epam / epam/Indigo

System doesn't calculate melting temperature for unsplit nucleotides if they are more then two

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Priority: Medium Severity: Medium
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

**Steps to Reproduce**
1. Go to Macromolecules mode - Flex canvas (empty)
2. Load from HELM: `RNA1{[2-damdA].[5hMedC].[Super-G].[AmMC6T].[Super-T].[5Br-dU]}|RNA2{[2-damdA].[2-damdA].[2-damdA].[5hMedC].[Super-G].[5Br-dU]}$RNA2,RNA1,6:pair-1:pair|RNA2,RNA1,5:pair-2:pair|RNA2,RNA1,4:pair-3:pair|RNA2,RNA1,3:pair-4:pair|RNA2,RNA1,2:pair-5:pair|RNA2,RNA1,1:pair-6:pair$$$V2.0`
![Image](https://github.com/user-attachments/assets/bd820f45-fd99-414d-a58f-9b1cbf139873)
3. Open Calculate properties (press `Alt+C`) and go to RNA/DNA tab

**Actual behavior**
Melting temperature is absent
![Image](https://github.com/user-attachments/assets/1cf58fa3-880c-4d3c-9a9a-69b523302786)

**Expected behavior**
Melting temperature is `35.9`
![Image](https://github.com/user-attachments/assets/2e8de458-72e1-432b-b66b-2d2a853f263d)
AC=10
CG=10
GT=10
TT=5
TU=5
SP (strength parameter per base) = 8 ( sum of pair strength (40) divide by number of pairs (5))
L (length of nucleotide sequence) = 6
UPC = 0,14 M
NAC = 0,2 M

Melting temperature = `7,35 * 8+LN(17,34 * 6)+LN(4,96 * 0,14)+LN(0,89 * 0,2)-25,42` = `35,9340966`

As per [requirement](https://github.com/epam/Indigo/issues/2552):

> 3. The equation for the melting temperature is as follows:
> Tm [°C] = 7,35 * SP + 17,34 * ln(L) + 4,96 * ln(UPC) + 0,89 * ln(NAC) - 25,42

**Environment details:**
- Ketcher Version 3.4.0-rc.3 Build at 2025-05-15; 19:51:50
- Indigo Version 1.32.0-rc.2.0-g94ab270bd-wasm32-wasm-clang-19.0.0
- Chrome Version 136.0.7103.93 (Official Build) (64-bit)
- Win10

Found while testing: https://github.com/epam/ketcher/issues/5727

Contributor guide

No contributing guide indexed for this repository

Research direction

No source files or tests are named. Reproduce the HELM example in Macromolecules mode, open Calculate properties on the RNA/DNA tab, and trace the melting-temperature calculation for unsplit nucleotides; done means the reported value is 35.9°C and matches the stated equation.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, wasm
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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