[Biojava-l] Isoelectric point and molecular weight calculations with BioJava - Conserns

[udana chathuranga]

Hi all,

I am starting a new thread regarding some concerns about BioJava 1.8 and
it's implementation of isoelectric point calculation and calculation the
mass of peptides.Also about mapping these to BioJava 3.0

1. Package org.biojava.bio.proteomics - Class_IsoelectricPointCalc
In the method "getIsoelectricPoint(SymbolList peptide)" they have used a
SymbolList type as the parameter ,if we are going to port to BioJava3.0
,What are the possible use of parameter instead of SymbolList in BioJava1.8?
SymbolList interface in org.biojava.bio.symbol not helpful in understanding
the use of SymbolList in Isoelectric Point calculation.

2. Package org.biojava.bio.proteomics - Class_MassCalc
In "calcTermMass" method they have added extra H if MH_PLUS is true.I am
little bit confuse why we have to add a extra H when calculating term mass?
and What is the importance of MH_PLUS prpperty?

If there are sample codes or demos how to use these classes and method, can
anyone guide me to those?


Thanks
Regards
Udana