MDAnalysis · orbeckst · Nov 8, 2023 · Nov 3, 2023 · Nov 3, 2023 · Nov 6, 2023
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -1,10 +1,51 @@
+=================
 API Documentation
 =================
 
-This documentation details the modules, classes, and functions in ``mdaencore``.
+The package contains implementations of similarity measures between protein
+ensembles described in :footcite:p:`LindorffLarsen2009`. The implementation and examples
+are described in :footcite:p:`Tiberti2015`.
+
+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:`~mdaencore.similarity.hes`
++ **Clustering Ensemble Similarity** : :func:`~mdaencore.similarity.ces`
++ **Dimensional Reduction Ensemble Similarity** : :func:`mdaencore.similarity.dres`
+
+as well as two methods to evaluate the convergence of trajectories:
+
++ **Clustering based convergence evaluation** : :func:`mdaencore.similarity.ces_convergence`
++ **Dimensionality-reduction based convergence evaluation** : :func:`mdaencore.similarity.dres_convergence`
+
+
+When using this module in published work please cite :footcite:p:`Tiberti2015`.
+
+
+Modules
+-------
+
+.. toctree::
+   :maxdepth: 1
+
+   encore/similarity
+   encore/clustering
+   encore/dimensionality_reduction
+   encore/confdistmatrix
+   encore/covariance
+   encore/bootstrap
+   encore/utils
+
 
-.. autosummary::
-   :toctree: autosummary
-   :recursive:
+References
+----------
 
-   mdaencore
+.. footbibliography::
diff --git a/docs/source/encore/bootstrap.rst b/docs/source/encore/bootstrap.rst
@@ -0,0 +1,6 @@
+===================================================
+Bootstrap procedures --- :mod:`mdaencore.bootstrap`
+===================================================
+
+.. automodule:: mdaencore.bootstrap
+   :members:
diff --git a/docs/source/encore/clustering.rst b/docs/source/encore/clustering.rst
@@ -0,0 +1,24 @@
+============
+ Clustering
+============
+
+.. automodule:: mdaencore.clustering.cluster
+   :members:
+
+.. automodule:: mdaencore.clustering.ClusterCollection
+   :members:
+
+.. automodule:: mdaencore.clustering.ClusteringMethod
+   :members:
+
+
+Clustering algorithms
+=====================
+
+The following clustering algorithms are always available:
+
+.. automodule:: mdaencore.clustering.affinityprop
+   :members:
+
+
+
diff --git a/docs/source/encore/confdistmatrix.rst b/docs/source/encore/confdistmatrix.rst
@@ -0,0 +1,6 @@
+================================================================
+Distance matrix calculations --- :mod:`mdaencore.confdistmatrix`
+================================================================
+
+.. automodule:: mdaencore.confdistmatrix
+   :members:
diff --git a/docs/source/encore/covariance.rst b/docs/source/encore/covariance.rst
@@ -0,0 +1,6 @@
+======================================================
+Covariance calculation --- :mod:`mdaencore.covariance`
+======================================================
+
+.. automodule:: mdaencore.covariance
+   :members:
diff --git a/docs/source/encore/dimensionality_reduction.rst b/docs/source/encore/dimensionality_reduction.rst
@@ -0,0 +1,18 @@
+==========================
+ Dimensionality reduction
+==========================
+
+.. automodule:: mdaencore.dimensionality_reduction.reduce_dimensionality
+   :members:
+
+.. automodule:: mdaencore.dimensionality_reduction.DimensionalityReductionMethod
+   :members:
+
+Dimensionality reduction algorithms
+===================================
+
+The following dimensionality reduction algorithms are always natively
+available:
+
+.. automodule:: mdaencore.dimensionality_reduction.stochasticproxembed
+   :members:
diff --git a/docs/source/encore/similarity.rst b/docs/source/encore/similarity.rst
@@ -0,0 +1,6 @@
+================================================================
+Ensemble Similarity Calculations --- :mod:`mdaencore.similarity`
+================================================================
+
+.. automodule:: mdaencore.similarity
+   :members:
diff --git a/docs/source/encore/utils.rst b/docs/source/encore/utils.rst
@@ -0,0 +1,8 @@
+==============================
+ Utility functions for ENCORE
+==============================
+
+.. automodule:: mdaencore.utils
+   :members:
+
+.. autofunction:: mdaencore.cutils.PureRMSD
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -7,7 +7,7 @@ Welcome to mdaencore's documentation!
 =========================================================
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Contents:
    :hidden:
 

diff --git a/mdaencore/clustering/cluster.py b/mdaencore/clustering/cluster.py
@@ -20,7 +20,11 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-"""The module defines a function serving as front-end for various clustering
+"""\
+clustering frontend --- :mod:`mdaencore.clustering.cluster`
+============================================================================
+
+The module defines a function serving as front-end for various clustering
 algorithms, wrapping them to allow them to be used interchangably.
 """
 import numpy as np

diff --git a/mdaencore/similarity.py b/mdaencore/similarity.py
@@ -50,7 +50,6 @@
 
 When using this module in published work please cite :footcite:p:`Tiberti2015`.
 
-.. _Examples:
 Examples
 ========