org.biojava3.phylo
public class ResidueProperties extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
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 |
Modifier and Type | Method and Description |
---|---|
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) |
public static java.util.Hashtable scoreMatrices
public static final int[] aaIndex
public static final int[] nucleotideIndex
public static final java.util.Hashtable aa3Hash
public static final java.util.Hashtable aa2Triplet
public static final java.util.Hashtable nucleotideName
public static final java.lang.String[] aa
public static final java.awt.Color midBlue
public static final java.util.Vector 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 ssHash
public static final java.awt.Color[] pidColours
public static final float[] pidThresholds
public static java.util.Hashtable codonHash
public static java.util.Vector Lys
public static java.util.Vector Asn
public static java.util.Vector Gln
public static java.util.Vector His
public static java.util.Vector Glu
public static java.util.Vector Asp
public static java.util.Vector Tyr
public static java.util.Vector Thr
public static java.util.Vector Pro
public static java.util.Vector Ala
public static java.util.Vector Ser
public static java.util.Vector Arg
public static java.util.Vector Gly
public static java.util.Vector Trp
public static java.util.Vector Cys
public static java.util.Vector Ile
public static java.util.Vector Met
public static java.util.Vector Leu
public static java.util.Vector Val
public static java.util.Vector Phe
public static java.util.Vector STOP
public static java.util.Hashtable codonHash2
public static java.util.Hashtable propHash
public static java.util.Hashtable hydrophobic
public static java.util.Hashtable polar
public static java.util.Hashtable small
public static java.util.Hashtable positive
public static java.util.Hashtable negative
public static java.util.Hashtable charged
public static java.util.Hashtable aromatic
public static java.util.Hashtable aliphatic
public static java.util.Hashtable tiny
public static java.util.Hashtable proline
public static java.util.Hashtable toDssp3State
public static double getHydmax()
public static double getHydmin()
public static double[] getHyd()
public static java.util.Hashtable 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)