Data structures #14

lilyminium · 2019-09-29T22:02:23Z

Universe

Universe creation
- Jupyter notebook for adding topology attributes
Explaining groups of atoms (residues, segments, fragments, molecules, residuegroups, segment groups)

AtomGroup

AtomGroup creation
Topology objects
Coordinate-related methods

doc/source/conf.py

lilyminium · 2019-10-10T16:23:12Z

@orbeckst Do you have any thoughts on the current content of the data-structures page: primarily ways to create Universes and AtomGroups, plus links to the Topology section for actions involving:

adding Residues/Segments
TopologyObjects
TopologyAttrs

orbeckst

Reads very nicely and I like the logical grouping. It's a lot of content, perhaps some of these pages can be split into smaller pages.

I'd also try to use sphinx linking as much as possible: use ref instead of hard links, use intersphinx linking to numpy, Python, and the MDAnalysis docs (which should become the API docs, similar to what you have tested here).

See comments inline.

doc/source/data_structures.rst

doc/source/selections.rst

doc/source/topology_system.rst

lilyminium · 2019-10-25T08:44:57Z

@orbeckst Unless you have any concerns I might merge this sometime late tomorrow (Australian) and ask the developer mailing list to comment.

richardjgowers · 2019-10-25T16:21:57Z

.travis.yml

 - source activate testenv
- pip install --upgrade sphinx sphinx-sitemap nbsphinx sphinx_rtd_theme ipython
+- jupyter-nbextension enable nglview --py --sys-prefix
 script:
 - make -C ${SPHINX_DIR} html && touch ${HTML_DIR}/.nojekyll
 deploy:


Kill the DS Store file below

Add a top-level .gitignore ! You can copy the MDA .gitignore

doc/source/atomgroup.rst

doc/source/groups_of_atoms.rst

orbeckst

Excellent stuff... just some nit-picking.

Notes on the notebooks (viewed via nbviewer)

https://nbviewer.jupyter.org/github/MDAnalysis/UserGuide/blob/229e589b370c4285a0822eb76a58181cd0d7bb18/doc/source/examples/constructing_universe.ipynb#Creating-a-blank-Universe : the list is formatted as fixed width/"pre", should be normal text
I do like the water example a lot. However, I wish you used a more realistic HOH angle (109º or whatever SPC has?) instead of 90º because invariably someone will copy&paste, even though we tell them not to. This guide will be around for a while so better get it right now. You can still generate coordinates on a grid by first making one molecule, putting them all in the same spot and then using translate() (or generate the grid with the translation vectors when making the initial array). Either way, this is already a medium/advanced tutorial so readers should be able to follow you.

P.S.: Extra cool: I can manipulate the image in the nbviewer static notebook. So awesome!!!! How did you do that?

General

I have various comments regarding "moving advanced stuff into extra sections and using links/footnotes". You can certainly just go ahead and merge and then potentially address these later. It would be great to get this PR merged.

Do you have something on the first page that says which minimum version of MDAnalysis this guide applies to? Also include the release of the guide and the date. (See MDAnalysisTutorial – I find all of this information very useful in assessing the relevance.)

orbeckst · 2019-10-25T18:09:26Z

.travis.yml

 - source activate testenv
- pip install --upgrade sphinx sphinx-sitemap nbsphinx sphinx_rtd_theme ipython
+- jupyter-nbextension enable nglview --py --sys-prefix
 script:
 - make -C ${SPHINX_DIR} html && touch ${HTML_DIR}/.nojekyll
 deploy:


Add a top-level .gitignore ! You can copy the MDA .gitignore

doc/source/groups_of_atoms.rst

orbeckst · 2019-10-25T18:42:20Z

doc/source/standard_selections.rst

+
+The below names are drawn from the CHARMM 27, OPLS-AA, GROMOS 53A6, AMBER 03, and AMBER 99sb*-ILDN force fields.
+
+------+------+------+------+------+------+------+------+


Is there a way to generate this table programmatically from the MDAnalysis version that the UserGuide pertains to?

Although this is not likely to change soon, when it does I guarantee that someone will forget to update the UserGuide.

I think @jbarnoud has written code to, for instance, dynamically create the AUTHORS list in the docs.

I think that sticking it in conf.py to run automatically would require installing MDAnalysis. If that isn't too heavy, this would be quite easy. Otherwise a script could be run manually from time-to-time to just regenerate standard_selections.rst?

