Metadata-Version: 2.1
Name: alchemlyb
Version: 0.7.0
Summary: the simple alchemistry library
Author: David Dotson
Author-email: dotsdl@gmail.com
Maintainer: Oliver Beckstein
Maintainer-email: orbeckst@gmail.com
License: BSD
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows 
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.7
Description-Content-Type: text/x-rst
License-File: LICENSE
License-File: AUTHORS

alchemlyb: the simple alchemistry library
=========================================

|doi| |docs| |build| |cov|

**alchemlyb** makes 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`_, `AMBER`_, `NAMD`_
   and `other simulation codes`_.

2. Subsamplers for obtaining uncorrelated samples from timeseries data
   (including extracting independent, equilibrated samples
   [Chodera2016]_ as implemented in the pymbar_ package).

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

.. _GROMACS: http://www.gromacs.org/
.. _AMBER: http://ambermd.org/
.. _NAMD: http://www.ks.uiuc.edu/Research/namd/
.. _`other simulation codes`: https://alchemlyb.readthedocs.io/en/latest/parsing.html
.. _`pymbar`: http://pymbar.readthedocs.io/
   

Getting involved
----------------

Contributions of all kinds are very welcome.

If you have questions or want to discuss alchemlyb please post in the `alchemlyb Discussions`_.

If you have bug reports or feature requests then please get in touch with us through the `Issue Tracker`_.

We also welcome code contributions: have a look at our `Developer Guide`_. Open an issue with the proposed fix or change in the `Issue Tracker`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository.

.. _`alchemlyb Discussions`: https://github.com/alchemistry/alchemlyb/discussions
.. _`Developer Guide`: https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide
.. _`Issue Tracker`: https://github.com/alchemistry/alchemlyb/issues
.. _`alchemistry/alchemlyb`: https://github.com/alchemistry/alchemlyb

   

References
----------

.. [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
    :alt: Zenodo DOI
    :scale: 100%
    :target: https://zenodo.org/badge/latestdoi/68669096

.. |docs| image:: https://readthedocs.org/projects/alchemlyb/badge/?version=latest
    :alt: Documentation
    :scale: 100%
    :target: http://alchemlyb.readthedocs.io/en/latest/

.. |build| image:: https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml/badge.svg?branch=master
    :alt: Build Status
    :scale: 100%
    :target: https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml

.. |cov| image:: https://codecov.io/gh/alchemistry/alchemlyb/branch/master/graph/badge.svg
    :alt: Code coverage
    :scale: 100%
    :target: https://codecov.io/gh/alchemistry/alchemlyb

