[Rdkit-discuss] SMILES Parse Error - '\n'

[Imran S. <imr...@gm...>]

Hi -

This is probably a trivial issue but if you're creating a database using the
rdkit postgres (Pg) cartridge it may save you some time.

I used the Wiki sample code to test ~400000 smiles structures,  and to write
the valid ones to a file.
E.g.
    smi = smi.replace('=N#N','=[N+]=[N-]').replace('N#N=','[N-]=[N+]=')
    mol =Chem.MolFromSmiles(smi)

Although there were errors like the following:-

SMILES Parse Error: syntax error while parsing
SMILES Parse Error: unclosed ring for input: [H]/N=c/1

The function returned a Mol object, which I wrote to a tab-delimited file
for loading into Pg using the  'copy table' command (using psql):
This failed due to the following:-

=# ERROR:  smiles 'Cc1cccc(c1)/N=N/C(=N' could not be parsed

It turns out there were '\n' (newline) chars in the smiles strings (which
obviously shouldn't be there).  Just a smi.replace('\n','') worked in this
case.

Hope this helps.

Cheers,

Imran