Index (strucmotif-search-core 0.12.3 API)

A B C D E G H I K L M N O P Q R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A0 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [0, 10) deg.
A100 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [90, 110) deg.
A120 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [110, 130) deg.
A140 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [130, 150) deg.
A160 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [150, 170) deg.
A180 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [170, 180]
A20 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [10, 30) deg.
A40 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [30, 50) deg.
A60 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [50, 70) deg.
A80 - Enum constant in enum org.rcsb.strucmotif.domain.motif.AngleType: [70, 90) deg.
add3d(float[], float[], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Adds 2 3D vectors.
addPositionSpecificExchange(LabelSelection, Collection<ResidueType>) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.OptionalStepBuilder: Register an exchange by specifying a 'range'/collection of component types.
ADENOSINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Adenosine
ALANINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Alanine
Algebra - Class in org.rcsb.strucmotif.math: A collection of algebraic or generic mathematical functions.
align(List<float[]>, float[], List<float[]>, float[]) - Static method in class org.rcsb.strucmotif.align.QuaternionAlignmentService: Align two set of residues.
align(List<Map<LabelAtomId, float[]>>, List<Map<LabelAtomId, float[]>>, AtomPairingScheme) - Method in interface org.rcsb.strucmotif.align.AlignmentService: Aligns 2 sets of residues to one another.
align(List<Map<LabelAtomId, float[]>>, List<Map<LabelAtomId, float[]>>, AtomPairingScheme) - Method in class org.rcsb.strucmotif.align.QuaternionAlignmentService
AlignmentResult - Interface in org.rcsb.strucmotif.domain.align: The result of an alignment.
AlignmentResultImpl - Class in org.rcsb.strucmotif.domain.align: The result of an alignment.
AlignmentResultImpl(Transformation, float) - Constructor for class org.rcsb.strucmotif.domain.align.AlignmentResultImpl: Construct an alignment result.
AlignmentService - Interface in org.rcsb.strucmotif.align: Superimpose sets of residues.
alignToReference(List<Map<LabelAtomId, float[]>>) - Method in class org.rcsb.strucmotif.core.HitScorer: Align a set of residues to the reference.
ALL - Enum constant in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme: Use everything.
ALPHA_CARBON - Enum constant in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme: Use alpha carbons only.
AMINO_ACID - Enum constant in enum org.rcsb.strucmotif.domain.structure.PolymerType: Amino acid chain.
angleTolerance(int) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Specify the angle tolerance (default: 1).
AngleType - Enum in org.rcsb.strucmotif.domain.motif: Binned representation of the angle between residues.
ARGININE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Arginine
ASPARAGINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Asparagine
ASPARTIC_ACID - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Aspartic acid
assemble(MotifSearchResult) - Method in interface org.rcsb.strucmotif.core.TargetAssembler: Search: i.e.
assemble(MotifSearchResult) - Method in class org.rcsb.strucmotif.core.TargetAssemblerImpl
AtomCorrespondence - Class in org.rcsb.strucmotif.domain.align: A wrapper which describes the correspondence between two collections of residues.
AtomCorrespondence(List<Map<LabelAtomId, float[]>>, List<Map<LabelAtomId, float[]>>, AtomPairingScheme) - Constructor for class org.rcsb.strucmotif.domain.align.AtomCorrespondence: Finds the correspondence between reference and candidate.
atomPairingScheme(AtomPairingScheme) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Controls which atoms will be considered for alignment.
AtomPairingScheme - Enum in org.rcsb.strucmotif.domain.align: Schemes on which atoms (by name) to use to align residues.

B

BACKBONE - Enum constant in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme: Use backbone atoms only.
backboneDistanceTolerance(int) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Specify the backbone distance tolerance (default: 1).
BETA_CARBON - Enum constant in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme: Use beta carbons only.
BIN_SIZE - Static variable in enum org.rcsb.strucmotif.domain.motif.AngleType: Width of an angle bin.
BIN_SIZE - Static variable in enum org.rcsb.strucmotif.domain.motif.DistanceType: Width of a distance bin.
blacklist(Collection<String>) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.OptionalStepBuilder: Filter out hits from the specified entries.
BOTH - Enum constant in enum org.rcsb.strucmotif.domain.motif.Overlap: Both sides overlap.
buildParameters() - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Creates a Parameters instance based on all values.
buildQuery() - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.OptionalStepBuilder: Build the actual container.

C

C - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C1_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C2_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C3_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C4 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C4_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C5 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C5_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C6 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
C8 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CA - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
capToInterval(float, float, float) - Static method in class org.rcsb.strucmotif.math.Algebra: Caps a value to a defined interval.
capToInterval(int, int, int) - Static method in class org.rcsb.strucmotif.math.Algebra: Caps a value to a defined interval.
CB - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CD - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CD1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CD2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CE - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CE1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CE2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CE3 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
centroid3d(Collection<float[]>) - Static method in class org.rcsb.strucmotif.math.Algebra: Computes the centroid of a collection of 3D vectors.
CG - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CG1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CG2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CH2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CHCH - Enum constant in enum org.rcsb.strucmotif.Motifs: Original zinc finger.
CHH - Enum constant in enum org.rcsb.strucmotif.Motifs: Simplified zinc finger.
composeTransformationMatrix(float[][], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Combine a rotation matrix and a translation vector into a 4x4 transformation matrix.
consume(InvertedIndexResiduePairIdentifier[], Overlap[]) - Method in class org.rcsb.strucmotif.domain.result.TargetStructure: Consumes a new 'generation' of residue pair identifiers which potentially resemble valid extensions to the registered paths.
crossProduct3d(float[], float[], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Computes the cross-produced of 2 3D vectors.
CYSTEINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Cysteine
CYTIDINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Cytidine
CZ - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CZ2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
CZ3 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId

