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::
@@ -33,8 +36,3 @@ RMSF values to make sense.
    /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