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

Packages that use Atom

Package	Description
de.bioforscher.singa.structure.algorithms.gyration
de.bioforscher.singa.structure.algorithms.superimposition
de.bioforscher.singa.structure.algorithms.superimposition.affinity
de.bioforscher.singa.structure.algorithms.superimposition.consensus
de.bioforscher.singa.structure.algorithms.superimposition.fit3d
de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations
de.bioforscher.singa.structure.model.families
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 Atom in de.bioforscher.singa.structure.algorithms.gyration

Methods in de.bioforscher.singa.structure.algorithms.gyration that return types with arguments of type Atom

Modifier and Type	Method and Description
List<Atom>	Gyration.getAtoms() Returns the atoms the gyration has been calculated from.

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

Methods in de.bioforscher.singa.structure.algorithms.superimposition that return types with arguments of type Atom

Modifier and Type	Method and Description
protected de.bioforscher.singa.core.utility.Pair<List<Atom>>	SubstructureSuperimposer.defineAtoms() Method to define the intersecting Atoms that should be used for the alignment.
protected de.bioforscher.singa.core.utility.Pair<List<Atom>>	FragmentSubstructureSuperimposer.defineAtoms()

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

Modifier and Type	Method and Description
static SubstructureSuperimposition	SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	SubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter)

Uses of Atom in de.bioforscher.singa.structure.algorithms.superimposition.affinity

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

Modifier and Type	Method and Description
AffinityAlignment.ParameterStep	AffinityAlignment.AtomStep.atomFilter(Predicate<Atom> atomFilter) Defines the StructuralEntityFilter.AtomFilter to be used for the computed alignments.
AffinityAlignment.ParameterStep	AffinityAlignment.Builder.atomFilter(Predicate<Atom> atomFilter)

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

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

Modifier and Type	Method and Description
ConsensusBuilder.ParameterStep	ConsensusBuilder.AtomStep.atomFilter(Predicate<Atom> atomFilter) Defines the StructuralEntityFilter.AtomFilter to be used during consensus calculation.
ConsensusBuilder.ParameterStep	ConsensusBuilder.Builder.atomFilter(Predicate<Atom> atomFilter)

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

Method parameters in de.bioforscher.singa.structure.algorithms.superimposition.fit3d with type arguments of type Atom

Modifier and Type	Method and Description
Fit3DBuilder.ParameterStep	Fit3DBuilder.AtomStep.atomFilter(Predicate<Atom> atomFilter) Defines a StructuralEntityFilter.AtomFilter filter to be used for the Fit3D alignment (e.g.
Fit3DBuilder.ParameterStep	Fit3DBuilder.Builder.atomFilter(Predicate<Atom> atomFilter)

Uses of Atom in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations

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

Modifier and Type	Method and Description
Atom	BetaCarbonRepresentationScheme.determineRepresentingAtom(LeafSubstructure<?> leafSubstructure)
Atom	CentroidRepresentationScheme.determineRepresentingAtom(LeafSubstructure<?> leafSubstructure)
Atom	SideChainCentroidRepresentationScheme.determineRepresentingAtom(LeafSubstructure<?> leafSubstructure)
Atom	RepresentationScheme.determineRepresentingAtom(LeafSubstructure<?> leafSubstructure) Determined the representing Atom for the concrete implementation.
Atom	LastHeavySidechainRepresentationScheme.determineRepresentingAtom(LeafSubstructure<?> leafSubstructure)
Atom	AlphaCarbonRepresentationScheme.determineRepresentingAtom(LeafSubstructure<?> leafSubstructure)

Uses of Atom in de.bioforscher.singa.structure.model.families

Method parameters in de.bioforscher.singa.structure.model.families with type arguments of type Atom

Modifier and Type	Method and Description
boolean	AminoAcidFamily.containsExpectedAtoms(List<Atom> atoms, AminoAcidFamily aminoAcidFamily) Returns true if the set of AtomFilter contains only Atom names, that can occur in the given residue type.

