Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 1234]

►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
►Nconrec
CConrecSegment
CtplHash
►NDistGeom
CBoundsMatrix	Class to store the distance bound
CChiralSet	Class used to store a quartet of points and chiral volume bounds on them
CChiralViolationContrib
CChiralViolationContribs
CChiralViolationContribsParams
CDistViolationContrib
CDistViolationContribs
CDistViolationContribsParams
CFourthDimContrib
CFourthDimContribs
CFourthDimContribsParams
►NForceFields
►NCrystalFF
CCrystalFFDetails
CExpTorsionAngle	A structure used to the experimental torsion patterns
CTorsionAngleContribM6	Torsion term for multiplicity m = 1 - 6
CTorsionAngleContribs
CTorsionAngleContribsParams
►NMMFF
CAngleBendContrib	The angle-bend term for MMFF
CBondStretchContrib	The bond-stretch term for MMFF
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
CStretchBendContrib	The angle-bend term for MMFF
CTorsionAngleContrib	Torsion term for MMFF
CVdWContrib	Van der Waals term for MMFF
►NUFF
CAngleBendContrib	The angle-bend term for the Universal Force Field
CAtomicParams	Class to store atomic parameters for the Universal Force Field
CBondStretchContrib	The bond-stretch term for the Universal Force Field
CInversionContrib	The inversion term for the Universal Force Field
CInversionContribs	A term to capture all Inversion Contributionss
CInversionContribsParams
CParamCollection	Singleton class for retrieving UFF AtomParams
CTorsionAngleContrib	Torsion term for the Universal Force Field
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
CAngleConstraintContrib	An angle range constraint modelled after a AngleBendContrib
CAngleConstraintContribs	A term to capture all flat bottom angle constraint potentials
CAngleConstraintContribsParams
CDistanceConstraintContrib	A distance range constraint modelled after a BondStretchContrib
CDistanceConstraintContribs	A term to capture all flat bottom distance constraint potentials
CDistanceConstraintContribsParams
CForceField	A class to store forcefields and handle minimization
CForceFieldContrib	Abstract base class for contributions to ForceFields
CPositionConstraintContrib	A position constraint of the type 0.5k * deltaX^2
CTorsionConstraintContrib	A dihedral angle range constraint modelled after a TorsionContrib
►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
►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
CCompute2DCoordParameters
CConstrainedDepictionParams
CCoordinateTemplates
CDepictException
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
CgtIIPair
►NRDFeatures
CExplicitFeature
CImplicitFeature
►NRDGeom
CGrid3D	Virtual base class for a grid object
CGridException
CPoint
CPoint2D
CPoint3D
CPointND
CTransform2D
CTransform3D
CUniformGrid3D
CUniformRealValueGrid3D
►NRDInfoTheory	Class used to rank bits based on a specified measure of information
CBitCorrMatGenerator
CInfoBitRanker
►NRDKit	Std stuff
►NAbbreviations
CAbbreviationDefinition
CAbbreviationMatch
►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
►NChirality
CBondWedgingParameters
CStereoInfo
CWedgeInfoAtropisomer
CWedgeInfoBase
CWedgeInfoChiral
►NCIPLabeler
CAtropisomerBond
CCIPMol
►CCIPMolSpan
CCIPMolIter
CConfiguration
CDigraph
CEdge
CMaxIterationsExceeded
CNode
CPairList
CPriority
CRule1a
CRule1b
CRule2
CRule3
CRule4a
CRule4b
CRule4c
CRule5
CRule5New
CRule6
CRules
CSequenceRule
CSort
CSp2Bond
CTetrahedral
CTooManyNodesException
►NDeprotect
CDeprotectData
►NDescriptors
CCrippenParamCollection	Singleton class for retrieving Crippen parameters
CCrippenParams	Class used to store Crippen parameters
CDoubleCubicLatticeVolume
CProperties	Holds a collection of properties for computation purposes
CPropertyFunctor
►Ndetail
CMCSParametersInternal
►NDGeomHelpers
CEmbedParameters	Parameter object for controlling embedding
►NFilterMatchOps
CAnd
CNot
COr
►NFMCS
CComposition2N
►CDuplicatedSeedCache
CTKey
CExecStatistics
CGraph
CMaximumCommonSubgraph
CMolFragment
CNewBond
CSeed
CSeedSet
►CSubstructureCache
CHashKey
CKeyNumericMetrics
CTarget
CTargetMatch
CTArray2D
►NGeneralizedSubstruct
CExtendedQueryMol
►NGeneralMolSupplier
CSupplierOptions
►NMHFPFingerprints
CMHFPEncoder
►NMMFF
►NTools
CDefaultTorsionBondSmarts
CMMFFAtomProperties
