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

Packages that use SubunitCluster

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

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

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

Modifier and Type	Method and Description
void	QsAlignResult.setClusters(List<SubunitCluster> clusters)

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

Methods in org.biojava.nbio.structure.cluster with parameters of type SubunitCluster

Modifier and Type	Method and Description
boolean	SubunitCluster.isIdenticalTo(SubunitCluster other) Tells whether the other SubunitCluster contains exactly the same Subunit.
boolean	SubunitCluster.mergeIdentical(SubunitCluster other) Merges the other SubunitCluster into this one if it contains exactly the same Subunit.
boolean	SubunitCluster.mergeSequence(SubunitCluster other, SubunitClustererParameters params) Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).
boolean	SubunitCluster.mergeSequence(SubunitCluster other, SubunitClustererParameters params, Alignments.PairwiseSequenceAlignerType alignerType, GapPenalty gapPenalty, SubstitutionMatrix<AminoAcidCompound> subsMatrix) Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).
boolean	SubunitCluster.mergeStructure(SubunitCluster other, SubunitClustererParameters params) Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (according to the criteria in params).

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

Constructor and Description
SubunitCluster(SubunitCluster other, List<Integer> subunitsToRetain) A copy constructor with the possibility of removing subunits.

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

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

Modifier and Type	Method and Description
List<SubunitCluster>	Stoichiometry.getClusters()
List<SubunitCluster>	QuatSymmetryResults.getSubunitClusters() Returns the List of SubunitCluster used to calculate symmetry.

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

Modifier and Type	Method and Description
void	Stoichiometry.setCustomStringGenerator(Function<List<SubunitCluster>,String> customStringGenerator) Let a user-defined function handle the entire string representation of a stoichiometry.

Constructor parameters in org.biojava.nbio.structure.symmetry.core with type arguments of type SubunitCluster

Constructor and Description
QuatSymmetrySubunits(List<SubunitCluster> clusters) Converts the List of SubunitCluster to a Subunit object.
Stoichiometry(List<SubunitCluster> clusters) Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, boolean resetAlphas) Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, Function<List<SubunitCluster>,String> customStringGenerator) Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, Function<List<SubunitCluster>,String> customStringGenerator) Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, Stoichiometry.StringOverflowStrategy strategy) Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, Stoichiometry.StringOverflowStrategy strategy, boolean resetAlphas) Constructor for Stoichiometry.