double Bond::getValenceContrib(const Atom *atom) const {
switch(getBondType()){
case UNSPECIFIED: return 0; break;
case IONIC: return 0; break;
case SINGLE: return 1; break;
case DOUBLE: return 2; break;
case TRIPLE: return 3; break;
case QUADRUPLE: return 4; break;
case QUINTUPLE: return 5; break;
case HEXTUPLE: return 6; break;
case ONEANDAHALF: return 1.5; break;
case TWOANDAHALF: return 2.5; break;
case THREEANDAHALF: return 3.5; break;
case FOURANDAHALF: return 4.5; break;
case FIVEANDAHALF: return 5.5; break;
case AROMATIC: return 1.5; break;
case DATIVEONE:
if(atom->getIdx()==getEndAtomIdx())return 1.0;
else return 0.0;
break;
case DATIVE:
if(atom->getIdx()==getEndAtomIdx())return 1.0;
else return 0.0;
break;
case ZERO: return 0; break;
default:
UNDER_CONSTRUCTION("Bad bond type");
}
}
d_saps.push_back({aIdx, lvIdx, idStr});
}
//! check if the bond is SubstanceGroup XBOND or CBOND
SubstanceGroup::BondType SubstanceGroup::getBondType(
unsigned int bondIdx) const {
PRECONDITION(
std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end(),
"bond is not part of the SubstanceGroup")
auto bond = dp_mol->getBondWithIdx(bondIdx);
bool begin_atom_in_sgroup =
std::find(d_atoms.begin(), d_atoms.end(), bond->getBeginAtomIdx()) !=
d_atoms.end();
bool end_atom_in_sgroup = std::find(d_atoms.begin(), d_atoms.end(),
bond->getEndAtomIdx()) != d_atoms.end();
if (begin_atom_in_sgroup && end_atom_in_sgroup) {
return SubstanceGroup::BondType::CBOND;
} else if (begin_atom_in_sgroup || end_atom_in_sgroup) {
return SubstanceGroup::BondType::XBOND;
} else {
std::ostringstream errout;
errout << "Neither beginning nor ending atoms of bond " << bond->getIdx()
<< " is in this SubstanceGroup.";
throw SubstanceGroupException(errout.str());
}
}
bool SubstanceGroupChecks::isValidType(const std::string &type) {
return std::find(SubstanceGroupChecks::sGroupTypes.begin(),
