com.hfg.bio.proteinproperty

Class IsoelectricPoint<S extends SimpleProteinPropertyCalcSettings>

java.lang.Object

com.hfg.bio.proteinproperty.SimpleProteinProperty<S,Float>

com.hfg.bio.proteinproperty.IsoelectricPoint<S>

All Implemented Interfaces:

SingleValueProteinProperty<S,Float>

public class IsoelectricPoint<S extends SimpleProteinPropertyCalcSettings>
extends SimpleProteinProperty<S,Float>

Isoelectric point calculation packaged as a protein property for ease of integration with other protein properties.

Field Summary

Fields

Modifier and Type	Field and Description
static IsoelectricPoint	BJELLQVIST
static IsoelectricPoint	EMBOSS
static IsoelectricPoint	EXPASY
static IsoelectricPoint	GRIMSLEY
static IsoelectricPoint	PATRICKIOS_SIMPLE
static IsoelectricPoint	SILLERO
static IsoelectricPoint	SILLERO_ABRIDGED
static IsoelectricPoint	STRYER_1995
static IsoelectricPoint	TAYLOR_NATIVE

Constructor Summary

Constructors

Constructor and Description
IsoelectricPoint(KaSet inKaSet)
IsoelectricPoint(KaSet inKaSet, String inReference)
IsoelectricPoint(String inName, KaSet inKaSet)

Method Summary

Modifier and Type	Method and Description
Float	calculate(Protein inProtein, S inSettings) Determines the isoelectric point (the pH at which the net charge is zero) for the protein.
protected Map<IonizableGroup,Integer>	constructIonizableGroupMap(Protein inProtein, S inSettings)
protected KaSet	getKaSet()
double	getNetCharge(double pH, Protein inProtein, S inSettings) Estimates the protein's net charge at the specified pH.
String	getType()
protected void	setKaSet(KaSet inValue)
static IsoelectricPoint	valueOf(KaSet inKaSet)
static Collection<IsoelectricPoint>	values()

Methods inherited from class com.hfg.bio.proteinproperty.SimpleProteinProperty

getDataType, getDescription, getReference, getReturnType, name, setDescription, setReference, toString, valueOf

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

BJELLQVIST

public static final IsoelectricPoint BJELLQVIST

EXPASY

public static final IsoelectricPoint EXPASY

EMBOSS

public static final IsoelectricPoint EMBOSS

SILLERO

public static final IsoelectricPoint SILLERO

SILLERO_ABRIDGED

public static final IsoelectricPoint SILLERO_ABRIDGED

PATRICKIOS_SIMPLE

public static final IsoelectricPoint PATRICKIOS_SIMPLE

STRYER_1995

public static final IsoelectricPoint STRYER_1995

GRIMSLEY

public static final IsoelectricPoint GRIMSLEY

TAYLOR_NATIVE

public static final IsoelectricPoint TAYLOR_NATIVE

Constructor Detail

IsoelectricPoint

public IsoelectricPoint(String inName,
                        KaSet inKaSet)

IsoelectricPoint

public IsoelectricPoint(KaSet inKaSet)

IsoelectricPoint

public IsoelectricPoint(KaSet inKaSet,
                        String inReference)

Method Detail

valueOf

public static IsoelectricPoint valueOf(KaSet inKaSet)

values

public static Collection<IsoelectricPoint> values()

getType

public String getType()

Specified by:

getType in class SimpleProteinProperty<S extends SimpleProteinPropertyCalcSettings,Float>

calculate

public Float calculate(Protein inProtein,
                       S inSettings)

Determines the isoelectric point (the pH at which the net charge is zero) for the protein.

Parameters:

inProtein - the protein on which the calculation should be performed

inSettings - settings for the calculation

Returns:

the calculated isoelectric point

getNetCharge

public double getNetCharge(double pH,
                           Protein inProtein,
                           S inSettings)

Estimates the protein's net charge at the specified pH.

Parameters:

pH - the pH at which the calculation should be performed

inProtein - the protein on which the calculation should be performed

inSettings - settings for the calculation

Returns:

the calculated net charge

setKaSet

protected void setKaSet(KaSet inValue)

getKaSet

protected KaSet getKaSet()

constructIonizableGroupMap

protected Map<IonizableGroup,Integer> constructIonizableGroupMap(Protein inProtein,
                                                                 S inSettings)