alchemlyb 0.3.1

alchemlyb: the simple alchemistry library
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|doi| |docs| |build| |cov|

**Warning**: This library is young. It is **not** API stable. It is a
nucleation point. By all means use and help improve it, but note that it will
change with time.

**alchemlyb** is an attempt to make alchemical free energy calculations easier
to do by leveraging the full power and flexibility of the PyData stack. It
includes:

1. Parsers for extracting raw data from output files of common molecular
dynamics engines such as GROMACS [Abraham2015]_.

2. Subsamplers for obtaining uncorrelated samples from timeseries data.

3. Estimators for obtaining free energies directly from this data, using
best-practices approaches for multistate Bennett acceptance ratio (MBAR)
[Shirts2008]_ and thermodynamic integration (TI).

In particular, it uses internally the excellent `pymbar
<http://pymbar.readthedocs.io/>`_ library for performing MBAR and extracting
independent, equilibrated samples [Chodera2016]_.

.. [Abraham2015] Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C.,
Hess, B., and Lindahl, E. (2015). GROMACS: High performance molecular
simulations through multi-level parallelism from laptops to supercomputers.
SoftwareX 1–2, 19–25.

.. [Shirts2008] Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal
analysis of samples from multiple equilibrium states. The Journal of Chemical
Physics 129, 124105.

.. [Chodera2016] Chodera, J.D. (2016). A Simple Method for Automated
Equilibration Detection in Molecular Simulations. Journal of Chemical Theory
and Computation 12, 1799–1805.

.. |doi| image:: https://zenodo.org/badge/68669096.svg
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.. |docs| image:: https://readthedocs.org/projects/alchemlyb/badge/?version=latest
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.. |build| image:: https://travis-ci.org/alchemistry/alchemlyb.svg?branch=master
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.. |cov| image:: https://codecov.io/gh/alchemistry/alchemlyb/branch/master/graph/badge.svg
:alt: Code coverage
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