On Mon, Sep 22, 2014 at 3:49 PM, JP <[email protected]> wrote:
>
> Ola RDKitters,
>
> I have a molecule in postgresql, and I would like to calculate the
overall formal charge of the molecule as separate + and - counts.
>
> I currently came up with (warning: hack ahead!)
>
> substruct_count(rdkitmol, mol_from_smarts('[-]'), true) +
(substruct_count(rdkitmol, mol_from_smarts('[--]'), true) * 2) +
(substruct_count(rdkitmol, mol_from_smarts('[---]'), true) * 3) as neg
>
> But this being RDKit, there probably is a better way (and what about my
[U+4] ?).
>
There's not really a good way that I can think of to do this.
If you were interested in the number of non-zero charged atoms, you could
do:
chembl_19=# select
substruct_count('[Na+].CCC.[Cl-]',mol_from_smarts('[!+0]'),true);
substruct_count
-----------------
2
(1 row)
but that doesn't seem to be what you're looking for.
There are also some string-manipulation games you could play on SMILES
columns that are still ugly, but which would probably be more efficient.
Here are a couple of queries that might be useful there:
chembl_19=# select count(*) from compound_structures where
length(canonical_smiles)-length(regexp_replace(canonical_smiles,'\+\]',''))
> 0;
count
--------
110832
(1 row)
Time: 2188.448 ms
chembl_19=# select count(*) from compound_structures where
length(canonical_smiles)-length(regexp_replace(canonical_smiles,'\+2\]',''))
> 0;
count
-------
274
(1 row)
Time: 2257.251 ms
chembl_19=# select count(*) from compound_structures where
length(canonical_smiles)-length(regexp_replace(canonical_smiles,'\-\]',''))
> 0;
count
-------
96973
(1 row)
Time: 2199.070 ms
-greg
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