Protease (com.hfg API Documentation)

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

All Implemented Interfaces:

Comparable
```
public class Protease
extends Object
implements Comparable
```
Chemical or biological proteolytic agent which can be used to theoretically digest a Protein.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

protected class Protease.SlidingWindow

Nested Classes
Modifier and Type	Class and Description
`protected class`	`Protease.SlidingWindow`

Field Summary

Fields
Modifier and Type	Field and Description
`static Protease`	`ASP_N`
`static Protease`	`ASP_N_DE`
`static Protease`	`CHYMOTRYPSIN`
`static Protease`	`ENTEROKINASE`
`static Protease`	`FACTOR_Xa` Factor Xa protease.
`static Protease`	`GLU_C`
`static Protease`	`HRV_3C` Human rhinovirus 3C protease.
`static Protease`	`LYS_C`
`static Protease`	`TEV` Tobacco Etch virus protease.
`static Protease`	`THROMBIN` Human thrombin protease.
`static Protease`	`TRYPSIN`

Constructor Summary

Constructors
Constructor and Description

Protease(String inName)

Constructors
Constructor and Description
`Protease(String inName)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(Object inObj2)`
`List<DigestFragment>`	`digest(Protein inProtein, DigestSettings inSettings)`
`boolean`	`equals(Object inObj2)`
`String`	`getExcludedP1PrimeResidues()`
`String`	`getExcludedP1Residues()`
`String`	`getExcludedP2PrimeResidues()`
`String`	`getExcludedP2Residues()`
`String`	`getExcludedP3Residues()`
`String`	`getExcludedP4Residues()`
`String`	`getExcludedP5Residues()`
`String`	`getExcludedP6Residues()`
`String`	`getP1PrimeSpecificity()`
`String`	`getP1Specificity()`
`String`	`getP2PrimeSpecificity()`
`String`	`getP2Specificity()`
`String`	`getP3PrimeSpecificity()`
`String`	`getP3Specificity()`
`String`	`getP4Specificity()`
`String`	`getP5Specificity()`
`String`	`getP6Specificity()`
`int`	`hashCode()`
`boolean`	`isCleavageSite(char inP1Residue, char inP1PrimeResidue)`
`boolean`	`isCleavageSite(CharSequence inNTerminalResidues, CharSequence inCTerminalResidues)`
`Protease`	`lock()`
`String`	`name()`
`Protease`	`setExcludedP1PrimeResidues(String inValue)`
`Protease`	`setExcludedP1Residues(String inValue)`
`Protease`	`setExcludedP2PrimeResidues(String inValue)`
`Protease`	`setExcludedP2Residues(String inValue)`
`Protease`	`setExcludedP3Residues(String inValue)`
`Protease`	`setExcludedP4Residues(String inValue)`
`Protease`	`setExcludedP5Residues(String inValue)`
`Protease`	`setExcludedP6Residues(String inValue)`
`Protease`	`setP1PrimeSpecificity(String inValue)`
`Protease`	`setP1Specificity(String inValue)`
`Protease`	`setP2PrimeSpecificity(String inValue)`
`Protease`	`setP2Specificity(String inValue)`
`Protease`	`setP3PrimeSpecificity(String inValue)`
`Protease`	`setP3Specificity(String inValue)`
`Protease`	`setP4Specificity(String inValue)`
`Protease`	`setP5Specificity(String inValue)`
`Protease`	`setP6Specificity(String inValue)`
`String`	`toString()`
`static Protease`	`valueOf(String inName)`
`static Protease[]`	`values()`

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

Field Detail
- TRYPSIN
```
public static final Protease TRYPSIN
```
- LYS_C
```
public static final Protease LYS_C
```
- CHYMOTRYPSIN
```
public static final Protease CHYMOTRYPSIN
```
- GLU_C
```
public static final Protease GLU_C
```
- ASP_N
```
public static final Protease ASP_N
```
- ASP_N_DE
```
public static final Protease ASP_N_DE
```
- THROMBIN
```
public static final Protease THROMBIN
```
  Human thrombin protease.
  Uses data from Gallwitz, M. et. al. (2012). "The extended cleavage specificity of human thrombin." PLoS ONE, 7 (2).
  Note: Experiments suggest a preference for P in P2 and R in P3'.
- TEV
```
public static final Protease TEV
```
  Tobacco Etch virus protease.
  Uses data from Kostallas, G. et. al. (2011). "Substrate profiling of tobacco Etch virus protease using a novel Fluorescence-Assisted whole-cell assay." PLoS ONE, 6 (1).
- HRV_3C
```
public static final Protease HRV_3C
```
  Human rhinovirus 3C protease.
  Uses data from Cordingley, M.G. et. al. (1990). "Substrate requirements of human rhinovirus 3C protease for peptide cleavage in vitro." Journal of Biological Chemistry, 265 (16), 9062-9065.
- FACTOR_Xa
```
public static final Protease FACTOR_Xa
```
  Factor Xa protease.
  Uses data from Harris, J. et. al. (2000). "Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries." PNAS, 97 (14), 7754-7759.
- ENTEROKINASE
```
public static final Protease ENTEROKINASE
```

