PBxplore API cookbook — Writing PB in file
==========================================

.. contents:: Table of Contents
   :local:
   :backlinks: none

.. note::

   This page is initialy a jupyter notebook. You can see a `notebook HTML
   render <WritePB_.html>`__ of it or download the `notebook
   itself <WritePB.ipynb>`__.


The PBxplore API allows to write all the files the command line tools
can. This includes the outputs of PBassign. The functions to handle
several file formats are available in the :mod:`pbxplore.io` module.

.. code:: python

    from __future__ import print_function, division
    from pprint import pprint
    %cd ../../../

::

    /Users/jon/dev/PBxplore

.. code:: python

    import pbxplore as pbx

Fasta files
-----------

The most common way to save PB sequences is to write them in a fasta
file.

PBxplore allows two ways to write fasta files. The sequences can be
written either all at once or one at a time. To write a batch of
sequences at once, we need a list of sequences and a list of the
corresponding sequence names. The writing function here is
:func:`pbxplore.io.write_fasta`.

.. code:: python

    names = []
    pb_sequences = []
    for chain_name, chain in pbx.chains_from_files(['demo1_assignation/2LFU.pdb']):
        dihedrals = chain.get_phi_psi_angles()
        pb_seq = pbx.assign(dihedrals)
        names.append(chain_name)
        pb_sequences.append(pb_seq)

    pprint(names)

    pprint(pb_sequences)

    with open('output.fasta', 'w') as outfile:
        pbx.io.write_fasta(outfile, pb_sequences, names)

::

    Read 10 chain(s) in demo1_assignation/2LFU.pdb
    ['demo1_assignation/2LFU.pdb | model 1 | chain A',
     'demo1_assignation/2LFU.pdb | model 2 | chain A',
     'demo1_assignation/2LFU.pdb | model 3 | chain A',
     'demo1_assignation/2LFU.pdb | model 4 | chain A',
     'demo1_assignation/2LFU.pdb | model 5 | chain A',
     'demo1_assignation/2LFU.pdb | model 6 | chain A',
     'demo1_assignation/2LFU.pdb | model 7 | chain A',
     'demo1_assignation/2LFU.pdb | model 8 | chain A',
     'demo1_assignation/2LFU.pdb | model 9 | chain A',
     'demo1_assignation/2LFU.pdb | model 10 | chain A']
    ['ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ',
     'ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghiadddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddfklpaccdddddfklmlmgcdehiaddddddfklmmgopZZ',
     'ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpacddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddefklpaccddddddfkgojbdfehpaddddddfkbccfbgZZ',
     'ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddddddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddfklmpccdddddddehiabghehiaddddddfklpccfkZZ',
     'ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadddddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddfklmaccddddddfbgghiafehiadddddddfklpacfZZ',
     'ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadddddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddfklmaccddddehiaehbgcdehiadddddddfehjlpcZZ',
     'ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapadddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddfklpaccdddddfklmaacdfehpadddddehjblckknZZ',
     'ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblbacddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddefklpaccdddddfklmbfbehehiaddddddffkgoiehZZ',
     'ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdcdddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddfklmpccddddehiacbcbdfehpadddddehjklmklmZZ',
     'ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapaccdddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddfklpaccddddddfbcfbacfehpadddddddekpghiaZZ']

.. code:: python

    !cat output.fasta
    !rm output.fasta

::

