Metadata-Version: 1.1
Name: GromacsWrapper
Version: 0.4.0
Summary: A python wrapper around the gromacs tools.
Home-page: https://github.com/Becksteinlab/GromacsWrapper
Author: Oliver Beckstein
Author-email: orbeckst@gmail.com
License: GPLv3
Download-URL: https://github.com/Becksteinlab/GromacsWrapper/downloads
Description: .. -*- mode: rst -*-
        .. The whole GromacsWrapper package is Copyright (c) 2009,2010,2011,2012 Oliver Beckstein,
        .. except where noted otherwise.
        
        
        ========================
         README: GromacsWrapper
        ========================
        
        |zenodo|
        
        A primitive wrapper around the Gromacs tools until we have proper
        python bindings. It also provides a small library (cook book) of
        often-used recipes and an optional analysis module with plugins for
        more complicated analysis tasks.
        
        `Documentation`_ is mostly provided through the python doc strings and
        available at http://gromacswrapper.readthedocs.org for recent releases.
        
        The source code is available in the `GromacsWrapper git repository`_.
        
        Please be aware that this is **alpha** software that most definitely
        contains bugs. It is *your* responsibility to ensure that you are
        running simulations with sensible parameters.
        
        
        .. _Documentation: 
           http://gromacswrapper.readthedocs.org/en/latest/
        .. _GromacsWrapper git repository:
           http://github.com/Becksteinlab/GromacsWrapper
        .. |zenodo| image:: https://zenodo.org/badge/13219/Becksteinlab/GromacsWrapper.svg
           :target: https://zenodo.org/badge/latestdoi/13219/Becksteinlab/GromacsWrapper
           :alt: Latest release on zenodo (with DOI)
        
        Licence
        =======
        
        The **GromacsWrapper** package is made available under the terms of
        the `GNU Public License v3`_ (or any higher version at your choice)
        except as noted below. See the file COPYING for the licensing terms
        for all modules.
        
        The **vmd** module is made available under the `LGPL v3`_ (see COPYING
        and COPYING.LESSER). **numkit** is provided under the "`Modified BSD
        Licence`_" (as it contains some code from scipy_).
        
        .. _GNU Public License v3: http://www.gnu.org/licenses/gpl.html
        .. _LGPL v3: http://www.gnu.org/licenses/lgpl.html
        .. _Modified BSD Licence: http://www.opensource.org/licenses/bsd-license.php
        .. _scipy: http://www.scipy.org
        
        The distribution contains third party software that is copyrighted by
        the authors but distributed under licences compatible with this
        package license. Where permitted and necessary, software/files were
        modified to integrate with GromacsWrapper.
        
        
        Installation
        ============
        
        Releases
        --------
        
        The `latest version of GromacsWrapper from PyPi`_ and can be installed
        with ::
        
          pip install GromacsWrapper
        
        .. _`latest version of GromacsWrapper from PyPi`:
           https://pypi.python.org/pypi/GromacsWrapper
        
        Development version
        -------------------
        
        The *develop* branch in the GitHub source repository generally
        contains useful code but nevertheless, things can break in weird and
        wonderful ways. Please report issues through the `Issue Tracker`_ and
        mention that you used the *develop branch*.
        
        To use the *development code base*:  checkout the ``develop`` branch::
        
           git clone https://github.com/Becksteinlab/GromacsWrapper.git
           cd GromacsWrapper
           git checkout -b develop origin/develop
        
        and install ::
        
           python setup.py install
        
        
        
        
        Download and Availability
        =========================
        
        The GromacsWrapper home page is
        http://github.com/Becksteinlab/GromacsWrapper.  The latest release of the
        package is being made available from https://github.com/Becksteinlab/GromacsWrapper/tags
        
        You can also clone the `GromacsWrapper git repository`_ or fork for
        your own development::
        
          git clone git://github.com/Becksteinlab/GromacsWrapper.git
        
        
        Reporting Bugs and Contributing to GromacsWrapper
        =================================================
        
        Please use the `Issue Tracker`_ to report bugs, installation problems,
        and feature requests.
        
        **Pull requests** for bug fixes and enhancements are very welcome.
        
        .. _Issue Tracker: http://github.com/Becksteinlab/GromacsWrapper/issues
        
        
        Citing
        ======
        
        |zenodo|
        
        If you find this package useful and use it in published work I'd be
        grateful if it was acknowledged in text as
        
          "... used GromacsWrapper (Oliver Beckstein,
          http://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)"
        
        or in the Acknowledgements section.
        
        If you use the ``gridmatmd`` plugin also cite [Allen2009]_.
        
        Thank you.
        
        
        .. rubric:: References
        
        .. [Allen2009]   W. J. Allen, J. A. Lemkul, and D. R. Bevan. (2009)
                         "GridMAT-MD: A Grid-based Membrane Analysis Tool for
                         Use With Molecular Dynamics."  J. Comput. Chem. 30,
                         1952-1958.
        
        
        
Keywords: science Gromacs analysis 'molecular dynamics'
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
