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
  • Constructor Details

  • Method Details

    • 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