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

boost |
logging |
rdLogger |
boost_adaptbx |
python |
ostream |
streambuf | A stream buffer getting data from and putting data into a Python file object
istream |
ostream |
streambuf_capsule |
ChemicalFeatures |
ChemicalFeature | Abstract base class for chemical feature
FreeChemicalFeature |
conrec |
ConrecSegment |
tplHash |
DistGeom |
BoundsMatrix | Class to store the distance bound
ChiralSet | Class used to store a quartet of points and chiral volume bounds on them
ChiralViolationContrib |
ChiralViolationContribs |
ChiralViolationContribsParams |
DistViolationContrib |
DistViolationContribs |
DistViolationContribsParams |
FourthDimContrib |
FourthDimContribs |
FourthDimContribsParams |
ForceFields |
CrystalFF |
CrystalFFDetails |
ExpTorsionAngle | A structure used to the experimental torsion patterns
TorsionAngleContribM6 | Torsion term for multiplicity m = 1 - 6
TorsionAngleContribs |
TorsionAngleContribsParams |
MMFF |
AngleBendContrib | The angle-bend term for MMFF
BondStretchContrib | The bond-stretch term for MMFF
EleContrib | Electrostatic term for MMFF
MMFFAngle | Class to store MMFF parameters for angle bending
MMFFAngleCollection |
MMFFAromCollection |
MMFFBndkCollection |
MMFFBond | Class to store MMFF parameters for bond stretching
MMFFBondCollection |
MMFFChg |
MMFFChgCollection |
MMFFCovRadPauEle |
MMFFCovRadPauEleCollection |
MMFFDef | Class to store MMFF atom type equivalence levels
MMFFDefCollection |
MMFFDfsbCollection |
MMFFHerschbachLaurie |
MMFFHerschbachLaurieCollection |
MMFFOop | Class to store MMFF parameters for out-of-plane bending
MMFFOopCollection |
MMFFPBCI | Class to store MMFF Partial Bond Charge Increments
MMFFPBCICollection |
MMFFProp | Class to store MMFF Properties
MMFFPropCollection |
MMFFStbn | Class to store MMFF parameters for stretch-bending
MMFFStbnCollection |
MMFFTor | Class to store MMFF parameters for torsions
MMFFTorCollection |
MMFFVdW | Class to store MMFF parameters for non-bonded Van der Waals
MMFFVdWCollection |
MMFFVdWRijstarEps |
OopBendContrib | Out-of-plane term for MMFF
StretchBendContrib | The angle-bend term for MMFF
TorsionAngleContrib | Torsion term for MMFF
VdWContrib | Van der Waals term for MMFF
UFF |
AngleBendContrib | The angle-bend term for the Universal Force Field
AtomicParams | Class to store atomic parameters for the Universal Force Field
BondStretchContrib | The bond-stretch term for the Universal Force Field
InversionContrib | The inversion term for the Universal Force Field
InversionContribs | A term to capture all Inversion Contributionss
InversionContribsParams |
ParamCollection | Singleton class for retrieving UFF AtomParams
TorsionAngleContrib | Torsion term for the Universal Force Field
UFFAngle | Class to store UFF parameters for angle bending
UFFBond | Class to store UFF parameters for bond stretching
UFFInv | Class to store UFF parameters for inversions
UFFTor | Class to store UFF parameters for torsions
UFFVdW | Class to store UFF parameters for van der Waals interactions
vdWContrib | Van der Waals term for the Universal Force Field
AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib
AngleConstraintContribs | A term to capture all flat bottom angle constraint potentials
AngleConstraintContribsParams |
DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib
DistanceConstraintContribs | A term to capture all flat bottom distance constraint potentials
DistanceConstraintContribsParams |
ForceField | A class to store forcefields and handle minimization
ForceFieldContrib | Abstract base class for contributions to ForceFields
PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2
TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib
Invar |
Invariant |
Queries |
AndQuery | Query implementing AND: requires all children to be `true`
EqualityQuery | Query implementing ==: arguments must match a particular value (within an optional tolerance)
GreaterEqualQuery | Query implementing >= using a particular value (and an optional tolerance)
GreaterQuery | Query implementing > using a particular value (and an optional tolerance)
Int2Type | Class to allow integer values to pick templates
LessEqualQuery | Query implementing <= using a particular value (and an optional tolerance)
LessQuery | Query implementing < using a particular value (and an optional tolerance)
OrQuery | Query implementing AND: requires any child to be `true`
Query | Base class for all queries
RangeQuery | Query implementing a range: arguments must fall in a particular range of values
SetQuery | Query implementing a set: arguments must one of a set of values
XOrQuery | Query implementing XOR: requires exactly one child to be `true`
RDCatalog |
Catalog | Abstract base class for a catalog object
CatalogEntry | Abstract base class to be used to represent an entry in a Catalog
CatalogParams | Abstract base class for the container used to create a catalog
HierarchCatalog | A Catalog with a hierarchical structure
vertex_entry_t | Used by the BGL to set up the node properties in our graph
RDDataManip |
MetricMatrixCalc | A generic metric matrix calculator (e.g similarity matrix or distance matrix)
RDDepict |
Compute2DCoordParameters |
ConstrainedDepictionParams |
CoordinateTemplates |
DepictException |
EmbeddedAtom | Class that contains the data for an atoms that has already been embedded
EmbeddedFrag | Class containing a fragment of a molecule that has already been embedded
gtIIPair |
RDFeatures |
ExplicitFeature |
ImplicitFeature |
RDGeom |
Grid3D | Virtual base class for a grid object
GridException |
Point |
Point2D |
Point3D |
PointND |
Transform2D |
Transform3D |
UniformGrid3D |
UniformRealValueGrid3D |
RDInfoTheory | Class used to rank bits based on a specified measure of information
BitCorrMatGenerator |
InfoBitRanker |
RDKit | Std stuff
Abbreviations |
AbbreviationDefinition |
AbbreviationMatch |
AtomPair |
AtomPairArguments | Class that holds atom-pair fingerprint specific arguments
AtomPairAtomEnv | Class that holds atom-environment data needed for atom-pair fingerprint generation
AtomPairAtomInvGenerator |
AtomPairEnvGenerator | Class that generates atom-environments for atom-pair fingerprint
Canon |
AtomCompareFunctor |
bondholder |
canon_atom |
ChiralAtomCompareFunctor |
MolStackElem | These are the actual elements in the molecular stack
MolStackUnion | Used to store components in the molecular stack
SpecialChiralityAtomCompareFunctor |
SpecialSymmetryAtomCompareFunctor |
Chirality |
BondWedgingParameters |
StereoInfo |
WedgeInfoAtropisomer |
WedgeInfoBase |
WedgeInfoChiral |
CIPLabeler |
AtropisomerBond |
CIPMol |
CIPMolSpan |
CIPMolIter |
Configuration |
Digraph |
Edge |
MaxIterationsExceeded |
Node |
PairList |
Priority |
Rule1a |
Rule1b |
Rule2 |
Rule3 |
Rule4a |
Rule4b |
Rule4c |
Rule5 |
Rule5New |
Rule6 |
Rules |
SequenceRule |
Sort |
Sp2Bond |
Tetrahedral |
TooManyNodesException |
Deprotect |
DeprotectData |
Descriptors |
CrippenParamCollection | Singleton class for retrieving Crippen parameters
CrippenParams | Class used to store Crippen parameters
DoubleCubicLatticeVolume |
Properties | Holds a collection of properties for computation purposes
PropertyFunctor |
detail |
MCSParametersInternal |
DGeomHelpers |
