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

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

.. _sphx_glr_examples_gallery_structure_nucleotide_base_pairs.py:


Plotting the base pairs of a tRNA-like-structure
================================================

In this example we plot a linear secondary-structure diagram of a tRNA
mimic (PDB ID: 4P5J) from the *turnip yellow mosaic virus* (TYMV).

.. GENERATED FROM PYTHON SOURCE LINES 8-93



.. image-sg:: /examples/gallery/structure/nucleotide/images/sphx_glr_base_pairs_001.png
   :alt: base pairs
   :srcset: /examples/gallery/structure/nucleotide/images/sphx_glr_base_pairs_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

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

    # Download the PDB file and read the structure
    pdb_file_path = rcsb.fetch("4p5j", "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)]

    # Get the residue names and residue ids of the nucleotides
    residue_ids = []
    residue_names = []
    for residue in struc.residue_iter(nucleotides):
        mapped_nucleotide, exact_match = struc.map_nucleotide(residue)
        if mapped_nucleotide is None:
            continue
        residue_ids.append(residue[0].res_id)
        if exact_match:
            residue_names.append(mapped_nucleotide)
        else:
            residue_names.append(mapped_nucleotide.lower())

    # Create a matplotlib pyplot
    fig, ax = plt.subplots(figsize=(8.0, 4.5))

    # Setup the axis
    ax.set_xlim(0.5, len(residue_ids) + 0.5)
    ax.set_ylim(0, len(residue_ids) / 2 + 0.5)
    ax.set_aspect("equal")
    ax.xaxis.set_major_locator(ticker.MultipleLocator(3))
    ax.tick_params(axis="both", which="major", labelsize=8)
    ax.set_yticks([])

    # Remove the frame
    plt.box(False)

    # Plot the residue names in order
    for residue_name, residue_id in zip(residue_names, residue_ids):
        ax.text(residue_id, 0, residue_name, ha="center", fontsize=8)

    # Compute the basepairs and pseudknot order (first result)
    base_pairs = struc.base_pairs(nucleotides)
    pseudoknot_order = struc.pseudoknots(base_pairs)[0]

    # Draw the arcs between base pairs
    for (base1, base2), order in zip(base_pairs, pseudoknot_order):
        arc_center = (np.mean((nucleotides.res_id[base1], nucleotides.res_id[base2])), 1.5)
        arc_diameter = abs(nucleotides.res_id[base2] - nucleotides.res_id[base1])
        name1 = nucleotides.res_name[base1]
        name2 = nucleotides.res_name[base2]
        if sorted([name1, name2]) in [["A", "U"], ["C", "G"]]:
            color = biotite.colors["dimorange"]
        else:
            color = biotite.colors["brightorange"]
        if order == 0:
            linestyle = "-"
        elif order == 1:
            linestyle = "--"
        else:
            linestyle = ":"
        arc = Arc(
            arc_center,
            arc_diameter,
            arc_diameter,
            theta1=0,
            theta2=180,
            color=color,
            linewidth=1.5,
            linestyle=linestyle,
        )
        ax.add_patch(arc)

    # Display the plot
    plt.show()


.. _sphx_glr_download_examples_gallery_structure_nucleotide_base_pairs.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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