Name from Structure

Name from Structure

This page covers local structure naming with the optional Orthonym engine and the exact read-back check required before a name is displayed or inserted.

Get a name for a drawing

Install the official Name from Structure (Orthonym) plugin through Installing and Updating Plugins. The plugin and the local naming engine are separate components: the plugin supplies commands and reports, while ChemDraft installs and manages the engine after explicit user action.

1. Select the molecule to name.
2. Choose Analyze → Name from Structure to open the naming panel.
3. If the engine is missing, review the installation offer and install it if wanted.
4. Read the accepted name's classification and any warnings, or the specific reason naming was declined.

The menus are app-wide on macOS and attached to the document window on Windows. When nothing is selected, the plugin can use the page's single molecule. With no molecule or several molecules on the page, select the intended structure. Multiple selected molecules are handled individually, up to ten; non-molecule selections are ignored.

The host also provides Structure → Convert Structure to Name for the plugin's Insert Name as Text command. This inserts a verified name below the structure. The patch is labelled Insert Name and contains new text objects. Each inserted name is its own undo step when several structures are processed.

What “verified” means

Orthonym proposes a name locally. ChemDraft accepts only fully verified engine results, distinguished as a preferred IUPAC name (PIN) or a systematic name. It then independently reads that name through the host's OPSIN parser.

Both the drawing and the parsed name are canonicalized to isomeric SMILES using RDKit. The canonical representations must match exactly. This check matters for charges, isotope labels, fragments, hydrogens, and supported stereochemistry: a name for a neutral form is not an acceptable substitute for a drawn zwitterion.

The host rejects results with unexpressed stereochemistry, incomplete verification, or a name that fails exact read-back. It also refuses a drawing that cannot first be exported as exact SMILES. Potentially chemical losses are not waived merely because the engine found a plausible name.

Verification establishes this structural read-back under these implementations. It does not prove that all nomenclature software interprets the name identically, or independently establish every preferred-name rule. Orthonym and the host check both use OPSIN, so a shared misinterpretation can escape this check.

Supported input and refusals

Naming has a limit of 500 heavy atoms and a 5000-character SMILES representation. A heavy atom is an atom other than hydrogen. Engine limits, unsupported elements, unnameable structures, and failed exact representation produce a refusal, rather than a guessed replacement name.

Represented abbreviations may be expanded to the exact molecular graph for naming; an informational warning discloses the expansion. R-group placeholders and other inexact representations can prevent naming. Accepted stereochemical names retain a warning that stereochemical naming has limited validation evidence.

A refusal does not mean the compound cannot exist or has no valid name. It means this engine and its verification gates did not establish an acceptable name for this drawing. Correct a drawing error if one is identified; otherwise retain the structure and the refusal reason.

Local engine and platforms

The installed engine uses Orthonym with a managed Python environment, RDKit, and Java-based verification components. Neither the engine nor its Python starts at app startup. Structures are not sent to a remote naming service; installation downloads the reviewed engine components.

The recorded Apple-silicon installation downloaded about 100 MB and occupied about 310 MB after installation. The installer requires 1 GB free to allow staging and an update's previous copy. Sizes vary by platform; the recorded Windows installation used about 265 MB of files after installation.

Platform	Current engine position
macOS, Apple silicon	Implemented; real installation measurements are recorded
macOS, Intel	Unsupported with the current dependency pins; refused before downloading
Windows x64	Implemented; real installs were measured, while cancellation, process cleanup, relocation edge cases, and other hands-on checks remain open in the architecture record

An interrupted or failed replacement rolls back rather than claiming a partial engine is ready. A broken installation, timeout, cancellation, or busy engine is distinct from a chemistry-based refusal.

Agent availability

The desktop plugin uses the shared naming policy. Structure-to-name support for the CLI and MCP is parked in the current plan; the CLI's existing name command must not be assumed to provide Orthonym naming. See the agent reference pages for the implemented headless interfaces.

See also

• Name to Structure
• Chemistry Guarantees
• Official Plugins
• Troubleshooting