RDKit: Class Hierarchy

| RDKit Open-source cheminformatics and machine learning.

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Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123456]

C better_enums::_eat_assign< EnumType > | Get intrinsic value of an (Enum::value) by taking advantage of
C better_enums::_initialize_at_program_start< Enum > |
C better_enums::_iterable< Element > |
C RDKit::Abbreviations::AbbreviationDefinition |
C RDKit::Abbreviations::AbbreviationMatch |
C RDKit::MolOps::AddHsParameters |
C RDKit::AdditionalOutput |
C RDKit::MolOps::AdjustQueryParameters | Parameters controlling the behavior of MolOps::adjustQueryProperties
C ForceFields::AngleConstraintContribsParams |
C RDKit::AromaticAtomIterator_< Atom_, Mol_ > | Iterate over aromatic atoms, this is bidirectional
C RDKit::Canon::AtomCompareFunctor |
C RDKit::AtomCoordsMatchFunctor |
C RDKit::atomicData |
C ForceFields::UFF::AtomicParams | Class to store atomic parameters for the Universal Force Field
C RDKit::AtomIterator_< Atom_, Mol_ > | A general random access iterator
►C RDKit::AtomMonomerInfo | The abstract base class for atom-level monomer info
C RDKit::AtomPDBResidueInfo | Captures atom-level information about peptide residues
C RDKit::MolDraw2D_detail::AtomSymbol |
C RDKit::SubstanceGroup::AttachPoint |
C RDKit::SLNParse::AttribType |
C RDKit::StructureCheck::AugmentedAtom |
►Cstd::basic_streambuf |
C boost_adaptbx::python::streambuf | A stream buffer getting data from and putting data into a Python file object
C RDKit::MolAlign::BestAlignmentParams |
C RDInfoTheory::BitCorrMatGenerator |
►C BitVect | Abstract base class for storing BitVectors
C ExplicitBitVect | Class for bit vectors that are densely occupied
C SparseBitVect | Class for bit vectors that are sparsely occupied
C RDKit::Canon::bondholder |
C RDKit::BondIterator_ | Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
C RDKit::Chirality::BondWedgingParameters |
C RDKit::Canon::canon_atom |
C RDKit::CartesianProduct | Iterate through all possible permutations of the rgroups
►C RDCatalog::Catalog< entryType, paramType > | Abstract base class for a catalog object
C RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int > |
C RDCatalog::HierarchCatalog< MolCatalogEntry, MolCatalogParams, int > |
C RDCatalog::HierarchCatalog< AcidBaseCatalogEntry, AcidBaseCatalogParams, int > |
C RDCatalog::HierarchCatalog< FragmentCatalogEntry, FragmentCatalogParams, int > |
C RDCatalog::HierarchCatalog< TransformCatalogEntry, TransformCatalogParams, int > |
C RDCatalog::HierarchCatalog< TautomerCatalogEntry, TautomerCatalogParams, int > |
C RDCatalog::HierarchCatalog< entryType, paramType, orderType > | A Catalog with a hierarchical structure
►C RDCatalog::Catalog< FilterCatalogEntry, FilterCatalogParams > |
C RDKit::FilterCatalog |
►C RDCatalog::CatalogEntry | Abstract base class to be used to represent an entry in a Catalog
C RDKit::FilterCatalogEntry |
C RDKit::FragCatalogEntry |
C RDKit::MolCatalogEntry | This class is used to store ROMol objects in a MolCatalog
C RDKit::MolStandardize::AcidBaseCatalogEntry |
C RDKit::MolStandardize::FragmentCatalogEntry |
C RDKit::MolStandardize::TautomerCatalogEntry |
C RDKit::MolStandardize::TransformCatalogEntry |
►C RDCatalog::CatalogParams | Abstract base class for the container used to create a catalog
C RDKit::FilterCatalogParams |
C RDKit::FragCatParams | Container for user parameters used to create a fragment catalog
C RDKit::MolCatalogParams | Container for user parameters used to create a mol catalog
C RDKit::MolStandardize::AcidBaseCatalogParams |
C RDKit::MolStandardize::FragmentCatalogParams |
C RDKit::MolStandardize::TautomerCatalogParams |
C RDKit::MolStandardize::TransformCatalogParams |
C RDKit::v2::CDXMLParser::CDXMLParserParams |
C RDKit::MolStandardize::ChargeCorrection |
C RDKit::StructureCheck::ChargeFix |
C RDKit::charptr_functor | Functor for comparing two strings
►C ChemicalFeatures::ChemicalFeature | Abstract base class for chemical feature
C ChemicalFeatures::FreeChemicalFeature |
C RDKit::MolChemicalFeature |
C RDKit::Canon::ChiralAtomCompareFunctor |
C DistGeom::ChiralSet | Class used to store a quartet of points and chiral volume bounds on them
C DistGeom::ChiralViolationContribsParams |
C RDKit::CIPLabeler::CIPMol |
C RDKit::CIPLabeler::CIPMolSpan< T, U >::CIPMolIter |
C RDKit::CIPLabeler::CIPMolSpan< T, U > |
C RDKit::MolStandardize::CleanupParameters |
C RDKit::RascalMCES::details::ClusNode |
C RDKit::FMCS::Composition2N |
C RDDepict::Compute2DCoordParameters |
►C RDKit::CIPLabeler::Configuration |
C RDKit::CIPLabeler::AtropisomerBond |
C RDKit::CIPLabeler::Sp2Bond |
