MassCalc is used to calculate the molecular mass of a protein Sequence. Since peptides are stored as Features on a sequence so MassCalc works with SymbolLists. The masses of the common amino acids are obtained from a SymbolPropertyTable which is stored statically in ProteinTools. Their is one static getMass method which does not allow for modification of the MassCalc object to compensate for post translational changes in the residue mass. If the masses of the common residues are to be modified then the user must create an instance of MassCalc and setSymbolModification.
MassCalc is used to calculate the molecular mass of a protein Sequence.
Since peptides are stored as Features on a sequence so MassCalc works with
SymbolLists. The masses of the common amino acids are obtained from a
SymbolPropertyTable which is stored statically in ProteinTools. Their
is one static getMass method which does not allow for modification
of the MassCalc object to compensate for post translational changes in
the residue mass. If the masses of the common residues are to be modified
then the user must create an instance of MassCalc and setSymbolModification.

Example Usage:

MassCalc massCalc = new MassCalc(SymbolPropertyTable.AVG_MASS);
massCalc.setSymbolModification('C', 161.01466);

double mass = massCalc.getMass(mySequence, true);


git-svn-id: ed25c26de1c5325e8eb0deed0b990ab8af8a4def@1051 7c6358e6-4a41-0410-a743-a5b2a554c398

sbliven/biojava,sbliven/biojava,sbliven/biojava