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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.
//
#include "MolChemicalFeature.h"
#include "MolChemicalFeatureDef.h"
#include "MolChemicalFeatureFactory.h"
#include "FeatureParser.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <vector>
#include <sstream>
#include <set>
#include <algorithm>
namespace RDKit {
FeatSPtrList MolChemicalFeatureFactory::getFeaturesForMol(const ROMol &mol,
const char* includeOnly) const {
PRECONDITION(includeOnly,"bad limits");
std::string limits(includeOnly);
#ifdef USE_VFLIB
AR_MOLGRAPH *molG=getMolGraph(mol);
#endif
FeatSPtrList res;
typedef std::vector< std::pair< std::string,std::set<int> > > MatchSetCollection;
MatchSetCollection matchSets;
for(MolChemicalFeatureDef::CollectionType::const_iterator featDefIt=beginFeatureDefs();
featDefIt!=endFeatureDefs();featDefIt++){
MolChemicalFeatureDef::CollectionType::value_type featDef=*featDefIt;
if(limits=="" || limits==featDef->getFamily()){
std::vector< MatchVectType > matches;
#ifdef USE_VFLIB
unsigned int numMatches=SubstructMatch(molG,*featDef->getPattern(),matches);
#else
unsigned int numMatches=SubstructMatch(mol,*featDef->getPattern(),matches);
#endif
for(unsigned int i=0;i<numMatches;i++){
const MatchVectType &match=matches[i];
std::set<int> matchSet;
for(MatchVectType::const_iterator mIt=match.begin();
mIt!=match.end();
++mIt){
matchSet.insert(mIt->second);
}
// loop over the matches we've already found and see if this one
// is unique:
bool unique=true;
for(MatchSetCollection::const_iterator vsiCI=matchSets.begin();
vsiCI!=matchSets.end();
++vsiCI){
if(vsiCI->first==featDef->getFamily() &&
std::includes(vsiCI->second.begin(),vsiCI->second.end(),
matchSet.begin(),matchSet.end())){
unique=false;
break;
}
}
if(unique){
matchSets.push_back(std::make_pair(featDef->getFamily(),matchSet));
// Set up the feature:
MolChemicalFeature *newFeat=new MolChemicalFeature(&mol,this,featDef.get());
MolChemicalFeature::AtomPtrContainer &atoms=newFeat->d_atoms;
atoms.resize(match.size());
// set up the atoms:
for(MatchVectType::const_iterator matchIt=match.begin();
matchIt!=match.end();matchIt++){
int atomIdx=matchIt->second;
int queryIdx=matchIt->first;
atoms[queryIdx]=mol.getAtomWithIdx(atomIdx);
}
// finally, add this to our result:
res.push_back(FeatSPtrList::value_type(newFeat));
}
}
}
}
#ifdef USE_VFLIB
#ifndef CACHE_ARMOLGRAPHS
delete molG;
#endif
#endif
return res;
}
MolChemicalFeatureFactory *buildFeatureFactory(const std::string &featureData){
std::stringstream ss(featureData);
return buildFeatureFactory(ss);
}
MolChemicalFeatureFactory *buildFeatureFactory(std::istream &inStream){
MolChemicalFeatureFactory *res=0;
MolChemicalFeatureDef::CollectionType featDefs;
if(parseFeatureData(inStream,featDefs)==0){
// everything parsed ok
res = new MolChemicalFeatureFactory();
//std::copy(featDefs.begin(),featDefs.end(),res->beginFeatureDefs());
for(MolChemicalFeatureDef::CollectionType::const_iterator ci=featDefs.begin();
ci!=featDefs.end();ci++){
res->addFeatureDef(*ci);
}
}
return res;
}
}
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