def exercise():
from scitbx.array_family import flex
from scitbx import matrix
from libtbx.test_utils import approx_equal, show_diff
import libtbx.load_env
if (libtbx.env.has_module(name="iotbx")):
from iotbx.shelx.parsers import decode_variables
import iotbx.shelx.errors
else:
decode_variables = None
mt = flex.mersenne_twister(seed=0)
for sgi, site, expected_expr, no_fvar in test_case_generator():
sps = sgi.any_compatible_crystal_symmetry(volume=1000) \
.special_position_settings()
ss = sps.site_symmetry(site)
assert approx_equal(ss.exact_site(), site)
sos = ss.special_op_simplified()
expr = str(sos)
assert not show_diff(expr, expected_expr)
def check(site):
ns = dict(zip("xyz", site))
expr_site = eval(expr, ns, {})
assert approx_equal(expr_site, site, 1e-4)
#
shifted_site = (matrix.col(site) +
matrix.col(mt.random_double_point_on_sphere()))
ns = dict(zip("xyz", shifted_site))
expr_shifted_site = eval(expr, ns, {})
expr_shifted_site_exact = ss.special_op() * expr_shifted_site
assert approx_equal(expr_shifted_site, expr_shifted_site_exact)
check(site)
for i_trial in range(3):
shifted_site = ss.special_op() * (matrix.col(site) + matrix.col(
mt.random_double_point_on_sphere()))
check(shifted_site)
fvars = [None] # placeholder for scale factor
if (decode_variables is not None):
try:
coded_variables = ss.shelx_fvar_encoding(site=site,
fvars=fvars)
except iotbx.shelx.errors.error:
if (not no_fvar): raise
else:
assert not no_fvar
if (not no_fvar):
values, behaviors = decode_variables(
free_variable=fvars, coded_variables=coded_variables)
mismatch = sps.unit_cell().mod_short_distance(site, values)
assert mismatch < 1e-10
def exercise():
from scitbx.array_family import flex
from scitbx import matrix
from libtbx.test_utils import approx_equal, show_diff
import libtbx.load_env
if (libtbx.env.has_module(name="iotbx")):
from iotbx.shelx.parsers import decode_variables
import iotbx.shelx.errors
else:
decode_variables = None
mt = flex.mersenne_twister(seed=0)
for sgi,site,expected_expr,no_fvar in test_case_generator():
sps = sgi.any_compatible_crystal_symmetry(volume=1000) \
.special_position_settings()
ss = sps.site_symmetry(site)
assert approx_equal(ss.exact_site(), site)
sos = ss.special_op_simplified()
expr = str(sos)
assert not show_diff(expr, expected_expr)
def check(site):
ns = dict(zip("xyz", site))
expr_site = eval(expr, ns, {})
assert approx_equal(expr_site, site, 1e-4)
#
shifted_site = (
matrix.col(site) + matrix.col(mt.random_double_point_on_sphere()))
ns = dict(zip("xyz", shifted_site))
expr_shifted_site = eval(expr, ns, {})
expr_shifted_site_exact = ss.special_op() * expr_shifted_site
assert approx_equal(expr_shifted_site, expr_shifted_site_exact)
check(site)
for i_trial in xrange(3):
shifted_site = ss.special_op() * (
matrix.col(site) + matrix.col(mt.random_double_point_on_sphere()))
check(shifted_site)
fvars = [None] # placeholder for scale factor
if (decode_variables is not None):
try:
coded_variables = ss.shelx_fvar_encoding(site=site, fvars=fvars)
except iotbx.shelx.errors.error:
if (not no_fvar): raise
else:
assert not no_fvar
if (not no_fvar):
values, behaviors = decode_variables(
free_variable=fvars, coded_variables=coded_variables)
mismatch = sps.unit_cell().mod_short_distance(site, values)
assert mismatch < 1e-10
def dev_build_shelx76_fvars(xray_structure, validation_tolerance=1e-10):
from iotbx.shelx.parsers import decode_variables
fvars = [1]
encoded_sites = []
scs = xray_structure.scatterers()
sstab = xray_structure.site_symmetry_table()
for i_sc in xray_structure.special_position_indices():
site = scs[i_sc].site
ss = sstab.get(i_sc)
coded_variables = ss.shelx_fvar_encoding(site=site, fvars=fvars)
if (validation_tolerance is not None):
values, behaviors = decode_variables(
free_variable=fvars, coded_variables=coded_variables)
mismatch = xray_structure.unit_cell().distance(site, values)
assert mismatch < validation_tolerance
encoded_sites.append(coded_variables)
return fvars, encoded_sites
def dev_build_shelx76_fvars(xray_structure, validation_tolerance=1e-10):
from iotbx.shelx.parsers import decode_variables
fvars = [1]
encoded_sites = []
scs = xray_structure.scatterers()
sstab = xray_structure.site_symmetry_table()
for i_sc in xray_structure.special_position_indices():
site = scs[i_sc].site
ss = sstab.get(i_sc)
coded_variables = ss.shelx_fvar_encoding(site=site, fvars=fvars)
if validation_tolerance is not None:
values, behaviors = decode_variables(free_variable=fvars, coded_variables=coded_variables)
mismatch = xray_structure.unit_cell().distance(site, values)
assert mismatch < validation_tolerance
encoded_sites.append(coded_variables)
return fvars, encoded_sites