Hi,
In a Jupyter notebook, the following code does not show renderings of the
molecules in a Pandas dataframe:
<code>
from rdkit import Chem
from rdkit.Chem import PandasTools
from rdkit.Chem.Draw import MolsToGridImage
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
IPythonConsole.ipython_useSVG = True
test_df = pd.read_csv('test.smi', delim_whitespace=True, header=None,
names=['smiles', 'id'])
PandasTools.RenderImagesInAllDataFrames(images=True)
PandasTools.AddMoleculeColumnToFrame(test_df, 'smiles', 'mol',
includeFingerprints=False)
test_df
</code>
Instead, string representations are shown (I think), i.e. every field in the
mol column starts with
<img src="data:image/png;base64..."
As far as I understand the documentation,
PandasTools.RenderImagesInAllDataFrames(images=True) should show the rendered
molecules. What am I doing wrong?
I'm using RDkit version 2019.03.4.0 via Anaconda.
Thanks
Markus
--
Markus Heller, PhD
Senior Scientist
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