.. 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 ==================================================== **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://orbeckst.github.com/GromacsWrapper/index.html .. Note that the online source code documentaion is only infrequently .. updated. Please refer to the code on github in GromacsWrapper git repository. .. _online source code documentation: http://sbcb.bioch.ox.ac.uk/oliver/software/GromacsWrapper/epydoc/index.html .. _GromacsWrapper git repository: http://github.com/orbeckst/GromacsWrapper .. _feedback, bug reports, suggestions: http://github.com/orbeckst/GromacsWrapper/issues Contents -------- .. toctree:: :maxdepth: 2 installation gromacs analysis auxiliary alternatives Indices and tables ------------------ * :ref:`genindex` * :ref:`modindex` * :ref:`search`