Welcome to grip-tomo’s documentation!

GRaph Identification of Proteins in TOMOgrams (grip-tomo).

The package consists of 3 core modules:

• pdb2graph.py - converts a PDB structure into a graph network.

• density2graph.py - converts a 3D density to a graph.

• graph2class.py - measures graph features and classifies

For more example usage see the included tutorial nobook.

If you found this tool helpful or want more information please cite: “Graph identification of proteins in tomograms (GRIP-Tomo)” by August George, et al. Preprint DOI: https://doi.org/10.48550/arXiv.2210.08194

Contents:

• pdb2graph module
  • PDB_df_to_G()
  • PDB_to_df()
  • get_hydrophobicity()
  • main()
  • plot_FA_and_CA_coordinates()
  • plot_coordinates()
  • save_data()
  • save_data_at_this_folder()
• density2graph module
  • add_Gaussian_noise()
  • cluster_data()
  • create_and_save_graph()
  • get_cluster_centroids()
  • load_density_file()
  • main()
  • normalize_and_threshold_data()
  • plot_clustering_results()
• graph2class module
  • calc_bc()
  • calc_graph_features()
  • calc_shortest_pthlen()
  • calc_similarity_score()
  • classify_graphs()
  • process_graphs()
  • process_similarity_df()
  • similarity_measure()

Indices and tables

• Index

• Module Index

• Search Page