de.bioforscher.singa.structure.model.oak

Class StructuralMotifs

java.lang.Object

de.bioforscher.singa.structure.model.oak.StructuralMotifs

public class StructuralMotifs
extends Object

Utility methods that deal with StructuralMotifs.

Author:

fk

Method Summary

Modifier and Type	Method and Description
static void	assignComplexExchanges(StructuralMotif structuralMotif, EnumSet<MatcherFamily> familyGroup) Assigns the given EnumSet of exchanges to the specified StructuralMotif.
static LabeledSymmetricMatrix<StructuralMotif>	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>	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 inherited from class java.lang.Object

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

Method Detail

assignComplexExchanges

public static void assignComplexExchanges(StructuralMotif structuralMotif,
                                          EnumSet<MatcherFamily> familyGroup)

Assigns the given EnumSet of exchanges to the specified StructuralMotif.

Parameters:

structuralMotif - The StructuralMotif to which the exchanges should be assigned.

familyGroup - The group of MatcherFamily to be assigned.

calculateRmsdMatrix

public static LabeledSymmetricMatrix<StructuralMotif> calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                          boolean idealSuperimposition)

Performs a superimposition of given StructuralMotifs using arbitrary atoms and returns the RMSD distance matrix between all elements.

Parameters:

structuralMotifs - The input structural motifs.

idealSuperimposition - If ideal superimposition should be performed.

Returns:

A LabeledSymmetricMatrix that contains all-against-all RMSD values.

calculateRmsdMatrix

public static LabeledSymmetricMatrix<StructuralMotif> 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.

Parameters:

structuralMotifs - The input structural motifs.

atomFilter - The StructuralEntityFilter.AtomFilter used for the superimposition.

idealSuperimposition - If ideal superimposition should be performed.

Returns:

A LabeledSymmetricMatrix that contains all-against-all RMSD values.