Yes, of course this is valid solution but this query gets even more
complicated if you want to return similarity as well. This will obviously
work, but how much simpler would it be it tanimoto_sml would accept cutoff
as optional parameter?
This is a kind of design flaw as having this parameter would also speed up
query execution.
On Thu, Jul 11, 2013 at 6:24 PM, James Swetnam <[email protected]> wrote:
> 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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>>
>>
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