def __init__(O, type, qE):
assert type in ["euler_params", "euler_angles_xyz"]
if (type == "euler_params"):
if (len(qE.elems) == 3):
qE = euler_angles_xyz_qE_as_euler_params_qE(qE=qE)
else:
if (len(qE.elems) == 4):
qE = euler_params_qE_as_euler_angles_xyz_qE(qE=qE)
O.type = type
O.qE = qE
O.q_size = len(qE)
#
if (type == "euler_params"):
O.unit_quaternion = qE.normalize() # RBDA, bottom of p. 86
O.E = RBDA_Eq_4_12(q=O.unit_quaternion)
else:
O.E = RBDA_Eq_4_7(q=qE)
#
O.Tps = matrix.rt((O.E, (0,0,0)))
O.Tsp = matrix.rt((O.E.transpose(), (0,0,0)))
O.Xj = T_as_X(O.Tps)
O.S = matrix.rec((
1,0,0,
0,1,0,
0,0,1,
0,0,0,
0,0,0,
0,0,0), n=(6,3))
def __init__(O, type, qE, qr, r_is_qr=False):
assert type in ["euler_params", "euler_angles_xyz"]
if (type == "euler_params"):
if (len(qE.elems) == 3):
qE = euler_angles_xyz_qE_as_euler_params_qE(qE=qE)
else:
if (len(qE.elems) == 4):
qE = euler_params_qE_as_euler_angles_xyz_qE(qE=qE)
O.type = type
O.qE = qE
O.qr = qr
O.r_is_qr = r_is_qr
O.q_size = len(qE) + len(qr)
#
if (type == "euler_params"):
O.unit_quaternion = qE.normalize() # RBDA, bottom of p. 86
O.E = RBDA_Eq_4_12(q=O.unit_quaternion)
else:
O.E = RBDA_Eq_4_7(q=qE)
if (r_is_qr):
O.r = qr
else:
O.r = O.E.transpose() * qr # RBDA Tab. 4.1
#
O.Tps = matrix.rt((O.E, -O.E * O.r)) # RBDA Eq. 2.28
O.Tsp = matrix.rt((O.E.transpose(), O.r))
O.Xj = T_as_X(O.Tps)
O.S = None
def __init__(O, type, qE, qr, r_is_qr=False):
assert type in ["euler_params", "euler_angles_xyz"]
if (type == "euler_params"):
if (len(qE.elems) == 3):
qE = euler_angles_xyz_qE_as_euler_params_qE(qE=qE)
else:
if (len(qE.elems) == 4):
qE = euler_params_qE_as_euler_angles_xyz_qE(qE=qE)
O.type = type
O.qE = qE
O.qr = qr
O.r_is_qr = r_is_qr
O.q_size = len(qE) + len(qr)
#
if (type == "euler_params"):
O.unit_quaternion = qE.normalize() # RBDA, bottom of p. 86
O.E = RBDA_Eq_4_12(q=O.unit_quaternion)
else:
O.E = RBDA_Eq_4_7(q=qE)
if (r_is_qr):
O.r = qr
else:
O.r = O.E.transpose() * qr # RBDA Tab. 4.1
#
O.Tps = matrix.rt((O.E, -O.E * O.r)) # RBDA Eq. 2.28
O.Tsp = matrix.rt((O.E.transpose(), O.r))
O.Xj = T_as_X(O.Tps)
O.S = None
def rt_from_string(string, default_r_identity=False, r_den=12**2, t_den=12**3):
from cctbx import sgtbx
from scitbx import matrix
result = None
s = string.strip()
if (len(s) == 0):
s = "a,b,c"
try:
cb_op = sgtbx.change_of_basis_op(symbol=s,
stop_chars="",
r_den=r_den,
t_den=t_den)
except ValueError as e:
pass
except RuntimeError as e:
pass
else:
return cb_op.c_inv().as_rational()
nums = nums_from_string(s)
if (nums is not None):
if (len(nums) == 12):
if (string.find("|") < 0):
result = matrix.rt((nums[:9], nums[9:]))
else:
result = matrix.rt((nums[:3] + nums[4:7] + nums[8:11],
(nums[3], nums[7], nums[11])))
elif (len(nums) == 9):
result = matrix.rt((nums[:9], (0, 0, 0)))
