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java.lang.Objectorg.biojava.bio.proteomics.IsoelectricPointCalc
public class IsoelectricPointCalc
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.
Nested Class Summary | |
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class |
IsoelectricPointCalc.ChargeCalculator
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Constructor Summary | |
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IsoelectricPointCalc()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public IsoelectricPointCalc()
Method Detail |
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public double getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm) throws IllegalAlphabetException, BioException
peptide
- peptide of which pI is required.hasFreeNTerm
- has free N-terminal amino group.hasFreeCTerm
- has free C-terminal carboxyl group.
IllegalAlphabetException
BioException
public static double getIsoelectricPoint(SymbolList peptide) throws IllegalAlphabetException, BioException
This method returns the same values as ExPASy's Compute pI/Mw program
peptide
- peptide of which pI is required.
IllegalAlphabetException
BioException
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