diff --git a/mdaencore/similarity.py b/mdaencore/similarity.py index 9d9b845..1999b75 100644 --- a/mdaencore/similarity.py +++ b/mdaencore/similarity.py @@ -30,11 +30,11 @@ described in :footcite:p:`Tiberti2015`. The module includes facilities for handling ensembles and trajectories through -the :class:`~MDAnalysis.core.universe.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. +the :class:`~MDAnalysis.core.universe.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: @@ -1045,13 +1045,13 @@ def ces(ensembles, -------- To calculate the Clustering Ensemble similarity, two ensembles are created as Universe object using a topology file and two trajectories. The - topology- and trajectory files used are obtained from the MDAnalysis - test suite for two different simulations of the protein AdK. - To use a different clustering method, set the parameter clustering_method - (Note that the sklearn module must be installed). Likewise, different parameters - for the same clustering method can be explored by adding different - instances of the same clustering class. - Here the simplest case of just two instances of :class:`~MDAnalysis.core.universe.Universe` is illustrated: + topology- and trajectory files used are obtained from the MDAnalysis test + suite for two different simulations of the protein AdK. To use a different + clustering method, set the parameter clustering_method (Note that the + sklearn module must be installed). Likewise, different parameters for the + same clustering method can be explored by adding different instances of + the same clustering class. Here the simplest case of just two instances + of :class:`~MDAnalysis.core.universe.Universe` is illustrated: >>> from MDAnalysis import Universe >>> import mdaencore as encore @@ -1325,8 +1325,8 @@ def dres(ensembles, To use a different dimensional reduction methods, simply set the parameter dimensionality_reduction_method. Likewise, different parameters for the same clustering method can be explored by adding different - instances of the same method class. - Here the simplest case of comparing just two instances of :class:`~MDAnalysis.core.universe.Universe` is + instances of the same method class. Here the simplest case of comparing + just two instances of :class:`~MDAnalysis.core.universe.Universe` is illustrated: >>> from MDAnalysis import Universe