Index

A

add_child() (commonnn._bundle.Bundle method) adjust_radius() (commonnn._types.MetricDummy method) (commonnn._types.MetricEuclidean method) (commonnn._types.MetricEuclideanReduced method) (commonnn._types.MetricExtInterface method)

alias (commonnn._bundle.Bundle attribute) assign() (commonnn._types.Neighbours method) (commonnn._types.NeighboursExtInterface method) (commonnn._types.NeighboursList method) (commonnn._types.NeighboursSet method)

B

build_tree() (commonnn._types.InputDataSklearnKDTree method) Builder (class in commonnn.recipes)

Bundle (class in commonnn._bundle) by_parts() (commonnn._types.InputDataExtComponentsMemoryview method)

C

calc_distance() (commonnn._types.Metric method) (commonnn._types.MetricDummy method) (commonnn._types.MetricEuclidean method) (commonnn._types.MetricEuclideanReduced method) (commonnn._types.MetricExtInterface method) calc_distance_other() (commonnn._types.Metric method) (commonnn._types.MetricDummy method) (commonnn._types.MetricEuclidean method) (commonnn._types.MetricEuclideanReduced method) (commonnn._types.MetricExtInterface method) check() (commonnn._types.SimilarityChecker method) (commonnn._types.SimilarityCheckerContains method) (commonnn._types.SimilarityCheckerExtInterface method) (commonnn._types.SimilarityCheckerSwitchContains method) children (commonnn.cluster.Clustering property) clear_cached() (commonnn._types.InputDataSklearnKDTree method) Clustering (class in commonnn.cluster) ClusterParameters (class in commonnn._types) commonnn._bundle module commonnn._fit module

commonnn._types module commonnn.cluster module commonnn.helper module commonnn.plot module commonnn.recipes module commonnn.report module CommonNNParameters (class in commonnn._types) CommonNNRecord (class in commonnn.report) compute_distances() (commonnn._types.InputDataExtInterface method) (commonnn._types.InputDataPairwiseDistancesComputer method) compute_neighbourhoods() (commonnn._types.InputDataExtInterface method) (commonnn._types.InputDataNeighbourhoodsComputer method) (commonnn._types.InputDataSklearnKDTree method) contains() (commonnn._types.Neighbours method) (commonnn._types.NeighboursExtInterface method) (commonnn._types.NeighboursList method) (commonnn._types.NeighboursSet method)

D

data (commonnn._types.InputData property) (commonnn._types.InputDataNeighbourhoodsSequence property) (commonnn._types.InputDataSklearnKDTree property) default_preparation_hook() (commonnn.recipes.Builder static method) DistanceGetter (class in commonnn._types)

DistanceGetterExtInterface (class in commonnn._types) DistanceGetterExtLookup (class in commonnn._types) DistanceGetterExtMetric (class in commonnn._types) DistanceGetterLookup (class in commonnn._types) DistanceGetterMetric (class in commonnn._types)

E

enough() (commonnn._types.Neighbours method) (commonnn._types.NeighboursExtInterface method) (commonnn._types.NeighboursList method) (commonnn._types.NeighboursSet method)

evaluate() (commonnn.cluster.Clustering method)

F

fit() (commonnn._fit.Fitter method) (commonnn._fit.FitterCommonNN method) (commonnn._fit.FitterExtCommonNNInterface method) (commonnn._fit.FitterExtInterface method) (commonnn._fit.HierarchicalFitter method) (commonnn._fit.HierarchicalFitterCommonNNMSTPrim method) (commonnn._fit.HierarchicalFitterRepeat method) (commonnn.cluster.Clustering method) fit_hierarchical() (commonnn.cluster.Clustering method) Fitter (class in commonnn._fit)

fitter (commonnn.cluster.Clustering property) FitterCommonNN (class in commonnn._fit) FitterCommonNNBFS (class in commonnn._fit) FitterCommonNNBFSDebug (class in commonnn._fit) FitterExtCommonNNBFS (class in commonnn._fit) FitterExtCommonNNInterface (class in commonnn._fit) FitterExtInterface (class in commonnn._fit) from_bundle() (commonnn.report.Record class method) from_length() (commonnn._types.Labels class method) from_mapping() (commonnn._types.ClusterParameters class method) from_sequence() (commonnn._types.Labels class method)

