Package org.biojava.bio.proteomics
Class IsoelectricPointCalc
- java.lang.Object
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- org.biojava.bio.proteomics.IsoelectricPointCalc
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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
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
IsoelectricPointCalc.ChargeCalculator
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Constructor Summary
Constructors Constructor Description IsoelectricPointCalc()
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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.
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Constructor Detail
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IsoelectricPointCalc
public IsoelectricPointCalc()
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Method Detail
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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
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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
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