How to subtrac a numpy array element-by-elemnt by another numpy array

Question

I have two numpy arrays, with just the 3-dimensional coordinates of two molecules.

I need to implement the following equation, and I'm having problems in the subtraction of each coordinate of one of the arrays by the second, and then square it.

I have tried the following, but since I'm still learning I feel that I am making some major mistake. The simple code I use is:

a = [math.sqrt(1/3*((i[:,0]-j[:,0])**2) + ((i[:,1] - j[:,1])**2) + ((i[:,2]-j[:,2])**2) for i, j in zip(coordenates_2, coordenates_1))]

math.sqrt only works with single values, not arrays. np.sqrt is best when using whole arrays. — hpaulj
– hpaulj, Commented Dec 6, 2020 at 20:04

David · Accepted Answer · 2020-12-06 18:37:19Z

1

It's numpy you can easily do it using the following example:

import numpy as np
x1 = np.random.randn(3,3,3)
x2 = np.random.randn(3,3,3)

res = np.sqrt(np.mean(np.power(x1-x2,2)))

answered Dec 6, 2020 at 18:37

David

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2 Comments

Jose Gracia Rodriguez Over a year ago

Thanks for your answer, sorry for the mess I made formulating the question. I have some questions about your answer, can I use np.square insted of ``` np.power``` and for my case would´t It be np.sum instead of np.mean. Finally I have used the following line, but I still cant get the exact results so perhaps Im making a mistake somewhere. np.sqrt((1/3)* np.sum(np.square(coordenadas_2-coordenadas_1)))

David Over a year ago

@JoseGraciaRodriguez can you share your data and expected result? It might be a small detail that is missed. And you can use square and sum it won’t matter

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