Uses of Class
org.biojava.nbio.structure.scop.ScopDomain
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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 -
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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 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 ScopDomain in org.biojava.nbio.structure.scop
Methods in org.biojava.nbio.structure.scop that return ScopDomain Modifier and Type Method Description ScopDomain
CachedRemoteScopInstallation. getDomainByScopID(String scopId)
ScopDomain
RemoteScopInstallation. getDomainByScopID(String scopId)
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>
CachedRemoteScopInstallation. filterByDomainName(String query)
List<ScopDomain>
RemoteScopInstallation. filterByDomainName(String query)
List<ScopDomain>
ScopDatabase. filterByDomainName(String query)
search through SCOP and filter based on domain nameList<ScopDomain>
ScopInstallation. filterByDomainName(String query)
List<ScopDomain>
CachedRemoteScopInstallation. getDomainsForPDB(String pdbId)
List<ScopDomain>
RemoteScopInstallation. getDomainsForPDB(String pdbId)
List<ScopDomain>
ScopDatabase. getDomainsForPDB(String pdbId)
Get a list of ScopDomains that have been assigned to a PDB IDList<ScopDomain>
ScopInstallation. getDomainsForPDB(String pdbId)
List<ScopDomain>
CachedRemoteScopInstallation. getScopDomainsBySunid(Integer sunid)
List<ScopDomain>
RemoteScopInstallation. getScopDomainsBySunid(Integer sunid)
List<ScopDomain>
ScopDatabase. getScopDomainsBySunid(Integer sunid)
Get a SCOP domain by its sunidList<ScopDomain>
ScopInstallation. getScopDomainsBySunid(Integer sunid)
Methods in org.biojava.nbio.structure.scop with parameters of type ScopDomain Modifier and Type Method Description List<ScopNode>
CachedRemoteScopInstallation. getTree(ScopDomain domain)
List<ScopNode>
RemoteScopInstallation. getTree(ScopDomain domain)
List<ScopNode>
ScopDatabase. getTree(ScopDomain domain)
get the SCOP sub-tree for a particular domain.List<ScopNode>
ScopInstallation. getTree(ScopDomain domain)
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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 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 Description List<ScopDomain>
ScopDomains. getScopDomain()
Methods in org.biojava.nbio.structure.scop.server with parameters of type ScopDomain Modifier and Type Method 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 Description static String
XMLUtil. getScopDomainsXML(List<ScopDomain> domains)
void
ScopDomains. setScopDomain(List<ScopDomain> domains)
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