def __init__(self,
map_data,
xray_structure,
ncs_restraints_group_list,
real_space_gradients_delta,
refine_selection=None,
use_ncs_constraints=True,
restraints_manager=None,
data_weight=None,
refine_sites=False,
refine_transformations=False):
adopt_init_args(self, locals())
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection,
number_of_atoms=self.xray_structure.sites_cart().size())
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=self.refine_selection)
self.unit_cell = self.xray_structure.unit_cell()
# get selection to refine
asu_size = xray_structure.scatterers().size()
if refine_sites:
# Use all atoms to refine
self.selection = flex.bool(asu_size, refine_selection)
elif refine_transformations:
# use only NCS related atoms (Without the Master NCS copy)
self.selection = nu.get_ncs_related_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
asu_size=asu_size)
def __init__(self,
fmodel,
ncs_restraints_group_list,
refine_selection=None,
use_ncs_constraints=True,
restraints_manager=None,
data_weight=None,
refine_sites=False,
refine_u_iso=False,
refine_transformations=False,
iso_restraints=None,
use_hd=False):
adopt_init_args(self, locals())
asu_size = self.fmodel.xray_structure.sites_cart().size()
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection, number_of_atoms=asu_size)
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=self.refine_selection)
self.fmodel.xray_structure.scatterers().flags_set_grads(state=False)
self.x_target_functor = self.fmodel.target_functor()
self.xray_structure = self.fmodel.xray_structure
if self.refine_sites:
xray.set_scatterer_grad_flags(
scatterers=self.fmodel.xray_structure.scatterers(), site=True)
elif self.refine_u_iso:
xray.set_scatterer_grad_flags(
scatterers=self.fmodel.xray_structure.scatterers(), u_iso=True)
elif self.refine_transformations:
xray.set_scatterer_grad_flags(
scatterers=self.fmodel.xray_structure.scatterers(), site=True)
def __init__(
self,
map_data,
xray_structure,
ncs_restraints_group_list,
real_space_gradients_delta,
refine_selection=None,
use_ncs_constraints=True,
restraints_manager=None,
data_weight=None,
refine_sites=False,
refine_transformations=False):
adopt_init_args(self, locals())
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection,
number_of_atoms=self.xray_structure.sites_cart().size())
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=self.refine_selection)
self.unit_cell = self.xray_structure.unit_cell()
# get selection to refine
asu_size = xray_structure.scatterers().size()
if refine_sites:
# Use all atoms to refine
self.selection = flex.bool(asu_size, refine_selection)
elif refine_transformations:
# use only NCS related atoms (Without the Master NCS copy)
self.selection = nu.get_ncs_related_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
asu_size=asu_size)
def test_ncs_selection(self):
"""
verify that extended_ncs_selection, which include the master ncs copy and
the portion of the protein we want to refine.
"""
# print sys._getframe().f_code.co_name
refine_selection = flex.size_t(range(30))
result = nu.get_extended_ncs_selection(
ncs_restraints_group_list=self.ncs_restraints_group_list,
refine_selection=refine_selection)
expected = [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29]
assert list(result) == expected
def test_ncs_selection(self):
"""
verify that extended_ncs_selection, which include the master ncs copy and
the portion of the protein we want to refine.