Constructor Detail
- Protease
```
public Protease(String inName)
```

Method Detail

values
```
public static Protease[] values()
```

valueOf

public static Protease valueOf(String inName)

hashCode
```
public int hashCode()
```
Overrides:

hashCode in class Object

equals
```
public boolean equals(Object inObj2)
```
Overrides:

equals in class Object

compareTo
```
public int compareTo(Object inObj2)
```
Specified by:

compareTo in interface Comparable

name
```
public String name()
```

toString
```
public String toString()
```
Overrides:

toString in class Object

setP6Specificity

public Protease setP6Specificity(String inValue)

getP6Specificity
```
public String getP6Specificity()
```

setExcludedP6Residues

public Protease setExcludedP6Residues(String inValue)

getExcludedP6Residues
```
public String getExcludedP6Residues()
```

setP5Specificity

public Protease setP5Specificity(String inValue)

getP5Specificity
```
public String getP5Specificity()
```

setExcludedP5Residues

public Protease setExcludedP5Residues(String inValue)

getExcludedP5Residues
```
public String getExcludedP5Residues()
```

setP4Specificity

public Protease setP4Specificity(String inValue)

getP4Specificity
```
public String getP4Specificity()
```

setExcludedP4Residues

public Protease setExcludedP4Residues(String inValue)

getExcludedP4Residues
```
public String getExcludedP4Residues()
```

setP3Specificity

public Protease setP3Specificity(String inValue)

getP3Specificity
```
public String getP3Specificity()
```

setExcludedP3Residues

public Protease setExcludedP3Residues(String inValue)

getExcludedP3Residues
```
public String getExcludedP3Residues()
```

setP2Specificity

public Protease setP2Specificity(String inValue)

getP2Specificity
```
public String getP2Specificity()
```

setExcludedP2Residues

public Protease setExcludedP2Residues(String inValue)

getExcludedP2Residues
```
public String getExcludedP2Residues()
```

setP1Specificity

public Protease setP1Specificity(String inValue)

getP1Specificity
```
public String getP1Specificity()
```

setExcludedP1PrimeResidues

public Protease setExcludedP1PrimeResidues(String inValue)

getExcludedP1PrimeResidues

public String getExcludedP1PrimeResidues()

setP1PrimeSpecificity

public Protease setP1PrimeSpecificity(String inValue)

getP1PrimeSpecificity
```
public String getP1PrimeSpecificity()
```

setExcludedP1Residues

public Protease setExcludedP1Residues(String inValue)

getExcludedP1Residues
```
public String getExcludedP1Residues()
```

setExcludedP2PrimeResidues

public Protease setExcludedP2PrimeResidues(String inValue)

getExcludedP2PrimeResidues

public String getExcludedP2PrimeResidues()

setP2PrimeSpecificity

public Protease setP2PrimeSpecificity(String inValue)

getP2PrimeSpecificity
```
public String getP2PrimeSpecificity()
```

setP3PrimeSpecificity

public Protease setP3PrimeSpecificity(String inValue)

getP3PrimeSpecificity
```
public String getP3PrimeSpecificity()
```

lock
```
public Protease lock()
```

digest

public List<DigestFragment> digest(Protein inProtein,
                                   DigestSettings inSettings)

isCleavageSite

public boolean isCleavageSite(char inP1Residue,
                              char inP1PrimeResidue)

isCleavageSite

public boolean isCleavageSite(CharSequence inNTerminalResidues,
                              CharSequence inCTerminalResidues)

Class Protease

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TRYPSIN

LYS_C

CHYMOTRYPSIN

GLU_C

ASP_N

ASP_N_DE

THROMBIN

TEV

HRV_3C

FACTOR_Xa

ENTEROKINASE

Constructor Detail

Protease

Method Detail

values

valueOf

hashCode

equals

compareTo

name

toString

setP6Specificity

getP6Specificity

setExcludedP6Residues

getExcludedP6Residues

setP5Specificity

getP5Specificity

setExcludedP5Residues

getExcludedP5Residues

setP4Specificity

getP4Specificity

setExcludedP4Residues

getExcludedP4Residues

setP3Specificity

getP3Specificity

setExcludedP3Residues

getExcludedP3Residues

setP2Specificity

getP2Specificity

setExcludedP2Residues

getExcludedP2Residues

setP1Specificity

getP1Specificity

setExcludedP1PrimeResidues

getExcludedP1PrimeResidues

setP1PrimeSpecificity

getP1PrimeSpecificity

setExcludedP1Residues

getExcludedP1Residues

setExcludedP2PrimeResidues

getExcludedP2PrimeResidues

setP2PrimeSpecificity

getP2PrimeSpecificity

setP3PrimeSpecificity

getP3PrimeSpecificity

lock

digest

isCleavageSite

isCleavageSite