Contents of configuration file

[kjogr12]

Hi.

I would like to use this repository and I have a question.
When training, what should I write as settings in the types file?
ex. https://github.com/RMeli/gnina-torch/blob/main/tests/data/test.types

I reckon the first column is label information, the fourth and fifth columns are PDB and ligand information, but what are the second and third columns?

[RMeli]

Hello.
Sorry for the scarce documentation, but the repository is still very much WIP. The .types file you linked is a test file, therefore it contains all possible labels.

Currently gnina-torch supports the following combinations:

• Ligand pose prediction: you only need the pose label (--label_pos )
• Ligand pose and binding affinity prediction (multi-task): you need the pose label (--label_pos) and the affinity label (--affinity_pos)
• Ligand pose and flexible residues pose prediction (multi-task): you need the ligand pose label (--label_pos) and the flexible residues pose label (--flexlabel_pos)

The CLI arguments --label_pos (default 0), --affinity_pos (default 1), and --flexlabel_pos (experimental!) allow you to tell gnina-torch in which column of the .types file the different quantities are located.

The last point in particular is still very experimental and under development/study.

If you only want to train for pose prediction, the following format is sufficient for the .types file:

pose_label protein_file ligand_file

If you want to train for both pose and binding affinity prediction, you need to use the following format for the .types file:

pose_label binding_affinity protein_file ligand_file

[kjogr12]

Thank you for the detailed explanation.
I understand the arguments and how to specify them. Although it is WIP, I can do what I want to do now with the current features, so I will give it a try!