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Calculating distances between adjacent points - chascp - Feb-19-2020
I have a code which will calculate the distances between all atoms in a cartesian coordinate system. However, I only want it to calculate it between the adjacent atoms e.g 1-2, 2-3, 3-4, 4-5, etc.
Can anyone recommend a way I can do this ? I have attached code below.
from scipy.spatial import distance
# Load data from file
with open('cartesian.csv') as datafile:
contents = [line.split() for line in datafile]
# Extract the xyz coordiantes, if there is an H in the last column
coords = []
for i, item in enumerate(contents):
#if item[-1] == 'H':
coords.append([[float(x) for x in item[0:2]], i+1])
# Show results
for i in range(len(coords)):
for j in range(i+1, len(coords)):
dist = distance.euclidean(coords[i][0], coords[j][0])
print('({}, {}): {:.5f}'.format(coords[i][1], coords[j][1], dist))Here is a small sample of my input file: atom x y z
1 0.0 0.0 1.2 2 0.0 0.0 2.4 3 0.0 0.0 3.6 4 0.0 0.0 4.8 5 0.0 0.0 6.0 6 0.0 0.0 7.2 7 0.0 0.0 8.4 8 0.0 0.0 9.6 9 0.0 0.0 10.8 10 0.0 0.0 12.0 11 0.0 0.0 13.2 12 0.0 0.0 14.4 13 0.0 0.0 15.6 14 0.0 0.0 16.8 15 0.0 0.0 18.0 16 0.0 0.0 19.2 17 0.0 0.0 20.4 18 0.0 0.0 21.6 19 0.0 0.0 22.8 20 0.0 0.0 24.0 1 2.10602 4.30161 15.4191 2 1.63363 3.84311 14.6922 3 1.0001799999999998 3.49724 14.0046 4 1.4663 2.88937 13.3751 5 0.9758450000000001 2.6336 12.8105 6 0.65735 1.4835200000000002 12.7484 7 0.46493 0.5138590000000001 12.9022 8 0.08873760000000001 -0.398863 12.5105 9 0.201499 -1.09372 11.6219 10 0.7903600000000001 -1.72045 11.0056 11 0.241616 -2.2128900000000002 11.9763 12 -0.20944000000000002 -2.29307 11.1821 13 -0.89938 -1.56606 11.1211 14 -1.41711 -2.4558 11.2009 15 -1.8840700000000001 -2.52969 12.2187 16 -1.81385 -1.49946 11.8263 17 -0.789176 -1.79308 12.1988 18 -1.17975 -1.1326 12.8 19 -1.0421200000000002 -0.111174 12.8198 20 -0.39158699999999996 -0.355446 13.5661 1 -0.453186 -0.8214870000000001 19.3475 2 -0.701328 -1.75309 19.3045 3 0.259701 -1.77368 18.8392 4 0.15001099999999998 -0.755324 18.3631 5 0.564654 -0.5530970000000001 17.6175 6 1.14706 -0.608927 16.8936 7 0.984617 -0.22286999999999998 15.9514 8 0.800405 -0.139544 14.949000000000002 9 0.823068 0.11181500000000001 13.8241 10 0.553984 -0.08825939999999999 12.8295 11 -0.23958600000000002 0.412857 12.4171 12 0.34061199999999997 0.7038409999999999 11.6287 13 0.191371 1.40337 10.6792 14 -0.615445 1.38181 9.71448 15 -0.735794 1.7825900000000001 8.84641 16 -0.457958 1.25463 7.86102 17 -0.81839 0.7253310000000001 6.93755 18 -1.0938 0.509904 5.79469 19 -0.45148999999999995 -0.237525 5.35572
RE: Calculating distances between adjacent points - scidam - Feb-21-2020
The following is the example for randomly generated data:
import numpy as np data = np.random.rand(30, 3) distances = ((data[:-1, ...] - data[1:, ...]) ** 2).sum(axis=1) ** 0.5