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d63f44cc0c
* backup commit * Change the names and meanings of MolOps::AdjustQueryWhichFlags What was there before was not flexible enough and was extremely confusing. This should clear that up. NOTE: this does break backwards compatibility with code that uses this enum, but given that this is new and has not been widely promoted, I suspect it should not affect that many people. The default behavior of MolOps::adjustQueryProperties() remains the same. * adjust to the new AdjustQueryWhichFlags * add mol_adjust_query_properties tests to the cartridge
97 lines
3.2 KiB
C++
97 lines
3.2 KiB
C++
//
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// Copyright (c) 2015 Greg Landrum
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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 <GraphMol/GraphMol.h>
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#include <GraphMol/QueryAtom.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/QueryOps.h>
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#include <GraphMol/AtomIterators.h>
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#include <GraphMol/BondIterators.h>
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#include <vector>
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#include <algorithm>
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namespace RDKit {
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namespace MolOps {
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ROMol *adjustQueryProperties(const ROMol &mol,
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const AdjustQueryParameters *params) {
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RWMol *res = new RWMol(mol);
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try {
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adjustQueryProperties(*res, params);
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} catch (MolSanitizeException &se) {
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delete res;
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throw se;
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}
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return static_cast<ROMol *>(res);
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}
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void adjustQueryProperties(RWMol &mol, const AdjustQueryParameters *inParams) {
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AdjustQueryParameters params;
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if (inParams) {
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params = *inParams;
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}
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const RingInfo *ringInfo = mol.getRingInfo();
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if (!ringInfo->isInitialized()) {
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MolOps::symmetrizeSSSR(mol);
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}
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for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
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Atom *at = mol.getAtomWithIdx(i);
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// pull properties we need from the atom here, once we
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// create a query atom they may no longer be valid.
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unsigned int nRings = ringInfo->numAtomRings(i);
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int atomicNum = at->getAtomicNum();
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if (params.adjustDegree &&
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!((params.adjustDegreeFlags & ADJUST_IGNORECHAINATOMS) && !nRings) &&
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!((params.adjustDegreeFlags & ADJUST_IGNORERINGATOMS) && nRings) &&
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!((params.adjustDegreeFlags & ADJUST_IGNOREDUMMIES) && !atomicNum) &&
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!((params.adjustDegreeFlags & ADJUST_IGNORENONDUMMIES) && atomicNum)) {
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QueryAtom *qa;
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if (!at->hasQuery()) {
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qa = new QueryAtom(*at);
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mol.replaceAtom(i, qa);
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delete qa;
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qa = static_cast<QueryAtom *>(mol.getAtomWithIdx(i));
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at = static_cast<Atom *>(qa);
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} else {
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qa = static_cast<QueryAtom *>(at);
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}
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qa->expandQuery(makeAtomExplicitDegreeQuery(qa->getDegree()));
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} // end of adjust degree
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if (params.adjustRingCount &&
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!((params.adjustRingCountFlags & ADJUST_IGNORECHAINATOMS) && !nRings) &&
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!((params.adjustRingCountFlags & ADJUST_IGNORERINGATOMS) && nRings) &&
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!((params.adjustRingCountFlags & ADJUST_IGNOREDUMMIES) && !atomicNum) &&
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!((params.adjustRingCountFlags & ADJUST_IGNORENONDUMMIES) &&
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atomicNum)) {
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QueryAtom *qa;
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if (!at->hasQuery()) {
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qa = new QueryAtom(*at);
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mol.replaceAtom(i, qa);
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delete qa;
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qa = static_cast<QueryAtom *>(mol.getAtomWithIdx(i));
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at = static_cast<Atom *>(qa);
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} else {
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qa = static_cast<QueryAtom *>(at);
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}
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qa->expandQuery(makeAtomInNRingsQuery(nRings));
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} // end of adjust ring count
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if (params.makeDummiesQueries && atomicNum == 0 && !at->hasQuery() &&
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!at->getIsotope()) {
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QueryAtom *qa = new QueryAtom();
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qa->setQuery(makeAtomNullQuery());
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mol.replaceAtom(i, qa);
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delete qa;
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at = mol.getAtomWithIdx(i);
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} // end of makeDummiesQueries
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} // end of loop over atoms
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}
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} // end of MolOps namespace
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} // end of RDKit namespace
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