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

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

.. _sphx_glr_examples_gallery_structure_transfer_rnas.py:


Comparison of a tRNA-like-structure with a tRNA
===============================================

In this example we plot a secondary-structure diagram of a tRNA mimic 
(PDB ID: 4P5J) from the *turnip yellow mosaic virus* (TYMV) and compare
it to a PHE-tRNA (PDB ID: 1EHZ).

.. GENERATED FROM PYTHON SOURCE LINES 9-88

.. code-block:: Python


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

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

    # Create a function to get the structures and compute information for 
    # the plots.
    def plot_rna(pdb_id, axes):
        # Download the PDB file and read the structure
        pdb_file_path = rcsb.fetch(pdb_id, "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 their pseudoknot order
        base_pairs = struc.base_pairs(nucleotides)
        base_pairs = struc.get_residue_positions(
            nucleotides, base_pairs.flatten()
        ).reshape(base_pairs.shape)
        pseudoknot_order = struc.pseudoknots(base_pairs)[0]

        # Set the linestyle according to the pseudoknot order
        linestyles = np.full(base_pairs.shape[0], '-', dtype=object)
        linestyles[pseudoknot_order == 1] = '--'
        linestyles[pseudoknot_order == 2] = ':'

        # Indicate canonical nucleotides with an upper case one-letter-code
        # and non-canonical nucleotides with a lower case one-letter-code
        base_labels = []
        for base in struc.residue_iter(nucleotides):
            one_letter_code, exact = struc.map_nucleotide(base)
            if exact:
                base_labels.append(one_letter_code)
            else:
                base_labels.append(one_letter_code.lower())

        # 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"]

        # Plot the secondary structure
        graphics.plot_nucleotide_secondary_structure(
            axes, base_labels, base_pairs, struc.get_residue_count(nucleotides),
            pseudoknot_order=pseudoknot_order, bond_linestyle=linestyles,
            bond_color=colors,
            # Margin to compensate for reduced axis limits in shared axis
            border=0.13
        )

        # Use the PDB ID to label each plot
        axes.set_title(pdb_id, loc="left")

    # Create a matplotlib pyplot
    fig, (ax1, ax2) = plt.subplots(
        2, 1, figsize=(8.0, 16.0),
        # Share both axes to ensure eqaul scaling of bath secondary structures
        sharex=True, sharey=True
    )

    # Plot the secondary structures
    plot_rna('1EHZ', ax1)
    plot_rna('4P5J', ax2)
    fig.tight_layout()

    plt.show()




.. image-sg:: /examples/gallery/structure/images/sphx_glr_transfer_rnas_001.png
   :alt: 1EHZ, 4P5J
   :srcset: /examples/gallery/structure/images/sphx_glr_transfer_rnas_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 89-97

The generated plots show that both structures consist of four hairpin 
loops. Two of those loops, which are opposite to each other, interact 
through two pseudoknotted base pairs in the otherwise unpaired loop of 
the respective hairpin structures. The fact that this interaction was 
mimicked indicates functional importance. 

A third hairpin loop is folded towards the centre of the tRNA mimic. 
This is not the case for the phenylalanine tRNA and thus signifies a 
major difference between the structures.


.. _sphx_glr_download_examples_gallery_structure_transfer_rnas.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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