def rt_mx_analysis(s):
print "<tr>"
print "<td><tt>" + str(s) + "</tt>"
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
if (r_info.type() == 1):
print "<td>1<td>-<td>-<td>-"
elif (r_info.type() == -1):
print "<td>%d<td>-<td>-<td>%s" % (
r_info.type(),
str(t_info.origin_shift()))
elif (abs(r_info.type()) == 2):
print "<td>%d<td>%s<td>%s<td>%s" % (
r_info.type(),
str_ev(r_info.ev()),
str(t_info.intrinsic_part()),
str(t_info.origin_shift()))
else:
print "<td>%d^%d<td>%s<td>%s<td>%s" % (
r_info.type(),
r_info.sense(),
str_ev(r_info.ev()),
str(t_info.intrinsic_part()),
str(t_info.origin_shift()))
print "</tr>"
def __init__(self, r, d, symmetry_agreement, status):
assert r.den() == 1
self.r = r
order = r.order()
self.r_info = sgtbx.rot_mx_info(r)
type = self.r_info.type()
axis = self.r_info.ev()
self.symmetry_agreement = symmetry_agreement
self.status = status
# compute intrinsic and location part of d, using p, which is
# the order times the projector onto r's invariant space
p = mat.sqr(r.accumulate().as_double())
t_i_num = (p*d).as_int()
t_l = d - t_i_num/order
t_i = sgtbx.tr_vec(sg_t_den//order*t_i_num, tr_den=sg_t_den)
# compute the origin corresponding to t_l by solving
# (1 - r) o = t_l
one_minus_r = -mat.sqr(self.r.minus_unit_mx().num())
one_minus_r_row_echelon = one_minus_r.as_flex_int_matrix()
q = mat.identity(3).as_flex_int_matrix()
rank = scitbx.math.row_echelon_form_t(one_minus_r_row_echelon, q)
qd = flex.double(mat.sqr(q)*t_l)[:rank]
o = flex.double((0,0,0))
scitbx.math.row_echelon_back_substitution_float(
one_minus_r_row_echelon, qd, o)
# construct object state
self.t_i, self.raw_origin = t_i, mat.col(o)
self.origin = None
self.one_minus_r = one_minus_r
def __init__(self, s ):
r_info = sgtbx.rot_mx_info( s.r() )
t_info = sgtbx.translation_part_info( s )
self.type = r_info.type()
self.ev = r_info.ev()
self.trans= t_info.intrinsic_part()
def possible_point_group_generators(self):
lattice_group = lattice_symmetry.group(self.f_in_p1.unit_cell(),
max_delta=1)
lattice_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
rot_parts = set()
decorated_rot_parts = []
for op in lattice_group:
r = op.r()
if r.is_unit_mx(): continue
if op.inverse() in rot_parts: continue
r_info = sgtbx.rot_mx_info(r)
if r_info.type() < -2: continue
rot_parts.add(op)
decorated_rot_parts.append((
r_info.type() == -1, # inversion shall come first,
list(r_info.ev()).count(
0), # axes // to unit cell shall come first
# note Python 2.5- compatibility
r_info.type() == -2, # mirrors preferred.
