Re: [Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

[Peter Schmidtke]

Hi Maciek,

I tried this today, and the trouble is that the erg fingerprints are neither 
sparse nor explicit rdkit bitvectors, but are represented as numpy arrays. As 
such they cannot even be used by current similarity functions in RDkit like 
Tanimoto similarity or other.

The only example I found on how to compare two erg fingerprints is the post by 
iwatobipen here:
https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit/
[https://iwatobipen.files.wordpress.com/2016/01/screen-shot-2016-01-16-at-10-19-47-pm.png]<https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit/>
ErGFingerprint in RDKit | Is life worth 
living?<https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit/>
Sometime, medicinal Chemists think about scaffold hopping approach in drug 
discovery project to overcome their issue. When I think about scaffold hopping, 
I consider about what's key interaction of molecule and protein. It's called 
pharmacophore. And also hopping approach is used me too approach to find 
another IP space. BTW, In 2006, researchers in Lilly…
iwatobipen.wordpress.com


Is there any documentation along those lines somewhere? The way I understand it 
 right now my options are:

  *   serialize numpy arrays to register them as binary to a postgresql database
 *   how to compare them in pgsql then?
  *   find a way / means to transform the numpy array into a sparse or explicit 
bitvector (would that make sense at all?)
  *   or just consider exact matches for erg fp's and do not integrate any 
similarity metric

Thanks in advance for ideas 

Peter






From: Maciek Wójcikowski 
Sent: Tuesday, December 17, 2019 20:18
To: Peter Schmidtke 
Cc: RDKit Discuss 
Subject: Re: [Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

While creating more detailed answer for you I stumbled upon very useful 
blogpost by Greg 
https://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html 
which explains in detail how custom fingerprints can be handled.

Both Tanimoto and Dice are supported for any sfp/bfp.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<mailto:mac...@wojcikowski.pl>


wt., 17 gru 2019 o 18:38 Maciek Wójcikowski 
mailto:mac...@wojcikowski.pl>> napisał(a):
Hi Peter,

You can index any binary fingerprint (both sparse and explicit). Also, you can 
create any custom fp in python and pass it over to postgresql. That said, I 
have not managed to transfer a sparse one from python to postgres, only the 
explicit.

Best,
Maciek

wt., 17 gru 2019, 13:00 użytkownik Peter Schmidtke 
mailto:peter.schmid...@discngine.com>> napisał:
Hi all,

is it possible to index the reduced graphs fingerprints in the pgsql cartridge 
as well? From my understanding the fingerprint provided by rdkit isn’t exactly 
in the same format as for standard morgan fingerprints.
Would this work anyhow? if yes with which similarity functions in pgsql? 
Anybody ever tried this and has a bit of documentation?

Thanks in advance

Peter
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Re: [Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

[Peter Schmidtke]

Thanks Maciek,

will check that out just wasn’t sure if this applies correctly to the reduced 
graph fingerprints which seemed a bit different:
ie: https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit

Anyway, we’ll try that out and write something up in case it’s working ;)

Cheers

Peter

On 17 Dec 2019, at 20:18, Maciek Wójcikowski 
mailto:mac...@wojcikowski.pl>> wrote:

While creating more detailed answer for you I stumbled upon very useful 
blogpost by Greg 
https://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html 
which explains in detail how custom fingerprints can be handled.

Both Tanimoto and Dice are supported for any sfp/bfp.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


wt., 17 gru 2019 o 18:38 Maciek Wójcikowski 
mailto:mac...@wojcikowski.pl>> napisał(a):
Hi Peter,

You can index any binary fingerprint (both sparse and explicit). Also, you can 
create any custom fp in python and pass it over to postgresql. That said, I 
have not managed to transfer a sparse one from python to postgres, only the 
explicit.

Best,
Maciek

wt., 17 gru 2019, 13:00 użytkownik Peter Schmidtke 
mailto:peter.schmid...@discngine.com>> napisał:
Hi all,

is it possible to index the reduced graphs fingerprints in the pgsql cartridge 
as well? From my understanding the fingerprint provided by rdkit isn’t exactly 
in the same format as for standard morgan fingerprints.
Would this work anyhow? if yes with which similarity functions in pgsql? 
Anybody ever tried this and has a bit of documentation?

Thanks in advance

Peter
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Re: [Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

[Maciek Wójcikowski]

While creating more detailed answer for you I stumbled upon very useful
blogpost by Greg
https://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html
which
explains in detail how custom fingerprints can be handled.

Both Tanimoto and Dice are supported for any sfp/bfp.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


wt., 17 gru 2019 o 18:38 Maciek Wójcikowski 
napisał(a):

> Hi Peter,
>
> You can index any binary fingerprint (both sparse and explicit). Also, you
> can create any custom fp in python and pass it over to postgresql. That
> said, I have not managed to transfer a sparse one from python to postgres,
> only the explicit.
>
> Best,
> Maciek
>
> wt., 17 gru 2019, 13:00 użytkownik Peter Schmidtke <
> peter.schmid...@discngine.com> napisał:
>
>> Hi all,
>>
>> is it possible to index the reduced graphs fingerprints in the pgsql
>> cartridge as well? From my understanding the fingerprint provided by rdkit
>> isn’t exactly in the same format as for standard morgan fingerprints.
>> Would this work anyhow? if yes with which similarity functions in pgsql?
>> Anybody ever tried this and has a bit of documentation?
>>
>> Thanks in advance
>>
>> Peter
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>
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Re: [Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

[Maciek Wójcikowski]

Hi Peter,

You can index any binary fingerprint (both sparse and explicit). Also, you
can create any custom fp in python and pass it over to postgresql. That
said, I have not managed to transfer a sparse one from python to postgres,
only the explicit.

Best,
Maciek

wt., 17 gru 2019, 13:00 użytkownik Peter Schmidtke <
peter.schmid...@discngine.com> napisał:

> Hi all,
>
> is it possible to index the reduced graphs fingerprints in the pgsql
> cartridge as well? From my understanding the fingerprint provided by rdkit
> isn’t exactly in the same format as for standard morgan fingerprints.
> Would this work anyhow? if yes with which similarity functions in pgsql?
> Anybody ever tried this and has a bit of documentation?
>
> Thanks in advance
>
> Peter
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