org.biojava3.phylo
Class ResidueProperties

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

public class ResidueProperties
extends Object


Field Summary
static String[] aa
           
static Hashtable aa2Triplet
           
static Hashtable aa3Hash
           
static int[] aaIndex
           
static Vector Ala
           
static Hashtable aliphatic
           
static Vector Arg
           
static Hashtable aromatic
           
static Vector Asn
           
static Vector Asp
           
static double[] buried
           
static double buriedmax
           
static double buriedmin
           
static Hashtable charged
           
static Hashtable codonHash
           
static Hashtable codonHash2
           
static Vector Cys
           
static Vector Gln
           
static Vector Glu
           
static Vector Gly
           
static double[] helix
           
static double helixmax
           
static double helixmin
           
static Vector His
           
static double[] hyd
           
static double[] hyd2
           
static double hydmax
           
static double hydmin
           
static Hashtable hydrophobic
           
static Vector Ile
           
static Vector Leu
           
static Vector Lys
           
static Vector Met
           
static Color midBlue
           
static Hashtable negative
           
static Color[] nucleotide
           
static int[] nucleotideIndex
           
static Hashtable nucleotideName
           
static Vector Phe
           
static Color[] pidColours
           
static float[] pidThresholds
           
static Hashtable polar
           
static Hashtable positive
           
static Vector Pro
           
static Hashtable proline
           
static Hashtable propHash
           
static Vector scaleColours
           
static Hashtable scoreMatrices
           
static Vector Ser
           
static Hashtable small
           
static Hashtable ssHash
           
static Vector STOP
           
static double[] strand
           
static double strandmax
           
static double strandmin
           
static Color[] taylor
           
static Vector Thr
           
static Hashtable tiny
           
static Hashtable toDssp3State
           
static Vector Trp
           
static double[] turn
           
static double turnmax
           
static double turnmin
           
static Vector Tyr
           
static Vector Val
           
static Color[] zappo
           
 
Method Summary
static String codonTranslate(String codon)
           
static Hashtable getAA3Hash()
           
static int[][] getBLOSUM62()
           
static int getBLOSUM62(char c1, char c2)
           
static Vector getCodons(String res)
           
static int[][] getDefaultDnaMatrix()
           
static int[][] getDefaultPeptideMatrix()
           
static int[][] getDNA()
           
static String getDssp3state(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(String A1, String A2)
           
static ScoreMatrix getScoreMatrix(String pwtype)
          get a ScoreMatrix based on its string name
static void main(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 Hashtable scoreMatrices

aaIndex

public static final int[] aaIndex

nucleotideIndex

public static final int[] nucleotideIndex

aa3Hash

public static final Hashtable aa3Hash

aa2Triplet

public static final Hashtable aa2Triplet

nucleotideName

public static final Hashtable nucleotideName

aa

public static final String[] aa

midBlue

public static final Color midBlue

scaleColours

public static final Vector scaleColours

taylor

public static final Color[] taylor

nucleotide

public static final Color[] nucleotide

zappo

public static final 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 Hashtable ssHash

pidColours

public static final Color[] pidColours

pidThresholds

public static final float[] pidThresholds

codonHash

public static Hashtable codonHash

Lys

public static Vector Lys

Asn

public static Vector Asn

Gln

public static Vector Gln

His

public static Vector His

Glu

public static Vector Glu

Asp

public static Vector Asp

Tyr

public static Vector Tyr

Thr

public static Vector Thr

Pro

public static Vector Pro

Ala

public static Vector Ala

Ser

public static Vector Ser

Arg

public static Vector Arg

Gly

public static Vector Gly

Trp

public static Vector Trp

Cys

public static Vector Cys

Ile

public static Vector Ile

Met

public static Vector Met

Leu

public static Vector Leu

Val

public static Vector Val

Phe

public static Vector Phe

STOP

public static Vector STOP

codonHash2

public static Hashtable codonHash2

propHash

public static Hashtable propHash

hydrophobic

public static Hashtable hydrophobic

polar

public static Hashtable polar

small

public static Hashtable small

positive

public static Hashtable positive

negative

public static Hashtable negative

charged

public static Hashtable charged

aromatic

public static Hashtable aromatic

aliphatic

public static Hashtable aliphatic

tiny

public static Hashtable tiny

proline

public static Hashtable proline

toDssp3State

public static Hashtable toDssp3State
Method Detail

getHydmax

public static double getHydmax()

getHydmin

public static double getHydmin()

getHyd

public static double[] getHyd()

getAA3Hash

public static Hashtable getAA3Hash()

getDNA

public static int[][] getDNA()

getBLOSUM62

public static int[][] getBLOSUM62()

getPAM250

public static int getPAM250(String A1,
                            String A2)

getBLOSUM62

public static int getBLOSUM62(char c1,
                              char c2)

getCodons

public static Vector getCodons(String res)

codonTranslate

public static String codonTranslate(String codon)

getDefaultPeptideMatrix

public static int[][] getDefaultPeptideMatrix()

getDefaultDnaMatrix

public static int[][] getDefaultDnaMatrix()

getScoreMatrix

public static ScoreMatrix getScoreMatrix(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 String getDssp3state(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(String[] args)