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Wrong stereochemistry when loading cdxml reaction #2739

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jblack-mestre opened this issue Jan 24, 2025 · 1 comment · Fixed by #2740
Closed

Wrong stereochemistry when loading cdxml reaction #2739

jblack-mestre opened this issue Jan 24, 2025 · 1 comment · Fixed by #2740
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-1.29.0-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 creating an .svg file with indigo-depict and wrong_stereochemistry.cdr, two identical product molecules are shown in the reaction, instead of two different isomers. The second product should have an upwards wedge, not a downwards dash.

Steps to Reproduce

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

Actual behavior
Indigo is reusing the stereochemistry data from the first product with the second product.
Image

Expected behavior
Indigo should clear the stereochemistry data from the first product, so the correct stereochemistry can be used in the second product.
Image

Environment details:

  • Windows 11
  • Indigo, commit 4960b8e

Attachments
wrong_stereochemistry.txt

Additional context
In MoleculeStereocenters::clear(), both the _stereocenters and _atropocenters maps need to be cleared

Comment from QA:
Reproduced on Indigo Version 1.28.0-rc.3.0-gd5bcc27cb-wasm32-wasm-clang-19.0.0
@AlexanderSavelyev AlexanderSavelyev linked a pull request Jan 24, 2025 that will close this issue
#2739 - Wrong stereochemistry when reading cdxml reaction #2740
Merged
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@AlexeyGirin AlexeyGirin added User`s Feedback Stereochemistry Bucket: Stereochemistry related issues Export to SVG/PNG Bucket: Bugs related to SVG/PNG export Priority: Medium Severity: High High level visibility to the user labels Jan 26, 2025
AlexanderSavelyev pushed a commit that referenced this issue Jan 30, 2025
@jblack-mestre @AliaksandrDziarkach
#2739 - Wrong stereochemistry when reading cdxml reaction (#2740)
1110103 
Co-authored-by: Aliakasndr Dziarkach <18146690+AliaksandrDziarkach@users.noreply.github.com>
@AlexeyGirin
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Verified.
Image

  • Ketcher Version 3.1.0-rc.1 Build at 2025-02-04; 21:27:02
  • Indigo Version 1.29.0-rc.1.0-g2e30df8f7-wasm32-wasm-clang-19.0.0
  • Chrome Version 133.0.6943.54 (Official Build) (64-bit)
  • Win10

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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-1.29.0-rc.1 (Current)
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Successfully merging a pull request may close this issue.

#2739 - Wrong stereochemistry when reading cdxml reaction mestrelab-chemoinformatics/Indigo
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@rrodionov91 @AlexeyGirin @jblack-mestre