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 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 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()
def create_geometric_rep(format='PDB', file=None, dir=None, compress_type=0, size=30.0, inc=36, force=False):
"""Create a PDB file containing a geometric object representing the frame order dynamics.
@keyword format: The format for outputting the geometric representation. Currently only the 'PDB' format is supported.
@type format: str
@keyword file: The name of the file of the PDB representation of the frame order dynamics to create.
@type file: str
@keyword dir: The name of the directory to place the PDB file into.
@type dir: str
@keyword compress_type: The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression.
@type compress_type: int
@keyword size: The size of the geometric object in Angstroms.
@type size: float
@keyword inc: The number of increments for the filling of the cone objects.
@type inc: int
@keyword force: Flag which if set to True will cause any pre-existing file to be overwritten.
@type force: bool
"""
# Printout.
subsection(file=sys.stdout, text="Creating a PDB file containing a geometric object representing the frame order dynamics.")
# Checks.
check_parameters(escalate=2)
# Initialise.
titles = []
structures = []
representation = []
sims = []
file_root = []
# Symmetry for inverted representations?
sym = True
if cdp.model in [MODEL_ROTOR, MODEL_FREE_ROTOR, MODEL_DOUBLE_ROTOR]:
sym = False
# The standard representation.
titles.append("Representation A")
structures.append(Internal())
if sym:
representation.append('A')
file_root.append("%s_A" % file)
else:
representation.append(None)
file_root.append(file)
sims.append(False)
# The inverted representation.
if sym:
titles.append("Representation A")
structures.append(Internal())
representation.append('B')
file_root.append("%s_B" % file)
sims.append(False)
# The standard MC simulation representation.
if hasattr(cdp, 'sim_number'):
titles.append("MC simulation representation A")
structures.append(Internal())
if sym:
representation.append('A')
file_root.append("%s_sim_A" % file)
else:
representation.append(None)
file_root.append("%s_sim" % file)
sims.append(True)
# The inverted MC simulation representation.
if hasattr(cdp, 'sim_number') and sym:
titles.append("MC simulation representation B")
structures.append(Internal())
representation.append('B')
file_root.append("%s_sim_B" % file)
sims.append(True)
# Loop over each structure and add the contents.
for i in range(len(structures)):
# Printout.
subsubsection(file=sys.stdout, text="Creating the %s." % titles[i])
# Create a model for each Monte Carlo simulation.
if sims[i]:
for sim_i in range(cdp.sim_number):
structures[i].add_model(model=sim_i+1)
# Add the pivots.
add_pivots(structure=structures[i], sims=sims[i])
# Add all rotor objects.
add_rotors(structure=structures[i], representation=representation[i], size=size, sims=sims[i])
# Add the axis systems.
add_axes(structure=structures[i], representation=representation[i], size=size, sims=sims[i])
# Add the cone objects.
if cdp.model not in [MODEL_ROTOR, MODEL_FREE_ROTOR, MODEL_DOUBLE_ROTOR]:
add_cones(structure=structures[i], representation=representation[i], size=size, inc=inc, sims=sims[i])
# Add atoms for creating titles.
add_titles(structure=structures[i], representation=representation[i], displacement=size+10, sims=sims[i])
# Create the PDB file.
if format == 'PDB':
pdb_file = open_write_file(file_root[i]+'.pdb', dir, compress_type=compress_type, force=force)
structures[i].write_pdb(pdb_file)
pdb_file.close()
def create_geometric_rep(format='PDB',
file=None,
dir=None,
compress_type=0,
size=30.0,
inc=36,
force=False):
"""Create a PDB file containing a geometric object representing the frame order dynamics.
@keyword format: The format for outputting the geometric representation. Currently only the 'PDB' format is supported.
@type format: str
@keyword file: The name of the file of the PDB representation of the frame order dynamics to create.
@type file: str
@keyword dir: The name of the directory to place the PDB file into.
@type dir: str
@keyword compress_type: The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression.
@type compress_type: int
@keyword size: The size of the geometric object in Angstroms.
@type size: float
@keyword inc: The number of increments for the filling of the cone objects.
@type inc: int
@keyword force: Flag which if set to True will cause any pre-existing file to be overwritten.
@type force: bool
"""
# Printout.
subsection(
file=sys.stdout,
text=
"Creating a PDB file containing a geometric object representing the frame order dynamics."
)
# Checks.
check_parameters(escalate=2)
# Initialise.
titles = []
structures = []
representation = []
sims = []
file_root = []
# Symmetry for inverted representations?
sym = True
if cdp.model in [MODEL_ROTOR, MODEL_FREE_ROTOR, MODEL_DOUBLE_ROTOR]:
sym = False
# The standard representation.
titles.append("Representation A")
structures.append(Internal())
if sym:
representation.append('A')
file_root.append("%s_A" % file)
else:
representation.append(None)
file_root.append(file)
sims.append(False)
# The inverted representation.
if sym:
titles.append("Representation A")
structures.append(Internal())
representation.append('B')
file_root.append("%s_B" % file)
sims.append(False)
# The standard MC simulation representation.
if hasattr(cdp, 'sim_number'):
titles.append("MC simulation representation A")
structures.append(Internal())
if sym:
representation.append('A')
file_root.append("%s_sim_A" % file)
else:
representation.append(None)
file_root.append("%s_sim" % file)
sims.append(True)
# The inverted MC simulation representation.
if hasattr(cdp, 'sim_number') and sym:
titles.append("MC simulation representation B")
structures.append(Internal())
representation.append('B')
file_root.append("%s_sim_B" % file)
sims.append(True)
# Loop over each structure and add the contents.
for i in range(len(structures)):
# Printout.
subsubsection(file=sys.stdout, text="Creating the %s." % titles[i])
# Create a model for each Monte Carlo simulation.
if sims[i]:
for sim_i in range(cdp.sim_number):
structures[i].add_model(model=sim_i + 1)
# Add the pivots.
add_pivots(structure=structures[i], sims=sims[i])
# Add all rotor objects.
add_rotors(structure=structures[i],
representation=representation[i],
size=size,
sims=sims[i])
# Add the axis systems.
add_axes(structure=structures[i],
representation=representation[i],
size=size,
sims=sims[i])
# Add the cone objects.
if cdp.model not in [
MODEL_ROTOR, MODEL_FREE_ROTOR, MODEL_DOUBLE_ROTOR
]:
add_cones(structure=structures[i],
representation=representation[i],
size=size,
inc=inc,
sims=sims[i])
# Add atoms for creating titles.
add_titles(structure=structures[i],
representation=representation[i],
displacement=size + 10,
sims=sims[i])
# Create the PDB file.
if format == 'PDB':
pdb_file = open_write_file(file_root[i] + '.pdb',
dir,
compress_type=compress_type,
force=force)
structures[i].write_pdb(pdb_file)
pdb_file.close()