epam / epam/Indigo

How does one collapse certain groups on a molecule, such as CF3?

Open
#1,805 1 comment 0 reactions 0 assignees View on GitHub
Priority: Medium Severity: Medium User`s Feedback
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

**Steps to Reproduce**
1. Use Indigo library version 1.18 in VB.Net environment, installed through NuGet;
2. Use a MolFile that contains a trifluoromethyl group such as TFA as indigo.loadMolecule();
3. Try to set rendering option 'render-superatom-mode'

**Expected behavior**
Expected to see CF3 as a collapsed group instead of CFFF, with a further possibility to selectively explode/collapse certain groups in a molecule discretely, such as R-NO2. Phenyl groups should not be collapsed into Ph but should retain their ring structure.

**Actual behavior**
'render-superatom-mode' not found as a rendering option;

**Environment details:**
Visual Studio Professional 2022, ver.17.9.2
Microsoft Windows 10 Pro, x64

**Attachments**
![Untitled](https://github.com/epam/Indigo/assets/163270436/2df011ec-8ae0-4c90-a6a9-30ce8e03454c)

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by inspecting Indigo's rendering-option handling and the indigo.loadMolecule() path for MolFile superatoms such as CF3. Check how render-superatom-mode is exposed in Indigo 1.18 and how selective collapse or expansion could preserve phenyl rings. Done means the option is available in the VB.Net environment and the requested groups render collapsed or expanded as specified.

Written by the indexing model from the issue text.

Assessment

Tech stack
visualbasic
Domain
computer-graphics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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