188.8.131.52.6. bootstrap procedures —
The module contains functions for bootstrapping either ensembles (Universe objects) or distance matrices, by resampling with replacement.
Matteo Tiberti, Wouter Boomsma, Tone Bengtsen
New in version 0.16.0.
- MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix(matrix, ensemble_assignment)
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.
- MDAnalysis.analysis.encore.bootstrap.get_distance_matrix_bootstrap_samples(distance_matrix, ensemble_assignment, samples=100, ncores=1)
Calculates distance matrices corresponding to bootstrapped ensembles, by resampling with replacement.
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)
- Return type
- MDAnalysis.analysis.encore.bootstrap.get_ensemble_bootstrap_samples(ensemble, samples=100)
Generates a bootstrapped ensemble by resampling with replacement.