def test_nrg_selection(self):
"""
test that a atom selection propagates correctly to ncs_restraints_group_list
"""
# print sys._getframe().f_code.co_name
nrg = self.ncs_restraints_group_list
m1 = list(nrg[0].master_iselection)
c1 = list(nrg[0].copies[0].iselection)
c2 = list(nrg[0].copies[1].iselection)
assert len(m1) == len(c1)
assert m1 == [0, 1, 2, 3, 4, 5, 6]
assert c1 == [7, 8, 9, 10, 11, 12, 13]
assert c2 == [14, 15, 16, 17, 18, 19, 20]
selection1 = flex.size_t([0,1,5,3,100,101])
selection2 = flex.size_t([0,1,5,3,7,8,9,12,100,101])
selection3 = flex.size_t([0,1,5,3,7,8,9,12,14,15,19,17,100,101])
new_nrg = nu.ncs_groups_selection(
ncs_restraints_group_list=nrg,
selection=selection1)
# only atoms in master are selected
mt = list(new_nrg[0].master_iselection)
c1t = list(new_nrg[0].copies[0].iselection)
assert mt == []
assert c1t == []
# atoms selected in both master and copies
new_nrg = nu.ncs_groups_selection(
ncs_restraints_group_list=nrg,
selection=selection2)
# only atoms in master are selected
mt = list(new_nrg[0].master_iselection)
c1t = list(new_nrg[0].copies[0].iselection)
assert mt == []
assert c1t == []
new_nrg = nu.ncs_groups_selection(
ncs_restraints_group_list=nrg,
selection=selection3)
# only atoms in master are selected
mt = list(new_nrg[0].master_iselection)
c1t = list(new_nrg[0].copies[0].iselection)
c2t = list(new_nrg[0].copies[1].iselection)
assert mt == [0, 1, 5]
assert c1t == [7, 8, 12]
assert c2t == [14, 15, 19]
def test_nrg_selection(self):
"""
test that a atom selection propagates correctly to ncs_restraints_group_list
"""
# print sys._getframe().f_code.co_name
nrg = self.ncs_restraints_group_list
m1 = list(nrg[0].master_iselection)
c1 = list(nrg[0].copies[0].iselection)
c2 = list(nrg[0].copies[1].iselection)
assert len(m1) == len(c1)
assert m1 == [0, 1, 2, 3, 4, 5, 6]
assert c1 == [7, 8, 9, 10, 11, 12, 13]
assert c2 == [14, 15, 16, 17, 18, 19, 20]
selection1 = flex.size_t([0, 1, 5, 3, 100, 101])
selection2 = flex.size_t([0, 1, 5, 3, 7, 8, 9, 12, 100, 101])
selection3 = flex.size_t(
[0, 1, 5, 3, 7, 8, 9, 12, 14, 15, 19, 17, 100, 101])
new_nrg = nu.ncs_groups_selection(ncs_restraints_group_list=nrg,
selection=selection1)
# only atoms in master are selected
mt = list(new_nrg[0].master_iselection)
c1t = list(new_nrg[0].copies[0].iselection)
assert mt == []
assert c1t == []
# atoms selected in both master and copies
new_nrg = nu.ncs_groups_selection(ncs_restraints_group_list=nrg,
selection=selection2)
# only atoms in master are selected
mt = list(new_nrg[0].master_iselection)
c1t = list(new_nrg[0].copies[0].iselection)
assert mt == []
assert c1t == []
new_nrg = nu.ncs_groups_selection(ncs_restraints_group_list=nrg,
selection=selection3)
# only atoms in master are selected
mt = list(new_nrg[0].master_iselection)
c1t = list(new_nrg[0].copies[0].iselection)
c2t = list(new_nrg[0].copies[1].iselection)
assert mt == [0, 1, 5]
assert c1t == [7, 8, 12]
assert c2t == [14, 15, 19]
def refine(self,
selection,
optimize_weight = True,
start_trial_weight_value = 50,
selection_buffer_radius=5,
box_cushion=2,
rms_bonds_limit = 0.03,
rms_angles_limit = 3.0):
if(self.ncs_groups is None): # no NCS constraints
sites_cart_moving = self.sites_cart
selection_within = self.xray_structure.selection_within(
radius = selection_buffer_radius,
selection = selection)
sel = selection.select(selection_within)
iselection = flex.size_t()
for i, state in enumerate(selection):
if state:
iselection.append(i)
box = utils.extract_box_around_model_and_map(
xray_structure = self.xray_structure,
map_data = self.target_map,
selection = selection_within,
box_cushion = box_cushion)
new_unit_cell = box.xray_structure_box.unit_cell()
geo_box = self.geometry_restraints_manager.select(box.selection)
geo_box = geo_box.discard_symmetry(new_unit_cell=new_unit_cell)
geo_box.remove_reference_coordinate_restraints_in_place() # disaster happens otherwise
map_box = box.map_box
sites_cart_box = box.xray_structure_box.sites_cart()
rsr_simple_refiner = simple(
target_map = map_box,
selection = sel,
real_space_gradients_delta = self.real_space_gradients_delta,
max_iterations = self.max_iterations,
geometry_restraints_manager = geo_box)
real_space_result = refinery(
refiner = rsr_simple_refiner,
xray_structure = box.xray_structure_box,
optimize_weight = optimize_weight,
start_trial_weight_value = start_trial_weight_value,