elif (len(nums) == 3):
if (default_r_identity):
r = (1, 0, 0, 0, 1, 0, 0, 0, 1)
else:
r = (0, 0, 0, 0, 0, 0, 0, 0, 0)
result = matrix.rt((r, nums))
return result
def __init__(O, qE, qr): O.qE = qE O.qr = qr # O.E = RBDA_Eq_4_12(qE) O.r = O.E.transpose() * qr # RBDA Tab. 4.1 # O.Tps = matrix.rt((O.E, -O.E * O.r)) # RBDA Eq. 2.28 O.Tsp = matrix.rt((O.E.transpose(), O.r))
def __init__(O, qE, qr):
O.qE = qE
O.qr = qr
#
O.E = RBDA_Eq_4_12(qE)
O.r = O.E.transpose() * qr # RBDA Tab. 4.1
#
O.Tps = matrix.rt((O.E, -O.E * O.r)) # RBDA Eq. 2.28
O.Tsp = matrix.rt((O.E.transpose(), O.r))
def __init__(O, qE):
O.qE = qE
O.q_size = len(qE)
#
c, s = math.cos(qE[0]), math.sin(qE[0])
O.E = matrix.sqr((c, s, 0, -s, c, 0, 0, 0, 1)) # RBDA Tab. 2.2
O.r = matrix.col((0, 0, 0))
#
O.Tps = matrix.rt((O.E, (0, 0, 0)))
O.Tsp = matrix.rt((O.E.transpose(), (0, 0, 0)))
O.Xj = T_as_X(O.Tps)
O.S = matrix.col((0, 0, 1, 0, 0, 0))
def __init__(O, qE): O.qE = qE O.q_size = len(qE) # c, s = math.cos(qE[0]), math.sin(qE[0]) O.E = matrix.sqr((c, s, 0, -s, c, 0, 0, 0, 1)) # RBDA Tab. 2.2 O.r = matrix.col((0,0,0)) # O.Tps = matrix.rt((O.E, (0,0,0))) O.Tsp = matrix.rt((O.E.transpose(), (0,0,0))) O.Xj = T_as_X(O.Tps) O.S = matrix.col((0,0,1,0,0,0))
def exercise_joint_lib_six_dof_aja_simplified():
tc = test_cases_tardy_pdb.test_cases[9]
tt = tc.tardy_tree_construct()
masses = [1.0]*len(tc.sites)
# arbitrary transformation so that the center of mass is not at the origin
rt_arbitrary = matrix.col((-0.21,-0.51,0.64)) \
.rt_for_rotation_around_axis_through(
point=matrix.col((-0.80, 0.28, -0.89)), angle=-37, deg=True)
sites = [rt_arbitrary * site for site in tc.sites]
tm = scitbx.rigid_body.essence.tardy.model(
labels=tc.labels,
sites=sites,
masses=masses,
tardy_tree=tt,
potential_obj=None)
assert len(tm.bodies) == 1
assert tm.q_packed_size == 7
mt = flex.mersenne_twister(seed=0)
for i_trial in xrange(3):
q = mt.random_double(size=tm.q_packed_size)*2-1
tm.unpack_q(q_packed=q)
sm = tm.sites_moved()
aja = matrix.rt(scitbx.rigid_body.joint_lib_six_dof_aja_simplified(
center_of_mass=tuple(flex.vec3_double(sites).mean()),
q=q))
sm2 = [aja * site for site in sites]
assert approx_equal(sm2, sm)
def exercise_joint_lib_six_dof_aja_simplified():
tc = test_cases_tardy_pdb.test_cases[9]
tt = tc.tardy_tree_construct()
masses = [1.0] * len(tc.sites)
# arbitrary transformation so that the center of mass is not at the origin
rt_arbitrary = matrix.col((-0.21,-0.51,0.64)) \
.rt_for_rotation_around_axis_through(
point=matrix.col((-0.80, 0.28, -0.89)), angle=-37, deg=True)
sites = [rt_arbitrary * site for site in tc.sites]
tm = scitbx.rigid_body.essence.tardy.model(labels=tc.labels,
sites=sites,
masses=masses,
tardy_tree=tt,
potential_obj=None)
assert len(tm.bodies) == 1
