Package org.biojava.bio.structure

Interfaces and classes for protein structure (PDB).

See:
          Description

Interface Summary
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
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.
Bond Simple bond - it's just an edge/vertex for two Atom nodes.
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.
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
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.
SVDSuperimposer A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...
 

Enum Summary
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
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).

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