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:[email protected]]
Sent: Monday, August 07, 2017 14:26
To: Bennion, Brian <[email protected]>
Cc: Chris Swain <[email protected]>; [email protected]
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
<[email protected]<mailto:[email protected]>> wrote:
The carbocations are in small heterocyclic molecules. see CHEMBL3815233
Brian
________________________________
From: Chris Swain <[email protected]<mailto:[email protected]>>
Sent: Monday, August 7, 2017 11:46:30 AM
To:
[email protected]<mailto:[email protected]>
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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