def test_should_raise_with_negative_k(self):
with self.assertRaises(RuntimeError):
restraints.DistanceRestraint(
self.system,
self.scaler,
self.ramp,
self.system.index.atom(0, "CA"),
self.system.index.atom(1, "CA"),
10.0 * u.nanometer,
10.0 * u.nanometer,
10.0 * u.nanometer,
10.0 * u.nanometer,
-1.0 * u.kilojoule_per_mole / u.nanometer**2,
)
def test_should_raise_with_negative_k(self):
with self.assertRaises(RuntimeError):
restraints.DistanceRestraint(
self.mock_system,
self.scaler,
self.ramp,
1,
"CA",
2,
"CA",
10.,
10.,
10.,
10.,
-1.0,
)
def test_should_raise_if_r4_less_than_r3(self):
with self.assertRaises(RuntimeError):
restraints.DistanceRestraint(
self.mock_system,
self.scaler,
self.ramp,
1,
"CA",
2,
"CA",
10.,
10.,
10.,
0.,
1.0,
)
def test_should_find_two_indices(self):
restraints.DistanceRestraint(
self.mock_system,
self.scaler,
self.ramp,
1,
"CA",
2,
"CA",
0,
0,
0.3,
999.,
1.0,
)
calls = [mock.call(1, "CA"), mock.call(2, "CA")]
self.mock_system.index_of_atom.assert_has_calls(calls)
def test_should_raise_on_bad_index(self):
self.mock_system.index_of_atom.side_effect = KeyError()
with self.assertRaises(KeyError):
restraints.DistanceRestraint(
self.mock_system,
self.scaler,
self.ramp,
1,
"BAD",
2,
"CA",
0,
0,
0.3,
999.,
1.0,
)
def get_secondary_structure_restraints(
system: interfaces.ISystem,
scaler: restraints.RestraintScaler,
ramp: Optional[restraints.TimeRamp] = None,
torsion_force_constant: Optional[u.Quantity] = None,
distance_force_constant: Optional[u.Quantity] = None,
quadratic_cut: Optional[u.Quantity] = None,
first_residue: Optional[indexing.ResidueIndex] = None,
min_secondary_match: int = 4,
filename: Optional[str] = None,
content: Optional[str] = None,
file: Optional[TextIO] = None,
) -> List[restraints.RestraintGroup]:
"""
Get a list of secondary structure restraints.
Args:
system: the system
scaler: the force scaler
ramp: the ramp, default is ConstantRamp
torsion_force_constant: force constant for torsions, default 2.5e-2 kJ/mol/deg^2
distance_force_constant: force constant for distances, default 2.5 kJ/mol/nm^2
quadratic_cut: switch from quadratic to linear beyond this distance, default 0.2 nm
min_secondary_match: minimum number of elements to match in secondary structure
first_residue: residue at which these secondary structure restraints start
filename: filename to open
content: contents to process
file: object to read from
Returns
A list of :class:`RestraintGroups`
.. note::
Specify exactly one of filename, contents, file.
"""
torsion_force_constant = (2.5e-2 * u.kilojoule_per_mole /
u.degree**2 if torsion_force_constant is None
else torsion_force_constant)
distance_force_constant = (2500 * u.kilojoule_per_mole / u.nanometer**2
if distance_force_constant is None else
distance_force_constant)
quadratic_cut = 0.2 * u.nanometer if quadratic_cut is None else quadratic_cut
if ramp is None:
ramp = restraints.ConstantRamp()
if first_residue is None:
first_residue = indexing.ResidueIndex(0)
else:
assert isinstance(first_residue, indexing.ResidueIndex)
if min_secondary_match > 5:
raise RuntimeError(
"Minimum number of elements to match in secondary structure "
"must be less than or equal to 5.")
