def get_groups(self):
groups = []<EOL>for a_index, m_index in enumerate(self.molecules):<EOL><INDENT>if m_index >= len(groups):<EOL><INDENT>groups.append([a_index])<EOL><DEDENT>else:<EOL><INDENT>groups[m_index].append(a_index)<EOL><DEDENT><DEDENT>return groups<EOL>
Return a list of groups of atom indexes

           Each atom in a group belongs to the same molecule or residue.