def find_space_group(self):
decorated_symmetry_pool = []
denominator = 12**3
for i, (r, d) in enumerate(self.cross_correlation_peaks()):
t = sgtbx.tr_vec((d * denominator).as_int(), tr_den=denominator)
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(r, t))
phi_sym = self.f_in_p1.symmetry_agreement_factor(
cb_op, assert_is_similar_symmetry=False)
if phi_sym < self.phi_sym_acceptance_cutoff:
status = possible_symmetry.accepted
elif phi_sym < self.phi_sym_rejection_cutoff:
status = possible_symmetry.unsure
else:
status = possible_symmetry.rejected
decorated_symmetry_pool.append(
(-status, i, possible_symmetry(r, d, phi_sym, status)))
decorated_symmetry_pool.sort()
self.symmetry_pool = [item[-1] for item in decorated_symmetry_pool]
self.origin = mat.mutable_zeros(3)
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.set_components_of_global_origin(self.origin)
if self.origin.elems.count(0) == 0: break
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.change_origin(self.origin)
self.space_group.expand_smx(symm.rt)
def find_space_group(self):
decorated_symmetry_pool = []
denominator = 12**3
for i, (r, d) in enumerate(self.cross_correlation_peaks()):
t = sgtbx.tr_vec((d*denominator).as_int(), tr_den=denominator)
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(r, t))
phi_sym = self.f_in_p1.symmetry_agreement_factor(
cb_op, assert_is_similar_symmetry=False)
if phi_sym < self.phi_sym_acceptance_cutoff:
status = possible_symmetry.accepted
elif phi_sym < self.phi_sym_rejection_cutoff:
status = possible_symmetry.unsure
else:
status = possible_symmetry.rejected
decorated_symmetry_pool.append(
(-status, i, possible_symmetry(r, d, phi_sym, status)))
decorated_symmetry_pool.sort()
self.symmetry_pool = [ item[-1] for item in decorated_symmetry_pool ]
self.origin = mat.mutable_zeros(3)
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.set_components_of_global_origin(self.origin)
if self.origin.elems.count(0) == 0: break
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.change_origin(self.origin)
self.space_group.expand_smx(symm.rt)
def change_of_basis_op_to(self, other):
""" The change of basis from self to other.
This method strives to return a mere origin shift.
"""
self_to_ref_op = self.change_of_basis_op_to_reference_setting()
other_to_ref_op = other.change_of_basis_op_to_reference_setting()
# early exit if other is not the same space group in a different setting
self_as_reference = self.change_basis(self_to_ref_op)
other_as_reference = other.change_basis(other_to_ref_op)
if self_as_reference.group() != other_as_reference.group(): return None
# the obvious answer: if it is a mere shift, return it
obvious_result = other_to_ref_op.inverse() * self_to_ref_op
if obvious_result.c().r().is_unit_mx(): return obvious_result
# otherwise, let's try to find an origin shift by hand
# see test case exercise_change_of_basis_between_arbitrary_space_groups
# in regression/tst_sgtbx.py for the motivation for this code.
self_z2p_op = self.change_of_basis_op_to_primitive_setting()
other_z2p_op = other.change_of_basis_op_to_primitive_setting()
primitive_self = self.change_basis(self_z2p_op)
primitive_other = other.change_basis(other_z2p_op)
if (set([op.r() for op in primitive_self.group()
]) == set([op.r() for op in primitive_other.group()])):
self_tr_info_for_r = dict([(op.r(), translation_part_info(op))
for op in primitive_self.group()])
origin_shift = matrix.mutable_zeros(3)
for op in primitive_other.group():
self_ti = self_tr_info_for_r[op.r()]
other_ti = translation_part_info(op)
if self_ti.intrinsic_part() != other_ti.intrinsic_part():
origin_shift = None
break
delta = other_ti.origin_shift().minus(
self_ti.origin_shift()).mod_positive()
delta_num = delta.num()
for i in range(3):
if origin_shift[i] == 0:
origin_shift[i] = 24 // delta.den() * delta_num[i]
if origin_shift.elems.count(0) == 0: break
if origin_shift is not None:
origin_shift = tr_vec(origin_shift, tr_den=24)
if not origin_shift.is_zero():
cb_op = change_of_basis_op(
rt_mx(origin_shift)).new_denominators(24, 144)
cb_op = other_z2p_op.inverse() * cb_op * self_z2p_op
cb_op.mod_positive_in_place()
tentative_other = self.change_basis(cb_op)
if tentative_other.group() == other.group():
return cb_op
# no origin shift has been found, so return the obvious answer
return obvious_result
def change_of_basis_op_to(self, other):
""" The change of basis from self to other.
This method strives to return a mere origin shift.
"""
self_to_ref_op = self.change_of_basis_op_to_reference_setting()
other_to_ref_op = other.change_of_basis_op_to_reference_setting()
# early exit if other is not the same space group in a different setting
self_as_reference = self.change_basis(self_to_ref_op)
other_as_reference = other.change_basis(other_to_ref_op)
if self_as_reference.group() != other_as_reference.group(): return None
# the obvious answer: if it is a mere shift, return it
obvious_result = other_to_ref_op.inverse()*self_to_ref_op
if obvious_result.c().r().is_unit_mx(): return obvious_result
# otherwise, let's try to find an origin shift by hand
# see test case exercise_change_of_basis_between_arbitrary_space_groups
# in regression/tst_sgtbx.py for the motivation for this code.
self_z2p_op = self.change_of_basis_op_to_primitive_setting()
other_z2p_op = other.change_of_basis_op_to_primitive_setting()
primitive_self = self.change_basis(self_z2p_op)
primitive_other = other.change_basis(other_z2p_op)
if ( set([ op.r() for op in primitive_self.group() ])
== set([ op.r() for op in primitive_other.group() ])):
self_tr_info_for_r = dict([ (op.r(), translation_part_info(op))
for op in primitive_self.group() ])
origin_shift = matrix.mutable_zeros(3)
for op in primitive_other.group():
self_ti = self_tr_info_for_r[op.r()]
other_ti = translation_part_info(op)
if self_ti.intrinsic_part() != other_ti.intrinsic_part():
origin_shift = None
break
delta = other_ti.origin_shift().minus(
self_ti.origin_shift()).mod_positive()
delta_num = delta.num()
for i in xrange(3):
if origin_shift[i] == 0:
origin_shift[i] = 24//delta.den()*delta_num[i]
if origin_shift.elems.count(0) == 0: break
if origin_shift is not None:
origin_shift = tr_vec(origin_shift, tr_den=24)
if not origin_shift.is_zero():
cb_op = change_of_basis_op(
rt_mx(origin_shift)).new_denominators(24, 144)
cb_op = other_z2p_op.inverse()*cb_op*self_z2p_op
cb_op.mod_positive_in_place()
tentative_other = self.change_basis(cb_op)
if tentative_other.group() == other.group():
return cb_op
# no origin shift has been found, so return the obvious answer
return obvious_result
