alchemlyb: the simple alchemistry library

Warning

This library is in an alpha state. The library and the documentation is incomplete. Use in production at your own risk.

alchemlyb is a library for doing alchemical free energy calculations more easily and with less prone for error. 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.

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.

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, with a Gitter channel for discussion among developers for fast turnaround on ideas.

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

User Documentation

For Developers