Uses of Interface
org.biojava.nbio.structure.scop.ScopDatabase
Packages that use ScopDatabase
Package
Description
This package deals with the server communication for auto-downloading pre-calculated alignments.
Parsers and API for SCOP, Structural Classification of Proteins.
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Uses of ScopDatabase in org.biojava.nbio.structure.align.client
Methods in org.biojava.nbio.structure.align.client with parameters of type ScopDatabaseModifier and TypeMethodDescriptionstatic ScopDomainStructureName.guessScopDomain(String name, ScopDatabase scopDB) Guess a scop domain. -
Uses of ScopDatabase in org.biojava.nbio.structure.align.util
Methods in org.biojava.nbio.structure.align.util with parameters of type ScopDatabaseModifier and TypeMethodDescriptionAtomCache.getStructureForDomain(String scopId, ScopDatabase scopDatabase) Returns the representation of aScopDomainas a BioJavaStructureobject.AtomCache.getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase) Returns the representation of aScopDomainas a BioJavaStructureobject.AtomCache.getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling) Returns the representation of aScopDomainas a BioJavaStructureobject. -
Uses of ScopDatabase in org.biojava.nbio.structure.gui.util
Methods in org.biojava.nbio.structure.gui.util that return ScopDatabase -
Uses of ScopDatabase in org.biojava.nbio.structure.scop
Subinterfaces of ScopDatabase in org.biojava.nbio.structure.scopModifier and TypeInterfaceDescriptioninterfaceClasses which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead.Classes in org.biojava.nbio.structure.scop that implement ScopDatabaseModifier and TypeClassDescriptionclassSCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).classAn extension of the RemoteScopInstallation that caches some of the data locally.classA class that fetches information about SCOP from a remote data-source.classThis class provides access to the SCOP protein structure classification.Methods in org.biojava.nbio.structure.scop that return ScopDatabaseModifier and TypeMethodDescriptionstatic ScopDatabaseScopFactory.getSCOP()Get the current default instance for the default versionstatic ScopDatabaseScopFactory.getSCOP(boolean forceLocalData) static ScopDatabaserequests a particular version of SCOP.static ScopDatabaseGets an instance of the specified scop version.Methods in org.biojava.nbio.structure.scop with parameters of type ScopDatabaseModifier and TypeMethodDescriptionstatic voidScopFactory.setScopDatabase(ScopDatabase scop) Set the default scop version and instance