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// $Id: MolChemicalFeatureFactory.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#define NO_IMPORT_ARRAY
#include <boost/python.hpp>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/types.h>
#include <RDBoost/Exceptions.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeature.h>
#include <boost/python/converter/shared_ptr_to_python.hpp>
namespace python = boost::python;
namespace RDKit {
// ----------------------------------------------------------------------------
// NOTE: the reason we don't provide an interface to get all the
// features from a molecule at the same time directly from C++ is a
// potential problem with the lifetime of molecules and features:
// Each Feature carries around a pointer to its owning molecule,
// and that pointer must remain valid. So we need to use the BPL's
// with_custodian_and_ward() functionality to tie the lifetime
// of the molecule to that of the feature. This is not currently
// possible in BPL v1.32 if we return a tuple of objects; so if
// we return a set of features, there's no way to use
// with_custodian_and_ward() to ensure that the molecule doesn't vanish
// underneath them. Access to all of a molecule's features is provided
// from within python (looping over getMolFeature() and gaining efficiency
// by not recomputing after the first call).
// ----------------------------------------------------------------------------
int getNumMolFeatures(const MolChemicalFeatureFactory &factory,
const ROMol &mol,
std::string includeOnly="") {
FeatSPtrList feats = factory.getFeaturesForMol(mol,includeOnly.c_str());
return feats.size();
}
FeatSPtr getMolFeature(const MolChemicalFeatureFactory &factory,
const ROMol &mol,
int idx,
std::string includeOnly="",
bool recompute=true) {
static FeatSPtrList feats;
if(recompute){
feats = factory.getFeaturesForMol(mol,includeOnly.c_str());
}
if(idx<0 || idx>=static_cast<int>(feats.size())){
throw IndexErrorException(idx);
}
FeatSPtrList_I fi=feats.begin();
for(int i=0;i<idx;++i){
++fi;
}
return (*fi);
}
python::tuple getFeatureFamilies(const MolChemicalFeatureFactory &factory){
python::list res;
MolChemicalFeatureDef::CollectionType::const_iterator iter;
for(iter=factory.beginFeatureDefs();iter!=factory.endFeatureDefs();++iter){
std::string fam= (*iter)->getFamily();
if(res.count(fam)==0) res.append(fam);
}
return python::tuple(res);
}
python::dict getFeatureDefs(const MolChemicalFeatureFactory &factory){
python::dict res;
MolChemicalFeatureDef::CollectionType::const_iterator iter;
for(iter=factory.beginFeatureDefs();iter!=factory.endFeatureDefs();++iter){
std::string key= (*iter)->getFamily()+"."+(*iter)->getType();
res[key]=(*iter)->getSmarts();
}
return res;
}
struct featfactory_wrapper {
static void wrap() {
std::string factoryClassDoc="Class to featurize a molecule\n";
// no direct constructor - use buildFactory function
python::class_<MolChemicalFeatureFactory>("MolChemicalFeatureFactory",
factoryClassDoc.c_str(), python::no_init)
.def("GetNumFeatureDefs", &MolChemicalFeatureFactory::getNumFeatureDefs,
"Get the number of feature definitions")
.def("GetFeatureFamilies", getFeatureFamilies,
"Get a tuple of feature types")
.def("GetFeatureDefs", getFeatureDefs,
"Get a dictionary with SMARTS definitions for each feature type")
.def("GetNumMolFeatures", getNumMolFeatures,
(python::arg("mol"),python::arg("includeOnly")=std::string("")),
"Get the number of features the molecule has")
.def("GetMolFeature", getMolFeature,
(python::arg("mol"),python::arg("idx"),
python::arg("includeOnly")=std::string(""),
python::arg("recompute")=true),
python::with_custodian_and_ward_postcall<0,2>(),
"returns a particular feature (by index)")
;
};
};
}
void wrap_factory() {
RDKit::featfactory_wrapper::wrap();
}
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