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80 lines
2.8 KiB
C++
80 lines
2.8 KiB
C++
//
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// Copyright (C) 2016 Novartis Institutes for BioMedical Research
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "../Substruct/SubstructMatch.h"
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#include "StructChecker.h"
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#include "Pattern.h"
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#include "Tautomer.h"
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namespace RDKit {
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namespace StructureCheck {
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bool StructCheckTautomer::applyTautomer(unsigned it) {
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if (Options.FromTautomer.size() <= it || Options.ToTautomer.size() <= it) {
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if (Options.Verbose)
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BOOST_LOG(rdInfoLog) << "ERROR: incorrect Tautomer index it=" << it
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<< "\n";
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return false;
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}
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const ROMol &fromTautomer = *Options.FromTautomer[it];
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const ROMol &toTautomer = *Options.ToTautomer[it];
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if (toTautomer.getNumAtoms() != fromTautomer.getNumAtoms()) {
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if (Options.Verbose)
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BOOST_LOG(rdInfoLog) << "ERROR: incorrect data toTautomer.getNumAtoms() "
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"!= fromTautomer.getNumAtoms()\n";
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// incorrect data
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// throw(.....);
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return false;
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}
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const unsigned nta = toTautomer.getNumAtoms();
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const unsigned ntb = toTautomer.getNumBonds();
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MatchVectType match; // The format is (queryAtomIdx, molAtomIdx)
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std::vector<unsigned> atomIdxMap(
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Mol.getNumAtoms()); // matched tau atom indeces
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if (!SubstructMatch(Mol, *Options.FromTautomer[it],
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match)) // SSMatch(mp, from_tautomer, SINGLE_MATCH);
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return false;
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if (Options.Verbose)
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BOOST_LOG(rdInfoLog) << "found match for from_tautomer with " << nta
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<< " atoms\n";
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// init
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for (unsigned i = 0; i < Mol.getNumAtoms(); i++) atomIdxMap[i] = -1;
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for (MatchVectType::const_iterator mit = match.begin(); mit != match.end();
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mit++) {
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unsigned tai = mit->first; // From and To Tautomer Atom index
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unsigned mai = mit->second; // Mol Atom index
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atomIdxMap[mai] = tai;
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}
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// scan for completely mapped bonds and replace bond order with mapped bond
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// from to_tautomer
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for (RDKit::BondIterator_ bond = Mol.beginBonds(); bond != Mol.endBonds();
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bond++) {
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unsigned ti = atomIdxMap[(*bond)->getBeginAtomIdx()];
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unsigned tj = atomIdxMap[(*bond)->getEndAtomIdx()];
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if (-1 == ti || -1 == tj) continue;
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const Bond *tb = toTautomer.getBondBetweenAtoms(ti, tj);
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if (tb && (*bond)->getBondType() != tb->getBondType()) {
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(*bond)->setBondType(tb->getBondType());
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}
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}
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// apply charge/radical fixes if any
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for (auto &i : match) {
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Atom &atom = *Mol.getAtomWithIdx(i.second);
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const Atom &ta = *toTautomer.getAtomWithIdx(i.first);
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atom.setFormalCharge(ta.getFormalCharge());
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atom.setNumRadicalElectrons(ta.getNumRadicalElectrons());
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}
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return true;
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}
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} // namespace StructureCheck
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} // namespace RDKit
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