Implement KDTree in PDB Coordinates

Concept

K-D Tree

In computer science, a k-d tree (short for k-dimensional tree) is a space-partitioning data structure for organizing points in a k-dimensional space. k-d trees are a useful data structure for several applications, such as searches involving a multidimensional search key (e.g. range searches and nearest neighbor searches). k-d trees are a special case of binary space partitioning trees.[1]

Reference

1. Wikipedia contributors. (2020, September 9). K-d tree. In Wikipedia, The Free Encyclopedia. Retrieved 13:47, September 18, 2020, from https://en.wikipedia.org/w/index.php?title=K-d_tree&oldid=977572387

Demo

2A01.A v.s 2LEM.A (via FATCAT)

Get all residues within the given radius from the source residue:

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query_sites = ["141","142"]

res_index_1 = tree1.query_radius(
    df_model['1'].query(f'atom_name == "CA" & residue_site in {query_sites}')[['x_coord','y_coord','z_coord']].to_numpy(), r=10)

res_index_2 = tree2.query_radius(
    df_model['2'].query(f'atom_name == "CA" & residue_site in {query_sites}')[['x_coord','y_coord','z_coord']].to_numpy(), r=10)

res_indexes = [np.intersect1d(*i) for i in zip(res_index_1,res_index_2)]