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Macro: Ket file does not include atom numbers associated with the leaving groups after saving #3691

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Zhirnoff opened this issue Dec 13, 2023 · 2 comments · Fixed by #3699
Closed

Macro: Ket file does not include atom numbers associated with the leaving groups after saving #3691

Zhirnoff opened this issue Dec 13, 2023 · 2 comments · Fixed by #3699
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@AlexeyGirin
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bug Macromolecules Priority: High
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Macromolecules Mi...

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@Zhirnoff
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Zhirnoff commented Dec 13, 2023 •
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Steps to Reproduce

  1. Switch to Macro mode
  2. Add any monomer on canvas
  3. Save structure in Ket format.
  4. Open saved Ket file and inspect the content of 'attachmentPoints'->'leavingGroup'->'atoms'

Actual behavior
When opening the Ket file, leaving groups information not correctly represented.
Leaving group atom numbers are missing.

2023-12-12_23h02_44

Also r-groups (rg-label) are indicated in the 'atoms' block
2023-12-13_14h24_53

Expected behavior
The Ket file should accurately represent leaving groups.
The leaving group atom should be specified.

2023-12-12_23h02_24

In the 'atoms' block, all r-groups should be replaced with H or O atoms

Desktop (please complete the following information):

  • OS: Windows 10
  • Browser Chrome
  • Version 112.0.5615.138 (Official Build) (64-bit)

Ketcher version
Version 2.17.0-rc.1
@Zhirnoff Zhirnoff added this to the Macromolecules Milestone 4 milestone Dec 13, 2023
@Zhirnoff Zhirnoff changed the title Macro: Missing living groups in Ket format after saving Macro: Ket file does not include atom numbers associated with the living groups after saving Dec 13, 2023
@Zhirnoff Zhirnoff changed the title Macro: Ket file does not include atom numbers associated with the living groups after saving Macro: Ket file does not include atom numbers associated with the leaving groups after saving Dec 13, 2023
@rrodionov91 rrodionov91 linked a pull request Dec 14, 2023 that will close this issue
Macro: #3691 - Ket file does not include atom numbers associated with the leaving groups after saving #3699
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@Zhirnoff
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Manual and autotest added

rrodionov91 added a commit that referenced this issue Dec 18, 2023
@rrodionov91 @Nitvex
Macro: #3691 - Ket file does not include atom numbers associated with…
d8277cf 
… the leaving groups after saving (#3699)

* fixed attachment points and leaving groups serializing/parsing in ket
* removed naturalAnalogCode property for CHEM-monomers from ket-format
* updated indigo version to 1.17.0-rc.3

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Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
Co-authored-by: Nikita_Vozisov <Nikita_Vozisov@epam.com>
@AlexeyGirin AlexeyGirin mentioned this issue Dec 20, 2023
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@AlexeyGirin
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Verified.

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@AlexeyGirin AlexeyGirin

Labels
bug Macromolecules Priority: High
Projects
Macromolecules Milestone 3
Status: Done
Milestone
Macromolecules Milestone 3
3 participants
@rrodionov91 @AlexeyGirin @Zhirnoff