end-to-end distance in python

One way to calculate the end-to-end distance of a polymer chain in Python is to use the Euclidean distance formula, which can be applied to the coordinates of the first and last monomers of the chain. Here is an example code to compute the end-to-end distance of a polymer chain using NumPy library:

main.py
import numpy as np

# define the coordinates of the first and last monomers
start = np.array([0, 0, 0])
end = np.array([3, 4, 4])

# calculate the Euclidean distance between the two points
distance = np.linalg.norm(end - start)

print("End-to-end distance:", distance)
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In this example, the np.array function is used to define the start and end points as 3-dimensional vectors, and the np.linalg.norm function is used to calculate the Euclidean distance between the two points. The resulting distance is printed to the console as output. This code can be easily adapted to calculate the end-to-end distance of longer polymer chains with more monomers, by using the coordinates of the first and last monomers as defined in the simulation output or experimental data.