Class IsoelectricPointCalc


  • public class IsoelectricPointCalc
    extends java.lang.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
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      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
    • Method Detail

      • 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