Add AntibodyFeatures reporter and R scripts, update InterfaceFeatures and R scripts, update AntibodyInfo and cdr clusters
NEWS:
==Antibody==
- closest North-Dunbrack CDR cluster now prints in AntibodyInfo show method
- have Antibody metrics Sasa calculations use SasaCalculator2 (which means default radii is now correctly reduce like InterfaceAnalyzerMover)
- add check for peptide bond C-N lengths in AntibodyInfo to check for missing cdr density or poorly closed loops. This check is default true and can be turned off using the option -antibody:check_cdr_chainbreaks false.
- add optional AntibodyInfo check for wonky peptide bond geometries in cdrs. This check is default false and can be enabled using the option -antibody:check_cdr_pep_bond_geom true. The function that is called has been added to loops/util and checks the deviations from the dunbrack/karplus Conformation Dependent Library values within some user-controlled cutoff value.
==Features==
- Add AntibodyFeatures reporter + many R scripts for analysis
- Update InterfaceFeatures reporter (add a few more columns), reorganize R scripts and add a few more
==Bugs==
-debug missing enums of some rare cdr clusters
-debug some antibody metrics via testing with thousands of antibodies
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Unit test status: Pass
Integration test status: Antibody integration tests will change - both cosmetically and any reporting Sasa metrics
*SnugDock integration test updated to not check CN peptide bond. There is a 2.56 A C-N bond at 31 H.