remap_speci.py

def specific_remap_dict(path_to_pdb):

    sd = {}
    idx = 0
    with open(path_to_pdb) as pdb_file:
        for line in pdb_file:
            if line.startswith('ATOM'):
                annotated = line[12].strip()
                specific_element = line[13:16].strip()
                if annotated:
                    element = annotated
                else:
                    element = line[13].strip()
                sd[specific_element] = element
                idx += 1

    return sd

fp = r'C:\Users\dealga\Documents\GitHub\BioBlender\Test_molecules\06_1L2Y_4GE.pdb'
sd = specific_remap_dict(path_to_pdb=fp)

import pprint
pprint.pprint(sd)