize (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) gaRandomSeed (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) Gaussian (rdkit.Chem.FeatMaps.FeatMaps.FeatMapParams.FeatProfile attribute) Gen2DFingerprint() (in module rdkit.Chem.Pharm2D.Generate) gen_primes() (in module rdkit.Chem.fmcs.fmcs) Generate2DCoords() (in module rdkit.Avalon.pyAvalonTools) generate_fraggle_fragmentation() (in module rdkit.Chem.Fraggle.FraggleSim) generate_smarts() (in module rdkit.Chem.fmcs.fmcs) generateCoordinates (rdkit.Chem.rdmolops.MolzipParams property) GenerateDepictionMatching2DStructure() (in module rdkit.Chem.rdDepictor) GenerateDepictionMatching3DStructure() (in module rdkit.Chem.rdDepictor) GenerateErGFingerprintForReducedGraph() (in module rdkit.Chem.rdReducedGraphs) GenerateMolExtendedReducedGraph() (in module rdkit.Chem.rdReducedGraphs) GenerateSubshapeShape() (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder method) GenerateSubshapeSkeleton() (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder method) Generic (rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType attribute) GenericBond (rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType attribute) GenericPicker (class in rdkit.SimDivFilters.SimilarityPickers) Get3DDistanceMatrix() (in module rdkit.Chem.rdmolops) get_canonical_bondtype_counts() (in module rdkit.Chem.fmcs.fmcs) get_canonical_bondtypes() (in module rdkit.Chem.fmcs.fmcs) get_closure_label() (in module rdkit.Chem.fmcs.fmcs) get_counts() (in module rdkit.Chem.fmcs.fmcs) get_initial_cangen_nodes() (in module rdkit.Chem.fmcs.fmcs) get_isotopes() (in module rdkit.Chem.fmcs.fmcs) get_mobile_h() (rdkit.Chem.MolKey.InchiInfo.InchiInfo method) get_selected_atom_classes() (in module rdkit.Chem.fmcs.fmcs) get_sp3_stereo() (rdkit.Chem.MolKey.InchiInfo.InchiInfo method) get_specified_types() (in module rdkit.Chem.fmcs.fmcs) get_typed_fragment() (in module rdkit.Chem.fmcs.fmcs) get_typed_molecule() (in module rdkit.Chem.fmcs.fmcs) GetAbundanceForIsotope() (rdkit.Chem.rdchem.PeriodicTable method) GetAcceptor1FeatVects() (in module rdkit.Chem.Features.FeatDirUtilsRD) GetAcceptor2FeatVects() (in module rdkit.Chem.Features.FeatDirUtilsRD) GetAcceptor3FeatVects() (in module rdkit.Chem.Features.FeatDirUtilsRD) GetActiveConformer() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) GetAdjacencyMatrix() (in module rdkit.Chem.rdmolops) GetAgents() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetAgentTemplate() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetAlignmentTransform() (in module rdkit.Chem.rdMolAlign) (in module rdkit.Numerics.rdAlignment) GetAllChildren() (rdkit.Chem.Recap.RecapHierarchyNode method) GetAllCombinations() (in module rdkit.Chem.Pharm2D.Utils) GetAllConformerBestRMS() (in module rdkit.Chem.rdMolAlign) GetAllData() (rdkit.ML.Data.MLData.MLDataSet method) (rdkit.ML.Data.MLData.MLQuantDataSet method) GetAllDescriptorNames() (in module rdkit.ML.Descriptors.CompoundDescriptors) GetAllowNontetrahedralChirality() (in module rdkit.Chem.rdmolops) GetAllPharmacophoreMatches() (in module rdkit.Chem.Pharm3D.EmbedLib) GetAltLoc() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetAngleDeg() (in module rdkit.Chem.rdMolTransforms) GetAngleRad() (in module rdkit.Chem.rdMolTransforms) getAnnotationColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) GetAPFingerprint() (in module rdkit.Chem.Draw.SimilarityMaps) GetAromaticAtoms() (rdkit.Chem.rdchem.Mol method) GetAromaticFeatVects() (in module rdkit.Chem.Features.FeatDirUtilsRD) GetAtomAlias() (in module rdkit.Chem.rdchem) GetAtomConjGrpIdx() (rdkit.Chem.rdchem.ResonanceMolSupplier method) GetAtomCoords() (rdkit.Chem.PyMol.MolViewer method) GetAtomCounts() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) GetAtomFeatInfo() (in module rdkit.Chem.FeatFinderCLI) GetAtomFeatures() (in module rdkit.Chem.rdMolDescriptors) GetAtomHeavyNeighbors() (in module rdkit.Chem.Pharm3D.EmbedLib) GetAtomicCharges() (rdkit.Chem.rdEHTTools.EHTResults method) GetAtomicData() (in module rdkit.utils.chemutils) GetAtomicNum() (rdkit.Chem.rdchem.Atom method) GetAtomicNumber() (rdkit.Chem.rdchem.PeriodicTable method) GetAtomicWeight() (rdkit.Chem.rdchem.PeriodicTable method) GetAtomicWeightsForFingerprint() (in module rdkit.Chem.Draw.SimilarityMaps) GetAtomicWeightsForModel() (in module rdkit.Chem.Draw.SimilarityMaps) GetAtomIds() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) GetAtomMapNum() (rdkit.Chem.rdchem.Atom method) GetAtomMatch() (in module rdkit.Chem.rdMolChemicalFeatures) GetAtomPairAtomCode() (in module rdkit.Chem.rdMolDescriptors) GetAtomPairAtomInvGen() (in module rdkit.Chem.rdFingerprintGenerator) GetAtomPairCode() (in module rdkit.Chem.rdMolDescriptors) GetAtomPairFingerprint() (in module rdkit.Chem.rdMolDescriptors) GetAtomPairFingerprintAsBitVect() (in module rdkit.Chem.AtomPairs.Pairs) GetAtomPairGenerator() (in module rdkit.Chem.rdFingerprintGenerator) GetAtomPosition() (rdkit.Chem.rdchem.Conformer method) GetAtomRLabel() (in module rdkit.Chem.rdchem) GetAtoms() (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.StereoGroup method) (rdkit.Chem.rdchem.SubstanceGroup method) GetAtomsMatchingBit() (in module rdkit.Chem.Pharm2D.Matcher) GetAtomsMatchingQuery() (rdkit.Chem.rdchem.Mol method) GetAtomToBits() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) GetAtomValue() (in module rdkit.Chem.rdchem) GetAtomWithIdx() (rdkit.Chem.rdchem.Mol method) GetAttachPoints() (rdkit.Chem.rdchem.SubstanceGroup method) GetAvailableProperties() (rdkit.Chem.rdMolDescriptors.Properties static method) GetAvailTransforms() (in module rdkit.ML.Data.Transforms) GetAvalonCountFP() (in module rdkit.Avalon.pyAvalonTools) GetAvalonFP() (in module rdkit.Avalon.pyAvalonTools) GetAvalonFPAsWords() (in module rdkit.Avalon.pyAvalonTools) getBackgroundColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) GetBeginAtom() (rdkit.Chem.rdchem.Bond method) GetBeginAtomIdx() (rdkit.Chem.rdchem.Bond method) GetBestAlignmentTransform() (in module rdkit.Chem.rdMolAlign) GetBestRMS() (in module rdkit.Chem.rdMolAlign) GetBestTFDBetweenMolecules() (in module rdkit.Chem.TorsionFingerprints) GetBins() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetBit() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) (rdkit.DataStructs.VectCollection.VectCollection method) GetBitDescription() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) (rdkit.Chem.rdfragcatalog.FragCatalog method) (rdkit.Chem.rdMolCatalog.MolCatalog method) GetBitDescriptionAsText() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetBitDiscrims() (rdkit.Chem.rdfragcatalog.FragCatalog method) GetBitEntryId() (rdkit.Chem.rdfragcatalog.FragCatalog method) (rdkit.Chem.rdMolCatalog.MolCatalog method) GetBitFuncGroupIds() (rdkit.Chem.rdfragcatalog.FragCatalog method) GetBitIdx() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetBitInfo() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetBitInfoMap() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) GetBitOrder() (rdkit.Chem.rdfragcatalog.FragCatalog method) GetBitPaths() (rdkit.Chem.rdFingerprintGenerator.AdditionalOutput method) GetBits() (rdkit.DataStructs.BitEnsemble.BitEnsemble method) GetBond() (rdkit.Chem.FragmentMatcher.FragmentMatcher method) GetBondBetweenAtoms() (rdkit.Chem.rdchem.Mol method) GetBondConjGrpIdx() (rdkit.Chem.rdchem.ResonanceMolSupplier method) GetBondDir() (rdkit.Chem.rdchem.Bond method) GetBondLength() (in module rdkit.Chem.rdMolTransforms) GetBonds() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) GetBondType() (rdkit.Chem.rdchem.Bond method) GetBondTypeAsDouble() (rdkit.Chem.rdchem.Bond method) GetBondWithIdx() (rdkit.Chem.rdchem.Mol method) GetBoolProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetBPFingerprint() (in module rdkit.Chem.AtomPairs.Sheridan) GetBrackets() (rdkit.Chem.rdchem.SubstanceGroup method) GetBTFingerprint() (in module rdkit.Chem.AtomPairs.Sheridan) GetBytes() (rdkit.DataStructs.cDataStructs.FPBReader method) GetCallback() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) GetCanonSmiles() (in module rdkit.Avalon.pyAvalonTools) GetCatalogParams() (rdkit.Chem.rdfragcatalog.FragCatalog method) GetChainId() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetCheckMolLog() (in module rdkit.Avalon.pyAvalonTools) GetChemDrawRxnAdjustParams() (in module rdkit.Chem.rdChemReactions) GetChildren() (rdkit.DataStructs.VectCollection.VectCollection method) (rdkit.ML.Cluster.Clusters.Cluster method) (rdkit.VLib.Node.VLibNode method) GetChiralTag() (rdkit.Chem.rdchem.Atom method) GetClusters() (rdkit.ML.InfoTheory.BitClusterer.BitClusterer method) GetColumnInfoFromCursor() (in module rdkit.Dbase.DbInfo) GetColumnNames() (in module rdkit.Dbase.DbInfo) (rdkit.Chem.Fingerprints.DbFpSupplier.DbFpSupplier method) (rdkit.Chem.Suppliers.DbMolSupplier.DbMolSupplier method) (rdkit.Dbase.DbConnection.DbConnect method) (rdkit.Dbase.DbResultSet.DbResultBase method) GetColumnNamesAndTypes() (in module rdkit.Dbase.DbInfo) (rdkit.Dbase.DbConnection.DbConnect method) (rdkit.Dbase.DbResultSet.DbResultBase method) GetColumns() (in module rdkit.Dbase.DbUtils) (rdkit.Dbase.DbConnection.DbConnect method) GetColumnTypes() (rdkit.Dbase.DbResultSet.DbResultBase method) GetCompactness() (rdkit.Chem.rdMolDescriptors.DoubleCubicLatticeVolume method) GetConfidenceInterval() (in module rdkit.ML.Data.Stats) GetConformer() (rdkit.Chem.rdchem.Mol method) GetConformerRMS() (in module rdkit.Chem.AllChem) GetConformerRMSMatrix() (in module rdkit.Chem.AllChem) GetConformers() (rdkit.Chem.rdchem.Mol method) GetConnectivityInvariants() (in module rdkit.Chem.rdMolDescriptors) GetContainingNeighbors() (rdkit.DataStructs.cDataStructs.FPBReader method) (rdkit.DataStructs.cDataStructs.MultiFPBReader method) GetCorrMatrix() (rdkit.ML.InfoTheory.rdInfoTheory.BitCorrMatGenerator method) GetCountFingerprint() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetCountFingerprintAsNumPy() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetCountFingerprints() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetCountFPs() (in module rdkit.Chem.rdFingerprintGenerator) GetCrippenO3A() (in module rdkit.Chem.rdMolAlign) GetCrippenO3AForProbeConfs() (in module rdkit.Chem.rdMolAlign) GetCStates() (rdkit.Chem.rdchem.SubstanceGroup method) GetCursor() (rdkit.Dbase.DbConnection.DbConnect method) GetData() (in module rdkit.Dbase.DbUtils) (rdkit.Dbase.DbConnection.DbConnect method) (rdkit.ML.Cluster.Clusters.Cluster method) GetDataCount() (rdkit.Dbase.DbConnection.DbConnect method) GetDbNames() (in module rdkit.Dbase.DbInfo) GetDefaultAbbreviations() (in module rdkit.Chem.rdAbbreviations) GetDefaultAdjustParams() (in module rdkit.Chem.rdChemReactions) GetDefaultLinkers() (in module rdkit.Chem.rdAbbreviations) GetDefaultPickleProperties() (in module rdkit.Chem.rdchem) GetDefaultValence() (rdkit.Chem.rdchem.PeriodicTable method) GetDegree() (rdkit.Chem.rdchem.Atom method) GetDeprotections() (in module rdkit.Chem.rdDeprotect) GetDescription() (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) (rdkit.Chem.rdMolCatalog.MolCatalogEntry method) GetDescriptorFuncs() (rdkit.ML.Descriptors.MoleculeDescriptors.MolecularDescriptorCalculator method) GetDescriptorNames() (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) (rdkit.ML.Descriptors.Descriptors.DescriptorCalculator method) (rdkit.ML.Descriptors.MoleculeDescriptors.MolecularDescriptorCalculator method) GetDescriptorSummaries() (rdkit.ML.Descriptors.MoleculeDescriptors.MolecularDescriptorCalculator method) GetDescriptorVersions() (rdkit.ML.Descriptors.MoleculeDescriptors.MolecularDescriptorCalculator method) GetDihedralDeg() (in module rdkit.Chem.rdMolTransforms) GetDihedralRad() (in module rdkit.Chem.rdMolTransforms) GetDirMatch() (rdkit.Chem.FeatMaps.FeatMapPoint.FeatMapPoint method) GetDist2() (rdkit.Chem.FeatMaps.FeatMapPoint.FeatMapPoint method) GetDistanceMatrix() (in module rdkit.Chem.Fingerprints.ClusterMols) (in module rdkit.Chem.rdmolops) GetDonor1FeatVects() (in module rdkit.Chem.Features.FeatDirUtilsRD) GetDonor2FeatVects() (in module rdkit.Chem.Features.FeatDirUtilsRD) GetDonor3FeatVects() (in module rdkit.Chem.Features.FeatDirUtilsRD) GetDoubleProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetDrawCoords() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) GetDrawingText() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo method) (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG method) GetElementName() (rdkit.Chem.rdchem.PeriodicTable method) GetElementSymbol() (rdkit.Chem.rdchem.PeriodicTable method) GetEndAtom() (rdkit.Chem.rdchem.Bond method) GetEndAtomIdx() (rdkit.Chem.rdchem.Bond method) GetEnergy() (rdkit.Chem.rdtrajectory.Snapshot method) GetEntry() (rdkit.Chem.rdfiltercatalog.FilterCatalog method) GetEntryBitId() (rdkit.Chem.rdfragcatalog.FragCatalog method) (rdkit.Chem.rdMolCatalog.MolCatalog method) GetEntryDescription() (rdkit.Chem.rdfragcatalog.FragCatalog method) (rdkit.Chem.rdMolCatalog.MolCatalog method) GetEntryDownIds() (rdkit.Chem.rdfragcatalog.FragCatalog method) (rdkit.Chem.rdMolCatalog.MolCatalog method) GetEntryFuncGroupIds() (rdkit.Chem.rdfragcatalog.FragCatalog method) GetEntryOrder() (rdkit.Chem.rdfragcatalog.FragCatalog method) GetEntryWithIdx() (rdkit.Chem.rdfiltercatalog.FilterCatalog method) GetEnumerator() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) GetEOFHitOnRead() (rdkit.Chem.rdmolfiles.ForwardSDMolSupplier method) GetErGFingerprint() (in module rdkit.Chem.rdReducedGraphs) GetEuclideanDistMat() (in module rdkit.DataManip.Metric.rdMetricMatrixCalc) GetExclusionSMARTS() (rdkit.Chem.FragmentMatcher.FragmentMatcher method) GetExperimentalTorsions() (in module rdkit.Chem.rdDistGeom) GetExplicitBitVectProp() (rdkit.Chem.rdchem.Atom method) GetExplicitValence() (rdkit.Chem.rdchem.Atom method) GetExtraPointPos() (rdkit.ForceField.rdForceField.ForceField method) GetExtras() (rdkit.DataStructs.TopNContainer.TopNContainer method) GetFactory() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) GetFailureCounts() (rdkit.Chem.rdDistGeom.EmbedParameters method) GetFamily() (rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature method) (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) GetFeatFamilies() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetFeatFeatDistMatrix() (in module rdkit.Chem.FeatMaps.FeatMapUtils) GetFeatFeatScore() (rdkit.Chem.FeatMaps.FeatMaps.FeatMap method) GetFeature() (rdkit.Chem.FeatMaps.FeatMaps.FeatMap method) getFeature() (rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore method) (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) GetFeatureDefs() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeatureFactory method) GetFeatureFamilies() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeatureFactory method) GetFeatureInvariants() (in module rdkit.Chem.rdMolDescriptors) GetFeatures() (rdkit.Chem.FeatMaps.FeatMaps.FeatMap method) getFeatures() (rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore method) (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) GetFeaturesForMol() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeatureFactory method) GetFilterMatches() (rdkit.Chem.rdfiltercatalog.FilterCatalog method) (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) GetFingerprint() (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions static method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) (rdkit.Chem.rdSubstructLibrary.FPHolderBase method) GetFingerprintAsNumPy() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetFingerprints() (in module rdkit.Chem.Fingerprints.MolSimilarity) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetFirstMatch() (rdkit.Chem.rdfiltercatalog.FilterCatalog method) GetFlattenedFunctionalGroupHierarchy() (in module rdkit.Chem.rdfiltercatalog) GetForceV3000() (rdkit.Chem.rdmolfiles.SDWriter method) GetFormalCharge() (in module rdkit.Chem.rdmolops) (rdkit.Chem.rdchem.Atom method) GetFP() (rdkit.DataStructs.cDataStructs.FPBReader method) GetFPForMol() (rdkit.Chem.rdfragcatalog.FragFPGenerator method) GetFpHolder() (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) GetFPLength() (rdkit.Chem.rdfragcatalog.FragCatalog method) (rdkit.Chem.rdMolCatalog.MolCatalog method) GetFPs() (in module rdkit.Chem.rdFingerprintGenerator) GetFraggleSimilarity() (in module rdkit.Chem.Fraggle.FraggleSim) GetFuncGroup() (rdkit.Chem.rdfragcatalog.FragCatParams method) GetFunctionalGroupHierarchy() (in module rdkit.Chem.rdfiltercatalog) GetGridIndex() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetGridIndices() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetGridPointIndex() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetGridPointLoc() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetGroupType() (rdkit.Chem.rdchem.StereoGroup method) GetHamiltonian() (rdkit.Chem.rdEHTTools.EHTResults method) GetHashedAtomPairFingerprint() (in module rdkit.Chem.rdMolDescriptors) GetHashedAtomPairFingerprintAsBitVect() (in module rdkit.Chem.rdMolDescriptors) GetHashedMorganFingerprint() (in module rdkit.Chem.rdMolDescriptors) GetHashedTopologicalTorsionFingerprint() (in module rdkit.Chem.rdMolDescriptors) GetHashedTopologicalTorsionFingerprintAsBitVect() (in module rdkit.Chem.rdMolDescriptors) GetHeterocycleReactions() (in module rdkit.Chem.EnumerateHeterocycles) GetHeterocycleReactionSmarts() (in module rdkit.Chem.EnumerateHeterocycles) getHighlightColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) GetHybridization() (rdkit.Chem.rdchem.Atom method) GetId() (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature method) (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) (rdkit.DataStructs.cDataStructs.FPBReader method) GetIdx() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) GetImplicitValence() (rdkit.Chem.rdchem.Atom method) GetInchiForCTAB() (in module rdkit.Chem.MolKey.MolKey) GetIndex() (rdkit.ML.Cluster.Clusters.Cluster method) GetIndexCombinations() (in module rdkit.Chem.Pharm2D.Utils) GetIndexInMol() (rdkit.Chem.rdchem.SubstanceGroup method) GetInfoString() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetInputData() (rdkit.ML.Data.MLData.MLDataSet method) (rdkit.ML.Data.MLData.MLQuantDataSet method) GetInsertionCode() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetIntProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetIsAromatic() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) GetIsConjugated() (rdkit.Chem.rdchem.Bond method) GetIsEnumerated() (rdkit.Chem.rdchem.ResonanceMolSupplier method) GetIsHeteroAtom() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetIsotope() (rdkit.Chem.rdchem.Atom method) GetItemText() (rdkit.Chem.rdmolfiles.SDMolSupplier method) (rdkit.Chem.rdmolfiles.SmilesMolSupplier method) (rdkit.Chem.rdmolfiles.TDTMolSupplier method) GetKekulize() (rdkit.Chem.rdmolfiles.SDWriter method) GetKey() (rdkit.Chem.rdSubstructLibrary.KeyHolderBase method) GetKeyForCTAB() (in module rdkit.Chem.MolKey.MolKey) GetKeyHolder() (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) GetKeys() (rdkit.Chem.rdSubstructLibrary.KeyHolderBase method) GetLastItemText() (rdkit.Chem.rdmolfiles.MultithreadedSDMolSupplier method) (rdkit.Chem.rdmolfiles.MultithreadedSmilesMolSupplier method) GetLastRecordId() (rdkit.Chem.rdmolfiles.MultithreadedSDMolSupplier method) (rdkit.Chem.rdmolfiles.MultithreadedSmilesMolSupplier method) GetLeaves() (rdkit.Chem.Recap.RecapHierarchyNode method) getLegendColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) GetLength() (rdkit.DataStructs.cDataStructs.IntSparseIntVect method) (rdkit.DataStructs.cDataStructs.LongSparseIntVect method) (rdkit.DataStructs.cDataStructs.UIntSparseIntVect method) (rdkit.DataStructs.cDataStructs.ULongSparseIntVect method) getLowerBound() (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) getLowerBound2D() (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) GetLowerFragLength() (rdkit.Chem.rdfragcatalog.FragCatParams method) GetMACCSKeysFingerprint() (in module rdkit.Chem.rdMolDescriptors) GetMass() (rdkit.Chem.rdchem.Atom method) GetMassForIsotope() (rdkit.Chem.rdchem.PeriodicTable method) GetMatch() (rdkit.Chem.FragmentMatcher.FragmentMatcher method) GetMatches() (rdkit.Chem.FilterCatalog.FilterMatcher method) (rdkit.Chem.FragmentMatcher.FragmentMatcher method) (rdkit.Chem.rdfiltercatalog.FilterCatalog method) (rdkit.Chem.rdfiltercatalog.FilterMatcherBase method) (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method)

