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RDKit
Open-source cheminformatics and machine learning.
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►Nboost | |
►Nlogging | |
CrdLogger | |
►Nboost_adaptbx | |
►Npython | |
Costream | |
►Cstreambuf | A stream buffer getting data from and putting data into a Python file object |
Cistream | |
Costream | |
Cstreambuf_capsule | |
►NChemicalFeatures | |
CChemicalFeature | Abstract base class for chemical feature |
CFreeChemicalFeature | Class for chemical features that do not orignate from molecules |
►Nconrec | |
CConrecSegment | |
►NDistGeom | |
CBoundsMatrix | Class to store the distance bound |
CChiralSet | Class used to store a quartet of points and chiral volume bounds on them |
CChiralViolationContrib | |
CDistViolationContrib | |
CFourthDimContrib | |
►NForceFields | |
►NCrystalFF | |
CCrystalFFDetails | |
CTorsionAngleContribM6 | Torsion term for multiplicity m = 1 - 6 |
►NMMFF | |
CAngleBendContrib | The angle-bend term for MMFF |
CAngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib |
CBondStretchContrib | The bond-stretch term for MMFF |
CDistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib |
CEleContrib | Electrostatic term for MMFF |
CMMFFAngle | Class to store MMFF parameters for angle bending |
CMMFFAngleCollection | |
CMMFFAromCollection | |
CMMFFBndkCollection | |
CMMFFBond | Class to store MMFF parameters for bond stretching |
CMMFFBondCollection | |
CMMFFChg | |
CMMFFChgCollection | |
CMMFFCovRadPauEle | |
CMMFFCovRadPauEleCollection | |
CMMFFDef | Class to store MMFF atom type equivalence levels |
CMMFFDefCollection | |
CMMFFDfsbCollection | |
CMMFFHerschbachLaurie | |
CMMFFHerschbachLaurieCollection | |
CMMFFOop | Class to store MMFF parameters for out-of-plane bending |
CMMFFOopCollection | |
CMMFFPBCI | Class to store MMFF Partial Bond Charge Increments |
CMMFFPBCICollection | |
CMMFFProp | Class to store MMFF Properties |
CMMFFPropCollection | |
CMMFFStbn | Class to store MMFF parameters for stretch-bending |
CMMFFStbnCollection | |
CMMFFTor | Class to store MMFF parameters for torsions |
CMMFFTorCollection | |
CMMFFVdW | Class to store MMFF parameters for non-bonded Van der Waals |
CMMFFVdWCollection | |
CMMFFVdWRijstarEps | |
COopBendContrib | Out-of-plane term for MMFF |
CPositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2 |
CStretchBendContrib | The angle-bend term for MMFF |
CTorsionAngleContrib | Torsion term for MMFF |
CTorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib |
CVdWContrib | Van der Waals term for MMFF |
►NUFF | |
CAngleBendContrib | The angle-bend term for the Universal Force Field |
CAngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib |
CAtomicParams | Class to store atomic parameters for the Universal Force Field |
CBondStretchContrib | The bond-stretch term for the Universal Force Field |
CDistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib |
CInversionContrib | The inversion term for the Universal Force Field |
CParamCollection | Singleton class for retrieving UFF AtomParams |
CPositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2 |
CTorsionAngleContrib | Torsion term for the Universal Force Field |
CTorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib |
CUFFAngle | Class to store UFF parameters for angle bending |
CUFFBond | Class to store UFF parameters for bond stretching |
CUFFInv | Class to store UFF parameters for inversions |
CUFFTor | Class to store UFF parameters for torsions |
CUFFVdW | Class to store UFF parameters for van der Waals interactions |
CvdWContrib | Van der Waals term for the Universal Force Field |
CForceField | A class to store forcefields and handle minimization |
CForceFieldContrib | Abstract base class for contributions to ForceFields |
►NInvar | |
CInvariant | |
►NQueries | |
