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Aromatic bonds are replaces with double bonds or disappear from structure after saving in inchi and inchi auxinfo-formats. #32

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AlexanderSavelyev opened this issue Sep 7, 2020 · 1 comment
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@AlexanderSavelyev
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Steps to reproduce:

  1. Launch Editor.
  2. Create any structure, for example, chain.
  3. Replace any of the structure bond with aromatic bond.
  4. Click "Save as..." button.
  5. Select inchi format. Click "Save to file".
  6. Click "Save as..." button.
  7. Select inchi auxinfo format. Click "Save to file".
  8. Clear the canvas.
  9. Open saved at 5 and 7 steps structures one by one.

Actual result:
Aromatic bond is replaced with double bond:
image

Scenario 2:
Steps to reproduce:

  1. Launch Editor.
  2. Create any structure, for example, chain.
  3. Replace neighborhood structure bonds through one with double bond.
  4. Replace the bond between double bonds with aromatic bond.
  5. Click "Save as..." button.
  6. Select inchi format. Click "Save to file".
  7. Click "Save as..." button.
  8. Select inchi auxinfo format. Click "Save to file".
  9. Clear the canvas.
  10. Open saved at 6 and 8 steps structures one by one.

Actual result:
The aromatic bond disappears from the structure.
image

@AlexanderSavelyev AlexanderSavelyev added this to To do in Ketcher Sep 7, 2020
@ensemenova ensemenova self-assigned this Jan 13, 2021
@ensemenova ensemenova moved this from To do to In progress in Ketcher Jan 13, 2021
@ensemenova
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ensemenova commented Jan 13, 2021

According to https://www.inchi-trust.org/technical-faq-2/ there is a format limitation on storing aromatic bonds in InChI

16.3. Are there any technical limitations for InChI input?
...
3. Allowed bond types are single, double, and triple. As an exception, “aromatic bonds” are also allowed only to be immediately converted into alternating single/double bonds by the InChI Software. Since this conversion is not bulletproof at all (partially because a formal definition of aromatic bonds accepted by everybody does not exist) the use of aromatic bonds is strongly discouraged.

Agreed with @AlexanderSavelyev on closing the issue

@ensemenova ensemenova moved this from In progress to Done in Ketcher Jan 19, 2021
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