org.biojava.nbio.structure

Enum EntityType

java.lang.Object

java.lang.Enum<EntityType>

org.biojava.nbio.structure.EntityType

All Implemented Interfaces:

Serializable, Comparable<EntityType>

public enum EntityType
extends Enum<EntityType>

The type of entity (polymer, non-polymer, water, macrolide) as defined in the mmCIF dictionary:

Entities are of four types: polymer, non-polymer, macrolide and water.

Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. It is not clear what macrolides are, but they appear to be supported since mmCIF 4.0.

Author:

Anthony Bradley, Jose Duarte

Enum Constant Summary

Enum Constants

Enum Constant and Description
MACROLIDE Macrolide.
NONPOLYMER Non-polymeric entities: ligands, metal ions, buffer molecules, etc
POLYMER Polymeric entities: poly-peptides and nucleotide chains
WATER Water

Method Summary

Modifier and Type	Method and Description
static EntityType	entityTypeFromString(String entityType) Creates a new EntityType from a String value.
String	getEntityType() Returns the type of the Entity as a String
static EntityType	valueOf(String name) Returns the enum constant of this type with the specified name.
static EntityType[]	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

Enum Constant Detail

POLYMER

public static final EntityType POLYMER

Polymeric entities: poly-peptides and nucleotide chains

NONPOLYMER

public static final EntityType NONPOLYMER

Non-polymeric entities: ligands, metal ions, buffer molecules, etc

WATER

public static final EntityType WATER

Water

MACROLIDE

public static final EntityType MACROLIDE

Macrolide. Supported in mmCIF 4.0 dictionary. Not clear what it refers to.

Method Detail

values

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

Returns:

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

valueOf

public static EntityType 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

getEntityType

public String getEntityType()

Returns the type of the Entity as a String

Returns:

String representation of the entity type.

entityTypeFromString

public static EntityType entityTypeFromString(String entityType)

Creates a new EntityType from a String value. Returns null if entityType is null or not one of the supported standard types.

Parameters:

entityType - String value , should be one of "polymer","non-polymer","water","macrolide"

Returns:

an EntityType object