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 <mac...@wojcikowski.pl> Sent: Tuesday, December 17, 2019 20:18 To: Peter Schmidtke <peter.schmid...@discngine.com> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net> 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 <mac...@wojcikowski.pl<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 <peter.schmid...@discngine.com<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 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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