def test_generate_conformers(self):
"""Test OpenEyeToolkitWrapper generate_conformers()"""
toolkit_wrapper = OpenEyeToolkitWrapper()
smiles = '[H]C([H])([H])C([H])([H])[H]'
molecule = toolkit_wrapper.from_smiles(smiles)
molecule.generate_conformers()
assert molecule.n_conformers != 0
assert not (molecule.conformers[0] == (0. * unit.angstrom)).all()
def test_compute_wiberg_bond_orders_charged(self):
"""Test OpenEyeToolkitWrapper compute_wiberg_bond_orders() on a molecule with net charge +1"""
toolkit_wrapper = OpenEyeToolkitWrapper()
smiles = '[H]C([H])([H])[N+]([H])([H])[H]'
molecule = toolkit_wrapper.from_smiles(smiles)
molecule.generate_conformers(toolkit_registry=toolkit_wrapper)
for charge_model in ['am1', 'pm3']:
molecule.compute_wiberg_bond_orders(
toolkit_registry=toolkit_wrapper, charge_model=charge_model)
def test_compute_wiberg_bond_orders(self):
"""Test OpenEyeToolkitWrapper compute_wiberg_bond_orders()"""
toolkit_wrapper = OpenEyeToolkitWrapper()
smiles = '[H]C([H])([H])C([H])([H])[H]'
molecule = toolkit_wrapper.from_smiles(smiles)
molecule.generate_conformers(toolkit_registry=toolkit_wrapper)
for charge_model in ['am1', 'pm3']:
molecule.compute_wiberg_bond_orders(
toolkit_registry=toolkit_wrapper, charge_model=charge_model)
print([bond.fractional_bond_order for bond in molecule.bonds])
def test_compute_wiberg_bond_orders_double_bond(self):
"""Test OpenEyeToolkitWrapper compute_wiberg_bond_orders() on a molecule with a double bond"""
toolkit_wrapper = OpenEyeToolkitWrapper()
smiles = r'C\C(F)=C(/F)C[C@@](C)(Cl)Br'
molecule = toolkit_wrapper.from_smiles(smiles)
molecule.generate_conformers(toolkit_registry=toolkit_wrapper)
for charge_model in ['am1', 'pm3']:
molecule.compute_wiberg_bond_orders(
toolkit_registry=toolkit_wrapper, charge_model=charge_model)
# TODO: Add test for equivalent Wiberg orders for equivalent bonds
double_bond_has_wbo_near_2 = False
for bond in molecule.bonds:
if bond.bond_order == 2:
if 1.75 < bond.fractional_bond_order < 2.25:
double_bond_has_wbo_near_2 = True
assert double_bond_has_wbo_near_2
def test_compute_partial_charges(self):
"""Test OpenEyeToolkitWrapper compute_partial_charges()"""
toolkit_wrapper = OpenEyeToolkitWrapper()
smiles = '[H]C([H])([H])C([H])([H])[H]'
molecule = toolkit_wrapper.from_smiles(smiles)
# Ensure that an exception is raised if no conformers are provided
with pytest.raises(Exception) as excinfo:
molecule.compute_partial_charges(toolkit_registry=toolkit_wrapper)
molecule.generate_conformers(toolkit_registry=toolkit_wrapper)
# Ensure that an exception is raised if an invalid charge model is passed in
with pytest.raises(Exception) as excinfo:
charge_model = 'notARealChargeModel'
molecule.compute_partial_charges(toolkit_registry=toolkit_wrapper,
charge_model=charge_model)
# TODO: Test all supported charge models
# Note: "amber" and "amberff94" only work for a subset of residue types, so we'll need to find testing data for
# those
# charge_model = [,'amber','amberff94']
# TODO: 'mmff' and 'mmff94' often assign charges of 0, presumably if the molecule is unrecognized.
# charge_model = ['mmff', 'mmff94']
for charge_model in [
'noop', 'am1bcc', 'am1bccnosymspt', 'am1bccelf10'
]:
with pytest.raises(NotImplementedError) as excinfo:
molecule.compute_partial_charges(
toolkit_registry=toolkit_wrapper
) # , charge_model=charge_model)
charge_sum = 0 * unit.elementary_charge
for pc in molecule._partial_charges:
charge_sum += pc
assert charge_sum < 0.001 * unit.elementary_charge
# For now, just test AM1-BCC while the SMIRNOFF spec for other charge models gets worked out
molecule.compute_partial_charges_am1bcc(
toolkit_registry=toolkit_wrapper) # , charge_model=charge_model)
charge_sum = 0 * unit.elementary_charge
for pc in molecule._partial_charges:
charge_sum += pc
assert charge_sum < 0.001 * unit.elementary_charge
def test_compute_partial_charges_net_charge(self):
"""Test OpenEyeToolkitWrapper compute_partial_charges() on a molecule with a net +1 charge"""
toolkit_wrapper = OpenEyeToolkitWrapper()
smiles = '[H]C([H])([H])[N+]([H])([H])[H]'
molecule = toolkit_wrapper.from_smiles(smiles)
molecule.generate_conformers(toolkit_registry=toolkit_wrapper)
with pytest.raises(NotImplementedError) as excinfo:
charge_model = 'notARealChargeModel'
molecule.compute_partial_charges(toolkit_registry=toolkit_wrapper
) #, charge_model=charge_model)
# TODO: Test all supported charge models
# TODO: "amber" and "amberff94" only work for a subset of residue types, so we'll need to find testing data for
# those
# charge_model = [,'amber','amberff94']
# The 'noop' charge model doesn't add up to the formal charge, so we shouldn't test it
# charge_model = ['noop']
for charge_model in [
'mmff', 'mmff94', 'am1bcc', 'am1bccnosymspt', 'am1bccelf10'
]:
with pytest.raises(NotImplementedError) as excinfo:
molecule.compute_partial_charges(
toolkit_registry=toolkit_wrapper
) #, charge_model=charge_model)
charge_sum = 0 * unit.elementary_charge
for pc in molecule._partial_charges:
charge_sum += pc
assert 0.999 * unit.elementary_charge < charge_sum < 1.001 * unit.elementary_charge
# For now, I'm just testing AM1-BCC (will test more when the SMIRNOFF spec for other charges is finalized)
molecule.compute_partial_charges_am1bcc(
toolkit_registry=toolkit_wrapper)
charge_sum = 0 * unit.elementary_charge
for pc in molecule._partial_charges:
charge_sum += pc
assert 0.999 * unit.elementary_charge < charge_sum < 1.001 * unit.elementary_charge