https://github.com/mdanalysis/solvation-analysis

A comprehensive tool for analyzing liquid solvation structure.
https://github.com/mdanalysis/solvation-analysis

Last synced: about 1 year ago
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A comprehensive tool for analyzing liquid solvation structure.

• Host: GitHub
• URL: https://github.com/mdanalysis/solvation-analysis
• Owner: MDAnalysis
• License: gpl-3.0
• Created: 2021-05-28T19:49:05.000Z (about 5 years ago)
• Default Branch: main
• Last Pushed: 2024-07-18T23:05:45.000Z (almost 2 years ago)
• Last Synced: 2025-01-12T15:06:21.267Z (over 1 year ago)
• Language: Python
• Homepage: https://solvation-analysis.readthedocs.io/en/latest/
• Size: 43.5 MB
• Stars: 46
• Watchers: 10
• Forks: 13
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

          
SolvationAnalysis

==============================

[//]: # (Badges)

[![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://www.numfocus.org/)

[![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)

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[![docs](https://img.shields.io/badge/docs-latest-brightgreen.svg)](https://solvation-analysis.readthedocs.io/en/latest/)

[![pub](https://joss.theoj.org/papers/10.21105/joss.05183/status.svg)](https://doi.org/10.21105/joss.05183)

[//]: # ([![DOI](https://zenodo.org/badge/371804402.svg)](https://zenodo.org/badge/latestdoi/371804402))

---

Solvation analysis implements a robust, cohesive, and fast set of methods

for analyzing the solvation structure of a liquid. It integrates with

[MDAnalysis](https://www.mdanalysis.org/) to seamlessly calculate, query,

and visualize solvation information.

Find documentation and tutorials on [readthedocs](https://solvation-analysis.readthedocs.io/en/latest/).

### Installing SolvationAnalysis

SolvationAnalysis is available on PyPI and conda-forge can be installed with pip or conda:

```bash

pip install solvation-analysis

# or

conda install -c conda-forge solvation_analysis

```

### Solvation Analysis Summarized

![summary](docs/tutorials/images/summary_figure.png)

### Visualization

With just a few lines of code, solvation analysis can calculate detailed

properties within and between solvent systems. A few examples are shown below.

![solvation_analysis.plotting.compare_coordination_numbers](docs/tutorials/images/coordination_plot.png)

![solvation_analysis.plotting.plot_speciation](docs/tutorials/images/speciation_plot.png)

![solvation_analysis.plotting.plot_rdfs](docs/tutorials/images/rdf_plot.png)

### Contributing

Contributions, both issues and PRs, are welcome. If you'd like to contribute, we ask that you

follow the community guidelines outlined in the [MDAnalysis Code of Conduct](https://www.mdanalysis.org/pages/conduct/).

Solvation Analysis uses [pre-commit](https://pre-commit.com/) for linting. Make sure to install

the pre-commit hooks if you are working on a contribution.

### Citation

This work is described in [JOSS](https://doi.org/10.21105/joss.05183), please cite it if you make

use of this package in published work.

---

Project based on the

[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.5.

[readthedocs]: (https://solvation-analysis.readthedocs.io/en/latest/)

[robust, cohesive, and fast set of methods]:(https://summerofcode.withgoogle.com/projects/#6227159028334592)

[Google Summer of Code]: https://summerofcode.withgoogle.com/

[MDAnalysis]: https://www.mdanalysis.org/