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epam / Indigo

Universal cheminformatics toolkit, utilities and database search tools
http://lifescience.opensource.epam.com
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Distorted structure representation when opening saved macromolecules in micro mode in CML, CDX, CDXML, Base 64 CDX formats #2523

Open Zhirnoff opened 4 weeks ago

Zhirnoff commented 4 weeks ago

Steps to Reproduce

  1. Open file in Macro mode (Flex mode) monomers-cycled.zip
  2. Switch to Micro mode 2024-10-07_19h16_31
  3. Save as CML, CDX, CDXML, Base 64 CDX
  4. Open saved files

Actual behavior Upon reopening the CML, CDX, CDXML, Base 64 CDX0 files, the structure appears distorted, with bonds incorrectly placed, resulting in a non-cyclic structure (as shown in the screenshot). The original intended shape and arrangement of monomers are lost. 2024-10-07_19h16_21 Screen from CDX also not fine: image

Expected behavior The saved structure should maintain its original form upon reopening, appearing as a cyclic structure similar to the screenshot.

2024-10-07_19h16_31

Desktop:

Ketcher version [Version 2.26.0-rc.1] Indigo version [Version 1.25.0-rc.1] Bug found during testing: https://github.com/epam/ketcher/issues/5400