CRDKit::AromaticAtomIterator_< Atom_, Mol_ > | Iterate over aromatic atoms, this is bidirectional |
►CRDKit::Atom | The class for representing atoms |
CRDKit::QueryAtom | Class for storing atomic queries |
CRDKit::Canon::AtomCompareFunctor | |
CRDKit::atomicData | |
CForceFields::UFF::AtomicParams | Class to store atomic parameters for the Universal Force Field |
CRDKit::AtomIterator_< Atom_, Mol_ > | A general random access iterator |
►CRDKit::AtomMonomerInfo | The abstract base class for atom-level monomer info |
CRDKit::AtomPDBResidueInfo | Captures atom-level information about peptide residues |
CRDKit::SLNParse::AttribType | |
►Cbasic_streambuf | |
Cboost_adaptbx::python::streambuf | A stream buffer getting data from and putting data into a Python file object |
►Cbinary_function | |
CRankers::argless< T > | |
CRankers::pairGreater< T1, T2 > | Functor for implementing > on two std::pairs. The first entries are compared |
CRankers::pairLess< T1, T2 > | Function for implementing < on two std::pairs. The first entries are compared |
CRDInfoTheory::BitCorrMatGenerator | |
►CBitVect | Abstract base class for storing BitVectors |
CExplicitBitVect | Class for bit vectors that are densely occupied |
CSparseBitVect | Class for bit vectors that are sparsely occupied |
►CRDKit::Bond | Class for representing a bond |
CRDKit::QueryBond | Class for storing Bond queries |
CRDKit::Canon::bondholder | |
CRDKit::BondIterator_ | Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess |
CRDKit::Canon::canon_atom | |
►CRDCatalog::Catalog< entryType, paramType > | Abstract base class for a catalog object |
CRDCatalog::HierarchCatalog< entryType, paramType, orderType > | A Catalog with a hierarchical structure |
►CRDCatalog::Catalog< entryType, orderType > | |
CRDCatalog::LinearCatalog< entryType, orderType > | Linear Catalog (analogous to an std::vector) |
►CRDCatalog::CatalogEntry | Abstract base class to be used to represent an entry in a Catalog |
CRDKit::FragCatalogEntry | |
CRDKit::MolCatalogEntry | This class is used to store ROMol objects in a MolCatalog |
►CRDCatalog::CatalogParams | Abstract base class for the container used to create a catalog |
CRDKit::FragCatParams | Container for user parameters used to create a fragment catalog |
CRDKit::MolCatalogParams | Container for user parameters used to create a mol catalog |
CRDKit::charptr_functor | Functor for comparing two strings |
►CChemicalFeatures::ChemicalFeature | Abstract base class for chemical feature |
CChemicalFeatures::FreeChemicalFeature | Class for chemical features that do not orignate from molecules |
CRDKit::MolChemicalFeature | |
CRDKit::ChemicalReaction | This is a class for storing and applying general chemical reactions |
CRDKit::Canon::ChiralAtomCompareFunctor | |
CDistGeom::ChiralSet | Class used to store a quartet of points and chiral volume bounds on them |
CRDKit::FMCS::Composition2N | |
CRDKit::Conformer | The class for representing 2D or 3D conformation of a molecule |
CRDKit::ConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess |
CRDKit::Descriptors::CrippenParamCollection | Singleton class for retrieving Crippen parameters |
CRDKit::Descriptors::CrippenParams | Class used to store Crippen parameters |
CRDKit::Dict | The Dict class can be used to store objects of arbitrary type keyed by strings |
CRDKit::DiscreteDistMat | |
CRDKit::DiscreteValueVect | Class for efficiently storing vectors of discrete values |
►CRDPickers::DistPicker | Abstract base class to do perform item picking (typically molecules) using a distance matrix |
CRDPickers::HierarchicalClusterPicker | Diversity picker based on hierarchical clustering |
CRDPickers::MaxMinPicker | Implements the MaxMin algorithm for picking a subset of item from a pool |
CRDKit::FMCS::DuplicatedSeedCache | |
CRDDepict::EmbeddedAtom | Class that contains the data for an atoms that has alredy been embedded |
CRDDepict::EmbeddedFrag | Class containing a fragment of a molecule that has already been embedded |
