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

Class Fit3DBuilder.Builder

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder

All Implemented Interfaces:

Fit3DBuilder.AtomStep, Fit3DBuilder.BatchParameterStep, Fit3DBuilder.ParameterStep, Fit3DBuilder.QueryStep, Fit3DBuilder.SiteConfigurationStep, Fit3DBuilder.SiteParameterConfigurationStep, Fit3DBuilder.SiteStep, Fit3DBuilder.TargetStep

Enclosing class:

Fit3DBuilder

public static class Fit3DBuilder.Builder
extends Object
implements Fit3DBuilder.QueryStep, Fit3DBuilder.SiteStep, Fit3DBuilder.SiteParameterConfigurationStep, Fit3DBuilder.SiteConfigurationStep, Fit3DBuilder.TargetStep, Fit3DBuilder.AtomStep, Fit3DBuilder.BatchParameterStep, Fit3DBuilder.ParameterStep

Constructor Summary

Constructors

Constructor and Description
Builder()

Method Summary

Modifier and Type	Method and Description
Fit3DBuilder.ParameterStep	atomFilter(Predicate<Atom> atomFilter) Defines a StructuralEntityFilter.AtomFilter filter to be used for the Fit3D alignment (e.g.
Fit3DBuilder.SiteParameterConfigurationStep	cutoffScore(double cutoffScore) The cutoff score that should be used when extending the site alignment.
Fit3DBuilder.ParameterStep	distanceTolerance(double distanceTolerance) Defines the distance tolerance that is accepted when extracting local environments.
Fit3DBuilder.AtomStep	exhaustive() Guarantees to find the ideal alignment of the input sites.
Fit3DBuilder.ParameterStep	filterEnvironments() Enables pre-filtering of extracted environments, i.e.
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	limitedParallelism(int limitedParallelism) Defines for a batch search the level of parallelism (number of cores) that should be used by Fit3D.
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.AtomStep	maximalParallelism() Allows Fit3D in search mode to use all available cores for processing.
Fit3DBuilder.TargetStep	query(StructuralMotif query) Defines the query motif for this Fit3D search.
Fit3DBuilder.ParameterStep	representationScheme(RepresentationSchemeType representationSchemeType) Defines a single point RepresentationScheme that should be used to represent single residues.
Fit3DBuilder.AtomStep	restrictToSpecifiedExchanges() Restricts the site alignment to the specified exchanges of the input sites.
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.SiteStep	site(StructuralMotif site1) Defines a site that should be aligned against another.
Fit3DBuilder.BatchParameterStep	skipAlphaCarbonTargets() Sets the option to skip all targets that consist of only alpha carbon atoms to avoid a lot of noise in the results.
Fit3DBuilder.BatchParameterStep	skipBackboneTargets() Sets the option to skip all targets that consist of only backbone atoms to avoid a lot of noise in the results.
Fit3DBuilder.ParameterStep	statisticalModel(StatisticalModel statisticalModel) Adds the specified StatisticalModel to the search to calculate significance of matches.
Fit3DBuilder.SiteParameterConfigurationStep	substitutionMatrix(SubstitutionMatrix substitutionMatrix) The SubstitutionMatrix to be used to calculate the Xie score.
Fit3DBuilder.AtomStep	target(LeafSubstructureContainer target) Defines the target against which this Fit3D search should be run.
Fit3DBuilder.BatchParameterStep	targets(StructureParser.MultiParser multiParser) Defines the targets against which this Fit3D search should be run in batch mode.
Fit3DBuilder.SiteParameterConfigurationStep	vs(StructuralMotif site2) Defines the second site for the pairwise site alignment.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Builder

public Builder()

Method Detail

query

public Fit3DBuilder.TargetStep query(StructuralMotif query)

Description copied from interface: Fit3DBuilder.QueryStep

Defines the query motif for this Fit3D search.

Specified by:

query in interface Fit3DBuilder.QueryStep

Parameters:

query - The query motif to be used.

Returns:

The Fit3DBuilder.TargetStep to define one or several targets.

site

public Fit3DBuilder.SiteStep site(StructuralMotif site1)

Description copied from interface: Fit3DBuilder.QueryStep

Defines a site that should be aligned against another.

Specified by:

site in interface Fit3DBuilder.QueryStep

Parameters:

site1 - The first site to be aligned.

