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bootstrap procedures --- :mod:`MDAnalysis.analysis.ensemble.bootstrap`
======================================================================
The module contains functions for bootstrapping either ensembles (Universe
objects) or distance matrices, by resampling with replacement.
:Author: Matteo Tiberti, Wouter Boomsma, Tone Bengtsen
.. versionadded:: 0.16.0
.. deprecated:: 2.8.0
This module is deprecated in favour of the
MDAKit `mdaencore `_ and will be removed
in MDAnalysis 3.0.0.
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Bootstrap an input square matrix. The resulting matrix will have the same
shape as the original one, but the order of its elements will be drawn
(with repetition). Separately bootstraps each ensemble.
Parameters
----------
matrix : encore.utils.TriangularMatrix
similarity/dissimilarity matrix
ensemble_assignment: numpy.array
array of ensemble assignments. This array must be matrix.size long.
Returns
-------
this_m : encore.utils.TriangularMatrix
bootstrapped similarity/dissimilarity matrix
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Calculates distance matrices corresponding to bootstrapped ensembles, by
resampling with replacement.
Parameters
----------
distance_matrix : encore.utils.TriangularMatrix
Conformational distance matrix
ensemble_assignment : str
Mapping from frames to which ensemble they are from (necessary because
ensembles are bootstrapped independently)
samples : int, optional
How many bootstrap samples to create.
ncores : int, optional
Maximum number of cores to be used (default is 1)
Returns
-------
confdistmatrix : list of encore.utils.TriangularMatrix
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Generates a bootstrapped ensemble by resampling with replacement.
Parameters
----------
ensemble : MDAnalysis.Universe
Conformational distance matrix
samples : int, optional
How many bootstrap samples to create.
Returns
-------
list of MDAnalysis.Universe objects
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