/**
* Make atom container from a given bond list. For each bond iterate over atoms and add them to the partContainer
*
* @param the atom
* @param List of parts
*
* @return partContainer
*/
private IAtomContainer makeAtomContainer(IAtom atom, List<IBond> parts)
{
var atoms = new List<IAtom>();
var bonds = new List<IBond>();
var atomsDone = new Dictionary<string, bool>();
atoms.Add(atom);
atomsDone[atom.getID()] = true;
foreach (var aBond in parts)
{
foreach (var bondedAtom in aBond.atoms().ToWindowsEnumerable<IAtom>())
{
var done = false;
atomsDone.TryGetValue(bondedAtom.getID(), out done);
//check if the atom is already contained
if (done)
{
continue;
}
atoms.Add(bondedAtom);
atomsDone[bondedAtom.getID()] = true;
}
bonds.Add(aBond);
}
IAtomContainer partContainer = new AtomContainer();
partContainer.setAtoms(atoms.ToArray());
partContainer.setBonds(bonds.ToArray());
return partContainer;
}