We are currently using Mol files, they’re large especially when urlencoded, we
would prefer smiles and smarts for queries, but we would need to be able to
normalize them.
As to sketchers Marvin JS seems to do a pretty good job with SMARTS.
Webster
From: Greg Landrum <greg.land...@gmail.com>
Sent: Friday, November 01, 2019 11:21 PM
To: Webster Homer <webster.ho...@milliporesigma.com>
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] SMARTS Query Normalization?
Hi Webster,
That's a really good question.
At the moment there isn't any way to do SMARTS normalization. The assumption
throughout the code is that if you've gone to the trouble to create a SMARTS
then you captured the aromaticity that you intend to search for there. I think
your use case makes sense though, so this would be an interesting thing for us
to take a look at for a future release.
What you might be able to do in the meantime, and what I usually suggest when
coming from a chemical sketcher, is to get an MDL molfile from the sketcher and
then use that to do your queries. You can use mol_from_ctab() in the cartridge
along with mol_adjust_query_properties:
chembl_25=# select * from rdk.mols where
m@>mol_adjust_query_properties(mol_from_ctab('
Mrv1810 11021905152D
9 9 0 0 0 0 999 V2000
-2.2782 -0.0547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9927 -0.4672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9927 -1.2922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2782 -1.7047 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5637 -1.2922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5637 -0.4672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2782 0.7703 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
-0.8493 -0.0547 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
-0.8493 -1.7047 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
1 6 2 0 0 0 0
1 7 1 0 0 0 0
6 8 1 0 0 0 0
5 9 1 0 0 0 0
M END
')) limit 5;
The chemical sketchers that I have tried tend to do a better job of generating
queries in Mol files, and the RDKit deals with converting from kekule->aromatic
form for you.
Does that help?
-greg
On Thu, Oct 31, 2019 at 5:42 PM Webster Homer
<webster.ho...@milliporesigma.com<mailto:webster.ho...@milliporesigma.com>>
wrote:
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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