Merge pull request #4252 from RosettaCommons/roccomoretti/fix_d_aa_loading_issues
Make DAAs and CCD components play more nicely together.
There were issues with loading in D-SER while the PDB components files were active. This PR adds a unit test for D-SER loading, as well as a few changes to address warnings/errors which occur during the process. We also adjust the exclude_pdb_components.txt list for the three letter code translation functionality which is currently in -alternate_3_letter_codes default.