def test_to_from_rdkit_core_props_unset(self): """Test RDKitToolkitWrapper to_rdkit() and from_rdkit() when given empty core property fields""" toolkit_wrapper = RDKitToolkitWrapper() # Replacing with a simple molecule with stereochemistry input_smiles = r'C\C(F)=C(/F)C[C@](C)(Cl)Br' expected_output_smiles = r'[H][C]([H])([H])/[C]([F])=[C](\[F])[C]([H])([H])[C@]([Cl])([Br])[C]([H])([H])[H]' molecule = Molecule.from_smiles(input_smiles, toolkit_registry=toolkit_wrapper) assert molecule.to_smiles( toolkit_registry=toolkit_wrapper) == expected_output_smiles # Ensure one atom has its stereochemistry specified central_carbon_stereo_specified = False for atom in molecule.atoms: if (atom.atomic_number == 6) and atom.stereochemistry == "R": central_carbon_stereo_specified = True assert central_carbon_stereo_specified # Do a first conversion to/from oemol rdmol = molecule.to_rdkit() molecule2 = Molecule.from_rdkit(rdmol) # Test that properties survived first conversion assert molecule.name == molecule2.name # NOTE: This expects the same indexing scheme in the original and new molecule central_carbon_stereo_specified = False for atom in molecule2.atoms: if (atom.atomic_number == 6) and atom.stereochemistry == "R": central_carbon_stereo_specified = True assert central_carbon_stereo_specified for atom1, atom2 in zip(molecule.atoms, molecule2.atoms): assert atom1.to_dict() == atom2.to_dict() for bond1, bond2 in zip(molecule.bonds, molecule2.bonds): assert bond1.to_dict() == bond2.to_dict() assert (molecule._conformers == None) assert (molecule2._conformers == None) for pc1, pc2 in zip(molecule._partial_charges, molecule2._partial_charges): pc1_ul = pc1 / unit.elementary_charge pc2_ul = pc2 / unit.elementary_charge assert_almost_equal(pc1_ul, pc2_ul, decimal=6) assert molecule2.to_smiles( toolkit_registry=toolkit_wrapper) == expected_output_smiles
def from_rdkit(self, molecule): """ It initializes an OpenForceField's Molecule object from an RDKit molecule. Parameters ---------- molecule : an offpele.topology.Molecule The offpele's Molecule object Returns ------- molecule : an openforcefield.topology.Molecule object The OpenForceField's Molecule """ from openforcefield.topology.molecule import Molecule rdkit_molecule = molecule.rdkit_molecule return Molecule.from_rdkit(rdkit_molecule)
def test_to_from_rdkit_core_props_filled(self): """Test RDKitToolkitWrapper to_rdkit() and from_rdkit() when given populated core property fields""" toolkit_wrapper = RDKitToolkitWrapper() # Replacing with a simple molecule with stereochemistry input_smiles = r'C\C(F)=C(/F)C[C@@](C)(Cl)Br' expected_output_smiles = r'[H][C]([H])([H])/[C]([F])=[C](\[F])[C]([H])([H])[C@@]([Cl])([Br])[C]([H])([H])[H]' molecule = Molecule.from_smiles(input_smiles, toolkit_registry=toolkit_wrapper) assert molecule.to_smiles( toolkit_registry=toolkit_wrapper) == expected_output_smiles # Populate core molecule property fields molecule.name = 'Alice' partial_charges = unit.Quantity( np.array([ -.9, -.8, -.7, -.6, -.5, -.4, -.3, -.2, -.1, 0., .1, .2, .3, .4, .5, .6, .7, .8 ]), unit.elementary_charge) molecule.partial_charges = partial_charges coords = unit.Quantity( np.array([['0.0', '1.0', '2.0'], ['3.0', '4.0', '5.0'], ['6.0', '7.0', '8.0'], ['9.0', '10.0', '11.0'], ['12.0', '13.0', '14.0'], ['15.0', '16.0', '17.0'], ['18.0', '19.0', '20.0'], ['21.0', '22.0', '23.0'], ['24.0', '25.0', '26.0'], ['27.0', '28.0', '29.0'], ['30.0', '31.0', '32.0'], ['33.0', '34.0', '35.0'], ['36.0', '37.0', '38.0'], ['39.0', '40.0', '41.0'], ['42.0', '43.0', '44.0'], ['45.0', '46.0', '47.0'], ['48.0', '49.0', '50.0'], ['51.0', '52.0', '53.0']]), unit.angstrom) molecule.add_conformer(coords) # Populate core atom property fields molecule.atoms[2].name = 'Bob' # Ensure one atom has its stereochemistry specified central_carbon_stereo_specified = False for atom in molecule.atoms: if (atom.atomic_number == 6) and atom.stereochemistry == "S": central_carbon_stereo_specified = True assert central_carbon_stereo_specified # Populate bond core property fields fractional_bond_orders = [float(val) for val in range(18)] for fbo, bond in zip(fractional_bond_orders, molecule.bonds): bond.fractional_bond_order = fbo # Do a first conversion to/from oemol rdmol = molecule.to_rdkit() molecule2 = Molecule.from_rdkit(rdmol) # Test that properties survived first conversion #assert molecule.to_dict() == molecule2.to_dict() assert molecule.name == molecule2.name # NOTE: This expects the same indexing scheme in the original and new molecule central_carbon_stereo_specified = False for atom in molecule2.atoms: if (atom.atomic_number == 6) and atom.stereochemistry == "S": central_carbon_stereo_specified = True assert central_carbon_stereo_specified for atom1, atom2 in zip(molecule.atoms, molecule2.atoms): assert atom1.to_dict() == atom2.to_dict() for bond1, bond2 in zip(molecule.bonds, molecule2.bonds): assert bond1.to_dict() == bond2.to_dict() assert (molecule._conformers[0] == molecule2._conformers[0]).all() for pc1, pc2 in zip(molecule._partial_charges, molecule2._partial_charges): pc1_ul = pc1 / unit.elementary_charge pc2_ul = pc2 / unit.elementary_charge assert_almost_equal(pc1_ul, pc2_ul, decimal=6) assert molecule2.to_smiles( toolkit_registry=toolkit_wrapper) == expected_output_smiles