PubChemPy

1.0.5 · active · verified Thu Apr 09

PubChemPy is a simple Python wrapper around the PubChem PUG REST API, providing an intuitive interface to query chemical information from PubChem. It allows programmatic access to compounds, substances, assays, and their properties. The current version is 1.0.5, and releases are infrequent, primarily addressing bug fixes and minor enhancements.

Warnings

gotcha PubChem imposes rate limits (e.g., 10 requests per second from a single IP address) on its PUG REST API. PubChemPy does not inherently manage these limits, so users must implement delays or batch queries (where applicable, like `as_dataframe=True` for `get_compounds`) to avoid HTTP 429 (Too Many Requests) errors.
Fix: Implement explicit delays (`time.sleep()`) between calls or use `PubChemPy` features that support batch processing for large numbers of queries.
gotcha API calls might return empty lists or `None` if no data is found, or raise `pubchempy.PubChemPyError` for issues like invalid CIDs or API errors. Robust error handling is crucial.
Fix: Always check if results are empty or `None` before accessing elements, and wrap API calls in `try...except PubChemPyError` blocks.
gotcha The behavior of `Compound.fingerprint` was corrected in v1.0.4 to align with the CACTVS fingerprint specification. Users relying on outputs from older versions might observe different fingerprint values.
Fix: If `Compound.fingerprint` was used in versions prior to 1.0.4, review any code that depends on its output, as the generated fingerprints might now be different and more accurate.
gotcha Proxy configuration was a known issue in older versions (addressed in v1.0.4). While PubChemPy leverages `requests` for HTTP, direct proxy configuration might still be needed via environment variables (`http_proxy`, `https_proxy`) or by passing a `proxies` dictionary to `requests` if direct `pubchempy` support is lacking for a specific function.
Fix: Ensure `http_proxy` and `https_proxy` environment variables are correctly set for system-wide proxy use, or explore `requests` library documentation for direct proxy configuration if `pubchempy` specific methods are not available for advanced proxy setups.

Install

pip install PubChemPy Install latest version

Imports

pubchempy
```
import pubchempy as pcp
```
Compound
```
from pubchempy import Compound
```
Substance
```
from pubchempy import Substance
```
PubChemPyError
```
from pubchempy import PubChemPyError
```

Quickstart

This example demonstrates how to search for a compound by name, retrieve its basic properties, and then fetch additional specific properties using its PubChem CID.

import pubchempy as pcp

try:
    # Search for compounds by name
    compounds = pcp.get_compounds('aspirin', 'name')

    if compounds:
        aspirin = compounds[0]
        print(f"Compound Name: {aspirin.iupac_name}")
        print(f"CID: {aspirin.cid}")
        print(f"Molecular Formula: {aspirin.molecular_formula}")
        print(f"Canonical SMILES: {aspirin.canonical_smiles}")

        # Retrieve specific properties for a compound
        properties = pcp.get_properties(
            ['molecular_weight', 'xlogp'], # List of properties to fetch
            aspirin.cid,
            'cid' # Namespace: 'cid' for compound IDs
        )
        if properties:
            print(f"Molecular Weight: {properties[0]['MolecularWeight']}")
            print(f"XLogP: {properties[0]['XLogP']}")
        else:
            print("Could not retrieve additional properties.")

    else:
        print("Aspirin not found in PubChem.")

except pcp.PubChemPyError as e:
    print(f"A PubChemPy API error occurred: {e}")
except Exception as e:
    print(f"An unexpected error occurred: {e}")

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