#5481 - Ambiguous CHEM shown wrong at Sequence mode

[Copilot]

Problem

When loading ambiguous CHEM monomers from HELM notation (e.g., CHEM1{(A:10+C:50)}$$V2.0) in Sequence mode, the symbol was incorrectly displayed as % instead of @.

Before:

After:

Root Cause

The AmbiguousSequenceItemRenderer was always displaying the monomer's label property, which defaults to % for all ambiguous monomers. However, when an ambiguous monomer contains different monomer types, it is classified as CHEM (via AmbiguousMonomer.getMonomerClass()), and should display the same symbol as regular CHEM monomers: @.

Solution

Modified AmbiguousSequenceItemRenderer.ts to check the monomer's classification:

get symbolToDisplay(): string {
  // Ambiguous CHEM monomers should display @ symbol
  if (
    this.node.monomer instanceof AmbiguousMonomer &&
    this.node.monomer.monomerClass === KetMonomerClass.CHEM
  ) {
    return '@';
  }
  return this.node.monomer.label;
}

This ensures symbol consistency across all monomer types in Sequence mode:

• Regular CHEM monomers: @
• Ambiguous CHEM monomers: @ ✓ (fixed)
• Ambiguous peptide monomers: %
• Other monomer types: their respective symbols

Testing

• ✅ All existing unit tests pass (298+ tests)
• ✅ TypeScript compilation succeeds with proper type guards
• ✅ Build succeeds for all packages
• ✅ No breaking changes introduced

Fixes #4556

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Ambiguous CHEM shown wrong at Sequence mode</issue_title>
<issue_description>Steps to Reproduce

1. Toggle to Macromolecules canvas - Sequence mode
2. Load from HELM: CHEM1{(A:10+C:50)}$$$$V2.0

Actual behavior
Ambiguous CHEM is shown as % symbol on sequence canvas

Expected behavior
Ambiguous CHEM is shown as @ symbol on sequence canvas

As per @ljubica-milovic:

Versions

• Ketcher Version 2.25.0-rc.1 Build at 2024-09-03; 15:31:03
• Indigo Toolkit Version 1.24.0-rc.1.0-gb8f099851-wasm32-wasm-clang-19.0.0
• Chrome Version 128.0.6613.114 (Official Build) (64-bit)
• Win10

Reference issues: #4556
</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes #5481

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