r.order(), # higher order preferred
op))
decorated_rot_parts.sort()
decorated_rot_parts.reverse()
for item in decorated_rot_parts:
yield item[-1]
def __init__(self, r, d, symmetry_agreement, status):
assert r.den() == 1
self.r = r
order = r.order()
self.r_info = sgtbx.rot_mx_info(r)
type = self.r_info.type()
axis = self.r_info.ev()
self.symmetry_agreement = symmetry_agreement
self.status = status
# compute intrinsic and location part of d, using p, which is
# the order times the projector onto r's invariant space
p = mat.sqr(r.accumulate().as_double())
t_i_num = (p * d).as_int()
t_l = d - t_i_num / order
t_i = sgtbx.tr_vec(sg_t_den // order * t_i_num, tr_den=sg_t_den)
# compute the origin corresponding to t_l by solving
# (1 - r) o = t_l
one_minus_r = -mat.sqr(self.r.minus_unit_mx().num())
one_minus_r_row_echelon = one_minus_r.as_flex_int_matrix()
q = mat.identity(3).as_flex_int_matrix()
rank = scitbx.math.row_echelon_form_t(one_minus_r_row_echelon, q)
qd = flex.double(mat.sqr(q) * t_l)[:rank]
o = flex.double((0, 0, 0))
scitbx.math.row_echelon_back_substitution_float(
one_minus_r_row_echelon, qd, o)
# construct object state
self.t_i, self.raw_origin = t_i, mat.col(o)
self.origin = None
self.one_minus_r = one_minus_r
def __init__(self, s):
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
self.type = r_info.type()
self.ev = r_info.ev()
self.trans = t_info.intrinsic_part()
def rt_mx_analysis(s):
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
t_intrinsic = str(t_info.intrinsic_part().mod_positive())
t_shift = str(t_info.origin_shift().mod_positive())
if (r_info.type() == 1):
return ("1", "-", "-", "-")
if (r_info.type() == -1):
return (str(r_info.type()), "-", "-", "(%s)" % (t_shift, ))
if (abs(r_info.type()) == 2):
return (str(r_info.type()), str_ev(r_info.ev()),
"(%s)" % (t_intrinsic, ), "(%s)" % (t_shift, ))
return (str(r_info.type()), str_ev(r_info.ev()), "(%s)" % (t_intrinsic, ),
"(%s)" % (t_shift, ))
def rt_mx_analysis(s):
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
t_intrinsic = str(t_info.intrinsic_part().mod_positive())
t_shift = str(t_info.origin_shift().mod_positive())
if (r_info.type() == 1):
return ("1", "-", "-", "-")
if (r_info.type() == -1):
return (str(r_info.type()), "-", "-", "location=(%s)" % (t_shift, ))
if (abs(r_info.type()) == 2):
return (str(r_info.type()), "axis=" + str_ev(r_info.ev()),
"(%s)" % (t_intrinsic, ), "location=(%s)" % (t_shift, ))
sense = "+"
if (r_info.sense() < 0):
sense = "-"
return (str(r_info.type()) + sense, "axis=" + str_ev(r_info.ev()),
"(%s)" % (t_intrinsic, ), "location=(%s)" % (t_shift, ))
def rt_mx_analysis(s):
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
t_intrinsic = str(t_info.intrinsic_part().mod_positive())
t_shift = str(t_info.origin_shift().mod_positive())
if (r_info.type() == 1):
return ("1", "-", "-", "-")
if (r_info.type() == -1):
return (str(r_info.type()), "-", "-", "(%s)" % (t_shift,))
if (abs(r_info.type()) == 2):
return (str(r_info.type()),
str_ev(r_info.ev()),
"(%s)" % (t_intrinsic,),
"(%s)" % (t_shift,))
return (str(r_info.type()),
str_ev(r_info.ev()),
"(%s)" % (t_intrinsic,),
"(%s)" % (t_shift,))
def rt_mx_analysis(s):
print("<tr>")
print("<td><tt>" + str(s) + "</tt>")
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
if (r_info.type() == 1):
print("<td>1<td>-<td>-<td>-")
elif (r_info.type() == -1):
print("<td>%d<td>-<td>-<td>%s" %
(r_info.type(), str(t_info.origin_shift())))
elif (abs(r_info.type()) == 2):
print("<td>%d<td>%s<td>%s<td>%s" %
(r_info.type(), str_ev(r_info.ev()), str(
t_info.intrinsic_part()), str(t_info.origin_shift())))
else:
print("<td>%d^%d<td>%s<td>%s<td>%s" %
(r_info.type(), r_info.sense(), str_ev(r_info.ev()),
str(t_info.intrinsic_part()), str(t_info.origin_shift())))
print("</tr>")
def possible_point_group_generators(self):
lattice_group = lattice_symmetry.group(self.f_in_p1.unit_cell(),
max_delta=1)
lattice_group.expand_inv(sgtbx.tr_vec((0,0,0)))
rot_parts = set()
decorated_rot_parts = []
for op in lattice_group:
r = op.r()
if r.is_unit_mx(): continue
if op.inverse() in rot_parts: continue
r_info = sgtbx.rot_mx_info(r)
if r_info.type() < -2: continue
rot_parts.add(op)
decorated_rot_parts.append(
(r_info.type() == -1, # inversion shall come first,
list(r_info.ev()).count(0), # axes // to unit cell shall come first
# note Python 2.5- compatibility
r_info.type() == -2, # mirrors preferred.
