epam / epam/Indigo

Using bond type 8 results in removal of implicit hydrogens from the whole molecule in png

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

Description

**Steps to Reproduce**
1. Open the attached molfile
[ketcher_2.txt](https://github.com/epam/ketcher/files/9943302/ketcher_2.txt)
2. Click on 'save as png'
3. See missing hydrogens of the CH3-group (as an example)

**Expected behavior**
groups/atoms that are not involved in the bond formation including bond type 8 should have implicit hydrogens given in the png (as it is expected from the ketcher editor - see attached screenshot
![Screenshot (123)](https://user-images.githubusercontent.com/7559189/200109711-5e3b2f9a-ca1b-4acf-a484-c362061beb3d.png)
)

**Actual behavior**
Currently, the implicit hydrogens are removed in the png
![image](https://github.com/epam/Indigo/assets/26869421/de84b007-f9b6-45f2-b74b-7982185a8a70)

Behavior is platform independent

Linked to https://github.com/epam/ketcher/issues/4539

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by opening the attached molfile and reproducing the issue through the “save as png” flow; the payload names no source files or tests. Trace PNG rendering and implicit-hydrogen handling for bond type 8, then verify that unrelated groups such as the CH3 group retain their hydrogens in the generated image.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
computer-graphics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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