Voronoia

Downloads


Voronoia - Standalone Version 1.0
Voronoia - Pymol Version 1.0


Installation Guidelines

Windows Linux
Installing the standalone version on Windows
Unzip the Voronoia_1.0.zip archive. In the 'standalone' directory, 'Voronoia_GUI.exe' starts the graphical user interface. You can create a link icon on your Desktop for this one. 'Voronoia.exe' provides a command-line-tool, which is best used from a text console (in the Start Menu or by executing the 'cmd'). Just type 'Voronoia.exe' there to get the program options listed. The 'standalone' directory may be moved as a whole to another place.
Installing the PyMOL plugin on Windows
Unzip the Voronoia_1.0_pymol.zip archive. To use the PyMOL plugin, all contents of the 'plugin\startup' directory must be copied to the 'PYMOL_DIR\modules\pmg_tk\startup' directory. The Voronoia GUI then can be activated from the PyMOL 'Plugin' menu. Substitute 'PYMOL_DIR' by the location where PyMOL is installed on your machine, most probably 'C:\Program Files\DeLano Scientific\PyMOL\'. We recommend using the 0.99 Version of PyMOL or newer.

If you want Voronoia to start each time with PyMOL, change the AUTOMATICALLY_OPEN_PYMOL_PLUGIN variable in the startup/voronoia.py file.
Technical Notes
Voronoia consists of a core algorithm compiled from Delphi (in get_volume.exe) and a wrapper software written in Python. It uses the Pmw and PIL libraries. All front-ends (Windows/Linux/GUI/PyMOL/commandline) use the same modules. The executables for Windows have been compiled using Py2exe and distutils.

The source code archive contains the precompiled Delphi executable (data/get_volume.exe) and several Python source files. Voronoia.py and Voronoia_GUI.py are the relevant ones providing the basic functionality. For the algorithm in 'get_volume.exe' you will still require Wine on Linux.

To see the logo, the PIL library is necessary (therefore we made it optional).



When using this software, please cite:
     Rother K, Preissner R, Goede A, Froemmel C.
     Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins.
     Bioinformatics. 2003 Nov 1;19(16):2112-21.