morellik / p3d Goto Github PK

INTRODUCTION

p3d was developed in order to offer a Python module that is powerful and fast,
yet intuitive to use. The simplicity of p3d is due to the usage of object 
oriented programming (i.e. atoms are treated as vectors), the implementation 
of a query parser that translates queries readable by humans into a combination
of algebra set operations the fact that no additional Python packages are 
necessary. The speed is due to the usage of a binary space partitioning (BSP)
tree which allows very fast queries in 3D (Henry et al. 1980). The additional 
synergy is obtained by the flexible combination of both speed and complexity in
the queries to the structural data. The combination of these factors makes p3d
the optimal module to rapidly develop new and powerful bioinformatic tools that
follow the Python philosophy of making the source code readable.

For more information please visit 
http://p3d.fufezan.net or http://www.biomedcentral.com/1471-2105/10/258


CITATION

Please cite us when using p3d for your publications. 

Fufezan C., Specht M (2009) p3d, python module for structural bioinformatics. 
BMC Bioinformatics 10, 258.


INSTALLATION

python setup.py install

(you might need admin privileges to write in the python site-package folder)


PARTICIPATE

If you like to participate, simply checkout the source code from our git hub at
http://github.com/fu/p3d, hack in your changes and submit them to us.


DOCUMENTATION

For more in depth documentation of the modules and examples, please refer to
the wiki pages at http://p3d.fufezan.net