epam / epam/Indigo

Exported string chosen for circular backbone is not first alphabetically

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BILN Priority: Low Severity: Low
Dominant language
C++
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Forks
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Avg merge
2d 11h
Merged PRs (30d)
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Description

Found while testing #3541

Note: after fixing this issue, requirement 2.1 of the Export section with the provided examples in https://github.com/epam/Indigo/issues/3541 should be re-tested.

**Steps to Reproduce:**

1. Open Macromolecules - Flex mode (clean canvas)
2. Paste the following HELM string from the clipboard: `PEPTIDE1{C.[Tza].A.A.[Tza]}|PEPTIDE2{[aIle].[Abu].[dE].[Bip]}$PEPTIDE2,PEPTIDE1,3:R3-1:R3|PEPTIDE1,PEPTIDE1,1:R1-5:R2|PEPTIDE2,PEPTIDE2,1:R1-4:R2$$$V2.0`
3. Click `Open as New` or `Add to Canvas` button
4. Click `Save as` button
5. Select BILN as the file format

**Actual Result:**
Strings chosen for circular backbones are not first alphabetically: `C-Tza-A-A-Tza` and `aIle-Abu-dE-Bip`

Image

**Expected Result:**
Strings chosen for the circular backbones are first alphabetically.
`A-A-Tza-C-Tza` is the first alphabetically (two 'a's), and `Abu-dE-Bib-alle` is the first alphabetically ('ab'). So the BILN string is `A(1,2)-A-Tza-C(2,3)-Tza(1,1).Abu(3,1)-dE(2,3)-Bip-alle(3,2)`

As per Req:
Image

**Found in Environment:**

- Ketcher Version 3.17.0-rc.1 Build at 2026-06-02; 21:27:10
- Indigo Version 1.45.0-rc.2.0-g168fb85f2-wasm32-wasm-clang-23.0.0
- Chrome Version 149.0.7827.156 (Official Build) (64-bit)
- Win11

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the issue in Macromolecules Flex mode with the provided HELM string, then export it as BILN and compare the circular-backbone ordering with the expected string. Re-test requirement 2.1 and the examples in issue #3541; done means both circular backbones use their alphabetically first representation.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
52/100

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