def simulate(file="simulation.pdb.bz2", dir=None, step_size=2.0, snapshot=10, total=1000, model=1, force=True):
"""Pseudo-Brownian dynamics simulation of the frame order motions.
@keyword file: The PDB file for storing the frame order pseudo-Brownian dynamics simulation. The compression is determined automatically by the file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
@type file: str
@keyword dir: The directory name to place the file into.
@type dir: str or None
@keyword step_size: The rotation will be of a random direction but with this fixed angle. The value is in degrees.
@type step_size: float
@keyword snapshot: The number of steps in the simulation when snapshots will be taken.
@type snapshot: int
@keyword total: The total number of snapshots to take before stopping the simulation.
@type total: int
@keyword model: Only one model from an analysed ensemble of structures can be used for the pseudo-Brownian simulation, as the simulation and corresponding PDB file consists of one model per simulation.
@type model: int
@keyword force: A flag which, if set to True, will overwrite the any pre-existing file.
@type force: bool
"""
# Printout.
print("Pseudo-Brownian dynamics simulation of the frame order motions.")
# Checks.
check_pipe()
check_model()
check_domain()
check_parameters()
check_pivot()
# Skip the rigid model.
if cdp.model == MODEL_RIGID:
print("Skipping the rigid model.")
return
# Open the output file.
file = open_write_file(file_name=file, dir=dir, force=force)
# The parameter values.
values = assemble_param_vector()
params = {}
i = 0
for name in cdp.params:
params[name] = values[i]
i += 1
# The structure.
structure = deepcopy(cdp.structure)
if structure.num_models() > 1:
structure.collapse_ensemble(model_num=model)
# The pivot points.
num_states = 1
if cdp.model == MODEL_DOUBLE_ROTOR:
num_states = 2
pivot = zeros((num_states, 3), float64)
for i in range(num_states):
pivot[i] = generate_pivot(order=i+1, pdb_limit=True)
# Shift to the average position.
average_position(structure=structure, models=[None])
# The motional eigenframe.
frame = generate_axis_system()
# Create the distribution.
brownian(file=file, model=cdp.model, structure=structure, parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(), step_size=step_size, snapshot=snapshot, total=total)
# Close the file.
file.close()
def distribute(file="distribution.pdb.bz2", dir=None, atom_id=None, total=1000, max_rotations=100000, model=1, force=True):
"""Create a uniform distribution of structures for the frame order motions.
@keyword file: The PDB file for storing the frame order motional distribution. The compression is determined automatically by the file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
@type file: str
@keyword dir: The directory name to place the file into.
@type dir: str or None
@keyword atom_id: The atom identification string to allow the distribution to be a subset of all atoms.
@type atom_id: None or str
@keyword total: The total number of states/model/structures in the distribution.
@type total: int
@keyword max_rotations: The maximum number of rotations to generate the distribution from. This prevents an execution for an infinite amount of time when a frame order amplitude parameter is close to zero so that the subset of all rotations within the distribution is close to zero.
@type max_rotations: int
@keyword model: Only one model from an analysed ensemble of structures can be used for the distribution, as the corresponding PDB file consists of one model per state.
@type model: int
@keyword force: A flag which, if set to True, will overwrite the any pre-existing file.
@type force: bool
"""
# Printout.
print("Uniform distribution of structures representing the frame order motions.")
# Check the total.
if total > 9999:
raise RelaxError("A maximum of 9999 models is allowed in the PDB format.")
