Package org.biojava.bio.structure
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 | AtomLearn 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
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Interface Summary Interface Description AminoAcid AGroup
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 recordsStructure 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 availableHetatomImpl Generic Implementation of a Group interface.JournalArticle PDB-specificMutator 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.