def helix_axis(sele='all', state=1):
xform = xform_between_chains('A',
'B',
sele=f'({sele}) and name CA',
state=state)
axis, ang, cen = hm.axis_ang_cen_of(xform)
return axis, cen
def show_with_axis(worms, idx=0):
"""TODO: Summary
Args:
worms (TYPE): Description
idx (int, optional): Description
"""
pose = worms.pose(idx, align=0, end=1)
x_from = worms.positions[idx][worms.criteria.from_seg]
x_to = worms.positions[idx][worms.criteria.to_seg]
x = x_to @ np.linalg.inv(x_from)
axis, ang, cen = homog.axis_ang_cen_of(x)
np.set_printoptions(precision=20)
print(x)
print(axis)
print(ang)
print(cen)
axis *= 100
showme(pose, name="unit")
util.xform_pose(x, pose)
showme(pose, name="sym1")
util.xform_pose(x, pose)
showme(pose, name="sym2")
showline(axis, cen)
showsphere(cen)
def score(self, segpos, *, verbosity=False, **kw):
x_from = segpos[self.from_seg]
x_to = segpos[self.to_seg]
xhat = x_to @ inv(x_from)
trans = xhat[..., :, 3]
if self.nfold is 1:
angle = hm.angle_of(xhat)
carterrsq = np.sum(trans[..., :3]**2, axis=-1)
roterrsq = angle**2
else:
if self.origin_seg is not None:
tgtaxis = segpos[self.origin_seg] @ [0, 0, 1, 0]
tgtcen = segpos[self.origin_seg] @ [0, 0, 0, 1]
axis, angle, cen = hm.axis_ang_cen_of(xhat)
carterrsq = hm.hnorm2(cen - tgtcen)
roterrsq = (1 - np.abs(hm.hdot(axis, tgtaxis))) * np.pi
else: # much cheaper if cen not needed
axis, angle = hm.axis_angle_of(xhat)
carterrsq = roterrsq = 0
carterrsq = carterrsq + hm.hdot(trans, axis)**2
roterrsq = roterrsq + (angle - self.symangle)**2
# if self.relweight is not None:
# # penalize 'relative' error
# distsq = np.sum(trans[..., :3]**2, axis=-1)
# relerrsq = carterrsq / distsq
# relerrsq[np.isnan(relerrsq)] = 9e9
# # too much of a hack??
# carterrsq += self.relweight * relerrsq
if verbosity > 0:
print('axis', axis[0])
print('trans', trans[0])
print('dot trans', hm.hdot(trans, axis)[0])
print('angle', angle[0] * 180 / np.pi)
return np.sqrt(carterrsq / self.tol**2 + roterrsq / self.rot_tol**2)
def primary_xform_commutator(units, state=1, **kw):
print('stub 0:')
print(units[0].stub)
closest = None
for j in range(1, 20):
x = hm.hinv(units[0].stub) @ units[j].stub
# print(f'stub {j}:')
# print(units[j].stub)
# print(x)
axis, ang, cen = hm.axis_ang_cen_of(x)
helical = hm.hdot(axis, x[:, 3])
print(j, helical, x[2, 3])
if abs(helical) > 0.01:
return x
return None
def alignment(self, segpos, **kwargs):
if self.origin_seg is not None:
return inv(segpos[self.origin_seg])
x_from = segpos[self.from_seg]
x_to = segpos[self.to_seg]
xhat = x_to @ inv(x_from)
axis, ang, cen = hm.axis_ang_cen_of(xhat)
# print('aln', axis)
# print('aln', ang * 180 / np.pi)
# print('aln', cen)
# print('aln', xhat[..., :, 3])
dotz = hm.hdot(axis, Uz)[..., None]
tgtaxis = np.where(dotz > 0, [0, 0, 1, 0], [0, 0, -1, 0])
align = hm.hrot((axis + tgtaxis) / 2, np.pi, cen)
align[..., :3, 3] -= cen[..., :3]
return align
def show_with_axis(worms, idx=0):
pose = worms.pose(idx, align=0, end=1)
x_from = worms.positions[idx][worms.criteria.from_seg]
x_to = worms.positions[idx][worms.criteria.to_seg]
x = x_to @ np.linalg.inv(x_from)
axis, ang, cen = homog.axis_ang_cen_of(x)
np.set_printoptions(precision=20)
print(x)
print(axis)
print(ang)
print(cen)
axis *= 100
showme(pose, name='unit')
util.xform_pose(x, pose)
showme(pose, name='sym1')
util.xform_pose(x, pose)
showme(pose, name='sym2')
showline(axis, cen)
showsphere(cen)