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.

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

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

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

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

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