r.order(), # higher order preferred
op))
decorated_rot_parts.sort()
decorated_rot_parts.reverse()
for item in decorated_rot_parts: yield item[-1]
def __init__(self,
input_symmetry,
angular_tolerance=None,
best_monoclinic_beta=True):
if (angular_tolerance is None):
angular_tolerance = 3
self._all_cells = []
space_group_number = input_symmetry.space_group_info().type().number()
if (space_group_number == 1):
self._cb_op = input_symmetry.change_of_basis_op_to_niggli_cell()
self._symmetry = input_symmetry.change_basis(self._cb_op)
self._all_cells.append(self._symmetry)
return
if (space_group_number < 3 or space_group_number >= 75):
self._cb_op = sgtbx.change_of_basis_op()
self._symmetry = input_symmetry
self._all_cells.append(self._symmetry)
return
standard_info = sgtbx.space_group_info(
symbol=space_group_number,
table_id="A1983")
cb_op_inp_ref = input_symmetry.space_group_info().type().cb_op()
cb_op_std_ref = standard_info.type().cb_op()
cb_op_std_inp = cb_op_inp_ref.inverse() * cb_op_std_ref
assert standard_info.group().change_basis(cb_op_std_inp) == input_symmetry.space_group()
best_cb_op = sgtbx.change_of_basis_op()
best_symmetry = input_symmetry
if (space_group_number <= 15):
two_fold_info = sgtbx.rot_mx_info(input_symmetry.space_group()(1).r())
assert abs(two_fold_info.type()) == 2
ev = list(two_fold_info.ev())
assert ev.count(0) == 2
unique_axis = ev.index(1)
affine = sgtbx.find_affine(input_symmetry.space_group())
for cb_mx in affine.cb_mx():
cb_op = sgtbx.change_of_basis_op(cb_mx).new_denominators(best_cb_op)
alt_symmetry = input_symmetry.change_basis(cb_op)
if (alt_symmetry.space_group() == input_symmetry.space_group()):
if (best_monoclinic_beta and unique_axis == 1):
cb_op_best_beta = alt_symmetry.unit_cell() \
.change_of_basis_op_for_best_monoclinic_beta()
if (not cb_op_best_beta.is_identity_op()):
cb_op.update(cb_op_best_beta)
alt_symmetry = input_symmetry.change_basis(cb_op)
self._all_cells.append(alt_symmetry)
cmp_result = best_symmetry.unit_cell().compare_monoclinic(
other=alt_symmetry.unit_cell(),
unique_axis=unique_axis,
angular_tolerance=angular_tolerance)
if (cmp_result > 0):
best_cb_op = cb_op
best_symmetry = alt_symmetry
else:
assert not str(standard_info).endswith(":2")
affine_group = sgtbx.space_group("P 4 3*").change_basis(
cb_op_std_inp)
for affine_s in affine_group:
cb_op = sgtbx.change_of_basis_op(affine_s) \
.new_denominators(best_cb_op)
alt_symmetry = input_symmetry.change_basis(cb_op)
if (alt_symmetry.space_group() == input_symmetry.space_group()):
self._all_cells.append(alt_symmetry)
cmp_result = best_symmetry.unit_cell().compare_orthorhombic(
alt_symmetry.unit_cell())
if (cmp_result > 0):
best_cb_op = cb_op
best_symmetry = alt_symmetry
self._cb_op = best_cb_op
self._symmetry = best_symmetry
def rlc_RTMxAnalysis(M):
r_info = sgtbx.rot_mx_info(M.r())
t_info = sgtbx.translation_part_info(M)
t_intrinsic = t_info.intrinsic_part().mod_positive().as_double()
t_shift = t_info.origin_shift().mod_positive().as_double()
#End = list_plus(Start + map(None,r_info.ev()))
####debug
### trans = 0
### length = 0
####debug
#if r_info.type() == 1:
if r_info.type() < 2:
#(rt, start, end) = ('1',(0,0,0),(0,0,0))
return None
#elif r_info.type() == -1:
# (rt, start, end) = (str(r_info.type()),t_shift,())
elif abs(r_info.type()) == 2:
trans = sum(t_intrinsic)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()), t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()) + "^1", t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type())+"^1",t_shift,tuple(list_plus(t_shift,r_info.ev())))
elif r_info.type() == 3:
if r_info.sense() >= 0:
# ignore opposite sense of rotation axes since they superimpose
trans = N.sqrt(
sum((map(lambda x, y: (y - x) * (y - x), (0, 0, 0),
t_intrinsic))))
# trans = N.sqrt(t_intrinsic[0]**2 + t_intrinsic[1]**2 + t_intrinsic[2]**2)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
