.. _gallery:

Jupyter Notebook Gallery
========================

.. |br| raw:: html

   </br>

The notebooks can be accessed locally by issuing::

 mdc_notebooks.py

from the CLI. This will create a local "sandboxed" copy of the notebooks,
which you can modify and play around with without breaking
the original notebooks. Note: all notebooks except the last two.

Tutorials
---------

.. list-table::

    * - .. figure:: _build/html/_images/interface.combined.png
           :target: notebooks/Tutorial.html
           :height: 100px

           ..

           |br| `One single notebook providing <notebooks/Tutorial.html>`_
           |br| `an overview of mdciao <notebooks/Tutorial.html>`_

FAQs
----
These are issue-specific notebooks. They are more verbose and explore
how particular optional parameters affect the output of some methods.

.. list-table::

    * - .. figure:: _build/doctrees/nbsphinx/notebooks_Missing_Contacts_15_1.png
           :target: notebooks/Missing_Contacts.html
           :height: 100px

           ..

           |br| `Missing Contacts <notebooks/Missing_Contacts.html>`_

      - .. figure:: _build/html/_images/notebooks_Comparing_CGs_Bars_41_1.png
           :target: notebooks/Comparing_CGs_Bars.html
           :height: 100px

           ..

           |br| `Comparing Frequencies: <notebooks/Comparing_CGs_Bars.html>`_
           |br| `Bar Plots <notebooks/Comparing_CGs_Bars.html>`_

    * - .. figure:: _build/html/_images/notebooks_Comparing_CGs_Flares_41_1.png
           :target: notebooks/Comparing_CGs_Flares.html
           :height: 100px

           ..

           |br| `Comparing Frequencies: <notebooks/Comparing_CGs_Flares.html>`_
           |br| `Flareplots <notebooks/Comparing_CGs_Flares.html>`_

      - .. figure:: _build/doctrees/nbsphinx/notebooks_Flareplot_Schemes_22_1.png
           :target: notebooks/Flareplot_Schemes.html
           :height: 100px

           ..

           |br| `Controlling Flareplots: <notebooks/Flareplot_Schemes.html>`_
           |br| `Schemes <notebooks/Flareplot_Schemes.html>`_

Examples
--------
These are worked out examples from the real world, from raw data to final results.
They are the best starting point to copy and modify with your own data.

.. list-table::

    * - .. figure:: _build/html/_images/notebooks_Manuscript_17_0.png
           :target: notebooks/Manuscript.html
           :height: 100px

           ..

           |br| `Interfaces: <notebooks/Manuscript.html>`_
           |br| `β2 Adrenergic Receptor in Complex with <notebooks/Manuscript.html>`_
           |br| `Empty Gs-Protein <notebooks/Manuscript.html>`_

      - .. figure:: _build/html/_images/notebooks_EGFR_Kinase_Inhibitors_14_0.png
           :target: notebooks/EGFR_Kinase_Inhibitors.html
           :height: 100px

           ..

           |br| `Binding-Pockets: <notebooks/EGFR_Kinase_Inhibitors.html>`_
           |br| `EGFR Kinase Inhibitors <notebooks/EGFR_Kinase_Inhibitors.html>`_

    * - .. figure:: _build/html/_images/notebooks_Covid-19-Spike-Protein-Example_23_1.png
           :target: notebooks/Covid-19-Spike-Protein-Example.html
           :height: 100px

           ..

           |br| `Covid-19 Spike Protein <notebooks/Covid-19-Spike-Protein-Example.html>`_
           |br| `Example 1: Residue Neighborhoods <notebooks/Covid-19-Spike-Protein-Example.html>`_

      - .. figure:: imgs/spike_intf.small.png
           :target: notebooks/Covid-19-Spike-Protein-Interface.html
           :height: 100px

           ..

           |br| `Covid-19 Spike Protein <notebooks/Covid-19-Spike-Protein-Interface.html>`_
           |br| `Example 2: Molecular Interfaces <notebooks/Covid-19-Spike-Protein-Interface.html>`_