Atom labels and owned indicators — 2026-09-20

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

Properties → Labels & chemistry → Atom labels & numbering… opens the display controls. Choose Whole drawing or Selected atoms, then choose skeletal, terminal, internal or all carbon labels. Implied hydrogens can be shown or hidden, with automatic, left, right, above or below placement on the affected atoms. These are display settings: changing them does not change the molecular graph or its formula. Drawing carbon/H/stereo defaults apply to newly added atoms. Hydrogen placement is a per-atom choice applied to the current scope.

To switch a hydroxyl label between OH and HO, select its oxygen and open Properties → Labels & chemistry → Atom labels & numbering…. With Selected atoms as the scope, choose Right for OH or Left for HO under Hydrogen position. Restore Automatic to follow the surrounding bonds. See the illustrated OH/HO walkthrough for the controls and an editable example.

Automatic placement uses the internal bond angles to choose an inline or stacked label. With two bonds it uses their angle bisector, including a stable choice for straight bonds. Terminal labels keep the usual inline form. It updates when a structure moves or rotates; explicit placement overrides it. Condensed display labels such as CCl₂ and NMe use the same placement logic, keeping the attachment element at the vertex and subscripts with their label. Unknown names remain intact. See the internal-label examples and scope.

Bonds meet the attachment atom inside a multi-atom text label (MeO, AcS, SPh), not the label’s center. Automatic attachment skips substituent nicknames (Me, Ac, Bn, Ph, TBS…), hydrogens and counts, and uses the atom nearest the bonds: the first atom when they arrive from the left, the last when they arrive from the right (the first atom for vertical bonds). Text naming no atom (Boc, M) stays centered, unless a long automatic terminal label would hide more than half of its single near-horizontal bond; that label meets the bond with its near edge. Text whose other letters would lie between the atom and a horizontal bond (MeO bonded from the left) also stays centered, so those letters do not hide the bond. Automatic labels with two or more bonds stay centered too. Contracted groups use the same rule on their displayed spelling, so a group without a reverse spelling still attaches at its anchor (OAc read from the right attaches at O, not at Ac). Bond attachment (text labels) overrides it per atom: Centered centers the label, Flush left/Flush right attach at the first or last atom, and Character N at that character. Native files store the choice as label_attachment. Editable CDXML/CDX clipboard data writes flush left/center/right as the text’s LabelJustification and the atom’s LabelDisplay, as ChemDraw saves its Text → Flush Left / Centered / Flush Right; ChemDraw lays a label without LabelDisplay out again as Automatic. Import reads LabelJustification (CDXML/CDX file export still refuses free text labels). Copying to ChemDraw 26.1 and back was checked on macOS: Flush left and Centered return unchanged. Flush right MeO returns as a contracted methoxy group aligned flush right, because ChemDraw reads a flush-right MeO as a methoxy fragment (it does the same for labels drawn in ChemDraw). A chosen character has no ChemDraw equivalent and is native only; changing the text returns it to Automatic.

Alternative lists such as [Cl,Br,I] with a single horizontal bond meet it with their near edge, so the text extends away from the molecule and the bond is trimmed at the label instead of running through it. Vertical and internal generic labels, including link nodes, stay centered.

Number assigns one sequence in creation/import order. Starts include 1, atom1, a, A, α and Α; letter sequences continue beyond the alphabet. A single selected atom also accepts a custom number such as Cα or 12a. Numbers are owned by atoms, independent of reaction atom-map numbers.

Show stereodescriptors (R/S, E/Z…) displays computed CIP assignments. Chemical edits invalidate cached assignments and trigger a quiet background refresh. Stale responses are ignored and rescheduled; refresh does not change selection, document dirtiness, drawn bond orders or Undo/Redo. Invalid chemistry produces an inspector error. Unassigned centers have no label.

Enantiomorphic double bonds display seqCis/seqTrans; native files and machine-facing exports retain the internal z/e codes. Axial descriptors chooses M/P (IUPAC preferred) or Ra/Sa for the whole drawing, independently of the selected scope. M maps to Ra and P to Sa; lowercase m/p map to ra/sa. The choice changes display only and can be undone. Every stereodescriptor uses the same italic indicator style. This option does not add axial stereo perception. Search CIP or pseudoasymmetric in the command palette (:) to show or hide stereodescriptors throughout the drawing.

