microsoft / microsoft/foldingdiff
Error when calculating Maximum training similarity TM scores
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Description
After generating the sampled_pdb and running the bin/tmscore_training.py, the following error always occurs:
File "~/foldingdiff/foldingdiff/tmalign.py", line 54, in run_tmalign
return results_dict["Chain_2"] # Normalize by reference length
KeyError: 'Chain_2'
After handling this with exception, I find that no sequence contains this key. And the warning of Cannot parse file: ~/foldingdiff/data/cath/dompdb/2qe7G01. Chain number 0. also appears for each pdb file.
May I ask which part I might have missed or is there a bug the the data/code?
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Research direction
Run bin/tmscore_training.py after generating sampled_pdb and reproduce the KeyError in foldingdiff/tmalign.py at run_tmalign. Inspect the warning for data/cath/dompdb/2qe7G01 and the TM-score parsing path to determine whether the input data or code causes the missing Chain_2 entry. Done means identifying and resolving the cause across the affected PDB files.
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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
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100