def __init__(self, ident, description=None, root_dir=None, pdb_file_type='mmtf'):
        Object.__init__(self, id=ident, description=description)

        self.pdb_file_type = pdb_file_type
        """str: ``pdb``, ``pdb.gz``, ``mmcif``, ``cif``, ``cif.gz``, ``xml.gz``, ``mmtf``, ``mmtf.gz`` - choose a file 
        type for files downloaded from the PDB"""

        # Create directories
        self._root_dir = None
        if root_dir:
            self.root_dir = root_dir

        # Sequences
        self.sequences = DictList()
        """DictList: Stored protein sequences which are related to this protein"""
        self.representative_sequence = None
        """SeqProp: Sequence set to represent this protein"""

        # Structures
        self.structures = DictList()
        """DictList: Stored protein structures which are related to this protein"""
        self.representative_structure = None
        """StructProp: Structure set to represent this protein, usually in monomeric form"""
        self.representative_chain = None
        """str: Chain ID in the representative structure which best represents a sequence"""
        self.representative_chain_seq_coverage = 0
        """float: Percent identity of sequence coverage for the representative chain"""

        # Alignments
        self.sequence_alignments = DictList()
        """DictList: Pairwise or multiple sequence alignments stored as ``Bio.Align.MultipleSeqAlignment`` objects"""
        self.structure_alignments = DictList()
        """DictList: Pairwise or multiple structure alignments - currently a placeholder"""
def __init__ ( self , ident , description = None , root_dir = None , pdb_file_type = 'mmtf' ) : Object . __init__ ( self , id = ident , description = description ) self . pdb_file_type = pdb_file_type self . _root_dir = None if root_dir : self . root_dir = root_dir self . sequences = DictList ( ) self . representative_sequence = None self . structures = DictList ( ) self . representative_structure = None self . representative_chain = None self . representative_chain_seq_coverage = 0 self . sequence_alignments = DictList ( ) self . structure_alignments = DictList ( )
str: ``pdb``, ``pdb.gz``, ``mmcif``, ``cif``, ``cif.gz``, ``xml.gz``, ``mmtf``, ``mmtf.gz`` - choose a file 
        type for files downloaded from the PDB