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7f71c7033df488479ec59104e81a552fc64b5c4b
rdkit/Code/GraphMol/Substruct/SubstructMatch.cpp
Paolo Tosco 7f71c7033d - made the ResonanceMolSupplier really lazy, i.e. resonance structure 
enumeration is only carried out when the user asks for a structure
  or when the user explicitly request that calling the enumerate()
  member function. This makes object creation fast and enables
  calling getNumConjGrps(), getBondConjGrpIdx() and getAtomConjGrpIdx()
  member function without incurring in the cost of necessarily
  enumerating resonance structures
- fixed some int/unsigned int inconsistencies
- now bonds and atoms with do not belong to conjugated groups
  get a -1 index
- added a few Python wrappers
- added a few tests
- removed unused variables from Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp
- fixed ResonanceMolSupplier Java wrappers which were really broken
2015-11-03 14:57:56 +00:00

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//
// Copyright (C) 2001-2015 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 <RDGeneral/RDThreads.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Resonance.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;
typedef struct {
ResonanceMolSupplier &resMolSupplier;
const ROMol &query;
bool uniquify;
bool recursionPossible;
bool useChirality;
bool useQueryQueryMatches;
unsigned int maxMatches;
} ResSubstructMatchHelperArgs_;
void MatchSubqueries(const ROMol &mol,QueryAtom::QUERYATOM_QUERY *q,bool useChirality,
SUBQUERY_MAP &subqueryMap,bool useQueryQueryMatches,
std::vector<RecursiveStructureQuery*> &locked
);
bool matchCompare(const std::pair<int, int> &a, const std::pair<int, int> &b);
bool matchVectCompare(const MatchVectType &a, const MatchVectType &b);
bool isToBeAddedToVector(std::vector<MatchVectType> &matches,
const MatchVectType &m);
void mergeMatchVect(std::vector<MatchVectType> &matches,
const std::vector<MatchVectType> &matchesTmp,
const ResSubstructMatchHelperArgs_ &args);
void ResSubstructMatchHelper_(const ResSubstructMatchHelperArgs_ &args,
std::vector<MatchVectType> *matches, unsigned int bi,
unsigned int ei);
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,
bool useQueryQueryMatches) :
d_query(query), d_mol(mol),df_useChirality(useChirality),
df_useQueryQueryMatches(useQueryQueryMatches) {};
bool operator()(MolGraph::edge_descriptor i,MolGraph::edge_descriptor j) const{
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;
}
}
bool res=bondCompat(d_query[i],d_mol[j]);
return res;
}
private:
const ROMol &d_query;
const ROMol &d_mol;
bool df_useChirality;
bool df_useQueryQueryMatches;
};
void mergeMatchVect(std::vector<MatchVectType> &matches,
const std::vector<MatchVectType> &matchesTmp,
const ResSubstructMatchHelperArgs_ &args) {
for (std::vector<MatchVectType>::const_iterator
it = matchesTmp.begin(); (matches.size() < args.maxMatches)
&& (it != matchesTmp.end()); ++it) {
if ((std::find(matches.begin(),
matches.end(), *it) == matches.end())
&& (!args.uniquify || isToBeAddedToVector(matches, *it)))
matches.push_back(*it);
}
};
void ResSubstructMatchHelper_(const ResSubstructMatchHelperArgs_ &args,
std::vector<MatchVectType> *matches, unsigned int bi, unsigned int ei) {
for (unsigned int i = bi; (matches->size() < args.maxMatches)
&& (i < ei); ++i) {
ROMol *mol = args.resMolSupplier[i];
std::vector<MatchVectType> matchesTmp;
SubstructMatch(*mol, args.query,
matchesTmp, args.uniquify, args.recursionPossible,
args.useChirality, args.useQueryQueryMatches, args.maxMatches);
mergeMatchVect(*matches, matchesTmp, args);
delete mol;
}
};
}
// ----------------------------------------------
//
// 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;
std::vector<RecursiveStructureQuery*> locked;
#ifdef RDK_THREADSAFE_SSS
locked.reserve(query.getNumAtoms());
#endif
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, locked);
}
}
}
//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,useQueryQueryMatches);
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) {
BOOST_FOREACH(RecursiveStructureQuery *v, locked)
v->d_mutex.unlock();
}
#endif
return res;
}
// ----------------------------------------------
//
// find one match in ResonanceMolSupplier object
//
bool SubstructMatch(ResonanceMolSupplier &resMolSupplier, const ROMol &query,
MatchVectType &matchVect, bool recursionPossible,
bool useChirality, bool useQueryQueryMatches)
{
bool match = false;
for (unsigned int i = 0; !match
&& (i < resMolSupplier.length()); ++i) {
ROMol *mol = resMolSupplier[i];
match = SubstructMatch(*mol, query, matchVect,
recursionPossible, useChirality, useQueryQueryMatches);
delete mol;
}
return match;
}
// ----------------------------------------------
//
// 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,
unsigned int maxMatches ){
std::vector<RecursiveStructureQuery*> locked;
