def exercise_lbfgs(test_case, use_geo, out, d_min=2):
sites_cart, geo_manager = cctbx.geometry_restraints.manager.\
construct_non_crystallographic_conserving_bonds_and_angles(
sites_cart=flex.vec3_double(test_case.sites),
edge_list_bonds=test_case.bonds,
edge_list_angles=test_case.angles())
scatterers = flex.xray_scatterer(sites_cart.size(),
xray.scatterer(scattering_type="C", b=20))
for sc, lbl in zip(scatterers, test_case.labels):
sc.label = lbl
structure = xray.structure(crystal_symmetry=geo_manager.crystal_symmetry,
scatterers=scatterers)
structure.set_sites_cart(sites_cart=sites_cart)
f_calc = structure.structure_factors(d_min=d_min,
anomalous_flag=False).f_calc()
fft_map = f_calc.fft_map()
fft_map.apply_sigma_scaling()
if (use_geo):
axis = matrix.col(flex.random_double_point_on_sphere())
rot = scitbx.math.r3_rotation_axis_and_angle_as_matrix(axis=axis,
angle=25,
deg=True)
trans = matrix.col(flex.random_double_point_on_sphere()) * 1.0
structure.apply_rigid_body_shift(rot=rot, trans=trans)
geo_manager.energies_sites(sites_cart=structure.sites_cart()).show(
f=out)
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
geometry_restraints_manager=geo_manager,
gradients_method="fd",
real_space_target_weight=1,
real_space_gradients_delta=d_min / 3)
geo_manager.energies_sites(sites_cart=minimized.sites_cart).show(f=out)
else:
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
unit_cell=structure.unit_cell(),
gradients_method="fd",
real_space_gradients_delta=d_min / 3)
rmsd_start = sites_cart.rms_difference(structure.sites_cart())
rmsd_final = sites_cart.rms_difference(minimized.sites_cart)
print("RMSD start, final:", rmsd_start, rmsd_final, file=out)
if (use_geo):
assert rmsd_start >= 1 - 1e-6
assert rmsd_final < 0.2
def show_f_g(label, f, g):
print(label, "f, |g|:", f, flex.mean_sq(g)**0.5, file=out)
show_f_g(label="start", f=minimized.f_start, g=minimized.g_start)
show_f_g(label="final", f=minimized.f_final, g=minimized.g_final)
assert minimized.f_final <= minimized.f_start
return minimized
def exercise_lbfgs(test_case, use_geo, out, d_min=2):
sites_cart, geo_manager = cctbx.geometry_restraints.manager.construct_non_crystallographic_conserving_bonds_and_angles(
sites_cart=flex.vec3_double(test_case.sites),
edge_list_bonds=test_case.bonds,
edge_list_angles=test_case.angles())
scatterers = flex.xray_scatterer(
sites_cart.size(), xray.scatterer(scattering_type="C", b=20))
for sc,lbl in zip(scatterers, test_case.labels):
sc.label = lbl
structure = xray.structure(
crystal_symmetry=geo_manager.crystal_symmetry,
scatterers=scatterers)
structure.set_sites_cart(sites_cart=sites_cart)
f_calc = structure.structure_factors(
d_min=d_min, anomalous_flag=False).f_calc()
fft_map = f_calc.fft_map()
fft_map.apply_sigma_scaling()
if (use_geo):
axis = matrix.col(flex.random_double_point_on_sphere())
rot = scitbx.math.r3_rotation_axis_and_angle_as_matrix(
axis=axis, angle=25, deg=True)
trans = matrix.col(flex.random_double_point_on_sphere()) * 1.0
structure.apply_rigid_body_shift(rot=rot, trans=trans)
geo_manager.energies_sites(sites_cart=structure.sites_cart()).show(f=out)
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
geometry_restraints_manager=geo_manager,
real_space_target_weight=1,
real_space_gradients_delta=d_min/3)
geo_manager.energies_sites(sites_cart=minimized.sites_cart).show(f=out)
else:
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
unit_cell=structure.unit_cell(),
real_space_gradients_delta=d_min/3)
rmsd_start = sites_cart.rms_difference(structure.sites_cart())
rmsd_final = sites_cart.rms_difference(minimized.sites_cart)
print >> out, "RMSD start, final:", rmsd_start, rmsd_final
