def test_update_rot_tran(self):
"""
Verify correct conversion from angles and translation
to rotation matrices and translations """
# print sys._getframe().f_code.co_name
x = flex.double([
-0.40177529, 1.20019851, 2.64221706, 0.5, -0.5, 0.0,
2.24044161, 1.57079633, 0.0, 0.0, 0.0, 0.0])
self.tr_obj1 = nu.update_rot_tran(
x=x,transforms_obj=self.tr_obj1)
rot_results, tran_results = nu.get_rotation_translation_as_list(
transforms_obj=self.tr_obj1)
rot_expected = [self.rotation1, self.rotation2]
tran_expected = [self.translation1,self.translation2]
assert approx_equal(tran_results,tran_expected,1.0e-4)
assert approx_equal(rot_results,rot_expected,1.0e-4)
def test_update_rot_tran(self):
"""
Verify correct conversion from angles and translation
to rotation matrices and translations """
# print sys._getframe().f_code.co_name
x = flex.double([
-0.40177529, 1.20019851, 2.64221706, 0.5, -0.5, 0.0, 2.24044161,
1.57079633, 0.0, 0.0, 0.0, 0.0
])
self.tr_obj1 = nu.update_rot_tran(x=x, transforms_obj=self.tr_obj1)
rot_results, tran_results = nu.get_rotation_translation_as_list(
transforms_obj=self.tr_obj1)
rot_expected = [self.rotation1, self.rotation2]
tran_expected = [self.translation1, self.translation2]
assert approx_equal(tran_results, tran_expected, 1.0e-4)
assert approx_equal(rot_results, rot_expected, 1.0e-4)
def run(prefix="tst", d_min=1.0):
"""
NCS constraints: xyz, adp, and operators.
"""
pdb_file_name_answer = "%s_answer.pdb"%prefix
of=open(pdb_file_name_answer, "w")
print >> of, pdb_str_answer
of.close()
#
pdb_file_name_poor = "%s_poor.pdb"%prefix
of=open(pdb_file_name_poor, "w")
print >> of, pdb_str_poor
of.close()
#
pdb_inp_answer = iotbx.pdb.input(file_name=pdb_file_name_answer)
ph_answer = pdb_inp_answer.construct_hierarchy()
ph_answer.atoms().reset_i_seq()
xrs_answer = pdb_inp_answer.xray_structure_simple()
#
pdb_inp_poor = iotbx.pdb.input(file_name=pdb_file_name_poor)
ph_poor = pdb_inp_poor.construct_hierarchy()
ph_poor_obj = iotbx.pdb.input(source_info=None, lines=pdb_str_poor2)
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp_poor.xray_structure_simple()
#
ppf = mmtbx.utils.process_pdb_file_srv(log=False).process_pdb_files(
raw_records=pdb_str_poor.splitlines())[0]
mmtbx.utils.assert_xray_structures_equal(
x1=ppf.xray_structure(show_summary = False),
x2=xrs_poor)
restraints_manager = mmtbx.restraints.manager(
geometry = ppf.geometry_restraints_manager(show_energies = False),
normalization = True)
#
fc = xrs_answer.structure_factors(d_min=d_min).f_calc()
fft_map = fc.fft_map(resolution_factor = 0.25)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
#
ncs_obj_poor = mmtbx.ncs.asu_ncs_converter(pdb_hierarchy = ph_answer,
add_identity=True)
ncs_obj_poor.write_pdb_file(file_name="asu.pdb",
crystal_symmetry=xrs_poor.crystal_symmetry(), mode="asu")
rm = ncs_obj_poor.back_rotation_matrices
tv = ncs_obj_poor.back_translation_vectors
ir = [rm[0]]
it = [tv[0]]
# create transformation object
transforms_obj = ncs.input(
hierarchy = ph_poor_obj.construct_hierarchy(),
rotations=rm,
translations=tv)
x = nu.concatenate_rot_tran(transforms_obj=transforms_obj)
x = nu.shake_transformations(
x = x,
shake_angles_sigma=1*math.pi/180,
shake_translation_sigma=0.1)
transforms_obj = nu.update_rot_tran(x=x, transforms_obj=transforms_obj)
rm,tv = nu.get_rotation_translation_as_list(transforms_obj=transforms_obj)
# just to see how result of shaking looks like
rm_ = ir+rm
tv_ = it+tv
ncs_obj_poor.back_rotation_matrices=rm_
ncs_obj_poor.back_translation_vectors=tv_
ncs_obj_poor.update_sites_cart(
sites_cart_master_ncs_copy=ncs_obj_poor.ph_first_chain.atoms().extract_xyz())
ncs_obj_poor.write_pdb_file(file_name="asu2.pdb",
crystal_symmetry=xrs_poor.crystal_symmetry(), mode="asu")
transforms_obj = nu.update_transforms(transforms_obj,rm,tv)
ncs_restraints_group_list = transforms_obj.get_ncs_restraints_group_list()
refine_selection = flex.size_t(xrange(transforms_obj.total_asu_length))
for i in xrange(5):
data_weight = 1
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_real_space(
map_data = map_data,
xray_structure = xrs_poor,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
real_space_gradients_delta = d_min/4,
restraints_manager = restraints_manager,
data_weight = data_weight,
refine_sites = True)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object = tfg_obj,
xray_structure = xrs_poor,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
finite_grad_differences_test = False,
max_iterations = 60,
refine_sites = True)
xrs_poor = tfg_obj.xray_structure
ph_poor.adopt_xray_structure(tfg_obj.xray_structure)
#
ncs_obj_poor = mmtbx.ncs.asu_ncs_converter(pdb_hierarchy = ph_poor,
add_identity=False)
rm,tv = nu.get_rotation_translation_as_list(
ncs_restraints_group_list= ncs_restraints_group_list)
#
ph_poor.write_pdb_file(file_name="refined.pdb")
def run(prefix="tst", d_min=1.0):
"""
NCS constraints: xyz, adp, and operators.
