def exercise_3():
from mmtbx import masks
from cctbx import sgtbx
xs = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("P1"),
elements=["C"] * 2,
unit_cell=(10, 20, 30, 70, 80, 120))
f_calc = xs.structure_factors(d_min=2.0).f_calc()
mp = masks.mask_master_params.extract()
mm1 = masks.manager(miller_array=f_calc, xray_structure=xs)
assert list(xs.scatterers().extract_occupancies()) == [1.0, 1.0]
fmasks1 = mm1.shell_f_masks()
assert len(fmasks1) == 1
assert flex.mean(flex.abs(fmasks1[0].data())) > 4.0
#
xs.set_occupancies(value=0)
mp.ignore_zero_occupancy_atoms = False
mp.use_asu_masks = False
mm2 = masks.manager(miller_array=f_calc, xray_structure=xs, mask_params=mp)
assert list(xs.scatterers().extract_occupancies()) == [0.0, 0.0]
fmasks1 = mm1.shell_f_masks()
assert len(fmasks1) == 1
fmasks2 = mm2.shell_f_masks()
assert len(fmasks2) == 1
assert flex.mean( flex.abs(fmasks1[0].data()) ) == \
flex.mean( flex.abs(fmasks2[0].data()) )
#
mp.ignore_zero_occupancy_atoms = True
mp.use_asu_masks = False
mm3 = masks.manager(miller_array=f_calc, xray_structure=xs, mask_params=mp)
assert list(xs.scatterers().extract_occupancies()) == [0.0, 0.0]
fmasks3 = mm3.shell_f_masks()
assert len(fmasks3) == 1
assert approx_equal(
flex.abs(fmasks3[0].data()).min_max_mean().as_tuple(), (0.0, 0.0, 0.0))
def exercise_3():
from mmtbx import masks
from cctbx import sgtbx
xs = random_structure.xray_structure(
space_group_info = sgtbx.space_group_info("P1"),
elements = ["C"]*2,
unit_cell = (10, 20, 30, 70, 80, 120))
f_calc = xs.structure_factors(d_min = 2.0).f_calc()
mp = masks.mask_master_params.extract()
mm1 = masks.manager(miller_array = f_calc,
xray_structure = xs)
assert list(xs.scatterers().extract_occupancies()) == [1.0, 1.0]
fmasks1 = mm1.shell_f_masks()
assert len(fmasks1) == 1
assert flex.mean( flex.abs(fmasks1[0].data()) ) > 4.0
#
xs.set_occupancies(value = 0)
mp.ignore_zero_occupancy_atoms = False
mp.use_asu_masks = False
mm2 = masks.manager(miller_array = f_calc,
xray_structure = xs,
mask_params = mp)
assert list(xs.scatterers().extract_occupancies()) == [0.0, 0.0]
fmasks1 = mm1.shell_f_masks()
assert len(fmasks1) == 1
fmasks2 = mm2.shell_f_masks()
assert len(fmasks2)==1
assert flex.mean( flex.abs(fmasks1[0].data()) ) == \
flex.mean( flex.abs(fmasks2[0].data()) )
#
mp.ignore_zero_occupancy_atoms = True
mp.use_asu_masks = False
mm3 = masks.manager(miller_array = f_calc,
xray_structure = xs,
mask_params = mp)
assert list(xs.scatterers().extract_occupancies()) == [0.0, 0.0]
fmasks3 = mm3.shell_f_masks()
assert len(fmasks3)==1
assert approx_equal(
flex.abs(fmasks3[0].data()).min_max_mean().as_tuple(), (0.0, 0.0, 0.0))
def get_f_mask(xrs, ma, step, option=2, r_shrink=None, r_sol=None):
#
result = ma.deep_copy()
sel = ma.d_spacings().data() >= 3
ma = ma.select(sel)
#
crystal_gridding = maptbx.crystal_gridding(
unit_cell=xrs.unit_cell(),
space_group_info=xrs.space_group_info(),
symmetry_flags=maptbx.use_space_group_symmetry,
step=step)
n_real = crystal_gridding.n_real()
atom_radii = vdw_radii_from_xray_structure(xray_structure=xrs)
mask_params = masks.mask_master_params.extract()
grid_step_factor = ma.d_min() / step
if (r_shrink is not None): mask_params.shrink_truncation_radius = r_shrink
if (r_sol is not None): mask_params.solvent_radius = r_sol
mask_params.grid_step_factor = grid_step_factor
# 1
if (option == 1):
asu_mask = ext.atom_mask(
unit_cell=xrs.unit_cell(),
group=xrs.space_group(),
resolution=ma.d_min(),
grid_step_factor=grid_step_factor,
solvent_radius=mask_params.solvent_radius,
shrink_truncation_radius=mask_params.shrink_truncation_radius)
asu_mask.compute(xrs.sites_frac(), atom_radii)
fm_asu = asu_mask.structure_factors(ma.indices())
f_mask = ma.set().array(data=fm_asu)
# 2
elif (option == 2):
asu_mask = ext.atom_mask(
unit_cell=xrs.unit_cell(),
space_group=xrs.space_group(),
gridding_n_real=n_real,
solvent_radius=mask_params.solvent_radius,