assert tm.q_packed_size == 7
mt = flex.mersenne_twister(seed=0)
for i_trial in xrange(3):
q = mt.random_double(size=tm.q_packed_size) * 2 - 1
tm.unpack_q(q_packed=q)
sm = tm.sites_moved()
aja = matrix.rt(
scitbx.rigid_body.joint_lib_six_dof_aja_simplified(
center_of_mass=tuple(flex.vec3_double(sites).mean()), q=q))
sm2 = [aja * site for site in sites]
assert approx_equal(sm2, sm)
def compute_operators(self, sites_cart):
for pair in self.selection_pairs:
superposition = superpose.least_squares_fit(
reference_sites=sites_cart.select(pair[0]),
other_sites=sites_cart.select(pair[1]))
rtmx = matrix.rt((superposition.r, superposition.t))
self.matrices.append(rtmx)
x = sites_cart.select(pair[0])
y = rtmx * sites_cart.select(pair[1])
d_sq = (x - y).dot()
self.rms.append(flex.mean(d_sq)**0.5)
def exercise_T_as_X(mersenne_twister):
for i_trial in xrange(10):
T1 = matrix.rt((mersenne_twister.random_double_r3_rotation_matrix(),
mersenne_twister.random_double(size=3) - 0.5))
T2 = matrix.rt((mersenne_twister.random_double_r3_rotation_matrix(),
mersenne_twister.random_double(size=3) - 0.5))
T12 = T1 * T2
T21 = T2 * T1
T1i = T1.inverse_assuming_orthogonal_r()
T2i = T2.inverse_assuming_orthogonal_r()
X1 = T_as_X(T1)
X2 = T_as_X(T2)
X12 = T_as_X(T12)
X21 = T_as_X(T21)
X1i = T_as_X(T1i)
X2i = T_as_X(T2i)
assert approx_equal(X1 * X2, X12)
assert approx_equal(X2 * X1, X21)
assert approx_equal(X1.inverse(), X1i)
assert approx_equal(X2.inverse(), X2i)
def exercise_T_as_X(mersenne_twister):
for i_trial in xrange(10):
T1 = matrix.rt((
mersenne_twister.random_double_r3_rotation_matrix(),
mersenne_twister.random_double(size=3)-0.5))
T2 = matrix.rt((
mersenne_twister.random_double_r3_rotation_matrix(),
mersenne_twister.random_double(size=3)-0.5))
T12 = T1 * T2
T21 = T2 * T1
T1i = T1.inverse_assuming_orthogonal_r()
T2i = T2.inverse_assuming_orthogonal_r()
X1 = T_as_X(T1)
X2 = T_as_X(T2)
X12 = T_as_X(T12)
X21 = T_as_X(T21)
X1i = T_as_X(T1i)
X2i = T_as_X(T2i)
assert approx_equal(X1*X2, X12)
assert approx_equal(X2*X1, X21)
assert approx_equal(X1.inverse(), X1i)
assert approx_equal(X2.inverse(), X2i)
def __init__(self, group, sites_cart):
self.group = group
self.matrices = []
self.rms = []
for pair in self.group.selection_pairs:
superposition = superpose.least_squares_fit(
reference_sites=sites_cart.select(pair[0]),
other_sites=sites_cart.select(pair[1]))
rtmx = matrix.rt((superposition.r, superposition.t))
self.matrices.append(rtmx)
x = sites_cart.select(pair[0])
y = rtmx * sites_cart.select(pair[1])
d_sq = (x - y).dot()
self.rms.append(flex.mean(d_sq)**0.5)
def __init__(self, group, sites_cart):
self.group = group
self.matrices = []
self.rms = []
for pair in self.group.selection_pairs:
superposition = superpose.least_squares_fit(
reference_sites=sites_cart.select(pair[0]),