D

D0 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [0, 0.5) A.
D1 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [0.5, 1.5) A.
D10 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [9.5, 10.5) A.
D11 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [10.5, 11.5) A.
D12 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [11.5, 12.5) A.
D13 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [12.5, 13.5) A.
D14 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [13.5, 14.5) A.
D15 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [14.5, 15.5) A.
D16 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [15.5, 16.5) A.
D17 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [16.5, 17.5) A.
D18 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [17.5, 18.5) A.
D19 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [18.5, 19.5) A.
D2 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [1.5, 2.5) A.
D20 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [19.5, 20.5) A.
D21 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [20.5, 21.5) A.
D22 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [21.5, 22.5) A.
D23 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [22.5, 23.5) A.
D24 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [23.5, 24.5) A.
D25 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [24.5, 25.5) A.
D26 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [25.5, 26.5) A.
D27 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [26.5, 27.5) A.
D28 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [27.5, 28.5) A.
D29 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [28.5, 29.5) A.
D3 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [2.5, 3.5) A.
D30 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [29.5, 30.5) A.
D31 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [30.5, 31.5) A.
D32 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [31.5, 32.5) A.
D33 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [32.5, 33.5) A.
D34 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [33.5, 34.5) A.
D35 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [34.5, 35.5) A.
D36 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [35.5, 36.5) A.
D37 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [36.5, 37.5) A.
D38 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [37.5, 38.5) A.
D39 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [38.5, 39.5) A.
D4 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [3.5, 4.5) A.
D40 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [39.5, 40.5) A.
D5 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [4.5, 5.5) A.
D6 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [5.5, 6.5) A.
D7 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [6.5, 7.5) A.
D8 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [7.5, 8.5) A.
D9 - Enum constant in enum org.rcsb.strucmotif.domain.motif.DistanceType: [8.5, 9.5) A.
defineByFile(InputStream) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder: Routine if stream of structure data contains extracted motif.
defineByFileAndSelection(InputStream, List<LabelSelection>) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder: Define a motif based on a stream of structure data and a selection of components.
defineByPdbIdAndSelection(String, List<LabelSelection>) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder: Define a motif based on the id of the reference structure and a selection of components.
defineByStructureAndSelection(Structure, List<LabelSelection>) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder: Routine if structure files contains extracted motif.
delete(Collection<String>) - Method in interface org.rcsb.strucmotif.io.InvertedIndex: Removes all information on a set of structures from the index.
delete(Collection<String>) - Method in class org.rcsb.strucmotif.io.InvertedIndexImpl
deleteDirty(Collection<String>) - Method in interface org.rcsb.strucmotif.io.StateRepository: Remove from 'dirty' collection.
deleteDirty(Collection<String>) - Method in class org.rcsb.strucmotif.io.StateRepositoryImpl
deleteKnown(Collection<String>) - Method in interface org.rcsb.strucmotif.io.StateRepository: Remove from 'known' collection.
deleteKnown(Collection<String>) - Method in class org.rcsb.strucmotif.io.StateRepositoryImpl
deleteRenumbered(String) - Method in interface org.rcsb.strucmotif.io.StructureDataProvider: Drop information on a renumbered structure.
deleteRenumbered(String) - Method in class org.rcsb.strucmotif.io.StructureDataProviderImpl
DEOXYADENOSINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Deoxyadenosine
DEOXYCYTIDINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Deoxycytidine
DEOXYGUANOSINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Deoxyguanosine
distance3d(float[], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Computes the distance between 2 3D vectors.
distanceSquared3d(float[], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Computes the squared distance between 2 3D vectors.
DistanceType - Enum in org.rcsb.strucmotif.domain.motif: Binned representation of the distance between residues.
divide3d(float[], float[], float) - Static method in class org.rcsb.strucmotif.math.Algebra: Divides a 3D vector by a scalar.
dotProduct3d(float[], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Computes the dot-product of 2 3D vectors.

E

equals(Object) - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor
equals(Object) - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairOccurrence
equals(Object) - Method in class org.rcsb.strucmotif.domain.structure.IndexSelection
equals(Object) - Method in class org.rcsb.strucmotif.domain.structure.LabelSelection
equals(Object) - Method in class org.rcsb.strucmotif.domain.structure.Revision

