ResidueProperties (biojava-phylo 4.0.0 API)

java.lang.Object
- org.biojava.nbio.phylo.ResidueProperties

public class ResidueProperties
extends Object

Field Summary

Fields
Modifier and Type	Field and Description
`static String[]`	`aa`
`static Hashtable<String,String>`	`aa2Triplet`
`static Hashtable<String,Integer>`	`aa3Hash`
`static int[]`	`aaIndex`
`static Vector<String>`	`Ala`
`static Hashtable<String,Integer>`	`aliphatic`
`static Vector<String>`	`Arg`
`static Hashtable<String,Integer>`	`aromatic`
`static Vector<String>`	`Asn`
`static Vector<String>`	`Asp`
`static double[]`	`buried`
`static double`	`buriedmax`
`static double`	`buriedmin`
`static Hashtable<String,Integer>`	`charged`
`static Hashtable<String,Vector<String>>`	`codonHash`
`static Hashtable<String,String>`	`codonHash2`
`static Vector<String>`	`Cys`
`static Vector<String>`	`Gln`
`static Vector<String>`	`Glu`
`static Vector<String>`	`Gly`
`static double[]`	`helix`
`static double`	`helixmax`
`static double`	`helixmin`
`static Vector<String>`	`His`
`static double[]`	`hyd`
`static double[]`	`hyd2`
`static double`	`hydmax`
`static double`	`hydmin`
`static Hashtable<String,Integer>`	`hydrophobic`
`static Vector<String>`	`Ile`
`static Vector<String>`	`Leu`
`static Vector<String>`	`Lys`
`static Vector<String>`	`Met`
`static Color`	`midBlue`
`static Hashtable<String,Integer>`	`negative`
`static Color[]`	`nucleotide`
`static int[]`	`nucleotideIndex`
`static Hashtable<String,String>`	`nucleotideName`
`static Vector<String>`	`Phe`
`static Color[]`	`pidColours`
`static float[]`	`pidThresholds`
`static Hashtable<String,Integer>`	`polar`
`static Hashtable<String,Integer>`	`positive`
`static Vector<String>`	`Pro`
`static Hashtable<String,Integer>`	`proline`
`static Hashtable<String,Hashtable<String,Integer>>`	`propHash`
`static Vector<Color>`	`scaleColours`
`static Hashtable<String,ScoreMatrix>`	`scoreMatrices`
`static Vector<String>`	`Ser`
`static Hashtable<String,Integer>`	`small`
`static Hashtable<String,Color>`	`ssHash`
`static Vector<String>`	`STOP`
`static double[]`	`strand`
`static double`	`strandmax`
`static double`	`strandmin`
`static Color[]`	`taylor`
`static Vector<String>`	`Thr`
`static Hashtable<String,Integer>`	`tiny`
`static Hashtable<String,String>`	`toDssp3State`
`static Vector<String>`	`Trp`
`static double[]`	`turn`
`static double`	`turnmax`
`static double`	`turnmin`
`static Vector<String>`	`Tyr`
`static Vector<String>`	`Val`
`static Color[]`	`zappo`

Method Summary

Methods
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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

scoreMatrices

public static Hashtable<String,ScoreMatrix> scoreMatrices

aaIndex
```
public static final int[] aaIndex
```

nucleotideIndex

public static final int[] nucleotideIndex

aa3Hash

public static final Hashtable<String,Integer> aa3Hash

aa2Triplet

public static final Hashtable<String,String> aa2Triplet

nucleotideName

public static final Hashtable<String,String> nucleotideName

aa
```
public static final String[] aa
```

midBlue
```
public static final Color midBlue
```

scaleColours

public static final Vector<Color> 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<String,Color> ssHash

pidColours
```
public static final Color[] pidColours
```

pidThresholds

public static final float[] pidThresholds

codonHash

public static Hashtable<String,Vector<String>> codonHash

Lys
```
public static Vector<String> Lys
```

Asn
```
public static Vector<String> Asn
```

Gln
```
public static Vector<String> Gln
```

His
```
public static Vector<String> His
```

Glu
```
public static Vector<String> Glu
```

Asp
```
public static Vector<String> Asp
```

Tyr
```
public static Vector<String> Tyr
```

Thr
```
public static Vector<String> Thr
```

Pro
```
public static Vector<String> Pro
```

Ala
```
public static Vector<String> Ala
```

Ser
```
public static Vector<String> Ser
```

Arg
```
public static Vector<String> Arg
```

Gly
```
public static Vector<String> Gly
```

Trp
```
public static Vector<String> Trp
```

Cys
```
public static Vector<String> Cys
```

Ile
```
public static Vector<String> Ile
```

Met
```
public static Vector<String> Met
```

Leu
```
public static Vector<String> Leu
```

Val
```
public static Vector<String> Val
```

Phe
```
public static Vector<String> Phe
```

STOP
```
public static Vector<String> STOP
```

codonHash2

public static Hashtable<String,String> codonHash2

propHash

public static Hashtable<String,Hashtable<String,Integer>> propHash

hydrophobic

public static Hashtable<String,Integer> hydrophobic

polar

public static Hashtable<String,Integer> polar

small

public static Hashtable<String,Integer> small

positive

public static Hashtable<String,Integer> positive

negative

public static Hashtable<String,Integer> negative

charged

public static Hashtable<String,Integer> charged

aromatic

public static Hashtable<String,Integer> aromatic

aliphatic

public static Hashtable<String,Integer> aliphatic

tiny

public static Hashtable<String,Integer> tiny

proline

public static Hashtable<String,Integer> proline

toDssp3State

public static Hashtable<String,String> toDssp3State

Method Detail

getHydmax
```
public static double getHydmax()
```

getHydmin
```
public static double getHydmin()
```

getHyd
```
public static double[] getHyd()
```

getAA3Hash

public static Hashtable<String,Integer> 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)

Class ResidueProperties

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

scoreMatrices

aaIndex

nucleotideIndex

aa3Hash

aa2Triplet

nucleotideName

aa

midBlue

scaleColours

taylor

nucleotide

zappo

hyd2

helix

helixmin

helixmax

strand

strandmin

strandmax

turn

turnmin

turnmax

buried

buriedmin

buriedmax

hyd

hydmax

hydmin

ssHash

pidColours

pidThresholds

codonHash

Lys

Asn

Gln

His

Glu

Asp

Tyr

Thr

Pro

Ala

Ser

Arg

Gly

Trp

Cys

Ile

Met

Leu

Val

Phe

STOP

codonHash2

propHash

hydrophobic

polar

small

positive

negative

charged

aromatic

aliphatic

tiny

proline

toDssp3State

Method Detail

getHydmax

getHydmin

getHyd

getAA3Hash

getDNA

getBLOSUM62

getPAM250

getBLOSUM62