Uses of Class
org.rcsb.strucmotif.domain.structure.Structure

Packages that use Structure

Package	Description
org.rcsb.strucmotif.core
org.rcsb.strucmotif.domain.query
org.rcsb.strucmotif.domain.result
org.rcsb.strucmotif.domain.structure
org.rcsb.strucmotif.io

Uses of Structure in org.rcsb.strucmotif.core

Methods in org.rcsb.strucmotif.core with parameters of type Structure

Modifier and Type	Method	Description
List<ResiduePairOccurrence>	KruskalMotifPruner.prune(Structure structure, List<LabelSelection> labelSelections, List<Map<LabelAtomId,float[]>> residues)
List<ResiduePairOccurrence>	MotifPruner.prune(Structure structure, List<LabelSelection> labelSelections, List<Map<LabelAtomId,float[]>> residues)	Perform pruning operation (e.g.
List<ResiduePairOccurrence>	NoOperationMotifPruner.prune(Structure structure, List<LabelSelection> labelSelections, List<Map<LabelAtomId,float[]>> residues)

Uses of Structure in org.rcsb.strucmotif.domain.query

Methods in org.rcsb.strucmotif.domain.query that return Structure

Modifier and Type	Method	Description
Structure	QueryStructure.getStructure()	Delegate to wrapped structure.

Methods in org.rcsb.strucmotif.domain.query with parameters of type Structure

Modifier and Type	Method	Description
QueryBuilder.MandatoryBuilder	QueryBuilder.defineByStructureAndSelection(Structure structure, List<LabelSelection> labelSelections)	Routine if structure files contains extracted motif.

Uses of Structure in org.rcsb.strucmotif.domain.result

Methods in org.rcsb.strucmotif.domain.result with parameters of type Structure

Modifier and Type	Method	Description
Stream<Hit>	TargetStructure.paths(List<Integer> residueIndexSwaps, Structure structure, HitScorer hitScorer, StateRepository stateRepository)	Traverses all paths of this structure.

Uses of Structure in org.rcsb.strucmotif.domain.structure

Constructors in org.rcsb.strucmotif.domain.structure with parameters of type Structure

Modifier	Constructor	Description
	ResidueGraph(Structure structure, float squaredCutoff, boolean allowTransformed)	Construct a new residue graph from a full structure.
	ResidueGraph(Structure structure, List<LabelSelection> labelSelections, List<Map<LabelAtomId,float[]>> residues, float squaredCutoff, boolean allowTransformed)	Construct a residue graph.

Uses of Structure in org.rcsb.strucmotif.io

Methods in org.rcsb.strucmotif.io that return Structure

Modifier and Type	Method	Description
Structure	StructureDataProvider.readFromInputStream(InputStream inputStream)	Read everything from an input stream.
Structure	StructureDataProviderImpl.readFromInputStream(InputStream inputStream)
Structure	StructureReader.readFromInputStream(InputStream inputStream)	Read from a InputStream and parse the corresponding Structure.
Structure	StructureReaderImpl.readFromInputStream(InputStream inputStream)
Structure	StructureDataProvider.readOriginal(String structureIdentifier)	Read a selected range from an original structure.
Structure	StructureDataProviderImpl.readOriginal(String structureIdentifier)
Structure	StructureDataProvider.readRenumbered(String structureIdentifier)	Read a renumbered structure entirely.
Structure	StructureDataProviderImpl.readRenumbered(String structureIdentifier)
Structure	StructureDataProvider.readSome(String structureIdentifier)	Read some structure entirely.
Structure	StructureDataProviderImpl.readSome(String structureIdentifier)