epam / epam/Indigo

Multiple backbones are exported in incorrect order

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BILN Priority: Low Severity: Low
Dominant language
C++
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406
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, requirements 2.2 and 2.2.1 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{D.D.D}|PEPTIDE2{C.C.C.C}|PEPTIDE3{A.A.A.A.A}|PEPTIDE4{F}|PEPTIDE5{E.E}$$$$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:**
Backbones are exported in the incorrect order: `D-D-D.C-C-C-C.A-A-A-A-A.F.E-E`
Image

**Expected Result:**
Backbones are exported in the correct order: `A-A-A-A-A.C-C-C-C.D-D-D.E-E.F`

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

Reproduce the issue in Macromolecules - Flex mode using the provided HELM string, then export it as BILN and trace the backbone ordering in the export path. Done means the output is A-A-A-A-A.C-C-C-C.D-D-D.E-E.F and the requirements 2.2 and 2.2.1 examples from issue #3541 pass on retest.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
55/100

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