FCFP_4 or FCFP_6 fingerprints in KNIME

Community Extensions RDKit
#1

hi !

is there any possibility to generat FCFP_4 or FCFP_6 (like in Pipeline Pilot) fingerprints (a fingerprint-list of several fragments of a molecule) with KNIME ?

I thought about using the Molecule fragmenter and then generating an FCFP fingerprint of every fragment of a molecule.. however, the fragmenter is very time-consuming so I´d like to know if there is any other possibility to generate fingerprint bit strings of molecule fragments directly (without prefixing the fragmenter node)? - Actually fingerprinting (especially FCFP) means also fragmenting in a way, but the result is always one bitstring (fingerprint) and we don´t obtain several fingerprints (e.g. as a list).

Thanks in advance !

#2

Hi,

The RDKit Fingerprint node defaults to 'morgan' fingerprint with radius=2.  This is essentially equivalent to ECFP_4 (diameter 4, ie radius=2).  If you want FCFP-like, then choose 'featmorgan'.

Kind regards

James