Fastest way to find the closest point to a given point in 3D, in Python

Question

So lets say I have 10,000 points in A and 10,000 points in B and want to find out the closest point in A for every B point.

Currently, I simply loop through every point

Answer 1

I typically use a kd-tree in such situations.

There is a C++ implementation wrapped with SWIG and bundled with BioPython that's easy to use.