    >demo1_assignation/2LFU.pdb | model 1 | chain A
    ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcd
    dddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddf
    klmaccddddddfbgniaghiapaddddddfklnoambZZ
    >demo1_assignation/2LFU.pdb | model 2 | chain A
    ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghia
    dddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddf
    klpaccdddddfklmlmgcdehiaddddddfklmmgopZZ
    >demo1_assignation/2LFU.pdb | model 3 | chain A
    ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpa
    cddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddef
    klpaccddddddfkgojbdfehpaddddddfkbccfbgZZ
    >demo1_assignation/2LFU.pdb | model 4 | chain A
    ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddd
    dddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddf
    klmpccdddddddehiabghehiaddddddfklpccfkZZ
    >demo1_assignation/2LFU.pdb | model 5 | chain A
    ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadd
    dddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddf
    klmaccddddddfbgghiafehiadddddddfklpacfZZ
    >demo1_assignation/2LFU.pdb | model 6 | chain A
    ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadd
    dddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddf
    klmaccddddehiaehbgcdehiadddddddfehjlpcZZ
    >demo1_assignation/2LFU.pdb | model 7 | chain A
    ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapa
    dddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddf
    klpaccdddddfklmaacdfehpadddddehjblckknZZ
    >demo1_assignation/2LFU.pdb | model 8 | chain A
    ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblba
    cddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddef
    klpaccdddddfklmbfbehehiaddddddffkgoiehZZ
    >demo1_assignation/2LFU.pdb | model 9 | chain A
    ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdc
    dddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddf
    klmpccddddehiacbcbdfehpadddddehjklmklmZZ
    >demo1_assignation/2LFU.pdb | model 10 | chain A
    ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapacc
    dddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddf
    klpaccddddddfbcfbacfehpadddddddekpghiaZZ

Sequences can be written once at a time using the
:func:`pbxplore.io.fasta._write_fasta_entry` function.

.. code:: python

    with open('output.fasta', 'w') as outfile:
        for chain_name, chain in pbx.chains_from_files(['demo1_assignation/2LFU.pdb']):
            dihedrals = chain.get_phi_psi_angles()
            pb_seq = pbx.assign(dihedrals)
            pbx.io.fasta._write_fasta_entry(outfile, pb_seq, chain_name)

::

    Read 10 chain(s) in demo1_assignation/2LFU.pdb

.. code:: python

    !cat output.fasta
    !rm output.fasta

::

    >demo1_assignation/2LFU.pdb | model 1 | chain A
    ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcd
    dddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddf
    klmaccddddddfbgniaghiapaddddddfklnoambZZ
    >demo1_assignation/2LFU.pdb | model 2 | chain A
    ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghia
    dddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddf
    klpaccdddddfklmlmgcdehiaddddddfklmmgopZZ
    >demo1_assignation/2LFU.pdb | model 3 | chain A
    ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpa
    cddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddef
    klpaccddddddfkgojbdfehpaddddddfkbccfbgZZ
    >demo1_assignation/2LFU.pdb | model 4 | chain A
    ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddd
    dddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddf
    klmpccdddddddehiabghehiaddddddfklpccfkZZ
    >demo1_assignation/2LFU.pdb | model 5 | chain A
    ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadd
    dddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddf
    klmaccddddddfbgghiafehiadddddddfklpacfZZ
    >demo1_assignation/2LFU.pdb | model 6 | chain A
    ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadd
    dddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddf
    klmaccddddehiaehbgcdehiadddddddfehjlpcZZ
    >demo1_assignation/2LFU.pdb | model 7 | chain A
    ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapa
    dddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddf
    klpaccdddddfklmaacdfehpadddddehjblckknZZ
    >demo1_assignation/2LFU.pdb | model 8 | chain A
    ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblba
    cddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddef
    klpaccdddddfklmbfbehehiaddddddffkgoiehZZ
    >demo1_assignation/2LFU.pdb | model 9 | chain A
    ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdc
    dddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddf
    klmpccddddehiacbcbdfehpadddddehjklmklmZZ
    >demo1_assignation/2LFU.pdb | model 10 | chain A
    ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapacc
    dddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddf
    klpaccddddddfbcfbacfehpadddddddekpghiaZZ

By default, the lines in fasta files are wrapped at 60 caracters as
defined in :const:`pbxplore.io.fasta.FASTA_WIDTH`. Both
:func:`pbxplore.io.write_fasta` and
:func:`pbxplore.io.fasta._write_fasta_entry` have a ``width``
optionnal argument that allows to control the wrapping.

