Hi Greg, about your comment on custom fingerprints:
"I'm not sure what you mean by substructures, but you can, from Python, use custom fingerprints in the cartridge. That's explained here: http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html"; For me and I suspect this is what Changge actually was asking if one can add a custom fingerprint for the substructure search part (the screen-out) and not just the similarity search (the blog post linked looks like it is only for similarity search). And with "custom substructure" I would assume a fully or partial substructure fingerprint. In some cases the Patternfingerprint doesn't have very good screenout rates and layeredfingerprint is much better. (Not really an issue for me just an obeservation).So from that point I can see and understand the need for using a custom fingerprint for the screenout step. Best Regards, Thomas ________________________________ Von: Greg Landrum <greg.land...@gmail.com> Gesendet: Samstag, 25. Januar 2020 06:11 An: Chicago Ji <chicago...@gmail.com> Cc: rdkit-discuss <rdkit-discuss@lists.sourceforge.net> Betreff: Re: [Rdkit-discuss] How does rdkit cartridge work? Hi Changge, On Fri, Jan 24, 2020 at 5:14 PM Chicago Ji <chicago...@gmail.com<mailto:chicago...@gmail.com>> wrote: I find that rdkit cartridge is quite efficient in substructure searching. Glad to hear that! :-) Is there any paper or similar paper that describes things behind rdkit cartridge? No, just the documentation. For example, what kind of substructures were indexed? The Pattern fingerprint is what's used to build the index for substructure searching. That fingerprint is described in the RDKit documentation here: https://www.rdkit.org/docs/RDKit_Book.html#pattern-fingerprints Is there a way that the users can add custom defined fingerprints and substructures? I'm not sure what you mean by substructures, but you can, from Python, use custom fingerprints in the cartridge. That's explained here: http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html Best, -greg Many thanks for your help! Best, Changge _______________________________________________ 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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