In addition to Brian's observation, there is also a "C1" early in the
SMILES, but no corresponding X1 to make a ring bond before or after it.
It appears that you might be reading the second half of a SMILES for some
reason. My guess is that the (C=C1) is associated with a preceding atom
that was not read.
-P
On Wed, Jan 18, 2017 at 6:32 PM, Brian Kelley <fustiga...@gmail.com> wrote:
> That doesn't look like a valid SMILES to me, I don't think a think a
> smiles string can start with a parenthesis ( branch ).
>
> ----
> Brian Kelley
>
> On Jan 18, 2017, at 6:18 PM, Larson Danes <lgda...@gmail.com> wrote:
>
> Hi all,
>
> I'm using the following query in postgresql (with the rdkit extension
> installed):
>
> "select casrn from mols where m @> CAST(? AS mol)"
>
>
> This returns "ERROR: could not create molecule from SMILES '...' " on
> occasion. One such SMILE that causes this error regularly is
> '(C=C1)[N+]([O-])=O'. I'm curious if there's documentation on this specific
> error message anywhere. I've looked and haven't had luck finding any.
>
> Any information about this error message is much appreciated.
>
>
> Thanks,
>
>
> Larson
>
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