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Dearomatization causes exception in case of Implicit H count query feature set to 4 (i.e. more than 2) #1478

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AlexeyGirin opened this issue Jan 4, 2024 · 5 comments · Fixed by #1570
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Dearomatization causes exception in case of Implicit H count query feature set to 4 (i.e. more than 2) #1478

AlexeyGirin opened this issue Jan 4, 2024 · 5 comments · Fixed by #1570
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Priority: High query features phase II
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Indigo-1.18.0-rc.4

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AlexeyGirin commented Jan 4, 2024 •
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Environment details (please complete the following information):

Describe the bug
Dearomatization causes exception in case of Implicit H count query feature set to 4 (i.e. more than 2)

Steps to Reproduce

  1. Load from file: Implicit H 4 (2).zip
  2. Press Dearomatize button (Ctrl+Alt+A)

Actual behavior
System throws exception:
Error Message
IndigoException: dearomatization: Dearomatization groups: atom_aromatic_connectivity < 0 on C having 6 drawn bonds, charge 0, and 0 radical electrons

Expected behavior
Exception don't happen
image
@AlexeyGirin AlexeyGirin added this to the Query Features - Phase II milestone Jan 4, 2024
@AlexeyGirin AlexeyGirin mentioned this issue Jan 5, 2024
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AlexeyGirin commented Jan 9, 2024 •
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Confirmed as bug
It must not dearmatize in that case (i.e. 4 and more)

TEST TWO ring case!

AliaksandrDziarkach added a commit that referenced this issue Jan 16, 2024
@AliaksandrDziarkach
#1478 Dearomatization causes exception in case of Implicit H count q…
5002ec1 
…uery feature set to 4 (i.e. more than 2)

Remove exception. Add UT
@AliaksandrDziarkach AliaksandrDziarkach self-assigned this Jan 16, 2024
@AliaksandrDziarkach AliaksandrDziarkach linked a pull request Jan 16, 2024 that will close this issue
#1478 Dearomatization causes exception in case of Implicit H count query feature set to 4 (i.e. more than 2) #1570
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AliaksandrDziarkach added a commit that referenced this issue Jan 17, 2024
@AliaksandrDziarkach
#1478 Dearomatization causes exception in case of Implicit H count q…
c661f9d 
…uery feature set to 4 (i.e. more than 2) (#1570)
AliaksandrDziarkach added a commit that referenced this issue Jan 17, 2024
@AliaksandrDziarkach
Backmerge: #1478 Dearomatization causes exception in case of Implicit…
9af5f13 
… H count query feature set to 4 (i.e. more than 2)

Backmerge by cherry-pick
AliaksandrDziarkach added a commit that referenced this issue Jan 17, 2024
@AliaksandrDziarkach
Backmerge: #1478 Dearomatization causes exception in case of Implicit…
235e5b4 
… H count query feature set to 4 (i.e. more than 2)

Fix UT
AlexanderSavelyev pushed a commit that referenced this issue Jan 22, 2024
@AliaksandrDziarkach
Backmerge: #1478 Dearomatization causes exception in case of Implicit…
e561c41 
… H count query feature set to 4 (i.e. more than 2) (#1583)
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AlexeyGirin commented Jan 29, 2024 •
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Not fixed.
Dearomatization simply clean up Implicit H value but not dearomatize the molecule.
More over - it seems that Implicit H value set on already aromatized ring is the different the same set on non-aromatized ring (it doesn't visible on the canvas, for example)

@AlexeyGirin AlexeyGirin reopened this Jan 29, 2024
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AliaksandrDziarkach commented Feb 5, 2024 •
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Expected behavior
Exception don't happen

Exception issue fixed.
If you found other issues - please fill separate corresponding bugs.

@AliaksandrDziarkach AliaksandrDziarkach removed their assignment Feb 5, 2024
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AlexeyGirin commented Feb 6, 2024 •
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If you found other issues - please fill separate corresponding bugs.

:-)))))

Moved to #1666

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AlexeyGirin commented Feb 6, 2024 •
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Fixed. No exception

  • Ketcher Version 2.18.0-rc.4 Build at 2024-02-06; 13:45:28
  • Indigo Toolkit Version 1.18.0-rc.6.0-g98bf384e0-x86_64-linux-gnu-11.2.1

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Priority: High query features phase II
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@AliaksandrDziarkach @vanoprenko @AlexeyGirin