static int DetermineFRJ(OBMol &mol)
{
vector<vector<int> >::iterator i;
vector<vector<int> > cfl;
//find all continuous graphs in the mol area
mol.ContigFragList(cfl);
if (cfl.empty())
return(0);
if (cfl.size() == 1)
return(mol.NumBonds() - mol.NumAtoms() + 1);
//count up the atoms and bonds belonging to each graph
OBBond *bond;
vector<OBBond*>::iterator j;
int numatoms,numbonds,frj=0;
OBBitVec frag;
for (i = cfl.begin();i != cfl.end();++i)
{
frag.Clear();
frag.FromVecInt(*i);
numatoms = (*i).size();
numbonds=0;
for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
if (frag.BitIsOn(bond->GetBeginAtomIdx()) &&
frag.BitIsOn(bond->GetEndAtomIdx()))
numbonds++;
frj += numbonds - numatoms + 1;
}
return(frj);
}
vector<OBBond*> OBResidue::GetBonds(bool exterior) const
{
OBAtom *atom;
vector<OBBond*> bonds;
OBBitVec idxs;
unsigned int sz;
sz = (unsigned int) _atoms.size();
for ( unsigned int i = 0 ; i < sz ; ++i )
{
atom = _atoms[i];
OBBond *bond;
vector<OBBond*>::iterator b;
for (bond = atom->BeginBond(b) ; bond ; bond = atom->NextBond(b))
{
if (!idxs.BitIsOn(bond->GetIdx()))
{
if (!exterior)
{
if (bond->GetNbrAtom(atom)->GetResidue() == this)
bonds.push_back(&(*bond));
}
else
bonds.push_back(&(*bond));
idxs.SetBitOn(bond->GetIdx());
}
}
}
return bonds;
}
