def get_equivalent_atoms(mol_file1, mol_file2):
"""Get a dictionary of equivalent atom pairs based on bonds
mol_file1 -- path to a .mol file
mol_file2 -- path to a second .mol file
Will return an empty dictionary if no mapping is found """
# Get coordinates and number atoms from a mol file
coords_and_bonds1 = Iab.coords_to_lists(mol_file1)
# Construct graph where nodes are atom numbers and edges are bonds
G1 = Iab.construct_graph(coords_and_bonds1)
# Get coordinates and number atoms for molecule 2
coords_and_bonds2 = Iab.coords_to_lists(mol_file2)
# Construct graph where nodes are atom numbers and edges are bonds
# for molecule 2
G2 = Iab.construct_graph(coords_and_bonds2)
# Find the combination of atoms that exclude the hydroxyl protons
# and return the mapping dictionary
return [Iab.get_redox_graph_mapping(G1, G2), coords_and_bonds1, \
coords_and_bonds2, G1, G2]
