Thanks, Takayuki, For both Repeated Bisection clustering and K-means clustering, they all need the number of clusters as input, right?
Best, Jing On Sun, Aug 23, 2015 at 1:17 AM, Taka Seri <serit...@gmail.com> wrote: > Dear Jing, > > How about your trying using bayon ? > https://code.google.com/p/bayon/ > It's not function of RDKit, but I think the library can cluster molecules > using ECFP4. > > Unfortunately, input file format of bayon is not distance matrix but easy > to prepare the format. > > Best regards. > > Takayuki > > > 2015年8月23日(日) 12:03 Jing Lu <ajin...@gmail.com>: > >> Currently, I prefer fingerprint based clustering, because it's hard to >> set the cutoff for scaffold based clustering. Does RDKit have scaffold >> based clustering? >> >> On Sat, Aug 22, 2015 at 10:56 PM, <abhik1...@gmail.com> wrote: >> >>> Hi, how about scaffold based clustering . You extract the scaffolds and >>> then cluster it and then put the respective scaffold compounds inside the >>> cluster . >>> >>> Sent from my iPhone >>> >>> > On Aug 22, 2015, at 8:43 PM, Jing Lu <ajin...@gmail.com> wrote: >>> > >>> > Dear RDKit users, >>> > >>> > If I want to cluster more than 1M molecules by ECFP4. How could I do >>> it? If I calculate the distance between every pair of molecules, the size >>> of distance matrix will be too big. Does RDKit support any heuristic >>> clustering algorithm without calculating the distance matrix of the whole >>> library? >>> > >>> > >>> > >>> > Thanks, >>> > Jing >>> > >>> ------------------------------------------------------------------------------ >>> > _______________________________________________ >>> > Rdkit-discuss mailing list >>> > Rdkit-discuss@lists.sourceforge.net >>> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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