shrink_truncation_radius=mask_params.shrink_truncation_radius)
asu_mask.compute(xrs.sites_frac(), atom_radii)
fm_asu = asu_mask.structure_factors(ma.indices())
f_mask = ma.set().array(data=fm_asu)
# 3
elif (option == 3):
mask_p1 = mmtbx.masks.mask_from_xray_structure(
xray_structure=xrs,
p1=True,
for_structure_factors=True,
solvent_radius=mask_params.solvent_radius,
shrink_truncation_radius=mask_params.shrink_truncation_radius,
n_real=n_real,
in_asu=False).mask_data
maptbx.unpad_in_place(map=mask_p1)
mask = asu_map_ext.asymmetric_map(
xrs.crystal_symmetry().space_group().type(), mask_p1).data()
f_mask = ma.structure_factors_from_asu_map(asu_map_data=mask,
n_real=n_real)
# 4
elif (option == 4):
f_mask = masks.bulk_solvent(
xray_structure=xrs,
ignore_zero_occupancy_atoms=False,
solvent_radius=mask_params.solvent_radius,
shrink_truncation_radius=mask_params.shrink_truncation_radius,
ignore_hydrogen_atoms=False,
grid_step=step,
atom_radii=atom_radii).structure_factors(miller_set=ma)
elif (option == 5):
o = mmtbx.masks.bulk_solvent(
xray_structure=xrs,
ignore_zero_occupancy_atoms=False,
solvent_radius=mask_params.solvent_radius,
shrink_truncation_radius=mask_params.shrink_truncation_radius,
ignore_hydrogen_atoms=False,
gridding_n_real=n_real,
atom_radii=atom_radii)
assert approx_equal(n_real, o.data.accessor().all())
f_mask = o.structure_factors(ma)
elif (option == 6):
# XXX No control over n_real, so results with others don't match
mask_manager = masks.manager(miller_array=ma,
miller_array_twin=None,
mask_params=mask_params)
f_mask = mask_manager.shell_f_masks(xray_structure=xrs,
force_update=True)[0]
else:
assert 0
#
data = flex.complex_double(result.indices().size(), 0)
data = data.set_selected(sel, f_mask.data())
result = result.array(data=data)
return result
def get_f_mask(xrs, ma, step, option=2):
crystal_gridding = maptbx.crystal_gridding(
unit_cell=xrs.unit_cell(),
space_group_info=xrs.space_group_info(),
symmetry_flags=maptbx.use_space_group_symmetry,
step=step)
n_real = crystal_gridding.n_real()
atom_radii = vdw_radii_from_xray_structure(xray_structure=xrs)
mask_params = masks.mask_master_params.extract()
grid_step_factor = ma.d_min() / step
# 1
if (option == 1):
asu_mask = ext.atom_mask(
unit_cell=xrs.unit_cell(),
group=xrs.space_group(),
resolution=ma.d_min(),
grid_step_factor=grid_step_factor,
solvent_radius=mask_params.solvent_radius,
shrink_truncation_radius=mask_params.shrink_truncation_radius)
asu_mask.compute(xrs.sites_frac(), atom_radii)
fm_asu = asu_mask.structure_factors(ma.indices())
f_mask = ma.set().array(data=fm_asu)
# 2
elif (option == 2):
asu_mask = ext.atom_mask(
unit_cell=xrs.unit_cell(),
space_group=xrs.space_group(),
gridding_n_real=n_real,
solvent_radius=mask_params.solvent_radius,
shrink_truncation_radius=mask_params.shrink_truncation_radius)
asu_mask.compute(xrs.sites_frac(), atom_radii)
fm_asu = asu_mask.structure_factors(ma.indices())
f_mask = ma.set().array(data=fm_asu)
# 3
elif (option == 3):
mask_params.grid_step_factor = grid_step_factor
mask_manager = masks.manager(miller_array=ma,
miller_array_twin=None,
mask_params=mask_params)
f_mask = mask_manager.shell_f_masks(xray_structure=xrs,
force_update=True)[0]
# 4
elif (option == 4):
mask_p1 = mmtbx.masks.mask_from_xray_structure(
xray_structure=xrs,
p1=True,
for_structure_factors=True,
n_real=n_real,
in_asu=False).mask_data
maptbx.unpad_in_place(map=mask_p1)
mask = asu_map_ext.asymmetric_map(
xrs.crystal_symmetry().space_group().type(), mask_p1).data()
f_mask = ma.structure_factors_from_asu_map(asu_map_data=mask,
n_real=n_real)
elif (option == 5):
o = mmtbx.masks.bulk_solvent(
xray_structure=xrs,
ignore_zero_occupancy_atoms=False,
solvent_radius=mask_params.solvent_radius,
shrink_truncation_radius=mask_params.shrink_truncation_radius,
ignore_hydrogen_atoms=False,
gridding_n_real=n_real,
atom_radii=atom_radii)
f_mask = o.structure_factors(ma)
else:
assert 0
#
return f_mask