GetMatchingCoreIdx() (rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition method) GetMaxAtomicNumber() (rdkit.Chem.rdchem.PeriodicTable method) GetMaxCount() (rdkit.Chem.rdfiltercatalog.SmartsMatcher method) GetMaxStructures() (rdkit.Chem.rdchem.ResonanceMolSupplierCallback method) GetMaxTautomers() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) GetMaxTransforms() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) GetMetric() (rdkit.ML.Cluster.Clusters.Cluster method) GetMetricName() (rdkit.Chem.Fingerprints.FingerprintMols.FingerprinterDetails method) GetMinCount() (rdkit.Chem.rdfiltercatalog.SmartsMatcher method) GetMMFFAngleBendParams() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetMMFFAtomType() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetMMFFBondStretchParams() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetMMFFFormalCharge() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetMMFFOopBendParams() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetMMFFPartialCharge() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetMMFFStretchBendParams() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetMMFFTorsionParams() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetMMFFVdWParams() (rdkit.ForceField.rdForceField.MMFFMolProperties method) GetModifiedAtoms() (rdkit.Chem.rdTautomerQuery.TautomerQuery method) GetModifiedBonds() (rdkit.Chem.rdTautomerQuery.TautomerQuery method) GetMol() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.MolBundle method) (rdkit.Chem.rdchem.RWMol method) (rdkit.Chem.rdMolCatalog.MolCatalogEntry method) (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) (rdkit.Chem.rdSubstructLibrary.MolHolderBase method) (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) GetMoleculeBoundsMatrix() (in module rdkit.Chem.rdDistGeom) GetMolFeats() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetMolFeature() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeatureFactory method) GetMolFrags() (in module rdkit.Chem.rdmolops) GetMolHash() (in module rdkit.Chem.RegistrationHash) GetMolHolder() (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) GetMolLayers() (in module rdkit.Chem.RegistrationHash) GetMolSize() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) GetMolsMatchingBit() (in module rdkit.Chem.FragmentCatalog) GetMolSubstanceGroups() (in module rdkit.Chem.rdchem) GetMolSubstanceGroupWithIdx() (in module rdkit.Chem.rdchem) GetMonomerInfo() (rdkit.Chem.rdchem.Atom method) GetMonomerType() (rdkit.Chem.rdchem.AtomMonomerInfo method) GetMoreTerminalPoints() (in module rdkit.Chem.Subshape.BuilderUtils) GetMorganAtomInvGen() (in module rdkit.Chem.rdFingerprintGenerator) GetMorganBondInvGen() (in module rdkit.Chem.rdFingerprintGenerator) GetMorganFeatureAtomInvGen() (in module rdkit.Chem.rdFingerprintGenerator) GetMorganFingerprint() (in module rdkit.Chem.Draw.SimilarityMaps) (in module rdkit.Chem.rdMolDescriptors) GetMorganFingerprintAsBitVect() (in module rdkit.Chem.rdMolDescriptors) GetMorganGenerator() (in module rdkit.Chem.rdFingerprintGenerator) GetMostCommonIsotope() (rdkit.Chem.rdchem.PeriodicTable method) GetMostCommonIsotopeMass() (rdkit.Chem.rdchem.PeriodicTable method) GetMostSubstitutedCoreMatch() (in module rdkit.Chem.rdmolops) GetName() (rdkit.Chem.FilterCatalog.FilterMatcher method) (rdkit.Chem.rdchem.AtomMonomerInfo method) (rdkit.Chem.rdfiltercatalog.FilterMatcherBase method) (rdkit.Chem.rdMolDescriptors.PropertyFunctor method) (rdkit.ML.Cluster.Clusters.Cluster method) GetNamedData() (rdkit.ML.Data.MLData.MLDataSet method) (rdkit.ML.Data.MLData.MLQuantDataSet method) GetNeighbors() (rdkit.Chem.rdchem.Atom method) GetNextId() (in module rdkit.Dbase.StorageUtils) GetNextRDId() (in module rdkit.Dbase.StorageUtils) GetNode() (in module rdkit.VLib.NodeLib.DbMolSupply) (in module rdkit.VLib.NodeLib.DbPickleSupplier) GetNodeList() (in module rdkit.ML.Cluster.ClusterUtils) GetNodesDownToCentroids() (in module rdkit.ML.Cluster.ClusterUtils) GetNoImplicit() (rdkit.Chem.rdchem.Atom method) GetNonzeroElements() (rdkit.DataStructs.cDataStructs.IntSparseIntVect method) (rdkit.DataStructs.cDataStructs.LongSparseIntVect method) (rdkit.DataStructs.cDataStructs.UIntSparseIntVect method) (rdkit.DataStructs.cDataStructs.ULongSparseIntVect method) GetNoStereoLayers() (in module rdkit.Chem.RegistrationHash) GetNOuterElecs() (rdkit.Chem.rdchem.PeriodicTable method) GetNPossibleVals() (rdkit.ML.Data.MLData.MLDataSet method) GetNPts() (rdkit.ML.Data.MLData.MLDataSet method) GetNResults() (rdkit.ML.Data.MLData.MLDataSet method) GetNumAgentTemplates() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetNumAtoms() (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) GetNumBins() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetNumBits() (rdkit.DataStructs.BitEnsemble.BitEnsemble method) (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.FPBReader method) (rdkit.DataStructs.cDataStructs.MultiFPBReader method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) (rdkit.DataStructs.VectCollection.VectCollection method) GetNumBonds() (rdkit.Chem.rdchem.Mol method) GetNumConformers() (rdkit.Chem.rdchem.Mol method) GetNumConjGrps() (rdkit.Chem.rdchem.ResonanceMolSupplier method) (rdkit.Chem.rdchem.ResonanceMolSupplierCallback method) GetNumDigits() (rdkit.Chem.rdmolfiles.TDTWriter method) GetNumDiverseStructures() (rdkit.Chem.rdchem.ResonanceMolSupplierCallback method) GetNumEntries() (rdkit.Chem.rdfiltercatalog.FilterCatalog method) (rdkit.Chem.rdfragcatalog.FragCatalog method) (rdkit.Chem.rdMolCatalog.MolCatalog method) GetNumExplicitHs() (rdkit.Chem.rdchem.Atom method) GetNumFeatureDefs() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeatureFactory method) GetNumFeatures() (rdkit.Chem.FeatMaps.FeatMaps.FeatMap method) GetNumFuncGroups() (rdkit.Chem.rdfragcatalog.FragCatParams method) GetNumHeavyAtoms() (rdkit.Chem.rdchem.Mol method) GetNumImplicitHs() (rdkit.Chem.rdchem.Atom method) GetNumMolFeatures() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeatureFactory method) GetNumOffBits() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) GetNumOnBits() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) GetNumPermutations() (rdkit.Chem.rdChemReactions.EnumerationStrategyBase method) GetNumPiElectrons() (in module rdkit.Chem.rdchem) GetNumProductTemplates() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetNumRadicalElectrons() (rdkit.Chem.rdchem.Atom method) GetNumReactantTemplates() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetNumStructures() (rdkit.Chem.rdchem.ResonanceMolSupplierCallback method) GetNumX() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetNumY() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetNumZ() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetNVars() (rdkit.ML.Data.MLData.MLDataSet method) GetO3A() (in module rdkit.Chem.rdMolAlign) GetO3AForProbeConfs() (in module rdkit.Chem.rdMolAlign) GetOccupancy() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetOccupancyVect() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetOffset() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetOnBits() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) (rdkit.DataStructs.VectCollection.VectCollection method) GetOptions() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetOrbitalEnergies() (rdkit.Chem.rdEHTTools.EHTResults method) GetOrder() (rdkit.Chem.rdMolCatalog.MolCatalogEntry method) GetOrVect() (rdkit.DataStructs.VectCollection.VectCollection method) GetOtherAtom() (rdkit.Chem.rdchem.Bond method) GetOtherAtomIdx() (rdkit.Chem.rdchem.Bond method) GetOverlapMatrix() (rdkit.Chem.rdEHTTools.EHTResults method) GetOwningMol() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.SubstanceGroup method) GetPackingDensity() (rdkit.Chem.rdMolDescriptors.DoubleCubicLatticeVolume method) GetParentAtoms() (rdkit.Chem.rdchem.SubstanceGroup method) GetParents() (rdkit.VLib.Node.VLibNode method) GetPattern() (rdkit.Chem.rdfiltercatalog.SmartsMatcher method) GetPDBResidueInfo() (rdkit.Chem.rdchem.Atom method) GetPeriodicTable() (in module rdkit.Chem.rdchem) GetPNG() (rdkit.Chem.PyMol.MolViewer method) GetPoint2D() (rdkit.Chem.rdtrajectory.Snapshot method) GetPoint3D() (rdkit.Chem.rdtrajectory.Snapshot method) GetPoints() (rdkit.ML.Cluster.Clusters.Cluster method) GetPointsPositions() (rdkit.ML.Cluster.Clusters.Cluster method) GetPos() (rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature method) (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) GetPosition() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) (rdkit.Chem.rdChemReactions.EnumerationStrategyBase method) (rdkit.ML.Cluster.Clusters.Cluster method) GetPositions() (rdkit.Chem.rdchem.Conformer method) GetPossibleScaffolds() (in module rdkit.Chem.Pharm2D.Utils) GetPreferCoordGen() (in module rdkit.Chem.rdDepictor) GetPrincipleQuantumNumber() (in module rdkit.Chem.EState.EState) GetProcessPropertyLists() (rdkit.Chem.rdmolfiles.ForwardSDMolSupplier method) (rdkit.Chem.rdmolfiles.MultithreadedSDMolSupplier method) (rdkit.Chem.rdmolfiles.SDMolSupplier method) GetProducts() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetProductTemplate() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetProgressCallback() (rdkit.Chem.rdchem.ResonanceMolSupplier method) GetProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) GetProperty() (rdkit.Chem.rdMolDescriptors.Properties static method) GetPropertyNames() (rdkit.Chem.rdMolDescriptors.Properties method) GetPropList() (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) GetPropName() (rdkit.Chem.rdSubstructLibrary.KeyFromPropHolder method) GetPropNames() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetPropsAsDict() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetPtNames() (rdkit.ML.Data.MLData.MLDataSet method) GetPts() (rdkit.DataStructs.TopNContainer.TopNContainer method) GetQuantBounds() (rdkit.ML.Data.MLData.MLDataSet method) getQueryColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) GetQueryText() (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions static method) GetQueryType() (rdkit.Chem.rdchem.Atom method) getRadii() (rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore method) getRadius() (rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore method) GetRb0() (rdkit.Chem.rdchem.PeriodicTable method) GetRcovalent() (rdkit.Chem.rdchem.PeriodicTable method) GetRDKFingerprint() (in module rdkit.Chem.Draw.SimilarityMaps) (in module rdkit.Chem.Fingerprints.FingerprintMols) GetRDKitAtomInvGen() (in module rdkit.Chem.rdFingerprintGenerator) GetRDKitFPGenerator() (in module rdkit.Chem.rdFingerprintGenerator) GetReactants() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetReactantTemplate() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetReactingAtoms() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetReaction() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) GetReader() (rdkit.DataStructs.cDataStructs.MultiFPBReader method) GetReadId() (rdkit.Chem.rdchem.StereoGroup method) GetReagents() (rdkit.Chem.rdChemReactions.EnumerateLibrary method) GetReassignStereo() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) GetReducedChargeMatrix() (rdkit.Chem.rdEHTTools.EHTResults method) GetReducedOverlapPopulationMatrix() (rdkit.Chem.rdEHTTools.EHTResults method) GetRemoveBondStereo() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) GetRemoveSp3Stereo() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) GetResidueName() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetResidueNumber() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetResults() (rdkit.ML.Data.MLData.MLDataSet method) (rdkit.ML.Data.MLData.MLQuantDataSet method) GetRGroupLabels() (rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition method) GetRGroupsAsColumns() (rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition method) GetRGroupsAsRows() (rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition method) GetRingInfo() (rdkit.Chem.rdchem.Mol method) GetRow() (rdkit.Chem.rdchem.PeriodicTable method) GetRvdw() (rdkit.Chem.rdchem.PeriodicTable method) GetScaffoldForMol() (in module rdkit.Chem.Scaffolds.MurckoScaffold) GetSearchOrder() (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) GetSecondaryStructure() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetSegmentNumber() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetSelectedAtoms() (rdkit.Chem.PyMol.MolViewer method) GetSerialNumber() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetShapeShapeDistance() (in module rdkit.Chem.Subshape.SubshapeAligner) GetShortestPath() (in module rdkit.Chem.rdmolops) GetSignature() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetSigSize() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) GetSimilarityMapForFingerprint() (in module rdkit.Chem.Draw.SimilarityMaps) GetSimilarityMapForModel() (in module rdkit.Chem.Draw.SimilarityMaps) GetSimilarityMapFromWeights() (in module rdkit.Chem.Draw.SimilarityMaps) GetSingleFingerprint() (rdkit.Chem.Fingerprints.SimilarityScreener.SimilarityScreener method) GetSize() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetSMARTS() (rdkit.Chem.FragmentMatcher.FragmentMatcher method) GetSmarts() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) GetSnapshot() (rdkit.Chem.rdtrajectory.Trajectory method) GetSpacing() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetSparseCountFingerprint() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetSparseCountFingerprints() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetSparseCountFPs() (in module rdkit.Chem.rdFingerprintGenerator) GetSparseFingerprint() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetSparseFingerprints() (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator32 method) (rdkit.Chem.rdFingerprintGenerator.FingerprintGenerator64 method) GetSparseFPs() (in module rdkit.Chem.rdFingerprintGenerator) GetSSSR() (in module rdkit.Chem.rdmolops) GetStandardizedWeights() (in module rdkit.Chem.Draw.SimilarityMaps) GetState() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) GetStereo() (rdkit.Chem.rdchem.Bond method) GetStereoAtoms() (rdkit.Chem.rdchem.Bond method) GetStereoGroups() (rdkit.Chem.rdchem.Mol method) GetStereoisomerCount() (in module rdkit.Chem.EnumerateStereoisomers) GetStereoTautomerHash() (in module rdkit.Chem.RegistrationHash) GetStringVectProp() (rdkit.Chem.rdchem.SubstanceGroup method) GetSubshapeAlignments() (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner method) GetSubstructMatch() (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.MolBundle method) (rdkit.Chem.rdchem.ResonanceMolSupplier method) (rdkit.Chem.rdTautomerQuery.TautomerQuery method) GetSubstructMatches() (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.MolBundle method) (rdkit.Chem.rdchem.ResonanceMolSupplier method) (rdkit.Chem.rdTautomerQuery.TautomerQuery method) GetSubstructMatchesWithTautomers() (rdkit.Chem.rdTautomerQuery.TautomerQuery method) GetSubstructParams() (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetSupplementalSmilesLabel() (in module rdkit.Chem.rdchem) GetSurfaceArea() (rdkit.Chem.rdMolDescriptors.DoubleCubicLatticeVolume method) GetSymbol() (rdkit.Chem.rdchem.Atom method) getSymbolColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) GetSymmSSSR() (in module rdkit.Chem.rdmolops) GetTableNames() (in module rdkit.Dbase.DbInfo) (rdkit.Dbase.DbConnection.DbConnect method) GetTanimoto() (rdkit.DataStructs.cDataStructs.FPBReader method) GetTanimotoDistMat() (in module rdkit.DataManip.Metric.rdMetricMatrixCalc) GetTanimotoNeighbors() (rdkit.DataStructs.cDataStructs.FPBReader method) (rdkit.DataStructs.cDataStructs.MultiFPBReader method) GetTanimotoSimMat() (in module rdkit.DataManip.Metric.rdMetricMatrixCalc) GetTautomers() (rdkit.Chem.rdTautomerQuery.TautomerQuery method) GetTempFactor() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) GetTemplateMolecule() (rdkit.Chem.rdTautomerQuery.TautomerQuery method) GetText() (rdkit.Chem.rdmolfiles.MaeWriter static method) (rdkit.Chem.rdmolfiles.SDWriter static method) GetTFDBetweenConformers() (in module rdkit.Chem.TorsionFingerprints) GetTFDBetweenMolecules() (in module rdkit.Chem.TorsionFingerprints) GetTFDMatrix() (in module rdkit.Chem.TorsionFingerprints) GetTolerance() (rdkit.Chem.rdfragcatalog.FragCatParams method) GetTopN() (rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRanker method) GetTopologicalTorsionFingerprint() (in module rdkit.Chem.rdMolDescriptors) GetTopologicalTorsionFingerprintAsIds() (in module rdkit.Chem.AtomPairs.Torsions) GetTopologicalTorsionGenerator() (in module rdkit.Chem.rdFingerprintGenerator) GetTotalDegree() (rdkit.Chem.rdchem.Atom method) GetTotalNumHs() (rdkit.Chem.rdchem.Atom method) GetTotalVal() (rdkit.DataStructs.cDataStructs.DiscreteValueVect method) (rdkit.DataStructs.cDataStructs.IntSparseIntVect method) (rdkit.DataStructs.cDataStructs.LongSparseIntVect method) (rdkit.DataStructs.cDataStructs.UIntSparseIntVect method) (rdkit.DataStructs.cDataStructs.ULongSparseIntVect method) GetTotalValence() (rdkit.Chem.rdchem.Atom method) GetTriangleMatches() (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner method) GetTriangles() (in module rdkit.Chem.Pharm2D.Utils) GetTTFingerprint() (in module rdkit.Chem.Draw.SimilarityMaps) GetTversky() (rdkit.DataStructs.cDataStructs.FPBReader method) GetTverskyNeighbors() (rdkit.DataStructs.cDataStructs.FPBReader method) (rdkit.DataStructs.cDataStructs.MultiFPBReader method) GetType() (rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature method) (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) GetTypeString() (rdkit.Chem.rdfragcatalog.FragCatParams method) GetTypeStrings() (in module rdkit.Dbase.DbUtils) GetUFFAngleBendParams() (in module rdkit.Chem.rdForceFieldHelpers) GetUFFBondStretchParams() (in module rdkit.Chem.rdForceFieldHelpers) GetUFFInversionParams() (in module rdkit.Chem.rdForceFieldHelpers) GetUFFTorsionParams() (in module rdkit.Chem.rdForceFieldHelpers) GetUFFVdWParams() (in module rdkit.Chem.rdForceFieldHelpers) getUltimateParents() (rdkit.Chem.Recap.RecapHierarchyNode method) GetUniqueCombinations() (in module rdkit.Chem.Pharm2D.Utils) GetUniqueCombinations_new() (in module rdkit.Chem.Pharm2D.Utils) GetUnsignedProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) GetUnsignedVectProp() (rdkit.Chem.rdchem.SubstanceGroup method) getUpperBound() (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) getUpperBound2D() (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) GetUpperFragLength() (rdkit.Chem.rdfragcatalog.FragCatParams method) GetUseLegacyStereoPerception() (in module rdkit.Chem.rdmolops) GetUSR() (in module rdkit.Chem.rdMolDescriptors) GetUSRCAT() (in module rdkit.Chem.rdMolDescriptors) GetUSRDistributions() (in module rdkit.Chem.rdMolDescriptors) GetUSRDistributionsFromPoints() (in module rdkit.Chem.rdMolDescriptors) GetUSRFromDistributions() (in module rdkit.Chem.rdMolDescriptors) GetUSRScore() (in module rdkit.Chem.rdMolDescriptors) GetV1TautomerEnumerator() (in module rdkit.Chem.MolStandardize.rdMolStandardize) GetVal() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetValenceContrib() (rdkit.Chem.rdchem.Bond method) GetValenceList() (rdkit.Chem.rdchem.PeriodicTable method) GetValPoint() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) GetValueType() (rdkit.DataStructs.cDataStructs.DiscreteValueVect method) getVariableAttachmentColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) GetVarNames() (rdkit.ML.Data.MLData.MLDataSet method) GetVDWVolume() (rdkit.Chem.rdMolDescriptors.DoubleCubicLatticeVolume method) GetVersion() (rdkit.Chem.rdMolDescriptors.PropertyFunctor method) GetVolume() (rdkit.Chem.rdMolDescriptors.DoubleCubicLatticeVolume method) GetWords() (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions static method) GetWrite2D() (rdkit.Chem.rdmolfiles.TDTWriter method) GetWriteId() (rdkit.Chem.rdchem.StereoGroup method) GetWriteNames() (rdkit.Chem.rdmolfiles.TDTWriter method) GOWER (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute) Greedy (rdkit.Chem.rdRGroupDecomposition.RGroupMatching attribute) GreedyChunks (rdkit.Chem.rdRGroupDecomposition.RGroupMatching attribute) grid (rdkit.Chem.Subshape.SubshapeObjects.ShapeWithSkeleton attribute) gridDims (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder attribute) gridResolution (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property) gridSpacing (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder attribute) guid (rdkit.Chem.MolDb.Loader_sa.Compound attribute)

H

HallKierAlpha() (in module rdkit.Chem.GraphDescriptors) HapticBondsToDative() (in module rdkit.Chem.rdmolops) HAS() (in module rdkit.ML.Descriptors.Parser) HasAgentTemplateSubstructMatch() (in module rdkit.Chem.rdChemReactions) HasBitVectPropWithValueQueryAtom() (in module rdkit.Chem.rdqueries) HasBoolPropWithValueQueryAtom() (in module rdkit.Chem.rdqueries) HasBoolPropWithValueQueryBond() (in module rdkit.Chem.rdqueries) HasChiralTagQueryAtom() (in module rdkit.Chem.rdqueries) HasDoublePropWithValueQueryAtom() (in module rdkit.Chem.rdqueries) HasDoublePropWithValueQueryBond() (in module rdkit.Chem.rdqueries) HasFilterMatch() (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) HashFunction (class in rdkit.Chem.rdMolHash) HashLayer (class in rdkit.Chem.RegistrationHash) HashScheme (class in rdkit.Chem.RegistrationHash) HasIntPropWithValueQueryAtom() (in module rdkit.Chem.rdqueries) HasIntPropWithValueQueryBond() (in module rdkit.Chem.rdqueries) HasMatch() (rdkit.Chem.FilterCatalog.FilterMatcher method) (rdkit.Chem.FragmentMatcher.FragmentMatcher method) (rdkit.Chem.rdfiltercatalog.FilterCatalog method) (rdkit.Chem.rdfiltercatalog.FilterMatcherBase method) (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) HasOwningMol() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) HasProductTemplateSubstructMatch() (in module rdkit.Chem.rdChemReactions) HasProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) HasPropQueryAtom() (in module rdkit.Chem.rdqueries) HasPropQueryBond() (in module rdkit.Chem.rdqueries) HasQuery() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Mol method) HasQueryHs() (in module rdkit.Chem.rdmolops) HasReactantTemplateSubstructMatch() (in module rdkit.Chem.rdChemReactions) HasReactionAtomMapping() (in module rdkit.Chem.rdChemReactions) HasReactionSubstructMatch() (in module rdkit.Chem.rdChemReactions)

HasStringPropWithValueQueryAtom() (in module rdkit.Chem.rdqueries) HasStringPropWithValueQueryBond() (in module rdkit.Chem.rdqueries) HasSubstructMatch() (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.MolBundle method) hasTitle (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) HasValenceViolation() (rdkit.Chem.rdchem.Atom method) HBA (rdkit.Chem.QED.QEDproperties attribute) HBD (rdkit.Chem.QED.QEDproperties attribute) HCountEqualsQueryAtom() (in module rdkit.Chem.rdqueries) HCountGreaterQueryAtom() (in module rdkit.Chem.rdqueries) HCountLessQueryAtom() (in module rdkit.Chem.rdqueries) heappop() (rdkit.Chem.fmcs.fmcs.VerboseHeapOps method) heappush() (rdkit.Chem.fmcs.fmcs.VerboseHeapOps method) HeavyAtomCount() (in module rdkit.Chem.Lipinski) HeavyAtomMolWt() (in module rdkit.Chem.Descriptors) Height() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) HetAtomProtomer (rdkit.Chem.rdMolHash.HashFunction attribute) HetAtomProtomerv2 (rdkit.Chem.rdMolHash.HashFunction attribute) HetAtomTautomer (rdkit.Chem.rdMolHash.HashFunction attribute) HetAtomTautomerv2 (rdkit.Chem.rdMolHash.HashFunction attribute) HEXTUPLE (rdkit.Chem.rdchem.BondType attribute) HideAll() (rdkit.Chem.PyMol.MolViewer method) hideColor (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) HideObject() (rdkit.Chem.PyMol.MolViewer method) hideWidth (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) HierarchicalClusterPicker (class in rdkit.SimDivFilters.rdSimDivPickers) highlightAtoms (rdkit.Chem.Draw.FingerprintEnv attribute) HighlightAtoms() (rdkit.Chem.PyMol.MolViewer method) highlightBonds (rdkit.Chem.Draw.FingerprintEnv attribute) highlightBondWidthMultiplier (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) highlightColor (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) highlightRad (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) highlightRadii (rdkit.Chem.Draw.FingerprintEnv attribute) highlightRadius (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) hueckelEnabled() (in module rdkit.Chem.rdDetermineBonds) HybridizationEqualsQueryAtom() (in module rdkit.Chem.rdqueries) HybridizationGreaterQueryAtom() (in module rdkit.Chem.rdqueries) HybridizationLessQueryAtom() (in module rdkit.Chem.rdqueries) HybridizationType (class in rdkit.Chem.rdchem) HYDROGEN (rdkit.Chem.rdchem.BondType attribute)

