This replaces the old mapping member by constructing it from self.chain_mapping. This function returns a mapping from
        chain IDs in pdb_name1 to chain IDs in pdb_name2.

def get_representative_chain_mapping(self, representative_id_1, representative_id_2):
        '''This replaces the old mapping member by constructing it from self.chain_mapping. This function returns a mapping from
        chain IDs in pdb_name1 to chain IDs in pdb_name2.'''
        d = {}
        for pdb1_chain_id, matched_chain_list in self.chain_mapping[(representative_id_1, representative_id_2)].iteritems():
            d[pdb1_chain_id] = matched_chain_list.get_related_chains_ids('EC{0}'.format(representative_id_2))
        return d