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Unable to add hydrogens for aromatic bonds outside the ring - system throws exception

Open AlexeyGirin opened this issue 1 year ago • 6 comments

Environment details (please complete the following information):

  • Indigo Toolkit Version 1.18.0-rc.3.0-ge65b5cde3-x86_64-linux-gnu-11.2.1
  • Ketcher Version 2.18.0-rc.2 Build at 2024-01-17; 16:42:55
  • Chrome Version 120.0.6099.130 (Official Build) (64-bit)
  • Win10
  • Issue found while testing https://github.com/epam/Indigo/issues/1436

Describe the bug Unable to add hydrogens for aromatic bonds outside the ring - system throws exception

Steps to Reproduce

  1. Load from file: Unable to add hydrogens for aromatic bonds outside the ring - system throws exception.zip (unzip first)
  2. Press Add/Remove explicit hydrogens button image

Actual behavior System throws exception: IndigoException: element: can not calculate implicit hydrogens on aromatic C, charge 0, degree 1, 0 radical electrons image image uat.test.lifescience.opensource.epam.com-1705525259112.log

Expected behavior image

AlexeyGirin avatar Jan 17 '24 21:01 AlexeyGirin

This is not query related issue. If you add 'aromatic' for any atom to use query molecule mode you can see that it will work

AliaksandrDziarkach avatar Jan 17 '24 21:01 AliaksandrDziarkach

I have no idea why "aromatic" bond placed in query bonds in ketcher. This is just a normal bond like single/double/triple. For example: if you add cyclohexane and change all bonds to aromatic - after change last bond to aromatic it will be re-drawn as aromatic benzene.

AliaksandrDziarkach avatar Jan 17 '24 21:01 AliaksandrDziarkach

Should not throw exceptopn

AlexeyGirin avatar Jan 22 '24 15:01 AlexeyGirin

No exception now - good, but works wrong (Version 1.18.0-rc.5.0-gb21ab5ad5-wasm32-wasm-clang-12.0.0) Actual behavior: image

Expected behavior: image

AlexeyGirin avatar Jan 29 '24 12:01 AlexeyGirin

MOved to RC7 as per @vanoprenko decision

AlexeyGirin avatar Feb 05 '24 10:02 AlexeyGirin

MOved to 1.19 as per @vanoprenko decision

AlexeyGirin avatar Feb 06 '24 10:02 AlexeyGirin

MOved to https://github.com/epam/Indigo/issues/1915

AlexeyGirin avatar Apr 16 '24 12:04 AlexeyGirin