Two new "standard" amino acids may need better integration

[nwmoriarty]

In 2014, the PDB designated SEC and PYL as standard amino acids and gave them the letters U and O, respectively. Nat made changes at the time but I think it's time to change it a little because the mmCIF format requires more details about the parent amino acid of any modified amino acid be specified. The SEC and PYL are, in fact, specified as the parents of a number of modified amino acids.

Nat also made the single letter code for UNK as U but I think it should be X. I have made changes in the two_new_standard_amino_acids branch but it breaks a number of tests.

Can we decide what is the best way forward. Make different changes or fix the tests? This may also impact other none tested scripts.

@bkpoon @olegsobolev @terwill @pafonine

[nwmoriarty]

I have updated the branch to contain working tests. You need to update GeoStd.

@terwill Can you, when you have fixed the bugs for the release,

git checkout two_new_standard_amino_acids

and check that you are happy with the changes.