Partial diffusion

[ulysse06]

Amazing project!

I would like to apply this tool for my research but I couldn't find an easy way to perform controlled partial diffusion with protpardelle. (I have been doing it with RFdiffusion until now)
Is it something that could be achieved or that you would eventually consider implementing?

[alexechu]

Thanks! You can definitely perform "partial diffusion" with protpardelle - for now as a hack, you could probably use the model.sample() function (with the default sampling configs) to do this: set the gt_coords and gt_cond_atom_mask to your input coordinates, and set apply_cond_proportion=0.8 for example to only generate for the last 20% of the reverse diffusion. You can do this with the aatype as well to fix the sequence up until the last 20%. We'll definitely look to add this as a more convenient feature in future updates.