Uses of Class
de.bioforscher.singa.structure.model.oak.StructuralMotif

Packages that use StructuralMotif

Package	Description
de.bioforscher.singa.structure.algorithms.superimposition.affinity
de.bioforscher.singa.structure.algorithms.superimposition.consensus
de.bioforscher.singa.structure.algorithms.superimposition.fit3d
de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics
de.bioforscher.singa.structure.model.oak
de.bioforscher.singa.structure.parser.pdb.structures

Uses of StructuralMotif in de.bioforscher.singa.structure.algorithms.superimposition.affinity

Methods in de.bioforscher.singa.structure.algorithms.superimposition.affinity that return types with arguments of type StructuralMotif

Modifier and Type	Method and Description
Map<StructuralMotif,List<StructuralMotif>>	AffinityAlignment.getClusters()
Map<StructuralMotif,List<StructuralMotif>>	AffinityAlignment.getClusters()
LabeledSymmetricMatrix<StructuralMotif>	AffinityAlignment.getDistanceMatrix()

Method parameters in de.bioforscher.singa.structure.algorithms.superimposition.affinity with type arguments of type StructuralMotif

Modifier and Type	Method and Description
AffinityAlignment.AtomStep	AffinityAlignment.InputStep.inputStructuralMotifs(List<StructuralMotif> structuralMotifs)
AffinityAlignment.AtomStep	AffinityAlignment.Builder.inputStructuralMotifs(List<StructuralMotif> structuralMotifs)

Uses of StructuralMotif in de.bioforscher.singa.structure.algorithms.superimposition.consensus

Methods in de.bioforscher.singa.structure.algorithms.superimposition.consensus that return StructuralMotif

Modifier and Type	Method and Description
StructuralMotif	ConsensusContainer.getStructuralMotif()

Method parameters in de.bioforscher.singa.structure.algorithms.superimposition.consensus with type arguments of type StructuralMotif

Modifier and Type	Method and Description
ConsensusBuilder.AtomStep	ConsensusBuilder.InputStep.inputStructuralMotifs(List<StructuralMotif> structuralMotifs) Defines the input StructuralMotifs for the ConsensusAlignment.
ConsensusBuilder.AtomStep	ConsensusBuilder.Builder.inputStructuralMotifs(List<StructuralMotif> structuralMotifs)

Constructors in de.bioforscher.singa.structure.algorithms.superimposition.consensus with parameters of type StructuralMotif

Constructor and Description
ConsensusContainer(StructuralMotif structuralMotif, boolean consensus)

Uses of StructuralMotif in de.bioforscher.singa.structure.algorithms.superimposition.fit3d

Methods in de.bioforscher.singa.structure.algorithms.superimposition.fit3d that return StructuralMotif

Modifier and Type	Method and Description
StructuralMotif	Fit3DMatch.getCandidateMotif()

Methods in de.bioforscher.singa.structure.algorithms.superimposition.fit3d with parameters of type StructuralMotif

Modifier and Type	Method and Description
Fit3DBuilder.TargetStep	Fit3DBuilder.QueryStep.query(StructuralMotif query) Defines the query motif for this Fit3D search.
Fit3DBuilder.TargetStep	Fit3DBuilder.Builder.query(StructuralMotif query)
Fit3DBuilder.SiteStep	Fit3DBuilder.QueryStep.site(StructuralMotif site) Defines a site that should be aligned against another.
Fit3DBuilder.SiteStep	Fit3DBuilder.Builder.site(StructuralMotif site1)
Fit3DBuilder.SiteParameterConfigurationStep	Fit3DBuilder.SiteStep.vs(StructuralMotif site) Defines the second site for the pairwise site alignment.
Fit3DBuilder.SiteParameterConfigurationStep	Fit3DBuilder.Builder.vs(StructuralMotif site2)

Uses of StructuralMotif in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics

Methods in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics with parameters of type StructuralMotif

Modifier and Type	Method and Description
static double	FofanovEstimation.determineEpsilon(StructuralMotif queryMotif, double modelCorrectnessCutoff) This calculates the cutoff epsilon up to which the RMSD distribution should be sampled for a desired model correctness.

Uses of StructuralMotif in de.bioforscher.singa.structure.model.oak

Methods in de.bioforscher.singa.structure.model.oak that return StructuralMotif

Modifier and Type	Method and Description
static StructuralMotif	StructuralMotif.fromLeafIdentifiers(Structure structure, List<LeafIdentifier> leafIdentifiers) Creates a StructuralMotif by extracting the given residues identified by a list of LeafIdentifiers.
static StructuralMotif	StructuralMotif.fromLeafSubstructures(List<LeafSubstructure<?>> leafSubstructures) Forms a StructuralMotif out of the given LeafSubstructures.
StructuralMotif	StructuralMotif.getCopy()

Methods in de.bioforscher.singa.structure.model.oak that return types with arguments of type StructuralMotif

Modifier and Type	Method and Description
static LabeledSymmetricMatrix<StructuralMotif>	StructuralMotifs.calculateRmsdMatrix(List<StructuralMotif> structuralMotifs, boolean idealSuperimposition) Performs a superimposition of given StructuralMotifs using arbitrary atoms and returns the RMSD distance matrix between all elements.
static LabeledSymmetricMatrix<StructuralMotif>	StructuralMotifs.calculateRmsdMatrix(List<StructuralMotif> structuralMotifs, Predicate<Atom> atomFilter, boolean idealSuperimposition) Performs a superimposition of given StructuralMotifs using the specified StructuralEntityFilter.AtomFilter and returns the RMSD distance matrix between all elements.

Methods in de.bioforscher.singa.structure.model.oak with parameters of type StructuralMotif

Modifier and Type	Method and Description
static void	StructuralMotifs.assignComplexExchanges(StructuralMotif structuralMotif, EnumSet<MatcherFamily> familyGroup) Assigns the given EnumSet of exchanges to the specified StructuralMotif.
static StructuralMotif.Type	StructuralMotif.Type.determine(StructuralMotif structuralMotif)

Method parameters in de.bioforscher.singa.structure.model.oak with type arguments of type StructuralMotif

Modifier and Type	Method and Description
static LabeledSymmetricMatrix<StructuralMotif>	StructuralMotifs.calculateRmsdMatrix(List<StructuralMotif> structuralMotifs, boolean idealSuperimposition) Performs a superimposition of given StructuralMotifs using arbitrary atoms and returns the RMSD distance matrix between all elements.
static LabeledSymmetricMatrix<StructuralMotif>	StructuralMotifs.calculateRmsdMatrix(List<StructuralMotif> structuralMotifs, Predicate<Atom> atomFilter, boolean idealSuperimposition) Performs a superimposition of given StructuralMotifs using the specified StructuralEntityFilter.AtomFilter and returns the RMSD distance matrix between all elements.

Uses of StructuralMotif in de.bioforscher.singa.structure.parser.pdb.structures

Methods in de.bioforscher.singa.structure.parser.pdb.structures with parameters of type StructuralMotif

Modifier and Type	Method and Description
static StructureSelector.StructuralModelStep	StructureSelector.selectFrom(StructuralMotif structuralMotif)

Constructors in de.bioforscher.singa.structure.parser.pdb.structures with parameters of type StructuralMotif

Constructor and Description
Selector(StructuralMotif structuralMotif)