Hi John, thanks for your response, I will use the mapping to the orig atoms to show the structural information.
> The fingerprints perform similarly well on classification benchmarks (i.e. > Birem Lessel). I am currently collecting data for QSAR classification experiments, are you refering to the dataset that is linked here: http://www.cheminformatics.org/datasets/#binary ? Could you give me a hint where I can find more data? Thanks, Martin Am 04.03.2015 um 20:45 schrieb John May: > Slight correction, CircularFingerprint does actually store the all the atoms > in the feature. It’s a simple patch to expose this if you want to add it. > > J > > On Mar 4, 2015, at 7:42 PM, John May <[email protected]> wrote: > >> Hi Martin, >> >> Yes and no. The CDK has two morgan/radial/circular/extended connectivity >> fingerprints. The newest CircularFingerprint calculates the bits/hashes >> without fragmenting the graph - that is it doesn’t at any point have the >> “feature” that encoded a certain bit. It does have atom a feature is centre >> on though, it doesn’t expose or store this. The other is the >> SignatureFingerprint that computes radial signatures first and then hashes >> these. A map of the features/count can obtained with the ‘getRawFingerprint’ >> method. The hash code is simply String.hashCode(). >> >> The fingerprints perform similarly well on classification benchmarks (i.e. >> Birem Lessel). >> >> Hope that helps. >> >> Regards, >> J >> >> On Mar 4, 2015, at 1:55 PM, Martin Gütlein <[email protected]> wrote: >> >>> Hi, >>> >>> How can I get the substructure/smarts from the (unfolded) ecfp fingerprint? >>> If thats not possible, is it hard to implement that? >>> >>> Kind regards, >>> Martin >>> >>> See corresponding functionality in chemaxon: >>> https://docs.chemaxon.com/pages/viewpage.action?pageId=14483752#ExtendedConnectivityFingerprint(ECFP)-FeatureRetrieval >>> >>> >>> ------------------------------------------------------------------------------ >>> Dive into the World of Parallel Programming The Go Parallel Website, >>> sponsored >>> by Intel and developed in partnership with Slashdot Media, is your hub for >>> all >>> things parallel software development, from weekly thought leadership blogs >>> to >>> news, videos, case studies, tutorials and more. Take a look and join the >>> conversation now. http://goparallel.sourceforge.net/ >>> _______________________________________________ >>> Cdk-user mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
