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

Interface Fit3DBuilder.ParameterStep

All Known Implementing Classes:

Fit3DBuilder.Builder

Enclosing class:

Fit3DBuilder

public static interface Fit3DBuilder.ParameterStep

Method Summary

Modifier and Type	Method and Description
Fit3DBuilder.ParameterStep	distanceTolerance(double distanceTolerance) Defines the distance tolerance that is accepted when extracting local environments.
Fit3DBuilder.ParameterStep	filterEnvironments() Enables pre-filtering of extracted environments, i.e.
Fit3DBuilder.ParameterStep	mapECNumbers() Enables mapping of each chain of a Fit3DMatch to an ECNumber using the SIFTS project.
Fit3DBuilder.ParameterStep	mapPfamIdentifiers() Enables mapping of each chain of a Fit3DMatch to a PfamIdentifier using the SIFTS project.
Fit3DBuilder.ParameterStep	mapUniProtIdentifiers() Enables mapping of each chain of a Fit3DMatch to a UniProtIdentifier using the SIFTS project.
Fit3DBuilder.ParameterStep	rmsdCutoff(double rmsdCutoff) Defines the RMSD cutoff up to which matches should be reported.
Fit3D	run() Creates a new Fit3D search and starts calculation.
Fit3DBuilder.ParameterStep	statisticalModel(StatisticalModel statisticalModel) Adds the specified StatisticalModel to the search to calculate significance of matches.

Method Detail

run

Fit3D run()
   throws SubstructureSuperimpositionException

Creates a new Fit3D search and starts calculation.

Returns:

A new Fit3D search when finished.

Throws:

SubstructureSuperimpositionException

rmsdCutoff

Fit3DBuilder.ParameterStep rmsdCutoff(double rmsdCutoff)

Defines the RMSD cutoff up to which matches should be reported. If a Fit3DSiteAlignment is performed this is the cutoff that is used for the internal call of the Fit3D algorithm.

Parameters:

rmsdCutoff - The RMSD cutoff up to which alignments should be reported.

Returns:

The Fit3DBuilder.ParameterStep that can be used to define optional parameters.

distanceTolerance

Fit3DBuilder.ParameterStep distanceTolerance(double distanceTolerance)

Defines the distance tolerance that is accepted when extracting local environments. If a Fit3DSiteAlignment is performed this is the cutoff that is used for the internal call of the Fit3D algorithm.

Parameters:

distanceTolerance - The distance tolerance considered when extracting local environments.

Returns:

The Fit3DBuilder.ParameterStep that can be used to define optional parameters.

statisticalModel

Fit3DBuilder.ParameterStep statisticalModel(StatisticalModel statisticalModel)

Adds the specified StatisticalModel to the search to calculate significance of matches. This may only be used when running a batch alignment. When running individual alignments the instance of the model should be passed to all individual Fit3D runs. After all runs completed call StatisticalModel.calculatePvalues(List)

Parameters:

statisticalModel - The StatisticalModel to be used.

Returns:

The Fit3DBuilder.BatchParameterStep that can be used to define optional parameters.

mapUniProtIdentifiers

Fit3DBuilder.ParameterStep mapUniProtIdentifiers()

Enables mapping of each chain of a Fit3DMatch to a UniProtIdentifier using the SIFTS project.

Returns:

The Fit3DBuilder.ParameterStep that can be used to define optional parameters.

mapPfamIdentifiers

Fit3DBuilder.ParameterStep mapPfamIdentifiers()

Enables mapping of each chain of a Fit3DMatch to a PfamIdentifier using the SIFTS project.

Returns:

The Fit3DBuilder.ParameterStep that can be used to define optional parameters.

mapECNumbers

Fit3DBuilder.ParameterStep mapECNumbers()

Enables mapping of each chain of a Fit3DMatch to an ECNumber using the SIFTS project.

Returns:

The Fit3DBuilder.ParameterStep that can be used to define optional parameters.

filterEnvironments

Fit3DBuilder.ParameterStep filterEnvironments()

Enables pre-filtering of extracted environments, i.e. each pair of residues has to have a compatible pair in the environment within distance cutoff.

Returns:

The Fit3DBuilder.ParameterStep that can be used to define optional parameters.