/// <summary> Checks the pathes if a ring has been found
///
/// </summary>
/// <param name="pathes"> The pathes to check for rings
/// </param>
/// <param name="ringSet"> The ringset to add the detected rings to
/// </param>
/// <param name="ac"> The AtomContainer with the original structure
/// </param>
private void detectRings(System.Collections.ArrayList pathes, IRingSet ringSet, IAtomContainer ac)
{
Path path = null;
IRing ring = null;
IBond bond = null;
for (int f = 0; f < pathes.Count; f++)
{
path = (Path)pathes[f];
if (path.Count > 3 && path[path.Count - 1] == path[0])
{
if (debug)
{
System.Console.Out.WriteLine("Removing path " + path.toString(originalAc) + " which is a ring.");
}
path.RemoveAt(0);
ring = ac.Builder.newRing();
for (int g = 0; g < path.Count; g++)
{
ring.addAtom((IAtom)path[g]);
}
IBond[] bonds = ac.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
bond = bonds[g];
if (ring.contains(bond.getAtomAt(0)) && ring.contains(bond.getAtomAt(1)))
{
ring.addBond(bond);
}
}
ringSet.addAtomContainer(ring);
}
}
}
private IRing combineRings(IRingSet ringset, int i, int j)
{
int c = 0;
for (int b = 0; b < cb[i].Length; b++)
{
c = cb[i][b] + cb[j][b];
if (c > 1)
{
break; //at least one common bond
}
}
if (c < 2)
{
return(null);
}
IRing ring = molecule.Builder.newRing();
IRing ring1 = (IRing)ringset.getAtomContainer(i);
IRing ring2 = (IRing)ringset.getAtomContainer(j);
for (int b = 0; b < cb[i].Length; b++)
{
c = cb[i][b] + cb[j][b];
if ((c == 1) && (cb[i][b] == 1))
{
ring.addBond(molecule.getBondAt(b));
}
else if ((c == 1) && (cb[j][b] == 1))
{
ring.addBond(molecule.getBondAt(b));
}
}
for (int a = 0; a < ring1.AtomCount; a++)
{
ring.addAtom(ring1.getAtomAt(a));
}
for (int a = 0; a < ring2.AtomCount; a++)
{
ring.addAtom(ring2.getAtomAt(a));
}
return(ring);
}
private IRing getRing(IAtomContainer spt, IBond bond)
{
IRing ring = spt.Builder.newRing();
PathTools.resetFlags(spt);
ring.addAtom(bond.getAtomAt(0));
PathTools.depthFirstTargetSearch(spt, bond.getAtomAt(0), bond.getAtomAt(1), ring);
ring.addBond(bond);
return(ring);
}