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

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

.. _sphx_glr_examples_gallery_structure_trajectory_sse.py:


Secondary structure during an MD simulation
===========================================

This script displays positional changes of secondary structure elements
(SSE) in the course of time of an MD simulation.

The trajectory file can be downloaded
:download:`here </examples/download/lysozyme_md.xtc>`
and the template PDB can be downloaded
:download:`here </examples/download/lysozyme_md.pdb>`.

.. GENERATED FROM PYTHON SOURCE LINES 13-91



.. image-sg:: /examples/gallery/structure/images/sphx_glr_trajectory_sse_001.png
   :alt: trajectory sse
   :srcset: /examples/gallery/structure/images/sphx_glr_trajectory_sse_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    # Code source: Daniel Bauer, Patrick Kunzmann
    # License: BSD 3 clause

    import numpy as np
    import matplotlib.pyplot as plt
    from matplotlib.lines import Line2D
    from matplotlib import colors
    import matplotlib as mpl
    import biotite.structure as struc
    import biotite.structure.io as strucio
    import biotite.structure.io.xtc as xtc
    from biotite.application.dssp import DsspApp


    # Put here the path of the downloaded files
    templ_file_path = "../../download/lysozyme_md.pdb"
    traj_file_path  = "../../download/lysozyme_md.xtc"


    xtc_file = xtc.XTCFile.read(traj_file_path)
    traj = xtc_file.get_structure(template=strucio.load_structure(templ_file_path))
    time = xtc_file.get_time()
    traj = traj[:, struc.filter_amino_acids(traj)]

    # DSSP does not assign an SSE to the last residue -> -1
    sse = np.empty((traj.shape[0], struc.get_residue_count(traj)-1), dtype='U1')
    for idx, frame in enumerate(traj):
        app = DsspApp(traj[idx])
        app.start()
        app.join()
        sse[idx] = app.get_sse()

    # Matplotlib needs numbers to assign colors correctly
    def sse_to_num(sse):
        num = np.empty(sse.shape, dtype=int)
        num[sse == 'C'] = 0
        num[sse == 'E'] = 1
        num[sse == 'B'] = 2
        num[sse == 'S'] = 3
        num[sse == 'T'] = 4
        num[sse == 'H'] = 5
        num[sse == 'G'] = 6
        num[sse == 'I'] = 7
        return num
    sse = sse_to_num(sse)


    # Plotting
    # SSE colormap
    color_assign = {
        r"coil": "white",
        r"$\beta$-sheet": "red",
        r"$\beta$-bridge": "black",
        r"bend": "green",
        r"turn": "yellow",
        r"$\alpha$-helix": "blue",
        r"$3_{10}$-helix": "gray",
        r"$\pi$-helix": "purple", 
    }
    cmap = colors.ListedColormap(color_assign.values())

    plt.figure(figsize=(8.0, 6.0))
    plt.imshow(sse.T, cmap=cmap, origin='lower')
    plt.xlabel("Time / ps")
    plt.ylabel("Residue")
    ticks = np.arange(0, len(traj), 10)
    plt.xticks(ticks, time[ticks].astype(int))

    # Custom legend below the DSSP plot
    custom_lines = [
        Line2D([0], [0], color=cmap(i), lw=4) for i in range(len(color_assign))
    ]
    plt.legend(
        custom_lines, color_assign.keys(), loc="upper center",
        bbox_to_anchor=(0.5, -0.15), ncol=len(color_assign), fontsize=8
    )
    plt.tight_layout()
    plt.show()

.. _sphx_glr_download_examples_gallery_structure_trajectory_sse.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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