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;
}
// Figure out the CIP ranks for the atoms of a molecule
void assignAtomCIPRanks(const ROMol &mol, UINT_VECT &ranks) {
PRECONDITION((!ranks.size() || ranks.size() >= mol.getNumAtoms()),
"bad ranks size");
if (!ranks.size()) ranks.resize(mol.getNumAtoms());
unsigned int numAtoms = mol.getNumAtoms();
#ifndef USE_NEW_STEREOCHEMISTRY
// get the initial invariants:
DOUBLE_VECT invars(numAtoms, 0);
buildCIPInvariants(mol, invars);
iterateCIPRanks(mol, invars, ranks, false);
#else
Canon::chiralRankMolAtoms(mol, ranks);
#endif
// copy the ranks onto the atoms:
for (unsigned int i = 0; i < numAtoms; ++i) {
mol[i]->setProp(common_properties::_CIPRank, ranks[i], 1);
}
}