.. code:: python

    print(pb_sequences[0])

::

    ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ

.. code:: python

    with open('output.fasta', 'w') as outfile:
        for width in (60, 70, 80):
            pbx.io.fasta._write_fasta_entry(outfile, pb_sequences[0],
                                            'width={} blocks'.format(width),
                                            width=width)

.. code:: python

    !cat output.fasta
    !rm output.fasta

::

    >width=60 blocks
    ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcd
    dddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddf
    klmaccddddddfbgniaghiapaddddddfklnoambZZ
    >width=70 blocks
    ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddf
    klopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniagh
    iapaddddddfklnoambZZ
    >width=80 blocks
    ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopaddddd
    fhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ

Flat records
------------

If we do not want to wrap the PB sequences, we can write a flat file.
Flat files contain raw sequences, one per line, with no header. Such
file can be easily written using the ``print`` built-in. Yet, PBxplore
offers a quick way to write flat records of a list of sequences: the
:func:`pbxplore.io.write_flat` function.

.. code:: python

    with open('output.flat', 'w') as outfile:
        pbx.io.write_flat(outfile, pb_sequences)

.. code:: python

    !cat output.flat
    !rm output.flat

::

    ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ
    ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghiadddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddfklpaccdddddfklmlmgcdehiaddddddfklmmgopZZ
    ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpacddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddefklpaccddddddfkgojbdfehpaddddddfkbccfbgZZ
    ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddddddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddfklmpccdddddddehiabghehiaddddddfklpccfkZZ
    ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadddddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddfklmaccddddddfbgghiafehiadddddddfklpacfZZ
    ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadddddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddfklmaccddddehiaehbgcdehiadddddddfehjlpcZZ
    ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapadddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddfklpaccdddddfklmaacdfehpadddddehjblckknZZ
    ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblbacddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddefklpaccdddddfklmbfbehehiaddddddffkgoiehZZ
    ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdcdddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddfklmpccddddehiacbcbdfehpadddddehjklmklmZZ
    ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapaccdddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddfklpaccddddddfbcfbacfehpadddddddekpghiaZZ

Dihedral angles
---------------

One needs the phi and psi dihedral angles to assign protein block
sequences. Having these angles, it is sometime convenient to store them
in a file. This can be done using the
:func:`pbxplore.io.write_phi_psi` function. This function works like
the :func:`pbxplore.io.write_fasta` one as it takes 3 arguments: the
output file, a list of dihedral angle records, and a list of names
corresponding to each record.

.. code:: python

    # Store the dihedral angles for all chains in a PDB file.
    # Store also the chain name for all chains.
    all_dihedrals = []
    names = []
    for chain_name, chain in pbx.chains_from_files(['demo1_assignation/2LFU.pdb']):
        all_dihedrals.append(chain.get_phi_psi_angles())
        names.append(chain_name)

    # Write the dihedral angles in a file
    with open('output.phipsi', 'w') as outfile:
        pbx.io.write_phipsi(outfile, all_dihedrals, names)

::

    Read 10 chain(s) in demo1_assignation/2LFU.pdb

The output is formated with one line per residue. The first columns
repeat the name given for the chain, then is the residue id followed by
the phi and the psi angle. If an angle is not defined, 'None' is written
instead.

.. code:: python

    !head output.phipsi
    !tail output.phipsi
    !rm output.phipsi

::

