Package org.biojava.nbio.structure

Enum 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 Detail

      • POLYMER

        public static final EntityType POLYMER
        Polymeric entities: poly-peptides and nucleotide chains

      • BRANCHED

        public static final EntityType BRANCHED
        The 'branched' type use mainly to represent carbohydrates. The type was introduced in these versions of the mmcif dictionary: 5.101 2012-08-22 5.291 2017-09-10 5.304 2018-08-01 The type will only be used for PDB-deposited files from July 2020, as part of the carbohydrate remediation project.
        Since:
        5.4.0

      • NONPOLYMER

        public static final EntityType NONPOLYMER
        Non-polymeric entities: ligands, metal ions, buffer molecules, etc

      • 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