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 that return types with arguments of type SubunitCluster

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

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, double minSeqid, double minCoverage) Merges the other SubunitCluster into this one if their representatives sequences are similar (higher sequence identity and coverage than the thresholds).
boolean	SubunitCluster.mergeSequence(SubunitCluster other, double minSeqid, double minCoverage, Alignments.PairwiseSequenceAlignerType alignerType, GapPenalty gapPenalty, SubstitutionMatrix<AminoAcidCompound> subsMatrix) Merges the other SubunitCluster into this one if their representatives sequences are similar (higher sequence identity and coverage than the thresholds).
boolean	SubunitCluster.mergeStructure(SubunitCluster other, double maxRmsd, double minCoverage) Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (lower RMSD and higher coverage than the thresholds).
boolean	SubunitCluster.mergeStructure(SubunitCluster other, double maxRmsd, double minCoverage, StructureAlignment aligner) Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (lower RMSD and higher coverage than the thresholds).

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

Modifier and Type	Method and Description
static String	SubunitClusterUtils.getStoichiometryString(List<SubunitCluster> clusters) Return a canonical String representation of the stoichiometry of a group of Subunits.
static boolean	SubunitClusterUtils.isPseudoStoichiometric(List<SubunitCluster> clusters) A pseudostoichiometric SubunitCluster was obtained using the SubunitClustererMethod.STRUCTURE similarity.

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>	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
static QuatSymmetryResults	QuatSymmetryDetector.calcGlobalSymmetry(List<SubunitCluster> clusters, QuatSymmetryParameters symmParams) Calculate GLOBAL symmetry results.
static List<QuatSymmetryResults>	QuatSymmetryDetector.calcLocalSymmetries(List<SubunitCluster> clusters, QuatSymmetryParameters symmParams) Returns a List of LOCAL symmetry results.

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

Constructor and Description
QuatSymmetryResults(List<SubunitCluster> clusters, HelixLayers helixLayers, SymmetryPerceptionMethod method) Constructor for roto-translational symmetries.
QuatSymmetryResults(List<SubunitCluster> clusters, RotationGroup rotationGroup, SymmetryPerceptionMethod method) Constructor for rotational symmetries.
QuatSymmetrySubunits(List<SubunitCluster> clusters) Converts the List of SubunitCluster to a Subunit object.