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)
def superimpose_coordinates(all_coordsets, iterpose = True):
all_superimposed_coordsets = []
for coordsets in all_coordsets:
calculator = RMSDCalculator(calculatorType = "QTRFIT_OMP_CALCULATOR",
fittingCoordsets = coordsets)
calculator.setNumberOfOpenMPThreads(4)
if iterpose:
print "\t- Using iterposition on trajectory (shape ", coordsets.shape, ")"
calculator.iterativeSuperposition()
all_superimposed_coordsets.append(coordsets)
else:
print "\t- Superimposing with first trajectory frame (shape ", coordsets.shape, ")"
_, superimposed_coordsets = calculator.oneVsTheOthers(0, get_superposed_coordinates = True)
all_superimposed_coordsets.append(superimposed_coordsets)
return all_superimposed_coordsets
def coords_rmsf(ca_coords):
calculator = RMSDCalculator(calculatorType="QTRFIT_OMP_CALCULATOR",
fittingCoordsets=ca_coords)
calculator.setNumberOfOpenMPThreads(4)
new_ca_coords = calculator.iterativeSuperposition()
# Calculate the actual rmsf
mean_conformation = new_ca_coords.mean(0)
ssqf = numpy.zeros(mean_conformation.shape)
for conf in new_ca_coords:
ssqf += (conf - mean_conformation)**2
return (ssqf.sum(1) / new_ca_coords.shape[0])**0.5
def superimpose_coordinates(all_coordsets, iterpose=True):
all_superimposed_coordsets = []
for coordsets in all_coordsets:
calculator = RMSDCalculator(calculatorType="QTRFIT_OMP_CALCULATOR",
fittingCoordsets=coordsets)
calculator.setNumberOfOpenMPThreads(4)
if iterpose:
print "\t- Using iterposition on trajectory (shape ", coordsets.shape, ")"
calculator.iterativeSuperposition()
all_superimposed_coordsets.append(coordsets)
else:
print "\t- Superimposing with first trajectory frame (shape ", coordsets.shape, ")"
_, superimposed_coordsets = calculator.oneVsTheOthers(
0, get_superposed_coordinates=True)
all_superimposed_coordsets.append(superimposed_coordsets)
return all_superimposed_coordsets
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)