other_sites=sites_cart.select(pair[1]))
rtmx = matrix.rt((superposition.r, superposition.t))
self.matrices.append(rtmx)
x = sites_cart.select(pair[0])
y = rtmx * sites_cart.select(pair[1])
d_sq = (x-y).dot()
self.rms.append(flex.mean(d_sq)**0.5)
def __init__(O, type, qE):
assert type in ["euler_params", "euler_angles_xyz"]
if (type == "euler_params"):
if (len(qE.elems) == 3):
qE = euler_angles_xyz_qE_as_euler_params_qE(qE=qE)
else:
if (len(qE.elems) == 4):
qE = euler_params_qE_as_euler_angles_xyz_qE(qE=qE)
O.type = type
O.qE = qE
O.q_size = len(qE)
#
if (type == "euler_params"):
O.unit_quaternion = qE.normalize() # RBDA, bottom of p. 86
O.E = RBDA_Eq_4_12(q=O.unit_quaternion)
else:
O.E = RBDA_Eq_4_7(q=qE)
#
O.Tps = matrix.rt((O.E, (0, 0, 0)))
O.Tsp = matrix.rt((O.E.transpose(), (0, 0, 0)))
O.Xj = T_as_X(O.Tps)
O.S = matrix.rec(
(1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0), n=(6, 3))
def get(i, delta):
fs = []
for signed_delta in [delta, -delta]:
q_delta[i] = q[i] + signed_delta
aja = matrix.rt(scitbx.rigid_body.joint_lib_six_dof_aja_simplified(
center_of_mass=center_of_mass,
q=q_delta))
sites_cart_delta = aja * sites_cart_0
rs_f = maptbx.real_space_target_simple(
unit_cell=unit_cell,
density_map=density_map,
sites_cart=sites_cart_delta,
selection=flex.bool(sites_cart_delta.size(),True))
fs.append(rs_f)
result.append((fs[0]-fs[1])/(2*delta))
def get(i, delta):
fs = []
for signed_delta in [delta, -delta]:
q_delta[i] = q[i] + signed_delta
aja = matrix.rt(scitbx.rigid_body.joint_lib_six_dof_aja_simplified(
center_of_mass=center_of_mass,
q=q_delta))
sites_cart_delta = aja * sites_cart_0
rs_f = maptbx.real_space_target_simple(
unit_cell=unit_cell,
density_map=density_map,
sites_cart=sites_cart_delta,
selection=flex.bool(sites_cart_delta.size(),True))
fs.append(rs_f)
result.append((fs[0]-fs[1])/(2*delta))
def rotate_about_2ptaxis(self, pdb_hier, coor1, coor2, rot):
# function that rotates a set of coordinates around an arbitrary
# axis defined by two points by a rotation in degrees
#coor1 is the center of rotation origin (input as 3tuple)
#coor2 gives the vector which forms the rotation axis
#a new copy of coords are returned as hierarchy
new_hier = pdb_hier.deep_copy()
x1, y1, z1 = coor1
x2, y2, z2 = coor2
rad = 2 * np.pi * rot / 360.0
(u, v, w) = (x2 - x1, y2 - y1, z2 - z1)
L = u**2 + v**2 + w**2
rt = matrix.rt(
([(u**2 + (v**2 + w**2) * math.cos(rad)) / L,
(u * v *
(1 - math.cos(rad)) - w * math.sqrt(L) * math.sin(rad)) / L,
(u * w *
(1 - math.cos(rad)) + v * math.sqrt(L) * math.sin(rad)) / L,
(u * v *
(1 - math.cos(rad)) + w * math.sqrt(L) * math.sin(rad)) / L,
(v**2 + (u**2 + w**2) * math.cos(rad)) / L,
(v * w *
(1 - math.cos(rad)) - u * math.sqrt(L) * math.sin(rad)) / L,
(u * w *
