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