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	Class for chemical features that do not orignate from molecules
►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
►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
CLinearCatalog	Linear Catalog (analogous to an std::vector)
►NRDDataManip
CMetricMatrixCalc	A generic metric matrix calculator (e.g similarity matrix or distance matrix)
►NRDDepict
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	Includes a bunch of functionality for handling Atom and Bond queries
►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
►NDrawing
►NFilterMatchOps
CAnd
CNot
COr
►NFMCS
CComposition2N
►CDuplicatedSeedCache
CTKey
CExecStatistics
CGraph
CMaximumCommonSubgraph
CMolFragment
CNewBond
CRingMatchTableSet
CSeed
CSeedSet
►CSubstructureCache
CHashKey
CKeyNumericMetrics
CTarget
CTargetMatch
CTArray2D
►NMMFF
CMMFFAtomProperties
CMMFFMolProperties
►NMolAlign
CLAP
CMolAlignException
CMolHistogram
CO3A
CO3AConstraint
CO3AConstraintVect
CO3AFuncData
CSDM
►NMolFragmenter
CFragmenterBondType
►NMolHash
CHashSet
►NMolOps	Groups a variety of molecular query and transformation operations
CAdjustQueryParameters
►NSLNParse
CAttribType
►NUFF
►NUtils
CLocaleSwitcher
CAromaticAtomIterator_	Iterate over aromatic atoms, this is bidirectional
CAtom	The class for representing atoms
CatomicData
CAtomIterator_	A general random access iterator
CAtomMonomerInfo	The abstract base class for atom-level monomer info
CAtomPDBResidueInfo	Captures atom-level information about peptide residues
CAtomRingQuery
CBadFileException	Used by various file parsing classes to indicate a bad file
CBond	Class for representing a bond
CBondIterator_	Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
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
CDict	The Dict class can be used to store objects of arbitrary type keyed by strings
CDiscreteDistMat
CDiscreteValueVect	Class for efficiently storing vectors of discrete values
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
CFilterMatch	Holds the atomPairs matched by the underlying matcher
CFilterMatcherBase
CFilterProperty_t
CForwardSDMolSupplier
CFPBReader	Class for reading and searching FPB files
CFragCatalogEntry
CFragCatGenerator
CFragCatParams	Container for user parameters used to create a fragment catalog
CFragFPGenerator
CGasteigerParams
CHasPropQuery
CHasPropWithValueQuery
CHasPropWithValueQuery< TargetPtr, std::string >
CHeteroatomIterator_	Iterate over heteroatoms, this is bidirectional
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
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
CMolDraw2DCairo
CMolDraw2DQt
CMolDraw2DSVG
CMolDraw2Dwx
CMolDrawOptions
CMolPickler	Handles pickling (serializing) molecules
CMolPicklerException	Used to indicate exceptions whilst pickling (serializing) molecules
CMolSanitizeException	Class for flagging sanitization errors
CMolSupplier
CMolWriter
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
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
CRingInfo	A class to store information about a molecule's rings
CROMol	ROMol is a molecule class that is intended to have a fixed topology
CRWMol	RWMol is a molecule class that is intended to be edited
CSDMolSupplier
CSDWriter
CSLNParseException
CSmartsMatcher
CSmilesMolSupplier	Lazy file parser for Smiles tables
CSmilesParseException
CSmilesWriter
CSparseIntVect	Class for efficiently storing sparse vectors of ints
CTDTMolSupplier	Lazy file parser for TDT files
CTDTWriter
►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
CMaxMinPicker	Implements the MaxMin algorithm for picking a subset of item from a pool
CBitVect	Abstract base class for storing BitVectors
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
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