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//
//
// 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
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