This directory contains example marimo notebooks demonstrating the usage of the marimo_chem_utils library for cheminformatics tasks.

This notebook demonstrates how to build an interactive cluster viewer.

• Features:
  • Reads a dataset of carbonic anhydrase inhibitors.
  • Generates fingerprints and performs Taylor-Butina clustering.
  • Aligns structures within clusters using MCS alignment.
  • Provides an interactive interface to select clusters and view aligned chemical structures.

This notebook shows how to run and visualize Rapid Elimination of Swill (REOS) filters.

• Features:
  • Applies structural filters (e.g., BMS rules) to remove undesirable compounds.
  • Summarizes filter results.
  • Interactive table to select specific filter rules and view matching molecules with the matching substructure highlighted.

This notebook creates an interactive scatterplot for chemical space visualization.

• Features:
  • Calculates TSNE coordinates from chemical fingerprints.
  • Displays an interactive scatterplot where points represent molecules.
  • Allows users to select points on the plot to view the corresponding chemical structures in a grid.

To run any of these examples, ensure you have the required dependencies installed (listed in the script metadata) and run the script using marimo:

marimo edit clustering.py
# or
marimo edit reos.py
# or
marimo edit scatterplot.py