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rdkit/Code/GraphMol/Substruct/SubstructMatch.cpp
Greg Landrum 4a14a52674 Fixes #153
2013-11-15 06:47:18 +01:00

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// $Id$
//
// Copyright (C) 2001-2010 Greg Landrum and 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 <RDGeneral/utils.h>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include "SubstructMatch.h"
#include "SubstructUtils.h"
#include <boost/smart_ptr.hpp>
#include <map>
#ifdef RDK_THREADSAFE_SSS
#include <boost/thread/mutex.hpp>
#endif
#include "ullmann.hpp"
#include "vf2.hpp"
namespace RDKit{
namespace detail {
typedef std::map<unsigned int,QueryAtom::QUERYATOM_QUERY *> SUBQUERY_MAP;
void MatchSubqueries(const ROMol &mol,QueryAtom::QUERYATOM_QUERY *q,bool useChirality,
SUBQUERY_MAP &subqueryMap,bool useQueryQueryMatches);
#ifdef RDK_THREADSAFE_SSS
void ClearSubqueryLocks(QueryAtom::QUERYATOM_QUERY *q);
#endif
typedef std::list<std::pair<MolGraph::vertex_descriptor,MolGraph::vertex_descriptor> > ssPairType;
class MolMatchFinalCheckFunctor {
public:
MolMatchFinalCheckFunctor(const ROMol &query,const ROMol &mol, bool useChirality) :
d_query(query), d_mol(mol), df_useChirality(useChirality) {};
bool operator()(const boost::detail::node_id c1[], const boost::detail::node_id c2[]) const {
//std::cerr<<" check! "<<df_useChirality<<std::endl;
if(!df_useChirality) return true;
//for(unsigned int i=0;i<d_query.getNumAtoms();++i){
// std::cerr<<" "<<c1[i]<<" "<<c2[i]<<std::endl;
//}
// check chiral atoms:
for(unsigned int i=0;i<d_query.getNumAtoms();++i){
const Atom *qAt=d_query.getAtomWithIdx(c1[i]);
if(qAt->getChiralTag()!=Atom::CHI_TETRAHEDRAL_CW &&
qAt->getChiralTag()!=Atom::CHI_TETRAHEDRAL_CCW) continue;
const Atom *mAt=d_mol.getAtomWithIdx(c2[i]);
if(mAt->getChiralTag()!=Atom::CHI_TETRAHEDRAL_CW &&
mAt->getChiralTag()!=Atom::CHI_TETRAHEDRAL_CCW) return false;
if(qAt->getDegree()!=mAt->getDegree()) return false;
INT_LIST qOrder;
for(unsigned int j=0;j<d_query.getNumAtoms();++j){
const Bond *qB = d_query.getBondBetweenAtoms(c1[i],c1[j]);
if(qB){
qOrder.push_back(qB->getIdx());
if(qOrder.size()==qAt->getDegree()) break;
}
}
int qPermCount=qAt->getPerturbationOrder(qOrder);
INT_LIST mOrder;
for(unsigned int j=0;j<d_query.getNumAtoms();++j){
const Bond *mB = d_mol.getBondBetweenAtoms(c2[i],c2[j]);
if(mB){
mOrder.push_back(mB->getIdx());
if(mOrder.size()==mAt->getDegree()) break;
}
}
int mPermCount=mAt->getPerturbationOrder(mOrder);
if((qPermCount%2 == mPermCount%2 &&
qAt->getChiralTag()!=mAt->getChiralTag()) ||
(qPermCount%2 != mPermCount%2 &&
qAt->getChiralTag()==mAt->getChiralTag())) return false;
}
// now check double bonds
for(unsigned int i=0;i<d_query.getNumBonds();++i){
const Bond *qBnd=d_query.getBondWithIdx(i);
if(qBnd->getBondType()!=Bond::DOUBLE ||
(qBnd->getStereo()!=Bond::STEREOZ &&
qBnd->getStereo()!=Bond::STEREOE)) continue;
// don't think this can actually happen, but check to be sure:
if(qBnd->getStereoAtoms().size()!=2) continue;
std::map<unsigned int,unsigned int> qMap;
for(unsigned int j=0;j<d_query.getNumAtoms();++j){
qMap[c1[j]]=j;
}
const Bond *mBnd=d_mol.getBondBetweenAtoms(c2[qMap[qBnd->getBeginAtomIdx()]],
c2[qMap[qBnd->getEndAtomIdx()]]);
CHECK_INVARIANT(mBnd,"Matching bond not found");
if(mBnd->getBondType()!=Bond::DOUBLE ||
(mBnd->getStereo()!=Bond::STEREOZ &&
mBnd->getStereo()!=Bond::STEREOE)) continue;
// don't think this can actually happen, but check to be sure:
if(mBnd->getStereoAtoms().size()!=2) continue;
