OpenFreeEnergy / OpenFreeEnergy/openfe
cli: Protein Parameter swallows error messages
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
From here:
https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/77
The actual error was a nonstandard residue in the PDB, this error message was swallowed by the strategy selector system in the CLI system however.
Ideally we'd have also seen the error message from the ProteinComponent.from_pdb call that was more informative
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the CLI strategy selector and the ProteinComponent.from_pdb call described in the issue, reproducing the nonstandard-residue case from ExampleNotebooks issue 77. Trace where the informative exception is caught or suppressed; done means the CLI exposes the underlying ProteinComponent.from_pdb error message to the user.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100