 |
RDKit
Open-source cheminformatics and machine learning.
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RDKit
Open-source cheminformatics and machine learning.
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| NBFGSOpt | |
| ►Nboost | |
| ►Nlogging | |
| CrdLogger | |
| ►Nboost_adaptbx | |
| ►Npython | |
| ►Cstreambuf | A stream buffer getting data from and putting data into a Python file object |
| Cistream | |
| Costream | |
| Cstreambuf_capsule | |
| Costream | |
| ►NChemicalFeatures | |
| CChemicalFeature | Abstract base class for chemical feature |
| CFreeChemicalFeature | Class for chemical features that do not originate 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 | |
| CTorsionAngleContribM6 | Torsion term for multiplicity m = 1 - 6 |
| CCrystalFFDetails | |
| ►NMMFF | |
| NUtils | |
| 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 |
| CVdWContrib | Van der Waals term for MMFF |
| CEleContrib | Electrostatic term for MMFF |
| COopBendContrib | Out-of-plane term for MMFF |
| CMMFFDef | Class to store MMFF atom type equivalence levels |
| CMMFFProp | Class to store MMFF Properties |
| CMMFFPBCI | Class to store MMFF Partial Bond Charge Increments |
| CMMFFChg | |
| CMMFFBond | Class to store MMFF parameters for bond stretching |
| CMMFFHerschbachLaurie | |
| CMMFFCovRadPauEle | |
| CMMFFAngle | Class to store MMFF parameters for angle bending |
| CMMFFStbn | Class to store MMFF parameters for stretch-bending |
| CMMFFOop | Class to store MMFF parameters for out-of-plane bending |
| CMMFFTor | Class to store MMFF parameters for torsions |
| CMMFFVdW | Class to store MMFF parameters for non-bonded Van der Waals |
| CMMFFVdWRijstarEps | |
| CMMFFAromCollection | |
| CMMFFDefCollection | |
| CMMFFPropCollection | |
| CMMFFPBCICollection | |
| CMMFFChgCollection | |
| CMMFFBondCollection | |
| CMMFFBndkCollection | |
| CMMFFHerschbachLaurieCollection | |
| CMMFFCovRadPauEleCollection | |
| CMMFFAngleCollection | |
| CMMFFStbnCollection | |
| CMMFFDfsbCollection | |
| CMMFFOopCollection | |
| CMMFFTorCollection | |
| CMMFFVdWCollection | |
| 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 |
| ►NUFF | |
| NParams | |
| NUtils | |
| CAngleBendContrib | The angle-bend term for the Universal Force Field |
| CAngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib |
| 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 |
| CvdWContrib | Van der Waals term for the Universal Force Field |
| CUFFBond | Class to store UFF parameters for bond stretching |
| CUFFAngle | Class to store UFF parameters for angle bending |
| CUFFTor | Class to store UFF parameters for torsions |
| CUFFInv | Class to store UFF parameters for inversions |
| CUFFVdW | Class to store UFF parameters for van der Waals interactions |
| CAtomicParams | Class to store atomic parameters 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 |
| CForceFieldContrib | Abstract base class for contributions to ForceFields |
| CForceField | A class to store forcefields and handle minimization |
| ►NInvar | |
| CInvariant | |
| NMolTransforms | |
| ►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) |
| 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 |
| CInt2Type | Class to allow integer values to pick templates |
| 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 |
| CpairGreater | Functor for implementing > on two std::pairs. The first entries are |
| CpairLess | Function for implementing < on two std::pairs. The first entries are |
| Cargless | |
| ►NRDCatalog | |
| CCatalog | Abstract base class for a catalog object |
| ►CHierarchCatalog | A Catalog with a hierarchical structure |
| Cvertex_entry_t | Used by the BGL to set up the node properties in our graph |
| 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 |
| ►NRDDataManip | |
