epam / epam/Indigo

Monomers with hyphens in names are loaded incorrectly

Open
#3,749 0 comments 0 reactions 0 assignees View on GitHub
BILN Priority: High Severity: High
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

Found while testing #3541

**Steps to Reproduce:**

1. Open Macromolecules - Flex mode (clean canvas)
2. Paste the following BILN string from the clipboard: `[D-2Thi]-[D-gGlu]-[Lys-al]`
3. Click `Open as New` or `Add to Canvas` button

**Actual Result:**
System treats hyphens within the square brackets as monomer connections and loads 6 monomers with incorrect names instead of 3 monomers that contain hyphens in their names

Image

**Expected Result:**
The system should correctly interpret monomer names containing hyphens and load three monomers with the names: `D-2Thi`,` D-gGlu`, and `Lys-al`
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 BILN input [D-2Thi]-[D-gGlu]-[Lys-al] in Macromolecules Flex mode using Open as New or Add to Canvas, then trace the BILN loading path in Indigo. Add a regression test showing that the input produces three monomers with hyphens in their names rather than six connected monomers.

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
68/100

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