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
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