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Distorted structure representation when opening saved macromolecules in micro mode in CML, CDX, CDXML, Base 64 CDX formats #2523

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Zhirnoff opened this issue Oct 7, 2024 · 0 comments
Open

Distorted structure representation when opening saved macromolecules in micro mode in CML, CDX, CDXML, Base 64 CDX formats #2523

Zhirnoff opened this issue Oct 7, 2024 · 0 comments
Labels
CML Bucket: CML format related issues Export to CDX Bucket: Bugs related to Export to CDX Export to CDXML Bucket: Bugs related to Export to CDXML Macro-Micro Bucket: Switching between Micro and Macro modes Priority: High
Milestone
Indigo-1.26.0-rc.3

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@Zhirnoff
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Zhirnoff commented Oct 7, 2024 •
edited by AlexeyGirin
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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:

  • OS: Windows 11
  • Browser Chrome
  • Version 128.0.6613.120 (Official Build) (64-bit)

Ketcher version
[Version 2.26.0-rc.1]
Indigo version
[Version 1.25.0-rc.1]
Bug found during testing: epam/ketcher#5400
@Zhirnoff Zhirnoff added Priority: High Macro-Micro Bucket: Switching between Micro and Macro modes CML Bucket: CML format related issues Export to CDXML Bucket: Bugs related to Export to CDXML Export to CDX Bucket: Bugs related to Export to CDX labels Oct 7, 2024
@Zhirnoff Zhirnoff added this to the Indigo-1.25.0-rc.2 milestone Oct 7, 2024
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Labels
CML Bucket: CML format related issues Export to CDX Bucket: Bugs related to Export to CDX Export to CDXML Bucket: Bugs related to Export to CDXML Macro-Micro Bucket: Switching between Micro and Macro modes Priority: High
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Milestone
Indigo-1.26.0-rc.3
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3 participants
@even1024 @AlexeyGirin @Zhirnoff