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

### - c -

- CachedMolHolder() : RDKit::CachedMolHolder
- CachedSmilesMolHolder() : RDKit::CachedSmilesMolHolder
- CachedTrustedSmilesMolHolder() : RDKit::CachedTrustedSmilesMolHolder
- calcAnnotationPosition() : RDKit::MolDraw2D_detail::DrawMol
- calcCanonicalRotation() : RDKit::GaussianShape::ShapeInput
- calcCanonicalTranslation() : RDKit::GaussianShape::ShapeInput
- calcCentre() : RDKit::MolDraw2D_detail::StringRect
- calcCorners() : RDKit::MolDraw2D_detail::StringRect
- calcDoubleBondLines() : RDKit::MolDraw2D_detail::DrawMol
- calcEigenValues() : RDKit::GaussianShape::ShapeInput
- calcEnergy() : ForceFields::ForceField, RDMIF::VdWaals
- calcExplicitValence() : RDKit::Atom
- calcExtremes() : RDKit::GaussianShape::ShapeInput
- calcGlyphBBox() : RDKit::MolDraw2D_detail::DrawTextFT
- calcGrad() : ForceFields::ForceField
- calcImplicitValence() : RDKit::Atom
- calcMeanBondLength() : RDKit::MolDraw2D_detail::DrawMol
- calcMetricMatrix() : RDDataManip::MetricMatrixCalc< vectType, entryType >
- calcMomentsOfInertia() : RDKit::GaussianShape::ShapeInput
- calcRadicalRect() : RDKit::MolDraw2D_detail::DrawMol
- calcScores() : RDKit::GaussianShape::SingleConformerAlignment
- calcSymbolEllipse() : RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine
- calcTripleBondLines() : RDKit::MolDraw2D_detail::DrawMol
- calculateScale() : RDKit::MolDraw2D_detail::DrawMol
- calcVolumeAndGradients() : RDKit::GaussianShape::SingleConformerAlignment
- canGrowBiggerThan() : RDKit::FMCS::Seed
- canonicalize() : RDKit::MolStandardize::TautomerEnumerator
- canonicalizeInPlace() : RDKit::MolStandardize::TautomerEnumerator
- canonicalizeOrientation() : RDDepict::EmbeddedFrag
- canSerialize() : RDKit::CustomPropHandler, RDKit::DataStructsExplicitBitVecPropHandler
- CaptureErrorLog() : RDLog::CaptureErrorLog
- CaptureLog() : RDLog::CaptureLog
- CartesianProduct() : RDKit::CartesianProduct
- CartesianProductStrategy() : RDKit::CartesianProductStrategy
- Catalog() : RDCatalog::Catalog< entryType, paramType >
- CDXMLParserParams() : RDKit::v2::CDXMLParser::CDXMLParserParams
- changeRoot() : RDKit::CIPLabeler::Digraph
- changeToDrawCoords() : RDKit::MolDraw2D_detail::DrawMol
- ChargeCorrection() : RDKit::MolStandardize::ChargeCorrection
- ChargeFix() : RDKit::StructureCheck::ChargeFix
- checkAllBondsToAttachmentPointPresent() : RDKit::RCore
- checkAllBondsToRGroupPresent() : RDKit::RCore
- checkedAtomBonds() : RDKit::ROMol
- checkedAtomNeighbors() : RDKit::ROMol
- checkedAtoms() : RDKit::ROMol
- checkedBonds() : RDKit::ROMol
- checkForEnd() : RDKit::v2::FileParsers::ForwardSDMolSupplier
- checkIfMatchAndAppend() : RDKit::FMCS::MaximumCommonSubgraph
- checkIterator() : RDKit::CXXAtomIterator< Graph, Vertex, Iterator, CheckedAtoms, CheckedBonds >::CXXAtomIter
- checkMolStructure() : RDKit::StructureCheck::StructChecker
- checkValid() : DistGeom::BoundsMatrix
- ChemicalFeature() : ChemicalFeatures::ChemicalFeature
- ChemicalReaction() : RDKit::ChemicalReaction
- ChemicalReactionException() : RDKit::ChemicalReactionException
- ChemicalReactionParserException() : RDKit::ChemicalReactionParserException
- ChiralAtomCompareFunctor() : RDKit::Canon::ChiralAtomCompareFunctor
- ChiralSet() : DistGeom::ChiralSet