| CMetricMatrixCalc | A generic metric matrix calculator (e.g similarity matrix or distance matrix) |
| ►NRDDepict | |
| CgtIIPair | |
| CEmbeddedAtom | Class that contains the data for an atoms that has already been embedded |
| CEmbeddedFrag | Class containing a fragment of a molecule that has already been embedded |
| CDepictException | |
| ►NRDFeatures | |
| CExplicitFeature | |
| CImplicitFeature | |
| ►NRDGeom | |
| CGridException | |
| CGrid3D | Virtual base class for a grid object |
| CPoint | |
| CPoint3D | |
| CPoint2D | |
| CPointND | |
| CTransform2D | |
| CTransform3D | |
| CUniformGrid3D | |
| ►NRDInfoTheory | Class used to rank bits based on a specified measure of information |
| CBitCorrMatGenerator | |
| CInfoBitRanker | |
| ►NRDKit | Std stuff |
| ►NAbbreviations | |
| Ncommon_properties | |
| NUtils | |
| CAbbreviationDefinition | |
| CAbbreviationMatch | |
| ►NAtomPair | |
| CAtomPairAtomInvGenerator | |
| CAtomPairArguments | Class that holds atom-pair fingerprint specific arguments |
| CAtomPairAtomEnv | Class that holds atom-environment data needed for atom-pair fingerprint generation |
| CAtomPairEnvGenerator | Class that generates atom-environments for atom-pair fingerprint |
| NAtomPairs | |
| ►NCanon | |
| CMolStackUnion | Used to store components in the molecular stack |
| CMolStackElem | These are the actual elements in the molecular stack |
| Cbondholder | |
| Ccanon_atom | |
| CSpecialChiralityAtomCompareFunctor | |
| CSpecialSymmetryAtomCompareFunctor | |
| CAtomCompareFunctor | |
| CChiralAtomCompareFunctor | |
| ►NChirality | |
| CStereoInfo | |
| ►NCIPLabeler | |
| ►CCIPMolSpan | |
| CCIPMolIter | |
| CCIPMol | |
| CConfiguration | |
| CSp2Bond | |
| CTetrahedral | |
| CDigraph | |
| CEdge | |
| CNode | |
| CPriority | |
| CPairList | |
| CRule1a | |
| CRule1b | |
| CRule2 | |
| CRule3 | |
| CRule4a | |
| CRule4b | |
| CRule4c | |
| CRule5 | |
| CRule5New | |
| CRule6 | |
| CRules | |
| CSequenceRule | |
| CSort | |
| CTooManyNodesException | |
| Ncommon_properties | |
| Nconstants | |
| ►NDeprotect | |
| CDeprotectData | |
| ►NDescriptors | |
| Ndetail | |
| CCrippenParams | Class used to store Crippen parameters |
| CCrippenParamCollection | Singleton class for retrieving Crippen parameters |
| CPropertyFunctor | |
| CProperties | Holds a collection of properties for computation purposes |
| Ndetail | |
| ►NDGeomHelpers | |
| CEmbedParameters | Parameter object for controlling embedding |
| NDTags | |
| NEnumerationStrategyPickler | |
| NEnumerationTypes | |
| NFileParserUtils | |
| ►NFilterMatchOps | |
| CAnd | |
| COr | |
| CNot | |
| ►NFMCS | |
| CComposition2N | |
| CExecStatistics | |
| ►CDuplicatedSeedCache | |
| CTKey | |
| CGraph | |
| CTArray2D | |
| CMaximumCommonSubgraph | |
| CRingMatchTableSet | |
| CMolFragment | |
| CNewBond | |
| CSeed | |
| CSeedSet | |
| ►CSubstructureCache | |
| CHashKey | |
| CKeyNumericMetrics | |
| CTarget | |
| CTargetMatch | |
| ►NForceFieldsHelper | |
| Ndetail | |
| ►NGeneralMolSupplier | |
| CSupplierOptions | |
| NLocal | |
| NMACCSFingerprints | |
| ►NMHFPFingerprints | |
| NFNV | |
| CMHFPEncoder | |
| ►NMMFF | |
| NDefaultParameters | |
| ►NTools | |
| CDefaultTorsionBondSmarts | |
| CMMFFAtomProperties | |
| CMMFFMolProperties | |
| NMMPA | |
| ►NMolAlign | |
| CMolAlignException | |
| CO3AFuncData | |
| CO3AConstraint | |
| CO3AConstraintVect | |
| CMolHistogram | |
| CLAP | |
| CSDM | |
| CO3A | |
| NMolDraw2D_detail | |
| ►NMolDraw2DUtils | |
| CContourParams | |
| ►NMolEnumerator | |
| CMolEnumeratorOp | Abstract base class for the a molecule enumeration operation |
| CPositionVariationOp | Molecule enumeration operation corresponding to position variation bonds |
| CLinkNodeOp | Molecule enumeration operation corresponding to LINKNODES |
| CMolEnumeratorParams | Parameters used to control the molecule enumeration |
