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        "author": "Eric J. Ma",
        "author_email": "ericmajinglong@gmail.com",
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        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
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            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
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        "description": "NOTICE: This package is going to be deprecated in favour of a peer-reviewed package, [`get-contacts`](https://getcontacts.github.io/). Please use that package going forward.\n\n# protein-graph\n\nComputes a molecular graph for protein structures.\n\n## why?\n\nProteins fold into 3D structures, and have a natural graph representation: amino acids are nodes, and biochemical interactions are edges.\n\nI 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.\n\nOne may be interested in the topology of proteins across species and over evolutionary time. This package can aid in answering this question.\n\n## how do I install this package?\n\nCurrently only `pip`-installable:\n\n```bash\n$ pip install proteingraph\n```\n\n## how do I use this package?\n\nThis 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.\n\nOnce that has been generated, the molecular graph can be generated using Python code.\n\n```python\nfrom proteingraph import ProteinInteractionNetwork\n\np = ProteinInteractionNetwork('my_model.pdb')\n```\n\nBecause 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.\n\nWhat this means is that all graph-theoretic metrics (e.g. degree centrality, betweenness centrality etc.) can be computed on the `ProteinInteractionNetwork` object.\n\nSee the HIV1 homology model example in the `examples/` directory for a minimal example.\n\n\n",
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        "keywords": "protein,biochemistry,structural biology,graph theory",
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