Intern Pubchem Name Conversion

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.