Installation

Requirements

CNotebook requires:

  • Python 3.11 or later

  • OpenEye Toolkits (2025.2.1 or later) with a valid license

Optional dependencies for DataFrame support:

  • Pandas support: pandas and oepandas

  • Polars support: polars and oepolars

Installing CNotebook

Install from PyPI:

pip install cnotebook

Or install from source:

git clone https://github.com/your-repo/cnotebook.git
cd cnotebook
pip install -e .

Installing Optional Dependencies

For Pandas DataFrame support:

pip install oepandas

For Polars DataFrame support:

pip install oepolars

CNotebook will automatically detect which backends are available and use them accordingly.

OpenEye Toolkits License

CNotebook requires a valid OpenEye Toolkits license (http://eyesopen.com/). Ensure your license file is properly configured before using CNotebook. Refer to the OpenEye documentation for license configuration details. Note that OpenEye offers free toolit licenses to academic institutions.

Verifying Installation

To verify your installation is working correctly:

import cnotebook
from openeye import oechem

# Check available backends
env = cnotebook.get_env()
print(f"Pandas available: {env.pandas_available} ({env.pandas_version})")
print(f"Polars available: {env.polars_available} ({env.polars_version})")
print(f"IPython available: {env.ipython_available} ({env.ipython_version})")
print(f"Marimo available: {env.marimo_available} ({env.marimo_version})")
print(f"MolGrid available: {env.molgrid_available}")

You should see something similar, depending on your environment and the notebook that you are using:

Pandas available: True (3.0.0)
Polars available: True (1.37.1)
IPython available: True (9.9.0)
Marimo available: False ()
MolGrid available: True