Michal-
Not pretty, but you could do
select mols.*, tanimoto_sml(morganbv_fp(':query_smiles'::mol),
morganbv_fp(mols.mol)) as similarity
from mols
where tanimoto_sml(morganbv_fp(':query_smiles'::mol),
morganbv_fp(mols.mol)) > :cutoff
or write your own C function is_similar(fp2, fp1, cutoff) and compile it
into the rdkit extension :)
How would having the parameter speed up query execution?
On Thu, Jul 11, 2013 at 10:33 AM, Michał Nowotka <[email protected]> wrote:
> 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]*
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>>
>
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