[Tutor] Euclidean Distances between Atoms in a Molecule.

[Stephen P. Molnar]

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
2   12.011  1.213336  0.948208 -0.033373
3   14.007  3.238650  1.041523  1.301322
4   12.011 -5.954489  0.650878  0.803379
5   12.011  5.654476  0.480066  0.013757
6   12.011  6.372043  2.731713 -1.662411
7   12.011  7.655753  0.168393  2.096802
8   12.011  5.563051 -1.990203 -1.511875
9    1.008 -2.939469 -1.327967 -1.247635
10   1.008 -1.460475  2.993912  2.415410
11   1.008  1.218042  0.451815 -2.057439
12   1.008 -6.255901  2.575035  1.496984
13   1.008 -6.560562 -0.695722  2.248982
14   1.008 -7.152500  0.390758 -0.864115
15   1.008  4.959548  3.061356 -3.139100
16   1.008  8.197613  2.429073 -2.588339
17   1.008  6.503322  4.471092 -0.543939
18   1.008  7.845274  1.892126  3.227577
19   1.008  9.512371 -0.273198  1.291080
20   1.008  7.147039 -1.365346  3.393778
21   1.008  4.191488 -1.928466 -3.057804
22   1.008  5.061650 -3.595015 -0.302810
23   1.008  7.402586 -2.392148 -2.374554

What I need for further calculation is a matrix of the Euclidean 
distances between the atoms.

So far in searching the Python literature I have only managed to confuse 
myself and would greatly appreciate any pointers towards a solution.

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.		Life is a fuzzy set
www.molecular-modeling.net		Stochastic and multivariate
(614)312-7528 (c)
Skype: smolnar1