Example 4

Example 4 for running the test on OctaDist PyPI

import octadist as oc

file = r"../example-input/Multiple-metals.xyz"

atom_full, coord_full = oc.molecule.extract_coord(file)

# If complex contains metal center more than one, you can specify the index metal
# whose octahedral structure will be computed.
# For example, this complex contains three metal atoms: Fe, Ru, and Rd.
# I add "2" as a second argument for choosing Ru as metal of interest.

atom, coord = oc.molecule.extract_octa(atom_full, coord_full, 2)

dist = oc.CalcDistortion(coord)
zeta = dist.zeta             # Zeta
delta = dist.delta           # Delta
sigma = dist.sigma           # Sigma
theta = dist.theta           # Theta

print("\nAll computed parameters")
print("-----------------------")
print("Zeta  =", zeta)
print("Delta =", delta)
print("Sigma =", sigma)
print("Theta =", theta)

# All computed parameters
# -----------------------
# Zeta  = 0.001616439510534251
# Delta = 3.5425830613072754e-08
# Sigma = 1.26579367508117
# Theta = 4.177042495798965