G

get(int) - Method in class org.rcsb.strucmotif.math.Partition
getAngle() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor: Binned angle for this pair.
getAngle(IndexSelection, IndexSelection) - Method in class org.rcsb.strucmotif.domain.structure.ResidueGraph: Reports the angle between 2 residues.
getAngleTolerance() - Method in class org.rcsb.strucmotif.domain.query.Parameters: The specified angle tolerance value.
getAssemblies() - Method in class org.rcsb.strucmotif.domain.structure.Structure: Access to assembly information.
getAssemblyIdentifier() - Method in class org.rcsb.strucmotif.domain.result.Hit
getAssemblyInformation() - Method in class org.rcsb.strucmotif.domain.structure.StructureInformation: Reports present assemblies and the struct_oper_ids needed to create them.
getAtomCount() - Method in class org.rcsb.strucmotif.domain.structure.Structure: Count of all atoms/rows in the source CIF file.
getAtomPairingScheme() - Method in class org.rcsb.strucmotif.core.HitScorer: Returns the used atom pairing scheme (e.g., all-atoms, side-chain, ...)
getAtomPairingScheme() - Method in class org.rcsb.strucmotif.domain.query.Parameters: How are atoms paired?
getBackboneDistance() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor: Binned backbone distance for this pair.
getBackboneDistance(IndexSelection, IndexSelection) - Method in class org.rcsb.strucmotif.domain.structure.ResidueGraph: Reports the distance of backbone of 2 residues.
getBackboneDistanceTolerance() - Method in class org.rcsb.strucmotif.domain.query.Parameters: The specified backbone distance tolerance value.
getBlacklist() - Method in class org.rcsb.strucmotif.domain.query.MotifSearchQuery: Returns disallowed entries of the search space.
getCandidateCentroid() - Method in class org.rcsb.strucmotif.domain.align.AtomCorrespondence: The centroid of the original candidate coordinates.
getCenteredCandidateVectors() - Method in class org.rcsb.strucmotif.domain.align.AtomCorrespondence: The centered vectors of the candidate.
getCenteredReferenceVectors() - Method in class org.rcsb.strucmotif.domain.align.AtomCorrespondence: The centered vectors of the reference.
getChainCount() - Method in class org.rcsb.strucmotif.domain.structure.Structure: Count of all chains in the source CIF file.
getCifFetchUrl() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: The URL where (Binary)CIF data will be fetched from if not present locally.
getDataSource() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Optional path to a local collection of structure data.
getDecimalPlacesMatrix() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: How many digits to write for matrices.
getDecimalPlacesScore() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: How many digits to write (e.g.
getDistanceCutoff() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Maximum distance of residue pairs.
getDownloadTries() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: How many tries are allowed for connection failures/timeouts during update.
getExchanges() - Method in class org.rcsb.strucmotif.domain.query.MotifSearchQuery: All specified exchanges.
getFirst() - Method in class org.rcsb.strucmotif.domain.Pair: The first element.
getFlattenedTransformation() - Method in class org.rcsb.strucmotif.domain.Transformation: The flattened transformation operation (row-major indexing).
getHits() - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: Access all (currently) valid hits.
getIndex() - Method in class org.rcsb.strucmotif.domain.structure.IndexSelection: The index of the referenced residue.
getIndex1() - Method in class org.rcsb.strucmotif.domain.motif.IndexResiduePairIdentifier
getIndex1() - Method in class org.rcsb.strucmotif.domain.motif.InvertedIndexResiduePairIdentifier
getIndex1() - Method in interface org.rcsb.strucmotif.domain.motif.ResiduePairIdentifier: The index of the first residue.
getIndex2() - Method in class org.rcsb.strucmotif.domain.motif.IndexResiduePairIdentifier
getIndex2() - Method in class org.rcsb.strucmotif.domain.motif.InvertedIndexResiduePairIdentifier
getIndex2() - Method in interface org.rcsb.strucmotif.domain.motif.ResiduePairIdentifier: The index of the second residue.
getIndexSelection1() - Method in class org.rcsb.strucmotif.domain.motif.IndexResiduePairIdentifier
getIndexSelection1() - Method in class org.rcsb.strucmotif.domain.motif.InvertedIndexResiduePairIdentifier
getIndexSelection1() - Method in interface org.rcsb.strucmotif.domain.motif.ResiduePairIdentifier: The complex IndexSelection of the first residue.
getIndexSelection2() - Method in class org.rcsb.strucmotif.domain.motif.IndexResiduePairIdentifier
getIndexSelection2() - Method in class org.rcsb.strucmotif.domain.motif.InvertedIndexResiduePairIdentifier
getIndexSelection2() - Method in interface org.rcsb.strucmotif.domain.motif.ResiduePairIdentifier: The complex IndexSelection of the second residue.
getIndexSelections() - Method in class org.rcsb.strucmotif.domain.query.QueryStructure: All selections of this query structure.
getIndicesContacts() - Method in class org.rcsb.strucmotif.domain.structure.ResidueGrid: All contacts registered.
getInMemoryStrategy() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: How is index and structure data acquired at runtime?
getInputStream(ResiduePairDescriptor) - Method in class org.rcsb.strucmotif.io.InvertedIndexImpl: Acquire the input stream for a descriptor.
getIntRepresentation() - Method in enum org.rcsb.strucmotif.domain.motif.AngleType: Convert enum to angle value in degree (basically the lower bound of the interval).
getIntRepresentation() - Method in enum org.rcsb.strucmotif.domain.motif.DistanceType: Convert enum to distance value in Angstrom (basically the lower bound of the interval).
getLabelAsymId() - Method in class org.rcsb.strucmotif.domain.structure.LabelSelection: The chain of interest.
getLabelAtomId() - Method in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
getLabelSelection() - Method in class org.rcsb.strucmotif.domain.query.PositionSpecificExchange: The position this exchange references.
getLabelSelection(int) - Method in class org.rcsb.strucmotif.domain.structure.Structure
getLabelSelections() - Method in class org.rcsb.strucmotif.domain.result.Hit
getLabelSelections() - Method in class org.rcsb.strucmotif.domain.structure.Structure: Access to all unique (label_asym_id, label_seq_id) pairs that exist in this structure.
getLabelSelections() - Method in enum org.rcsb.strucmotif.Motifs: The residues referenced by this motif.
getLabelSeqId() - Method in class org.rcsb.strucmotif.domain.structure.LabelSelection: The sequence position of interest.
getLimit() - Method in class org.rcsb.strucmotif.domain.query.Parameters: Terminate the search after this many hits have been accepted.
getMajor() - Method in class org.rcsb.strucmotif.domain.structure.Revision: The major version component.
getMaxMotifSize() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Maximum number of residues in a motif.
getMaxResults() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Maximum number of results returned.
getMeasuredTime(TimeUnit) - Method in class org.rcsb.strucmotif.domain.result.Timer: Retrieve the measured time.
getMillisecondTime() - Method in class org.rcsb.strucmotif.domain.result.Timer: Retrieve the measured time in milliseconds.
getMinor() - Method in class org.rcsb.strucmotif.domain.structure.Revision: The minor version component.
getMotifPruner() - Method in class org.rcsb.strucmotif.domain.query.Parameters: The motif pruning strategy applied.
getNumberOfPairings() - Method in class org.rcsb.strucmotif.domain.structure.ResidueGraph: Reports the number of pairings present in this graph.
getNumberOfPaths() - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: The number of valid paths in all target structures.
getNumberOfTargetStructures() - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: The number of referenced target structures.
getNumberOfValidPaths() - Method in class org.rcsb.strucmotif.domain.result.TargetStructure: Reports the number currently valid paths.
getNumberThreads() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: How many threads to use?
getOneLetterCode() - Method in enum org.rcsb.strucmotif.domain.structure.ResidueType: The one-letter code of this residue.
getOriginalInputStream(String) - Method in interface org.rcsb.strucmotif.io.StructureDataProvider: Acquire the input stream of an original structure.
getOriginalInputStream(String) - Method in class org.rcsb.strucmotif.io.StructureDataProviderImpl
getParameters() - Method in class org.rcsb.strucmotif.domain.query.MotifSearchQuery: All parameters defined for this search task.
getPathsTime() - Method in class org.rcsb.strucmotif.domain.result.Timings: Get the path assembly time in ms.
getPolymerType() - Method in enum org.rcsb.strucmotif.domain.structure.ResidueType: The polymer type of this residue.
getPositionSpecificExchanges() - Method in enum org.rcsb.strucmotif.Motifs: Potential position-specific exchanges for this motif.
getQuery() - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: The initial query.
getQueryStructure() - Method in class org.rcsb.strucmotif.domain.query.MotifSearchQuery: The structure used to define this query/motif.
getQueryTime() - Method in class org.rcsb.strucmotif.domain.result.Timings: Get the overall query timer in ms.
getReferenceCentroid() - Method in class org.rcsb.strucmotif.domain.align.AtomCorrespondence: The centroid of the original reference coordinates.
getRenumberedCoordinatePrecision() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: How many digits to write for renumbered files.
getResidueCount() - Method in class org.rcsb.strucmotif.domain.structure.Structure: Count of all residues in the source CIF file.
getResidueIdentifier() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairOccurrence: Where is this pair located?
getResidueIndex(String, int) - Method in class org.rcsb.strucmotif.domain.structure.Structure: Look up the index of a residue.
getResidueIndexSwaps() - Method in class org.rcsb.strucmotif.domain.query.QueryStructure: This allows re-arranging residues in hits so they have the same order as the query.
getResiduePairDescriptor() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairOccurrence: What are the properties of this pair?
getResiduePairDescriptors() - Method in class org.rcsb.strucmotif.domain.query.QueryStructure: All word descriptors in this query structure.
getResiduePairIdentifiers() - Method in class org.rcsb.strucmotif.domain.query.QueryStructure: All word identifiers in this query structure.
getResiduePairOccurrences() - Method in class org.rcsb.strucmotif.domain.query.QueryStructure: All word occurrences in this query structure.
getResidues() - Method in class org.rcsb.strucmotif.domain.query.QueryStructure
getResidueType(int) - Method in class org.rcsb.strucmotif.domain.structure.Structure: Reports the residue type/amino acid at a certain index.
getResidueType1() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor: Residue type (label_comp_id) of first element.
getResidueType2() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor: Residue type (label_comp_id) of second element.
getResidueTypes() - Method in class org.rcsb.strucmotif.domain.query.PositionSpecificExchange: The set of allowed component types at that position.
getResidueTypes() - Method in class org.rcsb.strucmotif.domain.result.Hit: Returns residue types (label_comp_id) of this hit.
getRevision() - Method in class org.rcsb.strucmotif.domain.structure.StructureInformation: The Revision of this entry.
getRmsdCutoff() - Method in class org.rcsb.strucmotif.domain.query.Parameters: At which RMSD are hits filtered?
getRootMeanSquareDeviation() - Method in interface org.rcsb.strucmotif.domain.align.AlignmentResult: The score of this superposition.
getRootMeanSquareDeviation() - Method in class org.rcsb.strucmotif.domain.align.AlignmentResultImpl
getRootMeanSquareDeviation() - Method in class org.rcsb.strucmotif.domain.result.Hit: Returns the RMSD of this hit.
getRootPath() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: The root path where data is read/written.
getScoreHitsTime() - Method in class org.rcsb.strucmotif.domain.result.Timings: Get the hit scoring time in ms.
getSecond() - Method in class org.rcsb.strucmotif.domain.Pair: The second element.
getSideChainDistance() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor: Binned side-chain distance for this pair.
getSideChainDistance(IndexSelection, IndexSelection) - Method in class org.rcsb.strucmotif.domain.structure.ResidueGraph: Reports the distance of side-chains of 2 residues.
getSideChainDistanceTolerance() - Method in class org.rcsb.strucmotif.domain.query.Parameters: The specified side-chain distance tolerance value.
getSquaredDistanceCutoff() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Convenience method to get squared distance cutoff.
getStructOperId() - Method in class org.rcsb.strucmotif.domain.structure.IndexSelection
getStructOperId() - Method in class org.rcsb.strucmotif.domain.structure.LabelSelection
getStructOperId() - Method in interface org.rcsb.strucmotif.domain.structure.Selection: The operator applied to the original coordinates.
getStructOperId1() - Method in class org.rcsb.strucmotif.domain.motif.IndexResiduePairIdentifier
getStructOperId1() - Method in class org.rcsb.strucmotif.domain.motif.InvertedIndexResiduePairIdentifier
getStructOperId1() - Method in interface org.rcsb.strucmotif.domain.motif.ResiduePairIdentifier: The operator expression applied to the first residue.
getStructOperId2() - Method in class org.rcsb.strucmotif.domain.motif.IndexResiduePairIdentifier
getStructOperId2() - Method in class org.rcsb.strucmotif.domain.motif.InvertedIndexResiduePairIdentifier
getStructOperId2() - Method in interface org.rcsb.strucmotif.domain.motif.ResiduePairIdentifier: The operator expression applied to the second residue.
getStructure() - Method in class org.rcsb.strucmotif.domain.query.QueryStructure: Delegate to wrapped structure.
getStructureIdentifier() - Method in class org.rcsb.strucmotif.domain.query.QueryStructure
getStructureIdentifier() - Method in class org.rcsb.strucmotif.domain.result.Hit
getStructureIdentifier() - Method in class org.rcsb.strucmotif.domain.result.TargetStructure: The identifier of this structure
getStructureIdentifier() - Method in class org.rcsb.strucmotif.domain.structure.Structure: This structure's identifier.
getStructureIdentifier() - Method in class org.rcsb.strucmotif.domain.structure.StructureInformation: The ID of this entry.
getStructureIdentifier() - Method in enum org.rcsb.strucmotif.Motifs: The structure identifier of this motif.
getTargetStructures() - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: Access to all currently referenced target structures.
getThreeLetterCode() - Method in enum org.rcsb.strucmotif.domain.structure.ResidueType: The (up to) three-letter code of this residue.
getTimings() - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: Associated timings.
getTransformation() - Method in interface org.rcsb.strucmotif.domain.align.AlignmentResult: The transformation which recreates this alignment when applied to the 2nd argument.
getTransformation() - Method in class org.rcsb.strucmotif.domain.align.AlignmentResultImpl
getTransformation() - Method in class org.rcsb.strucmotif.domain.result.Hit: Returns the transformation yielded by the underlying alignment.
getTransformation(String) - Method in class org.rcsb.strucmotif.domain.structure.Structure: Access to a specific transformation.
getTransformationMatrix() - Method in class org.rcsb.strucmotif.domain.Transformation: The actual transformation matrix.
getTransformations() - Method in class org.rcsb.strucmotif.domain.structure.Structure: Access to all transformations.
getUpdateChunkSize() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: How many structures to process before flushing to inverted index.
getWhitelist() - Method in class org.rcsb.strucmotif.domain.query.MotifSearchQuery: Returns the specified search space - no restrictions apply if empty.
GGGG - Enum constant in enum org.rcsb.strucmotif.Motifs: RNA G-tetrad.
GLUTAMIC_ACID - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Glutamic acid
GLUTAMINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Glutamine
GLYCINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Glycine
GUANOSINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Guanosine

