Hi! Thanks for the great package — it's been super helpful!

I noticed that there's currently no option to apply transformations (e.g., PBC corrections) to the Universe objects before featurization. As a workaround, I’ve been pre-processing my trajectories to remove PBC artifacts and then feeding the modified .xtc files to PENSA. While this works, it’s a bit cumbersome and bypasses the powerful, on-the-fly transformation capabilities that MDAnalysis provides.

It would be great if there were an option to apply custom transformations to universes before the featurization step. This would make the workflow more flexible and let users account for PBC and other preprocessing steps directly in their pipelines.

Thanks again for the awesome work!