I

id (rdkit.Chem.FragmentCatalog.BitGainsInfo attribute) (rdkit.Chem.rdchem.SubstanceGroupAttach property) Ignore (rdkit.Chem.FeatMaps.FeatMaps.FeatDirScoreMode attribute) ignoreAtomMapNumbers (rdkit.Chem.rdmolfiles.SmilesWriteParams property) IgnoreRingFusion (rdkit.Chem.rdFMCS.RingCompare attribute) ignoreSmoothingFailures (rdkit.Chem.rdDistGeom.EmbedParameters property) inchi (rdkit.Chem.MolKey.MolKey.InchiResult attribute) (rdkit.Chem.MolKey.MolKey.MolKeyResult attribute) InchiInfo (class in rdkit.Chem.MolKey.InchiInfo) InchiReadWriteError InchiResult (class in rdkit.Chem.MolKey.MolKey) InchiToInchiKey() (in module rdkit.Chem.inchi) (in module rdkit.Chem.rdinchi) InchiToMol() (in module rdkit.Chem.rdinchi) includeAgents (rdkit.Chem.rdChemReactions.ReactionFingerprintParams property) includeAtomNumbers (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) includeAtomTags (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) includeChiralFlagLabel (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) includeChirality (rdkit.Chem.rdFingerprintGenerator.FingerprintOptions property) includeDativeBonds (rdkit.Chem.rdmolfiles.SmilesWriteParams property) includeGenericBondScaffolds (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) includeGenericScaffolds (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) includeMetadata (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) includeRadicals (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) includeRedundantEnvironments (rdkit.Chem.rdFingerprintGenerator.MorganFingerprintOptions property) includeScaffoldsWithAttachments (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) includeScaffoldsWithoutAttachments (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) includeStereo (rdkit.Chem.rdmolfiles.MolWriterParams property) includeTargetMolInResults (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) index (rdkit.Chem.fmcs.fmcs.CangenNode attribute) IndexToRDId() (in module rdkit.Dbase.StorageUtils) InertialShapeFactor() (in module rdkit.Chem.Descriptors3D) inFileName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) info() (rdkit.RDLogger.logger method) InfoBitRanker (class in rdkit.ML.InfoTheory.rdInfoTheory) InfoEntropy() (in module rdkit.ML.InfoTheory.rdInfoTheory) InfoGain() (in module rdkit.ML.InfoTheory.rdInfoTheory) InfoType (class in rdkit.ML.InfoTheory.rdInfoTheory) Init() (rdkit.Chem.FragmentMatcher.FragmentMatcher method) (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) (rdkit.DataStructs.cDataStructs.FPBReader method) (rdkit.DataStructs.cDataStructs.MultiFPBReader method) InitFromDaylightString() (in module rdkit.DataStructs.cDataStructs) initFromFeat() (rdkit.Chem.FeatMaps.FeatMapPoint.FeatMapPoint method) initFromFile() (rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore method) initFromLines() (rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore method) InitFromStream() (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) initFromString() (rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore method) InitFromString() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) INITIAL_COORDS (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) Initialize (rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType attribute) Initialize() (rdkit.Chem.rdChemReactions.ChemicalReaction method) (rdkit.Chem.rdChemReactions.EnumerationStrategyBase method) (rdkit.ForceField.rdForceField.ForceField method) InitializeCheckMol() (in module rdkit.Avalon.pyAvalonTools) InitializePyMol() (rdkit.Chem.PyMol.MolViewer method) InitialSeed (rdkit.Chem.rdFMCS.MCSParameters property) initParser() (in module rdkit.Chem.ChemUtils.AlignDepict) (in module rdkit.Chem.ChemUtils.SDFToCSV) (in module rdkit.Chem.FeatFinderCLI) InitRandomNumbers() (in module rdkit.ML.Data.DataUtils) initStruchk() (in module rdkit.Chem.MolKey.MolKey) InNRingsEqualsQueryAtom() (in module rdkit.Chem.rdqueries) InNRingsGreaterQueryAtom() (in module rdkit.Chem.rdqueries)

InNRingsLessQueryAtom() (in module rdkit.Chem.rdqueries) INPUT_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) InputFormat (class in rdkit.Chem.SaltRemover) inputMolData (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineResult property) Insert() (rdkit.DataStructs.TopNContainer.TopNContainer method) InsertColumnData() (rdkit.Dbase.DbConnection.DbConnect method) InsertData() (rdkit.Dbase.DbConnection.DbConnect method) InsertMol() (rdkit.Chem.rdchem.RWMol method) InsertSnapshot() (rdkit.Chem.rdtrajectory.Trajectory method) InstallIPythonRenderer() (in module rdkit.Chem.Draw.IPythonConsole) InstallPandasTools() (in module rdkit.Chem.PandasTools) INTERSECT (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeCombineOperations attribute) intersect_counts() (in module rdkit.Chem.fmcs.fmcs) IntPair (class in rdkit.Chem.rdfiltercatalog) IntSparseIntVect (class in rdkit.DataStructs.cDataStructs) IntStringMap (class in rdkit.Chem.Draw.rdMolDraw2D) InvertChirality() (rdkit.Chem.rdchem.Atom method) IONIC (rdkit.Chem.rdchem.BondType attribute) Ipc() (in module rdkit.Chem.GraphDescriptors) IS2D_VALIDATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) Is2DValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) is2DZeroThreshold (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) Is3D() (rdkit.Chem.rdchem.Conformer method) is_in_ring (rdkit.Chem.fmcs.fmcs.Atom attribute) (rdkit.Chem.fmcs.fmcs.Bond attribute) IsAliphaticQueryAtom() (in module rdkit.Chem.rdqueries) IsAromaticQueryAtom() (in module rdkit.Chem.rdqueries) IsAtomInRingOfSize() (rdkit.Chem.rdchem.RingInfo method) IsBondInRingOfSize() (rdkit.Chem.rdchem.RingInfo method) IsBridgeheadQueryAtom() (in module rdkit.Chem.rdqueries) IsCoordGenSupportAvailable() (in module rdkit.Chem.rdDepictor) isDebugBuild() (in module rdkit.TestRunner) IsInitialized() (rdkit.Chem.rdChemReactions.ChemicalReaction method) IsInRing() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) IsInRingQueryAtom() (in module rdkit.Chem.rdqueries) IsInRingSize() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) IsMoleculeAgent() (rdkit.Chem.rdChemReactions.ChemicalReaction method) IsMoleculeProduct() (rdkit.Chem.rdChemReactions.ChemicalReaction method) IsMoleculeReactant() (rdkit.Chem.rdChemReactions.ChemicalReaction method) isNaN() (in module rdkit.Chem.Pharm3D.EmbedLib) Isotope (rdkit.Chem.rdmolops.MolzipLabel attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupLabelling attribute) IsotopeEqualsQueryAtom() (in module rdkit.Chem.rdqueries) IsotopeGreaterQueryAtom() (in module rdkit.Chem.rdqueries) isotopeLabels (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) IsotopeLabels (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) IsotopeLessQueryAtom() (in module rdkit.Chem.rdqueries) IsotopeParent() (in module rdkit.Chem.MolStandardize.rdMolStandardize) IsotopeParentInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) IsotopeValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) isovalScaleForQuantization (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property) IsReactionTemplateMoleculeAgent() (in module rdkit.Chem.rdChemReactions) IsRingFused() (rdkit.Chem.rdchem.RingInfo method) IsSubstructOf() (rdkit.Chem.rdTautomerQuery.TautomerQuery method) IsTerminal() (rdkit.ML.Cluster.Clusters.Cluster method) IsUnsaturatedQueryAtom() (in module rdkit.Chem.rdqueries) IsValid() (rdkit.Chem.FilterCatalog.FilterMatcher method) isValid() (rdkit.Chem.rdDeprotect.DeprotectData method) IsValid() (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) (rdkit.Chem.rdfiltercatalog.FilterMatcherBase method) (rdkit.Chem.rdfiltercatalog.SmartsMatcher method) isValidRingCut() (in module rdkit.Chem.Fraggle.FraggleSim) items() (rdkit.Chem.MolStandardize.rdMolStandardize.SmilesTautomerMap method)

J

JSONParseParameters (class in rdkit.Chem.rdMolInterchange)

JSONToMols() (in module rdkit.Chem.rdMolInterchange) JSONWriteParameters (class in rdkit.Chem.rdMolInterchange)

K

Kappa1() (in module rdkit.Chem.GraphDescriptors) Kappa2() (in module rdkit.Chem.GraphDescriptors) Kappa3() (in module rdkit.Chem.GraphDescriptors) KDG() (in module rdkit.Chem.rdDistGeom) keepOnlyFirstFragment (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) KEKULE_ALL (rdkit.Chem.rdchem.ResonanceFlags attribute) kekulize (rdkit.Chem.rdmolfiles.MolWriterParams property) Kekulize() (in module rdkit.Chem.rdmolops) kekulized (rdkit.Chem.MolStandardize.rdMolStandardize.Tautomer property) KekulizeException

KekulizeIfPossible() (in module rdkit.Chem.rdmolops) key() (rdkit.Chem.Draw.rdMolDraw2D.map_indexing_suite_IntStringMap_entry method) (rdkit.Chem.MolStandardize.rdMolStandardize.map_indexing_suite_SmilesTautomerMap_entry method) keyFeat (rdkit.Chem.Subshape.SubshapeObjects.SubshapeShape attribute) KeyFromPropHolder (class in rdkit.Chem.rdSubstructLibrary) KeyHolderBase (class in rdkit.Chem.rdSubstructLibrary) keys() (rdkit.Chem.MolStandardize.rdMolStandardize.SmilesTautomerMap method) KillCursor() (rdkit.Dbase.DbConnection.DbConnect method) KulczynskiSimilarity() (in module rdkit.DataStructs.cDataStructs) KulczynskiSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) KulczynskiSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs)

L

label (rdkit.Chem.FunctionalGroups.FGHierarchyNode attribute) (rdkit.Chem.rdAbbreviations.AbbreviationDefinition property) (rdkit.Chem.rdmolops.MolzipParams property) LabelMolAbbreviations() (in module rdkit.Chem.rdAbbreviations) labels (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) LabuteASA() (in module rdkit.Chem.MolSurf) LargestFragmentChooser (class in rdkit.Chem.MolStandardize.rdMolStandardize) largestFragmentChooserCountHeavyAtomsOnly (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) largestFragmentChooserUseAtomCount (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) Lasso (rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle attribute) LayeredFingerprint() (in module rdkit.Chem.rdmolops) LayeredOptions (class in rdkit.Chem.MolDb.FingerprintUtils) LAYOUT2D_VALIDATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) Layout2DValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) LazyBitVectorPick() (rdkit.SimDivFilters.rdSimDivPickers.LeaderPicker method) (rdkit.SimDivFilters.rdSimDivPickers.MaxMinPicker method) LazyBitVectorPickWithThreshold() (rdkit.SimDivFilters.rdSimDivPickers.MaxMinPicker method) LazyPick() (rdkit.SimDivFilters.rdSimDivPickers.LeaderPicker method) (rdkit.SimDivFilters.rdSimDivPickers.MaxMinPicker method) LazyPickWithThreshold() (rdkit.SimDivFilters.rdSimDivPickers.MaxMinPicker method) LazySig (class in rdkit.DataStructs.LazySignature) LeaderPicker (class in rdkit.SimDivFilters.rdSimDivPickers) LeeRichards (rdkit.Chem.rdFreeSASA.SASAAlgorithm attribute) legendFontSize (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) legendFraction (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) Length() (rdkit.Geometry.rdGeometry.Point2D method) (rdkit.Geometry.rdGeometry.Point3D method) (rdkit.Geometry.rdGeometry.PointND method) LengthSq() (rdkit.Geometry.rdGeometry.Point2D method) (rdkit.Geometry.rdGeometry.Point3D method) (rdkit.Geometry.rdGeometry.PointND method)

LINEAR_DOUBLE_BOND (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) lineColor (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) lineWidth (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) LineWidth() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) LinkNode (rdkit.Chem.rdMolEnumerator.EnumeratorType attribute) LoadDb() (in module rdkit.Chem.MolDb.Loader_orig) (in module rdkit.Chem.MolDb.Loader_sa) LoadDefaultRingSystemTemplates() (in module rdkit.Chem.rdDepictor) LoadFile() (rdkit.Chem.PyMol.MolViewer method) loadLayerFlags (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions attribute) LoadSDF() (in module rdkit.Chem.PandasTools) location (rdkit.Chem.Subshape.SubshapeObjects.SkeletonPoint attribute) log (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineResult property) log2() (in module rdkit.ML.SLT.Risk) LogDebugMsg() (in module rdkit.rdBase) LogErrorMsg() (in module rdkit.rdBase) logger (class in rdkit.RDLogger) LogInfoMsg() (in module rdkit.rdBase) logIt() (rdkit.RDLogger.logger method) LogMessage() (in module rdkit.rdBase) LogStatus() (in module rdkit.rdBase) LogToCppStreams() (in module rdkit.rdBase) LogToPythonLogger() (in module rdkit.rdBase) LogToPythonStderr() (in module rdkit.rdBase) LogWarningMsg() (in module rdkit.rdBase) LongSparseIntVect (class in rdkit.DataStructs.cDataStructs) lvIdx (rdkit.Chem.rdchem.SubstanceGroupAttach property)

M

MaeMolSupplier (class in rdkit.Chem.rdmolfiles) MaeWriter (class in rdkit.Chem.rdmolfiles) main() (in module rdkit.Chem.ChemUtils.AlignDepict) (in module rdkit.Chem.ChemUtils.SDFToCSV) (in module rdkit.Chem.FeatFinderCLI) (in module rdkit.Chem.fmcs.fmcs) make_arbitrary_smarts() (in module rdkit.Chem.fmcs.fmcs) make_canonical_smarts() (in module rdkit.Chem.fmcs.fmcs) make_complete_sdf() (in module rdkit.Chem.fmcs.fmcs) make_fragment_sdf() (in module rdkit.Chem.fmcs.fmcs) make_fragment_smiles() (in module rdkit.Chem.fmcs.fmcs) make_structure_format() (in module rdkit.Chem.fmcs.fmcs) makeAtomsGeneric (rdkit.Chem.rdmolops.AdjustQueryParameters property) makeAtomsGenericFlags (rdkit.Chem.rdmolops.AdjustQueryParameters property) makeBondsGeneric (rdkit.Chem.rdmolops.AdjustQueryParameters property) makeBondsGenericFlags (rdkit.Chem.rdmolops.AdjustQueryParameters property) makeDummiesQueries (rdkit.Chem.rdmolops.AdjustQueryParameters property) MakeFingerprint() (rdkit.Chem.rdSubstructLibrary.FPHolderBase method) MakeFreeSasaAPolarAtomQuery() (in module rdkit.Chem.rdFreeSASA) MakeFreeSasaPolarAtomQuery() (in module rdkit.Chem.rdFreeSASA) MakePicks() (rdkit.SimDivFilters.SimilarityPickers.GenericPicker method) (rdkit.SimDivFilters.SimilarityPickers.SpreadPicker method) (rdkit.SimDivFilters.SimilarityPickers.TopNOverallPicker method) MakePropertyRangeQuery() (in module rdkit.Chem.rdMolDescriptors) MakeScaffoldGeneric() (in module rdkit.Chem.Scaffolds.MurckoScaffold) map_indexing_suite_IntStringMap_entry (class in rdkit.Chem.Draw.rdMolDraw2D) map_indexing_suite_SmilesTautomerMap_entry (class in rdkit.Chem.MolStandardize.rdMolStandardize) MapToClusterFP() (rdkit.ML.InfoTheory.BitClusterer.BitClusterer method) MapToClusterScores() (rdkit.ML.InfoTheory.BitClusterer.BitClusterer method) mark() (rdkit.Chem.fmcs.fmcs.Timer method) MassEqualsQueryAtom() (in module rdkit.Chem.rdqueries) MassGreaterQueryAtom() (in module rdkit.Chem.rdqueries) MassLessQueryAtom() (in module rdkit.Chem.rdqueries) Match (rdkit.Chem.rdRGroupDecomposition.RGroupScore attribute) MATCH() (in module rdkit.Chem.fmcs.fmcs) Match() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdMolDescriptors.PropertyRangeQuery method) MatchChiralTag (rdkit.Chem.rdFMCS.MCSAtomCompareParameters property) MatchError Matches() (rdkit.Chem.rdMolAlign.O3A method) MatchFeatsToMol() (in module rdkit.Chem.Pharm3D.EmbedLib) MatchFormalCharge (rdkit.Chem.rdFMCS.MCSAtomCompareParameters property) MatchFusedRings (rdkit.Chem.rdFMCS.MCSBondCompareParameters property) MatchFusedRingsStrict (rdkit.Chem.rdFMCS.MCSBondCompareParameters property) matchingStrategy (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) MatchIsotope (rdkit.Chem.rdFMCS.MCSAtomCompareParameters property) MatchOnlyAtRgroupsAdjustParams() (in module rdkit.Chem.rdChemReactions) MatchPharmacophore() (in module rdkit.Chem.Pharm3D.EmbedLib) MatchPharmacophoreToMol() (in module rdkit.Chem.Pharm3D.EmbedLib) MatchStereo (rdkit.Chem.rdFMCS.MCSBondCompareParameters property) MatchTypeVect (class in rdkit.rdBase) matchValences (rdkit.Chem.fmcs.fmcs.Default attribute) MatchValences (rdkit.Chem.rdFMCS.MCSAtomCompareParameters property) MAtomQueryAtom() (in module rdkit.Chem.rdqueries) MAX() (in module rdkit.ML.Descriptors.Parser) (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) MaxAbsEStateIndex() (in module rdkit.Chem.EState.EState) MaxAbsPartialCharge() (in module rdkit.Chem.Descriptors) maxDistance (rdkit.Chem.rdFingerprintGenerator.AtomPairFingerprintOptions property) MaxDistance (rdkit.Chem.rdFMCS.MCSAtomCompareParameters property) MaxEStateIndex() (in module rdkit.Chem.EState.EState) maxFontSize (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) maximize (rdkit.Chem.fmcs.fmcs.Default attribute) MaximizeBonds (rdkit.Chem.rdFMCS.MCSParameters property) maxIsomers (rdkit.Chem.EnumerateStereoisomers.StereoEnumerationOptions attribute) maxIterations (rdkit.Chem.rdDistGeom.EmbedParameters property) maxMatches (rdkit.Chem.rdchem.SubstructMatchParameters property) MaxMinPicker (class in rdkit.SimDivFilters.rdSimDivPickers) MaxPartialCharge() (in module rdkit.Chem.Descriptors) maxPath (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions attribute) (rdkit.Chem.rdFingerprintGenerator.RDKitFingerprintOptions property) maxRecursiveMatches (rdkit.Chem.rdchem.SubstructMatchParameters property) maxRestarts (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) maxTautomers (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) MaxTautomersReached (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorStatus attribute) maxToEnumerate (rdkit.Chem.rdMolEnumerator.MolEnumeratorParams property) maxTransforms (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) MaxTransformsReached (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorStatus attribute) McConnaugheySimilarity() (in module rdkit.DataStructs.cDataStructs) McConnaugheySimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) McConnaugheySimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) MCFF_GetFeaturesForMol() (in module rdkit.Chem.ChemicalFeatures) MCQUITTY (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute) MCS (rdkit.Chem.rdRGroupDecomposition.RGroupCoreAlignment attribute) MCSAcceptance (class in rdkit.Chem.rdFMCS) MCSAtomCompare (class in rdkit.Chem.rdFMCS) MCSAtomCompareParameters (class in rdkit.Chem.rdFMCS) MCSBondCompare (class in rdkit.Chem.rdFMCS) MCSBondCompareParameters (class in rdkit.Chem.rdFMCS) MCSFinalMatchCheck (class in rdkit.Chem.rdFMCS) MCSParameters (class in rdkit.Chem.rdFMCS) MCSProgress (class in rdkit.Chem.rdFMCS) MCSProgressData (class in rdkit.Chem.rdFMCS) MCSResult (class in rdkit.Chem.fmcs.fmcs) (class in rdkit.Chem.rdFMCS) MDLRGroup (rdkit.Chem.rdRGroupDecomposition.RGroupLabelling attribute) MDLRGroupLabels (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) MEAN() (in module rdkit.ML.Descriptors.Parser) (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) MeanAndDev() (in module rdkit.ML.Data.Stats) MeanBondLength() (in module rdkit.Chem.Draw.rdMolDraw2D) medGridToleranceMult (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner attribute) MergeFeatPoints() (in module rdkit.Chem.FeatMaps.FeatMapUtils) mergeHs (rdkit.Chem.rdmolfiles.SmartsParserParams property) MergeMethod (class in rdkit.Chem.FeatMaps.FeatMapUtils) MergeMetric (class in rdkit.Chem.FeatMaps.FeatMapUtils) MergeQueryHs() (in module rdkit.Chem.rdmolops) Mesomer (rdkit.Chem.rdMolHash.HashFunction attribute) message() (in module rdkit.Chem.BuildFragmentCatalog) (in module rdkit.Chem.Fingerprints.FingerprintMols) (in module rdkit.Chem.FragmentCatalog) MetadataFromPNGFile() (in module rdkit.Chem.rdmolfiles) MetadataFromPNGString() (in module rdkit.Chem.rdmolfiles) METAL_STANDARDIZATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) MetalDisconnector (class in rdkit.Chem.MolStandardize.rdMolStandardize) MetalDisconnectorOptions (class in rdkit.Chem.MolStandardize.rdMolStandardize) MetalNof (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnector property) metalNof (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) MetalNon (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnector property) metalNon (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) METALS_DISCONNECTED (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) MHAtomQueryAtom() (in module rdkit.Chem.rdqueries) MHFPEncoder (class in rdkit.Chem.rdMHFPFingerprint) MIN() (in module rdkit.ML.Descriptors.Parser) (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) MinAbsEStateIndex() (in module rdkit.Chem.EState.EState) MinAbsPartialCharge() (in module rdkit.Chem.Descriptors) MinAtomRingSize() (rdkit.Chem.rdchem.RingInfo method) MinBondRingSize() (rdkit.Chem.rdchem.RingInfo method) minDistance (rdkit.Chem.rdFingerprintGenerator.AtomPairFingerprintOptions property) MinEStateIndex() (in module rdkit.Chem.EState.EState) minFontSize (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) Minimize() (rdkit.ForceField.rdForceField.ForceField method) MINIMIZE_FOURTH_DIMENSION (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) minimizerPrecision (rdkit.Chem.rdCoordGen.CoordGenParams property) MinimizeTrajectory() (rdkit.ForceField.rdForceField.ForceField method) minMedianBondLength (rdkit.Chem.MolStandardize.rdMolStandardize.Layout2DValidation property) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) MinPartialCharge() (in module rdkit.Chem.Descriptors) minPath (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions attribute) (rdkit.Chem.rdFingerprintGenerator.RDKitFingerprintOptions property) MinRingSizeEqualsQueryAtom() (in module rdkit.Chem.rdqueries) MinRingSizeGreaterQueryAtom() (in module rdkit.Chem.rdqueries) MinRingSizeLessQueryAtom() (in module rdkit.Chem.rdqueries) MissingChiralTagQueryAtom() (in module rdkit.Chem.rdqueries) MLDataSet (class in rdkit.ML.Data.MLData) MLQuantDataSet (class in rdkit.ML.Data.MLData) MMFFAddAngleConstraint() (rdkit.ForceField.rdForceField.ForceField method) MMFFAddDistanceConstraint() (rdkit.ForceField.rdForceField.ForceField method) MMFFAddPositionConstraint() (rdkit.ForceField.rdForceField.ForceField method) MMFFAddTorsionConstraint() (rdkit.ForceField.rdForceField.ForceField method) MMFFGetMoleculeForceField() (in module rdkit.Chem.rdForceFieldHelpers) MMFFGetMoleculeProperties() (in module rdkit.Chem.rdForceFieldHelpers) MMFFHasAllMoleculeParams() (in module rdkit.Chem.rdForceFieldHelpers) MMFFMolProperties (class in rdkit.ForceField.rdForceField) MMFFOptimizeMolecule() (in module rdkit.Chem.rdForceFieldHelpers) MMFFOptimizeMoleculeConfs() (in module rdkit.Chem.rdForceFieldHelpers) MMFFSanitizeMolecule() (in module rdkit.Chem.rdForceFieldHelpers) modifiedAtoms (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorResult property) modifiedBonds (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorResult property) module rdkit rdkit.Avalon rdkit.Avalon.pyAvalonTools rdkit.Chem rdkit.Chem.AllChem rdkit.Chem.AtomPairs rdkit.Chem.AtomPairs.Pairs rdkit.Chem.AtomPairs.Sheridan rdkit.Chem.AtomPairs.Torsions rdkit.Chem.AtomPairs.Utils rdkit.Chem.BRICS rdkit.Chem.BuildFragmentCatalog rdkit.Chem.ChemicalFeatures rdkit.Chem.ChemicalForceFields rdkit.Chem.ChemUtils rdkit.Chem.ChemUtils.AlignDepict rdkit.Chem.ChemUtils.BulkTester rdkit.Chem.ChemUtils.DescriptorUtilities rdkit.Chem.ChemUtils.SDFToCSV rdkit.Chem.ChemUtils.TemplateExpand rdkit.Chem.Crippen rdkit.Chem.Descriptors rdkit.Chem.Descriptors3D rdkit.Chem.Draw rdkit.Chem.Draw.IPythonConsole rdkit.Chem.Draw.MolDrawing rdkit.Chem.Draw.rdMolDraw2D rdkit.Chem.Draw.SimilarityMaps rdkit.Chem.EnumerateHeterocycles rdkit.Chem.EnumerateStereoisomers rdkit.Chem.EState rdkit.Chem.EState.AtomTypes rdkit.Chem.EState.EState rdkit.Chem.EState.EState_VSA rdkit.Chem.EState.Fingerprinter rdkit.Chem.FastSDMolSupplier rdkit.Chem.FeatFinderCLI rdkit.Chem.FeatMaps rdkit.Chem.FeatMaps.FeatMapParser rdkit.Chem.FeatMaps.FeatMapPoint rdkit.Chem.FeatMaps.FeatMaps rdkit.Chem.FeatMaps.FeatMapUtils rdkit.Chem.Features rdkit.Chem.Features.FeatDirUtilsRD rdkit.Chem.Features.ShowFeats rdkit.Chem.FilterCatalog rdkit.Chem.Fingerprints rdkit.Chem.Fingerprints.ClusterMols rdkit.Chem.Fingerprints.DbFpSupplier rdkit.Chem.Fingerprints.FingerprintMols rdkit.Chem.Fingerprints.MolSimilarity rdkit.Chem.Fingerprints.SimilarityScreener rdkit.Chem.fmcs rdkit.Chem.fmcs.fmcs rdkit.Chem.Fraggle rdkit.Chem.Fraggle.FraggleSim rdkit.Chem.FragmentCatalog rdkit.Chem.FragmentMatcher rdkit.Chem.Fragments rdkit.Chem.FunctionalGroups rdkit.Chem.GraphDescriptors rdkit.Chem.Graphs rdkit.Chem.inchi rdkit.Chem.Lipinski rdkit.Chem.MACCSkeys rdkit.Chem.MCS rdkit.Chem.MolCatalog rdkit.Chem.MolDb rdkit.Chem.MolDb.FingerprintUtils rdkit.Chem.MolDb.Loader rdkit.Chem.MolDb.Loader_orig rdkit.Chem.MolDb.Loader_sa rdkit.Chem.MolKey rdkit.Chem.MolKey.InchiInfo rdkit.Chem.MolKey.MolKey rdkit.Chem.MolStandardize.rdMolStandardize rdkit.Chem.MolSurf rdkit.Chem.PandasTools rdkit.Chem.PeriodicTable rdkit.Chem.Pharm2D rdkit.Chem.Pharm2D.Generate rdkit.Chem.Pharm2D.Gobbi_Pharm2D rdkit.Chem.Pharm2D.Matcher rdkit.Chem.Pharm2D.SigFactory rdkit.Chem.Pharm2D.Utils rdkit.Chem.Pharm3D rdkit.Chem.Pharm3D.EmbedLib rdkit.Chem.Pharm3D.ExcludedVolume rdkit.Chem.Pharm3D.Pharmacophore rdkit.Chem.PropertyMol rdkit.Chem.PyMol rdkit.Chem.QED rdkit.Chem.Randomize rdkit.Chem.rdAbbreviations rdkit.Chem.rdchem rdkit.Chem.rdChemicalFeatures rdkit.Chem.rdChemReactions rdkit.Chem.rdCIPLabeler rdkit.Chem.rdCoordGen rdkit.Chem.rdDepictor rdkit.Chem.rdDeprotect rdkit.Chem.rdDetermineBonds rdkit.Chem.rdDistGeom rdkit.Chem.rdEHTTools rdkit.Chem.rdfiltercatalog rdkit.Chem.rdFingerprintGenerator rdkit.Chem.rdFMCS rdkit.Chem.rdForceFieldHelpers rdkit.Chem.rdfragcatalog rdkit.Chem.rdFreeSASA rdkit.Chem.rdinchi rdkit.Chem.rdMHFPFingerprint rdkit.Chem.rdMMPA rdkit.Chem.rdMolAlign rdkit.Chem.rdMolCatalog rdkit.Chem.rdMolChemicalFeatures rdkit.Chem.rdMolDescriptors rdkit.Chem.rdMolEnumerator rdkit.Chem.rdmolfiles rdkit.Chem.rdMolHash rdkit.Chem.rdMolInterchange rdkit.Chem.rdmolops rdkit.Chem.rdMolTransforms rdkit.Chem.rdPartialCharges rdkit.Chem.rdqueries rdkit.Chem.rdReducedGraphs rdkit.Chem.rdRGroupDecomposition rdkit.Chem.rdShapeHelpers rdkit.Chem.rdSLNParse rdkit.Chem.rdSubstructLibrary rdkit.Chem.rdTautomerQuery rdkit.Chem.rdtrajectory rdkit.Chem.Recap rdkit.Chem.ReducedGraphs rdkit.Chem.RegistrationHash rdkit.Chem.SaltRemover rdkit.Chem.SATIS rdkit.Chem.Scaffolds rdkit.Chem.Scaffolds.MurckoScaffold rdkit.Chem.Scaffolds.rdScaffoldNetwork rdkit.Chem.ShowMols rdkit.Chem.SimpleEnum rdkit.Chem.SimpleEnum.Enumerator rdkit.Chem.SpacialScore rdkit.Chem.Subshape rdkit.Chem.Subshape.BuilderUtils rdkit.Chem.Subshape.SubshapeAligner rdkit.Chem.Subshape.SubshapeBuilder rdkit.Chem.Subshape.SubshapeObjects rdkit.Chem.Suppliers rdkit.Chem.Suppliers.DbMolSupplier rdkit.Chem.Suppliers.MolSupplier rdkit.Chem.TemplateAlign rdkit.Chem.TorsionFingerprints rdkit.DataManip rdkit.DataManip.Metric rdkit.DataManip.Metric.rdMetricMatrixCalc rdkit.DataStructs rdkit.DataStructs.BitEnsemble rdkit.DataStructs.BitEnsembleDb rdkit.DataStructs.BitUtils rdkit.DataStructs.cDataStructs rdkit.DataStructs.LazySignature rdkit.DataStructs.TopNContainer rdkit.DataStructs.VectCollection rdkit.Dbase rdkit.Dbase.DbConnection rdkit.Dbase.DbInfo rdkit.Dbase.DbModule rdkit.Dbase.DbResultSet rdkit.Dbase.DbUtils rdkit.Dbase.StorageUtils rdkit.DistanceGeometry rdkit.DistanceGeometry.DistGeom rdkit.ForceField rdkit.ForceField.rdForceField rdkit.Geometry rdkit.Geometry.rdGeometry rdkit.ML rdkit.ML.Cluster rdkit.ML.Cluster.Butina rdkit.ML.Cluster.Clustering rdkit.ML.Cluster.Clusters rdkit.ML.Cluster.ClusterUtils rdkit.ML.Cluster.ClusterVis rdkit.ML.Cluster.Murtagh rdkit.ML.Cluster.Resemblance rdkit.ML.Cluster.Standardize rdkit.ML.Composite rdkit.ML.Data rdkit.ML.Data.cQuantize rdkit.ML.Data.DataUtils rdkit.ML.Data.FindQuantBounds rdkit.ML.Data.MLData rdkit.ML.Data.Quantize rdkit.ML.Data.SplitData rdkit.ML.Data.Stats rdkit.ML.Data.Transforms rdkit.ML.DecTree rdkit.ML.Descriptors rdkit.ML.Descriptors.CompoundDescriptors rdkit.ML.Descriptors.Descriptors rdkit.ML.Descriptors.MoleculeDescriptors rdkit.ML.Descriptors.Parser rdkit.ML.files rdkit.ML.InfoTheory rdkit.ML.InfoTheory.BitClusterer rdkit.ML.InfoTheory.BitRank rdkit.ML.InfoTheory.entropy rdkit.ML.InfoTheory.rdInfoTheory rdkit.ML.KNN rdkit.ML.MatOps rdkit.ML.MLUtils rdkit.ML.MLUtils.VoteImg rdkit.ML.ModelPackage rdkit.ML.NaiveBayes rdkit.ML.Neural rdkit.ML.Scoring rdkit.ML.Scoring.Scoring rdkit.ML.SLT rdkit.ML.SLT.Risk rdkit.Numerics rdkit.Numerics.rdAlignment rdkit.rdBase rdkit.RDConfig rdkit.RDLogger rdkit.RDPaths rdkit.RDRandom rdkit.SimDivFilters rdkit.SimDivFilters.rdSimDivPickers rdkit.SimDivFilters.SimilarityPickers rdkit.TestRunner rdkit.utils rdkit.utils.cactvs rdkit.utils.chemutils rdkit.utils.fileutils rdkit.utils.listutils rdkit.utils.spiral rdkit.VLib rdkit.VLib.Filter rdkit.VLib.Node rdkit.VLib.NodeLib rdkit.VLib.NodeLib.DbMolSupply rdkit.VLib.NodeLib.DbPickleSupplier rdkit.VLib.NodeLib.SDSupply rdkit.VLib.NodeLib.SmartsMolFilter rdkit.VLib.NodeLib.SmartsRemover rdkit.VLib.NodeLib.SmilesDupeFilter rdkit.VLib.NodeLib.SmilesOutput rdkit.VLib.NodeLib.SmilesSupply rdkit.VLib.Output rdkit.VLib.Supply rdkit.VLib.Transform

