Merge pull request #2138 from RosettaCommons/roccomoretti/chain_in_InterfaceScoreCalculator
InterfaceScoreCalculator fixes
Previously, the ligand docking InterfaceScoreCalculator, while it takes a set of chain letters as the specification of the chain to use, instead bounced the chain specification through chain IDs, jump numbers, and even residue numbers. This resulted in difficulties when attempting to score poses which aren't set up with precise chain letter/chain ID/jump number/residue number correspondence, particularly with RMSD calculations on structures with differing numbers of (non-ligand) residues.
Rework the InterfaceScoreCalculator associate functions, so they work directly on chain letters (what the user is specifying). As an added bonus, reduce (but don't eliminate yet) the dependence on JD2.