bool OBBond::IsClosure()
{
OBMol *mol = (OBMol*)GetParent();
if (!mol)
return(false);
if (mol->HasClosureBondsPerceived())
return(HasFlag(OB_CLOSURE_BOND));
mol->SetClosureBondsPerceived();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::PerceiveClosureBonds", obAuditMsg);
OBBond *bond;
OBAtom *atom,*nbr;
OBBitVec uatoms,ubonds;
vector<OBAtom*> curr,next;
vector<OBAtom*>::iterator i;
vector<OBBond*>::iterator j;
uatoms.Resize(mol->NumAtoms()+1);
ubonds.Resize(mol->NumAtoms()+1);
for (;static_cast<unsigned int>(uatoms.CountBits()) < mol->NumAtoms();)
{
if (curr.empty())
for (atom = mol->BeginAtom(i);atom;atom = mol->NextAtom(i))
if (!uatoms[atom->GetIdx()])
{
uatoms |= atom->GetIdx();
curr.push_back(atom);
break;
}
for (;!curr.empty();)
{
for (i = curr.begin();i != curr.end();++i)
for (nbr = ((OBAtom*)*i)->BeginNbrAtom(j);nbr;nbr = ((OBAtom*)*i)->NextNbrAtom(j))
if (!uatoms[nbr->GetIdx()])
{
uatoms |= nbr->GetIdx();
ubonds |= (*j)->GetIdx();
next.push_back(nbr);
}
curr = next;
next.clear();
}
}
for (bond = mol->BeginBond(j);bond;bond = mol->NextBond(j))
if (!ubonds[bond->GetIdx()])
bond->SetClosure();
return(HasFlag(OB_CLOSURE_BOND));
}
/* A recursive O(N) traversal of the molecule */
static int FindRings(OBAtom *atom, int *avisit, unsigned char *bvisit,
unsigned int &frj, int depth)
{
OBBond *bond;
int result = -1;
vector<OBBond*>::iterator k;
for(bond = atom->BeginBond(k);bond;bond=atom->NextBond(k)) {
unsigned int bidx = bond->GetIdx();
if (bvisit[bidx] == 0) {
bvisit[bidx] = 1;
OBAtom *nbor = bond->GetNbrAtom(atom);
unsigned int nidx = nbor->GetIdx();
int nvisit = avisit[nidx];
if (nvisit == 0) {
avisit[nidx] = depth+1;
nvisit = FindRings(nbor,avisit,bvisit,frj,depth+1);
if (nvisit > 0) {
if (nvisit <= depth) {
bond->SetInRing();
if (result < 0 || nvisit < result)
result = nvisit;
}
}
} else {
if (result < 0 || nvisit < result)
result = nvisit;
bond->SetClosure();
bond->SetInRing();
frj++;
}
}
}
if (result > 0 && result <= depth)
atom->SetInRing();
return result;
}
