Uses of Interface
org.biojava.nbio.structure.StructureIdentifier

Packages that use StructureIdentifier

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align.client	This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.gui
org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.cath
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.domain
org.biojava.nbio.structure.ecod
org.biojava.nbio.structure.gui.util	Some utility classes for the protein structure GUIs.
org.biojava.nbio.structure.scop	Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.nbio.structure.symmetry.internal

Uses of StructureIdentifier in org.biojava.nbio.structure

Classes in org.biojava.nbio.structure that implement StructureIdentifier

Modifier and Type	Class and Description
class	BioAssemblyIdentifier
class	PassthroughIdentifier A stub StructureIdentifier, representing the full structure in all cases.
class	SubstructureIdentifier This is the canonical way to identify a part of a structure.
class	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

Methods in org.biojava.nbio.structure that return StructureIdentifier

Modifier and Type	Method and Description
StructureIdentifier	StructureImpl.getStructureIdentifier()
StructureIdentifier	Structure.getStructureIdentifier() Get an identifier corresponding to this structure

Methods in org.biojava.nbio.structure with parameters of type StructureIdentifier

Modifier and Type	Method and Description
void	StructureImpl.setStructureIdentifier(StructureIdentifier structureIdentifier)
void	Structure.setStructureIdentifier(StructureIdentifier structureIdentifier) Set the identifier corresponding to this structure

Uses of StructureIdentifier in org.biojava.nbio.structure.align.client

Classes in org.biojava.nbio.structure.align.client that implement StructureIdentifier

Modifier and Type	Class and Description
class	StructureName A utility class that makes working with names of structures, domains and ranges easier.

Methods in org.biojava.nbio.structure.align.client that return StructureIdentifier

Modifier and Type	Method and Description
StructureIdentifier	StructureName.getBaseIdentifier() StructureName wraps another StructureIdentifier.

Uses of StructureIdentifier in org.biojava.nbio.structure.align.gui

Methods in org.biojava.nbio.structure.align.gui that return StructureIdentifier

Modifier and Type	Method and Description
StructureIdentifier	SelectPDBPanel.getName1()
StructureIdentifier	SelectPDBPanel.getName2()

Constructor parameters in org.biojava.nbio.structure.align.gui with type arguments of type StructureIdentifier

Constructor and Description
MultipleAlignmentCalc(MultipleAlignmentGUI parent, List<Structure> structures, List<StructureIdentifier> names) Requests an alignment of the pdbs.

Uses of StructureIdentifier in org.biojava.nbio.structure.align.multiple

Methods in org.biojava.nbio.structure.align.multiple that return StructureIdentifier

Modifier and Type	Method and Description
StructureIdentifier	MultipleAlignment.getStructureIdentifier(int index) Returns the StructureIdentifier associated with the structure index from its parent Ensemble.
StructureIdentifier	MultipleAlignmentImpl.getStructureIdentifier(int index)

Methods in org.biojava.nbio.structure.align.multiple that return types with arguments of type StructureIdentifier

Modifier and Type	Method and Description
List<StructureIdentifier>	MultipleAlignmentEnsemble.getStructureIdentifiers() Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
List<StructureIdentifier>	MultipleAlignmentEnsembleImpl.getStructureIdentifiers()

Method parameters in org.biojava.nbio.structure.align.multiple with type arguments of type StructureIdentifier

Modifier and Type	Method and Description
void	MultipleAlignmentEnsemble.setStructureIdentifiers(List<StructureIdentifier> structureIdentifiers) Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
void	MultipleAlignmentEnsembleImpl.setStructureIdentifiers(List<StructureIdentifier> structureNames)

Constructor parameters in org.biojava.nbio.structure.align.multiple with type arguments of type StructureIdentifier

Constructor and Description
MultipleAlignmentEnsembleImpl(List<StructureIdentifier> structureIdentifiers) Constructor using structure identifiers.

Uses of StructureIdentifier in org.biojava.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util with parameters of type StructureIdentifier

Modifier and Type	Method and Description
Atom[]	AtomCache.getAtoms(StructureIdentifier name)
Atom[]	AtomCache.getRepresentativeAtoms(StructureIdentifier name)
Structure	AtomCache.getStructure(StructureIdentifier strucId) Get the structure corresponding to the given StructureIdentifier.

Uses of StructureIdentifier in org.biojava.nbio.structure.cath

Classes in org.biojava.nbio.structure.cath that implement StructureIdentifier

Modifier and Type	Class and Description
class	CathDomain A class which represents a single CATH domain.

Uses of StructureIdentifier in org.biojava.nbio.structure.cluster

Methods in org.biojava.nbio.structure.cluster that return StructureIdentifier

Modifier and Type	Method and Description
StructureIdentifier	Subunit.getIdentifier() The standard identifier of the Subunit.

Constructors in org.biojava.nbio.structure.cluster with parameters of type StructureIdentifier

Constructor and Description
Subunit(Atom[] reprAtoms, String name, StructureIdentifier identifier, Structure structure) A Subunit is solely defined by the coordinates of the representative Atoms of its residues.

Uses of StructureIdentifier in org.biojava.nbio.structure.domain

Classes in org.biojava.nbio.structure.domain that implement StructureIdentifier

Modifier and Type	Class and Description
class	PDPDomain

Uses of StructureIdentifier in org.biojava.nbio.structure.ecod

Classes in org.biojava.nbio.structure.ecod that implement StructureIdentifier

Modifier and Type	Class and Description
class	EcodDomain An EcodDomain contains all the information of the ECOD database: id, classification groups (from higher to lower in the tree: X,H,T,F), PDB code, chain, residue ranges and status (manual or automatic classification).

Uses of StructureIdentifier in org.biojava.nbio.structure.gui.util

Methods in org.biojava.nbio.structure.gui.util that return types with arguments of type StructureIdentifier

Modifier and Type	Method and Description
List<StructureIdentifier>	SelectMultiplePanel.getNames()

Uses of StructureIdentifier in org.biojava.nbio.structure.scop

Classes in org.biojava.nbio.structure.scop that implement StructureIdentifier

Modifier and Type	Class and Description
class	ScopDomain Container for the information for a domain.

Uses of StructureIdentifier in org.biojava.nbio.structure.symmetry.internal

Methods in org.biojava.nbio.structure.symmetry.internal that return StructureIdentifier

Modifier and Type	Method and Description
StructureIdentifier	CeSymmResult.getStructureId()

Methods in org.biojava.nbio.structure.symmetry.internal that return types with arguments of type StructureIdentifier

Modifier and Type	Method and Description
List<StructureIdentifier>	CeSymmResult.getRepeatsID() Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.

Methods in org.biojava.nbio.structure.symmetry.internal with parameters of type StructureIdentifier

Modifier and Type	Method and Description
void	CeSymmResult.setStructureId(StructureIdentifier structureId)