4.2.6.1.6. bootstrap procedures — 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

New in version 0.16.0.

MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix(matrix, ensemble_assignment)[source]

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 – bootstrapped similarity/dissimilarity matrix

Return type

encore.utils.TriangularMatrix

MDAnalysis.analysis.encore.bootstrap.get_distance_matrix_bootstrap_samples(distance_matrix, ensemble_assignment, samples=100, ncores=1)[source]

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

Return type

list of encore.utils.TriangularMatrix

MDAnalysis.analysis.encore.bootstrap.get_ensemble_bootstrap_samples(ensemble, samples=100)[source]

Generates a bootstrapped ensemble by resampling with replacement.

Parameters

  • ensemble (MDAnalysis.Universe) – Conformational distance matrix

  • samples (int, optional) – How many bootstrap samples to create.

Return type

list of MDAnalysis.Universe objects