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Ketcher part: Save to mol for micro and macro structures connected through attachment points works wrong #4879

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AlexeyGirin opened this issue Jun 24, 2024 · 1 comment · Fixed by #4966, #4970 or #4971
Closed

Ketcher part: Save to mol for micro and macro structures connected through attachment points works wrong #4879

AlexeyGirin opened this issue Jun 24, 2024 · 1 comment · Fixed by #4966, #4970 or #4971
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@rrodionov91
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bug external Issue depends on external services such as Indigo service
Milestone
Ketcher 2.22.0-rc.8

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@AlexeyGirin
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AlexeyGirin commented Jun 24, 2024 •
edited by Zhirnoff
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Original issue was created in Indigo - epam/Indigo#1993
@even1024 told that he did his part and now it require Ketcher side change to be done.

Summary
Save to mol for micro and macro structures connected through attachment points works wrong

Steps to Reproduce

  1. Open Ketcher.
  2. Draw a benzene ring
  3. Add an attachment point to the benzene ring via right click menu
  4. Switch to Macro mode and connect attachment point to a macro structure
  5. Switch to Micro mode
  6. Save structure in MOL V2000 format
  7. Open saved file in micro mode

If it is not possible to draw the structure, then you can open the prepared file (you just need to open it in macro mode and then switch to micro mode):
ketcher (53).zip

Actual behavior
Resulted file is incorrect:
image

Expected behavior
image

Desktop (please complete the following information):

  • OS: Windows 11
  • Browser Chrome
  • Version 124.0.6367.79 (Official Build) (64-bit)

Ketcher version
[Version 2.22.0-rc.2]
Indigo version
[Version 1.21.0-rc.1]

Refers to feature: #4530
Issue on Indigo side: epam/Indigo#1991
Attached saved files:

ketcherCDXML (1).zip
@AlexeyGirin AlexeyGirin added this to the Ketcher 2.22.0-rc.8 milestone Jun 24, 2024
@AlexeyGirin AlexeyGirin added the external Issue depends on external services such as Indigo service label Jun 24, 2024
@AlexeyGirin AlexeyGirin mentioned this issue Jun 26, 2024
Closed
@rrodionov91 rrodionov91 self-assigned this Jul 2, 2024
rrodionov91 added a commit that referenced this issue Jul 2, 2024
@rrodionov91
#4879 - Ketcher part: Save to mol for micro and macro structures conn…
5888985 
…ected through attachment points works wrong

- added removing the leavingGroup atom from structure before serialisation if there is connection to monomer
@rrodionov91 rrodionov91 linked a pull request Jul 2, 2024 that will close this issue
#4879 - Ketcher part: Save to mol for micro and macro structures connected through attachment points works wrong #4966
Merged
9 tasks
rrodionov91 added a commit that referenced this issue Jul 3, 2024
@rrodionov91
Merge pull request #4966 from epam/4879-remove-leaving-group-during-c…
98d6c08 
…onversion-indigo-2.22

#4879 - Ketcher part: Save to mol for micro and macro structures connected through attachment points works wrong
rrodionov91 added a commit that referenced this issue Jul 3, 2024
@rrodionov91
#4879 - Ketcher part: Save to mol for micro and macro structures conn…
a5431fe 
…ected through attachment points works wrong

- added removing the leavingGroup atom from structure before serialisation if there is connection to monomer
@rrodionov91 rrodionov91 linked a pull request Jul 3, 2024 that will close this issue
Backmerge: #4879 - Ketcher part: Save to mol for micro and macro structures connected through attachment points works wrong #4970
Merged
9 tasks
rrodionov91 added a commit that referenced this issue Jul 3, 2024
@rrodionov91
#4879 - Ketcher part: Save to mol for micro and macro structures conn…
692f0c6 
…ected through attachment points works wrong

- added removing the leavingGroup atom from structure before serialisation if there is connection to monomer
@rrodionov91 rrodionov91 linked a pull request Jul 3, 2024 that will close this issue
Backmerge: #4879 - Ketcher part: Save to mol for micro and macro structures connected through attachment points works wrong #4971
Merged
9 tasks
rrodionov91 added a commit that referenced this issue Jul 4, 2024
@rrodionov91
Backmerge: #4879 - Ketcher part: Save to mol for micro and macro stru…
c1c36a4 
…ctures connected through attachment points works wrong (#4970)

- added removing the leavingGroup atom from structure before serialisation if there is connection to monomer

* #4973 - Connection between molecule and monomer lost after opening and saving to ket

- fixed monomer atoms ids mapping during struct clone
- fixed removeLeavingGroupsFromConnectedAtoms
rrodionov91 added a commit that referenced this issue Jul 4, 2024
@rrodionov91
Backmerge: #4879 - Ketcher part: Save to mol for micro and macro stru…
d994377 
…ctures connected through attachment points works wrong (#4971)

- added removing the leavingGroup atom from structure before serialisation if there is connection to monomer

* #4973 - Connection between molecule and monomer lost after opening and saving to ket

- fixed monomer atoms ids mapping during struct clone
- fixed removeLeavingGroupsFromConnectedAtoms
@AnnaKosol
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Verified (title AND Enantiomer is verified too)
Снимок экрана 2024-07-05 в 14 42 46

Versions:
Ketcher Version 2.22.0-rc.9 https://lifescience.opensource.epam.com/ketcher/index.html Build at 2024-07-04; 15:58:14
Indigo Version 1.21.0-rc.3.0-g1570d3f9f-wasm32-wasm-clang-19.0.0
MacOs Sonoma version 14.5
Chrome Version 126.0.6478.127 (Официальная сборка), (arm64)

accmeboot pushed a commit that referenced this issue Jul 5, 2024
@rrodionov91
Backmerge: #4879 - Ketcher part: Save to mol for micro and macro stru…
ba63adc 
…ctures connected through attachment points works wrong (#4971)

- added removing the leavingGroup atom from structure before serialisation if there is connection to monomer

* #4973 - Connection between molecule and monomer lost after opening and saving to ket

- fixed monomer atoms ids mapping during struct clone
- fixed removeLeavingGroupsFromConnectedAtoms
@AlexeyGirin AlexeyGirin mentioned this issue Jul 9, 2024
Closed
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bug external Issue depends on external services such as Indigo service
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Ketcher 2.22.0-rc.8
3 participants
@rrodionov91 @AlexeyGirin @AnnaKosol