Chemical names

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

Chemical names turns a name into an editable structure and gives a molecule its systematic name. Names are converted on your computer; no internet connection, Java or naming service is needed.

Use it

Insert a structure from a name

1. Open Import, choose Name and type a name such as ethanol.
2. Choose Insert. Add name below is on at first and adds the name as a caption below the structure; turn it off to insert only the structure. Undo removes both, and Redo restores both.
3. Optional: choose Preview to check the structure first. Drag atoms to arrange the layout, or edit the SMILES and choose Apply. Reset restores the parsed structure.

Cancel stops a pending import. Editing the name or switching back to Structure cancels it too. If you change the chemistry in the preview, the typed name no longer matches, so ReShiki inserts the structure without it. Apply SMILES edits before you insert.

Show a molecule’s name

1. Right-click a molecule and choose Show chemical name. The name appears centered below the molecule; for ethanol it is ethan-1-ol.
2. Choose Hide chemical name in the same menu to remove it.

Show and Hide are each one Undo step. The clicked molecule is named even when other molecules are selected or grouped with it. The caption moves with the molecule. When the chemistry changes, the caption is removed in the same Undo step. Editing or dragging the caption turns it into ordinary text that stays.

To see or copy a name without placing it, select one whole molecule and choose Generate selected name in Import → Name → Details or in the Chemical names inspector. Then choose Copy name or Insert caption.

Curated offline aliases

1. In Import → Name, type a name and open ▸ Details. If Details is already open, choose Resolve name.
2. CURATED ALIASES · OFFLINE lists other names for the same structure, each with its source and license.
3. Choose Copy to copy an alias, or Use below to use it as the caption of the next insertion. Use original name below switches back to the typed name.
4. To name a drawn molecule, select it and choose Generate selected name in the same Details area. GENERATED SYSTEMATIC NAME · LOCAL RULES shows the result with Copy name and Insert caption.

Opening Details does not open the preview or insert anything. Changing the typed name clears the alias choice. An alias caption replaces the molecule’s existing name caption instead of adding a second one.

Chemical names inspector

Right-click a molecule and choose Chemical names…. ReShiki selects that molecule and opens the Chemical names inspector. It has two parts:

• NAME → STRUCTURE: enter a name and choose Parse name. Drag atoms in the preview to arrange the layout, or edit its SMILES and choose Update; Restore returns to the parsed structure. If the result has warnings, check I reviewed these warnings and the structure. Choose Insert to add the editable structure. It is inserted without a name caption.
• STRUCTURE → NAME: choose Generate selected name, then Copy name or Insert caption. Curated aliases for the molecule appear below the generated name.

‹ Properties returns to the Properties inspector, and Import opens the Import tab.

Limits

• Ambiguous names, unsupported or ignored stereo, relative or racemic qualifiers, radicals, polymers, queries and disconnected salts are rejected with a reason. A rejected name leaves the drawing and Undo history unchanged.
• Optical rotation signs are not turned into R/S. The one exception is (+)-lactic acid, which reads as (2S)-2-hydroxypropanoic acid.
• Generated names cover neutral organic molecules with up to 64 heavy atoms. Charged or isotope-labeled molecules and fused, spiro or bicyclic parents give an error.
• Generated names are systematic. They are not always the preferred IUPAC name.
• The alias catalog matches the exact structure, so stereo, charge and isotopes count. No curated aliases available in the bundled catalog. only means the catalog has no entry, not that the molecule has no other names.
• Other formats keep a caption’s text but not its link to the molecule.

Implementation notes

Name to structure

The Rust OPSIN port handles supported systematic and retained names, including substituted functional groups, bicyclic/spiro systems, heterocycles, supported absolute R/S and E/Z stereo, isotopes and formal charge. The editor accepts a connected graph with at most 512 atoms. ReShiki verifies the editable graph before inserting it. The specific retained name (+)-lactic acid is normalized locally to (2S)-2-hydroxypropanoic acid, using ChEBI:422, then parsed and checked against its explicit S graph. The parser result identifies this retained-name source. Other optical-rotation names, including derivatives, salts and conflicting descriptors, remain subject to strict rejection; this entry is not a general sign-to-configuration rule. The original input can be used for Add name below, while structure-to-name returns the verified (2S)-2-hydroxypropanoic acid. Older screenshots that show this name rejected predate this change. Changing the input or drawing invalidates pending or outdated results.

Structure to name

Abbreviated groups are expanded for naming. Showing an already named molecule reuses its caption. The ReShiki organic rules 1 profile covers supported neutral organic structures with at most 64 heavy atoms. Its declared subset includes carbon chains with supported branching and unsaturation, simple cycloalkanes, benzene and selected heteroaromatic parents; acids, simple esters, primary amides, nitriles, aldehydes, ketones, alcohols, primary amines, ethers and halogen substituents; and supported parent R/S and E/Z configurations. Carbon stems are limited to 20 atoms and substituent nesting to three levels. Unsupported functional groups and stereo contexts return an error. A generated name appears only after the local Rust parser reconstructs the same graph and specified stereo. Parent selection and naming rules also have independently expected tests. Comprehensive IUPAC coverage and preferred IUPAC name (PIN) selection are not claimed. Unspecified stereo remains unspecified.

Captions

The caption is ordinary editable text with an optional association to its complete molecule. It follows layout changes. A chemical identity change removes an obsolete automatic caption in the same Undo step; Undo restores it. Editing the caption text or dragging it independently detaches it, preserving that custom text through later chemical edits. Atom maps and visual atom numbers do not change name identity.

.rsk save, reopen and whole-molecule copy keep the association. Copying a caption alone keeps plain text. Figure export and CDXML/CDX keep visible caption text; external formats and older ReShiki readers cannot keep the association. The optional metadata uses the existing document-version convention, so an older reader may save the caption as ordinary text.

Alias catalog

The bundled catalog contains 40 retained or functional-class names for 30 identities, including ethyl alcohol for ethanol. Each alias displays its source, version, record and license. The complete catalog and provenance record the selected OPSIN data (MIT license) and one ChEBI equivalence (CC BY 4.0). The S, R and unspecified lactic acid graphs have separate entries. Neither charge nor isotope variants inherit the neutral, unlabeled alias. Reaction map labels do not change chemical identity. Looking up aliases needs no network connection, Java, Python or other program. Resolve name is disabled while parsing and for empty input. Changing preview chemistry prevents using aliases from the original graph. After chemistry changes, generate a new name before using it.

Records

The desktop review and fixtures cover an earlier build and an older design of the Chemical names inspector, with examples, provenance and reproducible checks. The dock and molecule-caption record covers the Import dock and captions, and the alias review covers the catalog.