[Biojava-l] Symbol / SymbolPropertyTable question

[mark.schreiber at novartis.com]

It really depends on what you want to do with it but it would seems like a 
good target for an Alphabet

- Mark





"Mark Southern" <msouthern at exsar.com>
Sent by: biojava-l-bounces at portal.open-bio.org
04/05/2005 03:26 AM

 
        To:     <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Symbol / SymbolPropertyTable question


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




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