C RDKit::CIPLabeler::Tetrahedral |
C conrec::ConrecSegment |
C RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator |
C set< K >::const_iterator | STL iterator class
C set< K >::const_reverse_iterator | STL iterator class
C RDKit::ConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
C RDDepict::ConstrainedDepictionParams |
C RDKit::MolDraw2DUtils::ContourParams |
C RDKit::ControlCHandler |
C RDDepict::CoordinateTemplates |
C RDMIF::Coulomb | Class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric)
C RDMIF::CoulombDielectric | Class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule by taking a distance-dependent dielectric into account:
C RDKit::Descriptors::CrippenParamCollection | Singleton class for retrieving Crippen parameters
C RDKit::Descriptors::CrippenParams | Class used to store Crippen parameters
C ForceFields::CrystalFF::CrystalFFDetails |
C RDKit::SubstanceGroup::CState |
►C RDKit::CustomPropHandler |
C RDKit::DataStructsExplicitBitVecPropHandler |
C RDKit::CXXAtomIterator< Graph, Vertex, Iterator >::CXXAtomIter |
C RDKit::CXXAtomIterator< Graph, Vertex, Iterator > |
C RDKit::CXXBondIterator< Graph, Edge, Iterator >::CXXBondIter |
C RDKit::CXXBondIterator< Graph, Edge, Iterator > |
C Data3Ddescriptors |
C RDKit::Deprotect::DeprotectData |
C RDKit::Dict | The `Dict` class can be used to store objects of arbitrary type keyed by `strings`
C RDKit::CIPLabeler::Digraph |
C RDKit::DiscreteDistMat |
C RDKit::DiscreteValueVect | Class for efficiently storing vectors of discrete values
C ForceFields::DistanceConstraintContribsParams |
►C RDPickers::DistPicker | Abstract base class to do perform item picking (typically molecules) using a distance matrix
C RDPickers::HierarchicalClusterPicker | Diversity picker based on hierarchical clustering
C RDPickers::LeaderPicker | Implements the Leader algorithm for picking a subset of item from a pool
C RDPickers::MaxMinPicker | Implements the MaxMin algorithm for picking a subset of item from a pool
C DistGeom::DistViolationContribsParams |
C RDKit::Descriptors::DoubleCubicLatticeVolume |
C RDKit::MolDraw2D_detail::DrawAnnotation |
C RDKit::DrawColour |
►C RDKit::MolDraw2D_detail::DrawMol |
►C RDKit::MolDraw2D_detail::DrawMolMCH |
C RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine |
C RDKit::MolDraw2D_detail::DrawMolMCHLasso |
►C RDKit::MolDraw2D_detail::DrawShape |
C RDKit::MolDraw2D_detail::DrawShapeArc |
C RDKit::MolDraw2D_detail::DrawShapeArrow |
C RDKit::MolDraw2D_detail::DrawShapeDashedWedge |
C RDKit::MolDraw2D_detail::DrawShapeEllipse |
C RDKit::MolDraw2D_detail::DrawShapePolyLine |
C RDKit::MolDraw2D_detail::DrawShapeSimpleLine |
C RDKit::MolDraw2D_detail::DrawShapeSolidWedge |
C RDKit::MolDraw2D_detail::DrawShapeWavyLine |
►C RDKit::MolDraw2D_detail::DrawText |
►C RDKit::MolDraw2D_detail::DrawTextFT |
C RDKit::MolDraw2D_detail::DrawTextFTCairo |
C RDKit::MolDraw2D_detail::DrawTextFTJS |
C RDKit::MolDraw2D_detail::DrawTextFTQt |
C RDKit::MolDraw2D_detail::DrawTextFTSVG |
►C RDKit::MolDraw2D_detail::DrawTextNotFT |
C RDKit::MolDraw2D_detail::DrawTextCairo |
C RDKit::MolDraw2D_detail::DrawTextJS |
C RDKit::MolDraw2D_detail::DrawTextQt |
C RDKit::MolDraw2D_detail::DrawTextSVG |
C RDKit::FMCS::DuplicatedSeedCache |
C RDKit::CIPLabeler::Edge |
C RDDepict::EmbeddedAtom | Class that contains the data for an atoms that has already been embedded
C RDDepict::EmbeddedFrag | Class containing a fragment of a molecule that has already been embedded
C RDKit::DGeomHelpers::EmbedParameters | Parameter object for controlling embedding
►Cboost::enable_shared_from_this |
►C RDKit::FilterMatcherBase |
C RDKit::ExclusionList |
C RDKit::FilterHierarchyMatcher |
C RDKit::FilterMatchOps::And |
C RDKit::FilterMatchOps::Not |
C RDKit::FilterMatchOps::Or |
C RDKit::SmartsMatcher |
►C RDKit::EnumerateLibraryBase |
C RDKit::EnumerateLibrary | This is a class for running reactions on sets of reagents
C RDKit::EnumerationParams |
►C RDKit::EnumerationStrategyBase |
C RDKit::CartesianProductStrategy |
C RDKit::EvenSamplePairsStrategy | EvenSamplePairsStrategy
C RDKit::RandomSampleAllBBsStrategy |
C RDKit::RandomSampleStrategy |
►Cstd::exception | STL class
C DatastructsException |
C RDDepict::DepictException |
C RDGeom::GridException |
C RDKit::ChemicalReactionException | Used to indicate an error in the chemical reaction engine
C RDKit::ChemicalReactionParserException | Used to indicate an error in parsing reaction data
C RDKit::ConformerException | Used to indicate errors from incorrect conformer access
C RDKit::EnumerationStrategyException | Class for flagging enumeration strategy errors
C RDKit::FeatureFileParseException | Class used to indicate errors in parsing feature definition files