CAndQuery | Query implementing AND: requires all children to be true |
CEqualityQuery | Query implementing ==: arguments must match a particular value (within an optional tolerance) |
CGreaterEqualQuery | Query implementing >= using a particular value (and an optional tolerance) |
CGreaterQuery | Query implementing > using a particular value (and an optional tolerance) |
CInt2Type | Class to allow integer values to pick templates |
CLessEqualQuery | Query implementing <= using a particular value (and an optional tolerance) |
CLessQuery | Query implementing < using a particular value (and an optional tolerance) |
COrQuery | Query implementing AND: requires any child to be true |
CQuery | Base class for all queries |
CRangeQuery | Query implementing a range: arguments must fall in a particular range of values |
CSetQuery | Query implementing a set: arguments must one of a set of values |
CXOrQuery | Query implementing XOR: requires exactly one child to be true |
►NRankers | Utility functionality used to rank sequences |
Cargless | |
CpairGreater | Functor for implementing > on two std::pairs. The first entries are |
CpairLess | Function for implementing < on two std::pairs. The first entries are |
►NRDCatalog | |
CCatalog | Abstract base class for a catalog object |
CCatalogEntry | Abstract base class to be used to represent an entry in a Catalog |
CCatalogParams | Abstract base class for the container used to create a catalog |
►CHierarchCatalog | A Catalog with a hierarchical structure |
Cvertex_entry_t | Used by the BGL to set up the node properties in our graph |
►NRDDataManip | |
CMetricMatrixCalc | A generic metric matrix calculator (e.g similarity matrix or distance matrix) |
►NRDDepict | |
CDepictException | |
CEmbeddedAtom | Class that contains the data for an atoms that has alredy been embedded |
CEmbeddedFrag | Class containing a fragment of a molecule that has already been embedded |
CgtIIPair | |
►NRDFeatures | |
CExplicitFeature | |
CImplicitFeature | |
►NRDGeom | |
CGrid3D | Virtual base class for a grid object |
CGridException | |
CPoint | |
CPoint2D | |
CPoint3D | |
CPointND | |
CTransform2D | |
CTransform3D | |
CUniformGrid3D | |
►NRDInfoTheory | Class used to rank bits based on a specified measure of infomation |
CBitCorrMatGenerator | |
CInfoBitRanker | |
►NRDKit | Std stuff |
►NAtomPair | |
CAtomPairArguments | Class that holds atom-pair fingerprint specific arguments |
CAtomPairAtomEnv | Class that holds atom-environment data needed for atom-pair fingerprint generation |
CAtomPairAtomInvGenerator | |
CAtomPairEnvGenerator | Class that generates atom-environments for atom-pair fingerprint |
►NCanon | |
CAtomCompareFunctor | |
Cbondholder | |
Ccanon_atom | |
CChiralAtomCompareFunctor | |
CMolStackElem | These are the actual elements in the molecular stack |
CMolStackUnion | Used to store components in the molecular stack |
CSpecialChiralityAtomCompareFunctor | |
CSpecialSymmetryAtomCompareFunctor | |
►NDescriptors | |
CCrippenParamCollection | Singleton class for retrieving Crippen parameters |
CCrippenParams | Class used to store Crippen parameters |
CProperties | Holds a collection of properties for computation purposes |
CPropertyFunctor | |
►NDGeomHelpers | |
CEmbedParameters | Parameter object for controlling embedding |
►NFilterMatchOps | |
CAnd | |
CNot | |
COr | |
►NFMCS | |
CComposition2N | |
►CDuplicatedSeedCache | |
CTKey | |
CExecStatistics | |
CGraph | |
CMaximumCommonSubgraph | |
CMolFragment | |
CNewBond | |
CRingMatchTableSet | |
CSeed | |
CSeedSet | |
►CSubstructureCache | |
CHashKey | |
CKeyNumericMetrics | |
CTarget | |
CTargetMatch | |
CTArray2D | |
►NForceFieldsHelper | |
►NMMFF | |
►NTools | |
CDefaultTorsionBondSmarts | |
CMMFFAtomProperties | |
CMMFFMolProperties | |
►NMolAlign | |
CLAP | |
CMolAlignException | |
CMolHistogram | |
