=============================================================================== ENCORE Ensemble Similarity Calculations --- :mod:`MDAnalysis.analysis.encore` =============================================================================== :Author: Matteo Tiberti, Wouter Boomsma, Tone Bengtsen :Year: 2015-2017 :Copyright: GNU Public License v3 :Maintainer: Matteo Tiberti , mtiberti on github .. versionadded:: 0.16.0 The module contains implementations of similarity measures between protein ensembles described in [Lindorff-Larsen2009a]_. The implementation and examples are described in [Tiberti2015a]_. The module includes facilities for handling ensembles and trajectories through the :class:`Universe` class, performing clustering or dimensionality reduction of the ensemble space, estimating multivariate probability distributions from the input data, and more. ENCORE can be used to compare experimental and simulation-derived ensembles, as well as estimate the convergence of trajectories from time-dependent simulations. ENCORE includes three different methods for calculations of similarity measures between ensembles implemented in individual functions: + **Harmonic Ensemble Similarity** : :func:`~MDAnalysis.analysis.encore.similarity.hes` + **Clustering Ensemble Similarity** : :func:`~MDAnalysis.analysis.encore.similarity.ces` + **Dimensional Reduction Ensemble Similarity** : :func:`~MDAnalysis.analysis.encore.similarity.dres` as well as two methods to evaluate the convergence of trajectories: + **Clustering based convergence evaluation** : :func:`~MDAnalysis.analysis.encore.similarity.ces_convergence` + **Dimensionality-reduction based convergence evaluation** : :func:`~MDAnalysis.analysis.encore.similarity.dres_convergence` When using this module in published work please cite [Tiberti2015a]_. Modules ------- .. toctree:: :maxdepth: 1 ./encore/similarity ./encore/clustering ./encore/dimensionality_reduction ./encore/confdistmatrix ./encore/covariance ./encore/bootstrap ./encore/utils References ---------- .. [Lindorff-Larsen2009a] Similarity Measures for Protein Ensembles. Lindorff-Larsen, K. Ferkinghoff-Borg, J. PLoS ONE 2008, 4, e4203. .. [Tiberti2015a] ENCORE: Software for Quantitative Ensemble.. Comparison. Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff- Larsen. PLoS Comput Biol. 2015, 11, e1004415