A function to replace the old constructor call where a PDB object was passed in and 'cloned'.

def clone(self, parse_ligands = False):
        '''A function to replace the old constructor call where a PDB object was passed in and 'cloned'.'''
        return PDB("\n".join(self.lines), pdb_id = self.pdb_id, strict = self.strict, parse_ligands = parse_ligands)