// find the neighbors for an atoms that are not connected by single bond that is
// not refBond
// if checkDir is true only neighbor atoms with bonds marked with a direction
// will be returned
void findAtomNeighborsHelper(const ROMol &mol, const Atom *atom,
const Bond *refBond, UINT_VECT &neighbors,
bool checkDir = false) {
PRECONDITION(atom, "bad atom");
PRECONDITION(refBond, "bad bond");
neighbors.clear();
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
const BOND_SPTR bond = mol[*beg];
Bond::BondDir dir = bond->getBondDir();
if (bond->getBondType() == Bond::SINGLE &&
bond->getIdx() != refBond->getIdx()) {
if (checkDir) {
if ((dir != Bond::ENDDOWNRIGHT) && (dir != Bond::ENDUPRIGHT)) {
++beg;
continue;
}
}
Atom *nbrAtom = bond->getOtherAtom(atom);
neighbors.push_back(nbrAtom->getIdx());
}
++beg;
}
}
std::string MolToSmarts(ROMol &inmol, bool doIsomericSmiles) {
RDUNUSED_PARAM(doIsomericSmiles); // does this parameter even make sense?
std::string res;
unsigned int nAtoms = inmol.getNumAtoms();
if (!nAtoms) return "";
ROMol mol(inmol);
UINT_VECT ranks;
ranks.resize(nAtoms);
// For smiles writing we would be canonicalizing but we will not do that here.
// We will simple use the atom indices as the rank
for (ROMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms();
atIt++) {
ranks.push_back((*atIt)->getIdx());
}
std::vector<AtomColors> colors;
colors.resize(nAtoms);
std::vector<AtomColors>::iterator colorIt;
for (colorIt = colors.begin(); colorIt != colors.end(); colorIt++)
*colorIt = Canon::WHITE_NODE;
colorIt = std::find(colors.begin(), colors.end(), Canon::WHITE_NODE);
while (colorIt != colors.end()) {
unsigned int nextAtomIdx = 0;
unsigned int nextRank;
std::string subSmi;
nextRank = nAtoms + 1;
for (unsigned int i = 0; i < nAtoms; i++) {
if (colors[i] == Canon::WHITE_NODE && ranks[i] < nextRank) {
nextRank = ranks[i];
nextAtomIdx = i;
}
}
subSmi = FragmentSmartsConstruct(mol, nextAtomIdx, colors, ranks);
res += subSmi;
colorIt = std::find(colors.begin(), colors.end(), Canon::WHITE_NODE);
if (colorIt != colors.end()) {
res += ".";
}
}
return res;
}