rdkit.Chem.rdMolChemicalFeatures module

Module containing from chemical feature and functions to generate the

rdkit.Chem.rdMolChemicalFeatures.BuildFeatureFactory((str)fileName) → MolChemicalFeatureFactory :

Construct a feature factory given a feature definition in a file

C++ signature :

RDKit::MolChemicalFeatureFactory* BuildFeatureFactory(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

rdkit.Chem.rdMolChemicalFeatures.BuildFeatureFactoryFromString((str)fdefString) → MolChemicalFeatureFactory :

Construct a feature factory given a feature definition block

C++ signature :

RDKit::MolChemicalFeatureFactory* BuildFeatureFactoryFromString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

rdkit.Chem.rdMolChemicalFeatures.GetAtomMatch((AtomPairsParameters)featMatch[, (int)maxAts=1024]) → object :

Returns an empty list if any of the features passed in share an atom.

Otherwise a list of lists of atom indices is returned.

C++ signature :

boost::python::api::object GetAtomMatch(boost::python::api::object [,int=1024])

class rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature

Bases: instance

Class to represent a chemical feature. These chemical features may or may not have been derived from molecule object; i.e. it is possible to have a chemical feature that was created just from its type and location.

Raises an exception This class cannot be instantiated from Python

ClearCache((MolChemicalFeature)self) → None :

Clears the cache used to store position information.

C++ signature :

void ClearCache(RDKit::MolChemicalFeature {lvalue})

GetActiveConformer((MolChemicalFeature)self) → int :

Gets the conformer to use.

C++ signature :

int GetActiveConformer(RDKit::MolChemicalFeature {lvalue})

GetAtomIds((MolChemicalFeature)self) → object :

Get the IDs of the atoms that participate in the feature

C++ signature :

_object* GetAtomIds(RDKit::MolChemicalFeature)

GetFactory((MolChemicalFeature)self) → MolChemicalFeatureFactory :

Get the factory used to generate this feature

C++ signature :

RDKit::MolChemicalFeatureFactory const* GetFactory(RDKit::MolChemicalFeature {lvalue})

GetFamily((MolChemicalFeature)self) → str :

Get the family to which the feature belongs; donor, acceptor, etc.

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetFamily(RDKit::MolChemicalFeature {lvalue})

GetId((MolChemicalFeature)self) → int :

Returns the identifier of the feature

C++ signature :

int GetId(RDKit::MolChemicalFeature {lvalue})

GetMol((MolChemicalFeature)self) → Mol :

Get the molecule used to derive the features

C++ signature :

RDKit::ROMol const* GetMol(RDKit::MolChemicalFeature {lvalue})

GetPos((MolChemicalFeature)self, (int)confId) → Point3D :

Get the location of the chemical feature

C++ signature :

RDGeom::Point3D GetPos(RDKit::MolChemicalFeature {lvalue},int)

GetPos( (MolChemicalFeature)self) -> Point3D :

Get the location of the default chemical feature (first position)

C++ signature :

RDGeom::Point3D GetPos(RDKit::MolChemicalFeature {lvalue})

GetType((MolChemicalFeature)self) → str :

Get the specific type for the feature

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetType(RDKit::MolChemicalFeature {lvalue})

SetActiveConformer((MolChemicalFeature)self, (int)confId) → None :

Sets the conformer to use (must be associated with a molecule).

C++ signature :

void SetActiveConformer(RDKit::MolChemicalFeature {lvalue},int)

class rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeatureFactory

Bases: instance

Class to featurize a molecule

Raises an exception This class cannot be instantiated from Python

GetFeatureDefs((MolChemicalFeatureFactory)self) → dict :

Get a dictionary with SMARTS definitions for each feature type

C++ signature :

boost::python::dict GetFeatureDefs(RDKit::MolChemicalFeatureFactory)

GetFeatureFamilies((MolChemicalFeatureFactory)self) → tuple :

Get a tuple of feature types

C++ signature :

boost::python::tuple GetFeatureFamilies(RDKit::MolChemicalFeatureFactory)

GetFeaturesForMol(mol, includeOnly='', confId=-1)

GetMolFeature((MolChemicalFeatureFactory)self, (Mol)mol, (int)idx[, (str)includeOnly=''[, (bool)recompute=True[, (int)confId=-1]]]) → MolChemicalFeature :

returns a particular feature (by index)

C++ signature :

boost::shared_ptr<RDKit::MolChemicalFeature> GetMolFeature(RDKit::MolChemicalFeatureFactory,RDKit::ROMol,int [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,bool=True [,int=-1]]])

GetNumFeatureDefs((MolChemicalFeatureFactory)self) → int :

Get the number of feature definitions

C++ signature :

int GetNumFeatureDefs(RDKit::MolChemicalFeatureFactory {lvalue})

GetNumMolFeatures((MolChemicalFeatureFactory)self, (Mol)mol[, (str)includeOnly='']) → int :

Get the number of features the molecule has

C++ signature :

int GetNumMolFeatures(RDKit::MolChemicalFeatureFactory,RDKit::ROMol [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’])