C RDKit::MolAlign::MolAlignException |
C RDKit::MolPicklerException | Used to indicate exceptions whilst pickling (serializing) molecules
►C RDKit::MolSanitizeException | Class for flagging sanitization errors
►C RDKit::AtomSanitizeException |
C RDKit::AtomKekulizeException |
C RDKit::AtomValenceException |
C RDKit::KekulizeException |
C RDKit::ReactionPicklerException | Used to indicate exceptions whilst pickling (serializing) reactions
C RDKit::RxnSanitizeException | Class for flagging sanitization errors
C RDKit::SLNParseException |
C RDKit::SmilesParse::SmilesParseException |
C RDKit::UnimplementedFPException |
C RDKit::v2::FileParsers::MolFileUnhandledFeatureException |
►Cstd::runtime_error | STL class
C IndexErrorException | Class to allow us to throw an `IndexError` from C++ and have it make it back to Python
C Invar::Invariant |
C KeyErrorException | Class to allow us to throw a `KeyError` from C++ and have it make it back to Python
C RDKit::BadFileException | Used by various file parsing classes to indicate a bad file
C RDKit::CIPLabeler::MaxIterationsExceeded |
C RDKit::CIPLabeler::TooManyNodesException |
C RDKit::ControlCCaught |
C RDKit::FileParseException | Used by various file parsing classes to indicate a parse error
C RDKit::MarvinWriterException |
C RDKit::MaxFindBondOrdersItersExceeded |
C RDKit::RigorousEnhancedStereoException |
C RDKit::SubstanceGroupException | Used to indicate errors from incorrect sgroup access
C ValueErrorException | Class to allow us to throw a `ValueError` from C++ and have it make it back to Python
C RDKit::FMCS::ExecStatistics |
C RDFeatures::ExplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE > |
C ForceFields::CrystalFF::ExpTorsionAngle | A structure used to the experimental torsion patterns
C RDKit::ExtendedQueryMol |
C RDKit::GeneralizedSubstruct::ExtendedQueryMol |
C RDKit::FilterData_t |
C RDKit::FilterMatch | Holds the atomPairs matched by the underlying matcher
C RDKit::FilterProperty_t |
►C RDKit::FingerprintArguments | Abstract base class that holds molecule independent arguments that are common amongst all fingerprint types and classes inherited from this would hold fingerprint type specific arguments
C RDKit::AtomPair::AtomPairArguments | Class that holds atom-pair fingerprint specific arguments
C RDKit::MorganFingerprint::MorganArguments | Class for holding Morgan fingerprint specific arguments
C RDKit::RDKitFP::RDKitFPArguments |
C RDKit::TopologicalTorsion::TopologicalTorsionArguments |
C RDKit::FingerprintFuncArguments | Struct that makes calling the fingerprint generation functions easier
C RDKit::FingerprintVarianceScoreData |
►C RDKit::EnumerateStereoisomers::details::Flipper |
C RDKit::EnumerateStereoisomers::details::AtomFlipper |
C RDKit::EnumerateStereoisomers::details::AtropisomerFlipper |
C RDKit::EnumerateStereoisomers::details::BondFlipper |
C RDKit::EnumerateStereoisomers::details::StereoGroupFlipper |
C ForceFields::ForceField | A class to store forcefields and handle minimization
►C ForceFields::ForceFieldContrib | Abstract base class for contributions to ForceFields
C DistGeom::ChiralViolationContribs |
C DistGeom::DistViolationContribs |
C DistGeom::FourthDimContribs |
C ForceFields::AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib
C ForceFields::AngleConstraintContribs | A term to capture all flat bottom angle constraint potentials
C ForceFields::CrystalFF::TorsionAngleContribM6 | Torsion term for multiplicity m = 1 - 6
C ForceFields::CrystalFF::TorsionAngleContribs |
C ForceFields::DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib
C ForceFields::DistanceConstraintContribs | A term to capture all flat bottom distance constraint potentials
C ForceFields::MMFF::AngleBendContrib | The angle-bend term for MMFF
C ForceFields::MMFF::BondStretchContrib | The bond-stretch term for MMFF
C ForceFields::MMFF::EleContrib | Electrostatic term for MMFF
C ForceFields::MMFF::NonbondedContrib | Combined vdW and charge terms for MMFF
C ForceFields::MMFF::OopBendContrib | Out-of-plane term for MMFF
C ForceFields::MMFF::StretchBendContrib | The angle-bend term for MMFF
C ForceFields::MMFF::TorsionAngleContrib | Torsion term for MMFF
C ForceFields::MMFF::VdWContrib | Van der Waals term for MMFF
C ForceFields::PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2
C ForceFields::TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib
C ForceFields::UFF::AngleBendContrib | The angle-bend term for the Universal Force Field
C ForceFields::UFF::BondStretchContrib | The bond-stretch term for the Universal Force Field
C ForceFields::UFF::InversionContrib | The inversion term for the Universal Force Field
