I had some time to check SVN blame:
http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/trunk/include/openbabel/bitvec.h?annotate=4853

So this is from Kevin Shepherd, which makes sense because he made some cleanups 
elsewhere in the bitvec code.

> Now the issue is if USE_64BIT_INTEGER should be dropped. I don't see it
> documented or referenced anywhere. Does anyone know where does it come
> from? Is user expected to set it at compile time or the compiler does it
> automatically? On which systems it is actually used if any?

This would have been set by autoconf and now by cmake.

> So that leaves us with the runtime option. It would be possible to
> determine the size of uint at runtime and construct appropriate
> variables for it

I think C99 is probably well-supported now, so we could simply go with:

#include <inttypes.h>

uint32_t …

Doing a run-time check would be a bad idea, IMHO. And as far as STL bitset, the 
bitvec type is more like a specialized vector<bool> (since it allows resizing) 
but offers some additional methods. I don't know how performance would compare 
with some of the optimized std::vector<bool> specialization classes. It might 
be worth benchmarking at some point.

-Geoff
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