unsigned int end1Matches=0;
unsigned int end2Matches=0;
if(c2[qMap[qBnd->getBeginAtomIdx()]]==mBnd->getBeginAtomIdx()){
// query Begin == mol Begin
if(c2[qMap[qBnd->getStereoAtoms()[0]]]==mBnd->getStereoAtoms()[0]) end1Matches=1;
if(c2[qMap[qBnd->getStereoAtoms()[1]]]==mBnd->getStereoAtoms()[1]) end2Matches=1;
} else {
// query End == mol Begin
if(c2[qMap[qBnd->getStereoAtoms()[0]]]==mBnd->getStereoAtoms()[1]) end1Matches=1;
if(c2[qMap[qBnd->getStereoAtoms()[1]]]==mBnd->getStereoAtoms()[0]) end2Matches=1;
}
//std::cerr<<" bnd: "<<qBnd->getIdx()<<":"<<qBnd->getStereo()<<" - "<<mBnd->getIdx()<<":"<<mBnd->getStereo()<<" -- "<<end1Matches<<" "<<end2Matches<<std::endl;
if(mBnd->getStereo()==qBnd->getStereo() && (end1Matches+end2Matches)==1) return false;
if(mBnd->getStereo()!=qBnd->getStereo() && (end1Matches+end2Matches)!=1) return false;
}
return true;
}
private:
const ROMol &d_query;
const ROMol &d_mol;
bool df_useChirality;
};
class AtomLabelFunctor{
public:
AtomLabelFunctor(const ROMol &query,const ROMol &mol, bool useChirality,
bool useQueryQueryMatches) :
d_query(query), d_mol(mol), df_useChirality(useChirality),
df_useQueryQueryMatches(useQueryQueryMatches) {};
bool operator()(unsigned int i,unsigned int j) const{
bool res=false;
if(df_useChirality){
const Atom *qAt=d_query.getAtomWithIdx(i);
if(qAt->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW ||
qAt->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW) {
const Atom *mAt=d_mol.getAtomWithIdx(j);
if(mAt->getChiralTag()!=Atom::CHI_TETRAHEDRAL_CW &&
mAt->getChiralTag()!=Atom::CHI_TETRAHEDRAL_CCW) return false;
}
}
res=atomCompat(d_query[i],d_mol[j],df_useQueryQueryMatches);
return res;
}
private:
const ROMol &d_query;
const ROMol &d_mol;
bool df_useChirality;
bool df_useQueryQueryMatches;
};
class BondLabelFunctor{
public:
BondLabelFunctor(const ROMol &query,const ROMol &mol,bool useChirality) :
d_query(query), d_mol(mol),df_useChirality(useChirality) {};
bool operator()(MolGraph::edge_descriptor i,MolGraph::edge_descriptor j) const{
bool res=bondCompat(d_query[i],d_mol[j]);
if(df_useChirality){
const BOND_SPTR qBnd=d_query[i];
if(qBnd->getBondType()==Bond::DOUBLE &&
(qBnd->getStereo()==Bond::STEREOZ ||
qBnd->getStereo()==Bond::STEREOE)){
const BOND_SPTR mBnd=d_mol[j];
if(mBnd->getBondType()==Bond::DOUBLE &&
!(mBnd->getStereo()==Bond::STEREOZ ||
mBnd->getStereo()==Bond::STEREOE))
return false;
}
}
return res;
}
private:
const ROMol &d_query;
const ROMol &d_mol;
bool df_useChirality;
};
}
// ----------------------------------------------
//
// find one match
//
bool SubstructMatch(const ROMol &mol,const ROMol &query,MatchVectType &matchVect,
bool recursionPossible,bool useChirality,bool useQueryQueryMatches)
{
//std::cerr<<"begin match"<<std::endl;
if(recursionPossible){
ROMol::ConstAtomIterator atIt;
detail::SUBQUERY_MAP subqueryMap;
for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
if((*atIt)->getQuery()){
detail::MatchSubqueries(mol,(*atIt)->getQuery(),useChirality,subqueryMap,
useQueryQueryMatches);
}
}
}
//std::cerr<<"main matching"<<std::endl;
matchVect.clear();
matchVect.resize(0);
detail::MolMatchFinalCheckFunctor matchChecker(query,mol,useChirality);
detail::AtomLabelFunctor atomLabeler(query,mol,useChirality,useQueryQueryMatches);
detail::BondLabelFunctor bondLabeler(query,mol,useChirality);
detail::ssPairType match;
#if 0
bool res=boost::ullmann(query.getTopology(),mol.getTopology(),
atomLabeler,bondLabeler,match);
#else
