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Reaction rendering always shows molecules in aromatic form #2976

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greglandrum opened this issue Feb 28, 2020 · 1 comment · Fixed by #3930
Closed

Reaction rendering always shows molecules in aromatic form #2976

greglandrum opened this issue Feb 28, 2020 · 1 comment · Fixed by #3930
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bug
Milestone
2021_03_1

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@greglandrum
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get2DCoordsForReaction() calls get2DCoordsMol(), which always sanitizes the reactants, agents, and products. There needs to be some control over this so that it's possible to draw reactions in kekule form (if desired).
@greglandrum greglandrum added this to the 2020_03_1 milestone Feb 28, 2020
@greglandrum greglandrum modified the milestones: 2020_03_1, 2020_09_1 Mar 29, 2020
@ChongLu121
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Hello,

I'd like to draw reactions in kekule form. Do you have any solution to convert the dashed line to kekulized ring?

rxn = AllChem.ReactionFromSmarts('CN.OC(=O)CCC1C2=C(C=CC=C2)C2=C1C=CC=C2>>CNC(=O)CCC1C2=C(C=CC=C2)C2=C1C=CC=C2',
useSmiles=True)
d = Draw.MolDraw2DSVG(600,200)
d.SetFontSize(0.6)
d.DrawReaction(rxn)
d.FinishDrawing()
svg = SVG(d.GetDrawingText())
display(svg)

Thanks.

@greglandrum greglandrum modified the milestones: 2020_09_1, 2021_03_1 Oct 20, 2020
greglandrum added a commit to greglandrum/rdkit that referenced this issue Mar 15, 2021
@greglandrum
Fixes rdkit#2976
8d56fa6 
Stops re-generating reaction coordinates when that's not required
@greglandrum greglandrum mentioned this issue Mar 15, 2021
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greglandrum added a commit that referenced this issue Mar 17, 2021
@greglandrum
MolDraw2D: collected tweaks and bug fixes (#3930)
fbc76ae 
* Fixes #2976
Stops re-generating reaction coordinates when that's not required

* add better test

* try to deal with bad font sizes from mol files

* one more expected result update

* try to be smarter about font changes

* suppress a compiler warning

* remove debug output

* update some expected test results
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MolDraw2D: collected tweaks and bug fixes greglandrum/rdkit
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@greglandrum @ChongLu121