Package org.biojava.bio.structure

Interfaces and classes for protein structure (PDB).

See: Description

Interface Summary

Interface	Description
AminoAcid	A Group that represents an AminoAcid.
Atom	A simple interface for an Atom.
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.

Class Summary

Class	Description
AlphaCTools	AlphaCTools is a collection of static convenience methods for dealing with Alpha Carbon Backbone Phi / Psi angles.
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.
Author	Describes author attributes for author information in a PDB file.
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.
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.
PDBHeader	A class that contains PDB Header information.
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.
SVDSuperimposer	A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...

Exception Summary

Exception	Description
StructureException	An exception during the parsing of a PDB file.

Package org.biojava.bio.structure Description

Interfaces and classes for protein structure (PDB).

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:

• PDBHeader
• DBRef
• Compound

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

• Calculate protein structure superimpositions
• Serialize PDB files to databases using Hibernate
• Tools for performing calculations
• Display structures in Jmol

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