Unhashed Morgan FPs ?

Hello there,

first of all, thanks a lot for your nice and useful RDKit contribution to KNIME!

I was wondering whether it would be possible to have an extension to the Morgan FP (in particular the FeatMorgan FP):

1) Instead of a hashed fixed sized FP I would rather prefer to have the entire set of found features. I already read here http://tech.knime.org/forum/rdkit/circular-fingerprint-feature-retrieval that you are working on something very similar, if not identical... however,

2)... I would also like to have the frequency of the features.

Strangely, I was always of the opinion that this was already possible with RDKit, but when I now came back to really use it I found it to be different - Maybe it was some other Chemistry Kit. As you already said you are working on point 1), I would be very happy if you could consider my second request!

thanks and keep up the good work!



Dear Ingo,

The RDKit itself can generate the unhashed fingerprints with counts. This is easily do-able from Python or Java.

There is not currently any support for this in knime since I don't think that knime supports the data types that are required (a different kind of fingerprint) and I haven't managed to figure out a sensible way of presenting the data.

If you have suggestions, please let me know.



Dear Greg,

thanks a lot, I will think about that!


thanks a lot