Metadata-Version: 1.1
Name: GromacsWrapper
Version: 0.3.2
Summary: A python wrapper around the gromacs tools.
Home-page: ://github.com/orbeckst/GromacsWrapper
Author: Oliver Beckstein
Author-email: orbeckst@gmail.com
License: GPLv3
Download-URL: https://github.com/orbeckst/GromacsWrapper/downloads
Description: .. -*- mode: rst -*-
        .. The whole GromacsWrapper package is Copyright (c) 2009,2010,2011,2012 Oliver Beckstein,
        .. except where noted otherwise.
        
        
        ========================
         README: GromacsWrapper
        ========================
        
        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.
        
        
        See :doc:`INSTALL` for installation instructions. `Documentation`_ is
        mostly provided through the python doc strings. See `Download and
        Availability`_ for download instructions if the instructions in
        :doc:`INSTALL` are not sufficient.
        
        The source code is also 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://orbeckst.github.com/GromacsWrapper/index.html
        .. _GromacsWrapper git repository:
           http://github.com/orbeckst/GromacsWrapper
        
        
        
        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
        
        
        Included Software
        =================
        
        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.
        
        In case of problems please direct error reports to `Oliver Beckstein`_
        in the first instance as these bugs might not have been present in the
        original software or files.
        
        Included third party content:
        
        GridMat-MD
          - Grid-based Membrane Analysis Tool for use with Molecular Dynamics
            [Allen2009]_
          - version: 1.0.2
          - license: GPL 3.0  
          - 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 (12): 1952-1958.
          - http://bevanlab.biochem.vt.edu/GridMAT-MD/
        
        
        ``odict.py``
          - a simple implementation of an ordered dictionary as proposed in :pep:`0372`
          - copyright: (c) 2008 by Armin Ronacher and PEP 273 authors.
          - license: modified BSD license (`compatible with GPL`_)
          - http://dev.pocoo.org/hg/sandbox/raw-file/tip/odict.py
        
          .. _compatible with GPL: http://www.fsf.org/licensing/licenses/index_html
        
        ``gromacs.fileformats.preprocess``
          - The preprocessor is based on ``pypreprocessor.py`` from
            `pypreprocessor`_, release 0.4.0.
          - copyright: (c) 2010 Evan Plaice
          - license: MIT (`compatible with GPL`_)
          - http://code.google.com/p/pypreprocessor/
        
          .. _pypreprocessor: http://code.google.com/p/pypreprocessor/
        
        
        Citing
        ======
        
        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/orbeckst/GromacsWrapper)"
        
        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.
        
        
        
        
        Download and Availability
        =========================
        
        The GromacsWrapper home page is
        http://github.com/orbeckst/GromacsWrapper.  The latest release of the
        package is being made available from https://github.com/orbeckst/GromacsWrapper/tags
        
        You can also clone the `GromacsWrapper git repository`_ or fork for
        your own development::
        
          git clone git://github.com/orbeckst/GromacsWrapper.git
        
        
        
        Contact
        =======
        
        Please use the `Issue Tracker`_ to report bugs and feature requests;
        general feedback and inquiries can be sent to `Oliver Beckstein`_ by
        e-mail.
        
        .. _Issue Tracker: http://github.com/orbeckst/GromacsWrapper/issues
        .. _Oliver Beckstein: orbeckst@gmail.com
        
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
