Uses of Class
org.biojava.nbio.structure.scop.ScopDomain

Packages that use ScopDomain

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.scop	Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.nbio.structure.scop.server

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

Methods in org.biojava.nbio.structure.align.client that return ScopDomain

Modifier and Type	Method and Description
static ScopDomain	StructureName.guessScopDomain(String name, ScopDatabase scopDB) Guess a scop domain.

Uses of ScopDomain in org.biojava.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util with parameters of type ScopDomain

Modifier and Type	Method and Description
Structure	AtomCache.getStructureForDomain(ScopDomain domain) Returns the representation of a ScopDomain as a BioJava Structure object.
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.

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

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

Modifier and Type	Method and Description
ScopDomain	ScopInstallation.getDomainByScopID(String scopId)
ScopDomain	ScopDatabase.getDomainByScopID(String scopId) get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
ScopDomain	RemoteScopInstallation.getDomainByScopID(String scopId)
ScopDomain	CachedRemoteScopInstallation.getDomainByScopID(String scopId)

Methods in org.biojava.nbio.structure.scop that return types with arguments of type ScopDomain

Modifier and Type	Method and Description
List<ScopDomain>	ScopInstallation.filterByDomainName(String query)
List<ScopDomain>	ScopDatabase.filterByDomainName(String query) search through SCOP and filter based on domain name
List<ScopDomain>	RemoteScopInstallation.filterByDomainName(String query)
List<ScopDomain>	CachedRemoteScopInstallation.filterByDomainName(String query)
List<ScopDomain>	ScopInstallation.getDomainsForPDB(String pdbId)
List<ScopDomain>	ScopDatabase.getDomainsForPDB(String pdbId) Get a list of ScopDomains that have been assigned to a PDB ID
List<ScopDomain>	RemoteScopInstallation.getDomainsForPDB(String pdbId)
List<ScopDomain>	CachedRemoteScopInstallation.getDomainsForPDB(String pdbId)
List<ScopDomain>	ScopInstallation.getScopDomainsBySunid(Integer sunid)
List<ScopDomain>	ScopDatabase.getScopDomainsBySunid(Integer sunid) Get a SCOP domain by its sunid
List<ScopDomain>	RemoteScopInstallation.getScopDomainsBySunid(Integer sunid)
List<ScopDomain>	CachedRemoteScopInstallation.getScopDomainsBySunid(Integer sunid)

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

Modifier and Type	Method and Description
List<ScopNode>	ScopInstallation.getTree(ScopDomain domain)
List<ScopNode>	ScopDatabase.getTree(ScopDomain domain) get the SCOP sub-tree for a particular domain.
List<ScopNode>	RemoteScopInstallation.getTree(ScopDomain domain)
List<ScopNode>	CachedRemoteScopInstallation.getTree(ScopDomain domain)

Uses of ScopDomain in org.biojava.nbio.structure.scop.server

Methods in org.biojava.nbio.structure.scop.server that return ScopDomain

Modifier and Type	Method and Description
static ScopDomain	XMLUtil.getScopDomainFromXML(String xml)

Methods in org.biojava.nbio.structure.scop.server that return types with arguments of type ScopDomain

Modifier and Type	Method and Description
List<ScopDomain>	ScopDomains.getScopDomain()

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

Modifier and Type	Method and Description
static String	XMLUtil.getScopDomainXML(ScopDomain domain)

Method parameters in org.biojava.nbio.structure.scop.server with type arguments of type ScopDomain

Modifier and Type	Method and Description
static String	XMLUtil.getScopDomainsXML(List<ScopDomain> domains)
void	ScopDomains.setScopDomain(List<ScopDomain> domains)