Package org.biojava.nbio.structure
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: 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 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
-
ClassDescriptionA
Groupthat represents an AminoAcid.AminoAcid inherits most from Hetatom.A simple interface for an Atom.Implementation of an Atom of a PDB file.an iterator over all atoms of a structure / group.A map fromResidueNumbersto ATOM record positions in a PDB file.Used as a Predicate to indicate whether a particular Atom should be mappedCreated by douglas on 1/23/15.Describes author attributes for author information in a PDB file.A simple bond -- it stores information about two atoms as well as information about its bond order.A simple bond -- it stores information about two atoms as well as information about its bond order.Work in progress - NOT final!Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.Defines the interface for a Chain.A Chain in a PDB file.Represents revision records for use byPDBHeader.A class to represent database cross references.Element is an enumeration of the elements of the periodic table.ElementType is an enumeration of the types of elements found in the periodic table.An object to contain the info from the PDB header for a Molecule.An enum to represent the experimental technique of a PDB structureThis is the data structure for a single Group of atoms.An iterator over all groups of a structure.This contains basic categories for Group types.Generic Implementation of a Group interface.Behaviors for how to balance memory vs. performance.PDB-specificAn internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.A class that can change one amino acid to another.A nucleotide group is almost the same as a Hetatm group.A stub StructureIdentifier, representing the full structure in all cases.A class to hold crystallographic information about a PDB structure.A class that contains PDB Header information.A wrapper class for the PDB identifier.An interface implemented by all classes that represent PDB records.Methods for getting the status of a PDB file (current, removed, unreleased) and for accessing different versions of the structure.Represents a simplified 3 state status of PDB IDs.Everything that is needed to uniquely describe a residue positionA chainName, a start residue, and an end residue.A chain, a start residue, and an end residue.Created by andreas on 9/11/15.Created by andreas on 9/11/15.Holds the data of sites presented in PDB files.A class that provides a set of standard amino acids.Interface for a structure object.An exception during the parsing of a PDB file.An identifier that uniquely identifies a wholeStructureor arbitrary substructure.Implementation of a PDB Structure.A class that provides static access methods for easy lookup of protein structure related componentsA class that provides some tool methods.This is the canonical way to identify a part of a structure.Represents a structure loaded from a URL (including a file URL)