antibody.py: output_cter_constraint(base,prefix,decoy) inconsistently omits decoy information
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Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 52/100
- Issue type
- Bug
- Clarity
- Clearly specified
- Activity status
- Stale
- Tech stack
- python
- Domain
- bioinformatics, tooling
Research direction
Start in antibody/antibody.py at output_cter_constraint, especially the file creation near line 1286 and the output near line 1306; compare these with the decoy-dependent invocation near line 1246. Done means the generated text retains the correct decoy information for each invocation without overwriting another decoy's output.
Written by the indexing model from the issue text.
Description
Hello,
I found this while I was commenting all the functions in antibody.py, see pull request https://github.com/RosettaCommons/tools/pull/31 .
The function output_cter_constraint(base,prefix,decoy) is meant to add information in a text file for a separate tool to interpret and further improve a cognate .pdb file. The routine is passed a decoy number, but that information is not used in line
https://github.com/RosettaCommons/tools/blob/master/antibody/antibody.py#L1286
where the file is created. Consequently, since the invocation is clearly dependent on that decoy number on line
https://github.com/RosettaCommons/tools/blob/9db2953dea18ba008e8c738e71df4074a44e32b1/antibody/antibody.py#L1246
there is some information overwritten. The decoy also needs to be added here
https://github.com/RosettaCommons/tools/blob/9db2953dea18ba008e8c738e71df4074a44e32b1/antibody/antibody.py#L1306
Cheers,
Steffen
- Dominant language
- Python
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- 9
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- 4
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