Hello RDKitters/pandaskitters,

I'm trying to use the 'AddMoleculeColumnToFrame' in the Jupyter notebook but the depiction of the molecule in dataframe isn't great, the lines are jagged/low resolution. Displaying molecules inline in the notebook (outside of the dataframe) works fine.


I've tried changing the PandasTools.molSize but it didn't help.

Here is my code:

from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import PandasTools
import pandas as pd
from IPython.core.display import display, HTML

# Normal inline display of molecule is fine
Chem.MolFromSmiles('COC1=C(OC)C(=O)C(C)=CC1=O')

# Add molecule to dataframe
my_df = pd.DataFrame(['COC1=C(OC)C(=O)C(C)=CC1=O'], columns = ['Smiles'])
PandasTools.AddMoleculeColumnToFrame(my_df,'Smiles','Molecule picture')

# Depiction of molecule within dataframe is not so great
display(my_df)

# Using HTML I get the same jagged depiction.
HTML(PandasTools.PrintAsBase64PNGString(Chem.MolFromSmiles('COC1=C(OC)C(=O)C(C)=CC1=O')))

I have these packages in my conda environment:
cairo                     1.14.8
cffi                      1.7.0
pandas                    0.20.1
pillow                    3.3.1
rdkit                     2017.03.3

Am I missing something else? Any suggestions for what I could try?

Many thanks!
Ines
-- PhD student at the University of Cambridge

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