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#6092 - Antisense creating doesn't work if ambiguous peptide present in the chain selection#9563

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6092-antisense-creating-doesn't-work-if-ambiguous-peptide-present-in-the-chain-selection
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#6092 - Antisense creating doesn't work if ambiguous peptide present in the chain selection#9563
mariam-khutuashvili wants to merge 3 commits intomasterfrom
6092-antisense-creating-doesn't-work-if-ambiguous-peptide-present-in-the-chain-selection

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@mariam-khutuashvili mariam-khutuashvili commented Mar 27, 2026 •
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  • Fix TypeError: Cannot read properties of undefined (reading 'map') crash when clicking "Create Antisense Strand" with an ambiguous peptide connected to an RNA chain
  • Root cause: in createAntisenseChain(), non-RNA nodes are cloned via this.addMonomer(monomer.monomerItem, ...). For AmbiguousMonomer, monomer.monomerItem is a synthetic MonomerItemType from the BaseMonomer super() call — it has isAmbiguous: true but no monomers array. When addMonomer detects isAmbiguous, it calls new AmbiguousMonomer(syntheticItem), whose constructor calls getAttachmentPoints(syntheticItem.monomers) → undefined.map() → crash
  • Fix: use monomer.variantMonomerItem (the real ambiguous template with the monomers array) instead of the synthetic monomerItem when the monomer is an AmbiguousMonomer

Check list

  • unit-tests written
  • e2e-tests written
  • documentation updated
  • PR name follows the pattern #1234 – issue name
  • branch name doesn't contain '#'
  • PR is linked with the issue
  • base branch (master or release/xx) is correct
  • task status changed to "Code review"
  • reviewers are notified about the pull request

@mariam-khutuashvili mariam-khutuashvili self-assigned this Mar 27, 2026
@auto-assign auto-assign bot requested a review from svvald March 27, 2026 09:34
@mariam-khutuashvili mariam-khutuashvili linked an issue Mar 27, 2026 that may be closed by this pull request
Antisense creating doesn't work if ambiguous peptide present in the chain selection #6092
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@mariam-khutuashvili
Use variantMonomerItem instead of synthetic monomerItem when cloning
5c8554e 
an AmbiguousMonomer during antisense strand creation, so the
AmbiguousMonomer constructor receives the real template with its
monomers array instead of the BaseMonomer synthetic item that lacks it.
@mariam-khutuashvili
#6092 – Antisense creating doesn't work if ambiguous peptide present …
c54faf7 
…in the chain selection
@mariam-khutuashvili
#6092 – Revert peptide skip in antisense creation: non-nucleotide bac…
3eddb94 
…kbone monomers should be copied
@mariam-khutuashvili mariam-khutuashvili force-pushed the 6092-antisense-creating-doesn't-work-if-ambiguous-peptide-present-in-the-chain-selection branch from 2680c51 to 3eddb94 Compare April 6, 2026 09:01
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@svvald svvald Awaiting requested review from svvald

@rrodionov91 rrodionov91 Awaiting requested review from rrodionov91

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Antisense creating doesn't work if ambiguous peptide present in the chain selection

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