/usr/include/rdkit/GraphMol/FMCS/RingMatchTableSet.h is in librdkit-dev 201503-3.
This file is owned by root:root, with mode 0o644.
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// Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
// @@ 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 <list>
#include <algorithm>
#include <math.h>
#include "SubstructMatchCustom.h"
namespace RDKit {
namespace FMCS {
class RingMatchTableSet {
class RingMatchTable {
FMCS::MatchTable MatchMatrix;
std::map<const INT_VECT*, unsigned> RingIndex;
public:
inline void clear() {
MatchMatrix.clear();
RingIndex.clear();
}
inline void resize(unsigned s1, unsigned s2) {
MatchMatrix.resize(s1, s2);
for(size_t i = 0; i < s1; i++)
for(size_t j = 0; j < s2; j++)
MatchMatrix.set(i, j, false);
}
inline void makeRingIndex(const ROMol* mol2) {
unsigned i=0;
// for each TARGET ring
const RingInfo::VECT_INT_VECT& rings2 = mol2->getRingInfo()->bondRings();
for(RingInfo::VECT_INT_VECT::const_iterator r2 = rings2.begin(); r2 != rings2.end(); r2++)
RingIndex[&*r2] = i++;
}
inline bool isEqual(unsigned i, const INT_VECT* r2)const {
return MatchMatrix.at(i, getRingIndex(r2));
}
inline void setMatch(unsigned i, const INT_VECT* r2) {
MatchMatrix.set(i, getRingIndex(r2), true);
}
private:
inline unsigned getRingIndex(const INT_VECT* r2)const {
std::map<const INT_VECT*, unsigned>::const_iterator j = RingIndex.find(r2);
if(RingIndex.end() == j)
throw -1;
return j->second;
}
};
private:
std::vector<std::vector<size_t> >* QueryBondRingsIndeces;
std::map<const ROMol*, std::vector<std::vector<size_t> > > TargetBondRingsIndecesSet; // by target molecules
std::map<const ROMol*, RingMatchTable> MatchMatrixSet; // by target molecules
std::map<const INT_VECT*, unsigned> QueryRingIndex;
public:
RingMatchTableSet() : QueryBondRingsIndeces(0) {}
inline void clear() {
if(QueryBondRingsIndeces)
QueryBondRingsIndeces->clear();
TargetBondRingsIndecesSet.clear();
MatchMatrixSet.clear();
QueryRingIndex.clear();
}
inline bool isQueryBondInRing(unsigned bi)const {
return (*QueryBondRingsIndeces)[bi].empty();
}
inline const std::vector<size_t>& getQueryBondRings(unsigned bi)const {
return (*QueryBondRingsIndeces)[bi];
}
inline bool isTargetBondInRing(const ROMol* target, unsigned bi)const {
std::map<const ROMol*, std::vector<std::vector<size_t> > >::const_iterator
i = TargetBondRingsIndecesSet.find(target);
if(TargetBondRingsIndecesSet.end() == i)
throw -1; //never
return i->second[bi].empty();
}
inline const std::vector<size_t>& getTargetBondRings(const ROMol* target, unsigned bi)const {
std::map<const ROMol*, std::vector<std::vector<size_t> > >::const_iterator
i = TargetBondRingsIndecesSet.find(target);
if(TargetBondRingsIndecesSet.end() == i)
throw -1; //never
return i->second[bi];
}
inline bool isEqual(const INT_VECT* r1, const INT_VECT* r2, const ROMol* mol2)const {
const RingMatchTable& m = getTargetMatchMatrix(mol2);
unsigned i = getQueryRingIndex(r1);
return m.isEqual(i,r2);
}
void init(const ROMol* query) {
MatchMatrixSet.clear();
// fill out QueryRingIndex
unsigned i=0;
const RingInfo::VECT_INT_VECT& rings = query->getRingInfo()->bondRings();
for(RingInfo::VECT_INT_VECT::const_iterator r = rings.begin(); r != rings.end(); r++)
QueryRingIndex[&*r] = i++;
TargetBondRingsIndecesSet.clear();
QueryBondRingsIndeces = &TargetBondRingsIndecesSet[query];
QueryBondRingsIndeces->resize(query->getNumBonds());
size_t ri = 0;
for(RingInfo::VECT_INT_VECT::const_iterator r = rings.begin(); r != rings.end(); r++, ri++)
