rdk/biskit

A Python platform for Structural Bioinformatics

Biskit

a software platform for structural bioinformatics

Please refer to http://biskit.pasteur.fr for installation and usage instructions, troubleshooting and everything else!

Biskit is a modular, object-oriented python library that provides intuitive classes for many typical tasks of structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories. At the same time, Biskit offers a software platform for the rapid integration of external programs and new algorithms into complex structural bioinformatics workflows. Calculations are thus often delegated to established programs like Xplor, Amber, Hex, Prosa, and DelPhi; interfaces to further software can be added easily. Moreover, Biskit simplifies the parallelisation of calculations via PVM (Parallel Virtual Machine).

Short Installation Instructions

git clone https://github.com/graik/biskit.git biskit
pip install -r biskit/requirements.txt
pip install -e biskit

Replace git clone by the appropriate tar xvf *tgz command to start from an official Biskit release bundle.

Note: if not already available, this will automatically install numpy, scipy, and BioPython. It will not however install the biggles plotting package, which is not strictly required but highly recommended. pip install biggles now works but compilation depends on third-party libraries (plotutils, python-dev, libplot-dev). On Ubuntu / Debian, a pre-compiled biggles can instead also be installed with sudo apt-get install python-pybiggles (currently only for Python 2.x).

See http://biskit.pasteur.fr/install/short for step-by-step instructions on alternative installation methods.

License

Biskit is distributed under the GNU GPL version 3. See LICENSE.txt. Contact us, in case you prefer a different licensing model.