A package for making graph representations of proteinstructures.
NOTICE: This package is going to be deprecated in favour of a peer-reviewed package,
get-contacts. Please use that package going forward.
Computes a molecular graph for protein structures.
Proteins fold into 3D structures, and have a natural graph representation: amino acids are nodes, and biochemical interactions are edges.
I wrote this package as part of a larger effort to do graph convolutional neural networks on protein structures (represented as graphs). However, that's not the only thing I can foresee doing with this.
One may be interested in the topology of proteins across species and over evolutionary time. This package can aid in answering this question.
how do I install this package?
$ pip install proteingraph
how do I use this package?
This package assumes that you have a standard protein structure file (e.g. a PDB file). This may be a file generated after solving the NMR or crystal structure of a protein, or it may be generated from homology modelling.
Once that has been generated, the molecular graph can be generated using Python code.
from proteingraph import ProteinInteractionNetwork p = ProteinInteractionNetwork('my_model.pdb')
ProteinInteractionNetwork class inherits from NetworkX's
Graph class, all methods that
Graph has are inherited by
ProteinInteractionNetwork, and it behaves just as a NetworkX graph does.
What this means is that all graph-theoretic metrics (e.g. degree centrality, betweenness centrality etc.) can be computed on the
See the HIV1 homology model example in the
examples/ directory for a minimal example.
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