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Molkit

PubChem Integration

Molkit uses the PubChem PUG REST API to identify the molecule you are working on. When you select atoms, the status bar fetches and displays the IUPAC name for the selection (a partial selection is looked up as a fragment). The same service supplies compound identifiers and synonyms for SVG exports that embed chemistry metadata. PubChem lookups require an internet connection; see SMILES Import & Export for the separate RDKit.js network dependency.

Name lookup in the status bar

Select all atoms of a molecule (for example, drag a box around it or press Ctrl+A). About half a second after the selection settles, the status bar shows “looking up name…” and then the IUPAC name reported by PubChem for the selection’s SMILES string. Clearing the selection clears the display.

Lookups are debounced and cached for the session, so repeated selections of the same structure do not trigger repeated network requests.

What you get:

  • The IUPAC name, displayed in the status bar. Click it to copy it to the clipboard; the display dims briefly to confirm.
  • A dropdown arrow when PubChem returns more than one name. Click it to open a list of alternates; click any entry to copy that name.
  • An external-link icon when PubChem matched a compound record (CID). Click it to open the compound’s PubChem page in a new tab.

You can also copy the current name from the command palette: press Ctrl+K and run “Copy IUPAC Name”.

PubChem data in SVG exports

When you export an SVG with the “Embed chemistry metadata” option enabled, Molkit also asks PubChem for the structure’s IUPAC name, CID, common-name synonyms, InChI, and InChIKey, and writes them into the exported file’s metadata. If the API is unreachable, the export still completes; only the PubChem fields are skipped.

Importing structures

Molkit does not import structures from PubChem by name or CID. To bring a structure in from text, paste a SMILES string instead. See SMILES.

Network and privacy

Every lookup sends the SMILES string of your selected structure to pubchem.ncbi.nlm.nih.gov as part of the request URL. No other document content is transmitted. If you work with structures you cannot share, avoid selecting them in full, or work offline.

Failure behavior

Lookups fail silently. If you are offline, PubChem is down, or the structure has no PubChem record, the status bar simply stays blank; no error dialog appears. Failed lookups are not cached, so re-selecting the structure retries.

See also