Mol (class in rdkit.Chem.rdchem) mol (rdkit.Chem.rdAbbreviations.AbbreviationDefinition property) (rdkit.Chem.Recap.RecapHierarchyNode attribute) MOL (rdkit.Chem.SaltRemover.InputFormat attribute) mol_key (rdkit.Chem.MolKey.MolKey.MolKeyResult attribute) MOL_SPTR_VECT (class in rdkit.Chem.rdChemReactions) MolAddRecursiveQueries() (in module rdkit.Chem.rdmolops) MolBlockToInchi() (in module rdkit.Chem.inchi) (in module rdkit.Chem.rdinchi) MolBlockToInchiAndAuxInfo() (in module rdkit.Chem.inchi) MolBundle (class in rdkit.Chem.rdchem) MolBundleCanSerialize() (in module rdkit.Chem.rdchem) MolCatalog (class in rdkit.Chem.rdMolCatalog) MolCatalogEntry (class in rdkit.Chem.rdMolCatalog) MolChemicalFeature (class in rdkit.Chem.rdMolChemicalFeatures) MolChemicalFeatureFactory (class in rdkit.Chem.rdMolChemicalFeatures) molCounts (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetwork property) MolDraw2D (class in rdkit.Chem.Draw.rdMolDraw2D) MolDraw2DCairo (class in rdkit.Chem.Draw.rdMolDraw2D) MolDraw2DSVG (class in rdkit.Chem.Draw.rdMolDraw2D) MolDrawing (class in rdkit.Chem.Draw.MolDrawing) MolDrawOptions (class in rdkit.Chem.Draw.rdMolDraw2D) MolecularDescriptorCalculator (class in rdkit.ML.Descriptors.MoleculeDescriptors) MolEnumeratorParams (class in rdkit.Chem.rdMolEnumerator) molFeatures (rdkit.Chem.Subshape.SubshapeObjects.SkeletonPoint attribute) MolFormula (rdkit.Chem.rdMolHash.HashFunction attribute) MolFragmentToCXSmarts() (in module rdkit.Chem.rdmolfiles) MolFragmentToCXSmiles() (in module rdkit.Chem.rdmolfiles) MolFragmentToSmarts() (in module rdkit.Chem.rdmolfiles) MolFragmentToSmiles() (in module rdkit.Chem.rdmolfiles) MolFromFASTA() (in module rdkit.Chem.rdmolfiles) MolFromHELM() (in module rdkit.Chem.rdmolfiles) MolFromInchi() (in module rdkit.Chem.inchi) MolFromMol2Block() (in module rdkit.Chem.rdmolfiles) MolFromMol2File() (in module rdkit.Chem.rdmolfiles) MolFromMolBlock() (in module rdkit.Chem.rdmolfiles) MolFromMolFile() (in module rdkit.Chem.rdmolfiles) MolFromMrvBlock() (in module rdkit.Chem.rdmolfiles) MolFromMrvFile() (in module rdkit.Chem.rdmolfiles) MolFromPDBBlock() (in module rdkit.Chem.rdmolfiles) MolFromPDBFile() (in module rdkit.Chem.rdmolfiles) MolFromPNGFile() (in module rdkit.Chem.rdmolfiles) MolFromPNGString() (in module rdkit.Chem.rdmolfiles) MolFromQuerySLN() (in module rdkit.Chem.rdSLNParse) MolFromRDKitSVG() (in module rdkit.Chem.rdmolfiles) MolFromSequence() (in module rdkit.Chem.rdmolfiles) MolFromSLN() (in module rdkit.Chem.rdSLNParse) MolFromSmarts() (in module rdkit.Chem.rdmolfiles) MolFromSmiles() (in module rdkit.Chem.rdmolfiles) MolFromTPLBlock() (in module rdkit.Chem.rdmolfiles) MolFromTPLFile() (in module rdkit.Chem.rdmolfiles) MolFromXYZBlock() (in module rdkit.Chem.rdmolfiles) MolFromXYZFile() (in module rdkit.Chem.rdmolfiles) MolHash() (in module rdkit.Chem.rdMolHash) MolHolder (class in rdkit.Chem.rdSubstructLibrary) MolHolderBase (class in rdkit.Chem.rdSubstructLibrary) MolIdentifierException MolKeyResult (class in rdkit.Chem.MolKey.MolKey) MolList (class in rdkit.Chem.rdfiltercatalog) MolLogP() (in module rdkit.Chem.Crippen) MolMetadataToPNGFile() (in module rdkit.Chem.rdmolfiles) MolMetadataToPNGString() (in module rdkit.Chem.rdmolfiles) MolMR() (in module rdkit.Chem.Crippen) molpkl (rdkit.Chem.MolDb.Loader_sa.Compound attribute) MolProps (rdkit.Chem.rdchem.PropertyPickleOptions attribute) MolSanitizeException MolsFromCDXML() (in module rdkit.Chem.rdmolfiles) MolsFromCDXMLFile() (in module rdkit.Chem.rdmolfiles) MolsFromPNGFile() (in module rdkit.Chem.rdmolfiles) MolsFromPNGString() (in module rdkit.Chem.rdmolfiles) MolsMatrixToGridImage() (in module rdkit.Chem.Draw) MolsToGridImage() (in module rdkit.Chem.Draw) MolsToImage() (in module rdkit.Chem.Draw) MolsToJSON() (in module rdkit.Chem.rdMolInterchange) MolSupplier (class in rdkit.Chem.Suppliers.MolSupplier) MolToACS1996SVG() (in module rdkit.Chem.Draw.rdMolDraw2D) MolToCMLBlock() (in module rdkit.Chem.rdmolfiles) MolToCMLFile() (in module rdkit.Chem.rdmolfiles) MolToCXSmarts() (in module rdkit.Chem.rdmolfiles) MolToCXSmiles() (in module rdkit.Chem.rdmolfiles) MolToFASTA() (in module rdkit.Chem.rdmolfiles) MolToFile() (in module rdkit.Chem.Draw) MolToHELM() (in module rdkit.Chem.rdmolfiles) MolToImage() (in module rdkit.Chem.Draw) MolToInchi() (in module rdkit.Chem.inchi) (in module rdkit.Chem.rdinchi) MolToInchiAndAuxInfo() (in module rdkit.Chem.inchi) MolToInchiKey() (in module rdkit.Chem.inchi) (in module rdkit.Chem.rdinchi) MolToJSON() (in module rdkit.Chem.rdMolInterchange) MolToMolBlock() (in module rdkit.Chem.rdmolfiles) MolToMolFile() (in module rdkit.Chem.rdmolfiles) MolToMrvBlock() (in module rdkit.Chem.rdmolfiles) MolToMrvFile() (in module rdkit.Chem.rdmolfiles) MolToPDBBlock() (in module rdkit.Chem.rdmolfiles) MolToPDBFile() (in module rdkit.Chem.rdmolfiles) MolToRandomSmilesVect() (in module rdkit.Chem.rdmolfiles) MolToSequence() (in module rdkit.Chem.rdmolfiles) MolToSmarts() (in module rdkit.Chem.rdmolfiles) MolToSmiles() (in module rdkit.Chem.rdmolfiles) MolToSVG() (in module rdkit.Chem.Draw.rdMolDraw2D) MolToTPLBlock() (in module rdkit.Chem.rdmolfiles) MolToTPLFile() (in module rdkit.Chem.rdmolfiles) MolToV2KMolBlock() (in module rdkit.Chem.rdmolfiles) MolToV3KMolBlock() (in module rdkit.Chem.rdmolfiles) MolToV3KMolFile() (in module rdkit.Chem.rdmolfiles) MolToXYZBlock() (in module rdkit.Chem.rdmolfiles) MolToXYZFile() (in module rdkit.Chem.rdmolfiles) MolViewer (class in rdkit.Chem.PyMol) MolVSValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) MolWriterParams (class in rdkit.Chem.rdmolfiles) MolWt() (in module rdkit.Chem.Descriptors) molzip() (in module rdkit.Chem.rdmolops) molzipFragments() (in module rdkit.Chem.rdmolops) MolzipLabel (class in rdkit.Chem.rdmolops) MolzipParams (class in rdkit.Chem.rdmolops) MorganFingerprintOptions (class in rdkit.Chem.rdFingerprintGenerator) MorganFP (rdkit.Chem.rdChemReactions.FingerprintType attribute) (rdkit.Chem.rdFingerprintGenerator.FPType attribute) MoveDummyNeighborsToBeginning() (in module rdkit.Chem.ChemUtils.TemplateExpand) MoveToMatchingLine() (in module rdkit.utils.fileutils) MQNs_() (in module rdkit.Chem.rdMolDescriptors) MrvBlockIsReaction() (in module rdkit.Chem.rdChemReactions) MrvFileIsReaction() (in module rdkit.Chem.rdChemReactions) MultiColourHighlightStyle (class in rdkit.Chem.Draw.rdMolDraw2D) multiColourHighlightStyle (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) MultiFPBReader (class in rdkit.DataStructs.cDataStructs) multipleBondOffset (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) MultithreadedSDMolSupplier (class in rdkit.Chem.rdmolfiles) MultithreadedSmilesMolSupplier (class in rdkit.Chem.rdmolfiles) MurckoDecompose() (in module rdkit.Chem.rdmolops) MurckoScaffold (rdkit.Chem.rdMolHash.HashFunction attribute) MurckoScaffoldSmiles() (in module rdkit.Chem.Scaffolds.MurckoScaffold) MurckoScaffoldSmilesFromSmiles() (in module rdkit.Chem.Scaffolds.MurckoScaffold) MurtaghCluster() (in module rdkit.ML.Cluster.Clustering) MurtaghDistCluster() (in module rdkit.ML.Cluster.Clustering) MW (rdkit.Chem.QED.QEDproperties attribute)

N

NACCESS (rdkit.Chem.rdFreeSASA.SASAClassifier attribute) nActs (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) name (rdkit.Chem.FunctionalGroups.FGHierarchyNode attribute) Name (rdkit.Chem.MolStandardize.rdMolStandardize.ChargeCorrection property) nameCol (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) names (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) (rdkit.Avalon.pyAvalonTools.StruChkResult attribute) (rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle attribute) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorStatus attribute) (rdkit.Chem.rdchem.AtomMonomerType attribute) (rdkit.Chem.rdchem.BondDir attribute) (rdkit.Chem.rdchem.BondStereo attribute) (rdkit.Chem.rdchem.BondType attribute) (rdkit.Chem.rdchem.ChiralType attribute) (rdkit.Chem.rdchem.CompositeQueryType attribute) (rdkit.Chem.rdchem.HybridizationType attribute) (rdkit.Chem.rdchem.PropertyPickleOptions attribute) (rdkit.Chem.rdchem.ResonanceFlags attribute) (rdkit.Chem.rdchem.StereoDescriptor attribute) (rdkit.Chem.rdchem.StereoGroupType attribute) (rdkit.Chem.rdchem.StereoSpecified attribute) (rdkit.Chem.rdchem.StereoType attribute) (rdkit.Chem.rdChemReactions.FingerprintType attribute) (rdkit.Chem.rdChemReactions.SanitizeFlags attribute) (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) (rdkit.Chem.rdFingerprintGenerator.FPType attribute) (rdkit.Chem.rdFMCS.AtomCompare attribute) (rdkit.Chem.rdFMCS.BondCompare attribute) (rdkit.Chem.rdFMCS.RingCompare attribute) (rdkit.Chem.rdFreeSASA.SASAAlgorithm attribute) (rdkit.Chem.rdFreeSASA.SASAClass attribute) (rdkit.Chem.rdFreeSASA.SASAClassifier attribute) (rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions attribute) (rdkit.Chem.rdMolEnumerator.EnumeratorType attribute) (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) (rdkit.Chem.rdmolfiles.RestoreBondDirOption attribute) (rdkit.Chem.rdMolHash.HashFunction attribute) (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) (rdkit.Chem.rdmolops.AromaticityModel attribute) (rdkit.Chem.rdmolops.MolzipLabel attribute) (rdkit.Chem.rdmolops.SanitizeFlags attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupCoreAlignment attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupLabelling attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupMatching attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupScore attribute) (rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType attribute) (rdkit.DataStructs.cDataStructs.DiscreteValueType attribute) (rdkit.ML.InfoTheory.rdInfoTheory.InfoType attribute) (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute) nBits (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) nbrCount (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder attribute) NeedsHs() (in module rdkit.Chem.rdmolops) NeedsUpdatePropertyCache() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Mol method) Negate() (rdkit.VLib.Filter.FilterNode method) neighbors (rdkit.Chem.fmcs.fmcs.CangenNode attribute) NetCharge (rdkit.Chem.rdMolHash.HashFunction attribute) NetworkEdge (class in rdkit.Chem.Scaffolds.rdScaffoldNetwork) NetworkEdge_VECT (class in rdkit.Chem.Scaffolds.rdScaffoldNetwork) NeutralValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) next() (rdkit.Chem.Fingerprints.DbFpSupplier.DbFpSupplier method) (rdkit.Chem.Fingerprints.SimilarityScreener.ThresholdScreener method) (rdkit.Chem.Fingerprints.SimilarityScreener.TopNScreener method) (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) (rdkit.Chem.rdChemReactions.EnumerationStrategyBase method) (rdkit.Chem.Suppliers.MolSupplier.MolSupplier method) (rdkit.Dbase.DbResultSet.DbResultSet method) (rdkit.Dbase.DbResultSet.RandomAccessDbResultSet method) (rdkit.VLib.Filter.FilterNode method) (rdkit.VLib.Node.VLibNode method) (rdkit.VLib.NodeLib.DbMolSupply.DbMolSupplyNode method) (rdkit.VLib.NodeLib.DbPickleSupplier.DbPickleSupplyNode method) (rdkit.VLib.NodeLib.SDSupply.SDSupplyNode method) (rdkit.VLib.NodeLib.SmilesSupply.SmilesSupplyNode method) (rdkit.VLib.Output.OutputNode method) (rdkit.VLib.Supply.SupplyNode method) (rdkit.VLib.Transform.TransformNode method) NextItem() (rdkit.Chem.Fingerprints.DbFpSupplier.ForwardDbFpSupplier method) (rdkit.Chem.Fingerprints.DbFpSupplier.RandomAccessDbFpSupplier method) NextMol() (rdkit.Chem.Suppliers.DbMolSupplier.ForwardDbMolSupplier method) (rdkit.Chem.Suppliers.DbMolSupplier.RandomAccessDbMolSupplier method) (rdkit.Chem.Suppliers.MolSupplier.MolSupplier method) nextSmiles() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) NHOHCount() (in module rdkit.Chem.Lipinski) NIH (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) NO_EVENT (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) NO_STEREO_SMILES (rdkit.Chem.RegistrationHash.HashLayer attribute) NO_STEREO_TAUTOMER_HASH (rdkit.Chem.RegistrationHash.HashLayer attribute) NoAdjustments() (rdkit.Chem.rdmolops.AdjustQueryParameters static method) NoAlignment (rdkit.Chem.rdRGroupDecomposition.RGroupCoreAlignment attribute) NOATOM (rdkit.Chem.rdchem.StereoInfo attribute) noAtomLabels (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) NoAtomValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) noCarbonSymbols (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute)

