Use MDAnalysis principal_axes() for single-UA molecules to prevent complex axes

[jkalayan]

Summary

Principal axes for molecules that were a single UA sometimes produced complex numbers when using the custom_principal_axes() function as the translational axes for forces added to the covariance matrices.

Changes

Change PA used for single UA molecules :

• Use the MDA principal_axes() function instead of the custom_principal_axes()

Update tests :

• Update tests to include the make_whole patch and remove redundant mocks

Impact

• Will fix bug that prevented forces to be translated for single UA molecules because some of these translational axes returned complex numbers when using the MOI tensor to get the PA.

[harryswift01]

This looks like a very clean fix. Using MDAnalysis’ principal_axes() for the single-UA case should prevent the complex axis issue from the custom MOI-based implementation, and it looks like the relevant tests have been updated accordingly. I’m happy to approve this, thank you!