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dead kernel for example notebooks without openeye license

Open schallerdavid opened this issue 2 years ago • 0 comments

Using OpenEye code without license leads to dead kernels. It would be great if the example notebooks can also be run without a valid OpenEye license or at least display a warning instead of a dying kernel without any further information.

  • getting_started.ipynb - cell 5 -> no dead kernel, but without toolkit="MDAnalysis" not working
  • kinoml_object_model - cell 7 -> dead kernel, will also likely happen below
  • OpenEye_structural_featurizer -> I guess failing is fine here, still a warning would be nice
  • Schrodinger_structural_featurizer -> reports missing SCHRODINGER installation at the appropriate level

I added an OpenEye license check in the Protein object initialization. However, this does not get used when using the from_pdb and from_file method. So one could add the checks there as well or find a more general solution.

In any case, if you stumble over dead kernels and don't have a valid OpenEye license specify toolkit="MDAnalysis" when working with Protein objects and DataSetProviders.

schallerdavid avatar May 27 '22 15:05 schallerdavid