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in af2_initial_guess/predict.py PDB mode skips checkpoints due to inconsistent naming in self.finished_structs #86

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xuqiqin opened this issue Jul 25, 2024 · 2 comments

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@xuqiqin
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xuqiqin commented Jul 25, 2024

When using pdb as input in af2_binder_design, the checkpoints are skipped due to a mismatch in naming conventions. The full pdb name is added to self.finished_structs, but the checkpoint check is performed using the tag name. Storing tag name to self.finished_structs fix the issue.

@Dan-Burns
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I'm having an issue where predict.py crashes a quarter of the way through the input pdbs folder and then when I restart it, it appears to ignore the checkpoint. Can you provide a little more detail on how you fix this? I can't find any scripts that contain a "finished_structs" method.

@alirezaomidi
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You can use this little tweak before every proteinmpnn run. This will fix the file:

awk -F/ '{split($NF, name, "."); print name[1]}' check.point > temp && mv temp check.point

A better way is to fix the bug in codebase.

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