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// $Id$
//
// 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 <RDBoost/python.h>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/types.h>
#include <RDGeneral/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, int confId) {
static FeatSPtrList feats;
if (recompute) {
feats = factory.getFeaturesForMol(mol, includeOnly.c_str(), confId);
}
if (idx < 0 || idx >= static_cast<int>(feats.size())) {
throw IndexErrorException(idx);
}
auto 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::arg("confId") = -1),
python::with_custodian_and_ward_postcall<0, 2>(),
"returns a particular feature (by index)");
};
};
} // namespace RDKit
void wrap_factory() { RDKit::featfactory_wrapper::wrap(); }
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