epam / epam/Indigo

No hydrogens for aromatic bonds as expected

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Hydrogens Priority: Low
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

**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](https://github.com/epam/Indigo/files/13968715/Unable.to.add.hydrogens.for.aromatic.bonds.outside.the.ring.-.system.throws.exception.zip) (unzip first)
2. Press Add/Remove explicit hydrogens button
![image](https://github.com/epam/Indigo/assets/26869421/5d4f119f-b7dc-4b0a-aff8-3ad7444097dd)

**Actual behavior:**
Some hydrogens are missing
![image](https://github.com/epam/Indigo/assets/26869421/3401fd60-41f2-4e7a-a1b2-f7270395f768)

**Expected behavior:**
![image](https://github.com/epam/Indigo/assets/26869421/1aeabf66-9211-40ee-a41f-ffc4822eaf4a)

**Versions:**
Windows 10
Chrome Version Version 123.0.6312.106 (Official Build) (64-bit)
Ketcher Version 2.21.0-rc.1 Build at 2024-04-15; 20:00:15
Indigo Toolkit Version 1.20.0-rc.1.0-g8e8ffc3c3-wasm32-wasm-clang-12.0.0

Contributor guide

No contributing guide indexed for this repository

Research direction

Unpack the attached reproduction archive and load it in the reported Ketcher/Indigo versions, then use the Add/Remove explicit hydrogens button to reproduce the exception and missing hydrogens. Trace the aromatic-bond hydrogen handling from that entry point; done means the sample processes without an exception and produces the expected hydrogens.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, wasm
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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