Colab? Update link in README.md.
fix_ligand_structure, etc., can be much simplified now. Might need to still add hydrogens for typing, but details not so important.
Be sure to remove existing charges.
Mention output is pK(affinity) somewhere. Output in terms of mM?
Need to add README.md. Done, but run through it from scratch to confirm works.
Need to update prepare_data/ files. Need to auto detect if user hasn't prepared that directory. Need to test. Perhaps move everyhting to train, organize scripts as best you can, but then say not supported.
To consider: at inference time, will users have to use gninatyper to prepare their molecules? That seems impractical.
What about centering the grid on the ligand center of geometry?
https://gnina.github.io/libmolgrid/python/index.html#the-gridmaker-class