RDKit: Class Members

| RDKit Open-source cheminformatics and machine learning.

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Here is a list of all class members with links to the classes they belong to:

### - a -

- a : RDKit::DrawColour, RDKit::RascalMCES::RascalClusterOptions, RDKit::RDTypeTag::detail::Value
- A_i : ForceFields::MMFF::MMFFVdW
- a_ij : ForceFields::MMFF::MMFFHerschbachLaurie
- abbrev : RDKit::Abbreviations::AbbreviationMatch
- abbreviation : RDKit::Deprotect::DeprotectData
- AbbreviationMatch() : RDKit::Abbreviations::AbbreviationMatch
- acceptFailure : RDDepict::ConstrainedDepictionParams
- accumulateVotes() : RDInfoTheory::InfoBitRanker
- AcidBaseCatalogEntry() : RDKit::MolStandardize::AcidBaseCatalogEntry
- AcidBaseCatalogParams() : RDKit::MolStandardize::AcidBaseCatalogParams
- acidbaseData : RDKit::MolStandardize::CleanupParameters
- acidbaseFile : RDKit::MolStandardize::CleanupParameters
- AcidicAtoms : RDKit::StructureCheck::StructCheckerOptions
- AcidityLimit : RDKit::StructureCheck::StructCheckerOptions
- activeAtmIdxOffset_ : RDKit::MolDraw2D_detail::DrawMol
- activeBndIdxOffset_ : RDKit::MolDraw2D_detail::DrawMol
- add() : RDKit::CIPLabeler::Node, RDKit::CIPLabeler::PairList, RDKit::CIPLabeler::Rules, RDKit::FMCS::DuplicatedSeedCache, RDKit::FMCS::SeedSet, RDKit::FMCS::SubstructureCache, RDKit::RGroupData, RDKit::RGroupDecompData::UsedLabels, RDKit::RGroupDecomposition
- addAgentTemplate() : RDKit::ChemicalReaction
- addAll() : RDKit::CIPLabeler::PairList
- addAtom() : RDKit::FMCS::DuplicatedSeedCache::TKey, RDKit::FMCS::Graph, RDKit::FMCS::Seed, RDKit::RWMol
- addAtomIndices : RDKit::MolDrawOptions
- addAtoms() : RDKit::RGroupDecompData
- addAtomWithBookmark() : RDKit::SubstanceGroup
- addAtomWithIdx() : RDKit::SubstanceGroup
- addAttachPoint() : RDKit::SubstanceGroup
- addBinary() : RDKit::CachedMolHolder
- addBond() : RDKit::FMCS::DuplicatedSeedCache::TKey, RDKit::FMCS::Graph, RDKit::FMCS::Seed, RDKit::RWMol
- addBondIndices : RDKit::MolDrawOptions
- addBondWithBookmark() : RDKit::SubstanceGroup
- addBondWithIdx() : RDKit::SubstanceGroup
- addBracket() : RDKit::SubstanceGroup
- addCatalog() : RDKit::FilterCatalogParams
- addChild() : Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >, RDKit::FilterHierarchyMatcher
- addConformer() : RDKit::ROMol
- addConformersToMol() : RDKit::Trajectory
- addContrib() : DistGeom::ChiralViolationContribs, DistGeom::DistViolationContribs, DistGeom::FourthDimContribs, ForceFields::AngleConstraintContribs, ForceFields::CrystalFF::TorsionAngleContribs, ForceFields::DistanceConstraintContribs, ForceFields::UFF::InversionContribs
- addCoords : RDKit::MolOps::AddHsParameters
- addCore() : RDKit::RGroupDecompData
- addCoreUserLabels() : RDKit::RGroupDecompData
- addCState() : RDKit::SubstanceGroup