| ►NMolFragmenter | |
| CFragmenterBondType | |
| NMolHash | |
| ►NMolInterchange | |
| CJSONParseParameters | |
| ►NMolOps | Groups a variety of molecular query and transformation operations |
| CRemoveHsParameters | |
| CAdjustQueryParameters | Parameters controlling the behavior of MolOps::adjustQueryProperties |
| NMolShapes | |
| ►NMolStandardize | |
| NTautomerScoringFunctions | |
| CAcidBaseCatalogEntry | |
| CAcidBaseCatalogParams | |
| CChargeCorrection | |
| CReionizer | The reionizer class to fix charges and reionize a molecule such that the |
| CUncharger | For neutralizing ionized acids and bases |
| CFragmentRemover | |
| ►CLargestFragmentChooser | |
| CLargest | |
| CFragmentCatalogEntry | |
| CFragmentCatalogParams | |
| CMetalDisconnector | |
| CCleanupParameters | The CleanupParameters structure defines the default parameters for the |
| CNormalizer | For applying Normalization transforms |
| CTautomer | |
| ►CTautomerEnumeratorResult | Contains results of tautomer enumeration |
| Cconst_iterator | |
| CTautomerEnumeratorCallback | |
| CTautomerEnumerator | |
| CTautomerCatalogEntry | |
| CTautomerCatalogParams | |
| CTautomerTransform | |
| CTransformCatalogEntry | |
| CTransformCatalogParams | |
| CValidationErrorInfo | Used to store the information returned by a |
| CValidationMethod | Abstract base class upon which all the |
| CRDKitValidation | Throws an error when there are no atoms in the |
| CMolVSValidations | Includes most of the same validations as |
| CNoAtomValidation | Throws an error if no atoms are present in the |
| CFragmentValidation | Logs if certain fragments are present |
| CNeutralValidation | Logs if not an overall neutral system |
| CIsotopeValidation | Logs if molecule contains isotopes |
| CMolVSValidation | Can be used to perform all MolVSValidions |
| CAllowedAtomsValidation | |
| CDisallowedAtomsValidation | |
| ►NMorganFingerprint | |
| CMorganAtomInvGenerator | Default atom invariants generator for Morgan fingerprint, generates ECFP-type invariants |
| CMorganFeatureAtomInvGenerator | Alternative atom invariants generator for Morgan fingerprint, generate FCFP-type invariants |
| CMorganBondInvGenerator | Bond invariants generator for Morgan fingerprint |
| 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 |
| CMorganEnvGenerator | Class that generates atom environments for Morgan fingerprint |
| ►NMorganFingerprints | |
| Css_matcher | |
| NPicklerOps | |
| NPNGData | Tags used for PNG metadata |
| NQueryOps | |
| ►NRDKitFP | |
| CRDKitFPArguments | |
| CRDKitFPAtomInvGenerator | |
| CRDKitFPAtomEnv | |
| CRDKitFPEnvGenerator | |
| NRDKitFPUtils | |
| ►NRDTypeTag | |
| ►Ndetail | |
| CValue | |
| NReactionRunnerUtils | |
| NReducedGraphs | |
| NRxnOps | |
| ►NScaffoldNetwork | |
| Ndetail | |
| CScaffoldNetworkParams | |
| CNetworkEdge | |
| CScaffoldNetwork | |
| NSGroupParsing | |
| NSGroupWriting | |
| ►NSLNParse | |
| CAttribType | |
| NSmartsWrite | |
| NSmilesWrite | |
| ►NStructureCheck | |
| CChargeFix | |
| CLigand | |
| CAugmentedAtom | |
| CIncEntry | |
| CPathEntry | |
| CStructCheckerOptions | Structure Check Options |
| CStructChecker | Class for performing structure validation and cleanup |
| CStructCheckTautomer | |
| CNeighbourhood | |
| NSubgraphs | |
| NSubstanceGroupChecks | |
| ►NTopologicalTorsion | |
| CTopologicalTorsionArguments | |
| CTopologicalTorsionAtomEnv | |
| CTopologicalTorsionEnvGenerator | |
| ►NUFF | |
| ►NTools | |
| CDefaultTorsionBondSmarts | |
| ►NUtils | |
| Ndetail | |
| CLocaleSwitcher | |
| CAtom | The class for representing atoms |
| CatomicData | |
| CAtomIterator_ | A general random access iterator |
| CHeteroatomIterator_ | Iterate over heteroatoms, this is bidirectional |
| CAromaticAtomIterator_ | Iterate over aromatic atoms, this is bidirectional |
