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

[Andreas Prlic]

Hi Udana,

> 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?

The counterpart in the 3.x series would be to use directly the
sequence interface or pass in a string representation of a sequence.

> 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?

not sure, somebody else might be able to say more about this

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


Did you see the cookbook ?

http://biojava.org/wiki/BioJava:CookBook1.7#Proteomics

Andreas