How to access elements of a list in a class object?

Question

I'm new to python and trying to understand the basics using the pyscal module. I am trying to find the positions of each atom in each molecule at each snapshot (timepoint). From what I understand, customkeys in the following defines a list, whereas sys is a class object containing the different snapshots of my system, where each snapshot is a timepoint containing the positions of all atoms in all molecules.

I want to do something like iterate over the class object to obtain the positions of all of the atoms in each molecules at each timepoint. So I do the following:

sys = ml.to_system(customkeys=["mol"])

for mol in sys:
    each_molec = atom.pos
    print(each_molec)
    print(mol)

The first print statement outputs only the positions of the very last atom in the system, and the second print statement outputs something that I don't understand like:

<pyscal.core.System object at 0x7f84eab9a900>

Alternatively, I can access the molecule number for a particular atom in an particular snapshot by something like:

sys[1].atoms[1].custom["mol"]

How, then, do I properly access the list in the class object and output the positions for each element (if that's the right word) of the list?

Answer 1

The System object contains a list of atoms. So, I suspect you need something like:

system = ml.to_system(customkeys=["mol"])
for mol in system.atoms:
    print("Another molecule")
    for atom in mol:
        print(atom.pos)

However, the pyscal module is large and complicated. It's possible I misunderstood the documentation.