[Deleted the previous contents of the thread because it was causing formatting problems for me in gmail, sorry]
One thing you might consider trying here is to build and install the RDKit (without the cartridge or Python wrappers) like a normal library using the standard RDKit build process. This should install all the header files (include export.h) and libraries you need. You can then put the cartridge source wherever is most convenient for you and then make sure your Makefile for the cartridge has the relevant -I and -L directives to point to where that install is. I *think* this would end up making things a lot easier in the end. -greg
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