# Checks.
check_pipe()
check_model()
check_domain()
check_parameters()
check_pivot()
# Skip the rigid model.
if cdp.model == MODEL_RIGID:
print("Skipping the rigid model.")
return
# Open the output file.
file = open_write_file(file_name=file, dir=dir, force=force)
# The parameter values.
values = assemble_param_vector()
params = {}
i = 0
for name in cdp.params:
params[name] = values[i]
i += 1
# The structure.
structure = deepcopy(cdp.structure)
if structure.num_models() > 1:
structure.collapse_ensemble(model_num=model)
# The pivot points.
num_states = 1
if cdp.model == MODEL_DOUBLE_ROTOR:
num_states = 2
pivot = zeros((num_states, 3), float64)
for i in range(num_states):
pivot[i] = generate_pivot(order=i+1, pdb_limit=True)
# Shift to the average position.
average_position(structure=structure, models=[None])
# The motional eigenframe.
frame = generate_axis_system()
# Only work with a subset.
if atom_id:
# The inverted selection.
selection = structure.selection(atom_id=atom_id, inv=True)
# Delete the data.
structure.delete(selection=selection, verbosity=0)
# Create the distribution.
uniform_distribution(file=file, model=cdp.model, structure=structure, parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(), total=total, max_rotations=max_rotations)
# Close the file.
file.close()
def permute_axes(permutation='A'):
"""Permute the axes of the motional eigenframe to switch between local minima.
@keyword permutation: The permutation to use. This can be either 'A' or 'B' to select between the 3 permutations, excluding the current combination.
@type permutation: str
"""
# Check that the model is valid.
allowed = MODEL_LIST_ISO_CONE + MODEL_LIST_PSEUDO_ELLIPSE
if cdp.model not in allowed:
raise RelaxError("The permutation of the motional eigenframe is only valid for the frame order models %s." % allowed)
# Check that the model parameters are setup.
if cdp.model in MODEL_LIST_ISO_CONE:
if not hasattr(cdp, 'cone_theta') or not is_float(cdp.cone_theta):
raise RelaxError("The parameter values are not set up.")
else:
if not hasattr(cdp, 'cone_theta_y') or not is_float(cdp.cone_theta_y):
raise RelaxError("The parameter values are not set up.")
# The iso cones only have one permutation.
if cdp.model in MODEL_LIST_ISO_CONE and permutation == 'B':
raise RelaxError("The isotropic cones only have one permutation.")
# The angles.
cone_sigma_max = 0.0
if cdp.model in MODEL_LIST_RESTRICTED_TORSION:
cone_sigma_max = cdp.cone_sigma_max
elif cdp.model in MODEL_LIST_FREE_ROTORS:
cone_sigma_max = pi
if cdp.model in MODEL_LIST_ISO_CONE:
angles = array([cdp.cone_theta, cdp.cone_theta, cone_sigma_max], float64)
else:
angles = array([cdp.cone_theta_x, cdp.cone_theta_y, cone_sigma_max], float64)
x, y, z = angles
# The axis system.
axes = generate_axis_system()
# Start printout for the isotropic cones.
if cdp.model in MODEL_LIST_ISO_CONE:
print("\nOriginal parameters:")
print("%-20s %20.10f" % ("cone_theta", cdp.cone_theta))
print("%-20s %20.10f" % ("cone_sigma_max", cone_sigma_max))
print("%-20s %20.10f" % ("axis_theta", cdp.axis_theta))
print("%-20s %20.10f" % ("axis_phi", cdp.axis_phi))
print("%-20s\n%s" % ("cone axis", axes[:, 2]))
print("%-20s\n%s" % ("full axis system", axes))
print("\nPermutation '%s':" % permutation)
# Start printout for the pseudo-ellipses.
else:
print("\nOriginal parameters:")
print("%-20s %20.10f" % ("cone_theta_x", cdp.cone_theta_x))
print("%-20s %20.10f" % ("cone_theta_y", cdp.cone_theta_y))
print("%-20s %20.10f" % ("cone_sigma_max", cone_sigma_max))
print("%-20s %20.10f" % ("eigen_alpha", cdp.eigen_alpha))
print("%-20s %20.10f" % ("eigen_beta", cdp.eigen_beta))
print("%-20s %20.10f" % ("eigen_gamma", cdp.eigen_gamma))
print("%-20s\n%s" % ("eigenframe", axes))
print("\nPermutation '%s':" % permutation)
