[Biojava-l] Symbol / SymbolPropertyTable question

[Mark Southern]

I thought I would ask the list for advice before I embarked on something. I
have some physiochemical properties of amino acids that I would like to
access. (Milne Acid/Base Lambda/Rho) It includes values for modified amino
acids, side groups and N and C termini. See below.

I could of course do a very simple String -> value mapping. The question is:
what would be the best way to implement this in biojava? I can imagine a
setup similar to ProteinTools which reads in per-symbol properties from xml
and creates SymbolPropertyTable instances but in this example I have
modified amino acids and non-aa entities so I might need to create a new
Alphabet?

Cheers,

Mark.

ALANINE		A
ARGININE		R
ASPARTIC ACID	D
ASP COOH		D+
ASPARAGINE		N
CYSTEIN		C
CYSTINE		C2
GLYCINE		G
GLUTAMIC ACID	E
GLU COOH		E+
GLUTAMINE		Q
HIS 			H
ISOLEUCINE		I
LEUCINE		L
LYSINE		K
METHIONINE		M
PHENYLALANINE	F
PROLINE		P
PRO cis		Pc
SERINE		S
THREONINE		T
TRYPTOPHANE		W
TYROSINE		Y
VALINE		V
N-Term		NT
C-Term		CT
-NHMe			NMe
H3CCO-		Ac