//
//
//  Copyright (C) 2020 Schrödinger, LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//

#include <GraphMol/MolOps.h>

#include "CIPMol.h"

namespace RDKit {
namespace CIPLabeler {

CIPMol::CIPMol(ROMol &mol) : d_mol{mol} {}

boost::rational<int> CIPMol::getFractionalAtomicNum(Atom *atom) const {
  PRECONDITION(atom, "bad atom")
  if (d_atomnums.empty()) {
    const_cast<CIPMol *>(this)->d_atomnums = calcFracAtomNums(*this);
  }
  return d_atomnums[atom->getIdx()];
}

unsigned CIPMol::getNumAtoms() const { return d_mol.getNumAtoms(); }

unsigned CIPMol::getNumBonds() const { return d_mol.getNumBonds(); };

Atom *CIPMol::getAtom(int idx) const { return d_mol.getAtomWithIdx(idx); };

CXXAtomIterator<MolGraph, Atom *> CIPMol::atoms() const {
  return d_mol.atoms();
}

Bond *CIPMol::getBond(int idx) const { return d_mol.getBondWithIdx(idx); };

CIPMolSpan<Bond *, ROMol::OEDGE_ITER> CIPMol::getBonds(Atom *atom) const {
  PRECONDITION(atom, "bad atom")
  return {d_mol, d_mol.getAtomBonds(atom)};
}

CIPMolSpan<Atom *, ROMol::ADJ_ITER> CIPMol::getNeighbors(Atom *atom) const {
  PRECONDITION(atom, "bad atom")
  return {d_mol, d_mol.getAtomNeighbors(atom)};
}

bool CIPMol::isInRing(Bond *bond) const {
  PRECONDITION(bond, "bad bond")
  const auto rings = d_mol.getRingInfo();

  if (!rings->isInitialized()) {
    MolOps::fastFindRings(d_mol);
  }

  return rings->numBondRings(bond->getIdx()) != 0u;
};

int CIPMol::getBondOrder(Bond *bond) const {
  PRECONDITION(bond, "bad bond")
  if (dp_kekulized_mol == nullptr) {
    auto tmp = new RWMol(d_mol);
    try {
      MolOps::Kekulize(*tmp);
    } catch (const MolSanitizeException &) {
    }
    const_cast<CIPMol *>(this)->dp_kekulized_mol.reset(tmp);
  }

  const auto kekulized_bond = dp_kekulized_mol->getBondWithIdx(bond->getIdx());

  // Dative bonds might need to be considered with a different bond order
  // for the end atom at the end of the bond.
  switch (kekulized_bond->getBondType()) {
    case Bond::ZERO:
    case Bond::HYDROGEN:
    case Bond::DATIVE:
    case Bond::DATIVEL:
    case Bond::DATIVER:
      return 0;
    case Bond::SINGLE:
      return 1;
    case Bond::AROMATIC:
      BOOST_LOG(rdWarningLog)
          << "non kekulizable aromatic bond being treated as bond order 1"
          << std::endl;
      return 1;
    case Bond::DOUBLE:
      return 2;
    case Bond::TRIPLE:
      return 3;
    case Bond::QUADRUPLE:
      return 4;
    case Bond::QUINTUPLE:
      return 5;
    case Bond::HEXTUPLE:
      return 6;
    default:
      throw std::runtime_error("Non integer-order bonds are not allowed.");
  }
};

}  // namespace CIPLabeler
}  // namespace RDKit