PubChemPy

PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.

Installation

Install PubChemPy with pip:

pip install pubchempy

Or with conda:

conda install -c conda-forge pubchempy

For detailed instructions, see the installation guide.

Example usage

Retrieve a compound by its PubChem Compound Identifier (CID) and print its SMILES and IUPAC name:

>>> import pubchempy as pcp
>>> comp = pcp.Compound.from_cid(1423)
>>> print(comp.smiles)
CCCCCCCNC1CCCC1CCCCCCC(=O)O
>>> print(comp.iupac_name)
7-[2-(heptylamino)cyclopentyl]heptanoic acid

Search compounds by name and print the SMILES and molecular weight of the first result:

>>> results = pcp.get_compounds("Aspirin", "name")
>>> print(results[0].smiles)
CC(=O)OC1=CC=CC=C1C(=O)O
>>> print(results[0].molecular_weight)
180.16

Documentation

Full documentation is available at https://docs.pubchempy.org.

This includes a step-by-step guide on how to use PubChemPy, as well as a complete API reference.

Contributing

• Feature ideas and bug reports are welcome on the Issue Tracker.
• Fork the source code on GitHub, make changes and file a pull request.

License

PubChemPy is licensed under the MIT license.