Uses of Class
de.bioforscher.singa.structure.algorithms.superimposition.scores.SubstitutionMatrix

Packages that use SubstitutionMatrix

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

Uses of SubstitutionMatrix in de.bioforscher.singa.structure.algorithms.superimposition

Methods in de.bioforscher.singa.structure.algorithms.superimposition with parameters of type SubstitutionMatrix

Modifier and Type	Method and Description
static SubstructureSuperimposition	SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, RepresentationScheme representationScheme, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, RepresentationScheme representationScheme, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)

Uses of SubstitutionMatrix in de.bioforscher.singa.structure.algorithms.superimposition.fit3d

Methods in de.bioforscher.singa.structure.algorithms.superimposition.fit3d with parameters of type SubstitutionMatrix

Modifier and Type	Method and Description
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.SiteParameterConfigurationStep	Fit3DBuilder.SiteParameterConfigurationStep.substitutionMatrix(SubstitutionMatrix substitutionMatrix) The SubstitutionMatrix to be used to calculate the Xie score.
Fit3DBuilder.SiteParameterConfigurationStep	Fit3DBuilder.Builder.substitutionMatrix(SubstitutionMatrix substitutionMatrix)

Uses of SubstitutionMatrix in de.bioforscher.singa.structure.algorithms.superimposition.scores

Methods in de.bioforscher.singa.structure.algorithms.superimposition.scores that return SubstitutionMatrix

Modifier and Type	Method and Description
static SubstitutionMatrix	SubstitutionMatrix.valueOf(String name) Returns the enum constant of this type with the specified name.
static SubstitutionMatrix[]	SubstitutionMatrix.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in de.bioforscher.singa.structure.algorithms.superimposition.scores with parameters of type SubstitutionMatrix

Modifier and Type	Method and Description
static XieScore	XieScore.of(SubstitutionMatrix substitutionMatrix, SubstructureSuperimposition substructureSuperimposition)