pandas_ext

Pandas DataFrame Accessor

The chem accessor provides chemistry-aware operations on Pandas DataFrames and Series containing molecule columns.

Usage

import cnotebook
import pandas as pd
import oepandas as oepd

# The accessor is automatically registered when cnotebook is imported
df = pd.DataFrame({"SMILES": ["CCO", "c1ccccc1"]})

# Convert SMILES to molecules
df.chem.as_molecule("SMILES", inplace=True)

# Highlight substructures
df.SMILES.chem.highlight("c1ccccc1")

# Align depictions
df.SMILES.chem.align_depictions("first")

# Create MolGrid
grid = df.SMILES.chem.molgrid()

DataFrame Methods

DataFrame.chem.as_molecule(column, inplace=False)

Convert a SMILES column to molecules.

DataFrame.chem.highlight_using_column(mol_col, pattern_col, inplace=False)

Highlight substructures using patterns from another column.

DataFrame.chem.fingerprint_similarity(mol_col, reference, inplace=False)

Color molecules by fingerprint similarity to a reference.

DataFrame.chem.molgrid(**kwargs)

Create a MolGrid from the DataFrame.

Series Methods

Series.chem.highlight(smarts)

Highlight a SMARTS pattern in the molecule column.

Series.chem.align_depictions(reference)

Align molecule depictions to a reference.

Series.chem.molgrid(**kwargs)

Create a MolGrid from the Series.