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
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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, etc.Defines the interface for a Chain.A Chain in a PDB file.An object to contain the info from the PDB header for a Molecule.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 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.Deprecated.PDB-specificA 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.An interface implemented by all classes that represent PDB recordsMethods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure.Represents the status of PDB IDs.Everything that is needed to uniquely describe a residue positionA chain, 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.A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...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 bySubstructureIdentifier
StructureNameinstead.