Uses of Interface
de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.AtomStep

Packages that use Fit3DBuilder.AtomStep

Package	Description
de.bioforscher.singa.structure.algorithms.superimposition.fit3d

Uses of Fit3DBuilder.AtomStep in de.bioforscher.singa.structure.algorithms.superimposition.fit3d

Classes in de.bioforscher.singa.structure.algorithms.superimposition.fit3d that implement Fit3DBuilder.AtomStep

Modifier and Type	Class and Description
static class	Fit3DBuilder.Builder

Methods in de.bioforscher.singa.structure.algorithms.superimposition.fit3d that return Fit3DBuilder.AtomStep

Modifier and Type	Method and Description
Fit3DBuilder.AtomStep	Fit3DBuilder.SiteConfigurationStep.exhaustive() Guarantees to find the ideal alignment of the input sites.
Fit3DBuilder.AtomStep	Fit3DBuilder.Builder.exhaustive()
Fit3DBuilder.AtomStep	Fit3DBuilder.SiteConfigurationStep.ignoreSpecifiedExchanges() Ignores the specified exchanges of the input sites and allows alignment of any type against any type using a heuristic that does not necessarily yield the best alignment possible.
Fit3DBuilder.AtomStep	Fit3DBuilder.Builder.ignoreSpecifiedExchanges()
Fit3DBuilder.AtomStep	Fit3DBuilder.SiteConfigurationStep.kuhnMunkres(SubstitutionMatrix substitutionMatrix, boolean restrictToExchanges) Assigns the alignment using Kuhn-Munkres optimization and scoring derived from the specified substitution matrix.
Fit3DBuilder.AtomStep	Fit3DBuilder.Builder.kuhnMunkres(SubstitutionMatrix substitutionMatrix, boolean restrictToExchanges)
Fit3DBuilder.AtomStep	Fit3DBuilder.BatchParameterStep.limitedParallelism(int limitedParallelism) Defines for a batch search the level of parallelism (number of cores) that should be used by Fit3D.
Fit3DBuilder.AtomStep	Fit3DBuilder.Builder.limitedParallelism(int limitedParallelism)
Fit3DBuilder.AtomStep	Fit3DBuilder.BatchParameterStep.maximalParallelism() Allows Fit3D in search mode to use all available cores for processing.
Fit3DBuilder.AtomStep	Fit3DBuilder.Builder.maximalParallelism()
Fit3DBuilder.AtomStep	Fit3DBuilder.SiteConfigurationStep.restrictToSpecifiedExchanges() Restricts the site alignment to the specified exchanges of the input sites.
Fit3DBuilder.AtomStep	Fit3DBuilder.Builder.restrictToSpecifiedExchanges()
Fit3DBuilder.AtomStep	Fit3DBuilder.TargetStep.target(LeafSubstructureContainer target) Defines the target against which this Fit3D search should be run.
Fit3DBuilder.AtomStep	Fit3DBuilder.Builder.target(LeafSubstructureContainer target)