Uses of Interface
org.biojava.nbio.structure.StructureIdentifier
Package
Description
Interfaces and classes for protein structure (PDB).
This package deals with the server communication for auto-downloading pre-calculated alignments.
Some utility classes for the protein structure GUIs.
Parsers and API for SCOP, Structural Classification of Proteins.
-
Uses of StructureIdentifier in org.biojava.nbio.structure
Modifier and TypeClassDescriptionclass
class
A stub StructureIdentifier, representing the full structure in all cases.class
This is the canonical way to identify a part of a structure.class
Represents a structure loaded from a URL (including a file URL)Modifier and TypeMethodDescriptionStructure.getStructureIdentifier()
Get an identifier corresponding to this structureStructureImpl.getStructureIdentifier()
Modifier and TypeMethodDescriptionvoid
Structure.setStructureIdentifier
(StructureIdentifier structureIdentifier) Set the identifier corresponding to this structurevoid
StructureImpl.setStructureIdentifier
(StructureIdentifier structureIdentifier) -
Uses of StructureIdentifier in org.biojava.nbio.structure.align.client
Modifier and TypeClassDescriptionclass
A utility class that makes working with names of structures, domains and ranges easier.Modifier and TypeMethodDescriptionStructureName.getBaseIdentifier()
StructureName wraps another StructureIdentifier. -
Uses of StructureIdentifier in org.biojava.nbio.structure.align.gui
-
Uses of StructureIdentifier in org.biojava.nbio.structure.align.multiple
Modifier and TypeMethodDescriptionMultipleAlignment.getStructureIdentifier
(int index) Returns the StructureIdentifier associated with the structure index from its parent Ensemble.MultipleAlignmentImpl.getStructureIdentifier
(int index) Modifier and TypeMethodDescriptionMultipleAlignmentEnsemble.getStructureIdentifiers()
Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).MultipleAlignmentEnsembleImpl.getStructureIdentifiers()
Modifier and TypeMethodDescriptionvoid
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) ModifierConstructorDescriptionMultipleAlignmentEnsembleImpl
(List<StructureIdentifier> structureIdentifiers) Constructor using structure identifiers. -
Uses of StructureIdentifier in org.biojava.nbio.structure.align.util
Modifier and TypeMethodDescriptionAtom[]
AtomCache.getAtoms
(StructureIdentifier name) Atom[]
AtomCache.getRepresentativeAtoms
(StructureIdentifier name) AtomCache.getStructure
(StructureIdentifier strucId) Get the structure corresponding to the givenStructureIdentifier
. -
Uses of StructureIdentifier in org.biojava.nbio.structure.cath
-
Uses of StructureIdentifier in org.biojava.nbio.structure.cluster
Modifier and TypeMethodDescriptionSubunit.getIdentifier()
The standard identifier of the Subunit.ModifierConstructorDescriptionSubunit
(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.ecod
Modifier and TypeClassDescriptionclass
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
-
Uses of StructureIdentifier in org.biojava.nbio.structure.scop
-
Uses of StructureIdentifier in org.biojava.nbio.structure.symmetry.internal
Modifier and TypeMethodDescriptionCeSymmResult.getRepeatsID()
Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.Modifier and TypeMethodDescriptionvoid
CeSymmResult.setStructureId
(StructureIdentifier structureId)