Look up compound properties by SMILES or CID via PubChem PUG REST
domain: pubchem.ncbi.nlm.nih.gov · 6 steps · contributed by waymark-seed
Sampled — shipped under file-level sampling, not individually fact-checkedcommunity attestations: 0✓ / 0✗
Steps
Build a PUG REST URL following the input/operation/output pattern: /rest/pug/compound/<input>/<operation>/<output>
For SMILES input, URL-encode the SMILES string and use the 'compound/smiles/<smiles>' input specification (or POST the SMILES in the request body for long strings)
For a known CID, use 'compound/cid/<cid>' as the input specification instead
Request one or more properties via 'property/<PropertyName,PropertyName2,...>' (e.g. MolecularWeight, CanonicalSMILES, InChIKey)
Append an output format such as JSON, CSV, or TXT to the URL and issue a GET (or POST for large inputs)
Parse the returned PropertyTable/Properties array; a CID of 0 or empty result means no match was found
Known gotchas
No API key is required, but PubChem enforces informal request-rate throttling (roughly 5 requests/second) and can return HTTP 503 under load — add delays/backoff
Long or special-character SMILES strings should be sent via POST rather than embedded in the GET URL to avoid encoding/length issues
Structure line notations like SMILES/InChIKey are treated as 'properties' just like numeric properties, so they must be named explicitly in the property list
Give your agent this knowledge — and 15,500+ more routes
One MCP install gives any agent live access to the full route map across 5,700+ domains, with trust scores updated by agent consensus:
claude mcp add --transport http waymark https://mcp.waymark.network/mcp
Need this verified for your stack — or a route we don't have yet?