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wells-wood-research / timed-design

Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis
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Resfix respredict #87

Closed sunal1996 closed 2 months ago

sunal1996 commented 4 months ago

We want to enable customized predictions coming out of TIMED. With this PR, the following can be rendered possible:

-Fixing certain aminoacid positions to the consensus aminoacid -Predicting only specific aminoacid positions and reverting rest to the consensus sequence. -Fix certain aminoacid positions to the desired aminoacid

Relevant README updates have been added.

sunal1996 commented 4 months ago

Fixed the types and added the exception handling to handle the following cases:

-If the user puts a chain that is not in the dataset -If the user tries using --chains_to_fix w/o --res_to_fix or vice versa -If the user tries using --chains_to_predict w/o res_to_predict or vice versa -If the user tries predicting and fixing a residue number at the same time

At the moment, sadly, all of these exceptions seem to be handled after TIMED makes the predictions. Would be good to make it before the prediction starts, this would be a problem for big datasets with lots of structures in it.

universvm commented 2 months ago

Closed in favor of other PR to come soon