#9866 - Additional elements appear when inserting a file saved in mol format the expand monomers package

[Lianamirru]

How the feature works? / How did you fix the issue?

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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

[claude]

The bare true as the 11th positional arg to Struct.clone(...) is opaque — a reader has to jump to struct.ts:192 to learn it means "clone attachment points." The sibling change in this same PR (ketSerializer.ts:967) introduces const needCloneAttachmentPoints = true; precisely to self-document the call. Mirroring that pattern here would keep the two new call sites consistent:

Suggested change

	true,
	bondIdMap,
	true /* needCloneAttachmentPoints */,

[claude]

A one-liner explaining why a per-atom StereoLabel.Abs must also raise the chiral header flag would help — this is exactly the bug being fixed, and without context a future maintainer is likely to "simplify" it back. Something like // Atoms can carry an Abs stereo label even when no fragment is flagged as Abs (e.g., after copy/paste); both paths must raise the chiral flag. above the assignment would suffice.

Minor: Array.from(map.values()).some(...) materialises both maps before short-circuiting. For typical molecules this is negligible, but a small forEach/for…of helper would avoid the throwaway arrays if you're already touching this block.

[claude]

Targeted bug-fix PR — the two correctness changes (cloning attachment points so leaving-group hydrogens get dropped, and raising the chiral header flag for per-atom Abs labels) are sound and the fixture updates are consistent with the behaviour change. No security concerns; perf impact of the new Array.from(...).some(...) and the propagated needCloneAttachmentPoints flag is negligible (monomer-count bounded, not atom-count bounded).

Two small things noted inline. One broader follow-up worth flagging separately:

Struct.clone ergonomics (struct.ts:192-204). The signature now takes 11 optional positional params, and this PR adds a new call site that passes ten undefineds to reach the 11th (ketSerializer.ts:968-980). It also has no JSDoc despite needCloneAttachmentPoints materially changing production output. Converting to a single options object (clone({ needCloneAttachmentPoints: true })) — and documenting the flag — would eliminate the undefined-padding, the magic-boolean problem in Editor.ts:3047, and the docs gap in one pass. Out of scope here, but worth a follow-up issue.