org.biojava3.phylo
Class ResidueProperties

java.lang.Object
  org.biojava3.phylo.ResidueProperties

public class ResidueProperties
extends java.lang.Object

Field Summary

static java.lang.String[]	aa
static java.util.Hashtable	aa2Triplet
static java.util.Hashtable	aa3Hash
static int[]	aaIndex
static java.util.Vector	Ala
static java.util.Hashtable	aliphatic
static java.util.Vector	Arg
static java.util.Hashtable	aromatic
static java.util.Vector	Asn
static java.util.Vector	Asp
static double[]	buried
static double	buriedmax
static double	buriedmin
static java.util.Hashtable	charged
static java.util.Hashtable	codonHash
static java.util.Hashtable	codonHash2
static java.util.Vector	Cys
static java.util.Vector	Gln
static java.util.Vector	Glu
static java.util.Vector	Gly
static double[]	helix
static double	helixmax
static double	helixmin
static java.util.Vector	His
static double[]	hyd
static double[]	hyd2
static double	hydmax
static double	hydmin
static java.util.Hashtable	hydrophobic
static java.util.Vector	Ile
static java.util.Vector	Leu
static java.util.Vector	Lys
static java.util.Vector	Met
static java.awt.Color	midBlue
static java.util.Hashtable	negative
static java.awt.Color[]	nucleotide
static int[]	nucleotideIndex
static java.util.Hashtable	nucleotideName
static java.util.Vector	Phe
static java.awt.Color[]	pidColours
static float[]	pidThresholds
static java.util.Hashtable	polar
static java.util.Hashtable	positive
static java.util.Vector	Pro
static java.util.Hashtable	proline
static java.util.Hashtable	propHash
static java.util.Vector	scaleColours
static java.util.Hashtable	scoreMatrices
static java.util.Vector	Ser
static java.util.Hashtable	small
static java.util.Hashtable	ssHash
static java.util.Vector	STOP
static double[]	strand
static double	strandmax
static double	strandmin
static java.awt.Color[]	taylor
static java.util.Vector	Thr
static java.util.Hashtable	tiny
static java.util.Hashtable	toDssp3State
static java.util.Vector	Trp
static double[]	turn
static double	turnmax
static double	turnmin
static java.util.Vector	Tyr
static java.util.Vector	Val
static java.awt.Color[]	zappo

Method Summary

static java.lang.String	codonTranslate(java.lang.String codon)
static java.util.Hashtable	getAA3Hash()
static int[][]	getBLOSUM62()
static int	getBLOSUM62(char c1, char c2)
static java.util.Vector	getCodons(java.lang.String res)
static int[][]	getDefaultDnaMatrix()
static int[][]	getDefaultPeptideMatrix()
static int[][]	getDNA()
static java.lang.String	getDssp3state(java.lang.String ssstring) translate from other dssp secondary structure alphabets to 3-state
static double[]	getHyd()
static double	getHydmax()
static double	getHydmin()
static int	getPAM250(char c, char d)
static int	getPAM250(java.lang.String A1, java.lang.String A2)
static ScoreMatrix	getScoreMatrix(java.lang.String pwtype) get a ScoreMatrix based on its string name
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

scoreMatrices

public static java.util.Hashtable scoreMatrices

aaIndex

public static final int[] aaIndex

nucleotideIndex

public static final int[] nucleotideIndex

aa3Hash

public static final java.util.Hashtable aa3Hash

aa2Triplet

public static final java.util.Hashtable aa2Triplet

nucleotideName

public static final java.util.Hashtable nucleotideName

aa

public static final java.lang.String[] aa

midBlue

public static final java.awt.Color midBlue

scaleColours

public static final java.util.Vector scaleColours

taylor

public static final java.awt.Color[] taylor

nucleotide

public static final java.awt.Color[] nucleotide

zappo

public static final java.awt.Color[] zappo

hyd2

public static final double[] hyd2

helix

public static final double[] helix

helixmin

public static final double helixmin

See Also:

Constant Field Values

helixmax

public static final double helixmax

See Also:

Constant Field Values

strand

public static final double[] strand

strandmin

public static final double strandmin

See Also:

Constant Field Values

strandmax

public static final double strandmax

See Also:

Constant Field Values

turn

public static final double[] turn

turnmin

public static final double turnmin

See Also:

Constant Field Values

turnmax

public static final double turnmax

See Also:

Constant Field Values

buried

public static final double[] buried

buriedmin

public static final double buriedmin

See Also:

Constant Field Values

buriedmax

public static final double buriedmax

See Also:

Constant Field Values

hyd

public static final double[] hyd

hydmax

public static final double hydmax

See Also:

Constant Field Values

hydmin

public static final double hydmin

See Also:

Constant Field Values

ssHash

public static final java.util.Hashtable ssHash

pidColours

public static final java.awt.Color[] pidColours

pidThresholds

public static final float[] pidThresholds

codonHash

public static java.util.Hashtable codonHash

Lys

public static java.util.Vector Lys

Asn

public static java.util.Vector Asn

Gln

public static java.util.Vector Gln

His

public static java.util.Vector His

Glu

public static java.util.Vector Glu

Asp

public static java.util.Vector Asp

Tyr

public static java.util.Vector Tyr

Thr

public static java.util.Vector Thr

Pro

public static java.util.Vector Pro

Ala

public static java.util.Vector Ala

Ser

public static java.util.Vector Ser

Arg

public static java.util.Vector Arg

Gly

public static java.util.Vector Gly

Trp

public static java.util.Vector Trp

Cys

public static java.util.Vector Cys

Ile

public static java.util.Vector Ile

Met

public static java.util.Vector Met

Leu

public static java.util.Vector Leu

Val

public static java.util.Vector Val

Phe

public static java.util.Vector Phe

STOP

public static java.util.Vector STOP

codonHash2

public static java.util.Hashtable codonHash2

propHash

public static java.util.Hashtable propHash

hydrophobic

public static java.util.Hashtable hydrophobic

polar

public static java.util.Hashtable polar

small

public static java.util.Hashtable small

positive

public static java.util.Hashtable positive

negative

public static java.util.Hashtable negative

charged

public static java.util.Hashtable charged

aromatic

public static java.util.Hashtable aromatic

aliphatic

public static java.util.Hashtable aliphatic

tiny

public static java.util.Hashtable tiny

proline

public static java.util.Hashtable proline

toDssp3State

public static java.util.Hashtable toDssp3State

Method Detail

getHydmax

public static double getHydmax()

getHydmin

public static double getHydmin()

getHyd

public static double[] getHyd()

getAA3Hash

public static java.util.Hashtable getAA3Hash()

getDNA

public static int[][] getDNA()

getBLOSUM62

public static int[][] getBLOSUM62()

getPAM250

public static int getPAM250(java.lang.String A1,
                            java.lang.String A2)

getBLOSUM62

public static int getBLOSUM62(char c1,
                              char c2)

getCodons

public static java.util.Vector getCodons(java.lang.String res)

codonTranslate

public static java.lang.String codonTranslate(java.lang.String codon)

getDefaultPeptideMatrix

public static int[][] getDefaultPeptideMatrix()

getDefaultDnaMatrix

public static int[][] getDefaultDnaMatrix()

getScoreMatrix

public static ScoreMatrix getScoreMatrix(java.lang.String pwtype)

get a ScoreMatrix based on its string name

Parameters:

pwtype -

Returns:

matrix in scoreMatrices with key pwtype or null

getPAM250

public static int getPAM250(char c,
                            char d)

getDssp3state

public static java.lang.String getDssp3state(java.lang.String ssstring)

translate from other dssp secondary structure alphabets to 3-state

Parameters:

ssstring -

Returns:

ssstring as a three-state secondary structure assignment.

main

public static void main(java.lang.String[] args)