Add the star atom (*) to the special nodes section of the extended table

[eloyfelix]

Background
It doesn't seem possible to add dummy (*) atoms in Ketcher. We would like to use Ketcher in the new ChEBI database development and this is an important feature since in ChEBI * and R groups, and A (any) atoms have a very defined meaning

Differenciating * from A is quite important for ChEBI since they have a meaning (related to the Ontology):
* = attaches to something (meaning it is a fragment)
R = something attaches here (meaning it is a core structure where a fragment will attach)
A = any single atom

Solution
button allowing the insertion of * atoms like MarvinJS has.

Requirements

1. The star atom should be added to the special nodes section of the extended table.

2. Tooltip text for hover over the box containing the star atom should read: "Any atom, including hydrogen".

3. The special nodes section of the extended table should be reorganized (see mockup).

4. Hotkey for adding the star atom is shift+8.

5. "Special atom" * should be added to the canvas the same way as all other special atoms.

Replace the existing atom with the star atom: r-click -> edit -> atom type: special -> open the extended table -> choose the star atom from the special nodes section -> add -> apply
Add the atom directly from the extended table on the sidebar: open the extended table -> choose the star atom from the special nodes section -> add to canvas
Add using a hotkey: shift+8 -> add to canvas

6. Export/import of structures with star atoms should be supported in KET format.

Support on the Indigo side: #2713.

UX

[AlexeyGirin]

Hi @eloyfelix
Thanks for your request.
Could you please provide some examples in different formats (SMILES, Mol etc) with such atom (please try to provide small molecules) and expected output on the canvas

[eloyfelix]

First example:

https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47265

molfile: ChEBI_47265.mol.zip
SMILES: Br*

It should show in canvas (see the selected button in MarvinJS in the image would be the expected functionality):

Second example:

https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:142521

molfile: ChEBI_142521.mol.zip
SMILES: [C@@]1(O[C@]([C@H](NC(=O)C)[C@H](C1)O)([C@@H]([C@H](O)CO)O)[H])(C(O)=O)O[C@H]2[C@H]([C@H](O[C@H]([C@@H]2O)*)CO)O[C@H]3[C@@H]([C@H]([C@@H](O)[C@H](O3)CO)O)NC(C)=O

Many thanks for looking into it!

[AlexeyGirin]

Meeting note: Considered as moderate to fix.
Preliminary milestone - 3.1

[eloyfelix]

Many thanks, @AlexeyGirin! I noticed there are no dates for the milestones. Do you have a rough idea of when this might happen? Even something like "sometime in 2025" would be helpful.

Thanks again for considering the feature.

[ljubica-milovic]

Hello, @eloyfelix!

Thank you again for your interest.

We will be adding the star/dummy atom in release 3.1. You can expect the final version of it in mid-March 2025 (with the beta version available a little sooner than that).

[eloyfelix]

Hi @ljubica-milovic!

Many thanks for implementing this feature - it's going to be really helpful for us!
Wishing you and the team a wonderful New Year 2025! 🎉

Best regards