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Image missing stereochemistry information when using abbreviations #2741

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jblack-mestre opened this issue Jan 24, 2025 · 0 comments · Fixed by #2742
Closed

Image missing stereochemistry information when using abbreviations #2741

jblack-mestre opened this issue Jan 24, 2025 · 0 comments · Fixed by #2742
Labels
Export to SVG/PNG Bucket: Bugs related to SVG/PNG export Priority: Medium Severity: High High level visibility to the user Stereochemistry Bucket: Stereochemistry related issues User`s Feedback
Milestone
Indigo-1.30.0-rc....

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@jblack-mestre
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jblack-mestre commented Jan 24, 2025 •
edited by AlexeyGirin
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Summary
When generating an .svg image with indigo-depict missing_stereochemistry_info.cdr, the product is missing a downward dash bond connecting to the CN. This problem doesn't happen when the CN is displayed in expanded notation.

Steps to Reproduce

  1. indigo-depict.exe missing_stereochemistry_info.cdr missing_stereochemistry_info.svg

Actual behavior
The svg image is missing a downward dash bond in the product when connecting to the CN group.
Image

Expected behavior
Indigo should display the correct steroechemistry as described in the cdxml file.
Image

Environment details:

Attachments
missing_stereochemistry_info.txt
expanded_not_missing_steroechemistry.txt

Additional context
In MoleculeRenderInternal::_prepareSGroups, the bond direction should be set when creating a new bond between the super atom and the neighboring atom.

Comment from QA:
Reproduced on Indigo Version 1.28.0-rc.3.0-gd5bcc27cb-wasm32-wasm-clang-19.0.0
jblack-mestre added a commit to mestrelab-chemoinformatics/Indigo that referenced this issue Jan 24, 2025
@jblack-mestre
epam#2741 set bond direction when creating a new bond with a super atom
b8c8d91
@AlexeyGirin AlexeyGirin added User`s Feedback Export to SVG/PNG Bucket: Bugs related to SVG/PNG export Priority: Medium Severity: High High level visibility to the user Stereochemistry Bucket: Stereochemistry related issues labels Jan 26, 2025
@AlexanderSavelyev AlexanderSavelyev linked a pull request Jan 27, 2025 that will close this issue
#2741 Image missing stereochemistry information when using abbreviations #2742
Merged
7 tasks
jblack-mestre added a commit to mestrelab-chemoinformatics/Indigo that referenced this issue Jan 31, 2025
@jblack-mestre
epam#2741 remove unit test
9c71539
jblack-mestre added a commit to mestrelab-chemoinformatics/Indigo that referenced this issue Jan 31, 2025
@jblack-mestre
epam#2741 add render regression test
f5d1553
jblack-mestre added a commit to mestrelab-chemoinformatics/Indigo that referenced this issue Feb 4, 2025
@jblack-mestre
epam#2741 update render_reactions.py.out
9ef822d
jblack-mestre added a commit to mestrelab-chemoinformatics/Indigo that referenced this issue Feb 4, 2025
@jblack-mestre
epam#2741 add linux and mac reference pngs
e27605e
AlexanderSavelyev pushed a commit that referenced this issue Feb 4, 2025
@jblack-mestre
#2741 Image missing stereochemistry information when using abbreviati…
121b7d2 
…ons (#2742)
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Labels
Export to SVG/PNG Bucket: Bugs related to SVG/PNG export Priority: Medium Severity: High High level visibility to the user Stereochemistry Bucket: Stereochemistry related issues User`s Feedback
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Milestone
Indigo-1.30.0-rc.1 (Current)
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@AlexanderSavelyev @AlexeyGirin @jblack-mestre