R pseudoatom is replaced with R# (RGroup) after saving in Extended SMILES and CML formats.
- Dominant language
- C++
- Stars
- 406
- Forks
- 134
- Avg merge
- 2d 11h
- Merged PRs (30d)
- 24
Description
**Steps to reproduce**
1. Create any structure, for example, chain.
2. Click Periodic table.
3. Open Extended tab.
4. Click the "R" button in the Special nodes section, click the OK button and click any structure atom.
5. Click "Save as" button. Select Extended SMILE format. Click OK.
6. Clear the canvas.
7. Open the structure saved at 5th step.
**Actual result**
The R pseudoatom is replaced with R#.

If user clicks R# with Selection Tool R-Group window is opened. If user clicks Check Structure, the window contains the information "R-Groups warning: Structure contains RGroup components".

**Expected result**
R should stay R pseudoatom after saving in Extended SMILE and should not became RGroup.
The same problem is when user saves the structure in CML-format.
Contributor guide
No contributing guide indexed for this repository
Research direction
Reproduce the issue using the listed canvas steps, then inspect the Extended SMILES and CML save/load paths for pseudoatom handling. Compare the saved and reopened structures; done means an R pseudoatom remains R in both formats and does not trigger R-Group behavior or warnings.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100