DescriptorEngine.process() is inexplicable getting stuck processing descriptors for certain molecules. Attached is a SD File containing four such molecules. I left it running over night (over 12 hours) and it was still stuck on these same 4 molecules (4 threads). Each thread was using 100% CPU so it is either just churning away at something which isn't terminating, or there is some sort of busy wait going on.
This is with CDK 1.0.x.