Uses of Class
de.bioforscher.singa.structure.model.molecules.MoleculeAtom

Packages that use MoleculeAtom

Package	Description
de.bioforscher.singa.structure.algorithms.molecules
de.bioforscher.singa.structure.algorithms.superimposition
de.bioforscher.singa.structure.model.molecules

Uses of MoleculeAtom in de.bioforscher.singa.structure.algorithms.molecules

Methods in de.bioforscher.singa.structure.algorithms.molecules that return types with arguments of type MoleculeAtom

Modifier and Type	Method and Description
static List<LinkedList<MoleculeAtom>>	MoleculePathFinder.findMultiPathInMolecule(MoleculeGraph molecule, LinkedList<Set<Element>> multiPath)
static List<LinkedList<MoleculeAtom>>	MoleculePathFinder.findPathInMolecule(MoleculeGraph molecule, LinkedList<Element> path)
List<de.bioforscher.singa.core.utility.Pair<MoleculeAtom>>	MoleculeIsomorphism.getAtomPairs(MoleculeGraph fullMatch)
static BiFunction<MoleculeAtom,MoleculeAtom,Boolean>	MoleculeIsomorphismFinder.AtomConditions.isArbitrary()
static BiFunction<MoleculeAtom,MoleculeAtom,Boolean>	MoleculeIsomorphismFinder.AtomConditions.isArbitrary()
static BiFunction<MoleculeAtom,MoleculeAtom,Boolean>	MoleculeIsomorphismFinder.AtomConditions.isSameElement()
static BiFunction<MoleculeAtom,MoleculeAtom,Boolean>	MoleculeIsomorphismFinder.AtomConditions.isSameElement()

Method parameters in de.bioforscher.singa.structure.algorithms.molecules with type arguments of type MoleculeAtom

Modifier and Type	Method and Description
static MoleculeIsomorphism	MoleculeIsomorphismFinder.of(MoleculeGraph pattern, MoleculeGraph target, BiFunction<MoleculeAtom,MoleculeAtom,Boolean> atomCondition, BiFunction<MoleculeBond,MoleculeBond,Boolean> bondCondition)
static MoleculeIsomorphism	MoleculeIsomorphismFinder.of(MoleculeGraph pattern, MoleculeGraph target, BiFunction<MoleculeAtom,MoleculeAtom,Boolean> atomCondition, BiFunction<MoleculeBond,MoleculeBond,Boolean> bondCondition)

Constructor parameters in de.bioforscher.singa.structure.algorithms.molecules with type arguments of type MoleculeAtom

Constructor and Description
MoleculeIsomorphism(RISubgraphFinder<MoleculeAtom,MoleculeBond,Vector2D,Integer,MoleculeGraph> finder)

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

Method parameters in de.bioforscher.singa.structure.algorithms.superimposition with type arguments of type MoleculeAtom

Modifier and Type	Method and Description
static SubstructureSuperimposition	FragmentSubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, BiFunction<MoleculeAtom,MoleculeAtom,Boolean> atomCondition, BiFunction<MoleculeBond,MoleculeBond,Boolean> bondCondition)
static SubstructureSuperimposition	FragmentSubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, BiFunction<MoleculeAtom,MoleculeAtom,Boolean> atomCondition, BiFunction<MoleculeBond,MoleculeBond,Boolean> bondCondition)

Uses of MoleculeAtom in de.bioforscher.singa.structure.model.molecules

Methods in de.bioforscher.singa.structure.model.molecules that return MoleculeAtom

Modifier and Type	Method and Description
MoleculeAtom	MoleculeAtom.getCopy()

Methods in de.bioforscher.singa.structure.model.molecules that return types with arguments of type MoleculeAtom

Modifier and Type	Method and Description
static List<LinkedList<MoleculeAtom>>	MoleculeGraphs.findMultiPathOfElements(MoleculeGraph graph, LinkedList<Set<Element>> path)
static List<LinkedList<MoleculeAtom>>	MoleculeGraphs.findPathOfElements(MoleculeGraph graph, LinkedList<Element> path)
static Predicate<MoleculeAtom>	MoleculeGraphs.isElement(Element element)
static Predicate<MoleculeAtom>	MoleculeGraphs.isOneOfElements(Set<Element> elements)

Methods in de.bioforscher.singa.structure.model.molecules with parameters of type MoleculeAtom

Modifier and Type	Method and Description
int	MoleculeGraph.addEdgeBetween(int identifier, MoleculeAtom source, MoleculeAtom target)
int	MoleculeGraph.addEdgeBetween(MoleculeAtom source, MoleculeAtom target)
int	MoleculeGraph.addEdgeBetween(MoleculeAtom source, MoleculeAtom target, MoleculeBondType bondType)

Constructors in de.bioforscher.singa.structure.model.molecules with parameters of type MoleculeAtom

Constructor and Description
MoleculeBond(int identifier, MoleculeAtom source, MoleculeAtom target, MoleculeBondType type)