# The axis inversion structure.
inv = ones(3, float64)
# The starting condition x <= y <= z.
if x <= y and y <= z:
# Printout.
print("%-20s %-20s" % ("Starting condition", "x <= y <= z"))
# The cone angle and axes permutations.
if permutation == 'A':
perm_angles = [0, 2, 1]
perm_axes = [2, 1, 0]
inv[perm_axes[2]] = -1.0
else:
perm_angles = [1, 2, 0]
perm_axes = [2, 0, 1]
# The starting condition x <= z <= y.
elif x <= z and z <= y:
# Printout.
print("%-20s %-20s" % ("Starting condition", "x <= z <= y"))
# The cone angle and axes permutations.
if permutation == 'A':
perm_angles = [0, 2, 1]
perm_axes = [2, 1, 0]
inv[perm_axes[2]] = -1.0
else:
perm_angles = [2, 1, 0]
perm_axes = [0, 2, 1]
inv[perm_axes[2]] = -1.0
# The starting condition z <= x <= y.
elif z <= x and x <= y:
# Printout.
print("%-20s %-20s" % ("Starting condition", "z <= x <= y"))
# The cone angle and axes permutations.
if permutation == 'A':
perm_angles = [2, 0, 1]
perm_axes = [1, 2, 0]
else:
perm_angles = [2, 1, 0]
perm_axes = [0, 2, 1]
inv[perm_axes[2]] = -1.0
# Cannot be here.
else:
raise RelaxFault
# Printout.
print("%-20s %-20s" % ("Cone angle permutation", perm_angles))
print("%-20s %-20s" % ("Axes permutation", perm_axes))
# Permute the angles.
if cdp.model in MODEL_LIST_ISO_CONE:
cdp.cone_theta = (angles[perm_angles[0]] + angles[perm_angles[1]]) / 2.0
else:
cdp.cone_theta_x = angles[perm_angles[0]]
cdp.cone_theta_y = angles[perm_angles[1]]
if cdp.model in MODEL_LIST_RESTRICTED_TORSION:
cdp.cone_sigma_max = angles[perm_angles[2]]
elif cdp.model in MODEL_LIST_FREE_ROTORS:
cdp.cone_sigma_max = pi
# Permute the axes (iso cone).
if cdp.model in MODEL_LIST_ISO_CONE:
# Convert the y-axis to spherical coordinates (the x-axis would be ok too, or any vector in the x-y plane due to symmetry of the original permutation).
axis_new = axes[:, 1]
r, cdp.axis_theta, cdp.axis_phi = cartesian_to_spherical(axis_new)
# Permute the axes (pseudo-ellipses).
else:
axes_new = transpose(array([inv[0]*axes[:, perm_axes[0]], inv[1]*axes[:, perm_axes[1]], inv[2]*axes[:, perm_axes[2]]], float64))
# Convert the permuted frame to Euler angles and store them.
cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma = R_to_euler_zyz(axes_new)
# End printout.
if cdp.model in MODEL_LIST_ISO_CONE:
print("\nPermuted parameters:")
print("%-20s %20.10f" % ("cone_theta", cdp.cone_theta))
if cdp.model == MODEL_ISO_CONE:
print("%-20s %20.10f" % ("cone_sigma_max", cdp.cone_sigma_max))
print("%-20s %20.10f" % ("axis_theta", cdp.axis_theta))
print("%-20s %20.10f" % ("axis_phi", cdp.axis_phi))
print("%-20s\n%s" % ("cone axis", axis_new))
else:
print("\nPermuted parameters:")
print("%-20s %20.10f" % ("cone_theta_x", cdp.cone_theta_x))
print("%-20s %20.10f" % ("cone_theta_y", cdp.cone_theta_y))
if cdp.model == MODEL_PSEUDO_ELLIPSE:
print("%-20s %20.10f" % ("cone_sigma_max", cdp.cone_sigma_max))
print("%-20s %20.10f" % ("eigen_alpha", cdp.eigen_alpha))
print("%-20s %20.10f" % ("eigen_beta", cdp.eigen_beta))
print("%-20s %20.10f" % ("eigen_gamma", cdp.eigen_gamma))
print("%-20s\n%s" % ("eigenframe", axes_new))
def simulate(file="simulation.pdb.bz2",
dir=None,
step_size=2.0,
snapshot=10,
total=1000,
model=1,
force=True):
"""Pseudo-Brownian dynamics simulation of the frame order motions.
