That explains the problem. Glad everything is working.
On Thu, May 31, 2018 at 4:29 PM Alfredo Quevedo <[email protected]>
wrote:
> Hi Greg,
>
> thank you for your feedback.
>
> the tests you mentioned worked ok for me and both molecules are matched
> using the specified smiles. I found that the matching problem was really
> silly: I was expecting to match both molecules in the CHEMBL database I
> downloaded (i.e. CHEMBL1517804 and CHEMBL2442053) which are accesible
> though a search using the web interface of CHEMBL. However, for some reason
> compound CHEMBL2442053 is not present in the downloadable database (and
> obviously not being matched)
>
> best regards
>
> Alfredo
>
> El 31/05/2018 a las 1:09, Greg Landrum escribió:
>
> 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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>
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