G

get() (commonnn._types.NeighboursGetter method) (commonnn._types.NeighboursGetterBruteForce method) (commonnn._types.NeighboursGetterExtInterface method) (commonnn._types.NeighboursGetterLookup method) (commonnn._types.NeighboursGetterRecomputeLookup method) (commonnn._types.SimilarityChecker method) (commonnn._types.SimilarityCheckerContains method) (commonnn._types.SimilarityCheckerExtInterface method) (commonnn._types.SimilarityCheckerSwitchContains method) get_builder_kwargs() (commonnn._fit.FitterCommonNNBFS class method) (commonnn._fit.FitterCommonNNBFSDebug class method) (commonnn._fit.FitterExtCommonNNBFS class method) (commonnn._fit.HierarchicalFitterCommonNNMSTPrim class method) (commonnn._fit.HierarchicalFitterRepeat class method) (commonnn._fit.PredictorCommonNNFirstmatch class method) (commonnn._types.DistanceGetter class method) (commonnn._types.DistanceGetterExtInterface class method) (commonnn._types.DistanceGetterExtMetric class method) (commonnn._types.DistanceGetterMetric class method) (commonnn._types.InputData class method) (commonnn._types.InputDataExtInterface class method) (commonnn._types.MetricExtInterface class method) (commonnn._types.Neighbours class method) (commonnn._types.NeighboursExtInterface class method) (commonnn._types.NeighboursGetter class method) (commonnn._types.NeighboursGetterBruteForce class method) (commonnn._types.NeighboursGetterExtBruteForce class method) (commonnn._types.NeighboursGetterExtInterface class method) (commonnn._types.PriorityQueue class method) (commonnn._types.PriorityQueueExtInterface class method) (commonnn._types.Queue class method) (commonnn._types.QueueExtInterface class method) (commonnn._types.SimilarityChecker class method) (commonnn._types.SimilarityCheckerExtInterface class method) get_child() (commonnn._bundle.Bundle method) get_component() (commonnn._types.InputDataComponents method) (commonnn._types.InputDataExtInterface method) (commonnn._types.InputDataSklearnKDTree method) get_dict_attribute() (in module commonnn.helper) get_distance() (commonnn._types.InputDataExtInterface method) (commonnn._types.InputDataPairwiseDistances method)

get_fit_signature() (commonnn._fit.FitterCommonNN method) (commonnn._fit.FitterExtCommonNNInterface method) (commonnn._fit.PredictorCommonNN method) get_fparam() (commonnn._types.ClusterParameters method) get_iparam() (commonnn._types.ClusterParameters method) get_member() (commonnn._types.Neighbours method) (commonnn._types.NeighboursExtInterface method) (commonnn._types.NeighboursList method) (commonnn._types.NeighboursSet method) get_n_neighbours() (commonnn._types.InputDataExtInterface method) (commonnn._types.InputDataExtNeighbourhoodsVector method) (commonnn._types.InputDataNeighbourhoods method) (commonnn._types.InputDataNeighbourhoodsSequence method) (commonnn._types.InputDataSklearnKDTree method) get_neighbour() (commonnn._types.InputDataExtInterface method) (commonnn._types.InputDataExtNeighbourhoodsVector method) (commonnn._types.InputDataNeighbourhoods method) (commonnn._types.InputDataNeighbourhoodsSequence method) (commonnn._types.InputDataSklearnKDTree method) get_other() (commonnn._types.NeighboursGetter method) (commonnn._types.NeighboursGetterBruteForce method) (commonnn._types.NeighboursGetterExtInterface method) (commonnn._types.NeighboursGetterLookup method) (commonnn._types.NeighboursGetterRecomputeLookup method) get_single() (commonnn._types.DistanceGetter method) (commonnn._types.DistanceGetterExtInterface method) (commonnn._types.DistanceGetterExtMetric method) (commonnn._types.DistanceGetterLookup method) (commonnn._types.DistanceGetterMetric method) get_single_other() (commonnn._types.DistanceGetter method) (commonnn._types.DistanceGetterExtInterface method) (commonnn._types.DistanceGetterExtMetric method) (commonnn._types.DistanceGetterLookup method) (commonnn._types.DistanceGetterMetric method) get_subset() (commonnn._types.InputData method) (commonnn._types.InputDataExtComponentsMemoryview method) (commonnn._types.InputDataExtDistancesLinearMemoryview method) (commonnn._types.InputDataExtDistancesMemoryview method) (commonnn._types.InputDataExtNeighbourhoodsMemoryview method) (commonnn._types.InputDataExtNeighbourhoodsVector method) (commonnn._types.InputDataNeighbourhoodsSequence method) (commonnn._types.InputDataSklearnKDTree method)

H

HierarchicalFitter (class in commonnn._fit) HierarchicalFitterCommonNNMSTPrim (class in commonnn._fit)

