def from_dict(d):
''' Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
Returns:
The crystal model
'''
from dxtbx.model import Crystal
# If None, return None
if d is None:
return None
# Check the version and id
if str(d['__id__']) != "crystal":
raise ValueError("\"__id__\" does not equal \"crystal\"")
# Extract from the dictionary
real_space_a = d['real_space_a']
real_space_b = d['real_space_b']
real_space_c = d['real_space_c']
# str required to force unicode to ascii conversion
space_group = str("Hall:" + d['space_group_hall_symbol'])
xl = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group_symbol=space_group)
# Isoforms used for stills
try:
xl.identified_isoform = d['identified_isoform']
except KeyError:
pass
# Extract scan point setting matrices, if present
try:
A_at_scan_points = d['A_at_scan_points']
xl.set_A_at_scan_points(A_at_scan_points)
except KeyError:
pass
# Extract covariance of B, if present
try:
cov_B = d['B_covariance']
xl.set_B_covariance(cov_B)
except KeyError:
pass
# Extract covariance of B at scan points, if present
cov_B_at_scan_points = d.get('B_covariance_at_scan_points')
if cov_B_at_scan_points is not None:
from scitbx.array_family import flex
cov_B_at_scan_points = flex.double(cov_B_at_scan_points).as_1d()
cov_B_at_scan_points.reshape(flex.grid(xl.num_scan_points, 9, 9))
xl.set_B_covariance_at_scan_points(cov_B_at_scan_points)
return xl
def from_dict(d):
''' Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
Returns:
The crystal model
'''
from dxtbx.model import Crystal
# If None, return None
if d is None:
return None
# Check the version and id
if str(d['__id__']) != "crystal":
raise ValueError("\"__id__\" does not equal \"crystal\"")
# Extract from the dictionary
real_space_a = d['real_space_a']
real_space_b = d['real_space_b']
real_space_c = d['real_space_c']
# str required to force unicode to ascii conversion
space_group = str("Hall:" + d['space_group_hall_symbol'])
xl = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group_symbol=space_group)
# New parameters for maximum likelihood values
try:
xl._ML_half_mosaicity_deg = d['ML_half_mosaicity_deg']
except KeyError:
pass
try:
xl._ML_domain_size_ang = d['ML_domain_size_ang']
except KeyError:
pass
# Isoforms used for stills
try:
xl.identified_isoform = d['identified_isoform']
except KeyError:
pass
# Extract scan point setting matrices, if present
try:
A_at_scan_points = d['A_at_scan_points']
xl.set_A_at_scan_points(A_at_scan_points)
except KeyError:
pass
# Extract covariance of B, if present
try:
cov_B = d['B_covariance']
xl.set_B_covariance(cov_B)
except KeyError:
pass
# Extract mosaicity, if present
try:
mosaicity = d['mosaicity']
xl.set_mosaicity(mosaicity)
except KeyError:
pass
return xl