Hi Brian,
It's not that surprising. The RDKit is stricter about allowing unreasonable
chemistry that the tool the ChEMBL group uses to produce SMILES or mol
blocks.
There are always some molecules that the RDKit just won't process.
If you are concerned and see any in that group of failures that you think
should have been processed, please let me know.
-greg
On Mon, Aug 7, 2017 at 6:36 PM, Bennion, Brian wrote:
> Hello,
>
>
>
> This might be a nit picky question. I am attempting to read in the smiles
> string for the 1.7 million non-biological compounds in the latest chembl23
> release. As it turns out 382 compounds fail to be read by RDkit.
>
> The errors are either kekulization failure or valence errors.
>
>
>
> Has anyone attempted this task before?
>
> Brian
>
>
>
>
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