RDKit: Class List

| RDKit Open-source cheminformatics and machine learning.

- Main Page
- Namespaces
- Classes
- Files

- Class List
- Class Hierarchy
- Class Members

Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 1234]

►N boost |
►N logging |
C rdLogger |
►N boost_adaptbx |
►N python |
C ostream |
►C streambuf | A stream buffer getting data from and putting data into a Python file object
C istream |
C ostream |
C streambuf_capsule |
►N ChemicalFeatures |
C ChemicalFeature | Abstract base class for chemical feature
C FreeChemicalFeature | Class for chemical features that do not orignate from molecules
►N DistGeom |
C BoundsMatrix | Class to store the distance bound
C ChiralSet | Class used to store a quartet of points and chiral volume bounds on them
C ChiralViolationContrib |
C DistViolationContrib |
C FourthDimContrib |
►N ForceFields |
►N CrystalFF |
C TorsionAngleContribM6 | Torsion term for multiplicity m = 1 - 6
►N MMFF |
C AngleBendContrib | The angle-bend term for MMFF
C AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib
C BondStretchContrib | The bond-stretch term for MMFF
C DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib
C EleContrib | Electrostatic term for MMFF
C MMFFAngle | Class to store MMFF parameters for angle bending
C MMFFAngleCollection |
C MMFFAromCollection |
C MMFFBndkCollection |
C MMFFBond | Class to store MMFF parameters for bond stretching
C MMFFBondCollection |
C MMFFChg |
C MMFFChgCollection |
C MMFFCovRadPauEle |
C MMFFCovRadPauEleCollection |
C MMFFDef | Class to store MMFF atom type equivalence levels
C MMFFDefCollection |
C MMFFDfsbCollection |
C MMFFHerschbachLaurie |
C MMFFHerschbachLaurieCollection |
C MMFFOop | Class to store MMFF parameters for out-of-plane bending
C MMFFOopCollection |
C MMFFPBCI | Class to store MMFF Partial Bond Charge Increments
C MMFFPBCICollection |
C MMFFProp | Class to store MMFF Properties
C MMFFPropCollection |
C MMFFStbn | Class to store MMFF parameters for stretch-bending
C MMFFStbnCollection |
C MMFFTor | Class to store MMFF parameters for torsions
C MMFFTorCollection |
C MMFFVdW | Class to store MMFF parameters for non-bonded Van der Waals
C MMFFVdWCollection |
C MMFFVdWRijstarEps |
C OopBendContrib | Out-of-plane term for MMFF
C PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2
C StretchBendContrib | The angle-bend term for MMFF
C TorsionAngleContrib | Torsion term for MMFF
C TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib
C VdWContrib | Van der Waals term for MMFF
►N UFF |
C AngleBendContrib | The angle-bend term for the Universal Force Field
C AngleConstraintContrib | An angle range constraint modelled after a AngleBendContrib
C AtomicParams | Class to store atomic parameters for the Universal Force Field
C BondStretchContrib | The bond-stretch term for the Universal Force Field
C DistanceConstraintContrib | A distance range constraint modelled after a BondStretchContrib
C InversionContrib | The inversion term for the Universal Force Field
C ParamCollection | Singleton class for retrieving UFF AtomParams
C PositionConstraintContrib | A position constraint of the type 0.5k * deltaX^2
C TorsionAngleContrib | Torsion term for the Universal Force Field
C TorsionConstraintContrib | A dihedral angle range constraint modelled after a TorsionContrib
C UFFAngle | Class to store UFF parameters for angle bending
C UFFBond | Class to store UFF parameters for bond stretching
C UFFInv | Class to store UFF parameters for inversions
C UFFTor | Class to store UFF parameters for torsions
C UFFVdW | Class to store UFF parameters for van der Waals interactions
C vdWContrib | Van der Waals term for the Universal Force Field
C ForceField | A class to store forcefields and handle minimization
C ForceFieldContrib | Abstract base class for contributions to ForceFields
►N Invar |
C Invariant |
►N Queries |
C AndQuery | Query implementing AND: requires all children to be `true`
C EqualityQuery | Query implementing ==: arguments must match a particular value (within an optional tolerance)
C GreaterEqualQuery | Query implementing >= using a particular value (and an optional tolerance)
C GreaterQuery | Query implementing > using a particular value (and an optional tolerance)
C Int2Type | Class to allow integer values to pick templates