C ForceFields::UFF::InversionContribs | A term to capture all Inversion Contributionss
C ForceFields::UFF::TorsionAngleContrib | Torsion term for the Universal Force Field
C ForceFields::UFF::vdWContrib | Van der Waals term for the Universal Force Field
C DistGeom::FourthDimContribsParams |
C RDKit::FPBReader | Class for reading and searching FPB files
►C RDKit::FPHolderBase | Base FPI for the fingerprinter used to rule out impossible matches
►C RDKit::PatternHolder |
C RDKit::TautomerPatternHolder |
C RDKit::FragCatGenerator |
C RDKit::FragFPGenerator |
C RDKit::MolFragmenter::FragmenterBondType |
C RDKit::MolStandardize::FragmentRemover |
►CGaBase |
C RDKit::RGroupGa |
C RDKit::GaResult |
C RDKit::GasteigerParams |
►CGraph_t |
C RDKit::FMCS::Graph |
C RDGeom::Grid3D< VectorType, ValueType1, ValueType2 > | Virtual base class for a grid object
►C RDGeom::Grid3D< RDKit::DiscreteValueVect, int, unsigned int > |
C RDGeom::UniformGrid3D |
►C RDGeom::Grid3D< RDKit::RealValueVect, double, double > |
C RDGeom::UniformRealValueGrid3D |
C RDDepict::gtIIPair |
C RDKit::FMCS::SubstructureCache::HashKey |
►C RDKit::HasPropWithValueQueryBase |
C RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect > |
C RDKit::HasPropWithValueQuery< TargetPtr, std::string > |
C RDKit::HasPropWithValueQuery< TargetPtr, T > |
C RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect > |
C RDKit::HasPropWithValueQuery< TargetPtr, std::string > |
C RDMIF::HBond | Class for calculation of hydrogen bond potential between probe and molecule
C RDKit::HeteroatomIterator_< Atom_, Mol_ > | Iterate over heteroatoms, this is bidirectional
C RDKit::MolOps::Hybridizations |
C RDMIF::Hydrophilic | Class for calculation of hydrophilic field of molecule
C RDFeatures::ImplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE > |
C RDKit::StructureCheck::IncEntry |
C RDInfoTheory::InfoBitRanker |
C Queries::Int2Type< v > | Class to allow integer values to pick templates
►CIntegerStringChromosome |
C RDKit::RGroupDecompositionChromosome |
C ForceFields::UFF::InversionContribsParams |
►Cstd::ios_base | STL class
►Cstd::basic_ios< Char > | STL class
►Cstd::basic_istream< Char > | STL class
►Cstd::istream | STL class
C boost_adaptbx::python::streambuf::istream |
►Cstd::basic_ostream< Char > | STL class
►Cstd::ostream | STL class
►C boost_adaptbx::python::streambuf::ostream |
C boost_adaptbx::python::ostream |
C set< K >::iterator | STL iterator class
C RDKit::MolInterchange::JSONParseParameters |
C RDKit::MolInterchange::JSONWriteParameters |
►C RDKit::KeyHolderBase |
C RDKit::KeyFromPropHolder |
C RDKit::FMCS::SubstructureCache::KeyNumericMetrics |
C RDKit::MolAlign::LAP |
C RDKit::larger_of< T > | Functor for returning the larger of two values
C RDKit::MolStandardize::LargestFragmentChooser::Largest |
C RDKit::MolStandardize::LargestFragmentChooser |
C RDPickers::LeaderPickerState< T > |
C RDKit::StructureCheck::Ligand |
C RDKit::MolDraw2D_detail::LinePair |
C RDKit::MolEnumerator::LinkNode |
C RDKit::Utils::LocaleSwitcher |
C RDKit::ltDouble | Functor to compare two doubles with a tolerance
C better_enums::map< Enum, T, Compare > |
C better_enums::map_compare< T > |
C better_enums::map_compare< const char * > |
C better_enums::map_compare< const wchar_t * > |
C RDKit::MarvinArrow |
C RDKit::MarvinAtom |
C RDKit::MarvinAttachmentPoint |
C RDKit::MarvinBond |
C RDKit::MarvinBondStereo |
C RDKit::MarvinCondition |
►C RDKit::MarvinMolBase |
C RDKit::MarvinDataSgroup |
C RDKit::MarvinGenericSgroup |
C RDKit::MarvinMol |
C RDKit::MarvinMonomerSgroup |
C RDKit::MarvinMulticenterSgroup |
C RDKit::MarvinMultipleSgroup |
C RDKit::MarvinSruCoModSgroup |
C RDKit::MarvinSuperatomSgroup |
C RDKit::MarvinSuperatomSgroupExpanded |
C RDKit::MarvinPlus |
C RDKit::MarvinReaction |
C RDKit::MarvinRectangle |
C RDKit::MarvinStereoGroup |
C RDKit::MatchingAtomIterator_< Atom_, Mol_ > | Iterate over atoms matching a query function. This is bidirectional
►C RDNumeric::Matrix< TYPE > | A matrix class for general, non-square matrices
C RDNumeric::SquareMatrix< TYPE > |
►C RDNumeric::Matrix< double > |
►C RDNumeric::SquareMatrix< double > |
C DistGeom::BoundsMatrix | Class to store the distance bound
C RDGeom::Transform2D |
C RDGeom::Transform3D |
C RDKit::FMCS::MaximumCommonSubgraph |
C RDPickers::MaxMinPickInfo |
C RDKit::MCSAtomCompareParameters |
C RDKit::MCSBondCompareParameters |
►C RDKit::MCSParameters |
C RDKit::detail::MCSParametersInternal |
C RDKit::MCSProgressData |
C RDKit::MCSResult |
C RDKit::SynthonSpaceSearch::details::MemoryMappedFileReader |
C RDKit::MolStandardize::MetalDisconnector |
C RDKit::MolStandardize::MetalDisconnectorOptions |
