org.biojava.bio.structure

Interface Summary
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 Summary
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 Summary
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 Summary
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.

Package org.biojava.bio.structure Description

Interfaces and classes for protein structure (PDB).

See also the BioJava 3 tutorial for more information on the protein structure modules.

Parse PDB files

To load a PDB file see the PDBFileReader class in the IO subpackage.

Parse mmCif files

To laod a mmCif file see the MMCIFFileReader class.

The Structure object

The Structure object allows to access the PDB header information as well as to the data from the ATOM records. The header information is currently available through the following objects:

The structure object provides access to the data from the ATOM records through a hierarchy of sub-object:

  Structure
          |
          Chain
              |
              Group
                  |
                  Atom

Learn more how to work with groups.

Other Features

For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure