Metadata-Version: 1.1
Name: alchemlyb
Version: 0.1.0
Summary: the simple alchemistry library
Home-page: UNKNOWN
Author: David Dotson
Author-email: dotsdl@gmail.com
License: BSD
Description: alchemlyb: the simple alchemistry library
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        |doi| |docs| |build| |cov| |gitter|
        
        **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
            :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://travis-ci.org/alchemistry/alchemlyb.svg?branch=master
            :alt: Build Status
            :scale: 100%
            :target: https://travis-ci.org/alchemistry/alchemlyb
        
        .. |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
        
        .. |gitter| image:: https://badges.gitter.im/alchemistry/alchemlyb.png
            :alt: Gitter chat
            :scale: 100%
            :target: https://gitter.im/alchemistry/alchemlyb
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering
