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epam / ketcher

Web-based molecule sketcher
https://lifescience.opensource.epam.com/ketcher/demo.html
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Aromatization of 5-membered, nitrogen-containing aromatic rings results in invalid SMILES #4566

Closed gio-hlx closed 4 months ago

gio-hlx commented 6 months ago

Steps to Reproduce

  1. Draw a 5-membered, nitrogen-containing aromatic ring (e.g. pyrrole, indole, etc.).
  2. Click on the aromatization button
  3. Look at the represented molecule structure and especially the generated SMILES string.

Actual behavior The molecule is converted from the kekule to the aromatic representation but the H atom connected to the aromatic N is removed (e.g. pyrrole: “C1NC=CC=1” -> “c1cccn1”)

Expected behavior The molecule is converted from the kekule to the aromatic representation keeping the hydrogen atom connected to the aromatic nitrogen (e.g. pyrrole: “C1NC=CC=1” -> “c1ccc[nH]1”)

Screenshots See screenshot of pyrrole case where the hydrogen atom attached to the aromatic nitrogen is removed generating an invalid SMILES.

pyrrole_kekule pyrrole_aromatic

Ketcher version Ketcher 2.7.2

Additional context I’m using Ketcher 2.7.2 integrated in the “Molecule Widget (Labs)” node from KNIME. I’ve noticed this problem during the aromatisation of common heteroaromatic molecules containing 5-membered aromatic rings with N (e.g. pyrrole, indole, etc.). The generated SMILES (and the corresponding molecular structures) are not valid and cannot be parsed by and used in other molecular tools (e.g. RDKit).

AlexeyGirin commented 4 months ago

Hi @gio-hlx ! Thanks for your report.

It seems that issue you describe is already fixed in the latest releases. Please consider Ketcher version update (to 2.21 at least) image

rrodionov91 commented 4 months ago

[heart] Roman Rodionov reacted to your message:

From: Alexey Girin @.> Sent: Thursday, July 4, 2024 9:02:08 PM To: epam/ketcher @.> Cc: Subscribed @.***> Subject: Re: [epam/ketcher] Aromatization of 5-membered, nitrogen-containing aromatic rings results in invalid SMILES (Issue #4566)

Hi @gio-hlxhttps://urldefense.com/v3/__https://github.com/gio-hlx__;!!GF_29dbcQIUBPA!xcelVGkfjyqeovqEACRqvMM5NUqHi3eRqwmoHuMualLTTyaGjTWK9fLA9nfvVmD03PiYrnsUlAyGSsqAMVf7K53fmA8$ ! Thanks for your report.

It seems that issue you describe is already fixed in the latest releases. Please consider Ketcher version update (to 2.21 at least) image.png (view on web)https://urldefense.com/v3/__https://github.com/epam/ketcher/assets/26869421/defd0d0d-6508-4ed2-8952-30add66e9499__;!!GF_29dbcQIUBPA!xcelVGkfjyqeovqEACRqvMM5NUqHi3eRqwmoHuMualLTTyaGjTWK9fLA9nfvVmD03PiYrnsUlAyGSsqAMVf7LuFH2zE$

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