Clean Up function is applied to the unselected part within Superatom S-Group

**Description:**
In the opened clean2.mol file when a user selects the chain part and applies Clean Up function to it, the unselected part within Superatom S-Group is cleaned up too.
But when a user selects the part within Superatom S-Group and applies Clean Up function to it, the part within Superatom S-Group is not cleaned up.
The issue was discussed with Alexander Savelyev.

**Steps to reproduce:**
1) Open the clean2.mol file.
2) Distort the structure in the different parts.
3) Select the chain part of structure.
4) Click the Clean Up button.
5) Click Undo.
6) Select the part within within Superatom S-Group.
7) Click the Clean Up button.

**Actual result:**
The unselected part within Superatom S-Group is cleaned up at the same time as the selected chain part is cleaned up.
The part within Superatom S-Group is not cleaned up when it is selected.

**Expected result:**
Only the selected chain part is cleaned up.
The part within Superatom S-Group is cleaned up when it is selected.