GRIP-Tomo: GRaph Identification of Proteins in Tomograms

A pipeline to help identify and classify structures in tomography data using global and local topological (network) features.

The package consists of 3 core modules:

1. pdb2graph.py - converts a PDB structure into a graph network.
2. density2graph.py - converts a 3D density to a graph.
3. graph2class.py - measures graph features and classifies

Documentation

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Quickstart guide:

0. open terminal / command prompt
1. clone the repository: git clone https://github.com/EMSL-Computing/grip-tomo
2. install the dependencies: pip install -r /path/to/requirements.txt
3. run tests: cd path/to/grip_tomo/ then python _test_basic.py
4. review example notebook, grip_tomo/example_notebook.ipynb
   • To interact with .ipynb files install Jupyter-lab

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Citation

Please cite our publication and accompanying software if you use it:

George, A, Kim, DN, Moser, T, Gildea, IT, Evans, JE, Cheung, MS. Graph identification of proteins in tomograms (GRIP-Tomo). Protein Science. 2023; 32( 1):e4538. https://doi.org/10.1002/pro.4538

George, A, Kim, DN, Moser, T, Gildea, IT, Evans, JE, Cheung, MS. EMSL-Computing/grip-tomo: Version 1.0. Zenodo; 2023. https://doi.org/10.5281/zenodo.17127842

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See the included license and disclaimer files

August George, PNNL, 2022