# fudge to make sure that PyMOL actually draws the axis (move it slightly off [1,-1,1]) !!!
r[0] = r[0] * 1.000001
(rt, start, end) = (str(r_info.type()), t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
#(rt, start, end) = (str(r_info.type())+ "^" + subscript ,t_shift,tuple(list_plus(t_shift,r)))
(start, end) = (t_shift, tuple(list_plus(t_shift, r)))
length = N.sqrt(
sum((map(lambda x, y: (y - x) * (y - x), start, end))))
# r_info.sense() for 3^1 and 3^2 seems always to be "1" ???
# if r_info.sense() < 0:
# subscript = str(1-r_info.sense())
# else:
# subscript = str(r_info.sense())
# use ratio of trans to length to get the correct axis symbol:
# fudged the value to get the right numbers. (using length/2., rather than length/3.)
if trans < length * 0.5:
subscript = '1'
else:
subscript = '2'
rt = str(r_info.type()) + "^" + subscript
#(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
### print "Type, sense, Start, End, length, trans", rt, r_info.sense(), start, end, length, trans
# print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length)
# print "(rt, start, end)", (rt,start,end)
else:
return None
#return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
elif r_info.sense() > 0:
# ignore opposite sense of rotation axes since they superimpose
trans = sum(t_intrinsic)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()), t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
subscript = str(int(trans * r_info.type() +
.5)) # add 0.5 to fix rounding errors
(rt, start, end) = (str(r_info.type()) + "^" + subscript, t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
#return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
else:
return None
# print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length),
# print "(rt, start, end)", (rt,start,end)
return (rt, start, end)
def rlc_RTMxAnalysis(M):
r_info = sgtbx.rot_mx_info(M.r())
t_info = sgtbx.translation_part_info(M)
t_intrinsic = t_info.intrinsic_part().mod_positive().as_double()
t_shift = t_info.origin_shift().mod_positive().as_double()
#End = list_plus(Start + map(None,r_info.ev()))
####debug
### trans = 0
### length = 0
####debug
#if (r_info.type() == 1):
if (r_info.type() < 2):
#(rt, start, end) = ('1',(0,0,0),(0,0,0))
return None
#elif (r_info.type() == -1):
# (rt, start, end) = (str(r_info.type()),t_shift,())
elif (abs(r_info.type()) == 2):
trans = reduce(lambda x,y:x+y,t_intrinsic)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type())+"^1",t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type())+"^1",t_shift,tuple(list_plus(t_shift,r_info.ev())))
elif (r_info.type() == 3):
if (r_info.sense() >= 0) :
# ignore opposite sense of rotation axes since they superimpose
trans = N.sqrt(reduce(lambda x,y:x+y,(map(lambda x,y:(y-x)*(y-x),(0,0,0),t_intrinsic))))
# trans = N.sqrt(t_intrinsic[0]**2 + t_intrinsic[1]**2 + t_intrinsic[2]**2)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
# fudge to make sure that PyMOL actually draws the axis (move it slightly off [1,-1,1]) !!!
r[0] = r[0]*1.000001
(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
#(rt, start, end) = (str(r_info.type())+ "^" + subscript ,t_shift,tuple(list_plus(t_shift,r)))
(start, end) = (t_shift,tuple(list_plus(t_shift,r)))
length = N.sqrt(reduce(lambda x,y:x+y,(map(lambda x,y:(y-x)*(y-x),start, end))))