CO3A | |
CO3AConstraint | |
CO3AConstraintVect | |
CO3AFuncData | |
CSDM | |
►NMolDraw2DUtils | |
CContourParams | |
►NMolFragmenter | |
CFragmenterBondType | |
►NMolHash | |
CHashSet | |
►NMolInterchange | |
CJSONParseParameters | |
►NMolOps | Groups a variety of molecular query and transformation operations |
CAdjustQueryParameters | |
►NMolStandardize | |
CAcidBaseCatalogEntry | |
CAcidBaseCatalogParams | |
CAllowedAtomsValidation | |
CChargeCorrection | |
CCleanupParameters | The CleanupParameters structure defines the default parameters for the |
CDisallowedAtomsValidation | |
CFragmentCatalogEntry | |
CFragmentCatalogParams | |
CFragmentRemover | |
CFragmentValidation | Logs if certain fragments are present |
CIsotopeValidation | Logs if molecule contains isotopes |
►CLargestFragmentChooser | |
CLargest | |
CMetalDisconnector | |
CMolVSValidation | Can be used to perform all MolVSValidions |
CMolVSValidations | Includes most of the same validations as |
CNeutralValidation | Logs if not an overall neutral system |
CNoAtomValidation | Throws an error if no atoms are present in the |
►CNormalizer | For applying Normalization transforms |
CProduct | |
CRDKitValidation | Throws an error when there are no atoms in the |
CReionizer | The reionizer class to fix charges and reionize a molecule such that the |
CTautomerCanonicalizer | |
CTautomerCatalogEntry | |
CTautomerCatalogParams | |
CTautomerEnumerator | |
CTautomerTransform | |
CTransformCatalogEntry | |
CTransformCatalogParams | |
CUncharger | For neutralizing ionized acids and bases |
CValidationErrorInfo | Used to store the information returned by a |
CValidationMethod | Abstract base class upon which all the |
►NMorganFingerprint | |
CMorganArguments | Class for holding Morgan fingerprint specific arguments |
CMorganAtomEnv | Class for holding the bit-id created from Morgan fingerprint environments and the additional data necessary extra outputs |
CMorganAtomInvGenerator | Default atom invariants generator for Morgan fingerprint, generates ECFP-type invariants |
CMorganBondInvGenerator | Bond invariants generator for Morgan fingerprint |
CMorganEnvGenerator | Class that generates atom environments for Morgan fingerprint |
CMorganFeatureAtomInvGenerator | Alternative atom invariants generator for Morgan fingerprint, generate FCFP-type invariants |
►NMorganFingerprints | |
Css_matcher | |
►NRDKitFP | |
CRDKitFPArguments | |
CRDKitFPAtomEnv | |
CRDKitFPAtomInvGenerator | |
CRDKitFPEnvGenerator | |
►NRDTypeTag | |
►Ndetail | |
CValue | |
►NSLNParse | |
CAttribType | |
►NStructureCheck | |
CAugmentedAtom | |
CChargeFix | |
CIncEntry | |
CLigand | |
CNeighbourhood | |
CPathEntry | |
CStructChecker | Class for performing structure validation and cleanup |
CStructCheckerOptions | Structure Check Options |
CStructCheckTautomer | |
►NTopologicalTorsion | |
CTopologicalTorsionArguments | |
CTopologicalTorsionAtomEnv | |
CTopologicalTorsionEnvGenerator | |
►NUFF | |
►NTools | |
CDefaultTorsionBondSmarts | |
►NUtils | |
CLocaleSwitcher | |
CAdditionalOutput | |
CAromaticAtomIterator_ | Iterate over aromatic atoms, this is bidirectional |
CAtom | The class for representing atoms |
CAtomEnvironment | Abstract base class that holds atom-environments that will be hashed to generate the fingerprint |
CAtomEnvironmentGenerator | Abstract base class that generates atom-environments from a molecule |
CatomicData | |
CAtomInvariantsGenerator | Abstract base class for atom invariants generators |
CAtomIterator_ | A general random access iterator |
CAtomKekulizeException | |
CAtomMonomerInfo | The abstract base class for atom-level monomer info |
CAtomPDBResidueInfo | Captures atom-level information about peptide residues |
CAtomRingQuery | |
CAtomSanitizeException | |
CAtomValenceException | |