bool res=boost::vf2(query.getTopology(),mol.getTopology(),
atomLabeler,bondLabeler,matchChecker,match);
#endif
if(res){
matchVect.resize(query.getNumAtoms());
for(detail::ssPairType::const_iterator iter=match.begin();iter!=match.end();++iter){
matchVect[iter->first]=std::pair<int,int>(iter->first,iter->second);
}
}
#ifdef RDK_THREADSAFE_SSS
if(recursionPossible){
ROMol::ConstAtomIterator atIt;
for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
if((*atIt)->getQuery()){
detail::ClearSubqueryLocks((*atIt)->getQuery());
}
}
}
#endif
return res;
}
// ----------------------------------------------
//
// find all matches
//
// NOTE: this blows out the contents of matches
//
unsigned int SubstructMatch(const ROMol &mol,const ROMol &query,
std::vector< MatchVectType > &matches,
bool uniquify,bool recursionPossible,
bool useChirality,bool useQueryQueryMatches){
if(recursionPossible){
detail::SUBQUERY_MAP subqueryMap;
ROMol::ConstAtomIterator atIt;
for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
if((*atIt)->getQuery()){
//std::cerr<<"recurse from atom "<<(*atIt)->getIdx()<<std::endl;
detail::MatchSubqueries(mol,(*atIt)->getQuery(),useChirality,subqueryMap,
useQueryQueryMatches);
}
}
}
matches.clear();
matches.resize(0);
detail::AtomLabelFunctor atomLabeler(query,mol,useChirality,useQueryQueryMatches);
detail::BondLabelFunctor bondLabeler(query,mol,useChirality);
detail::MolMatchFinalCheckFunctor matchChecker(query,mol,useChirality);
std::list<detail::ssPairType> pms;
#if 0
bool found=boost::ullmann_all(query.getTopology(),mol.getTopology(),
atomLabeler,bondLabeler,pms);
#else
bool found=boost::vf2_all(query.getTopology(),mol.getTopology(),
atomLabeler,bondLabeler,matchChecker,pms);
#endif
unsigned int res=0;
if(found){
unsigned int nQueryAtoms=query.getNumAtoms();
matches.reserve(pms.size());
for(std::list<detail::ssPairType>::const_iterator iter1=pms.begin();
iter1!=pms.end();++iter1){
MatchVectType matchVect;
matchVect.resize(nQueryAtoms);
for(detail::ssPairType::const_iterator iter2=iter1->begin();
iter2!=iter1->end();++iter2){
matchVect[iter2->first]=std::pair<int,int>(iter2->first,iter2->second);
}
matches.push_back(matchVect);
}
if(uniquify){
removeDuplicates(matches,mol.getNumAtoms());
}
res = matches.size();
}
#ifdef RDK_THREADSAFE_SSS
if(recursionPossible){
ROMol::ConstAtomIterator atIt;
for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
if((*atIt)->getQuery()){
detail::ClearSubqueryLocks((*atIt)->getQuery());
}
}
}
#endif
return res;
}
namespace detail {
unsigned int RecursiveMatcher(const ROMol &mol,const ROMol &query,
std::vector< int > &matches,bool useChirality,
SUBQUERY_MAP &subqueryMap,bool useQueryQueryMatches)
{
ROMol::ConstAtomIterator atIt;
for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
if((*atIt)->getQuery()){
MatchSubqueries(mol,(*atIt)->getQuery(),useChirality,subqueryMap,
useQueryQueryMatches);
}
}
detail::AtomLabelFunctor atomLabeler(query,mol,useChirality,useQueryQueryMatches);
detail::BondLabelFunctor bondLabeler(query,mol,useChirality);
detail::MolMatchFinalCheckFunctor matchChecker(query,mol,useChirality);
matches.clear();
matches.resize(0);
std::list<detail::ssPairType> pms;
#if 0
bool found=boost::ullmann_all(query.getTopology(),mol.getTopology(),
atomLabeler,bondLabeler,pms);
#else
bool found=boost::vf2_all(query.getTopology(),mol.getTopology(),
atomLabeler,bondLabeler,matchChecker,pms);
#endif
unsigned int res=0;
if(found){
matches.reserve(pms.size());
for(std::list<detail::ssPairType>::const_iterator iter1=pms.begin();