- addCustomPropHandler() : RDKit::MolPickler
- addDummyAtomsToUnlabelledCoreAtoms() : RDKit::RGroupDecompositionParameters
- addEdge() : RDCatalog::HierarchCatalog< entryType, paramType, orderType >
- addEntry() : RDCatalog::Catalog< entryType, paramType >, RDCatalog::HierarchCatalog< entryType, paramType, orderType >, RDKit::FilterCatalog
- addFeatureDef() : RDKit::MolChemicalFeatureFactory
- addFingerprint() : RDKit::FPHolderBase
- addFP : RDKit::SynthonSpaceSearch::SynthonSpaceFPHitSet
- addFragsFromMol() : RDKit::FragCatGenerator
- additionalAtomLabelPadding : RDKit::MolDrawOptions
- additionalOutput : RDKit::FingerprintFuncArguments
- addKey() : RDKit::KeyFromPropHolder, RDKit::KeyHolderBase
- addMol() : RDKit::CachedMolHolder, RDKit::CachedSmilesMolHolder, RDKit::CachedTrustedSmilesMolHolder, RDKit::FixedMolSizeMolBundle, RDKit::FPHolderBase, RDKit::KeyFromPropHolder, RDKit::KeyHolderBase, RDKit::MolBundle, RDKit::MolHolder, RDKit::MolHolderBase, RDKit::SubstructLibrary
- addMoleculeMetadata() : RDKit::MolDraw2DSVG
- addNode() : RDKit::CIPLabeler::Digraph
- addNoLineArcs() : RDKit::MolDraw2D_detail::DrawMolMCHLasso
- addNonRingAtom() : RDDepict::EmbeddedFrag
- addParentAtomWithBookmark() : RDKit::SubstanceGroup
- addParentAtomWithIdx() : RDKit::SubstanceGroup
- addPattern() : RDKit::ExclusionList
- addPoint() : RDFeatures::ImplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE >
- addProductTemplate() : RDKit::ChemicalReaction
- addReactantTemplate() : RDKit::ChemicalReaction
- addReactionToPool() : RDKit::SynthonSpaceSearch::SynthonSpace
- addReader() : RDKit::MultiFPBReader
- addResidueInfo : RDKit::MolOps::AddHsParameters
- addRgroupData() : RDKit::VarianceDataForLabel
- addRing() : RDKit::RingInfo
- addRingSystemTemplates() : RDDepict::CoordinateTemplates
- addSgroupsToPtree() : RDKit::MarvinMolBase
- addSmiles() : RDKit::CachedSmilesMolHolder, RDKit::CachedTrustedSmilesMolHolder
- addSnapshot() : RDKit::Trajectory
- addStereoAnnotation : RDKit::MolDrawOptions
- addSynthon() : RDKit::SynthonSpaceSearch::SynthonSet
- addSynthonToPool() : RDKit::SynthonSpaceSearch::SynthonSpace
- addTerm() : ForceFields::MMFF::AngleBendContrib, ForceFields::MMFF::BondStretchContrib, ForceFields::MMFF::EleContrib, ForceFields::MMFF::NonbondedContrib, ForceFields::MMFF::OopBendContrib, ForceFields::MMFF::StretchBendContrib, ForceFields::MMFF::TorsionAngleContrib, ForceFields::MMFF::VdWContrib
- addVarianceData() : RDKit::FingerprintVarianceScoreData
- adjustBondEndsForLabels() : RDKit::MolDraw2D_detail::DrawMol
- adjustBondsOnSolidWedgeEnds() : RDKit::MolDraw2D_detail::DrawMol
- adjustCharges : RDKit::MolStandardize::MetalDisconnectorOptions
- adjustColons() : RDKit::MolDraw2D_detail::AtomSymbol
- adjustConjugatedFiveRings : RDKit::MolOps::AdjustQueryParameters
- adjustDegree : RDKit::MolOps::AdjustQueryParameters