@keyword file: The PDB file for storing the frame order pseudo-Brownian dynamics simulation. The compression is determined automatically by the file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
@type file: str
@keyword dir: The directory name to place the file into.
@type dir: str or None
@keyword step_size: The rotation will be of a random direction but with this fixed angle. The value is in degrees.
@type step_size: float
@keyword snapshot: The number of steps in the simulation when snapshots will be taken.
@type snapshot: int
@keyword total: The total number of snapshots to take before stopping the simulation.
@type total: int
@keyword model: Only one model from an analysed ensemble of structures can be used for the pseudo-Brownian simulation, as the simulation and corresponding PDB file consists of one model per simulation.
@type model: int
@keyword force: A flag which, if set to True, will overwrite the any pre-existing file.
@type force: bool
"""
# Printout.
print("Pseudo-Brownian dynamics simulation of the frame order motions.")
# Checks.
check_pipe()
check_model()
check_domain()
check_parameters()
check_pivot()
# Skip the rigid model.
if cdp.model == MODEL_RIGID:
print("Skipping the rigid model.")
return
# Open the output file.
file = open_write_file(file_name=file, dir=dir, force=force)
# The parameter values.
values = assemble_param_vector()
params = {}
i = 0
for name in cdp.params:
params[name] = values[i]
i += 1
# The structure.
structure = deepcopy(cdp.structure)
if structure.num_models() > 1:
structure.collapse_ensemble(model_num=model)
# The pivot points.
num_states = 1
if cdp.model == MODEL_DOUBLE_ROTOR:
num_states = 2
pivot = zeros((num_states, 3), float64)
for i in range(num_states):
pivot[i] = generate_pivot(order=i + 1, pdb_limit=True)
# Shift to the average position.
average_position(structure=structure, models=[None])
# The motional eigenframe.
frame = generate_axis_system()
# Create the distribution.
brownian(file=file,
model=cdp.model,
structure=structure,
parameters=params,
eigenframe=frame,
pivot=pivot,
atom_id=domain_moving(),
step_size=step_size,
snapshot=snapshot,
total=total)
# Close the file.
file.close()
def distribute(file="distribution.pdb.bz2",
dir=None,
atom_id=None,
total=1000,
max_rotations=100000,
model=1,
force=True):
"""Create a uniform distribution of structures for the frame order motions.
@keyword file: The PDB file for storing the frame order motional distribution. The compression is determined automatically by the file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
@type file: str
@keyword dir: The directory name to place the file into.
@type dir: str or None
@keyword atom_id: The atom identification string to allow the distribution to be a subset of all atoms.
@type atom_id: None or str
@keyword total: The total number of states/model/structures in the distribution.
@type total: int
@keyword max_rotations: The maximum number of rotations to generate the distribution from. This prevents an execution for an infinite amount of time when a frame order amplitude parameter is close to zero so that the subset of all rotations within the distribution is close to zero.
@type max_rotations: int
@keyword model: Only one model from an analysed ensemble of structures can be used for the distribution, as the corresponding PDB file consists of one model per state.
@type model: int
@keyword force: A flag which, if set to True, will overwrite the any pre-existing file.
@type force: bool
"""
# Printout.
print(
"Uniform distribution of structures representing the frame order motions."
)
# Check the total.
if total > 9999:
raise RelaxError(
"A maximum of 9999 models is allowed in the PDB format.")
