def run_test(self):
# Refinement
params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
params.algorithm = "direct"
# Get the xray_structure of the shaken ASU
xrs_shaken_asu, dummy, transform_info, ph, ph2 = step_1(
file_name="one_ncs_in_asu_shaken.pdb",
crystal_symmetry=self.xrs_one_ncs.crystal_symmetry(),
write_name='asu_shaken.pdb')
tr_obj = iotbx.ncs.input(
hierarchy = ph,
transform_info = transform_info,
exclude_selection=None)
self.ncs_restraints_group_list = tr_obj.get_ncs_restraints_group_list()
# refine both ncs related and not related atoms
self.refine_selection = flex.size_t(range(tr_obj.total_asu_length))
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=tr_obj.get_ncs_restraints_group_list(),
refine_selection=self.refine_selection)
assert self.refine_selection.size() == 21, self.refine_selection.size()
self.fmodel = mmtbx.f_model.manager(
f_obs = self.f_obs,
r_free_flags = self.r_free_flags,
xray_structure = xrs_shaken_asu,
sf_and_grads_accuracy_params = params,
target_name = "ls_wunit_k1")
r_start = self.fmodel.r_work()
assert r_start > 0.1, r_start
print "start r_factor: %6.4f" % r_start
for macro_cycle in xrange(self.n_macro_cycle):
data_weight = None
if(self.use_geometry_restraints):
self.transformations=False
data_weight = nu.get_weight(minimized_obj=self)
target_and_grads_object = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_reciprocal_space(
fmodel = self.fmodel,
ncs_restraints_group_list = self.ncs_restraints_group_list,
refine_selection = self.refine_selection,
restraints_manager = self.grm,
data_weight = data_weight,
refine_sites = self.sites,
refine_u_iso = self.u_iso,
iso_restraints = self.iso_restraints)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object = target_and_grads_object,
xray_structure = self.fmodel.xray_structure,
ncs_restraints_group_list = self.ncs_restraints_group_list,
refine_selection = self.refine_selection,
finite_grad_differences_test = self.finite_grad_differences_test,
max_iterations = 100,
refine_sites = self.sites,
refine_u_iso = self.u_iso)
refine_type = 'adp'*self.u_iso + 'sites'*self.sites
outstr = " macro_cycle {0:3} ({1}) r_factor: {2:6.4f} " + \
self.finite_grad_differences_test * \
"finite_grad_difference_val: {3:.4f}"
print outstr.format(
macro_cycle, refine_type,self.fmodel.r_work(),
minimized.finite_grad_difference_val)
assert (minimized.finite_grad_difference_val < 1.0e-3)
assert approx_equal(self.fmodel.r_work(), target_and_grads_object.fmodel.r_work())
# break test if r_work is very small
if target_and_grads_object.fmodel.r_work() < 1.0e-6: break
# check results
if(self.u_iso):
assert approx_equal(self.fmodel.r_work(), 0, 1.e-5)
elif(self.sites):
if(self.use_geometry_restraints):
assert approx_equal(self.fmodel.r_work(), 0, 0.00018)
else:
assert approx_equal(self.fmodel.r_work(), 0, 3.e-4)
else: assert 0
# output refined model
xrs_refined = self.fmodel.xray_structure
output_file_name = "refined_u_iso%s_sites%s.pdb"%(str(self.u_iso),
str(self.sites))
assert ph2.atoms().size() == self.fmodel.xray_structure.scatterers().size()
ph2.atoms().set_xyz(self.fmodel.xray_structure.sites_cart())
ph2.atoms().set_b(
self.fmodel.xray_structure.extract_u_iso_or_u_equiv()*adptbx.u_as_b(1.))