"""
# print sys._getframe().f_code.co_name
refine_selection = flex.size_t(range(30))
result = nu.get_extended_ncs_selection(
ncs_restraints_group_list=self.ncs_restraints_group_list,
refine_selection=refine_selection)
expected = [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29]
assert list(result) == expected
def __init__(self,
xray_structure,
ncs_restraints_group_list,
refine_selection=None,
use_ncs_constraints=True,
restraints_manager=None,
refine_sites=False,
refine_transformations=False):
adopt_init_args(self, locals())
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection,
number_of_atoms=self.xray_structure.sites_cart().size())
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=self.refine_selection)
self.unit_cell = self.xray_structure.unit_cell()
def __init__(
self,
xray_structure,
ncs_restraints_group_list,
refine_selection=None,
use_ncs_constraints=True,
restraints_manager=None,
refine_sites=False,
refine_transformations=False):
adopt_init_args(self, locals())
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection,
number_of_atoms=self.xray_structure.sites_cart().size())
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=self.refine_selection)
self.unit_cell = self.xray_structure.unit_cell()
def __init__(self,
map_data,
xray_structure,
ncs_restraints_group_list,
real_space_gradients_delta,
refine_selection=None,
use_ncs_constraints=True,
restraints_manager=None,
data_weight=None,
refine_sites=False):
adopt_init_args(self, locals())
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection,
number_of_atoms=self.xray_structure.sites_cart().size())
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=self.refine_selection)
self.unit_cell = self.xray_structure.unit_cell()
# get selection to refine
asu_size = xray_structure.scatterers().size()
self.selection = flex.bool(asu_size, refine_selection)
def test_grads_one_ncs_to_asu(self):
# No more NAGs in NCS selection
# print sys._getframe().f_code.co_name
pdb_inp = iotbx.pdb.input(lines=test_pdb_1,source_info=None)
ncs_inp = ncs.input(hierarchy=pdb_inp.construct_hierarchy(),
exclude_selection=None)
pdb_inp = iotbx.pdb.input(source_info=None, lines=test_pdb_1)
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
#
nrgl = ncs_inp.get_ncs_restraints_group_list()
asu_length = ncs_inp.total_asu_length
#
refine_selection = nu.get_refine_selection(number_of_atoms=asu_length)
extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=nrgl,
refine_selection=refine_selection)
#
self.assertEqual(asu_length, ph.atoms_size())
self.assertEqual(asu_length, 18)
#
xrs_one_ncs_copy = xrs.select(extended_ncs_selection)
master_grad = xrs_one_ncs_copy.extract_u_iso_or_u_equiv()
#
g = grads_one_ncs_to_asu(
ncs_restraints_group_list=nrgl,
total_asu_length=asu_length,
extended_ncs_selection=extended_ncs_selection,
master_grad=master_grad)
#
self.assertEqual(g.size(),18)
masters = [[0,1,12],[2, 3, 13]]
copies = [[[4, 5, 14],[8, 9, 16]],[[6, 7, 15],[10, 11, 17]]]
for m,cs in zip(masters,copies):
ml = list(g.select(flex.size_t(m)))
for c in cs:
cl = list(g.select(flex.size_t(c)))
self.assertEqual(ml,cl)
def __init__(
self,
fmodel,
ncs_restraints_group_list,
refine_selection=None,
use_ncs_constraints=True,
restraints_manager=None,
data_weight=None,
refine_sites=False,
refine_u_iso=False,
refine_transformations=False,
iso_restraints = None,
use_hd = False):
adopt_init_args(self, locals())
asu_size = self.fmodel.xray_structure.sites_cart().size()
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection,
number_of_atoms=asu_size)
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=self.refine_selection)
self.fmodel.xray_structure.scatterers().flags_set_grads(state=False)
self.x_target_functor = self.fmodel.target_functor()
self.xray_structure = self.fmodel.xray_structure
if self.refine_sites:
xray.set_scatterer_grad_flags(
scatterers = self.fmodel.xray_structure.scatterers(),
