Uses of Interface
org.biojava.nbio.structure.scop.ScopDatabase

Packages that use ScopDatabase

Package	Description
org.biojava.nbio.structure.align.client	This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.util
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.

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

Methods in org.biojava.nbio.structure.align.client with parameters of type ScopDatabase

Modifier and Type	Method and Description
static ScopDomain	StructureName.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 ScopDatabase

Modifier and Type	Method and Description
Structure	AtomCache.getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase) Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	AtomCache.getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling) Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	AtomCache.getStructureForDomain(String scopId, ScopDatabase scopDatabase) Returns the representation of a ScopDomain as a BioJava Structure object.

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

Methods in org.biojava.nbio.structure.gui.util that return ScopDatabase

Modifier and Type	Method and Description
ScopDatabase	ScopInstallationInstance.getSCOP()

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

Subinterfaces of ScopDatabase in org.biojava.nbio.structure.scop

Modifier and Type	Interface and Description
interface	LocalScopDatabase Classes 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 ScopDatabase

Modifier and Type	Class and Description
class	BerkeleyScopInstallation SCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).
class	CachedRemoteScopInstallation An extension of the RemoteScopInstallation that caches some of the data locally.
class	RemoteScopInstallation A class that fetches information about SCOP from a remote data-source.
class	ScopInstallation This class provides access to the SCOP protein structure classification.

Methods in org.biojava.nbio.structure.scop that return ScopDatabase

Modifier and Type	Method and Description
static ScopDatabase	ScopFactory.getSCOP() Get the current default instance for the default version
static ScopDatabase	ScopFactory.getSCOP(boolean forceLocalData)
static ScopDatabase	ScopFactory.getSCOP(String version) requests a particular version of SCOP.
static ScopDatabase	ScopFactory.getSCOP(String version, boolean forceLocalData) Gets an instance of the specified scop version.

Methods in org.biojava.nbio.structure.scop with parameters of type ScopDatabase

Modifier and Type	Method and Description
static void	ScopFactory.setScopDatabase(ScopDatabase scop) Set the default scop version and instance