Returns:

The Fit3DBuilder.SiteStep to define the antagonist.

target

public Fit3DBuilder.AtomStep target(LeafSubstructureContainer target)

Description copied from interface: Fit3DBuilder.TargetStep

Defines the target against which this Fit3D search should be run.

Specified by:

target in interface Fit3DBuilder.TargetStep

Parameters:

target - The target LeafSubstructureContainer against which the search should be run.

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

targets

public Fit3DBuilder.BatchParameterStep targets(StructureParser.MultiParser multiParser)

Description copied from interface: Fit3DBuilder.TargetStep

Defines the targets against which this Fit3D search should be run in batch mode. This can either be a list of PDB-IDs or file paths pointing to target files in PDB format.

Specified by:

targets in interface Fit3DBuilder.TargetStep

Parameters:

multiParser - The StructureParser.MultiParser that provides the structures to that should be run in batch mode.

Returns:

The Fit3DBuilder.BatchParameterStep to define the level of parallelism the batch search should use.

run

public Fit3D run()
          throws SubstructureSuperimpositionException

Description copied from interface: Fit3DBuilder.AtomStep

Creates a new Fit3D search and starts calculation.

Specified by:

run in interface Fit3DBuilder.AtomStep

Specified by:

run in interface Fit3DBuilder.ParameterStep

Returns:

A new Fit3D search when finished.

Throws:

SubstructureSuperimpositionException

rmsdCutoff

public Fit3DBuilder.ParameterStep rmsdCutoff(double rmsdCutoff)

Description copied from interface: Fit3DBuilder.ParameterStep

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.

Specified by:

rmsdCutoff in interface Fit3DBuilder.ParameterStep

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

public Fit3DBuilder.ParameterStep distanceTolerance(double distanceTolerance)

Description copied from interface: Fit3DBuilder.ParameterStep

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.

Specified by:

distanceTolerance in interface Fit3DBuilder.ParameterStep

Parameters:

distanceTolerance - The distance tolerance considered when extracting local environments.

Returns:

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

atomFilter

public Fit3DBuilder.ParameterStep atomFilter(Predicate<Atom> atomFilter)

Description copied from interface: Fit3DBuilder.AtomStep

Defines a StructuralEntityFilter.AtomFilter filter to be used for the Fit3D alignment (e.g. only sidechain atoms).

Specified by:

atomFilter in interface Fit3DBuilder.AtomStep

Parameters:

atomFilter - The StructuralEntityFilter.AtomFilter filter to be used for the alignment.

Returns:

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

representationScheme

public Fit3DBuilder.ParameterStep representationScheme(RepresentationSchemeType representationSchemeType)

Description copied from interface: Fit3DBuilder.AtomStep

Defines a single point RepresentationScheme that should be used to represent single residues.

Specified by:

representationScheme in interface Fit3DBuilder.AtomStep

Parameters:

representationSchemeType - The RepresentationSchemeType that should be used.

Returns:

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

limitedParallelism

public Fit3DBuilder.AtomStep limitedParallelism(int limitedParallelism)

Description copied from interface: Fit3DBuilder.BatchParameterStep

Defines for a batch search the level of parallelism (number of cores) that should be used by Fit3D.

Specified by:

limitedParallelism in interface Fit3DBuilder.BatchParameterStep

Parameters:

limitedParallelism - The desired level of parallelism.

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

maximalParallelism

public Fit3DBuilder.AtomStep maximalParallelism()

Description copied from interface: Fit3DBuilder.BatchParameterStep

Allows Fit3D in search mode to use all available cores for processing.

Specified by:

maximalParallelism in interface Fit3DBuilder.BatchParameterStep

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

skipAlphaCarbonTargets

public Fit3DBuilder.BatchParameterStep skipAlphaCarbonTargets()

Description copied from interface: Fit3DBuilder.BatchParameterStep

Sets the option to skip all targets that consist of only alpha carbon atoms to avoid a lot of noise in the results.

Specified by:

skipAlphaCarbonTargets in interface Fit3DBuilder.BatchParameterStep

Returns:

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

skipBackboneTargets

public Fit3DBuilder.BatchParameterStep skipBackboneTargets()

Description copied from interface: Fit3DBuilder.BatchParameterStep

Sets the option to skip all targets that consist of only backbone atoms to avoid a lot of noise in the results.

