RosettaCommons / RosettaCommons/foundry
[BUG] Residue and/or chain IDs not matching when using select_fixed_atoms constraint
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- Dominant language
- Python
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Description
At the start of a new batch - so some designs are created successfully - an assertion error is raised with this message:
File "/path/to/miniforge3/envs/foundry/lib/python3.12/site-packages/rfd3/trainer/trainer_utils.py", line 406, in process_unindexed_outputs
assert (res_id_ == res_id) & (chain_id_ == chain_id)
This also only seems to occur when specific atoms are chosen in the select_fixed_atoms constraint.
See full conversation in the Protein Design Slack.
In the chat linked above the user supplied files for an example that produces this error and error logs from his attempts.
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 process_unindexed_outputs in trainer_utils.py around line 406 and review the select_fixed_atoms constraint, using the example files and error logs linked in the Protein Design Slack conversation. Reproduce the residue or chain ID mismatch and confirm that the supplied example completes without the assertion.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100