Uses of Class
org.biojava.nbio.structure.scop.ScopDomain
Packages that use ScopDomain
Package
Description
This package deals with the server communication for auto-downloading pre-calculated alignments.
Parsers and API for SCOP, Structural Classification of Proteins.
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Uses of ScopDomain in org.biojava.nbio.structure.align.client
Methods in org.biojava.nbio.structure.align.client that return ScopDomainModifier and TypeMethodDescriptionstatic ScopDomainStructureName.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 ScopDomainModifier and TypeMethodDescriptionAtomCache.getStructureForDomain(ScopDomain domain) Returns the representation of aScopDomainas a BioJavaStructureobject.AtomCache.getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase) Returns the representation of aScopDomainas a BioJavaStructureobject.AtomCache.getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling) Returns the representation of aScopDomainas a BioJavaStructureobject. -
Uses of ScopDomain in org.biojava.nbio.structure.scop
Methods in org.biojava.nbio.structure.scop that return ScopDomainModifier and TypeMethodDescriptionCachedRemoteScopInstallation.getDomainByScopID(String scopId) RemoteScopInstallation.getDomainByScopID(String scopId) ScopDatabase.getDomainByScopID(String scopId) get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)ScopInstallation.getDomainByScopID(String scopId) Methods in org.biojava.nbio.structure.scop that return types with arguments of type ScopDomainModifier and TypeMethodDescriptionCachedRemoteScopInstallation.filterByDomainName(String query) RemoteScopInstallation.filterByDomainName(String query) ScopDatabase.filterByDomainName(String query) search through SCOP and filter based on domain nameScopInstallation.filterByDomainName(String query) CachedRemoteScopInstallation.getDomainsForPDB(String pdbId) RemoteScopInstallation.getDomainsForPDB(String pdbId) ScopDatabase.getDomainsForPDB(String pdbId) Get a list of ScopDomains that have been assigned to a PDB IDScopInstallation.getDomainsForPDB(String pdbId) CachedRemoteScopInstallation.getScopDomainsBySunid(Integer sunid) RemoteScopInstallation.getScopDomainsBySunid(Integer sunid) ScopDatabase.getScopDomainsBySunid(Integer sunid) Get a SCOP domain by its sunidScopInstallation.getScopDomainsBySunid(Integer sunid) Methods in org.biojava.nbio.structure.scop with parameters of type ScopDomainModifier and TypeMethodDescriptionCachedRemoteScopInstallation.getTree(ScopDomain domain) RemoteScopInstallation.getTree(ScopDomain domain) ScopDatabase.getTree(ScopDomain domain) get the SCOP sub-tree for a particular domain.ScopInstallation.getTree(ScopDomain domain) -
Uses of ScopDomain in org.biojava.nbio.structure.scop.server
Methods in org.biojava.nbio.structure.scop.server that return ScopDomainMethods in org.biojava.nbio.structure.scop.server that return types with arguments of type ScopDomainMethods in org.biojava.nbio.structure.scop.server with parameters of type ScopDomainMethod parameters in org.biojava.nbio.structure.scop.server with type arguments of type ScopDomainModifier and TypeMethodDescriptionstatic StringXMLUtil.getScopDomainsXML(List<ScopDomain> domains) voidScopDomains.setScopDomain(List<ScopDomain> domains)