// $Id$
//
//  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++)];
    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++)];
    int molRxnRole;
    if (oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole,
                                molRxnRole)) {
      return molRxnRole;
    }
  }
  return -1;
}
}  // namespace

namespace RDKit {

ChemicalReaction *RxnMolToChemicalReaction(const ROMol &mol) {
  auto *rxn = new ChemicalReaction();

  MOL_SPTR_VECT fragments = MolOps::getMolFrags(mol);

  unsigned countFragments = 0;
  for (auto 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;
}
}  // namespace RDKit