Package org.biojava.nbio.aaproperties

Class Constraints

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