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//
// Copyright (c) 2015 Greg Landrum
//
// @@ 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 <GraphMol/GraphMol.h>
#include <GraphMol/QueryAtom.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/QueryOps.h>
#include <GraphMol/AtomIterators.h>
#include <GraphMol/BondIterators.h>
#include <vector>
#include <algorithm>
namespace RDKit {
namespace MolOps {
ROMol *adjustQueryProperties(const ROMol &mol,
const AdjustQueryParameters *params) {
RWMol *res = new RWMol(mol);
try {
adjustQueryProperties(*res, params);
} catch (MolSanitizeException &se) {
delete res;
throw se;
}
return static_cast<ROMol *>(res);
}
void adjustQueryProperties(RWMol &mol, const AdjustQueryParameters *inParams) {
AdjustQueryParameters params;
if (inParams) {
params = *inParams;
}
const RingInfo *ringInfo = mol.getRingInfo();
if (!ringInfo->isInitialized()) {
MolOps::symmetrizeSSSR(mol);
}
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
Atom *at = mol.getAtomWithIdx(i);
// pull properties we need from the atom here, once we
// create a query atom they may no longer be valid.
unsigned int nRings = ringInfo->numAtomRings(i);
int atomicNum = at->getAtomicNum();
if (params.adjustDegree &&
!((params.adjustDegreeFlags & ADJUST_RINGSONLY) && !nRings) &&
!((params.adjustDegreeFlags & ADJUST_IGNOREDUMMIES) && !atomicNum)) {
QueryAtom *qa;
if (!at->hasQuery()) {
qa = new QueryAtom(*at);
mol.replaceAtom(i, qa);
delete qa;
qa = static_cast<QueryAtom *>(mol.getAtomWithIdx(i));
at = static_cast<Atom *>(qa);
} else {
qa = static_cast<QueryAtom *>(at);
}
qa->expandQuery(makeAtomExplicitDegreeQuery(qa->getDegree()));
} // end of adjust degree
if (params.adjustRingCount &&
!((params.adjustRingCountFlags & ADJUST_RINGSONLY) && !nRings) &&
!((params.adjustRingCountFlags & ADJUST_IGNOREDUMMIES) && !atomicNum)) {
QueryAtom *qa;
if (!at->hasQuery()) {
qa = new QueryAtom(*at);
mol.replaceAtom(i, qa);
delete qa;
qa = static_cast<QueryAtom *>(mol.getAtomWithIdx(i));
at = static_cast<Atom *>(qa);
} else {
qa = static_cast<QueryAtom *>(at);
}
qa->expandQuery(makeAtomInNRingsQuery(nRings));
} // end of adjust ring count
if (params.makeDummiesQueries && atomicNum == 0 && !at->hasQuery() &&
!at->getIsotope()) {
QueryAtom *qa = new QueryAtom();
qa->setQuery(makeAtomNullQuery());
mol.replaceAtom(i, qa);
delete qa;
at = mol.getAtomWithIdx(i);
} // end of makeDummiesQueries
} // end of loop over atoms
}
} // end of MolOps namespace
} // end of RDKit namespace
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