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 ``OEDesignUnit`` - **Substructure 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. .. image:: _static/molecule_with_style.png :align: center =========================== Pandas and Polars in Marimo =========================== Works with the native Marimo table UI. .. image:: _static/marimo_pandas_polars.png :align: center ============================ Pandas and Polars in Jupyter ============================ Keep the same look-and-feel without changing any ``DataFrame`` rendering in Jupyter notebooks. .. raw:: html
Molecule Name MolWt
0 Image benzene 78.11184
1 Image 2-acetoxybenzoic acid 180.15742000000003
2 Image 2-(4-isobutylphenyl)propanoic acid 206.28082
3 Image 1,3,7-trimethylpurine-2,6-dione 194.1906
4 Image ~{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. .. image:: _static/molgrid_example.png :align: center Contents -------- .. toctree:: :maxdepth: 2 :caption: Getting Started installation quickstart .. toctree:: :maxdepth: 2 :caption: User Guide rendering dataframes molgrid c3d advanced_rendering .. toctree:: :maxdepth: 2 :caption: API Reference api/index Indices and Tables ------------------ * :ref:`genindex` * :ref:`modindex` * :ref:`search`