rms_bonds_limit = rms_bonds_limit,
rms_angles_limit = rms_angles_limit)
self.weight_optimal = real_space_result.weight_final
sites_cart_box_refined = real_space_result.sites_cart_result
sites_cart_box_refined_shifted_back = \
sites_cart_box_refined + box.shift_to_map_boxed_sites_back
sites_cart_refined = sites_cart_box_refined_shifted_back.select(sel)
sites_cart_moving = sites_cart_moving.set_selected(
iselection, sites_cart_refined)
self.xray_structure.set_sites_cart(sites_cart_moving)
self.sites_cart = self.xray_structure.sites_cart()
else: # NCS constraints are present
# select on xrs, grm, ncs_groups
grm = self.geometry_restraints_manager.select(selection)
xrs = self.xray_structure.select(selection)
sel = flex.bool(xrs.scatterers().size(), True)
size = self.xray_structure.scatterers().size()
ncs_groups_ = ncs_utils.ncs_groups_selection(
ncs_restraints_group_list = self.ncs_groups,
selection = selection)
#
rsr_simple_refiner = simple(
target_map = self.target_map,
selection = sel,
real_space_gradients_delta = self.real_space_gradients_delta,
max_iterations = self.max_iterations,
geometry_restraints_manager = grm,
ncs_groups = ncs_groups_)
real_space_result = refinery(
refiner = rsr_simple_refiner,
xray_structure = xrs,
optimize_weight = optimize_weight,
start_trial_weight_value = start_trial_weight_value,
rms_bonds_limit = rms_bonds_limit,
rms_angles_limit = rms_angles_limit)
self.weight_optimal = real_space_result.weight_final
def refine(self,
selection,
optimize_weight=True,
start_trial_weight_value=50,
selection_buffer_radius=5,
box_cushion=2,
rms_bonds_limit=0.03,
rms_angles_limit=3.0):
if (self.ncs_groups is None): # no NCS constraints
sites_cart_moving = self.sites_cart
selection_within = self.xray_structure.selection_within(
radius=selection_buffer_radius, selection=selection)
sel = selection.select(selection_within)
iselection = flex.size_t()
for i, state in enumerate(selection):
if state:
iselection.append(i)
box = utils.extract_box_around_model_and_map(
xray_structure=self.xray_structure,
map_data=self.target_map,
selection=selection_within,
box_cushion=box_cushion)
new_unit_cell = box.xray_structure_box.unit_cell()
geo_box = self.geometry_restraints_manager.select(box.selection)
geo_box = geo_box.discard_symmetry(new_unit_cell=new_unit_cell)
geo_box.remove_reference_coordinate_restraints_in_place(
) # disaster happens otherwise
map_box = box.map_box
sites_cart_box = box.xray_structure_box.sites_cart()
rsr_simple_refiner = simple(
target_map=map_box,
selection=sel,
real_space_gradients_delta=self.real_space_gradients_delta,
max_iterations=self.max_iterations,
geometry_restraints_manager=geo_box,
gradients_method=self.gradients_method)
real_space_result = refinery(
refiner=rsr_simple_refiner,
xray_structure=box.xray_structure_box,
optimize_weight=optimize_weight,
start_trial_weight_value=start_trial_weight_value,
rms_bonds_limit=rms_bonds_limit,
rms_angles_limit=rms_angles_limit)
self.weight_optimal = real_space_result.weight_final
sites_cart_box_refined = real_space_result.sites_cart_result
shift_back = [-box.shift_cart[i] for i in xrange(3)]
sites_cart_box_refined_shifted_back = \
sites_cart_box_refined + shift_back # Sure + not - ?
sites_cart_refined = sites_cart_box_refined_shifted_back.select(
sel)
sites_cart_moving = sites_cart_moving.set_selected(
iselection, sites_cart_refined)
self.xray_structure.set_sites_cart(sites_cart_moving)
self.sites_cart = self.xray_structure.sites_cart()
else: # NCS constraints are present
# select on xrs, grm, ncs_groups
grm = self.geometry_restraints_manager.select(selection)
xrs = self.xray_structure.select(selection)
sel = flex.bool(xrs.scatterers().size(), True)
size = self.xray_structure.scatterers().size()
ncs_groups_ = ncs_utils.ncs_groups_selection(
ncs_restraints_group_list=self.ncs_groups, selection=selection)
#
rsr_simple_refiner = simple(
target_map=self.target_map,
selection=sel,
real_space_gradients_delta=self.real_space_gradients_delta,
max_iterations=self.max_iterations,
geometry_restraints_manager=grm,
ncs_groups=ncs_groups_)
real_space_result = refinery(
refiner=rsr_simple_refiner,
xray_structure=xrs,
optimize_weight=optimize_weight,
start_trial_weight_value=start_trial_weight_value,
rms_bonds_limit=rms_bonds_limit,
rms_angles_limit=rms_angles_limit)
self.weight_optimal = real_space_result.weight_final
