Hi Fio,
Thanks for the tips. I’ve found that I need PandasTools to convert a smiles to a mol though, I’ve not had MolFromSmiles work on a dataframe. Have you found that this works? Cheers, mike From: Fiorella Ruggiu <[email protected]> Sent: 31 October 2019 15:48 To: Mike Mazanetz <[email protected]> Cc: Jan Halborg Jensen <[email protected]>; RDKit Discuss <[email protected]> Subject: Re: [Rdkit-discuss] failed mols in converting SMILES to Pandas dataframe Molecule Hello Mike, you could create a function with your if else structure and use apply on the pandas dataframe. For example, if you have a SMILES column in your df: def addMol(smiles): if Chem.MolFromSmiles(smiles) is None: Etc return None # or whatever you wish to return when it fails else: Etc return Chem.MolFromSmiles(smiles) df['RDKitMol']=df.apply(lambda row: addMol(row['SMILES']), axis=1) Might not be as efficient as the build-in PandasTools though. Best, Fio On Thu, Oct 31, 2019 at 8:07 AM Mike Mazanetz <[email protected] <mailto:[email protected]> > wrote: Dear RDKit’ers I’ve been trying to skip failed molecules in PandasTools.AddMoleculeColumnToFrame. This is possible if I chuck each row to a different processor, but what I really want to do is return a missing row entry. Normally I’d go: If mol is None: Etc Else: Etc But Pandas DF’s seem to being playing hard-ball. Any thoughts? Cheers, mike _______________________________________________ Rdkit-discuss mailing list [email protected] <mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
