Get all of the SequenceMaps - Rosetta->ATOM, ATOM->SEQRES/FASTA, SEQRES->UniParc.

def _create_sequence_maps(self):
        '''Get all of the SequenceMaps - Rosetta->ATOM, ATOM->SEQRES/FASTA, SEQRES->UniParc.'''

        if self.sifts:
            self.sifts_atom_to_seqres_sequence_maps = self.sifts.atom_to_seqres_sequence_maps
            self.sifts_seqres_to_uniparc_sequence_maps = self.sifts.seqres_to_uniparc_sequence_maps
            self.sifts_atom_to_uniparc_sequence_maps = self.sifts.atom_to_uniparc_sequence_maps
            if self.pdb_id in pdbs_with_do_not_use_SIFTS_for_these_chains:
                for chain_id in self.sifts_atom_to_seqres_sequence_maps.keys() + self.sifts_seqres_to_uniparc_sequence_maps.keys() + self.sifts_atom_to_uniparc_sequence_maps.keys():
                    if (self.pdb_id, chain_id) in do_not_use_SIFTS_for_these_chains:
                        self.sifts_atom_to_seqres_sequence_maps[chain_id] = SequenceMap()
                        self.sifts_seqres_to_uniparc_sequence_maps = SequenceMap()
                        self.sifts_atom_to_uniparc_sequence_maps = SequenceMap()

        if self.pdb_to_rosetta_residue_map_error:
            self.rosetta_to_atom_sequence_maps = {}
            for c in self.atom_sequences.keys():
                self.rosetta_to_atom_sequence_maps[c] = SequenceMap()
        else:
            self.rosetta_to_atom_sequence_maps = self.pdb.rosetta_to_atom_sequence_maps

        # If we removed atoms from the PDB file, we need to remove them from the maps so that our validations hold later on
        self.pdbml_atom_to_seqres_sequence_maps = self.pdbml.atom_to_seqres_sequence_maps
        if self.pdb_id in ROSETTA_HACKS_residues_to_remove:
            for residue_to_remove in ROSETTA_HACKS_residues_to_remove[self.pdb_id]:
                chain_id = residue_to_remove[0]
                self.pdbml_atom_to_seqres_sequence_maps[chain_id].remove(residue_to_remove)
                #if self.sifts:
                #    self.sifts_atom_to_seqres_sequence_maps[chain_id].remove(residue_to_remove)

        if self.pdb_id not in do_not_use_the_sequence_aligner:
            self.clustal_seqres_to_uniparc_sequence_maps = self.PDB_UniParc_SA.seqres_to_uniparc_sequence_maps