QMzyme 0.0.7.dev0

QM-based enzyme model generation and validation.

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 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.

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:

• 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:

• 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.