(1 - math.cos(rad)) - v * math.sqrt(L) * math.sin(rad)) / L,
(v * w *
(1 - math.cos(rad)) + u * math.sqrt(L) * math.sin(rad)) / L,
(w**2 + (u**2 + v**2) * math.cos(rad)) / L], [
((x1 * (v**2 + w**2) - u *
(y1 * v + z1 * w)) * (1 - math.cos(rad)) +
(y1 * w - z1 * v) * math.sqrt(L) * math.sin(rad)) / L,
((y1 * (u**2 + w**2) - v *
(x1 * u + z1 * w)) * (1 - math.cos(rad)) +
(z1 * u - x1 * w) * math.sqrt(L) * math.sin(rad)) / L,
((z1 * (u**2 + v**2) - w *
(x1 * u + y1 * v)) * (1 - math.cos(rad)) +
(x1 * v - y1 * u) * math.sqrt(L) * math.sin(rad)) / L,
]))
atoms = new_hier.atoms()
sites = atoms.extract_xyz()
atoms.set_xyz(rt.r.elems * sites + rt.t.elems)
return new_hier
def axis_rt(axis, setting=None):
if axis.type == b"rotation":
if setting:
a = setting.angle_start_range_incr[0]
else:
a = 0.0
v = matrix.col(axis.vector)
r = v.axis_and_angle_as_r3_rotation_matrix(a, deg=True)
t = matrix.col(axis.offset)
elif axis.type == b"translation":
if setting:
t = setting.displacement_start_range_incr[0]
else:
t = 0.0
v = matrix.col(axis.vector)
r = matrix.sqr((1, 0, 0, 0, 1, 0, 0, 0, 1))
o = matrix.col(axis.offset)
t = v * t + o
rt = matrix.rt((r, t))
return rt
def run():
osType = sys.platform
if osType.startswith('win'):
directory_path = 'c:\Phenix\Dev\Work\work'
else:
directory_path = '/net/cci-filer2/raid1/home/youval/Work/work'
print os.getcwd()
os.chdir(directory_path)
f = open('mtrix_not_included_in_pdb.txt','w')
good_MTRIX_pdb_files = pickle.load(open('dict_good_MTRIX_pdb_files','r'))
MTRIX_with_Straucture_Factor = pickle.load(open('MTRIX_with_Straucture_Factor_file_list','r'))
results = []
n = len(MTRIX_with_Straucture_Factor)
for file_name in MTRIX_with_Straucture_Factor:
pdb_inp = pdb.input(file_name=good_MTRIX_pdb_files[file_name]) # read the pdb file data
TRASFORM_info = pdb_inp.process_mtrix_records(error_handle=False,eps=1e-2)
TRASFORM_info = [matrix.rt(x.values) for x in TRASFORM_info if not x.coordinates_present]
if TRASFORM_info != []:
f.write(file_name + '\n')
print '*'*60
results.append(file_name)
f.close()
print 'files with MTRIX records that are not already include in pdb file: {}'.format(len(results))
print 'Total files with mtrix records: {}'.format(n)
def __init__(O, sites): O.pivot = center_of_mass_from_sites(sites=sites) O.normal = None O.T0b = matrix.rt(((1,0,0,0,1,0,0,0,1), -O.pivot)) O.Tb0 = matrix.rt(((1,0,0,0,1,0,0,0,1), O.pivot))
def rt(self):
return matrix.rt( ( self.r, self.t ) )
def sgtbx_rt_mx_as_matrix_rt(s):
return matrix.rt((s.r().as_double(), s.t().as_double()))
def setT(O): O.Tps = matrix.rt((O.E, (0,0,0))) O.Tsp = matrix.rt((O.E.transpose(), (0,0,0)))
def run(server_info, inp, status):
print "<pre>"
from scitbx import matrix
p = p_from_string(string=inp.cb_expr)
assert inp.p_or_q in ["P", "Q"]
