Aromaticity and Gasteiger charges guessers by cbouy · Pull Request #2926 · MDAnalysis/mdanalysis

cbouy · 2020-08-31T17:36:12Z

Part of #2468

Changes made in this Pull Request:

Add a guesser for the aromaticities TopologyAttr
Add a guesser for partial charges (Gasteiger)

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

cbouy · 2020-08-31T17:39:09Z

@richardjgowers @IAlibay @fiona-naughton Not sure who I'm supposed to ping now that GSoC ended 😅

IAlibay

Overall lgtm, but needs tests and usage docs (there's some example use docstring at the top that could be good to add to, although we might want to migrate to user guide, @lilyminium thoughts?).

Couple of comments, there's a long term thought about how we want our guessers to look like in a multi-converter world. Overall we might need to completely overhaul the guessers, so I'm not convinced it needs to be addressed here.

package/MDAnalysis/topology/guessers.py

IAlibay · 2020-08-31T18:01:27Z

package/MDAnalysis/topology/guessers.py

+    return np.array([atom.GetIsAromatic() for atom in atoms])
+
+
+def guess_gasteiger_charges(atomgroup):


I think for now it's fine, although long term we might want to consider how we want this to look API-wise. In a hypothetical world where we have converters for things like openbabel, we might end up with multiple possible charge assignment methods. It'd be nice to have them all accessible from the same entry point.

IAlibay · 2020-08-31T18:07:21Z

Forgot to add; can't speak for everyone, but I don't mind if you keep pinging me for the RDKit things. I get the email notifications whether or not you do so anyways :)

codecov · 2020-09-01T10:57:09Z

Codecov Report

Merging #2926 (28998be) into develop (8a5ef48) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop    #2926   +/-   ##
========================================
  Coverage    92.81%   92.81%           
========================================
  Files          170      170           
  Lines        22801    22811   +10     
  Branches      3239     3243    +4     
========================================
+ Hits         21162    21172   +10     
  Misses        1591     1591           
  Partials        48       48

Impacted Files	Coverage Δ
package/MDAnalysis/topology/guessers.py	`100.00% <100.00%> (ø)`

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 8a5ef48...28998be. Read the comment docs.

IAlibay · 2021-04-10T10:40:59Z

Slowly going back into the RDKIT stuff.

@cbouy if you're still interested in progressing here, I think what's stalling the PR is the lack of tests.

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

pep8speaks · 2021-04-10T16:28:24Z

Hello @cbouy! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-04-10 16:29:49 UTC

IAlibay

This looks fine to me. @lilyminium can you have a glance at this?

lilyminium

LGTM. I am curious what the performance would be like for a molecule from a non-rdkit (e.g. PDB) format, but problems deriving aromaticity/charges should be solved in the RDKitConverter I would say.

IAlibay · 2021-04-23T21:39:26Z

Thanks @cbouy ! -- squash merging

IAlibay · 2021-04-23T21:53:41Z

😱 We forgot the changelog!
@cbouy can you add a changelog entry for this in #2942?

Towards MDAnalysis#2468 ## Work done in this PR * Add aromaticity and Gasteiger charges guessers which work via the RDKIT converter.

* added get_connections * modified tests for atoms.bonds/angles/dihedrals etc * modified parsers and things to use get_connections or bonds * updated CHANGELOG * pep8 * undo half of PR 3160 * add intra stuff * Update package/MDAnalysis/core/groups.py Co-authored-by: Jonathan Barnoud <jonathan@barnoud.net> * tighten up base class checking * update docstring * suppres warnings * Use absolute file paths in ITPParser (#3108) Fixes #3037 Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> * Adds aromaticity and Gasteiger charges guessers (#2926) Towards #2468 ## Work done in this PR * Add aromaticity and Gasteiger charges guessers which work via the RDKIT converter. * BLD: handle gcc on MacOS (#3234) Fixes #3109 ## Work done in this PR * gracefully handle the case where `gcc` toolchain in use on MacOS has been built from source using `clang` by `spack` (so it really is `gcc` in use, not `clang`) ## Notes * we could try to add regression testing, but a few problems: - `using_clang()` is inside `setup.py`, which probably can't be safely imported because it has unguarded statements/ code blocks that run right away - testing build issues is typically tricky with mocking, etc. (though in this case, probably just need to move `using_clang()` somewhere else and then test it against a variety of compiler metadata strings * Remove ParmEd Timestep writing "support" (#3240) Fixes #3031 * Adding py3.9 to gh actions CI matrix (#3245) * Fixes #2974 * Python 3.9 officially supported * Add Python 3.9 to testing matrix * Adds macOS CI entry, formalises 3.9 support * fix changelog * special metaclass * move function down * tidy code Co-authored-by: Jonathan Barnoud <jonathan@barnoud.net> Co-authored-by: Aditya Kamath <48089312+aditya-kamath@users.noreply.github.com> Co-authored-by: Cédric Bouysset <bouysset.cedric@gmail.com> Co-authored-by: Tyler Reddy <tyler.je.reddy@gmail.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

