java.lang.Object

org.biojava.nbio.aaproperties.Constraints

public class Constraints extends Object

This class is used to support the implementation of properties stated in IPeptideProperties. It initializes several values that would be needed for the computation of properties such as

Molecular weight
Instability index
Hydropathy value
pKa

Version:

2011.05.21

Author:

kohchuanhock

See Also:

IPeptideProperties

Field Summary

Fields

Modifier and Type

Field

Description

static AminoAcidCompound

A

static Map<AminoAcidCompound,Double>

aa2CTerminalPka

static Map<AminoAcidCompound,Double>

aa2ExtinctionCoefficient

static Map<AminoAcidCompound,Double>

aa2Hydrophathicity

static Map<AminoAcidCompound,Double>

aa2MolecularWeight

static Map<AminoAcidCompound,Double>

aa2NTerminalPka

static Map<AminoAcidCompound,Double>

aa2PKa

static AminoAcidCompound

C

static AminoAcidCompound

D

static Map<String,Double>

diAA2Instability

static AminoAcidCompound

E

static AminoAcidCompound

F

static AminoAcidCompound

G

static AminoAcidCompound

H

static AminoAcidCompound

I

static AminoAcidCompound

K

static AminoAcidCompound

L

static AminoAcidCompound

M

static AminoAcidCompound

N

static AminoAcidCompound

P

static AminoAcidCompound

Q

static AminoAcidCompound

R

static AminoAcidCompound

S

static AminoAcidCompound

T

static AminoAcidCompound

V

static AminoAcidCompound

W

static AminoAcidCompound

Y
Constructor Summary

Constructors

Constructor

Description

Constraints()
Method Summary

Modifier and Type

Method

Description

static void

initExtinctionCoefficient()

Does the initialization of extinction coefficient based on http://au.expasy.org/tools/protparam-doc.html

static void

initMolecularWeight()

Does the initialization of molecular weights based on http://au.expasy.org/tools/findmod/findmod_masses.html#AA

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

Field Details
- A
  
  public static AminoAcidCompound A
- R
  
  public static AminoAcidCompound R
- N
  
  public static AminoAcidCompound N
- D
  
  public static AminoAcidCompound D
- C
  
  public static AminoAcidCompound C
- E
  
  public static AminoAcidCompound E
- Q
  
  public static AminoAcidCompound Q
- G
  
  public static AminoAcidCompound G
- H
  
  public static AminoAcidCompound H
- I
  
  public static AminoAcidCompound I
- L
  
  public static AminoAcidCompound L
- K
  
  public static AminoAcidCompound K
- M
  
  public static AminoAcidCompound M
- F
  
  public static AminoAcidCompound F
- P
  
  public static AminoAcidCompound P
- S
  
  public static AminoAcidCompound S
- T
  
  public static AminoAcidCompound T
- W
  
  public static AminoAcidCompound W
- Y
  
  public static AminoAcidCompound Y
- V
  
  public static AminoAcidCompound V
- aa2ExtinctionCoefficient
  
  public static Map<AminoAcidCompound,Double> aa2ExtinctionCoefficient
- aa2MolecularWeight
  
  public static Map<AminoAcidCompound,Double> aa2MolecularWeight
- aa2Hydrophathicity
  
  public static Map<AminoAcidCompound,Double> aa2Hydrophathicity
- aa2PKa
  
  public static Map<AminoAcidCompound,Double> aa2PKa
- diAA2Instability
  
  public static Map<String,Double> diAA2Instability
- aa2NTerminalPka
  
  public static Map<AminoAcidCompound,Double> aa2NTerminalPka
- aa2CTerminalPka
  
  public static Map<AminoAcidCompound,Double> aa2CTerminalPka
Constructor Details
- Constraints
  
  public Constraints()
Method Details
- initMolecularWeight
  
  public static void initMolecularWeight()
  
  Does the initialization of molecular weights based on http://au.expasy.org/tools/findmod/findmod_masses.html#AA
- initExtinctionCoefficient
  
  public static void initExtinctionCoefficient()
  
  Does the initialization of extinction coefficient based on http://au.expasy.org/tools/protparam-doc.html

Class Constraints

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

A

R

N

D

C

E

Q

G

H

I

L

K

M

F

P

S

T

W

Y

V

aa2ExtinctionCoefficient

aa2MolecularWeight

aa2Hydrophathicity

aa2PKa

diAA2Instability

aa2NTerminalPka

aa2CTerminalPka

Constructor Details

Constraints

Method Details

initMolecularWeight

initExtinctionCoefficient