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703fe5a225
* remove include from headers * update implementation files * completely remove BOOST_FOREACH (#7) * convert those changes to use auto * get rid of all usage of BOOST_FOREACH Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
106 lines
3.2 KiB
C++
106 lines
3.2 KiB
C++
//
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// Copyright (C) 2013 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/MolOps.h>
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#include <RDGeneral/Exceptions.h>
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#include <GraphMol/AtomIterators.h>
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#include <GraphMol/BondIterators.h>
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namespace RDKit {
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namespace MolOps {
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ROMol *renumberAtoms(const ROMol &mol,
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const std::vector<unsigned int> &newOrder) {
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unsigned int nAts = mol.getNumAtoms();
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PRECONDITION(newOrder.size() == nAts, "bad newOrder size");
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std::vector<unsigned int> revOrder(nAts);
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for (unsigned int nIdx = 0; nIdx < nAts; ++nIdx) {
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unsigned int oIdx = newOrder[nIdx];
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if (oIdx > nAts) {
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throw ValueErrorException("idx value exceeds numAtoms");
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}
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revOrder[oIdx] = nIdx;
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}
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// ------
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// newOrder[i] : which atom should be in position i of the new mol
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// revOrder[i] : where atom i of the original mol landed in the new mol
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auto *res = new RWMol();
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// copy over the atoms:
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for (unsigned int nIdx = 0; nIdx < nAts; ++nIdx) {
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unsigned int oIdx = newOrder[nIdx];
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const Atom *oAtom = mol.getAtomWithIdx(oIdx);
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Atom *nAtom = oAtom->copy();
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res->addAtom(nAtom, false, true);
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// take care of atom-numbering-dependent properties:
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INT_VECT nAtoms;
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if (nAtom->getPropIfPresent(common_properties::_ringStereoAtoms, nAtoms)) {
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// FIX: ought to be able to avoid this copy.
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for (auto &val : nAtoms) {
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if (val < 0) {
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val = -1 * (revOrder[(-val - 1)] + 1);
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} else {
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val = revOrder[val - 1] + 1;
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}
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}
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nAtom->setProp(common_properties::_ringStereoAtoms, nAtoms, true);
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}
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}
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// now the bonds:
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for (ROMol::ConstBondIterator bi = mol.beginBonds(); bi != mol.endBonds();
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++bi) {
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const Bond *oBond = (*bi);
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Bond *nBond = oBond->copy();
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nBond->setBeginAtomIdx(revOrder[oBond->getBeginAtomIdx()]);
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nBond->setEndAtomIdx(revOrder[oBond->getEndAtomIdx()]);
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res->addBond(nBond, true);
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// take care of atom-numbering-dependent properties:
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for (auto &idx : nBond->getStereoAtoms()) {
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idx = revOrder[idx];
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}
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}
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// Conformers:
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for (auto oConf = mol.beginConformers(); oConf != mol.endConformers();
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++oConf) {
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auto *nConf = new Conformer(nAts);
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for (unsigned int i = 0; i < nAts; ++i) {
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nConf->setAtomPos(i, (*oConf)->getAtomPos(newOrder[i]));
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}
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nConf->setId((*oConf)->getId());
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nConf->set3D((*oConf)->is3D());
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res->addConformer(nConf);
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}
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// update the ring info:
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const RingInfo *oRings = mol.getRingInfo();
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if (oRings && oRings->isInitialized()) {
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RingInfo *nRings = res->getRingInfo();
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nRings->reset();
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nRings->initialize();
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for (unsigned int i = 0; i < oRings->numRings(); ++i) {
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const INT_VECT &oRing = oRings->atomRings()[i];
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INT_VECT nRing(oRing.size());
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for (unsigned int j = 0; j < oRing.size(); ++j) {
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nRing[j] = revOrder[oRing[j]];
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}
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nRings->addRing(nRing, oRings->bondRings()[i]);
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}
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}
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return dynamic_cast<ROMol *>(res);
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}
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}; // end of namespace MolOps
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}; // end of namespace RDKit
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