Uses of Class
org.biojava.nbio.structure.domain.pdp.Domain

Packages that use Domain

Package	Description
org.biojava.nbio.structure.domain
org.biojava.nbio.structure.domain.pdp
org.biojava.nbio.structure.scop.server

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 and Description
static java.util.List<Domain>	LocalProteinDomainParser.suggestDomains(Atom[] ca) Suggest domains for a set of Calpha atoms
static java.util.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 and Description
static java.util.List<Domain>	ClusterDomains.cluster(java.util.List<Domain> domains, PDPDistanceMatrix pdpDistMatrix)
java.util.List<Domain>	CutDomain.getDomains()

Methods in org.biojava.nbio.structure.domain.pdp with parameters of type Domain

Modifier and Type	Method and 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 and Description
static void	ShortSegmentRemover.cleanup(java.util.List<Domain> domains)
static java.util.List<Domain>	ClusterDomains.cluster(java.util.List<Domain> domains, PDPDistanceMatrix pdpDistMatrix)

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 and Description
static java.util.SortedSet<Domain>	XMLUtil.getDomainsFromXML(java.lang.String xml)

Method parameters in org.biojava.nbio.structure.scop.server with type arguments of type Domain

Modifier and Type	Method and Description
static java.lang.String	XMLUtil.getDomainsXML(java.util.SortedSet<Domain> domains)