if (use_geo):
assert rmsd_start >= 1-1e-6
assert rmsd_final < 0.2
def show_f_g(label, f, g):
print >> out, label, "f, |g|:", f, flex.mean_sq(g)**0.5
show_f_g(label="start", f=minimized.f_start, g=minimized.g_start)
show_f_g(label="final", f=minimized.f_final, g=minimized.g_final)
assert minimized.f_final <= minimized.f_start
return minimized
def run():
def compute_map(xray_structure, d_min=1.5, resolution_factor=1. / 4):
fc = xray_structure.structure_factors(d_min=d_min).f_calc()
fft_map = fc.fft_map(resolution_factor=resolution_factor)
fft_map.apply_sigma_scaling()
result = fft_map.real_map_unpadded()
return result, fc, fft_map
xrs = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("P212121"),
elements=["N", "C", "O", "S", "P"] * 10,
volume_per_atom=50)
map_target, tmp, tmp = compute_map(xray_structure=xrs)
xrs_sh = xrs.deep_copy_scatterers()
xrs_sh.shake_sites_in_place(mean_distance=0.8)
start_error = flex.mean(xrs.distances(other=xrs_sh))
print "Start:", start_error
map_current, miller_array, crystal_gridding = compute_map(
xray_structure=xrs_sh)
for step in [miller_array.d_min() / 4] * 5:
if (1):
minimized = real_space_target_and_gradients.minimization(
xray_structure=xrs_sh,
miller_array=miller_array,
crystal_gridding=crystal_gridding,
map_target=map_target,
max_iterations=500,
min_iterations=25,
step=step,
geometry_restraints_manager=None,
target_type="diff_map")
xrs_sh = minimized.xray_structure
map_current = minimized.map_current
final_error = flex.mean(
xrs.distances(other=minimized.xray_structure))
if (0):
minimized = real_space_refinement_simple.lbfgs(
sites_cart=xrs_sh.sites_cart(),
density_map=map_target,
unit_cell=xrs_sh.unit_cell(),
geometry_restraints_manager=None,
real_space_gradients_delta=step)
xrs_sh = xrs_sh.replace_sites_cart(minimized.sites_cart)
final_error = flex.mean(xrs.distances(other=xrs_sh))
print "Final:", final_error
assert approx_equal(start_error, 0.8, 1.e-3)
assert final_error < 1.e-4
print "OK"
def run():
def compute_map(xray_structure, d_min=1.5, resolution_factor=1./4):
fc = xray_structure.structure_factors(d_min = d_min).f_calc()
fft_map = fc.fft_map(resolution_factor=resolution_factor)
fft_map.apply_sigma_scaling()
result = fft_map.real_map_unpadded()
return result, fc, fft_map
xrs = random_structure.xray_structure(
space_group_info = sgtbx.space_group_info("P212121"),
elements = ["N","C","O","S","P"]*10,
volume_per_atom = 50)
map_target,tmp,tmp = compute_map(xray_structure = xrs)
xrs_sh = xrs.deep_copy_scatterers()
xrs_sh.shake_sites_in_place(mean_distance=0.8)
start_error = flex.mean(xrs.distances(other = xrs_sh))
print "Start:", start_error
map_current, miller_array, crystal_gridding = compute_map(
xray_structure = xrs_sh)
for step in [miller_array.d_min()/4]*5:
if(1):
minimized = real_space_target_and_gradients.minimization(
xray_structure = xrs_sh,
miller_array = miller_array,
crystal_gridding = crystal_gridding,
map_target = map_target,
max_iterations = 500,
min_iterations = 25,
step = step,
geometry_restraints_manager = None,
target_type = "diff_map")
xrs_sh = minimized.xray_structure
map_current = minimized.map_current
final_error = flex.mean(xrs.distances(other = minimized.xray_structure))
if(0):
minimized = real_space_refinement_simple.lbfgs(
sites_cart=xrs_sh.sites_cart(),
density_map=map_target,
unit_cell=xrs_sh.unit_cell(),
geometry_restraints_manager=None,
real_space_gradients_delta=step)
xrs_sh = xrs_sh.replace_sites_cart(minimized.sites_cart)
final_error = flex.mean(xrs.distances(other = xrs_sh))
print "Final:", final_error
assert approx_equal(start_error, 0.8, 1.e-3)
assert final_error < 1.e-4
print "OK"
