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