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

[Greg L. <gre...@gm...>]

Dear Adrian,

Quick one: the svn version of the cartridge code now has the function
is_valid_smiles()

On Fri, Oct 29, 2010 at 5:08 PM, Adrian Schreyer <ma...@ad...> wrote:
>
> Creating the mol types is actually not that slow I thought, compared
> to creating the indexes (based on the latest version of chembl).

The index generation is certainly slower than loading the molecules.

> Simplifying the database creation is definitely worth it, and those
> costly operations are done only once. Another suggestion I had was to
> refactor the naming of the functions in the cartridge to make them
> more similar to the underlying functions in the Python/C++ libraries,
> e.g. mol_in ~ mol_from_smiles / mol_out ~ mol_to_smiles.

I believe that the current naming scheme is more consistent with the
way postgresql does things. That's not an automatic "it has to be done
that way", but I think it is an argument for maintaining the current
naming.

>
> Given the context, maybe it is possible to reduce the number of
> instances where a smiles string cannot be parsed. From what I have
> seen so far, this happens in three cases: the smiles string contains a
> non-daylight extension (not rdkit's fault), exotic inorganic chemistry
> (negligible) or the valence system in rdkit is violated. The last case
> is something where I often encounter problems, for example bromic acid
>
> Chem.MolFromSmiles('OBr(=O)=O')
> [15:21:29] Explicit valence for atom # 1 Br, 5, is greater than permitted
>
> Is there a definition for the valence model used in rdkit somewhere in
> the source tree? I assume the valence model is nothing that can be
> manually changed by the user without breaking other aspects of the
> software.

If you want to allow additional valence states for atoms, you can edit
$RDBASE/Code/GraphMol/atomic_data.cpp, but that's about the only way
to do changes at the moment. The topic of supporting other valences,
like 5 for Br, has come up in the past. If we can identify a limited
number of additional valences that are required, I'd be willing to add
them to the standard RDKit parameters.[1] I'm happy to hear
suggestions about what those additional valences should be. We should
probably do this in a separate thread on the -discuss list.

Best Regards,
-greg
[1] Within reason... I will balk at changing anything in the first row
of the periodic table and will probably resist changing anything in
the second row other than chlorine (to allow chlorate anions).