Uses of Class
org.biojava.nbio.structure.cluster.SubunitCluster
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Packages that use SubunitCluster Package Description org.biojava.nbio.structure.align.quaternary org.biojava.nbio.structure.cluster org.biojava.nbio.structure.symmetry.core -
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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 Description void
QsAlignResult. setClusters(List<SubunitCluster> clusters)
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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 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 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 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 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 Description QuatSymmetrySubunits(List<SubunitCluster> clusters)
Converts the List ofSubunitCluster
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.
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