What do you think the "raw" fingerprint is? Why would you expect it for the Substructure one?
On Fri, 21 Feb 2020 at 09:47, Maria Sorokina <maria.ssorok...@gmail.com> wrote: > I tried in total 7 fingerprinters (PubChem, Substructure, MACCS, > KlekotaRoth, Circular, ShortestPath and Hybrifization) and none worked. For > some, I’m not surprised, but I was really expecting to have the raw > fingerprints for the Substructure one > > > Dr. Maria Sorokina > Steinbeck Research Group > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > http://cheminf.uni-jena.de > > Le 21 févr. 2020 à 10:39, John Mayfield <john.wilkinson...@gmail.com> a > écrit : > > ... I do have some patches for an updated fingerprint API stack that would > also add this in to more places. Essentially it was added to the public API > but only implemented in a few places and left as a "ToDo" elsewhere. Might > be something for the hack-a-thon. > > I should PubChem fingerprints are binary in nature though so you would > probably never want the RAW version. *getBitFingerprint()* it implemented > always. > > John > > On Fri, 21 Feb 2020 at 09:34, John Mayfield <john.wilkinson...@gmail.com> > wrote: > >> Hi Maria, >> >> Not all fingerprint support the "RAW" option and Count options. >> >> John >> >> On Fri, 21 Feb 2020 at 09:31, Maria Sorokina <maria.ssorok...@gmail.com> >> wrote: >> >>> Dear community, >>> >>> It is decidedly substructure search and fingerprinting period of the >>> year! >>> >>> I want to create (to store) raw fingerprints of a range of different >>> fingerprint types for a big number of complex molecules (natural products). >>> >>> For example this: >>> >>> PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( >>> SilentChemObjectBuilder.getInstance() ); >>> >>> System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer)); >>> >>> For all my molecules I am getting an" UnsupportedOperationException", >>> which according to the documentation reflects only the fact that the >>> fingerprinter >>> cannot produce the raw fingerprint. >>> I am using the latest (2.3) version of the CDK. >>> Can anybody help me with this issue? >>> >>> >>> Kind regards, >>> Maria >>> >>> >>> Dr. Maria Sorokina >>> Steinbeck Research Group >>> Analytical Chemistry - Cheminformatics and Chemometrics >>> Friedrich-Schiller-University Jena, Germany >>> http://cheminf.uni-jena.de >>> >>> _______________________________________________ >>> Cdk-user mailing list >>> Cdk-user@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >> >
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