H

handleKnownSplit(String[]) - Method in class org.rcsb.strucmotif.io.StateRepositoryImpl: Split a line into a structure information object.
hashCode() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor
hashCode() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairOccurrence
hashCode() - Method in class org.rcsb.strucmotif.domain.structure.IndexSelection
hashCode() - Method in class org.rcsb.strucmotif.domain.structure.LabelSelection
hashCode() - Method in class org.rcsb.strucmotif.domain.structure.Revision
hasLimit() - Method in class org.rcsb.strucmotif.domain.query.Parameters: Report if the result count is limited.
HDS - Enum constant in enum org.rcsb.strucmotif.Motifs: Catalytic triad.
HEAP - Enum constant in enum org.rcsb.strucmotif.config.InMemoryStrategy: Load all data into heap during initialization.
HISTIDINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Histidine
Hit - Class in org.rcsb.strucmotif.domain.result: The result of a structural motif search.
Hit(String, String, List<LabelSelection>, List<ResidueType>, float, Transformation) - Constructor for class org.rcsb.strucmotif.domain.result.Hit: Construct a transformed hit (i.e., scored by an alignment).
HitScorer - Class in org.rcsb.strucmotif.core: Scores hits by computing the RMSD with respect to the reference motif.
HitScorer(List<Map<LabelAtomId, float[]>>, AtomPairingScheme, AlignmentService) - Constructor for class org.rcsb.strucmotif.core.HitScorer: Construct a query-specific hit scorer.

I

IDENTITY_MATRIX_4D - Static variable in class org.rcsb.strucmotif.domain.Transformation: Neutral/identity transformation.
IDENTITY_TRANSFORMATION - Static variable in class org.rcsb.strucmotif.domain.Transformation
IllegalQueryDefinitionException - Exception in org.rcsb.strucmotif.core: Indicates invalid query definitions.
IllegalQueryDefinitionException() - Constructor for exception org.rcsb.strucmotif.core.IllegalQueryDefinitionException: Default constructor.
IllegalQueryDefinitionException(String) - Constructor for exception org.rcsb.strucmotif.core.IllegalQueryDefinitionException: Construct with message.
IllegalQueryDefinitionException(String, Throwable) - Constructor for exception org.rcsb.strucmotif.core.IllegalQueryDefinitionException: Construct with message and cause.
IllegalQueryDefinitionException(Throwable) - Constructor for exception org.rcsb.strucmotif.core.IllegalQueryDefinitionException: Construct with cause.
incrementAndGetPathGeneration() - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: Called internally after a descriptor has been processed.
INDEX_DIRECTORY - Static variable in class org.rcsb.strucmotif.config.MotifSearchConfig: Name of the inverted index directory.
IndexResiduePairIdentifier - Class in org.rcsb.strucmotif.domain.motif: A ResiduePairIdentifier based on IndexSelection instances, created by the residue graph.
IndexResiduePairIdentifier(IndexSelection, IndexSelection) - Constructor for class org.rcsb.strucmotif.domain.motif.IndexResiduePairIdentifier: Construct an identifier from 2 IndexSelections.
IndexSelection - Class in org.rcsb.strucmotif.domain.structure: Selects a residue by its index in the source structure file.
IndexSelection(String, int) - Constructor for class org.rcsb.strucmotif.domain.structure.IndexSelection: Constructs an IndexSelection.
indexSelections() - Method in interface org.rcsb.strucmotif.domain.motif.ResiduePairIdentifier: Convenience method to access both IndexSelections.
initializeRenumberedStructureCache() - Method in interface org.rcsb.strucmotif.io.StructureDataProvider: If `strucmotif.in-memory-strategy` is active: Initialize caching by reading all structures and keeping them in memory for fast access.
initializeRenumberedStructureCache() - Method in class org.rcsb.strucmotif.io.StructureDataProviderImpl
InMemoryStrategy - Enum in org.rcsb.strucmotif.config: Keep structure data in memory? Requires ~30 GB of memory for 180k structures.
insert(ResiduePairDescriptor, Map<String, Collection<ResiduePairIdentifier>>) - Method in interface org.rcsb.strucmotif.io.InvertedIndex: Insert operation for new data.
insert(ResiduePairDescriptor, Map<String, Collection<ResiduePairIdentifier>>) - Method in class org.rcsb.strucmotif.io.InvertedIndexImpl
insertDirty(Collection<String>) - Method in interface org.rcsb.strucmotif.io.StateRepository: Insert into 'dirty' collection.
insertDirty(Collection<String>) - Method in class org.rcsb.strucmotif.io.StateRepositoryImpl
insertKnown(Collection<StructureInformation>) - Method in interface org.rcsb.strucmotif.io.StateRepository: Insert into 'known' collection.
insertKnown(Collection<StructureInformation>) - Method in class org.rcsb.strucmotif.io.StateRepositoryImpl
InvertedIndex - Interface in org.rcsb.strucmotif.io: The specification on how to insert and select residue pair occurrences.
InvertedIndexImpl - Class in org.rcsb.strucmotif.io: The implementation of the inverted index.
InvertedIndexImpl(MotifSearchConfig) - Constructor for class org.rcsb.strucmotif.io.InvertedIndexImpl: Construct a inverted index instance.
InvertedIndexResiduePairIdentifier - Class in org.rcsb.strucmotif.domain.motif: A ResiduePairIdentifier defined by data from the inverted index.
InvertedIndexResiduePairIdentifier(Object[], boolean) - Constructor for class org.rcsb.strucmotif.domain.motif.InvertedIndexResiduePairIdentifier: Construct an identifier based on raw data.
isFlipped() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor: We have to keep track whether this descriptor should match an original one (i.e.
ISOLEUCINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Isoleucine
isRenumberedGzip() - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Gzip renumbered files?

