[Tutor] Euclidean Distances between Atoms in a Molecule.

[Asurin]

Dr. Molnar:

This might be your solution:
>>> import numpy
>>> a = numpy.array((-3.265636,  0.198894,  0.090858))
>>> b = numpy.array((-1.307161,  1.522212,  1.003463))
>>> dist = numpy.linalg.norm(a-b)
>>> dist
2.5337013913983633
>>> 


Qiao Qiao
> On Apr 2, 2017, at 1:41 PM, Stephen P. Molnar <s.molnar at sbcglobal.net> 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
> 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
> _______________________________________________
> Tutor maillist  -  Tutor at python.org
> To unsubscribe or change subscription options:
> https://mail.python.org/mailman/listinfo/tutor