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123 lines
4.0 KiB
C++
123 lines
4.0 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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#include "MolChemicalFeature.h"
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#include "MolChemicalFeatureDef.h"
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#include "MolChemicalFeatureFactory.h"
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#include "FeatureParser.h"
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <vector>
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#include <sstream>
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#include <set>
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#include <algorithm>
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namespace RDKit {
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FeatSPtrList MolChemicalFeatureFactory::getFeaturesForMol(const ROMol &mol,
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const char* includeOnly) const {
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PRECONDITION(includeOnly,"bad limits");
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std::string limits(includeOnly);
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#ifdef USE_VFLIB
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AR_MOLGRAPH *molG=getMolGraph(mol);
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#endif
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FeatSPtrList res;
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int idx = 1;
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typedef std::vector< std::pair< std::string,std::set<int> > > MatchSetCollection;
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MatchSetCollection matchSets;
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for(MolChemicalFeatureDef::CollectionType::const_iterator featDefIt=beginFeatureDefs();
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featDefIt!=endFeatureDefs();featDefIt++){
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MolChemicalFeatureDef::CollectionType::value_type featDef=*featDefIt;
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if(limits=="" || limits==featDef->getFamily()){
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std::vector< MatchVectType > matches;
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#ifdef USE_VFLIB
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unsigned int numMatches=SubstructMatch(molG,*featDef->getPattern(),matches);
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#else
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unsigned int numMatches=SubstructMatch(mol,*featDef->getPattern(),matches);
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#endif
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for(unsigned int i=0;i<numMatches;i++){
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const MatchVectType &match=matches[i];
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std::set<int> matchSet;
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for(MatchVectType::const_iterator mIt=match.begin();
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mIt!=match.end();
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++mIt){
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matchSet.insert(mIt->second);
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}
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// loop over the matches we've already found and see if this one
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// is unique:
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bool unique=true;
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for(MatchSetCollection::const_iterator vsiCI=matchSets.begin();
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vsiCI!=matchSets.end();
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++vsiCI){
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if(vsiCI->first==featDef->getFamily() &&
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std::includes(vsiCI->second.begin(),vsiCI->second.end(),
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matchSet.begin(),matchSet.end())){
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unique=false;
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break;
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}
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}
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if(unique){
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matchSets.push_back(std::make_pair(featDef->getFamily(),matchSet));
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// Set up the feature:
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MolChemicalFeature *newFeat=new MolChemicalFeature(&mol,this,featDef.get(),idx++);
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MolChemicalFeature::AtomPtrContainer &atoms=newFeat->d_atoms;
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atoms.resize(match.size());
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// set up the atoms:
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for(MatchVectType::const_iterator matchIt=match.begin();
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matchIt!=match.end();matchIt++){
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int atomIdx=matchIt->second;
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int queryIdx=matchIt->first;
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atoms[queryIdx]=mol.getAtomWithIdx(atomIdx);
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}
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// finally, add this to our result:
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res.push_back(FeatSPtrList::value_type(newFeat));
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}
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}
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}
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}
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#ifdef USE_VFLIB
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#ifndef CACHE_ARMOLGRAPHS
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delete molG;
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#endif
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#endif
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return res;
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}
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MolChemicalFeatureFactory *buildFeatureFactory(const std::string &featureData){
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std::stringstream ss(featureData);
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return buildFeatureFactory(ss);
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}
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MolChemicalFeatureFactory *buildFeatureFactory(std::istream &inStream){
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MolChemicalFeatureFactory *res=0;
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MolChemicalFeatureDef::CollectionType featDefs;
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if(parseFeatureData(inStream,featDefs)==0){
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// everything parsed ok
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res = new MolChemicalFeatureFactory();
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//std::copy(featDefs.begin(),featDefs.end(),res->beginFeatureDefs());
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for(MolChemicalFeatureDef::CollectionType::const_iterator ci=featDefs.begin();
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ci!=featDefs.end();ci++){
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res->addFeatureDef(*ci);
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}
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}
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return res;
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}
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}
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