Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

dead kernel for example notebooks without openeye license #122

Open
schallerdavid opened this issue May 27, 2022 · 0 comments
Open

dead kernel for example notebooks without openeye license #122

schallerdavid opened this issue May 27, 2022 · 0 comments
Labels
bug Something isn't working documentation Improvements or additions to documentation

Comments

@schallerdavid
Copy link
Contributor

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 schallerdavid added bug Something isn't working documentation Improvements or additions to documentation labels May 27, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working documentation Improvements or additions to documentation
Projects
None yet
Development

No branches or pull requests

1 participant