- ChiralViolationContribs() : DistGeom::ChiralViolationContribs
- ChiralViolationContribsParams() : DistGeom::ChiralViolationContribsParams
- choose() : RDKit::MolStandardize::LargestFragmentChooser
- chooseInPlace() : RDKit::MolStandardize::LargestFragmentChooser
- chromosomeLength() : RDKit::RGroupGa
- CIPMol() : RDKit::CIPLabeler::CIPMol
- CIPMolIter() : RDKit::CIPLabeler::CIPMolSpan< T, U >::CIPMolIter
- CIPMolSpan() : RDKit::CIPLabeler::CIPMolSpan< T, U >
- cleanup() : RDKit::Dict::Pair, RDKit::FPBReader
- cleanup_rdvalue() : RDKit::RDValue
- cleanUpNumbering() : RDKit::MarvinMolBase
- cleanUpNumberingMolsAtomsBonds() : RDKit::MarvinMolBase, RDKit::MarvinSuperatomSgroup
- CleanupParameters() : RDKit::MolStandardize::CleanupParameters
- cleanUpSgNumbering() : RDKit::MarvinMolBase
- clear() : Queries::SetQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, RDKit::FingerprintVarianceScoreData, RDKit::FMCS::DuplicatedSeedCache, RDKit::FMCS::SeedSet, RDKit::FMCS::TargetMatch, RDKit::FMCS::TArray2D< T >, RDKit::RDProps, RDKit::RWMol, RDKit::StructureCheck::StructCheckerOptions, RDKit::Trajectory
- clearAllAtomBookmarks() : RDKit::ROMol
- clearAllBondBookmarks() : RDKit::ROMol
- clearAtomBookmark() : RDKit::ROMol
- clearAttachPoints() : RDKit::SubstanceGroup
- clearBits() : BitVect, ExplicitBitVect, SparseBitVect
- clearBondBookmark() : RDKit::ROMol
- clearBrackets() : RDKit::SubstanceGroup
- clearCache() : RDKit::MolChemicalFeature
- clearComputedProps() : RDKit::RDProps, RDKit::ROMol
- clearConformers() : RDKit::ROMol
- clearCStates() : RDKit::SubstanceGroup
- clearDrawing() : RDKit::MolDraw2D, RDKit::MolDraw2DCairo, RDKit::MolDraw2DJS, RDKit::MolDraw2DQt, RDKit::MolDraw2DSVG, RDKit::MolDraw2Dwx
- clearProp() : RDKit::FilterCatalogEntry, RDKit::FragCatalogEntry, RDKit::MolCatalogEntry, RDKit::RDProps
- clearPropertyCache() : RDKit::Atom, RDKit::ROMol
- ClearTee() : boost::logging::rdLogger
- clearTieStore() : RDKit::RGroupScorer
- clearVal() : RDKit::Dict
- Clone() : RDKit::FilterMatcherBase
- clone() : RDKit::AtomInvariantsGenerator, RDKit::AtomPair::AtomPairAtomInvGenerator, RDKit::BondInvariantsGenerator, RDKit::CustomPropHandler, RDKit::DataStructsExplicitBitVecPropHandler, RDKit::MorganFingerprint::MorganAtomInvGenerator, RDKit::MorganFingerprint::MorganBondInvGenerator, RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator, RDKit::RDKitFP::RDKitFPAtomInvGenerator
- close() : RDKit::MolWriter, RDKit::PDBWriter, RDKit::SDWriter, RDKit::SmilesWriter, RDKit::TDTWriter, RDKit::v1::MolSupplier, RDKit::v2::FileParsers::MolSupplier
- cluster() : RDPickers::HierarchicalClusterPicker
- collectVotes() : RDInfoTheory::BitCorrMatGenerator
- colour() : RDKit::MolDraw2D, RDKit::MolDraw2D_detail::DrawText
- commitBatchEdit() : RDKit::RWMol
- commonArgumentsString() : RDKit::FingerprintArguments
- compact() : RDPickers::LeaderPickerState< T >
- compact_next() : RDPickers::LeaderPickerState< T >
- compare() : RDKit::Canon::bondholder, RDKit::CIPLabeler::Rule1a, RDKit::CIPLabeler::Rule1b, RDKit::CIPLabeler::Rule2, RDKit::CIPLabeler::Rule3, RDKit::CIPLabeler::Rule4a, RDKit::CIPLabeler::Rule4b, RDKit::CIPLabeler::Rule4c, RDKit::CIPLabeler::Rule5, RDKit::CIPLabeler::Rule5New, RDKit::CIPLabeler::Rule6, RDKit::CIPLabeler::Rules, RDKit::CIPLabeler::SequenceRule
