def setUp(self):
self.ramp = restraints.ConstantRamp()
def setUp(self):
p = SubSystemFromSequence("GLY GLY GLY GLY")
b = SystemBuilder()
self.system = b.build_system([p])
self.scaler = restraints.ConstantScaler()
self.ramp = restraints.ConstantRamp()
def get_rdc_restraints(
system: interfaces.ISystem,
patcher: patchers.RdcAlignmentPatcher,
scaler: restraints.RestraintScaler,
ramp: Optional[restraints.TimeRamp] = None,
quadratic_cut: Optional[u.Quantity] = None,
scale_factor: float = 1.0e4,
filename: Optional[str] = None,
content: Optional[str] = None,
file: Optional[TextIO] = None,
) -> List[restraints.RdcRestraint]:
"""
Reads restraints from file and returns as RdcRestraint object.
Args:
system: the system object for the restraints to be added to.
patcher: the patcher that was used to add alignment tensor dummy atoms
scaler: object to scale the force constant.
ramp: ramp, default is ConstantRamp()
quadratic_cut: restraints become linear beyond this deviation, default 999 Hz
scale_factor: scale factor for kappa and alignment tensor
filename : filename to open
content : contents to process
file : object to read from
Returns:
list of restraints from input
.. note::
The value of `kappa` will be scaled down by `scale_factor`. This will
result in the alignment tensor being scaled up by `scale_factor`.
Ideally, the largest values of the scaled alignment tensor should be
approximately 1. As typical values of the alignment are on the order
of 1e-4, the default value of 1e4 is a reasonable guess. The value
of `scale_factor` must be the same for all experiments that share the
same alignment.
.. note::
The value of kappa is assumed to be in units of Hz A^3.
"""
quadratic_cut = 999.0 / u.seconds if quadratic_cut is None else quadratic_cut
if ramp is None:
ramp = restraints.ConstantRamp()
contents = _handle_arguments(filename, content, file)
lines = contents.splitlines()
lines = [line.strip() for line in lines if not line.startswith("#")]
restraint_list = []
for line in lines:
cols = line.split()
res_i = int(cols[0])
atom_i = cols[1]
res_j = int(cols[2])
atom_j = cols[3]
obs = float(cols[4])
expt = int(cols[5])
tolerance = float(cols[6])
kappa = float(cols[7]) / scale_factor
force_const = float(cols[8])
weight = float(cols[9])
atom_index_i = system.index.atom(res_i, atom_i, one_based=True)
atom_index_j = system.index.atom(res_j, atom_j, one_based=True)
rest = restraints.RdcRestraint(
system,
scaler,
ramp,
atom_index_i,
atom_index_j,
kappa * u.second**-1 * u.angstrom**3,
obs * u.second**-1,
tolerance * u.second**-1,
force_const * u.kilojoule_per_mole * u.second**2,
quadratic_cut,
weight,
expt,
patcher,
)
restraint_list.append(rest)
return restraint_list
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
def setUp(self):
self.mock_system = mock.Mock()
self.scaler = restraints.ConstantScaler()
self.ramp = restraints.ConstantRamp()
def setUp(self):
p = system.ProteinMoleculeFromSequence("GLY GLY GLY GLY")
b = system.SystemBuilder()
self.system = b.build_system_from_molecules([p])
self.scaler = restraints.ConstantScaler()
self.ramp = restraints.ConstantRamp()