How about
select * from mols where tanimoto_sml(morganbv_fp(':query_smiles'::mol),
morganbv_fp(mols.mol)) > :cutoff ?
where 'query_smiles' is your desired query molecule, 'cutoff' is the
minimum similarity and mols.mol is the serialized RDkit::ROMol extension
On Thu, Jul 11, 2013 at 9:50 AM, Rodrigo Ochoa <[email protected]>wrote:
> Hi Michal
>
> This a problem that can be solved through two ways:
>
> 1) Execute a single query like this before calling the
> rdkit.tanimoto_threshold:
>
> select 'c1ccccc1O'::mol;
>
> Then you can set a tanimoto threshold without problems. Is an internal
> bug, that can be solved according to the second way
>
> 2) You can add this line to the postgressql.conf file:
>
> shared_preload_libraries = 'rdkit'
>
> This is a link with the explanation:
> https://code.google.com/p/rdkit/wiki/BuildingTheCartridge
>
> I hope it helps
>
>
> On Thu, Jul 11, 2013 at 5:52 PM, Michał Nowotka <[email protected]> wrote:
>
>> Is is possible to specify similarity threshold for single query instead
>> of relying on global "rdkit.tanimoto_threshold" which I'm having problems
>> with?
>>
>> It would be much more intuitive to do so, otherwise I need to surround my
>> similarity search SQL with statements changing global threshold and
>> restoring it afterwards.
>>
>> Regards,
>>
>> Michał Nowotka
>>
>>
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>
>
> --
>
> ----------------------------------------------------------------------------------------------------
> *Rodrigo Alonso Ochoa Deossa
> **Bioengineer - MSc(c) Basic Biomedical Sciences*
> *University of Antioquia - SIU - PECET
> Medellín, Colombia
> **e: [email protected]*
> *t: +57-4-2196622*
> *m: +57-3004505174*
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