Package org.biojava.nbio.structure
Enum GroupType
- java.lang.Object
-
- java.lang.Enum<GroupType>
-
- org.biojava.nbio.structure.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.
-
-
-
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 namejava.lang.NullPointerException
- if the argument is null
-
toString
public java.lang.String toString()
- Overrides:
toString
in classjava.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
-
-