Patch CTERM_AMIDATION has property issues

[josephlubin]

The CTERM_AMIDATION has some issues that make working with it challenging. For one, it removes too many properties, making it difficult to select the terminal residue. I have also encountered errors when trying to use it in combination with NCAAs, though I think @roccomoretti may have fixed that aready.

Here is a C-terminal alanine with and without capping:
Vanilla:

Base: ALA
 Properties: POLYMER PROTEIN CANONICAL_AA UPPER_TERMINUS ALIPHATIC METALBINDING ALPHA_AA L_AA
 Variant types: UPPER_TERMINUS_VARIANT

Capped:

Base: ALA
 Properties: POLYMER PROTEIN ALIPHATIC METALBINDING ALPHA_AA L_AA
 Variant types: CTERM_AMIDATION

In contrast, this problem does not exist with ACETYLATED_NTERMINUS_VARIANT, which retains the LOWER_TERMINUS property and gains an ACETYLATED_NTERMINUS property.

Vanilla:

Base: ALA
 Properties: POLYMER PROTEIN CANONICAL_AA LOWER_TERMINUS ALIPHATIC METALBINDING ALPHA_AA L_AA
 Variant types: LOWER_TERMINUS_VARIANT

Capped:

Base: ALA
 Properties: POLYMER PROTEIN CANONICAL_AA LOWER_TERMINUS ALIPHATIC METALBINDING ACETYLATED_NTERMINUS ALPHA_AA L_AA
 Variant types: ACETYLATED_NTERMINUS_VARIANT

Andy Watkins mentioned that METHYLATED_CTERMINUS_VARIANT works well, so that may be a good template for comparison.

[josephlubin]

I also found an error with ACETYLATED_NTERMINUS_VARIANT in tandem with NCAAs, albeit not a very informative one. I attempted to use a MutateResidueMover, setting the capped terminus to my NCAA, and get the following.

File: /Volumes/scratch/b3.r/rosetta/commits/rosetta/source/src/core/conformation/Residue.cc:202
[ ERROR ] UtilityExitException
ERROR: 

This is mitigated if I remove the cap, make the substitution, then re-add the cap.