Uses of Interface
org.biojava.nbio.structure.StructureIdentifier
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Packages that use StructureIdentifier Package Description org.biojava.nbio.structure 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 org.biojava.nbio.structure.scop Parsers and API for SCOP, Structural Classification of Proteins.org.biojava.nbio.structure.symmetry.internal -
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Uses of StructureIdentifier in org.biojava.nbio.structure
Classes in org.biojava.nbio.structure that implement StructureIdentifier Modifier and Type Class 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 bySubstructureIdentifier
Methods in org.biojava.nbio.structure that return StructureIdentifier Modifier and Type Method Description StructureIdentifier
Structure. getStructureIdentifier()
Get an identifier corresponding to this structureStructureIdentifier
StructureImpl. getStructureIdentifier()
Methods in org.biojava.nbio.structure with parameters of type StructureIdentifier Modifier and Type Method Description void
Structure. setStructureIdentifier(StructureIdentifier structureIdentifier)
Set the identifier corresponding to this structurevoid
StructureImpl. setStructureIdentifier(StructureIdentifier structureIdentifier)
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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 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 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 Description StructureIdentifier
SelectPDBPanel. getName1()
StructureIdentifier
SelectPDBPanel. getName2()
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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 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 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 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 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 Description Atom[]
AtomCache. getAtoms(StructureIdentifier name)
Atom[]
AtomCache. getRepresentativeAtoms(StructureIdentifier name)
Structure
AtomCache. getStructure(StructureIdentifier strucId)
Get the structure corresponding to the givenStructureIdentifier
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Uses of StructureIdentifier in org.biojava.nbio.structure.cath
Classes in org.biojava.nbio.structure.cath that implement StructureIdentifier Modifier and Type Class 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 Description StructureIdentifier
Subunit. getIdentifier()
The standard identifier of the Subunit.Constructors in org.biojava.nbio.structure.cluster with parameters of type StructureIdentifier Constructor 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 Description class
PDPDomain
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Uses of StructureIdentifier in org.biojava.nbio.structure.ecod
Classes in org.biojava.nbio.structure.ecod that implement StructureIdentifier Modifier and Type Class 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 Description List<StructureIdentifier>
SelectMultiplePanel. getNames()
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Uses of StructureIdentifier in org.biojava.nbio.structure.scop
Classes in org.biojava.nbio.structure.scop that implement StructureIdentifier Modifier and Type Class 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 Description StructureIdentifier
CeSymmResult. getStructureId()
Methods in org.biojava.nbio.structure.symmetry.internal that return types with arguments of type StructureIdentifier Modifier and Type Method 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 Description void
CeSymmResult. setStructureId(StructureIdentifier structureId)
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