| Queries::AndQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing AND: requires all children to be true |
| ForceFields::UFF::AngleBendContrib | The angle-bend term for the Universal Force Field |
| RankAtoms::argless< T > | |
| RDKit::AromaticAtomIterator_< Atom_, Mol_, PMAP_ > | Iterate over aromatic atoms, this is bidirectional |
| RDKit::Atom | The class for representing atoms |
| RDKit::atomicData | |
| ForceFields::UFF::AtomicParams | Class to store atomic parameters for the Universal Force Field |
| RDKit::AtomIterator_< Atom_, Mol_, PMAP_ > | A general random access iterator |
| RDKit::AtomRingQuery | |
| RDKit::BadFileException | Used by various file parsing classes to indicate a bad file |
| RDInfoTheory::BitCorrMatGenerator | |
| BitVect | Abstract base class for storing BitVectors |
| RDKit::Bond | Class for representing a bond |
| RDKit::BondIterator_ | Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess |
| ForceFields::UFF::BondStretchContrib | The bond-stretch term for the Universal Force Field |
| DistGeom::BoundsMatrix | Class to store the distance bound |
| RDCatalog::Catalog< entryType, paramType > | Abstract base class for a catalog object |
| RDCatalog::CatalogEntry | Abstract base class to be used to represent an entry in a Catalog |
| RDCatalog::CatalogParams | Abstract base class for the container used to create a catalog |
| RDKit::charptr_functor | Functor for comparing two strings |
| ChemicalFeatures::ChemicalFeature | Abstract base class for chemical feature |
| RDKit::ChemicalReaction | This is a class for storing and applying general chemical reactions |
| RDKit::ChemicalReactionException | Used to indicate an error in the chemical reaction engine |
| RDKit::ChemicalReactionParserException | Used to indicate an error in parsing reaction data |
| DistGeom::ChiralSet | Class used to store a quartet of points and chiral volume bounds on them |
| DistGeom::ChiralViolationContrib | |
| RDKit::Conformer | The class for representing 2D or 3D conformation of a molecule |
| RDKit::ConformerException | Used to indicate errors from incorrect confomer access |
| RDKit::ConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess |
| RDKit::Descriptors::CrippenParamCollection | Singleton class for retrieving Crippen parameters |
| RDKit::Descriptors::CrippenParams | Class used to store Crippen parameters |
| DatastructsException | |
| RDKit::Dict | The Dict class can be used to store objects of arbitrary type keyed by strings |
| RDKit::DiscreteDistMat | |
| RDKit::DiscreteValueVect | Class for efficiently storing vectors of discrete values |
| ForceFields::UFF::DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib |
| RDPickers::DistPicker | Abstract base class to do perform item picking (typically molecules) using a distance matrix |
| DistGeom::DistViolationContrib | |
| RDKit::edge_bond_t | |
| RDKit::edge_wght_t | |
| RDDepict::EmbeddedAtom | Class that contains the data for an atoms that has alredy been embedded |
| RDDepict::EmbeddedFrag | Class containing a fragment of a molecule that has already been embedded |
| Queries::EqualityQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing ==: arguments must match a particular value (within an optional tolerance) |
| ExplicitBitVect | Class for bit vectors that are densely occupied |
| RDFeatures::ExplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE > | |
| RDKit::FeatureFileParseException | Class used to indicate errors in parsing feature definition files |
| RDKit::FileParseException | Used by various file parsing classes to indicate a parse error |
| ForceFields::ForceField | A class to store forcefields and handle minimization |
| ForceFields::ForceFieldContrib | Abstract base class for contributions to ForceFields |
| DistGeom::FourthDimContrib | |
| RDKit::FragCatalogEntry | |
| RDKit::FragCatGenerator | |
| RDKit::FragCatParams | Container for user parameters used to create a fragment catalog |
| RDKit::FragFPGenerator | |
| ChemicalFeatures::FreeChemicalFeature | Class for chemical features that do not orignate from molecules |
| RDKit::GasteigerParams | |
| Queries::GreaterEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing >= using a particular value (and an optional tolerance) |
| Queries::GreaterQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing > using a particular value (and an optional tolerance) |
| RDGeom::Grid3D | Virtual base class for a grid object |
| RDGeom::GridException | |
| RDDepict::gtIIPair | |
| RDKit::HeteroatomIterator_< Atom_, Mol_, PMAP_ > | Iterate over heteroatoms, this is bidirectional |
| RDCatalog::HierarchCatalog< entryType, paramType, orderType > | A Catalog with a hierarchical structure |
