epam / epam/Indigo

CHEMs cannot be imported; system treats them as amino acids

Open
#3,744 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

Note: after fixing this issue, requirement 4 of Import 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 BILN string from the clipboard: `EG-C-C-C-EG`
3. Click `Open as New` or `Add to Canvas` button

**Actual Result:**
CHEM `EG` is imported as an amino acid
Image

**Expected Result:**
CHEM `EG` is imported correctly as a CHEM
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 149.0.7827.103 (Official Build) (64-bit)
- Win11

Contributor guide

No contributing guide indexed for this repository

Research direction

Start at the BILN import path used by Macromolecules in Flex mode and reproduce the issue with `EG-C-C-C-EG`, checking how tokens are classified during `Open as New` or `Add to Canvas`. Done means `EG` is imported as a CHEM rather than an amino acid, and requirement 4 with the examples in issue #3541 passes when re-tested.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, wasm
Domain
tooling
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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