Metadata-Version: 2.1
Name: alchemlyb
Version: 0.6.0
Summary: the simple alchemistry library
Home-page: UNKNOWN
Author: David Dotson
Author-email: dotsdl@gmail.com
Maintainer: Oliver Beckstein
Maintainer-email: orbeckst@gmail.com
License: BSD
Description: 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
        
        
Platform: UNKNOWN
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
Description-Content-Type: text/x-rst
