RosettaCommons / RosettaCommons/foundry
[BUG]
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- Dominant language
- Python
- Stars
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- Forks
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- Avg merge
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- Merged PRs (30d)
- 2
Description
Describe the bug
When I want to introduce symmetry module into my json file, there are always some problems. I noticed that the hotspot and symmetry are in conflict. So I want to ask whether the parameters like select_exposed or buried and unindexed are in the range of hotspots.
To Reproduce
Please describe any:
- prepare the json file and pdb file, submit the files to predict
- system architectures (if relevant)
- structure files - if it refers to output file, there is a photo shown below.
- input file : a motif combined with dummy ligand and small molecule.
- errors:JSONDecodeError: Expecting property name enclosed in double quotes: line 19
column 9 (char 529)
Expected behavior
I will get protein structures with desired symmetry and ideal pocket to bury the small molecule.
Screenshots
I don't get valid output under symmetric condition.
But the following graph shows that the generated protein has a large percentage of disordered secondary structures.
Additional context
json file:
err file:
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 the attached symmetry.json.txt and 869663.txt files, checking the JSONDecodeError at line 19, column 9 and how the hotspot and symmetry parameters interact. Compare the requested symmetry and buried-pocket settings with the generated structure; done means the configuration parses and produces valid symmetric output with the intended pocket rather than the reported disordered result.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100