found more links

Author: lilyminium

doc/source/examples/analysis/trajectory_similarity/README.rst

@@ -5,7 +5,11 @@
 Trajectory similarity
 ======================
 
-A molecular dynamics trajectory with :math:`N` atoms can be considered through a path through :math:`3N`-dimensional molecular configuration space. MDAnalysis contains a number of algorithms to compare the conformational ensembles of different trajectories. Most of these are in the :mod:`MDAnalysis.analysis.encore` module (:cite:`tiberti_encore_2015`) and compare estimated probability distributions to measure similarity. The `path similarity analysis </examples/analysis/trajectory_similarity/psa.html>`_ compares the RMSD between pairs of structures in conformation transition paths. :mod:`MDAnalysis.analysis.encore` also contains functions for evaluating the conformational convergence of a trajectory using the `similarity over conformation clusters </examples/analysis/trajectory_similarity/clustering_ensemble_similarity.html>`_ or `similarity in a reduced dimensional space </examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity.html>`_.
+A molecular dynamics trajectory with :math:`N` atoms can be considered through a path through :math:`3N`-dimensional molecular configuration space. MDAnalysis contains a number of algorithms to compare the conformational ensembles of different trajectories. Most of these are in the :mod:`MDAnalysis.analysis.encore` module (:cite:`tiberti_encore_2015`) and compare estimated probability distributions to measure similarity.
+The :ref:`/examples/analysis/trajectory_similarity/psa.ipynb` tutorial compares the RMSD between pairs of structures in conformation transition paths.
+:mod:`MDAnalysis.analysis.encore` also contains functions for evaluating the conformational convergence of a trajectory using the
+:ref:`similarity over conformation clusters </examples/analysis/trajectory_similarity/clustering_ensemble_similarity.ipynb>`
+or :ref:`similarity in a reduced dimensional space </examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity.ipynb>`.
 
 
 .. toctree::