sokrypton / sokrypton/ColabFold
batch.get_queries signature and bug in sorting
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Description
Expected Behavior
-
Sorting queries by sequence length in
batch.get_queriesshould work for multimers (i.e. should sort by total sequence length, not by number of monomer chains). -
The problem arises from multiple types allowed for
query_sequence(listfor multimers andstrfor monomers). That is also not correctly specified in the return type of thebatch.get_queriesfunction (onlystris listed, here).
Current Behavior
Multimers are sorted by number of chains and not by total sequence length, here.
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 in colabfold/batch.py at the get_queries definition around line 596 and the sorting logic around line 669. Inspect how query_sequence represents monomers and multimers, then verify that the return type documents both forms and that sorting uses total sequence length for multimers. Confirm the behavior with the relevant existing query-sorting checks, if present.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 48/100