def exercise_random_traceless_symmetry_constrained_b_cart():
from cctbx import crystal
cs = crystal.symmetry((10,20,30,90,90,90), "P212121")
bc = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry = cs, u_scale=1, u_min=0.1)
assert approx_equal(bc[0]+bc[1]+bc[2], 0)
assert approx_equal(bc[3],0)
assert approx_equal(bc[4],0)
assert approx_equal(bc[5],0)
def exercise_random_traceless_symmetry_constrained_b_cart():
from cctbx import crystal
cs = crystal.symmetry((10, 20, 30, 90, 90, 90), "P212121")
bc = adptbx.random_traceless_symmetry_constrained_b_cart(crystal_symmetry=cs, u_scale=1, u_min=0.1)
assert approx_equal(bc[0] + bc[1] + bc[2], 0)
assert approx_equal(bc[3], 0)
assert approx_equal(bc[4], 0)
assert approx_equal(bc[5], 0)
def run_0(symbol = "C 2"):
space_group_info = sgtbx.space_group_info(symbol = symbol)
xrs = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*50,
volume_per_atom = 100.0,
random_u_iso = True)
#
b_cart = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=xrs.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(), adptbx.b_as_u(b_cart))
#
F = xrs.structure_factors(d_min = 1.5).f_calc()
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
#
bin_selections = []
F.setup_binner(reflections_per_bin=50)
for i_bin in F.binner().range_used():
sel = F.binner().selection(i_bin)
bin_selections.append(sel)
#
d_spacings = F.d_spacings().data()
ss = 1./flex.pow2(d_spacings) / 4.
k_mask_tmp = mmtbx.f_model.ext.k_mask(ss, 0.35, 80.)
k_mask = flex.double(F.data().size(), 0)
k_isotropic = flex.double(F.data().size(), 0)
for s in bin_selections:
d = d_spacings.select(s)
k_mask.set_selected(s, flex.mean(k_mask_tmp.select(s)))
k_isotropic.set_selected(s, random.randint(1,10))
#
fmodel = mmtbx.f_model.manager(
xray_structure = xrs,
f_obs = abs(F),
k_isotropic = k_isotropic,
k_anisotropic = k_anisotropic,
k_mask = k_mask)
f_calc = fmodel.f_calc()
f_masks = fmodel.f_masks()
f_model = fmodel.f_model()
f_obs = abs(f_model)
r_free_flags = f_obs.generate_r_free_flags(use_lattice_symmetry=False)
#
assert approx_equal(bulk_solvent.r_factor(f_obs.data(), f_model.data()), 0)
aso = scaler.run(
f_obs = f_obs,
f_calc = f_calc,
f_mask = f_masks,
r_free_flags = r_free_flags,
bin_selections = bin_selections,
number_of_cycles = 500,
auto_convergence_tolerance = 1.e-9,
ss = ss,
try_poly = True,
try_expanal = True,
try_expmin = True,
verbose = False)
assert approx_equal(aso.r_final, 0.00037, 0.00001)
assert approx_equal(aso.r_low, 0.00002, 0.00001)
assert approx_equal(aso.r_high, 0.00006, 0.00001)
assert approx_equal(
bulk_solvent.r_factor(f_obs.data(), abs(aso.core.f_model).data(), 1),
bulk_solvent.r_factor(f_obs.data(), abs(aso.core.f_model).data()))
def run_0(symbol="C 2"):
space_group_info = sgtbx.space_group_info(symbol=symbol)
xrs = random_structure.xray_structure(space_group_info=space_group_info,
elements=["N"] * 50,
volume_per_atom=100.0,
random_u_iso=True)
#
b_cart = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=xrs.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(), adptbx.b_as_u(b_cart))
#
F = xrs.structure_factors(d_min=1.5).f_calc()
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
#
bin_selections = []
F.setup_binner(reflections_per_bin=50)
for i_bin in F.binner().range_used():
sel = F.binner().selection(i_bin)
bin_selections.append(sel)
#
d_spacings = F.d_spacings().data()
ss = 1. / flex.pow2(d_spacings) / 4.
k_mask_tmp = mmtbx.f_model.ext.k_mask(ss, 0.35, 80.)
