... 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 <[email protected]> wrote: > Hi Maria, > > Not all fingerprint support the "RAW" option and Count options. > > John > > On Fri, 21 Feb 2020 at 09:31, Maria Sorokina <[email protected]> > 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 >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> >
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