EmbedParameters | Parameter object for controlling embedding
FilterMatchOps |
And |
Not |
Or |
FMCS |
Composition2N |
DuplicatedSeedCache |
TKey |
ExecStatistics |
Graph |
MaximumCommonSubgraph |
MolFragment |
NewBond |
Seed |
SeedSet |
SubstructureCache |
HashKey |
KeyNumericMetrics |
Target |
TargetMatch |
TArray2D |
GeneralizedSubstruct |
ExtendedQueryMol |
GeneralMolSupplier |
SupplierOptions |
MHFPFingerprints |
MHFPEncoder |
MMFF |
Tools |
DefaultTorsionBondSmarts |
MMFFAtomProperties |
MMFFMolProperties |
MolAlign |
LAP |
MolAlignException |
MolHistogram |
O3A |
O3AConstraint |
O3AConstraintVect |
O3AFuncData |
SDM |
MolDraw2D_detail |
AtomSymbol |
DrawAnnotation |
DrawMol |
DrawMolMCH |
DrawMolMCHCircleAndLine |
DrawMolMCHLasso |
DrawShape |
DrawShapeArc |
DrawShapeArrow |
DrawShapeDashedWedge |
DrawShapeEllipse |
DrawShapePolyLine |
DrawShapeSimpleLine |
DrawShapeSolidWedge |
DrawShapeWavyLine |
DrawText |
DrawTextCairo |
DrawTextFT |
DrawTextFTCairo |
DrawTextFTJS |
DrawTextFTQt |
DrawTextFTSVG |
DrawTextJS |
DrawTextNotFT |
DrawTextQt |
DrawTextSVG |
LinePair |
StringRect |
MolDraw2DUtils |
ContourParams |
MolEnumerator |
LinkNode |
LinkNodeOp | Molecule enumeration operation corresponding to LINKNODES
MolEnumeratorOp | Abstract base class for the a molecule enumeration operation
MolEnumeratorParams | Parameters used to control the molecule enumeration
PositionVariationOp | Molecule enumeration operation corresponding to position variation bonds
RepeatUnitOp | Molecule enumeration operation corresponding to SRUs
MolFragmenter |
FragmenterBondType |
MolInterchange |
JSONParseParameters |
JSONWriteParameters |
MolOps | Groups a variety of molecular query and transformation operations
AdjustQueryParameters | Parameters controlling the behavior of MolOps::adjustQueryProperties
Hybridizations |
RemoveHsParameters |
MolStandardize |
TautomerScoringFunctions |
SubstructTerm |
AcidBaseCatalogEntry |
AcidBaseCatalogParams |
AllowedAtomsValidation |
ChargeCorrection |
CleanupParameters |
CompositeValidation | Simple way to apply a collection of
DisallowedAtomsValidation |
DisallowedRadicalValidation |
FeaturesValidation |
FragmentCatalogEntry |
FragmentCatalogParams |
FragmentRemover |
FragmentValidation | Logs if certain fragments are present
Is2DValidation |
IsotopeValidation | Logs if molecule contains isotopes
LargestFragmentChooser |
Largest |
Layout2DValidation |
MetalDisconnector |
MetalDisconnectorOptions |
MolVSValidation |
NeutralValidation | Logs if not an overall neutral system
NoAtomValidation | MolVS Validations
Normalizer | For applying Normalization transforms
Pipeline |
PipelineLogEntry |
PipelineOptions |
PipelineResult |
RDKitValidation |
Reionizer |
StereoValidation |
Tautomer |
TautomerCatalogEntry |
TautomerCatalogParams |
TautomerEnumerator |
TautomerEnumeratorCallback |
TautomerEnumeratorResult | Contains results of tautomer enumeration
const_iterator |
TautomerTransform |
TransformCatalogEntry |
TransformCatalogParams |
Uncharger | For neutralizing ionized acids and bases
ValidationMethod |
MorganFingerprint |
MorganArguments | Class for holding Morgan fingerprint specific arguments
MorganAtomEnv | Class for holding the bit-id created from Morgan fingerprint environments and the additional data necessary extra outputs
MorganAtomInvGenerator | Default atom invariants generator for Morgan fingerprint, generates ECFP-type invariants
MorganBondInvGenerator | Bond invariants generator for Morgan fingerprint
MorganEnvGenerator | Class that generates atom environments for Morgan fingerprint
MorganFeatureAtomInvGenerator | Alternative atom invariants generator for Morgan fingerprint, generate FCFP-type invariants
