//! Sets atom->IsChiral() to true for chiral atoms
void OBMol::FindChiralCenters()
{
if (HasChiralityPerceived())
return;
SetChiralityPerceived();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::FindChiralCenters", obAuditMsg);
//do quick test to see if there are any possible chiral centers
bool mayHaveChiralCenter=false;
OBAtom *atom,*nbr;
vector<OBAtom*>::iterator i;
for (atom = BeginAtom(i);atom;atom = NextAtom(i))
if (atom->GetHyb() == 3 && atom->GetHvyValence() >= 3)
{
mayHaveChiralCenter=true;
break;
}
if (!mayHaveChiralCenter)
return;
OBBond *bond;
vector<OBBond*>::iterator j;
for (bond = BeginBond(j);bond;bond = NextBond(j))
if (bond->IsWedge() || bond->IsHash())
(bond->GetBeginAtom())->SetChiral();
vector<unsigned int> vgid;
GetGIDVector(vgid);
vector<unsigned int> tlist;
vector<unsigned int>::iterator k;
bool ischiral;
for (atom = BeginAtom(i);atom;atom = NextAtom(i))
if (atom->GetHyb() == 3 && atom->GetHvyValence() >= 3 && !atom->IsChiral())
{
tlist.clear();
ischiral = true;
for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
{
for (k = tlist.begin();k != tlist.end();++k)
if (vgid[nbr->GetIdx()-1] == *k)
ischiral = false;
if (ischiral)
tlist.push_back(vgid[nbr->GetIdx()-1]);
else
break;
}
if (ischiral)
atom->SetChiral();
}
}
void OBMol::FindSSSR()
{
if (HasSSSRPerceived())
return;
SetSSSRPerceived();
obErrorLog.ThrowError(__FUNCTION__,
"Ran OpenBabel::FindSSSR", obAuditMsg);
// Delete any old data before we start finding new rings
// The following procedure is slow
// So if client code is multi-threaded, we don't want to make them wait
if (HasData("SSSR")) {
DeleteData("SSSR");
}
OBRing *ring;
vector<OBRing*>::iterator j;
//get Frèrejacque taking int account multiple possible spanning graphs
int frj = DetermineFRJ(*this);
if (frj)
{
vector<OBRing*> vr;
FindRingAtomsAndBonds();
OBBond *bond;
vector<OBBond*> cbonds;
vector<OBBond*>::iterator k;
//restrict search for rings around closure bonds
for (bond = BeginBond(k);bond;bond = NextBond(k))
if (bond->IsClosure())
cbonds.push_back(bond);
if (!cbonds.empty())
{
OBRingSearch rs;
//search for all rings about closures
vector<OBBond*>::iterator i;
for (i = cbonds.begin();i != cbonds.end();++i)
rs.AddRingFromClosure(*this,(OBBond*)*i);
rs.SortRings();
rs.RemoveRedundant(frj);
//store the SSSR set
for (j = rs.BeginRings();j != rs.EndRings();++j)
{
ring = new OBRing ((*j)->_path,NumAtoms()+1);
ring->SetParent(this);
vr.push_back(ring);
}
//rs.WriteRings();
}
OBRingData *rd = new OBRingData();
rd->SetOrigin(perceived); // to separate from user or file input
rd->SetAttribute("SSSR");
rd->SetData(vr);
SetData(rd);
}
}
