pubchem-database

What this skill does

# 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**:
```python
import pubchempy as pcp
compounds = pcp.get_compounds('aspirin', 'name')
compound = compounds[0]
```

**By CID (Compound ID)**:
```python
compound = pcp.Compound.from_cid(2244)  # Aspirin
```

**By SMILES**:
```python
compound = pcp.get_compounds('CC(=O)OC1=CC=CC=C1C(=O)O', 'smiles')[0]
```

**By InChI**:
```python
compound = pcp.get_compounds('InChI=1S/C9H8O4/...', 'inchi')[0]
```

**By Molecular Formula**:
```python
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)**:
```python
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**:
```python
# Request only specific properties
properties = pcp.get_properties(
    ['MolecularFormula', 'MolecularWeight', 'CanonicalSMILES', 'XLogP'],
    'aspirin',
    'name'
)
# Returns list of dictionaries
```

**Batch Property Retrieval**:
```python
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:

```python
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:

```python
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:

```python
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:

```python
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:

```python
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:

```python
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:

```python
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**:
```python
# 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:

```bash
uv pip install pubchempy
```

For direct API access and bioactivity queries:

```bash
uv pip install requests
```

Optional for data analysis:

```bash
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 pro