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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.

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  • $\begingroup$ Please provide a small example file $\endgroup$ Feb 5 at 0:13
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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')
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