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LBM-EPFL / PeSTo

Geometric deep learning method to predict protein binding interfaces from a protein structure.
https://pesto.epfl.ch
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PeSTo/md_analysis/data_manager /data_manager.py, "meta" does not exist #6

Closed rubenalv closed 1 month ago

rubenalv commented 1 year ago

I have tried to run PeSTo/md_analysis/apply_model_md.ipynb. The folder "model" does not exist here, but I copied it from the root directory. The from X import statements need to refer to "model."

In from CLoNe.clone import CLoNe "CLoNe" does not exist

The data "meta" does not exist, so the data_manager.py just throws a FileNotFoundError: [Errno 2] No such file or directory: 'database/meta'

Also, the symlink for directory datasets/ points to an non-existent location

Could you upload the data, for testing?

chiarinival commented 7 months ago

Hi Ruben!!!

We have faced the very same problem while attempting to run the "apply_model_md.ipynb" notebook. We encountered a keynote complaint in cell 7, probably linked to the missing "meta" file. As you, we created an ex-novo database folder under md_analysis and transferred there our .xtc and .pdb files.

I wonder, did you manage to solve the error since you last reported? Any feedback would be greatly apprecciated.

I share with you the last part of our error:

243 except KeyError as err: --> 244 raise UndefinedVariableError(key, is_local) from err UndefinedVariableError: name 'pdbid' is not defined

Thanks a lot,

Valerio

rubenalv commented 7 months ago

@chiarinival, I could not solve the actual error due to the missing directories, but I proposed a working solution here https://github.com/LBM-EPFL/PeSTo/issues/5 Unless you specifically want to run the apply_model_md.ipynb file, I would hope you can recreate that solution. Cheers, R