CBadFileException | Used by various file parsing classes to indicate a bad file |
CBond | Class for representing a bond |
CBondInvariantsGenerator | Abstract base class for bond invariants generators |
CBondIterator_ | Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess |
CCachedMolHolder | Concrete class that holds binary cached molecules in memory |
CCachedSmilesMolHolder | Concrete class that holds smiles strings in memory |
CCachedTrustedSmilesMolHolder | Concrete class that holds trusted smiles strings in memory |
CCartesianProductStrategy | This is a class for enumerating reagents using Cartesian Products of |
Ccharptr_functor | Functor for comparing two strings |
CChemicalReaction | This is a class for storing and applying general chemical reactions |
CChemicalReactionException | Used to indicate an error in the chemical reaction engine |
CChemicalReactionParserException | Used to indicate an error in parsing reaction data |
CConformer | The class for representing 2D or 3D conformation of a molecule |
CConformerException | Used to indicate errors from incorrect confomer access |
CConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess |
CCustomPropHandler | |
►CCXXAtomIterator | |
CCXXAtomIter | |
►CCXXBondIterator | |
CCXXBondIter | |
CDataStructsExplicitBitVecPropHandler | |
►CDict | The Dict class can be used to store objects of arbitrary type keyed by strings |
CPair | |
CDiscreteDistMat | |
CDiscreteValueVect | Class for efficiently storing vectors of discrete values |
CDrawColour | |
CEnumerateLibrary | This is a class for running reactions on sets of reagents |
CEnumerateLibraryBase | Base class for enumerating chemical reactions from collections of |
CEnumerationParams | This is a class for providing enumeration options that control |
CEnumerationStrategyBase | |
CEnumerationStrategyException | Class for flagging enumeration strategy errors |
CEvenSamplePairsStrategy | EvenSamplePairsStrategy |
CExclusionList | |
CFeatureFileParseException | Class used to indicate errors in parsing feature definition files |
CFileParseException | Used by various file parsing classes to indicate a parse error |
CFilterCatalog | |
CFilterCatalogEntry | |
CFilterCatalogParams | |
CFilterData_t | |
CFilterHierarchyMatcher | |
CFilterMatch | Holds the atomPairs matched by the underlying matcher |
CFilterMatcherBase | |
CFilterProperty_t | |
CFingerprintArguments | 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 |
CFingerprintGenerator | Class that generates same fingerprint style for different output formats |
CForwardSDMolSupplier | |
CFPBReader | Class for reading and searching FPB files |
CFPHolderBase | Base FPI for the fingerprinter used to rule out impossible matches |
CFragCatalogEntry | |
CFragCatGenerator | |
CFragCatParams | Container for user parameters used to create a fragment catalog |
CFragFPGenerator | |
CGasteigerParams | |
CHasPropQuery | |
CHasPropWithValueQuery | |
CHasPropWithValueQuery< TargetPtr, ExplicitBitVect > | |
CHasPropWithValueQuery< TargetPtr, std::string > | |
CHeteroatomIterator_ | Iterate over heteroatoms, this is bidirectional |
CKekulizeException | |
Clarger_of | Functor for returning the larger of two values |
CltDouble | Functor to compare two doubles with a tolerance |
CMatchingAtomIterator_ | Iterate over atoms matching a query function. This is bidirectional |
CMCSAtomCompareParameters | |
CMCSBondCompareParameters | |
CMCSParameters | |
CMCSProgressData | |
CMCSResult | |
CMolBundle | |
CMolCatalogEntry | This class is used to store ROMol objects in a MolCatalog |
CMolCatalogParams | Container for user parameters used to create a mol catalog |
CMolChemicalFeature | |
CMolChemicalFeatureDef | |
CMolChemicalFeatureFactory | The class for finding chemical features in molecules |
CMolDraw2D | MolDraw2D is the base class for doing 2D renderings of molecules |