K

KDDDE - Enum constant in enum org.rcsb.strucmotif.Motifs: Aminopeptidase.
KDEEH - Enum constant in enum org.rcsb.strucmotif.Motifs: Enolase superfamily.
KDEEH_EXCHANGES - Enum constant in enum org.rcsb.strucmotif.Motifs: Enolase superfamily with exchanges.
KRUSKAL - Enum constant in enum org.rcsb.strucmotif.config.MotifPruningStrategy: Minimal spanning tree, determined by Kruskal's algorithm.
KruskalMotifPruner - Class in org.rcsb.strucmotif.core: A motif may be best described by the minimal spanning tree which connects all vertices in the most compact fashion.
KruskalMotifPruner(MotifSearchConfig) - Constructor for class org.rcsb.strucmotif.core.KruskalMotifPruner: Injectable constructor.

L

LabelAtomId - Enum in org.rcsb.strucmotif.domain.structure: Enumerates all 'common' atoms by name.
LabelSelection - Class in org.rcsb.strucmotif.domain.structure: Identifies a residue unambiguously by label_asym_id, struct_oper_id, and label_seq_id.
LabelSelection(String, String, int) - Constructor for class org.rcsb.strucmotif.domain.structure.LabelSelection: Construct a label selection.
LEFT_LEFT - Enum constant in enum org.rcsb.strucmotif.domain.motif.Overlap: Left identifier of first word corresponds to left identifier of second word.
LEFT_RIGHT - Enum constant in enum org.rcsb.strucmotif.domain.motif.Overlap: Left identifier of first word corresponds to right identifier of second word.
LEUCINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Leucine
limitResults(int) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Stop after a certain number of accepted hits.
LYSINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Lysine

M

main(String[]) - Static method in class org.rcsb.strucmotif.MotifSearchApplication: Default entry point.
manifestResidue(int) - Method in class org.rcsb.strucmotif.domain.structure.Structure: Manifest a residue by its index.
manifestResidue(int, String) - Method in class org.rcsb.strucmotif.domain.structure.Structure: 'Manifests' a residue, i.e.
manifestResidue(LabelSelection) - Method in class org.rcsb.strucmotif.domain.structure.Structure: Manifest a residue by its LabelSelection.
manifestResidues(List<LabelSelection>) - Method in class org.rcsb.strucmotif.domain.structure.Structure: Manifest a collection of residues by their LabelSelection.
METHIONINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Methionine
MotifPruner - Interface in org.rcsb.strucmotif.core: Pruning motifs is advantageous as it saves time (less lookups) and avoids too rigid criteria enforced during search.
motifPruningStrategy(MotifPruningStrategy) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Specify the motif pruning strategy.
motifPruningStrategy(MotifPruner) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Specify the motif pruning strategy.
MotifPruningStrategy - Enum in org.rcsb.strucmotif.config: How to simplify/prune motifs?
Motifs - Enum in org.rcsb.strucmotif: Motif definitions used in examples and tests.
MotifSearch - Class in org.rcsb.strucmotif: The entry point to perform motif searches.
MotifSearchApplication - Class in org.rcsb.strucmotif: The entry point of the strucmotif-search application.
MotifSearchApplication(QueryBuilder) - Constructor for class org.rcsb.strucmotif.MotifSearchApplication: Constructor.
MotifSearchConfig - Class in org.rcsb.strucmotif.config: All properties used throughout the strucmotif-search application.
MotifSearchConfig() - Constructor for class org.rcsb.strucmotif.config.MotifSearchConfig
MotifSearchQuery - Class in org.rcsb.strucmotif.domain.query: The immutable container for a structural motif query.
MotifSearchResult - Class in org.rcsb.strucmotif.domain.result: The state and results of a motif search run.
MotifSearchResult(MotifSearchQuery) - Constructor for class org.rcsb.strucmotif.domain.result.MotifSearchResult: Construct a result container.
MotifSearchRuntime - Interface in org.rcsb.strucmotif.core: Performs motif search queries and returns the corresponding result object.
MotifSearchRuntimeImpl - Class in org.rcsb.strucmotif.core: The default strucmotif-search runtime.
MotifSearchRuntimeImpl(TargetAssembler, ThreadPool, MotifSearchConfig, AlignmentService, StructureDataProvider, StateRepository) - Constructor for class org.rcsb.strucmotif.core.MotifSearchRuntimeImpl: Injectable constructor.
multiply3d(float[], float[][], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Left-multiplies a 3D vector with a 3x3 matrix.
multiply3d(float[], float[], float) - Static method in class org.rcsb.strucmotif.math.Algebra: Multiplies a 3D vector with a scalar.
multiply4d(float[][], float[][]) - Static method in class org.rcsb.strucmotif.math.Algebra: Multiplies 2 4x4 matrices.
multiply4d(float[], float[][], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Left-multiplies a 3D vector with a 4x4 matrix.

N

N - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
N1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
N2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
N3 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
N4 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
N6 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
N7 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
N9 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
ND1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
ND2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
NE - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
NE1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
NE2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
newQuery() - Static method in class org.rcsb.strucmotif.MotifSearch: Start a new query using the QueryBuilder.
NH1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
NH2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
NONE - Enum constant in enum org.rcsb.strucmotif.config.MotifPruningStrategy: Merely extract ResiduePairOccurrence.
NONE - Enum constant in enum org.rcsb.strucmotif.domain.motif.Overlap: No overlap.
NoOperationMotifPruner - Class in org.rcsb.strucmotif.core: Don't prune query motif.
NoOperationMotifPruner(MotifSearchConfig) - Constructor for class org.rcsb.strucmotif.core.NoOperationMotifPruner: Injectable constructor.
norm3d(float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Computes the norm of a vector.
normalize3d(float[], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Normalizes a vector (i.e.
NUCLEOTIDE - Enum constant in enum org.rcsb.strucmotif.domain.structure.PolymerType: Nucleotide chain.
NZ - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId

O

O - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O1P - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O2_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O2P - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O3_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O4 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O4_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O5_PRIME - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
O6 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OD1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OD2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OE1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OE2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
of(float[][]) - Static method in class org.rcsb.strucmotif.domain.Transformation
ofAngle(float) - Static method in enum org.rcsb.strucmotif.domain.motif.AngleType: Convert angle in degrees to enum value.
ofDistance(float) - Static method in enum org.rcsb.strucmotif.domain.motif.DistanceType: Convert distance in Angstrom to enum value.
OFF - Enum constant in enum org.rcsb.strucmotif.config.InMemoryStrategy: Access file-system any time structure data is requested.
ofIntRepresentation(int) - Static method in enum org.rcsb.strucmotif.domain.motif.AngleType: Convert the ordinal to enum value.
ofIntRepresentation(int) - Static method in enum org.rcsb.strucmotif.domain.motif.DistanceType: Convert the ordinal to enum value.
ofLabelAtomId(String) - Static method in enum org.rcsb.strucmotif.domain.structure.LabelAtomId: Resolve a label_atom_id.
ofOneLetterCode(String) - Static method in enum org.rcsb.strucmotif.domain.structure.ResidueType: Resolve a one-letter-code.
ofResiduePairIdentifiers(IndexResiduePairIdentifier, IndexResiduePairIdentifier) - Static method in enum org.rcsb.strucmotif.domain.motif.Overlap: Determines the overlap between 2 IndexResiduePairIdentifier instances.
ofThreeLetterCode(String) - Static method in enum org.rcsb.strucmotif.domain.structure.ResidueType: Maps labelCompId values to the correct ResidueType.
OG - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OG1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OH - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OP1 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OP2 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
OP3 - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
org.rcsb.strucmotif - package org.rcsb.strucmotif
org.rcsb.strucmotif.align - package org.rcsb.strucmotif.align
org.rcsb.strucmotif.config - package org.rcsb.strucmotif.config
org.rcsb.strucmotif.core - package org.rcsb.strucmotif.core
org.rcsb.strucmotif.domain - package org.rcsb.strucmotif.domain
org.rcsb.strucmotif.domain.align - package org.rcsb.strucmotif.domain.align
org.rcsb.strucmotif.domain.motif - package org.rcsb.strucmotif.domain.motif
org.rcsb.strucmotif.domain.query - package org.rcsb.strucmotif.domain.query
org.rcsb.strucmotif.domain.result - package org.rcsb.strucmotif.domain.result
org.rcsb.strucmotif.domain.structure - package org.rcsb.strucmotif.domain.structure
org.rcsb.strucmotif.io - package org.rcsb.strucmotif.io
org.rcsb.strucmotif.math - package org.rcsb.strucmotif.math
Overlap - Enum in org.rcsb.strucmotif.domain.motif: Describes the overlap between two ResiduePairIdentifier instances.
OXT - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId

P

P - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
Pair<F,S> - Class in org.rcsb.strucmotif.domain: Defines a relation between 2 objects.
Pair(F, S) - Constructor for class org.rcsb.strucmotif.domain.Pair: Construct a pair.
pairingsParallel() - Method in class org.rcsb.strucmotif.domain.structure.ResidueGraph: Allows to traverse all pairings.
pairingsSequential() - Method in class org.rcsb.strucmotif.domain.structure.ResidueGraph: Allows to sequentially traverse all pairings.
Parameters - Class in org.rcsb.strucmotif.domain.query: Immutable instance capturing all parameters of a given search job.
Partition<T> - Class in org.rcsb.strucmotif.math: Partitions a collection into (roughly) equal-sized chunks.
Partition(Collection<T>, int) - Constructor for class org.rcsb.strucmotif.math.Partition: Split a collection into partitions up to a defined size.
paths(List<Integer>, Structure, HitScorer, StateRepository) - Method in class org.rcsb.strucmotif.domain.result.TargetStructure: Traverses all paths of this structure.
pathsStart() - Method in class org.rcsb.strucmotif.domain.result.Timings: Start the path assembly timer.
pathsStop() - Method in class org.rcsb.strucmotif.domain.result.Timings: Stop the path assembly timer.
performSearch(MotifSearchQuery) - Method in interface org.rcsb.strucmotif.core.MotifSearchRuntime: Performs a structural motif search run for a given query.
performSearch(MotifSearchQuery) - Method in class org.rcsb.strucmotif.core.MotifSearchRuntimeImpl
performSearch(MotifSearchQuery, Consumer<Hit>) - Method in interface org.rcsb.strucmotif.core.MotifSearchRuntime: Performs a structural motif search for a given query.
performSearch(MotifSearchQuery, Consumer<Hit>) - Method in class org.rcsb.strucmotif.core.MotifSearchRuntimeImpl
PHENYLALANINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Phenylalanine
PolymerType - Enum in org.rcsb.strucmotif.domain.structure: Reports the polymer type for a component.
PositionSpecificExchange - Class in org.rcsb.strucmotif.domain.query: Defines a position-specific exchange for a particular position in the query structure.
PositionSpecificExchange(LabelSelection, Set<ResidueType>) - Constructor for class org.rcsb.strucmotif.domain.query.PositionSpecificExchange: Constructs a new position-specific exchange.
PositionSpecificExchange(LabelSelection, ResidueType...) - Constructor for class org.rcsb.strucmotif.domain.query.PositionSpecificExchange
PROLINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Proline
prune(Structure, List<LabelSelection>, List<Map<LabelAtomId, float[]>>) - Method in class org.rcsb.strucmotif.core.KruskalMotifPruner
prune(Structure, List<LabelSelection>, List<Map<LabelAtomId, float[]>>) - Method in interface org.rcsb.strucmotif.core.MotifPruner: Perform pruning operation (e.g.
prune(Structure, List<LabelSelection>, List<Map<LabelAtomId, float[]>>) - Method in class org.rcsb.strucmotif.core.NoOperationMotifPruner
PSEUDO_ATOMS - Enum constant in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme: Use pseudo-atoms defined by ResiduePairDescriptor.

Q

QuaternionAlignmentService - Class in org.rcsb.strucmotif.align: Align 2 sets of residues by a quaternion-based characteristic polynomial.
QuaternionAlignmentService() - Constructor for class org.rcsb.strucmotif.align.QuaternionAlignmentService
QueryBuilder - Class in org.rcsb.strucmotif.domain.query: The entry point to create MotifSearchQuery instances.
QueryBuilder(StructureDataProvider, KruskalMotifPruner, NoOperationMotifPruner, MotifSearchRuntime, MotifSearchConfig) - Constructor for class org.rcsb.strucmotif.domain.query.QueryBuilder: Construct a new query builder.
QueryBuilder.MandatoryBuilder - Class in org.rcsb.strucmotif.domain.query: Parameters are considered mandatory arguments (in the sense that some value has to be given - nonetheless, default values will be used).
QueryBuilder.OptionalStepBuilder - Class in org.rcsb.strucmotif.domain.query: Optional parameters of the algorithm.
queryStop() - Method in class org.rcsb.strucmotif.domain.result.Timings: Stop the overall query timer.
QueryStructure - Class in org.rcsb.strucmotif.domain.query: A query structure wraps a Structure and provides additional functionality needed to employ it as motif definition during a structural motif query job.