C RDDataManip::MetricMatrixCalc< vectType, entryType > | A generic metric matrix calculator (e.g similarity matrix or distance matrix)
C RDKit::MHFPFingerprints::MHFPEncoder |
C ForceFields::MMFF::MMFFAngle | Class to store MMFF parameters for angle bending
C ForceFields::MMFF::MMFFAngleCollection |
C ForceFields::MMFF::MMFFAromCollection |
C RDKit::MMFF::MMFFAtomProperties |
C ForceFields::MMFF::MMFFBndkCollection |
C ForceFields::MMFF::MMFFBond | Class to store MMFF parameters for bond stretching
C ForceFields::MMFF::MMFFBondCollection |
C ForceFields::MMFF::MMFFChg |
C ForceFields::MMFF::MMFFChgCollection |
C ForceFields::MMFF::MMFFCovRadPauEle |
C ForceFields::MMFF::MMFFCovRadPauEleCollection |
C ForceFields::MMFF::MMFFDef | Class to store MMFF atom type equivalence levels
C ForceFields::MMFF::MMFFDefCollection |
C ForceFields::MMFF::MMFFDfsbCollection |
C ForceFields::MMFF::MMFFHerschbachLaurie |
C ForceFields::MMFF::MMFFHerschbachLaurieCollection |
C RDKit::MMFF::MMFFMolProperties |
C ForceFields::MMFF::MMFFOop | Class to store MMFF parameters for out-of-plane bending
C ForceFields::MMFF::MMFFOopCollection |
C ForceFields::MMFF::MMFFPBCI | Class to store MMFF Partial Bond Charge Increments
C ForceFields::MMFF::MMFFPBCICollection |
C ForceFields::MMFF::MMFFProp | Class to store MMFF Properties
C ForceFields::MMFF::MMFFPropCollection |
C ForceFields::MMFF::MMFFStbn | Class to store MMFF parameters for stretch-bending
C ForceFields::MMFF::MMFFStbnCollection |
C ForceFields::MMFF::MMFFTor | Class to store MMFF parameters for torsions
C ForceFields::MMFF::MMFFTorCollection |
C ForceFields::MMFF::MMFFVdW | Class to store MMFF parameters for non-bonded Van der Waals
C ForceFields::MMFF::MMFFVdWCollection |
C ForceFields::MMFF::MMFFVdWRijstarEps |
C RDKit::v2::FileParsers::Mol2ParserParams |
C RDKit::MolChemicalFeatureDef |
C RDKit::MolChemicalFeatureFactory | The class for finding chemical features in molecules
C MolData3Ddescriptors |
►C RDKit::MolDraw2D | MolDraw2D is the base class for doing 2D renderings of molecules
C RDKit::MolDraw2DCairo |
C RDKit::MolDraw2DJS |
C RDKit::MolDraw2DQt |
C RDKit::MolDraw2DSVG |
C RDKit::MolDraw2Dwx |
C RDKit::MolDrawOptions |
►C RDKit::MolEnumerator::MolEnumeratorOp | Abstract base class for the a molecule enumeration operation
C RDKit::MolEnumerator::LinkNodeOp | Molecule enumeration operation corresponding to LINKNODES
C RDKit::MolEnumerator::PositionVariationOp | Molecule enumeration operation corresponding to position variation bonds
C RDKit::MolEnumerator::RepeatUnitOp | Molecule enumeration operation corresponding to SRUs
C RDKit::MolEnumerator::MolEnumeratorParams | Parameters used to control the molecule enumeration
C RDKit::v2::FileParsers::MolFileParserParams |
C RDKit::FMCS::MolFragment |
C RDKit::v2::FileParsers::MolFromSCSRParams |
C RDKit::MolAlign::MolHistogram |
►C RDKit::MolHolderBase | Base class API for holding molecules to substructure search
C RDKit::CachedMolHolder | Concrete class that holds binary cached molecules in memory
C RDKit::CachedSmilesMolHolder | Concrete class that holds smiles strings in memory
C RDKit::CachedTrustedSmilesMolHolder | Concrete class that holds trusted smiles strings in memory
C RDKit::MolHolder | Concrete class that holds molecules in memory
C RDKit::MolMatchFinalCheckFunctor |
C RDKit::MolPickler | Handles pickling (serializing) molecules
C RDKit::Canon::MolStackElem | These are the actual elements in the molecular stack
C RDKit::Canon::MolStackUnion | Used to store components in the molecular stack
►C RDKit::MolSupplier |
►C RDKit::v1::ForwardSDMolSupplier |
C RDKit::v1::SDMolSupplier |
C RDKit::v1::SmilesMolSupplier | Lazy file parser for Smiles tables
C RDKit::v1::TDTMolSupplier | Lazy file parser for TDT files
►C RDKit::v1::MolSupplier |
C RDKit::v1::ForwardSDMolSupplier |
C RDKit::v1::SmilesMolSupplier | Lazy file parser for Smiles tables
C RDKit::v1::TDTMolSupplier | Lazy file parser for TDT files
►C RDKit::v2::FileParsers::MolSupplier |
►C RDKit::v2::FileParsers::ForwardSDMolSupplier |
C RDKit::v2::FileParsers::SDMolSupplier |
C RDKit::v2::FileParsers::SmilesMolSupplier | Lazy file parser for Smiles tables
C RDKit::v2::FileParsers::TDTMolSupplier | Lazy file parser for TDT files
C RDKit::MolWriterParams |
C RDKit::MolzipParams |
C RDKit::v2::MarvinParser::MrvParserParams |
C RDKit::MrvWriterParams |
C RDKit::MultiFPBReader | Class for reading and searching multiple FPB files
C RDKit::StructureCheck::Neighbourhood |
C RDKit::ScaffoldNetwork::NetworkEdge |
C RDKit::FMCS::NewBond |
C RDKit::CIPLabeler::Node |
►Cboost::noncopyable |
C RDKit::AtomEnvironmentGenerator< std::uint64_t > |
