Intern PubChem Name Conversion

Convert molecules between IUPAC, SMILES, and molecular formula using PubChem as the source of truth. Use this whenever the user asks to convert, normalize, o...

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.