| CQueryAtomIterator_ | Iterate over atoms matching a query. This is bidirectional |
| CMatchingAtomIterator_ | Iterate over atoms matching a query function. This is bidirectional |
| CBond | Class for representing a bond |
| CBondIterator_ | Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess |
| CConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess |
| CCartesianProductStrategy | This is a class for enumerating reagents using Cartesian Products of |
| CEnumerationParams | This is a class for providing enumeration options that control |
| CEnumerateLibrary | This is a class for running reactions on sets of reagents |
| CEnumerateLibraryBase | Base class for enumerating chemical reactions from collections of |
| CEnumerationStrategyException | Class for flagging enumeration strategy errors |
| CEnumerationStrategyBase | |
| CEvenSamplePairsStrategy | EvenSamplePairsStrategy |
| CRandomSampleStrategy | This is a class for fully randomly sampling reagents |
| CRandomSampleAllBBsStrategy | This is a class for randomly enumerating reagents that ensures all reagents |
| CChemicalReactionException | Used to indicate an error in the chemical reaction engine |
| CChemicalReaction | This is a class for storing and applying general chemical reactions |
| CReactionFingerprintParams | |
| CChemicalReactionParserException | Used to indicate an error in parsing reaction data |
| CReactionPicklerException | Used to indicate exceptions whilst pickling (serializing) reactions |
| CReactionPickler | Handles pickling (serializing) reactions |
| CRxnSanitizeException | Class for flagging sanitization errors |
| CConformerException | Used to indicate errors from incorrect conformer access |
| CConformer | The class for representing 2D or 3D conformation of a molecule |
| CMolFileUnhandledFeatureException | |
| CMolSupplier | |
| CForwardSDMolSupplier | |
| CSDMolSupplier | |
| CSmilesMolSupplier | Lazy file parser for Smiles tables |
| CTDTMolSupplier | Lazy file parser for TDT files |
| CPDBMolSupplier | Lazy file parser for PDB files |
| CMolWriter | |
| CSmilesWriter | |
| CSDWriter | |
| CTDTWriter | |
| CPDBWriter | |
| CFilterCatalogParams | |
| CFilterCatalog | |
| CFilterCatalogEntry | |
| CFilterMatch | Holds the atomPairs matched by the underlying matcher |
| CFilterMatcherBase | |
| CSmartsMatcher | |
| CExclusionList | |
| CFilterHierarchyMatcher | |
| CFilterData_t | |
| CFilterProperty_t | |
| CAdditionalOutput | |
| 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 |
| 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 |
| CAtomInvariantsGenerator | Abstract base class for atom invariants generators |
| CBondInvariantsGenerator | Abstract base class for bond invariants generators |
| CFingerprintGenerator | Class that generates same fingerprint style for different output formats |
| CUnimplementedFPException | Used to indicate errors for unimplemented fp types in convenience functions |
| CMCSAtomCompareParameters | |
| CMCSBondCompareParameters | |
| CMCSProgressData | |
| CMCSParameters | |
| CMCSResult | |
| CFragCatalogEntry | |
| CFragCatGenerator | |
| CFragCatParams | Container for user parameters used to create a fragment catalog |
| CFragFPGenerator | |
| CMolBundle | MolBundle contains a collection of related ROMols |
| CFixedMolSizeMolBundle | |
| CMolCatalogEntry | This class is used to store ROMol objects in a MolCatalog |
| CMolCatalogParams | Container for user parameters used to create a mol catalog |
| CFeatureFileParseException | Class used to indicate errors in parsing feature definition files |
| CMolChemicalFeature | |
| CMolChemicalFeatureDef | |
| CMolChemicalFeatureFactory | The class for finding chemical features in molecules |
| CDrawText | |
| CDrawTextCairo | |
| CDrawTextFT | |
| CDrawTextFTCairo | |
| CDrawTextFTJS | |
