Uses of Class
de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition

Packages that use SubstructureSuperimposition

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

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

Methods in de.bioforscher.singa.structure.algorithms.superimposition that return SubstructureSuperimposition

Modifier and Type	Method and Description
static SubstructureSuperimposition	SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, RepresentationScheme representationScheme)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, RepresentationScheme representationScheme)
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)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, RepresentationScheme representationScheme)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
static SubstructureSuperimposition	FragmentSubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
static SubstructureSuperimposition	FragmentSubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, BiFunction<MoleculeAtom,MoleculeAtom,Boolean> atomCondition, BiFunction<MoleculeBond,MoleculeBond,Boolean> bondCondition)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, RepresentationScheme representationScheme)
protected SubstructureSuperimposition	SubstructureSuperimposer.calculateSuperimposition() Finds the superimposition for a list of LeafSubstructure according to their input order

Uses of SubstructureSuperimposition in de.bioforscher.singa.structure.algorithms.superimposition.consensus

Methods in de.bioforscher.singa.structure.algorithms.superimposition.consensus that return SubstructureSuperimposition

Modifier and Type	Method and Description
SubstructureSuperimposition	ConsensusContainer.getSuperimposition()

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

Modifier and Type	Method and Description
void	ConsensusContainer.setSuperimposition(SubstructureSuperimposition superimposition)

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

Methods in de.bioforscher.singa.structure.algorithms.superimposition.fit3d that return SubstructureSuperimposition

Modifier and Type	Method and Description
SubstructureSuperimposition	Fit3DMatch.getSubstructureSuperimposition()

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

Modifier and Type	Method and Description
static Fit3DMatch	Fit3DMatch.of(double rmsd, SubstructureSuperimposition substructureSuperimposition)
static Fit3DMatch	Fit3DMatch.of(double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)

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

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

Modifier and Type	Method and Description
static XieScore	XieScore.of(SubstitutionMatrix substitutionMatrix, SubstructureSuperimposition substructureSuperimposition)
static PsScore	PsScore.of(SubstructureSuperimposition substructureSuperimposition, int referenceLength, int queryLength) Calculates the PsScore for the given SubstructureSuperimposition.