Hi Rajarshi,
Here's what RDKit says from the interactive shell:
>>> from rdkit import Chem
>>> Chem.MolFromSmiles("C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3")
[23:02:36] Explicit valence for atom # 6 N, 4, is greater than permitted
RDKit is pretty strict about accepting chemically reasonable structures, and
will reject a lot of structures which other programs accept.
This warning about a too-high valence on a nitrogen is probably the most common
failure message I get from RDKit's SMILES parser.
Cheers,
Andrew
[email protected]
> On Jan 13, 2018, at 22:52, Rajarshi Guha <[email protected]> wrote:
>
> Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query is
> failing when the query SMILES is
>
> C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3
>
> The error reported from Postgres is
>
> PSQLException: ERROR: could not create molecule from SMILES
> 'C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3'
> Position: 81
>
>
> The SMILES is parsed by CDK and JChem and I can't see why this should fail.
>
> I must be missing something obvious (?)
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
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