C RDKit::FingerprintGenerator< std::uint64_t > |
►C RDKit::AtomEnvironment< OutputType > | Abstract base class that holds atom-environments that will be hashed to generate the fingerprint
C RDKit::AtomPair::AtomPairAtomEnv< OutputType > | Class that holds atom-environment data needed for atom-pair fingerprint generation
C RDKit::MorganFingerprint::MorganAtomEnv< OutputType > | Class for holding the bit-id created from Morgan fingerprint environments and the additional data necessary extra outputs
C RDKit::RDKitFP::RDKitFPAtomEnv< OutputType > |
C RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv< OutputType > |
►C RDKit::AtomEnvironmentGenerator< OutputType > | Abstract base class that generates atom-environments from a molecule
C RDKit::AtomPair::AtomPairEnvGenerator< OutputType > | Class that generates atom-environments for atom-pair fingerprint
C RDKit::MorganFingerprint::MorganEnvGenerator< OutputType > | Class that generates atom environments for Morgan fingerprint
C RDKit::RDKitFP::RDKitFPEnvGenerator< OutputType > |
C RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator< OutputType > |
►C RDKit::AtomInvariantsGenerator | Abstract base class for atom invariants generators
C RDKit::AtomPair::AtomPairAtomInvGenerator |
C RDKit::MorganFingerprint::MorganAtomInvGenerator | Default atom invariants generator for Morgan fingerprint, generates ECFP-type invariants
C RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator | Alternative atom invariants generator for Morgan fingerprint, generate FCFP-type invariants
C RDKit::RDKitFP::RDKitFPAtomInvGenerator |
►C RDKit::BondInvariantsGenerator | Abstract base class for bond invariants generators
C RDKit::MorganFingerprint::MorganBondInvGenerator | Bond invariants generator for Morgan fingerprint
C RDKit::FingerprintGenerator< OutputType > | Class that generates same fingerprint style for different output formats
C RDKit::MMFF::Tools::DefaultTorsionBondSmarts |
►C RDKit::MolWriter |
C RDKit::PDBWriter |
C RDKit::SDWriter |
C RDKit::SmilesWriter |
C RDKit::TDTWriter |
C RDKit::UFF::Tools::DefaultTorsionBondSmarts |
C RDLog::LogStateSetter |
C RDKit::MolStandardize::Normalizer | For applying Normalization transforms
C RDKit::MolAlign::O3A |
C RDKit::MolAlign::O3AConstraint |
C RDKit::MolAlign::O3AConstraintVect |
C RDKit::MolAlign::O3AFuncData |
C better_enums::optional< T > |
►C RDKit::Dict::Pair |
C RDKit::PairHolder |
C RDKit::CIPLabeler::PairList |
C ForceFields::UFF::ParamCollection | Singleton class for retrieving UFF AtomParams
C RDKit::RascalMCES::PartitionSet |
C RDKit::StructureCheck::PathEntry |
C RDKit::v1::PDBParserParams |
C RDKit::v2::FileParsers::PDBParserParams |
C RDKit::PeriodicTable | Singleton class for retrieving information about atoms
C RDKit::MolStandardize::Pipeline |
C RDKit::MolStandardize::PipelineLogEntry |
C RDKit::MolStandardize::PipelineOptions |
C RDKit::MolStandardize::PipelineResult |
C RDKit::PNGMetadataParams |
►C RDGeom::Point |
C RDGeom::Point2D |
C RDGeom::Point3D |
C RDGeom::PointND |
C RDKit::CIPLabeler::Priority |
C RDKit::Descriptors::Properties | Holds a collection of properties for computation purposes
C RDKit::Descriptors::PropertyFunctor |
C PySequenceHolder< T > | Class to hold sequences (lists, tuples, arrays, etc.) passed from Python -> C++
►C Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion > | Base class for all queries
C Queries::AndQuery< int, const ROMol &, true > |
C Queries::AndQuery< int, Atom const *, true > |
C Queries::AndQuery< int, Bond const *, true > |
C Queries::EqualityQuery< double, const ROMol &, true > |
C Queries::EqualityQuery< int, Atom const *, true > |
C Queries::EqualityQuery< int, Bond const *, true > |
C Queries::OrQuery< int, const ROMol &, true > |
C Queries::OrQuery< int, Atom const *, true > |
C Queries::OrQuery< int, Bond const *, true > |
C Queries::RangeQuery< double, const ROMol &, true > |
C Queries::RangeQuery< int, Atom const *, true > |
C Queries::RangeQuery< int, Bond const *, true > |
►C Queries::SetQuery< int, Atom const *, true > |
C RDKit::RecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS)
C Queries::SetQuery< int, Bond const *, true > |
C Queries::XOrQuery< int, const ROMol &, true > |
C Queries::XOrQuery< int, Atom const *, true > |
C Queries::XOrQuery< int, Bond const *, true > |
►C Queries::Query< int, ConstAtomPtr, needsConversion > |
►C Queries::EqualityQuery< int, ConstAtomPtr, true > |
C RDKit::AtomRingQuery |
►C Queries::Query< int, TargetPtr, needsConversion > |
►C Queries::EqualityQuery< int, TargetPtr, true > |
C RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect > |
C RDKit::HasPropWithValueQuery< TargetPtr, std::string > |