MorganFingerprints |
ss_matcher |
RascalMCES |
details |
ClusNode |
PartitionSet |
RascalClusterOptions |
RascalOptions |
RascalResult |
RDKitFP |
RDKitFPArguments |
RDKitFPAtomEnv |
RDKitFPAtomInvGenerator |
RDKitFPEnvGenerator |
RDTypeTag |
detail |
Value |
ScaffoldNetwork |
NetworkEdge |
ScaffoldNetwork |
ScaffoldNetworkParams |
SLNParse |
AttribType |
SmilesParse |
SmilesParseException |
StructureCheck |
AugmentedAtom |
ChargeFix |
IncEntry |
Ligand |
Neighbourhood |
PathEntry |
StructChecker | Class for performing structure validation and cleanup
StructCheckerOptions |
StructCheckTautomer |
SynthonSpaceSearch |
details |
Stepper |
SearchResults |
Synthon |
SynthonSet |
SynthonSpace |
SynthonSpaceFingerprintSearcher |
SynthonSpaceHitSet |
SynthonSpaceSearcher |
SynthonSpaceSearchParams |
SynthonSpaceSubstructureSearcher |
TopologicalTorsion |
TopologicalTorsionArguments |
TopologicalTorsionAtomEnv |
TopologicalTorsionEnvGenerator |
UFF |
Tools |
DefaultTorsionBondSmarts |
Utils |
LocaleSwitcher |
v1 |
ForwardSDMolSupplier |
MolSupplier |
SDMolSupplier |
SmartsParserParams |
SmilesMolSupplier | Lazy file parser for Smiles tables
SmilesParserParams |
TDTMolSupplier | Lazy file parser for TDT files
v2 |
CDXMLParser |
CDXMLParserParams |
FileParsers |
ForwardSDMolSupplier |
Mol2ParserParams |
MolFileParserParams |
MolFileUnhandledFeatureException |
MolSupplier |
PDBParserParams |
SDMolSupplier |
SmilesMolSupplier | Lazy file parser for Smiles tables
SmilesMolSupplierParams |
TDTMolSupplier | Lazy file parser for TDT files
TDTMolSupplierParams |
TPLParserParams |
MarvinParser |
MrvParserParams |
AdditionalOutput |
AromaticAtomIterator_ | Iterate over aromatic atoms, this is bidirectional
Atom | The class for representing atoms
AtomEnvironment | Abstract base class that holds atom-environments that will be hashed to generate the fingerprint
AtomEnvironmentGenerator | Abstract base class that generates atom-environments from a molecule
atomicData |
AtomInvariantsGenerator | Abstract base class for atom invariants generators
AtomIterator_ | A general random access iterator
AtomKekulizeException |
AtomMonomerInfo | The abstract base class for atom-level monomer info
AtomPDBResidueInfo | Captures atom-level information about peptide residues
AtomRingQuery |
AtomSanitizeException |
AtomValenceException |
BadFileException | Used by various file parsing classes to indicate a bad file
Bond | Class for representing a bond
BondInvariantsGenerator | Abstract base class for bond invariants generators
BondIterator_ | Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
CachedMolHolder | Concrete class that holds binary cached molecules in memory
CachedSmilesMolHolder | Concrete class that holds smiles strings in memory
CachedTrustedSmilesMolHolder | Concrete class that holds trusted smiles strings in memory
CartesianProduct | Iterate through all possible permutations of the rgroups
CartesianProductStrategy |
charptr_functor | Functor for comparing two strings
ChemicalReaction | This is a class for storing and applying general chemical reactions
ChemicalReactionException | Used to indicate an error in the chemical reaction engine
ChemicalReactionParserException | Used to indicate an error in parsing reaction data
Conformer | The class for representing 2D or 3D conformation of a molecule
ConformerException | Used to indicate errors from incorrect conformer access
ConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
ControlCHandler |
CustomPropHandler |
CXXAtomIterator |
CXXAtomIter |
CXXBondIterator |
CXXBondIter |
DataStructsExplicitBitVecPropHandler |
