That worked! Thanks Greg and everyone who worked on that, brilliant!
Ines

On 2017-10-25 07:09, Greg Landrum wrote:
Hi Ines,

This problem should go away if you update to the most recent version
of the RDKit.

-greg

On Tue, Oct 24, 2017 at 4:19 PM, Ines Smit <ia...@cam.ac.uk> wrote:

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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