C RDKit::HasPropQuery< TargetPtr > |
C RDKit::HasPropWithValueQuery< TargetPtr, T > |
C RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect > |
C RDKit::HasPropWithValueQuery< TargetPtr, std::string > |
►C Queries::Query< MatchFuncArgType, MatchFuncArgType, false > |
C Queries::AndQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing AND: requires all children to be `true`
►C Queries::EqualityQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing ==: arguments must match a particular value (within an optional tolerance)
C Queries::GreaterEqualQuery< double, const ROMol &, true > |
C Queries::GreaterEqualQuery< int, Atom const *, true > |
C Queries::GreaterEqualQuery< int, Bond const *, true > |
C Queries::GreaterQuery< double, const ROMol &, true > |
C Queries::GreaterQuery< int, Atom const *, true > |
C Queries::GreaterQuery< int, Bond const *, true > |
C Queries::LessEqualQuery< double, const ROMol &, true > |
C Queries::LessEqualQuery< int, Atom const *, true > |
C Queries::LessEqualQuery< int, Bond const *, true > |
C Queries::LessQuery< double, const ROMol &, true > |
C Queries::LessQuery< int, Atom const *, true > |
C Queries::LessQuery< int, Bond const *, true > |
C Queries::OrQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing AND: requires any child to be `true`
C Queries::RangeQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing a range: arguments must fall in a particular range of values
C Queries::SetQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing a set: arguments must one of a set of values
C Queries::XOrQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing XOR: requires exactly one child to be `true`
►C Queries::Query< MatchFuncArgType, MatchFuncArgType, needsConversion > |
►C Queries::EqualityQuery< MatchFuncArgType, MatchFuncArgType, false > |
C Queries::GreaterEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing >= using a particular value (and an optional tolerance)
C Queries::GreaterQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing > using a particular value (and an optional tolerance)
C Queries::LessEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing <= using a particular value (and an optional tolerance)
C Queries::LessQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing < using a particular value (and an optional tolerance)
C RDKit::QueryAtomIterator_< Atom_, Mol_ > | Iterate over atoms matching a query. This is bidirectional
C RDKit::RascalMCES::RascalClusterOptions |
C RDKit::RascalMCES::RascalOptions |
C RDKit::RascalMCES::RascalResult |
C RDKit::RCore | RCore is the core common to a series of molecules
C RDKit::RDAny |
C boost::logging::rdLogger |
►C RDKit::RDProps |
►C RDKit::Atom | The class for representing atoms
C RDKit::QueryAtom | Class for storing atomic queries
►C RDKit::Bond | Class for representing a bond
C RDKit::QueryBond | Class for storing Bond queries
C RDKit::ChemicalReaction | This is a class for storing and applying general chemical reactions
C RDKit::Conformer | The class for representing 2D or 3D conformation of a molecule
►C RDKit::MolBundle | MolBundle contains a collection of related ROMols
C RDKit::FixedMolSizeMolBundle |
►C RDKit::ROMol |
C RDKit::RWMol | RWMol is a molecule class that is intended to be edited
C RDKit::SubstanceGroup | The class for representing SubstanceGroups
C RDKit::RDValue |
C RDKit::ReactionFingerprintParams |
C RDKit::ReactionPickler | Handles pickling (serializing) reactions
C RDKit::v2::ReactionParser::ReactionSmartsParserParams |
C RDKit::RealValueVect |
C RDKit::MolStandardize::Reionizer |
C RDKit::MolOps::RemoveHsParameters |
C RDKit::ResonanceMolSupplier |
C RDKit::ResonanceMolSupplierCallback |
C set< K >::reverse_iterator | STL iterator class
C RDKit::RGroupData | A single rgroup attached to a given core
C RDKit::RGroupDecompData |
C RDKit::RGroupDecomposition |
C RDKit::RGroupDecompositionParameters |
C RDKit::RGroupDecompositionProcessResult |
C RDKit::RGroupMatch | RGroupMatch is the decomposition for a single molecule
C RDKit::RGroupScorer |
C RDKit::RingInfo |
C RDKit::ScaffoldNetwork::ScaffoldNetwork |
C RDKit::ScaffoldNetwork::ScaffoldNetworkParams |
C RDKit::MolAlign::SDM |
C RDKit::SynthonSpaceSearch::SearchResults |
C RDKit::FMCS::Seed |
C RDKit::FMCS::SeedSet |
►C RDKit::CIPLabeler::SequenceRule |
C RDKit::CIPLabeler::Rule1a |
C RDKit::CIPLabeler::Rule1b |
C RDKit::CIPLabeler::Rule2 |
C RDKit::CIPLabeler::Rule3 |
C RDKit::CIPLabeler::Rule4a |
C RDKit::CIPLabeler::Rule4b |
C RDKit::CIPLabeler::Rule4c |
C RDKit::CIPLabeler::Rule5 |
C RDKit::CIPLabeler::Rule5New |
C RDKit::CIPLabeler::Rule6 |
C RDKit::CIPLabeler::Rules |
