Package org.biojava.nbio.structure

Enum Class GroupType

java.lang.Object
java.lang.Enum<GroupType>
org.biojava.nbio.structure.GroupType
All Implemented Interfaces:
Serializable, Comparable<GroupType>, Constable
public enum GroupType extends Enum<GroupType>
This contains basic categories for Group types. It reflects the categorization used in old PDB file (e.g. for storing whether a residue is composed of ATOM or HETATM records. It is less specific than the mmCIF/PDBx-defined ResidueType enum, which may be more suitable for future applications.
Since:
1.7
Author:
Andreas Prlic, Spencer Bliven
See Also:

  • Enum Constant Details

    • AMINOACID

      public static final GroupType AMINOACID
      The type for amino acids (L-peptides)

    • NUCLEOTIDE

      public static final GroupType NUCLEOTIDE
      The type for nucleotide groups (dna and rna)

    • HETATM

      public static final GroupType HETATM
      The type for hetero groups (everything else)

  • Field Details

    • WATERNAMES

      public static final List<String> WATERNAMES
      The 3-letter codes used in the PDB to identify water molecules
      See Also:

  • Method Details

    • values

      public static GroupType[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared

    • valueOf

      public static GroupType valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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 class has no constant with the specified name
      NullPointerException - if the argument is null

    • toString

      public String toString()
      Overrides:
      toString in class Enum<GroupType>
      Returns:
      The name of this GroupType. One of "amino", "nucleotide", or "hetatm"

    • getResidueTypes

      public Set<ResidueType> getResidueTypes()
      Get a set of ResidueTypes loosely equivalent to this GroupType.

      Because mmCIF and PDB handle modified residues differently, some Groups may have a well-defined ResidueType yet still be HETATMs.

      Returns:
      A Set of ResidueTypes commonly classified as this GroupType