OpenFreeEnergy / OpenFreeEnergy/openfe

CLI does not properly return PDB parsing errors

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#1,335 3 comments 0 reactions 1 assignee View on GitHub

@atravitz is already working on this.

Since Jun 3, 2025.

cli usability
Dominant language
Python
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332
Forks
56
Avg merge
3d 9h
Merged PRs (30d)
13

Description

If you load a bad PDB and ProteinComponent.from_pdb_file fails, the CLI will automatically catch the ValueError and try to load from PDBx instead. Since you are still attempting to read a PDB file, this both suppresses the error message from PDB reading and yields a very unspecific PDBx reading error. This is an issue for users since they can't debug why their systems aren't working.

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