generation of pickle file

[amrhamedp]

Hi,
where is the script that generates the pickle file? It is interesting to know cause it will affect much the size of the graph. I can see that the protein atoms in your files have small number of atoms so what was the cutoff used to get those atoms and are they selected from native pose only or differ according to the docked pose?

[jaechanglim]

Each pickle file is a tuple of two RDKit molecule objects. Each RDKit object corresponds to a ligand and protein. As you pointed, the protein has a large number of atoms, so we chose protein atoms close to the docked ligand. So the selected protein atoms vary depending on 3D binding structures of the ligand. The criteria is 8 angstrom.