Uses of Class
de.bioforscher.singa.structure.model.identifiers.LeafIdentifier

Packages that use LeafIdentifier

Package	Description
de.bioforscher.singa.structure.model.identifiers
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.tokens
de.bioforscher.singa.structure.parser.plip
de.bioforscher.singa.structure.parser.sifts

Uses of LeafIdentifier in de.bioforscher.singa.structure.model.identifiers

Fields in de.bioforscher.singa.structure.model.identifiers declared as LeafIdentifier

Modifier and Type	Field and Description
static LeafIdentifier	LeafIdentifier.DEFAULT_LEAF_IDENTIFIER

Methods in de.bioforscher.singa.structure.model.identifiers that return LeafIdentifier

Modifier and Type	Method and Description
static LeafIdentifier	LeafIdentifier.fromSimpleString(String simpleString) Constructs a LeafIdentifier from the given simple string.

Methods in de.bioforscher.singa.structure.model.identifiers that return types with arguments of type LeafIdentifier

Modifier and Type	Method and Description
static List<LeafIdentifier>	LeafIdentifiers.of(String... identifers)

Methods in de.bioforscher.singa.structure.model.identifiers with parameters of type LeafIdentifier

Modifier and Type	Method and Description
int	LeafIdentifier.compareTo(LeafIdentifier o)

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

Methods in de.bioforscher.singa.structure.model.interfaces that return LeafIdentifier

Modifier and Type	Method and Description
LeafIdentifier	LeafSubstructure.getIdentifier() Returns the complete leaf identifier.

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

Modifier and Type	Method and Description
default Optional<AminoAcid>	LeafSubstructureContainer.getAminoAcid(LeafIdentifier leafIdentifier) Returns an Optional of the AminoAcid with the given identifier.
Optional<LeafSubstructure<?>>	LeafSubstructureContainer.getLeafSubstructure(LeafIdentifier leafIdentifier) Returns an Optional of the LeafSubstructure with the given identifier.
default Optional<Ligand>	LeafSubstructureContainer.getLigand(LeafIdentifier leafIdentifier) Returns an Optional of the Ligand with the given identifier.
default Optional<Nucleotide>	LeafSubstructureContainer.getNucleotide(LeafIdentifier leafIdentifier) Returns an Optional of the Nucleotide with the given identifier.
boolean	LeafSubstructureContainer.removeLeafSubstructure(LeafIdentifier leafIdentifier) Removes a LeafSubstructure from this container.

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

Methods in de.bioforscher.singa.structure.model.mmtf that return LeafIdentifier

Modifier and Type	Method and Description
LeafIdentifier	MmtfLeafSubstructure.getIdentifier()

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

Modifier and Type	Method and Description
Optional<LeafSubstructure<?>>	MmtfModel.getLeafSubstructure(LeafIdentifier leafIdentifier)
Optional<LeafSubstructure<?>>	MmtfStructure.getLeafSubstructure(LeafIdentifier leafIdentifier)
Optional<LeafSubstructure<?>>	MmtfChain.getLeafSubstructure(LeafIdentifier leafIdentifier)
boolean	MmtfModel.removeLeafSubstructure(LeafIdentifier leafIdentifier)
boolean	MmtfStructure.removeLeafSubstructure(LeafIdentifier leafIdentifier)
boolean	MmtfChain.removeLeafSubstructure(LeafIdentifier leafIdentifier)

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

Fields in de.bioforscher.singa.structure.model.oak with type parameters of type LeafIdentifier

Modifier and Type	Field and Description
LinkedHashMap<LeafIdentifier,LeafSubstructure<?>>	StructuralMotif.leafSubstructures

Methods in de.bioforscher.singa.structure.model.oak that return LeafIdentifier

Modifier and Type	Method and Description
LeafIdentifier	OakLeafSubstructure.getIdentifier()
LeafIdentifier	OakChain.getNextLeafIdentifier()

