def tests(Cls):
initializer = Cls(os.path.join(os.getcwd()+r"/test_files", "beta.res"))
print initializer.symmetry._unit_cell
for scatterer in initializer.scatterers:
print getattr(scatterer,"label"), getattr(scatterer,"site"),\
adptbx.u_star_as_u_iso(initializer.symmetry._unit_cell,
scatterer.u_star)
def _initialize_from_ins(self, **kwargs):
iucr_structure = from_ins.from_ins(self.fname, **kwargs)
self.scatterers = iucr_structure.scatterers()
self.symmetry = iucr_structure.crystal_symmetry()
for scatterer in self.scatterers:
setattr(scatterer, "u_iso",
adptbx.u_star_as_u_iso(self.unit_cell, scatterer.u_star))
def exercise_tensor_rank_2_orth_and_frac_linear_maps():
from cctbx import adptbx, sgtbx
p1 = sgtbx.space_group_info('P1')
for i in xrange(100):
uc = p1.any_compatible_unit_cell(27)
u_star = matrix.col.random(n=6, a=0, b=1)
u_iso_ref = adptbx.u_star_as_u_iso(uc, u_star)
u_iso = matrix.col(uc.u_star_to_u_iso_linear_form()).dot(u_star)
assert approx_equal(u_iso, u_iso_ref, eps=1e-15)
u_cart_ref = adptbx.u_star_as_u_cart(uc, u_star)
u_cart = matrix.sqr(uc.u_star_to_u_cart_linear_map()) * u_star
assert approx_equal(u_cart, u_cart_ref, eps=1e-15)
u_cif_ref = adptbx.u_star_as_u_cif(uc, u_star)
u_cif = matrix.diag(uc.u_star_to_u_cif_linear_map())*(u_star)
assert approx_equal(u_cif, u_cif_ref)
def exercise_tensor_rank_2_orth_and_frac_linear_maps():
from cctbx import adptbx, sgtbx
p1 = sgtbx.space_group_info('P1')
for i in range(100):
uc = p1.any_compatible_unit_cell(27)
u_star = matrix.col.random(n=6, a=0, b=1)
u_iso_ref = adptbx.u_star_as_u_iso(uc, u_star)
u_iso = matrix.col(uc.u_star_to_u_iso_linear_form()).dot(u_star)
assert approx_equal(u_iso, u_iso_ref, eps=1e-15)
u_cart_ref = adptbx.u_star_as_u_cart(uc, u_star)
u_cart = matrix.sqr(uc.u_star_to_u_cart_linear_map()) * u_star
assert approx_equal(u_cart, u_cart_ref, eps=1e-15)
u_cif_ref = adptbx.u_star_as_u_cif(uc, u_star)
u_cif = matrix.diag(uc.u_star_to_u_cif_linear_map()) * (u_star)
assert approx_equal(u_cif, u_cif_ref)
def split_u(u_eq, xray_structure, tls_selections, offset):
global time_split_u
timer = user_plus_sys_time()
uc = xray_structure.unit_cell()
for tls_selection in tls_selections:
if (offset):
offset_ = adptbx.b_as_u(5.0)
else:
offset_ = 0.0
for i_seq in tls_selection:
sc = xray_structure.scatterers()[i_seq]
u_nm = sc.u_star
u_nm_iso = adptbx.u_star_as_u_iso(uc, u_nm)
u_iso_new = u_eq[i_seq] - u_nm_iso
if u_iso_new < 0.0:
u_iso_new = 0.0
assert u_iso_new >= 0.0
sc.u_iso = u_iso_new
assert sc.flags.use_u_aniso()
assert sc.flags.use_u_iso()
u_iso = xray_structure.scatterers().extract_u_iso().select(
xray_structure.use_u_iso())
assert (u_iso < 0.0).count(True) == 0
time_split_u += timer.elapsed()
def u_star_minus_u_iso_airlie(unit_cell, u_star): u_iso = adptbx.u_star_as_u_iso(unit_cell,u_star) u_star_as_beta = adptbx.u_star_as_beta(u_star) u_iso_as_beta = adptbx.u_iso_as_beta(unit_cell,u_iso) beta_minus_u_iso = [a-i for a,i in zip(u_star_as_beta,u_iso_as_beta)] return adptbx.beta_as_u_star(beta_minus_u_iso)
def u_star_minus_u_iso_airlie(unit_cell, u_star):
u_iso = adptbx.u_star_as_u_iso(unit_cell, u_star)
u_star_as_beta = adptbx.u_star_as_beta(u_star)
u_iso_as_beta = adptbx.u_iso_as_beta(unit_cell, u_iso)
beta_minus_u_iso = [a - i for a, i in zip(u_star_as_beta, u_iso_as_beta)]
return adptbx.beta_as_u_star(beta_minus_u_iso)