IAlibay self-requested a review August 31, 2020 17:40

IAlibay self-assigned this Aug 31, 2020

IAlibay requested changes Aug 31, 2020

View reviewed changes

orbeckst added the GSoC GSoC project label Sep 2, 2020

IAlibay added this to the 2.0 milestone Apr 6, 2021

Cédric Bouysset and others added 4 commits April 10, 2021 18:28

add aromaticity and gasteiger charges guessers

8cb5df0

Update package/MDAnalysis/topology/guessers.py

9966478

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Update package/MDAnalysis/topology/guessers.py

91014da

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

add tests

17a4923

cbouy force-pushed the rdkit-guessers branch from 88f7245 to 17a4923 Compare April 10, 2021 16:28

pep8

28998be

IAlibay approved these changes Apr 22, 2021

View reviewed changes

IAlibay requested a review from lilyminium April 22, 2021 18:39

lilyminium approved these changes Apr 23, 2021

View reviewed changes

IAlibay merged commit 32e3254 into MDAnalysis:develop Apr 23, 2021

IAlibay mentioned this pull request May 10, 2021

Improving the RDKitConverter caching system #2942

Merged

4 tasks

fiona-naughton added enhancement Component-Readers labels Sep 25, 2023

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Aromaticity and Gasteiger charges guessers#2926

Aromaticity and Gasteiger charges guessers#2926
IAlibay merged 5 commits intoMDAnalysis:developfrom
cbouy:rdkit-guessers

cbouy commented Aug 31, 2020 •

edited

Loading

Uh oh!

cbouy commented Aug 31, 2020

Uh oh!

IAlibay left a comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

IAlibay Aug 31, 2020

Uh oh!

IAlibay commented Aug 31, 2020

Uh oh!

codecov bot commented Sep 1, 2020 •

edited

Loading

Uh oh!

IAlibay commented Apr 10, 2021

Uh oh!

pep8speaks commented Apr 10, 2021 •

edited

Loading

Uh oh!

IAlibay left a comment

Uh oh!

lilyminium left a comment

Uh oh!

IAlibay commented Apr 23, 2021

Uh oh!

IAlibay commented Apr 23, 2021

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

6 participants

		return np.array([atom.GetIsAromatic() for atom in atoms])


		def guess_gasteiger_charges(atomgroup):

Conversation

cbouy commented Aug 31, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

PR Checklist

Uh oh!

cbouy commented Aug 31, 2020

Uh oh!

IAlibay left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

IAlibay Aug 31, 2020

Choose a reason for hiding this comment

Uh oh!

IAlibay commented Aug 31, 2020

Uh oh!

codecov bot commented Sep 1, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

IAlibay commented Apr 10, 2021

Uh oh!

pep8speaks commented Apr 10, 2021 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Comment last updated at 2021-04-10 16:29:49 UTC

Uh oh!

IAlibay left a comment

Choose a reason for hiding this comment

Uh oh!

lilyminium left a comment

Choose a reason for hiding this comment

Uh oh!

IAlibay commented Apr 23, 2021

Uh oh!

IAlibay commented Apr 23, 2021

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

6 participants

cbouy commented Aug 31, 2020 •

edited

Loading

codecov bot commented Sep 1, 2020 •

edited

Loading

pep8speaks commented Apr 10, 2021 •

edited

Loading