Improve LocalRelax to work with DNA and be non-directional (#4971)
I had a complex I wanted to use LocalRelax on but because of the directionality code it was incompatible with DNA.
These changes remove the directionality, but allow non-protein residues to work with this code!
I also updated a few XRW_TODO comments, and compared this to the previous implementation.
compared to the previous LocalRelax, this code packs slightly more residues at a time (from ~140 -> ~200) but keeps approximately the same number of residues minimzing at each step (~50).
K used to be some function of the distance between two CA/CB residues * directionality parameters * 0.28. now it's just based on the NBR_radius so it's triggered when the distance between two nbr atoms is <= nbr_radius_1 + nbr_radius_2.
That's what I found to make the # residues that minimize/pack the most similar to the old version