def test_transforms(self):
from MDAnalysis.lib.distances import transform_StoR, transform_RtoS
# To check the cython coordinate transform, the same operation is done in numpy
# Is a matrix multiplication of Coords x Box = NewCoords, so can use np.dot
# Test transformation
R_mol1 = transform_StoR(self.S_mol1, self.box)
R_np1 = np.dot(self.S_mol1, self.box)
# Test transformation when given box in different form
R_mol2 = transform_StoR(self.S_mol2, self.boxV)
R_np2 = np.dot(self.S_mol2, self.box)
assert_almost_equal(R_mol1, R_np1, self.prec, err_msg="StoR transform failed with box")
assert_almost_equal(R_mol2, R_np2, self.prec, err_msg="StoR transform failed with boxV")
# Round trip test
S_test1 = transform_RtoS(R_mol1, self.boxV) # boxV here althought initial transform with box
S_test2 = transform_RtoS(R_mol2, self.box) # and vice versa, should still work
assert_almost_equal(S_test1, self.S_mol1, self.prec, err_msg="Round trip failed in transform")
assert_almost_equal(S_test2, self.S_mol2, self.prec, err_msg="Round trip failed in transform")
def test_transforms(self):
from MDAnalysis.lib.distances import transform_StoR, transform_RtoS
# To check the cython coordinate transform, the same operation is done in numpy
# Is a matrix multiplication of Coords x Box = NewCoords, so can use np.dot
# Test transformation
R_mol1 = transform_StoR(self.S_mol1, self.box)
R_np1 = np.dot(self.S_mol1, self.box)
# Test transformation when given box in different form
R_mol2 = transform_StoR(self.S_mol2, self.boxV)
R_np2 = np.dot(self.S_mol2, self.box)
assert_almost_equal(R_mol1,
R_np1,
self.prec,
err_msg="StoR transform failed with box")
assert_almost_equal(R_mol2,
R_np2,
self.prec,
err_msg="StoR transform failed with boxV")
# Round trip test
S_test1 = transform_RtoS(
R_mol1,
self.boxV) # boxV here althought initial transform with box
S_test2 = transform_RtoS(R_mol2,
self.box) # and vice versa, should still work
assert_almost_equal(S_test1,
self.S_mol1,
self.prec,
err_msg="Round trip failed in transform")
assert_almost_equal(S_test2,
self.S_mol2,
self.prec,
err_msg="Round trip failed in transform")
def assert_in_box(positions, box):
"""Asserts that all `positions` are strictly within the primary periodic
image as defined by `box`
"""
relpos = transform_RtoS(positions, box)
assert np.all((relpos >= 0.0) & (relpos < 1.0))