name: pubchem-database description: Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. license: Unknown metadata: skill-author: K-Dense Inc.

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]

# Access individual properties
molecular_formula = compound.molecular_formula
molecular_weight = compound.molecular_weight
iupac_name = compound.iupac_name
smiles = compound.canonical_smiles
inchi = compound.inchi
xlogp = compound.xlogp  # Partition coefficient
tpsa = compound.tpsa    # Topological polar surface area

Get Specific Properties:

# Request only specific properties
properties = pcp.get_properties(
    ['MolecularFormula', 'MolecularWeight', 'CanonicalSMILES', 'XLogP'],
    'aspirin',
    'name'
)
# Returns list of dictionaries

Batch Property Retrieval:

import pandas as pd

compound_names = ['aspirin', 'ibuprofen', 'paracetamol']
all_properties = []

for name in compound_names:
    props = pcp.get_properties(
        ['MolecularFormula', 'MolecularWeight', 'XLogP'],
        name,
        'name'
    )
    all_properties.extend(props)

df = pd.DataFrame(all_properties)

Available Properties: MolecularFormula, MolecularWeight, CanonicalSMILES, IsomericSMILES, InChI, InChIKey, IUPACName, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBondCount, Complexity, Charge, and many more (see references/api_reference.md for complete list).

3. Similarity Search

Find structurally similar compounds using Tanimoto similarity:

import pubchempy as pcp

# Start with a query compound
query_compound = pcp.get_compounds('gefitinib', 'name')[0]
query_smiles = query_compound.canonical_smiles

# Perform similarity search
similar_compounds = pcp.get_compounds(
    query_smiles,
    'smiles',
    searchtype='similarity',
    Threshold=85,  # Similarity threshold (0-100)
    MaxRecords=50
)

# Process results
for compound in similar_compounds[:10]:
    print(f"CID {compound.cid}: {compound.iupac_name}")
    print(f"  MW: {compound.molecular_weight}")

Note: Similarity searches are asynchronous for large queries and may take 15-30 seconds to complete. PubChemPy handles the asynchronous pattern automatically.

4. Substructure Search

Find compounds containing a specific structural motif:

import pubchempy as pcp

# Search for compounds containing pyridine ring
pyridine_smiles = 'c1ccncc1'

matches = pcp.get_compounds(
    pyridine_smiles,
    'smiles',
    searchtype='substructure',
    MaxRecords=100
)

print(f"Found {len(matches)} compounds containing pyridine")

Common Substructures:

Benzene ring: c1ccccc1
Pyridine: c1ccncc1
Phenol: c1ccc(O)cc1
Carboxylic acid: C(=O)O

5. Format Conversion

Convert between different chemical structure formats:

import pubchempy as pcp

compound = pcp.get_compounds('aspirin', 'name')[0]

# Convert to different formats
smiles = compound.canonical_smiles
inchi = compound.inchi
inchikey = compound.inchikey
cid = compound.cid

# Download structure files
pcp.download('SDF', 'aspirin', 'name', 'aspirin.sdf', overwrite=True)
pcp.download('JSON', '2244', 'cid', 'aspirin.json', overwrite=True)

6. Structure Visualization

Generate 2D structure images:

import pubchempy as pcp

# Download compound structure as PNG
pcp.download('PNG', 'caffeine', 'name', 'caffeine.png', overwrite=True)

# Using direct URL (via requests)
import requests

cid = 2244  # Aspirin
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/PNG?image_size=large"
response = requests.get(url)

with open('structure.png', 'wb') as f:
    f.write(response.content)

7. Synonym Retrieval

Get all known names and synonyms for a compound:

import pubchempy as pcp

synonyms_data = pcp.get_synonyms('aspirin', 'name')

if synonyms_data:
    cid = synonyms_data[0]['CID']
    synonyms = synonyms_data[0]['Synonym']

    print(f"CID {cid} has {len(synonyms)} synonyms:")
    for syn in synonyms[:10]:  # First 10
        print(f"  - {syn}")

8. Bioactivity Data Access

Retrieve biological activity data from assays:

import requests
import json

# Get bioassay summary for a compound
cid = 2244  # Aspirin
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/assaysummary/JSON"

response = requests.get(url)
if response.status_code == 200:
    data = response.json()
    # Process bioassay information
    table = data.get('Table', {})
    rows = table.get('Row', [])
    print(f"Found {len(rows)} bioassay records")

