Note: This function ignores any DNA.

def GetRosettaResidueMap(self, ConvertMSEToAtom = False, RemoveIncompleteFinalResidues = False, RemoveIncompleteResidues = False):
        '''Note: This function ignores any DNA.'''
        raise Exception('This code looks to be deprecated. Use construct_pdb_to_rosetta_residue_map instead.')
        chain = None
        sequences = {}
        residue_map = {}
        resid_set = set()
        resid_list = []

        DNA_residues = set([' DA', ' DC', ' DG', ' DT'])
        chains = []
        self.RAW_ATOM_SEQUENCE = []
        essential_atoms_1 = set(['CA', 'C', 'N'])#, 'O'])
        essential_atoms_2 = set(['CA', 'C', 'N'])#, 'OG'])
        current_atoms = set()
        atoms_read = {}
        oldchainID = None
        removed_residue = {}
        for line in self.lines:
            if line[0:4] == 'ATOM' or (ConvertMSEToAtom and (line[0:6] == 'HETATM') and (line[17:20] == 'MSE')):
                chainID = line[21]
                if missing_chain_ids.get(self.pdb_id):
                    chainID = missing_chain_ids[self.pdb_id]
                if chainID not in chains:
                    chains.append(chainID)
                residue_longname = line[17:20]
                if residue_longname in DNA_residues:
                    # Skip DNA
                    continue
                if residue_longname == 'UNK':
                    # Skip unknown residues
                    continue
                if residue_longname not in allowed_PDB_residues_types and not(ConvertMSEToAtom and residue_longname == 'MSE'):
                    if not self.strict:
                        # Skip unknown residues
                        continue
                    else:
                        raise NonCanonicalResidueException("Residue %s encountered: %s" % (line[17:20], line))
                else:
                    resid = line[21:27]
                    #print(chainID, residue_longname, resid)
                    #print(line)
                    #print(resid_list)
                    if resid not in resid_set:
                        removed_residue[chainID] = False
                        add_residue = True
                        if current_atoms:
                            if RemoveIncompleteResidues and essential_atoms_1.intersection(current_atoms) != essential_atoms_1 and essential_atoms_2.intersection(current_atoms) != essential_atoms_2:
                                oldChain = resid_list[-1][0]
                                oldResidueID = resid_list[-1][1:]
                                print("The last residue '%s', %s, in chain %s is missing these atoms: %s." % (resid_list[-1], residue_longname, oldChain, essential_atoms_1.difference(current_atoms) or essential_atoms_2.difference(current_atoms)))
                                resid_set.remove(resid_list[-1])
                                #print("".join(resid_list))
                                resid_list = resid_list[:-1]
                                if oldchainID:
                                    removed_residue[oldchainID] = True
                                #print("".join(resid_list))
                                #print(sequences[oldChain])
                                if sequences.get(oldChain):
                                    sequences[oldChain] = sequences[oldChain][:-1]

                                if residue_map.get(oldChain):
                                    residue_map[oldChain] = residue_map[oldChain][:-1]

                                #print(sequences[oldChain]
                        else:
                            assert(not(resid_set))
                        current_atoms = set()
                        atoms_read[chainID] = set()
                        atoms_read[chainID].add(line[12:15].strip())
                        resid_set.add(resid)
                        resid_list.append(resid)
                        chainID = line[21]

                        sequences[chainID] = sequences.get(chainID, [])
                        if residue_longname in non_canonical_amino_acids:
                            sequences[chainID].append(non_canonical_amino_acids[residue_longname])
                        else:
                            sequences[chainID].append(residue_type_3to1_map[residue_longname])

                        residue_map[chainID] = residue_map.get(chainID, [])
                        if residue_longname in non_canonical_amino_acids:
                            residue_map[chainID].append((resid, non_canonical_amino_acids[residue_longname]))
                        else:
                            residue_map[chainID].append((resid, residue_type_3to1_map[residue_longname]))

                        oldchainID = chainID
                    else:
                        #atoms_read[chainID] = atoms_read.get(chainID, set())
                        atoms_read[chainID].add(line[12:15].strip())
                    current_atoms.add(line[12:15].strip())
        if RemoveIncompleteFinalResidues:
            # These are (probably) necessary for Rosetta to keep the residue. Rosetta does throw away residues where only the N atom is present if that residue is at the end of a chain.
            for chainID, sequence_list in sequences.iteritems():
                if not(removed_residue[chainID]):
                    if essential_atoms_1.intersection(atoms_read[chainID]) != essential_atoms_1 and essential_atoms_2.intersection(atoms_read[chainID]) != essential_atoms_2:
                        print("The last residue %s of chain %s is missing these atoms: %s." % (sequence_list[-1], chainID, essential_atoms_1.difference(atoms_read[chainID]) or essential_atoms_2.difference(atoms_read[chainID])))
                        oldResidueID = sequence_list[-1][1:]
                        residue_map[chainID] = residue_map[chainID][0:-1]
                        sequences[chainID] = sequence_list[0:-1]


        for chainID, sequence_list in sequences.iteritems():
            sequences[chainID] = "".join(sequence_list)
            assert(sequences[chainID] == "".join([res_details[1] for res_details in residue_map[chainID]]))
        for chainID in chains:
            for a_acid in sequences.get(chainID, ""):
                self.RAW_ATOM_SEQUENCE.append((chainID, a_acid))

        residue_objects = {}
        for chainID in residue_map.keys():
            residue_objects[chainID] = []
        for chainID, residue_list in residue_map.iteritems():
            for res_pair in residue_list:
                resid = res_pair[0]
                resaa = res_pair[1]
                assert(resid[0] == chainID)
                residue_objects[chainID].append((resid[1:].strip(), resaa))

        return sequences, residue_objects