mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
ba12d98ad0
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers * Actually delete atoms and bonds... * RWMol::clear now calls destroy to handle atom/bond deletion * Changes broken Atom lookup for windows/gcc * Adds tests for running with valgrind * Adds test designed for valgrind and molecule deletions * Removes RNG, actually tests bond deletions * update swig wrappers * deal with most recent changes on the main branch
104 lines
3.7 KiB
C++
104 lines
3.7 KiB
C++
// $Id$
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//
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// Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#include <GraphMol/ChemReactions/Reaction.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/ChemReactions/ReactionParser.h>
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namespace {
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bool testForSameRXNRoleOfAllMoleculeAtoms(const RDKit::ROMol &mol, int role) {
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RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
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while (atItP.first != atItP.second) {
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const RDKit::Atom *oAtom = mol[*(atItP.first++)];
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int current_role;
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if (oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole,
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current_role) &&
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current_role != role) {
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return false;
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}
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}
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return true;
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}
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int getRXNRoleOfMolecule(const RDKit::ROMol &mol) {
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RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
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while (atItP.first != atItP.second) {
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const RDKit::Atom *oAtom = mol[*(atItP.first++)];
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int molRxnRole;
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if (oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole,
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molRxnRole)) {
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return molRxnRole;
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}
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}
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return -1;
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}
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}
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namespace RDKit {
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ChemicalReaction *RxnMolToChemicalReaction(const ROMol &mol) {
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auto *rxn = new ChemicalReaction();
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MOL_SPTR_VECT fragments = MolOps::getMolFrags(mol);
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unsigned countFragments = 0;
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for (auto iter = fragments.begin(); iter != fragments.end();
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++iter, countFragments++) {
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int role = getRXNRoleOfMolecule(*iter->get());
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if (!testForSameRXNRoleOfAllMoleculeAtoms(*iter->get(), role)) {
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BOOST_LOG(rdWarningLog)
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<< ">> Atoms within one molecule have different RXN roles.\n";
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continue;
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}
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switch (role) {
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case 1:
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rxn->addReactantTemplate(*iter);
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break;
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case 2:
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rxn->addProductTemplate(*iter);
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break;
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case 3:
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rxn->addAgentTemplate(*iter);
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break;
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default:
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BOOST_LOG(rdWarningLog) << ">> Fragment " << countFragments
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<< " not included in the reaction, atoms do "
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"not have a correct RXN role.\n";
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}
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}
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return rxn;
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}
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}
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