public class ResidueProperties extends Object
| Modifier and Type | Field and Description |
|---|---|
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 |
| Modifier and Type | Method and Description |
|---|---|
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) |
public static Hashtable scoreMatrices
public static final int[] aaIndex
public static final int[] nucleotideIndex
public static final Hashtable aa2Triplet
public static final Hashtable nucleotideName
public static final Vector scaleColours
public static final Color[] nucleotide
public static final double[] hyd2
public static final double[] helix
public static final double helixmin
public static final double helixmax
public static final double[] strand
public static final double strandmin
public static final double strandmax
public static final double[] turn
public static final double turnmin
public static final double turnmax
public static final double[] buried
public static final double buriedmin
public static final double buriedmax
public static final double[] hyd
public static final double hydmax
public static final double hydmin
public static final Color[] pidColours
public static final float[] pidThresholds
public static Hashtable codonHash2
public static Hashtable hydrophobic
public static Hashtable toDssp3State
public static double getHydmax()
public static double getHydmin()
public static double[] getHyd()
public static Hashtable getAA3Hash()
public static int[][] getDNA()
public static int[][] getBLOSUM62()
public static int getBLOSUM62(char c1, char c2)
public static String codonTranslate(String codon)
public static int[][] getDefaultPeptideMatrix()
public static int[][] getDefaultDnaMatrix()
public static ScoreMatrix getScoreMatrix(String pwtype)
pwtype - public static int getPAM250(char c, char d)
public static String getDssp3state(String ssstring)
ssstring - Copyright © 2012 BioJava. All Rights Reserved.