NoConformers (rdkit.Chem.rdchem.PropertyPickleOptions attribute) NOCount() (in module rdkit.Chem.Lipinski) nodeColor (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) nodeRad (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) nodes (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetwork property) NoMatchFoundError NoMerge (rdkit.Chem.FeatMaps.FeatMapUtils.DirMergeMode attribute) (rdkit.Chem.FeatMaps.FeatMapUtils.MergeMetric attribute) nonAgentWeight (rdkit.Chem.rdChemReactions.ReactionFingerprintParams property) NONE (rdkit.Chem.rdchem.BondDir attribute) None (rdkit.Chem.rdRGroupDecomposition.RGroupCoreAlignment attribute) nonempty_powerset() (in module rdkit.Chem.fmcs.fmcs) NonHydrogenDegreeEqualsQueryAtom() (in module rdkit.Chem.rdqueries) NonHydrogenDegreeGreaterQueryAtom() (in module rdkit.Chem.rdqueries) NonHydrogenDegreeLessQueryAtom() (in module rdkit.Chem.rdqueries) NonStrict (rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions attribute) NoProps (rdkit.Chem.rdchem.PropertyPickleOptions attribute) NORMALIZATION_APPLIED (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) normalizationsFile (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) Normalize() (in module rdkit.Chem.MolStandardize.rdMolStandardize) normalize() (rdkit.Chem.MolStandardize.rdMolStandardize.Normalizer method) Normalize() (rdkit.Geometry.rdGeometry.Point2D method) (rdkit.Geometry.rdGeometry.Point3D method) (rdkit.Geometry.rdGeometry.PointND method) NormalizeDepiction() (in module rdkit.Chem.rdDepictor) NormalizeInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) normalizeInPlace() (rdkit.Chem.MolStandardize.rdMolStandardize.Normalizer method) Normalizer (class in rdkit.Chem.MolStandardize.rdMolStandardize) NORMALIZER_STANDARDIZATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) normalizerData (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) NormalizerFromData() (in module rdkit.Chem.MolStandardize.rdMolStandardize) NormalizerFromParams() (in module rdkit.Chem.MolStandardize.rdMolStandardize) normalizerMaxRestarts (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) NoSymmetrization (rdkit.Chem.rdRGroupDecomposition.RGroupMatching attribute) NoValue (rdkit.Chem.rdchem.StereoDescriptor attribute) nPerClass (rdkit.Chem.FragmentCatalog.BitGainsInfo attribute) NPR1() (in module rdkit.Chem.Descriptors3D) NPR2() (in module rdkit.Chem.Descriptors3D) NumAliphaticCarbocycles() (in module rdkit.Chem.Lipinski) NumAliphaticHeteroatomNeighborsEqualsQueryAtom() (in module rdkit.Chem.rdqueries) NumAliphaticHeteroatomNeighborsGreaterQueryAtom() (in module rdkit.Chem.rdqueries) NumAliphaticHeteroatomNeighborsLessQueryAtom() (in module rdkit.Chem.rdqueries) NumAliphaticHeterocycles() (in module rdkit.Chem.Lipinski) NumAliphaticRings() (in module rdkit.Chem.Lipinski) NumAromaticCarbocycles() (in module rdkit.Chem.Lipinski) NumAromaticHeterocycles() (in module rdkit.Chem.Lipinski) NumAromaticRings() (in module rdkit.Chem.Lipinski) numAtomPairFingerprintBits (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) NumAtomRings() (rdkit.Chem.rdchem.RingInfo method) numAtoms (rdkit.Chem.rdFMCS.MCSProgressData property) (rdkit.Chem.rdFMCS.MCSResult property) NumBitsInCommon() (in module rdkit.DataStructs.cDataStructs) numBitsPerFeature (rdkit.Chem.rdFingerprintGenerator.FingerprintOptions property) NumBondRings() (rdkit.Chem.rdchem.RingInfo method) numBonds (rdkit.Chem.rdFMCS.MCSProgressData property) (rdkit.Chem.rdFMCS.MCSResult property) numBranchBits (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) NumChildren() (rdkit.DataStructs.VectCollection.VectCollection method) numChiralBits (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) NumCombinations() (in module rdkit.Chem.Pharm2D.Utils) numElectrons (rdkit.Chem.rdEHTTools.EHTResults property) numFeatThresh (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner attribute) NumFusedBonds() (rdkit.Chem.rdchem.RingInfo method) NumHAcceptors() (in module rdkit.Chem.Lipinski) NumHDonors() (in module rdkit.Chem.Lipinski) NumHeteroatomNeighborsEqualsQueryAtom() (in module rdkit.Chem.rdqueries) NumHeteroatomNeighborsGreaterQueryAtom() (in module rdkit.Chem.rdqueries) NumHeteroatomNeighborsLessQueryAtom() (in module rdkit.Chem.rdqueries) NumHeteroatoms() (in module rdkit.Chem.Lipinski) numMols (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) NumMols() (rdkit.Chem.rdmolfiles.MaeWriter method) (rdkit.Chem.rdmolfiles.PDBWriter method) (rdkit.Chem.rdmolfiles.SDWriter method) (rdkit.Chem.rdmolfiles.SmilesWriter method) (rdkit.Chem.rdmolfiles.TDTWriter method) numOrbitals (rdkit.Chem.rdEHTTools.EHTResults property) numPathBits (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) numPiBits (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) NumPiElectrons() (in module rdkit.Chem.AtomPairs.Utils) NumPoints() (rdkit.Chem.rdtrajectory.Trajectory method) (rdkit.ForceField.rdForceField.ForceField method) NumRadicalElectrons() (in module rdkit.Chem.Descriptors) NumRadicalElectronsEqualsQueryAtom() (in module rdkit.Chem.rdqueries) NumRadicalElectronsGreaterQueryAtom() (in module rdkit.Chem.rdqueries) NumRadicalElectronsLessQueryAtom() (in module rdkit.Chem.rdqueries) NumRelevantCycles() (rdkit.Chem.rdchem.RingInfo method) NumRingFamilies() (rdkit.Chem.rdchem.RingInfo method) NumRings() (rdkit.Chem.rdchem.RingInfo method) NumRotatableBonds() (in module rdkit.Chem.Lipinski) NumRotatableBondsOptions (class in rdkit.Chem.rdMolDescriptors) NumSaturatedCarbocycles() (in module rdkit.Chem.Lipinski) NumSaturatedHeterocycles() (in module rdkit.Chem.Lipinski) NumSaturatedRings() (in module rdkit.Chem.Lipinski) numThreads (rdkit.Chem.rdchem.SubstructMatchParameters property) (rdkit.Chem.rdDistGeom.EmbedParameters property) numTypeBits (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) NumValenceElectrons() (in module rdkit.Chem.Descriptors) numZeroFail (rdkit.Chem.rdDistGeom.EmbedParameters property) nWords (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions attribute)

O

O3A (class in rdkit.Chem.rdMolAlign) ObsoleteCodeError OffBitProjSimilarity() (in module rdkit.DataStructs.cDataStructs) OffBitsInCommon() (in module rdkit.DataStructs.cDataStructs) Offset() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) OnBitProjSimilarity() (in module rdkit.DataStructs.cDataStructs) OnBitSimilarity() (in module rdkit.DataStructs.cDataStructs) OnBitsInCommon() (in module rdkit.DataStructs.cDataStructs) onBitsName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) ONEANDAHALF (rdkit.Chem.rdchem.BondType attribute) ONEBITVALUE (rdkit.DataStructs.cDataStructs.DiscreteValueType attribute) onlyHeavyAtomsForRMS (rdkit.Chem.rdDistGeom.EmbedParameters property) onlyMatchAtRGroups (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) onlyNonzeroInvariants (rdkit.Chem.rdFingerprintGenerator.MorganFingerprintOptions property) onlyShortestPaths (rdkit.Chem.rdFingerprintGenerator.TopologicalTorsionFingerprintOptions property) onlyStereoGroups (rdkit.Chem.EnumerateStereoisomers.StereoEnumerationOptions attribute) onlyUnassigned (rdkit.Chem.EnumerateStereoisomers.StereoEnumerationOptions attribute) OONS (rdkit.Chem.rdFreeSASA.SASAClassifier attribute) OptimizeMol() (in module rdkit.Chem.Pharm3D.EmbedLib) OptimizeMolecule() (in module rdkit.Chem.rdForceFieldHelpers)

OptimizeMoleculeConfs() (in module rdkit.Chem.rdForceFieldHelpers) optimizerForceTol (rdkit.Chem.rdDistGeom.EmbedParameters property) OrderTriangle() (in module rdkit.Chem.Pharm2D.Utils) orVect (rdkit.DataStructs.VectCollection.VectCollection property) ostream (class in rdkit.rdBase) OTHER (rdkit.Chem.rdchem.AtomMonomerType attribute) (rdkit.Chem.rdchem.BondType attribute) (rdkit.Chem.rdchem.HybridizationType attribute) other_node (rdkit.Chem.fmcs.fmcs.OutgoingEdge attribute) other_node_idx (rdkit.Chem.fmcs.fmcs.OutgoingEdge attribute) outgoing_edges (rdkit.Chem.fmcs.fmcs.CangenNode attribute) OutgoingEdge (class in rdkit.Chem.fmcs.fmcs) OUTPUT_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) OutputGainsData() (in module rdkit.Chem.BuildFragmentCatalog) outputMolData (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineResult property) OutputNode (class in rdkit.VLib.NodeLib.SmilesOutput) (class in rdkit.VLib.Output) OutputRedirectC (class in rdkit.TestRunner) outputV2000 (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) Overlap (rdkit.Chem.FeatMaps.FeatMapUtils.MergeMetric attribute)

P

padding (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) PAINS (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) PAINS_A (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) PAINS_B (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) PAINS_C (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) params (rdkit.Chem.FeatMaps.FeatMaps.FeatMap attribute) parent (rdkit.Chem.FunctionalGroups.FGHierarchyNode attribute) parentMolData (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineResult property) parents (rdkit.Chem.Recap.RecapHierarchyNode attribute) Parse() (rdkit.Chem.FeatMaps.FeatMapParser.FeatMapParser method) parse_num_atoms() (in module rdkit.Chem.fmcs.fmcs) parse_select() (in module rdkit.Chem.fmcs.fmcs) parse_threshold() (in module rdkit.Chem.fmcs.fmcs) parse_timeout() (in module rdkit.Chem.fmcs.fmcs) ParseAbbreviations() (in module rdkit.Chem.rdAbbreviations) ParseArgs() (in module rdkit.Chem.BuildFragmentCatalog) (in module rdkit.Chem.Fingerprints.FingerprintMols) parseConformers (rdkit.Chem.rdMolInterchange.JSONParseParameters property) ParseFeatPointBlock() (rdkit.Chem.FeatMaps.FeatMapParser.FeatMapParser method) ParseLinkers() (in module rdkit.Chem.rdAbbreviations) ParseMolQueryDefFile() (in module rdkit.Chem.rdmolops) parseName (rdkit.Chem.rdmolfiles.SmartsParserParams property) (rdkit.Chem.rdmolfiles.SmilesParserParams property) ParseParamBlock() (rdkit.Chem.FeatMaps.FeatMapParser.FeatMapParser method) parseProperties (rdkit.Chem.rdMolInterchange.JSONParseParameters property) PARSING_INPUT (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) PassesFilter() (rdkit.Chem.rdSubstructLibrary.FPHolderBase method) PathToSubmol() (in module rdkit.Chem.rdmolops) pattern (rdkit.Chem.FunctionalGroups.FGHierarchyNode attribute) PatternFingerprint() (in module rdkit.Chem.rdmolops) PatternFingerprintTautomerTarget() (in module rdkit.Chem.rdTautomerQuery) PatternFingerprintTemplate() (rdkit.Chem.rdTautomerQuery.TautomerQuery method) PatternFP (rdkit.Chem.rdChemReactions.FingerprintType attribute) PatternHolder (class in rdkit.Chem.rdSubstructLibrary) PBF() (in module rdkit.Chem.Descriptors3D) PDBRESIDUE (rdkit.Chem.rdchem.AtomMonomerType attribute) PDBWriter (class in rdkit.Chem.rdmolfiles) PEOE_VSA1() (in module rdkit.Chem.MolSurf) PEOE_VSA10() (in module rdkit.Chem.MolSurf) PEOE_VSA11() (in module rdkit.Chem.MolSurf) PEOE_VSA12() (in module rdkit.Chem.MolSurf) PEOE_VSA13() (in module rdkit.Chem.MolSurf) PEOE_VSA14() (in module rdkit.Chem.MolSurf) PEOE_VSA2() (in module rdkit.Chem.MolSurf) PEOE_VSA3() (in module rdkit.Chem.MolSurf) PEOE_VSA4() (in module rdkit.Chem.MolSurf) PEOE_VSA5() (in module rdkit.Chem.MolSurf) PEOE_VSA6() (in module rdkit.Chem.MolSurf) PEOE_VSA7() (in module rdkit.Chem.MolSurf) PEOE_VSA8() (in module rdkit.Chem.MolSurf) PEOE_VSA9() (in module rdkit.Chem.MolSurf) PEOE_VSA_() (in module rdkit.Chem.rdMolDescriptors) PeriodicTable (class in rdkit.Chem.rdchem) PermissiveRingFusion (rdkit.Chem.rdFMCS.RingCompare attribute) permutation (rdkit.Chem.rdchem.StereoInfo property) permutation() (in module rdkit.ML.Data.DataUtils) Pharmacophore (class in rdkit.Chem.Pharm3D.Pharmacophore) Pick() (rdkit.SimDivFilters.rdSimDivPickers.HierarchicalClusterPicker method) (rdkit.SimDivFilters.rdSimDivPickers.MaxMinPicker method) PickCanonical() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) Pipeline (class in rdkit.Chem.MolStandardize.rdMolStandardize) PIPELINE_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) PipelineLog (class in rdkit.Chem.MolStandardize.rdMolStandardize) PipelineLogEntry (class in rdkit.Chem.MolStandardize.rdMolStandardize) PipelineOptions (class in rdkit.Chem.MolStandardize.rdMolStandardize) PipelineResult (class in rdkit.Chem.MolStandardize.rdMolStandardize) PipelineStage (class in rdkit.Chem.MolStandardize.rdMolStandardize)

PipelineStatus (class in rdkit.Chem.MolStandardize.rdMolStandardize) PMI1() (in module rdkit.Chem.Descriptors3D) PMI2() (in module rdkit.Chem.Descriptors3D) PMI3() (in module rdkit.Chem.Descriptors3D) Point2D (class in rdkit.Geometry.rdGeometry) Point3D (class in rdkit.Geometry.rdGeometry) PointND (class in rdkit.Geometry.rdGeometry) Polar (rdkit.Chem.rdFreeSASA.SASAClass attribute) Positions() (rdkit.ForceField.rdForceField.ForceField method) PositionVariation (rdkit.Chem.rdMolEnumerator.EnumeratorType attribute) powerset() (in module rdkit.Chem.fmcs.fmcs) precision (rdkit.Chem.rdmolfiles.MolWriterParams property) preferOrganic (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) PREPARE_FOR_STANDARDIZATION (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) PREPARE_FOR_STANDARDIZATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) PREPARE_FOR_VALIDATION (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) PREPARE_FOR_VALIDATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) PrepareAndDrawMolecule() (in module rdkit.Chem.Draw.rdMolDraw2D) PrepareMolForDrawing() (in module rdkit.Chem.Draw.rdMolDraw2D) prepareMolsBeforeDrawing (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) PreprocessReaction() (in module rdkit.Chem.rdChemReactions) (in module rdkit.Chem.SimpleEnum.Enumerator) PrincipalComponents() (in module rdkit.ML.Data.Stats) Print() (rdkit.ML.Cluster.Clusters.Cluster method) PrintAsImageString() (in module rdkit.Chem.PandasTools) PrivateProps (rdkit.Chem.rdchem.PropertyPickleOptions attribute) probeRadius (rdkit.Chem.rdFreeSASA.SASAOpts property) Process() (rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition method) ProcessAndScore() (rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition method) processArgs() (in module rdkit.Chem.ChemUtils.AlignDepict) (in module rdkit.Chem.FeatFinderCLI) ProcessCompoundList() (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) ProcessGainsData() (in module rdkit.Chem.BuildFragmentCatalog) ProcessGainsFile() (in module rdkit.Chem.FragmentCatalog) ProcessMol() (in module rdkit.Chem.MolDb.Loader_orig) (in module rdkit.Chem.MolDb.Loader_sa) ProcessSimpleList() (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) ProgressCallback (rdkit.Chem.rdFMCS.MCSParameters property) Properties (class in rdkit.Chem.rdMolDescriptors) properties() (in module rdkit.Chem.QED) PropertyFunctor (class in rdkit.Chem.Descriptors) (class in rdkit.Chem.rdMolDescriptors) PropertyMol (class in rdkit.Chem.PropertyMol) PropertyPickleOptions (class in rdkit.Chem.rdchem) PropertyRangeQuery (class in rdkit.Chem.rdMolDescriptors) PROTONATION_CHANGED (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) Protor (rdkit.Chem.rdFreeSASA.SASAClassifier attribute) PROTRUDE (rdkit.Chem.Subshape.SubshapeAligner.SubshapeDistanceMetric attribute) ProtrudeDistance() (in module rdkit.Geometry.rdGeometry) prune_maximize_atoms() (in module rdkit.Chem.fmcs.fmcs) prune_maximize_bonds() (in module rdkit.Chem.fmcs.fmcs) pruneBeforeFragmenting (rdkit.Chem.Scaffolds.rdScaffoldNetwork.ScaffoldNetworkParams property) PruneMatchesUsingDirection() (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner method) PruneMatchesUsingFeatures() (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner method) PruneMatchesUsingShape() (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner method) pruneRmsThresh (rdkit.Chem.rdDistGeom.EmbedParameters property) PSA (rdkit.Chem.QED.QEDproperties attribute) PyInfoEntropy() (in module rdkit.ML.InfoTheory.entropy) PyInfoGain() (in module rdkit.ML.InfoTheory.entropy) pyLabuteASA() (in module rdkit.Chem.MolSurf) pyPEOE_VSA_() (in module rdkit.Chem.MolSurf) pyScorePair() (in module rdkit.Chem.AtomPairs.Pairs) pyScorePath() (in module rdkit.Chem.AtomPairs.Torsions) pySlogP_VSA_() (in module rdkit.Chem.MolSurf) pySMR_VSA_() (in module rdkit.Chem.MolSurf) PythonFilterMatcher (class in rdkit.Chem.rdfiltercatalog) PythonPropertyFunctor (class in rdkit.Chem.rdMolDescriptors)

Q

QAtomQueryAtom() (in module rdkit.Chem.rdqueries) qed() (in module rdkit.Chem.QED) QEDproperties (class in rdkit.Chem.QED) QHAtomQueryAtom() (in module rdkit.Chem.rdqueries) QUADRUPLE (rdkit.Chem.rdchem.BondType attribute) query (rdkit.Chem.rdfiltercatalog.IntPair property)

QueryAtom (class in rdkit.Chem.rdchem) QueryAtomData (rdkit.Chem.rdchem.PropertyPickleOptions attribute) QueryBond (class in rdkit.Chem.rdchem) queryMol (rdkit.Chem.rdFMCS.MCSResult property) queryTri (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment attribute) QuickSmartsMatch() (in module rdkit.Chem) QUINTUPLE (rdkit.Chem.rdchem.BondType attribute)

R

R2() (in module rdkit.ML.Data.Stats) radicalSymbol (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) radius (rdkit.Chem.FeatMaps.FeatMaps.FeatMapParams attribute) (rdkit.Chem.rdFingerprintGenerator.MorganFingerprintOptions property) RadiusOfGyration() (in module rdkit.Chem.Descriptors3D) rand (rdkit.Chem.EnumerateStereoisomers.StereoEnumerationOptions attribute) randNegEig (rdkit.Chem.rdDistGeom.EmbedParameters property) random() (in module rdkit.RDRandom) RandomAccessDbFpSupplier (class in rdkit.Chem.Fingerprints.DbFpSupplier) RandomAccessDbMolSupplier (class in rdkit.Chem.Suppliers.DbMolSupplier) RandomAccessDbResultSet (class in rdkit.Dbase.DbResultSet) RandomizeActivities() (in module rdkit.ML.Data.DataUtils) RandomizeMol() (in module rdkit.Chem.Randomize) RandomizeMolBlock() (in module rdkit.Chem.Randomize) RandomSampleAllBBsStrategy (class in rdkit.Chem.rdChemReactions) RandomSampleStrategy (class in rdkit.Chem.rdChemReactions) randomSeed (rdkit.Chem.rdDistGeom.EmbedParameters property) (rdkit.Chem.rdMolEnumerator.MolEnumeratorParams property) RandomTransform() (in module rdkit.Chem.rdMolAlign) rank (rdkit.Chem.fmcs.fmcs.CangenNode attribute) RankBits() (in module rdkit.ML.InfoTheory.BitRank) RDIdToInt() (in module rdkit.Dbase.StorageUtils) RDKFingerprint() (in module rdkit.Chem.rdmolops) rdkit module rdkit.Avalon module rdkit.Avalon.pyAvalonTools module rdkit.Chem module rdkit.Chem.AllChem module rdkit.Chem.AtomPairs module rdkit.Chem.AtomPairs.Pairs module rdkit.Chem.AtomPairs.Sheridan module rdkit.Chem.AtomPairs.Torsions module rdkit.Chem.AtomPairs.Utils module rdkit.Chem.BRICS module rdkit.Chem.BuildFragmentCatalog module rdkit.Chem.ChemicalFeatures module rdkit.Chem.ChemicalForceFields module rdkit.Chem.ChemUtils module rdkit.Chem.ChemUtils.AlignDepict module rdkit.Chem.ChemUtils.BulkTester module rdkit.Chem.ChemUtils.DescriptorUtilities module rdkit.Chem.ChemUtils.SDFToCSV module rdkit.Chem.ChemUtils.TemplateExpand module rdkit.Chem.Crippen module rdkit.Chem.Descriptors module rdkit.Chem.Descriptors3D module rdkit.Chem.Draw module rdkit.Chem.Draw.IPythonConsole module rdkit.Chem.Draw.MolDrawing module rdkit.Chem.Draw.rdMolDraw2D module rdkit.Chem.Draw.SimilarityMaps module rdkit.Chem.EnumerateHeterocycles module rdkit.Chem.EnumerateStereoisomers module rdkit.Chem.EState module rdkit.Chem.EState.AtomTypes module rdkit.Chem.EState.EState module rdkit.Chem.EState.EState_VSA module rdkit.Chem.EState.Fingerprinter module rdkit.Chem.FastSDMolSupplier module rdkit.Chem.FeatFinderCLI module rdkit.Chem.FeatMaps module rdkit.Chem.FeatMaps.FeatMapParser module rdkit.Chem.FeatMaps.FeatMapPoint module rdkit.Chem.FeatMaps.FeatMaps module rdkit.Chem.FeatMaps.FeatMapUtils module rdkit.Chem.Features module rdkit.Chem.Features.FeatDirUtilsRD module rdkit.Chem.Features.ShowFeats module rdkit.Chem.FilterCatalog module rdkit.Chem.Fingerprints module rdkit.Chem.Fingerprints.ClusterMols module rdkit.Chem.Fingerprints.DbFpSupplier module rdkit.Chem.Fingerprints.FingerprintMols module rdkit.Chem.Fingerprints.MolSimilarity module rdkit.Chem.Fingerprints.SimilarityScreener module rdkit.Chem.fmcs module rdkit.Chem.fmcs.fmcs module rdkit.Chem.Fraggle module rdkit.Chem.Fraggle.FraggleSim module rdkit.Chem.FragmentCatalog module rdkit.Chem.FragmentMatcher module rdkit.Chem.Fragments module rdkit.Chem.FunctionalGroups module rdkit.Chem.GraphDescriptors module rdkit.Chem.Graphs module rdkit.Chem.inchi module rdkit.Chem.Lipinski module rdkit.Chem.MACCSkeys module rdkit.Chem.MCS module rdkit.Chem.MolCatalog module rdkit.Chem.MolDb module rdkit.Chem.MolDb.FingerprintUtils module rdkit.Chem.MolDb.Loader module rdkit.Chem.MolDb.Loader_orig module rdkit.Chem.MolDb.Loader_sa module rdkit.Chem.MolKey module rdkit.Chem.MolKey.InchiInfo module rdkit.Chem.MolKey.MolKey module rdkit.Chem.MolStandardize.rdMolStandardize module rdkit.Chem.MolSurf module rdkit.Chem.PandasTools module rdkit.Chem.PeriodicTable module rdkit.Chem.Pharm2D module rdkit.Chem.Pharm2D.Generate module rdkit.Chem.Pharm2D.Gobbi_Pharm2D module rdkit.Chem.Pharm2D.Matcher module rdkit.Chem.Pharm2D.SigFactory module rdkit.Chem.Pharm2D.Utils module rdkit.Chem.Pharm3D module rdkit.Chem.Pharm3D.EmbedLib module rdkit.Chem.Pharm3D.ExcludedVolume module rdkit.Chem.Pharm3D.Pharmacophore module rdkit.Chem.PropertyMol module rdkit.Chem.PyMol module rdkit.Chem.QED module rdkit.Chem.Randomize module rdkit.Chem.rdAbbreviations module rdkit.Chem.rdchem module rdkit.Chem.rdChemicalFeatures module rdkit.Chem.rdChemReactions module rdkit.Chem.rdCIPLabeler module rdkit.Chem.rdCoordGen module rdkit.Chem.rdDepictor module rdkit.Chem.rdDeprotect module rdkit.Chem.rdDetermineBonds module rdkit.Chem.rdDistGeom module rdkit.Chem.rdEHTTools module rdkit.Chem.rdfiltercatalog module rdkit.Chem.rdFingerprintGenerator module rdkit.Chem.rdFMCS module rdkit.Chem.rdForceFieldHelpers module rdkit.Chem.rdfragcatalog module rdkit.Chem.rdFreeSASA module rdkit.Chem.rdinchi module rdkit.Chem.rdMHFPFingerprint module rdkit.Chem.rdMMPA module rdkit.Chem.rdMolAlign module rdkit.Chem.rdMolCatalog module rdkit.Chem.rdMolChemicalFeatures module rdkit.Chem.rdMolDescriptors module rdkit.Chem.rdMolEnumerator module rdkit.Chem.rdmolfiles module rdkit.Chem.rdMolHash module rdkit.Chem.rdMolInterchange module rdkit.Chem.rdmolops module rdkit.Chem.rdMolTransforms module rdkit.Chem.rdPartialCharges module rdkit.Chem.rdqueries module rdkit.Chem.rdReducedGraphs module rdkit.Chem.rdRGroupDecomposition module rdkit.Chem.rdShapeHelpers module rdkit.Chem.rdSLNParse module rdkit.Chem.rdSubstructLibrary module rdkit.Chem.rdTautomerQuery module rdkit.Chem.rdtrajectory module rdkit.Chem.Recap module rdkit.Chem.ReducedGraphs module rdkit.Chem.RegistrationHash module rdkit.Chem.SaltRemover module rdkit.Chem.SATIS module rdkit.Chem.Scaffolds module rdkit.Chem.Scaffolds.MurckoScaffold module rdkit.Chem.Scaffolds.rdScaffoldNetwork module rdkit.Chem.ShowMols module rdkit.Chem.SimpleEnum module rdkit.Chem.SimpleEnum.Enumerator module rdkit.Chem.SpacialScore module rdkit.Chem.Subshape module rdkit.Chem.Subshape.BuilderUtils module rdkit.Chem.Subshape.SubshapeAligner module rdkit.Chem.Subshape.SubshapeBuilder module rdkit.Chem.Subshape.SubshapeObjects module rdkit.Chem.Suppliers module rdkit.Chem.Suppliers.DbMolSupplier module rdkit.Chem.Suppliers.MolSupplier module rdkit.Chem.TemplateAlign module rdkit.Chem.TorsionFingerprints module rdkit.DataManip module rdkit.DataManip.Metric module rdkit.DataManip.Metric.rdMetricMatrixCalc module rdkit.DataStructs module rdkit.DataStructs.BitEnsemble module rdkit.DataStructs.BitEnsembleDb module rdkit.DataStructs.BitUtils module rdkit.DataStructs.cDataStructs module rdkit.DataStructs.LazySignature module rdkit.DataStructs.TopNContainer module rdkit.DataStructs.VectCollection module rdkit.Dbase module rdkit.Dbase.DbConnection module rdkit.Dbase.DbInfo module rdkit.Dbase.DbModule module rdkit.Dbase.DbResultSet module rdkit.Dbase.DbUtils module

