Uses of Interface
org.biojava.nbio.structure.scop.ScopDatabase
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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 org.biojava.nbio.structure.scop 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 ScopDatabase Modifier and Type Method 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 Description Structure
AtomCache. getStructureForDomain(String scopId, ScopDatabase scopDatabase)
Returns the representation of aScopDomain
as a BioJavaStructure
object.Structure
AtomCache. getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase)
Returns the representation of aScopDomain
as a BioJavaStructure
object.Structure
AtomCache. getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling)
Returns the representation of aScopDomain
as a BioJavaStructure
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 Description ScopDatabase
ScopInstallationInstance. getSCOP()
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Uses of ScopDatabase in org.biojava.nbio.structure.scop
Subinterfaces of ScopDatabase in org.biojava.nbio.structure.scop Modifier and Type Interface 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 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 Description static ScopDatabase
ScopFactory. getSCOP()
Get the current default instance for the default versionstatic 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 Description static void
ScopFactory. setScopDatabase(ScopDatabase scop)
Set the default scop version and instance
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