Scaffold Hopping

[sirine90]

Hello!

Thank you for sharing the code.

Could you please share an example how you do scaffold hopping (or scaffold elaboration/ fragment merging/ fragment growing).
I tried using the inpaint_ligand function, but it does not seem to work.

Thanks in advance :)

[Pang-chao]

Hello. I don't know if you have solved the problem. I just had the same problem. The problem is due to a wrong parameter in line 113 of the inpaint.py file.
That line should be changed to
ligand, pocket, lig_fixed, pocket_fixed,
At the same time, insert a new line below line 92.
pocket_fixed = torch.ones_like(pocket['mask'])
This line of code makes all the pocket nodes fixed during inpaint.