For more complex bioactivity queries, use the scripts/bioactivity_query.py helper script which provides:

Bioassay summaries with activity outcome filtering
Assay target identification
Search for compounds by biological target
Active compound lists for specific assays

9. Comprehensive Compound Annotations

Access detailed compound information through PUG-View:

import requests

cid = 2244
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON"

response = requests.get(url)
if response.status_code == 200:
    annotations = response.json()
    # Contains extensive data including:
    # - Chemical and Physical Properties
    # - Drug and Medication Information
    # - Pharmacology and Biochemistry
    # - Safety and Hazards
    # - Toxicity
    # - Literature references
    # - Patents

Get Specific Section:

# Get only drug information
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON?heading=Drug and Medication Information"

Installation Requirements

Install PubChemPy for Python-based access:

uv pip install pubchempy

For direct API access and bioactivity queries:

uv pip install requests

Optional for data analysis:

uv pip install pandas

Helper Scripts

This skill includes Python scripts for common PubChem tasks:

scripts/compound_search.py

Provides utility functions for searching and retrieving compound information:

Key Functions:

search_by_name(name, max_results=10): Search compounds by name
search_by_smiles(smiles): Search by SMILES string
get_compound_by_cid(cid): Retrieve compound by CID
get_compound_properties(identifier, namespace, properties): Get specific properties
similarity_search(smiles, threshold, max_records): Perform similarity search
substructure_search(smiles, max_records): Perform substructure search
get_synonyms(identifier, namespace): Get all synonyms
batch_search(identifiers, namespace, properties): Batch search multiple compounds
download_structure(identifier, namespace, format, filename): Download structures
print_compound_info(compound): Print formatted compound information

Usage:

from scripts.compound_search import search_by_name, get_compound_properties

# Search for a compound
compounds = search_by_name('ibuprofen')

# Get specific properties
props = get_compound_properties('aspirin', 'name', ['MolecularWeight', 'XLogP'])

scripts/bioactivity_query.py

Provides functions for retrieving biological activity data:

Key Functions:

get_bioassay_summary(cid): Get bioassay summary for compound
get_compound_bioactivities(cid, activity_outcome): Get filtered bioactivities
get_assay_description(aid): Get detailed assay information
get_assay_targets(aid): Get biological targets for assay
search_assays_by_target(target_name, max_results): Find assays by target
get_active_compounds_in_assay(aid, max_results): Get active compounds
get_compound_annotations(cid, section): Get PUG-View annotations
summarize_bioactivities(cid): Generate bioactivity summary statistics
find_compounds_by_bioactivity(target, threshold, max_compounds): Find compounds by target

Usage:

from scripts.bioactivity_query import get_bioassay_summary, summarize_bioactivities

# Get bioactivity summary
summary = summarize_bioactivities(2244)  # Aspirin
print(f"Total assays: {summary['total_assays']}")
print(f"Active: {summary['active']}, Inactive: {summary['inactive']}")

API Rate Limits and Best Practices

Rate Limits:

Maximum 5 requests per second
Maximum 400 requests per minute
Maximum 300 seconds running time per minute

Best Practices:

Use CIDs for repeated queries: CIDs are more efficient than names or structures
Cache results locally: Store frequently accessed data
Batch requests: Combine multiple queries when possible
Implement delays: Add 0.2-0.3 second delays between requests
Handle errors gracefully: Check for HTTP errors and missing data
Use PubChemPy: Higher-level abstraction handles many edge cases
Leverage asynchronous pattern: For large similarity/substructure searches
Specify MaxRecords: Limit results to avoid timeouts

Error Handling:

from pubchempy import BadRequestError, NotFoundError, TimeoutError

try:
    compound = pcp.get_compounds('query', 'name')[0]
except NotFoundError:
    print("Compound not found")
except BadRequestError:
    print("Invalid request format")
except TimeoutError:
    print("Request timed out - try reducing scope")
except IndexError:
    print("No results returned")

Common Workflows

Workflow 1: Chemical Identifier Conversion Pipeline

Convert between different chemical identifiers:

import pubchempy as pcp

# Start with any identifier type
compound = pcp.get_compounds('caffeine', 'name')[0]

# Extract all identifier formats
identifiers = {
    'CID': compound.cid,
    'Name': compound.iupac_name,
    'SMILES': compound.canonical_smiles,
    'InChI': compound.inchi,
    'InChIKey': compound.inchikey,
    'Formula': compound.molecular_formula
}

