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 > <mailto: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 > <mailto: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 <http://cheminf.uni-jena.de/> > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net <mailto:Cdk-user@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/cdk-user > <https://lists.sourceforge.net/lists/listinfo/cdk-user>
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