Uses of Package
org.biojava.nbio.structure

Packages that use org.biojava.nbio.structure

Package	Description
demo
org.biojava.nbio.protmod.structure
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align	Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.client	This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.fatcat	Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.fatcat.calc
org.biojava.nbio.structure.align.gui
org.biojava.nbio.structure.align.gui.aligpanel
org.biojava.nbio.structure.align.gui.jmol	Utility methods for better interaction with Jmol.
org.biojava.nbio.structure.align.helper	Helper classes for structural alignment.
org.biojava.nbio.structure.align.model
org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.multiple.mc
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.align.pairwise	Classes for the pairwise alignment of structures.
org.biojava.nbio.structure.align.quaternary
org.biojava.nbio.structure.align.seq
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.align.xml	Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.nbio.structure.asa
org.biojava.nbio.structure.basepairs
org.biojava.nbio.structure.cath
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.contact
org.biojava.nbio.structure.domain
org.biojava.nbio.structure.domain.pdp
org.biojava.nbio.structure.ecod
org.biojava.nbio.structure.gui	A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.nbio.structure.gui.events	Some event classes for the protein structure GUIs.
org.biojava.nbio.structure.gui.util	Some utility classes for the protein structure GUIs.
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.io.cif
org.biojava.nbio.structure.io.mmcif	Input and Output of mmcif files.
org.biojava.nbio.structure.io.mmtf
org.biojava.nbio.structure.quaternary
org.biojava.nbio.structure.scop	Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.nbio.structure.secstruc
org.biojava.nbio.structure.symmetry.core
org.biojava.nbio.structure.symmetry.gui
org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.utils
org.biojava.nbio.structure.xtal

Classes in org.biojava.nbio.structure used by demo

Class and Description
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.protmod.structure

Class and Description
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.
ResidueNumber Everything that is needed to uniquely describe a residue position
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure

Class and Description
AminoAcid A Group that represents an AminoAcid.
Atom A simple interface for an Atom.
AtomPositionMap A map from ResidueNumbers to ATOM record positions in a PDB file.
AtomPositionMap.GroupMatcher Used as a Predicate to indicate whether a particular Atom should be mapped
Author Describes author attributes for author information in a PDB file.
Bond A simple bond -- it stores information about two atoms as well as information about its bond order.
BondType Work in progress - NOT final!
Chain Defines the interface for a Chain.
DBRef A class to represent database cross references.
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.
EntityInfo An object to contain the info from the PDB header for a Molecule.
EntityType The type of entity (polymer, non-polymer, water, macrolide) as defined in the mmCIF dictionary: Entities are of four types: polymer, non-polymer, macrolide and water.
ExperimentalTechnique An enum to represent the experimental technique of a PDB structure
Group This is the data structure for a single Group of atoms.
GroupType This contains basic categories for Group types.
HetatomImpl Generic Implementation of a Group interface.
HetatomImpl.PerformanceBehavior Behaviors for how to balance memory vs. performance.
JournalArticle PDB-specific
PDBCrystallographicInfo A class to hold crystallographic information about a PDB structure.
PDBHeader A class that contains PDB Header information.
PDBRecord An interface implemented by all classes that represent PDB records.
PDBStatus.Status Represents the status of PDB IDs.
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.
SeqMisMatch Created by andreas on 9/11/15.
Site Holds the data of sites presented in PDB files.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.
StructureIO.StructureFiletype
SubstructureIdentifier This is the canonical way to identify a part of a structure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align

Class and Description
Atom A simple interface for an Atom.
Group This is the data structure for a single Group of atoms.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.ce

Class and Description
Atom A simple interface for an Atom.
Group This is the data structure for a single Group of atoms.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.client

Class and Description
Atom A simple interface for an Atom.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.
SubstructureIdentifier This is the canonical way to identify a part of a structure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.fatcat

Class and Description
Atom A simple interface for an Atom.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.fatcat.calc

