Uses of Class org.biojava.nbio.structure.scop.ScopDomain (biojava 6.0.0 API)

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)`