Analysis notebooks for 0.20.1

.gitignore

@@ -26,14 +26,23 @@ doc/build
 
 # ignore generated files
 *.vmd
+*.crd
 *.dcd
 *.xyz
 *.pdb
 *.trr
 *.ndx
 *.xtc
+*.pkl
+*.dat
 
 # example files
-doc/source/examples/*
-!doc/source/examples/**/*.rst
+doc/source/examples/**/*.*
 !doc/source/examples/**/*.ipynb
+!doc/source/examples/**/*.rst
+!doc/source/examples/**/*.gif
+!doc/source/examples/**/*.png
+
+# backup files
+doc/source/examples/**/.*.ipynb
+

doc/source/conf.py

@@ -54,7 +54,8 @@
     'nbsphinx',
     'sphinx_rtd_theme',
     'IPython.sphinxext.ipython_console_highlighting',
-    'IPython.sphinxext.ipython_directive'
+    'IPython.sphinxext.ipython_directive',
+    'sphinxcontrib.bibtex',
 ]
 
 pygments_style = 'default'
@@ -71,9 +72,11 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
+
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store',
                     '.ipynb_checkpoints', '**/.ipynb_checkpoints', 'scripts', '.*.ipynb']
 
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -112,7 +115,7 @@
     # Toc options
     'collapse_navigation': True,
     'sticky_navigation': True,
-    'navigation_depth': 5,
+    'navigation_depth': 4,
     'includehidden': True,
     'titles_only': False,
 }
@@ -156,6 +159,14 @@
 ]
 
 ipython_warning_is_error = False
+nbsphinx_prolog = r"""
+.. raw:: html
+
+    <script src='http://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js'></script>
+    <script>require=requirejs;</script>
+
+
+"""
 
 # substitutions
 MDAnalysis_version = '0.20.1'

doc/source/examples/README.rst

@@ -12,3 +12,17 @@ MDAnalysis maintains a collection of Jupyter notebooks as examples of what the c
 
    quickstart
    constructing_universe
+   transformations/README
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Analysis
+
+   analysis/alignment_and_rms/README
+   analysis/distances_and_contacts/README
+   analysis/trajectory_similarity/README
+   analysis/structure/README
+   analysis/reduced_dimensions/README
+   analysis/polymers_and_membranes/README
+   analysis/volumetric/README
+

doc/source/examples/analysis/README.rst

@@ -0,0 +1,52 @@
+.. -*- coding: utf-8 -*-
+.. _analysis:
+
+========
+Analysis
+========
+
+The :mod:`~MDAnalysis.analysis` module of MDAnalysis provides the tools needed to analyse your data. 
+Several analyses are included with the package. These range from standard algorithms 
+(e.g. :ref:`calculating root mean squared quantities <alignment-and-rms>`) to unique algorithms such as 
+the `path similarity analysis <examples/analysis/trajectory_similarity/psa.ipynb>`__.
+
+Generally these bundled analyses are contributed by various researchers who use the code for their own work. 
+Please refer to the individual module documentation or relevant user guide tutorials for additional 
+references and citation information.
+
+If you need functionality that is not already provided in MDAnalysis, there are 
+`several ways to write your own analysis <examples/analysis/custom_trajectory_analysis.ipynb>`__.
+
+
+
+Imports and dependencies
+========================
+
+Analysis modules are not imported by default. In order to use them, you will need to import 
+them separately, e.g.::
+
+    from MDAnalysis.analysis import align
+
+.. note::
+
+    Several modules in :mod:`MDAnalysis.analysis` require additional Python packages. 
+    For example, :mod:`~MDAnalysis.analysis.encore` makes use of `scikit-learn <http://scikit-learn.org/>`__. 
+    The Python packages are not automatically installed with `pip`, although they are with `conda`.
+
+    Other modules require external programs. For example, :mod:`~MDAnalysis.analysis.hole` requires 
+    the `HOLE <http://www.holeprogram.org/>`_ programs. You will need to install these yourself.
+
+
+.. include:: /examples/analysis/alignment_and_rms/README.rst
+
+.. include:: /examples/analysis/distances_and_contacts/README.rst
+
+.. include:: /examples/analysis/trajectory_similarity/README.rst
+
+.. include:: /examples/analysis/structure/README.rst
+
+.. include:: /examples/analysis/volumetric/README.rst
+
+.. include:: /examples/analysis/reduced_dimensions/README.rst
+
+.. include:: /examples/analysis/polymers_and_membranes/README.rst

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

@@ -0,0 +1,25 @@
+.. -*- coding: utf-8 -*-
+
+.. _alignment-and-rms:
+
+==========================
+Alignments and RMS fitting
+==========================
+
+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. 
+
+.. note::
+
+    These modules use the fast QCP algorithm to calculate the root mean
+    square distance (RMSD) between two coordinate sets :cite:`theobald_rapid_2005` and
+    the rotation matrix *R* that minimizes the RMSD :cite:`liu_fast_2009`. Please
+    cite these references when using these modules.
+
+.. toctree::
+   :maxdepth: 1
+
+   /examples/analysis/alignment_and_rms/aligning_structure_to_another
+   /examples/analysis/alignment_and_rms/aligning_trajectory_to_first_frame
+   /examples/analysis/alignment_and_rms/aligning_trajectory
+   /examples/analysis/alignment_and_rms/rmsd
+   /examples/analysis/alignment_and_rms/pairwise_rmsd