#ifdef RDK_THREADSAFE_SSS
locked.reserve(query.getNumAtoms());
#endif
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, locked);
}
}
}
matches.clear();
matches.resize(0);
detail::AtomLabelFunctor atomLabeler(query,mol,useChirality,useQueryQueryMatches);
detail::BondLabelFunctor bondLabeler(query,mol,useChirality,useQueryQueryMatches);
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,maxMatches);
#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) {
BOOST_FOREACH(RecursiveStructureQuery *v, locked)
v->d_mutex.unlock();
}
#endif
return res;
}
// ----------------------------------------------
//
// find all matches in a ResonanceMolSupplier object
//
// NOTE: this blows out the contents of matches
//
unsigned int SubstructMatch(ResonanceMolSupplier &resMolSupplier,
const ROMol &query,
std::vector<MatchVectType> &matches,
bool uniquify, bool recursionPossible,
bool useChirality, bool useQueryQueryMatches,
unsigned int maxMatches, int numThreads)
{
matches.clear();
detail::ResSubstructMatchHelperArgs_ args = {
resMolSupplier, query, uniquify, recursionPossible,
useChirality, useQueryQueryMatches, maxMatches
};
unsigned int nt = std::min(resMolSupplier.length(),
getNumThreadsToUse(numThreads));
if (nt == 1)
detail::ResSubstructMatchHelper_(args, &matches,
0, resMolSupplier.length());
#ifdef RDK_THREADSAFE_SSS
else {
boost::thread_group tg;
std::vector<std::vector<MatchVectType> *> matchesThread(nt);
unsigned int ei = 0;
double dpt = static_cast<double>(resMolSupplier.length())
/ static_cast<double>(nt);
double dc = 0.0;
for (unsigned int ti = 0; ti < nt; ++ti) {
matchesThread[ti] = new std::vector<MatchVectType>();
unsigned int bi = ei;
dc += dpt;
ei = static_cast<unsigned int>(floor(dc));
tg.add_thread(new boost::thread(detail::ResSubstructMatchHelper_,
args, matchesThread[ti], bi, ei));
}
tg.join_all();
unsigned int matchSize = 0;
for (unsigned int ti = 0; ti < nt; ++ti)
matchSize += matchesThread[ti]->size();
matches.reserve(matchSize);
for (unsigned int ti = 0; ti < nt; ++ti) {
mergeMatchVect(matches, *(matchesThread[ti]), args);
delete matchesThread[ti];
}
}
#endif
std::sort(matches.begin(), matches.end(), detail::matchVectCompare);
return matches.size();
}
namespace detail {
unsigned int RecursiveMatcher(const ROMol &mol,const ROMol &query,
std::vector< int > &matches,bool useChirality,
SUBQUERY_MAP &subqueryMap,bool useQueryQueryMatches,
std::vector<RecursiveStructureQuery*> &locked)
{
ROMol::ConstAtomIterator atIt;
for(atIt=query.beginAtoms();atIt!=query.endAtoms();atIt++){
if((*atIt)->getQuery()){
MatchSubqueries(mol,(*atIt)->getQuery(),useChirality,subqueryMap,
useQueryQueryMatches, locked);
}
}
detail::AtomLabelFunctor atomLabeler(query,mol,useChirality,useQueryQueryMatches);
detail::BondLabelFunctor bondLabeler(query,mol,useChirality,useQueryQueryMatches);
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(common_properties::_queryRootAtom)){
matches.push_back(iter1->begin()->second);
} else {
int rootIdx;
query.getProp(common_properties::_queryRootAtom,rootIdx);
bool found=false;
for(detail::ssPairType::const_iterator pairIter=iter1->begin();
pairIter!=iter1->end();++pairIter){
if(pairIter->first==static_cast<unsigned int>(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,
std::vector<RecursiveStructureQuery*> &locked){
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;
#ifdef RDK_THREADSAFE_SSS
rsq->d_mutex.lock();
locked.push_back(rsq);
#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, locked);
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,
locked);
}
//std::cout << "<<- back " << (int)query << std::endl;
}
bool matchCompare(const std::pair<int, int> &a,
const std::pair<int, int> &b)
{
return (a.second < b.second);
}
bool matchVectCompare(const MatchVectType &a, const MatchVectType &b)
{
for (unsigned int i = 0; i < std::min(a.size(), b.size()); ++i) {
if (a[i].second != b[i].second)
return (a[i].second < b[i].second);
}
return (a.size() < b.size());
}
bool isToBeAddedToVector(std::vector<MatchVectType> &matches,
const MatchVectType &m)
{
bool isToBeAdded = true;
MatchVectType mCopy = m;
std::sort(mCopy.begin(), mCopy.end(), matchCompare);
for (std::vector<MatchVectType>::iterator it = matches.end();
isToBeAdded && it-- != matches.begin();) {
isToBeAdded = (it->size() != mCopy.size());
if (!isToBeAdded) {
MatchVectType matchCopy = *it;
std::sort(matchCopy.begin(), matchCopy.end(), matchCompare);
for (unsigned int i = 0; !isToBeAdded && (i < matchCopy.size()); ++i)
isToBeAdded = (mCopy[i].second != matchCopy[i].second);
if (!isToBeAdded) {
for (unsigned int i = 0; !isToBeAdded && (i < m.size()); ++i)
isToBeAdded = (m[i].second < (*it)[i].second);
if (isToBeAdded) {
matches.erase(it);
break;
}
}
}
}
return isToBeAdded;
}
} // end of namespace detail
}
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