R

RCSB_ENTRY_LIST - Static variable in class org.rcsb.strucmotif.config.MotifSearchConfig: RCSB URL that reports currently present identifiers in archive.
readFromInputStream(InputStream) - Method in interface org.rcsb.strucmotif.io.StructureDataProvider: Read everything from an input stream.
readFromInputStream(InputStream) - Method in class org.rcsb.strucmotif.io.StructureDataProviderImpl
readFromInputStream(InputStream) - Method in interface org.rcsb.strucmotif.io.StructureReader: Read from a InputStream and parse the corresponding Structure.
readFromInputStream(InputStream) - Method in class org.rcsb.strucmotif.io.StructureReaderImpl
readOriginal(String) - Method in interface org.rcsb.strucmotif.io.StructureDataProvider: Read a selected range from an original structure.
readOriginal(String) - Method in class org.rcsb.strucmotif.io.StructureDataProviderImpl
readRenumbered(String) - Method in interface org.rcsb.strucmotif.io.StructureDataProvider: Read a renumbered structure entirely.
readRenumbered(String) - Method in class org.rcsb.strucmotif.io.StructureDataProviderImpl
readSome(String) - Method in interface org.rcsb.strucmotif.io.StructureDataProvider: Read some structure entirely.
readSome(String) - Method in class org.rcsb.strucmotif.io.StructureDataProviderImpl
RENUMBERED_DIRECTORY - Static variable in class org.rcsb.strucmotif.config.MotifSearchConfig: Name of the renumbered directory.
ResidueGraph - Class in org.rcsb.strucmotif.domain.structure: Represents the pseudo-graph defined by all residues.
ResidueGraph(Structure, float, boolean) - Constructor for class org.rcsb.strucmotif.domain.structure.ResidueGraph: Construct a new residue graph from a full structure.
ResidueGraph(Structure, List<LabelSelection>, List<Map<LabelAtomId, float[]>>, float, boolean) - Constructor for class org.rcsb.strucmotif.domain.structure.ResidueGraph: Construct a residue graph.
ResidueGrid - Class in org.rcsb.strucmotif.domain.structure: Efficiently determine residues in contacts by a spatial hashing approach.
ResidueGrid(List<float[]>, float) - Constructor for class org.rcsb.strucmotif.domain.structure.ResidueGrid: Construct a residue grid from a structure.
ResiduePairDescriptor - Class in org.rcsb.strucmotif.domain.motif: Captures all properties of a residue pair (i.e.
ResiduePairDescriptor(ResidueType, ResidueType, DistanceType, DistanceType, AngleType) - Constructor for class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor: Construct a residue pair descriptor capturing all properties of this pair.
residuePairDescriptorsByTolerance(int, int, int, Map<IndexSelection, Set<ResidueType>>) - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairOccurrence: Traverse all ResiduePairDescriptor instances which are compatible to this one given the specified parameters and registered position-specific exchanges (if any).
ResiduePairIdentifier - Interface in org.rcsb.strucmotif.domain.motif: Residue pair identifiers combine the Selection of each residue making up this pair.
ResiduePairOccurrence - Class in org.rcsb.strucmotif.domain.motif: A residue pair occurrence is the combination of its properties (ResiduePairDescriptor) and both identifiers (wrapped as ResiduePairIdentifier).
ResiduePairOccurrence(ResiduePairDescriptor, ResiduePairIdentifier) - Constructor for class org.rcsb.strucmotif.domain.motif.ResiduePairOccurrence: Construct a pair occurrence.
residuePairOccurrencesParallel() - Method in class org.rcsb.strucmotif.domain.structure.ResidueGraph: Allows to traverse all residue pair occurrences.
residuePairOccurrencesSequential() - Method in class org.rcsb.strucmotif.domain.structure.ResidueGraph: Allows to traverse all residue pair occurrences.
ResidueType - Enum in org.rcsb.strucmotif.domain.structure: Registry of known residues.
Revision - Class in org.rcsb.strucmotif.domain.structure: The version of a PDB entry.
Revision(int, int) - Constructor for class org.rcsb.strucmotif.domain.structure.Revision: Construct a version tag.
RIGHT_LEFT - Enum constant in enum org.rcsb.strucmotif.domain.motif.Overlap: Right identifier of first word corresponds to left identifier of second word.
RIGHT_RIGHT - Enum constant in enum org.rcsb.strucmotif.domain.motif.Overlap: Right identifier of first word corresponds to right identifier of second word.
rmsdCutoff(double) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Filter hits based on RMSD.
run() - Method in class org.rcsb.strucmotif.domain.query.MotifSearchQuery: Dispatch this query and perform the corresponding search.
runAndConsume(Consumer<Hit>) - Method in class org.rcsb.strucmotif.domain.query.MotifSearchQuery: Dispatch this query and consume each accepted hit on-the-fly.
runAndWriteToPath(Path) - Method in class org.rcsb.strucmotif.domain.query.MotifSearchQuery: Dispatch this query and write each accepted hit to a file.

S

scoreHitsStart() - Method in class org.rcsb.strucmotif.domain.result.Timings: Start the hit scoring timer.
scoreHitsStop() - Method in class org.rcsb.strucmotif.domain.result.Timings: Stop the hit scoring timer.
SD - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
select(ResiduePairDescriptor) - Method in interface org.rcsb.strucmotif.io.InvertedIndex: Perform lookup for a particular bin.
select(ResiduePairDescriptor) - Method in class org.rcsb.strucmotif.io.InvertedIndexImpl
selectAssemblyMap(String) - Method in interface org.rcsb.strucmotif.io.StateRepository: Provides assembly information.
selectAssemblyMap(String) - Method in class org.rcsb.strucmotif.io.StateRepositoryImpl
selectDirty() - Method in interface org.rcsb.strucmotif.io.StateRepository: The set of currently 'dirty' ids.
selectDirty() - Method in class org.rcsb.strucmotif.io.StateRepositoryImpl
Selection - Interface in org.rcsb.strucmotif.domain.structure: A selection within a Structure.
selectKnown() - Method in interface org.rcsb.strucmotif.io.StateRepository: Returns all registered revisions.
selectKnown() - Method in class org.rcsb.strucmotif.io.StateRepositoryImpl
SERINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Serine
setCifFetchUrl(String) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: The URL where (Binary)CIF data will be fetched from if not present locally.
setDataSource(String) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Optional path to a local collection of structure data.
setDecimalPlacesMatrix(int) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set how many digits to write for matrices.
setDecimalPlacesScore(int) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set how many digits to write (e.g.
setDistanceCutoff(float) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set maximum distance of residue pairs.
setDownloadTries(int) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set how many tries should be allowed for connection failures/timeouts during update.
setHits(List<Hit>) - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: Update the collection of currently valid hits.
setInMemoryStrategy(InMemoryStrategy) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set how index and structure data is acquired at runtime.
setMaxMotifSize(int) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set maximum number of residues in a motif.
setMaxResults(int) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set maximum number of results returned.
setNumberOfPaths(int) - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: Update the number of valid paths.
setNumberOfTargetStructures(int) - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: Update the number of referenced target structures.
setNumberThreads(int) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set how many threads to use?
setRenumberedCoordinatePrecision(int) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set how many digits to write for renumbered files.
setRenumberedGzip(boolean) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set gzip renumbered files?
setRootPath(String) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set the root path where data is read/written.
setTargetStructures(Map<String, TargetStructure>) - Method in class org.rcsb.strucmotif.domain.result.MotifSearchResult: Update the currently referenced target structures.
setUpdateChunkSize(int) - Method in class org.rcsb.strucmotif.config.MotifSearchConfig: Set how many structures to process before flushing to inverted index.
SG - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
SIDE_CHAIN - Enum constant in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme: Use side-chain atoms only.
sideChainDistanceTolerance(int) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder: Specify the side-chain distance tolerance (default: 1).
size() - Method in class org.rcsb.strucmotif.math.Partition
start() - Method in class org.rcsb.strucmotif.domain.result.Timer: Start the time.
STATE_DIRTY_LIST - Static variable in class org.rcsb.strucmotif.config.MotifSearchConfig: List of all identifiers needed to recover if update operation fails.
STATE_KNOWN_LIST - Static variable in class org.rcsb.strucmotif.config.MotifSearchConfig: List of all identifiers ever registered.
StateRepository - Interface in org.rcsb.strucmotif.io: The state of the application consists of two lists of structure identifiers: known: entries that have been processed (might become invalid if e.g.
StateRepositoryImpl - Class in org.rcsb.strucmotif.io: A file-system-based state repository.
StateRepositoryImpl(MotifSearchConfig) - Constructor for class org.rcsb.strucmotif.io.StateRepositoryImpl: Construct a state repository instance.
stop() - Method in class org.rcsb.strucmotif.domain.result.Timer: Stop the time and 'freeze' the measurement for later retrieval/output.
Structure - Class in org.rcsb.strucmotif.domain.structure: The structure object wraps categories of a mmCIF file and allows access via some utility methods.
Structure(String, Map<String, int[]>, int[], int[], byte[], byte[], short[], short[], short[], Map<String, List<String>>, Map<String, Transformation>) - Constructor for class org.rcsb.strucmotif.domain.structure.Structure: Create a structure view.
StructureDataProvider - Interface in org.rcsb.strucmotif.io: Access structure data.
StructureDataProviderImpl - Class in org.rcsb.strucmotif.io: Default implementation of a structure data provider.
StructureDataProviderImpl(StructureReader, StructureWriter, MotifSearchConfig) - Constructor for class org.rcsb.strucmotif.io.StructureDataProviderImpl: Construct a structure provider.
StructureInformation - Class in org.rcsb.strucmotif.domain.structure: Reports global properties of a structure.
StructureInformation(String, Revision, Map<String, Set<String>>) - Constructor for class org.rcsb.strucmotif.domain.structure.StructureInformation: Wraps info on a structure.
StructureReader - Interface in org.rcsb.strucmotif.io: Read structures from CIF files.
StructureReaderImpl - Class in org.rcsb.strucmotif.io: A simple structure reader that parses CIF data into structure instances.
StructureReaderImpl() - Constructor for class org.rcsb.strucmotif.io.StructureReaderImpl
StructureWriter - Interface in org.rcsb.strucmotif.io: The contract to write optimized structure data that don't contain non-polymers, hydrogen, model afters #1 etc.
StructureWriterImpl - Class in org.rcsb.strucmotif.io: This implementation keeps a sparse representation of structure data including: label_asym_id label_seq_id label_comp_id label_atom_id coordinates entry identifier and data used for assembly generation
StructureWriterImpl() - Constructor for class org.rcsb.strucmotif.io.StructureWriterImpl: Construct a writer.
submit(Callable<R>) - Method in interface org.rcsb.strucmotif.core.ThreadPool: Dispatch a Callable.
submit(Callable<R>) - Method in class org.rcsb.strucmotif.core.ThreadPoolImpl
subtract3d(float[], float[], float[]) - Static method in class org.rcsb.strucmotif.math.Algebra: Subtracts 2 3D vectors.