- adjustDegreeFlags : RDKit::MolOps::AdjustQueryParameters
- adjustHeavyDegree : RDKit::MolOps::AdjustQueryParameters
- adjustHeavyDegreeFlags : RDKit::MolOps::AdjustQueryParameters
- adjustLineEndForHighlight() : RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine
- adjustLineForString() : RDKit::MolDraw2D_detail::DrawText
- adjustMolBlockWedging : RDDepict::ConstrainedDepictionParams
- AdjustQueryParameters() : RDKit::MolOps::AdjustQueryParameters
- adjustRingChain : RDKit::MolOps::AdjustQueryParameters
- adjustRingChainFlags : RDKit::MolOps::AdjustQueryParameters
- adjustRingCount : RDKit::MolOps::AdjustQueryParameters
- adjustRingCountFlags : RDKit::MolOps::AdjustQueryParameters
- adjustSingleBondsBetweenAromaticAtoms : RDKit::MolOps::AdjustQueryParameters
- adjustSingleBondsToDegreeOneNeighbors : RDKit::MolOps::AdjustQueryParameters
- adjustStringRectsForSuperSubScript() : RDKit::MolDraw2D_detail::DrawText
- adjustToRemovedAtom() : RDKit::SubstanceGroup
- adjustToRemovedBond() : RDKit::SubstanceGroup
- agents : RDKit::MarvinReaction
- agentWeight : RDKit::ReactionFingerprintParams
- aid : RDDepict::EmbeddedAtom
- aIdx : RDKit::SubstanceGroup::AttachPoint
- ALIAS_CONVERSION_FAILED : RDKit::StructureCheck::StructChecker
- align() : RDKit::MolAlign::O3A
- align_ : RDKit::MolDraw2D_detail::DrawAnnotation
- alignCoordinates : RDKit::MolzipParams
- alignment : RDKit::RGroupDecompositionParameters
- alignOnly : RDDepict::ConstrainedDepictionParams
- alignString() : RDKit::MolDraw2D_detail::DrawText, RDKit::MolDraw2D_detail::DrawTextNotFT
- ALL : RDKit::FilterCatalogParams
- allBestMCESs : RDKit::RascalMCES::RascalOptions
- allBondsExplicit : RDKit::SmilesWriteParams
- allHsExplicit : RDKit::SmilesWriteParams
- allocateAtomCounts() : RDKit::AdditionalOutput
- allocateAtomsPerBit() : RDKit::AdditionalOutput
- allocateAtomToBits() : RDKit::AdditionalOutput
- allocateBitInfoMap() : RDKit::AdditionalOutput
- allocateBitPaths() : RDKit::AdditionalOutput
- ALLOW_CHARGE_SEPARATION : RDKit::ResonanceMolSupplier
- ALLOW_INCOMPLETE_OCTETS : RDKit::ResonanceMolSupplier
- allowAromaticBondType : RDKit::MolStandardize::FeaturesValidation, RDKit::MolStandardize::PipelineOptions
- allowAtomAliases : RDKit::MolStandardize::FeaturesValidation
- allowAtomBondClashExemption : RDKit::MolStandardize::Layout2DValidation, RDKit::MolStandardize::PipelineOptions
- allowCXSMILES : RDKit::v1::SmartsParserParams, RDKit::v1::SmilesParserParams, RDKit::v2::ReactionParser::ReactionSmartsParserParams, RDKit::v2::SmilesParse::SmartsParserParams, RDKit::v2::SmilesParse::SmilesParserParams
- allowDativeBondType : RDKit::MolStandardize::FeaturesValidation, RDKit::MolStandardize::PipelineOptions
- allowDummies : RDKit::MolStandardize::FeaturesValidation
- AllowedAtomsValidation() : RDKit::MolStandardize::AllowedAtomsValidation
