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

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

.. _sphx_glr_examples_gallery_structure_misc_diameter.py:


Calculation of protein diameter
===============================

This script calculates the diameter of a protein
defined as the maximum pairwise atom distance.

.. GENERATED FROM PYTHON SOURCE LINES 8-36




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

 .. code-block:: none

    Diameter of 1QAW: 88.78395 Angstrom






|

.. code-block:: Python


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

    from tempfile import gettempdir
    import numpy as np
    import biotite.database.rcsb as rcsb
    import biotite.structure as struc
    import biotite.structure.io as strucio


    def get_diameter(pdb_id):
        file_name = rcsb.fetch(pdb_id, "bcif", gettempdir())
        atom_array = strucio.load_structure(file_name)
        # Remove all non-amino acids
        atom_array = atom_array[struc.filter_amino_acids(atom_array)]
        coord = atom_array.coord
        # Calculate all pairwise difference vectors
        diff = coord[:, np.newaxis, :] - coord[np.newaxis, :, :]
        # Calculate absolute of difference vectors -> square distances
        sq_dist = np.sum(diff * diff, axis=-1)
        # Maximum distance is diameter
        diameter = np.sqrt(np.max(sq_dist))
        return diameter


    # Example application
    print("Diameter of 1QAW:", get_diameter("1QAW"), "Angstrom")


.. _sphx_glr_download_examples_gallery_structure_misc_diameter.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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