Uses of Class
org.biojava.nbio.structure.cluster.Subunit

Packages that use Subunit

Package	Description
org.biojava.nbio.structure.align.quaternary
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.symmetry.core

Uses of Subunit in org.biojava.nbio.structure.align.quaternary

Methods in org.biojava.nbio.structure.align.quaternary that return types with arguments of type Subunit

Modifier and Type	Method	Description
List<Subunit>	QsAlignResult.getAlignedSubunits1()	Return the aligned subunits of the first Subunit group, in the alignment order.
List<Subunit>	QsAlignResult.getAlignedSubunits2()	Return the aligned subunits of the second Subunit group, in the alignment order.
List<Subunit>	QsAlignResult.getSubunits1()	Original Subunits of the first group.
List<Subunit>	QsAlignResult.getSubunits2()	Original Subunits of the second group.

Method parameters in org.biojava.nbio.structure.align.quaternary with type arguments of type Subunit

Modifier and Type	Method	Description
static QsAlignResult	QsAlign.align(List<Subunit> s1, List<Subunit> s2, SubunitClustererParameters cParams, QsAlignParameters aParams)

Constructor parameters in org.biojava.nbio.structure.align.quaternary with type arguments of type Subunit

Modifier	Constructor	Description
	QsAlignResult(List<Subunit> subunits1, List<Subunit> subunits2)	The Constructor of the result takes the same inputs as the QsAlign algorithm.

Uses of Subunit in org.biojava.nbio.structure.cluster

Methods in org.biojava.nbio.structure.cluster that return types with arguments of type Subunit

Modifier and Type	Method	Description
static List<Subunit>	SubunitExtractor.extractSubunits(Structure structure, int absMinLen, double fraction, int minLen)	Extract the information of each protein Chain in a Structure and converts them into a List of Subunit.
List<Subunit>	SubunitCluster.getSubunits()	Subunits contained in the SubunitCluster.

Method parameters in org.biojava.nbio.structure.cluster with type arguments of type Subunit

Modifier and Type	Method	Description
static Stoichiometry	SubunitClusterer.cluster(List<Subunit> subunits, SubunitClustererParameters params)

Constructors in org.biojava.nbio.structure.cluster with parameters of type Subunit

Modifier	Constructor	Description
	SubunitCluster(Subunit subunit)	A constructor from a single Subunit.

Constructor parameters in org.biojava.nbio.structure.cluster with type arguments of type Subunit

Modifier	Constructor	Description
	SubunitCluster(List<Subunit> subunits, List<List<Integer>> subunitEQR)	Create the cluster manually by specifying subunits and the equivalent residues

Uses of Subunit in org.biojava.nbio.structure.symmetry.core

Methods in org.biojava.nbio.structure.symmetry.core that return types with arguments of type Subunit

Modifier and Type	Method	Description
List<Subunit>	QuatSymmetryResults.getSubunits()	Returns the List of Subunits used to calculate symmetry.

Method parameters in org.biojava.nbio.structure.symmetry.core with type arguments of type Subunit

Modifier and Type	Method	Description
static QuatSymmetryResults	QuatSymmetryDetector.calcGlobalSymmetry(List<Subunit> subunits, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)	Calculate GLOBAL symmetry results.
static List<QuatSymmetryResults>	QuatSymmetryDetector.calcLocalSymmetries(List<Subunit> subunits, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)	Returns a List of LOCAL symmetry results.