if (inp.p_or_q == "Q"):
p = p.inverse()
assert inp.p_transpose in ["off", "on"]
if (inp.p_transpose == "on"):
p = matrix.rt((p.r.transpose(), p.t))
print "P:"
display_rt(p)
print
q = p.inverse()
print "Q:"
display_rt(q)
print
if (len(inp.obj_expr.strip()) != 0):
if (inp.obj_type in ["xyz", "hkl"]):
triple = xyz_from_string(string=inp.obj_expr)
if (inp.obj_type == "xyz"):
print "Transformation law: (Q,q) xyz"
print
print " xyz:", triple
print
print " xyz':", (q.r * matrix.col(triple) + q.t).elems
print
else:
print "Transformation law: hkl P"
print
print " hkl:", triple
print
print " hkl':", (matrix.row(triple) * p.r).elems
print
elif (inp.obj_type == "unit_cell"):
from cctbx import uctbx
uc = uctbx.unit_cell(inp.obj_expr)
print "Transformation law: Pt G P"
print
print "unit cell:", uc
print
g = matrix.sym(sym_mat3=uc.metrical_matrix())
print "metrical matrix:"
display_r(g)
print
gp = p.r.transpose() * g * p.r
print "metrical matrix':"
display_r(gp)
print
ucp = uctbx.unit_cell(metrical_matrix=gp.as_sym_mat3())
print "unit cell':", ucp
print
elif (inp.obj_type == "Ww"):
w = w_from_string(string=inp.obj_expr)
print "Transformation law: (Q,q) (W,w) (P,p)"
print
print "(W, w):"
display_rt(w)
print
wp = q * w * p
print "(W, w)':"
display_rt(wp)
print
else:
raise RuntimeError("Unknown obj_type: %s" % inp.obj_type)
print "</pre>"
def as_rational(self): return matrix.rt((self.r().as_rational(), self.t().as_rational()))
if (len(s) == 0):
s = "a,b,c"
try:
cb_op = sgtbx.change_of_basis_op(
symbol=s, stop_chars="", r_den=r_den, t_den=t_den)
except ValueError, e:
pass
except RuntimeError, e :
pass
else:
return cb_op.c_inv().as_rational()
nums = nums_from_string(s)
if (nums is not None):
if (len(nums) == 12):
if (string.find("|") < 0):
result = matrix.rt((nums[:9], nums[9:]))
else:
result = matrix.rt(
(nums[:3]+nums[4:7]+nums[8:11],
(nums[3], nums[7], nums[11])))
elif (len(nums) == 9):
result = matrix.rt((nums[:9], (0,0,0)))
elif (len(nums) == 3):
if (default_r_identity):
r = (1,0,0,0,1,0,0,0,1)
else:
r = (0,0,0,0,0,0,0,0,0)
result = matrix.rt((r, nums))
return result
def raise_uninterpretable(what, expression):
def run(server_info, inp, status):
print "<pre>"
from scitbx import matrix
p = p_from_string(string=inp.cb_expr)
assert inp.p_or_q in ["P", "Q"]
if (inp.p_or_q == "Q"):
p = p.inverse()
assert inp.p_transpose in ["off", "on"]
if (inp.p_transpose == "on"):
p = matrix.rt((p.r.transpose(), p.t))
print "P:"
display_rt(p)
print
q = p.inverse()
print "Q:"
display_rt(q)
print
if (len(inp.obj_expr.strip()) != 0):
if (inp.obj_type in ["xyz", "hkl"]):
triple = xyz_from_string(string=inp.obj_expr)
if (inp.obj_type == "xyz"):
print "Transformation law: (Q,q) xyz"
print
print " xyz:", triple
print
print " xyz':", (
q.r * matrix.col(triple) + q.t).elems
