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()