Unhashed Morgan FPs ?

Community Extensions
1

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!

 

ingo

2

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.

-greg

 

3

Dear Greg,

thanks a lot, I will think about that!

 

thanks a lot

ingo

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