def test_double_conversion(self, templates):
# Pick some OPLS parameters at random
params = {
'k0': 1.38 * u.Unit('kJ/mol'),
'k1': -0.51 * u.Unit('kJ/mol'),
'k2': 2.2 * u.Unit('kJ/mol'),
'k3': -0.25 * u.Unit('kJ/mol'),
'k4': 1.44 * u.Unit('kJ/mol')
}
opls_torsion_potential = templates['OPLSTorsionPotential']
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = opls_torsion_potential.independent_variables
opls_connection_type = DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=params)
# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
# Convert connection back to OPLS
final_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
assert_allclose_units([*opls_connection_type.parameters.values()],
[*final_connection_type.parameters.values()],
rtol=1e-5,
atol=1e-8)
def test_double_conversion(self):
# Pick some OPLS parameters at random
params = { 'k0' : 1.38 * u.Unit('kJ/mol'),
'k1' : -0.51 * u.Unit('kJ/mol'),
'k2' : 2.2 * u.Unit('kJ/mol'),
'k3' : -0.25 * u.Unit('kJ/mol'),
'k4' : 1.44 * u.Unit('kJ/mol')
}
name = OPLSTorsionPotential().name
expression = OPLSTorsionPotential().expression
variables = OPLSTorsionPotential().independent_variables
opls_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params)
# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
# Convert connection back to OPLS
final_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
assert np.allclose([*opls_connection_type.parameters.values()],
[*final_connection_type.parameters.values()])
def test_opls_to_ryckaert(self, templates):
# Pick some OPLS parameters at random
params = {
"k0": 1.38 * u.Unit("kJ/mol"),
"k1": -0.51 * u.Unit("kJ/mol"),
"k2": 2.2 * u.Unit("kJ/mol"),
"k3": -0.25 * u.Unit("kJ/mol"),
"k4": 1.44 * u.Unit("kJ/mol"),
}
opls_torsion_potential = templates["OPLSTorsionPotential"]
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = opls_torsion_potential.independent_variables
opls_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
# Pick some angles to check
angles = [-2.38, -1.31, -0.44, 0.0, 0.26, 0.92, 1.84, 3.10]
for angle in angles:
assert np.isclose(
float(
ryckaert_connection_type.expression.subs([
(param, val) for param, val in {
**ryckaert_connection_type.parameters,
"phi":
angle - np.pi,
}.items()
])),
float(
opls_connection_type.expression.subs([
(param, val) for param, val in {
**opls_connection_type.parameters,
"phi": angle,
}.items()
])),
)
def test_opls_to_ryckaert(self, templates):
# Pick some OPLS parameters at random
params = {
'k0': 1.38 * u.Unit('kJ/mol'),
'k1': -0.51 * u.Unit('kJ/mol'),
'k2': 2.2 * u.Unit('kJ/mol'),
'k3': -0.25 * u.Unit('kJ/mol'),
'k4': 1.44 * u.Unit('kJ/mol')
}
opls_torsion_potential = templates['OPLSTorsionPotential']
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = opls_torsion_potential.independent_variables
opls_connection_type = DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=params)
# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
# Pick some angles to check
angles = [-2.38, -1.31, -0.44, 0.0, 0.26, 0.92, 1.84, 3.10]
for angle in angles:
assert np.isclose(
float(
ryckaert_connection_type.expression.subs([
(param, val) for param, val in {
**ryckaert_connection_type.parameters, 'phi':
angle - np.pi
}.items()
])),
float(
opls_connection_type.expression.subs([
(param, val) for param, val in {
**opls_connection_type.parameters, 'phi': angle
}.items()
])),
)
def test_invalid_connection_type(self, templates):
params = {
'c0': 1.53 * u.Unit('kJ/mol'),
'c1': 0.76 * u.Unit('kJ/mol'),
'c2': -0.22 * u.Unit('kJ/mol'),
'c3': 3.55 * u.Unit('kJ/mol'),
'c4': 0.94 * u.Unit('kJ/mol'),
'c5': 0.0 * u.Unit('kJ/mol')
}
ryckaert_bellemans_torsion_potential = templates[
'RyckaertBellemansTorsionPotential']
name = ryckaert_bellemans_torsion_potential.name
expression = ryckaert_bellemans_torsion_potential.expression
variables = ['phi', 'psi']
ryckaert_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params)
with pytest.raises(GMSOError, match='Cannot use'):
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
expression = 'c0+c1+c2+c3+c4+c5+phi'
variables = ryckaert_bellemans_torsion_potential.independent_variables
ryckaert_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params)
with pytest.raises(GMSOError, match='Cannot use'):
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
# Pick some OPLS parameters at random
params = {
'k0': 1.38 * u.Unit('kJ/mol'),
'k1': -0.51 * u.Unit('kJ/mol'),
'k2': 2.2 * u.Unit('kJ/mol'),
'k3': -0.25 * u.Unit('kJ/mol'),
'k4': 1.44 * u.Unit('kJ/mol')
}
opls_torsion_potential = templates['OPLSTorsionPotential']
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = ['phi', 'psi']
opls_connection_type = DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=params)
with pytest.raises(GMSOError, match=''):
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
variables = opls_torsion_potential.independent_variables
expression = 'k0+k1+k2+k3+k4+phi'
opls_connection_type = DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=params)
with pytest.raises(GMSOError, match=''):
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
def test_invalid_connection_type(self, templates):
params = {
"c0": 1.53 * u.Unit("kJ/mol"),
"c1": 0.76 * u.Unit("kJ/mol"),
"c2": -0.22 * u.Unit("kJ/mol"),
"c3": 3.55 * u.Unit("kJ/mol"),
"c4": 0.94 * u.Unit("kJ/mol"),
"c5": 0.0 * u.Unit("kJ/mol"),
}
ryckaert_bellemans_torsion_potential = templates[
"RyckaertBellemansTorsionPotential"]
name = ryckaert_bellemans_torsion_potential.name
expression = (str(ryckaert_bellemans_torsion_potential.expression) +
" + 3 * psi")
variables = ["phi", "psi"]
ryckaert_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
with pytest.raises(GMSOError, match="Cannot use"):
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
expression = "c0+c1+c2+c3+c4+c5+phi"
variables = ryckaert_bellemans_torsion_potential.independent_variables
ryckaert_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
with pytest.raises(GMSOError, match="Cannot use"):
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
# Pick some OPLS parameters at random
params = {
"k0": 1.38 * u.Unit("kJ/mol"),
"k1": -0.51 * u.Unit("kJ/mol"),
"k2": 2.2 * u.Unit("kJ/mol"),
"k3": -0.25 * u.Unit("kJ/mol"),
"k4": 1.44 * u.Unit("kJ/mol"),
}
opls_torsion_potential = templates["OPLSTorsionPotential"]
name = opls_torsion_potential.name
expression = (str(opls_torsion_potential.expression) +
" + 0.5 * k1 * (1 + cos(psi))")
variables = ["phi", "psi"]
opls_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
with pytest.raises(GMSOError, match=""):
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
variables = opls_torsion_potential.independent_variables
expression = "k0+k1+k2+k3+k4+phi"
opls_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
with pytest.raises(GMSOError, match=""):
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