Specified by:

skipBackboneTargets in interface Fit3DBuilder.BatchParameterStep

Returns:

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

statisticalModel

public Fit3DBuilder.ParameterStep statisticalModel(StatisticalModel statisticalModel)

Description copied from interface: Fit3DBuilder.ParameterStep

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)

Specified by:

statisticalModel in interface Fit3DBuilder.ParameterStep

Parameters:

statisticalModel - The StatisticalModel to be used.

Returns:

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

mapUniProtIdentifiers

public Fit3DBuilder.ParameterStep mapUniProtIdentifiers()

Description copied from interface: Fit3DBuilder.ParameterStep

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

Specified by:

mapUniProtIdentifiers in interface Fit3DBuilder.ParameterStep

Returns:

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

mapPfamIdentifiers

public Fit3DBuilder.ParameterStep mapPfamIdentifiers()

Description copied from interface: Fit3DBuilder.ParameterStep

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

Specified by:

mapPfamIdentifiers in interface Fit3DBuilder.ParameterStep

Returns:

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

mapECNumbers

public Fit3DBuilder.ParameterStep mapECNumbers()

Description copied from interface: Fit3DBuilder.ParameterStep

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

Specified by:

mapECNumbers in interface Fit3DBuilder.ParameterStep

Returns:

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

filterEnvironments

public Fit3DBuilder.ParameterStep filterEnvironments()

Description copied from interface: Fit3DBuilder.ParameterStep

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

Specified by:

filterEnvironments in interface Fit3DBuilder.ParameterStep

Returns:

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

vs

public Fit3DBuilder.SiteParameterConfigurationStep vs(StructuralMotif site2)

Description copied from interface: Fit3DBuilder.SiteStep

Defines the second site for the pairwise site alignment.

Specified by:

vs in interface Fit3DBuilder.SiteStep

Parameters:

site2 - The second site to be aligned.

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

cutoffScore

public Fit3DBuilder.SiteParameterConfigurationStep cutoffScore(double cutoffScore)

Description copied from interface: Fit3DBuilder.SiteParameterConfigurationStep

The cutoff score that should be used when extending the site alignment.

Specified by:

cutoffScore in interface Fit3DBuilder.SiteParameterConfigurationStep

Parameters:

cutoffScore - The cutoff score.

Returns:

The Fit3DBuilder.SiteParameterConfigurationStep to configure other parameters.

substitutionMatrix

public Fit3DBuilder.SiteParameterConfigurationStep substitutionMatrix(SubstitutionMatrix substitutionMatrix)

Description copied from interface: Fit3DBuilder.SiteParameterConfigurationStep

The SubstitutionMatrix to be used to calculate the Xie score.

Specified by:

substitutionMatrix in interface Fit3DBuilder.SiteParameterConfigurationStep

Parameters:

substitutionMatrix - The substitution matrix.

Returns:

The Fit3DBuilder.SiteParameterConfigurationStep to configure other parameters.

restrictToSpecifiedExchanges

public Fit3DBuilder.AtomStep restrictToSpecifiedExchanges()

Description copied from interface: Fit3DBuilder.SiteConfigurationStep

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

Specified by:

restrictToSpecifiedExchanges in interface Fit3DBuilder.SiteConfigurationStep

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

ignoreSpecifiedExchanges

public Fit3DBuilder.AtomStep ignoreSpecifiedExchanges()

Description copied from interface: Fit3DBuilder.SiteConfigurationStep

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.

Specified by:

ignoreSpecifiedExchanges in interface Fit3DBuilder.SiteConfigurationStep

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

exhaustive

public Fit3DBuilder.AtomStep exhaustive()

Description copied from interface: Fit3DBuilder.SiteConfigurationStep

Guarantees to find the ideal alignment of the input sites.

Specified by:

exhaustive in interface Fit3DBuilder.SiteConfigurationStep

Returns:

The Fit3DBuilder.AtomStep to define optional restrictions on Atoms.

kuhnMunkres

public Fit3DBuilder.AtomStep kuhnMunkres(SubstitutionMatrix substitutionMatrix,
                                         boolean restrictToExchanges)

Description copied from interface: Fit3DBuilder.SiteConfigurationStep

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.

Specified by:

kuhnMunkres in interface Fit3DBuilder.SiteConfigurationStep

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.