Finally, support for calculating the Avalon fingerprint has been added to the RDKit Fingerprint node.
The Avalon fingerprint was described in the following publication:
Gedeck, P., Rohde, B. & Bartels, C. QSAR − How Good Is It in Practice? Comparison of Descriptor Sets on an Unbiased Cross Section of Corporate Data Sets. Journal of Chemical Information and Modeling46, 1924-1936 (2006).
Thanks to Manuel Schwarze, Dillip Kumar Mohanty, Swarnaprava Singh, and Sudip Ghosh for their work on the Knime nodes and for Bernd Rohde for the Avalon toolkit.
I like the Functional Group Filter! Could this be improved to include any metal as a filter in the list selection ? This can be useful to remove non-organic molecules.
The functional group definitions that are used by the Functional Group Filter node are read from a text file and you have the option to provide your own version of that (there's an option in the Configure dialog for this). You can download a "clean" copy of the default file here: http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Data/Functional_Group_Hierarchy.txt
However, if you would like to just remove molecules that match any of a particular set of queries, I would recommend using the "RDKit Dictionary Substructure Filter" and providing the list of SMARTS that you don't want to see as input to that. That's probably somewhat simpler.
Note that I had to reformat the original file some to make it work with the knime file reader. I also only use the first set of filters that's in the file (that's why I included the Row Filter). I have attached the modified file.