def test_torsion_handler_charmm_potential(self):
"""
Test creation of TorsionHandlers with the deprecated 0.2 potential value "charmm" instead of the current
supported potential value "fourier".
"""
import re
# Test creating ProperTorsionHandlers
err_msg = re.escape(
"Attempted to set ProperTorsionHandler.potential to charmm. Currently, "
"only the following values are supported: ['k*(1+cos(periodicity*theta-phase))']."
)
with pytest.raises(SMIRNOFFSpecError, match=err_msg):
ph1 = ProperTorsionHandler(potential='charmm',
skip_version_check=True)
ph1 = ProperTorsionHandler(
potential='k*(1+cos(periodicity*theta-phase))',
skip_version_check=True)
# Same test, but with ImproperTorsionHandler
err_msg = re.escape(
"Attempted to set ImproperTorsionHandler.potential to charmm. Currently, "
"only the following values are supported: ['k*(1+cos(periodicity*theta-phase))']."
)
with pytest.raises(SMIRNOFFSpecError, match=err_msg):
ph1 = ImproperTorsionHandler(potential='charmm',
skip_version_check=True)
ph1 = ImproperTorsionHandler(
potential='k*(1+cos(periodicity*theta-phase))',
skip_version_check=True)
def test_single_term_proper_torsion(self):
"""
Test creation and serialization of a single-term proper torsion
"""
from simtk import unit
p1 = ProperTorsionHandler.ProperTorsionType(
smirks='[*:1]-[*:2]-[*:3]-[*:4]',
phase1=30 * unit.degree,
periodicity1=2,
k1=5 * unit.kilocalorie_per_mole)
param_dict = p1.to_dict()
assert ('k1', 5 * unit.kilocalorie_per_mole) in param_dict.items()
assert ('phase1', 30 * unit.degree) in param_dict.items()
assert ('periodicity1', 2) in param_dict.items()
assert 'idivf' not in param_dict
def test_multi_term_proper_torsion_skip_index(self):
"""
Test creation and serialization of a multi-term proper torsion where
the indices are not consecutive and a SMIRNOFFSpecError is raised
"""
from simtk import unit
with pytest.raises(SMIRNOFFSpecError, match="Unexpected kwarg (phase3: 31 deg)*") as context:
p1 = ProperTorsionHandler.ProperTorsionType(smirks='[*:1]-[*:2]-[*:3]-[*:4]',
phase1=30 * unit.degree,
periodicity1=2,
k1=5 * unit.kilocalorie_per_mole,
phase3=31 * unit.degree,
periodicity3=3,
k3=6 * unit.kilocalorie_per_mole,
)
def test_multi_term_proper_torsion_bad_units(self):
"""
Test creation and serialization of a multi-term proper torsion where
one of the terms has incorrect units
"""
from simtk import unit
with pytest.raises(IncompatibleUnitError, match="should have units of")\
as context:
p1 = ProperTorsionHandler.ProperTorsionType(smirks='[*:1]-[*:2]-[*:3]-[*:4]',
phase1=30 * unit.degree,
periodicity1=2,
k1=5 * unit.kilocalorie_per_mole,
phase2=31 * unit.angstrom, # This should be caught
periodicity2=3,
k2=6 * unit.kilocalorie_per_mole,
)
def test_multi_term_proper_torsion(self):
"""
Test creation and serialization of a multi-term proper torsion
"""
from simtk import unit
p1 = ProperTorsionHandler.ProperTorsionType(smirks='[*:1]-[*:2]-[*:3]-[*:4]',
phase1=30 * unit.degree,
periodicity1=2,
k1=5 * unit.kilocalorie_per_mole,
phase2=31 * unit.degree,
periodicity2=3,
k2=6 * unit.kilocalorie_per_mole,
)
param_dict = p1.to_dict()
assert param_dict['k1'] == 5 * unit.kilocalorie_per_mole
assert param_dict['phase1'] == 30 * unit.degree
assert param_dict['periodicity1'] == 2
assert param_dict['k2'] == 6 * unit.kilocalorie_per_mole
assert param_dict['phase2'] == 31 * unit.degree
assert param_dict['periodicity2'] == 3