org.biojava.nbio.structure

Enum GroupType

java.lang.Object

java.lang.Enum<GroupType>

org.biojava.nbio.structure.GroupType

All Implemented Interfaces:

Serializable, Comparable<GroupType>

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:

ResidueType

Enum Constant Summary

Enum Constants

Enum Constant and 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 and Description
static List<String>	WATERNAMES The 3-letter codes used in the PDB to identify water molecules

Method Summary

Methods

Modifier and Type	Method and Description
Set<ResidueType>	getResidueTypes() Get a set of ResidueTypes loosely equivalent to this GroupType.
String	toString()
static GroupType	valueOf(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 List<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(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

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