pmx: alchemistry in gromacs
===========================
|build| |cov|
**PMX_BIOBB DISTRIBUTION VERSION**: 2.0.0
**Based on the PMX Icolos branch commit**: https://github.com/deGrootLab/pmx/commit/80f4f8a1552c37e3d926f950d91db77cd4dea9cf
**Warning:** this is a development version of ``pmx``, 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
:scale: 100%
:target: https://travis-ci.org/deGrootLab/pmx
.. |cov| image:: https://codecov.io/gh/deGrootLab/pmx/branch/develop/graph/badge.svg
:alt: Code coverage
:scale: 100%
:target: https://codecov.io/gh/deGrootLab/pmx
Raw data
{
"_id": null,
"home_page": "https://github.com/deGrootLab/pmx/tree/develop",
"name": "pmx-biobb",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": "",
"keywords": "",
"author": "Daniel Seeliger",
"author_email": "seeliger.biosoft@gmail.de",
"download_url": "https://files.pythonhosted.org/packages/6f/b2/61607c93aa5d3c34838e44ed7df748137d3b266a06a32b6d521a19ddedb4/pmx_biobb-3.0.3.tar.gz",
"platform": null,
"description": "pmx: alchemistry in gromacs\n===========================\n\n|build| |cov|\n\n**PMX_BIOBB DISTRIBUTION VERSION**: 2.0.0\n**Based on the PMX Icolos branch commit**: https://github.com/deGrootLab/pmx/commit/80f4f8a1552c37e3d926f950d91db77cd4dea9cf\n\n**Warning:** this is a development version of ``pmx``, it is not stable or reliable yet. You are welcome to\ntry/test it and provide feedback, but use at your own risk. The current stable version of ``pmx`` can\nbe found in the master branch: https://github.com/deGrootLab/pmx\n\n``pmx`` is a python library that allows users to setup and analyse molecular\ndynamics simulations with the `Gromacs <http://gromacs.org>`_ package.\nAmong its main features are the setup and analysis of alchemical free energy\ncalculations for protein, nucleic acid, and small molecule mutations.\n\nhttps://degrootlab.github.io/pmx/\n\nCitations\n---------\n``pmx`` is a research software. If you make use of it in scientific publications, please cite the following papers::\n\n @article{Gapsys2015pmx,\n title = {pmx: Automated protein structure and topology\n generation for alchemical perturbations},\n author = {Gapsys, Vytautas and Michielssens, Servaas\n and Seeliger, Daniel and de Groot, Bert L.},\n journal = {Journal of Computational Chemistry},\n volume = {36},\n number = {5},\n pages = {348--354},\n year = {2015},\n doi = {10.1002/jcc.23804}\n }\n\n @article{Seeliger2010pmx,\n title = {Protein Thermostability Calculations Using\n Alchemical Free Energy Simulations},\n author = {Seeliger, Daniel and de Groot, Bert L.},\n journal = {Biophysical Journal},\n volume = {98},\n number = {10},\n pages = {2309--2316},\n year = {2010},\n doi = {10.1016/j.bpj.2010.01.051}\n }\n\n\nLicense\n-------\n``pmx`` is licensed under the GNU Lesser General Public License v3.0 (LGPL v3).\n\n.. |build| image:: https://travis-ci.org/deGrootLab/pmx.svg?branch=master\n :alt: Build Status\n :scale: 100%\n :target: https://travis-ci.org/deGrootLab/pmx\n\n.. |cov| image:: https://codecov.io/gh/deGrootLab/pmx/branch/develop/graph/badge.svg\n :alt: Code coverage\n :scale: 100%\n :target: https://codecov.io/gh/deGrootLab/pmx\n\n\n",
"bugtrack_url": null,
"license": "GPL 3",
"summary": "Toolkit for free-energy calculation setup/analysis and biomolecular structure handling",
"version": "3.0.3",
"project_urls": {
"Homepage": "https://github.com/deGrootLab/pmx/tree/develop"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "8a703744fd3fd4d13d0fcd04c50740aa9584ba6c5b7eb43e1a4dd65a7c223cf2",
"md5": "bdd2945ebdc7c5bf444c772ce3dc99d5",
"sha256": "31b89ebbbdc319f2d60989786809c57fc899cdd22759036bc7aa1e05ee67e9e1"
},
"downloads": -1,
"filename": "pmx_biobb-3.0.3-cp37-cp37m-macosx_10_9_x86_64.whl",
"has_sig": false,
"md5_digest": "bdd2945ebdc7c5bf444c772ce3dc99d5",
"packagetype": "bdist_wheel",
"python_version": "cp37",
"requires_python": ">=3.7",
"size": 5822575,
"upload_time": "2023-05-26T10:34:43",
"upload_time_iso_8601": "2023-05-26T10:34:43.666127Z",
"url": "https://files.pythonhosted.org/packages/8a/70/3744fd3fd4d13d0fcd04c50740aa9584ba6c5b7eb43e1a4dd65a7c223cf2/pmx_biobb-3.0.3-cp37-cp37m-macosx_10_9_x86_64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "6fb261607c93aa5d3c34838e44ed7df748137d3b266a06a32b6d521a19ddedb4",
"md5": "947cc6aaa6ea2c597d6cdcdcead7a8da",
"sha256": "09f90d49519ccfdc1b60aa83d38ca2c32a038133416a5bf4043ecd80b5886db0"
},
"downloads": -1,
"filename": "pmx_biobb-3.0.3.tar.gz",
"has_sig": false,
"md5_digest": "947cc6aaa6ea2c597d6cdcdcead7a8da",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 5332938,
"upload_time": "2023-05-26T10:34:47",
"upload_time_iso_8601": "2023-05-26T10:34:47.791994Z",
"url": "https://files.pythonhosted.org/packages/6f/b2/61607c93aa5d3c34838e44ed7df748137d3b266a06a32b6d521a19ddedb4/pmx_biobb-3.0.3.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-05-26 10:34:47",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "deGrootLab",
"github_project": "pmx",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "pmx-biobb"
}
JSON
