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f42f479d28
smarts queries run faster (like vector bindings). Though there is an addition to the smarts parser exposed here, I do not recommend using it in client code.
282 lines
8.9 KiB
C++
Executable File
282 lines
8.9 KiB
C++
Executable File
// $Id$
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//
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// Copyright (C) 2001-2010 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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//
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#include <RDGeneral/utils.h>
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include "SubstructMatch.h"
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#include "SubstructUtils.h"
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#include <boost/smart_ptr.hpp>
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#include <map>
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#include "ullmann.hpp"
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#include "vf2.hpp"
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namespace RDKit{
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namespace detail {
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typedef std::map<unsigned int,QueryAtom::QUERYATOM_QUERY *> SUBQUERY_MAP;
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void MatchSubqueries(const ROMol &mol,QueryAtom::QUERYATOM_QUERY *q,bool useChirality,
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bool registerQuery,
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SUBQUERY_MAP &subqueryMap );
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typedef std::list<std::pair<MolGraph::vertex_descriptor,MolGraph::vertex_descriptor> > ssPairType;
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class AtomLabelFunctor{
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public:
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AtomLabelFunctor(const ROMol &query,const ROMol &mol, bool useChirality) :
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d_query(query), d_mol(mol), df_useChirality(useChirality) {};
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bool operator()(unsigned int i,unsigned int j) const{
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bool res=false;
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if(!df_useChirality){
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res=atomCompat(d_query[i],d_mol[j]);
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} else {
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res=chiralAtomCompat(d_query[i],d_mol[j]);
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}
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//std::cerr<<" alf: "<<i<<" - "<<j<<"? "<<res<<std::endl;
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return res;
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}
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private:
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const ROMol &d_query;
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const ROMol &d_mol;
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bool df_useChirality;
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};
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class BondLabelFunctor{
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public:
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BondLabelFunctor(const ROMol &query,const ROMol &mol) :
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d_query(query), d_mol(mol) {};
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bool operator()(MolGraph::edge_descriptor i,MolGraph::edge_descriptor j) const{
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bool res=bondCompat(d_query[i],d_mol[j]);
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//std::cerr<<" blf: "<<i<<" - "<<j<<"? "<<res<<std::endl;
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return res;
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}
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private:
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const ROMol &d_query;
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const ROMol &d_mol;
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};
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}
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// ----------------------------------------------
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//
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// find one match
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//
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bool SubstructMatch(const ROMol &mol,const ROMol &query,MatchVectType &matchVect,
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bool recursionPossible,bool useChirality,bool registerQuery)
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{
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//std::cerr<<"begin match"<<std::endl;
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if(recursionPossible){
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ROMol::ConstAtomIterator atIt;
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detail::SUBQUERY_MAP subqueryMap;
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for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
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if((*atIt)->getQuery()){
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detail::MatchSubqueries(mol,(*atIt)->getQuery(),useChirality,registerQuery,
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subqueryMap);
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}
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}
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}
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//std::cerr<<"main matching"<<std::endl;
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matchVect.clear();
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matchVect.resize(0);
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detail::AtomLabelFunctor atomLabeler(query,mol,useChirality);
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detail::BondLabelFunctor bondLabeler(query,mol);
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detail::ssPairType match;
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#if 0
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bool res=boost::ullmann(query.getTopology(),mol.getTopology(),
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atomLabeler,bondLabeler,match);
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#else
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bool res=boost::vf2(query.getTopology(),mol.getTopology(),
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atomLabeler,bondLabeler,match);
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#endif
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if(res){
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matchVect.resize(query.getNumAtoms());
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for(detail::ssPairType::const_iterator iter=match.begin();iter!=match.end();++iter){
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matchVect[iter->first]=std::pair<int,int>(iter->first,iter->second);
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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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//
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// find all matches
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//
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// NOTE: this blows out the contents of matches
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//
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unsigned int SubstructMatch(const ROMol &mol,const ROMol &query,
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std::vector< MatchVectType > &matches,
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bool uniquify,bool recursionPossible,
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bool useChirality,bool registerQuery) {
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if(recursionPossible){
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detail::SUBQUERY_MAP subqueryMap;
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ROMol::ConstAtomIterator atIt;
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for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
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if((*atIt)->getQuery()){
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//std::cerr<<"recurse from atom "<<(*atIt)->getIdx()<<std::endl;
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detail::MatchSubqueries(mol,(*atIt)->getQuery(),useChirality,registerQuery,subqueryMap);
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}
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}
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}
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matches.clear();
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matches.resize(0);
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detail::AtomLabelFunctor atomLabeler(query,mol,useChirality);
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detail::BondLabelFunctor bondLabeler(query,mol);
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std::list<detail::ssPairType> pms;
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#if 0
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bool found=boost::ullmann_all(query.getTopology(),mol.getTopology(),
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atomLabeler,bondLabeler,pms);
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#else
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bool found=boost::vf2_all(query.getTopology(),mol.getTopology(),
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atomLabeler,bondLabeler,pms);
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#endif
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unsigned int res=0;
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if(found){
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unsigned int nQueryAtoms=query.getNumAtoms();
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matches.reserve(pms.size());