T

TargetAssembler - Interface in org.rcsb.strucmotif.core: Where the magic happens.
TargetAssemblerImpl - Class in org.rcsb.strucmotif.core: The default strucmotif-search target assembler.
TargetAssemblerImpl(InvertedIndex, ThreadPool) - Constructor for class org.rcsb.strucmotif.core.TargetAssemblerImpl: Injectable constructor.
TargetStructure - Class in org.rcsb.strucmotif.domain.result: A container keeping track of paths in a target structure.
TargetStructure(String, InvertedIndexResiduePairIdentifier[]) - Constructor for class org.rcsb.strucmotif.domain.result.TargetStructure: Construct a target structure instance.
test(InvertedIndexResiduePairIdentifier, InvertedIndexResiduePairIdentifier) - Method in enum org.rcsb.strucmotif.domain.motif.Overlap
test(LabelAtomId) - Method in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme
ThreadPool - Interface in org.rcsb.strucmotif.core: An application-wide shared thread pool with a configurable number of threads.
ThreadPoolImpl - Class in org.rcsb.strucmotif.core: Wraps a ForkJoinPool.
ThreadPoolImpl(MotifSearchConfig) - Constructor for class org.rcsb.strucmotif.core.ThreadPoolImpl: Constructor.
THREONINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Threonine
THYMIDINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Thymidine
Timer - Class in org.rcsb.strucmotif.domain.result: Tracks timings.
Timer() - Constructor for class org.rcsb.strucmotif.domain.result.Timer
Timings - Class in org.rcsb.strucmotif.domain.result: A helper class keeping track of internal timings.
Timings() - Constructor for class org.rcsb.strucmotif.domain.result.Timings: Constructs a new timer instance.
toString() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairDescriptor
toString() - Method in class org.rcsb.strucmotif.domain.motif.ResiduePairOccurrence
toString() - Method in class org.rcsb.strucmotif.domain.Pair
toString() - Method in class org.rcsb.strucmotif.domain.structure.IndexSelection
toString() - Method in class org.rcsb.strucmotif.domain.structure.LabelSelection
transform(float[], float[]) - Method in class org.rcsb.strucmotif.domain.Transformation: Transform a vector.
Transformation - Class in org.rcsb.strucmotif.domain: A transformation described by a 4x4 matrix.
transpose3d(float[][]) - Static method in class org.rcsb.strucmotif.math.Algebra: Transpose a 3x3 matrix.
TRYPTOPHAN - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Tryptophan
TYROSINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Tyrosine

U

UNKNOWN_AMINO_ACID - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Some unknown amino acid.
UNKNOWN_ATOM - Enum constant in enum org.rcsb.strucmotif.domain.structure.LabelAtomId
UNKNOWN_COMPONENT - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Some unknown, yet polymeric component.
UNKNOWN_NUCLEOTIDE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Some unknown nucleotide.
URIDINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Uridine

V

VALINE - Enum constant in enum org.rcsb.strucmotif.domain.structure.ResidueType: Valine
valueOf(String) - Static method in enum org.rcsb.strucmotif.config.InMemoryStrategy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.config.MotifPruningStrategy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.domain.motif.AngleType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.domain.motif.DistanceType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.domain.motif.Overlap: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.domain.structure.LabelAtomId: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.domain.structure.PolymerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.domain.structure.ResidueType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.rcsb.strucmotif.Motifs: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.rcsb.strucmotif.config.InMemoryStrategy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.config.MotifPruningStrategy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.domain.align.AtomPairingScheme: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.domain.motif.AngleType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.domain.motif.DistanceType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.domain.motif.Overlap: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.domain.structure.LabelAtomId: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.domain.structure.PolymerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.domain.structure.ResidueType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.rcsb.strucmotif.Motifs: Returns an array containing the constants of this enum type, in the order they are declared.

W

whitelist(Collection<String>) - Method in class org.rcsb.strucmotif.domain.query.QueryBuilder.OptionalStepBuilder: Narrow down the search space to the specified entries.
write(MmCifFile, Path) - Method in interface org.rcsb.strucmotif.io.StructureWriter: Write structure data to the file system.
write(MmCifFile, Path) - Method in class org.rcsb.strucmotif.io.StructureWriterImpl
writeRenumbered(String, MmCifFile) - Method in interface org.rcsb.strucmotif.io.StructureDataProvider: Write a renumbered structure.
writeRenumbered(String, MmCifFile) - Method in class org.rcsb.strucmotif.io.StructureDataProviderImpl

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