Yes, I can confirm that this is a problem caused by changes in Pandas v0.25.x
Now we just need to figure out what those changes are and how to work around them. Here's a github issue to track the problem: https://github.com/rdkit/rdkit/issues/2673 -greg On Tue, Nov 5, 2019 at 12:21 PM Jan Halborg Jensen <jhjen...@chem.ku.dk> wrote: > 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> 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 > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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