Dict | The `Dict` class can be used to store objects of arbitrary type keyed by `strings`
Pair |
DiscreteDistMat |
DiscreteValueVect | Class for efficiently storing vectors of discrete values
DrawColour |
EnumerateLibrary | This is a class for running reactions on sets of reagents
EnumerateLibraryBase |
EnumerationParams |
EnumerationStrategyBase |
EnumerationStrategyException | Class for flagging enumeration strategy errors
EvenSamplePairsStrategy | EvenSamplePairsStrategy
ExclusionList |
FeatureFileParseException | Class used to indicate errors in parsing feature definition files
FileParseException | Used by various file parsing classes to indicate a parse error
FilterCatalog |
FilterCatalogEntry |
FilterCatalogParams |
FilterData_t |
FilterHierarchyMatcher |
FilterMatch | Holds the atomPairs matched by the underlying matcher
FilterMatcherBase |
FilterProperty_t |
FingerprintArguments | 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
FingerprintFuncArguments | Struct that makes calling the fingerprint generation functions easier
FingerprintGenerator | Class that generates same fingerprint style for different output formats
FingerprintVarianceScoreData |
FixedMolSizeMolBundle |
ForwardSDMolSupplier |
FPBReader | Class for reading and searching FPB files
FPHolderBase | Base FPI for the fingerprinter used to rule out impossible matches
FragCatalogEntry |
FragCatGenerator |
FragCatParams | Container for user parameters used to create a fragment catalog
FragFPGenerator |
GaResult |
GasteigerParams |
HasPropQuery |
HasPropWithValueQuery |
HasPropWithValueQuery< TargetPtr, ExplicitBitVect > |
HasPropWithValueQuery< TargetPtr, std::string > |
HasPropWithValueQueryBase |
HeteroatomIterator_ | Iterate over heteroatoms, this is bidirectional
KekulizeException |
KeyFromPropHolder |
KeyHolderBase |
larger_of | Functor for returning the larger of two values
ltDouble | Functor to compare two doubles with a tolerance
MarvinArrow |
MarvinAtom |
MarvinAttachmentPoint |
MarvinBond |
MarvinBondStereo |
MarvinCondition |
MarvinDataSgroup |
MarvinGenericSgroup |
MarvinMol |
MarvinMolBase |
MarvinMonomerSgroup |
MarvinMulticenterSgroup |
MarvinMultipleSgroup |
MarvinPlus |
MarvinReaction |
MarvinRectangle |
MarvinSruCoModSgroup |
MarvinStereoGroup |
MarvinSuperatomSgroup |
MarvinSuperatomSgroupExpanded |
MarvinWriterException |
MatchingAtomIterator_ | Iterate over atoms matching a query function. This is bidirectional
MCSAtomCompareParameters |
MCSBondCompareParameters |
MCSParameters |
MCSProgressData |
MCSResult |
MolBundle | MolBundle contains a collection of related ROMols
MolCatalogEntry | This class is used to store ROMol objects in a MolCatalog
MolCatalogParams | Container for user parameters used to create a mol catalog
MolChemicalFeature |
MolChemicalFeatureDef |
MolChemicalFeatureFactory | The class for finding chemical features in molecules
MolDraw2D | MolDraw2D is the base class for doing 2D renderings of molecules
MolDraw2DCairo |
MolDraw2DJS |
MolDraw2DQt |
MolDraw2DSVG |
MolDraw2Dwx |
MolDrawOptions |
MolHolder | Concrete class that holds molecules in memory
MolHolderBase | Base class API for holding molecules to substructure search
MolMatchFinalCheckFunctor |
MolPickler | Handles pickling (serializing) molecules
MolPicklerException | Used to indicate exceptions whilst pickling (serializing) molecules
MolSanitizeException | Class for flagging sanitization errors
MolSupplier |
MolWriter |
MolWriterParams |
MolzipParams |
MrvWriterParams |
MultiFPBReader | Class for reading and searching multiple FPB files
PairHolder |
PatternHolder |
PDBWriter |
