def mag_superimpose(a1, a2):
sup = SVDSuperimposer()
a1 = np.asarray(a1)
a2 = np.asarray(a2)
mags = [norm(v) for v in a2]
if len(a1) <= 7:
min_dist = (1.0E6, 'foo', 'bar')
for l in itertools.permutations(a1):
p = np.array([m * v / norm(v) for m, v in zip(mags, l)])
sup.set(a2, p)
sup.run()
rot, tran = sup.get_rotran()
rms = sup.get_rms()
if rms < min_dist[0]:
min_dist = (rms, rot, tran)
else:
a1, a2 = match_vectors(a1, a2, 6)
mags = [norm(v) for v in a2]
min_dist = (1.0E6, 'foo', 'bar')
for l in itertools.permutations(a1):
p = np.array([m * v / norm(v) for m, v in zip(mags, l)])
sup.set(a2, p)
sup.run()
rot, tran = sup.get_rotran()
rms = sup.get_rms()
if rms < min_dist[0]:
min_dist = (rms, rot, tran)
return min_dist
def superimpose(a1,a2): sup = SVDSuperimposer() a1 = np.asarray(a1) a2 = np.asarray(a2) if len(a1) <= 7: min_dist = (1.0E6, 'foo', 'bar') for l in itertools.permutations(a1): p = np.asarray(l) sup.set(a2,p) sup.run() rot,tran = sup.get_rotran() aff_a1 = np.dot(l,rot) + tran rms = sup.get_rms() if rms < min_dist[0]: min_dist = (rms,rot,tran) else: a1,a2 = match_vectors(a1,a2,6) min_dist = (1.0E6, 'foo', 'bar') for l in itertools.permutations(a1): p = np.asarray(l) sup.set(a2,p) sup.run() rot,tran = sup.get_rotran() aff_a1 = np.dot(l,rot) + tran rms = sup.get_rms() if rms < min_dist[0]: min_dist = (rms,rot,tran) return min_dist
[50.22, -0.02, 52.85]], 'f')
y = array([[51.30, -2.99, 46.54], [51.09, -1.88, 47.58], [52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]], 'f')
sup = SVDSuperimposer()
# set the coords
# y will be rotated and translated on x
sup.set(x, y)
# do the lsq fit
sup.run()
# get the rmsd
rms = sup.get_rms()
# get rotation (right multiplying!) and the translation
rot, tran = sup.get_rotran()
# rotate y on x manually
y_on_x1 = dot(y, rot) + tran
# same thing
y_on_x2 = sup.get_transformed()
def simple_matrix_print(matrix):
"""Simple string to display a floating point matrix
This should give the same output on multiple systems. This is
y=array([[51.30, -2.99, 46.54],
[51.09, -1.88, 47.58],
[52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]], 'f')
sup=SVDSuperimposer()
# set the coords
# y will be rotated and translated on x
sup.set(x, y)
# do the lsq fit
sup.run()
# get the rmsd
rms=sup.get_rms()
# get rotation (right multiplying!) and the translation
rot, tran=sup.get_rotran()
# rotate y on x manually
y_on_x1=dot(y, rot)+tran
# same thing
y_on_x2=sup.get_transformed()
def simple_matrix_print(matrix):
"""Simple string to display a floating point matrix
This should give the same output on multiple systems. This is
needed because a simple "print matrix" uses scientific notation