chemspace-marimo

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Interactive chemical space viewer built with marimo.

Explore chemical space on a t-SNE scatter plot, tune embedding and clustering parameters, and inspect selected molecules in a reactive table.

Demo

Features

• 2000 NCI molecules from RDKit built-in dataset
• Morgan fingerprints (ECFP4) + Tanimoto distance matrix
• scikit-learn TSNE 2D embedding with precomputed distances
• HDBSCAN density-based clustering
• Reactive parameter controls for t-SNE and HDBSCAN (mo.ui.number)
• mo.ui.matplotlib interactive box / lasso selection
• Inline SVG structures in the property table via format_mapping
• Noise filtering (cluster = -1) for selected rows

Quick Start

No install needed — just run with PEP 723 inline metadata:

uvx marimo edit ./app.py --sandbox

Or with a local virtual environment:

uv sync
uv run marimo edit app.py