static unsigned int FindRingAtomsAndBonds2(OBMol &mol)
{
mol.SetRingAtomsAndBondsPerceived(); // mol.SetFlag(OB_RINGFLAGS_MOL);
mol.SetClosureBondsPerceived(); // mol.SetFlag(OB_CLOSURE_MOL);
unsigned int bsize = mol.NumBonds()+1;
unsigned char *bvisit = (unsigned char*)malloc(bsize);
memset(bvisit,0,bsize);
unsigned int acount = mol.NumAtoms();
unsigned int asize = (unsigned int)((acount+1)*sizeof(int));
int *avisit = (int*)malloc(asize);
memset(avisit,0,asize);
unsigned int frj = 0;
for(unsigned int i=1; i<=acount; i++ )
if(avisit[i] == 0) {
avisit[i] = 1;
OBAtom *atom = mol.GetAtom(i);
FindRings(atom,avisit,bvisit,frj,1);
}
free(avisit);
free(bvisit);
return frj;
}
void OBMol::FindRingAtomsAndBonds()
{
if (HasFlag(OB_RINGFLAGS_MOL))
return;
SetFlag(OB_RINGFLAGS_MOL);
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::FindRingAtomsAndBonds", obAuditMsg);
OBBitVec avisit,bvisit;
avisit.Resize(NumAtoms()+1);
bvisit.Resize(NumAtoms()+1);
vector<int> path;
path.resize(NumAtoms()+1);
for(unsigned int i=1; i<= NumAtoms(); i++ )
if(!avisit[i])
FindRings(*this,path,avisit,bvisit,i,0);
}
static void FindRings(OBMol &mol,vector<int> &path,OBBitVec &avisit,
OBBitVec &bvisit, int natom,int depth )
{
OBAtom *atom;
OBBond *bond;
vector<OBBond*>::iterator k;
// don't return if all atoms are visited
// (For example, some atoms are in multiple rings!) -GRH
if (avisit[natom])
{
int j = depth-1;
bond=mol.GetBond(path[j--]);
bond->SetInRing();
while( j >= 0 )
{
bond=mol.GetBond(path[j--]);
bond->SetInRing();
(bond->GetBeginAtom())->SetInRing();
(bond->GetEndAtom())->SetInRing();
if(bond->GetBeginAtomIdx()==static_cast<unsigned int>(natom) || bond->
GetEndAtomIdx()==static_cast<unsigned int>(natom))
break;
}
}
else
{
avisit.SetBitOn(natom);
atom = mol.GetAtom(natom);
for(bond = atom->BeginBond(k);bond;bond=atom->NextBond(k))
if( !bvisit[bond->GetIdx()])
{
path[depth] = bond->GetIdx();
bvisit.SetBitOn(bond->GetIdx());
FindRings(mol,path,avisit,bvisit,bond->GetNbrAtomIdx(atom),
depth+1);
}
}
}
/* 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;
}
