Skip to main content

A package for making graph representations of proteinstructures.

Project description

# protein-graph

Computes a molecular graph for protein structures.

## why?

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 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.

```python
from pin import ProteinInteractionNetwork

p = pin.ProteinInteractionNetwork('my_model.pdb')
```

Because the `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 `ProteinInteractionNetwork` object.

See the HIV1 homology model example in the `examples/` directory for a minimal example.


Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

proteingraph-0.1.1.tar.gz (2.9 kB view hashes)

Uploaded Source

Built Distribution

proteingraph-0.1.1-py3-none-any.whl (3.6 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page