// finds cycles
void dfsFindCycles(ROMol &mol, int atomIdx, int inBondIdx,
std::vector<AtomColors> &colors, const UINT_VECT &ranks,
INT_VECT &atomOrders, VECT_INT_VECT &atomRingClosures,
const boost::dynamic_bitset<> *bondsInPlay,
const std::vector<std::string> *bondSymbols, bool doRandom) {
Atom *atom = mol.getAtomWithIdx(atomIdx);
atomOrders.push_back(atomIdx);
colors[atomIdx] = GREY_NODE;
// ---------------------
//
// Build the list of possible destinations from here
//
// ---------------------
std::vector<PossibleType> possibles;
possibles.resize(0);
ROMol::OBOND_ITER_PAIR bondsPair = mol.getAtomBonds(atom);
possibles.reserve(bondsPair.second - bondsPair.first);
while (bondsPair.first != bondsPair.second) {
Bond *theBond = mol[*(bondsPair.first)];
bondsPair.first++;
if (bondsInPlay && !(*bondsInPlay)[theBond->getIdx()]) continue;
if (inBondIdx < 0 ||
theBond->getIdx() != static_cast<unsigned int>(inBondIdx)) {
int otherIdx = theBond->getOtherAtomIdx(atomIdx);
long rank = ranks[otherIdx];
// ---------------------
//
// things are a bit more complicated if we are sitting on a
// ring atom. we would like to traverse first to the
// ring-closure atoms, then to atoms outside the ring first,
// then to atoms in the ring that haven't already been visited
// (non-ring-closure atoms).
//
// Here's how the black magic works:
// - non-ring atom neighbors have their original ranks
// - ring atom neighbors have this added to their ranks:
// (MAX_BONDTYPE - bondOrder)*MAX_NATOMS*MAX_NATOMS
// - ring-closure neighbors lose a factor of:
// (MAX_BONDTYPE+1)*MAX_NATOMS*MAX_NATOMS
//
// This tactic biases us to traverse to non-ring neighbors first,
// original ordering if bond orders are all equal... crafty, neh?
//
// ---------------------
if (!doRandom) {
if (colors[otherIdx] == GREY_NODE) {
rank -= static_cast<int>(MAX_BONDTYPE + 1) * MAX_NATOMS * MAX_NATOMS;
if (!bondSymbols) {
rank += static_cast<int>(MAX_BONDTYPE - theBond->getBondType()) *
MAX_NATOMS;
} else {
const std::string &symb = (*bondSymbols)[theBond->getIdx()];
std::uint32_t hsh = gboost::hash_range(symb.begin(), symb.end());
rank += (hsh % MAX_NATOMS) * MAX_NATOMS;
}
} else if (theBond->getOwningMol().getRingInfo()->numBondRings(
theBond->getIdx())) {
if (!bondSymbols) {
rank += static_cast<int>(MAX_BONDTYPE - theBond->getBondType()) *
MAX_NATOMS * MAX_NATOMS;
} else {
const std::string &symb = (*bondSymbols)[theBond->getIdx()];
std::uint32_t hsh = gboost::hash_range(symb.begin(), symb.end());
rank += (hsh % MAX_NATOMS) * MAX_NATOMS * MAX_NATOMS;
}
}
} else {
// randomize the rank
rank = std::rand();
}
// std::cerr << " " << atomIdx << ": " << otherIdx << " " <<
// rank
// << std::endl;
// std::cerr<<"aIdx: "<< atomIdx <<" p: "<<otherIdx<<" Rank:
// "<<ranks[otherIdx] <<" "<<colors[otherIdx]<<"
// "<<theBond->getBondType()<<" "<<rank<<std::endl;
possibles.push_back(PossibleType(rank, otherIdx, theBond));
}
}
// ---------------------
//
// Sort on ranks
//
// ---------------------
std::sort(possibles.begin(), possibles.end(), _possibleCompare());
// if (possibles.size())
// std::cerr << " aIdx1: " << atomIdx
// << " first: " << possibles.front().get<0>() << " "
// << possibles.front().get<1>() << std::endl;
// // ---------------------
//
// Now work the children
//
// ---------------------
for (auto &possible : possibles) {
int possibleIdx = possible.get<1>();
Bond *bond = possible.get<2>();
switch (colors[possibleIdx]) {
case WHITE_NODE:
// -----
// we haven't seen this node at all before, traverse
// -----
dfsFindCycles(mol, possibleIdx, bond->getIdx(), colors, ranks,
atomOrders, atomRingClosures, bondsInPlay, bondSymbols,
doRandom);
break;
case GREY_NODE:
// -----
// we've seen this, but haven't finished it (we're finishing a ring)
// -----
atomRingClosures[possibleIdx].push_back(bond->getIdx());
atomRingClosures[atomIdx].push_back(bond->getIdx());
break;
default:
// -----
// this node has been finished. don't do anything.
// -----
break;
}
}
colors[atomIdx] = BLACK_NODE;
} // namespace Canon
