On Sun, Apr 02, 2017 at 01:41:27PM -0400, Stephen P. Molnar wrote:
> I am trying to port a program that I wrote in FORTRAN twenty years ago
> into Python 3 and am having a hard time trying to calculate the
> Euclidean distance between each atom in the molecule and every other
> atom in the molecule.
>
> Here is a typical table of coordinates:
>
>
> MASS X Y Z
> 0 12.011 -3.265636 0.198894 0.090858
> 1 12.011 -1.307161 1.522212 1.003463
[...]
> What I need for further calculation is a matrix of the Euclidean
> distances between the atoms.
It is quite likely that the third-party Numpy or Scipy packages include
read-made solutions to this. It sounds like the sort of thing that they
will do, and probably much more efficiently than pure Python code.
But as a simple example, if I have two coordinates written as tuples:
p = (-3.265636, 0.198894, 0.090858)
q = (-1.307161, 1.522212, 1.003463)
I can write a Euclidean distance function like this:
import math
def distance(a, b):
"""Return the Euclidean distance between 3D points a and b."""
return math.sqrt(
(a[0] - b[0])**2 + (a[1] - b[1])**2 + (a[2] - b[2])**2
)
and then call the function:
result = distance(p, q)
which will return 2.5337013913983633 and assign it to the variable
"result".
Does that help?
--
Steve
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