Metadata-Version: 2.4
Name: pmx_biobb
Version: 5.2.2
Summary: Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
Home-page: https://github.com/deGrootLab/pmx/tree/develop
Author: Daniel Seeliger, Vytautas Gapsys
Author-email: d.seeliger@gmx.net, vytautas.gapsys@gmail.com
License: LGPL-3.0
Classifier: Programming Language :: Python
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.9
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: matplotlib
Requires-Dist: rdkit
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license
Dynamic: license-file
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pmx: alchemistry in gromacs
===========================

|build| |cov|

**Warning:** this is a development version of ``pmx`` (`commit b8d83d0 <https://github.com/deGrootLab/pmx/tree/b8d83d0679b9728057c6ac18a04c86cebed72b47>`_), it is not stable or reliable yet. You are welcome to
try/test it and provide feedback, but use at your own risk. The current stable version of ``pmx`` can
be found in the master branch: https://github.com/deGrootLab/pmx

``pmx`` is a python library that allows users to setup and analyse molecular
dynamics simulations with the `Gromacs <http://gromacs.org>`_ package.
Among its main features are the setup and analysis of alchemical free energy
calculations for protein, nucleic acid, and small molecule mutations.

https://degrootlab.github.io/pmx/

Citations
---------
``pmx`` is a research software. If you make use of it in scientific publications, please cite the following papers::

    @article{Gapsys2015pmx,
        title = {pmx: Automated protein structure and topology
        generation for alchemical perturbations},
        author = {Gapsys, Vytautas and Michielssens, Servaas
        and Seeliger, Daniel and de Groot, Bert L.},
        journal = {Journal of Computational Chemistry},
        volume = {36},
        number = {5},
        pages = {348--354},
        year = {2015},
        doi = {10.1002/jcc.23804}
    }

    @article{Seeliger2010pmx,
        title = {Protein Thermostability Calculations Using
        Alchemical Free Energy Simulations},
        author = {Seeliger, Daniel and de Groot, Bert L.},
        journal = {Biophysical Journal},
        volume = {98},
        number = {10},
        pages = {2309--2316},
        year = {2010},
        doi = {10.1016/j.bpj.2010.01.051}
    }


License
-------
``pmx`` is licensed under the GNU Lesser General Public License v3.0 (LGPL v3).

.. |build| image:: https://travis-ci.org/deGrootLab/pmx.svg?branch=master
    :alt: Build Status
    :target: https://travis-ci.org/deGrootLab/pmx

.. |cov| image:: https://codecov.io/gh/deGrootLab/pmx/branch/develop/graph/badge.svg
    :alt: Code coverage
    :target: https://codecov.io/gh/deGrootLab/pmx