# Checks.
check_pipe()
check_model()
check_domain()
check_parameters()
check_pivot()
# Skip the rigid model.
if cdp.model == MODEL_RIGID:
print("Skipping the rigid model.")
return
# Open the output file.
file = open_write_file(file_name=file, dir=dir, force=force)
# The parameter values.
values = assemble_param_vector()
params = {}
i = 0
for name in cdp.params:
params[name] = values[i]
i += 1
# The structure.
structure = deepcopy(cdp.structure)
if structure.num_models() > 1:
structure.collapse_ensemble(model_num=model)
# The pivot points.
num_states = 1
if cdp.model == MODEL_DOUBLE_ROTOR:
num_states = 2
pivot = zeros((num_states, 3), float64)
for i in range(num_states):
pivot[i] = generate_pivot(order=i + 1, pdb_limit=True)
# Shift to the average position.
average_position(structure=structure, models=[None])
# The motional eigenframe.
frame = generate_axis_system()
# Only work with a subset.
if atom_id:
# The inverted selection.
selection = structure.selection(atom_id=atom_id, inv=True)
# Delete the data.
structure.delete(selection=selection, verbosity=0)
# Create the distribution.
uniform_distribution(file=file,
model=cdp.model,
structure=structure,
parameters=params,
eigenframe=frame,
pivot=pivot,
atom_id=domain_moving(),
total=total,
max_rotations=max_rotations)
# Close the file.
file.close()
def permute_axes(permutation='A'):
"""Permute the axes of the motional eigenframe to switch between local minima.
@keyword permutation: The permutation to use. This can be either 'A' or 'B' to select between the 3 permutations, excluding the current combination.
@type permutation: str
"""
# Check that the model is valid.
allowed = MODEL_LIST_ISO_CONE + MODEL_LIST_PSEUDO_ELLIPSE
if cdp.model not in allowed:
raise RelaxError(
"The permutation of the motional eigenframe is only valid for the frame order models %s."
% allowed)
# Check that the model parameters are setup.
if cdp.model in MODEL_LIST_ISO_CONE:
if not hasattr(cdp, 'cone_theta') or not is_float(cdp.cone_theta):
raise RelaxError("The parameter values are not set up.")
else:
if not hasattr(cdp, 'cone_theta_y') or not is_float(cdp.cone_theta_y):
raise RelaxError("The parameter values are not set up.")
# The iso cones only have one permutation.
if cdp.model in MODEL_LIST_ISO_CONE and permutation == 'B':
raise RelaxError("The isotropic cones only have one permutation.")
# The angles.
cone_sigma_max = 0.0
if cdp.model in MODEL_LIST_RESTRICTED_TORSION:
cone_sigma_max = cdp.cone_sigma_max
elif cdp.model in MODEL_LIST_FREE_ROTORS:
cone_sigma_max = pi
if cdp.model in MODEL_LIST_ISO_CONE:
angles = array([cdp.cone_theta, cdp.cone_theta, cone_sigma_max],
float64)
else:
angles = array([cdp.cone_theta_x, cdp.cone_theta_y, cone_sigma_max],
float64)
x, y, z = angles
# The axis system.
axes = generate_axis_system()
# Start printout for the isotropic cones.
if cdp.model in MODEL_LIST_ISO_CONE:
print("\nOriginal parameters:")
print("%-20s %20.10f" % ("cone_theta", cdp.cone_theta))
print("%-20s %20.10f" % ("cone_sigma_max", cone_sigma_max))
print("%-20s %20.10f" % ("axis_theta", cdp.axis_theta))
print("%-20s %20.10f" % ("axis_phi", cdp.axis_phi))
print("%-20s\n%s" % ("cone axis", axes[:, 2]))
print("%-20s\n%s" % ("full axis system", axes))
print("\nPermutation '%s':" % permutation)
