This program takes the molecular coordinates from an input file and calculates the bond distances between all atoms. There is a built-in conditional that performs a soft bond check using specific distance cutoff criteria (0-1.5 Angstroms).
The following is the contents of a water geometry input file:
3
Water xyz file
O 0.000000 -0.007156 0.965491
H1 -0.000000 0.001486 -0.003471
H2 0.000000 0.931026 1.207929
The code formats and writes the calculated bond lengths and the total number of atoms to a text file called distance_file.txt
Here are the results for water:
Number of atoms in molecule: 3
O - H1 | Atom Distance: 0.96900 Angstroms
O - H2 | Atom Distance: 0.96900 Angstroms
This program contains unit tests on the functions defined in geom_analysis.py
collected 2 items
test_geom_analysis.py::test_calculate_distance PASSED [ 50%]
test_geom_analysis.py::test_bond_check PASSED [100%]
The functions are determined to be stable.