KaSet (com.hfg API Documentation)

java.lang.Object
- com.hfg.bio.KaSet

All Implemented Interfaces:

Cloneable, Comparable<KaSet>
```
public class KaSet
extends Object
implements Cloneable, Comparable<KaSet>
```
Encapsulation for a group of K_a (dissociation constant) values. Most commonly used for protein isoelectric point prediction.

Field Summary

Fields
Modifier and Type	Field and Description
`static KaSet`	`BJELLQVIST` Bjellqvist B, Hughes GJ, Pasquali C, et al.
`static KaSet`	`EMBOSS` Method from EMBOSS's iep tool.
`static KaSet`	`EXPASY` Method from Expasy's Compute pI/Mw tool which implements the values from Bjellqvist but mistakenly treats C-terminal Asp and Glu sidechain values as C-terminal values.
`static KaSet`	`GRIMSLEY` Grimsley GR, Scholtz JM, Pace CN (2009).
`static KaSet`	`PATRICKIOS_SIMPLE` Patrickios, CS, Yamasaki, EN.
`static KaSet`	`SILLERO` Sillero A, Ribeiro JM.
`static KaSet`	`SILLERO_ABRIDGED` Sillero A, Ribeiro JM.
`static KaSet`	`STRYER_1995` Biochemistry by Lubert Stryer, 1995
`static KaSet`	`TAYLOR_NATIVE` Intended for use with native proteins.

Constructor Summary

Constructors
Constructor and Description

KaSet(String inName)

KaSet(XMLNode inXML)

Constructors
Constructor and Description
`KaSet(String inName)`
`KaSet(XMLNode inXML)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`KaSet`	`addpKa(AminoAcid inResidue, float inpKa, Charge inProtonatedForm)` Adds a pKa value for the specified amino acid to the set.
`KaSet`	`addpKa(Molecule inMolecule, IonizableGroup inIonizableGroup)` Adds a pKa value for the specified molecule to the set.
`KaSet`	`clone()`
`int`	`compareTo(KaSet inObj2)`
`boolean`	`equals(Object inObj2)`
`IonizableGroup`	`getCTerminalKa(CTerminalGroup inCTerminalGroup, AminoAcid inCTerminalResidue)`
`IonizableGroup`	`getCTerminalSidechainKa(AminoAcid inResidue)`
`ProteinAnalysisMode`	`getDefaultProteinAnalysisMode()`
`List<IonizableGroup>`	`getIonizableGroups(Molecule inResidue)`
`IonizableGroup`	`getNTerminalKa(NTerminalGroup inNTerminalGroup, AminoAcid inNTerminalResidue)`
`boolean`	`isLocked()`
`KaSet`	`lock()`
`String`	`name()`
`KaSet`	`setCTerminalpKa(AminoAcid inResidue, float inpKa, Charge inProtonatedForm)`
`KaSet`	`setCTerminalpKa(CTerminalGroup inCTerminalGroup, float inpKa, Charge inProtonatedForm)`
`KaSet`	`setCTerminalSidechainpKa(AminoAcid inResidue, float inpKa, Charge inProtonatedForm)`
`KaSet`	`setDefaultProteinAnalysisMode(ProteinAnalysisMode inValue)`
`KaSet`	`setName(String inValue)`
`KaSet`	`setNTerminalpKa(AminoAcid inResidue, float inpKa, Charge inProtonatedForm)`
`KaSet`	`setNTerminalpKa(NTerminalGroup inNTerminalGroup, float inpKa, Charge inProtonatedForm)`
`String`	`toString()`
`XMLNode`	`toXMLNode()`
`static KaSet`	`valueOf(String inName)`
`static Collection<KaSet>`	`values()`

