Wrap RDKit drawing code for AtomGroups

[cbouy]

Part of #2468 Depends on #2775

Changes made in this Pull Request:

• In notebooks, by importing from MDAnalysis.visualization.RDKit import RDKitDrawer, the default representation of the AtomGroup is changed for small molecules: it displays an image of the AtomGroup using RDKit's drawing code (and the default representation for large AtomGroups)
• The default drawer displays PNG images for atomgroups below 200 atoms, removes non-polar hydrogens, kekulizes and flattens the structure, although all of these are configurable
• You can reuse the code that is used to generate the PNG/SVG by calling drawer.atomgroup_to_image(ag, ...). There is also some code to automatically display or save gifs from an atomgroup:
• And all of this can be cancelled at any point

PR Checklist

• [ ] Tests?
• [x] Docs?
• [ ] CHANGELOG updated?
• [x] Issue raised/referenced?

Tagging @MDAnalysis/coredevs

I'm not sure if I've put the code in the right place but "visualization" made sense to me

[pep8speaks]

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

• In the file package/MDAnalysis/visualization/RDKit.py:

Line 146:80: E501 line too long (98 > 79 characters)

• In the file package/MDAnalysis/visualization/base.py:

Line 64:73: W291 trailing whitespace Line 87:73: W291 trailing whitespace

• In the file testsuite/MDAnalysisTests/visualization/test_base.py:

Line 41:9: E731 do not assign a lambda expression, use a def Line 44:1: W293 blank line contains whitespace Line 46:9: E731 do not assign a lambda expression, use a def Line 52:9: E731 do not assign a lambda expression, use a def Line 56:46: W292 no newline at end of file

• In the file testsuite/MDAnalysisTests/visualization/test_rdkit.py:

Line 72:62: W291 trailing whitespace

Comment last updated at 2020-08-31 16:50:33 UTC

[cbouy]

I added a metaclass and a base class for "formatters" (i.e. classes that can modify the representation of other objects in interactive shells/notebooks), in case we want to add another visualization package like nglview to display atomgroups directly.

Also, I'm not sure how to test the AtomGroup representation and the generation of images...
Does anyone have some pointers ?

[codecov[bot]]

Codecov Report

Merging #2900 into develop will increase coverage by 5.37%. The diff coverage is 1.02%.

@@             Coverage Diff             @@
##           develop    #2900      +/-   ##
===========================================
+ Coverage    87.20%   92.57%   +5.37%     
===========================================
  Files          167      189      +22     
  Lines        21744    24690    +2946     
  Branches      3186     3196      +10     
===========================================
+ Hits         18961    22857    +3896     
+ Misses        2258     1787     -471     
+ Partials       525       46     -479     

Impacted Files	Coverage Δ
package/MDAnalysis/visualization/RDKit.py	0.00% <0.00%> (ø)
package/MDAnalysis/visualization/base.py	0.00% <0.00%> (ø)
package/MDAnalysis/__init__.py	92.68% <100.00%> (+0.18%)	:arrow_up:
package/MDAnalysis/topology/tpr/obj.py	96.96% <0.00%> (-3.04%)	:arrow_down:
package/MDAnalysis/lib/formats/libdcd.pyx	88.48% <0.00%> (-0.85%)	:arrow_down:
package/MDAnalysis/lib/formats/libmdaxdr.pyx	89.81% <0.00%> (-0.16%)	:arrow_down:
package/MDAnalysis/core/topology.py	100.00% <0.00%> (ø)
package/MDAnalysis/analysis/polymer.py	100.00% <0.00%> (ø)
package/MDAnalysis/coordinates/MMTF.py	100.00% <0.00%> (ø)
package/MDAnalysis/coordinates/NAMDBIN.py	100.00% <0.00%> (ø)
... and 124 more

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[IAlibay]

I'm moving this to the 2.1.0 milestone

[ldomic]

Maybe this helps with the SVG testing? https://github.com/ldomic/mdanalysis/blob/2af2d99447cc06d96fd3695b400b9f3bcbb0f4d5/testsuite/MDAnalysisTests/visualization/test_lintools.py