ph2.write_pdb_file(file_name = output_file_name,
crystal_symmetry=self.fmodel.xray_structure.crystal_symmetry())
self.test_files_names.append(output_file_name)
# check final model
if(not self.use_geometry_restraints):
# XXX fix later for case self.use_geometry_restraints=True
pdb_inp_answer = iotbx.pdb.input(source_info=None, lines=ncs_1_copy)
pdb_inp_refined = iotbx.pdb.input(file_name=output_file_name)
xrs1 = pdb_inp_answer.xray_structure_simple(
crystal_symmetry=self.fmodel.xray_structure.crystal_symmetry())
xrs2 = pdb_inp_refined.xray_structure_simple().select(
minimized.extended_ncs_selection)
print xrs1.crystal_symmetry().unit_cell().parameters()
print xrs2.crystal_symmetry().unit_cell().parameters()
mmtbx.utils.assert_xray_structures_equal(
x1 = xrs1,
x2 = xrs2,
sites = False)
delta = flex.vec3_double([xrs1.center_of_mass()]*xrs2.scatterers().size())-\
flex.vec3_double([xrs2.center_of_mass()]*xrs2.scatterers().size())
xrs2.set_sites_cart(sites_cart = xrs2.sites_cart()+delta)
mmtbx.utils.assert_xray_structures_equal(
x1 = xrs1,
x2 = xrs2,
eps=1.e-4)
def run_test(self):
# Refinement
params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
params.algorithm = "direct"
# Get the xray_structure of the shaken ASU
m_shaken = multimer(
file_name="one_ncs_in_asu_shaken.pdb",
round_coordinates=False,
reconstruction_type='cau',error_handle=True,eps=1e-2)
xrs_shaken_asu = m_shaken.assembled_multimer.extract_xray_structure(
crystal_symmetry=self.xrs_one_ncs.crystal_symmetry())
# force non-rounded coordinates into xray structure
xrs_shaken_asu.set_sites_cart(m_shaken.sites_cart())
# Save the shaken ASU for inspection
m_shaken.write(
pdb_output_file_name='asu_shaken.pdb',
crystal_symmetry=self.xrs_one_ncs.crystal_symmetry())
tr_obj = m_shaken.transforms_obj
self.ncs_restraints_group_list = tr_obj.get_ncs_restraints_group_list()
# refine both ncs related and not related atoms
self.refine_selection = flex.size_t(range(tr_obj.total_asu_length))
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=tr_obj.get_ncs_restraints_group_list(),
refine_selection=self.refine_selection)
assert self.refine_selection.size() == 21
self.fmodel = mmtbx.f_model.manager(
f_obs = self.f_obs,
r_free_flags = self.r_free_flags,
xray_structure = xrs_shaken_asu,
sf_and_grads_accuracy_params = params,
target_name = "ls_wunit_k1")
r_start = self.fmodel.r_work()
assert r_start > 0.1, r_start
print "start r_factor: %6.4f" % r_start
for macro_cycle in xrange(self.n_macro_cycle):
if self.transformations and \
not self.ncs_restraints_group_list: continue
data_weight = None
if(self.use_geometry_restraints):
data_weight = nu.get_weight(minimized_obj=self)
target_and_grads_object = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_reciprocal_space(
fmodel = self.fmodel,
ncs_restraints_group_list = self.ncs_restraints_group_list,
refine_selection = self.refine_selection,
restraints_manager = self.grm,
data_weight = data_weight,
refine_sites = self.sites,
refine_u_iso = self.u_iso,
refine_transformations = self.transformations,
iso_restraints = self.iso_restraints)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object = target_and_grads_object,
xray_structure = self.fmodel.xray_structure,
ncs_restraints_group_list = self.ncs_restraints_group_list,
refine_selection = self.refine_selection,
finite_grad_differences_test = self.finite_grad_differences_test,
max_iterations = 100,
refine_sites = self.sites,
refine_u_iso = self.u_iso,
refine_transformations = self.transformations)
refine_type = 'adp'*self.u_iso + 'sites'*self.sites \
+ 'transformation'*self.transformations
outstr = " macro_cycle {0:3} ({1}) r_factor: {2:6.4f} " + \
self.finite_grad_differences_test * \
"finite_grad_difference_val: {3:.4f}"
print outstr.format(
macro_cycle, refine_type,self.fmodel.r_work(),
minimized.finite_grad_difference_val)
assert (minimized.finite_grad_difference_val < 1.0e-3)
assert approx_equal(self.fmodel.r_work(), target_and_grads_object.fmodel.r_work())
# break test if r_work is very small
if target_and_grads_object.fmodel.r_work() < 1.0e-6: break
# check results
if(self.u_iso):
assert approx_equal(self.fmodel.r_work(), 0, 1.e-5)
elif(self.sites):
if(self.use_geometry_restraints):
assert approx_equal(self.fmodel.r_work(), 0, 0.00015)
else:
assert approx_equal(self.fmodel.r_work(), 0, 1.e-5)
elif self.transformations:
assert approx_equal(self.fmodel.r_work(), 0, 0.0001)
else: assert 0
# output refined model
xrs_refined = self.fmodel.xray_structure
m_shaken.assembled_multimer.adopt_xray_structure(self.fmodel.xray_structure)
output_file_name = "refined_u_iso%s_sites%s.pdb"%(str(self.u_iso),
str(self.sites))
m_shaken.write(output_file_name)
self.test_files_names.append(output_file_name)
# check final model
if(not self.use_geometry_restraints):
# XXX fix later for case self.use_geometry_restraints=True
pdb_inp_answer = iotbx.pdb.input(source_info=None, lines=ncs_1_copy)
pdb_inp_refined = iotbx.pdb.input(file_name=output_file_name)
xrs1 = pdb_inp_answer.xray_structure_simple()
xrs2 = pdb_inp_refined.xray_structure_simple().select(
minimized.extended_ncs_selection)
mmtbx.utils.assert_xray_structures_equal(
x1 = xrs1,
x2 = xrs2,
sites = False)
delta = flex.vec3_double([xrs1.center_of_mass()]*xrs2.scatterers().size())-\
flex.vec3_double([xrs2.center_of_mass()]*xrs2.scatterers().size())
xrs2.set_sites_cart(sites_cart = xrs2.sites_cart()+delta)
mmtbx.utils.assert_xray_structures_equal(
x1 = xrs1,
x2 = xrs2)