def structure_factors_from_fcf(file_path, xs=None):
cif = iotbx.cif.reader(file_path=file_path).model()
cif_block = cif.values()[0]
if '_shelx_refln_list_code' in cif_block:
assert cif_block['_shelx_refln_list_code'] == '4'
arrays = iotbx.cif.builders.miller_array_builder(cif_block).arrays()
fo2 = arrays['_refln_F_squared_meas']
fc2 = arrays['_refln_F_squared_calc']
if xs is None:
fc = fc2.f_sq_as_f().phase_transfer(flex.double(fc2.size(), 0))
scale = 1
else:
fc = fo2.structure_factors_from_scatterers(xs, algorithm="direct").f_calc()
scale = fo2.scale_factor(fc)
return xs, fo2, fc, scale
def run_once(file_path,
nu=None,
log=None,
atomic_form_factors=None,
inelastic_form_factors="henke",
chiral_space_groups_only=False,
outlier_cutoff_factor=2):
if log is None:
log = sys.stdout
file_root, file_ext = os.path.splitext(file_path)
hkl_path = file_root + '.hkl'
fcf_path = file_root + '.fcf'
if file_ext in ('.fcf', '.hkl'):
xs, fo2, fc, scale = structure_factors_from_fcf(file_path)
elif file_ext == '.cif':
cif = iotbx.cif.reader(file_path=file_path).model()
cif_block = cif.values()[0]
wavelength = float(cif_block['_diffrn_radiation_wavelength'])
xs = iotbx.cif.builders.crystal_structure_builder(cif_block).structure
xs.set_inelastic_form_factors(photon=wavelength,
table=inelastic_form_factors)
if os.path.exists(fcf_path):
xs, fo2, fc, scale = structure_factors_from_fcf(fcf_path, xs)
elif os.path.exists(hkl_path):
try:
xs, fo2, fc, scale = structure_factors_from_hkl(hkl_path, xs)
except RuntimeError:
xs, fo2, fc, scale = structure_factors_from_fcf(hkl_path, xs)
else:
return
else:
if not os.path.exists(hkl_path): return
xs, fo2, fc, scale = structure_factors_from_ins_res(file_path)
if fc.space_group().is_centric() or (chiral_space_groups_only
and not fc.space_group().is_chiral()):
return
print >> log, file_path
fc.space_group_info().show_summary(f=log)
print >> log, "space_group.is_chiral(): " + str(
fc.space_group().is_chiral())
absolute_structure_analysis(xs,
fo2,
fc,
scale,
nu=nu,
log=log,
outlier_cutoff_factor=outlier_cutoff_factor)
log.flush()
def structure_factors_from_fcf(file_path, xs=None):
cif = iotbx.cif.reader(file_path=file_path).model()
cif_block = cif.values()[0]
if '_shelx_refln_list_code' in cif_block:
assert cif_block['_shelx_refln_list_code'] == '4'
arrays = iotbx.cif.builders.miller_array_builder(cif_block).arrays()
fo2 = arrays['_refln_F_squared_meas']
fc2 = arrays['_refln_F_squared_calc']
if xs is None:
fc = fc2.f_sq_as_f().phase_transfer(flex.double(fc2.size(), 0))
scale = 1
else:
fc = fo2.structure_factors_from_scatterers(
xs, algorithm="direct").f_calc()
scale = fo2.scale_factor(fc)
return xs, fo2, fc, scale
def run_once(file_path, nu=None, log=None, atomic_form_factors=None,
inelastic_form_factors="henke", chiral_space_groups_only=False,
outlier_cutoff_factor=2):
if log is None:
log = sys.stdout
file_root, file_ext = os.path.splitext(file_path)
hkl_path = file_root + '.hkl'
fcf_path = file_root + '.fcf'
if file_ext in ('.fcf', '.hkl'):
xs, fo2, fc, scale = structure_factors_from_fcf(file_path)
elif file_ext == '.cif':
cif = iotbx.cif.reader(file_path=file_path).model()
cif_block = cif.values()[0]
wavelength = float(cif_block['_diffrn_radiation_wavelength'])
xs = iotbx.cif.builders.crystal_structure_builder(cif_block).structure
xs.set_inelastic_form_factors(
photon=wavelength, table=inelastic_form_factors)
if os.path.exists(fcf_path):
xs, fo2, fc, scale = structure_factors_from_fcf(fcf_path, xs)
elif os.path.exists(hkl_path):
try:
xs, fo2, fc, scale = structure_factors_from_hkl(hkl_path, xs)
except RuntimeError:
xs, fo2, fc, scale = structure_factors_from_fcf(hkl_path, xs)
else: return
else:
if not os.path.exists(hkl_path): return
xs, fo2, fc, scale = structure_factors_from_ins_res(file_path)
if fc.space_group().is_centric() or (chiral_space_groups_only and
not fc.space_group().is_chiral()):
return
print >> log, file_path
fc.space_group_info().show_summary(f=log)
print >> log, "space_group.is_chiral(): " + str(fc.space_group().is_chiral())
absolute_structure_analysis(xs, fo2, fc, scale, nu=nu, log=log,
outlier_cutoff_factor=outlier_cutoff_factor)
log.flush()