- allowEmptyMolecules : RDKit::MolStandardize::PipelineOptions, RDKit::MolStandardize::RDKitValidation
- allowEnhancedStereo : RDKit::MolStandardize::FeaturesValidation, RDKit::MolStandardize::PipelineOptions
- allowLongBondsInRings : RDKit::MolStandardize::Layout2DValidation, RDKit::MolStandardize::PipelineOptions
- allowMultipleCoresInSameMol : RDKit::RGroupDecompositionParameters
- allowMultipleRGroupsOnUnlabelled : RDKit::RGroupDecompositionParameters
- allowNonTerminalRGroups : RDKit::RGroupDecompositionParameters
- allowQueries : RDKit::MolStandardize::FeaturesValidation
- allowRGroups : RDDepict::ConstrainedDepictionParams
- Alpha : RDKit::StructureCheck::StructCheckerOptions
- alpha_i : ForceFields::MMFF::MMFFVdW
- alpha_inc_used : RDKit::StructureCheck::IncEntry
- AlphaInc : RDKit::StructureCheck::IncEntry
- AlphaPathTable : RDKit::StructureCheck::StructCheckerOptions
- And() : RDKit::FilterMatchOps::And
- AndQuery() : Queries::AndQuery< MatchFuncArgType, DataFuncArgType, needsConversion >
- ang1_ : RDKit::MolDraw2D_detail::DrawShapeArc
- ang2_ : RDKit::MolDraw2D_detail::DrawShapeArc
- angle : RDDepict::EmbeddedAtom
- angle1 : RDKit::MolDraw2D_detail::LinePair
- angle2 : RDKit::MolDraw2D_detail::LinePair
- angle_ : RDKit::MolDraw2D_detail::DrawShapeArrow
- AngleBendContrib() : ForceFields::MMFF::AngleBendContrib, ForceFields::UFF::AngleBendContrib
- AngleConstraintContrib() : ForceFields::AngleConstraintContrib
- AngleConstraintContribs() : ForceFields::AngleConstraintContribs
- AngleConstraintContribsParams() : ForceFields::AngleConstraintContribsParams
- angles : ForceFields::CrystalFF::CrystalFFDetails
- angleTo() : Point2D, RDGeom::Point2D, RDGeom::Point3D, RDGeom::PointND
- annotateProperties() : RDKit::Descriptors::Properties
- annotationColour : RDKit::MolDrawOptions
- annotationFontScale : RDKit::MolDrawOptions
- annotations_ : RDKit::MolDraw2D_detail::DrawMol
- AnyOverLappingAtoms() : RDKit::MarvinMolBase
- append() : RDKit::MolAlign::O3AConstraintVect, RDKit::MolStandardize::PipelineResult
- ApplyMask : RDKit::RDValue
- ApplyPtrMask : RDKit::RDValue
- applyTautomer() : RDKit::StructureCheck::StructCheckTautomer
- approxSimilarityAdjuster : RDKit::SynthonSpaceSearch::SynthonSpaceSearchParams
- areAtomsInSameRing() : RDKit::RingInfo
- areAtomsInSameRingOfSize() : RDKit::RingInfo
- areBondsInSameRing() : RDKit::RingInfo
- areBondsInSameRingOfSize() : RDKit::RingInfo
- areRingsFused() : RDKit::RingInfo
- arom : ForceFields::MMFF::MMFFProp
- AROMATIC : RDKit::Bond
- AromaticAtomIterator_() : RDKit::AromaticAtomIterator_< Atom_, Mol_ >
- aromaticMatchesConjugated : RDKit::SubstructMatchParameters
- aromaticMatchesSingleOrDouble : RDKit::SubstructMatchParameters
- aromatizeIfPossible : RDKit::MolOps::AdjustQueryParameters
- arrow : RDKit::MarvinReaction