for(INT_VECT::const_iterator bi = r->begin(); bi != r->end(); bi++) // all bonds in the ring
(*QueryBondRingsIndeces)[*bi].push_back(ri);
}
inline void addTargetBondRingsIndeces(const ROMol* mol2) {
std::vector<std::vector<size_t> >& m = TargetBondRingsIndecesSet[mol2];
m.resize(mol2->getNumBonds());
size_t ri = 0;
const RingInfo::VECT_INT_VECT& rings = mol2->getRingInfo()->bondRings();
for(RingInfo::VECT_INT_VECT::const_iterator r = rings.begin(); r != rings.end(); r++, ri++)
for(INT_VECT::const_iterator bi = r->begin(); bi != r->end(); bi++) // all bonds in the ring
m[*bi].push_back(ri);
}
void computeRingMatchTable(const ROMol* query, const ROMol* targetMolecule, const MCSParameters& parameters) { // call it for all targets
const RingInfo::VECT_INT_VECT& rings1 = query->getRingInfo()->bondRings();
const RingInfo::VECT_INT_VECT& rings2 = targetMolecule->getRingInfo()->bondRings();
RingMatchTable& m = addTargetMatchMatrix(targetMolecule, rings1.size(), rings2.size());
unsigned i=0;
// for each query ring
for(RingInfo::VECT_INT_VECT::const_iterator r1 = rings1.begin(); r1 != rings1.end(); r1++, i++) {
FMCS::Graph graph1;
makeRingGraph(graph1, *r1, query); // for each query ring bond ADD all atoms and bonds
// for each TARGET ring
for(RingInfo::VECT_INT_VECT::const_iterator r2 = rings2.begin(); r2 != rings2.end(); r2++) {
if(r1->size() != r2->size()) // rings are different
continue;
FMCS::Graph graph2;
makeRingGraph(graph2, *r2, targetMolecule); // for each TAG ring bond ADD all atoms and bonds
// check ring substruct match
MCSBondCompareParameters bp = parameters.BondCompareParameters;
bp.RingMatchesRingOnly = false;
bp.CompleteRingsOnly = false;
bool match =
#ifdef NEVER_xxx_PRECOMPUTED_TABLES_MATCH // not computed yet, because MatchTable computation usees this ring info table
FMCS::SubstructMatchCustomTable(graph2, graph1, tag->AtomMatchTable, tag->BondMatchTable);
#else //noticable slowly:
FMCS::SubstructMatchCustom( graph2, *targetMolecule , graph1, *query
, parameters.AtomTyper, parameters.BondTyper, NULL, parameters.AtomCompareParameters, bp, NULL);
#endif
if(match)
m.setMatch(i, &*r2);
}
}
}
private:
void makeRingGraph(FMCS::Graph& g, const INT_VECT& ring, const ROMol* mol)const { // ADD all atoms and bonds
std::map<const Atom*, unsigned> atomMap;
for(size_t i=0; i < ring.size(); i++) {
const Bond* bond = mol->getBondWithIdx(ring[i]);
const Atom* atom1= bond->getBeginAtom();
const Atom* atom2= bond->getEndAtom();
unsigned j1 = -1;
unsigned j2 = -1;
std::map<const Atom*, unsigned>::const_iterator ai;
ai = atomMap.find(atom1);
if(atomMap.end() != ai)
j1 = ai->second;
ai = atomMap.find(atom2);
if(atomMap.end() != ai)
j2 = ai->second;
if(-1==j1) {
j1 = g.m_vertices.size();
atomMap[atom1] = j1;
g.addAtom(atom1->getIdx());
}
if(-1==j2) {
j2 = g.m_vertices.size();
atomMap[atom2] = j2;
g.addAtom(atom2->getIdx());
}
g.addBond(ring[i], j1, j2);
}
}
inline unsigned getQueryRingIndex(const INT_VECT* r1)const {
std::map<const INT_VECT*, unsigned>::const_iterator i = QueryRingIndex.find(r1);
if(QueryRingIndex.end() == i)
throw -1; //never
return i->second;
}
inline const RingMatchTable& getTargetMatchMatrix(const ROMol* mol2)const {
std::map<const ROMol*, RingMatchTable>::const_iterator mi = MatchMatrixSet.find(mol2);
if(MatchMatrixSet.end() == mi)
throw -1; //never
return mi->second;
}
inline RingMatchTable& addTargetMatchMatrix(const ROMol* mol2, unsigned s1, unsigned s2) {
RingMatchTable& m = MatchMatrixSet[mol2];
m.resize(s1, s2);
m.makeRingIndex(mol2);
return m;
}
};
}
} // namespace RDKit
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