def build(cls, data_handler, matrix_creation_parameters):
"""
Generates a matrix with the method used in the handler creation.
@param trajectory_handler:
@param matrix_creation_parameters:
@return: The created matrix.
"""
calculator_type = matrix_creation_parameters.get_value("calculator_type",
default_value = "QTRFIT_OMP_CALCULATOR")
calculator_options = matrix_creation_parameters.get_value("calculator_options",
default_value = ProtocolParameters({"number_of_threads":8,
"blocks_per_grid":8,
"threads_per_block":32}))
calculator_options = ProtocolParameters(calculator_options)
structure = data_handler.get_data()
fit_selection_coordsets = structure.getFittingCoordinates()
calc_selection_coordsets = structure.getCalculationCoordinates()
if calc_selection_coordsets is None:
calculator = RMSDCalculator(calculatorType = calculator_type,
fittingCoordsets = fit_selection_coordsets)
else:
symm_groups = []
if "symmetries" in matrix_creation_parameters:
# Then prepare it to handle calculation symmetries
# Description of equivalences must have the same number of atoms
symm_groups = cls.process_symm_groups(matrix_creation_parameters,
structure,
calc_selection_coordsets)
print "Using symmetries", symm_groups
calculator = RMSDCalculator(calculatorType = calculator_type,
fittingCoordsets = fit_selection_coordsets,
calculationCoordsets = calc_selection_coordsets,
calcSymmetryGroups = symm_groups)
try:
calculator.setNumberOfOpenMPThreads(calculator_options.get_value("number_of_threads",
default_value = 8))
except KeyError:
pass
try:
calculator.setCUDAKernelThreadsPerBlock(calculator_options.get_value("threads_per_block",
default_value = 32),
calculator_options.get_value("blocks_per_grid",
default_value = 8))
except KeyError:
pass
rmsds = calculator.pairwiseRMSDMatrix()
return CondensedMatrix(rmsds)
class WorkspaceHandler(Observable):
def __init__(self, workspace_parameters, observer):
super(WorkspaceHandler,self).__init__(observer)
self.parameters = ProtocolParameters(workspace_parameters.get_value("parameters", default_value = ProtocolParameters({
"overwrite":True,
"clear_after_exec":["tmp"]
})))
self.data = {
"results": os.path.join(workspace_parameters["base"], workspace_parameters.get_value("results", default_value="results")),
"tmp" : os.path.join(workspace_parameters["base"], workspace_parameters.get_value("tmp", default_value= "tmp")),
"clusters" : os.path.join(workspace_parameters["base"], workspace_parameters.get_value("clusters", default_value= "clusters")),
"matrix" : os.path.join(workspace_parameters["base"], workspace_parameters.get_value("matrix", default_value= "matrix"))
}
def __getitem__(self,key):
return self.data[key]
def __str__(self):
return json.dumps(self.data, sort_keys=False, indent=4, separators=(',', ': '))
def create_directories(self):
"""
Recreates the workspace structure. Removes the old location if necessary.
"""
self.notify("MSG","Creating workspace...")
if self.parameters.get_value("overwrite", default_value = True) :
self.clear_directories(self.data.keys())
for folder_key in self.data:
scripts_common.create_directory(self.data[folder_key])
def clear_directories(self, directory_keys):
"""
Removes the directories given as parameters.
@param directory_keys: The keys of the 'data' object which defined paths will be erased.
"""
for folder_key in directory_keys:
folder_path = self.data[folder_key]
if os.path.exists(folder_path):
shutil.rmtree(folder_path)
self.notify("MSG","Removing %s ..."%folder_path)
# print "Removing %s ..."%folder_path
def __enter__(self):
self.create_directories()
return self
def __exit__(self, exception_type, exception_val, trace):
self.clear_directories(self.parameters["clear_after_exec"])
def build(cls, data_handler, matrix_creation_parameters):
"""
Generates a matrix with the method used in the handler creation.
@param trajectory_handler:
@param matrix_creation_parameters:
@return: The created matrix.
"""
calculator_type = matrix_creation_parameters.get_value(
"calculator_type", default_value="QTRFIT_OMP_CALCULATOR")
calculator_options = matrix_creation_parameters.get_value(
"calculator_options",
default_value=ProtocolParameters({
"number_of_threads": 8,
"blocks_per_grid": 8,
"threads_per_block": 32
}))
calculator_options = ProtocolParameters(calculator_options)
structure = data_handler.get_data()
fit_selection_coordsets = structure.getFittingCoordinates()
calc_selection_coordsets = structure.getCalculationCoordinates()
if calc_selection_coordsets is None:
calculator = RMSDCalculator(
calculatorType=calculator_type,
fittingCoordsets=fit_selection_coordsets)
else:
symm_groups = []
if "symmetries" in matrix_creation_parameters:
# Then prepare it to handle calculation symmetries
# Description of equivalences must have the same number of atoms
symm_groups = cls.process_symm_groups(
matrix_creation_parameters, structure,
calc_selection_coordsets)
print "Using symmetries", symm_groups
calculator = RMSDCalculator(
calculatorType=calculator_type,
fittingCoordsets=fit_selection_coordsets,
calculationCoordsets=calc_selection_coordsets,
calcSymmetryGroups=symm_groups)
try:
calculator.setNumberOfOpenMPThreads(
calculator_options.get_value("number_of_threads",
default_value=8))
except KeyError:
pass
try:
calculator.setCUDAKernelThreadsPerBlock(
calculator_options.get_value("threads_per_block",
default_value=32),
calculator_options.get_value("blocks_per_grid",
default_value=8))
except KeyError:
pass
rmsds = calculator.pairwiseRMSDMatrix()
return CondensedMatrix(rmsds)
class WorkspaceHandler(Observable):
def __init__(self, workspace_parameters, observer):
super(WorkspaceHandler, self).__init__(observer)
self.parameters = ProtocolParameters(
workspace_parameters.get_value(
"parameters", default_value=ProtocolParameters({"overwrite": True, "clear_after_exec": ["tmp"]})
)
)
self.data = {
"results": os.path.join(
workspace_parameters["base"], workspace_parameters.get_value("results", default_value="results")
),
"tmp": os.path.join(
workspace_parameters["base"], workspace_parameters.get_value("tmp", default_value="tmp")
),
"clusters": os.path.join(
workspace_parameters["base"], workspace_parameters.get_value("clusters", default_value="clusters")
),
"matrix": os.path.join(
workspace_parameters["base"], workspace_parameters.get_value("matrix", default_value="matrix")
),
}
def __getitem__(self, key):
return self.data[key]
def __str__(self):
return json.dumps(self.data, sort_keys=False, indent=4, separators=(",", ": "))
def create_directories(self):
"""
Recreates the workspace structure. Removes the old location if necessary.
"""
self.notify("MSG", "Creating workspace...")
if self.parameters.get_value("overwrite", default_value=True):
self.clear_directories(self.data.keys())
for folder_key in self.data:
scripts_common.create_directory(self.data[folder_key])
def clear_directories(self, directory_keys):
"""
Removes the directories given as parameters.
@param directory_keys: The keys of the 'data' object which defined paths will be erased.
"""
for folder_key in directory_keys:
folder_path = self.data[folder_key]
if os.path.exists(folder_path):
shutil.rmtree(folder_path)
self.notify("MSG", "Removing %s ..." % folder_path)
# print "Removing %s ..."%folder_path
def __enter__(self):
self.create_directories()
return self
def __exit__(self, exception_type, exception_val, trace):
self.clear_directories(self.parameters["clear_after_exec"])
