pubchem-compounds 1.1.3

A Python wrapper for the PubChem PUG REST API. Provides convenient methods to retrieve chemical information using CIDs, SIDs, CAS numbers, SMILES, and InChIKeys, and to convert between chemical identifiers. Built-in rate limiting and retry logic; RDKit integration for SDF/mol retrieval.

pubchem-compounds

A Python wrapper for the PubChem PUG REST API, focused on Compounds and Substances. It provides:

• Identifier conversion: CAS → CID / SID, InChIKey → CID, SMILES → CID, CID → CAS / EINECS / DTXSID
• Batch property fetching from lists of CIDs
• SDF / RDKit mol retrieval for CIDs, SIDs, or CAS numbers
• SMILES and InChI extraction for any PubChem synonym
• PFAS classification tree node queries
• Built-in rate limiting (max 5 req/s, 400 req/min) and automatic retry on HTTP 403

Installation

From PyPI

pip install pubchem-compounds

Note: RDKit is required only for functions that return molecules (get_mols_from_cids, cas_to_mols, synonyms_to_smiles, etc.). Install it separately:

pip install rdkit          # rdkit ≥ 2023.03
# or via conda:
conda install -c conda-forge rdkit

From source

git clone https://gitlab.com/lucmiaz/pubchem.git
cd pubchem
pip install -e .

Install with optional dependencies:

pip install -e ".[dev]"   # pytest, pylint
pip install -e ".[docs]"  # sphinx, sphinx-rtd-theme

Quick start

import pubchem_compounds as pc

CAS → CID

mapping, failed = pc.cas_to_cid("7732-18-5")  # water
print(mapping)   # {'7732-18-5': [962]}

Batch CAS lookup

cas_list = ["7732-18-5", "74-82-8", "71-43-2"]
mapping, failed = pc.cas_to_cid(cas_list)
# {'7732-18-5': [962], '74-82-8': [297], '71-43-2': [241]}

CAS → SMILES

processed, failed = pc.cas_to_smiles(["7732-18-5", "74-82-8"])
print(processed["7732-18-5"])  # 'O'
print(processed["74-82-8"])    # 'C'

CAS → RDKit molecules

mols = pc.cas_to_mols(["7732-18-5", "74-82-8"])
for cas, mol_list in mols.items():
    for mol in mol_list:
        print(cas, mol.GetNumAtoms())

Fetch compound properties for a list of CIDs

data = pc.get_from_cids([962, 297, 241], target="property/MolecularFormula,MolecularWeight")
for prop in data["PropertyTable"]["Properties"]:
    print(prop["CID"], prop["MolecularFormula"], prop["MolecularWeight"])

CID → CAS (reverse lookup)

cas_list = pc.cid_to_cas(962)
print(cas_list)  # ['7732-18-5']

InChIKey → CID

cids = pc.inchikey_to_pubchem("XLYOFNOQVPJJNP-UHFFFAOYSA-N")
print(cids)  # [962]

DTXSID → SMILES

Via PubChem

processed, failed = pc.dtxsid_to_smiles(["DTXSID9020584"])
print(processed["DTXSID9020584"])

Via CompTox

from pubchemcompounds import mols_from_comptox
mols = mols_from_comptox(["DTXSID4059916"])

PFAS classification tree

# Fetch all CIDs from the OECD PFAS list node (default hnid = 5517102)
cids = pc.pubchem_pfas_tree()
print(f"{len(cids)} PFAS CIDs found")

For a full API reference and more examples, see the documentation.

Dependencies

Package	Purpose
requests	HTTP requests
numpy	Rate-limiting random intervals
regex	CAS / EINECS / DTXSID pattern matching
tqdm	Progress bars for batch operations
rdkit (optional)	SDF parsing and mol/SMILES generation

Licence

Copyright © 2024–2026 Luc T. Miaz.
Licensed under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) licence.

Acknowledgments

Developed under the ZeroPM project (WP2) funded by the European Union's Horizon 2020 research and innovation programme (grant agreement No 101036756). Developed at the Department of Environmental Science, Stockholm University.