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for(std::list<detail::ssPairType>::const_iterator iter1=pms.begin();
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iter1!=pms.end();++iter1){
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MatchVectType matchVect;
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matchVect.resize(nQueryAtoms);
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for(detail::ssPairType::const_iterator iter2=iter1->begin();
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iter2!=iter1->end();++iter2){
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matchVect[iter2->first]=std::pair<int,int>(iter2->first,iter2->second);
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}
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matches.push_back(matchVect);
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}
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if(uniquify){
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removeDuplicates(matches,mol.getNumAtoms());
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}
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res = matches.size();
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}
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return res;
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}
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namespace detail {
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unsigned int RecursiveMatcher(const ROMol &mol,const ROMol &query,
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std::vector< int > &matches,bool useChirality,
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bool registerQuery,SUBQUERY_MAP &subqueryMap)
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{
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ROMol::ConstAtomIterator atIt;
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for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
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if((*atIt)->getQuery()){
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MatchSubqueries(mol,(*atIt)->getQuery(),useChirality,registerQuery,subqueryMap);
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}
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}
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detail::AtomLabelFunctor atomLabeler(query,mol,useChirality);
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detail::BondLabelFunctor bondLabeler(query,mol);
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matches.clear();
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matches.resize(0);
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std::list<detail::ssPairType> pms;
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#if 0
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bool found=boost::ullmann_all(query.getTopology(),mol.getTopology(),
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atomLabeler,bondLabeler,pms);
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#else
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bool found=boost::vf2_all(query.getTopology(),mol.getTopology(),
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atomLabeler,bondLabeler,pms);
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#endif
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unsigned int res=0;
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if(found){
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matches.reserve(pms.size());
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for(std::list<detail::ssPairType>::const_iterator iter1=pms.begin();
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iter1!=pms.end();++iter1){
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if(!query.hasProp("_queryRootAtom")){
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matches.push_back(iter1->begin()->second);
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} else {
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int rootIdx;
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query.getProp("_queryRootAtom",rootIdx);
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bool found=false;
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for(detail::ssPairType::const_iterator pairIter=iter1->begin();
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pairIter!=iter1->end();++pairIter){
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if(pairIter->first==rootIdx){
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matches.push_back(pairIter->second);
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found=true;
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break;
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}
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}
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if(!found){
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BOOST_LOG(rdErrorLog)<<"no match found for queryRootAtom"<<std::endl;
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}
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}
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}
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res = matches.size();
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}
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//std::cout << " <<< RecursiveMatcher: " << int(query) << std::endl;
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return res;
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}
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void MatchSubqueries(const ROMol &mol,QueryAtom::QUERYATOM_QUERY *query,bool useChirality,
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bool registerQuery,SUBQUERY_MAP &subqueryMap){
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PRECONDITION(query,"bad query");
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//std::cout << "*-*-* MS: " << (int)query << std::endl;
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//std::cout << "\t\t" << typeid(*query).name() << std::endl;
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if(query->getDescription()=="RecursiveStructure"){
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RecursiveStructureQuery *rsq=(RecursiveStructureQuery *)query;
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rsq->clear();
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bool matchDone=false;
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if(rsq->getSerialNumber() &&
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subqueryMap.find(rsq->getSerialNumber()) != subqueryMap.end()){
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// we've matched an equivalent serial number before, just
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// copy in the matches:
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matchDone=true;
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const RecursiveStructureQuery *orsq=
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(const RecursiveStructureQuery *)subqueryMap[rsq->getSerialNumber()];
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for(RecursiveStructureQuery::CONTAINER_TYPE::const_iterator setIter=orsq->beginSet();
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setIter!=orsq->endSet();++setIter){
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rsq->insert(*setIter);
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}
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//std::cerr<<" copying results for query serial number: "<<rsq->getSerialNumber()<<std::endl;
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}
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if(!matchDone){
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ROMol const *queryMol = rsq->getQueryMol();
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// in case we are reusing this query, clear its contents now.
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if(queryMol){
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std::vector< int > matchStarts;
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unsigned int res = RecursiveMatcher(mol,*queryMol,matchStarts,useChirality,
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registerQuery,subqueryMap);
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if(res){
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for(std::vector<int>::iterator i=matchStarts.begin();
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i!=matchStarts.end();
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i++){
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rsq->insert(*i);
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}
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}
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}
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if(rsq->getSerialNumber()){
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subqueryMap[rsq->getSerialNumber()]=query;
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//std::cerr<<" storing results for query serial number: "<<rsq->getSerialNumber()<<std::endl;
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}
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}
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} else {
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//std::cout << "\tmsq1: ";
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}
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// now recurse over our children (these things can be nested)
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Queries::Query<int,Atom const*,true>::CHILD_VECT_CI childIt;
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//std::cout << query << " " << query->endChildren()-query->beginChildren() << std::endl;
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for(childIt=query->beginChildren();childIt!=query->endChildren();childIt++){
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MatchSubqueries(mol,childIt->get(),useChirality,registerQuery,subqueryMap);
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}
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//std::cout << "<<- back " << (int)query << std::endl;
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}
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} // end of namespace detail
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}
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