Workflow 2: Drug-Like Property Screening

Screen compounds using Lipinski's Rule of Five:

import pubchempy as pcp

def check_drug_likeness(compound_name):
    compound = pcp.get_compounds(compound_name, 'name')[0]

    # Lipinski's Rule of Five
    rules = {
        'MW <= 500': compound.molecular_weight <= 500,
        'LogP <= 5': compound.xlogp <= 5 if compound.xlogp else None,
        'HBD <= 5': compound.h_bond_donor_count <= 5,
        'HBA <= 10': compound.h_bond_acceptor_count <= 10
    }

    violations = sum(1 for v in rules.values() if v is False)
    return rules, violations

rules, violations = check_drug_likeness('aspirin')
print(f"Lipinski violations: {violations}")

Workflow 3: Finding Similar Drug Candidates

Identify structurally similar compounds to a known drug:

import pubchempy as pcp

# Start with known drug
reference_drug = pcp.get_compounds('imatinib', 'name')[0]
reference_smiles = reference_drug.canonical_smiles

# Find similar compounds
similar = pcp.get_compounds(
    reference_smiles,
    'smiles',
    searchtype='similarity',
    Threshold=85,
    MaxRecords=20
)

# Filter by drug-like properties
candidates = []
for comp in similar:
    if comp.molecular_weight and 200 <= comp.molecular_weight <= 600:
        if comp.xlogp and -1 <= comp.xlogp <= 5:
            candidates.append(comp)

print(f"Found {len(candidates)} drug-like candidates")

Workflow 4: Batch Compound Property Comparison

Compare properties across multiple compounds:

import pubchempy as pcp
import pandas as pd

compound_list = ['aspirin', 'ibuprofen', 'naproxen', 'celecoxib']

properties_list = []
for name in compound_list:
    try:
        compound = pcp.get_compounds(name, 'name')[0]
        properties_list.append({
            'Name': name,
            'CID': compound.cid,
            'Formula': compound.molecular_formula,
            'MW': compound.molecular_weight,
            'LogP': compound.xlogp,
            'TPSA': compound.tpsa,
            'HBD': compound.h_bond_donor_count,
            'HBA': compound.h_bond_acceptor_count
        })
    except Exception as e:
        print(f"Error processing {name}: {e}")

df = pd.DataFrame(properties_list)
print(df.to_string(index=False))

Workflow 5: Substructure-Based Virtual Screening

Screen for compounds containing specific pharmacophores:

import pubchempy as pcp

# Define pharmacophore (e.g., sulfonamide group)
pharmacophore_smiles = 'S(=O)(=O)N'

# Search for compounds containing this substructure
hits = pcp.get_compounds(
    pharmacophore_smiles,
    'smiles',
    searchtype='substructure',
    MaxRecords=100
)

# Further filter by properties
filtered_hits = [
    comp for comp in hits
    if comp.molecular_weight and comp.molecular_weight < 500
]

print(f"Found {len(filtered_hits)} compounds with desired substructure")

Reference Documentation

For detailed API documentation, including complete property lists, URL patterns, advanced query options, and more examples, consult references/api_reference.md. This comprehensive reference includes:

Complete PUG-REST API endpoint documentation
Full list of available molecular properties
Asynchronous request handling patterns
PubChemPy API reference
PUG-View API for annotations
Common workflows and use cases
Links to official PubChem documentation

Troubleshooting

Compound Not Found:

Try alternative names or synonyms
Use CID if known
Check spelling and chemical name format

Timeout Errors:

Reduce MaxRecords parameter
Add delays between requests
Use CIDs instead of names for faster queries

Empty Property Values:

Not all properties are available for all compounds
Check if property exists before accessing: if compound.xlogp:
Some properties only available for certain compound types

Rate Limit Exceeded:

Implement delays (0.2-0.3 seconds) between requests
Use batch operations where possible
Consider caching results locally

Similarity/Substructure Search Hangs:

These are asynchronous operations that may take 15-30 seconds
PubChemPy handles polling automatically
Reduce MaxRecords if timing out

Additional Resources

PubChem Home: https://pubchem.ncbi.nlm.nih.gov/
PUG-REST Documentation: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest
PUG-REST Tutorial: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest-tutorial
PubChemPy Documentation: https://pubchempy.readthedocs.io/
PubChemPy GitHub: https://github.com/mcs07/PubChemPy

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