# Start printout for the pseudo-ellipses.
else:
print("\nOriginal parameters:")
print("%-20s %20.10f" % ("cone_theta_x", cdp.cone_theta_x))
print("%-20s %20.10f" % ("cone_theta_y", cdp.cone_theta_y))
print("%-20s %20.10f" % ("cone_sigma_max", cone_sigma_max))
print("%-20s %20.10f" % ("eigen_alpha", cdp.eigen_alpha))
print("%-20s %20.10f" % ("eigen_beta", cdp.eigen_beta))
print("%-20s %20.10f" % ("eigen_gamma", cdp.eigen_gamma))
print("%-20s\n%s" % ("eigenframe", axes))
print("\nPermutation '%s':" % permutation)
# The axis inversion structure.
inv = ones(3, float64)
# The starting condition x <= y <= z.
if x <= y and y <= z:
# Printout.
print("%-20s %-20s" % ("Starting condition", "x <= y <= z"))
# The cone angle and axes permutations.
if permutation == 'A':
perm_angles = [0, 2, 1]
perm_axes = [2, 1, 0]
inv[perm_axes[2]] = -1.0
else:
perm_angles = [1, 2, 0]
perm_axes = [2, 0, 1]
# The starting condition x <= z <= y.
elif x <= z and z <= y:
# Printout.
print("%-20s %-20s" % ("Starting condition", "x <= z <= y"))
# The cone angle and axes permutations.
if permutation == 'A':
perm_angles = [0, 2, 1]
perm_axes = [2, 1, 0]
inv[perm_axes[2]] = -1.0
else:
perm_angles = [2, 1, 0]
perm_axes = [0, 2, 1]
inv[perm_axes[2]] = -1.0
# The starting condition z <= x <= y.
elif z <= x and x <= y:
# Printout.
print("%-20s %-20s" % ("Starting condition", "z <= x <= y"))
# The cone angle and axes permutations.
if permutation == 'A':
perm_angles = [2, 0, 1]
perm_axes = [1, 2, 0]
else:
perm_angles = [2, 1, 0]
perm_axes = [0, 2, 1]
inv[perm_axes[2]] = -1.0
# Cannot be here.
else:
raise RelaxFault
# Printout.
print("%-20s %-20s" % ("Cone angle permutation", perm_angles))
print("%-20s %-20s" % ("Axes permutation", perm_axes))
# Permute the angles.
if cdp.model in MODEL_LIST_ISO_CONE:
cdp.cone_theta = (angles[perm_angles[0]] +
angles[perm_angles[1]]) / 2.0
else:
cdp.cone_theta_x = angles[perm_angles[0]]
cdp.cone_theta_y = angles[perm_angles[1]]
if cdp.model in MODEL_LIST_RESTRICTED_TORSION:
cdp.cone_sigma_max = angles[perm_angles[2]]
elif cdp.model in MODEL_LIST_FREE_ROTORS:
cdp.cone_sigma_max = pi
# Permute the axes (iso cone).
if cdp.model in MODEL_LIST_ISO_CONE:
# Convert the y-axis to spherical coordinates (the x-axis would be ok too, or any vector in the x-y plane due to symmetry of the original permutation).
axis_new = axes[:, 1]
r, cdp.axis_theta, cdp.axis_phi = cartesian_to_spherical(axis_new)
# Permute the axes (pseudo-ellipses).
else:
axes_new = transpose(
array([
inv[0] * axes[:, perm_axes[0]], inv[1] * axes[:, perm_axes[1]],
inv[2] * axes[:, perm_axes[2]]
], float64))
# Convert the permuted frame to Euler angles and store them.
cdp.eigen_alpha, cdp.eigen_beta, cdp.eigen_gamma = R_to_euler_zyz(
axes_new)
