.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/gallery/structure/nucleotide/leontis_westhof.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_nucleotide_leontis_westhof.py>`
        to download the full example code

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

.. _sphx_glr_examples_gallery_structure_nucleotide_leontis_westhof.py:


Leontis-Westhof Nomenclature
============================

In this example we plot a secondary structure diagram annotated with
Leontis-Westhof nomenclature :footcite:`Leontis2001` of the sarcin-ricin
loop from E. coli (PDB ID: 6ZYB).

.. GENERATED FROM PYTHON SOURCE LINES 9-76

.. code-block:: Python


    # Code source: Tom David Müller
    # License: BSD 3 clause

    from tempfile import gettempdir
    import matplotlib.pyplot as plt
    import numpy as np
    import biotite
    import biotite.database.rcsb as rcsb
    import biotite.structure as struc
    import biotite.structure.graphics as graphics
    import biotite.structure.io.pdb as pdb

    # Download the PDB file and read the structure
    pdb_file_path = rcsb.fetch("6ZYB", "pdb", gettempdir())
    pdb_file = pdb.PDBFile.read(pdb_file_path)
    atom_array = pdb.get_structure(pdb_file)[0]
    nucleotides = atom_array[struc.filter_nucleotides(atom_array)]

    # Compute the base pairs and the Leontis-Westhof nomenclature
    base_pairs = struc.base_pairs(nucleotides)
    glycosidic_bonds = struc.base_pairs_glycosidic_bond(nucleotides, base_pairs)
    edges = struc.base_pairs_edge(nucleotides, base_pairs)
    base_pairs = struc.get_residue_positions(nucleotides, base_pairs.flatten()).reshape(
        base_pairs.shape
    )

    # Get the one-letter-codes of the bases
    base_labels = []
    for base in struc.residue_iter(nucleotides):
        base_labels.append(base.res_name[0])

    # Color canonical Watson-Crick base pairs with a darker orange and
    # non-canonical base pairs with a lighter orange
    colors = np.full(base_pairs.shape[0], biotite.colors["brightorange"])
    for i, (base1, base2) in enumerate(base_pairs):
        name1 = base_labels[base1]
        name2 = base_labels[base2]
        if sorted([name1, name2]) in [["A", "U"], ["C", "G"]]:
            colors[i] = biotite.colors["dimorange"]

    # Use the base labels to indicate the Leontis-Westhof nomenclature
    for bases, edge_types, orientation in zip(base_pairs, edges, glycosidic_bonds):
        for base, edge in zip(bases, edge_types):
            if orientation == 1:
                annotation = "c"
            else:
                annotation = "t"
            if edge == 1:
                annotation += "W"
            elif edge == 2:
                annotation += "H"
            else:
                annotation += "S"
            base_labels[base] = annotation

    # Create a matplotlib pyplot
    fig, ax = plt.subplots(figsize=(8.0, 8.0))

    # Plot the secondary structure
    graphics.plot_nucleotide_secondary_structure(
        ax, base_labels, base_pairs, struc.get_residue_count(nucleotides), bond_color=colors
    )

    # Display the plot
    plt.show()




.. image-sg:: /examples/gallery/structure/nucleotide/images/sphx_glr_leontis_westhof_001.png
   :alt: leontis westhof
   :srcset: /examples/gallery/structure/nucleotide/images/sphx_glr_leontis_westhof_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/biotite/structure/hbond.py:270: UserWarning: Input structure has no associated 'BondList', Hydrogen atoms bonded to donors are detected by distance
      warnings.warn(




.. GENERATED FROM PYTHON SOURCE LINES 77-100

The sarcin-ricin loop is part of the 23s rRNA and is considered
crucial to the ribosome‘s activity. The incorporation of the
Leontis-Westhof nomenclature into the 2D-plot shows how the individual
base pairs are oriented and how their glycosidic bonds are oriented
relative to each other.

This visualization enables one to see a pattern that cannot be
communicated through the 2D structure alone. The upper part of the
sarcin-ricin loop consists of only cis (c) oriented glycosidic bonds.
All bases interact through their Watson-Crick edge (W). On the other
hand, the lower part of the sarcin ricin loop looks strikingly
different. The glycosidic bonds are oriented in cis (c) and trans (t)
orientation. The bases interact through all three edges: Watson-Crick
(W), Hoogsteen (H), and Sugar (S).

Thus, it can be concluded that the upper part of the sarcin ricin loop
represents a highly organized helix, while the lower part of the loop
is comparatively unorganized.

References
----------

.. footbibliography::


.. _sphx_glr_download_examples_gallery_structure_nucleotide_leontis_westhof.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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