I see the problem. Well, originally, I wanted to checkout how the raw fingerprints look like. I am storing all the data (and the fingerprints) in MongoDB, and I am still not sure if in case I save the BitFingerprints directly in there (with is possible when the field has an Object type), if they will be parseable by the mongo engine as fingerprints (without retrieving them to be read with CDK). So this is why I wanted to check the raw fingerprints, as they should be more JSON-friendly format, and mongo engine would be able to read those integers and strings for further similarity search.
Kind regards, Maria 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 19:31, John Mayfield <john.wilkinson...@gmail.com> a écrit > : > > Okay looking at it the Substructure fingerprint would be easy to adapt... but > it's not hard to just count the substructures. Utility code like that is > difficult to justify, every line is more to maintain. > > The other problem is I don't like the fingerprint APIs so it's a toss-up > between using effort to implement something I (or hopefully someone else) > will ultimately rewrite in future. "Deprecated on arrival" I believe Egon has > said before. > > On Fri, 21 Feb 2020 at 18:25, John Mayfield <john.wilkinson...@gmail.com > <mailto:john.wilkinson...@gmail.com>> wrote: > 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 > <mailto: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 <http://cheminf.uni-jena.de/> > >> Le 21 févr. 2020 à 10:39, John Mayfield <john.wilkinson...@gmail.com >> <mailto: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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