sokrypton / sokrypton/ColabFold
colabfold_search without an index and --db-load-mode
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Description
Hi All,
I see that colabfold_search hardcodes --db-load-mode to 0 if there is no index (.idx files) present.
Is there a particular reason for this?
Running with a GPU, I see a substantial speedup if I hack search.py to use --db-load-mode 2, even though the index is not present.
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 search.py and trace how colabfold_search selects --db-load-mode when .idx files are absent. Compare the existing mode 0 path with mode 2 on a GPU, then verify the expected behavior with representative searches; done means the rationale and supported behavior are clear and the observed speedup or any limitation is covered.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100