Dear Greg (and, of course, Thorsten and Bernd!)
Great job on the Knime nodes! I have been giving these a go and am
impressed (and excited about the future development!). A couple of
observations / comments / questions:
1. I have observed that sometimes the FP node seems to generate blank
fingerprints (doesn't appear to just be the rendering - eg blank if I
swap to 'Bit Scratch' render as well. I have mainly been trying the
default Morgan FPs, and find that if I reset the node and re-run, the FP
is still blank. If, however, I swap the node to eg atompair, run, then
swap back to Morgan - it seems to work... I am running on knime 2.2.2
on Windows 32-bit.
2. The next point is probably down to cheminformatics / knime naivety,
but I must confess I am struggling a little to cluster compounds based
on the FP... I have used the 'Distance Matrix Calculate' node (with
Tanimoto similarity) to get a matrix that can be used by the
'Heirarchical Clustering (DistMatrix)' or 'k-Medoids' nodes. However,
both of these appear to perform VERY slowly for a set of ~ 4000
compounds. I also attempted to cluster on the fingerprints directly,
using the Neighborgrams nodes - but must confess I am some way off
understanding what I am doing! My limited experience of using the RDKit
functionality to cluster compounds and eg select a representative set
(based on the FP Tanimoto distances and the Murtagh clustering) was that
it performed rather rapidly. Is there the intention to expose this
functionality in knime (or is the functionality already there and I just
don't know how?)
3. Any plans for Windows 64-bit support?
4. I would be interested to know what the team views as the next
priorities - property calcs, 3D conformations, pharmacophores,
rendering? So much great stuff to choose from! :-)
Kind regards
James
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