Enum GroupType

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<GroupType>

    public enum GroupType
    extends java.lang.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:
    ResidueType
    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description
      AMINOACID
      The type for amino acids (L-peptides)
      HETATM
      The type for hetero groups (everything else)
      NUCLEOTIDE
      The type for nucleotide groups (dna and rna)
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.util.List<java.lang.String> WATERNAMES
      The 3-letter codes used in the PDB to identify water molecules
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.Set<ResidueType> getResidueTypes()
      Get a set of ResidueTypes loosely equivalent to this GroupType.
      java.lang.String toString()  
      static GroupType valueOf​(java.lang.String name)
      Returns the enum constant of this type with the specified name.
      static GroupType[] 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, valueOf
      • Methods inherited from class java.lang.Object

        getClass, notify, notifyAll, wait, wait, wait
    • Enum Constant Detail

      • 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 Detail

      • WATERNAMES

        public static final java.util.List<java.lang.String> WATERNAMES
        The 3-letter codes used in the PDB to identify water molecules
        See Also:
        Group.isWater()
    • Method Detail

      • values

        public static GroupType[] 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 (GroupType c : GroupType.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static GroupType valueOf​(java.lang.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:
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        java.lang.NullPointerException - if the argument is null
      • toString

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

        public java.util.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