RDKit: Class Hierarchy

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

C RDKit::MolOps::AdjustQueryParameters |
C RDKit::AromaticAtomIterator_< Atom_, Mol_ > | Iterate over aromatic atoms, this is bidirectional
►C RDKit::Atom | The class for representing atoms
C RDKit::QueryAtom | Class for storing atomic queries
C RDKit::Canon::AtomCompareFunctor |
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::SLNParse::AttribType |
►Cbasic_streambuf |
C boost_adaptbx::python::streambuf | A stream buffer getting data from and putting data into a Python file object
►Cbinary_function |
C Rankers::argless< T > |
C Rankers::pairGreater< T1, T2 > | Functor for implementing > on two std::pairs. The first entries are
C Rankers::pairLess< T1, T2 > | Function for implementing < on two std::pairs. The first entries are
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::Bond | Class for representing a bond
C RDKit::QueryBond | Class for storing Bond queries
C RDKit::Canon::bondholder |
C RDKit::BondIterator_ | Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
C RDKit::Canon::canon_atom |
►C RDCatalog::Catalog< entryType, paramType > | Abstract base class for a catalog object
C RDCatalog::HierarchCatalog< entryType, paramType, orderType > | A Catalog with a hierarchical structure
C RDKit::FilterCatalog |
►C RDCatalog::Catalog< entryType, orderType > |
C RDCatalog::LinearCatalog< entryType, orderType > | Linear Catalog (analogous to an std::vector)
►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 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::charptr_functor | Functor for comparing two strings
►C ChemicalFeatures::ChemicalFeature | Abstract base class for chemical feature
C ChemicalFeatures::FreeChemicalFeature | Class for chemical features that do not orignate from molecules
C RDKit::MolChemicalFeature |
C RDKit::ChemicalReaction | This is a class for storing and applying general chemical reactions
C RDKit::Canon::ChiralAtomCompareFunctor |
C DistGeom::ChiralSet | Class used to store a quartet of points and chiral volume bounds on them
C RDKit::FMCS::Composition2N |
C RDKit::Conformer | The class for representing 2D or 3D conformation of a molecule
C RDKit::ConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
C RDKit::Descriptors::CrippenParamCollection | Singleton class for retrieving Crippen parameters
C RDKit::Descriptors::CrippenParams | Class used to store Crippen parameters
C RDKit::Dict | The `Dict` class can be used to store objects of arbitrary type keyed by `strings`
C RDKit::DiscreteDistMat |
C RDKit::DiscreteValueVect | Class for efficiently storing vectors of discrete values
►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::MaxMinPicker | Implements the MaxMin algorithm for picking a subset of item from a pool
C RDKit::FMCS::DuplicatedSeedCache |
C RDDepict::EmbeddedAtom | Class that contains the data for an atoms that has alredy been embedded
C RDDepict::EmbeddedFrag | Class containing a fragment of a molecule that has already been embedded
►Cenable_shared_from_this |
►C RDKit::FilterMatcherBase |
C RDKit::ExclusionList |
C RDKit::FilterMatchOps::And |
C RDKit::FilterMatchOps::Not |
C RDKit::FilterMatchOps::Or |
C RDKit::SmartsMatcher |
►Cstd::exception | STL class
C DatastructsException |
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 confomer access
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::ReactionPicklerException | Used to indicate exceptions whilst pickling (serializing) reactions
C RDKit::SLNParseException |
C RDKit::SmilesParseException |
►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::FileParseException | Used by various file parsing classes to indicate a parse error
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 RDKit::FilterData_t |
C RDKit::FilterMatch | Holds the atomPairs matched by the underlying matcher
C RDKit::FilterProperty_t |
C ForceFields::ForceField | A class to store forcefields and handle minimization
►C ForceFields::ForceFieldContrib | Abstract base class for contributions to ForceFields
C DistGeom::ChiralViolationContrib |
C DistGeom::DistViolationContrib |
C DistGeom::FourthDimContrib |
C ForceFields::CrystalFF::TorsionAngleContribM6 | Torsion term for multiplicity m = 1 - 6
C ForceFields::MMFF::AngleBendContrib | The angle-bend term for MMFF
C ForceFields::MMFF::AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib
C ForceFields::MMFF::BondStretchContrib | The bond-stretch term for MMFF
C ForceFields::MMFF::DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib
C ForceFields::MMFF::EleContrib | Electrostatic term for MMFF
C ForceFields::MMFF::OopBendContrib | Out-of-plane term for MMFF
C ForceFields::MMFF::PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2
C ForceFields::MMFF::StretchBendContrib | The angle-bend term for MMFF
C ForceFields::MMFF::TorsionAngleContrib | Torsion term for MMFF
C ForceFields::MMFF::TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib
C ForceFields::MMFF::VdWContrib | Van der Waals term for MMFF