At least, you can have the table in a separate file that gets included here. This way, you can generate the table with a script without having to deal with the rest of the page in the script. I have an example in MDAnalysis/mdanalysis#2176; it is a bit of a monster, but mostly because of what gets written in the external file.

doc/source/standard_selections.rst

orbeckst · 2019-10-25T18:44:04Z

doc/source/selections.rst

+
+    MDAnalysis will ignore everything after the ``*``. ``u.select_atoms("resname *E")`` will not select atoms whose residue name ends in E, but instead select every atom.
+
+


Is there a way that we only maintain this nice documentation of selections in a single place? If we update it in the code then we mustn't forget to update it here. (Not something to be solved in this PR but generally something to think about: How do we avoid duplicating docs that need to be updated.)

orbeckst · 2019-10-25T18:45:14Z

doc/source/trajectories.rst

+Trajectories
+===============
+
+MDAnalysis groups dynamic data about a :code:`Universe` into its trajectory. This is typically loaded from a trajectory file.


* changed fragment example * added advanced topology section * now auto-generates standard selections

lilyminium · 2019-10-26T14:24:35Z

Thanks for the reviews @richardjgowers and @orbeckst, and for the pointer to the script @jbarnoud. I have now:

switched the KALP fragment example to lysozyme in water
updated the constructing universes notebook to have a correct water geometry and added a section on tiling
I hope removed .DS_Store?
added a script to generate files for the tables in standard_selections.rst

@orbeckst NGLView is cool! You can save the notebook widget state, and I think I had to include the javascript for widgets with this for it to render:

html_js_files = [
    'https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js',
    DEFAULT_EMBED_REQUIREJS_URL,
]

(from this issue)

re: the MDAnalysis version -- I think ideally the UserGuide should apply to the most up-to-date one, with notes on when major changes happened? The tutorials should definitely have minimum versions on them. I haven't added them yet, but will once I work out which versions they work with.

orbeckst · 2019-10-29T00:34:10Z

Sorry, my comments are too late to the party – but they were all basically 👍 .

lilyminium added the in progress label Sep 29, 2019

orbeckst reviewed Sep 30, 2019

View reviewed changes

doc/source/conf.py Outdated Show resolved Hide resolved

Lily Wang added 5 commits October 10, 2019 11:55

got started on data structures

453b271

removed own path

79f98a4

added images and combined data structures

972bc1b

removed generated files

73f1c44

removed autosummary

a00d87f

lilyminium force-pushed the data-structures branch from 56a34a2 to a00d87f Compare October 10, 2019 00:57

Lily Wang added 2 commits October 11, 2019 02:25

split coordinate and topology sections from data structures

6b726c3

updated atomgroup methods and universe properties

bfefbbc

orbeckst reviewed Oct 13, 2019

View reviewed changes

Lily Wang added 7 commits October 23, 2019 13:55

split data structures and added refs

65d91c6

checked atom selections

1b6a11d

removed periodicity

b2fd1cb

updated universe construction example

f72e981

travis for nglview

bd666ae

fixed typo

357e772

added link to notebook

229e589

richardjgowers requested changes Oct 25, 2019

View reviewed changes

orbeckst requested changes Oct 25, 2019

View reviewed changes

Lily Wang added 2 commits October 26, 2019 14:09

removed DS_Store

5c95874

implemented review changes

8b694c5

* changed fragment example * added advanced topology section * now auto-generates standard selections

updated travis

f7b5c1c

lilyminium merged commit 48dd10c into master Oct 26, 2019

lilyminium deleted the data-structures branch October 26, 2019 21:54

lilyminium mentioned this pull request Oct 26, 2019

Slicing and selection #6

Closed

7 tasks

This was referenced Dec 28, 2019

Building a Universe #3

Closed

Using Universe #2

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Data structures #14

Data structures #14

lilyminium commented Sep 29, 2019 •

edited

Loading

lilyminium commented Oct 10, 2019

orbeckst left a comment

lilyminium commented Oct 25, 2019 •

edited

Loading

richardjgowers Oct 25, 2019

orbeckst Oct 25, 2019

orbeckst left a comment

orbeckst Oct 25, 2019

orbeckst Oct 25, 2019

lilyminium Oct 26, 2019

jbarnoud Oct 26, 2019

orbeckst Oct 25, 2019

orbeckst Oct 25, 2019

lilyminium commented Oct 26, 2019

orbeckst commented Oct 29, 2019


		The below names are drawn from the CHARMM 27, OPLS-AA, GROMOS 53A6, AMBER 03, and AMBER 99sb*-ILDN force fields.

		+------+------+------+------+------+------+------+------+


		MDAnalysis will ignore everything after the ````. ``u.select_atoms("resname E")`` will not select atoms whose residue name ends in E, but instead select every atom.

Data structures #14

Data structures #14

Conversation

lilyminium commented Sep 29, 2019 • edited Loading

lilyminium commented Oct 10, 2019

orbeckst left a comment

Choose a reason for hiding this comment

lilyminium commented Oct 25, 2019 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

orbeckst left a comment

Choose a reason for hiding this comment

Notes on the notebooks (viewed via nbviewer)

General

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

lilyminium commented Oct 26, 2019

orbeckst commented Oct 29, 2019

lilyminium commented Sep 29, 2019 •

edited

Loading

lilyminium commented Oct 25, 2019 •

edited

Loading