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//
// Copyright (c) 2010-2018, 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/ChemReactions/ReactionParser.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/MolOps.h>
#include <sstream>
namespace {
void setRXNRoleOfAllMoleculeAtoms(RDKit::ROMol &mol, int role) {
RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
while (atItP.first != atItP.second) {
RDKit::Atom *oAtom = mol[*(atItP.first++)];
oAtom->setProp(RDKit::common_properties::molRxnRole, role);
}
}
std::string molToString(RDKit::ROMol &mol, bool toSmiles) {
std::string res = "";
if (toSmiles) {
res = MolToSmiles(mol, true);
} else {
res = MolToSmarts(mol, true);
}
std::vector<int> mapping;
if (RDKit::MolOps::getMolFrags(mol, mapping) > 1) {
res = "(" + res + ")";
}
return res;
}
std::string chemicalReactionTemplatesToString(
const RDKit::ChemicalReaction &rxn, RDKit::ReactionMoleculeType type,
bool toSmiles, bool canonical) {
std::string res = "";
std::vector<std::string> vfragsmi;
auto begin = getStartIterator(rxn, type);
auto end = getEndIterator(rxn, type);
for (; begin != end; ++begin) {
vfragsmi.push_back(molToString(**begin, toSmiles));
}
if (canonical) {
std::sort(vfragsmi.begin(), vfragsmi.end());
}
for (unsigned i = 0; i < vfragsmi.size(); ++i) {
res += vfragsmi[i];
if (i < vfragsmi.size() - 1) {
res += ".";
}
}
return res;
}
std::string chemicalReactionToRxnToString(const RDKit::ChemicalReaction &rxn,
bool toSmiles, bool canonical) {
std::string res = "";
res += chemicalReactionTemplatesToString(rxn, RDKit::Reactant, toSmiles,
canonical);
res += ">";
res +=
chemicalReactionTemplatesToString(rxn, RDKit::Agent, toSmiles, canonical);
res += ">";
res += chemicalReactionTemplatesToString(rxn, RDKit::Product, toSmiles,
canonical);
return res;
}
} // namespace
namespace RDKit {
//! returns the reaction SMARTS for a reaction
std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn) {
return chemicalReactionToRxnToString(rxn, false, false);
};
//! returns the reaction SMILES for a reaction
std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn,
bool canonical) {
return chemicalReactionToRxnToString(rxn, true, canonical);
};
#if 1
//! returns an RXN block for a reaction
std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn,
bool separateAgents) {
std::ostringstream res;
res << "$RXN\n\n RDKit\n\n";
if (separateAgents) {
res << std::setw(3) << rxn.getNumReactantTemplates() << std::setw(3)
<< rxn.getNumProductTemplates() << std::setw(3)
<< rxn.getNumAgentTemplates() << "\n";
} else {
res << std::setw(3)
<< (rxn.getNumReactantTemplates() + rxn.getNumAgentTemplates())
<< std::setw(3) << rxn.getNumProductTemplates() << "\n";
}
for (auto iter = rxn.beginReactantTemplates();
iter != rxn.endReactantTemplates(); ++iter) {
// to write the mol block, we need ring information:
MolOps::findSSSR(**iter);
res << "$MOL\n";
res << MolToMolBlock(**iter, true, -1, false);
}
if (!separateAgents) {
for (auto iter = rxn.beginAgentTemplates(); iter != rxn.endAgentTemplates();
++iter) {
// to write the mol block, we need ring information:
MolOps::findSSSR(**iter);
res << "$MOL\n";
res << MolToMolBlock(**iter, true, -1, false);
}
}
for (auto iter = rxn.beginProductTemplates();
iter != rxn.endProductTemplates(); ++iter) {
// to write the mol block, we need ring information:
MolOps::findSSSR(**iter);
res << "$MOL\n";
res << MolToMolBlock(**iter, true, -1, false);
}
if (separateAgents) {
for (auto iter = rxn.beginAgentTemplates(); iter != rxn.endAgentTemplates();
++iter) {
// to write the mol block, we need ring information:
MolOps::findSSSR(**iter);
res << "$MOL\n";
res << MolToMolBlock(**iter, true, -1, false);
}
}
return res.str();
};
#endif
//! returns a ROMol with RXNMolRole used for a reaction
ROMol *ChemicalReactionToRxnMol(const ChemicalReaction &rxn) {
auto *res = new RWMol();
for (auto iter = rxn.beginReactantTemplates();
iter != rxn.endReactantTemplates(); ++iter) {
setRXNRoleOfAllMoleculeAtoms(*iter->get(), 1);
res->insertMol(*iter->get());
}
for (auto iter = rxn.beginProductTemplates();
iter != rxn.endProductTemplates(); ++iter) {
setRXNRoleOfAllMoleculeAtoms(*iter->get(), 2);
res->insertMol(*iter->get());
}
for (auto iter = rxn.beginAgentTemplates(); iter != rxn.endAgentTemplates();
++iter) {
setRXNRoleOfAllMoleculeAtoms(*iter->get(), 3);
res->insertMol(*iter->get());
}
return (ROMol *)res;
}
} // namespace RDKit
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