epam / epam/Indigo

V3000 export loses emsc labels for peptide template attachment atoms

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#3,667 0 comments 0 reactions 1 assignee Claimed by @even1024 View on GitHub
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Description

**Summary**
When a peptide MOL V3000 file is loaded into Ketcher and exported back to MOL V3000, template attachment/leaving atom labels are lost.

**Steps to Reproduce**
1. Open the attached input MOL V3000 file in Ketcher.
2. Export the structure as MOL V3000.
3. Compare the exported file with the attached expected MOL V3000 file.

**Actual behavior**
Template attachment/leaving atom labels are missing in the exported MOL V3000 file.

Example:

```diff
- M V30 6 emsc 1.59031 0.205733 0.0 0
+ M V30 6 1.59031 0.205733 0.0 0
```

**Expected behavior**
Peptide template attachment/leaving atoms inside V3000 `TEMPLATE` CTABs should be exported with the `emsc` label.

Example:

```mol
M V30 6 emsc 1.59031 0.205733 0.0 0
M V30 7 emsc -1.82323 0.0707134 0.0 0
```

**Environment details:**
- Back-end version: Indigo `release/1.44`
- Front-end version: Ketcher with Indigo `release/1.44`
- Indigo version: `1.44.0-dev.1.20-g6a192d848-x86_64-win-msvc-1940`
- OS version: Windows

**Attachments**
Input and expected MOL V3000 files are attached separately.

**Additional context**
The issue affects peptide `TEMPLATE` CTAB attachment/leaving atoms. These atoms should be treated as template placeholders and exported as `emsc`.

Molfile links:
- Input: https://github.com/epam/ketcher/blob/master/ketcher-autotests/tests/test-data/Molfiles-V3000/Chromium-popup/snake-mode-peptides-on-canvas.mol
- Expected: https://github.com/epam/ketcher/blob/master/ketcher-autotests/tests/test-data/Molfiles-V3000/Chromium-popup/snake-mode-peptides-on-canvas-expected.mol

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