Nicholas, this is an O(n^2) problem (many-to-many) and difficult to make efficient. It is, however, 'embarrassingly parallel' so you can take advantage of multiple cores.
Have a look at how these 2 KNIME workflows implement the PAINS filters with the RDKit nodes in KNIME: http://www.myexperiment.org/workflows/1841.html http://www.myexperiment.org/workflows/2485.html -- Cheers, Simon ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
