Merge pull request #1856 from RosettaCommons/aleaverfay/close_contact_selector
New neighborhood selector using atom-pair distances
My other residue selector, the NeighborhoodResidueSelector, uses the same logic that the packer uses to decide neighbor relationships. Namely: under any rotamer assignment for two residues, would they interact? It does this by considering each residue as a sphere centered at the neighbor atom (e.g. cbeta), and then asking are the spheres get within the interaction cutoff. Modeling residues as spheres, however, is not always what you want.
This new neighborhood selector, the "CloseContactResidueSelector" identifies residues that have atoms within a certain distance cutoff -- that is, it's using the current atomic coordinates to make the neighborhood decision, instead of "any possible rotamer assignment," which often includes residues that couldn't realistically move into contact distance because there are other residues in the way.