Hi Taka and Jan,
Thanks for your help. Worked out that I shouldn’t have added the names=[] when I read in my csv file (woops). It fails if you have a mol which is None, I’ll have to add a line asking it to check that ROMol isn’t None first. Annoying. Thanks for your help, mike From: Taka Seri <[email protected]> Sent: 31 October 2019 10:15 To: Jan Halborg Jensen <[email protected]> Cc: Mike Mazanetz <[email protected]>; RDKit Discuss <[email protected]> Subject: Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule Hi, Pandas apply function will work too. AddMoleculeColumnToFrame(DF, "Smiles") at first. Default setting, rdkit mol object will be added "ROMol" column in your dataframe. https://www.rdkit.org/docs/source/rdkit.Chem.PandasTools.html Then call apply function to apply a calculation function an axis of ROMol. https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.apply.html DF['HAC'] = DF["ROMol"].apply(Chem.Lipinski.HeavyAtomCount) Best regards, Taka 2019年10月31日(木) 18:30 Jan Halborg Jensen <[email protected] <mailto:[email protected]> >: Hi Mike This should work DF[‘HAC’] = [Chem.Lipinski.HeavyAtomCount(mol) for mol in DF[‘Molecule’]] Best regards, Jan On 31 Oct 2019, at 10.16, Mike Mazanetz <[email protected] <mailto:[email protected]> > wrote: Hi RDKit Gurus, I’ve followed the docs and created a molecule column in my Pandas dataframe. However, I do not seem to be able to do molecular operations on the column. For example, if you had a SMILES column, how would you calculate heavy atom count and append this result to a new column? This doesn’t work: DF[‘HAC’] = Chem.Lipinski.HeavyAtomCount(DF[‘Molecule’]) Where the Molecule column is generated by PandasTools.AddMoleculeColumnToFrame Thanks, mike _______________________________________________ Rdkit-discuss mailing list <mailto:[email protected]> [email protected] <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list [email protected] <mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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