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

Modifier and Type	Method and Description
void	StructuralMotif.addExchangeableFamily(LeafIdentifier leafIdentifier, AminoAcidFamily aminoAcidFamily) For a given LeafIdentifier a possible exchange is added.
void	StructuralMotif.addExchangeableFamily(LeafIdentifier leafIdentifier, MatcherFamily matcherFamily) For a given LeafIdentifier a possible exchange is added.
void	StructuralMotif.addExchangeableFamily(LeafIdentifier leafIdentifier, NucleotideFamily nucleotideFamily) For a given LeafIdentifier a possible exchange is added.
static OakAminoAcid	LeafSubstructureFactory.createAminoAcidFromAtoms(LeafIdentifier leafIdentifier, AminoAcidFamily aminoAcidFamily, Map<String,OakAtom> atoms, StructureParserOptions options)
static OakLeafSubstructure<?>	LeafSubstructureFactory.createLeafSubstructure(LeafIdentifier leafIdentifier, StructuralFamily family)
static OakNucleotide	LeafSubstructureFactory.createNucleotideFromAtoms(LeafIdentifier leafIdentifier, NucleotideFamily nucleotideFamily, Map<String,OakAtom> atoms, StructureParserOptions options)
Optional<LeafSubstructure<?>>	StructuralMotif.getLeafSubstructure(LeafIdentifier leafIdentifier)
Optional<LeafSubstructure<?>>	OakStructure.getLeafSubstructure(LeafIdentifier leafIdentifier)
Optional<LeafSubstructure<?>>	OakChain.getLeafSubstructure(LeafIdentifier leafIdentifier)
Optional<LeafSubstructure<?>>	OakModel.getLeafSubstructure(LeafIdentifier leafIdentifier)
boolean	StructuralMotif.removeLeafSubstructure(LeafIdentifier leafIdentifier)
boolean	OakStructure.removeLeafSubstructure(LeafIdentifier leafIdentifier)
boolean	OakChain.removeLeafSubstructure(LeafIdentifier leafIdentifier)
boolean	OakModel.removeLeafSubstructure(LeafIdentifier leafIdentifier)

Method parameters in de.bioforscher.singa.structure.model.oak with type arguments of type LeafIdentifier

Modifier and Type	Method and Description
static StructuralMotif	StructuralMotif.fromLeafIdentifiers(Structure structure, List<LeafIdentifier> leafIdentifiers) Creates a StructuralMotif by extracting the given residues identified by a list of LeafIdentifiers.

Constructors in de.bioforscher.singa.structure.model.oak with parameters of type LeafIdentifier

Constructor and Description
OakAminoAcid(LeafIdentifier leafIdentifier, AminoAcidFamily family)
OakAminoAcid(LeafIdentifier identifer, AminoAcidFamily aminoAcidFamily, String threeLetterCode)
OakLeafSubstructure(LeafIdentifier leafIdentifier, FamilyType family)
OakLeafSubstructure(LeafIdentifier identifer, FamilyType aminoAcidFamily, String threeLetterCode)
OakLigand(LeafIdentifier leafIdentifier, LigandFamily family)
OakNucleotide(LeafIdentifier leafIdentifier, NucleotideFamily family)
OakNucleotide(LeafIdentifier identifer, NucleotideFamily nucleotideFamily, String threeLetterCode)

Uses of LeafIdentifier in de.bioforscher.singa.structure.parser.pdb.structures.tokens

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

Modifier and Type	Method and Description
OakLeafSubstructure<?>	LeafSkeleton.toRealLeafSubstructure(LeafIdentifier identifer, Map<String,OakAtom> atoms)

Uses of LeafIdentifier in de.bioforscher.singa.structure.parser.plip

Methods in de.bioforscher.singa.structure.parser.plip that return LeafIdentifier

Modifier and Type	Method and Description
LeafIdentifier	Interaction.getSource()
LeafIdentifier	Interaction.getTarget()

Methods in de.bioforscher.singa.structure.parser.plip with parameters of type LeafIdentifier

Modifier and Type	Method and Description
List<Interaction>	InteractionContainer.getInteractionsBetween(LeafIdentifier first, LeafIdentifier second) Returns all Interactions between two leaves (i.e.
boolean	InteractionContainer.hasInteractions(LeafIdentifier first, LeafIdentifier second) Returns true if any interaction between the two leaves is annotated in this container.
void	Interaction.setSource(LeafIdentifier source)
void	Interaction.setTarget(LeafIdentifier target)

Uses of LeafIdentifier in de.bioforscher.singa.structure.parser.sifts

Fields in de.bioforscher.singa.structure.parser.sifts with type parameters of type LeafIdentifier

Modifier and Type	Field and Description
Map<LeafIdentifier,Integer>	ResidueMapContentHandler.mapping

Methods in de.bioforscher.singa.structure.parser.sifts that return types with arguments of type LeafIdentifier

Modifier and Type	Method and Description
Map<LeafIdentifier,Integer>	ResidueMapContentHandler.getMapping()
Map<LeafIdentifier,Integer>	UniProtResidueMapParser.parse()
static Map<LeafIdentifier,Integer>	UniProtResidueMapParser.parse(PDBIdentifier pdbIdentifier)
static Map<LeafIdentifier,Integer>	UniProtResidueMapParser.parse(String pdbIdentifier)