Charles R Harris
Mon Nov 3 11:30:57 CST 2008
On Mon, Nov 3, 2008 at 1:36 AM, Anne Archibald
> 2008/11/3 Charles R Harris <email@example.com>:
> > I usually want a complete list of points in some neighborhood. I looked
> > through your cython code and I think the loops can be improved a bit to
> > better use of low level C code.
> The C implementation doesn't currently do this at all. It'd be a good
> addition, though I think you'd have to use object arrays of lists,
> which have always made me faintly queasy. You'd want a whole separate
> tree-traversal routine here, with short-circuit branches for both
> all-in-the-neighborhood and all-outside-the-neighborhood. Since kdtree
> construction is rather fast, does it perhaps make sense to write a
> two-tree version?
Looks like the BioPython folks have been busy. The KDTree code has been
updated to use numpy and converted to C from C++. You can view the code in
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