[Feedback] Redesign Specific Residues only about timed-design HOT 2 OPEN

Working on it at the moment. Managed to implement it for single structures and single chains, and there is a clear path for doing it for multiple structures. However, what if the user wants to specifically fix residues in chain B, C, D etc.? It appears to me that the chain information gets lost when we generate frame datasets, and TIMED puts everything into chain A. If this is correct, I think it gives us two paths:

a) User has to accept that instead of specifying the chain B 15th residue, they will have to specify X+15th residue where X is the length of chain A. Or, if they want to change chain D 3rd residue, they will have to specify the X+Y+Z+3rd residue where X-Y-Z are the lengths of chain A-B-C
b) We will have to figure out a way to not lose this information in frame generation. Later, instead of TIMED outputting the sequence into just one chain (x_A where x is the protein name and A is chain A), maybe it should give x_A, x_B, x_C separately for each chain.

Thoughts? @universvm

from timed-design.

@sunal1996 Output should include chains as we store them in the frames. This is likely a bug #79 . Once that's fixed we should be able to use your implementation :)

from timed-design.