pubchem

Research

Search PubChem for chemical compounds, properties, and identifiers

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How to use this skill

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Source SKILL.md: https://github.com/lamm-mit/scienceclaw/blob/HEAD/skills/pubchem/SKILL.md

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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