public class ResidueProperties
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String[] |
aa |
static java.util.Hashtable<java.lang.String,java.lang.String> |
aa2Triplet |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
aa3Hash |
static int[] |
aaIndex |
static java.util.Vector<java.lang.String> |
Ala |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
aliphatic |
static java.util.Vector<java.lang.String> |
Arg |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
aromatic |
static java.util.Vector<java.lang.String> |
Asn |
static java.util.Vector<java.lang.String> |
Asp |
static double[] |
buried |
static double |
buriedmax |
static double |
buriedmin |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
charged |
static java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>> |
codonHash |
static java.util.Hashtable<java.lang.String,java.lang.String> |
codonHash2 |
static java.util.Vector<java.lang.String> |
Cys |
static java.util.Vector<java.lang.String> |
Gln |
static java.util.Vector<java.lang.String> |
Glu |
static java.util.Vector<java.lang.String> |
Gly |
static double[] |
helix |
static double |
helixmax |
static double |
helixmin |
static java.util.Vector<java.lang.String> |
His |
static double[] |
hyd |
static double[] |
hyd2 |
static double |
hydmax |
static double |
hydmin |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
hydrophobic |
static java.util.Vector<java.lang.String> |
Ile |
static java.util.Vector<java.lang.String> |
Leu |
static java.util.Vector<java.lang.String> |
Lys |
static java.util.Vector<java.lang.String> |
Met |
static java.awt.Color |
midBlue |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
negative |
static java.awt.Color[] |
nucleotide |
static int[] |
nucleotideIndex |
static java.util.Hashtable<java.lang.String,java.lang.String> |
nucleotideName |
static java.util.Vector<java.lang.String> |
Phe |
static java.awt.Color[] |
pidColours |
static float[] |
pidThresholds |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
polar |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
positive |
static java.util.Vector<java.lang.String> |
Pro |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
proline |
static java.util.Hashtable<java.lang.String,java.util.Hashtable<java.lang.String,java.lang.Integer>> |
propHash |
static java.util.Vector<java.awt.Color> |
scaleColours |
static java.util.Hashtable<java.lang.String,ScoreMatrix> |
scoreMatrices |
static java.util.Vector<java.lang.String> |
Ser |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
small |
static java.util.Hashtable<java.lang.String,java.awt.Color> |
ssHash |
static java.util.Vector<java.lang.String> |
STOP |
static double[] |
strand |
static double |
strandmax |
static double |
strandmin |
static java.awt.Color[] |
taylor |
static java.util.Vector<java.lang.String> |
Thr |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
tiny |
static java.util.Hashtable<java.lang.String,java.lang.String> |
toDssp3State |
static java.util.Vector<java.lang.String> |
Trp |
static double[] |
turn |
static double |
turnmax |
static double |
turnmin |
static java.util.Vector<java.lang.String> |
Tyr |
static java.util.Vector<java.lang.String> |
Val |
static java.awt.Color[] |
zappo |
Modifier and Type | Method and Description |
---|---|
static java.lang.String |
codonTranslate(java.lang.String codon) |
static java.util.Hashtable<java.lang.String,java.lang.Integer> |
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) |
public static java.util.Hashtable<java.lang.String,ScoreMatrix> scoreMatrices
public static final int[] aaIndex
public static final int[] nucleotideIndex
public static final java.util.Hashtable<java.lang.String,java.lang.Integer> aa3Hash
public static final java.util.Hashtable<java.lang.String,java.lang.String> aa2Triplet
public static final java.util.Hashtable<java.lang.String,java.lang.String> nucleotideName
public static final java.lang.String[] aa
public static final java.awt.Color midBlue
public static final java.util.Vector<java.awt.Color> scaleColours
public static final java.awt.Color[] taylor
public static final java.awt.Color[] nucleotide
public static final java.awt.Color[] zappo
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 java.util.Hashtable<java.lang.String,java.awt.Color> ssHash
public static final java.awt.Color[] pidColours
public static final float[] pidThresholds
public static java.util.Hashtable<java.lang.String,java.util.Vector<java.lang.String>> codonHash
public static java.util.Vector<java.lang.String> Lys
public static java.util.Vector<java.lang.String> Asn
public static java.util.Vector<java.lang.String> Gln
public static java.util.Vector<java.lang.String> His
public static java.util.Vector<java.lang.String> Glu
public static java.util.Vector<java.lang.String> Asp
public static java.util.Vector<java.lang.String> Tyr
public static java.util.Vector<java.lang.String> Thr
public static java.util.Vector<java.lang.String> Pro
public static java.util.Vector<java.lang.String> Ala
public static java.util.Vector<java.lang.String> Ser
public static java.util.Vector<java.lang.String> Arg
public static java.util.Vector<java.lang.String> Gly
public static java.util.Vector<java.lang.String> Trp
public static java.util.Vector<java.lang.String> Cys
public static java.util.Vector<java.lang.String> Ile
public static java.util.Vector<java.lang.String> Met
public static java.util.Vector<java.lang.String> Leu
public static java.util.Vector<java.lang.String> Val
public static java.util.Vector<java.lang.String> Phe
public static java.util.Vector<java.lang.String> STOP
public static java.util.Hashtable<java.lang.String,java.lang.String> codonHash2
public static java.util.Hashtable<java.lang.String,java.util.Hashtable<java.lang.String,java.lang.Integer>> propHash
public static java.util.Hashtable<java.lang.String,java.lang.Integer> hydrophobic
public static java.util.Hashtable<java.lang.String,java.lang.Integer> polar
public static java.util.Hashtable<java.lang.String,java.lang.Integer> small
public static java.util.Hashtable<java.lang.String,java.lang.Integer> positive
public static java.util.Hashtable<java.lang.String,java.lang.Integer> negative
public static java.util.Hashtable<java.lang.String,java.lang.Integer> charged
public static java.util.Hashtable<java.lang.String,java.lang.Integer> aromatic
public static java.util.Hashtable<java.lang.String,java.lang.Integer> aliphatic
public static java.util.Hashtable<java.lang.String,java.lang.Integer> tiny
public static java.util.Hashtable<java.lang.String,java.lang.Integer> proline
public static java.util.Hashtable<java.lang.String,java.lang.String> toDssp3State
public static double getHydmax()
public static double getHydmin()
public static double[] getHyd()
public static java.util.Hashtable<java.lang.String,java.lang.Integer> getAA3Hash()
public static int[][] getDNA()
public static int[][] getBLOSUM62()
public static int getPAM250(java.lang.String A1, java.lang.String A2)
public static int getBLOSUM62(char c1, char c2)
public static java.util.Vector<?> getCodons(java.lang.String res)
public static java.lang.String codonTranslate(java.lang.String codon)
public static int[][] getDefaultPeptideMatrix()
public static int[][] getDefaultDnaMatrix()
public static ScoreMatrix getScoreMatrix(java.lang.String pwtype)
pwtype
- public static int getPAM250(char c, char d)
public static java.lang.String getDssp3state(java.lang.String ssstring)
ssstring
- public static void main(java.lang.String[] args)