Takes a list, pdb_list, of pdb names e.g. ['Model', 'Scaffold', ...] with which the object was created.
            Using the first element of this list as a base, get the sequence alignments with chains in other members
            of the list. For simplicity, if a chain in the first PDB matches multiple chains in another PDB, we only
            return the alignment for one of the chains. If pdb_list is empty then the function defaults to the object's
            members.

            Returns one sequence alignment string for each chain mapping. Each line is a concatenation of lines of the
            specified width, separated by the specified line separator.

def get_sequence_alignment_strings(self, pdb_list = [], reversed = True, width = 80, line_separator = '\n'):
        '''Takes a list, pdb_list, of pdb names e.g. ['Model', 'Scaffold', ...] with which the object was created.
            Using the first element of this list as a base, get the sequence alignments with chains in other members
            of the list. For simplicity, if a chain in the first PDB matches multiple chains in another PDB, we only
            return the alignment for one of the chains. If pdb_list is empty then the function defaults to the object's
            members.

            Returns one sequence alignment string for each chain mapping. Each line is a concatenation of lines of the
            specified width, separated by the specified line separator.'''

        raise Exception('Re-implement using the equivalence classes.')

        sequence_alignment_printer_tuples = self.get_sequence_alignment_printer_objects(pdb_list = pdb_list, reversed = reversed, width = width, line_separator = line_separator)
        alignment_strings = []
        for sequence_alignment_printer_tuple in sequence_alignment_printer_tuples:
            primary_pdb_chain = sequence_alignment_printer_tuple[0]
            sap = sequence_alignment_printer_tuple[1]
            alignment_strings.append(sap.to_lines(reversed = reversed, width = width, line_separator = line_separator))

        return alignment_strings