"""
pdb_file_name_answer = "%s_answer.pdb"%prefix
of=open(pdb_file_name_answer, "w")
print >> of, pdb_str_answer
of.close()
#
pdb_file_name_poor = "%s_poor.pdb"%prefix
of=open(pdb_file_name_poor, "w")
print >> of, pdb_str_poor
of.close()
#
pdb_inp_answer = iotbx.pdb.input(file_name=pdb_file_name_answer)
ph_answer = pdb_inp_answer.construct_hierarchy()
ph_answer.atoms().reset_i_seq()
xrs_answer = pdb_inp_answer.xray_structure_simple()
#
pdb_inp_poor = iotbx.pdb.input(file_name=pdb_file_name_poor)
ph_poor = pdb_inp_poor.construct_hierarchy()
ph_poor_obj = iotbx.pdb.hierarchy.input(pdb_string=pdb_str_poor2)
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp_poor.xray_structure_simple()
#
ppf = mmtbx.utils.process_pdb_file_srv(log=False).process_pdb_files(
raw_records=pdb_str_poor.splitlines())[0]
mmtbx.utils.assert_xray_structures_equal(
x1=ppf.xray_structure(show_summary = False),
x2=xrs_poor)
restraints_manager = mmtbx.restraints.manager(
geometry = ppf.geometry_restraints_manager(show_energies = False),
normalization = True)
#
fc = xrs_answer.structure_factors(d_min=d_min).f_calc()
fft_map = fc.fft_map(resolution_factor = 0.25)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
#
ncs_obj_poor = mmtbx.ncs.asu_ncs_converter(pdb_hierarchy = ph_answer,
add_identity=True)
ncs_obj_poor.write_pdb_file(file_name="asu.pdb",
crystal_symmetry=xrs_poor.crystal_symmetry(), mode="asu")
rm = ncs_obj_poor.back_rotation_matrices
tv = ncs_obj_poor.back_translation_vectors
ir = [rm[0]]
it = [tv[0]]
# create transformation object
transforms_obj = ncs.input(
pdb_hierarchy_inp = ph_poor_obj,
rotations=rm,
translations=tv)
x = nu.concatenate_rot_tran(transforms_obj=transforms_obj)
x = nu.shake_transformations(
x = x,
shake_angles_sigma=1*math.pi/180,
shake_translation_sigma=0.1)
transforms_obj = nu.update_rot_tran(x=x, transforms_obj=transforms_obj)
rm,tv = nu.get_rotation_translation_as_list(transforms_obj=transforms_obj)
# just to see how result of shaking looks like
rm_ = ir+rm
tv_ = it+tv
ncs_obj_poor.back_rotation_matrices=rm_
ncs_obj_poor.back_translation_vectors=tv_
ncs_obj_poor.update_sites_cart(
sites_cart_master_ncs_copy=ncs_obj_poor.ph_first_chain.atoms().extract_xyz())
ncs_obj_poor.write_pdb_file(file_name="asu2.pdb",
crystal_symmetry=xrs_poor.crystal_symmetry(), mode="asu")
transforms_obj = nu.update_transforms(transforms_obj,rm,tv)
ncs_restraints_group_list = transforms_obj.get_ncs_restraints_group_list()
refine_selection = flex.size_t(xrange(transforms_obj.total_asu_length))
for i in xrange(5):
data_weight = 1
for action in [[False, True], [True, False]]:
refine_sites, refine_transformations = action
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_real_space(
map_data = map_data,
xray_structure = xrs_poor,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
real_space_gradients_delta = d_min/4,
restraints_manager = restraints_manager,
data_weight = data_weight,
refine_sites = refine_sites,
refine_transformations = refine_transformations)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object = tfg_obj,
xray_structure = xrs_poor,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
finite_grad_differences_test = False,
max_iterations = 60,
refine_sites = refine_sites,
refine_transformations = refine_transformations)
xrs_poor = tfg_obj.xray_structure
ph_poor.adopt_xray_structure(tfg_obj.xray_structure)
#
ncs_obj_poor = mmtbx.ncs.asu_ncs_converter(pdb_hierarchy = ph_poor,
add_identity=False)
rm,tv = nu.get_rotation_translation_as_list(
ncs_restraints_group_list= ncs_restraints_group_list)
#
ph_poor.write_pdb_file(file_name="refined.pdb")
