LeafletFinder Removal in MDAnalysis 3.0.0

[m-a-r-i-u-s]

Is your feature request related to a problem?

The LeafletFinder function will be removed in MDAnalysis 3.0.0 (see https://github.com/MDAnalysis/mdanalysis/issues/4544#issue-2216069497)

Describe the solution you'd like

DomHMM's core functionality is not, and should be not, leaflet identification. The flipping of phospholipids happens only rarely on MD relevant time scales. I would suggest that users should provide their own leaflet assignments by default. However, we have the code for automatically leaflet assignment already at hand. We could therefore offer this as an option that must be explicitly triggered by the user.

I would suggest this workflow

• User-defined leaflet selection (default) -> No update of leaflets (default) / Update leaflets every n steps (non-default)

• Automatic leaflet selection (non-default) -> No update of leaflets (default) / Update leaflets every n steps (non-default)

• [ ] User-defined leaflet selection as default option.

• [ ] Automatic leaflet assignment must be explicitly triggered.

• [ ] Add implementation of LeafletFinder.

[yusuferentunc]

In the MDAnalysis issue, they redirect users to use a MDAKits implementation for LeafletFinder https://lipyds.readthedocs.io/en/latest/leafletfinder.html

However, that kit's implementation doesn't seem robust for current time