rNets is an innovative python tool designed for visualization of reaction networks with a simple and robust command-line interface. rNets was conceptualized with the core principles of modularity, and easy integration with existing software packages by reducing dependencies to the minimum. This tool not only simplifies the visualization process but also opens new avenues for exploring complex reaction networks in diverse research contexts.

These instructions will get you a copy of the project up and running on your local machine.

• python >= 3.12

rNets only depends on the python standard library that usually comes with the cpython interpreter, the default one adopted by the python community. This means the the only requisite for installing rNets is python. The python community has placed a lot of effort into the documentation and actively maintains it so for further instructions on how to install python into your computer we highly recommend to check the official python documentation.

Although for being able to install and run rNets only python is required, rNets relies heavily on graphviz for the actual rendering of the images, as the output of rNets is tipically a .dot file. Installing graphviz is tipically a straightforward and quick process. Graphviz may be downloaded from their official webpage.

rNets can be directly installed through pip as a version of the package is hosted at the Python Package Index (PyPI):

$ python -m pip install rNets

However, if the user does prefer it, it can also be easily installed from the source code. For that we will start by downloading the source code using git.

$ git clone https://codeberg.org/spgarcica/rNets.git rnets-source

Next we proceed to install it using pip

$ python -m pip install rnets-source/

If you do not have git or do prefer to download manually the source code as a .zip or .tar.gz do it install it.

$ python -m pip install rNets.tar.gz

Completely uninstalling rNets is also quite easy due to its lack of dependencies. All that is needed is to command pip to uninstall the package

$ python -m pip uninstall rNets

• python 3.12

The examples folders contains with corresponding readme files the instructions and necessary data to generate a variety of different reaction networks and animations.

The documentation of rNets can be accessed at https://spgarcica.github.io/rNets/ . Here a more detailed description of the examples can also be found.

List of main developers and contact emails:

• Sergio Pablo-García [ ORCID , Github ]
• Raúl Pérez-Soto [ ORCID , Github ]
• Albert Sabadell-Rendón [ ORCID , Github ]
• Diego Garay-Ruiz [ ORCID , Github ]
• Vladyslav Nosylevskyi [ ORCID Github ]
• Nuria Lopez [ ORCID ]

rNets is freely available under an MIT License

To cite rNets please cite the following publications:

@misc{pablo-garcia_rnets_2024,
    title = {{rNets}: {A} standalone package to visualize reaction networks.},
    shorttitle = {{rNets}},
    url = {https://chemrxiv.org/engage/chemrxiv/article-details/660c5ccae9ebbb4db9378cc1},
    doi = {10.26434/chemrxiv-2024-l7gf5},
    language = {en},
    urldate = {2024-04-04},
    publisher = {ChemRxiv},
    author = {Pablo-García, Sergio and Pérez-Soto, Raúl and Sabadell-Rendón, Albert and Garay-Ruiz, Diego and Nosylevskyi, Vladyslav and López, Nuria},
    month = apr,
    year = {2024},
    keywords = {catalysis, computational chemistry, density functional theory, dft, graphviz, microkinetics, python, reaction networks, visualization},
}