CMolDraw2DCairo | |
CMolDraw2DQt | |
CMolDraw2DSVG | |
CMolDraw2Dwx | |
CMolDrawOptions | |
CMolFileUnhandledFeatureException | |
CMolHolder | Concrete class that holds molecules in memory |
CMolHolderBase | Base class API for holding molecules to substructure search |
CMolPickler | Handles pickling (serializing) molecules |
CMolPicklerException | Used to indicate exceptions whilst pickling (serializing) molecules |
CMolSanitizeException | Class for flagging sanitization errors |
CMolSupplier | |
CMolWriter | |
CMultiFPBReader | Class for reading and searching multiple FPB files |
CMultiMolDraw2D | |
CPatternHolder | Uses the pattern fingerprinter to rule out matches |
CPDBMolSupplier | Lazy file parser for PDB files |
CPDBWriter | |
CPeriodicTable | Singleton class for retrieving information about atoms |
CQueryAtom | Class for storing atomic queries |
CQueryAtomIterator_ | Iterate over atoms matching a query. This is bidirectional |
CQueryBond | Class for storing Bond queries |
CRandomSampleAllBBsStrategy | This is a class for randomly enumerating reagents that ensures all reagents |
CRandomSampleStrategy | This is a class for fully randomly sampling reagents |
CRDAny | |
CRDProps | |
CRDValue | |
CReactionFingerprintParams | |
CReactionPickler | Handles pickling (serializing) reactions |
CReactionPicklerException | Used to indicate exceptions whilst pickling (serializing) reactions |
CRecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS) |
CResonanceMolSupplier | |
CRGroupDecomposition | |
CRGroupDecompositionParameters | |
CRingInfo | A class to store information about a molecule's rings |
CROMol | |
CRWMol | RWMol is a molecule class that is intended to be edited |
CRxnSanitizeException | Class for flagging sanitization errors |
CSDMolSupplier | |
CSDWriter | |
CSLNParseException | |
CSmartsMatcher | |
CSmilesMolSupplier | Lazy file parser for Smiles tables |
CSmilesParseException | |
CSmilesParserParams | |
CSmilesWriter | |
CSnapshot | |
CSparseIntVect | Class for efficiently storing sparse vectors of ints |
CStereoGroup | |
►CSubstanceGroup | The class for representing SubstanceGroups |
CAttachPoint | |
CCState | |
CSubstanceGroupException | Used to indicate errors from incorrect sgroup access |
CSubstructLibrary | Substructure Search a library of molecules |
CSubstructMatchParameters | |
CTDTMolSupplier | Lazy file parser for TDT files |
CTDTWriter | |
CTrajectory | |
CUnimplementedFPException | Used to indicate errors for unimplemented fp types in convenience functions |
►NRDNumeric | |
CMatrix | A matrix class for general, non-square matrices |
CSquareMatrix | |
CSymmMatrix | A symmetric matrix class |
CVector | A class to represent vectors of numbers |
►NRDPickers | |
CDistPicker | Abstract base class to do perform item picking (typically molecules) using a distance matrix |
CHierarchicalClusterPicker | Diversity picker based on hierarchical clustering |
CLeaderPicker | Implements the Leader algorithm for picking a subset of item from a pool |
CLeaderPickerState | |
CMaxMinPicker | Implements the MaxMin algorithm for picking a subset of item from a pool |
CMaxMinPickInfo | |
CBitVect | Abstract base class for storing BitVectors |
CData3Ddescriptors | |
CDatastructsException | |
CExplicitBitVect | Class for bit vectors that are densely occupied |
CIndexErrorException | Class to allow us to throw an IndexError from C++ and have it make it back to Python |
CKeyErrorException | Class to allow us to throw a KeyError from C++ and have it make it back to Python |
CMolData3Ddescriptors | |
CPySequenceHolder | Class to hold sequences (lists, tuples, arrays, etc.) passed from Python -> C++ |
CSparseBitVect | Class for bit vectors that are sparsely occupied |
CValueErrorException | Class to allow us to throw a ValueError from C++ and have it make it back to Python |