bool atomIsCandidateForRingStereochem(const ROMol &mol, const Atom *atom) {
PRECONDITION(atom, "bad atom");
bool res = false;
if (!atom->getPropIfPresent(common_properties::_ringStereochemCand, res)) {
const RingInfo *ringInfo = mol.getRingInfo();
if (ringInfo->isInitialized() && ringInfo->numAtomRings(atom->getIdx())) {
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
std::vector<const Atom *> nonRingNbrs;
std::vector<const Atom *> ringNbrs;
while (beg != end) {
const BOND_SPTR bond = mol[*beg];
if (!ringInfo->numBondRings(bond->getIdx())) {
nonRingNbrs.push_back(bond->getOtherAtom(atom));
} else {
ringNbrs.push_back(bond->getOtherAtom(atom));
}
++beg;
}
unsigned int rank1 = 0, rank2 = 0;
switch (nonRingNbrs.size()) {
case 0:
// don't do spiro:
res = false;
break;
case 1:
if (ringNbrs.size() == 2) res = true;
break;
case 2:
if (nonRingNbrs[0]->getPropIfPresent(common_properties::_CIPRank,
rank1) &&
nonRingNbrs[1]->getPropIfPresent(common_properties::_CIPRank,
rank2)) {
if (rank1 == rank2) {
res = false;
} else {
res = true;
}
}
break;
default:
res = false;
}
}
atom->setProp(common_properties::_ringStereochemCand, res, 1);
}
return res;
}
// 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;
}
}
// construct a vector with <atomIdx,direction> pairs for
// neighbors of a given atom. This list will only be
// non-empty if at least one of the bonds has its direction
// set.
void findAtomNeighborDirHelper(const ROMol &mol, const Atom *atom,
const Bond *refBond, UINT_VECT &ranks,
INT_PAIR_VECT &neighbors,
bool &hasExplicitUnknownStereo) {
PRECONDITION(atom, "bad atom");
PRECONDITION(refBond, "bad bond");
bool seenDir = false;
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
const BOND_SPTR bond = mol[*beg];
// check whether this bond is explictly set to have unknown stereo
if (!hasExplicitUnknownStereo) {
int explicit_unknown_stereo;
if (bond->getBondDir() == Bond::UNKNOWN // there's a squiggle bond
|| (bond->getPropIfPresent<int>(common_properties::_UnknownStereo,
explicit_unknown_stereo) &&
explicit_unknown_stereo))
hasExplicitUnknownStereo = true;
}
Bond::BondDir dir = bond->getBondDir();
if (bond->getIdx() != refBond->getIdx()) {
if (dir == Bond::ENDDOWNRIGHT || dir == Bond::ENDUPRIGHT) {
seenDir = true;
// If we're considering the bond "backwards", (i.e. from end
// to beginning, reverse the effective direction:
if (atom != bond->getBeginAtom()) {
if (dir == Bond::ENDDOWNRIGHT)
dir = Bond::ENDUPRIGHT;
else
dir = Bond::ENDDOWNRIGHT;
}
}
Atom *nbrAtom = bond->getOtherAtom(atom);
neighbors.push_back(std::make_pair(nbrAtom->getIdx(), dir));
}
++beg;
}
if (!seenDir) {
neighbors.clear();
} else {
if (neighbors.size() == 2 &&
ranks[neighbors[0].first] == ranks[neighbors[1].first]) {
// the two substituents are identical, no stereochemistry here:
neighbors.clear();
} else {
// it's possible that direction was set only one of the bonds, set the
// other
// bond's direction to be reversed:
if (neighbors[0].second != Bond::ENDDOWNRIGHT &&
neighbors[0].second != Bond::ENDUPRIGHT) {
CHECK_INVARIANT(neighbors.size() > 1, "too few neighbors");
neighbors[0].second = neighbors[1].second == Bond::ENDDOWNRIGHT
? Bond::ENDUPRIGHT
: Bond::ENDDOWNRIGHT;
} else if (neighbors.size() > 1 &&
neighbors[1].second != Bond::ENDDOWNRIGHT &&
neighbors[1].second != Bond::ENDUPRIGHT) {
neighbors[1].second = neighbors[0].second == Bond::ENDDOWNRIGHT
? Bond::ENDUPRIGHT
: Bond::ENDDOWNRIGHT;
}
}
}
}