Hello Peter,
Great, that just made me realize that I was not using my most recent conda 
environment version of RDkit.
I reread the 2D sdf file with the latest rdkit version and now only 31 
molecules are tossed out by the SDMolsupplier in RDKit.  51 compounds had 
errors when reading in the smiles strings.
Brian


From: Peter S. Shenkin [mailto:shen...@gmail.com]
Sent: Monday, August 07, 2017 14:26
To: Bennion, Brian <benni...@llnl.gov>
Cc: Chris Swain <sw...@mac.com>; rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million 
compounds

That molecule's SMILES is correctly rendered by RDKit, or at least by the 
version of RDKit behind Slack:

[Inline image 1]


-P.

On Mon, Aug 7, 2017 at 3:54 PM, Bennion, Brian 
<benni...@llnl.gov<mailto:benni...@llnl.gov>> wrote:

The carbocations are in small heterocyclic molecules. see CHEMBL3815233

Brian



________________________________
From: Chris Swain <sw...@mac.com<mailto:sw...@mac.com>>
Sent: Monday, August 7, 2017 11:46:30 AM
To: 
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Subject: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million 
compounds

I've not tried to read in ChEMBL but I have tried to process other large 
datasets e.g. ZINC. My impression was that problems arose with small 
heterocyclic systems, particularly if fused or containing multiple different 
heteroatoms. I did wonder if the different aromaticity models might be the 
issue.

Chris
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