Uses of Class
de.bioforscher.singa.structure.model.oak.OakAtom

Packages that use OakAtom

Package	Description
de.bioforscher.singa.structure.model.oak
de.bioforscher.singa.structure.parser.pdb.structures.tokens

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

Fields in de.bioforscher.singa.structure.model.oak declared as OakAtom

Modifier and Type	Field and Description
protected OakAtom	OakBond.source
protected OakAtom	OakBond.target

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

Modifier and Type	Method and Description
OakAtom	OakAtom.getCopy()
OakAtom	OakBond.getSource()
OakAtom	OakBond.getTarget()

Methods in de.bioforscher.singa.structure.model.oak that return types with arguments of type OakAtom

Modifier and Type	Method and Description
Set<OakAtom>	OakAtom.getNeighbours()

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

Modifier and Type	Method and Description
void	OakLeafSubstructure.addAtom(OakAtom atom)
int	OakLeafSubstructure.addBondBetween(OakAtom source, OakAtom target)
int	OakLeafSubstructure.addBondBetween(OakAtom source, OakAtom target, BondType bondType)
int	OakLeafSubstructure.addBondBetween(OakBond edge, OakAtom source, OakAtom target) Adds a bond connecting the the given atoms.
void	OakAtom.addNeighbour(OakAtom node)
boolean	OakBond.connectsAtom(OakAtom oakAtom)
void	OakBond.setSource(OakAtom source)
void	OakBond.setTarget(OakAtom target)

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

Modifier and Type	Method and Description
static OakAminoAcid	LeafSubstructureFactory.createAminoAcidFromAtoms(LeafIdentifier leafIdentifier, AminoAcidFamily aminoAcidFamily, Map<String,OakAtom> atoms, StructureParserOptions options)
static OakNucleotide	LeafSubstructureFactory.createNucleotideFromAtoms(LeafIdentifier leafIdentifier, NucleotideFamily nucleotideFamily, Map<String,OakAtom> atoms, StructureParserOptions options)

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

Constructor and Description
OakAtom(OakAtom atom) This is a copy constructor.

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

Methods in de.bioforscher.singa.structure.parser.pdb.structures.tokens that return OakAtom

Modifier and Type	Method and Description
static OakAtom	AtomToken.assembleAtom(String atomLine)

Method parameters in de.bioforscher.singa.structure.parser.pdb.structures.tokens with type arguments of type OakAtom

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