Uses of Class
org.biojava.nbio.structure.domain.pdp.Domain
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Packages that use Domain Package Description org.biojava.nbio.structure.domain org.biojava.nbio.structure.domain.pdp org.biojava.nbio.structure.scop.server -
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Uses of Domain in org.biojava.nbio.structure.domain
Methods in org.biojava.nbio.structure.domain that return types with arguments of type Domain Modifier and Type Method Description static List<Domain>
LocalProteinDomainParser. suggestDomains(Atom[] ca)
Suggest domains for a set of Calpha atomsstatic List<Domain>
LocalProteinDomainParser. suggestDomains(Structure s)
Suggest domains for a protein structure -
Uses of Domain in org.biojava.nbio.structure.domain.pdp
Methods in org.biojava.nbio.structure.domain.pdp that return types with arguments of type Domain Modifier and Type Method Description static List<Domain>
ClusterDomains. cluster(List<Domain> domains, PDPDistanceMatrix pdpDistMatrix)
List<Domain>
CutDomain. getDomains()
Methods in org.biojava.nbio.structure.domain.pdp with parameters of type Domain Modifier and Type Method Description int
Domain. compareTo(Domain other)
int
Cut. cut(Atom[] ca, Domain dom, CutValues val, int[][] dist, PDPDistanceMatrix pdpMatrix)
void
CutDomain. cutDomain(Domain dom, CutSites cut_sites, PDPDistanceMatrix pdpMatrix)
Method parameters in org.biojava.nbio.structure.domain.pdp with type arguments of type Domain Modifier and Type Method Description static void
ShortSegmentRemover. cleanup(List<Domain> domains)
static List<Domain>
ClusterDomains. cluster(List<Domain> domains, PDPDistanceMatrix pdpDistMatrix)
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Uses of Domain in org.biojava.nbio.structure.scop.server
Methods in org.biojava.nbio.structure.scop.server that return types with arguments of type Domain Modifier and Type Method Description static SortedSet<Domain>
XMLUtil. getDomainsFromXML(String xml)
Method parameters in org.biojava.nbio.structure.scop.server with type arguments of type Domain Modifier and Type Method Description static String
XMLUtil. getDomainsXML(SortedSet<Domain> domains)
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