org.biojava.bio.proteomics
Class IsoelectricPointCalc

java.lang.Object
  extended by org.biojava.bio.proteomics.IsoelectricPointCalc

public class IsoelectricPointCalc
extends Object

Class that computes isoelectric point for denaturated proteins. These pIs are useful for predicting the position of a protein on a 2D gel.

The pK values are taken from Bjellqvist B. et al., "Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions", Electrophoresis 1994, 15, 529-539.

Since:
1.22
Author:
David Huen, George Waldon

Nested Class Summary
 class IsoelectricPointCalc.ChargeCalculator
           
 
Constructor Summary
IsoelectricPointCalc()
           
 
Method Summary
static double getIsoelectricPoint(SymbolList peptide)
          Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends.
 double getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)
          Computes isoelectric point of specified peptide.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

IsoelectricPointCalc

public IsoelectricPointCalc()
Method Detail

getPI

public double getPI(SymbolList peptide,
                    boolean hasFreeNTerm,
                    boolean hasFreeCTerm)
             throws IllegalAlphabetException,
                    BioException
Computes isoelectric point of specified peptide.

Parameters:
peptide - peptide of which pI is required.
hasFreeNTerm - has free N-terminal amino group.
hasFreeCTerm - has free C-terminal carboxyl group.
Throws:
IllegalAlphabetException
BioException

getIsoelectricPoint

public static double getIsoelectricPoint(SymbolList peptide)
                                  throws IllegalAlphabetException,
                                         BioException
Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends. Various ambiguity symbols, symbols for which pK data are not available, or illegal symbols are not contributing to the calculated pI.

This method returns the same values as ExPASy's Compute pI/Mw program

Parameters:
peptide - peptide of which pI is required.
Returns:
the calculated pI
Throws:
IllegalAlphabetException
BioException
Since:
1.5