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    "info": {
        "author": "Oliver Beckstein",
        "author_email": "orbeckst@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License (GPL)",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: POSIX",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Chemistry",
            "Topic :: Software Development :: Libraries :: Python Modules"
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        "description": ".. -*- mode: rst, coding: utf-8 -*-\n.. The whole GromacsWrapper package is Copyright (c) 2009-2018 Oliver\n.. Beckstein and AUTHORS except where noted otherwise.\n\n\n========================\n README: GromacsWrapper\n========================\n\n|build| |cov| |docs| |zenodo| |PRsWelcome|\n\nA primitive Python wrapper around the Gromacs_ tools. The library is\ntested with Gromacs 4.6.5, 2018.x, 2019.x (and 2016.x also works) and\nis tested with Python 2.7 and 3.6.\n\nGromacsWrapper also provides a small library (cook book) of often-used\nrecipes and helper functions to set up MD simulations.\n\n`Documentation`_ is mostly provided through the python doc strings and\navailable at https://gromacswrapper.readthedocs.org for recent releases.\n\nThe source code is available in the `GromacsWrapper git repository`_.\n\nPlease be aware that this is **beta** software that most definitely\ncontains bugs. It is *your* responsibility to ensure that you are\nrunning simulations with sensible parameters.\n\n.. _Gromacs: http://www.gromacs.org\n.. _Documentation: \n   https://gromacswrapper.readthedocs.org/en/latest/\n.. _GromacsWrapper git repository:\n   https://github.com/Becksteinlab/GromacsWrapper\n.. |build| image:: https://travis-ci.org/Becksteinlab/GromacsWrapper.svg\n   :target: https://travis-ci.org/Becksteinlab/GromacsWrapper\n   :alt: Build Status\n.. |cov| image:: https://codecov.io/gh/Becksteinlab/GromacsWrapper/badge.svg\n   :target: https://codecov.io/gh/Becksteinlab/GromacsWrapper\n   :alt: Code Coverage\n   :scale: 100%\n.. |zenodo| image:: https://zenodo.org/badge/13219/Becksteinlab/GromacsWrapper.svg\n   :target: https://zenodo.org/badge/latestdoi/13219/Becksteinlab/GromacsWrapper\n   :alt: Latest release on zenodo (with DOI)\n.. |docs| image:: https://readthedocs.org/projects/gromacswrapper/badge/?version=latest\n   :target: https://gromacswrapper.readthedocs.org/en/latest/?badge=latest\n   :alt: Documentation\n.. |PRsWelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg\n   :target: http://makeapullrequest.com\n   :alt: PRs Welcome!\n\nQuick Start\n===========\n\nGiven a PDB file ``1iee.pdb``, set up and run a simple simulation (assuming\nyou have all other input files at hand such as the MDP files)::\n\n  >>> import gromacs\n  >>> print(gromacs.release)\n  2018.2\n  >>> help(gromacs.pdb2gmx)\n  DESCRIPTION\n\n  gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files,\n  adds hydrogens to the molecules and generates coordinates in GROMACS\n  ...\n  ...\n  OPTIONS\n\n  Options to specify input files:\n\n  -f      [<.gro/.g96/...>]  (eiwit.pdb)\n            Structure file: gro g96 pdb brk ent esp tpr\n  ...\n  ...\n  >>> gromacs.pdb2gmx(f=\"1ake.pdb\", o=\"protein.gro\", p=\"topol.top\",\n  ...                 ff=\"oplsaa\", water=\"tip4p\")\n  >>> gromacs.editconf(f=\"protein.gro\", o=\"boxed.gro\",\n  ...                  bt=\"dodecahedron\", d=1.5, princ=True,\n  ...                  input=\"Protein\")\n  >>> gromacs.solvate(cp=\"boxed.gro\", cs=\"tip4p\", p=\"topol.top\",\n  ...                 o=\"solvated.gro\")\n  >>> gromacs.grompp(f=\"emin.mdp\", c=\"solvated.gro\", p=\"topol.top\",\n  ...                o=\"emin.tpr\")\n  >>> gromacs.mdrun(v=True, deffnm=\"emin\")\n  >>> gromacs.grompp(f=\"md.mdp\", c=\"md.gro\", p=\"topol.top\", o=\"md.tpr\")\n  >>> gromacs.mdrun(v=True, deffnm=\"md\")\n\n\n\nLicense\n=======\n\nThe **GromacsWrapper** package is made available under the terms of\nthe `GNU Public License v3`_ (or any higher version at your choice)\nexcept as noted below. See the file COPYING for the licensing terms\nfor all modules.\n\n.. _GNU Public License v3: http://www.gnu.org/licenses/gpl.html\n\nThe distribution contains third party software that is copyrighted by\nthe authors but distributed under licences compatible with this\npackage license. Where permitted and necessary, software/files were\nmodified to integrate with GromacsWrapper.\n\n\nInstallation\n============\n\nReleases\n--------\n\nThe `latest version of GromacsWrapper from PyPi`_ and can be installed\nwith ::\n\n  pip install GromacsWrapper\n\n.. _`latest version of GromacsWrapper from PyPi`:\n   https://pypi.org/project/GromacsWrapper/\n\nDevelopment version\n-------------------\n\nThe *master* branch in the GitHub source repository generally\ncontains useful code but nevertheless, things can break in weird and\nwonderful ways. Please report issues through the `Issue Tracker`_ and\nmention that you used the *develop branch*.\n\nTo use the *development code base*:  checkout the ``master`` branch::\n\n   git clone https://github.com/Becksteinlab/GromacsWrapper.git\n   cd GromacsWrapper\n\nand install ::\n\n   python setup.py install\n\n\n\n\nDownload and Availability\n=========================\n\nThe GromacsWrapper home page is\nhttp://github.com/Becksteinlab/GromacsWrapper.  The latest release of the\npackage is being made available from https://github.com/Becksteinlab/GromacsWrapper/releases\n\nYou can also clone the `GromacsWrapper git repository`_ or fork for\nyour own development::\n\n  git clone git://github.com/Becksteinlab/GromacsWrapper.git\n\nQuestions\n=========\n\nPlease ask questions in the `Issue Tracker`_ (instead of private email).\n\n\nReporting Bugs and Contributing to GromacsWrapper\n=================================================\n\nPlease use the `Issue Tracker`_ to report bugs, installation problems,\nand feature requests.\n\n**Pull requests** for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a \ngeneral introduction on how make a pull request and contribute to open source projects.\n\n.. _Issue Tracker: http://github.com/Becksteinlab/GromacsWrapper/issues\n\n\nBuilding Documentation\n======================\n\nInstall Sphinx::\n\n   pip install sphinx\n\nand compile::\n\n   cd package/doc/sphinx\n   make html\n\n\nCiting\n======\n\n|zenodo|\n\nGromacsWrapper was written by Oliver Beckstein with contributions from\nmany other people. Please see the file AUTHORS_ for all the names.\n\nIf you find this package useful and use it in published work I'd be\ngrateful if it was acknowledged in text as\n\n  \"... used GromacsWrapper (Oliver Beckstein et al,\n  https://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)\"\n\nor in the Acknowledgements section.\n\nThank you.\n\n.. _AUTHORS:\n   https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/master/AUTHORS\n\n\n\n",
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