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:

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 alignments with CE and FATCAT.
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

@since 1.5