Example
==========

Before running the code, the user should edit the `config.yaml` to tailor the application of VizChemoton to the given
specific system. Even so, the default `config.yaml` is set so that the user can run VizChemoton out-of-the-box
with the data in the *./vizchemoton/resources* folder. In the *docs/manual.md*, we provide a detailed explanation
of the parameters in `config.yaml`.

.. code-block:: bash

    # Activate conda environment 
    conda activate my_env

    # Edit the config file
    vi config.yaml

    # Run the code of this repository (at the /vizchemoton level) to obtain the html
    python3 -m vizchemoton

The code renders a `.html` file, with the path and name specified by the user, which contains the compounds and
reactions of the reaction network.

Double-clicking the `.html` file will open a dashboard similar to the diagram below, where we have
depicted the description of the main built-in functionalities.

.. image:: ../html_manual.png
    :alt: Example HTML dashboard

.. note::
   
   VizChemoton has been applied to the ozonation of model olefins in water. The reader can download the 3 associated    HTML files from the `Zenodo repository <https://zenodo.org/records/14448899>`_. We recommend downloading the
   **CRN_T_network.html** file since it's the smallest in size, and thus more manageable. 

If the reader wishes to find a specific molecule in the network, we recommend using the Find module of
`ioChem-BD <https://www.iochem-bd.org/>`_. The diagram below shows the three steps: (1) select search by structure, (2)
draw the chemical structure that you are interested in, (3) if *Results* is greater than 0 press the button *go*.
This will redirect you to the *Browse* module, where all the calculations involving the drawn structure will be listed.
Next, you should search on the right side of the screen for the box named *Author*, and click the name *Enric Petrus*.
The *Title* name of the searched structure will be the same as the one in the network HTML file.

.. image:: ../iochem_find.png
    :alt: ioChem-BD search steps