HierarchicalFitterRepeat (class in commonnn._fit) hierarchy_level (commonnn._bundle.Bundle attribute)

I

info() (commonnn._bundle.Bundle method) input_data (commonnn.cluster.Clustering property) InputData (class in commonnn._types) InputDataComponents (class in commonnn._types) InputDataExtComponentsMemoryview (class in commonnn._types) InputDataExtDistancesLinearMemoryview (class in commonnn._types) InputDataExtDistancesMemoryview (class in commonnn._types) InputDataExtInterface (class in commonnn._types) InputDataExtNeighbourhoodsMemoryview (class in commonnn._types) InputDataExtNeighbourhoodsVector (class in commonnn._types) InputDataNeighbourhoods (class in commonnn._types) InputDataNeighbourhoodsComputer (class in commonnn._types) InputDataNeighbourhoodsSequence (class in commonnn._types) InputDataPairwiseDistances (class in commonnn._types) InputDataPairwiseDistancesComputer (class in commonnn._types) InputDataSklearnKDTree (class in commonnn._types) insert() (commonnn.report.Summary method)

is_empty() (commonnn._types.PriorityQueue method) (commonnn._types.PriorityQueueExtInterface method) (commonnn._types.PriorityQueueMaxHeap method) (commonnn._types.Queue method) (commonnn._types.QueueExtInterface method) (commonnn._types.QueueFIFODeque method) is_selfcounting (commonnn._types.NeighboursGetter property) (commonnn._types.NeighboursGetterBruteForce property) (commonnn._types.NeighboursGetterExtInterface attribute) (commonnn._types.NeighboursGetterLookup property) (commonnn._types.NeighboursGetterRecomputeLookup property) is_sorted (commonnn._types.NeighboursGetter property) (commonnn._types.NeighboursGetterBruteForce property) (commonnn._types.NeighboursGetterExtInterface attribute) (commonnn._types.NeighboursGetterLookup property) (commonnn._types.NeighboursGetterRecomputeLookup property) isolate() (commonnn._bundle.Bundle method) (commonnn.cluster.Clustering method)

L

Labels (class in commonnn._types)

labels (commonnn.cluster.Clustering property)

M

make_parameters() (commonnn._fit.Fitter method) (commonnn._fit.FitterCommonNN method) (commonnn._fit.FitterExtCommonNNInterface method) (commonnn._fit.FitterExtInterface method) (commonnn._fit.HierarchicalFitterCommonNNMSTPrim method) (commonnn._fit.Predictor method) (commonnn._fit.PredictorCommonNN method) make_typed_DataFrame() (in module commonnn.report) meta (commonnn._types.InputData property) Metric (class in commonnn._types) MetricDummy (class in commonnn._types) MetricEuclidean (class in commonnn._types) MetricEuclideanReduced (class in commonnn._types) MetricExtDummy (class in commonnn._types)

MetricExtEuclidean (class in commonnn._types) MetricExtEuclideanPeriodicReduced (class in commonnn._types) MetricExtEuclideanReduced (class in commonnn._types) MetricExtInterface (class in commonnn._types) MetricExtPrecomputed (class in commonnn._types) module commonnn._bundle commonnn._fit commonnn._types commonnn.cluster commonnn.helper commonnn.plot commonnn.recipes commonnn.report

N

n_dim (commonnn._types.InputDataComponents property) (commonnn._types.InputDataSklearnKDTree property) n_neighbours (commonnn._types.InputDataNeighbourhoodsSequence property) (commonnn._types.InputDataSklearnKDTree property) n_points (commonnn._types.InputData property) (commonnn._types.InputDataNeighbourhoodsSequence property) (commonnn._types.InputDataSklearnKDTree property) (commonnn._types.Neighbours property) (commonnn._types.NeighboursList property) (commonnn._types.NeighboursSet property) Neighbours (class in commonnn._types) neighbours (commonnn._types.NeighboursList property) (commonnn._types.NeighboursSet property)

NeighboursExtInterface (class in commonnn._types) NeighboursExtSet (class in commonnn._types) NeighboursExtUnorderedSet (class in commonnn._types) NeighboursExtVector (class in commonnn._types) NeighboursExtVectorUnorderedSet (class in commonnn._types) NeighboursGetter (class in commonnn._types) NeighboursGetterBruteForce (class in commonnn._types) NeighboursGetterExtBruteForce (class in commonnn._types) NeighboursGetterExtInterface (class in commonnn._types) NeighboursGetterExtLookup (class in commonnn._types) NeighboursGetterLookup (class in commonnn._types) NeighboursGetterRecomputeLookup (class in commonnn._types) NeighboursList (class in commonnn._types) NeighboursSet (class in commonnn._types)

