Puckepy

April 18, 2025 · View on GitHub

A library to describe and characterise molecules.

  • puckepy.formalism to describe molecules quantitatively through various puckering formalisms
  • puckepy.confsampling to provide the functionality from pucke.rs in Python
  • puckepy.geometry to describe molecules by elementary geometrical attributes

Documentation

Consult the API documentation here !

Installation

  • Available for linux on python3 --version >=3.12. Consider making a new .venv or conda environment if your python version is older.
  • Requires no python dependencies, so it is safe to install in any base environment.
# pip venv
$ python3.12 -m venv .venv
$ source activate .venv

# Conda
$ conda create --name myenv python=3.12
$ conda activate myenv

Install puckepy in the environment.

$ pip install puckepy

If you are not on Linux, you might benefit from a local installation method. If you are on Windows, I suggest using Windows Subsystem for Linux (WSL2).
Local installation protocol can be found here !

Citation

If you've used pucke.py or any of its parts, please cite the following published article :

[1] Rihon, J., Reynders, S., Bernardes Pinheiro, V. et al. The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers. J Cheminform 17, 53 (2025). https://doi.org/10.1186/s13321-025-00977-7

@article{Rihon_2025,
    title={The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers},
    volume={17},
    ISSN={1758-2946},
    url={http://dx.doi.org/10.1186/s13321-025-00977-7},
    DOI={10.1186/s13321-025-00977-7},
    number={1},
    journal={Journal of Cheminformatics},
    publisher={Springer Science and Business Media LLC},
    author={Rihon, Jérôme and Reynders, Sten and Bernardes Pinheiro, Vitor and Lescrinier, Eveline},
    year={2025},
    month=apr
}

Author

Written and designed by Jérôme Rihon