Example notebooks for HydrogenBondAnalysis

.readthedocs.yml

@@ -19,4 +19,4 @@ python:
   version: 3.7
 
 conda:
-  environment: environment.yml
+  environment: environment.yml

README.rst

@@ -2,11 +2,10 @@
   MDAnalysis User Guide
 ================================
 
-|build| 
+|build| |binder|
 
 |usergroup| |developergroup|
 
-
 MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in `many popular formats`_. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
 
 This repository contains the `user guide`_ for MDAnalysis. The user guide originated as a `project for Google Season of Docs 2019-2020`_ .
@@ -31,3 +30,7 @@ This repository contains the `user guide`_ for MDAnalysis. The user guide origin
 .. |build| image:: https://travis-ci.com/MDAnalysis/UserGuide.svg?branch=master
    :alt: Build Status
    :target: https://travis-ci.com/MDAnalysis/UserGuide
+
+.. |binder| image:: https://mybinder.org/badge_logo.svg
+   :alt: Binder
+   :target: https://mybinder.org/v2/gh/MDAnalysis/UserGuide/HEAD?urlpath=tree%2Fdoc%2Fsource%2Fexamples

doc/source/AUTHORS

@@ -26,4 +26,7 @@ Chronological list of authors
 2020
   - Rocco Meli
   - Irfan Alibay
-
+  - Yuxuan Zhuang
+  - Mieczyslaw Torchala
+2021
+  - Paul Smith

doc/source/conf.py

@@ -182,9 +182,10 @@ def sort_authors(filename):
 
 # Configuration for intersphinx: refer to the Python standard library
 # and other packages used by MDAnalysis
+mda_version = mda.__version__
 intersphinx_mapping = {'https://docs.python.org/': None,
                        'https://docs.scipy.org/doc/numpy/': None,
-                       'https://www.mdanalysis.org/docs/': None,
+                       f'https://docs.mdanalysis.org/{mda_version}/': None,
                        'https://docs.pytest.org/en/latest/': None,
                        'https://chemfiles.org/chemfiles.py/latest/': None,
                        'http://parmed.github.io/ParmEd/html/': None,

doc/source/examples/README.rst

@@ -25,4 +25,4 @@ MDAnalysis maintains a collection of Jupyter notebooks as examples of what the c
    analysis/reduced_dimensions/README
    analysis/polymers_and_membranes/README
    analysis/volumetric/README
-
+   analysis/hydrogen_bonds/README

doc/source/examples/analysis/README.rst

@@ -8,15 +8,17 @@ 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>`__.
+the `path similarity 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>`__.
+`several ways to write your own analysis <custom_trajectory_analysis.ipynb>`__.
 
+If you want to run your own script in parallel in MDAnalysis, here is a `tutorial on make your code parallelizable
+<custom_parallel_analysis.ipynb>`__.
 
 
 Imports and dependencies
@@ -49,4 +51,6 @@ them separately, e.g.::
 
 .. include:: /examples/analysis/reduced_dimensions/README.rst
 
-.. include:: /examples/analysis/polymers_and_membranes/README.rst
+.. include:: /examples/analysis/polymers_and_membranes/README.rst
+
+.. include:: /examples/analysis/hydrogen_bonds/README.rst

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

@@ -19,8 +19,8 @@ The :mod:`MDAnalysis.analysis.align` and :mod:`MDAnalysis.analysis.rms` modules
    :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/aligning_trajectory_to_frame
    /examples/analysis/alignment_and_rms/rmsd
    /examples/analysis/alignment_and_rms/pairwise_rmsd
    /examples/analysis/alignment_and_rms/rmsf