old_contents: # will merge this file with test_toolkits.py later, currently doing it separately
  
  
  from simtk.openmm.app import PDBFile
  from openforcefield.topology import Molecule, Topology
  from openforcefield.typing.engines.smirnoff import ForceField
  
  def test_compute_partial_charges(self):
      """Test computation/retrieval of partial charges"""
      # TODO: Test only one molecule for speed?
      # TODO: Do we need to deepcopy each molecule, or is setUp called separately for each test method?
      from simtk import unit
      import numpy as np
  
      return
  
  
  # Create a simple molecule from SMILES and turn it into a topology.
  mol1 = Molecule.from_smiles("C1=NC=CC(=C1)C2=CC=C(C=C2)O")
  mol1.generate_conformers(n_conformers=1)
  mol1.compute_wiberg_bond_orders()
  for i in mol1.bonds: 
     print(i.fractional_bond_order)
  print("Total number of bonds:", len(mol1.bonds))
  
  mol2 = Molecule.from_smiles("C1=NC=CC(=C1)C2=CC=C(C=C2)[O-]")
  mol2.generate_conformers(n_conformers=1)
  mol2.compute_wiberg_bond_orders()
  for i in mol2.bonds: 
     print(i.fractional_bond_order)
  print("Total number of bonds:", len(mol1.bonds))
  
  
  #from IPython import embed
  #embed();
  #exit()
  
new_contents: # will merge this file with test_toolkits.py later, currently doing it separately
  
  
  from simtk.openmm.app import PDBFile
  from openforcefield.topology import Molecule, Topology
  from openforcefield.typing.engines.smirnoff import ForceField
  from openforcefield.utils import get_data_file_path
  
  
  ## Create a simple molecule from SMILES and turn it into a topology.
  #mol1 = Molecule.from_smiles("C1=NC=CC(=C1)C2=CC=C(C=C2)O")
  #mol1.generate_conformers(n_conformers=1)
  #mol1.compute_wiberg_bond_orders()
  #
  #mol2 = Molecule.from_smiles("C1=NC=CC(=C1)C2=CC=C(C=C2)[O-]")
  #mol2.generate_conformers(n_conformers=1)
  #mol2.compute_wiberg_bond_orders()
  
  # Reading neutral molecule from file
  filename = get_data_file_path('molecules/molecule_neutral.sdf')
  molecule1 = Molecule.from_file(filename)  # not using toolkitwrapper flag
  molecule1.compute_wiberg_bond_orders()
  # Fetching wiberg bond order of of C-C bond
  for i in molecule1.atoms[4].bonds:
      if i.atom1_index == 6 or i.atom2_index == 6:
          wbo_neutral = i.fractional_bond_order
  
  # Reading negative molecule from file
  filename = get_data_file_path('molecules/molecule_anion.sdf')
  molecule2 = Molecule.from_file(filename)  # not using toolkitwrapper flag
  molecule2.compute_wiberg_bond_orders()
  # Fetching wiberg bond order of of C-C bond
  for i in molecule2.atoms[4].bonds:
      if i.atom1_index == 6 or i.atom2_index == 6:
          wbo_anion = i.fractional_bond_order
  
  # Checking that only one additional bond is present ihe neutral molecule
  assert (len(molecule1.bonds)==len(molecule2.bonds)+1)
  # Wiberg bond order is higher in the anion
  assert (wbo_anion > wbo_neutral)
  
  
  
  #from IPython import embed
  #embed();
  #exit()
  
subject: test for wbo