Error: create_conditional_graphs_from_files() got an unexpected keyword argument 'pocket_definition'

[spyda90]

Hi,

I've tryed the the new mol2pharm script and it works fine.
The JSON is readble and easy to be edited with the "enabled" keyword. Thank you.

I am now running new generation using --task fixed_protein_pharmacophore_ligand_denovo_condensed. I see that now the options are slightly different, since the task is asking for option --pocket_ligand instead of --ligand_file. However, I am encountering the following error.

Error: create_conditional_graphs_from_files() got an unexpected keyword argument 'pocket_definition'

I have never encountered such an error with the previous version.

Thank you in advance.

[ras425]

Hi! I’m not able to recreate this error; it might be a version mismatch. Try running pip install -e . and if that doesn’t fix it, let me know the full command you are running. Thanks!

[spyda90]

Hi,

Thank you for following this.

Running pip install -e . the output is:

Installing collected packages: omtra
  Attempting uninstall: omtra
    Found existing installation: omtra 0.0.0
    Uninstalling omtra-0.0.0:
      Successfully uninstalled omtra-0.0.0
Successfully installed omtra-0.0.0

Is that correct?

Btw, the command line I am running is the following:
omtra --task fixed_protein_pharmacophore_ligand_denovo_condensed --protein_file proteins/protein.pdb --pocket_ligand reference_ligands/ligand_from_x-ray.sdf --pharmacophore_file pharmacophore/pharmacophore.json --n_samples 100 --output_dir outputs/fixed_protein_pharmacophore_ligand_denovo_condensed___pharmacophore

[Dunni3]

That's correct. Can you confirm your sampling command still breaks?

[spyda90]

Yes, it is. Can you reproduce the same error?

[spyda90]

Any news? Thank you!

[Dunni3]

@ras425 can you reproduce that example command?

Apologies for the delay. Defending my thesis tomorrow :) will be more active in the coming weeks!

[ras425]

Hi, I still can't reproduce the error with that command. Check if python -c "import omtra; print(omtra.__file__)" points to your local OMTRA repo. If not you could try python -m pip uninstall omtra -y and then python -m pip install -e .
You could also try find . -name "*.pyc" -delete to clear cached python files just in case. Let me know if this helps!

[spyda90]

Thank you both and good luck for the thesis defense!
Next week we will try to make a clean reinstall of the current version and let you know.

Best