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

Interface Fit3DBuilder.SiteConfigurationStep

All Known Subinterfaces:

Fit3DBuilder.SiteParameterConfigurationStep

All Known Implementing Classes:

Fit3DBuilder.Builder

Enclosing class:

Fit3DBuilder

public static interface Fit3DBuilder.SiteConfigurationStep

Method Summary

Modifier and Type	Method and Description
Fit3DBuilder.AtomStep	exhaustive() Guarantees to find the ideal alignment of the input sites.
Fit3DBuilder.AtomStep	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	kuhnMunkres(SubstitutionMatrix substitutionMatrix, boolean restrictToExchanges) Assigns the alignment using Kuhn-Munkres optimization and scoring derived from the specified substitution matrix.
Fit3DBuilder.AtomStep	restrictToSpecifiedExchanges() Restricts the site alignment to the specified exchanges of the input sites.

Method Detail

restrictToSpecifiedExchanges

Fit3DBuilder.AtomStep restrictToSpecifiedExchanges()

Restricts the site alignment to the specified exchanges of the input sites.

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

ignoreSpecifiedExchanges

Fit3DBuilder.AtomStep 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.

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

exhaustive

Fit3DBuilder.AtomStep exhaustive()

Guarantees to find the ideal alignment of the input sites.

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

kuhnMunkres

Fit3DBuilder.AtomStep kuhnMunkres(SubstitutionMatrix substitutionMatrix,
                                  boolean restrictToExchanges)

Assigns the alignment using Kuhn-Munkres optimization and scoring derived from the specified substitution matrix. This is a heuristic alignment that does not necessarily yield the best alignment possible.

Parameters:

substitutionMatrix - The SubstitutionMatrix to be used for calculation of the assignment.

restrictToExchanges - If set true specified exchanges of the input sites are considered.

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.