marimo-chem-utils 0.2.0

A collection of cheminformatics utility functions for use with marimo notebooks.

marimo-chem-utils

A collection of cheminformatics utility functions for use with marimo, an open-source reactive notebook for Python.

Installation

You can install marimo-chem-utils using pip:

pip install marimo-chem-utils

Usage

Here is an example of how to use some of the functions in this library.

import pandas as pd
import marimo as mo
from marimo_chem_utils import (
    add_fingerprint_column,
    add_image_column,
    add_inchi_key_column,
    add_tsne_columns,
    interactive_chart
)

# Load some data
df = pd.read_csv("https://raw.githubusercontent.com/PatWalters/datafiles/refs/heads/main/carbonic.csv")

# Add fingerprints, images, and InChI keys
df = add_fingerprint_column(df, fp_type="counts_fp")
df = add_image_column(df, smiles_column="SMILES")
df = add_inchi_key_column(df, smiles_column="SMILES")

# Generate t-SNE coordinates
df = add_tsne_columns(df)

# Create an interactive plot
chart = interactive_chart(df, x_col="TSNE_x", y_col="TSNE_y", color_col="PIC50", image_col="image")

# In a marimo cell, you would display the chart like this:
# mo.ui.altair_chart(chart)

This will create a pandas.DataFrame with additional columns for fingerprints, images, and InChI keys, and then generate an interactive t-SNE plot that you can explore in your marimo notebook. The plot will display molecule images in the tooltips.