de.bioforscher.singa.structure.model.families

Enum MatcherFamily

java.lang.Object

java.lang.Enum<MatcherFamily>

de.bioforscher.singa.structure.model.families.MatcherFamily

All Implemented Interfaces:

StructuralFamily<MatcherFamily>, Serializable, Comparable<MatcherFamily>

public enum MatcherFamily
extends Enum<MatcherFamily>
implements StructuralFamily<MatcherFamily>

This is a StructuralFamily that groups others. Using this, one can employ the definition of exchanges to be allowed for a group of residues.

Author:

fk

Enum Constant Summary

Enum Constants

Enum Constant and Description
ALL
FUNCTIONAL_AROMATIC
FUNCTIONAL_NEGATIVE
FUNCTIONAL_POLAR
FUNCTIONAL_POSITIVE
FUNCTIONAL_UNPOLAR
GUTTERIDGE_AMIDE
GUTTERIDGE_AMINE
GUTTERIDGE_CARBOXYLATE
GUTTERIDGE_GUANIDIUM
GUTTERIDGE_HYDROXYL
GUTTERIDGE_IMIDAZOLE
GUTTERIDGE_OTHERS
GUTTERIDGE_THIOL

Field Summary

Fields

Modifier and Type	Field and Description
static EnumSet<MatcherFamily>	ALL_AMINO_ACIDS
static EnumSet<MatcherFamily>	FUNCTIONAL The following types are grouped according to functional chemical groups:
static EnumSet<MatcherFamily>	GUTTERIDGE The following types are grouped according to

Method Summary

Modifier and Type	Method and Description
EnumSet<AminoAcidFamily>	getMembers()
String	getOneLetterCode()
String	getThreeLetterCode()
static MatcherFamily	valueOf(String name) Returns the enum constant of this type with the specified name.
static MatcherFamily[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Comparable

compareTo

Enum Constant Detail

ALL

public static final MatcherFamily ALL

GUTTERIDGE_IMIDAZOLE

public static final MatcherFamily GUTTERIDGE_IMIDAZOLE

GUTTERIDGE_AMINE

public static final MatcherFamily GUTTERIDGE_AMINE

GUTTERIDGE_CARBOXYLATE

public static final MatcherFamily GUTTERIDGE_CARBOXYLATE

GUTTERIDGE_AMIDE

public static final MatcherFamily GUTTERIDGE_AMIDE

GUTTERIDGE_HYDROXYL

public static final MatcherFamily GUTTERIDGE_HYDROXYL

GUTTERIDGE_THIOL

public static final MatcherFamily GUTTERIDGE_THIOL

GUTTERIDGE_GUANIDIUM

public static final MatcherFamily GUTTERIDGE_GUANIDIUM

GUTTERIDGE_OTHERS

public static final MatcherFamily GUTTERIDGE_OTHERS

FUNCTIONAL_AROMATIC

public static final MatcherFamily FUNCTIONAL_AROMATIC

FUNCTIONAL_NEGATIVE

public static final MatcherFamily FUNCTIONAL_NEGATIVE

FUNCTIONAL_POSITIVE

public static final MatcherFamily FUNCTIONAL_POSITIVE

FUNCTIONAL_POLAR

public static final MatcherFamily FUNCTIONAL_POLAR

FUNCTIONAL_UNPOLAR

public static final MatcherFamily FUNCTIONAL_UNPOLAR

Field Detail

GUTTERIDGE

public static final EnumSet<MatcherFamily> GUTTERIDGE

The following types are grouped according to

      Gutteridge, A. and Thornton, J. M.:
      Understanding nature's catalytic toolkit Trends in biochemical sciences, Elsevier, 2005, 30, 622-629.
 

FUNCTIONAL

public static EnumSet<MatcherFamily> FUNCTIONAL

The following types are grouped according to functional chemical groups:

      aromatic (a)             F,Y,W
      negatively charged (n)   D,E
      positively charged (p)   K,R,H
      polar, uncharged (o)     P,N,Q,C,T,S
      nonpolar, aliphatic (i)  G,A,V,L,M,I
 

ALL_AMINO_ACIDS

public static EnumSet<MatcherFamily> ALL_AMINO_ACIDS

Method Detail

values

public static MatcherFamily[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (MatcherFamily c : MatcherFamily.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static MatcherFamily valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

getMembers

public EnumSet<AminoAcidFamily> getMembers()

getOneLetterCode

public String getOneLetterCode()

Specified by:

getOneLetterCode in interface StructuralFamily<MatcherFamily>

getThreeLetterCode

public String getThreeLetterCode()

Specified by:

getThreeLetterCode in interface StructuralFamily<MatcherFamily>