Replace links with refs (#406)

* replace links with refs

Author: lilyminium

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

@@ -10,10 +10,13 @@ The :mod:`MDAnalysis.analysis.align` and :mod:`MDAnalysis.analysis.rms`
 modules contain the functions used for aligning structures,
 aligning trajectories, and calculating root mean squared quantities.
 
-Demonstrations of alignment are in `align_structure <aligning_structure_to_another.ipynb>`__,
-`align_trajectory_first <aligning_trajectory_to_frame.ipynb>`__, and `align_trajectory <aligning_trajectory.ipynb>`__. Another example of
-generating an average structure from an alignment is demonstrated in
-`rmsf <rmsf.ipynb>`__. Typically, trajectories need to be aligned for RMSD and
+Demonstrations of alignment are in
+:ref:`/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb`,
+:ref:`/examples/analysis/alignment_and_rms/aligning_trajectory_to_frame.ipynb`,
+and :ref:`/examples/analysis/alignment_and_rms/aligning_trajectory.ipynb`.
+Another example of generating an average structure from an alignment is demonstrated in
+:ref:`/examples/analysis/alignment_and_rms/rmsf.ipynb`.
+Typically, trajectories need to be aligned for RMSD and
 RMSF values to make sense.
 
 .. note::
@@ -32,9 +35,3 @@ RMSF values to make sense.
    /examples/analysis/alignment_and_rms/rmsd
    /examples/analysis/alignment_and_rms/pairwise_rmsd
    /examples/analysis/alignment_and_rms/rmsf
-
-.. _rmsd: /examples/analysis/alignment_and_rms/rmsd.ipynb
-.. _pairwise: /examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb
-.. _align_structure: aligning_structure_to_another.ipynb
-.. _align_trajectory: aligning_trajectory.ipynb
-.. _align_trajectory_frame: aligning_trajectory_to_frame.ipynb

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::