    demo1_assignation/2LFU.pdb | model 1 | chain A    276     None    44.77 
    demo1_assignation/2LFU.pdb | model 1 | chain A    277   -81.67    15.27 
    demo1_assignation/2LFU.pdb | model 1 | chain A    278   -79.03   -21.52 
    demo1_assignation/2LFU.pdb | model 1 | chain A    279  -144.43    64.08 
    demo1_assignation/2LFU.pdb | model 1 | chain A    280   -84.23   144.90 
    demo1_assignation/2LFU.pdb | model 1 | chain A    281    70.83   -64.01 
    demo1_assignation/2LFU.pdb | model 1 | chain A    282  -107.77    93.35 
    demo1_assignation/2LFU.pdb | model 1 | chain A    283   -71.42   108.03 
    demo1_assignation/2LFU.pdb | model 1 | chain A    284   -72.99    99.31 
    demo1_assignation/2LFU.pdb | model 1 | chain A    285   -92.93     2.32 
    demo1_assignation/2LFU.pdb | model 10 | chain A    426   -88.16   127.99 
    demo1_assignation/2LFU.pdb | model 10 | chain A    427  -107.40  -161.76 
    demo1_assignation/2LFU.pdb | model 10 | chain A    428   -72.12   -14.94 
    demo1_assignation/2LFU.pdb | model 10 | chain A    429    66.62   -81.17 
    demo1_assignation/2LFU.pdb | model 10 | chain A    430  -141.67   111.76 
    demo1_assignation/2LFU.pdb | model 10 | chain A    431   -69.37   141.19 
    demo1_assignation/2LFU.pdb | model 10 | chain A    432    76.08   -75.91 
    demo1_assignation/2LFU.pdb | model 10 | chain A    433  -149.23   167.34 
    demo1_assignation/2LFU.pdb | model 10 | chain A    434   -63.43   -27.06 
    demo1_assignation/2LFU.pdb | model 10 | chain A    435  -166.70     None 

Read fasta files
----------------

We want to read sequences that we wrote in files. PBxplore provides a
function to read fasta files: the :func:`pbxplore.io.read_fasta`
function.

.. code:: python

    def pdb_to_fasta_pb(pdb_path, fasta_path):
        """
        Write a fasta file with all the PB sequences from a PDB
        """
        with open(fasta_path, 'w') as outfile:
            for chain_name, chain in pbx.chains_from_files([pdb_path]):
                dihedrals = chain.get_phi_psi_angles()
                pb_seq = pbx.assign(dihedrals)
                pbx.io.fasta._write_fasta_entry(outfile, pb_seq, chain_name)

    # Write a fasta file
    pdb_to_fasta_pb('demo1_assignation/2LFU.pdb', 'output.fasta')

    # Read a list of headers and a list of sequences from a fasta file
    names, sequences = pbx.io.read_fasta('output.fasta')

    print('names:')
    pprint(names)
    print('sequences:')
    pprint(sequences)

    !rm output.fasta

::

    Read 10 chain(s) in demo1_assignation/2LFU.pdb
    read 10 sequences in output.fasta
    names:
    ['demo1_assignation/2LFU.pdb | model 1 | chain A',
     'demo1_assignation/2LFU.pdb | model 2 | chain A',
     'demo1_assignation/2LFU.pdb | model 3 | chain A',
     'demo1_assignation/2LFU.pdb | model 4 | chain A',
     'demo1_assignation/2LFU.pdb | model 5 | chain A',
     'demo1_assignation/2LFU.pdb | model 6 | chain A',
     'demo1_assignation/2LFU.pdb | model 7 | chain A',
     'demo1_assignation/2LFU.pdb | model 8 | chain A',
     'demo1_assignation/2LFU.pdb | model 9 | chain A',
     'demo1_assignation/2LFU.pdb | model 10 | chain A']
    sequences:
    ['ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ',
     'ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghiadddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddfklpaccdddddfklmlmgcdehiaddddddfklmmgopZZ',
     'ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpacddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddefklpaccddddddfkgojbdfehpaddddddfkbccfbgZZ',
     'ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddddddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddfklmpccdddddddehiabghehiaddddddfklpccfkZZ',
     'ZZpaehiehkaccdddddehjbccdddddddddfklggcddddddddddddddfbhpadddddddddddfklopadddddehiamlmmpccdddddeehiadddddfbacddcddddddfklmaccddddddfbgghiafehiadddddddfklpacfZZ',
     'ZZmghbacfkbccdddddeehpacdddddddddfklggcdddddddddddddehiacadddddddddddfklopadddddehiaklnopcddddddeehiadddehjlnopacddddddfklmaccddddehiaehbgcdehiadddddddfehjlpcZZ',
     'ZZcchbacfkbccdddddfehpacdddddddddfklggcdddddddddddddddehjapadddddddddfknopadddddfklmmmnopcddddddehjiddddddfknopacddddddfklpaccdddddfklmaacdfehpadddddehjblckknZZ',
     'ZZcehjdeehiacdjdddedjbdcdddddddddfklggcdddddddddddddddbfblbacddddddddfklopacddddehiamlnopaddddddehjacddddfehpaaccdddddefklpaccdddddfklmbfbehehiaddddddffkgoiehZZ',
     'ZZpccdjdfkbccdddddehhpacdddddddddfklggcdddddddddddddehiacbdcdddddddddfklopadddddehiammnopcddddddeejiadddehjlgobacddddddfklmpccddddehiacbcbdfehpadddddehjklmklmZZ',
     'ZZccfklcfkbccdddddehjbdcdddddddddfklggcdddddddddddddehiapaccdddddddddfklopadddddehjamlnopaddddddehjddcdddfbfghpacddddddfklpaccddddddfbcfbacfehpadddddddekpghiaZZ']

