Re: [Rdkit-discuss] RDKit "cannot create mol from SMILE" error

This all explains a lot. Thanks very much, Brian and Peter! On Wed, Jan 18, 2017 at 6:05 PM, Peter S. Shenkin wrote: > 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

Re: [Rdkit-discuss] RDKit "cannot create mol from SMILE" error

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

Re: [Rdkit-discuss] RDKit "cannot create mol from SMILE" error

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 wrote: > > Hi all, > > I'm using the following query in postgresql (with the rdkit

[Rdkit-discuss] RDKit "cannot create mol from SMILE" error

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'.