code: private static Atom[] getAtoms(Atom[] ca, int[] positions, int length,
  			boolean clone) {
  
  		List<Atom> atoms = new ArrayList<Atom>();
  		for (int i = 0; i < length; i++) {
  			int p = positions[i];
  			Atom a;
  			if (clone) {
  				a = (Atom) ca[p].clone();
  				a.setGroup((Group) ca[p].getGroup().clone());
  			} else {
  				a = ca[p];
  			}
  			atoms.add(a);
  		}
  		return atoms.toArray(new Atom[atoms.size()]);
  	}
docs: most likely the clone flag is not needed