Bond tools and exchange

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

Added 2026-09-20. The bond palette and contextual menu now offer 17 presets. Single, double and triple bonds have direct toolbar buttons. Other styles open from the separate bond palette. Select a bond to change its preset, RGB color and double-line position in Properties. The drawing canvas, SVG, PDF and PNG use the same geometry.

Preset	Meaning in ReShiki
Single, double, triple	Ordinary covalent orders; existing midpoint click cycling remains available
Solid wedge, hashed wedge	Tetrahedral up/down depiction from the first endpoint
Hollow wedge, parallel hashed	Alternate up/down depictions
Bold	Up depiction for a single bond; thick stroke
Wavy	Unspecified single-bond stereochemistry
Coordination (dashed), dative	Directed donor-to-acceptor dative bond; dashed line or arrow
Hydrogen bond	Noncovalent interaction from an explicit bonded H to an acceptor
Partial (solid / dashed), partial (double dashed)	Fractional 1.5 order and the indicated line pattern; see semantic limits below
Bold double	Bold primary line and ordinary secondary line
Crossed double	Double bond with unspecified E/Z stereochemistry
Quadruple	Four-line bond and quadruple order; shortcut 4

Workflow

• Choose a palette tool, then use its contextual preset menu for the full set. Drag to see the actual bond style before release. Existing carbon-chain growth and attachment still work.
• Click an existing bond to apply a style. Repeated clicks with a matching solid/hashed/hollow wedge, parallel hash, bold, dative or coordination tool reverse its endpoints. Ordinary single/double/triple bonds retain their order cycle; aromatic edges follow the appearance rules below.
• On the first conversion of a plain single bond to a solid, hashed or hollow wedge, the narrow end starts at the sole plausible stereocenter: an endpoint without multiple bonds that can have four substituents (including attached or implicit H, with a simple P/S extension), or a nonterminal endpoint opposite a terminal atom. If both endpoints or neither qualify, the existing direction stays. Clicking the matching wedge again still reverses it. Aromatic, dative and retained projection bonds keep their existing direction rules; drag previews use the same endpoint choice as the committed edit.
• With Select (V), click a bond’s middle to select both endpoint atoms. Properties applies bond edits to edges whose two endpoints are selected. A larger selection can style multiple bonds together; mixed presets are indicated.
• Double and partial bonds offer Automatic, Centered, Left and Right second-line placement. For explicit Left/Right placement, reversing an edge or reflecting the drawing adjusts its relative side.
• Automatic double bonds point into their ring. A fusion double prefers the incident ring with more other double or aromatic bonds, then a six-membered ring on a tie. Substituted chain doubles offset toward an attached ring or, when no attached ring selects a side, the side with more substituent bonds. Equal counts then place the second line on the negative-cross-product side of the bond’s stored start-to-end direction, using drawing coordinates with y increasing downward; CDXML retains its B-to-E direction. Unlabeled terminal carbons such as =CH₂ follow the substituent-side rule; terminal heteroatom doubles such as C=O remain centered. The chain tie and terminal-carbon rules follow ChemDraw 26.1’s ACS Document 1996 style. Center chain double bonds in Document Style restores centered chain placement. Explicit positions remain available.
• Offset inner lines shorten at each adjoining angle bisector, with the established minimum setback retained for five- and six-membered rings. Small rings receive more shortening; an end without a neighbour on the offset side receives none. Drawing, crossings, arrow attachments and SVG/PNG/PDF exports share this geometry. Tilted 3D rings retain their existing face selection and polygon clipping.
• Enter a hex color and press Enter or Color. Colors, line placement and aromatic projection styles do not change molecular identity. Chemical order/stereochemical changes invalidate chemistry so Check recomputes it.
• Hydrogen bonds must start at an existing explicit H with a covalent bond to another atom, and end at N, O, F or S with nonpositive formal charge. Unsupported endpoints leave the drawing unchanged. The interaction does not increase the hydrogen atom’s valence.
• Drawing, restyling and direction changes are undoable. Save .rsk to retain the complete state.

Aromatic ring appearance

On an aromatic edge, solid/hashed/hollow wedges, bold, parallel hashes and wavy styles preserve the aromatic bond order. They depict the ring’s projection without assigning tetrahedral stereochemistry. The aromatic circle or partial inner curve remains visible, including after a 3D tilt. Clicking the same wedge again reverses its direction; Single restores a plain edge while keeping the ring aromatic. Explicit Double/Triple and coordination presets still change the bond order.

This behavior is shared by bond clicks, drag previews, committed drags and Properties, with Undo/Redo. Native files and SVG/PNG/PDF retain the appearance. CDXML/CDX preserve aromatic bold edges and solid wedges, bold double bonds, supported Haworth projections and single-bond projection wedges/hashes whose narrow end is an unassigned coordination metal. Other projection styles still require plain edges before editable file export. Coordination-frame wedges carry no tetrahedral stereo; ordinary single-bond wedges retain their stereochemical meaning.

Export marks such a metal with ChemDraw’s no-stereocentre flag (AS="N"). On import, a flagged metal’s single-bond wedges/hashes are read without tetrahedral stereo and become projections, as do metal wedges that specify no tetrahedral centre (for example at a six-coordinate metal). Unflagged wedges at a four-coordinate metal keep their tetrahedral meaning.

Checking and redrawing stereochemistry

Check drawing reports stereobonds with no effect or a probably reversed narrow end, ambiguous wedge geometry, conflicting wedges, and undefined stereocentres or stereogenic double bonds. The notices select the affected atoms and bonds; clicking a notice in Stereochemistry selects that item again. Reverse fixes the probably reversed bonds in one Undo step. Explicitly unknown stereochemistry, such as a wavy bond, is excluded from the undefined count.