iter1!=pms.end();++iter1){
if(!query.hasProp("_queryRootAtom")){
matches.push_back(iter1->begin()->second);
} else {
int rootIdx;
query.getProp("_queryRootAtom",rootIdx);
bool found=false;
for(detail::ssPairType::const_iterator pairIter=iter1->begin();
pairIter!=iter1->end();++pairIter){
if(pairIter->first==rootIdx){
matches.push_back(pairIter->second);
found=true;
break;
}
}
if(!found){
BOOST_LOG(rdErrorLog)<<"no match found for queryRootAtom"<<std::endl;
}
}
}
res = matches.size();
}
//std::cout << " <<< RecursiveMatcher: " << int(query) << std::endl;
return res;
}
void MatchSubqueries(const ROMol &mol,QueryAtom::QUERYATOM_QUERY *query,bool useChirality,
SUBQUERY_MAP &subqueryMap,bool useQueryQueryMatches){
PRECONDITION(query,"bad query");
//std::cout << "*-*-* MS: " << (int)query << std::endl;
//std::cout << "\t\t" << typeid(*query).name() << std::endl;
if(query->getDescription()=="RecursiveStructure"){
RecursiveStructureQuery *rsq=(RecursiveStructureQuery *)query;
//std::cerr<<"lock: "<<rsq<<std::endl;
#ifdef RDK_THREADSAFE_SSS
rsq->d_mutex.lock();
#endif
rsq->clear();
bool matchDone=false;
if(rsq->getSerialNumber() &&
subqueryMap.find(rsq->getSerialNumber()) != subqueryMap.end()){
// we've matched an equivalent serial number before, just
// copy in the matches:
matchDone=true;
const RecursiveStructureQuery *orsq=
(const RecursiveStructureQuery *)subqueryMap[rsq->getSerialNumber()];
for(RecursiveStructureQuery::CONTAINER_TYPE::const_iterator setIter=orsq->beginSet();
setIter!=orsq->endSet();++setIter){
rsq->insert(*setIter);
}
//std::cerr<<" copying results for query serial number: "<<rsq->getSerialNumber()<<std::endl;
}
if(!matchDone){
ROMol const *queryMol = rsq->getQueryMol();
// in case we are reusing this query, clear its contents now.
if(queryMol){
std::vector< int > matchStarts;
unsigned int res = RecursiveMatcher(mol,*queryMol,matchStarts,useChirality,
subqueryMap,useQueryQueryMatches);
if(res){
for(std::vector<int>::iterator i=matchStarts.begin();
i!=matchStarts.end();
i++){
rsq->insert(*i);
}
}
}
if(rsq->getSerialNumber()){
subqueryMap[rsq->getSerialNumber()]=query;
//std::cerr<<" storing results for query serial number: "<<rsq->getSerialNumber()<<std::endl;
}
}
} else {
//std::cout << "\tmsq1: ";
}
// now recurse over our children (these things can be nested)
Queries::Query<int,Atom const*,true>::CHILD_VECT_CI childIt;
//std::cout << query << " " << query->endChildren()-query->beginChildren() << std::endl;
for(childIt=query->beginChildren();childIt!=query->endChildren();childIt++){
MatchSubqueries(mol,childIt->get(),useChirality,subqueryMap,useQueryQueryMatches);
}
//std::cout << "<<- back " << (int)query << std::endl;
}
#ifdef RDK_THREADSAFE_SSS
void ClearSubqueryLocks(QueryAtom::QUERYATOM_QUERY *query){
PRECONDITION(query,"bad query");
if(query->getDescription()=="RecursiveStructure"){
RecursiveStructureQuery *rsq=(RecursiveStructureQuery *)query;
//std::cerr<<"unlock: "<<rsq<<std::endl;
rsq->d_mutex.unlock();
for(ROMol::ConstAtomIterator atIt=rsq->getQueryMol()->beginAtoms();
atIt!=rsq->getQueryMol()->endAtoms();atIt++){
if((*atIt)->getQuery()){
ClearSubqueryLocks((*atIt)->getQuery());
}
}
}
// now recurse over our children (these things can be nested)
for(Queries::Query<int,Atom const*,true>::CHILD_VECT_CI childIt=query->beginChildren();
childIt!=query->endChildren();childIt++){
ClearSubqueryLocks(childIt->get());
}
}
#endif
} // end of namespace detail
}
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