void dfsBuildStack(ROMol &mol,int atomIdx,int inBondIdx,
std::vector<AtomColors> &colors,
VECT_INT_VECT &cycles,
const UINT_VECT &ranks,
INT_VECT &cyclesAvailable,
MolStack &molStack,
INT_VECT &atomOrders,
INT_VECT &bondVisitOrders,
VECT_INT_VECT &atomRingClosures,
std::vector<INT_LIST> &atomTraversalBondOrder,
const boost::dynamic_bitset<> *bondsInPlay,
const std::vector<std::string> *bondSymbols
){
#if 0
std::cerr<<"traverse from atom: "<<atomIdx<<" via bond "<<inBondIdx<<" num cycles available: "
<<std::count(cyclesAvailable.begin(),cyclesAvailable.end(),1)<<std::endl;
#endif
Atom *atom = mol.getAtomWithIdx(atomIdx);
INT_LIST directTravList,cycleEndList;
boost::dynamic_bitset<> seenFromHere(mol.getNumAtoms());
seenFromHere.set(atomIdx);
molStack.push_back(MolStackElem(atom));
atomOrders[atom->getIdx()] = molStack.size();
colors[atomIdx] = GREY_NODE;
INT_LIST travList;
if(inBondIdx>=0) travList.push_back(inBondIdx);
// ---------------------
//
// Add any ring closures
//
// ---------------------
if(atomRingClosures[atomIdx].size()){
std::vector<unsigned int> ringsClosed;
BOOST_FOREACH(int bIdx,atomRingClosures[atomIdx]){
travList.push_back(bIdx);
Bond *bond = mol.getBondWithIdx(bIdx);
seenFromHere.set(bond->getOtherAtomIdx(atomIdx));
unsigned int ringIdx;
if(bond->getPropIfPresent(common_properties::_TraversalRingClosureBond, ringIdx)){
// this is end of the ring closure
// we can just pull the ring index from the bond itself:
molStack.push_back(MolStackElem(bond,atomIdx));
bondVisitOrders[bIdx]=molStack.size();
molStack.push_back(MolStackElem(ringIdx));
// don't make the ring digit immediately available again: we don't want to have the same
// ring digit opening and closing rings on an atom.
ringsClosed.push_back(ringIdx-1);
} else {
// this is the beginning of the ring closure, we need to come up with a ring index:
INT_VECT::const_iterator cAIt=std::find(cyclesAvailable.begin(),
cyclesAvailable.end(),1);
if(cAIt==cyclesAvailable.end()){
throw ValueErrorException("Too many rings open at once. SMILES cannot be generated.");
}
unsigned int lowestRingIdx = cAIt-cyclesAvailable.begin();
cyclesAvailable[lowestRingIdx] = 0;
++lowestRingIdx;
bond->setProp(common_properties::_TraversalRingClosureBond,lowestRingIdx);
molStack.push_back(MolStackElem(lowestRingIdx));
}
}
