See: Description
Interface | Description |
---|---|
AminoAcid |
A
Group that represents an AminoAcid. |
Atom |
A simple interface for an Atom.
|
AtomPositionMap.GroupMatcher | |
Chain |
Defines the interface for a Chain.
|
Group |
This is the data structure for a single Group of atoms.
|
PDBRecord |
An interface implemented by all classes that represent PDB records
|
Structure |
Interface for a structure object.
|
StructureIdentifier |
An identifier that uniquely identifies a whole
Structure or arbitrary substructure,
including whole chains, ScopDomains , and CathDomains . |
Class | Description |
---|---|
AminoAcidImpl |
AminoAcid inherits most from Hetatom.
|
AtomImpl |
Implementation of an Atom of a PDB file.
|
AtomIterator |
an iterator over all atoms of a structure / group.
|
AtomPositionMap |
A map from
ResidueNumbers to ATOM record positions in a PDB file. |
Author |
Describes author attributes for author information in a PDB file.
|
Bond |
A simple bond -- it stores information about two atoms as well as information
about its bond order.
|
Calc |
utility operations on Atoms, AminoAcids, etc.
|
ChainImpl |
A Chain in a PDB file.
|
Compound |
Created by IntelliJ IDEA.
|
DBRef |
A class to represent database cross references.
|
GroupIterator |
An iterator over all groups of a structure.
|
GroupType |
contains only the static declaration of which types of Groups are available
|
HetatomImpl |
Generic Implementation of a Group interface.
|
Identifier |
A collection of utilities to create
StructureIdentifiers . |
JournalArticle |
PDB-specific
|
Mutator |
A class that can change one amino acid to another.
|
NucleotideImpl |
A nucleotide group is almost the same as a Hetatm group.
|
PDBCrystallographicInfo |
A class to hold crystallographic information about a PDB structure.
|
PDBHeader |
A class that contains PDB Header information.
|
PDBStatus |
Methods for getting the status of a PDB file (current, obsolete, etc)
and for accessing different versions of the structure.
|
ResidueNumber |
Everything that is needed to uniquely describe a residue position
|
ResidueRange |
A chain, a start residue, and an end residue.
|
Site |
Holds the data of sites presented in PDB files.
|
SSBond |
A simple bean to store disulfid bridge information, the SSBOND records in the PDB files.
|
StandardAminoAcid |
A class that provides a set of standard amino acids.
|
StructureImpl |
Implementation of a PDB Structure.
|
StructureTools |
A class that provides some tool methods.
|
SubstructureIdentifier |
An arbitrary collection of residues in a
Structure . |
SVDSuperimposer |
A class that calculates the superimposition between two sets of atoms
inspired by the biopython SVDSuperimposer class...
|
UriIdentifier |
A
StructureIdentifier that uses URIs to identify structures. |
Enum | Description |
---|---|
BondType |
Work in progress - NOT final!
|
Element |
Element is an enumeration of the elements of the periodic table.
|
ElementType |
ElementType is an enumeration of the types of elements found in the periodic table.
|
PDBStatus.Status |
Represents the status of PDB IDs.
|
Exception | Description |
---|---|
StructureException |
An exception during the parsing of a PDB file.
|
UnknownPdbAminoAcidException |
An exception for use during translating amino acids in a PDB file.
|
Interfaces and classes for protein structure (PDB).
See also the BioJava 3 tutorial for more information on the protein structure modules.
Structure | Chain | Group | AtomLearn more how to work with groups.
For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure