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 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 > 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 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 >> >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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 not read. -P On Wed, Jan 18, 2017 at 6:32 PM, Brian Kelley 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 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 > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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 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 > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[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'. 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss