https://github.com/tinaccil/gretobape_cleaning

Cleaning Astrochemical Reaction network via Thermodynamics principles
https://github.com/tinaccil/gretobape_cleaning

astrochemistry chemoinformatics graph networks quantum-chemistry reaction-network

Last synced: about 2 months ago
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Cleaning Astrochemical Reaction network via Thermodynamics principles

• Host: GitHub
• URL: https://github.com/tinaccil/gretobape_cleaning
• Owner: TinacciL
• License: mit
• Created: 2022-02-18T16:04:24.000Z (almost 3 years ago)
• Default Branch: master
• Last Pushed: 2023-12-24T15:43:27.000Z (about 1 year ago)
• Last Synced: 2023-12-24T16:23:35.189Z (about 1 year ago)
• Topics: astrochemistry, chemoinformatics, graph, networks, quantum-chemistry, reaction-network
• Language: Jupyter Notebook
• Homepage:
• Size: 2.18 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Cleaning Astrochemical Reaction network via Thermodynamics principles

This is a Python 3.8 script that permits to read and work with an astrochemical reaction network in [KIDA format](https://kida.astrochem-tools.org/) .

## Installation

This program used a python3 interface, to run this code you must install on your machine this list of packages:

* ```networkx```

* ```numpy```

* ```pandas```

## Script Structure

All the codes for the cleaning are inside the ```Cleaning_script.ipynb``` ipython notebook, the ```lib.py``` python file is where many functions are stored.

An example on how encode a KIDA Reaction Network and visualize is in the ```reaction_network_to_graph.ipynb``` file.

## Database

Networks and molecules information are inside the ```Database``` directory. A dedicated ```ReadMe``` file is inside the directory.

## Associated publications

Please refer to the following publication to cite our work or retrieve the info:

[The GRETOBAPE gas-phase reaction network: the importance of being exothermic, L.Tinacci et al 2023 Arxiv](https://doi.org/10.48550/arXiv.2302.14799)

```bibtex

@article{Tinacci_Gretobape,

  title={The GRETOBAPE gas-phase reaction network: the importance of being exothermic},

  author={Tinacci, Lorenzo and Ferrada-Chamorro, Sim{\'o}n and Ceccarelli, Cecilia and Pantaleone, Stefano and Ascenzi, Daniela and Maranzana, Andrea and Balucani, Nadia and Ugliengo, Piero},

  journal={arXiv preprint arXiv:2302.14799},

  year={2023}

}

```

[Structures and Properties of Known and Postulated Interstellar Cations, L.Tinacci et al 2021 ApJS 256 35](https://doi.org/10.3847/1538-4365/ac194c)

```bibtex

@article{Tinacci_ISM_cations,

title={Structures and Properties of Known and Postulated Interstellar Cations},

author={Tinacci, Lorenzo and Pantaleone, Stefano and Maranzana, Andrea and Balucani, Nadia and Ceccarelli, Cecilia and Ugliengo, Piero},

journal={The Astrophysical Journal Supplement Series},

volume={256},

number={2},

pages={35},

year={2021},

doi={10.3847/1538-4365/ac194c},

publisher={IOP Publishing}

}

```

All the data are store in the following ZENODO link:

DOI:[10.5281/zenodo.7799421](https://zenodo.org/record/7799421)

## Acknowledgments

This project has received funding within the European Union’s Horizon 2020 research and innovation programme from the Marie Sklodowska-Curie for the project ”Astro-Chemical Origins” (ACO), grant agreement No 811312.