Methods inherited from class java.lang.Object
finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - BJELLQVIST
```
public static final KaSet BJELLQVIST
```
    Bjellqvist B, Hughes GJ, Pasquali C, et al. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis. 1993;14(10):1023-31. Available at: http://www.ncbi.nlm.nih.gov/pubmed/8125050. Intended for use with reduced and denatured proteins on 2D gels.
  - EXPASY
```
public static final KaSet EXPASY
```
    Method from Expasy's Compute pI/Mw tool which implements the values from Bjellqvist but mistakenly treats C-terminal Asp and Glu sidechain values as C-terminal values. Intended for use with reduced and denatured proteins on 2D gels.
  - EMBOSS
```
public static final KaSet EMBOSS
```
    Method from EMBOSS's iep tool. Intended for use with reduced and denatured proteins on 2D gels.
  - SILLERO
```
public static final KaSet SILLERO
```
    Sillero A, Ribeiro JM. Isoelectric points of proteins: theoretical determination. Analytical biochemistry. 1989;179(2):319-325. Available at: http://www.ncbi.nlm.nih.gov/pubmed/2774179. Intended for use with reduced and denatured proteins on 2D gels.
  - SILLERO_ABRIDGED
```
public static final KaSet SILLERO_ABRIDGED
```
    Sillero A, Ribeiro JM. Isoelectric points of proteins: theoretical determination. Analytical biochemistry. 1989;179(2):319-325. Available at: http://www.ncbi.nlm.nih.gov/pubmed/2774179. Intended for use with reduced and denatured proteins on 2D gels. An oversimplification for ease of calculation.
  - PATRICKIOS_SIMPLE
```
public static final KaSet PATRICKIOS_SIMPLE
```
    Patrickios, CS, Yamasaki, EN. Polypeptide amino acid composition and isoelectric point. II. Comparison between experiment and theory. Analytical Biochemistry. 1995:231(1):82-91. http://doi.org/10.1006/abio.1995.1506. An oversimplification for ease of calculation.
  - STRYER_1995
```
public static final KaSet STRYER_1995
```
    Biochemistry by Lubert Stryer, 1995
  - GRIMSLEY
```
public static final KaSet GRIMSLEY
```
    Grimsley GR, Scholtz JM, Pace CN (2009). A summary of the measured pK values of the ionizable groups in folded proteins. Protein Science 18(1), 247-251. Note that they do not provide a value for Arginine so a default value of 12 is used. Intended for use with native proteins.
  - TAYLOR_NATIVE
```
public static final KaSet TAYLOR_NATIVE
```
    Intended for use with native proteins.
- Constructor Detail
  - KaSet
```
public KaSet(String inName)
```
  - KaSet
```
public KaSet(XMLNode inXML)
```
- Method Detail
  - values
```
public static Collection<KaSet> values()
```
  - valueOf
```
public static KaSet valueOf(String inName)
```
  - name
```
public String name()
```
  - setName
```
public KaSet setName(String inValue)
```
  - isLocked
```
public boolean isLocked()
```
  - lock
```
public KaSet lock()
```
  - setDefaultProteinAnalysisMode
```
public KaSet setDefaultProteinAnalysisMode(ProteinAnalysisMode inValue)
```
  - getDefaultProteinAnalysisMode
```
public ProteinAnalysisMode getDefaultProteinAnalysisMode()
```
  - toXMLNode
```
public XMLNode toXMLNode()
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - equals
```
public boolean equals(Object inObj2)
```
    Overrides:
    
    equals in class Object
  - compareTo
```
public int compareTo(KaSet inObj2)
```
    Specified by:
    
    compareTo in interface Comparable<KaSet>
  - clone
```
public KaSet clone()
```
    Overrides:
    
    clone in class Object
  - addpKa
```
public KaSet addpKa(AminoAcid inResidue,
                    float inpKa,
                    Charge inProtonatedForm)
```
    Adds a pKa value for the specified amino acid to the set. Ka = 10^(-pKa)
    
    Parameters:
    
    inResidue - the amino acid that the pKa value should apply to
    
    inpKa - the pKa value to associate with the specified amino acid
    
    inProtonatedForm - the charge of the group's protonated form
    
    Returns:
    
    this KaSet to enable method chaining
  - addpKa
```
public KaSet addpKa(Molecule inMolecule,
                    IonizableGroup inIonizableGroup)
```
    Adds a pKa value for the specified molecule to the set. This form of addpKa() can be used to to assign pKa values to monosaccharide groups in a glycan. Ka = 10^(-pKa)
    
    Parameters:
    
    inMolecule - the amino acid that the pKa value should apply to
    
    inIonizableGroup - the ionizable group to associate with the given molecule
    
    Returns:
    
    this KaSet to enable method chaining
  - getIonizableGroups
```
public List<IonizableGroup> getIonizableGroups(Molecule inResidue)
```
  - getNTerminalKa
```
public IonizableGroup getNTerminalKa(NTerminalGroup inNTerminalGroup,
                                     AminoAcid inNTerminalResidue)
```
  - setNTerminalpKa
```
public KaSet setNTerminalpKa(NTerminalGroup inNTerminalGroup,
                             float inpKa,
                             Charge inProtonatedForm)
```
  - setNTerminalpKa
```
public KaSet setNTerminalpKa(AminoAcid inResidue,
                             float inpKa,
                             Charge inProtonatedForm)
```
  - getCTerminalKa
```
public IonizableGroup getCTerminalKa(CTerminalGroup inCTerminalGroup,
                                     AminoAcid inCTerminalResidue)
```
  - setCTerminalpKa
```
public KaSet setCTerminalpKa(CTerminalGroup inCTerminalGroup,
                             float inpKa,
                             Charge inProtonatedForm)
```
  - setCTerminalpKa
```
public KaSet setCTerminalpKa(AminoAcid inResidue,
                             float inpKa,
                             Charge inProtonatedForm)
```
  - setCTerminalSidechainpKa
```
public KaSet setCTerminalSidechainpKa(AminoAcid inResidue,
                                      float inpKa,
                                      Charge inProtonatedForm)
```
  - getCTerminalSidechainKa
```
public IonizableGroup getCTerminalSidechainKa(AminoAcid inResidue)
```

Class KaSet

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BJELLQVIST

EXPASY

EMBOSS

SILLERO

SILLERO_ABRIDGED

PATRICKIOS_SIMPLE

STRYER_1995

GRIMSLEY

TAYLOR_NATIVE

Constructor Detail

KaSet

KaSet

Method Detail

values

valueOf

name

setName

isLocked

lock

setDefaultProteinAnalysisMode

getDefaultProteinAnalysisMode

toXMLNode

toString

equals

compareTo

clone

addpKa

addpKa

getIonizableGroups

getNTerminalKa

setNTerminalpKa

setNTerminalpKa

getCTerminalKa

setCTerminalpKa

setCTerminalpKa

setCTerminalSidechainpKa

getCTerminalSidechainKa