.. |basic_usage_example| graphviz:: ../resources/basic_usage.dot

============
Basic Usage
============

Aside from the python library, rNets comes with a command line executable. In 
order to generate a reaction network with rnets we will require 
2 files (one containing the species and another containing the reactions), and to
visualize it we will also require to have graphviz or any other 
software capable of rendering image files from :code:`.dot` files.

To illustrate the basic usage pipeline, lets assume that we have the files: 
compounds.csv and reactions.csv with the following contents: 

:code:`compounds.csv`

.. code:: none

   name,energy,fflags
   reactant,0,b
   intermediate,0,b
   product,0,b

:code:`reactions.csv`

.. code:: none

   cleft,cleft,cright,cright,energy,direction,name
   reactant,,intermediate,,0.5,<->,R0
   intermediate,,product,,0.4,<->,R1

For a detailed explanation on the contents and format of these files please 
check the :doc:`file_formats` section

The first step will be to generate a :code:`.dot` file using the command line 
executable: 

.. code:: shell 

   python -m rnets -cf compounds.csv -rf reactions.csv -o output.dot

Here, we do not need to specify if we want a graph colored based only on 
thermochemistry or based on concentrations. In the presence of concentration 
values it will default to a concentration-based graph, while its absence will 
default to a thermochemistry-based graph. :code:`output.dot` is the name of the 
:code:`.dot` file that will be generated.

Next, we proceed to render the drawing into a png. For this we will use the 
:code:`dot` executable that comes with graphviz.

.. code:: shell 

   dot -Tpng output.dot -o output.png

With this we have generated the final graph of our reaction network. 

.. centered:: |basic_usage_example|

.. todo:: 
   
   A more detailed control of the graph format, as well as specifying the 
   temperature or energy units can be achieved using the configuration files. 
   
   Add section on how to use configuration files or generate them