I think we should separate the discussion for
fine coarsening ( up to 5 residues)
coarse coarsening ( more than 5 residues).
For fine coarsening I think the helper function is fine and most
restraints would work will well with it.
I still have the question of why bother keeping consecutive residues
together? As far as I can tell, it produces uniformly worse results
than allowing them to be separate. Unless there is some advantage, it
isn't something that should be there.
Coarse coarsening, on the other hand, is needed mostly for flexible
chain representation for which we can not apply either of these
methods, as we do not have a structure, and so I think that for now
relaxing the restraints is sufficient.
It also makes sense in the case where you have structures of some of
the components, but not others and just want to preserve overall shape.