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

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

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

Methods in de.bioforscher.singa.structure.model.interfaces that return types with arguments of type Atom

Modifier and Type	Method and Description
default List<Atom>	LeafSubstructureContainer.getAllAtoms() Returns all Atoms.
List<Atom>	AtomContainer.getAllAtoms() Returns all Atoms.
default Optional<Atom>	LeafSubstructureContainer.getAtom(int atomIdentifier) Returns an Optional of the Atom with the given identifier.
Optional<Atom>	AtomContainer.getAtom(Integer atomIdentifier) Returns an Optional of the Atom with the given identifier.
Optional<Atom>	LeafSubstructure.getAtomByName(String atomName)

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

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

Modifier and Type	Class and Description
class	MmtfAtom The implementation of Atom for mmtf structures.

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

Modifier and Type	Method and Description
Atom	MmtfAtom.getCopy()

Methods in de.bioforscher.singa.structure.model.mmtf that return types with arguments of type Atom

Modifier and Type	Method and Description
List<Atom>	MmtfLeafSubstructure.getAllAtoms()
Optional<Atom>	MmtfModel.getAtom(Integer atomIdentifier)
Optional<Atom>	MmtfStructure.getAtom(Integer atomIdentifier)
Optional<Atom>	MmtfChain.getAtom(Integer atomIdentifier)
Optional<Atom>	MmtfLeafSubstructure.getAtom(Integer internalAtomIndex)
Optional<Atom>	MmtfLeafSubstructure.getAtomByName(String atomName)

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

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

Modifier and Type	Class and Description
class	OakAtom

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

Modifier and Type	Method and Description
static Atom	AminoAcids.createVirtualCBAtom(AminoAcid aminoAcid) This creates a virtual beta carbon for glycine by superimposing alanine.

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

Modifier and Type	Method and Description
static LabeledSymmetricMatrix<Atom>	Structures.calculateAtomDistanceMatrix(AtomContainer atomContainer) Returns the distance matrix of the given Atoms.
static LabeledSymmetricMatrix<Atom>	Structures.calculateAtomDistanceMatrix(List<Atom> atoms) Returns the distance matrix of the given Atoms.
List<Atom>	OakLeafSubstructure.getAllAtoms()
Optional<Atom>	StructuralMotif.getAtom(Integer atomIdentifier)
Optional<Atom>	OakStructure.getAtom(Integer atomIdentifier)
Optional<Atom>	OakChain.getAtom(Integer atomIdentifier)
Optional<Atom>	OakLeafSubstructure.getAtom(Integer atomIdentifier)
Optional<Atom>	OakModel.getAtom(Integer atomIdentifier)
Optional<Atom>	OakLeafSubstructure.getAtomByName(String atomName)
Predicate<Atom>	StructuralEntityFilter.AtomFilterType.getFilter()
Optional<Map.Entry<UniqueAtomIdentifer,Atom>>	OakStructure.getUniqueAtomEntry(int atomSerial)
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.hasAtomName(AtomName atomName)
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.hasAtomName(String atomName)
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.hasAtomNames(String... atomNames)
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.hasIdentifier(int identifier)
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isAlphaCarbon()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isArbitrary()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isBackbone()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isBackboneCarbon()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isBackboneNitrogen()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isBackboneOxygen()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isBetaCarbon()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isCarbon()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isHydrogen()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isNitrogen()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isOxygen()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isPhosphorus()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isSideChain()
static Predicate<Atom>	StructuralEntityFilter.AtomFilter.isWithinRange(int startId, int endId)

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

Modifier and Type	Method and Description
static LabeledSymmetricMatrix<Atom>	Structures.calculateAtomDistanceMatrix(List<Atom> atoms) Returns the distance matrix of the given Atoms.
static LabeledSymmetricMatrix<StructuralMotif>	StructuralMotifs.calculateRmsdMatrix(List<StructuralMotif> structuralMotifs, Predicate<Atom> atomFilter, boolean idealSuperimposition) Performs a superimposition of given StructuralMotifs using the specified StructuralEntityFilter.AtomFilter and returns the RMSD distance matrix between all elements.

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

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

Modifier and Type	Method and Description
Atom	StructureSelector.SelectStep.selectAtom()
Atom	StructureSelector.Selector.selectAtom()