rdkit.Dbase.StorageUtils module rdkit.DistanceGeometry module rdkit.DistanceGeometry.DistGeom module rdkit.ForceField module rdkit.ForceField.rdForceField module rdkit.Geometry module rdkit.Geometry.rdGeometry module rdkit.ML module rdkit.ML.Cluster module rdkit.ML.Cluster.Butina module rdkit.ML.Cluster.Clustering module rdkit.ML.Cluster.Clusters module rdkit.ML.Cluster.ClusterUtils module rdkit.ML.Cluster.ClusterVis module rdkit.ML.Cluster.Murtagh module rdkit.ML.Cluster.Resemblance module rdkit.ML.Cluster.Standardize module rdkit.ML.Composite module rdkit.ML.Data module rdkit.ML.Data.cQuantize module rdkit.ML.Data.DataUtils module rdkit.ML.Data.FindQuantBounds module rdkit.ML.Data.MLData module rdkit.ML.Data.Quantize module rdkit.ML.Data.SplitData module rdkit.ML.Data.Stats module rdkit.ML.Data.Transforms module rdkit.ML.DecTree module rdkit.ML.Descriptors module rdkit.ML.Descriptors.CompoundDescriptors module rdkit.ML.Descriptors.Descriptors module rdkit.ML.Descriptors.MoleculeDescriptors module rdkit.ML.Descriptors.Parser module rdkit.ML.files module rdkit.ML.InfoTheory module rdkit.ML.InfoTheory.BitClusterer module rdkit.ML.InfoTheory.BitRank module rdkit.ML.InfoTheory.entropy module rdkit.ML.InfoTheory.rdInfoTheory module rdkit.ML.KNN module rdkit.ML.MatOps module rdkit.ML.MLUtils module rdkit.ML.MLUtils.VoteImg module rdkit.ML.ModelPackage module rdkit.ML.NaiveBayes module rdkit.ML.Neural module rdkit.ML.Scoring module rdkit.ML.Scoring.Scoring module rdkit.ML.SLT module rdkit.ML.SLT.Risk module rdkit.Numerics module rdkit.Numerics.rdAlignment module rdkit.rdBase module rdkit.RDConfig module rdkit.RDLogger module rdkit.RDPaths module rdkit.RDRandom module rdkit.SimDivFilters module rdkit.SimDivFilters.rdSimDivPickers module rdkit.SimDivFilters.SimilarityPickers module rdkit.TestRunner module rdkit.utils module rdkit.utils.cactvs module rdkit.utils.chemutils module rdkit.utils.fileutils module rdkit.utils.listutils module rdkit.utils.spiral module rdkit.VLib module rdkit.VLib.Filter module rdkit.VLib.Node module rdkit.VLib.NodeLib module rdkit.VLib.NodeLib.DbMolSupply module rdkit.VLib.NodeLib.DbPickleSupplier module rdkit.VLib.NodeLib.SDSupply module rdkit.VLib.NodeLib.SmartsMolFilter module rdkit.VLib.NodeLib.SmartsRemover module rdkit.VLib.NodeLib.SmilesDupeFilter module rdkit.VLib.NodeLib.SmilesOutput module rdkit.VLib.NodeLib.SmilesSupply module rdkit.VLib.Output module rdkit.VLib.Supply module rdkit.VLib.Transform module RDKitFingerprintOptions (class in rdkit.Chem.rdFingerprintGenerator) RDKitFP (rdkit.Chem.rdChemReactions.FingerprintType attribute) (rdkit.Chem.rdFingerprintGenerator.FPType attribute) RDKitValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) reaction_smarts (rdkit.Chem.rdDeprotect.DeprotectData property) ReactionFingerprintParams (class in rdkit.Chem.rdChemReactions) ReactionFromMolecule() (in module rdkit.Chem.rdChemReactions) ReactionFromMrvBlock() (in module rdkit.Chem.rdChemReactions) ReactionFromMrvFile() (in module rdkit.Chem.rdChemReactions) ReactionFromPNGFile() (in module rdkit.Chem.rdChemReactions) ReactionFromPNGString() (in module rdkit.Chem.rdChemReactions) ReactionFromRxnBlock() (in module rdkit.Chem.rdChemReactions) ReactionFromRxnFile() (in module rdkit.Chem.rdChemReactions) ReactionFromSmarts() (in module rdkit.Chem.rdChemReactions) ReactionMetadataToPNGFile() (in module rdkit.Chem.rdChemReactions) ReactionMetadataToPNGString() (in module rdkit.Chem.rdChemReactions) ReactionsFromCDXMLBlock() (in module rdkit.Chem.rdChemReactions) ReactionsFromCDXMLFile() (in module rdkit.Chem.rdChemReactions) ReactionToImage() (in module rdkit.Chem.Draw) ReactionToMolecule() (in module rdkit.Chem.rdChemReactions) ReactionToMrvBlock() (in module rdkit.Chem.rdChemReactions) ReactionToMrvFile() (in module rdkit.Chem.rdChemReactions) ReactionToRxnBlock() (in module rdkit.Chem.rdChemReactions) ReactionToSmarts() (in module rdkit.Chem.rdChemReactions) ReactionToSmiles() (in module rdkit.Chem.rdChemReactions) ReactionToV3KRxnBlock() (in module rdkit.Chem.rdChemReactions) ReadAmberTrajectory() (in module rdkit.Chem.rdtrajectory) ReadDataFile() (in module rdkit.ML.files) ReadGeneralExamples() (in module rdkit.ML.Data.DataUtils) ReadGromosTrajectory() (in module rdkit.Chem.rdtrajectory) readline() (rdkit.ML.files.ReFile method) readlines() (rdkit.ML.files.ReFile method) ReadQuantExamples() (in module rdkit.ML.Data.DataUtils) ReadVars() (in module rdkit.ML.Data.DataUtils) reagentMaxMatchCount (rdkit.Chem.rdChemReactions.EnumerationParams property) real_atom (rdkit.Chem.fmcs.fmcs.Atom attribute) real_bond (rdkit.Chem.fmcs.fmcs.Bond attribute) ReapplyMolBlockWedging() (in module rdkit.Chem.rdmolops) RecapDecompose() (in module rdkit.Chem.Recap) RecapHierarchyNode (class in rdkit.Chem.Recap) recharged (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) recursionPossible (rdkit.Chem.rdchem.SubstructMatchParameters property) redirect_stderr (class in rdkit.TestRunner) redirect_stdout (class in rdkit.TestRunner) RedoxPair (rdkit.Chem.rdMolHash.HashFunction attribute) Redraw() (rdkit.Chem.PyMol.MolViewer method) ReduceProductToSideChains() (in module rdkit.Chem.rdChemReactions) ReFile (class in rdkit.ML.files) Regioisomer (rdkit.Chem.rdMolHash.HashFunction attribute) RegisterItem() (in module rdkit.Dbase.StorageUtils) RegisterItems() (in module rdkit.Dbase.StorageUtils) RegisterProperty() (rdkit.Chem.rdMolDescriptors.Properties static method) RegisterSchema() (in module rdkit.Chem.MolDb.Loader_sa) Reionize() (in module rdkit.Chem.MolStandardize.rdMolStandardize) reionize() (rdkit.Chem.MolStandardize.rdMolStandardize.Reionizer method) ReionizeInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) reionizeInPlace() (rdkit.Chem.MolStandardize.rdMolStandardize.Reionizer method) Reionizer (class in rdkit.Chem.MolStandardize.rdMolStandardize) ReionizerFromData() (in module rdkit.Chem.MolStandardize.rdMolStandardize) RelabelDuplicateLabels (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) RelabelMappedDummies() (in module rdkit.Chem.rdRGroupDecomposition) removalReaction (rdkit.Chem.FunctionalGroups.FGHierarchyNode attribute) remove() (rdkit.Chem.MolStandardize.rdMolStandardize.FragmentRemover method) remove_unknown_bondtypes() (in module rdkit.Chem.fmcs.fmcs) REMOVE_WEIGHTS (rdkit.Chem.RegistrationHash.EnhancedStereoUpdateMode attribute) RemoveAgentTemplates() (rdkit.Chem.rdChemReactions.ChemicalReaction method) RemoveAllConformers() (rdkit.Chem.rdchem.Mol method) RemoveAllHs() (in module rdkit.Chem.rdmolops) removeAllHydrogenRGroups (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) removeAllHydrogenRGroupsAndLabels (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) removeAndTrackIsotopes (rdkit.Chem.rdmolops.RemoveHsParameters property) RemoveAtom() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) RemoveAttachment (rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType attribute) RemoveBond() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) RemoveChild() (rdkit.ML.Cluster.Clusters.Cluster method) (rdkit.VLib.Node.VLibNode method) RemoveConformer() (rdkit.Chem.rdchem.Mol method) removeDefiningBondStereo (rdkit.Chem.rdmolops.RemoveHsParameters property) removeDegreeZero (rdkit.Chem.rdmolops.RemoveHsParameters property) removeDummyNeighbors (rdkit.Chem.rdmolops.RemoveHsParameters property) RemoveEntry() (rdkit.Chem.rdfiltercatalog.FilterCatalog method) RemoveFragments() (in module rdkit.Chem.MolStandardize.rdMolStandardize) RemoveFragmentsInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) removeHapticDummies (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnectorOptions property) removeHigherDegrees (rdkit.Chem.rdmolops.RemoveHsParameters property) removeHs (rdkit.Chem.rdmolfiles.SmilesParserParams property) RemoveHs() (in module rdkit.Chem.rdmolops) RemoveHsParameters (class in rdkit.Chem.rdmolops) removeHydrides (rdkit.Chem.rdmolops.RemoveHsParameters property) removeHydrogensPostMatch (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) removeInPlace() (rdkit.Chem.MolStandardize.rdMolStandardize.FragmentRemover method) removeInSGroups (rdkit.Chem.rdmolops.RemoveHsParameters property) removeIsotopes (rdkit.Chem.rdmolops.RemoveHsParameters property) removeMapped (rdkit.Chem.rdmolops.RemoveHsParameters property) RemoveMappingNumbersFromReactions() (in module rdkit.Chem.rdChemReactions) RemoveNonExplicit3DChirality() (in module rdkit.Chem.rdmolops) removeNonimplicit (rdkit.Chem.rdmolops.RemoveHsParameters property) removeNontetrahedralNeighbors (rdkit.Chem.rdmolops.RemoveHsParameters property) removeOnlyHNeighbors (rdkit.Chem.rdmolops.RemoveHsParameters property) RemoveParent() (rdkit.VLib.Node.VLibNode method) RemoveSaltsFromFrame() (in module rdkit.Chem.PandasTools) RemoveSnapshot() (rdkit.Chem.rdtrajectory.Trajectory method) RemoveStereochemistry() (in module rdkit.Chem.rdmolops) RemoveUnmappedProductTemplates() (rdkit.Chem.rdChemReactions.ChemicalReaction method) RemoveUnmappedReactantTemplates() (rdkit.Chem.rdChemReactions.ChemicalReaction method) removeWithQuery (rdkit.Chem.rdmolops.RemoveHsParameters property) removeWithWedgedBond (rdkit.Chem.rdmolops.RemoveHsParameters property) RenderImagesInAllDataFrames() (in module rdkit.Chem.PandasTools) RenumberAtoms() (in module rdkit.Chem.rdmolops) RepeatUnit (rdkit.Chem.rdMolEnumerator.EnumeratorType attribute) ReplaceAtom() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) ReplaceAtomWithQueryAtom() (in module rdkit.Chem.rdqueries) ReplaceBond() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) ReplaceCore() (in module rdkit.Chem.rdmolops) ReplaceGroup() (in module rdkit.Chem.Pharm3D.EmbedLib) ReplaceSidechains() (in module rdkit.Chem.rdmolops) ReplaceSubstructs() (in module rdkit.Chem.rdmolops) report() (rdkit.Chem.fmcs.fmcs.VerboseCachingTargetsMatcher method) (rdkit.Chem.fmcs.fmcs.VerboseHeapOps method) reportAllFailures (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) rerank() (in module rdkit.Chem.fmcs.fmcs) reset() (rdkit.Chem.Fingerprints.DbFpSupplier.ForwardDbFpSupplier method) (rdkit.Chem.Fingerprints.DbFpSupplier.RandomAccessDbFpSupplier method) Reset() (rdkit.Chem.Fingerprints.SimilarityScreener.SimilarityScreener method) (rdkit.Chem.Fingerprints.SimilarityScreener.ThresholdScreener method) (rdkit.Chem.Fingerprints.SimilarityScreener.TopNScreener method) reset() (rdkit.Chem.rdchem.ResonanceMolSupplier method) (rdkit.Chem.rdmolfiles.MaeMolSupplier method) (rdkit.Chem.rdmolfiles.SDMolSupplier method) (rdkit.Chem.rdmolfiles.SmilesMolSupplier method) (rdkit.Chem.rdmolfiles.TDTMolSupplier method) Reset() (rdkit.Chem.Suppliers.DbMolSupplier.ForwardDbMolSupplier method) (rdkit.Chem.Suppliers.DbMolSupplier.RandomAccessDbMolSupplier method) (rdkit.Chem.Suppliers.MolSupplier.MolSupplier method) (rdkit.DataStructs.VectCollection.VectCollection method) (rdkit.Dbase.DbResultSet.DbResultBase method) (rdkit.Dbase.DbResultSet.DbResultSet method) (rdkit.Dbase.DbResultSet.RandomAccessDbResultSet method) reset() (rdkit.VLib.Node.VLibNode method) (rdkit.VLib.NodeLib.DbMolSupply.DbMolSupplyNode method) (rdkit.VLib.NodeLib.DbPickleSupplier.DbPickleSupplyNode method) (rdkit.VLib.NodeLib.SDSupply.SDSupplyNode method) (rdkit.VLib.NodeLib.SmilesDupeFilter.DupeFilter method) (rdkit.VLib.NodeLib.SmilesOutput.OutputNode method) (rdkit.VLib.NodeLib.SmilesSupply.SmilesSupplyNode method) (rdkit.VLib.Supply.SupplyNode method) ResetState() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) ResonanceFlags (class in rdkit.Chem.rdchem) ResonanceMolSupplier (class in rdkit.Chem.rdchem) ResonanceMolSupplierCallback (class in rdkit.Chem.rdchem) restore_isotopes() (in module rdkit.Chem.fmcs.fmcs) RestoreBondDirOption (class in rdkit.Chem.rdmolfiles) RestoreBondDirOptionClear (rdkit.Chem.rdmolfiles.RestoreBondDirOption attribute) RestoreBondDirOptionTrue (rdkit.Chem.rdmolfiles.RestoreBondDirOption attribute) reverse() (rdkit.DataStructs.TopNContainer.TopNContainer method) rewind() (rdkit.ML.files.ReFile method) RGroupCoreAlignment (class in rdkit.Chem.rdRGroupDecomposition) RGroupDecompose() (in module rdkit.Chem.rdRGroupDecomposition) RGroupDecomposition (class in rdkit.Chem.rdRGroupDecomposition) RGroupDecompositionParameters (class in rdkit.Chem.rdRGroupDecomposition) RGroupDecompositionToFrame() (in module rdkit.Chem.PandasTools) RGroupLabelling (class in rdkit.Chem.rdRGroupDecomposition) rgroupLabelling (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) RGroupLabels (class in rdkit.Chem.rdRGroupDecomposition) RGroupMatching (class in rdkit.Chem.rdRGroupDecomposition) RGroupScore (class in rdkit.Chem.rdRGroupDecomposition) RingBondCountEqualsQueryAtom() (in module rdkit.Chem.rdqueries) RingBondCountGreaterQueryAtom() (in module rdkit.Chem.rdqueries) RingBondCountLessQueryAtom() (in module rdkit.Chem.rdqueries) RingCompare (class in rdkit.Chem.rdFMCS) RingCount() (in module rdkit.Chem.Lipinski) RingInfo (class in rdkit.Chem.rdchem) ringMatchesRingOnly (rdkit.Chem.fmcs.fmcs.Default attribute) RingMatchesRingOnly (rdkit.Chem.rdFMCS.MCSAtomCompareParameters property) (rdkit.Chem.rdFMCS.MCSBondCompareParameters property) RogotGoldbergSimilarity() (in module rdkit.DataStructs.cDataStructs) RogotGoldbergSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) RogotGoldbergSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) RollbackBatchEdit() (rdkit.Chem.rdchem.EditableMol method) (rdkit.Chem.rdchem.RWMol method) rootedAtAtom (rdkit.Chem.rdmolfiles.SmilesWriteParams property) rotate (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) ROTB (rdkit.Chem.QED.QEDproperties attribute) run() (rdkit.Chem.MolStandardize.rdMolStandardize.Pipeline method) RunDetails (class in rdkit.Chem.BuildFragmentCatalog) RunFilterCatalog() (in module rdkit.Chem.rdfiltercatalog) runIt() (in module rdkit.ML.Data.FindQuantBounds) RunMol() (in module rdkit.Chem.rdEHTTools) RunReactant() (rdkit.Chem.rdChemReactions.ChemicalReaction method) RunReactantInPlace() (rdkit.Chem.rdChemReactions.ChemicalReaction method) RunReactants() (rdkit.Chem.rdChemReactions.ChemicalReaction method) RusselSimilarity() (in module rdkit.DataStructs.cDataStructs) RusselSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) RusselSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) RWMol (class in rdkit.Chem.rdchem) rxnSmarts (rdkit.Chem.FunctionalGroups.FGHierarchyNode attribute)

