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 | Class for chemical features that do not orignate from molecules
conrec |
ConrecSegment |
DistGeom |
BoundsMatrix | Class to store the distance bound
ChiralSet | Class used to store a quartet of points and chiral volume bounds on them
ChiralViolationContrib |
DistViolationContrib |
FourthDimContrib |
ForceFields |
CrystalFF |
CrystalFFDetails |
TorsionAngleContribM6 | Torsion term for multiplicity m = 1 - 6
MMFF |
AngleBendContrib | The angle-bend term for MMFF
AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib
BondStretchContrib | The bond-stretch term for MMFF
DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib
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
PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2
StretchBendContrib | The angle-bend term for MMFF
TorsionAngleContrib | Torsion term for MMFF
TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib
VdWContrib | Van der Waals term for MMFF
UFF |
AngleBendContrib | The angle-bend term for the Universal Force Field
AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib
AtomicParams | Class to store atomic parameters for the Universal Force Field
BondStretchContrib | The bond-stretch term for the Universal Force Field
DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib
InversionContrib | The inversion term for the Universal Force Field
ParamCollection | Singleton class for retrieving UFF AtomParams
PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2
TorsionAngleContrib | Torsion term for the Universal Force Field
TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib
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
ForceField | A class to store forcefields and handle minimization
ForceFieldContrib | Abstract base class for contributions to ForceFields
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`
Rankers | Utility functionality used to rank sequences
argless |
pairGreater | Functor for implementing > on two std::pairs. The first entries are
pairLess | Function for implementing < on two std::pairs. The first entries are
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 |
DepictException |
EmbeddedAtom | Class that contains the data for an atoms that has alredy 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 |
RDInfoTheory | Class used to rank bits based on a specified measure of infomation
BitCorrMatGenerator |
InfoBitRanker |
RDKit | Std stuff
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 |
Descriptors |
CrippenParamCollection | Singleton class for retrieving Crippen parameters
CrippenParams | Class used to store Crippen parameters
Properties | Holds a collection of properties for computation purposes
PropertyFunctor |
DGeomHelpers |
EmbedParameters | Parameter object for controlling embedding
FilterMatchOps |
And |
Not |
Or |
FMCS |
Composition2N |
DuplicatedSeedCache |
TKey |
ExecStatistics |
Graph |
MaximumCommonSubgraph |
MolFragment |
NewBond |
RingMatchTableSet |
Seed |
SeedSet |
SubstructureCache |
HashKey |
KeyNumericMetrics |
Target |
TargetMatch |
TArray2D |
ForceFieldsHelper |
MMFF |
Tools |
DefaultTorsionBondSmarts |
MMFFAtomProperties |
MMFFMolProperties |
MolAlign |
LAP |
MolAlignException |
MolHistogram |
O3A |
O3AConstraint |
O3AConstraintVect |
O3AFuncData |
SDM |
MolDraw2DUtils |
ContourParams |
MolFragmenter |
FragmenterBondType |
MolHash |
HashSet |
MolInterchange |
JSONParseParameters |
MolOps | Groups a variety of molecular query and transformation operations
AdjustQueryParameters |
MolStandardize |
AcidBaseCatalogEntry |
AcidBaseCatalogParams |
AllowedAtomsValidation |
ChargeCorrection |
CleanupParameters | The CleanupParameters structure defines the default parameters for the
DisallowedAtomsValidation |
FragmentCatalogEntry |
FragmentCatalogParams |
FragmentRemover |
FragmentValidation | Logs if certain fragments are present
IsotopeValidation | Logs if molecule contains isotopes
LargestFragmentChooser |
Largest |
MetalDisconnector |
MolVSValidation | Can be used to perform all MolVSValidions
MolVSValidations | Includes most of the same validations as
NeutralValidation | Logs if not an overall neutral system
NoAtomValidation | Throws an error if no atoms are present in the
Normalizer | For applying Normalization transforms
Product |