- assertValidTemplate() : RDDepict::CoordinateTemplates
- assessRingFormers() : RDKit::SynthonSpaceSearch::SynthonSet
- assign() : RDNumeric::Matrix< TYPE >, RDNumeric::Vector< TYPE >
- assignConnectorsUsed() : RDKit::SynthonSpaceSearch::SynthonSet
- at() : RDKit::FMCS::TArray2D< T >, RDKit::MolStandardize::TautomerEnumeratorResult
- at1Cds_ : RDKit::MolDraw2D_detail::DrawShapeDashedWedge
- at2AtomicNum : ForceFields::UFF::InversionContribsParams
- atCds_ : RDKit::MolDraw2D_detail::DrawMol
- atEnd() : RDKit::ResonanceMolSupplier, RDKit::v1::MolSupplier, RDKit::v2::FileParsers::ForwardSDMolSupplier, RDKit::v2::FileParsers::MolSupplier, RDKit::v2::FileParsers::SDMolSupplier, RDKit::v2::FileParsers::SmilesMolSupplier, RDKit::v2::FileParsers::TDTMolSupplier
- atIdx_ : RDKit::MolDraw2D_detail::AtomSymbol
- atno : ForceFields::MMFF::MMFFProp
- Atom() : RDKit::Atom
- atom : RDKit::Canon::canon_atom, RDKit::Canon::MolStackUnion, RDKit::MarvinAttachmentPoint, RDKit::MolDraw2D_detail::LinePair
- atom1_ : RDKit::MolDraw2D_detail::DrawShape
- atom1Label : RDKit::MolFragmenter::FragmenterBondType
- atom1Type : RDKit::MolFragmenter::FragmenterBondType
- atom2_ : RDKit::MolDraw2D_detail::DrawShape
- atom2Label : RDKit::MolFragmenter::FragmenterBondType
- atom2Type : RDKit::MolFragmenter::FragmenterBondType
- ATOM_CHARGE : RDKit::MolPickler
- ATOM_CHECK_FAILED : RDKit::StructureCheck::StructChecker
- ATOM_CHIRALTAG : RDKit::MolPickler
- ATOM_CLASH : RDKit::StructureCheck::StructChecker
- ATOM_DUMMYLABEL : RDKit::MolPickler
- ATOM_INDEX : RDKit::MolPickler
- ATOM_ISAROMATIC : RDKit::MolPickler
- ATOM_MAPNUMBER : RDKit::MolPickler
- ATOM_MASS : RDKit::MolPickler
- ATOM_NEXPLICIT : RDKit::MolPickler
- ATOM_NUMBER : RDKit::MolPickler
- ATOM_PDB_RESIDUE_ALTLOC : RDKit::MolPickler
- ATOM_PDB_RESIDUE_CHAINID : RDKit::MolPickler
- ATOM_PDB_RESIDUE_INSERTIONCODE : RDKit::MolPickler
- ATOM_PDB_RESIDUE_ISHETEROATOM : RDKit::MolPickler
- ATOM_PDB_RESIDUE_OCCUPANCY : RDKit::MolPickler
- ATOM_PDB_RESIDUE_RESIDUENAME : RDKit::MolPickler
- ATOM_PDB_RESIDUE_RESIDUENUMBER : RDKit::MolPickler
- ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE : RDKit::MolPickler
- ATOM_PDB_RESIDUE_SEGMENTNUMBER : RDKit::MolPickler
- ATOM_PDB_RESIDUE_SERIALNUMBER : RDKit::MolPickler
- ATOM_PDB_RESIDUE_TEMPFACTOR : RDKit::MolPickler
- ATOM_POS : RDKit::MolPickler
- AtomAcidity : RDKit::StructureCheck::StructCheckerOptions
- atomBonds() : RDKit::ROMol
- atomClashLimit : RDKit::MolStandardize::PipelineOptions
- atomColourPalette : RDKit::MolDrawOptions
- AtomCompareCalls : RDKit::FMCS::ExecStatistics
- AtomCompareFunctor() : RDKit::Canon::AtomCompareFunctor
- AtomCompareParameters : RDKit::MCSParameters
- atomCoords() : RDKit::MolDraw2D
- AtomCoordsMatchFunctor() : RDKit::AtomCoordsMatchFunctor
- atomCounts : RDKit::AdditionalOutput
