def test_subsubsection(self):
"""Test of the lib.text.sectioning.subsubsection() function."""
# Write out the subsubsection.
file = DummyFileObject()
subsubsection(file=file, text='Test subsubsection')
# Read the results.
lines = file.readlines()
print("Formatted subsubsection lines: %s" % lines)
# Check the title.
real_lines = [
'\n',
'Test subsubsection\n',
'~~~~~~~~~~~~~~~~~~\n',
'\n',
]
self.assertEqual(len(lines), len(real_lines))
for i in range(len(lines)):
self.assertEqual(lines[i], real_lines[i])
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_ave_pos(format='PDB', file=None, dir=None, compress_type=0, model=1, force=False):
"""Create a PDB file of the molecule with the moving domains shifted to the average position.
@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 for the average molecule structure.
@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 model: Only one model from an analysed ensemble can be used for the PDB representation of the Monte Carlo simulations, as these consists of one model per simulation.
@type model: 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 with the moving domains shifted to the average position.")
# Checks.
if not hasattr(cdp, 'structure'):
warn(RelaxWarning("No structural data is present, cannot create the average position representation."))
return
# Initialise.
titles = []
sims = []
file_root = []
models = []
structures = []
# The real average position.
titles.append("real average position")
sims.append(False)
file_root.append(file)
models.append([None])
# The positive MC simulation representation.
if hasattr(cdp, 'sim_number'):
titles.append("MC simulation representation")
sims.append(True)
file_root.append("%s_sim" % file)
models.append([i+1 for i in range(cdp.sim_number)])
# Make a copy of the structural object (so as to preserve the original structure).
structures.append(deepcopy(cdp.structure))
if hasattr(cdp, 'sim_number'):
structures.append(deepcopy(cdp.structure))
# Delete all but the chosen model for the simulations.
if hasattr(cdp, 'sim_number') and len(structures[-1].structural_data) > 1:
# Determine the models to delete.
to_delete = []
for model_cont in structures[-1].model_loop():
if model_cont.num != model:
to_delete.append(model_cont.num)
to_delete.reverse()
# Delete them.
for num in to_delete:
structures[-1].structural_data.delete_model(model_num=num)
# Loop over each representation and add the contents.
for i in range(len(titles)):
# Printout.
subsubsection(file=sys.stdout, text="Creating the %s." % titles[i])
# Loop over each model.
for j in range(len(models[i])):
# Create or set the models, if needed.
if models[i][j] == 1:
structures[i].set_model(model_new=1)
elif models[i][j] != None:
structures[i].add_model(model=models[i][j])
# Shift to the average position.
average_position(structure=structures[i], models=models[i], sim=sims[i])
# Output to PDB format.
if format == 'PDB':
pdb_file = open_write_file(file_name=file_root[i]+'.pdb', dir=dir, compress_type=compress_type, force=force)
structures[i].write_pdb(file=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()
def create_ave_pos(format='PDB',
file=None,
dir=None,
compress_type=0,
model=1,
force=False):
"""Create a PDB file of the molecule with the moving domains shifted to the average position.
@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 for the average molecule structure.
@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 model: Only one model from an analysed ensemble can be used for the PDB representation of the Monte Carlo simulations, as these consists of one model per simulation.
@type model: 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 with the moving domains shifted to the average position."
)
# Checks.
if not hasattr(cdp, 'structure'):
warn(
RelaxWarning(
"No structural data is present, cannot create the average position representation."
))
return
# Initialise.
titles = []
sims = []
file_root = []
models = []
structures = []
# The real average position.
titles.append("real average position")
sims.append(False)
file_root.append(file)
models.append([None])
# The positive MC simulation representation.
if hasattr(cdp, 'sim_number'):
titles.append("MC simulation representation")
sims.append(True)
file_root.append("%s_sim" % file)
models.append([i + 1 for i in range(cdp.sim_number)])
# Make a copy of the structural object (so as to preserve the original structure).
structures.append(deepcopy(cdp.structure))
if hasattr(cdp, 'sim_number'):
structures.append(deepcopy(cdp.structure))
# Delete all but the chosen model for the simulations.
if hasattr(cdp, 'sim_number') and len(structures[-1].structural_data) > 1:
# Determine the models to delete.
to_delete = []
for model_cont in structures[-1].model_loop():
if model_cont.num != model:
to_delete.append(model_cont.num)
to_delete.reverse()
# Delete them.
for num in to_delete:
structures[-1].structural_data.delete_model(model_num=num)
# Loop over each representation and add the contents.
for i in range(len(titles)):
# Printout.
subsubsection(file=sys.stdout, text="Creating the %s." % titles[i])
# Loop over each model.
for j in range(len(models[i])):
# Create or set the models, if needed.
if models[i][j] == 1:
structures[i].set_model(model_new=1)
elif models[i][j] != None:
structures[i].add_model(model=models[i][j])
# Shift to the average position.
average_position(structure=structures[i],
models=models[i],
sim=sims[i])
# Output to PDB format.
if format == 'PDB':
pdb_file = open_write_file(file_name=file_root[i] + '.pdb',
dir=dir,
compress_type=compress_type,
force=force)
structures[i].write_pdb(file=pdb_file)
pdb_file.close()
