Macro: RNA Builder allows creating an invalid preset with disconnected sugar

[olganaz]

RNA Builder allows user to select a sugar without R3 connection (e.g. '3SS6') while creating a new preset and save this preset in monomer library. If user further tries to add this preset to canvas, Uncaught ReferenceError: process is not defined error appears in browser console and the operation doesn't succeed.

Instead, RNA Builder should not allow using sugar, base or phosphate as a building block if corresponding monomer doesn't have connection point required for connecting with other monomers in the nucleotide. If user selects a monomer while RNA Builder is in editing mode, the following checks should be applied:

Action	Validation rule	Error message if violated
Select base	Base has R1 connection point	Base without R1 connection point cannot make nucleotide
Select base	If sugar is selected, it should have R3 connection point	Sugar without R3 connection point cannot make this nucleotide
Select sugar	If base is selected, sugar should have R3 connection point	Sugar without R3 connection point cannot make this nucleotide
Select phosphate	Phosphate has R1 connection point	Phosphate without R1 connection point cannot make nucleotide
Select phosphate	If sugar is selected, it should have R2 connection point	Sugar without R2 connection point cannot make this nucleotide
Select sugar	If phosphate is selected, sugar should have R2 connection point	Sugar without R2 connection point cannot make this nucleotide

A preset can only have the following structures:

• Sugar+Base
• Sugar+Phosphate
• Sugar+Base+Phosphate

If user validation rule is violated corresponding error should be shown in a pop-up error box and 'Save'/'Add to presets' button should be disabled

Ketcher version
[Version 2.17.0-rc.2]
Related issue: #3615

[ilya-asiyuk-epam]

Merged into 2.21 branch - #4721

[AlexeyGirin]

Not fixed.
I still able to create preset with 3SS6 sugar:

1. Open RNA builder
2. Click New Preset button
3. Select Phosphate (P in my case)
4. Select Base (A in my case)
5. Select 3SS6 sugar
   
6. Press Add to Presets button
   

• Indigo Toolkit Version 1.21.0-rc.1.0-g9194599b2-wasm32-wasm-clang-19.0.0
• Ketcher Version 2.22.0-rc.2 Build at 2024-06-03; 18:43:00
• Chrome Version 125.0.6422.142 (Official Build) (64-bit)
• Windows 10

[NataliaLoginova]

Alexey and I agreed that the task would be closed. An issue will be created for the case found by Alexey.

[NataliaLoginova]

Alexey Girin will create issue for the case that he found.

[Zhirnoff]

Tested. We still can create forbidden RNA preset. We have bug for it in 2.23 #4763
Desktop:

• OS: Windows 11
• Browser Chrome
• Version 124.0.6367.79 (Official Build) (64-bit)

Ketcher version
[Version 2.21.0-rc.3]
Indigo version
[Version 1.20.0-rc.3]