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.chem
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.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	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	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	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.
DatabasePDBRevRecord	Represents revision records for use by PDBHeader.
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:
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.
PdbId	A wrapper class for the PDB identifier.
PDBRecord	An interface implemented by all classes that represent PDB records.
PDBStatus.Status	Represents a simplified 3 state 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.
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	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	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	Description
PdbId	A wrapper class for the PDB identifier.
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	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	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	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	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	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	Description
Atom	A simple interface for an Atom.

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

Class	Description
Atom	A simple interface for an Atom.

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

Class	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	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	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	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	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	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	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.
PdbId	A wrapper class for the PDB identifier.
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	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	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	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	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.chem

Class	Description
Group	This is the data structure for a single Group of atoms.

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

Class	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	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	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.domain.pdp

Class	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	Description
PdbId	A wrapper class for the PDB identifier.
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	Description
Structure	Interface for a structure object.

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

Class	Description
Structure	Interface for a structure object.

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

Class	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	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.
PdbId	A wrapper class for the PDB identifier.
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	Description
Atom	A simple interface for an Atom.
Chain	Defines the interface for a Chain.
Structure	Interface for a structure object.

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

Class	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	Description
Structure	Interface for a structure object.

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

Class	Description
PdbId	A wrapper class for the PDB identifier.
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	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	Description
Structure	Interface for a structure object.

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

Class	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	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	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	Description
Structure	Interface for a structure object.