def test_to_list(self): """Test basic ParameterList.to_list() function, ensuring units are preserved""" from simtk import unit p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.01 * unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom**2) p2 = BondHandler.BondType(smirks='[*:1]=[*:2]', length=1.02 * unit.angstrom, k=6 * unit.kilocalorie_per_mole / unit.angstrom**2) p3 = BondHandler.BondType(smirks='[*:1]#[*:3]', length=1.03 * unit.angstrom, k=7 * unit.kilocalorie_per_mole / unit.angstrom**2) parameter_list = ParameterList([p1, p2, p3]) ser_param_list = parameter_list.to_list() assert len(ser_param_list) == 3 assert ser_param_list[0]['length'] == 1.01 * unit.angstrom
def test_read_write_optional_parameter_attribute(self): """ Test ParameterTypes' ability to store and write out optional attributes passed to __init__() """ from simtk import unit p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.02 * unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom**2, id='b1') param_dict = p1.to_dict() assert ('id', 'b1') in param_dict.items()
def test_round_trip(self): """Test basic ParameterList.to_list() function and constructor""" from simtk import unit p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.01 * unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom**2) p2 = BondHandler.BondType(smirks='[*:1]=[*:2]', length=1.02 * unit.angstrom, k=6 * unit.kilocalorie_per_mole / unit.angstrom**2) p3 = BondHandler.BondType(smirks='[*:1]#[*:3]', length=1.03 * unit.angstrom, k=7 * unit.kilocalorie_per_mole / unit.angstrom**2) parameter_list = ParameterList([p1, p2, p3]) param_dict_list = parameter_list.to_list() parameter_list_2 = ParameterList() for param_dict in param_dict_list: new_parameter = BondHandler.BondType(**param_dict) parameter_list_2.append(new_parameter) assert parameter_list.to_list() == parameter_list_2.to_list()
def test_error_cosmetic_parameter_attribute(self): """ Test that ParameterTypes raise an error on receiving unexpected attributes passed to __init__() """ from simtk import unit with pytest.raises(SMIRNOFFSpecError, match="Unexpected kwarg (pilot: alice)*") as context: p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.02*unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2, pilot='alice', allow_cosmetic_attributes=False )
def test_read_but_dont_write_cosmetic_parameter_attribute(self): """ Test ParameterTypes' ability to ignore cosmetic attributes passed to __init__() if instructed """ from simtk import unit p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.02 * unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom**2, pilot='alice', allow_cosmetic_attributes=True) param_dict = p1.to_dict(discard_cosmetic_attributes=True) assert ('pilot', 'alice') not in param_dict.items()
def test_bondtype_to_dict_custom_output_units(self): """ Test BondType to_dict with custom output units. """ from simtk import unit p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.02 * unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom**2) param_dict = p1.to_dict() param_dict_unitless, attached_units = detach_units( param_dict, output_units={'length_unit': unit.nanometer}) assert attached_units['length_unit'] == unit.nanometer assert abs(param_dict_unitless['length'] - 0.102) < 1e-10
def test_bondtype_to_dict_invalid_output_units(self): """ Test ParameterType to_dict with invalid output units. """ from simtk import unit p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.02*unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2 ) param_dict = p1.to_dict() with pytest.raises(ValueError, match='Requested output unit calorie is not compatible with quantity unit angstrom .' ) as context: param_dict_unitless, attached_units = detach_units(param_dict, output_units = {'length_unit': unit.calorie})
def test_bondtype_to_dict(self): """ Test BondType to_dict. """ from simtk import unit p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.02 * unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2 ) param_dict = p1.to_dict() param_dict_unitless, attached_units = detach_units(param_dict) assert param_dict_unitless == {'smirks': '[*:1]-[*:2]', 'length': 1.02, 'k': 5,} assert attached_units == {'length_unit': unit.angstrom, 'k_unit': (unit.angstrom ** -2) * (unit.mole ** -1) * (unit.kilocalorie ** 1) }
def test_add_delete_cosmetic_attrib(self): """ Test adding and deleting cosmetic attributes for already-initialized ParameterType objects """ from simtk import unit p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', length=1.02*unit.angstrom, k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2, ) # Ensure the cosmetic attribute is present by default during output p1.add_cosmetic_attribute('pilot', 'alice') param_dict = p1.to_dict() assert ('pilot', 'alice') in param_dict.items() # Ensure the cosmetic attribute isn't present if we request that it be discarded param_dict = p1.to_dict(discard_cosmetic_attributes=True) assert ('pilot', 'alice') not in param_dict.items() # Manually delete the cosmetic attribute and ensure it doesn't get written out p1.delete_cosmetic_attribute('pilot') param_dict = p1.to_dict() assert ('pilot', 'alice') not in param_dict.items()