C ForceFields::UFF::AngleBendContrib | The angle-bend term for the Universal Force Field
C ForceFields::UFF::AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib
C ForceFields::UFF::BondStretchContrib | The bond-stretch term for the Universal Force Field
C ForceFields::UFF::DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib
C ForceFields::UFF::InversionContrib | The inversion term for the Universal Force Field
C ForceFields::UFF::PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2
C ForceFields::UFF::TorsionAngleContrib | Torsion term for the Universal Force Field
C ForceFields::UFF::TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib
C ForceFields::UFF::vdWContrib | Van der Waals term for the Universal Force Field
C RDKit::FPBReader | Class for reading and searching FPB files
C RDKit::FragCatGenerator |
C RDKit::FragFPGenerator |
C RDKit::MolFragmenter::FragmenterBondType |
C RDKit::GasteigerParams |
►CGraph_t |
C RDKit::FMCS::Graph |
►C RDGeom::Grid3D | Virtual base class for a grid object
C RDGeom::UniformGrid3D |
C RDDepict::gtIIPair |
C RDKit::FMCS::SubstructureCache::HashKey |
C RDKit::MolHash::HashSet |
C RDKit::HeteroatomIterator_< Atom_, Mol_ > | Iterate over heteroatoms, this is bidirectional
C RDFeatures::ImplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE > |
C RDInfoTheory::InfoBitRanker |
C Queries::Int2Type< v > | Class to allow integer values to pick templates
►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 RDKit::FMCS::SubstructureCache::KeyNumericMetrics |
C RDKit::MolAlign::LAP |
C RDKit::larger_of< T > | Functor for returning the larger of two values
C RDKit::Utils::LocaleSwitcher |
C RDKit::ltDouble | Functor to compare two doubles with a tolerance
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 RDKit::MCSAtomCompareParameters |
C RDKit::MCSBondCompareParameters |
C RDKit::MCSParameters |
C RDKit::MCSProgressData |
C RDKit::MCSResult |
C RDDataManip::MetricMatrixCalc< vectType, entryType > | A generic metric matrix calculator (e.g similarity matrix or distance matrix)
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::MolChemicalFeatureDef |
C RDKit::MolChemicalFeatureFactory | The class for finding chemical features in molecules
►C RDKit::MolDraw2D |
C RDKit::MolDraw2DCairo |
C RDKit::MolDraw2DQt |
C RDKit::MolDraw2DSVG |
C RDKit::MolDraw2Dwx |
C RDKit::MolDrawOptions |
C RDKit::FMCS::MolFragment |
C RDKit::MolAlign::MolHistogram |
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::ForwardSDMolSupplier |
C RDKit::SDMolSupplier |
C RDKit::PDBMolSupplier | Lazy file parser for PDB files
C RDKit::SmilesMolSupplier | Lazy file parser for Smiles tables
C RDKit::TDTMolSupplier | Lazy file parser for TDT files
►C RDKit::MolWriter |
C RDKit::PDBWriter |
C RDKit::SDWriter |
C RDKit::SmilesWriter |
C RDKit::TDTWriter |
C RDKit::FMCS::NewBond |
C RDKit::MolAlign::O3A |
C RDKit::MolAlign::O3AConstraint |
C RDKit::MolAlign::O3AConstraintVect |
C RDKit::MolAlign::O3AFuncData |
C ForceFields::UFF::ParamCollection | Singleton class for retrieving UFF AtomParams
C RDKit::PeriodicTable | Singleton class for retrieving information about atoms
►C RDGeom::Point |
C RDGeom::Point2D |
C RDGeom::Point3D |
C RDGeom::PointND |
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< 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< 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 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< int, Atom const *, needsConversion > |
►C Queries::SetQuery< int, Atom const *, true > |
C RDKit::RecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS)
►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::HasPropQuery< TargetPtr > |
C RDKit::HasPropWithValueQuery< TargetPtr, T > |
C RDKit::HasPropWithValueQuery< TargetPtr, std::string > |
C RDKit::QueryAtomIterator_< Atom_, Mol_ > | Iterate over atoms matching a query. This is bidirectional
C boost::logging::rdLogger |
C RDKit::ReactionFingerprintParams |
C RDKit::ReactionPickler | Handles pickling (serializing) reactions
C RDKit::ResonanceMolSupplier |
C RDKit::RingInfo | A class to store information about a molecule's rings
C RDKit::FMCS::RingMatchTableSet |
►C RDKit::ROMol | ROMol is a molecule class that is intended to have a fixed topology
C RDKit::RWMol | RWMol is a molecule class that is intended to be edited
C RDKit::MolAlign::SDM |
C RDKit::FMCS::Seed |
C RDKit::FMCS::SeedSet |
C RDKit::SparseIntVect< IndexType > | Class for efficiently storing sparse vectors of ints
C RDKit::Canon::SpecialChiralityAtomCompareFunctor |
C RDKit::Canon::SpecialSymmetryAtomCompareFunctor |
►C boost_adaptbx::python::streambuf_capsule |
C boost_adaptbx::python::ostream |
C RDKit::FMCS::SubstructureCache |
C RDNumeric::SymmMatrix< TYPE > | A symmetric matrix class
C RDKit::FMCS::Target |
C RDKit::FMCS::TargetMatch |
C RDKit::FMCS::TArray2D< T > |
C RDKit::FMCS::TArray2D< bool > |
C RDKit::FMCS::DuplicatedSeedCache::TKey |
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 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