P

pie() (commonnn.cluster.Clustering method) pop() (commonnn._types.PriorityQueue method) (commonnn._types.PriorityQueueExtInterface method) (commonnn._types.PriorityQueueMaxHeap method) (commonnn._types.Queue method) (commonnn._types.QueueExtInterface method) (commonnn._types.QueueFIFODeque method) predict() (commonnn._fit.Predictor method) (commonnn._fit.PredictorCommonNN method) (commonnn.cluster.Clustering method) Predictor (class in commonnn._fit)

PredictorCommonNN (class in commonnn._fit) PredictorCommonNNFirstmatch (class in commonnn._fit) PriorityQueue (class in commonnn._types) PriorityQueueExtInterface (class in commonnn._types) PriorityQueueMaxHeap (class in commonnn._types) push() (commonnn._types.PriorityQueue method) (commonnn._types.PriorityQueueExtInterface method) (commonnn._types.PriorityQueueMaxHeap method) (commonnn._types.Queue method) (commonnn._types.QueueExtInterface method) (commonnn._types.QueueFIFODeque method)

Q

Queue (class in commonnn._types) QueueExtFIFOQueue (class in commonnn._types)

QueueExtInterface (class in commonnn._types) QueueExtLIFOVector (class in commonnn._types) QueueFIFODeque (class in commonnn._types)

R

RadiusParameters (class in commonnn._types) Record (class in commonnn.report) reel() (commonnn._bundle.Bundle method) (commonnn.cluster.Clustering method) ReferenceIndices (class in commonnn._types) reset() (commonnn._types.Neighbours method) (commonnn._types.NeighboursExtInterface method) (commonnn._types.NeighboursList method) (commonnn._types.NeighboursSet method) (commonnn._types.PriorityQueue method) (commonnn._types.PriorityQueueExtInterface method) (commonnn._types.PriorityQueueMaxHeap method)

root (commonnn.cluster.Clustering property)

S

set_dict_attribute() (in module commonnn.helper) SimilarityChecker (class in commonnn._types) SimilarityCheckerContains (class in commonnn._types) SimilarityCheckerExtContains (class in commonnn._types) SimilarityCheckerExtInterface (class in commonnn._types) SimilarityCheckerExtScreensorted (class in commonnn._types) SimilarityCheckerExtSwitchContains (class in commonnn._types) SimilarityCheckerSwitchContains (class in commonnn._types) size() (commonnn._types.PriorityQueue method) (commonnn._types.PriorityQueueExtInterface method) (commonnn._types.PriorityQueueMaxHeap method) (commonnn._types.Queue method) (commonnn._types.QueueExtInterface method) (commonnn._types.QueueFIFODeque method)

sort_by_size() (commonnn._types.Labels method) summarize() (commonnn.cluster.Clustering method) Summary (class in commonnn.report) summary (commonnn.cluster.Clustering property)

T

timed() (in module commonnn.report) to_components_array() (commonnn._types.InputDataComponents method) (commonnn._types.InputDataExtComponentsMemoryview method) (commonnn._types.InputDataSklearnKDTree method) to_DataFrame() (commonnn.report.Summary method) to_dict() (commonnn._types.ClusterParameters method) to_distance_array() (commonnn._types.InputDataExtDistancesLinearMemoryview method) (commonnn._types.InputDataExtDistancesMemoryview method) to_dtrajs() (commonnn.cluster.Clustering method) to_mapping() (commonnn._types.Labels method) to_n_neighbours_array() (commonnn._types.InputDataExtNeighbourhoodsMemoryview method) (commonnn._types.InputDataExtNeighbourhoodsVector method) (commonnn._types.InputDataNeighbourhoodsSequence method) (commonnn._types.InputDataSklearnKDTree method)

to_neighbourhoods_array() (commonnn._types.InputDataExtNeighbourhoodsMemoryview method) (commonnn._types.InputDataExtNeighbourhoodsVector method) (commonnn._types.InputDataNeighbourhoodsSequence method) to_neighbours_array() (commonnn._types.Neighbours method) (commonnn._types.NeighboursExtSet method) (commonnn._types.NeighboursExtUnorderedSet method) (commonnn._types.NeighboursExtVector method) (commonnn._types.NeighboursExtVectorUnorderedSet method) (commonnn._types.NeighboursList method) (commonnn._types.NeighboursSet method) to_nx_DiGraph() (commonnn.cluster.Clustering method) to_set() (commonnn._types.Labels method) tree() (commonnn.cluster.Clustering method) trim() (commonnn.cluster.Clustering method)