Construction of an adjacency matrix

In this example we create an adjacency matrix of the CA atoms in the lysozyme crystal structure (PDB: 1AKI). The values in the adjacency matrix m are m[i,j] = 1 if distance(i,j) <= threshold else 0.

# Code source: Patrick Kunzmann
# License: BSD 3 clause

from tempfile import gettempdir
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
import biotite
import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io as strucio

file_name = rcsb.fetch("1aki", "bcif", gettempdir())
array = strucio.load_structure(file_name)
# We only consider CA atoms
ca = array[array.atom_name == "CA"]
# 7 Angstrom adjacency threshold
threshold = 7
# Create cell list of the CA atom array
# for efficient measurement of adjacency
cell_list = struc.CellList(ca, cell_size=threshold)
adjacency_matrix = cell_list.create_adjacency_matrix(threshold)

figure = plt.figure()
ax = figure.add_subplot(111)
cmap = ListedColormap(["white", biotite.colors["dimgreen"]])
ax.matshow(adjacency_matrix, cmap=cmap, origin="lower")
ax.xaxis.tick_bottom()
ax.set_aspect("equal")
ax.set_xlabel("Residue number")
ax.set_ylabel("Residue number")
ax.set_title("Adjacency matrix of the lysozyme crystal structure")
figure.tight_layout()
plt.show()