lamm-mit PubChem Compound Lookup
Query the PubChem database for chemical compounds, molecular properties, SMILES, InChI, and related data. PubChem is NCBI's open chemistry database.
Overview
- Search compounds by name or identifier
- Retrieve molecular formula, weight, SMILES, InChI, InChIKey
- Find related compounds and synonyms
- No API key required (rate limit: 5 requests/second)
Usage
Search by compound name:
python3 {baseDir}/scripts/pubchem_search.py --query "aspirin"
Get compound by CID:
python3 {baseDir}/scripts/pubchem_search.py --cid 2244
Get detailed properties:
python3 {baseDir}/scripts/pubchem_search.py --cid 2244 --format detailed
Search with max results:
python3 {baseDir}/scripts/pubchem_search.py --query "caffeine" --max-results 5
Parameters
| Parameter | Description | Default |
|---|---|---|
--query |
Compound name or search term | - |
--cid |
PubChem Compound ID | - |
--max-results |
Max results for search | 10 |
--format |
Output: summary, detailed, json | summary |
Output
- Summary: CID, name, molecular formula, molecular weight, SMILES
- Detailed: Adds InChI, InChIKey, synonyms, related CIDs
- JSON: Full API response
Notes
- Rate limit: 5 requests per second (no API key)
- Use --cid for exact compound when you know the ID
- Use --query for name or text search