Selection cleanup

Implementation notes and historical checks. Open the visual guide →.

Clean up requires selected atoms. Double-click an atom to select its connected molecule, or use the rectangle/lasso tools for a smaller region.

• Selected atoms redraws only the selection. Unselected atoms remain fixed, including atoms bonded to the selection.
• Selected molecules redraws connected molecules touched by the selection. Other molecules remain unchanged, and each cleaned molecule retains its own center.
• Keep orientation fits the new coordinates to the original orientation without reflecting the structure. Disable it to use the generated orientation.

The canvas first shows a preview. Use Show original to compare, then Apply or Cancel. Apply creates one Undo step. Cancelling an in-flight refresh prevents its late result from reopening the preview. Text, arrows, graphics, groups, colors and label styles are retained.

Components containing multi-center or variable attachments are kept unchanged with an explicit warning. This includes collapsed or expanded Cp/Cp* groups. Independent ordinary molecules in the same selection can still be cleaned. Automatic geometry cleanup of attachment-containing complexes is not yet supported; retaining them does not claim molecular identifier or coordination valence validation. Malformed attachment targets and solver errors remain errors.

Cleanup checks molecular identity, including stereochemistry. Fixed-atom constraints can prevent a satisfactory layout; an error leaves the drawing unchanged. If regenerated coordinates would assign previously unspecified alkene stereochemistry, an affected double bond receives a crossed depiction and the preview explains why. Invalid chemistry outside a selected component does not prevent that component from being cleaned; a warning explains when whole-document properties cannot be computed.

A stereochemistry refusal suggests including the whole molecule only when some of its atoms were held fixed. If the whole molecule was already included, the message confirms that the drawing was left unchanged.

Automated coverage includes separate molecule centers, fixed unselected atoms, partial side-chain cleanup, selected-molecule expansion, abbreviations, unselected invalid chemistry, orientation control, tetrahedral and alkene identity, and cancellation of late cleanup results. Reaction layout and general geometric optimization remain separate work.