org.biojava.bio.proteomics
Class IsoelectricPointCalc

java.lang.Object
  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