public class ResidueProperties extends Object
| Modifier and Type | Method and Description |
|---|---|
static String |
codonTranslate(String codon) |
static Hashtable<String,Integer> |
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<String,ScoreMatrix> scoreMatrices
public static final int[] aaIndex
public static final int[] nucleotideIndex
public static final String[] aa
public static final Color midBlue
public static final Color[] taylor
public static final Color[] nucleotide
public static final 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 Color[] pidColours
public static final float[] pidThresholds
public static double getHydmax()
public static double getHydmin()
public static double[] getHyd()
public static int[][] getDNA()
public static int[][] getBLOSUM62()
public static int getBLOSUM62(char c1,
char c2)
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 - public static void main(String[] args)
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