As promised in part 1, this article will provide a Python script for processing the .json text file generated as output by the Residue Interaction Network Generator (RING) and then plot the data as a 3D protein structure network (PSN) using Plotly. In Part 1 we described in detail the workflow diagram shown below to generate a 3D PSN using Python scripts to process the RING generated json file. Because much of the code in Part 2 is similar in structure to Part 1, the reader should feel confident in simply copying and pasting the code into a .py file and running the script — very straightforward. The json file shown here can be generated using the steps described in Part 1 or you can download the text file from GitHub. Since this article is on the short side I will go into more detail as to what the code is doing. First, recall from part 1 that the .json contact network file referenced in this story was generated in the pipeline diagrammed below:
