def build(cls, data_handler, matrix_params):
"""
- "distance": Euclidean distance of the geometrical center of one body.
"parameters":{
"fit_selection": String,
"body_selection": String,
}
"fit_selection": The Prody selection string used to describe the atoms to be superposed.
"body_selection": Another Prody selection string that describes the element that will be used
to get the euclidean distances.
"""
# Build calculator with fitting coordinate sets ...
fit_selection_coordsets = data_handler.get_data(
).getFittingCoordinates()
# and calculation coordsets (we want them to be moved along with the fitting ones)
body_selection_coordsets = data_handler.get_data(
).getCalculationCoordinates()
calculator = RMSDCalculator(
calculatorType="QTRFIT_OMP_CALCULATOR",
fittingCoordsets=fit_selection_coordsets,
calculationCoordsets=body_selection_coordsets)
# Superpose iteratively (will modify all coordinates)
calculator.iterativeSuperposition()
#centers = body_selection_coordsets.mean(1)
from prody.measure import calcCenter
centers = calcCenter(body_selection_coordsets)
return centers
def build(cls, data_handler, matrix_params):
"""
- "distance": Euclidean distance of the geometrical center of one body.
"parameters":{
"fit_selection": String,
"body_selection": String,
}
"fit_selection": The Prody selection string used to describe the atoms to be superposed.
"body_selection": Another Prody selection string that describes the element that will be used
to get the euclidean distances.
"""
# Build calculator with fitting coordinate sets ...
fit_selection_coordsets = data_handler.get_data().getFittingCoordinates()
# and calculation coordsets (we want them to be moved along with the fitting ones)
body_selection_coordsets = data_handler.get_data().getCalculationCoordinates()
calculator = RMSDCalculator(calculatorType = "QTRFIT_OMP_CALCULATOR",
fittingCoordsets = fit_selection_coordsets,
calculationCoordsets = body_selection_coordsets)
# Superpose iteratively (will modify all coordinates)
calculator.iterativeSuperposition()
#centers = body_selection_coordsets.mean(1)
from prody.measure import calcCenter
centers = calcCenter(body_selection_coordsets)
return centers
def testMultiCoordsetsWithWeights(self):
assert_equal(
calcCenter(ATOMS.getCoordsets(), weights=ones(len(ATOMS))),
CENTERS)
def testMultiCoordsets(self):
assert_equal(calcCenter(ATOMS.getCoordsets()), CENTERS)
def testCenterWithWeights(self):
assert_equal(calcCenter(ATOMS, weights=ones(len(ATOMS))), CENTERS[0])
def testCenter(self):
assert_equal(calcCenter(ATOMS), CENTERS[0])
def testMultiCoordsetsWithWeights(self):
assert_equal(calcCenter(ATOMS.getCoordsets(),
weights=ones(len(ATOMS))), CENTERS)
def testMultiCoordsets(self):
assert_equal(calcCenter(ATOMS.getCoordsets()), CENTERS)
def testCenterWithWeights(self):
assert_equal(calcCenter(ATOMS, weights=ones(len(ATOMS))),
CENTERS[0])
def testCenter(self):
assert_equal(calcCenter(ATOMS), CENTERS[0])