If the sequences we want to read are spread amongst several fasta files,
then we can use the :func:`pbxplore.io.read_several_fasta` function
that takes a list of fasta file path as argument instead of a single
path.

.. code:: python

    # Write several fasta files
    pdb_to_fasta_pb('demo1_assignation/1BTA.pdb', '1BTA.fasta')
    pdb_to_fasta_pb('demo1_assignation/2LFU.pdb', '2FLU.fasta')

    # Read the fasta files
    names, sequences = pbx.io.read_several_fasta(['1BTA.fasta', '2FLU.fasta'])

    # Print the first entries
    print('names:')
    pprint(names[:5])
    print('sequences:')
    pprint(sequences[:5])

    !rm 1BTA.fasta 2FLU.fasta

::

    Read 1 chain(s) in demo1_assignation/1BTA.pdb
    Read 10 chain(s) in demo1_assignation/2LFU.pdb
    read 1 sequences in 1BTA.fasta
    read 10 sequences in 2FLU.fasta
    names:
    ['demo1_assignation/1BTA.pdb | chain A',
     'demo1_assignation/2LFU.pdb | model 1 | chain A',
     'demo1_assignation/2LFU.pdb | model 2 | chain A',
     'demo1_assignation/2LFU.pdb | model 3 | chain A',
     'demo1_assignation/2LFU.pdb | model 4 | chain A']
    sequences:
    ['ZZdddfklonbfklmmmmmmmmnopafklnoiaklmmmmmnoopacddddddehkllmmmmngoilmmmmmmmmmmmmnopacdcddZZ',
     'ZZbghiacfkbccdddddehiadddddddddddfklggcdddddddddddddehifbdcddddddddddfklopadddddfhpamlnopcddddddehjadddddehjacbddddddddfklmaccddddddfbgniaghiapaddddddfklnoambZZ',
     'ZZpcfblcffbccdddddeehjacdddddddddfklggcddddddddddddddfblghiadddddddddfklopadddddehpmmmnopcddddddeehiacdddfblopadcddddddfklpaccdddddfklmlmgcdehiaddddddfklmmgopZZ',
     'ZZmgghiafbbccdddddehjbdcdddddddddfklggcddddddddddddddfbfghpacddddddddfklopadddddehiaklmmmgcdddddeehiaddddfkbgciacdddddefklpaccddddddfkgojbdfehpaddddddfkbccfbgZZ',
     'ZZcghiacfkbacdddddfbhpacdddddddddfklmcfdddddddddddddehiacddddddddddddfknopadddddfkpamlnopaddddddehjaccdddfklnopacddddddfklmpccdddddddehiabghehiaddddddfklpccfkZZ']