bionoi

Conversion of biomolecules to Voronoi diagrams.

Description

bionoi constructs the voronoi diagram (VD) of protein binding site/pocket or ligand structure based on the 3D or 2D coordinate structure.

Requirements

1. Python 3
2. numpy 1.14+
3. scipy 0.18+
4. Pandas 0.19+
5. scikit-spatial 0.12.0
6. matplotlib 2.0.2+
7. biopandas ; eg : pip/conda install biopandas

Getting started

1. copy/download the code from GitHub
2. If input is a 3D coordinate of protein/ligand, it will be projected to 2D plane
3. Run voronoi.py with a .mol2 file (see Examples)

Examples

create a 2D image using mol2 file in 2D or 3D format

./voronoi.py
or
./voronoi.py -mol 4v94E.mol2 -out out.jpg -dpi 120 -alpha 0.5 -size 128

An example of voronoi image of ATP-binding site protein pocket colored by atom types:

chaperonin (4v94, chain E)

Contributors:

Rajiv Gandhi Govindaraj, Jeffrey Lemoine, Limeng Pu, Ye Fang and Michal Brylinski.