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 _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
