A program for visualizing gnina's protein-ligand affinity scoring.
Gnina can be found at: https://github.com/gnina/gnina
This functionality will eventually be integrated into gnina.

removal.py generates .pdb files with the necessary information stored in the b-factor fields.
visualize.py is a script that can be run within PyMol to color the relevant molecules according to their b-factor scores.

1. Run removal.py to generate the output .pdb files.
   It requires gnina to be installed, and you will have to modify the path to gnina within removal.py, as it is hard-coded.

2. Open the output files in PyMol.

3. Run visualize command.

To use visualize.py, run the following command in PyMol:

run /path/to/visualize.py

This will add the visualize command to pymol.

Its usage is pretty straightforward:

visualize ligand_name, receptor_name

This will color the atoms in both molecules according to their b-factor score, with green representing a positive contribution to the CNN score, and red representing a negative contribution.