(incremental) Support for D-AminoAcids

[aalhossary]

Support of D-AminoAcids (to be recognized as AminoAcids instead of HetAtomGroups).

Other modoficatiosn may follow to support bigger ChemComp names.

Related to #993

[JonStargaryen]

Brief question: Does this fix a particular problem or is the motivation solely completeness?

At least according to the docs it seems as treating D-amino acids as hetatms is the desired behavior:

biojava/biojava-structure/src/main/java/org/biojava/nbio/structure/GroupType.java

Line 45 in ebb6eb0

* The type for amino acids (L-peptides)

[aalhossary]

Does this fix a particular problem or is the motivation solely completeness?

It fixes a particular problem. I am searching the PDB for different types of cross links (e.g. isopeptide) which are present in D as well as L aminoacids. Treating D-AminoAcids as just HetAtom group limits me to a great extent.

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Regarding completeness, technically they are not different from L-AminoAcids and different bonds can form between them and L-AminoAcids.
Add to this that nucleotide- analogues and D-AminoAcids are increasingly being deposited in PDB nowadays, in contrast to when BioJava 1.7 was designed.

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I am willing to take the responsibility of this initiative, but we need to discuss any major design change thoroughly first.

[josemduarte]

See my comments in #993

[aalhossary]

Let's keep this pull request for the implementation discussions, and keep the design discussions to the #993 .