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

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

.. _sphx_glr_examples_gallery_structure_misc_pdb_statistics.py:


Annual releases of PDB structures
=================================

This script creates a plot showing the number of annually released PDB
structures since 1990, very similar to the
`official statistics <https://www.rcsb.org/stats/growth/growth-released-structures>`_.

.. GENERATED FROM PYTHON SOURCE LINES 9-80



.. image-sg:: /examples/gallery/structure/misc/images/sphx_glr_pdb_statistics_001.png
   :alt: PDB release statistics
   :srcset: /examples/gallery/structure/misc/images/sphx_glr_pdb_statistics_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

    from datetime import datetime, time
    import matplotlib.pyplot as plt
    import numpy as np
    import biotite
    import biotite.database.rcsb as rcsb

    years = np.arange(1990, datetime.today().year + 1)
    xray_count = np.zeros(len(years), dtype=int)
    nmr_count = np.zeros(len(years), dtype=int)
    em_count = np.zeros(len(years), dtype=int)
    tot_count = np.zeros(len(years), dtype=int)
    # For each year fetch the list of released PDB IDs
    # and count the number
    for i, year in enumerate(years):
        # A query that comprises one year
        date_query = rcsb.FieldQuery(
            "rcsb_accession_info.initial_release_date",
            range_closed=(
                datetime.combine(datetime(year, 1, 1), time.min),
                datetime.combine(datetime(year, 12, 31), time.max),
            ),
        )
        xray_query = rcsb.FieldQuery("exptl.method", exact_match="X-RAY DIFFRACTION")
        nmr_query = rcsb.FieldQuery("exptl.method", exact_match="SOLUTION NMR")
        em_query = rcsb.FieldQuery("exptl.method", exact_match="ELECTRON MICROSCOPY")
        # Get the amount of structures, that were released in that year
        # AND were elucidated with the respective method
        xray_count[i], nmr_count[i], em_count[i] = [
            rcsb.count(date_query & method_query)
            for method_query in [xray_query, nmr_query, em_query]
        ]
        # Get the total amount of structures released in that year
        tot_count[i] = rcsb.count(date_query)

    fig, ax = plt.subplots(figsize=(8.0, 5.0))
    ax.set_title("PDB release statistics")
    ax.set_xlim(years[0] - 1, years[-1] + 1)
    ax.set_xticks(years)
    ax.set_xticklabels([str(y) for y in years], rotation=45)
    ax.set_xlabel("Year")
    ax.set_ylabel("Released structures per year")
    ax.bar(years, xray_count, color=biotite.colors["darkorange"], label="X-Ray")
    ax.bar(
        years,
        nmr_count,
        bottom=xray_count,
        color=biotite.colors["orange"],
        label="Solution NMR",
    )
    ax.bar(
        years,
        em_count,
        bottom=xray_count + nmr_count,
        color=biotite.colors["brightorange"],
        label="Electron Microscopy",
    )
    ax.bar(
        years,
        tot_count - xray_count - nmr_count - em_count,
        bottom=xray_count + nmr_count + em_count,
        color="gray",
        label="Miscellaneous",
    )
    ax.legend(loc="upper left")
    fig.tight_layout()

    plt.show()


.. _sphx_glr_download_examples_gallery_structure_misc_pdb_statistics.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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