mgm79 / biographs

Python class to easily deal with protein networks.

biographs: Amino acid networks in Python

What is biographs?

Biographs is a python module converting structural files formats like pdb or cif into amino acid networks. It is written over the packages biopython and networkx. This allows for a flexible and powerful handling of both: protein networks and protein structures.

Notably biographs uses the great Bio.PDB module to construct the network given a cutoff distance. Here, the network is a networkx.Graph object, which allows high customization of the network and tons of tools for networks analysis.

To use biographs just type in a terminal:

	$ git clone https://github.com/rodogi/biographs.git

Here is an example to build the amino acid network of the cholera toxin (PDB id: 1eei):

import biographs as bg

molecule = bg.Pmolecule('1eei.pdb')
network = molecule.network()
network.nodes()[:10]
['G26', 'G27', 'G24', 'G25', 'G22', 'G23', 'G20', 'G21', 'G28', 'G29']

Required packages

biopython Great to read and work with structure files such as pdb found in the protein data bank. You can listen to the voices of three of the main contributors of biopython in this podcast.

networkx Has an extensive set of functions to deal with networks.

scipy Mainstream package for scientific computation, here used mainly for numpy and geometrical algorithms.