def _refine_bravais(self): # type: () -> None
"""Run `dials.refine_bravais_settings` to determine the space group."""
dials_start = timeit.default_timer()
info("\nRefining Bravais settings...")
self.refls = eliminate_sys_absent(self.expts, self.refls)
map_to_primitive(self.expts, self.refls)
try:
refined_settings = refined_settings_from_refined_triclinic(
self.expts, self.refls, self.params.dials_refine_bravais)
except RuntimeError as e:
warning("dials.refine_bravais_settings failed.\nGiving up.")
sys.exit(e)
possible_bravais_settings = {
solution["bravais"]
for solution in refined_settings
}
bravais_lattice_to_space_group_table(possible_bravais_settings)
try:
# Old version of dials with as_str() method
logger.info(refined_settings.as_str())
except AttributeError:
# Newer versions of dials (>= 2.2.2) has proper __str__ method
logger.info(refined_settings)
info(
"Successfully completed (%.1f sec)",
timeit.default_timer() - dials_start,
)
def refine_bravais_settings(self, reflections, experiments):
# configure DIALS logging
if self.dials_log:
log.config(verbosity=0, logfile=self.dials_log)
proc_scope = phil_scope.format(python_object=self.params)
sgparams = sg_scope.fetch(proc_scope).extract()
sgparams.refinement.reflections.outlier.algorithm = 'tukey'
crystal_P1 = copy.deepcopy(experiments[0].crystal)
# Generate Bravais settings
try:
Lfat = refined_settings_factory_from_refined_triclinic(sgparams,
experiments,
reflections,
lepage_max_delta=5)
except Exception as e:
# If refinement fails, reset to P1 (experiments remain modified by Lfat
# if there's a refinement failure, which causes issues down the line)
for expt in experiments:
expt.crystal = crystal_P1
return None
Lfat.labelit_printout()
# Filter out not-recommended (i.e. too-high rmsd and too-high max angular
# difference) solutions
Lfat_recommended = [s for s in Lfat if s.recommended]
# If none are recommended, return None (do not reindex)
if len(Lfat_recommended) == 0:
return None
# Find the highest symmetry group
possible_bravais_settings = set(solution['bravais'] for solution in
Lfat_recommended)
bravais_lattice_to_space_group_table(possible_bravais_settings)
lattice_to_sg_number = {
'aP': 1, 'mP': 3, 'mC': 5, 'oP': 16, 'oC': 20, 'oF': 22, 'oI': 23,
'tP': 75, 'tI': 79, 'hP': 143, 'hR': 146, 'cP': 195, 'cF': 196, 'cI': 197
}
filtered_lattices = {}
for key, value in lattice_to_sg_number.items():
if key in possible_bravais_settings:
filtered_lattices[key] = value
highest_sym_lattice = max(filtered_lattices, key=filtered_lattices.get)
highest_sym_solutions = [s for s in Lfat if s['bravais'] == highest_sym_lattice]
if len(highest_sym_solutions) > 1:
highest_sym_solution = sorted(highest_sym_solutions,
key=lambda x: x['max_angular_difference'])[0]
else:
highest_sym_solution = highest_sym_solutions[0]
return highest_sym_solution
def refine_bravais_settings(self, reflections, experiments):
# configure DIALS logging
if self.dials_log:
log.config(verbosity=1, logfile=self.dials_log)
proc_scope = phil_scope.format(python_object=self.params)
sgparams = sg_scope.fetch(proc_scope).extract()
sgparams.refinement.reflections.outlier.algorithm = "tukey"
crystal_P1 = copy.deepcopy(experiments[0].crystal)
try:
refined_settings = refined_settings_from_refined_triclinic(
experiments=experiments,
reflections=reflections,
params=sgparams)
possible_bravais_settings = {
s["bravais"]
for s in refined_settings
}
bravais_lattice_to_space_group_table(possible_bravais_settings)
except Exception:
for expt in experiments:
expt.crystal = crystal_P1
return None
# Generate Bravais settings
# try:
# Lfat = refined_settings_factory_from_refined_triclinic(sgparams,
# experiments,
# reflections,
# lepage_max_delta=5)
# except Exception as e:
# # If refinement fails, reset to P1 (experiments remain modified by Lfat
# # if there's a refinement failure, which causes issues down the line)
# for expt in experiments:
# expt.crystal = crystal_P1
# return None
#
# Lfat.labelit_printout()
#
# # Filter out not-recommended (i.e. too-high rmsd and too-high max angular
# # difference) solutions
# Lfat_recommended = [s for s in Lfat if s.recommended]
#
# # If none are recommended, return None (do not reindex)
# if len(Lfat_recommended) == 0:
# return None
#
# # Find the highest symmetry group
# possible_bravais_settings = set(solution['bravais'] for solution in
# Lfat_recommended)
# bravais_lattice_to_space_group_table(possible_bravais_settings)
lattice_to_sg_number = {
"aP": 1,
"mP": 3,
"mC": 5,
"oP": 16,
"oC": 20,
"oF": 22,
"oI": 23,
"tP": 75,
"tI": 79,
"hP": 143,
"hR": 146,
"cP": 195,
"cF": 196,
"cI": 197,
}
filtered_lattices = {}
for key, value in lattice_to_sg_number.items():
if key in possible_bravais_settings:
filtered_lattices[key] = value
highest_sym_lattice = max(filtered_lattices, key=filtered_lattices.get)
highest_sym_solutions = [
s for s in refined_settings if s["bravais"] == highest_sym_lattice
]
if len(highest_sym_solutions) > 1:
highest_sym_solution = sorted(
highest_sym_solutions,
key=lambda x: x["max_angular_difference"])[0]
else:
highest_sym_solution = highest_sym_solutions[0]
return highest_sym_solution