.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/gallery/nucleotide_contacts.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        Click :ref:`here <sphx_glr_download_examples_gallery_nucleotide_contacts.py>`
        to download the full example code

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

.. _sphx_glr_examples_gallery_nucleotide_contacts.py:


Contacts between nucleotides in a tetracycline aptamer
======================================================

This example reproduces a figure from the publication
*"StreAM-Tg: algorithms for analyzing coarse grained RNA dynamics based
on Markov models of connectivity-graphs"* [1]_.

The figure displays a coarse grained model of a tetracycline aptamer
and highlights interacting nucleotides based on a cutoff distance.

.. [1] S Jager, B Schiller, P Babel, M Blumenroth, T Strufe and K Hamacher,
   "StreAM-Tg: algorithms for analyzing coarse grained RNA dynamics based
   on Markov models of connectivity-graphs."
   Algorithms Mol Biol 12 (2017).

.. GENERATED FROM PYTHON SOURCE LINES 17-30

.. code-block:: default


    # Code source: Patrick Kunzmann
    # License: CC0

    import numpy as np
    import biotite.structure as struc
    import biotite.structure.io.mmtf as mmtf
    import biotite.database.rcsb as rcsb
    import ammolite


    PNG_SIZE = (800, 800)








.. GENERATED FROM PYTHON SOURCE LINES 31-60

.. code-block:: default


    mmtf_file = mmtf.MMTFFile.read(rcsb.fetch("3EGZ", "mmtf"))
    structure = mmtf.get_structure(mmtf_file, model=1)
    aptamer = structure[struc.filter_nucleotides(structure)]

    # Coarse graining: Represent each nucleotide using its C3' atom
    aptamer = aptamer[aptamer.atom_name == "C3'"]
    # Connect consecutive nucleotides
    indices = np.arange(aptamer.array_length())
    aptamer.bonds = struc.BondList(
        aptamer.array_length(),
        np.stack((indices[:-1], indices[1:]), axis=-1)
    )

    pymol_obj = ammolite.PyMOLObject.from_structure(aptamer)
    pymol_obj.show("sticks")
    pymol_obj.show("spheres")
    pymol_obj.color("black")
    ammolite.cmd.set("stick_color", "red")
    ammolite.cmd.set("stick_radius", 0.5)
    ammolite.cmd.set("sphere_scale", 1.0)
    ammolite.cmd.set("sphere_quality", 4)

    # Adjust camera
    pymol_obj.orient()
    pymol_obj.zoom(buffer=10)
    ammolite.cmd.rotate("z", 90)
    ammolite.show(PNG_SIZE)




.. image-sg:: /examples/gallery/images/sphx_glr_nucleotide_contacts_001.png
   :alt: nucleotide contacts
   :srcset: /examples/gallery/images/sphx_glr_nucleotide_contacts_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 61-78

.. code-block:: default


    CUTOFF = 13

    # Find contacts within cutoff distance
    adjacency_matrix = struc.CellList(aptamer, CUTOFF) \
                       .create_adjacency_matrix(CUTOFF)
    for i, j in zip(*np.where(adjacency_matrix)):
        pymol_obj.distance("", i, j, show_label=False, gap=0)

    ammolite.cmd.set("dash_color", "firebrick")

    # Add black outlines
    ammolite.cmd.bg_color("white")
    ammolite.cmd.set("ray_trace_mode", 1)
    ammolite.cmd.set("ray_trace_disco_factor", 0.5)

    ammolite.show(PNG_SIZE)
    # sphinx_gallery_thumbnail_number = 2


.. image-sg:: /examples/gallery/images/sphx_glr_nucleotide_contacts_002.png
   :alt: nucleotide contacts
   :srcset: /examples/gallery/images/sphx_glr_nucleotide_contacts_002.png
   :class: sphx-glr-single-img






.. _sphx_glr_download_examples_gallery_nucleotide_contacts.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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