CMMFFMolProperties
►NMolAlign
CLAP
CMolAlignException
CMolHistogram
CO3A
CO3AConstraint
CO3AConstraintVect
CO3AFuncData
CSDM
►NMolDraw2D_detail
CAtomSymbol
CDrawAnnotation
CDrawMol
CDrawMolMCH
CDrawMolMCHCircleAndLine
CDrawMolMCHLasso
CDrawShape
CDrawShapeArc
CDrawShapeArrow
CDrawShapeDashedWedge
CDrawShapeEllipse
CDrawShapePolyLine
CDrawShapeSimpleLine
CDrawShapeSolidWedge
CDrawShapeWavyLine
CDrawText
CDrawTextCairo
CDrawTextFT
CDrawTextFTCairo
CDrawTextFTJS
CDrawTextFTQt
CDrawTextFTSVG
CDrawTextJS
CDrawTextNotFT
CDrawTextQt
CDrawTextSVG
CLinePair
CStringRect
►NMolDraw2DUtils
CContourParams
►NMolEnumerator
CLinkNode
CLinkNodeOp	Molecule enumeration operation corresponding to LINKNODES
CMolEnumeratorOp	Abstract base class for the a molecule enumeration operation
CMolEnumeratorParams	Parameters used to control the molecule enumeration
CPositionVariationOp	Molecule enumeration operation corresponding to position variation bonds
CRepeatUnitOp	Molecule enumeration operation corresponding to SRUs
►NMolFragmenter
CFragmenterBondType
►NMolInterchange
CJSONParseParameters
CJSONWriteParameters
►NMolOps	Groups a variety of molecular query and transformation operations
CAdjustQueryParameters	Parameters controlling the behavior of MolOps::adjustQueryProperties
CHybridizations
CRemoveHsParameters
►NMolStandardize
►NTautomerScoringFunctions
CSubstructTerm
CAcidBaseCatalogEntry
CAcidBaseCatalogParams
CAllowedAtomsValidation
CChargeCorrection
CCleanupParameters
CCompositeValidation	Simple way to apply a collection of
CDisallowedAtomsValidation
CDisallowedRadicalValidation
CFeaturesValidation
CFragmentCatalogEntry
CFragmentCatalogParams
CFragmentRemover
CFragmentValidation	Logs if certain fragments are present
CIs2DValidation
CIsotopeValidation	Logs if molecule contains isotopes
►CLargestFragmentChooser
CLargest
CLayout2DValidation
CMetalDisconnector
CMetalDisconnectorOptions
CMolVSValidation
CNeutralValidation	Logs if not an overall neutral system
CNoAtomValidation	MolVS Validations
CNormalizer	For applying Normalization transforms
CPipeline
CPipelineLogEntry
CPipelineOptions
CPipelineResult
CRDKitValidation
CReionizer
CStereoValidation
CTautomer
CTautomerCatalogEntry
CTautomerCatalogParams
CTautomerEnumerator
CTautomerEnumeratorCallback
►CTautomerEnumeratorResult	Contains results of tautomer enumeration
Cconst_iterator
CTautomerTransform
CTransformCatalogEntry
CTransformCatalogParams
CUncharger	For neutralizing ionized acids and bases
CValidationMethod
►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
►NRascalMCES
►Ndetails
CClusNode
CPartitionSet
CRascalClusterOptions
CRascalOptions
CRascalResult
►NRDKitFP
CRDKitFPArguments
CRDKitFPAtomEnv
CRDKitFPAtomInvGenerator
CRDKitFPEnvGenerator
►NRDTypeTag
►Ndetail
CValue
►NScaffoldNetwork
CNetworkEdge
CScaffoldNetwork
CScaffoldNetworkParams
►NSLNParse
CAttribType
►NSmilesParse
CSmilesParseException
►NStructureCheck
CAugmentedAtom
CChargeFix
CIncEntry
CLigand
CNeighbourhood
CPathEntry
CStructChecker	Class for performing structure validation and cleanup
CStructCheckerOptions
CStructCheckTautomer
►NSynthonSpaceSearch
►Ndetails
CStepper
CSearchResults
CSubstructureResults
CSynthon
CSynthonSet
CSynthonSpace
CSynthonSpaceFingerprintSearcher
CSynthonSpaceHitSet
CSynthonSpaceSearcher
CSynthonSpaceSearchParams
CSynthonSpaceSubstructureSearcher
►NTopologicalTorsion
CTopologicalTorsionArguments
CTopologicalTorsionAtomEnv
CTopologicalTorsionEnvGenerator
►NUFF
►NTools
CDefaultTorsionBondSmarts
►NUtils
CLocaleSwitcher
►Nv1
CForwardSDMolSupplier
CMolSupplier
CSDMolSupplier
CSmartsParserParams
CSmilesMolSupplier	Lazy file parser for Smiles tables
CSmilesParserParams
CTDTMolSupplier	Lazy file parser for TDT files
►Nv2
►NCDXMLParser
CCDXMLParserParams
►NFileParsers
CForwardSDMolSupplier
CMol2ParserParams
CMolFileParserParams
CMolFileUnhandledFeatureException
CMolSupplier
CPDBParserParams
CSDMolSupplier
CSmilesMolSupplier	Lazy file parser for Smiles tables
CSmilesMolSupplierParams
CTDTMolSupplier	Lazy file parser for TDT files
CTDTMolSupplierParams
CTPLParserParams
►NMarvinParser
CMrvParserParams
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
CCartesianProduct	Iterate through all possible permutations of the rgroups
CCartesianProductStrategy
