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Can't render fragments with multiple external connections #2778

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jblack-mestre opened this issue Feb 19, 2025 · 1 comment · Fixed by #2800
Closed

Can't render fragments with multiple external connections #2778

jblack-mestre opened this issue Feb 19, 2025 · 1 comment · Fixed by #2800

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@jblack-mestre
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Summary
When you try to render a fragment from a CDXML file with more than 1 external connection, indigo will not render any of the connections.

Steps to Reproduce

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

Actual behavior
The bonds are missing between the alkane group and the OH functional groups. As a side effect, OH is turned into H2O.
Image
(The C10H20 fragment is displaced due to a different bug #2747)

Expected behavior
Bonds are drawn between OH-C10H20-OH, as in chemdraw:
Image

Environment details:

Attachments
multiple_external_connections.cdr.txt

Additional context
MoleculeCdxmlLoader::_parseCollections and MoleculeCdxmlLoader::_checkFragmentConnection are only coded to handle a single external connection for each fragment (possibly because it is becomes ambiguous to assign a set of external connections to a set of bonds).

jblack-mestre added a commit to mestrelab-chemoinformatics/Indigo that referenced this issue Feb 20, 2025
jblack-mestre added a commit to mestrelab-chemoinformatics/Indigo that referenced this issue Mar 6, 2025
@jblack-mestre jblack-mestre changed the title Can't rednder fragments with multiple external connections Can't render fragments with multiple external connections Mar 7, 2025
@AlexanderSavelyev AlexanderSavelyev linked a pull request Mar 7, 2025 that will close this issue
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jblack-mestre added a commit to mestrelab-chemoinformatics/Indigo that referenced this issue Mar 7, 2025
@Zhirnoff Zhirnoff added this to the Indigo-1.31.0-rc.1 milestone Apr 4, 2025
@AlexeyGirin
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AlexeyGirin commented Apr 4, 2025

Verified.
Follow up issue created: epam/ketcher#6851

Image

  • Ketcher Version 3.3.0-rc.1 Build at 2025-04-02; 09:36:56
  • Indigo Version 1.31.0-rc.1.0-g859747ec7-wasm32-wasm-clang-19.0.0
  • Chrome Version 135.0.7049.42 (Official Build) (64-bit)
  • Win10

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3 participants