[Rdkit-devel] PostgreSQL cartridge: Function to check whether a SMILES string is valid or not in RDKit

[Adrian S. <am...@ca...>]

Hi Greg,

I moved to PostgreSQL 9.0 recently and installed the RDKit cartridge
which was easy to compile and install. It is also one of the fastest
cartridges I have used so far, definitely a great extension of RDKit!

At the moment I am trying to create rdkit molecules and fingerprints
for the latest version of the ChEMBL database, there is however a
problem which can be solved easily. Since I already had the ChEMBL
database (including the SMILES strings), I added tables to hold the
mol and fp types for every compound and tried to populate it through
"insert into... select mol_in(ism::cstring)..." which works nicely
unless it finds a SMILES string it cannot parse such as this
"CCCC1234B567B89%10B%11%12%13B8%14%15B%11%16%17B%12%18%19B59%13B16%18C2%16%19(c%20ccc(Oc%21ccc(cc%21)C(=O)O)cc%20)B3%14%17B47%10%15"
(ChEBI: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A105310).
The query will fail then, and the only way to populate these table is
to download the SMILES and filter them manually in Python. Is it
possible to have a boolean function (is_valid(cstring)?) in the
cartridge that simply checks if a SMILES can be parsed with RDKit or
not? This would make it possible to add this check to a where clause
in a query and as a result make the creation of mol types much easier.

Cheers

Adrian