site = True)
elif self.refine_u_iso:
xray.set_scatterer_grad_flags(
scatterers = self.fmodel.xray_structure.scatterers(),
u_iso = True)
elif self.refine_transformations:
xray.set_scatterer_grad_flags(
scatterers = self.fmodel.xray_structure.scatterers(),
site = True)
def test_grads_one_ncs_to_asu(self):
# No more NAGs in NCS selection
# print sys._getframe().f_code.co_name
pdb_inp = iotbx.pdb.input(lines=test_pdb_1, source_info=None)
ncs_inp = ncs.input(hierarchy=pdb_inp.construct_hierarchy(),
exclude_selection=None)
pdb_inp = iotbx.pdb.input(source_info=None, lines=test_pdb_1)
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
#
nrgl = ncs_inp.get_ncs_restraints_group_list()
asu_length = ncs_inp.total_asu_length
#
refine_selection = nu.get_refine_selection(number_of_atoms=asu_length)
extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=nrgl, refine_selection=refine_selection)
#
self.assertEqual(asu_length, ph.atoms_size())
self.assertEqual(asu_length, 18)
#
xrs_one_ncs_copy = xrs.select(extended_ncs_selection)
master_grad = xrs_one_ncs_copy.extract_u_iso_or_u_equiv()
#
g = grads_one_ncs_to_asu(ncs_restraints_group_list=nrgl,
total_asu_length=asu_length,
extended_ncs_selection=extended_ncs_selection,
master_grad=master_grad)
#
self.assertEqual(g.size(), 18)
masters = [[0, 1, 12], [2, 3, 13]]
copies = [[[4, 5, 14], [8, 9, 16]], [[6, 7, 15], [10, 11, 17]]]
for m, cs in zip(masters, copies):
ml = list(g.select(flex.size_t(m)))
for c in cs:
cl = list(g.select(flex.size_t(c)))
self.assertEqual(ml, cl)
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 __init__(self,
ncs_restraints_group_list,
target_and_grads_object,
xray_structure,
refine_selection=None,
finite_grad_differences_test=False,
finite_grad_difference_val=0,
max_iterations=35,
refine_sites=False,
refine_u_iso=False,
refine_transformations=False):
"""
NCS constrained ADP and coordinates refinement. Also refines NCS operators.
"""
adopt_init_args(self,
args=locals(),
exclude=['ncs_restraints_group_list'])
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection,
number_of_atoms=self.xray_structure.sites_cart().size())
self.use_ncs_constraints = target_and_grads_object.use_ncs_constraints
self.ncs_restraints_group_list = nu.ncs_restraints_group_list_copy(
ncs_restraints_group_list)
self.ncs_groups_coordinates_centers = []
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=self.ncs_restraints_group_list,
refine_selection=self.refine_selection)
assert [
self.refine_sites, self.refine_u_iso, self.refine_transformations
].count(True) == 1
self.total_asu_length = len(xray_structure.sites_cart())
traditional_convergence_test_eps = 1.0e-6
if self.use_ncs_constraints:
xray_structure_one_ncs_copy = xray_structure.select(
self.extended_ncs_selection)
else:
xray_structure_one_ncs_copy = xray_structure.select(
self.refine_selection)
if self.refine_sites:
self.x = xray_structure_one_ncs_copy.sites_cart().as_double()
elif self.refine_u_iso:
assert xray_structure_one_ncs_copy.scatterers().size() == \
xray_structure_one_ncs_copy.use_u_iso().count(True)
self.x = xray_structure_one_ncs_copy.extract_u_iso_or_u_equiv()
elif self.refine_transformations:
# move refinable parameters to coordinate center
self.ncs_groups_coordinates_centers = nu.get_ncs_groups_centers(
xray_structure=self.xray_structure,
ncs_restraints_group_list=self.ncs_restraints_group_list)
self.ncs_restraints_group_list = nu.shift_translation_to_center(
shifts=self.ncs_groups_coordinates_centers,
ncs_restraints_group_list=self.ncs_restraints_group_list)
self.x = nu.concatenate_rot_tran(
ncs_restraints_group_list=self.ncs_restraints_group_list)
minimizer = scitbx.lbfgs.run(
target_evaluator=self,
termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=max_iterations,
traditional_convergence_test_eps=
traditional_convergence_test_eps),
exception_handling_params=scitbx.lbfgs.
