Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

https://github.com/alchemistry/alchemlyb

the simple alchemistry library
https://github.com/alchemistry/alchemlyb

free-energy library molecular-dynamics python science

Last synced: about 1 month ago
JSON representation

the simple alchemistry library

Lists

README 

        
alchemlyb: the simple alchemistry library

=========================================



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



**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/



Installation

------------



**Install** via ``pip`` from `PyPi (alchemlyb)`_ ::



  pip install alchemlyb



or as a `conda`_ package from the `conda-forge (alchemlyb)`_ channel

::



  conda install -c conda-forge alchemlyb 



**Update** with ``pip`` ::



  pip install --update alchemlyb



or with ``conda`` run ::



  conda update -c conda-forge alchemlyb



to get the latest released version.



.. _`PyPi (alchemlyb)`: https://pypi.org/project/alchemlyb/

.. _`conda`: https://conda.io/

.. _`conda-forge (alchemlyb)`: https://anaconda.org/conda-forge/alchemlyb



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



.. |anaconda| image:: https://anaconda.org/conda-forge/alchemlyb/badges/version.svg

   :alt: anaconda package

   :scale: 100%	 

   :target: https://anaconda.org/conda-forge/alchemlyb