Hi Alfredo,
I can't think of any reason this would be true based on the molecules you
provide.
Certainly each of the molecules has a substructure match:
chembl_23=# select 'CCc1ccc(-n2nc3ccc(NC(=O)c4ccc5c(c4)OCO5)cc3n2)cc1'::mol@
>'c1c[nH]nn1'::mol;
?column?
----------
t
(1 row)
chembl_23=# select
'COc1ncc(-c2ccc(N(Cc3ccsc3)C(=O)Cn3nnc4ccccc43)cc2)cn1'::mol@
>'c1c[nH]nn1'::mol;
?column?
----------
t
(1 row)
And if I put them in a small table, add an index, and search, I also get
the expected results:
chembl_23=# create temporary table twomols (smiles text,m mol);
CREATE TABLE
chembl_23=# insert into twomols values
('CCc1ccc(-n2nc3ccc(NC(=O)c4ccc5c(c4)OCO5)cc3n2)cc1',
'CCc1ccc(-n2nc3ccc(NC(=O)c4ccc5c(c4)OCO5)cc3n2)cc1'::mol);
INSERT 0 1
chembl_23=# insert into twomols values
('COc1ncc(-c2ccc(N(Cc3ccsc3)C(=O)Cn3nnc4ccccc43)cc2)cn1',
'COc1ncc(-c2ccc(N(Cc3ccsc3)C(=O)Cn3nnc4ccccc43)cc2)cn1'::mol);
INSERT 0 1
chembl_23=# select smiles from twomols where m@>'c1c[nH]nn1'::mol;
smiles
-------------------------------------------------------
CCc1ccc(-n2nc3ccc(NC(=O)c4ccc5c(c4)OCO5)cc3n2)cc1
COc1ncc(-c2ccc(N(Cc3ccsc3)C(=O)Cn3nnc4ccccc43)cc2)cn1
(2 rows)
chembl_23=# create index tidx on twomols using gist(m);
CREATE INDEX
chembl_23=# select smiles from twomols where m@>'c1c[nH]nn1'::mol;
smiles
-------------------------------------------------------
CCc1ccc(-n2nc3ccc(NC(=O)c4ccc5c(c4)OCO5)cc3n2)cc1
COc1ncc(-c2ccc(N(Cc3ccsc3)C(=O)Cn3nnc4ccccc43)cc2)cn1
(2 rows)
Can you please check to see if this simple test works for you?
To do more detailed troubleshooting I will need to know which version of
the cartridge you are using and one which operating system.
Best,
-greg
On Tue, May 29, 2018 at 8:00 PM Alfredo Quevedo <[email protected]>
wrote:
> Dear user,
>
> I am trying to perform a substructure search using smiles notation under
> the ChEMBL database I have already loaded into my postgreSQL database. I
> am here providing two sample molecules in smiles format as read by the
> RDKit cartrigde into the database:
>
> Molecule 1: CCc1ccc(-n2nc3ccc(NC(=O)c4ccc5c(c4)OCO5)cc3n2)cc1
>
> Molecule 2: COc1ncc(-c2ccc(N(Cc3ccsc3)C(=O)Cn3nnc4ccccc43)cc2)cn1
>
>
> Both molecules contains a triazole scaffold, and I am trying to select
> both compounds among a whole database using the following smiles
> genereated by RDKit for a triazole: ´c1c[nH]nn1´
>
> My problem is that the search is only able to match molecule 1 but not
> molecule 2. Which may be the problem? Since I am serching in a database
> of compounds previously processed with the RDKit cartrigde, shouldnt the
> subtructure match?
>
> thanks in advance for the help
>
> regards
>
> Alfredo
>
>
>
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