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  • The dynsight workflow
    • Trj
    • Insight
    • ClusterInsight
    • OnionInsight
    • OnionSmoothInsight

Tutorials

  • Tutorials
    • Getting Started
    • Spatial Denoising
    • Cleaning Cluster Population

dynsight

  • vision
    • label_tool
    • VisionInstance
  • track
    • track_xyz
  • descriptors
    • SOAP
      • saponify_trajectory
      • fill_soap_vector_from_dscribe
      • normalize_soap
      • soap_distance
    • timeSOAP
      • timesoap
    • LENS
      • list_neighbours_along_trajectory
      • compute_lens
    • many_body_tica
    • velocity_alignment
    • orientational_order_param
  • onion clustering
    • onion_uni_smooth
    • OnionUniSmooth
    • onion_multi_smooth
    • OnionMultiSmooth
    • onion_uni
    • OnionUni
    • onion_multi
    • OnionMulti
  • analysis
    • shannon
    • info_gain
    • compute_negentropy
    • sample_entropy
    • compute_shannon
    • compute_kl_entropy
    • compute_entropy_gain
    • compute_shannon_multi
    • compute_kl_entropy_multi
    • compute_entropy_gain_multi
    • compute_rdf
    • self_time_correlation
    • cross_time_correlation
    • spatialaverage
  • data processing
    • kernelsoap
    • simplekernelsoap
    • soapdistance
    • soapdistancenormalized
    • simplesoapdistance
    • createreferencesfromtrajectory
    • getdistancebetween
    • getdistancesfromref
    • getdistancesfromrefnormalized
    • mergereferences
    • savereferences
    • getreferencesfromdataset
    • applyclassification
    • cleaning_cluster_population
  • HDF5er
    • mda_to_hdf5
    • universe_to_hdf5
    • create_universe_from_slice
  • logs
    • Logs
      • dynsight.logs.Logger

Modules

  • Modules
    • dynsight
      • dynsight.analysis
        • dynsight.analysis.compute_entropy_gain
        • dynsight.analysis.compute_entropy_gain_multi
        • dynsight.analysis.compute_kl_entropy
        • dynsight.analysis.compute_kl_entropy_multi
        • dynsight.analysis.compute_negentropy
        • dynsight.analysis.compute_rdf
        • dynsight.analysis.compute_shannon
        • dynsight.analysis.compute_shannon_multi
        • dynsight.analysis.cross_time_correlation
        • dynsight.analysis.info_gain
        • dynsight.analysis.sample_entropy
        • dynsight.analysis.self_time_correlation
        • dynsight.analysis.shannon
        • dynsight.analysis.spatialaverage
        • dynsight.analysis.two_nn_estimator
      • dynsight.data_processing
        • dynsight.data_processing.applyclassification
        • dynsight.data_processing.cleaning_cluster_population
        • dynsight.data_processing.createreferencesfromtrajectory
        • dynsight.data_processing.getdistancebetween
        • dynsight.data_processing.getdistancesfromref
        • dynsight.data_processing.getdistancesfromrefnormalized
        • dynsight.data_processing.getreferencesfromdataset
        • dynsight.data_processing.kernelsoap
        • dynsight.data_processing.mergereferences
        • dynsight.data_processing.savereferences
        • dynsight.data_processing.simplekernelsoap
        • dynsight.data_processing.simplesoapdistance
        • dynsight.data_processing.soapdistance
        • dynsight.data_processing.soapdistancenormalized
      • dynsight.descriptors
        • dynsight.descriptors.compute_mean_alignment
        • dynsight.descriptors.many_body_tica
        • dynsight.descriptors.orientational_order_param
        • dynsight.descriptors.velocity_alignment
      • dynsight.hdf5er
        • dynsight.hdf5er.create_universe_from_slice
        • dynsight.hdf5er.mda_to_hdf5
        • dynsight.hdf5er.universe_to_hdf5
      • dynsight.lens
        • dynsight.lens.compute_lens
        • dynsight.lens.list_neighbours_along_trajectory
      • dynsight.logs
        • dynsight.logs.Logger
      • dynsight.onion
        • dynsight.onion.onion_multi
        • dynsight.onion.onion_multi_smooth
        • dynsight.onion.onion_uni
        • dynsight.onion.onion_uni_smooth
        • dynsight.onion.OnionMulti
        • dynsight.onion.OnionMultiSmooth
        • dynsight.onion.OnionUni
        • dynsight.onion.OnionUniSmooth
      • dynsight.soap
        • dynsight.soap.fill_soap_vector_from_dscribe
        • dynsight.soap.normalize_soap
        • dynsight.soap.saponify_trajectory
        • dynsight.soap.soap_distance
        • dynsight.soap.timesoap
      • dynsight.track
        • dynsight.track.track_xyz
      • dynsight.trajectory
        • dynsight.trajectory.ClusterInsight
        • dynsight.trajectory.Insight
        • dynsight.trajectory.OnionInsight
        • dynsight.trajectory.OnionSmoothInsight
        • dynsight.trajectory.Trj
      • dynsight.utilities
        • dynsight.utilities.find_extrema_points
        • dynsight.utilities.load_or_compute_soap
        • dynsight.utilities.normalize_array
        • dynsight.utilities.read_xyz
        • dynsight.utilities.save_xyz_from_ndarray
      • dynsight.vision
        • dynsight.vision.label_tool
        • dynsight.vision.VisionInstance
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HDF5er¶

This module requires to install cpctools. This can be done with with pip:

$ pip install cpctools
  • mda_to_hdf5
  • universe_to_hdf5
  • create_universe_from_slice

Acknowledgement¶

The original cpctools code was written by Daniele Rapetti.

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