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

Packages that use SubunitClustererParameters

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

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

Methods in org.biojava.nbio.structure.align.quaternary with parameters of type SubunitClustererParameters

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

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

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

Modifier and Type	Method and Description
static Stoichiometry	SubunitClusterer.cluster(List<Subunit> subunits, SubunitClustererParameters params)
static Stoichiometry	SubunitClusterer.cluster(Structure structure, SubunitClustererParameters params)
boolean	SubunitCluster.divideInternally(SubunitClustererParameters clusterParams) Analyze the internal symmetry of the SubunitCluster and divide its Subunit into the internal repeats (domains) if they are internally symmetric.
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).

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

Methods in org.biojava.nbio.structure.symmetry.core with parameters of type SubunitClustererParameters

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