# End printout.
if cdp.model in MODEL_LIST_ISO_CONE:
print("\nPermuted parameters:")
print("%-20s %20.10f" % ("cone_theta", cdp.cone_theta))
if cdp.model == MODEL_ISO_CONE:
print("%-20s %20.10f" % ("cone_sigma_max", cdp.cone_sigma_max))
print("%-20s %20.10f" % ("axis_theta", cdp.axis_theta))
print("%-20s %20.10f" % ("axis_phi", cdp.axis_phi))
print("%-20s\n%s" % ("cone axis", axis_new))
else:
print("\nPermuted parameters:")
print("%-20s %20.10f" % ("cone_theta_x", cdp.cone_theta_x))
print("%-20s %20.10f" % ("cone_theta_y", cdp.cone_theta_y))
if cdp.model == MODEL_PSEUDO_ELLIPSE:
print("%-20s %20.10f" % ("cone_sigma_max", cdp.cone_sigma_max))
print("%-20s %20.10f" % ("eigen_alpha", cdp.eigen_alpha))
print("%-20s %20.10f" % ("eigen_beta", cdp.eigen_beta))
print("%-20s %20.10f" % ("eigen_gamma", cdp.eigen_gamma))
print("%-20s\n%s" % ("eigenframe", axes_new))
def decompose(root="decomposed", dir=None, atom_id=None, model=1, force=True):
"""Structural representation of the individual frame order motional components.
@keyword root: The file root for the PDB files created. Each motional component will be represented by a different PDB file appended with '_mode1.pdb', '_mode2.pdb', '_mode3.pdb', etc.
@type root: str
@keyword dir: The directory name to place the file into.
@type dir: str or None
@keyword atom_id: The atom identification string to allow the decomposition to be applied to subset of all atoms.
@type atom_id: None or str
@keyword model: Only one model from an analysed ensemble of structures can be used for the decomposition, as the corresponding PDB file consists of one model per state.
@type model: int
@keyword force: A flag which, if set to True, will overwrite the any pre-existing file.
@type force: bool
"""
# Printout.
print(
"PDB representation of the individual components of the frame order motions."
)
# Checks.
check_pipe()
check_model()
check_domain()
check_parameters()
check_pivot()
# Skip any unsupported models.
unsupported = [MODEL_RIGID, MODEL_DOUBLE_ROTOR]
if cdp.model in unsupported:
print("Skipping the unsupported '%s' model." % cdp.model)
return
# Initialise the angle vector (cone opening angle 1, cone opening angle 2, torsion angle).
angles = zeros(3, float64)
# Cone opening.
if cdp.model in MODEL_LIST_ISO_CONE:
angles[0] = angles[1] = cdp.cone_theta
elif cdp.model in MODEL_LIST_PSEUDO_ELLIPSE:
angles[0] = cdp.cone_theta_y
angles[1] = cdp.cone_theta_x
# Non-zero torsion angle.
if cdp.model in MODEL_LIST_FREE_ROTORS:
angles[2] = pi
elif cdp.model in MODEL_LIST_RESTRICTED_TORSION:
angles[2] = cdp.cone_sigma_max
# The motional eigenframe.
frame = generate_axis_system()
# Mode ordering from largest to smallest.
indices = argsort(angles)
angles = angles[indices[::-1]]
frame = transpose(transpose(frame)[indices[::-1]])
# The pivot point.
pivot = generate_pivot(order=1, pdb_limit=True)
# Loop over each mode.
for i in range(3):
# Skip modes with no motion.
if angles[i] < 1e-7:
continue
# Open the output file.
file_name = "%s_mode%i.pdb" % (root, i + 1)
file = open_write_file(file_name=file_name, dir=dir, force=force)
# The structure.
structure = deepcopy(cdp.structure)
if structure.num_models() > 1:
structure.collapse_ensemble(model_num=model)
# Shift to the average position.
average_position(structure=structure, models=[None])
# Create the representation.
mode_distribution(file=file,
structure=structure,
axis=frame[:, i],
angle=angles[i],
pivot=pivot,
atom_id=domain_moving())
# Close the file.
file.close()
