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

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

.. _sphx_glr_examples_gallery_structure_misc_gap_bars.py:


Identifying unresolved regions in protein structures
====================================================

This script creates two bars, each indicating gaps in the structure
of DNA-PKcs. The top bar indicates the missing residues in a recent
crystal structure (PDB: 5LUQ), the bottom bar indicates missing
residues in a recent cryo-EM structure (PDB: 5W1R).

* *Green*:  Space-resolved residues
* *Yellow*: Residues with merely polyalanine annotation
* *Red*:    Unresolved residues

.. GENERATED FROM PYTHON SOURCE LINES 14-98



.. image-sg:: /examples/gallery/structure/misc/images/sphx_glr_gap_bars_001.png
   :alt: 5luq, 5w1r
   :srcset: /examples/gallery/structure/misc/images/sphx_glr_gap_bars_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

    from tempfile import gettempdir
    import matplotlib.pyplot as plt
    import numpy as np
    from matplotlib.patches import Rectangle
    import biotite.database.rcsb as rcsb
    import biotite.structure.io as strucio


    def plot_gaps(pdb_id, chain_id, ax):
        # Download and parse structure file
        path = rcsb.fetch(pdb_id, "bcif", gettempdir())
        atom_array = strucio.load_structure(path)
        # Consider only one chain
        atom_array = atom_array[atom_array.chain_id == chain_id]
        # Array for saving the 'green', 'yellow' and 'red' state
        states = np.zeros(atom_array.res_id[-1], dtype=int)
        for i in range(len(states)):
            # Get array for only one residue ID
            residue = atom_array[atom_array.res_id == i + 1]
            if len(residue) == 0:
                # not existing
                states[i] = 0
            elif residue.res_name[0] == "UNK":
                # exisiting but polyalanine
                states[i] = 1
            else:
                # existing
                states[i] = 2

        # Find the intervals for each state
        state_intervals = []
        curr_state = None
        curr_start = None
        for i in range(len(states)):
            if curr_start is None:
                curr_start = i
                curr_state = states[i]
            else:
                if states[i] != states[i - 1]:
                    state_intervals.append((curr_start, i, curr_state))
                    curr_start = i
                    curr_state = states[i]
        state_intervals.append((curr_start, i, curr_state))

        # Draw the state intervals as colored rectangles
        for interval in state_intervals:
            start = interval[0]
            stop = interval[1]
            state = interval[2]
            if state == 0:
                color = "firebrick"
            elif state == 1:
                color = "gold"
            elif state == 2:
                color = "forestgreen"
            ax.add_patch(
                Rectangle(
                    (start + 1 - 0.5, 0), stop - start, 1, edgecolor="None", facecolor=color
                )
            )
        # Some other visual stuff
        ax.spines["left"].set_visible(False)
        ax.spines["bottom"].set_visible(False)
        ax.spines["right"].set_visible(False)
        ax.spines["top"].set_visible(False)
        ax.yaxis.set_visible(False)
        ax.set_xlim(0.5, len(states) + 0.5)
        ax.set_ylim(0, 2)


    fig = plt.figure(figsize=(8.0, 2.5))
    ax = fig.add_subplot(211)
    ax.set_title("5luq", loc="left")
    plot_gaps("5luq", "A", ax)
    ax = fig.add_subplot(212)
    ax.set_title("5w1r", loc="left")
    plot_gaps("5w1r", "A", ax)
    ax.set_xlabel(r"$Residue \ number$")
    fig.tight_layout()
    plt.show()


.. _sphx_glr_download_examples_gallery_structure_misc_gap_bars.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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