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_filePDBxFile

The file object.

data_blockstring, optional

The name of the data block. Default is the first (and most times only) data block of the file.

Returns
sequenceslist of Sequence

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