# r_info.sense() for 3^1 and 3^2 seems always to be "1" ???
# if r_info.sense() < 0:
# subscript = str(1-r_info.sense())
# else:
# subscript = str(r_info.sense())
# use ratio of trans to length to get the correct axis symbol:
# fudged the value to get the right numbers. (using length/2., rather than length/3.)
if trans < length*0.5 :
subscript = '1'
else:
subscript = '2'
rt = str(r_info.type())+ "^" + subscript
#(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
### print "Type, sense, Start, End, length, trans", rt, r_info.sense(), start, end, length, trans
# print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length)
# print "(rt, start, end)", (rt,start,end)
else:
return None
#return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
elif (r_info.sense() > 0):
# ignore opposite sense of rotation axes since they superimpose
trans = reduce(lambda x,y:x+y,t_intrinsic)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
subscript = str(int(trans*r_info.type()+.5)) # add 0.5 to fix rounding errors
(rt, start, end) = (str(r_info.type())+ "^" + subscript ,t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
#return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
else:
return None
# print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length),
# print "(rt, start, end)", (rt,start,end)
return (rt, start, end)
def __init__(self,symop): self.symop = symop # an instance of rt_mx from cctbx import sgtbx self.r_info = sgtbx.rot_mx_info(self.symop.r()) self.t_info = sgtbx.translation_part_info(self.symop)
def __init__(self,
input_symmetry,
angular_tolerance=None,
best_monoclinic_beta=True):
if (angular_tolerance is None):
angular_tolerance = 3
self._all_cells = []
space_group_number = input_symmetry.space_group_info().type().number()
if (space_group_number == 1):
self._cb_op = input_symmetry.change_of_basis_op_to_niggli_cell()
self._symmetry = input_symmetry.change_basis(self._cb_op)
self._all_cells.append(self._symmetry)
return
if (space_group_number < 3 or space_group_number >= 75):
self._cb_op = sgtbx.change_of_basis_op()
self._symmetry = input_symmetry
self._all_cells.append(self._symmetry)
return
standard_info = sgtbx.space_group_info(symbol=space_group_number,
table_id="A1983")
cb_op_inp_ref = input_symmetry.space_group_info().type().cb_op()
cb_op_std_ref = standard_info.type().cb_op()
cb_op_std_inp = cb_op_inp_ref.inverse() * cb_op_std_ref
assert standard_info.group().change_basis(
cb_op_std_inp) == input_symmetry.space_group()
best_cb_op = sgtbx.change_of_basis_op()
best_symmetry = input_symmetry
if (space_group_number <= 15):
two_fold_info = sgtbx.rot_mx_info(
input_symmetry.space_group()(1).r())
assert abs(two_fold_info.type()) == 2
ev = list(two_fold_info.ev())
assert ev.count(0) == 2
unique_axis = ev.index(1)
affine = sgtbx.find_affine(input_symmetry.space_group())
for cb_mx in affine.cb_mx():
cb_op = sgtbx.change_of_basis_op(cb_mx).new_denominators(
best_cb_op)
alt_symmetry = input_symmetry.change_basis(cb_op)
if (alt_symmetry.space_group() == input_symmetry.space_group()
):
if (best_monoclinic_beta and unique_axis == 1):
cb_op_best_beta = alt_symmetry.unit_cell() \
.change_of_basis_op_for_best_monoclinic_beta()
if (not cb_op_best_beta.is_identity_op()):
cb_op.update(cb_op_best_beta)
alt_symmetry = input_symmetry.change_basis(cb_op)
self._all_cells.append(alt_symmetry)
cmp_result = best_symmetry.unit_cell().compare_monoclinic(
other=alt_symmetry.unit_cell(),
unique_axis=unique_axis,
angular_tolerance=angular_tolerance)
if (cmp_result > 0):
best_cb_op = cb_op
best_symmetry = alt_symmetry
else:
assert not str(standard_info).endswith(":2")
affine_group = sgtbx.space_group("P 4 3*").change_basis(
cb_op_std_inp)
for affine_s in affine_group:
cb_op = sgtbx.change_of_basis_op(affine_s) \
.new_denominators(best_cb_op)
alt_symmetry = input_symmetry.change_basis(cb_op)
if (alt_symmetry.space_group() == input_symmetry.space_group()
):
self._all_cells.append(alt_symmetry)
cmp_result = best_symmetry.unit_cell(
).compare_orthorhombic(alt_symmetry.unit_cell())
if (cmp_result > 0):
best_cb_op = cb_op
best_symmetry = alt_symmetry
self._cb_op = best_cb_op
self._symmetry = best_symmetry
def __init__(self, symop):
self.symop = symop # an instance of rt_mx
from cctbx import sgtbx
self.r_info = sgtbx.rot_mx_info(self.symop.r())
self.t_info = sgtbx.translation_part_info(self.symop)