Class and Description
Atom A simple interface for an Atom.
Group This is the data structure for a single Group of atoms.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.gui

Class and Description
Atom A simple interface for an Atom.
Group This is the data structure for a single Group of atoms.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.gui.aligpanel

Class and Description
Atom A simple interface for an Atom.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.gui.jmol

Class and Description
Atom A simple interface for an Atom.
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.helper

Class and Description
Atom A simple interface for an Atom.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.model

Class and Description
Atom A simple interface for an Atom.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.multiple

Class and Description
Atom A simple interface for an Atom.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.multiple.mc

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

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.multiple.util

Class and Description
Atom A simple interface for an Atom.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.pairwise

Class and Description
Atom A simple interface for an Atom.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.quaternary

Class and Description
Atom A simple interface for an Atom.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.seq

Class and Description
Atom A simple interface for an Atom.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.util

Class and Description
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.
ResidueNumber Everything that is needed to uniquely describe a residue position
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.xml

Class and Description
Atom A simple interface for an Atom.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.asa

Class and Description
Atom A simple interface for an Atom.
Group This is the data structure for a single Group of atoms.
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.basepairs

Class and Description
Chain Defines the interface for a Chain.
Group This is the data structure for a single Group of atoms.
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.cath

Class and Description
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.
SubstructureIdentifier This is the canonical way to identify a part of a structure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.cluster

Class and Description
Atom A simple interface for an Atom.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.contact

Class and Description
Atom A simple interface for an Atom.
Chain Defines the interface for a Chain.
EntityInfo An object to contain the info from the PDB header for a Molecule.
Group This is the data structure for a single Group of atoms.
ResidueNumber Everything that is needed to uniquely describe a residue position
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.domain

Class and Description
Atom A simple interface for an Atom.
ResidueRange A chainName, a start residue, and an end residue.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.
SubstructureIdentifier This is the canonical way to identify a part of a structure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.domain.pdp

Class and Description
Atom A simple interface for an Atom.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.ecod

Class and Description
ResidueRange A chainName, a start residue, and an end residue.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.
SubstructureIdentifier This is the canonical way to identify a part of a structure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.gui

Class and Description
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.gui.events

Class and Description
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.gui.util

Class and Description
Chain Defines the interface for a Chain.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.io

Class and Description
Atom A simple interface for an Atom.
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.
EntityInfo An object to contain the info from the PDB header for a Molecule.
Group This is the data structure for a single Group of atoms.
PDBRecord An interface implemented by all classes that represent PDB records.
ResidueNumber Everything that is needed to uniquely describe a residue position
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.io.cif

Class and Description
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.io.mmcif

Class and Description
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.
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.io.mmtf

Class and Description
Atom A simple interface for an Atom.
Chain Defines the interface for a Chain.
ExperimentalTechnique An enum to represent the experimental technique of a PDB structure
Group This is the data structure for a single Group of atoms.
PDBCrystallographicInfo A class to hold crystallographic information about a PDB structure.
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.quaternary

Class and Description
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.scop

Class and Description
ResidueRange A chainName, a start residue, and an end residue.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.
SubstructureIdentifier This is the canonical way to identify a part of a structure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.secstruc

Class and Description
Group This is the data structure for a single Group of atoms.
ResidueNumber Everything that is needed to uniquely describe a residue position
ResidueRangeAndLength A chain, a start residue, and an end residue.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.symmetry.core

Class and Description
Structure Interface for a structure object.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.symmetry.gui

Class and Description
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.symmetry.internal

Class and Description
Atom A simple interface for an Atom.
StructureException An exception during the parsing of a PDB file.
StructureIdentifier An identifier that uniquely identifies a whole Structure or arbitrary substructure.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.symmetry.utils

Class and Description
Atom A simple interface for an Atom.
Group This is the data structure for a single Group of atoms.
Structure Interface for a structure object.
StructureException An exception during the parsing of a PDB file.

Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.xtal

Class and Description
Structure Interface for a structure object.