RosettaCommons / RosettaCommons/RFdiffusion
How to use the trb file in combination with ProteinMPNN
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- Python
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Description
Hi, RF diffusion team,
I am inpainting a protein with varied AA length.
For a fixed length of design, I can use --fixed_positions_jsonl function in ProteinMPNN.
For a varied length of designs, the .trb file outputs which residues were fixed during RFdiffusion nicely.
Is there a way I can fed this trb information to ProteinMPNN?
Contributor guide
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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 by reviewing the RFdiffusion documentation and the workflow around the .trb output, then compare it with ProteinMPNN's --fixed_positions_jsonl input. The issue does not name a file, test, or entry point, so first determine whether existing documentation or scripts describe converting residue information between the two tools. Done would be a documented, reproducible way to use varied-length fixed-residue information with ProteinMPNN.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100