def exercise():
from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex
sc = xray.scatterer
xs = xray.structure(
# COD entry 2103456, selected atoms
crystal_symmetry=crystal.symmetry(unit_cell=(10.1053, 10.1053, 10.1053,
90, 90, 90),
space_group_symbol="P 21 3"),
scatterers=flex.xray_scatterer((sc(label='ER1',
site=(-0.16698, 0.66698, 0.33302)),
sc(label='ER2',
site=(0.39957, 0.60043, 0.10043)))))
#
from iotbx.shelx import fvar_encoding
xsm = fvar_encoding.move_sites_if_necessary_for_shelx_fvar_encoding(xs)
from six.moves import cStringIO as StringIO
sio = StringIO()
xsm.show_scatterers(f=sio)
from libtbx.test_utils import show_diff
assert not show_diff(
sio.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
ER1 Er 4 (-0.1670 -0.3330 0.3330) 1.00 0.0000 [ - ]
ER2 Er 4 ( 0.3996 -0.3996 0.1004) 1.00 0.0000 [ - ]
""")
#
from iotbx.shelx.errors import error
from libtbx.test_utils import Exception_expected, approx_equal
try:
fvar_encoding.dev_build_shelx76_fvars(xs)
except error:
pass
else:
raise Exception_expected
#
fvars, encoded_sites = fvar_encoding.dev_build_shelx76_fvars(xsm)
assert approx_equal(fvars, [1, 0.33396, 0.79914])
assert approx_equal(encoded_sites,
[[19.5, -19.5, -20.5], [30.5, 29.5, -30.5]])
def process(params, pickle_file_name):
cod_id = op.basename(pickle_file_name).split(".", 1)[0]
print "cod_id:", cod_id
c_obs, structure_prep, edge_list = easy_pickle.load(
file_name=pickle_file_name)
changes = structure_prep.make_scatterer_labels_shelx_compatible_in_place()
if (params.sites_mod_short):
structure_prep = structure_prep.sites_mod_short()
from iotbx.shelx import fvar_encoding
structure_prep = \
fvar_encoding.move_sites_if_necessary_for_shelx_fvar_encoding(
xray_structure=structure_prep)
structure_prep.show_summary().show_scatterers()
if (len(changes) != 0):
from libtbx.utils import plural_s
print "INFO: %d atom name%s changed for compatibility with SHELXL:" \
% plural_s(len(changes))
for change in changes:
print ' changed: "%s" -> "%s"' % change
structure_prep.scattering_type_registry(table="it1992").show()
fvar_encoding.dev_build_shelx76_fvars(structure_prep) # only an exercise
print "." * 79
#
if (len(params.optimizers) == 0):
return
#
assert c_obs.is_xray_intensity_array() or c_obs.is_xray_amplitude_array()
if (c_obs.is_xray_intensity_array()):
i_obs = c_obs
f_obs = c_obs.f_sq_as_f(algorithm="xtal_3_7")
else:
f_obs = c_obs
i_obs = c_obs.f_as_f_sq(algorithm="shelxl")
process_continue(params=params,
cod_id=cod_id,
c_obs=c_obs,
i_obs=i_obs,
f_obs=f_obs,
structure_prep=structure_prep)
def process(params, pickle_file_name):
cod_id = op.basename(pickle_file_name).split(".",1)[0]
print "cod_id:", cod_id
c_obs, structure_prep, edge_list = easy_pickle.load(
file_name=pickle_file_name)
changes = structure_prep.make_scatterer_labels_shelx_compatible_in_place()
if (params.sites_mod_short):
structure_prep = structure_prep.sites_mod_short()
from iotbx.shelx import fvar_encoding
structure_prep = \
fvar_encoding.move_sites_if_necessary_for_shelx_fvar_encoding(
xray_structure=structure_prep)
structure_prep.show_summary().show_scatterers()
if (len(changes) != 0):
from libtbx.utils import plural_s
print "INFO: %d atom name%s changed for compatibility with SHELXL:" \
% plural_s(len(changes))
for change in changes:
print ' changed: "%s" -> "%s"' % change
structure_prep.scattering_type_registry(table="it1992").show()
fvar_encoding.dev_build_shelx76_fvars(structure_prep) # only an exercise
print "."*79
#
if (len(params.optimizers) == 0):
return
#
assert c_obs.is_xray_intensity_array() or c_obs.is_xray_amplitude_array()
if (c_obs.is_xray_intensity_array()):
i_obs = c_obs
f_obs = c_obs.f_sq_as_f(algorithm="xtal_3_7")
else:
f_obs = c_obs
i_obs = c_obs.f_as_f_sq(algorithm="shelxl")
process_continue(
params=params,
cod_id=cod_id,
c_obs=c_obs, i_obs=i_obs, f_obs=f_obs,
structure_prep=structure_prep)
def exercise():
from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex
sc = xray.scatterer
xs = xray.structure(
# COD entry 2103456, selected atoms
crystal_symmetry=crystal.symmetry(
unit_cell=(10.1053, 10.1053, 10.1053, 90, 90, 90),
space_group_symbol="P 21 3"),
scatterers=flex.xray_scatterer((
sc(label='ER1', site=(-0.16698, 0.66698, 0.33302)),
sc(label='ER2', site=(0.39957, 0.60043, 0.10043)))))
#
from iotbx.shelx import fvar_encoding
xsm = fvar_encoding.move_sites_if_necessary_for_shelx_fvar_encoding(xs)
from cStringIO import StringIO
sio = StringIO()
xsm.show_scatterers(f=sio)
from libtbx.test_utils import show_diff
assert not show_diff(sio.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
ER1 Er 4 (-0.1670 -0.3330 0.3330) 1.00 0.0000 [ - ]
ER2 Er 4 ( 0.3996 -0.3996 0.1004) 1.00 0.0000 [ - ]
""")
#
from iotbx.shelx.errors import error
from libtbx.test_utils import Exception_expected, approx_equal
try: fvar_encoding.dev_build_shelx76_fvars(xs)
except error: pass
else: raise Exception_expected
#
fvars, encoded_sites = fvar_encoding.dev_build_shelx76_fvars(xsm)
assert approx_equal(fvars, [1, 0.33396, 0.79914])
assert approx_equal(encoded_sites,
[[19.5, -19.5, -20.5], [30.5, 29.5, -30.5]])
