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//
// Copyright (C) 2016 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 "../Substruct/SubstructMatch.h"
#include "StructChecker.h"
#include "Pattern.h"
#include "Tautomer.h"
namespace RDKit {
namespace StructureCheck {
bool StructCheckTautomer::applyTautomer(unsigned it) {
if (Options.FromTautomer.size() <= it || Options.ToTautomer.size() <= it) {
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "ERROR: incorrect Tautomer index it=" << it
<< "\n";
return false;
}
const ROMol &fromTautomer = *Options.FromTautomer[it];
const ROMol &toTautomer = *Options.ToTautomer[it];
if (toTautomer.getNumAtoms() != fromTautomer.getNumAtoms()) {
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "ERROR: incorrect data toTautomer.getNumAtoms() "
"!= fromTautomer.getNumAtoms()\n";
// incorrect data
// throw(.....);
return false;
}
const unsigned nta = toTautomer.getNumAtoms();
MatchVectType match; // The format is (queryAtomIdx, molAtomIdx)
if (!SubstructMatch(Mol, *Options.FromTautomer[it],
match)) // SSMatch(mp, from_tautomer, SINGLE_MATCH);
return false;
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "found match for from_tautomer with " << nta
<< " atoms\n";
// init
size_t invalid_idx = 1 + Mol.getNumAtoms();
std::vector<unsigned> atomIdxMap(Mol.getNumAtoms(), invalid_idx); // matched tau atom indeces
for (MatchVectType::const_iterator mit = match.begin(); mit != match.end();
++mit) {
unsigned tai = mit->first; // From and To Tautomer Atom index
unsigned mai = mit->second; // Mol Atom index
atomIdxMap[mai] = tai;
}
// scan for completely mapped bonds and replace bond order with mapped bond
// from to_tautomer
for (RDKit::BondIterator_ bond = Mol.beginBonds(); bond != Mol.endBonds();
++bond) {
unsigned ti = atomIdxMap[(*bond)->getBeginAtomIdx()];
unsigned tj = atomIdxMap[(*bond)->getEndAtomIdx()];
if (invalid_idx == ti || invalid_idx == tj) {
continue;
}
const Bond *tb = toTautomer.getBondBetweenAtoms(ti, tj);
if (tb && (*bond)->getBondType() != tb->getBondType()) {
(*bond)->setBondType(tb->getBondType());
}
}
// apply charge/radical fixes if any
for (auto &i : match) {
Atom &atom = *Mol.getAtomWithIdx(i.second);
const Atom &ta = *toTautomer.getAtomWithIdx(i.first);
atom.setFormalCharge(ta.getFormalCharge());
atom.setNumRadicalElectrons(ta.getNumRadicalElectrons());
}
return true;
}
} // namespace StructureCheck
} // namespace RDKit
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