RDKitValidation | Throws an error when there are no atoms in the
Reionizer | The reionizer class to fix charges and reionize a molecule such that the
TautomerCanonicalizer |
TautomerCatalogEntry |
TautomerCatalogParams |
TautomerEnumerator |
TautomerTransform |
TransformCatalogEntry |
TransformCatalogParams |
Uncharger | For neutralizing ionized acids and bases
ValidationErrorInfo | Used to store the information returned by a
ValidationMethod | Abstract base class upon which all the
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 |
RDKitFP |
RDKitFPArguments |
RDKitFPAtomEnv |
RDKitFPAtomInvGenerator |
RDKitFPEnvGenerator |
RDTypeTag |
detail |
Value |
SLNParse |
AttribType |
StructureCheck |
AugmentedAtom |
ChargeFix |
IncEntry |
Ligand |
Neighbourhood |
PathEntry |
StructChecker | Class for performing structure validation and cleanup
StructCheckerOptions | Structure Check Options
StructCheckTautomer |
TopologicalTorsion |
TopologicalTorsionArguments |
TopologicalTorsionAtomEnv |
TopologicalTorsionEnvGenerator |
UFF |
Tools |
DefaultTorsionBondSmarts |
Utils |
LocaleSwitcher |
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
CartesianProductStrategy | This is a class for enumerating reagents using Cartesian Products of
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 confomer access
ConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
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 | Base class for enumerating chemical reactions from collections of
EnumerationParams | This is a class for providing enumeration options that control
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
FingerprintGenerator | Class that generates same fingerprint style for different output formats
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 |
GasteigerParams |
HasPropQuery |
HasPropWithValueQuery |
HasPropWithValueQuery< TargetPtr, ExplicitBitVect > |
HasPropWithValueQuery< TargetPtr, std::string > |
HeteroatomIterator_ | Iterate over heteroatoms, this is bidirectional
KekulizeException |
larger_of | Functor for returning the larger of two values
ltDouble | Functor to compare two doubles with a tolerance
MatchingAtomIterator_ | Iterate over atoms matching a query function. This is bidirectional
MCSAtomCompareParameters |
MCSBondCompareParameters |
MCSParameters |
MCSProgressData |
MCSResult |
MolBundle |
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 |
MolDraw2DQt |
MolDraw2DSVG |
MolDraw2Dwx |
MolDrawOptions |
MolFileUnhandledFeatureException |
MolHolder | Concrete class that holds molecules in memory
MolHolderBase | Base class API for holding molecules to substructure search
MolPickler | Handles pickling (serializing) molecules
MolPicklerException | Used to indicate exceptions whilst pickling (serializing) molecules
MolSanitizeException | Class for flagging sanitization errors
MolSupplier |
MolWriter |
MultiFPBReader | Class for reading and searching multiple FPB files
MultiMolDraw2D |
PatternHolder | Uses the pattern fingerprinter to rule out matches
PDBMolSupplier | Lazy file parser for PDB files
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 | This is a class for randomly enumerating reagents that ensures all reagents
RandomSampleStrategy | This is a class for fully randomly sampling reagents
RDAny |
RDProps |
RDValue |
ReactionFingerprintParams |
ReactionPickler | Handles pickling (serializing) reactions
ReactionPicklerException | Used to indicate exceptions whilst pickling (serializing) reactions
RecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS)
ResonanceMolSupplier |
RGroupDecomposition |
RGroupDecompositionParameters |
RingInfo | A class to store information about a molecule's rings
ROMol |
RWMol | RWMol is a molecule class that is intended to be edited
RxnSanitizeException | Class for flagging sanitization errors
SDMolSupplier |
SDWriter |
SLNParseException |
SmartsMatcher |
SmilesMolSupplier | Lazy file parser for Smiles tables
SmilesParseException |
SmilesParserParams |
SmilesWriter |
Snapshot |
SparseIntVect | Class for efficiently storing sparse vectors of ints
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 |
TDTMolSupplier | Lazy file parser for TDT files
TDTWriter |
Trajectory |
UnimplementedFPException | Used to indicate errors for unimplemented fp types in convenience functions
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