de.bioforscher.singa.structure.model.families

Enum AminoAcidFamily

java.lang.Object

java.lang.Enum<AminoAcidFamily>

de.bioforscher.singa.structure.model.families.AminoAcidFamily

All Implemented Interfaces:

StructuralFamily<AminoAcidFamily>, Serializable, Comparable<AminoAcidFamily>

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

A AminoAcidFamily contains the general information of a type of amino acid.

Author:

cl

Enum Constant Summary

Enum Constants

Enum Constant and Description
ALANINE
ARGININE
ASPARAGINE
ASPARTIC_ACID
CYSTEINE
GAP
GLUTAMIC_ACID
GLUTAMINE
GLYCINE
HISTIDINE
ISOLEUCINE
LEUCINE
LYSINE
METHIONINE
PHENYLALANINE
PROLINE
SERINE
THREONINE
TRYPTOPHAN
TYROSINE
UNKNOWN
VALINE

Method Summary

Modifier and Type	Method and Description
boolean	containsExpectedAtoms(List<Atom> atoms, AminoAcidFamily aminoAcidFamily) Returns true if the set of AtomFilter contains only Atom names, that can occur in the given residue type.
EnumSet<AtomName>	getAllowedAtoms()
static Optional<AminoAcidFamily>	getAminoAcidTypeByOneLetterCode(char oneLetterCode)
static Optional<AminoAcidFamily>	getAminoAcidTypeByOneLetterCode(String oneLetterCode)
static Optional<AminoAcidFamily>	getAminoAcidTypeByThreeLetterCode(String threeLetterCode)
String	getName()
String	getOneLetterCode()
AminoAcid	getPrototype() Returns a prototype of the AminoAcid that are deposited in the project resources.
String	getThreeLetterCode()
static AminoAcidFamily	valueOf(String name) Returns the enum constant of this type with the specified name.
static AminoAcidFamily[]	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

ALANINE

public static final AminoAcidFamily ALANINE

ARGININE

public static final AminoAcidFamily ARGININE

ASPARAGINE

public static final AminoAcidFamily ASPARAGINE

ASPARTIC_ACID

public static final AminoAcidFamily ASPARTIC_ACID

CYSTEINE

public static final AminoAcidFamily CYSTEINE

GLUTAMINE

public static final AminoAcidFamily GLUTAMINE

GLUTAMIC_ACID

public static final AminoAcidFamily GLUTAMIC_ACID

GLYCINE

public static final AminoAcidFamily GLYCINE

HISTIDINE

public static final AminoAcidFamily HISTIDINE

ISOLEUCINE

public static final AminoAcidFamily ISOLEUCINE

LEUCINE

public static final AminoAcidFamily LEUCINE

LYSINE

public static final AminoAcidFamily LYSINE

METHIONINE

public static final AminoAcidFamily METHIONINE

PHENYLALANINE

public static final AminoAcidFamily PHENYLALANINE

PROLINE

public static final AminoAcidFamily PROLINE

SERINE

public static final AminoAcidFamily SERINE

THREONINE

public static final AminoAcidFamily THREONINE

TRYPTOPHAN

public static final AminoAcidFamily TRYPTOPHAN

TYROSINE

public static final AminoAcidFamily TYROSINE

VALINE

public static final AminoAcidFamily VALINE

UNKNOWN

public static final AminoAcidFamily UNKNOWN

GAP

public static final AminoAcidFamily GAP

Method Detail

values

public static AminoAcidFamily[] 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 (AminoAcidFamily c : AminoAcidFamily.values())
    System.out.println(c);

Returns:

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

valueOf

public static AminoAcidFamily 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

getAminoAcidTypeByThreeLetterCode

public static Optional<AminoAcidFamily> getAminoAcidTypeByThreeLetterCode(String threeLetterCode)

getAminoAcidTypeByOneLetterCode

public static Optional<AminoAcidFamily> getAminoAcidTypeByOneLetterCode(char oneLetterCode)

getAminoAcidTypeByOneLetterCode

public static Optional<AminoAcidFamily> getAminoAcidTypeByOneLetterCode(String oneLetterCode)

getName

public String getName()

getOneLetterCode

public String getOneLetterCode()

Specified by:

getOneLetterCode in interface StructuralFamily<AminoAcidFamily>

getThreeLetterCode

public String getThreeLetterCode()

Specified by:

getThreeLetterCode in interface StructuralFamily<AminoAcidFamily>

getAllowedAtoms

public EnumSet<AtomName> getAllowedAtoms()

containsExpectedAtoms

public boolean containsExpectedAtoms(List<Atom> atoms,
                                     AminoAcidFamily aminoAcidFamily)

Returns true if the set of AtomFilter contains only Atom names, that can occur in the given residue type.

Parameters:

atoms - The atoms to be checked.

aminoAcidFamily - The expected type of residue.

Returns:

True, if the set of AtomFilter contains only Atom names, that can occur in the given residue type.

getPrototype

public AminoAcid getPrototype()

Returns a prototype of the AminoAcid that are deposited in the project resources.

Returns:

A AminoAcid prototype.