print
else:
print "Transformation law: hkl P"
print
print " hkl:", triple
print
print " hkl':", (matrix.row(triple) * p.r).elems
print
elif (inp.obj_type == "unit_cell"):
from cctbx import uctbx
uc = uctbx.unit_cell(inp.obj_expr)
print "Transformation law: Pt G P"
print
print "unit cell:", uc
print
g = matrix.sym(sym_mat3=uc.metrical_matrix())
print "metrical matrix:"
display_r(g)
print
gp = p.r.transpose() * g * p.r
print "metrical matrix':"
display_r(gp)
print
ucp = uctbx.unit_cell(metrical_matrix=gp.as_sym_mat3())
print "unit cell':", ucp
print
elif (inp.obj_type == "Ww"):
w = w_from_string(string=inp.obj_expr)
print "Transformation law: (Q,q) (W,w) (P,p)"
print
print "(W, w):"
display_rt(w)
print
wp = q * w * p
print "(W, w)':"
display_rt(wp)
print
else:
raise RuntimeError("Unknown obj_type: %s" % inp.obj_type)
print "</pre>"
try:
cb_op = sgtbx.change_of_basis_op(symbol=s,
stop_chars="",
r_den=r_den,
t_den=t_den)
except ValueError, e:
pass
except RuntimeError, e:
pass
else:
return cb_op.c_inv().as_rational()
nums = nums_from_string(s)
if (nums is not None):
if (len(nums) == 12):
if (string.find("|") < 0):
result = matrix.rt((nums[:9], nums[9:]))
else:
result = matrix.rt((nums[:3] + nums[4:7] + nums[8:11],
(nums[3], nums[7], nums[11])))
elif (len(nums) == 9):
result = matrix.rt((nums[:9], (0, 0, 0)))
elif (len(nums) == 3):
if (default_r_identity):
r = (1, 0, 0, 0, 1, 0, 0, 0, 1)
else:
r = (0, 0, 0, 0, 0, 0, 0, 0, 0)
result = matrix.rt((r, nums))
return result
def raise_uninterpretable(what, expression):
def GetMatrix (self) : from scitbx import matrix r = [ c.GetPhilValue() for c in self._r_ctrls ] t = [ c.GetPhilValue() for c in self._t_ctrls ] return matrix.rt((r,t))
def setT(O):
O.Tps = matrix.rt((O.E, (0, 0, 0)))
O.Tsp = matrix.rt((O.E.transpose(), (0, 0, 0)))
def __init__(O, sites):
O.pivot = center_of_mass_from_sites(sites=sites)
O.normal = None
O.T0b = matrix.rt(((1, 0, 0, 0, 1, 0, 0, 0, 1), -O.pivot))
O.Tb0 = matrix.rt(((1, 0, 0, 0, 1, 0, 0, 0, 1), O.pivot))
def rt(self): return matrix.rt(tuple_r_t=(self.r, self.t))
def __init__(O, pivot, normal): O.pivot = pivot O.normal = normal r = normal.vector_to_001_rotation() O.T0b = matrix.rt((r, -r * pivot)) O.Tb0 = matrix.rt((r.transpose(), pivot))
def sgtbx_rt_mx_as_matrix_rt(s): return matrix.rt((s.r().as_double(), s.t().as_double()))
def __init__(O, pivot, normal):
O.pivot = pivot
O.normal = normal
r = normal.vector_to_001_rotation()
O.T0b = matrix.rt((r, -r * pivot))
O.Tb0 = matrix.rt((r.transpose(), pivot))
def as_rational(self):
return matrix.rt((self.r().as_rational(), self.t().as_rational()))
def GetMatrix(self):
from scitbx import matrix
r = [c.GetPhilValue() for c in self._r_ctrls]
t = [c.GetPhilValue() for c in self._t_ctrls]
return matrix.rt((r, t))