C set< K > | STL class
C RDKit::SmartsParserParams |
C RDKit::v1::SmartsParserParams |
C RDKit::v2::SmilesParse::SmartsParserParams |
C RDKit::v2::FileParsers::SmilesMolSupplierParams |
C RDKit::SmilesParserParams |
C RDKit::v1::SmilesParserParams |
C RDKit::v2::SmilesParse::SmilesParserParams |
C RDKit::SmilesWriteParams |
C RDKit::Snapshot |
C RDKit::CIPLabeler::Sort |
C RDKit::SparseIntVect< IndexType > | Class for efficiently storing sparse vectors of ints
C RDKit::Canon::SpecialChiralityAtomCompareFunctor |
C RDKit::Canon::SpecialSymmetryAtomCompareFunctor |
C RDKit::MorganFingerprints::ss_matcher |
C RDKit::SynthonSpaceSearch::details::Stepper |
C RDKit::StereoBondThresholds |
C RDKit::EnumerateStereoisomers::StereoEnumerationOptions |
C RDKit::StereoGroup |
C RDKit::Chirality::StereoInfo |
C RDKit::EnumerateStereoisomers::StereoisomerEnumerator |
►C boost_adaptbx::python::streambuf_capsule |
C boost_adaptbx::python::ostream |
C RDKit::MolDraw2D_detail::StringRect |
C RDKit::StructureCheck::StructChecker | Class for performing structure validation and cleanup
C RDKit::StructureCheck::StructCheckerOptions |
C RDKit::StructureCheck::StructCheckTautomer |
C RDKit::SubsetInfo |
C RDKit::SubsetOptions | Subsetting Options for copyMolSubset
C RDKit::SubstructLibrary | Substructure Search a library of molecules
C RDKit::SubstructMatchParameters |
C RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm |
C RDKit::FMCS::SubstructureCache |
C RDKit::GeneralMolSupplier::SupplierOptions |
C RDNumeric::SymmMatrix< TYPE > | A symmetric matrix class
C RDKit::SynthonSpaceSearch::Synthon |
C RDKit::SynthonSpaceSearch::SynthonSet |
C RDKit::SynthonSpaceSearch::SynthonSpace |
►C RDKit::SynthonSpaceSearch::SynthonSpaceHitSet |
C RDKit::SynthonSpaceSearch::SynthonSpaceFPHitSet |
►C RDKit::SynthonSpaceSearch::SynthonSpaceSearcher |
C RDKit::SynthonSpaceSearch::SynthonSpaceFingerprintSearcher |
C RDKit::SynthonSpaceSearch::SynthonSpaceRascalSearcher |
C RDKit::SynthonSpaceSearch::SynthonSpaceSubstructureSearcher |
C RDKit::SynthonSpaceSearch::SynthonSpaceSearchParams |
C RDKit::FMCS::Target |
C RDKit::FMCS::TargetMatch |
C RDKit::FMCS::TArray2D< T > |
C RDKit::MolStandardize::Tautomer |
C RDKit::MolStandardize::TautomerEnumerator |
C RDKit::MolStandardize::TautomerEnumeratorCallback |
C RDKit::MolStandardize::TautomerEnumeratorResult | Contains results of tautomer enumeration
C RDKit::TautomerQuery |
C RDKit::MolStandardize::TautomerTransform |
C RDKit::v2::FileParsers::TDTMolSupplierParams |
C RDKit::FMCS::DuplicatedSeedCache::TKey |
C ForceFields::CrystalFF::TorsionAngleContribsParams |
C conrec::tplHash |
C RDKit::v2::FileParsers::TPLParserParams |
C RDKit::Trajectory |
C ForceFields::UFF::UFFAngle | Class to store UFF parameters for angle bending
C ForceFields::UFF::UFFBond | Class to store UFF parameters for bond stretching
C ForceFields::UFF::UFFInv | Class to store UFF parameters for inversions
C ForceFields::UFF::UFFTor | Class to store UFF parameters for torsions
C ForceFields::UFF::UFFVdW | Class to store UFF parameters for van der Waals interactions
C RDKit::MolStandardize::Uncharger | For neutralizing ionized acids and bases
C RDKit::UsedLabelMap |
C RDKit::RGroupDecompData::UsedLabels |
►C RDKit::MolStandardize::ValidationMethod |
C RDKit::MolStandardize::AllowedAtomsValidation |
►C RDKit::MolStandardize::CompositeValidation | Simple way to apply a collection of
C RDKit::MolStandardize::MolVSValidation |
C RDKit::MolStandardize::DisallowedAtomsValidation |
C RDKit::MolStandardize::DisallowedRadicalValidation |
C RDKit::MolStandardize::FeaturesValidation |
C RDKit::MolStandardize::FragmentValidation | Logs if certain fragments are present
C RDKit::MolStandardize::Is2DValidation |
C RDKit::MolStandardize::IsotopeValidation | Logs if molecule contains isotopes
C RDKit::MolStandardize::Layout2DValidation |
C RDKit::MolStandardize::NeutralValidation | Logs if not an overall neutral system
C RDKit::MolStandardize::NoAtomValidation | MolVS Validations
C RDKit::MolStandardize::RDKitValidation |
C RDKit::MolStandardize::StereoValidation |
C RDKit::RDTypeTag::detail::Value |
C RDKit::VarianceDataForLabel |
►C RDMIF::VdWaals | Abstract class for calculation of Van der Waals interaction between probe and molecule at gridpoint `pt`
C RDMIF::MMFFVdWaals |
C RDMIF::UFFVdWaals |
C RDNumeric::Vector< TYPE > | A class to represent vectors of numbers
C RDCatalog::HierarchCatalog< entryType, paramType, orderType >::vertex_entry_t | Used by the BGL to set up the node properties in our graph
►C RDKit::Chirality::WedgeInfoBase |
C RDKit::Chirality::WedgeInfoAtropisomer |
C RDKit::Chirality::WedgeInfoChiral |