epam / epam/Indigo

Ketcher does not produce correct SMARTS with atom lists in aromatic rings

Open
#3,713 3 comments 0 reactions 0 assignees View on GitHub
Export to SMARTS Priority: High User`s Feedback
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

**Steps to Reproduce**
1. Go to https://lifescience.opensource.epam.com/KetcherDemo/index.html?api_path=/v2
2. Sketch benzene ring
3. Aromatize
4. Click Periodic Table
5. Click list
6. Click C and N
7. Put list on three atoms
8. Click save
9. Choose SMARTS

**Actual behavior**
`[#6,#7;h0]1:[#6,#7;h0]:[#6,#7;h0]:[#6]:[#6]:[#6]:1`

**Expected behavior**
`[#6,#7]1:[#6,#7]:[#6,#7]:[#6]:[#6]:[#6]:1`

or at least with correct operator precedence

`[#6,#7&h0]1:[#6,#7&h0]:[#6,#7&h0]:[#6]:[#6]:[#6]:1`

**Screenshots**
Screenshot 2024-11-08 at 10 20 50

**Desktop (please complete the following information):**
- OS: macOS 14.6.1
- Browser: Chrome
- Version: 130.0.6723.117 arm64

**Ketcher version** [e.g. v2.4.2].
Your own demo. Version 2.25.0

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce the issue from the KetcherDemo URL using the listed benzene, aromatization, atom-list, and SMARTS-save steps. Start by tracing the SMARTS output for aromatic atom lists and verify completion when the result matches the expected operator precedence and no longer adds h0 incorrectly.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
42/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.