biotite.structure.io.pdbx.get_sequence

biotite.structure.io.pdbx.get_sequence(pdbx_file, data_block=None)[source]

Get the protein and nucleotide sequences from the entity_poly.pdbx_seq_one_letter_code_can entry.

Supported polymer types (_entity_poly.type) are: 'polypeptide(D)', 'polypeptide(L)', 'polydeoxyribonucleotide', 'polyribonucleotide' and 'polydeoxyribonucleotide/polyribonucleotide hybrid'. Uracil is converted to Thymine.

Parameters
pdbx_fileCIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock

The file object.

data_blockstr, optional

The name of the data block. Default is the first (and most times only) data block of the file. If the data block object is passed directly to pdbx_file, this parameter is ignored.

Returns
sequenceslist of Sequence

The protein and nucleotide sequences for each entity (equivalent to chains in most cases).