S

S (rdkit.Chem.rdchem.HybridizationType attribute) SaltRemover (class in rdkit.Chem.SaltRemover) SampleSubshape() (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder method) sanePartialProducts (rdkit.Chem.rdChemReactions.EnumerationParams property) sanitize (rdkit.Chem.rdMolEnumerator.MolEnumeratorParams property) (rdkit.Chem.rdmolfiles.SmilesParserParams property) SANITIZE_ADJUST_REACTANTS (rdkit.Chem.rdChemReactions.SanitizeFlags attribute) SANITIZE_ADJUSTHS (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_ALL (rdkit.Chem.rdChemReactions.SanitizeFlags attribute) (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_ATOM_MAPS (rdkit.Chem.rdChemReactions.SanitizeFlags attribute) SANITIZE_CLEANUP (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_CLEANUP_ORGANOMETALLICS (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_CLEANUPATROPISOMERS (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_CLEANUPCHIRALITY (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_FINDRADICALS (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_KEKULIZE (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_MERGEHS (rdkit.Chem.rdChemReactions.SanitizeFlags attribute) SANITIZE_NONE (rdkit.Chem.rdChemReactions.SanitizeFlags attribute) (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_PROPERTIES (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_RGROUP_NAMES (rdkit.Chem.rdChemReactions.SanitizeFlags attribute) SANITIZE_SETAROMATICITY (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_SETCONJUGATION (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_SETHYBRIDIZATION (rdkit.Chem.rdmolops.SanitizeFlags attribute) SANITIZE_SYMMRINGS (rdkit.Chem.rdmolops.SanitizeFlags attribute) SanitizeFlags (class in rdkit.Chem.rdChemReactions) (class in rdkit.Chem.rdmolops) SanitizeMol() (in module rdkit.Chem.rdmolops) SanitizeRxn() (in module rdkit.Chem.rdChemReactions) SanitizeRxnAsMols() (in module rdkit.Chem.rdChemReactions) SASAAlgorithm (class in rdkit.Chem.rdFreeSASA) SASAClass (class in rdkit.Chem.rdFreeSASA) SASAClassifier (class in rdkit.Chem.rdFreeSASA) SASAOpts (class in rdkit.Chem.rdFreeSASA) SATISTypes() (in module rdkit.Chem.SATIS) save_atom_classes() (in module rdkit.Chem.fmcs.fmcs) save_isotopes() (in module rdkit.Chem.fmcs.fmcs) SaveFile() (rdkit.Chem.PyMol.MolViewer method) SaveSMILESFromFrame() (in module rdkit.Chem.PandasTools) SaveState() (rdkit.ML.Descriptors.Descriptors.DescriptorCalculator method) (rdkit.ML.Descriptors.MoleculeDescriptors.MolecularDescriptorCalculator method) SaveXlsxFromFrame() (in module rdkit.Chem.PandasTools) ScaffoldNetwork (class in rdkit.Chem.Scaffolds.rdScaffoldNetwork) ScaffoldNetworkParams (class in rdkit.Chem.Scaffolds.rdScaffoldNetwork) ScaffoldPasses() (in module rdkit.Chem.Pharm2D.Utils) scaleAndCenter() (rdkit.Chem.Draw.MolDrawing.MolDrawing method) scaleBondWidth (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) scaledMedianBondLength (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) scaleHighlightBondWidth (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) scalingFactor (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) Score() (rdkit.Chem.rdMolAlign.O3A method) ScoreFeats() (rdkit.Chem.FeatMaps.FeatMaps.FeatMap method) ScoreFromLists() (in module rdkit.Chem.BuildFragmentCatalog) scoreMethod (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) scoreMode (rdkit.Chem.FeatMaps.FeatMaps.FeatMap attribute) ScoreMolecules() (in module rdkit.Chem.BuildFragmentCatalog) scoresName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) ScoreTautomer() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator static method) ScoreWithIndex() (rdkit.DataStructs.BitEnsemble.BitEnsemble method) ScoreWithOnBits() (rdkit.DataStructs.BitEnsemble.BitEnsemble method) ScreenFingerprints() (in module rdkit.Chem.Fingerprints.MolSimilarity) ScreenFromDetails() (in module rdkit.Chem.Fingerprints.MolSimilarity) ScreenInDb() (in module rdkit.Chem.Fingerprints.MolSimilarity) SDMolSupplier (class in rdkit.Chem.rdmolfiles) SDSupplyNode (class in rdkit.VLib.NodeLib.SDSupply) SDWriter (class in rdkit.Chem.rdmolfiles) searchLayerFlags (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions attribute) seedProcessed (rdkit.Chem.rdFMCS.MCSProgressData property) SeedRandomNumberGenerator() (in module rdkit.rdBase) select_fragments() (in module rdkit.Chem.Fraggle.FraggleSim) SelectAtoms() (rdkit.Chem.PyMol.MolViewer method) selectColor (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) SelectProteinNeighborhood() (rdkit.Chem.PyMol.MolViewer method) Serialize() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) (rdkit.Chem.rdfiltercatalog.FilterCatalog method) (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) (rdkit.Chem.rdfragcatalog.FragCatalog method) (rdkit.Chem.rdfragcatalog.FragCatParams method) (rdkit.Chem.rdMolCatalog.MolCatalog method) (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) SERIALIZING_OUTPUT (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) Set3D() (rdkit.Chem.rdchem.Conformer method) set_isotopes() (in module rdkit.Chem.fmcs.fmcs) SetACS1996Mode() (in module rdkit.Chem.Draw.rdMolDraw2D) SetActiveConformer() (rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature method) SetAllowNontetrahedralChirality() (in module rdkit.Chem.rdmolops) SetAltLoc() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetAngleDeg() (in module rdkit.Chem.rdMolTransforms) SetAngleRad() (in module rdkit.Chem.rdMolTransforms) setAnnotationColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) setAromaticBonds (rdkit.Chem.rdMolInterchange.JSONParseParameters property) SetAromaticity() (in module rdkit.Chem.rdmolops) SetAtomAlias() (in module rdkit.Chem.rdchem) SetAtomicNum() (rdkit.Chem.rdchem.Atom method) SetAtomMapNum() (rdkit.Chem.rdchem.Atom method) setAtomPalette() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) SetAtomPosition() (rdkit.Chem.rdchem.Conformer method) SetAtomRLabel() (in module rdkit.Chem.rdchem) SetAtoms() (rdkit.Chem.rdchem.SubstanceGroup method) setAtomSymbols() (rdkit.Chem.rdmolops.MolzipParams method) SetAtomValue() (in module rdkit.Chem.rdchem) setBackgroundColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) SetBiasList() (rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRanker method) SetBins() (rdkit.Chem.Pharm2D.SigFactory.SigFactory method) SetBit() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) SetBitList() (rdkit.ML.InfoTheory.rdInfoTheory.BitCorrMatGenerator method) SetBits() (rdkit.DataStructs.BitEnsemble.BitEnsemble method) SetBitsFromList() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) SetBondDir() (rdkit.Chem.rdchem.Bond method) SetBondLength() (in module rdkit.Chem.rdMolTransforms) SetBonds() (rdkit.Chem.rdchem.SubstanceGroup method) SetBondStereoFromDirections() (in module rdkit.Chem.rdmolops) SetBondType() (rdkit.Chem.rdchem.Bond method) SetBoolProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) SetBoundsMat() (rdkit.Chem.rdDistGeom.EmbedParameters method) SetCallback() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) SetChainId() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetChiralTag() (rdkit.Chem.rdchem.Atom method) SetClusters() (rdkit.ML.InfoTheory.BitClusterer.BitClusterer method) SetColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) setColourMap() (rdkit.Chem.Draw.rdMolDraw2D.ContourParams method) SetComicMode() (in module rdkit.Chem.Draw) SetConjugation() (in module rdkit.Chem.rdmolops) setContourColour() (rdkit.Chem.Draw.rdMolDraw2D.ContourParams method) SetCoordMap() (rdkit.Chem.rdCoordGen.CoordGenParams method) (rdkit.Chem.rdDistGeom.EmbedParameters method) SetCountBounds() (rdkit.Chem.rdFingerprintGenerator.FingerprintOptions method) SetCPCI() (rdkit.Chem.rdDistGeom.EmbedParameters method) SetDarkMode() (in module rdkit.Chem.Draw.rdMolDraw2D) SetData() (rdkit.Chem.FeatMaps.FeatMapParser.FeatMapParser method) (rdkit.Chem.rdmolfiles.MaeMolSupplier method) (rdkit.Chem.rdmolfiles.SDMolSupplier method) (rdkit.Chem.rdmolfiles.SmilesMolSupplier method) (rdkit.Chem.rdmolfiles.TDTMolSupplier method) (rdkit.ML.Cluster.Clusters.Cluster method) SetDefaultPickleProperties() (in module rdkit.Chem.rdchem) SetDefaultTemplateFileDir() (in module rdkit.Chem.rdCoordGen) SetDescription() (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) (rdkit.Chem.rdMolCatalog.MolCatalogEntry method) setDescriptorVersion() (in module rdkit.Chem.ChemUtils.DescriptorUtilities) SetDihedralDeg() (in module rdkit.Chem.rdMolTransforms) SetDihedralRad() (in module rdkit.Chem.rdMolTransforms) SetDisplayStyle() (rdkit.Chem.PyMol.MolViewer method) SetDisplayUpdate() (rdkit.Chem.PyMol.MolViewer method) SetDoubleBondNeighborDirections() (in module rdkit.Chem.rdmolops) SetDoubleProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) SetDrawOptions() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) SetEnergy() (rdkit.Chem.rdtrajectory.Snapshot method) SetEnumerationOperator() (rdkit.Chem.rdMolEnumerator.MolEnumeratorParams method) SetExclusionPatterns() (rdkit.Chem.rdfiltercatalog.ExclusionList method) SetExplicitBitVectProp() (rdkit.Chem.rdchem.Atom method) setExtraFinalCheck() (rdkit.Chem.rdchem.SubstructMatchParameters method) SetFamily() (rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature method) SetFillPolys() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) SetFlexiMode() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) SetFontSize() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) SetForceV3000() (rdkit.Chem.rdmolfiles.SDWriter method) SetFormalCharge() (rdkit.Chem.rdchem.Atom method) SetGenericQueriesFromProperties() (in module rdkit.Chem.rdmolops) setHighlightColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) SetHybridization() (in module rdkit.Chem.rdmolops) (rdkit.Chem.rdchem.Atom method) SetId() (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature method) SetIndex() (rdkit.ML.Cluster.Clusters.Cluster method) SetInsertionCode() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetIntProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) SetIsAromatic() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) SetIsConjugated() (rdkit.Chem.rdchem.Bond method) SetIsHeteroAtom() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetIsotope() (rdkit.Chem.rdchem.Atom method) SetKekulize() (rdkit.Chem.rdmolfiles.SDWriter method) setLegendColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) setLevel() (rdkit.RDLogger.logger method) SetLineWidth() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) setLowerBound() (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) setLowerBound2D() (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) SetMaskBits() (rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRanker method) SetMaxCount() (rdkit.Chem.rdfiltercatalog.SmartsMatcher method) SetMaxTautomers() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) SetMaxTransforms() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) setMDLFiveRingAromaticity (rdkit.Chem.rdmolops.AdjustQueryParameters property) SetMetalNof() (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnector method) SetMetalNon() (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnector method) SetMetric() (rdkit.ML.Cluster.Clusters.Cluster method) SetMetricFromName() (rdkit.Chem.Fingerprints.FingerprintMols.FingerprinterDetails method) SetMinCount() (rdkit.Chem.rdfiltercatalog.SmartsMatcher method) SetMMFFAngleTerm() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFBondTerm() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFDielectricConstant() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFDielectricModel() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFEleTerm() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFOopTerm() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFStretchBendTerm() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFTorsionTerm() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFVariant() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFVdWTerm() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMMFFVerbosity() (rdkit.ForceField.rdForceField.MMFFMolProperties method) SetMol() (rdkit.Chem.rdMolCatalog.MolCatalogEntry method) SetMonochromeMode() (in module rdkit.Chem.Draw.rdMolDraw2D) SetMonomerInfo() (rdkit.Chem.rdchem.Atom method) SetMonomerType() (rdkit.Chem.rdchem.AtomMonomerInfo method) SetName() (rdkit.Chem.rdchem.AtomMonomerInfo method) (rdkit.ML.Cluster.Clusters.Cluster method) SetNegate() (rdkit.VLib.Filter.FilterNode method) SetNoImplicit() (rdkit.Chem.rdchem.Atom method) SetNumDigits() (rdkit.Chem.rdmolfiles.TDTWriter method) SetNumExplicitHs() (rdkit.Chem.rdchem.Atom method) SetNumRadicalElectrons() (rdkit.Chem.rdchem.Atom method) SetNumThreads() (rdkit.Chem.rdchem.ResonanceMolSupplier method) SetOccupancy() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetOffset() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) SetOrder() (rdkit.Chem.rdMolCatalog.MolCatalogEntry method) SetParentAtoms() (rdkit.Chem.rdchem.SubstanceGroup method) SetPattern() (rdkit.Chem.rdfiltercatalog.FilterHierarchyMatcher method) (rdkit.Chem.rdfiltercatalog.SmartsMatcher method) SetPDBResidueInfo() (rdkit.Chem.rdchem.Atom method) SetPos() (rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature method) SetPosition() (rdkit.ML.Cluster.Clusters.Cluster method) SetPositions() (rdkit.Chem.rdchem.Conformer method) SetPreferCoordGen() (in module rdkit.Chem.rdDepictor) SetProbe() (rdkit.Chem.Fingerprints.SimilarityScreener.SimilarityScreener method) SetProcessPropertyLists() (rdkit.Chem.rdmolfiles.ForwardSDMolSupplier method) (rdkit.Chem.rdmolfiles.MultithreadedSDMolSupplier method) (rdkit.Chem.rdmolfiles.SDMolSupplier method) SetProgressCallback() (rdkit.Chem.rdchem.ResonanceMolSupplier method) SetProp() (rdkit.Chem.PropertyMol.PropertyMol method) (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) (rdkit.Chem.rdfiltercatalog.FilterCatalogEntry method) SetProps() (rdkit.Chem.rdmolfiles.MaeWriter method) (rdkit.Chem.rdmolfiles.SDWriter method) (rdkit.Chem.rdmolfiles.SmilesWriter method) (rdkit.Chem.rdmolfiles.TDTWriter method)

SetQuery() (rdkit.Chem.rdchem.QueryAtom method) (rdkit.Chem.rdchem.QueryBond method) setQueryColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) setRadius() (rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore method) SetReassignStereo() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) SetRemoveBondStereo() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) SetRemoveSp3Stereo() (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator method) SetResidueName() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetResidueNumber() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetRingSystemTemplates() (in module rdkit.Chem.rdDepictor) setScale (rdkit.Chem.Draw.rdMolDraw2D.ContourParams property) SetScale() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) SetSearchOrder() (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) SetSecondaryStructure() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetSegmentNumber() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetSerialNumber() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetSphereOccupancy() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) SetState() (rdkit.Chem.rdChemReactions.EnumerateLibraryBase method) SetStereo() (rdkit.Chem.rdchem.Bond method) SetStereoAtoms() (rdkit.Chem.rdchem.Bond method) SetStereoGroups() (rdkit.Chem.rdchem.RWMol method) SetSupplementalSmilesLabel() (in module rdkit.Chem.rdchem) setSymbolColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) SetTempFactor() (rdkit.Chem.rdchem.AtomPDBResidueInfo method) SetTemplateMol() (rdkit.Chem.rdCoordGen.CoordGenParams method) SetTerminalAtomCoords() (in module rdkit.Chem.rdmolops) SetType() (rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature method) SetUnsignedProp() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Bond method) (rdkit.Chem.rdchem.Conformer method) (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.SubstanceGroup method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) setupAUTOCorrDescriptors() (in module rdkit.Chem.Descriptors) setUpperBound() (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) setUpperBound2D() (rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore method) SetUseLegacyStereoPerception() (in module rdkit.Chem.rdmolops) SetVal() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) SetValPoint() (rdkit.Geometry.rdGeometry.UniformGrid3D_ method) setVariableAttachmentColour() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) SetWrite2D() (rdkit.Chem.rdmolfiles.TDTWriter method) SetWriteId() (rdkit.Chem.rdchem.StereoGroup method) SetWriteNames() (rdkit.Chem.rdmolfiles.TDTWriter method) SGROUP_DATA (rdkit.Chem.RegistrationHash.HashLayer attribute) shapeDirs (rdkit.Chem.Subshape.SubshapeObjects.SkeletonPoint attribute) shapeDist (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment attribute) shapeDistTol (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner attribute) shapeMoments (rdkit.Chem.Subshape.SubshapeObjects.SkeletonPoint attribute) ShapeProtrudeDist() (in module rdkit.Chem.rdShapeHelpers) shapes (rdkit.Chem.Subshape.SubshapeObjects.SubshapeShape attribute) ShapeTanimotoDist() (in module rdkit.Chem.rdShapeHelpers) ShapeTverskyIndex() (in module rdkit.Chem.rdShapeHelpers) ShapeWithSkeleton (class in rdkit.Chem.Subshape.SubshapeObjects) shift_targets() (rdkit.Chem.fmcs.fmcs.CachingTargetsMatcher method) (rdkit.Chem.fmcs.fmcs.VerboseCachingTargetsMatcher method) ShouldAcceptMCS (rdkit.Chem.rdFMCS.MCSParameters property) shouldKekulize() (in module rdkit.Chem.Draw) ShowArrow() (in module rdkit.Chem.Features.ShowFeats) ShowDescriptors() (rdkit.ML.Descriptors.Descriptors.DescriptorCalculator method) ShowDetails() (in module rdkit.Chem.BuildFragmentCatalog) ShowMetricMat() (in module rdkit.ML.Cluster.Resemblance) ShowMol() (in module rdkit.Chem.Draw) (rdkit.Chem.PyMol.MolViewer method) ShowMolFeats() (in module rdkit.Chem.Features.ShowFeats) ShowMols() (in module rdkit.Chem.Draw.IPythonConsole) showUnknownDoubleBonds (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) showWarnings (rdkit.Chem.rdmolops.RemoveHsParameters property) ShrakeRupley (rdkit.Chem.rdFreeSASA.SASAAlgorithm attribute) shuffle() (in module rdkit.RDRandom) SigFactory (class in rdkit.Chem.Pharm2D.SigFactory) SignedAngleTo() (rdkit.Geometry.rdGeometry.Point2D method) (rdkit.Geometry.rdGeometry.Point3D method) SimilarityScreener (class in rdkit.Chem.Fingerprints.SimilarityScreener) simplifiedStereoGroupLabel (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) SimplifyEnhancedStereo() (in module rdkit.Chem.rdmolops) SINGLE (rdkit.Chem.rdchem.BondType attribute) SingleBestAtoms (class in rdkit.Chem.fmcs.fmcs) SingleBestAtomsCompleteRingsOnly (class in rdkit.Chem.fmcs.fmcs) SingleBestBonds (class in rdkit.Chem.fmcs.fmcs) SingleBestBondsCompleteRingsOnly (class in rdkit.Chem.fmcs.fmcs) singleColourWedgeBonds (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) SIXTEENBITVALUE (rdkit.DataStructs.cDataStructs.DiscreteValueType attribute) Size() (rdkit.Chem.rdchem.MolBundle method) size_check_failed (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) SkeletonPoint (class in rdkit.Chem.Subshape.SubshapeObjects) skelPts (rdkit.Chem.Subshape.SubshapeObjects.ShapeWithSkeleton attribute) sketcherBestPrecision (rdkit.Chem.rdCoordGen.CoordGenParams property) sketcherCoarsePrecision (rdkit.Chem.rdCoordGen.CoordGenParams property) sketcherQuickPrecision (rdkit.Chem.rdCoordGen.CoordGenParams property) sketcherStandardPrecision (rdkit.Chem.rdCoordGen.CoordGenParams property) Skip() (rdkit.Chem.rdChemReactions.EnumerationStrategyBase method) SLINK (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute) SlogP_VSA1() (in module rdkit.Chem.MolSurf) SlogP_VSA10() (in module rdkit.Chem.MolSurf) SlogP_VSA11() (in module rdkit.Chem.MolSurf) SlogP_VSA12() (in module rdkit.Chem.MolSurf) SlogP_VSA2() (in module rdkit.Chem.MolSurf) SlogP_VSA3() (in module rdkit.Chem.MolSurf) SlogP_VSA4() (in module rdkit.Chem.MolSurf) SlogP_VSA5() (in module rdkit.Chem.MolSurf) SlogP_VSA6() (in module rdkit.Chem.MolSurf) SlogP_VSA7() (in module rdkit.Chem.MolSurf) SlogP_VSA8() (in module rdkit.Chem.MolSurf) SlogP_VSA9() (in module rdkit.Chem.MolSurf) SlogP_VSA_() (in module rdkit.Chem.rdMolDescriptors) SmallWorldIndexBR (rdkit.Chem.rdMolHash.HashFunction attribute) SmallWorldIndexBRL (rdkit.Chem.rdMolHash.HashFunction attribute) smarts (rdkit.Chem.FunctionalGroups.FGHierarchyNode attribute) Smarts (rdkit.Chem.MolStandardize.rdMolStandardize.ChargeCorrection property) SMARTS (rdkit.Chem.SaltRemover.InputFormat attribute) SmartsFilter (class in rdkit.VLib.NodeLib.SmartsMolFilter) SmartsMatcher (class in rdkit.Chem.rdfiltercatalog) SmartsParserParams (class in rdkit.Chem.rdmolfiles) SmartsRemover (class in rdkit.VLib.NodeLib.SmartsRemover) smartsString (rdkit.Chem.rdFMCS.MCSResult property) smiCol (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) smiles (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorResult property) (rdkit.Chem.Recap.RecapHierarchyNode attribute) SMILES (rdkit.Chem.SaltRemover.InputFormat attribute) SmilesMolSupplier (class in rdkit.Chem.rdmolfiles) SmilesMolSupplierFromText() (in module rdkit.Chem.rdmolfiles) smilesOut() (rdkit.VLib.NodeLib.SmilesOutput.OutputNode method) SmilesParserParams (class in rdkit.Chem.rdmolfiles) SmilesSupplyNode (class in rdkit.VLib.NodeLib.SmilesSupply) SmilesTautomerMap (class in rdkit.Chem.MolStandardize.rdMolStandardize) smilesTautomerMap (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorResult property) SmilesToGif() (in module rdkit.utils.cactvs) SmilesToImage() (in module rdkit.utils.cactvs) SmilesWriteParams (class in rdkit.Chem.rdmolfiles) SmilesWriter (class in rdkit.Chem.rdmolfiles) SMR_VSA1() (in module rdkit.Chem.MolSurf) SMR_VSA10() (in module rdkit.Chem.MolSurf) SMR_VSA2() (in module rdkit.Chem.MolSurf) SMR_VSA3() (in module rdkit.Chem.MolSurf) SMR_VSA4() (in module rdkit.Chem.MolSurf) SMR_VSA5() (in module rdkit.Chem.MolSurf) SMR_VSA6() (in module rdkit.Chem.MolSurf) SMR_VSA7() (in module rdkit.Chem.MolSurf) SMR_VSA8() (in module rdkit.Chem.MolSurf) SMR_VSA9() (in module rdkit.Chem.MolSurf) SMR_VSA_() (in module rdkit.Chem.rdMolDescriptors) Snapshot (class in rdkit.Chem.rdtrajectory) SokalSimilarity() (in module rdkit.DataStructs.cDataStructs) SokalSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) SokalSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) SortMatchesByDegreeOfCoreSubstitution() (in module rdkit.Chem.rdmolops) SP (rdkit.Chem.rdchem.HybridizationType attribute) SP2 (rdkit.Chem.rdchem.HybridizationType attribute) SP2D (rdkit.Chem.rdchem.HybridizationType attribute) SP3 (rdkit.Chem.rdchem.HybridizationType attribute) SP3D (rdkit.Chem.rdchem.HybridizationType attribute) SP3D2 (rdkit.Chem.rdchem.HybridizationType attribute) SparseBitVect (class in rdkit.DataStructs.cDataStructs) SparseRankBits() (in module rdkit.ML.InfoTheory.BitRank) specified (rdkit.Chem.rdchem.StereoInfo property) Specified (rdkit.Chem.rdchem.StereoSpecified attribute) SpherocityIndex() (in module rdkit.Chem.Descriptors3D) splitAromaticC (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnectorOptions property) splitBonds (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) SplitComposition() (in module rdkit.utils.chemutils) SplitDataSet() (in module rdkit.ML.Data.SplitData) SplitDbData() (in module rdkit.ML.Data.SplitData) splitGrignards (rdkit.Chem.MolStandardize.rdMolStandardize.MetalDisconnectorOptions property) SplitIndices() (in module rdkit.ML.Data.SplitData) SplitIntoNClusters() (in module rdkit.ML.Cluster.ClusterUtils) SplitMolByPDBChainId() (in module rdkit.Chem.rdmolops) SplitMolByPDBResidues() (in module rdkit.Chem.rdmolops) SpreadPicker (class in rdkit.SimDivFilters.SimilarityPickers) SPS() (in module rdkit.Chem.SpacialScore) srETKDGv3() (in module rdkit.Chem.rdDistGeom) stage (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineResult property) STANDARDIZATION (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) STANDARDIZATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) StandardizeMatrix() (in module rdkit.ML.Data.Stats) StandardizeSmiles() (in module rdkit.Chem.MolStandardize.rdMolStandardize) starting_from (class in rdkit.Chem.fmcs.fmcs) Stats() (rdkit.Chem.rdChemReactions.EvenSamplePairsStrategy method) status (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineLogEntry property) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineResult property) (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorResult property) std_ostream (class in rdkit.rdBase) StdDev() (in module rdkit.ML.Cluster.Standardize) stepSize (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder attribute) STEREO_ABSOLUTE (rdkit.Chem.rdchem.StereoGroupType attribute) STEREO_AND (rdkit.Chem.rdchem.StereoGroupType attribute) stereo_code (rdkit.Chem.MolKey.MolKey.MolKeyResult attribute) stereo_comment (rdkit.Chem.MolKey.MolKey.MolKeyResult attribute) stereo_error (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) stereo_forced_bad (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) STEREO_INSENSITIVE_LAYERS (rdkit.Chem.RegistrationHash.HashScheme attribute) STEREO_OR (rdkit.Chem.rdchem.StereoGroupType attribute) stereo_transformed (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) STEREO_VALIDATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) STEREOANY (rdkit.Chem.rdchem.BondStereo attribute) STEREOATROPCCW (rdkit.Chem.rdchem.BondStereo attribute) STEREOATROPCW (rdkit.Chem.rdchem.BondStereo attribute) StereoBondThresholds (class in rdkit.Chem.rdmolops) STEREOCIS (rdkit.Chem.rdchem.BondStereo attribute) StereoDescriptor (class in rdkit.Chem.rdchem) STEREOE (rdkit.Chem.rdchem.BondStereo attribute) StereoEnumerationOptions (class in rdkit.Chem.EnumerateStereoisomers) StereoGroup (class in rdkit.Chem.rdchem) StereoGroup_vect (class in rdkit.Chem.rdchem) StereoGroupType (class in rdkit.Chem.rdchem) StereoInfo (class in rdkit.Chem.rdchem) STEREONONE (rdkit.Chem.rdchem.BondStereo attribute) StereoParent() (in module rdkit.Chem.MolStandardize.rdMolStandardize) StereoParentInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) StereoSpecified (class in rdkit.Chem.rdchem) STEREOTRANS (rdkit.Chem.rdchem.BondStereo attribute) StereoType (class in rdkit.Chem.rdchem) StereoValidation (class in rdkit.Chem.MolStandardize.rdMolStandardize) STEREOZ (rdkit.Chem.rdchem.BondStereo attribute) StoreAll (rdkit.Chem.rdFMCS.MCSParameters property) StraightenDepiction() (in module rdkit.Chem.rdDepictor) streambuf (class in rdkit.rdBase) strict (rdkit.Chem.MolStandardize.rdMolStandardize.IsotopeValidation property) Strict (rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions attribute) strictCXSMILES (rdkit.Chem.rdmolfiles.SmartsParserParams property) (rdkit.Chem.rdmolfiles.SmilesParserParams property) StrictLinkages (rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions attribute) strictParsing (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineOptions property) StrictRingFusion (rdkit.Chem.rdFMCS.RingCompare attribute) strictValenceCheck (rdkit.Chem.rdMolInterchange.JSONParseParameters property) StripMol() (rdkit.Chem.SaltRemover.SaltRemover method) StripMolWithDeleted() (rdkit.Chem.SaltRemover.SaltRemover method) StruChkFlag (class in rdkit.Avalon.pyAvalonTools) StruChkResult (class in rdkit.Avalon.pyAvalonTools) STRUCTURE_MODIFICATION (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) Subgraph (class in rdkit.Chem.fmcs.fmcs) subgraph_to_fragment() (in module rdkit.Chem.fmcs.fmcs) submol (rdkit.Chem.Draw.FingerprintEnv attribute) SubshapeAligner (class in rdkit.Chem.Subshape.SubshapeAligner) SubshapeAlignment (class in rdkit.Chem.Subshape.SubshapeAligner) SubshapeBuilder (class in rdkit.Chem.Subshape.SubshapeBuilder) SubshapeCombineOperations (class in rdkit.Chem.Subshape.SubshapeBuilder) SubshapeDistanceMetric (class in rdkit.Chem.Subshape.SubshapeAligner) SubshapeShape (class in rdkit.Chem.Subshape.SubshapeObjects) SubstanceGroup (class in rdkit.Chem.rdchem) SubstanceGroup_VECT (class in rdkit.Chem.rdchem) SubstanceGroupAttach (class in rdkit.Chem.rdchem) SubstanceGroupCState (class in rdkit.Chem.rdchem) SubstructLibrary (class in rdkit.Chem.rdSubstructLibrary) SubstructLibraryCanSerialize() (in module rdkit.Chem.rdSubstructLibrary) SubstructMatchParameters (class in rdkit.Chem.rdchem) substructMatchParams (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) success (rdkit.Avalon.pyAvalonTools.StruChkResult attribute) Sum (rdkit.Chem.FeatMaps.FeatMapUtils.DirMergeMode attribute) SUM (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeCombineOperations attribute) SUM() (in module rdkit.ML.Descriptors.Parser) (rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator method) SuperParent() (in module rdkit.Chem.MolStandardize.rdMolStandardize) SuperParentInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) SupplierFromDetails() (in module rdkit.Chem.BuildFragmentCatalog) SupplierFromFilename() (in module rdkit.Chem) SupplyNode (class in rdkit.VLib.Supply) symmetrizeConjugatedTerminalGroupsForPruning (rdkit.Chem.rdDistGeom.EmbedParameters property)