- atomCountsType : RDKit::AdditionalOutput
- AtomFlipper() : RDKit::EnumerateStereoisomers::details::AtomFlipper
- AtomFunctorCalls : RDKit::FMCS::ExecStatistics
- atomHighlightsAreCircles : RDKit::MolDrawOptions
- atomicData() : RDKit::atomicData
- AtomicNum() : RDKit::atomicData
- atomicNums_ : RDKit::MolDraw2D_detail::DrawMol
- AtomIterator_() : RDKit::AtomIterator_< Atom_, Mol_ >
- AtomKekulizeException() : RDKit::AtomKekulizeException
- atomLabelDeuteriumTritium : RDKit::MolDrawOptions
- atomLabels : RDKit::MolDrawOptions
- atomLabels_ : RDKit::MolDraw2D_detail::DrawMol
- atomMapping : RDKit::SubsetInfo
- AtomMatchTable : RDKit::FMCS::Target
- atomMembers() : RDKit::RingInfo
- AtomMonomerInfo() : RDKit::AtomMonomerInfo
- AtomMonomerType : RDKit::AtomMonomerInfo
- atomNeighbors() : RDKit::ROMol
- atomNoteColour : RDKit::MolDrawOptions
- atomNums : ForceFields::CrystalFF::CrystalFFDetails
- AtomPairArguments() : RDKit::AtomPair::AtomPairArguments
- AtomPairAtomEnv() : RDKit::AtomPair::AtomPairAtomEnv< OutputType >
- AtomPairAtomInvGenerator() : RDKit::AtomPair::AtomPairAtomInvGenerator
- atomPairs : RDKit::FilterMatch
- AtomPDBResidueInfo() : RDKit::AtomPDBResidueInfo
- atomProperties : RDKit::SubstructMatchParameters
- atomProperty : RDKit::MolzipParams
- AtomPtrContainer : RDKit::MolChemicalFeature
- AtomPtrContainer_CI : RDKit::MolChemicalFeature
- atomRefInAtoms() : RDKit::MarvinMolBase
- atomRefs2 : RDKit::MarvinBond
- atomRegions : RDKit::MolDrawOptions
- AtomRingQuery() : RDKit::AtomRingQuery
- atomRings() : RDKit::RingInfo
- atomRingSizes() : RDKit::RingInfo
- Atoms : RDKit::FMCS::MolFragment, RDKit::StructureCheck::Neighbourhood
- atoms() : RDKit::CIPLabeler::CIPMol, RDKit::MarvinMolBase, RDKit::MarvinStereoGroup, RDKit::ROMol
- AtomSanitizeException() : RDKit::AtomSanitizeException
- atomsPerBit : RDKit::AdditionalOutput
- atomsPerBitType : RDKit::AdditionalOutput
- AtomSymbol() : RDKit::MolDraw2D_detail::AtomSymbol, RDKit::StructureCheck::AugmentedAtom, RDKit::StructureCheck::IncEntry, RDKit::StructureCheck::Ligand
- atomSymbols : RDKit::MolzipParams
- atomSyms() : RDKit::MolDraw2D
- atomSyms_ : RDKit::MolDraw2D_detail::DrawMol
- atomToBits : RDKit::AdditionalOutput
- atomToBitsType : RDKit::AdditionalOutput
- AtomTyper : RDKit::MCSParameters
- AtomTypeScheme : RDKit::MolAlign::O3A
- AtomValenceException() : RDKit::AtomValenceException
- AtropisomerBond() : RDKit::CIPLabeler::AtropisomerBond
- AtropisomerFlipper() : RDKit::EnumerateStereoisomers::details::AtropisomerFlipper
- attachmentPoints : RDKit::MarvinSuperatomSgroup
- attachments : RDKit::RGroupData
- AttribType() : RDKit::SLNParse::AttribType
- AugmentedAtom() : RDKit::StructureCheck::AugmentedAtom
- AugmentedAtomPairs : RDKit::StructureCheck::StructCheckerOptions
- autoGetLabels() : RDKit::RGroupDecompositionParameters