Index

A

applyclassification() (in module dynsight.data_processing)

C

cleaning_cluster_population() (in module dynsight.data_processing) clear_history() (dynsight.logs.Logger method) ClusterInsight (class in dynsight.trajectory) compute_entropy_gain() (in module dynsight.analysis) compute_entropy_gain_multi() (in module dynsight.analysis) compute_kl_entropy() (in module dynsight.analysis) compute_kl_entropy_multi() (in module dynsight.analysis) compute_lens() (in module dynsight.lens) compute_mean_alignment() (in module dynsight.descriptors)

compute_negentropy() (in module dynsight.analysis) compute_rdf() (in module dynsight.analysis) compute_shannon() (in module dynsight.analysis) compute_shannon_multi() (in module dynsight.analysis) configure() (dynsight.logs.Logger method) create_dataset_from_predictions() (dynsight.vision.VisionInstance method) create_universe_from_slice() (in module dynsight.hdf5er) createreferencesfromtrajectory() (in module dynsight.data_processing) cross_time_correlation() (in module dynsight.analysis)

D

dataset (dynsight.trajectory.Insight attribute) dump_colored_trj() (dynsight.trajectory.OnionSmoothInsight method) (dynsight.trajectory.Trj method) dump_to_json() (dynsight.trajectory.ClusterInsight method) (dynsight.trajectory.Insight method) (dynsight.trajectory.OnionInsight method) (dynsight.trajectory.OnionSmoothInsight method) dump_xyz_with_insight() (dynsight.trajectory.Trj method) dynsight module dynsight.analysis module dynsight.data_processing module dynsight.descriptors module dynsight.hdf5er module

dynsight.lens module dynsight.logs module dynsight.onion module dynsight.soap module dynsight.track module dynsight.trajectory module dynsight.utilities module dynsight.vision module

E

export_prediction_to_xyz() (dynsight.vision.VisionInstance method)

extract_datasets() (dynsight.logs.Logger method)

F

fill_soap_vector_from_dscribe() (in module dynsight.soap) find_extrema_points() (in module dynsight.utilities) fit() (dynsight.onion.OnionMulti method) (dynsight.onion.OnionMultiSmooth method) (dynsight.onion.OnionUni method) (dynsight.onion.OnionUniSmooth method)

fit_predict() (dynsight.onion.OnionMulti method) (dynsight.onion.OnionMultiSmooth method) (dynsight.onion.OnionUni method) (dynsight.onion.OnionUniSmooth method)

G

get() (dynsight.logs.Logger method) get_angular_velocity() (dynsight.trajectory.Insight method) get_coord_number() (dynsight.trajectory.Trj method) get_coordinates() (dynsight.trajectory.Trj method) get_lens() (dynsight.trajectory.Trj method) get_onion() (dynsight.trajectory.Insight method) get_onion_analysis() (dynsight.trajectory.Insight method) get_onion_smooth() (dynsight.trajectory.Insight method) get_orientational_op() (dynsight.trajectory.Trj method) get_params() (dynsight.onion.OnionMulti method) (dynsight.onion.OnionUni method)

get_rdf() (dynsight.trajectory.Trj method) get_slice() (dynsight.trajectory.Trj method) get_soap() (dynsight.trajectory.Trj method) get_tica() (dynsight.trajectory.Insight method) get_time_correlation() (dynsight.trajectory.Insight method) get_timesoap() (dynsight.trajectory.Trj method) get_velocity_alignment() (dynsight.trajectory.Trj method) getdistancebetween() (in module dynsight.data_processing) getdistancesfromref() (in module dynsight.data_processing) getdistancesfromrefnormalized() (in module dynsight.data_processing) getreferencesfromdataset() (in module dynsight.data_processing)

I

info_gain() (in module dynsight.analysis) init_from_universe() (dynsight.trajectory.Trj class method)

init_from_xtc() (dynsight.trajectory.Trj class method) init_from_xyz() (dynsight.trajectory.Trj class method) Insight (class in dynsight.trajectory)

K

kernelsoap() (in module dynsight.data_processing)

