Merging vmullig/ncaas into master to get my changes to NCAAs.
--Add 4,5-dihydroxyisoleucine (a component of alpha-amanitin) to the l-ncaas part of the database.
--Change is_D_aa() function in core/chemical/AA.cc to is_canonical_D_aa()
--Removed some code duplication in Ramachandran.cc.
--Added BACKBONE_AA lines to params files. This can be used to tell Rosetta that the rama and p_aa_pp scoring functions should treat a particular noncanonical amino acid like a designated canonical amino acid. (For example, in the 4,5-dihydroxyisoleucine params file, we have "BACKBONE_AA ILE").
--Added ALPHA_AA, BETA_AA, L_AA, and D_AA properties for alpha, beta, L-alpha, and D-alpha amino acids, respectively.
--Updates D-proline with shadow atoms so that it scores and minimizes identically to (i.e. like the mirror image of) L-proline.
--Fixes one more dependency problem in core/pose/util.cc, which should hopefully fix any remaining build problems not fixed by my last tweak to master.
These changes have not yet been described on the Gollum Wiki, but will soon.
TODO:
--Update BPY.params.
Unit test status: Pass
Integration test status: ZERO changed tests!