Support of D-AminoAcids

aalhossary

D-AminoAcids (https://proteopedia.org/wiki/index.php/Amino_Acids) are optical isomers or enantiomers (mirror images) of naturally occuring L-AminoAcids. They have the same structure but with opposite chirality.
When I parse structures that contain D-AminoAcids, they are parser as hetatoms.

Here are some of my notes:

I tried adding the D-AminoAcids to StructureTools lookup table, but that was not enough.
HetatomImpl.isAminoAcid() returns false for cases like DAL (D-Alanine), because it tests whether PolymerType.PROTEIN_ONLY.contains(pt).
Although PolymerType includes types for both peptide("polypeptide(L)") and dpeptide("polypeptide(D)"), PolymerType.PROTEIN_ONLY contains the peptide type only.
Also I see a lot of redundancy between StructureTools and ChemCompTools. Is there a need to keep both of them?, or we can simply deprecate the former for the sake of the later.

I think a restructuring task can be done in conjunction with supporting longer ChecmComp names expected in 2022.
We can schedule refactoring this feature to the new version of BioJava. However, we need to start by supporting D-AminoAcids soon.