I am confused about a particular part of the code

[demainchen]

Sorry, I don't know much about CPP, but I find you use it. I notice after I run the preprocessor. sh, some CPP programs are executed. Such a program will create some JSON files,I am confused about the context of these JSON files.
First, how you calculate the res_index? and why there so many atoms are the same with this index.
Second, for example [2,3] in the bonds part, I think it means protein 2 and protein 3 have PPI. If my idea is right, how you get it from the raw data? PDB files just tells us the basic information about the protein, but do not tell us the PPI information.
Third, I notice in the contacts part, all the contexts are 9-dimension arrays, I am confused about what's the mean. It looks like you don't mention it in your paper.
Sorry for disturbing you and my poor English! Thank you!