Merge pull request #3483 from RosettaCommons/roccomoretti/seq_rec_metric
Add a simple metric which can calculate sequence recovery.
There's several options for how to calculate the sequence recovery.
* Standard sequence recovery, which is calculated from a subset of residues, comparing their seqeunce with that of a specified reference structures (potentially a "native")
* PSSM recovery - This is a pass/fail based approach from DeLuca et al 2011 - Basically, everything with a positive PSSM score is counted as "not a mutation" (No reference structure needed.)
* Average PSSM score for designed residues. (No reference structure needed).
* Delta PSSM score for designed residues (Uses reference structure.)