mohebifar / gromacswrapper

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.

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.

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.

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).

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

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/releases

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.

Building Documentation

Install Sphinx:

apt-get install python-sphinx

and compile:

cd package/doc/sphinx
make html

Citing

GromacsWrapper was written by Oliver Beckstein with contributions from many other people. Please see the file AUTHORS for all the names.

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 et al, http://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)"

or in the Acknowledgements section.

Thank you.