| CDrawTextFTQt | |
| CDrawTextFTSVG | |
| CDrawTextJS | |
| CDrawTextQt | |
| CDrawTextSVG | |
| CDrawColour | |
| CStringRect | |
| CMolDrawOptions | |
| CMolDraw2D | MolDraw2D is the base class for doing 2D renderings of molecules |
| CMolDraw2DCairo | |
| CMolDraw2DJS | |
| CMolDraw2DQt | |
| CMolDraw2DSVG | |
| CMolDraw2Dwx | |
| CMultiMolDraw2D | |
| CMolPicklerException | Used to indicate exceptions whilst pickling (serializing) molecules |
| CMolPickler | Handles pickling (serializing) molecules |
| CAtomMonomerInfo | The abstract base class for atom-level monomer info |
| CAtomPDBResidueInfo | Captures atom-level information about peptide residues |
| CGasteigerParams | |
| CPeriodicTable | Singleton class for retrieving information about atoms |
| CQueryAtom | Class for storing atomic queries |
| CQueryBond | Class for storing Bond queries |
| CAtomRingQuery | |
| CRecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS) |
| CHasPropQuery | |
| CHasPropWithValueQuery | |
| CHasPropWithValueQuery< TargetPtr, std::string > | |
| CHasPropWithValueQuery< TargetPtr, ExplicitBitVect > | |
| CResonanceMolSupplierCallback | |
| CResonanceMolSupplier | |
| CRCore | RCore is the core common to a series of molecules |
| CRGroupData | A single rgroup attached to a given core. |
| CRGroupDecompositionParameters | |
| CRGroupDecomposition | |
| ►CRGroupDecompData | |
| CUsedLabels | |
| CRGroupMatch | RGroupMatch is the decomposition for a single molecule |
| CCartesianProduct | Iterate through all possible permutations of the rgroups |
| CRingInfo | A class to store information about a molecule's rings |
| ►CCXXAtomIterator | |
| CCXXAtomIter | |
| ►CCXXBondIterator | |
| CCXXBondIter | |
| CROMol | |
| CRWMol | RWMol is a molecule class that is intended to be edited |
| CMolSanitizeException | Class for flagging sanitization errors |
| CAtomSanitizeException | |
| CAtomValenceException | |
| CAtomKekulizeException | |
| CKekulizeException | |
| CSLNParseException | |
| CSmilesParserParams | |
| CSmilesParseException | |
| CStereoGroup | |
| CSubstanceGroupException | Used to indicate errors from incorrect sgroup access |
| ►CSubstanceGroup | The class for representing SubstanceGroups |
| CAttachPoint | |
| CCState | |
| CSubstructMatchParameters | |
| CMolHolderBase | Base class API for holding molecules to substructure search |
| CMolHolder | Concrete class that holds molecules in memory |
| 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 |
| CFPHolderBase | Base FPI for the fingerprinter used to rule out impossible matches |
| CPatternHolder | Uses the pattern fingerprinter to rule out matches |
| CSubstructLibrary | Substructure Search a library of molecules |
| CTautomerQuery | |
| CSnapshot | |
| CTrajectory | |
| CDataStructsExplicitBitVecPropHandler | |
| CDiscreteDistMat | |
| CDiscreteValueVect | Class for efficiently storing vectors of discrete values |
| CFPBReader | Class for reading and searching FPB files |
| CMultiFPBReader | Class for reading and searching multiple FPB files |
| CSparseIntVect | Class for efficiently storing sparse vectors of ints |
| CBadFileException | Used by various file parsing classes to indicate a bad file |
| ►CDict | The Dict class can be used to store objects of arbitrary type keyed by strings |
| CPair | |
| CFileParseException | Used by various file parsing classes to indicate a parse error |
| CRDAny | |
| CRDProps | |
| CRDValue | |
| CCustomPropHandler | |
| CltDouble | Functor to compare two doubles with a tolerance |
| Clarger_of | Functor for returning the larger of two values |
| Ccharptr_functor | Functor for comparing two strings |
| ►NRDLog | |
| CBlockLogs | |
| ►NRDNumeric | |
| NAlignments | |
| NEigenSolvers | |
| 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 | |
| NRingUtils | |
| NSmilesParseOps |
1.9.1