C LessEqualQuery | Query implementing <= using a particular value (and an optional tolerance)
C LessQuery | Query implementing < using a particular value (and an optional tolerance)
C OrQuery | Query implementing AND: requires any child to be `true`
C Query | Base class for all queries
C RangeQuery | Query implementing a range: arguments must fall in a particular range of values
C SetQuery | Query implementing a set: arguments must one of a set of values
C XOrQuery | Query implementing XOR: requires exactly one child to be `true`
►N Rankers | Utility functionality used to rank sequences
C argless |
C pairGreater | Functor for implementing > on two std::pairs. The first entries are
C pairLess | Function for implementing < on two std::pairs. The first entries are
►N RDCatalog |
C Catalog | Abstract base class for a catalog object
C CatalogEntry | Abstract base class to be used to represent an entry in a Catalog
C CatalogParams | Abstract base class for the container used to create a catalog
►C HierarchCatalog | A Catalog with a hierarchical structure
C vertex_entry_t | Used by the BGL to set up the node properties in our graph
C LinearCatalog | Linear Catalog (analogous to an std::vector)
►N RDDataManip |
C MetricMatrixCalc | A generic metric matrix calculator (e.g similarity matrix or distance matrix)
►N RDDepict |
C EmbeddedAtom | Class that contains the data for an atoms that has alredy been embedded
C EmbeddedFrag | Class containing a fragment of a molecule that has already been embedded
C gtIIPair |
►N RDFeatures |
C ExplicitFeature |
C ImplicitFeature |
►N RDGeom |
C Grid3D | Virtual base class for a grid object
C GridException |
C Point |
C Point2D |
C Point3D |
C PointND |
C Transform2D |
C Transform3D |
C UniformGrid3D |
►N RDInfoTheory | Class used to rank bits based on a specified measure of infomation
C BitCorrMatGenerator |
C InfoBitRanker |
►N RDKit | Includes a bunch of functionality for handling Atom and Bond queries
►N Canon |
C AtomCompareFunctor |
C bondholder |
C canon_atom |
C ChiralAtomCompareFunctor |
C MolStackElem | These are the actual elements in the molecular stack
C MolStackUnion | Used to store components in the molecular stack
C SpecialChiralityAtomCompareFunctor |
C SpecialSymmetryAtomCompareFunctor |
►N Descriptors |
C CrippenParamCollection | Singleton class for retrieving Crippen parameters
C CrippenParams | Class used to store Crippen parameters
►N Drawing |
►N FilterMatchOps |
C And |
C Not |
C Or |
►N FMCS |
C Composition2N |
►C DuplicatedSeedCache |
C TKey |
C ExecStatistics |
C Graph |
C MaximumCommonSubgraph |
C MolFragment |
C NewBond |
C RingMatchTableSet |
C Seed |
C SeedSet |
►C SubstructureCache |
C HashKey |
C KeyNumericMetrics |
C Target |
C TargetMatch |
C TArray2D |
►N MMFF |
C MMFFAtomProperties |
C MMFFMolProperties |
►N MolAlign |
C LAP |
C MolAlignException |
C MolHistogram |
C O3A |
C O3AConstraint |
C O3AConstraintVect |
C O3AFuncData |
C SDM |
►N MolFragmenter |
C FragmenterBondType |
►N MolHash |
C HashSet |
►N MolOps | Groups a variety of molecular query and transformation operations
C AdjustQueryParameters |
►N SLNParse |
C AttribType |
►N UFF |
►N Utils |
C LocaleSwitcher |
C AromaticAtomIterator_ | Iterate over aromatic atoms, this is bidirectional
C Atom | The class for representing atoms
C atomicData |
C AtomIterator_ | A general random access iterator
C AtomMonomerInfo | The abstract base class for atom-level monomer info
C AtomPDBResidueInfo | Captures atom-level information about peptide residues
C AtomRingQuery |
C BadFileException | Used by various file parsing classes to indicate a bad file
C Bond | Class for representing a bond
C BondIterator_ | Iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
C charptr_functor | Functor for comparing two strings
C ChemicalReaction | This is a class for storing and applying general chemical reactions
C ChemicalReactionException | Used to indicate an error in the chemical reaction engine
C ChemicalReactionParserException | Used to indicate an error in parsing reaction data
C Conformer | The class for representing 2D or 3D conformation of a molecule
C ConformerException | Used to indicate errors from incorrect confomer access
