.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/gallery/structure/alphabet/msa.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_gallery_structure_alphabet_msa.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_gallery_structure_alphabet_msa.py:


Multiple Structural alignment of orthologous proteins
=====================================================

In this example we perform a structural alignment of multiple lysozyme
variants from different organisms.
A feasible approach to perfrom such a multiple structure alignment is the
usage of a structural alphabet:
At first the structure is translated into a sequence that represents
the structure.
Then the sequences can be aligned with the standard sequence alignment
techniques, using the substitution matrix of the structural alphabet.

In this example, the structural alphabet we will use is called
*Protein Blocks* (PBs) :footcite:`Brevern2000, Barnoud2017`:
There are 16 different PBs, represented by the symbols ``a`` to ``p``.
Each one depicts a different set of the backbone dihedral angles of a
peptide 5-mer.

.. footbibliography::

.. GENERATED FROM PYTHON SOURCE LINES 22-88



.. image-sg:: /examples/gallery/structure/alphabet/images/sphx_glr_msa_001.png
   :alt: msa
   :srcset: /examples/gallery/structure/alphabet/images/sphx_glr_msa_001.png, /examples/gallery/structure/alphabet/images/sphx_glr_msa_001_2_00x.png 2.00x
   :class: sphx-glr-single-img





.. code-block:: Python


    # Code source: Patrick Kunzmann
    # License: BSD 3 clause

    import matplotlib.pyplot as plt
    import biotite.database.rcsb as rcsb
    import biotite.sequence.align as align
    import biotite.sequence.graphics as graphics
    import biotite.structure as struc
    import biotite.structure.alphabet as strucalph
    import biotite.structure.io.pdbx as pdbx

    PDB_IDS = ["1REX", "1AKI", "1DKJ", "1GD6"]

    # Create a PB sequence from each structure
    structural_sequences = []
    organisms = []
    for pdb_id in PDB_IDS:
        file = pdbx.BinaryCIFFile.read(rcsb.fetch(pdb_id, "bcif"))
        # Take only the first model into account
        array = pdbx.get_structure(file, model=1)
        # We are only interested in the first protein chain
        array = array[struc.filter_amino_acids(array)]
        array = array[array.chain_id == array.chain_id[0]]
        pb_sequences, _ = strucalph.to_protein_blocks(array)
        structural_sequences.append(pb_sequences[0].remove_undefined())

        try:
            organism_name = file.block["entity_src_nat"][
                "pdbx_organism_scientific"
            ].as_item()
        except KeyError:
            organism_name = file.block["entity_src_gen"][
                "pdbx_gene_src_scientific_name"
            ].as_item()
        generic, specific = organism_name.split(" ")
        abbreviation = f"{generic[0]}. {specific}"
        organisms.append(abbreviation)


    # Perform a multiple sequence alignment of the PB sequences
    matrix = align.SubstitutionMatrix.std_protein_blocks_matrix()
    alignment, order, _, _ = align.align_multiple(
        structural_sequences, matrix, gap_penalty=(-500, -100), terminal_penalty=False
    )

    # Visualize the alignment
    # Order alignment according to guide tree
    alignment = alignment[:, order.tolist()]
    labels = [organisms[i] for i in order]
    fig = plt.figure(figsize=(8.0, 4.0))
    ax = fig.add_subplot(111)
    # The color scheme was generated with the 'Gecos' software
    graphics.plot_alignment_type_based(
        ax,
        alignment,
        labels=labels,
        symbols_per_line=45,
        spacing=2,
        show_numbers=True,
        color_scheme="flower",
    )
    # Organism names in italic
    ax.set_yticklabels(ax.get_yticklabels(), fontdict={"fontstyle": "italic"})
    fig.tight_layout()
    plt.show()


.. _sphx_glr_download_examples_gallery_structure_alphabet_msa.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: msa.ipynb <msa.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: msa.py <msa.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: msa.zip <msa.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_