org.biojava3.phylo
Class ResidueProperties
java.lang.Object
org.biojava3.phylo.ResidueProperties
public class ResidueProperties
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
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)