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

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

.. _sphx_glr_examples_gallery_structure_contacts_domain_hbonds.py:


Hydrogen bonds between protein domains
======================================

In this example we will identify the hydrogen bonds between the p-Helix
and the selecivity filter of the channel protein KcsA (PDB: 2KB1).
The structure was resolved using NMR, so multiple models are present
in the structure.
Hence, we can also calculate the frequency of each bond.

.. GENERATED FROM PYTHON SOURCE LINES 11-56



.. image-sg:: /examples/gallery/structure/contacts/images/sphx_glr_domain_hbonds_001.png
   :alt: domain hbonds
   :srcset: /examples/gallery/structure/contacts/images/sphx_glr_domain_hbonds_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/biotite/structure/hbond.py:270: UserWarning: Input structure has no associated 'BondList', Hydrogen atoms bonded to donors are detected by distance
      warnings.warn(






|

.. code-block:: Python


    # Code source: Daniel Bauer
    # License: BSD 3 clause

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

    file_name = rcsb.fetch("2KB1", "bcif", gettempdir())
    stack = strucio.load_structure(file_name)
    # Four identical chains, consider only chain A
    chain_a = stack[:, stack.chain_id == "A"]
    # Selection for p-helix
    p_helix = (chain_a.res_id >= 40) & (chain_a.res_id <= 52)
    # Selection for selectivity filter
    sf = (chain_a.res_id >= 53) & (chain_a.res_id <= 58)

    # Calculate the hydrogen bonds and the frequency of each bond
    triplets, mask = struc.hbond(chain_a, selection1=p_helix, selection2=sf)
    freq = struc.hbond_frequency(mask)

    # Create names of bonds
    label = "{d_resid}{d_resnm}-{d_a} -- {a_resid}{a_resnm}-{a_a}"
    names = [
        label.format(
            d_resid=chain_a.res_id[donor],
            d_resnm=chain_a.res_name[donor],
            d_a=chain_a.atom_name[donor],
            a_resid=chain_a.res_id[acceptor],
            a_resnm=chain_a.res_name[acceptor],
            a_a=chain_a.atom_name[acceptor],
        )
        for donor, _, acceptor in triplets
    ]

    plt.subplots(figsize=(11, 4.5))
    plt.bar(names, freq, color=biotite.colors["orange"])
    plt.xlabel("Hydrogen bond")
    plt.ylabel("Hydrogen bond frequency")
    plt.xticks(rotation=45)
    plt.tight_layout()
    plt.show()


.. _sphx_glr_download_examples_gallery_structure_contacts_domain_hbonds.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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