Macro: Support of unsplit nucleotides

[olganaz]

Background
In some cases there is no need to divide modified nucleotides to submonomers (sugar, base, phosphate). Such nucleotides should be supported as single monomers.

Requirements

1. Unsplit nucleotides are nucleotides which have chemical structure, but submonomers (sugar, base, phosphate) are not specified

2. Additional chapter 'Nucleotides' should be introduced in a RNA tab of Ketcher library

3. Unsplit nucleotides should have base natural analog

4. Unsplit nucleotides should be grouped by natural analog in a library.
   - Nucleotides, for which a natural analogue is not specified, should be grouped in a separate section in a library ("No natural analogue")

5. Unsplit nucleotides should not interrupt enumeration of RNA chain in flex mode

6. Unsplit nucleotides should be displayed:

   • in flex/snake modes - as a pentagon with name (see mockups)
   • in sequence view - as natural analog symbol if it's specified, otherwise - as '@' symbol

7. On preview chemical structure together with name and IDT alias should be displayed.

8. Establishing connections between unsplit nucleotides should be performed as for peptide monomers (center-to-center, center-to-point , point-to-center, point-to-point).

Examples
Unsplit_nucleotides.zip
iAmMC6T.zip - has 4 AP

IDT name	Full name	Natural analog
/5Super-dG/	5' Super G	G
/55Br-dU/	5' 5-Bromo dU	U
/5Super-dT/	5' Super T	T
/55HydMe-dC/	5' 5-Hydroxymethyl dC	C
/55NitInd/	5' 5-Nitroindole	X
/5AmdA/	5' 2, 6-Diaminopurine	A
/iAmMC6T/	Int Amino Modifier C6 dT	T

UX

[olganaz]

Attached files with examples suitable for testing

[AlexeyGirin]

Unsplit nucleotides is a new entity, it's like CHEMS, only different

Questions to @olganaz

1. Where are nucleotides located if they do not have a natural analogue? (we sort them by it). - X group?
2. How do you understand that a nucleotide does not have a natural analogue? - no grouping in the library
3. Displaying Unsplit nucleotides as ordinary nucleotides in sequence mode is not very convenient - mixing two different entities - do we really want this?

[olganaz]

1. Added the requirement
2. separate group in library
3. TBC

[Zhirnoff]

Tested.
We have many bugs described above
Desktop:

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

Ketcher version
[Version 2.23.0-rc.1]
Indigo version
[Version 1.22.0-rc.1]