def refinable_params_one_ncs_to_asu(self, x=None):
"""
Expand refinabale parameters corresponding to one NCS copy to parameters
corresponding to whole ASU.
"""
x_old = self.xray_structure.sites_cart()
if not x: x = self.x
if self.refine_sites or self.refine_transformations:
if self.use_ncs_constraints or self.refine_transformations:
new_x = nu.apply_transforms(
ncs_coordinates=flex.vec3_double(x),
ncs_restraints_group_list=self.ncs_restraints_group_list,
total_asu_length=x_old.size(),
extended_ncs_selection=self.extended_ncs_selection,
round_coordinates=False,
center_of_coordinates=self.ncs_groups_coordinates_centers)
new_x = new_x.select(self.refine_selection)
new_x = x_old.set_selected(self.refine_selection, new_x)
else:
new_x = self.x
return new_x.as_double()
elif self.refine_u_iso:
if self.use_ncs_constraints:
return grads_one_ncs_to_asu(
ncs_restraints_group_list=self.ncs_restraints_group_list,
extended_ncs_selection=self.extended_ncs_selection,
total_asu_length=x_old.size(),
master_grad=x)
else:
return flex.double(list(x))
def refinable_params_one_ncs_to_asu(self, x=None):
"""
Expand refinabale parameters corresponding to one NCS copy to parameters
corresponding to whole ASU.
"""
x_old = self.xray_structure.sites_cart()
if not x : x = self.x
if self.refine_sites or self.refine_transformations:
if self.use_ncs_constraints or self.refine_transformations:
new_x = nu.apply_transforms(
ncs_coordinates = flex.vec3_double(x),
ncs_restraints_group_list = self.ncs_restraints_group_list,
total_asu_length = x_old.size(),
extended_ncs_selection = self.extended_ncs_selection,
round_coordinates = False,
center_of_coordinates = self.ncs_groups_coordinates_centers)
new_x = new_x.select(self.refine_selection)
new_x = x_old.set_selected(self.refine_selection,new_x)
else:
new_x = self.x
return new_x.as_double()
elif self.refine_u_iso:
if self.use_ncs_constraints:
return grads_one_ncs_to_asu(
ncs_restraints_group_list = self.ncs_restraints_group_list,
extended_ncs_selection = self.extended_ncs_selection,
total_asu_length = x_old.size(),
master_grad = x)
else:
return flex.double(list(x))
def test_MTRIX(self):
'''Test MTRIX record processing'''
# print sys._getframe().f_code.co_name
cau_expected_results = [
[1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [-0.366025, 1.366025, 1.0], [-1.366025, 0.366025, 1.0],
[1.0, 1.5, 1.0], [94.618, -5.253, 91.582],
[94.618, -91.582, -5.253], [51.858229, 79.315053, 91.582], [-42.759771, 84.568053, 91.582],
[94.618, -4.753, 91.582], [62.395, 51.344, 80.786],
[62.395, -80.786, 51.344], [-13.267688, 79.70763, 80.786], [-75.662688, 28.36363, 80.786],
[62.395, 51.844, 80.786], [39.954, 51.526, 72.372],
[39.954, -72.372, 51.526], [-24.645804, 60.364163, 72.372], [-64.599804, 8.838163, 72.372],
[39.954, 52.026, 72.372]]
# use MTRIX data
multimer_data = multimer(
file_name='multimer_test_data.pdb',
reconstruction_type='cau')
cau_multimer_xyz = list(multimer_data.sites_cart())
cau_multimer_xyz.sort()
cau_expected_results.sort()
assert approx_equal(cau_expected_results,cau_multimer_xyz,eps=0.001)
# Test that the number of MTRIX record to process is correct
self.assertEqual(multimer_data.number_of_transforms,4)
# Test getting non-rounded ASU
source_xyz = multimer_data.get_ncs_hierarchy().atoms().extract_xyz()
xyz = apply_transforms(
ncs_coordinates = source_xyz,
ncs_restraints_group_list = multimer_data.get_ncs_restraints_group_list(),
total_asu_length = multimer_data.total_asu_length(),
extended_ncs_selection = flex.size_t_range(source_xyz.size()),
round_coordinates=False)
cau_multimer_xyz = list(xyz)
cau_multimer_xyz.sort()
assert approx_equal(cau_expected_results,cau_multimer_xyz,eps=0.00001)
# Test multimer without rounding
multimer_data = multimer(
file_name='multimer_test_data.pdb',
round_coordinates=False,
reconstruction_type='cau')
cau_multimer_xyz = list(multimer_data.sites_cart())
cau_multimer_xyz.sort()
cau_expected_results.sort()
assert approx_equal(cau_expected_results,cau_multimer_xyz,eps=0.00001)