I am working on evaluating the RD Kit Postgresql data cartridge for use as the
back end of a Web Application. The app will use a JavaScript sketcher to allow
the user to input a SMILES of SMARTS that will be sent to the RD Kit cartridge.
In evaluating RD Kit I found that it doesn't support aromatic normalization on
SMARTS. As a test case I used Marvin JS to generate a SMARTS:
C(=CN=C1)C(=C1N2)N=C2
Used it as a query:
select structure_id from rdk.mols where
m@>mol_adjust_query_properties(mol_from_smarts('C(=CN=C1)C(=C1N2)N=C2'));
structure_id
--------------
(0 rows)
Not surprisingly it had no hits. Looked at the mol_adjust_query_properties
function:
select mol_adjust_query_properties(mol_from_smarts('C(=CN=C1)C(=C1N2)N=C2'));
mol_adjust_query_properties
-----------------------------
c1cc2ncnc2cn1
That looked good.
select structure_id from rdk.mols where
m@>mol_adjust_query_properties(mol_from_smarts('c1cc2ncnc2cn1'));
structure_id
--------------
30183725
(1 row)
But wait there should be more hits!
select count(*) from rdk.mols where m@>'c1cc2ncnc2cn1'::qmol;
count
-------
27
Then I tried this:
select structure_id from rdk.mols where
m@>mol_adjust_query_properties(mol_from_smarts('c1cc2ncnc2cn1'),'{"adjustDegree":false}');
(27 rows)
OK, but what I really need to have work is this:
select structure_id from rdk.mols where
m@>mol_adjust_query_properties(mol_from_smarts('C(=CN=C1)C(=C1N2)N=C2'),'{"adjustDegree":false}');
structure_id
--------------
(0 rows)
Which it does not. Is mol_adjust_query_properties misnamed? It doesn't really
seem to want a query. Am I missing an option? Unless I can make this work I
don't see how I can use RD Kit in my application.
What am I missing? Or does RD Kit just not allow for normalizing SMARTS?
Thanks
Webster Homer
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