If you grep the source for KDTree, you should find a couple examples of its use. It may be a bit slower than the fortran kdtree, but it is at least readily available.
(Chiming in from the great beyond)
Britton makes a good suggestion, but I think that people should be aware of two things:
It wouldn't be difficult to add periodicity to KDTree, but I just didn't do it.
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