How to convert a SDF molecular structure file to a pandas dataframe with Python?

Question

What is the best python tool to convert a SDF file to a structured data frame (pandas.DataFrame). Similar to Molconvert from ChemAxon? SDF can have different datafields for each compound which I would like to have in a dataframe. The 2D or 3D structures can be disregarded.

Sören · Accepted Answer

It is easily done with RDKit:
from rdkit.Chem import PandasTools

fn = '/mypath/dataset.sdf'

df = PandasTools.LoadSDF(fn, embedProps=True, molColName=None, smilesName='smiles')

How to convert a SDF molecular structure file to a pandas dataframe with Python?

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