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// $Id$
//
// Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
namespace {
bool testForSameRXNRoleOfAllMoleculeAtoms(const RDKit::ROMol &mol, int role) {
RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
while (atItP.first != atItP.second) {
const RDKit::Atom *oAtom = mol[*(atItP.first++)].get();
int current_role;
if (oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole,
current_role) &&
current_role != role) {
return false;
}
}
return true;
}
int getRXNRoleOfMolecule(const RDKit::ROMol &mol) {
RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
while (atItP.first != atItP.second) {
const RDKit::Atom *oAtom = mol[*(atItP.first++)].get();
int molRxnRole;
if (oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole,
molRxnRole)) {
return molRxnRole;
}
}
return -1;
}
}
namespace RDKit {
ChemicalReaction *RxnMolToChemicalReaction(const ROMol &mol) {
ChemicalReaction *rxn = new ChemicalReaction();
MOL_SPTR_VECT fragments = MolOps::getMolFrags(mol);
unsigned countFragments = 0;
for (MOL_SPTR_VECT::iterator iter = fragments.begin();
iter != fragments.end(); ++iter, countFragments++) {
int role = getRXNRoleOfMolecule(*iter->get());
if (!testForSameRXNRoleOfAllMoleculeAtoms(*iter->get(), role)) {
BOOST_LOG(rdWarningLog)
<< ">> Atoms within one molecule have different RXN roles.\n";
continue;
}
switch (role) {
case 1:
rxn->addReactantTemplate(*iter);
break;
case 2:
rxn->addProductTemplate(*iter);
break;
case 3:
rxn->addAgentTemplate(*iter);
break;
default:
BOOST_LOG(rdWarningLog) << ">> Fragment " << countFragments
<< " not included in the reaction, atoms do "
"not have a correct RXN role.\n";
}
}
return rxn;
}
}
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