L

label_tool() (in module dynsight.vision) labels (dynsight.trajectory.ClusterInsight attribute) (dynsight.trajectory.OnionInsight attribute) (dynsight.trajectory.OnionSmoothInsight attribute) labels_ (dynsight.onion.OnionMulti attribute) (dynsight.onion.OnionMultiSmooth attribute) (dynsight.onion.OnionUni attribute) (dynsight.onion.OnionUniSmooth attribute)

list_neighbours_along_trajectory() (in module dynsight.lens) load_from_json() (dynsight.trajectory.ClusterInsight class method) (dynsight.trajectory.Insight class method) (dynsight.trajectory.OnionInsight class method) (dynsight.trajectory.OnionSmoothInsight class method) load_or_compute_soap() (in module dynsight.utilities) log() (dynsight.logs.Logger method) Logger (class in dynsight.logs)

M

many_body_tica() (in module dynsight.descriptors) mda_to_hdf5() (in module dynsight.hdf5er) mergereferences() (in module dynsight.data_processing) meta (dynsight.trajectory.Insight attribute) (dynsight.trajectory.OnionInsight attribute) (dynsight.trajectory.OnionSmoothInsight attribute) module dynsight dynsight.analysis dynsight.data_processing dynsight.descriptors dynsight.hdf5er dynsight.lens dynsight.logs dynsight.onion dynsight.soap dynsight.track dynsight.trajectory dynsight.utilities dynsight.vision

N

normalize_array() (in module dynsight.utilities)

normalize_soap() (in module dynsight.soap)

O

onion_multi() (in module dynsight.onion) onion_multi_smooth() (in module dynsight.onion) onion_uni() (in module dynsight.onion) onion_uni_smooth() (in module dynsight.onion) OnionInsight (class in dynsight.trajectory)

OnionMulti (class in dynsight.onion) OnionMultiSmooth (class in dynsight.onion) OnionSmoothInsight (class in dynsight.trajectory) OnionUni (class in dynsight.onion) OnionUniSmooth (class in dynsight.onion) orientational_order_param() (in module dynsight.descriptors)

P

plot_medoids() (dynsight.trajectory.OnionInsight method) plot_one_trj() (dynsight.trajectory.OnionInsight method) (dynsight.trajectory.OnionSmoothInsight method) plot_output() (dynsight.trajectory.OnionInsight method) (dynsight.trajectory.OnionSmoothInsight method)

plot_sankey() (dynsight.trajectory.OnionInsight method) (dynsight.trajectory.OnionSmoothInsight method) plot_state_populations() (dynsight.trajectory.OnionInsight method) (dynsight.trajectory.OnionSmoothInsight method) predict() (dynsight.vision.VisionInstance method)

R

read_xyz() (in module dynsight.utilities)

record_data() (dynsight.logs.Logger method) reshaped_data (dynsight.trajectory.OnionInsight attribute)

S

sample_entropy() (in module dynsight.analysis) saponify_trajectory() (in module dynsight.soap) save_history() (dynsight.logs.Logger method) save_xyz_from_ndarray() (in module dynsight.utilities) savereferences() (in module dynsight.data_processing) self_time_correlation() (in module dynsight.analysis) set_params() (dynsight.onion.OnionMulti method) (dynsight.onion.OnionUni method) set_training_dataset() (dynsight.vision.VisionInstance method) shannon() (in module dynsight.analysis) simplekernelsoap() (in module dynsight.data_processing)

simplesoapdistance() (in module dynsight.data_processing) soap_distance() (in module dynsight.soap) soapdistance() (in module dynsight.data_processing) soapdistancenormalized() (in module dynsight.data_processing) spatial_average() (dynsight.trajectory.Insight method) spatialaverage() (in module dynsight.analysis) state_list (dynsight.trajectory.OnionInsight attribute) (dynsight.trajectory.OnionSmoothInsight attribute) state_list_ (dynsight.onion.OnionMulti attribute) (dynsight.onion.OnionMultiSmooth attribute) (dynsight.onion.OnionUni attribute) states_list_ (dynsight.onion.OnionUniSmooth attribute)

T

timesoap() (in module dynsight.soap) track_xyz() (in module dynsight.track) train() (dynsight.vision.VisionInstance method)

Trj (class in dynsight.trajectory) tune_hyperparams() (dynsight.vision.VisionInstance method) two_nn_estimator() (in module dynsight.analysis)

U

universe (dynsight.trajectory.Trj attribute)

universe_to_hdf5() (in module dynsight.hdf5er)

V

velocity_alignment() (in module dynsight.descriptors)

VisionInstance (class in dynsight.vision)

W

warning() (dynsight.logs.Logger method)

with_slice() (dynsight.trajectory.Trj method)