PeriodicTable | Singleton class for retrieving information about atoms
QueryAtom | Class for storing atomic queries
QueryAtomIterator_ | Iterate over atoms matching a query. This is bidirectional
QueryBond | Class for storing Bond queries
RandomSampleAllBBsStrategy |
RandomSampleStrategy |
RCore | RCore is the core common to a series of molecules
RDAny |
RDProps |
RDValue |
ReactionFingerprintParams |
ReactionPickler | Handles pickling (serializing) reactions
ReactionPicklerException | Used to indicate exceptions whilst pickling (serializing) reactions
RealValueVect |
RecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS)
ResonanceMolSupplier |
ResonanceMolSupplierCallback |
RGroupData | A single rgroup attached to a given core
RGroupDecompData |
UsedLabels |
RGroupDecomposition |
RGroupDecompositionChromosome |
RGroupDecompositionParameters |
RGroupDecompositionProcessResult |
RGroupGa |
RGroupMatch | RGroupMatch is the decomposition for a single molecule
RGroupScorer |
RigorousEnhancedStereoException |
RingInfo |
ROMol |
RWMol | RWMol is a molecule class that is intended to be edited
RxnSanitizeException | Class for flagging sanitization errors
SDMolSupplier |
SDWriter |
SLNParseException |
SmartsMatcher |
SmartsParserParams |
SmilesMolSupplier | Lazy file parser for Smiles tables
SmilesParserParams |
SmilesWriteParams |
SmilesWriter |
Snapshot |
SparseIntVect | Class for efficiently storing sparse vectors of ints
StereoBondThresholds |
StereoGroup |
SubstanceGroup | The class for representing SubstanceGroups
AttachPoint |
CState |
SubstanceGroupException | Used to indicate errors from incorrect sgroup access
SubstructLibrary | Substructure Search a library of molecules
SubstructMatchParameters |
TautomerPatternHolder |
TautomerQuery |
TDTMolSupplier | Lazy file parser for TDT files
TDTWriter |
Trajectory |
UnimplementedFPException |
UsedLabelMap |
VarianceDataForLabel |
RDMIF |
Coulomb | Class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric)
CoulombDielectric | Class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule by taking a distance-dependent dielectric into account:
HBond | Class for calculation of hydrogen bond potential between probe and molecule
Hydrophilic | Class for calculation of hydrophilic field of molecule
MMFFVdWaals |
UFFVdWaals |
VdWaals | Abstract class for calculation of Van der Waals interaction between probe and molecule at gridpoint `pt`
RDNumeric |
Matrix | A matrix class for general, non-square matrices
SquareMatrix |
SymmMatrix | A symmetric matrix class
Vector | A class to represent vectors of numbers
RDPickers |
DistPicker | Abstract base class to do perform item picking (typically molecules) using a distance matrix
HierarchicalClusterPicker | Diversity picker based on hierarchical clustering
LeaderPicker | Implements the Leader algorithm for picking a subset of item from a pool
LeaderPickerState |
MaxMinPicker | Implements the MaxMin algorithm for picking a subset of item from a pool
MaxMinPickInfo |
BitVect | Abstract base class for storing BitVectors
Data3Ddescriptors |
DatastructsException |
ExplicitBitVect | Class for bit vectors that are densely occupied
IndexErrorException | Class to allow us to throw an `IndexError` from C++ and have it make it back to Python
KeyErrorException | Class to allow us to throw a `KeyError` from C++ and have it make it back to Python
MolData3Ddescriptors |
PySequenceHolder | Class to hold sequences (lists, tuples, arrays, etc.) passed from Python -> C++
SparseBitVect | Class for bit vectors that are sparsely occupied
ValueErrorException | Class to allow us to throw a `ValueError` from C++ and have it make it back to Python