alchemlyb: the simple alchemistry library

alchemlyb is a library for doing alchemical free energy calculations more easily. It includes functions for parsing data from formats common to existing MD engines, subsampling these data, and fitting these data with an estimator to obtain free energies. These functions are simple in usage and pure in scope, and can be chained together to build customized analyses of data.

alchemlyb seeks to be as boring and simple as possible to enable more complex work. Its components allow work at all scales, from use on small systems using a single workstation to larger datasets that require distributed computing using libraries such as dask.

The library is under active development and the API is still somewhat in flux. However, it is used by multiple groups in a production environment. We use semantic versioning to indicate clearly what kind of changes you may expect between releases. See Contributing for how to get in touch if you have questions or find problems.

Core philosophy

With its goal to remain simple to use, alchemlyb’s design philosophy follows the following points:

  1. Use functions when possible, classes only when necessary (or for estimators, see (2)).

  2. For estimators, mimic the scikit-learn API as much as possible.

  3. Aim for a consistent interface throughout, e.g. all parsers take similar inputs and yield a common set of outputs.

For more details, see the Roadmap.

Development model

This is an open-source project, the hope of which is to produce a library with which the community is happy. To enable this, the library is a community effort. Development is done in the open on GitHub.

Software engineering best-practices are used throughout, including continuous integration testing via Travis CI, up-to-date documentation, and regular releases.


Contributions are very welcome. If you have bug reports or feature requests or questions then please get in touch with us through the Issue Tracker. We also welcome code contributions: have a look at our Developer Guide and submit a pull request against the alchemistry/alchemlyb GitHub repository.

For Developers