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

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

.. _sphx_glr_examples_gallery_structure_adjacency_matrix.py:


Construction of an adjacency matrix
===================================

In this example we create an adjacency matrix of the CA atoms in the
lysozyme crystal structure (PDB: 1AKI).
The values in the adjacency matrix ``m`` are
``m[i,j] = 1 if distance(i,j) <= threshold else 0``.

.. GENERATED FROM PYTHON SOURCE LINES 10-44



.. image-sg:: /examples/gallery/structure/images/sphx_glr_adjacency_matrix_001.png
   :alt: Adjacency matrix of the lysozyme crystal structure
   :srcset: /examples/gallery/structure/images/sphx_glr_adjacency_matrix_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

    from tempfile import gettempdir
    import biotite
    import biotite.structure as struc
    import biotite.structure.io as strucio
    import biotite.database.rcsb as rcsb
    import matplotlib.pyplot as plt
    from matplotlib.colors import ListedColormap


    file_name = rcsb.fetch("1aki", "bcif", gettempdir())
    array = strucio.load_structure(file_name)
    # We only consider CA atoms
    ca = array[array.atom_name == "CA"]
    # 7 Angstrom adjacency threshold
    threshold = 7
    # Create cell list of the CA atom array
    # for efficient measurement of adjacency
    cell_list = struc.CellList(ca, cell_size=threshold)
    adjacency_matrix = cell_list.create_adjacency_matrix(threshold)

    figure = plt.figure()
    ax = figure.add_subplot(111)
    cmap = ListedColormap(["white", biotite.colors["dimgreen"]])
    ax.matshow(adjacency_matrix, cmap=cmap, origin="lower")
    ax.xaxis.tick_bottom()
    ax.set_aspect("equal")
    ax.set_xlabel("Residue number")
    ax.set_ylabel("Residue number")
    ax.set_title("Adjacency matrix of the lysozyme crystal structure")
    figure.tight_layout()
    plt.show()

.. _sphx_glr_download_examples_gallery_structure_adjacency_matrix.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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