epam / epam/Indigo

AxoLabs: incorrect auto‑pairing / hydrogen bonds for complementary sequences

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

Description

**Source task:**
https://github.com/epam/Indigo/issues/3250

**Preconditions:**

Macromolecules mode enabled.
Paste from clipboard, format = AxoLabs.

**Steps to reproduce (case 1):**

1. Open Paste from clipboard.
2. Paste:
```
5'-AAAp-3'
5'-UUUp-3'
```
3. Add to canvas.

**Actual behavior**
Image

**Expected behavior**
Image

**Steps to reproduce (case 2):**

1. Open Paste from clipboard.
2. Paste:
```
5'-GCUA-3'
5'-CGAU-3'
```
3. Add to canvas.

**Actual behavior**
Image

**Expected behavior**
Image

**Environment details:**
- OS: MacOs Tahoe version 26.2
- Browser Chrome Version 143.0.7499.170
- Version Ketcher 3.12.0-rc.1
- Version Indigo 1.40.0-rc.1.0-g63d8f2068-wasm32-wasm-clang-19.0.0

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce both cases through Paste from clipboard in Macromolecules mode using the AxoLabs inputs shown. Trace the AxoLabs parsing and complementary-sequence auto-pairing path; done means both examples produce the expected pairing and hydrogen-bond structures in Ketcher.

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
38/100

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