►Cstd::exception | STL class |
CDatastructsException | |
CRDGeom::GridException | |
CRDKit::ChemicalReactionException | Used to indicate an error in the chemical reaction engine |
CRDKit::ChemicalReactionParserException | Used to indicate an error in parsing reaction data |
CRDKit::ConformerException | Used to indicate errors from incorrect confomer access |
CRDKit::FeatureFileParseException | Class used to indicate errors in parsing feature definition files |
CRDKit::MolAlign::MolAlignException | |
CRDKit::MolPicklerException | Used to indicate exceptions whilst pickling (serializing) molecules |
CRDKit::MolSanitizeException | Class for flagging sanitization errors |
CRDKit::ReactionPicklerException | Used to indicate exceptions whilst pickling (serializing) reactions |
CRDKit::SLNParseException | |
CRDKit::SmilesParseException | |
►Cstd::runtime_error | STL class |
CIndexErrorException | Class to allow us to throw an IndexError from C++ and have it make it back to Python |
CInvar::Invariant | |
CKeyErrorException | Class to allow us to throw a KeyError from C++ and have it make it back to Python |
CRDKit::BadFileException | Used by various file parsing classes to indicate a bad file |
CRDKit::FileParseException | Used by various file parsing classes to indicate a parse error |
CValueErrorException | Class to allow us to throw a ValueError from C++ and have it make it back to Python |
CRDKit::FMCS::ExecStatistics | |
CRDFeatures::ExplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE > | |
CForceFields::ForceField | A class to store forcefields and handle minimization |
►CForceFields::ForceFieldContrib | Abstract base class for contributions to ForceFields |
CDistGeom::ChiralViolationContrib | |
CDistGeom::DistViolationContrib | |
CDistGeom::FourthDimContrib | |
CForceFields::MMFF::AngleBendContrib | The angle-bend term for MMFF |
CForceFields::MMFF::AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib |
CForceFields::MMFF::BondStretchContrib | The bond-stretch term for MMFF |
CForceFields::MMFF::DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib |
CForceFields::MMFF::EleContrib | Electrostatic term for MMFF |
CForceFields::MMFF::OopBendContrib | Out-of-plane term for MMFF |
CForceFields::MMFF::PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2 |
CForceFields::MMFF::StretchBendContrib | The angle-bend term for MMFF |
CForceFields::MMFF::TorsionAngleContrib | Torsion term for MMFF |
CForceFields::MMFF::TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib |
CForceFields::MMFF::VdWContrib | Van der Waals term for MMFF |
CForceFields::UFF::AngleBendContrib | The angle-bend term for the Universal Force Field |
CForceFields::UFF::AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib |
CForceFields::UFF::BondStretchContrib | The bond-stretch term for the Universal Force Field |
CForceFields::UFF::DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib |
CForceFields::UFF::InversionContrib | The inversion term for the Universal Force Field |
CForceFields::UFF::PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2 |
CForceFields::UFF::TorsionAngleContrib | Torsion term for the Universal Force Field |
CForceFields::UFF::TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib |
CForceFields::UFF::vdWContrib | Van der Waals term for the Universal Force Field |
CRDKit::FragCatGenerator | |
CRDKit::FragFPGenerator | |
CRDKit::MolFragmenter::FragmenterBondType | |
CRDKit::GasteigerParams | |
►CGraph_t | |
CRDKit::FMCS::Graph | |
►CRDGeom::Grid3D | Virtual base class for a grid object |
CRDGeom::UniformGrid3D | |
CRDDepict::gtIIPair | |
CRDKit::FMCS::SubstructureCache::HashKey | |
CRDKit::MolHash::HashSet | |
CRDKit::HeteroatomIterator_< Atom_, Mol_ > | Iterate over heteroatoms, this is bidirectional |
CRDFeatures::ImplicitFeature< FAMILYMARKER, TYPEMARKER, LOCTYPE > | |
CRDInfoTheory::InfoBitRanker | |
CQueries::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 |
Cboost_adaptbx::python::streambuf::istream | |