C ConstBondIterator_ | Const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess
C Dict | The `Dict` class can be used to store objects of arbitrary type keyed by `strings`
C DiscreteDistMat |
C DiscreteValueVect | Class for efficiently storing vectors of discrete values
C ExclusionList |
C FeatureFileParseException | Class used to indicate errors in parsing feature definition files
C FileParseException | Used by various file parsing classes to indicate a parse error
C FilterCatalog |
C FilterCatalogEntry |
C FilterCatalogParams |
C FilterData_t |
C FilterMatch | Holds the atomPairs matched by the underlying matcher
C FilterMatcherBase |
C FilterProperty_t |
C ForwardSDMolSupplier |
C FPBReader | Class for reading and searching FPB files
C FragCatalogEntry |
C FragCatGenerator |
C FragCatParams | Container for user parameters used to create a fragment catalog
C FragFPGenerator |
C GasteigerParams |
C HasPropQuery |
C HasPropWithValueQuery |
C HasPropWithValueQuery< TargetPtr, std::string > |
C HeteroatomIterator_ | Iterate over heteroatoms, this is bidirectional
C larger_of | Functor for returning the larger of two values
C ltDouble | Functor to compare two doubles with a tolerance
C MatchingAtomIterator_ | Iterate over atoms matching a query function. This is bidirectional
C MCSAtomCompareParameters |
C MCSBondCompareParameters |
C MCSParameters |
C MCSProgressData |
C MCSResult |
C MolCatalogEntry | This class is used to store ROMol objects in a MolCatalog
C MolCatalogParams | Container for user parameters used to create a mol catalog
C MolChemicalFeature |
C MolChemicalFeatureDef |
C MolChemicalFeatureFactory | The class for finding chemical features in molecules
C MolDraw2D |
C MolDraw2DCairo |
C MolDraw2DQt |
C MolDraw2DSVG |
C MolDraw2Dwx |
C MolDrawOptions |
C MolPickler | Handles pickling (serializing) molecules
C MolPicklerException | Used to indicate exceptions whilst pickling (serializing) molecules
C MolSanitizeException | Class for flagging sanitization errors
C MolSupplier |
C MolWriter |
C PDBMolSupplier | Lazy file parser for PDB files
C PDBWriter |
C PeriodicTable | Singleton class for retrieving information about atoms
C QueryAtom | Class for storing atomic queries
C QueryAtomIterator_ | Iterate over atoms matching a query. This is bidirectional
C QueryBond | Class for storing Bond queries
C ReactionFingerprintParams |
C ReactionPickler | Handles pickling (serializing) reactions
C ReactionPicklerException | Used to indicate exceptions whilst pickling (serializing) reactions
C RecursiveStructureQuery | Allows use of recursive structure queries (e.g. recursive SMARTS)
C ResonanceMolSupplier |
C RingInfo | A class to store information about a molecule's rings
C ROMol | ROMol is a molecule class that is intended to have a fixed topology
C RWMol | RWMol is a molecule class that is intended to be edited
C SDMolSupplier |
C SDWriter |
C SLNParseException |
C SmartsMatcher |
C SmilesMolSupplier | Lazy file parser for Smiles tables
C SmilesParseException |
C SmilesWriter |
C SparseIntVect | Class for efficiently storing sparse vectors of ints
C TDTMolSupplier | Lazy file parser for TDT files
C TDTWriter |
►N RDNumeric |
C Matrix | A matrix class for general, non-square matrices
C SquareMatrix |
C SymmMatrix | A symmetric matrix class
C Vector | A class to represent vectors of numbers
►N RDPickers |
C DistPicker | Abstract base class to do perform item picking (typically molecules) using a distance matrix
C HierarchicalClusterPicker | Diversity picker based on hierarchical clustering
C MaxMinPicker | Implements the MaxMin algorithm for picking a subset of item from a pool
C BitVect | Abstract base class for storing BitVectors
C DatastructsException |
C ExplicitBitVect | Class for bit vectors that are densely occupied
C IndexErrorException | Class to allow us to throw an `IndexError` from C++ and have it make it back to Python
C KeyErrorException | Class to allow us to throw a `KeyError` from C++ and have it make it back to Python
C PySequenceHolder | Class to hold sequences (lists, tuples, arrays, etc.) passed from Python -> C++
C SparseBitVect | Class for bit vectors that are sparsely occupied
C ValueErrorException | Class to allow us to throw a `ValueError` from C++ and have it make it back to Python