.. GromacsWrapper documentation master file, created by sphinx-quickstart on Tue Jun 23 19:38:56 2009.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

====================================================
  GromacsWrapper --- a Python framework for Gromacs
====================================================

:Release: |release|
:Date: |today|


**GromacsWrapper** is a Python package that wraps system calls to
Gromacs_ tools into thin classes. This allows for fairly seamless
integration of the gromacs tools into Python_ scripts. This is
generally superior to shell scripts because of Python's better error
handling and superior data structures. It also allows for
modularization and code re-use. In addition, commands, warnings and
errors are logged to a file so that there exists a complete history of
what has been done.

See :doc:`INSTALL` for download and installation instructions. `Documentation`_
is primarily provided through the Python doc strings (from which most of the
online documentation is generated).

The source code itself is available in the `GromacsWrapper git
repository`_.

.. warning:: Please be aware that this is **alpha** software that most
  definitely contains bugs. The API is not stable yet and can change
  between releases.
  
  It is *your* responsibility to ensure that you are running
  simulations with sensible parameters.

The package and the documentation are still in flux and any 
`feedback, bug reports, suggestions`_ and contributions are very welcome. See the
package :doc:`README` for contact details.

.. SeeAlso:: Other approaches to interfacing Python_ and Gromacs_
             are listed under :doc:`alternatives`.


.. _Gromacs: http://www.gromacs.org
.. _Python: http://www.python.org
.. _Documentation: http://becksteinlab.github.io/GromacsWrapper/
.. _GromacsWrapper git repository:
   http://github.com/Becksteinlab/GromacsWrapper
.. _feedback, bug reports, suggestions:
   http://github.com/Becksteinlab/GromacsWrapper/issues


Contents
--------

.. toctree::
   :maxdepth: 2

   installation
   configuration
   gromacs
   analysis
   auxiliary
   alternatives



Indices and tables
------------------

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

