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epam / Indigo

Universal cheminformatics toolkit, utilities and database search tools
http://lifescience.opensource.epam.com
Apache License 2.0
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Macro: V3000 export: leaving groups are displayed as side chain connections for standard presets added to canvas #1598

Closed Zhirnoff closed 6 months ago

Zhirnoff commented 8 months ago

Steps to Reproduce

  1. Go to 'Macromolecules'
  2. Add several RNA presets on canvas (for ex. A, C, G) and connect them with bonds.
  3. Remove the last phosphate
  4. Go to 'Open structure' -> 'Paste from clipboard' (AG: Seems it is mol v3000 way)
  5. Type RNA:ACG
  6. Save to mol file
  7. Open this file in another sketcher

Actual behavior Sequences look different. The one, that was created on canvas, has explicit living groups connected to the main sequence. Chemical structure is correct for both sequences.

Expected behavior Sequences should look the same. Leaving groups should be hidden inside Sgroup.

Screenshots image

Sequence_vs_preset_on_canvas_export_v3000.zip ketcher (24).zip

Desktop (please complete the following information):

Ketcher version [e.g. v2.4.2]. Version 2.18.0-rc.2 Indigo Toolkit Version 1.18.0-rc.3.0-ge65b5cde3-wasm32-wasm-clang-12.0.0

Zhirnoff commented 8 months ago

@even1024 When exporting a single chain on canvas to external editor, everything appears normal, and hydrogens are not shown. However, when exporting two chains, they overlap, and one of the chains displays hydrogens. Additionally, when saving in mol V3000 format, SEQID is not assigned to the second structure. 2024-02-01_20h51_43

https://github.com/epam/Indigo/assets/62464241/209afe71-a85a-4eb5-b720-9a7d73c93de2

File saved in Ketcher: structure.zip File saved in external editor: ExternalEditor.zip

AlexeyGirin commented 8 months ago

MOved to RC7 since we decided to release RC6 today because it has all features for Query Features Phase II done and remained tasks (Macromolecules) definitely out of scope

Zhirnoff commented 7 months ago

As I wrote above when exporting two chains, they overlap each other. This behavior has not been fixed.

https://github.com/epam/Indigo/assets/62464241/1ade8a6a-2bad-4eac-bb41-246f57709369

files.zip

AlexeyGirin commented 6 months ago

Not fully fixed. Actual behavior System creates mol file with RNAs stacked in one image

Expected behavior System creates mol file with one RNA above other image

AlexeyGirin commented 6 months ago

Non fixed part moved to https://github.com/epam/Indigo/issues/1877