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 conformer 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
CEnumerationParams
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
CFingerprintFuncArguments	Struct that makes calling the fingerprint generation functions easier
CFingerprintGenerator	Class that generates same fingerprint style for different output formats
CFingerprintVarianceScoreData
CFixedMolSizeMolBundle
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
CGaResult
CGasteigerParams
CHasPropQuery
CHasPropWithValueQuery
CHasPropWithValueQuery< TargetPtr, ExplicitBitVect >
CHasPropWithValueQuery< TargetPtr, std::string >
CHasPropWithValueQueryBase
CHeteroatomIterator_	Iterate over heteroatoms, this is bidirectional
CKekulizeException
CKeyFromPropHolder
CKeyHolderBase
Clarger_of	Functor for returning the larger of two values
CltDouble	Functor to compare two doubles with a tolerance
CMarvinArrow
CMarvinAtom
CMarvinAttachmentPoint
CMarvinBond
CMarvinBondStereo
CMarvinCondition
CMarvinDataSgroup
CMarvinGenericSgroup
CMarvinMol
CMarvinMolBase
CMarvinMonomerSgroup
CMarvinMulticenterSgroup
CMarvinMultipleSgroup
CMarvinPlus
CMarvinReaction
CMarvinRectangle
CMarvinSruCoModSgroup
CMarvinStereoGroup
CMarvinSuperatomSgroup
CMarvinSuperatomSgroupExpanded
CMarvinWriterException
CMatchingAtomIterator_	Iterate over atoms matching a query function. This is bidirectional
CMCSAtomCompareParameters
CMCSBondCompareParameters
CMCSParameters
CMCSProgressData
CMCSResult
CMolBundle	MolBundle contains a collection of related ROMols
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
CMolDraw2DJS
CMolDraw2DQt
CMolDraw2DSVG
CMolDraw2Dwx
CMolDrawOptions
CMolHolder	Concrete class that holds molecules in memory
CMolHolderBase	Base class API for holding molecules to substructure search
CMolMatchFinalCheckFunctor
CMolPickler	Handles pickling (serializing) molecules
CMolPicklerException	Used to indicate exceptions whilst pickling (serializing) molecules
CMolSanitizeException	Class for flagging sanitization errors
CMolSupplier
CMolWriter
CMolWriterParams
CMolzipParams
CMrvWriterParams
CMultiFPBReader	Class for reading and searching multiple FPB files
CPairHolder
CPatternHolder
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
CRandomSampleStrategy
CRCore	RCore is the core common to a series of molecules
CRDAny
CRDProps
CRDValue
CReactionFingerprintParams
CReactionPickler	Handles pickling (serializing) reactions
CReactionPicklerException	Used to indicate exceptions whilst pickling (serializing) reactions
CRealValueVect
CRecursiveStructureQuery	Allows use of recursive structure queries (e.g. recursive SMARTS)
CResonanceMolSupplier
CResonanceMolSupplierCallback
CRGroupData	A single rgroup attached to a given core
►CRGroupDecompData
CUsedLabels
CRGroupDecomposition
CRGroupDecompositionChromosome
CRGroupDecompositionParameters
CRGroupDecompositionProcessResult
CRGroupGa
CRGroupMatch	RGroupMatch is the decomposition for a single molecule
CRGroupScorer
CRigorousEnhancedStereoException
CRingInfo
CROMol
CRWMol	RWMol is a molecule class that is intended to be edited
CRxnSanitizeException	Class for flagging sanitization errors
CSDMolSupplier
CSDWriter
CSLNParseException
CSmartsMatcher
CSmartsParserParams
CSmilesMolSupplier	Lazy file parser for Smiles tables
CSmilesParserParams
CSmilesWriteParams
CSmilesWriter
CSnapshot
CSparseIntVect	Class for efficiently storing sparse vectors of ints
CStereoBondThresholds
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
CTautomerPatternHolder
CTautomerQuery
CTDTMolSupplier	Lazy file parser for TDT files
CTDTWriter
CTrajectory
CUnimplementedFPException
CUsedLabelMap
CVarianceDataForLabel
►NRDMIF
CCoulomb	Class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric)
CCoulombDielectric	Class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule by taking a distance-dependent dielectric into account:
CHBond	Class for calculation of hydrogen bond potential between probe and molecule
CHydrophilic	Class for calculation of hydrophilic field of molecule
CMMFFVdWaals
CUFFVdWaals
CVdWaals	Abstract class for calculation of Van der Waals interaction between probe and molecule at gridpoint pt
►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