Package org.biojava.nbio.structure

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

Interface Summary

Interface	Description
AminoAcid	A Group that represents an AminoAcid.
Atom	A simple interface for an Atom.
AtomPositionMap.GroupMatcher	Used as a Predicate to indicate whether a particular Atom should be mapped
Bond	A simple bond -- it stores information about two atoms as well as information about its bond order.
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.
SeqMisMatch	Created by andreas on 9/11/15.
Structure	Interface for a structure object.
StructureIdentifier	An identifier that uniquely identifies a whole Structure or arbitrary substructure.

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.
AugmentedResidueRange	Created by douglas on 1/23/15.
Author	Describes author attributes for author information in a PDB file.
BioAssemblyIdentifier
BondImpl	A simple bond -- it stores information about two atoms as well as information about its bond order.
Calc	Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
ChainImpl	A Chain in a PDB file.
DatabasePDBRevRecord	Represents revision records for use by PDBHeader.
DBRef	A class to represent database cross references.
EntityInfo	An object to contain the info from the PDB header for a Molecule.
GroupIterator	An iterator over all groups of a structure.
HetatomImpl	Generic Implementation of a Group interface.
JournalArticle	PDB-specific
Model	An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.
Mutator	A class that can change one amino acid to another.
NucleotideImpl	A nucleotide group is almost the same as a Hetatm group.
PassthroughIdentifier	A stub StructureIdentifier, representing the full structure in all cases.
PDBCrystallographicInfo	A class to hold crystallographic information about a PDB structure.
PDBHeader	A class that contains PDB Header information.
PdbId	A wrapper class for the PDB identifier.
PDBStatus	Methods for getting the status of a PDB file (current, removed, unreleased) and for accessing different versions of the structure.
ResidueNumber	Everything that is needed to uniquely describe a residue position
ResidueRange	A chainName, a start residue, and an end residue.
ResidueRangeAndLength	A chain, a start residue, and an end residue.
SeqMisMatchImpl	Created by andreas on 9/11/15.
Site	Holds the data of sites presented in PDB files.
StandardAminoAcid	A class that provides a set of standard amino acids.
StructureImpl	Implementation of a PDB Structure.
StructureIO	A class that provides static access methods for easy lookup of protein structure related components
StructureTools	A class that provides some tool methods.
SubstructureIdentifier	This is the canonical way to identify a part of a structure.
URLIdentifier	Represents a structure loaded from a URL (including a file URL) A few custom query parameters are supported: format=[pdb|cif] Specify the file format (will otherwise be guessed from the extension) pdbId=[String] Specify the PDB ID (also guessed from the filename) chainID=[String] A single chain from the structure residues=[String] Residue ranges, in a form understood by SubstructureIdentifier

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.
EntityType	The type of entity (polymer, non-polymer, water, macrolide) as defined in the mmCIF dictionary:
ExperimentalTechnique	An enum to represent the experimental technique of a PDB structure
GroupType	This contains basic categories for Group types.
HetatomImpl.PerformanceBehavior	Behaviors for how to balance memory vs. performance.
PDBStatus.Status	Represents a simplified 3 state status of PDB IDs.

Exception Summary

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