k_mask = flex.double(F.data().size(), 0)
k_isotropic = flex.double(F.data().size(), 0)
for s in bin_selections:
d = d_spacings.select(s)
k_mask.set_selected(s, flex.mean(k_mask_tmp.select(s)))
k_isotropic.set_selected(s, random.randint(1, 10))
#
fmodel = mmtbx.f_model.manager(xray_structure=xrs,
f_obs=abs(F),
k_isotropic=k_isotropic,
k_anisotropic=k_anisotropic,
k_mask=k_mask)
f_calc = fmodel.f_calc()
f_masks = fmodel.f_masks()
f_model = fmodel.f_model()
f_obs = abs(f_model)
r_free_flags = f_obs.generate_r_free_flags(use_lattice_symmetry=False)
#
assert approx_equal(bulk_solvent.r_factor(f_obs.data(), f_model.data()), 0)
aso = scaler.run(f_obs=f_obs,
f_calc=f_calc,
f_mask=f_masks,
r_free_flags=r_free_flags,
bin_selections=bin_selections,
number_of_cycles=500,
auto_convergence_tolerance=1.e-9,
ss=ss,
try_poly=True,
try_expanal=True,
try_expmin=True,
verbose=True)
print("r_f:", aso.r_final)
print("r_l:", aso.r_low)
print("r_h:", aso.r_high)
assert aso.r_final < 0.0009, [aso.r_final, 0.0009]
assert aso.r_low < 0.0017, [aso.r_low, 0.0017]
assert aso.r_high < 0.0006, [aso.r_high, 0.0006]
assert approx_equal(
bulk_solvent.r_factor(f_obs.data(),
abs(aso.core.f_model).data(), 1),
bulk_solvent.r_factor(f_obs.data(),
abs(aso.core.f_model).data()))
def exercise_6_instantiate_consistency(symbol = "C 2"):
random.seed(0)
flex.set_random_seed(0)
for scale in [1.e-4, 1.0, 1.e+4]:
for k_sol in [0, 0.3]:
for b_sol in [0, 50]:
for set_h_occ_to_zero in [True, False]:
for update_f_part1 in [True, False]:
for apply_scale_to in ["f_obs", "f_model"]:
# Simulate Fobs START
x = random_structure.xray_structure(
space_group_info = sgtbx.space_group_info(symbol=symbol),
elements =(("O","N","C")*3+("H",)*10),
volume_per_atom = 50,
min_distance = 3,
general_positions_only = True,
random_u_iso = True,
random_occupancy = False)
x.scattering_type_registry(table="wk1995")
x.set_occupancies(value=0.8, selection = x.hd_selection())
f_calc = x.structure_factors(d_min = 2.0).f_calc()
mask_manager = mmtbx.masks.manager(miller_array = f_calc)
f_mask = mask_manager.shell_f_masks(xray_structure = x)[0]
assert flex.mean(abs(f_mask).data()) > 0
b_cart=adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=x.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(x.unit_cell(), adptbx.b_as_u(b_cart))
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(f_calc.indices(), u_star)
ss = 1./flex.pow2(f_calc.d_spacings().data()) / 4.
k_mask = mmtbx.f_model.ext.k_mask(ss, k_sol, b_sol)
if(apply_scale_to=="f_model"):
k_isotropic = flex.double(f_calc.data().size(), scale)
else:
k_isotropic = flex.double(f_calc.data().size(), 1)
f_model_data = scale*k_anisotropic*(f_calc.data()+k_mask*f_mask.data())
f_model = f_calc.customized_copy(data = f_model_data)
f_obs = abs(f_model)
if(apply_scale_to=="f_obs"):
f_obs = f_obs.customized_copy(data = f_obs.data()*scale)
r_free_flags = f_obs.generate_r_free_flags()
# Simulate Fobs END
if(set_h_occ_to_zero):
x.set_occupancies(value=0.0, selection = x.hd_selection())
x.shake_sites_in_place(mean_distance=5)
sel = x.random_remove_sites_selection(fraction=0.3)
x = x.select(sel)
fmodel = mmtbx.f_model.manager(
xray_structure = x,
f_obs = f_obs,
r_free_flags = r_free_flags)
fmodel.update_all_scales(fast=True, show=False,
update_f_part1=update_f_part1)
f_part1_data = fmodel.f_calc().data()*flex.random_double(
fmodel.f_calc().data().size())
f_part1 = fmodel.f_calc().customized_copy(data = f_part1_data)
