lamm-mit/pubchem
skills/pubchem/SKILL.md
Search PubChem for chemical compounds, properties, and identifiers
$ install --global
skillsauthnpx skillsauth add lamm-mit/scienceclaw pubchemInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Last scanned: Apr 6, 2026, 12:54 PM21.2s2 files scanned
SKILL.md
- name:
- pubchem
- description:
- Search PubChem for chemical compounds, properties, and identifiers
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
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