[FIXED] Can't figure how to stop dictionary keys from overwriting themselves

Issue

I'm trying to create a dictionary and my dictionary keys keep overwriting themselves. I don't understand how I can handle this issue.

Here's the script:

import MDAnalysis as mda


u = mda.Universe('rps5.prmtop', 'rps5.inpcrd')

ca = u.select_atoms('protein')

charges = ca.charges
atom_types = ca.names
resnames = ca.resnames


charge_dict = {}

for i in range(len(charges)):
    #print(i+1 ,resnames[i], atom_types[i], charges[i])
    charge_dict[resnames[i]] =  {}
    charge_dict[resnames[i]][atom_types[i]] = charges[i]

print(charge_dict)

The charges, atom_types and resnames are all lists, with the same number of elements.

I want my dictionary to look like this: charge_dict[resname][atom_types] = charges (charge_dict['MET']['CA'] = 0.32198, for example).

Could you please help me with this issue?

Solution

Without actually seeing a complete problem description, my guess is that your final result is that each charge_dict[name] is a dictionary with just one key. That's not because the keys "overwrite themselves". Your program overwrites them explicitly: charge_dict[resnames[i]] = {}.

What you want is to only reset the value for that key if it is not already set. You could easily do that by first testing if resnames[i] not in charge_dict:, but the Python standard library provides an even simpler mechanism: collections.defaultdict. A defaultdict is a dictionary with an associated default value creator. So you can do the following:

from collections import defaultdict
charge_dict = defaultdict(dict)

After that, you won't need to worry about initializing charge_dict[name] because a new dictionary will automatically spring into existence when the default value function (dict) is called.

Answered By - rici