QMzyme 0.0.7.dev0
QM-based enzyme model generation and validation.
License: MIT
Requires Python: >=3.11


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*QMzyme is currently under-development. Please note the user interface may change! The first stable API version will be released as QMzyme==1.0.0 on PyPi.*

QMzyme is a Python toolkit to facilitate (quantum mechanical) QM-based enzyme calculations. The GenerateModel module guides the process of generating calculation ready truncated or partitioned molecule regions. Any input file(s) accepted by [MDAnalysis to create a Universe](https://userguide.mdanalysis.org/stable/universe.html) object can be used to start working in QMzyme. From there, the code relies on more flexible QMzyme objects: QMzymeAtom, QMzymeResidue, QMzymeRegion and QMzymeModel. 

Full documentation with installation instructions, technical details and examples can be found in [Read the Docs](https://qmzyme.readthedocs.io/).

## Contributing to QMzyme
For suggestions and improvements of the code (greatly appreciated!), please reach out through the issues and pull requests options of Github.  

## References

QMzyme has not been formally published. Please refer back here for the proper citation once it has.

QMzyme's main dependency is MDAnalysis. When using QMzyme please [cite MDAnalysis accordingly](https://www.mdanalysis.org/pages/citations/):

* R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 98-105, Austin, TX, 2016. SciPy, doi:10.25080/majora-629e541a-00e.

* N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319-2327, doi:10.1002/jcc.21787. PMCID:PMC3144279

If you use QMzyme to write QM software calculation input files, please include this citation for [AQME](https://aqme.readthedocs.io/en/latest/):  

* Alegre-Requena, J. V.; Sowndarya, S.; Pérez-Soto, R.; Alturaifi, T.; Paton, R. AQME: Automated Quantum Mechanical Environments for Researchers and Educators. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2023, 13, e1663. (DOI: 10.1002/wcms.1663).  


#### Copyright
Copyright (c) 2024, Heidi Klem

#### Acknowledgements
Project architecture initially inspired by [MolSSI CMS Cookiecutter](https://github.com/molssi/cookiecutter-cms).