def test_add_delete_cosmetic_attributes(self):
"""Test ParameterHandler.to_dict() function when some parameters are in
different units (proper behavior is to convert all quantities to the last-
read unit)
"""
from simtk import unit
bh = BondHandler(skip_version_check=True)
bh.add_parameter({
'smirks': '[*:1]-[*:2]',
'length': 1 * unit.angstrom,
'k': 10 * unit.kilocalorie_per_mole / unit.angstrom**2
})
bh.add_parameter({
'smirks': '[*:1]=[*:2]',
'length': 0.2 * unit.nanometer,
'k': 0.4 * unit.kilojoule_per_mole / unit.nanometer**2
})
assert not (bh.attribute_is_cosmetic('pilot'))
# Ensure the cosmetic attribute is present by default during output
bh.add_cosmetic_attribute('pilot', 'alice')
param_dict = bh.to_dict()
assert ('pilot', 'alice') in param_dict.items()
assert bh.attribute_is_cosmetic('pilot')
# Ensure the cosmetic attribute isn't present if we request that it be discarded
param_dict = bh.to_dict(discard_cosmetic_attributes=True)
assert 'pilot' not in param_dict
# Manually delete the cosmetic attribute and ensure it doesn't get written out
bh.delete_cosmetic_attribute('pilot')
param_dict = bh.to_dict()
assert 'pilot' not in param_dict
assert not (bh.attribute_is_cosmetic('pilot'))
def test_to_dict_maintain_units(self):
"""Test ParameterHandler.to_dict() function when parameters were provided in different units
"""
from simtk import unit
bh = BondHandler(skip_version_check=True)
bh.add_parameter({'smirks': '[*:1]-[*:2]',
'length': 1*unit.angstrom,
'k': 10*unit.kilocalorie_per_mole/unit.angstrom**2})
bh.add_parameter({'smirks': '[*:1]=[*:2]',
'length': 0.2*unit.nanometer,
'k': 0.4*unit.kilojoule_per_mole/unit.nanometer**2})
bh_dict = bh.to_dict()
assert bh_dict['Bond'][0]['length'] == unit.Quantity(1., unit.angstrom)
assert bh_dict['Bond'][0]['length'].unit == unit.angstrom
assert bh_dict['Bond'][1]['length'] == unit.Quantity(0.2, unit.nanometer)
assert bh_dict['Bond'][1]['length'].unit == unit.nanometer
def test_different_units_to_dict(self):
"""Test ParameterHandler.to_dict() function when some parameters are in
different units (proper behavior is to convert all quantities to the last-
read unit)
"""
from simtk import unit
bh = BondHandler(skip_version_check=True)
bh.add_parameter({'smirks': '[*:1]-[*:2]',
'length': 1*unit.angstrom,
'k': 10*unit.kilocalorie_per_mole/unit.angstrom**2})
bh.add_parameter({'smirks': '[*:1]=[*:2]',
'length': 0.2*unit.nanometer,
'k': 0.4*unit.kilojoule_per_mole/unit.nanometer**2})
bh_dict = bh.to_dict()
assert bh_dict['Bond'][0]['length'] == unit.Quantity(value=1, unit=unit.angstrom)
assert bh_dict['Bond'][1]['length'] == unit.Quantity(value=2, unit=unit.angstrom)
def test_get_parameter(self):
"""Test that ParameterHandler.get_parameter can lookup function
"""
from simtk import unit
bh = BondHandler(skip_version_check=True, allow_cosmetic_attributes=True)
bh.add_parameter({'smirks': '[*:1]-[*:2]',
'length': 1*unit.angstrom,
'k': 10*unit.kilocalorie_per_mole/unit.angstrom**2,
'id': 'b0'})
bh.parameters[0].add_cosmetic_attribute('foo', 'bar')
# Check base behavior
params = bh.get_parameter({'smirks': '[*:1]-[*:2]'})
assert params[0].length == unit.Quantity(1.0, unit.angstrom)
assert params[0].k == unit.Quantity(10.0, unit.kilocalorie_per_mole/unit.angstrom**2)
# Ensure a query with no matches returns an empty list
assert not bh.get_parameter({'smirks': 'xyz'})
# Ensure searching for a nonexistent attr does not raise an exception
assert not bh.get_parameter({'bAdAttR': '0'})
# Check for optional and cosmetic attrs
optional_params = bh.get_parameter({'id': 'b0'})
cosmetic_params = bh.get_parameter({'foo': 'bar'})
assert optional_params[0].id == 'b0'
assert cosmetic_params[0]._foo == 'bar'
# Ensure selection behaves a "OR" not "AND"
bh.add_parameter({'smirks': '[#1:1]-[#6:2]',
'length': 1*unit.angstrom,
'k': 10*unit.kilocalorie_per_mole/unit.angstrom**2,
'id': 'b1'})
params = bh.get_parameter({'id': 'b0', 'smirks': '[#1:1]-[#6:2]'})
assert 'b0' in [param.id for param in params]
assert '[*:1]-[*:2]' in [param.smirks for param in params]
# Ensure selection does not return duplicates if multiple matches
params = bh.get_parameter({'id': 'b1', 'smirks': '[#1:1]-[#6:2]'})
assert len(params) == 1