exception_handling_parameters(
ignore_line_search_failed_rounding_errors=True,
ignore_line_search_failed_step_at_lower_bound=True,
ignore_line_search_failed_maxfev=True))
# change transforms to the original coordinate system
if self.refine_transformations:
self.ncs_restraints_group_list = nu.shift_translation_back_to_place(
shifts=self.ncs_groups_coordinates_centers,
ncs_restraints_group_list=self.ncs_restraints_group_list)
if (getattr(self.target_and_grads_object, "finalize", None)):
self.target_and_grads_object.finalize()
# pass the refined ncs_restraints_group_list to original object
for g1, g2 in zip(ncs_restraints_group_list,
self.ncs_restraints_group_list):
for tr1, tr2 in zip(g1.copies, g2.copies):
tr1.r = tr2.r
tr1.t = tr2.t
def __init__(self,
ncs_restraints_group_list,
target_and_grads_object,
xray_structure,
refine_selection = None,
finite_grad_differences_test = False,
finite_grad_difference_val = 0,
max_iterations = 35,
refine_sites = False,
refine_u_iso = False,
refine_transformations = False):
"""
NCS constrained ADP and coordinates refinement. Also refines NCS operators.
"""
adopt_init_args(self, args=locals(),exclude=['ncs_restraints_group_list'])
self.refine_selection = nu.get_refine_selection(
refine_selection=self.refine_selection,
number_of_atoms=self.xray_structure.sites_cart().size())
self.use_ncs_constraints = target_and_grads_object.use_ncs_constraints
self.ncs_restraints_group_list = nu.ncs_restraints_group_list_copy(
ncs_restraints_group_list)
self.ncs_groups_coordinates_centers = []
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=self.ncs_restraints_group_list,
refine_selection=self.refine_selection)
assert [self.refine_sites,
self.refine_u_iso, self.refine_transformations].count(True) == 1
self.total_asu_length = len(xray_structure.sites_cart())
traditional_convergence_test_eps = 1.0e-6
if self.use_ncs_constraints:
xray_structure_one_ncs_copy = xray_structure.select(
self.extended_ncs_selection)
else:
xray_structure_one_ncs_copy = xray_structure.select(self.refine_selection)
if self.refine_sites:
self.x = xray_structure_one_ncs_copy.sites_cart().as_double()
elif self.refine_u_iso:
assert xray_structure_one_ncs_copy.scatterers().size() == \
xray_structure_one_ncs_copy.use_u_iso().count(True)
self.x = xray_structure_one_ncs_copy.extract_u_iso_or_u_equiv()
elif self.refine_transformations:
# move refinable parameters to coordinate center
self.ncs_groups_coordinates_centers = nu.get_ncs_groups_centers(
xray_structure=self.xray_structure,
ncs_restraints_group_list=self.ncs_restraints_group_list)
self.ncs_restraints_group_list = nu.shift_translation_to_center(
shifts = self.ncs_groups_coordinates_centers,
ncs_restraints_group_list = self.ncs_restraints_group_list)
self.x = nu.concatenate_rot_tran(
ncs_restraints_group_list=self.ncs_restraints_group_list)
minimizer = scitbx.lbfgs.run(
target_evaluator=self,
termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=max_iterations,
traditional_convergence_test_eps=traditional_convergence_test_eps),
exception_handling_params=scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_rounding_errors=True,
ignore_line_search_failed_step_at_lower_bound=True,
ignore_line_search_failed_maxfev=True))
# change transforms to the original coordinate system
if self.refine_transformations:
self.ncs_restraints_group_list = nu.shift_translation_back_to_place(
shifts = self.ncs_groups_coordinates_centers,
ncs_restraints_group_list = self.ncs_restraints_group_list)
if(getattr(self.target_and_grads_object, "finalize", None)):
self.target_and_grads_object.finalize()
# pass the refined ncs_restraints_group_list to original object
for g1,g2 in zip(ncs_restraints_group_list,self.ncs_restraints_group_list):
for tr1,tr2 in zip(g1.copies,g2.copies):
tr1.r = tr2.r
tr1.t = tr2.t
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)
