Intern PubChem Name Conversion

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name: intern_pubchem_name_conversion description: Convert molecules between IUPAC, SMILES, and molecular formula using PubChem as the source of truth. Use this whenever the user asks to convert, normalize, or cross-check molecular representations in chemistry/science workflows (including Intern research tasks). Prefer API lookup over memory; do not guess. homepage: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest metadata: { "openclaw": { "emoji": "🧪", "requires": { "bins": ["curl", "python3"] } } }

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Intern PubChem Name Conversion

Convert one molecular representation into all three fields:

smiles

iupac

formula

When to use

Use this skill when the user asks to:

convert IUPAC <-> SMILES

fetch molecular formula from IUPAC/SMILES

validate molecule identity against PubChem

Do not use this skill for:

reaction mechanism explanation

quantum chemistry simulation

docking or property prediction beyond PubChem identifiers

Input contract

Expect one input value and one type:

input_type: iupac or smiles

input_value: raw string

If the user gives only one string without type:

treat strings with many bond symbols (=, #, [, ], @) as smiles

otherwise treat as iupac/name query

Required behavior

Always query PubChem first. Do not answer from memory when tools are available.

1) URL-encode the full input string:

ENCODED=$(python3 -c 'import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1], safe=""))' "$INPUT_VALUE")

2) Build the primary endpoint:

If input_type == iupac:

- https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{ENCODED}/property/SMILES,IUPACName,MolecularFormula/JSON

If input_type == smiles:

- https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/{ENCODED}/property/SMILES,IUPACName,MolecularFormula/JSON

3) If smiles primary endpoint is non-200, retry once with:

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/smiles/{ENCODED}/property/SMILES,IUPACName,MolecularFormula/JSON

4) If still non-200, do CID fallback:

Resolve CID:

- iupac: .../compound/name/{ENCODED}/cids/JSON - smiles: .../compound/smiles/{ENCODED}/cids/JSON

Then fetch properties by CID:

- .../compound/cid/{CID}/property/SMILES,IUPACName,MolecularFormula/JSON

5) Parse PropertyTable.Properties[0] and map:

smiles <- SMILES (fallback ConnectivitySMILES)

iupac <- IUPACName

formula <- MolecularFormula

Output format

Return JSON only (no markdown fences, no extra prose):

{
  "smiles": "...",
  "iupac": "...",
  "formula": "..."
}

If all attempts fail, still return the same schema with empty strings:

{
  "smiles": "",
  "iupac": "",
  "formula": ""
}

Quality rules

Keep PubChem values verbatim; do not rewrite or normalize names.

If multiple records are returned, use the first record consistently.

Do not silently swap stereochemistry markers.