用python实现两个文件间原子距离的成对计算

def read_coordinates(filename):
    coordinates = []
    with open(filename, 'r') as file:
        for line in file:
            atom_type, x, y, z = line.split()
            coordinates.append((atom_type, float(x), float(y), float(z)))
    return coordinates

file1_coordinates = read_coordinates('file1.txt')
file2_coordinates = read_coordinates('file2.txt')

import numpy as np

def calculate_distances(coordinates1, coordinates2):
    distances = np.zeros((len(coordinates1), len(coordinates2)))
    for i, atom1 in enumerate(coordinates1):
        for j, atom2 in enumerate(coordinates2):
            distance = np.sqrt((atom1[1] - atom2[1])**2 + (atom1[2] - atom2[2])**2 + (atom1[3] - atom2[3])**2)
            distances[i, j] = distance
    return distances

distances_matrix = calculate_distances(file1_coordinates, file2_coordinates)

print(distances_matrix)