Enable IUPAC style notes in Check drawing in Stereochemistry for optional advice about bonds between stereocentres, mixed hash styles, alternate-only depictions, wavy bonds beside alkenes, re-entrant ring atoms and T-shaped geometry. This preference starts off and does not alter how bonds are interpreted.

Redraw stereo bonds, available in the selection context menu, command palette and stereo notices, lets the automatic wedge chooser place the wedges again. It acts on the molecules touched by the selection, or the whole drawing with no selection. It normalises solid/hollow/bold and hash depictions to solid or hashed wedges while retaining configuration, coordinates, colours and other bond properties. Wavy and projection bonds stay as drawn. The command is undoable.

Under Show R/S and E/Z labels, enable Mark undefined stereocentres to show muted (?) markers at undefined stereocentres and stereogenic double bonds. The document option starts off. Markers appear in figure exports only while visible; they are separate from chemical CIP labels. Enable Use Ξ/ξ for undefined (IUPAC) below it to draw (Ξ) instead, or (ξ) at a pseudoasymmetric centre, the IUPAC descriptors for unknown configuration (P-91.2.1.2.1). Generated-name notices list the specific units whose configurations are left unspecified. With Write Ξ/ξ for unknown configuration on in Chemical names, the generated name writes those units as Ξ/ξ too, for example (2Ξ,3R)-3-chlorobutan-2-ol.

Native and chemical representation

Native document version 6 added double_position, secondary_display and per-bond RGB color, with defaults for older files. The app still accepts native versions 1–5. Order 4 means aromatic; version 6 added order values 0 hydrogen, 5 dative, 6 quadruple and 7 fractional 1.5. These numeric values belong to ReShiki’s file format, not chemical bond-order notation.

Cleanup preserves bond appearance and restates visible tetrahedral stereochemistry against the new coordinates. Tests remove stored atom stereochemistry and infer identity from the resulting drawing independently. Bold/hollow up depictions can become parallel hashes when a reflected or regenerated projection requires a down depiction; exact stylistic restoration is not guaranteed by two reflections. Undo restores the original style.

CDXML exchange

The public SDK describes bond display, secondary display, double-line position and order. Interchange behavior is verified with saved fixtures and regression tests.

Live file exchange exposed encoding details absent from the older SDK:

• The supported external hydrogen-bond encoding is Display="Dash" Display2="DottedHydrogen", with ordinary/default order. ReShiki restores its noncovalent meaning and emits that encoding.
• Dashed coordination saves as an ordinary/default order plus Display="Dash"; ReShiki imports it as directed dative chemistry.
• Double-dashed partial bonds need an explicit second Dash display when exported.
• Import supplies the ordinary secondary display when a bold double bond omits it.

A saved interchange gallery under tests/fixtures/ contains 18 bonds. These cover all 17 presets plus the donor–H covalent bond. Tests assert styles, chemical orders, selected line patterns and hydrogen valence after import. Atom association must be unambiguous; an incomplete or ambiguous fragment parse cancels import rather than attaching styles to the wrong atoms.

Verification and limits

74 Rust tests and 23 Python tests pass, alongside formatting and Clippy. Added coverage includes all presets through native and CDXML round trips; cleanup; visible tetrahedral identity; reflection; manual line position; SVG/PNG colors; PDF generation; selected-bond history; hydrogen valence; dative MOL round trips; and rejection of lossy molecular exports.

Desktop checks drew and reversed a hollow wedge, changed a selected double bond’s side and color, exercised Undo/Redo, and saved native version 6. The interchange gallery was visually inspected after save/reopen. Local QA files are under ignored artifacts/bond-qa-20260920/.

The rebuilt standalone bundle passed signature verification and its engine check from /tmp with RESHIKI_ROOT=/nonexistent. Its bundled worker imported the interchange fixture as 35 atoms and 18 bonds with formula C26H75Cu2N3ORe2+4. The packaged desktop app opened that file, saved it as native version 6, reopened the styled native review drawing and successfully checked its chemistry. The review drawing includes one additional hollow-wedge bond; its long formula now fits the Properties panel, and the saved red color/right-side double-line controls reappear on selection.

Remaining boundaries:

• ReShiki currently stores these as fractional 1.5 bonds. It does not implement the full tautomer/query or delocalized-resonance behavior associated with those tools. The ordinary aromatic-ring workflow remains separate.
• Hydrogen endpoint validation is a local heuristic, not comprehensive hydrogen-bond perception. It does not create an explicit H automatically or assess geometry/interaction energy.
• SMILES export rejects hydrogen and fractional bonds; InChI also rejects dative and quadruple bonds. MOL export rejects hydrogen, fractional and quadruple bonds. Dative MOL exchange is tested. Native and drawing exports retain the supported styles; molecular formats do not retain all drawing appearance.
• Query/multiorder bonds, multicenter attachments, full metal/non-tetrahedral stereochemistry and perspective tools remain incomplete or absent. The subsequent chain tools update adds straight/snaking drags and fixed-angle/length controls.
• Unusual aromatic systems, dense metal complexes, source-specific CDXML attributes and broad chemical equivalence require additional differential fixtures. The gallery is a feature sample, not exhaustive chemical validation.

See the broader feature-gap audit for the remaining workspace and chemistry features.

The Style palette now offers All selected, Text, and Bonds color scopes. Choose Bonds to recolor selected bond strokes while retaining label colors, or All selected to recolor the complete selected drawing. Click a bond’s middle to select both endpoints; Shift-click adds more. The selection summary explicitly counts selected bonds.

Clicking an existing double bond with the matching double-bond tool cycles centered, left and right placement. Its order, chemical identity and color stay unchanged. Hovering or selecting a bond supports 1/2/3 for single/double/triple; repeated 2 also cycles line position. Each change is one Undo step.