#8249: prevent hanging hydrogen bond when typing after antisense ove…

[guranda2626]

Summary

Fixes a bug where an indestructible hanging hydrogen bond appears on the canvas after pressing Enter at the end of an antisense sequence and typing a nucleotide in Sequence mode.

Steps to reproduce:

1. Open Macromolecules canvas → Sequence mode (clear canvas)
2. Load from HELM via clipboard:
   RNA1{r(A)p.r(A)p.r(A)p.r(A)}|RNA2{r(U)p.r(U)p.r(U)p.r(U)}$RNA1,RNA2,11:pair-11:pair$$$V2.0
3. Switch to edit mode at the end of the antisense sequence
4. Press Enter, then press A

Before: A hanging dashed bond appears — disconnected from any antisense nucleotide, impossible to select or delete.

After: The new A nucleotide is added as a standalone sense node with no bond.

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Root cause

When a HELM structure has a partially-paired antisense chain, the SequenceViewModel places unmatched antisense nucleotides into overflow positions — TwoStrandedChainItem nodes where senseNode is EmptySequenceNode and antisenseNode is a real unmatched nucleotide.

Pressing Enter at such a position calls splitCurrentChain(), which detaches the last unmatched antisense nucleotide from the backbone. After re-render, the caret lands at the chain's end node, whose previousNodeInSameChain is {EmptySeq, U2}.

When the user then presses A in sync edit mode, the antisense-creation condition:

// before fix
previousTwoStrandedNodeInSameChain?.antisenseNode ??
currentTwoStrandedNode?.antisenseNode

evaluated U2 as truthy and fired, inserting a new antisense U into U2's existing chain and creating a hydrogen bond between a new sense A (isolated chain) and that antisense U — a bond crossing incompatible chains, making it unremovable.

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Fix

The sync-mode branch of the antisense condition in add-sequence-item (SequenceMode.ts) now also requires that the triggering node's senseNode is present and not an EmptySequenceNode:

// after fix
(previousTwoStrandedNodeInSameChain?.senseNode &&
  !(previousTwoStrandedNodeInSameChain.senseNode instanceof EmptySequenceNode) &&
  previousTwoStrandedNodeInSameChain.antisenseNode) ||
(currentTwoStrandedNode?.senseNode &&
  !(currentTwoStrandedNode.senseNode instanceof EmptySequenceNode) &&
  currentTwoStrandedNode.antisenseNode)

Issue link

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