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// $Id$
//
// Copyright (C) 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 <boost/dynamic_bitset.hpp>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/types.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeature.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h>
#include <ChemicalFeatures/FreeChemicalFeature.h>
namespace python = boost::python;
namespace RDKit {
python::object GetAtomMatch(python::object featMatch, int maxAts = 1024) {
python::list res;
unsigned int nEntries =
python::extract<unsigned int>(featMatch.attr("__len__")());
boost::dynamic_bitset<> indices(maxAts);
for (unsigned int i = 0; i < nEntries; ++i) {
MolChemicalFeature *feat =
python::extract<MolChemicalFeature *>(featMatch[i]);
const MolChemicalFeature::AtomPtrContainer &atoms = feat->getAtoms();
MolChemicalFeature::AtomPtrContainer_CI aci;
python::list local;
for (aci = atoms.begin(); aci != atoms.end(); ++aci) {
unsigned int idx = (*aci)->getIdx();
if (indices[idx]) {
return python::list();
} else {
indices[idx] = 1;
}
local.append(idx);
}
res.append(local);
}
return res;
}
#if 0
// defined in MolChemicalFeatureFactory.cpp
python::tuple getFeatsForMol(const MolChemicalFeatureFactory &factory,
const ROMol &mol,
std::string includeOnly);
// Moving this into C++ didn't provide any speed improvement in our profiling,
// so, rather than adding additional complications to the wrapper interface,
// we'll just leave it out
//
// In the event it should be re-integrated, here's the def:
//python::def("GetFeatureMatchDict",GetFeatMatchDict,(python::arg("mol"),
// python::arg("factory"),
// python::arg("feats")),
// );
python::dict GetFeatMatchDict(const ROMol *mol,const MolChemicalFeatureFactory *factory,
python::object feats){
python::dict res;
unsigned int nEntries=python::extract<unsigned int>(feats.attr("__len__")());
for(unsigned int i=0;i<nEntries;++i){
const char *family;
python::extract<MolChemicalFeature *> cfX(feats[i]);
if(cfX.check()){
family=cfX()->getFamily().c_str();
} else {
python::extract<ChemicalFeatures::FreeChemicalFeature *> fcfX(feats[i]);
family=fcfX()->getFamily().c_str();
}
if(!res.has_key(family)){
res[family] = getFeatsForMol(factory,mol,family);
}
}
return res;
}
#endif
struct ChemicalFeatureUtils_wrapper {
static void wrap() {
python::def(
"GetAtomMatch", GetAtomMatch,
(python::arg("featMatch"), python::arg("maxAts") = 1024),
"Returns an empty list if any of the features passed in share an atom.\n\
Otherwise a list of lists of atom indices is returned.\n");
}
};
} // end of namespace RDKit
void wrap_ChemicalFeatureUtils() {
RDKit::ChemicalFeatureUtils_wrapper::wrap();
}
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