Merge pull request #1213 from RosettaCommons/dimaio/PolymerBondedContainer_fixes
Small bugfixes for cart_bonded/PolymerBondedEnergyContainer.
Previously there was special logic in the container specifically for cart_bonded. Instead, the special case is handled by cart_bonded (moving some logic to compute intrares energies/derivatives), and the energy container behaves more reasonably. In doing so, we fix a bug where cart_bonded was not getting scored for some terminal residues.