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
