I want to make a python script that will load an xyz file. From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms.
If I have a xyz coordinate in this matrix form:
4 test O 0.0 0.0 0.0 H 1.0 0.0 0.0 H 0.0 1.0 0.0
Then I want to find the bond parameters by simply using pythagoras formula using only the indices of the matrix. If I need to find the OH distance, I can give the indices and the value will come up.
Now this is easy for a small system, It will get tiresome for a large one. This is why I want to use a small script, that can load a xyz file, set index and allow user to find the bond parameters.