Chain.write() — write out chain sequence to an alignment file

write(file, atom_file, align_code, comment='', format='PIR', chop_nonstd_termini=True)

This writes out the residue sequence of the chain to an alignment file.

file can be either a file name or a modfile.File() object open in write mode (in which case the structure is appended to the file).

atom_file and align_code specify the name of the chain's associated atom file, and its alignment code, respectively; suitable values can be obtained from Chain.atom_file_and_code(). comment, if given, specifies a comment to prepend to the alignment file.

format specifies the format of the output file; see alignment.write(). PIR or FASTA formats are supported.

chop_nonstd_termini trims non-standard terminal residues in exactly the same way as for Chain.filter().

This command is not available for alignment sequences, because the PDB residue numbers (only available in template structures or models) are needed to write the PIR header.

Example: See Chain.filter() command.