CNotebook Documentation
CNotebook provides ergonomic chemistry visualization in Jupyter Notebooks and Marimo with the OpenEye Toolkits. Simply import the package and your molecular data will be automatically rendered as chemical structures.
Key Features
Zero Configuration: Just import and molecules render as structures
Multiple Environments: Supports Jupyter Notebooks and Marimo
DataFrame Integration: Works with Pandas and Polars DataFrames
MolGrid Interactive Grids: Browse, search, and select molecules
C3D 3D Viewer: Interactive 3Dmol.js viewer with built-in GUI
Design Unit Support: Render protein-ligand complexes from
OEDesignUnitSubstructure Highlighting: SMARTS pattern highlighting
Molecular Alignment: Align molecules to reference structures
Native Object Support
Make OEMol, OEGraphMol, OE2DMolDisplay, and OEDesignUnit
first-class citizens in your notebook with native, highly configurable rendering.
Pandas and Polars in Marimo
Works with the native Marimo table UI.
Pandas and Polars in Jupyter
Keep the same look-and-feel without changing any DataFrame rendering in Jupyter notebooks.
| Molecule | Name | MolWt | |
|---|---|---|---|
| 0 |  |
benzene | 78.11184 |
| 1 |  |
2-acetoxybenzoic acid | 180.15742000000003 |
| 2 |  |
2-(4-isobutylphenyl)propanoic acid | 206.28082 |
| 3 |  |
1,3,7-trimethylpurine-2,6-dione | 194.1906 |
| 4 |  |
~{N}-(4-hydroxyphenyl)acetamide | 151.16255999999998 |
Molecule Grid Support
Access searchable, interactive molecule grids from iterables of molecule objects,
and directly from DataFrame or Series in Pandas and Polars.
Contents
Getting Started
User Guide
API Reference