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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