Show D/L for amino acids and sugars is off by default and applies to the whole drawing. When stereodescriptors are visible, recognized structures show an upright D or L before their CIP assignment, for example L (S). The CIP code keeps its italic style; Upright stereo parentheses also keeps the parentheses upright. Search D/L in the command palette to toggle this display. The choice is saved in native documents and does not alter stereochemistry.

For an alpha amino acid with N, C(=O)X (X = O, N, S or H, not a ketone) and carbon side-chain neighbors plus one hydrogen, D/L follows the assigned R/S code and the carbonyl versus side-chain CIP priority. This includes peptide residues and handles L-cysteine as L (R). The comparison uses atomic numbers through the second sphere, including multiple-bond duplicates and hydrogens. A tie omits D/L rather than guessing from incomplete priorities. Glycine and unrelated stereocentres keep their usual indicators.

Recognized Haworth monosaccharides show D/L only at the last configurational carbon. If ring closure involves a terminal CH2, the preceding stereocentre supplies the name. Open-chain aldoses with stored configurations, such as the Fischer templates, show D/L at the stereocentre next to CH₂OH. Both forms read stored stereochemical parity and connectivity, so turning a Fischer projection by 90° (which draws the enantiomer) changes D to L rather than hiding the name.

Indicators start at 7.5 pt Arial; stereo labels are italic. Change their size or apply the current toolbar font/color. Position numbers & stereo labels shows handles: drag a number or stereo indicator, then Escape to finish. Each drag is one Undo step. Automatic positions consider nearby labels, captions and bonds. A custom number longer than one character starts beside its atom on the open side and is left- or right-justified so extra text runs away from the structure; above or below an atom it stays centred. Restore automatic positions removes manual offsets; a dragged indicator keeps its exact position. Copying, grouping and transforming a structure retain indicator ownership.

Canvas, SVG, PDF and PNG share the indicator geometry. Drawing exports refresh computed labels on a snapshot before rendering. JACS remains the new-document default: Arial 10 pt atom/caption text, black, 14.4 pt bonds and 0.6 pt lines. New clears label overrides and restores skeletal carbons, visible implied H, and no atom numbers or stereo indicators. Native format 9 stores the settings, styles and offsets; previous supported document versions remain readable.

CDXML imports and exports use node/bond-owned objecttag records, plus label-display attributes. Atom numbers do not become detached captions. Imported CIP text is never trusted as chemistry; Rust recomputes the assignment. Desktop exports provide measured positions. Protocol clients that omit the atom_indicators payload receive a simple positional fallback.

CIP assignments use the Rust implementation, independently checked against RDKit’s CIP labeler. The numbered phenylalanine interchange fixture retains C9H11NO2, the same InChIKey, 12 atom-owned numbers and an (S) label.

Limits: tetrahedral R/S/r/s, ordinary double-bond E/Z, enantiomorphic double-bond seqCis/seqTrans, biaryl atropisomer M/P and three-carbon allene M/P (m/p for pseudoasymmetry) are supported. Biaryl axes require an authored wedge or hash originating at an axis atom; distant substituent wedges do not specify the axis. Rotation barriers are not inferred. Allene stereo requires terminal substituent wedges at one end only; wedges at both ends receive an ST-1.6 drawing note. Its indicator belongs to the central carbon. SMILES retains @AL1/@AL2, and MOL/CDXML retain terminal wedges. Longer cumulenes and enhanced-group stereochemistry are not implemented. InChI generation uses verified terminal wedges with real 2D coordinates; coordinate-free or projected allene input cannot use that path. The raw InChI adapter maps allene parity, but native InChI import still discards it with a diagnostic because the pinned dependency does not expose its parity records. Naming still excludes allene stereo. Unknown object tags, unsupported indicator formatting and ambiguous atom matches are rejected. Dense diagrams can still need manual indicator positioning. Numbering is an explicit command; it does not automatically renumber after every edit. Further features remain listed in the feature status.

Original update validation: 125 Rust and 36 Python tests passed, covering identity, sequences, native/CDXML ownership, transform/copy, exported geometry, stale refreshes and history. Native computer checks cover the imported interchange fixture, numbering, manual drag, Undo/Redo, native persistence and external reopening of the export. Local artifacts and logs: artifacts/atom-labels-qa-20260920/.