►Cstd::basic_ostream< Char > | STL class |
►Cstd::ostream | STL class |
►Cboost_adaptbx::python::streambuf::ostream | |
Cboost_adaptbx::python::ostream | |
CRDKit::FMCS::SubstructureCache::KeyNumericMetrics | |
CRDKit::MolAlign::LAP | |
CRDKit::larger_of< T > | Functor for returning the larger of two values |
CRDKit::Utils::LocaleSwitcher | |
CRDKit::ltDouble | Functor to compare two doubles with a tolerance |
CRDKit::MatchingAtomIterator_< Atom_, Mol_ > | Iterate over atoms matching a query function. This is bidirectional |
►CRDNumeric::Matrix< TYPE > | A matrix class for general, non-square matrices |
CRDNumeric::SquareMatrix< TYPE > | |
►CRDNumeric::Matrix< double > | |
►CRDNumeric::SquareMatrix< double > | |
CDistGeom::BoundsMatrix | Class to store the distance bound |
CRDGeom::Transform2D | |
CRDGeom::Transform3D | |
CRDKit::FMCS::MaximumCommonSubgraph | |
CRDKit::MCSAtomCompareParameters | |
CRDKit::MCSBondCompareParameters | |
CRDKit::MCSParameters | |
CRDKit::MCSProgressData | |
CRDKit::MCSResult | |
CRDDataManip::MetricMatrixCalc< vectType, entryType > | A generic metric matrix calculator (e.g similarity matrix or distance matrix) |
CForceFields::MMFF::MMFFAngle | Class to store MMFF parameters for angle bending |
CForceFields::MMFF::MMFFAngleCollection | |
CForceFields::MMFF::MMFFAromCollection | |
CRDKit::MMFF::MMFFAtomProperties | |
CForceFields::MMFF::MMFFBndkCollection | |
CForceFields::MMFF::MMFFBond | Class to store MMFF parameters for bond stretching |
CForceFields::MMFF::MMFFBondCollection | |
CForceFields::MMFF::MMFFChg | |
CForceFields::MMFF::MMFFChgCollection | |
CForceFields::MMFF::MMFFCovRadPauEle | |
CForceFields::MMFF::MMFFCovRadPauEleCollection | |
CForceFields::MMFF::MMFFDef | Class to store MMFF atom type equivalence levels |
CForceFields::MMFF::MMFFDefCollection | |
CForceFields::MMFF::MMFFDfsbCollection | |
CForceFields::MMFF::MMFFHerschbachLaurie | |
CForceFields::MMFF::MMFFHerschbachLaurieCollection | |
CRDKit::MMFF::MMFFMolProperties | |
CForceFields::MMFF::MMFFOop | Class to store MMFF parameters for out-of-plane bending |
CForceFields::MMFF::MMFFOopCollection | |
CForceFields::MMFF::MMFFPBCI | Class to store MMFF Partial Bond Charge Increments |
CForceFields::MMFF::MMFFPBCICollection | |
CForceFields::MMFF::MMFFProp | Class to store MMFF Properties |
CForceFields::MMFF::MMFFPropCollection | |
CForceFields::MMFF::MMFFStbn | Class to store MMFF parameters for stretch-bending |
CForceFields::MMFF::MMFFStbnCollection | |
CForceFields::MMFF::MMFFTor | Class to store MMFF parameters for torsions |
CForceFields::MMFF::MMFFTorCollection | |
CForceFields::MMFF::MMFFVdW | Class to store MMFF parameters for non-bonded Van der Waals |
CForceFields::MMFF::MMFFVdWCollection | |
CForceFields::MMFF::MMFFVdWRijstarEps | |
CRDKit::MolChemicalFeatureDef | |
CRDKit::MolChemicalFeatureFactory | The class for finding chemical features in molecules |
►CRDKit::MolDraw2D | |
CRDKit::MolDraw2DCairo | |
CRDKit::MolDraw2DQt | |
CRDKit::MolDraw2DSVG | |
CRDKit::MolDraw2Dwx | |
CRDKit::MolDrawOptions | |
CRDKit::FMCS::MolFragment | |
CRDKit::MolAlign::MolHistogram | |
CRDKit::MolPickler | Handles pickling (serializing) molecules |
CRDKit::Canon::MolStackElem | These are the actual elements in the molecular stack |
CRDKit::Canon::MolStackUnion | Used to store components in the molecular stack |
►CRDKit::MolSupplier | |
►CRDKit::ForwardSDMolSupplier | |
CRDKit::SDMolSupplier | |
CRDKit::PDBMolSupplier | Lazy file parser for PDB files |
CRDKit::SmilesMolSupplier | Lazy file parser for Smiles tables |
CRDKit::TDTMolSupplier | Lazy file parser for TDT files |
►CRDKit::MolWriter | |
CRDKit::PDBWriter | |
CRDKit::SDWriter | |
CRDKit::SmilesWriter | |
CRDKit::TDTWriter | |
CRDKit::FMCS::NewBond | |
CRDKit::MolAlign::O3A | |
CRDKit::MolAlign::O3AConstraint | |
CRDKit::MolAlign::O3AConstraintVect | |
CRDKit::MolAlign::O3AFuncData | |
CForceFields::UFF::ParamCollection | Singleton class for retrieving UFF AtomParams |
