PGT (Python GROMACS Toolkit)
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README.md

README.md

PGT (Python GROMACS Toolkit, version 0.1)

This is a toolbox written in Python to ease the work with GROMACS. It is documented via the docstring-feature of Python.

This toolkit is currently very much a work in progress and not to be considered being an end-product of any kind. Publication is done in hope to inspire / ease someone else's work or to help him/her not having to reinvent the wheel.

Most of the stuff implemented is directly related to my work as a grad student in the field of biomolecular dynamics. If you, however, find this stuff useful, implement further functionality, add comments or (most important) find bugs, feel free to contact me via email or github.

Cheers, Florian (www.lettis.net)

License

This software is licensed under the simplified BSD-License:

Copyright (c) 2012, Florian Sittel (www.lettis.net)

All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of the PGT project.

Prerequesites

* Python >= 2.7.X
* SciPy / Numpy
* pexpect (Python expect module)
* matplotlib
* python-sphinx (autodoc tool)