RosettaCommons / RosettaCommons/RFdiffusion
Partial diffusion errors
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- Python
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Description
Hello, I've bumped into a contig error when doing partial diffusion of a PDB composed of chains 'A' and 'B'
When I want to keep fixed chain A but diffuse some residues in chain B by using this contigs code [A1-124/0 B1-2/3-3/B6-121], I get this error:
AssertionError: for partial diffusion there can be no offset between the index of a residue in the input and the index of the residue in the output
However, I can run the partial diffusion without any problem if I diffuse a random residue in chain A: [A1-123/1-1/0 B1-2/3-3/B6-121]
I can also run this: [A1-124/0 B1-121]
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First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the assertion with the reported contigs for chains A and B, then compare it with the two partial-diffusion cases that succeed. Trace the partial-diffusion handling of residue indices and offsets; done means the failing contig runs successfully without breaking the existing successful cases.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100