fmodel.update(f_part1 = f_part1)
r1 = fmodel.r_work()
#
zero=fmodel.f_calc().customized_copy(data=fmodel.f_calc().data()*0)
fmodel_dc = mmtbx.f_model.manager(
f_obs = fmodel.f_obs(),
r_free_flags = fmodel.r_free_flags(),
k_isotropic = fmodel.k_isotropic(),
k_anisotropic = fmodel.k_anisotropic(),
f_calc = fmodel.f_model_no_scales(),
f_part1 = fmodel.f_part1(),
f_part2 = fmodel.f_part2(),
f_mask = zero)
r2 = fmodel_dc.r_work()
if(0):
print "r1=%8.6f r2=%8.6f fp1=%6.3f fp2=%6.3f fc=%6.3f"%(r1, r2,
flex.mean(abs(fmodel.f_part1()).data()), \
flex.mean(abs(fmodel.f_part2()).data()), \
flex.mean(abs(fmodel.f_calc()).data())), \
"set_h_occ_to_zero=", set_h_occ_to_zero,\
"update_f_part1=", update_f_part1
assert approx_equal(r1, r2), [r1, r2]
def exercise_6_instantiate_consistency(symbol="C 2"):
random.seed(0)
flex.set_random_seed(0)
for scale in [1.e-4, 1.0, 1.e+4]:
for k_sol in [0, 0.3]:
for b_sol in [0, 50]:
for set_h_occ_to_zero in [True, False]:
for update_f_part1 in [True, False]:
for apply_scale_to in ["f_obs", "f_model"]:
# Simulate Fobs START
x = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info(
symbol=symbol),
elements=(("O", "N", "C") * 3 + ("H", ) * 10),
volume_per_atom=50,
min_distance=3,
general_positions_only=True,
random_u_iso=True,
random_occupancy=False)
x.scattering_type_registry(table="wk1995")
x.set_occupancies(value=0.8,
selection=x.hd_selection())
f_calc = x.structure_factors(d_min=2.0).f_calc()
mask_manager = mmtbx.masks.manager(
miller_array=f_calc)
f_mask = mask_manager.shell_f_masks(
xray_structure=x)[0]
assert flex.mean(abs(f_mask).data()) > 0
b_cart = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=x.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(
x.unit_cell(), adptbx.b_as_u(b_cart))
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(
f_calc.indices(), u_star)
ss = 1. / flex.pow2(
f_calc.d_spacings().data()) / 4.
k_mask = mmtbx.f_model.ext.k_mask(ss, k_sol, b_sol)
if (apply_scale_to == "f_model"):
k_isotropic = flex.double(
f_calc.data().size(), scale)
else:
k_isotropic = flex.double(
f_calc.data().size(), 1)
f_model_data = scale * k_anisotropic * (
f_calc.data() + k_mask * f_mask.data())
f_model = f_calc.customized_copy(data=f_model_data)
f_obs = abs(f_model)
if (apply_scale_to == "f_obs"):
f_obs = f_obs.customized_copy(
data=f_obs.data() * scale)
r_free_flags = f_obs.generate_r_free_flags()
# Simulate Fobs END
if (set_h_occ_to_zero):
x.set_occupancies(value=0.0,
selection=x.hd_selection())
x.shake_sites_in_place(mean_distance=5)
sel = x.random_remove_sites_selection(fraction=0.3)
x = x.select(sel)
fmodel = mmtbx.f_model.manager(
xray_structure=x,
f_obs=f_obs,
r_free_flags=r_free_flags)
fmodel.update_all_scales(
fast=True,
show=False,
update_f_part1=update_f_part1)
f_part1_data = fmodel.f_calc().data(
) * flex.random_double(
fmodel.f_calc().data().size())
f_part1 = fmodel.f_calc().customized_copy(
data=f_part1_data)
fmodel.update(f_part1=f_part1)
r1 = fmodel.r_work()
#
zero = fmodel.f_calc().customized_copy(
data=fmodel.f_calc().data() * 0)
fmodel_dc = mmtbx.f_model.manager(
f_obs=fmodel.f_obs(),
r_free_flags=fmodel.r_free_flags(),
k_isotropic=fmodel.k_isotropic(),
k_anisotropic=fmodel.k_anisotropic(),
f_calc=fmodel.f_model_no_scales(),
f_part1=fmodel.f_part1(),
f_part2=fmodel.f_part2(),
f_mask=zero)
r2 = fmodel_dc.r_work()
if (0):
print("r1=%8.6f r2=%8.6f fp1=%6.3f fp2=%6.3f fc=%6.3f"%(r1, r2,
