PubChem Database

Overview

PubChem is the world's largest freely available chemical database with 110M+ compounds and 270M+ bioactivities. Query chemical structures by name, CID, or SMILES, retrieve molecular properties, perform similarity and substructure searches, access bioactivity data using PUG-REST API and PubChemPy.

When to Use This Skill

This skill should be used when:

• Searching for chemical compounds by name, structure (SMILES/InChI), or molecular formula
• Retrieving molecular properties (MW, LogP, TPSA, hydrogen bonding descriptors)
• Performing similarity searches to find structurally related compounds
• Conducting substructure searches for specific chemical motifs
• Accessing bioactivity data from screening assays
• Converting between chemical identifier formats (CID, SMILES, InChI)
• Batch processing multiple compounds for drug-likeness screening or property analysis

Core Capabilities

1. Chemical Structure Search

Search for compounds using multiple identifier types:

By Chemical Name:

import pubchempy as pcp
compounds = pcp.get_compounds('aspirin', 'name')
compound = compounds[0]

By CID (Compound ID):

compound = pcp.Compound.from_cid(2244)  # Aspirin

By SMILES:

compound = pcp.get_compounds('CC(=O)OC1=CC=CC=C1C(=O)O', 'smiles')[0]

By InChI:

compound = pcp.get_compounds('InChI=1S/C9H8O4/...', 'inchi')[0]

By Molecular Formula:

compounds = pcp.get_compounds('C9H8O4', 'formula')
# Returns all compounds matching this formula

2. Property Retrieval

Retrieve molecular properties for compounds using either high-level or low-level approaches:

Using PubChemPy (Recommended):

import pubchempy as pcp

# Get compound object with all properties
compound = pcp.get_compounds('caffeine', 'name')[0]