CRDKit::PeriodicTable | Singleton class for retrieving information about atoms |
►CRDGeom::Point | |
CRDGeom::Point2D | |
CRDGeom::Point3D | |
CRDGeom::PointND | |
CPySequenceHolder< T > | Class to hold sequences (lists, tuples, arrays, etc.) passed from Python -> C++ |
►CQueries::Query< MatchFuncArgType, DataFuncArgType, needsConversion > | Base class for all queries |
CQueries::AndQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing AND: requires all children to be true |
►CQueries::EqualityQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing ==: arguments must match a particular value (within an optional tolerance) |
CQueries::GreaterEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing >= using a particular value (and an optional tolerance) |
CQueries::GreaterQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing > using a particular value (and an optional tolerance) |
CQueries::LessEqualQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing <= using a particular value (and an optional tolerance) |
CQueries::LessQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing < using a particular value (and an optional tolerance) |
CQueries::OrQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing AND: requires any child to be true |
CQueries::RangeQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing a range: arguments must fall in a particular range of values |
CQueries::SetQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing a set: arguments must one of a set of values |
CQueries::XOrQuery< MatchFuncArgType, DataFuncArgType, needsConversion > | Query implementing XOR: requires exactly one child to be true |
►CQueries::Query< int, Atom const *, needsConversion > | |
►CQueries::SetQuery< int, Atom const *, true > | |
CRDKit::RecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS) |
►CQueries::Query< int, ConstAtomPtr, needsConversion > | |
►CQueries::EqualityQuery< int, ConstAtomPtr, true > | |
CRDKit::AtomRingQuery | |
►CQueries::Query< int, TargetPtr, needsConversion > | |
►CQueries::EqualityQuery< int, TargetPtr, true > | |
CRDKit::HasPropQuery< TargetPtr > | |
CRDKit::HasPropWithValueQuery< TargetPtr, T > | |
CRDKit::HasPropWithValueQuery< TargetPtr, std::string > | |
CRDKit::QueryAtomIterator_< Atom_, Mol_ > | Iterate over atoms matching a query. This is bidirectional |
Cboost::logging::rdLogger | |
CRDKit::ReactionFingerprintParams | |
CRDKit::ReactionPickler | Handles pickling (serializing) reactions |
CRDKit::RingInfo | A class to store information about a molecule's rings |
CRDKit::FMCS::RingMatchTableSet | |
►CRDKit::ROMol | ROMol is a molecule class that is intended to have a fixed topology |
CRDKit::RWMol | RWMol is a molecule class that is intended to be edited |
CRDKit::MolAlign::SDM | |
CRDKit::FMCS::Seed | |
CRDKit::FMCS::SeedSet | |
CRDKit::SparseIntVect< IndexType > | Class for efficiently storing sparse vectors of ints |
CRDKit::Canon::SpecialChiralityAtomCompareFunctor | |
CRDKit::Canon::SpecialSymmetryAtomCompareFunctor | |
►Cboost_adaptbx::python::streambuf_capsule | |
Cboost_adaptbx::python::ostream | |
CRDKit::FMCS::SubstructureCache | |
CRDNumeric::SymmMatrix< TYPE > | A symmetric matrix class |
CRDKit::FMCS::Target | |
CRDKit::FMCS::TargetMatch | |
CRDKit::FMCS::TArray2D< T > | |
CRDKit::FMCS::TArray2D< bool > | |
CRDKit::FMCS::DuplicatedSeedCache::TKey | |
CForceFields::UFF::UFFAngle | Class to store UFF parameters for angle bending |
CForceFields::UFF::UFFBond | Class to store UFF parameters for bond stretching |
CForceFields::UFF::UFFInv | Class to store UFF parameters for inversions |
CForceFields::UFF::UFFTor | Class to store UFF parameters for torsions |
CForceFields::UFF::UFFVdW | Class to store UFF parameters for van der Waals interactions |
CRDNumeric::Vector< TYPE > | A class to represent vectors of numbers |
CRDCatalog::HierarchCatalog< entryType, paramType, orderType >::vertex_entry_t | Used by the BGL to set up the node properties in our graph |