def next(self):
# obtain first index for first call
if self.idx2_1 is None:
self.idx2_1 = self.iter1.next()
# toggle inversion if inversion is possible
if self.can_invert and self.invert == False and self.idx2_2 is not None:
self.invert = True
else:
# determine next pair of indices
self.invert = False
# try to increment 2nd iterator
try:
self.idx2_2 = self.iter2.next()
except StopIteration:
# end of list, start over again
self.iter2 = iter(self.candidates2)
# and increment iter1
self.idx2_1 = self.iter1.next()
self.idx2_2 = None
return self.next()
if self.idx2_1 == self.idx2_2:
return self.next()
x1 = self.x1
x2 = self.x2
idx1_1 = self.idx1_1
idx1_2 = self.idx1_2
idx2_1 = self.idx2_1
idx2_2 = self.idx2_2
assert idx1_1 is not None
assert idx1_2 is not None
assert idx2_1 is not None
assert idx2_2 is not None
# we can immediately trash the match if angle does not match
try:
cos_theta2 = np.dot(x2[idx2_1], x2[idx2_2]) / \
(np.linalg.norm(x2[idx2_1])*np.linalg.norm(x2[idx2_2]))
except ValueError:
raise
if np.abs(cos_theta2 - self.cos_theta1) > 0.5:
return self.next()
mul = 1.0
if self.invert:
mul = -1.0
# get rotation for current atom match candidates
dist, rot = rmsfit.findrotation(x1[[idx1_1, idx1_2]],
mul * x2[[idx2_1, idx2_2]],
align_com=False)
return rot, self.invert
def next(self):
# obtain first index for first call
if self.idx2_1 is None:
self.idx2_1 = self.iter1.next()
# toggle inversion if inversion is possible
if self.can_invert and self.invert == False and self.idx2_2 is not None:
self.invert = True
else:
# determine next pair of indices
self.invert = False
# try to increment 2nd iterator
try:
self.idx2_2 = self.iter2.next()
except StopIteration:
# end of list, start over again
self.iter2 = iter(self.candidates2)
# and increment iter1
self.idx2_1 = self.iter1.next()
self.idx2_2 = None
return self.next()
if self.idx2_1 == self.idx2_2:
return self.next()
x1 = self.x1
x2 = self.x2
idx1_1 = self.idx1_1
idx1_2 = self.idx1_2
idx2_1 = self.idx2_1
idx2_2 = self.idx2_2
assert idx1_1 is not None
assert idx1_2 is not None
assert idx2_1 is not None
assert idx2_2 is not None
# we can immediately trash the match if angle does not match
try:
cos_theta2 = np.dot(x2[idx2_1], x2[idx2_2]) / \
(np.linalg.norm(x2[idx2_1])*np.linalg.norm(x2[idx2_2]))
except ValueError:
raise
if(np.abs(cos_theta2 - self.cos_theta1) > 0.5):
return self.next()
mul = 1.0
if(self.invert):
mul=-1.0
# get rotation for current atom match candidates
dist, rot = rmsfit.findrotation( \
x1[[idx1_1, idx1_2]], mul*x2[[idx2_1, idx2_2]], align_com=False)
return rot, self.invert
def find_rotation(self, X1, X2):
dist, mx = findrotation(X1, X2)
return dist, mx
def find_rotation(self, X1, X2):
dist, mx = findrotation(X1, X2)
return dist, mx
def getAlignRotation(XA, XB):
print "WARNING: getAlignRotation is obsolete, use find_rotation"
return rotations.mx2q(findrotation(XA, XB))
def getAlignRotation(XA, XB):
print "WARNING: getAlignRotation is obsolete, use find_rotation"
return rotations.mx2q(findrotation(XA, XB))
