Certara Brings Chemaxon Cheminformatics Natively to Python with New Python API

Radnor, PA – July 20, 2026, Certara, Inc. (Nasdaq: CERT), a global leader in model-informed drug development, today announced that a native Python toolkit that brings Chemaxon’s cheminformatics engine, including molecular conversions, property calculations, fingerprinting and similarity checks directly into Python via an API is now available for use.

Python has surpassed specialized scripting languages in all areas of modern discovery organizations, from data science and machine learning teams to bench scientists building their own analysis notebooks.

With the new API, compounds are mapped to native Python objects that drop into any Jupyter notebook, analytics pipeline, or real-time workflow using standard Pythonic tools without the need for external API calls, CLI wrappers or Java bridge.

“Discovery scientists are increasingly standardizing new automation, screening, and modeling projects on Python while continuing to rely on Chemaxon cheminformatics toolkits. The new Python API is designed to meet that shift directly,” said Roland Knispel, Senior Product Manager, Core Chemistry Toolkits.

 

The Chemaxon Python API delivers value for discovery scientists in the following ways:

Designed for frictionless adoption

Alongside the release, Certara is changing how Chemaxon interfaces are packaged. Rather than licensing the Python API as a separate add-on, it’s included with the toolkits and products customers already own – no separate purchase required to start using it.

Coverage expands with every release

The new Python API ships with the foundational cheminformatics tools scientists rely on most. Certara is bringing over additional functionality from its established Java API incrementally, prioritized by customer demand. The list of current capabilities is continuously updated in their documentation, so customers know what’s available today.

Built to get scientists running in minutes

Getting started takes a single line: pip install chemaxon. No separate package to stand up, no external dependencies. Certara also provides a growing library of ready-to-run Jupyter notebooks covering common tasks like structure conversion, property and fingerprint calculation, and similarity screening, so scientists can go from install to a working notebook the same day.

Learn more about the new Python API in the Chemaxon documentation.

Join the first Python API webinar on July 30.