User Guide
==========
The default version of the dataset (the full dataset as a CSV file based on the newest ChEMBL version) can be generated by calling 

::

    python main.py -o <output_path>

with further options explained in `Arguments`_.

An overview of the available arguments is also available by calling 

::

    python main.py --help

The output will always contain the full dataset as a CSV file. 
The arguments only allow for the output of additional files or modify how the full dataset is extracted.  



Arguments
*********
.. csv-table:: 
   :file: tables/userguide.csv
   :widths: 20, 10, 10, 10, 50
   :header-rows: 1



Accessing ChEMBL
****************
ChEMBL is accessed either through a given path to an SQLite database download or through the `chembl_downloader package`_. 
In both cases, SQLite is used to query ChEMBL. 
Some of the earlier ChEMBL versions are missing tables or fields required to calculate the dataset. 
Therefore, the earliest ChEMBL version for which the dataset can be calculated is ChEMBL 26.


.. _chembl_downloader package: https://github.com/cthoyt/chembl-downloader