- compareGrids() : RDGeom::UniformRealValueGrid3D
- compareParams() : RDGeom::UniformGrid3D, RDGeom::UniformRealValueGrid3D
- compareRectanglesByX() : RDKit::MarvinRectangle
- compareRectanglesByYReverse() : RDKit::MarvinRectangle
- compareStereo() : RDKit::Canon::bondholder
- compareTo() : RDKit::CIPLabeler::PairList
- compareVectors() : RDGeom::UniformRealValueGrid3D, RDKit::RealValueVect
- CompositeValidation() : RDKit::MolStandardize::CompositeValidation
- Composition2N() : RDKit::FMCS::Composition2N
- compute2N() : RDKit::FMCS::Composition2N
- computeBox() : RDDepict::EmbeddedFrag
- computeCostMatrix() : RDKit::MolAlign::LAP
- computeDistMat() : RDDepict::EmbeddedFrag
- computeKey() : RDKit::FMCS::SubstructureCache::HashKey
- computeMinCostPath() : RDKit::MolAlign::LAP
- computeMMFFCharges() : RDKit::MMFF::MMFFMolProperties
- computeProperties() : RDKit::Descriptors::Properties
- computeRemainingSize() : RDKit::FMCS::Seed
- Configuration() : RDKit::CIPLabeler::Configuration
- Conformer() : RDKit::Conformer
- ConformerException() : RDKit::ConformerException
- ConicToFunctionImpl() : RDKit::MolDraw2D_detail::DrawTextFT, RDKit::MolDraw2D_detail::DrawTextFTCairo, RDKit::MolDraw2D_detail::DrawTextFTJS, RDKit::MolDraw2D_detail::DrawTextFTQt, RDKit::MolDraw2D_detail::DrawTextFTSVG
- ConrecSegment() : conrec::ConrecSegment
- const_iterator() : RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator
- ConstBondIterator_() : RDKit::ConstBondIterator_
- contractOneMultipleSgroup() : RDKit::MarvinMultipleSgroup
- contribs() : ForceFields::ForceField
- ControlCCaught() : RDKit::ControlCCaught
- ControlCHandler() : RDKit::ControlCHandler
- convertFromOneSuperAtom() : RDKit::MarvinSuperatomSgroup
- convertToOneSuperAtom() : RDKit::MarvinSuperatomSgroupExpanded
- copy() : DistGeom::ChiralViolationContribs, DistGeom::DistViolationContribs, DistGeom::FourthDimContribs, ForceFields::AngleConstraintContrib, ForceFields::AngleConstraintContribs, ForceFields::CrystalFF::PlanarityContribs, ForceFields::CrystalFF::TorsionAngleContribM6, ForceFields::CrystalFF::TorsionAngleContribs, ForceFields::DistanceConstraintContrib, ForceFields::DistanceConstraintContribs, ForceFields::ForceFieldContrib, ForceFields::MMFF::AngleBendContrib, ForceFields::MMFF::BondStretchContrib, ForceFields::MMFF::EleContrib, ForceFields::MMFF::NonbondedContrib, ForceFields::MMFF::OopBendContrib, ForceFields::MMFF::StretchBendContrib, ForceFields::MMFF::TorsionAngleContrib, ForceFields::MMFF::VdWContrib, ForceFields::PositionConstraintContrib, ForceFields::TorsionConstraintContrib, ForceFields::UFF::AngleBendContrib, ForceFields::UFF::BondStretchContrib, ForceFields::UFF::InversionContrib, ForceFields::UFF::InversionContribs, ForceFields::UFF::TorsionAngleContrib, ForceFields::UFF::vdWContrib, Point2D, Queries::AndQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::EqualityQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::GreaterEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::GreaterQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::LessEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::LessQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::OrQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::RangeQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::SetQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, Queries::XOrQuery< MatchFuncArgType, DataFuncArgType, needsConversion >, RDGeom::Point2D, RDGeom::Point3D, RDGeom::Point, RDGeom::PointND, RDKit::Atom, RDKit::AtomKekulizeException, RDKit::AtomMonomerInfo, RDKit::AtomPDBResidueInfo, RDKit::AtomRingQuery, RDKit::AtomSanitizeException, RDKit::AtomValenceException, RDKit::Bond, RDKit::CartesianProductStrategy, RDKit::EnumerationStrategyBase, RDKit::EvenSamplePairsStrategy, RDKit::ExclusionList, RDKit::FilterHierarchyMatcher, RDKit::FilterMatcherBase, RDKit::FilterMatchOps::And, RDKit::FilterMatchOps::Not, RDKit::FilterMatchOps::Or, RDKit::HasPropQuery< TargetPtr >, RDKit::HasPropWithValueQuery< TargetPtr, T >, RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >, RDKit::HasPropWithValueQuery< TargetPtr, std::string >, RDKit::KekulizeException, RDKit::MolEnumerator::LinkNodeOp, RDKit::MolEnumerator::MolEnumeratorOp, RDKit::MolEnumerator::PositionVariationOp, RDKit::MolEnumerator::RepeatUnitOp, RDKit::MolSanitizeException, RDKit::MolStandardize::AllowedAtomsValidation, RDKit::MolStandardize::CompositeValidation, RDKit::MolStandardize::DisallowedAtomsValidation, RDKit::MolStandardize::DisallowedRadicalValidation, RDKit::MolStandardize::FeaturesValidation, RDKit::MolStandardize::FragmentValidation, RDKit::MolStandardize::Is2DValidation, RDKit::MolStandardize::IsotopeValidation, RDKit::MolStandardize::Layout2DValidation, RDKit::MolStandardize::MolVSValidation, RDKit::MolStandardize::NeutralValidation, RDKit::MolStandardize::NoAtomValidation, RDKit::MolStandardize::RDKitValidation, RDKit::MolStandardize::StereoValidation, RDKit::MolStandardize::ValidationMethod, RDKit::QueryAtom, RDKit::QueryBond, RDKit::RandomSampleAllBBsStrategy, RDKit::RandomSampleStrategy, RDKit::RecursiveStructureQuery, RDKit::SmartsMatcher
- copyGene() : RDKit::RGroupDecompositionChromosome
- copyMol() : RDKit::MarvinDataSgroup, RDKit::MarvinGenericSgroup, RDKit::MarvinMol, RDKit::MarvinMolBase, RDKit::MarvinMonomerSgroup, RDKit::MarvinMulticenterSgroup, RDKit::MarvinMultipleSgroup, RDKit::MarvinSruCoModSgroup, RDKit::MarvinSuperatomSgroup, RDKit::MarvinSuperatomSgroupExpanded
- Coulomb() : RDMIF::Coulomb
- CoulombDielectric() : RDMIF::CoulombDielectric
- countMatches() : RDKit::SubstructLibrary
- countUserRGroups() : RDKit::RCore
- createChromosome() : RDKit::RGroupGa
- createDrawObjects() : RDKit::MolDraw2D_detail::DrawMol
- createFromParent() : RDKit::FMCS::Seed
- createPartialBond() : RDKit::RWMol
- CreateShingling() : RDKit::MHFPFingerprints::MHFPEncoder
- CrippenParamCollection() : RDKit::Descriptors::CrippenParamCollection
- crossProduct() : RDGeom::Point3D
- CubicToFunctionImpl() : RDKit::MolDraw2D_detail::DrawTextFT, RDKit::MolDraw2D_detail::DrawTextFTCairo, RDKit::MolDraw2D_detail::DrawTextFTJS, RDKit::MolDraw2D_detail::DrawTextFTQt, RDKit::MolDraw2D_detail::DrawTextFTSVG
- CustomFeature() : RDKit::GaussianShape::CustomFeature
- CXXAtomIter() : RDKit::CXXAtomIterator< Graph, Vertex, Iterator, CheckedAtoms, CheckedBonds >::CXXAtomIter
- CXXAtomIterator() : RDKit::CXXAtomIterator< Graph, Vertex, Iterator, CheckedAtoms, CheckedBonds >
- CXXBondIter() : RDKit::CXXBondIterator< Graph, Edge, Iterator, Checked >::CXXBondIter
- CXXBondIterator() : RDKit::CXXBondIterator< Graph, Edge, Iterator, Checked >