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 __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 = ncs_restraints_group_list.get_extended_ncs_selection(
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 = ncs_restraints_group_list.get_extended_ncs_selection(
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)
p = ncs.input.get_default_params()
p.ncs_search.exclude_selection = None
ncs_inp = ncs.input(hierarchy=pdb_inp.construct_hierarchy(),
params=p.ncs_search)
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.truncated_hierarchy.atoms_size()
#
refine_selection = nu.get_refine_selection(number_of_atoms=asu_length)
extended_ncs_selection = nrgl.get_extended_ncs_selection(
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 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 __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
