Chemical symbols and orbitals

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

JACS / ACS remains the default: Arial 10 pt, black, 14.4 pt bonds and 0.6 pt lines. New restores those settings even after changing tool styles.

Drawing and editing

The Chemical symbols palette button opens 18 choices: circled/plain charges, radicals/diradicals, lone pairs/bars, radical ions, H-dot/H-dash, attachment diamond/star/wave/bead and single/double daggers. Properties previews the actual styled geometry.

With Attach to atoms enabled, click an atom to add a charge, radical or lone pair. Drag from an atom to place its mark at a specific offset. Charges and radicals change the molecular graph’s chemical state; lone pairs/bars are annotations. A check refreshes implicit hydrogen labels and reports unpaired electrons. Charge changes release imported implicit-label hydrogen counts so ammonium can become ammonia again.

Select the atom and use Position atom marks to drag individual mark handles. Rotate turns a mark 45°. Remove deletes the mark and clears its represented charge/radical state. Movement, duplication and transforms carry marks with their owner; native undo/redo includes each edit. Atom-label color also colors its marks. Lone-pair annotations do not infer valence, electron count or orbital occupancy.

Free symbols are ordinary selectable graphics. H-dot/H-dash and attachment markers currently use free placement only; they do not define stereochemical hydrogen bonds, R-groups, polymers or reaction attachment semantics. Use an explicit H atom and stereobond for chemical hydrogen stereochemistry.

The Orbitals palette offers s, sigma, single lobe, p, sp³ hybrid, dxy and dz². Drag from the node to choose size/direction; Shift constrains to 15°. Click uses one default bond length. Outline, solid and flat-gray phases have live previews; multi-lobe orbitals support phase reversal. Node snapping places an orbital at a nearby atom, but the orbital is a drawing object. Group it with the molecule when they should move together. Gray fill is not gradient shading.

Persistence and exchange

• Native format 8 retains orbital parameters, phases and atom-owned marks; earlier document versions still open.
• Canvas, SVG, PDF and PNG use shared vector geometry, including differently filled orbital lobes and rotated marks.
• SMILES/MOL/CDXML retain supported one/two-unpaired-electron chemistry; molecular formats omit drawing annotations.
• Free symbols and orbitals export to CDXML as grouped editable vector curves. Importing those vectors retains their appearance, but not their parametric orbital/symbol controls.
• CDXML plain/solid orbital and supported free-symbol objects import as editable ReShiki objects. Gradient-shaded orbitals are rejected explicitly.
• CDXML atom-owned single charges, radical dots and supported lone pairs use represent ownership links. Carbon lone-pair annotation export is rejected because an external drawing application interprets it as diradical chemistry. Positioned multiple-charge marks, combined radical-ion marks, bars and colored attached marks require native/SVG/PDF/PNG; unsupported per-symbol CDXML overrides are rejected. External saves can discard ownership of distant marks, so export requires marks within 1.05 label sizes of their owner and closer to that atom than any other atom. A visible atom label and hydrogen count are written explicitly.
• Template attachment rejects marked or radical anchor atoms; free insertion of these templates retains their full drawing.

This is a bounded drawing/chemistry subset, not complete chemical-symbol or orbital parity. Automatic lone-pair placement, collision avoidance, arbitrary mark colors/sizes in the inspector, gradient shading, orbital fixed-length constraints and 3D orbital semantics remain incomplete.

Verification

Interchange fixtures in tests/fixtures/ cover a p orbital, a free circled plus and an atom-owned circled charge. The charge changes ammonia to ammonium and stores its owner with a represent child.

Tests cover all shapes/phases, native and vector persistence, atom ownership through transforms/copy, atomic rejection, history, radical/charge chemistry, supported exchange and explicit exchange failures. The complete suite passes 102 Rust and 30 Python tests.

Desktop checks used a standalone app launched from /tmp: ammonia → circled ammonium; mark repositioning with Undo/Redo; a rotated p orbital with reversed gray/blue phases; native save/reopen; vector/raster export; and NH₄⁺ → NH₃⁺ with one unpaired electron. New was exercised after setting 18 pt bold red text, a 3 pt graphic line and reversed phases; it restored JACS defaults. The final mark position was adjusted to clear the label while meeting the interchange proximity constraint.

A ReShiki-exported attached charge was opened and saved in an external drawing application, then re-imported and checked as [NH4+]; the saved result is retained under tests/fixtures/. A distant-position counterexample exposed loss of the charge/ownership link, and now causes an explicit export error. Desktop artifacts, drawings, screenshots and standalone checks are under artifacts/symbols-qa-20260920/. The exported PNG was visually inspected; the orbital phase and atom mark match the canvas.