Thanks for the hint, Mark. I found that the NameTokenization class could be
used for this purpose, although it can't deal with the ambiguous amino acid
"Xaa". The following code will work for regular amino acid such as "Cys"
Alphabet ap = AlphabetManager.alphabetForName("PROTEIN");
NameTokenization nt = new NameTokenization((FiniteAlphabet)ap);
Symbol s = nt.parseToken("Cys");
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