| RDCatalog::HierarchCatalog< entryType, paramType, orderType >::vertex_entry_t | Used by the BGL to set up the node properties in our graph |
| RDPickers::HierarchicalClusterPicker | Diversity picker based on hierarchical clustering |
| RDFeatures::ImplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE > | |
| IndexErrorException | Class to allow us to throw an IndexError from C++ and have it make it back to Python |
| RDInfoTheory::InfoBitRanker | |
| Queries::Int2Type< v > | Class to allow integer values to pick templates |
| Invar::Invariant | |
| KeyErrorException | Class to allow us to throw a KeyError from C++ and have it make it back to Python |
| RDKit::larger_of< T > | Functor for returning the larger of two values |
| Queries::LessEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing <= using a particular value (and an optional tolerance) |
| Queries::LessQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing < using a particular value (and an optional tolerance) |
| RDCatalog::LinearCatalog< entryType, orderType > | Linear Catalog (analogous to an std::vector) |
| RDKit::ltDouble | Functor to compare two doubles with a tolerance |
| RDNumeric::Matrix< TYPE > | A matrix class for general, non-square matrices |
| RDPickers::MaxMinPicker | Implements the MaxMin algorithm for picking a subset of item from a pool |
| RDDataManip::MetricMatrixCalc< vectType, entryType > | A generic metric matrix calculator (e.g similarity matrix or distance matrix) |
| RDKit::MolAlign::MolAlignException | |
| RDKit::MolCatalogEntry | This class is used to store ROMol objects in a MolCatalog |
| RDKit::MolCatalogParams | Container for user parameters used to create a mol catalog |
| RDKit::MolChemicalFeature | |
| RDKit::MolChemicalFeatureDef | |
| RDKit::MolChemicalFeatureFactory | The class for finding chemical features in molecules |
| RDKit::MolPickler | Handles pickling (serializing) molecules |
| RDKit::MolPicklerException | Used to indicate exceptions whilst pickling (serializing) molecules |
| RDKit::MolSanitizeException | Class for flagging sanitization errors |
| Canon::MolStackElem | These are the actual elements in the molecular stack |
| Canon::MolStackUnion | Used to store components in the molecular stack |
| RDKit::MolSupplier | |
| RDKit::MolWriter | |
| Queries::OrQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing AND: requires any child to be true |
| RankAtoms::pairGTFunctor< T > | Functor for implementing > on two std::pairs. The first entries are compared |
| ForceFields::UFF::ParamCollection | Singleton class for retrieving UFF AtomParams |
| RDKit::PeriodicTable | Singleton class for retrieving information about atoms |
| RDGeom::Point | |
| RDGeom::Point2D | |
| RDGeom::Point3D | |
| RDGeom::PointND | |
| PySequenceHolder< T > | Class to hold sequences (lists, tuples, arrays, etc.) passed from Python -> C++ |
| Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion > | Base class for all queries |
| RDKit::QueryAtom | Class for storing atomic queries |
| RDKit::QueryAtomIterator_< Atom_, Mol_, PMAP_ > | Iterate over atoms matching a query. This is bidirectional |
| RDKit::QueryBond | Class for storing Bond queries |
| Queries::RangeQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing a range: arguments must fall in a particular range of values |
| RDKit::RecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS) |
| RDKit::RingInfo | A class to store information about a molecule's rings |
| RDKit::ROMol | ROMol is a molecule class that is intended to have a fixed topology |
| RDKit::RWMol | RWMol is a molecule class that is intended to be edited |
| RDKit::SDMolSupplier | |
| RDKit::SDWriter | |
| Queries::SetQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing a set: arguments must one of a set of values |
| RDKit::SmilesMolSupplier | Lazy file parser for Smiles tables |
| RDKit::SmilesParseException | |
| RDKit::SmilesWriter | |
| SparseBitVect | Class for bit vectors that are sparsely occupied |
| RDKit::SparseIntVect< IndexType > | Class for efficiently storing sparse vectors of ints |
| RDNumeric::SquareMatrix< TYPE > | |
| RDNumeric::SymmMatrix< TYPE > | A symmetric matrix class |
| RDKit::TDTMolSupplier | Lazy file parser for TDT files |
| RDKit::TDTWriter | |
| ForceFields::UFF::TorsionAngleContrib | Torsion term for the Universal Force Field |
| RDGeom::Transform2D | |
| RDGeom::Transform3D | |
| RDGeom::UniformGrid3D | |
| ValueErrorException | Class to allow us to throw a ValueError from C++ and have it make it back to Python |
| ForceFields::UFF::vdWContrib | Van der Waals term for the Universal Force Field |
| RDNumeric::Vector< TYPE > | A class to represent vectors of numbers |
| RDKit::vertex_atom_t | |
| Queries::XOrQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing XOR: requires exactly one child to be true |
