Uses of Interface
de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer

Packages that use LeafSubstructureContainer

Package	Description
de.bioforscher.singa.structure.algorithms.superimposition
de.bioforscher.singa.structure.algorithms.superimposition.fit3d
de.bioforscher.singa.structure.model.interfaces
de.bioforscher.singa.structure.model.mmtf
de.bioforscher.singa.structure.model.oak
de.bioforscher.singa.structure.parser.pdb.structures

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

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

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.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.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)

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

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

Modifier and Type	Method and Description
Fit3DBuilder.AtomStep	Fit3DBuilder.TargetStep.target(LeafSubstructureContainer target) Defines the target against which this Fit3D search should be run.
Fit3DBuilder.AtomStep	Fit3DBuilder.Builder.target(LeafSubstructureContainer target)

Uses of LeafSubstructureContainer in de.bioforscher.singa.structure.model.interfaces

Subinterfaces of LeafSubstructureContainer in de.bioforscher.singa.structure.model.interfaces

Modifier and Type	Interface and Description
interface	Chain Chains that represent one continuous macro molecule (most often the biggest macro molecules and its ligands are collected in one model).
interface	Model Models represent macro molecular structures.
interface	Structure Structures represent chemical objects in three dimensional space.

Methods in de.bioforscher.singa.structure.model.interfaces with type parameters of type LeafSubstructureContainer

Modifier and Type	Method and Description
<ContainerType extends LeafSubstructureContainer> ContainerType	LeafSubstructureContainer.getCopy()

Methods in de.bioforscher.singa.structure.model.interfaces with parameters of type LeafSubstructureContainer

Modifier and Type	Method and Description
default void	LeafSubstructureContainer.removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep) Removes all LeafSubstructures from this container that are not referenced in the given LeafSubstructureContainer.

Uses of LeafSubstructureContainer in de.bioforscher.singa.structure.model.mmtf

Classes in de.bioforscher.singa.structure.model.mmtf that implement LeafSubstructureContainer

Modifier and Type	Class and Description
class	MmtfChain The implementation of Chain for mmtf structures.
class	MmtfModel The implementation of Model for mmtf structures.
class	MmtfStructure The implementation of Structures for mmtf structures.

Methods in de.bioforscher.singa.structure.model.mmtf with parameters of type LeafSubstructureContainer

Modifier and Type	Method and Description
void	MmtfModel.removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)
void	MmtfStructure.removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)
void	MmtfChain.removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep) Removes all LeafSubstructures from this container that are not referenced in the given LeafSubstructureContainer.

Uses of LeafSubstructureContainer in de.bioforscher.singa.structure.model.oak

Classes in de.bioforscher.singa.structure.model.oak that implement LeafSubstructureContainer

Modifier and Type	Class and Description
class	OakChain
class	OakModel
class	OakStructure
class	StructuralMotif

Methods in de.bioforscher.singa.structure.model.oak with parameters of type LeafSubstructureContainer

Modifier and Type	Method and Description
static LabeledSymmetricMatrix<LeafSubstructure<?>>	Structures.calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer) Returns the distance matrix of the given LeafSubstructureContainer.
static double	Structures.calculateExtent(LeafSubstructureContainer leafSubstructureContainer) Returns the maximal extent of the given LeafSubstructureContainer.
static LabeledSymmetricMatrix<LeafSubstructure<?>>	Structures.calculateSquaredDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer) Returns the squared distance matrix of the given LeafSubstructureContainer.
static double	Structures.calculateSquaredExtent(LeafSubstructureContainer leafSubstructureContainer) Returns the maximal squared extent of the given LeafSubstructureContainer.

Uses of LeafSubstructureContainer in de.bioforscher.singa.structure.parser.pdb.structures

Methods in de.bioforscher.singa.structure.parser.pdb.structures with parameters of type LeafSubstructureContainer

Modifier and Type	Method and Description
static void	StructureWriter.writeLeafSubstructureContainer(LeafSubstructureContainer leafSubstructureContainer, Path outputPath) Writes a given LeafSubstructureContainer in PDB format.