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 <ruggiu.fiore...@gmail.com>
Sent: 31 October 2019 15:48
To: Mike Mazanetz <mi...@novadatasolutions.co.uk>
Cc: Jan Halborg Jensen <jhjen...@chem.ku.dk>; RDKit Discuss
<rdkit-discuss@lists.sourceforge.net>
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 <mi...@novadatasolutions.co.uk
<mailto:mi...@novadatasolutions.co.uk> > 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
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