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 <mhel...@admarebio.com<mailto:mhel...@admarebio.com>> 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 Direct: 604.827.1122 Main: 604.827.1147 <image001.png> 2405 Wesbrook Mall, 4th Floor, Vancouver, BC V6T 1Z3 This email and any attachments thereto may contain confidential material for the sole use of the intended recipient. Anyreview, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not theintended recipient, please contact the sender immediately and permanently delete the original and any copies of this emailand any attachments thereto. _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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