flex.mean(abs(fmodel.f_part1()).data()), \
flex.mean(abs(fmodel.f_part2()).data()), \
flex.mean(abs(fmodel.f_calc()).data())), \
"set_h_occ_to_zero=", set_h_occ_to_zero,\
"update_f_part1=", update_f_part1)
assert approx_equal(r1, r2), [r1, r2]
def exercise_5_bulk_sol_and_scaling_and_H(symbol = "C 2"):
random.seed(0)
flex.set_random_seed(0)
x = random_structure.xray_structure(
space_group_info = sgtbx.space_group_info(symbol=symbol),
elements =(("O","N","C")*5+("H",)*10),
volume_per_atom = 200,
min_distance = 1.5,
general_positions_only = True,
random_u_iso = True,
random_occupancy = False)
x.scattering_type_registry(table="wk1995")
x.set_occupancies(value=0.6, selection = x.hd_selection())
f_calc = x.structure_factors(d_min = 1.5, algorithm="direct").f_calc()
mask_manager = mmtbx.masks.manager(miller_array = f_calc)
f_mask = mask_manager.shell_f_masks(xray_structure = x)[0]
assert flex.mean(abs(f_mask).data()) > 0
b_cart=adptbx.random_traceless_symmetry_constrained_b_cart(crystal_symmetry=x.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(x.unit_cell(), adptbx.b_as_u(b_cart))
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(f_calc.indices(), u_star)
ss = 1./flex.pow2(f_calc.d_spacings().data()) / 4.
k_mask = mmtbx.f_model.ext.k_mask(ss, 0.37, 64.0)
scale = 17.
k_isotropic = flex.double(f_calc.data().size(), scale)
f_model_data = scale*k_anisotropic*(f_calc.data()+k_mask*f_mask.data())
f_model = f_calc.customized_copy(data = f_model_data)
f_obs = abs(f_model)
r_free_flags = f_obs.generate_r_free_flags()
sfg_params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
sfg_params.algorithm = "direct"
for it in [(0,0.6), (1,-0.4), (0.2,0.4), (-0.2,0.8)]:
value, k_h_ = it
x.set_occupancies(value=value, selection = x.hd_selection())
fmodel = mmtbx.f_model.manager(
xray_structure = x,
f_obs = f_obs,
k_mask = k_mask,
k_anisotropic = k_anisotropic,
k_isotropic = k_isotropic,
r_free_flags = r_free_flags,
sf_and_grads_accuracy_params = sfg_params)
fmodel_dc = fmodel.deep_copy()
assert fmodel.r_work() > 0.02, fmodel.r_work()
fmodel.update_f_hydrogens_grid_search()
assert approx_equal(fmodel.k_h, k_h_), [it, fmodel.k_h, fmodel.r_work()]
assert approx_equal(fmodel.b_h, 0)
assert approx_equal(fmodel.r_work(), 0)
fmodel_dc.update_f_hydrogens()
assert fmodel_dc.r_work() < 0.01
# test 2
fmodel = mmtbx.f_model.manager(
xray_structure = x,
f_obs = f_obs,
r_free_flags = r_free_flags,
sf_and_grads_accuracy_params = sfg_params)
fmodel_dc = fmodel.deep_copy()
assert fmodel.r_work() > 0.25
fmodel.update_all_scales(cycles=6, fast=False, update_f_part1=False,
refine_hd_scattering_method="slow")
assert approx_equal(fmodel.k_h, k_h_)
assert approx_equal(fmodel.b_h, 0)
assert approx_equal(fmodel.r_work(), 0)
fmodel_dc.update_all_scales(update_f_part1=False,
refine_hd_scattering_method="fast")
assert fmodel_dc.r_work() < 0.05
# test 3
fmodel = mmtbx.f_model.manager(
xray_structure = x,
f_obs = f_obs,
r_free_flags = r_free_flags,
sf_and_grads_accuracy_params = sfg_params)
assert fmodel.r_work() > 0.25
fmodel.update_all_scales(cycles=6, fast=True, show=False,
update_f_part1=False, refine_hd_scattering_method="slow")
assert approx_equal(fmodel.k_h, k_h_)
assert approx_equal(fmodel.b_h, 0)
assert fmodel.r_work() < 0.025
map_coeffs = fmodel.map_coefficients(map_type="2mFo-DFc")
fmodel.export_f_obs_flags_as_mtz(file_name="tmp_tst_fmodel.mtz")
assert os.path.isfile("tmp_tst_fmodel.mtz")
