On Mon, Jan 27, 2020 at 6:13 AM Thomas Strunz <beginn...@hotmail.de> wrote:
> > 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 > <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. > Unfortunately the way the pattern fingerprints are used with the index makes it impossible to change this without building and installing your own version of the cartridge. There's now way that I know of to get this setup so that one can provide the fingerprints externally. In some cases the Patternfingerprint doesn't have very good screenout rates > and layeredfingerprint is much better. > If/when you come across cases like this, I would be interested to hear about them so that I can think about improving the pattern fingerprint (adding new patterns isn't that hard at the C++ level). Best, -greg > (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> 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 > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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