[Biopython-dev] KD tree module

[Thomas Hamelryck]

Hi,

I just finished a KD tree python extension module in C++. A KD tree
is a data structure that allows fast range queries in vector space. 
My implementation also does fixed radius neighbor search (ie. it finds
all point pairs closer than a given radius). It requires Numpy.

I'm going to use the thing to find bonds between atoms and to find all atoms 
close to a bound ligand in a cystal structure, and similar things. 

Of course, a KD tree can also be very useful for other purposes, e.g. 
for a fast implementation of the K-means algorithm.

I'd like to put the code in Bio.Tools.KDTree, if that's OK for everybody.

I also welcome any suggestions/criticism/remarks/requests with respect  to 
the structure code. BTW, where am I supposed to put the hand written 
documentation for it? Add it to the tutorial tex file?

Cheers,

---
Thomas Hamelryck      Vrije Universiteit Brussel (VUB)
Intitute for Molecular Biology            ULTR Department
Paardenstraat 65    1640 Sint-Gensius-Rode, Belgium
                http://ultr.vub.ac.be/~thomas