min_secondary_match = int(min_secondary_match)
contents = _get_secondary_sequence(filename, content, file)
groups = []
helices = _extract_secondary_runs(contents, "H", 5, min_secondary_match,
first_residue)
for helix in helices:
rests: List[restraints.SelectableRestraint] = []
for index in range(helix.start + 1, helix.end - 1):
phi = restraints.TorsionRestraint(
system,
scaler,
ramp,
system.index.atom(index - 1, "C"),
system.index.atom(index, "N"),
system.index.atom(index, "CA"),
system.index.atom(index, "C"),
-62.5 * u.degree,
17.5 * u.degree,
torsion_force_constant,
)
psi = restraints.TorsionRestraint(
system,
scaler,
ramp,
system.index.atom(index, "N"),
system.index.atom(index, "CA"),
system.index.atom(index, "C"),
system.index.atom(index + 1, "N"),
-42.5 * u.degree,
17.5 * u.degree,
torsion_force_constant,
)
rests.append(phi)
rests.append(psi)
d1 = restraints.DistanceRestraint(
system,
scaler,
ramp,
system.index.atom(helix.start, "CA"),
system.index.atom(helix.start + 3, "CA"),
0 * u.nanometer,
0.485 * u.nanometer,
0.561 * u.nanometer,
0.561 * u.nanometer + quadratic_cut,
distance_force_constant,
)
d2 = restraints.DistanceRestraint(
system,
scaler,
ramp,
system.index.atom(helix.start + 1, "CA"),
system.index.atom(helix.start + 4, "CA"),
0 * u.nanometer,
0.485 * u.nanometer,
0.561 * u.nanometer,
0.561 * u.nanometer + quadratic_cut,
distance_force_constant,
)
d3 = restraints.DistanceRestraint(
system,
scaler,
ramp,
system.index.atom(helix.start, "CA"),
system.index.atom(helix.start + 4, "CA"),
0 * u.nanometer,
0.581 * u.nanometer,
0.684 * u.nanometer,
0.684 * u.nanometer + quadratic_cut,
distance_force_constant,
)
rests.append(d1)
rests.append(d2)
rests.append(d3)
group = restraints.RestraintGroup(rests, len(rests))
groups.append(group)
extended = _extract_secondary_runs(contents, "E", 5, min_secondary_match,
first_residue)
for ext in extended:
rests = []
for index in range(ext.start + 1, ext.end - 1):
phi = restraints.TorsionRestraint(
system,
scaler,
ramp,
system.index.atom(index - 1, "C"),
system.index.atom(index, "N"),
system.index.atom(index, "CA"),
system.index.atom(index, "C"),
-117.5 * u.degree,
27.5 * u.degree,
torsion_force_constant,
)
psi = restraints.TorsionRestraint(
system,
scaler,
ramp,
system.index.atom(index, "N"),
system.index.atom(index, "CA"),
system.index.atom(index, "C"),
system.index.atom(index + 1, "N"),
145 * u.degree,
25.0 * u.degree,
torsion_force_constant,
)
rests.append(phi)
rests.append(psi)
d1 = restraints.DistanceRestraint(
system,
scaler,
ramp,
system.index.atom(ext.start, "CA"),
system.index.atom(ext.start + 3, "CA"),
0 * u.nanometer,
0.785 * u.nanometer,
1.063 * u.nanometer,
1.063 * u.nanometer + quadratic_cut,
distance_force_constant,
)
d2 = restraints.DistanceRestraint(
system,
scaler,
ramp,
system.index.atom(ext.start + 1, "CA"),
system.index.atom(ext.start + 4, "CA"),
0 * u.nanometer,
0.785 * u.nanometer,
1.063 * u.nanometer,
1.063 * u.nanometer + quadratic_cut,
distance_force_constant,
)
d3 = restraints.DistanceRestraint(
system,
scaler,
ramp,
system.index.atom(ext.start, "CA"),
system.index.atom(ext.start + 4, "CA"),
0 * u.nanometer,
1.086 * u.nanometer,
1.394 * u.nanometer,
1.394 * u.nanometer + quadratic_cut,
distance_force_constant,
)
rests.append(d1)
rests.append(d2)
rests.append(d3)
group = restraints.RestraintGroup(rests, len(rests))
groups.append(group)
return groups