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Molfile with SuperAtoms render shows a disconnected superAtom group at the corner #500

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gandha9394 opened this issue Oct 16, 2024 · 0 comments

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@gandha9394
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Describe the bug
I use Ketcher molecule editor and extract the molfile and use the molfile to display. On Ketcher I can add super atoms or abbreviations like tBu or OAc or COOH. When I try to render the molfile with RDKITJs (svg/canvas mode), I see a detached abbreviation at the corner. It looks weird and confusing.

To Reproduce
Steps to reproduce the behavior:

  1. Go to 'Ketcher demo'
  2. Add a molecule with a superAtom (type OAc -> Enter -> and place it)
  3. Export molfile
  4. Use molfile to render on RDKit. And you will see OAc at the left corner (mostly)

Expected behavior
RDKit should understand super atoms and should either ignore it or render appropriately. Would be great if it can be tied to condense_abbreviations() function.

Screenshots
Screenshot 2024-10-17 at 1 52 00 AM

Desktop (please complete the following information):

  • OS: All OS. But I tried this on Mac and Windows.
  • Browser: Chrome mostly. But I think its independent of the browser. Its part of the SVG
  • Version: 2024.3.5-1.0.0

Smartphone (please complete the following information):

  • NA
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