Re: [Rdkit-discuss] Molecules not rendere in Dataframe

[Jan H. J. <jhj...@ch...>]

Hi again,

Since I thought it might be a Colab problem I also posted the question on Stackoverflow, and got an answer from Oliver Scott
https://stackoverflow.com/questions/58656572/problem-using-addmoleculecolumntoframe-on-google-colab/58690736#58690736

"Seems like this is a problem with all pandas versions above 0.25.0, So I guess for now the easiest fix is to downgrade pandas. Or you can use this method which seemed to work for me:


from IPython.display import HTML
HTML(df.to_html())

I haven’t managed to downgrade pandas on Colab (almost certainly a Colab issue) but the other workaround works fine.

Best regards, Jan

On 4 Nov 2019, at 19.47, Markus Heller <mh...@ad...<mailto:mh...@ad...>> wrote:

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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