T

tableName (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) TagAtoms() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG method) TakeEnsemble() (in module rdkit.ML.Data.DataUtils) TANIMOTO (rdkit.Chem.Subshape.SubshapeAligner.SubshapeDistanceMetric attribute) TanimotoDistance() (in module rdkit.Geometry.rdGeometry) TanimotoSimilarity() (in module rdkit.Chem.ReducedGraphs) (in module rdkit.DataStructs.cDataStructs) TanimotoSimilarityNeighbors() (in module rdkit.DataStructs.cDataStructs) TanimotoSimilarityNeighbors_sparse() (in module rdkit.DataStructs.cDataStructs) target (rdkit.Chem.rdfiltercatalog.IntPair property) targetTri (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment attribute) Tautomer (class in rdkit.Chem.MolStandardize.rdMolStandardize) tautomer (rdkit.Chem.MolStandardize.rdMolStandardize.Tautomer property) TAUTOMER_HASH (rdkit.Chem.RegistrationHash.HashLayer attribute) TAUTOMER_INSENSITIVE_LAYERS (rdkit.Chem.RegistrationHash.HashScheme attribute) TautomerEnumerator (class in rdkit.Chem.MolStandardize.rdMolStandardize) TautomerEnumeratorCallback (class in rdkit.Chem.MolStandardize.rdMolStandardize) TautomerEnumeratorResult (class in rdkit.Chem.MolStandardize.rdMolStandardize) TautomerEnumeratorStatus (class in rdkit.Chem.MolStandardize.rdMolStandardize) TautomerParent() (in module rdkit.Chem.MolStandardize.rdMolStandardize) TautomerParentInPlace() (in module rdkit.Chem.MolStandardize.rdMolStandardize) TautomerPatternHolder (class in rdkit.Chem.rdSubstructLibrary) TautomerQuery (class in rdkit.Chem.rdTautomerQuery) TautomerQueryCanSerialize() (in module rdkit.Chem.rdTautomerQuery) tautomerReassignStereo (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) tautomerRemoveBondStereo (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) tautomerRemoveIsotopicHs (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) tautomerRemoveSp3Stereo (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) tautomers (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorResult property) tautomerScoreVersion (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumerator attribute) tautomerTransformsFile (rdkit.Chem.MolStandardize.rdMolStandardize.CleanupParameters property) TDTMolSupplier (class in rdkit.Chem.rdmolfiles) TDTWriter (class in rdkit.Chem.rdmolfiles) template_transformed (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) templateFileDir (rdkit.Chem.rdCoordGen.CoordGenParams property) terminalColors (rdkit.ML.Cluster.ClusterVis.VisOpts attribute) terminalPtRadScale (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder attribute) test1() (rdkit.Chem.Recap.TestCase method) test2() (rdkit.Chem.Recap.TestCase method) test3() (rdkit.Chem.Recap.TestCase method) testAmideRxn() (rdkit.Chem.Recap.TestCase method) testAmineRxn() (rdkit.Chem.Recap.TestCase method) testAromCAromCRxn() (rdkit.Chem.Recap.TestCase method) testAromNAliphCRxn() (rdkit.Chem.Recap.TestCase method) testAromNAromCRxn() (rdkit.Chem.Recap.TestCase method) TestCase (class in rdkit.Chem.PandasTools) (class in rdkit.Chem.Recap) Tester() (rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRanker method) testEsterRxn() (rdkit.Chem.Recap.TestCase method) testEtherRxn() (rdkit.Chem.Recap.TestCase method) testGithub1507() (rdkit.Chem.PandasTools.TestCase method) testGithub3701() (rdkit.Chem.PandasTools.TestCase method) testLactamNAliphCRxn() (rdkit.Chem.Recap.TestCase method) testMinFragmentSize() (rdkit.Chem.Recap.TestCase method) TestMolecule() (in module rdkit.Chem.ChemUtils.BulkTester) testOlefinRxn() (rdkit.Chem.Recap.TestCase method) testSFNetIssue1801871() (rdkit.Chem.Recap.TestCase method) testSFNetIssue1804418() (rdkit.Chem.Recap.TestCase method) testSFNetIssue1881803() (rdkit.Chem.Recap.TestCase method) testSulfonamideRxn() (rdkit.Chem.Recap.TestCase method) TestSupplier() (in module rdkit.Chem.ChemUtils.BulkTester) testUreaRxn() (rdkit.Chem.Recap.TestCase method) Tet_CCW (rdkit.Chem.rdchem.StereoDescriptor attribute) Tet_CW (rdkit.Chem.rdchem.StereoDescriptor attribute) TextFileToData() (in module rdkit.ML.Data.DataUtils) TextFileToDatabase() (in module rdkit.Dbase.DbUtils) TextToData() (in module rdkit.ML.Data.DataUtils) THREEANDAHALF (rdkit.Chem.rdchem.BondType attribute) THREECENTER (rdkit.Chem.rdchem.BondType attribute) threshold (rdkit.Chem.MolStandardize.rdMolStandardize.Is2DValidation property) Threshold (rdkit.Chem.rdFMCS.MCSParameters property) ThresholdScreener (class in rdkit.Chem.Fingerprints.SimilarityScreener) tiebreaker() (in module rdkit.Chem.fmcs.fmcs) timeout (rdkit.Chem.fmcs.fmcs.Default attribute)

Timeout (rdkit.Chem.rdFMCS.MCSParameters property) timeout (rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters property) timeoutString (rdkit.Chem.fmcs.fmcs.Default attribute) Timer (class in rdkit.Chem.fmcs.fmcs) ToBase64() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) ToBinary() (rdkit.Chem.rdchem.Mol method) (rdkit.Chem.rdchem.MolBundle method) (rdkit.Chem.rdChemReactions.ChemicalReaction method) (rdkit.Chem.rdTautomerQuery.TautomerQuery method) (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.IntSparseIntVect method) (rdkit.DataStructs.cDataStructs.LongSparseIntVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) (rdkit.DataStructs.cDataStructs.UIntSparseIntVect method) (rdkit.DataStructs.cDataStructs.ULongSparseIntVect method) ToBitString() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) ToList() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.IntSparseIntVect method) (rdkit.DataStructs.cDataStructs.LongSparseIntVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) (rdkit.DataStructs.cDataStructs.UIntSparseIntVect method) (rdkit.DataStructs.cDataStructs.ULongSparseIntVect method) topN (rdkit.Chem.BuildFragmentCatalog.RunDetails attribute) TopNContainer (class in rdkit.DataStructs.TopNContainer) TopNOverallPicker (class in rdkit.SimDivFilters.SimilarityPickers) TopNScreener (class in rdkit.Chem.Fingerprints.SimilarityScreener) TopologicalTorsion (rdkit.Chem.rdChemReactions.FingerprintType attribute) TopologicalTorsionFingerprintOptions (class in rdkit.Chem.rdFingerprintGenerator) TopologicalTorsionFP (rdkit.Chem.rdFingerprintGenerator.FPType attribute) torsionAtomCount (rdkit.Chem.rdFingerprintGenerator.TopologicalTorsionFingerprintOptions property) tossit() (in module rdkit.Chem.rdchem) ToStream() (rdkit.Chem.rdSubstructLibrary.SubstructLibrary method) TotalDegreeEqualsQueryAtom() (in module rdkit.Chem.rdqueries) TotalDegreeGreaterQueryAtom() (in module rdkit.Chem.rdqueries) TotalDegreeLessQueryAtom() (in module rdkit.Chem.rdqueries) totalEnergy (rdkit.Chem.rdEHTTools.EHTResults property) TotalValenceEqualsQueryAtom() (in module rdkit.Chem.rdqueries) TotalValenceGreaterQueryAtom() (in module rdkit.Chem.rdqueries) TotalValenceLessQueryAtom() (in module rdkit.Chem.rdqueries) TPSA() (in module rdkit.Chem.MolSurf) trackFailures (rdkit.Chem.rdDistGeom.EmbedParameters property) Trajectory (class in rdkit.Chem.rdtrajectory) Trans() (rdkit.Chem.rdMolAlign.O3A method) transform (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment attribute) transform() (rdkit.VLib.NodeLib.SmartsRemover.SmartsRemover method) TransformConformer() (in module rdkit.Chem.rdMolTransforms) transformed (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) transformed_set (rdkit.Avalon.pyAvalonTools.StruChkResult attribute) TransformMol() (in module rdkit.Chem.AllChem) (in module rdkit.Chem.Subshape.SubshapeAligner) TransformNode (class in rdkit.VLib.Transform) transformPoint() (rdkit.Chem.Draw.MolDrawing.MolDrawing method) TransformPoints() (in module rdkit.ML.Data.Stats) TranslateChiralFlagToStereoGroups() (in module rdkit.Chem.rdmolops) treatNonterminalBondsToMetalAsZOBs (rdkit.Chem.rdCoordGen.CoordGenParams property) Triangle (rdkit.Chem.FeatMaps.FeatMaps.FeatMapParams.FeatProfile attribute) triangleRMSTol (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner attribute) triangleSSD (rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment attribute) trigger_report() (rdkit.Chem.fmcs.fmcs.VerboseHeapOps method) TRIPLE (rdkit.Chem.rdchem.BondType attribute) tryEmbedding (rdkit.Chem.EnumerateStereoisomers.StereoEnumerationOptions attribute) TverskyIndex() (in module rdkit.Geometry.rdGeometry) TverskySimilarity() (in module rdkit.DataStructs.cDataStructs) TWOANDAHALF (rdkit.Chem.rdchem.BondType attribute) TWOBITVALUE (rdkit.DataStructs.cDataStructs.DiscreteValueType attribute) type (rdkit.Chem.rdchem.StereoInfo property) (rdkit.Chem.Scaffolds.rdScaffoldNetwork.NetworkEdge property) Type() (rdkit.Chem.rdChemReactions.EnumerationStrategyBase method) TypeAtoms() (in module rdkit.Chem.EState.AtomTypes) TypedFragment (class in rdkit.Chem.fmcs.fmcs) TypedMolecule (class in rdkit.Chem.fmcs.fmcs) TypeFinder() (in module rdkit.Dbase.DbUtils)

U

UFFAddAngleConstraint() (rdkit.ForceField.rdForceField.ForceField method) UFFAddDistanceConstraint() (rdkit.ForceField.rdForceField.ForceField method) UFFAddPositionConstraint() (rdkit.ForceField.rdForceField.ForceField method) UFFAddTorsionConstraint() (rdkit.ForceField.rdForceField.ForceField method) UFFGetMoleculeForceField() (in module rdkit.Chem.rdForceFieldHelpers) UFFHasAllMoleculeParams() (in module rdkit.Chem.rdForceFieldHelpers) UFFOptimizeMolecule() (in module rdkit.Chem.rdForceFieldHelpers) UFFOptimizeMoleculeConfs() (in module rdkit.Chem.rdForceFieldHelpers) UIntSparseIntVect (class in rdkit.DataStructs.cDataStructs) ULongSparseIntVect (class in rdkit.DataStructs.cDataStructs) uncharge() (rdkit.Chem.MolStandardize.rdMolStandardize.Uncharger method) unchargeInPlace() (rdkit.Chem.MolStandardize.rdMolStandardize.Uncharger method) Uncharger (class in rdkit.Chem.MolStandardize.rdMolStandardize) Unclassified (rdkit.Chem.rdFreeSASA.SASAClass attribute) UNCONSTRAINED_ANIONS (rdkit.Chem.rdchem.ResonanceFlags attribute) UNCONSTRAINED_CATIONS (rdkit.Chem.rdchem.ResonanceFlags attribute) UnfoldedRDKFingerprintCountBased() (in module rdkit.Chem.rdmolops) UniformGrid3D() (in module rdkit.Geometry.rdGeometry) UniformGrid3D_ (class in rdkit.Geometry.rdGeometry) UnimplementedCodeError UninstallIPythonRenderer() (in module rdkit.Chem.Draw.IPythonConsole) UninstallPandasTools() (in module rdkit.Chem.PandasTools) UNION (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeCombineOperations attribute) unique (rdkit.Chem.EnumerateStereoisomers.StereoEnumerationOptions attribute) Uniquer (class in rdkit.Chem.fmcs.fmcs) uniquify (rdkit.Chem.rdchem.SubstructMatchParameters property) Uniquify() (rdkit.DataStructs.VectCollection.VectCollection method) UniquifyCombinations() (in module rdkit.Chem.Pharm2D.Utils) UNKNOWN (rdkit.Chem.rdchem.AtomMonomerType attribute) (rdkit.Chem.rdchem.BondDir attribute) Unknown (rdkit.Chem.rdchem.StereoSpecified attribute) UnSetBit() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) UnSetBitsFromList() (rdkit.DataStructs.cDataStructs.ExplicitBitVect method) (rdkit.DataStructs.cDataStructs.SparseBitVect method) UnsignedLong_Vect (class in rdkit.rdBase) UNSPECIFIED (rdkit.Chem.rdchem.BondType attribute) (rdkit.Chem.rdchem.HybridizationType attribute) Unspecified (rdkit.Chem.rdchem.StereoSpecified attribute) (rdkit.Chem.rdchem.StereoType attribute) unspecifiedStereoIsUnknown (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) updateAtomPalette() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) UpdateDrawerParamsFromJSON() (in module rdkit.Chem.Draw.rdMolDraw2D)

updateExplicitCount (rdkit.Chem.rdmolops.RemoveHsParameters property) UpdateFromSequence() (rdkit.DataStructs.cDataStructs.IntSparseIntVect method) (rdkit.DataStructs.cDataStructs.LongSparseIntVect method) (rdkit.DataStructs.cDataStructs.UIntSparseIntVect method) (rdkit.DataStructs.cDataStructs.ULongSparseIntVect method) UpdateMolDrawOptionsFromJSON() (in module rdkit.Chem.Draw.rdMolDraw2D) UpdateParamsFromJSON() (in module rdkit.Chem.MolStandardize.rdMolStandardize) UpdatePharmacophoreBounds() (in module rdkit.Chem.Pharm3D.EmbedLib) UpdateProductsStereochemistry() (in module rdkit.Chem.rdChemReactions) UpdatePropertyCache() (rdkit.Chem.rdchem.Atom method) (rdkit.Chem.rdchem.Mol method) UpdateScaffoldNetwork() (in module rdkit.Chem.Scaffolds.rdScaffoldNetwork) UPGMA (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute) Usage() (in module rdkit.Chem.BuildFragmentCatalog) (in module rdkit.Chem.ChemUtils.TemplateExpand) (in module rdkit.Chem.Fingerprints.FingerprintMols) (in module rdkit.ML.Data.FindQuantBounds) (in module rdkit.ML.MLUtils.VoteImg) use2D (rdkit.Chem.rdFingerprintGenerator.AtomPairFingerprintOptions property) useAvalonAtomPalette() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) useBasicKnowledge (rdkit.Chem.rdDistGeom.EmbedParameters property) useBondOrder (rdkit.Chem.rdFingerprintGenerator.RDKitFingerprintOptions property) useBWAtomPalette() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) useCDKAtomPalette() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) useChirality (rdkit.Chem.rdchem.SubstructMatchParameters property) useComplexQueryAtomSymbols (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) useDefaultAtomPalette() (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions method) useEnhancedStereo (rdkit.Chem.rdchem.SubstructMatchParameters property) useExpTorsionAnglePrefs (rdkit.Chem.rdDistGeom.EmbedParameters property) useFraction (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) useGenericMatchers (rdkit.Chem.rdchem.SubstructMatchParameters property) useHCounts (rdkit.Chem.rdMolInterchange.JSONParseParameters property) useHs (rdkit.Chem.rdFingerprintGenerator.RDKitFingerprintOptions property) UseLarger (rdkit.Chem.FeatMaps.FeatMapUtils.MergeMethod attribute) useMacrocycle14config (rdkit.Chem.rdDistGeom.EmbedParameters property) useMacrocycleTorsions (rdkit.Chem.rdDistGeom.EmbedParameters property) useMolBlockWedging (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) useQueryQueryMatches (rdkit.Chem.rdchem.SubstructMatchParameters property) useRandomCoords (rdkit.Chem.rdDistGeom.EmbedParameters property) useRDKitExtensions (rdkit.Chem.rdMolInterchange.JSONWriteParameters property) useSmallRingTorsions (rdkit.Chem.rdDistGeom.EmbedParameters property) useStereoCareForBonds (rdkit.Chem.rdmolops.AdjustQueryParameters property) useSymmetryForPruning (rdkit.Chem.rdDistGeom.EmbedParameters property) UsingCoordGen (class in rdkit.Chem.rdDepictor)

V

valid() (rdkit.Chem.FeatMaps.FeatMapUtils.DirMergeMode class method) (rdkit.Chem.FeatMaps.FeatMapUtils.MergeMethod class method) (rdkit.Chem.FeatMaps.FeatMapUtils.MergeMetric class method) validate() (rdkit.Chem.MolStandardize.rdMolStandardize.ValidationMethod method) Validate() (rdkit.Chem.rdChemReactions.ChemicalReaction method) ValidateRDId() (in module rdkit.Dbase.StorageUtils) ValidateSmiles() (in module rdkit.Chem.MolStandardize.rdMolStandardize) VALIDATION (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) VALIDATION_ERROR (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) ValidationMethod (class in rdkit.Chem.MolStandardize.rdMolStandardize) value (rdkit.Chem.fmcs.fmcs.CangenNode attribute) values (rdkit.Avalon.pyAvalonTools.StruChkFlag attribute) (rdkit.Avalon.pyAvalonTools.StruChkResult attribute) (rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle attribute) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStage attribute) (rdkit.Chem.MolStandardize.rdMolStandardize.PipelineStatus attribute) (rdkit.Chem.MolStandardize.rdMolStandardize.TautomerEnumeratorStatus attribute) (rdkit.Chem.rdchem.AtomMonomerType attribute) (rdkit.Chem.rdchem.BondDir attribute) (rdkit.Chem.rdchem.BondStereo attribute) (rdkit.Chem.rdchem.BondType attribute) (rdkit.Chem.rdchem.ChiralType attribute) (rdkit.Chem.rdchem.CompositeQueryType attribute) (rdkit.Chem.rdchem.HybridizationType attribute) (rdkit.Chem.rdchem.PropertyPickleOptions attribute) (rdkit.Chem.rdchem.ResonanceFlags attribute) (rdkit.Chem.rdchem.StereoDescriptor attribute) (rdkit.Chem.rdchem.StereoGroupType attribute) (rdkit.Chem.rdchem.StereoSpecified attribute) (rdkit.Chem.rdchem.StereoType attribute) (rdkit.Chem.rdChemReactions.FingerprintType attribute) (rdkit.Chem.rdChemReactions.SanitizeFlags attribute) (rdkit.Chem.rdDistGeom.EmbedFailureCauses attribute) (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) (rdkit.Chem.rdFingerprintGenerator.FPType attribute) (rdkit.Chem.rdFMCS.AtomCompare attribute) (rdkit.Chem.rdFMCS.BondCompare attribute) (rdkit.Chem.rdFMCS.RingCompare attribute) (rdkit.Chem.rdFreeSASA.SASAAlgorithm attribute) (rdkit.Chem.rdFreeSASA.SASAClass attribute) (rdkit.Chem.rdFreeSASA.SASAClassifier attribute) (rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions attribute) (rdkit.Chem.rdMolEnumerator.EnumeratorType attribute) (rdkit.Chem.rdmolfiles.CXSmilesFields attribute) (rdkit.Chem.rdmolfiles.RestoreBondDirOption attribute) (rdkit.Chem.rdMolHash.HashFunction attribute) (rdkit.Chem.rdmolops.AdjustQueryWhichFlags attribute) (rdkit.Chem.rdmolops.AromaticityModel attribute) (rdkit.Chem.rdmolops.MolzipLabel attribute) (rdkit.Chem.rdmolops.SanitizeFlags attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupCoreAlignment attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupLabelling attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupLabels attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupMatching attribute) (rdkit.Chem.rdRGroupDecomposition.RGroupScore attribute) (rdkit.Chem.Scaffolds.rdScaffoldNetwork.EdgeType attribute) (rdkit.DataStructs.cDataStructs.DiscreteValueType attribute) (rdkit.ML.InfoTheory.rdInfoTheory.InfoType attribute) (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute)

values() (rdkit.Chem.MolStandardize.rdMolStandardize.SmilesTautomerMap method) variableAtomRadius (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) variableBondWidthMultiplier (rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions property) VectCollection (class in rdkit.DataStructs.VectCollection) VectFilterMatch (class in rdkit.Chem.rdfiltercatalog) VectIter (class in rdkit) VectMolVect (class in rdkit.Chem.rdChemReactions) vector (rdkit.Chem.rdchem.SubstanceGroupCState property) VectorDescriptorNamespace (class in rdkit.Chem.ChemUtils.DescriptorUtilities) VectorDescriptorWrapper (class in rdkit.Chem.ChemUtils.DescriptorUtilities) VectorOfStringVectors (class in rdkit.rdBase) verbose (rdkit.Chem.rdDistGeom.EmbedParameters property) Verbose (rdkit.Chem.rdFMCS.MCSParameters property) VerboseCachingTargetsMatcher (class in rdkit.Chem.fmcs.fmcs) VerboseHeapOps (class in rdkit.Chem.fmcs.fmcs) version (rdkit.Chem.rdMolDescriptors.AtomPairsParameters attribute) VisOpts (class in rdkit.ML.Cluster.ClusterVis) VLibNode (class in rdkit.VLib.Node) VoteAndBuildImage() (in module rdkit.ML.MLUtils.VoteImg) VSA_EState1() (in module rdkit.Chem.EState.EState_VSA) VSA_EState10() (in module rdkit.Chem.EState.EState_VSA) VSA_EState2() (in module rdkit.Chem.EState.EState_VSA) VSA_EState3() (in module rdkit.Chem.EState.EState_VSA) VSA_EState4() (in module rdkit.Chem.EState.EState_VSA) VSA_EState5() (in module rdkit.Chem.EState.EState_VSA) VSA_EState6() (in module rdkit.Chem.EState.EState_VSA) VSA_EState7() (in module rdkit.Chem.EState.EState_VSA) VSA_EState8() (in module rdkit.Chem.EState.EState_VSA) VSA_EState9() (in module rdkit.Chem.EState.EState_VSA) VSA_EState_() (in module rdkit.Chem.EState.EState_VSA)

W

WARD (rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod attribute) warning() (in module rdkit.Chem.Suppliers.DbMolSupplier) (rdkit.RDLogger.logger method) WasCanceled() (rdkit.Chem.rdchem.ResonanceMolSupplier method) WedgeBond() (in module rdkit.Chem.rdmolops) wedgeDashedBonds (rdkit.Chem.Draw.MolDrawing.DrawingOptions attribute) WedgeMolBonds() (in module rdkit.Chem.rdmolops) wedgeTwoBondsIfPossible (rdkit.Chem.rdmolops.BondWedgingParameters property) weight (rdkit.Chem.FeatMaps.FeatMapPoint.FeatMapPoint attribute) WeightedAverage (rdkit.Chem.FeatMaps.FeatMapUtils.MergeMethod attribute) Weights() (rdkit.Chem.rdMolAlign.O3A method) weights_max() (in module rdkit.Chem.QED) weights_mean() (in module rdkit.Chem.QED) weights_none() (in module rdkit.Chem.QED) width (rdkit.Chem.FeatMaps.FeatMaps.FeatMapParams attribute)

Width() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D method) winRad (rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder attribute) wordSize (rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions attribute) WrapLogs() (in module rdkit.rdBase) write() (rdkit.Chem.rdmolfiles.MaeWriter method) (rdkit.Chem.rdmolfiles.PDBWriter method) (rdkit.Chem.rdmolfiles.SDWriter method) (rdkit.Chem.rdmolfiles.SmilesWriter method) (rdkit.Chem.rdmolfiles.TDTWriter method) WriteData() (in module rdkit.ML.Data.DataUtils) WriteDrawingText() (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo method) WriteGridToFile() (in module rdkit.Geometry.rdGeometry) WritePickledData() (in module rdkit.ML.Data.DataUtils) WriteSDF() (in module rdkit.Chem.PandasTools) WriteTopBitsToFile() (rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRanker method)

X

x (rdkit.Geometry.rdGeometry.Point2D property) (rdkit.Geometry.rdGeometry.Point3D property)

XAtomQueryAtom() (in module rdkit.Chem.rdqueries) XHAtomQueryAtom() (in module rdkit.Chem.rdqueries) xOffset (rdkit.ML.Cluster.ClusterVis.VisOpts attribute)

Y

y (rdkit.Geometry.rdGeometry.Point2D property) (rdkit.Geometry.rdGeometry.Point3D property)

yOffset (rdkit.ML.Cluster.ClusterVis.VisOpts attribute)

Z

z (rdkit.Geometry.rdGeometry.Point3D property) ZERO (rdkit.Chem.rdchem.BondType attribute)

ZINC (rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs attribute) Zoom() (rdkit.Chem.PyMol.MolViewer method)