def run():
target_structure = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("I432"),
elements=['C']*6+['O'],
use_u_iso=False,
use_u_aniso=True,
)
shift = tuple(flex.random_double(3))
print "shift to be found: (%.3f, %.3f, %.3f)" % shift
target_structure_in_p1 = target_structure.expand_to_p1().apply_shift(shift)
miller_indices = miller.build_set(
crystal_symmetry=target_structure,
anomalous_flag=True,
d_min=0.8)
f_obs = miller_indices.structure_factors_from_scatterers(
xray_structure=target_structure,
algorithm="direct").f_calc().amplitudes()
miller_indices_in_p1 = miller.build_set(
crystal_symmetry=target_structure_in_p1,
anomalous_flag=True,
d_min=0.8)
f_calc = miller_indices_in_p1.structure_factors_from_scatterers(
xray_structure=target_structure_in_p1,
algorithm="direct").f_calc()
crystal_gridding = f_calc.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False,
have_f_part=False),
resolution_factor=1/2
)
omptbx.env.num_threads = 1
t_fast_tf = show_times()
fast_tf_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_obs.space_group(),
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_f_obs=f_obs.indices(),
f_obs=f_obs.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_calc.indices(),
p1_f_calc=f_calc.data()).target_map()
print
print "Fast translation function"
t_fast_tf()
t_cross_corr = show_times()
for op in target_structure.space_group():
f, op_times_f = f_calc.original_and_transformed(op)
cross_corr_map = miller.fft_map(crystal_gridding,
f * op_times_f.conjugate().data())
print
print "Traditional cross-correlation"
t_cross_corr()
def run():
target_structure = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("I432"),
elements=['C'] * 6 + ['O'],
use_u_iso=False,
use_u_aniso=True,
)
shift = tuple(flex.random_double(3))
print "shift to be found: (%.3f, %.3f, %.3f)" % shift
target_structure_in_p1 = target_structure.expand_to_p1().apply_shift(shift)
miller_indices = miller.build_set(crystal_symmetry=target_structure,
anomalous_flag=True,
d_min=0.8)
f_obs = miller_indices.structure_factors_from_scatterers(
xray_structure=target_structure,
algorithm="direct").f_calc().amplitudes()
miller_indices_in_p1 = miller.build_set(
crystal_symmetry=target_structure_in_p1,
anomalous_flag=True,
d_min=0.8)
f_calc = miller_indices_in_p1.structure_factors_from_scatterers(
xray_structure=target_structure_in_p1, algorithm="direct").f_calc()
crystal_gridding = f_calc.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False, have_f_part=False),
resolution_factor=1 / 2)
omptbx.env.num_threads = 1
t_fast_tf = show_times()
fast_tf_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_obs.space_group(),
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_f_obs=f_obs.indices(),
f_obs=f_obs.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_calc.indices(),
p1_f_calc=f_calc.data()).target_map()
print
print "Fast translation function"
t_fast_tf()
t_cross_corr = show_times()
for op in target_structure.space_group():
f, op_times_f = f_calc.original_and_transformed(op)
cross_corr_map = miller.fft_map(crystal_gridding,
f * op_times_f.conjugate().data())
print
print "Traditional cross-correlation"
t_cross_corr()
def run(args):
timer = show_times(time_start="now")
if (len(args) == 5):
exercise(
lbfgs_impl=eval(args[0]),
n=int(args[1]),
m=int(args[2]),
iprint=[int(args[3]), int(args[4])])
return
assert args in [[], ["--once"], ["--endless"]]
if (not have_lbfgs_fem):
print "Skipping some tests: lbfgs_fem.cpp not linked into scitbx_lbfgs_ext."
once = "--once" in args
endless = "--endless" in args
if (once or endless):
while 1:
if (have_lbfgs_fem):
exercise(lbfgs_impl=fortran)
exercise(lbfgs_impl=raw_reference)
exercise(lbfgs_impl=raw)
if (not endless): break
else:
compare_implementations()
timer()
print "OK"
def run(args):
timer = show_times(time_start="now")
if len(args) == 5:
exercise(lbfgs_impl=eval(args[0]),
n=int(args[1]),
m=int(args[2]),
iprint=[int(args[3]), int(args[4])])
return
assert args in [[], ["--once"], ["--endless"]]
if not have_lbfgs_fem:
print(
"Skipping some tests: lbfgs_fem.cpp not linked into scitbx_lbfgs_ext."
)
once = "--once" in args
endless = "--endless" in args
while once or endless:
if have_lbfgs_fem:
exercise(lbfgs_impl=fortran)
exercise(lbfgs_impl=raw_reference)
exercise(lbfgs_impl=raw)
once = False
else:
compare_implementations()
timer()
print("OK")
def run_program(program_class=None,
custom_process_arguments=None,
args=None,
logger=None):
'''
Function for running programs using CCTBXParser and the program template
:param program_class: ProgramTemplate type (required)
:param custom_process_arguments:
Custom function to parse unknown arguments (optional)
:param args: list of command-line arguments (optional)
:param logger: logger (e.g. multi_out) for output (optional)
:rtype: whatever is returned from program_class.get_results()
'''
assert program_class is not None
if args is None:
args = sys.argv[1:]
# create logger
if logger is None:
logger = multi_out()
logger.register('stdout', sys.stdout)
logger.register('parser_log', StringIO())
# start timer
t = show_times(out=logger)
# create parser
parser = CCTBXParser(program_class=program_class,
custom_process_arguments=custom_process_arguments,
logger=logger)
namespace = parser.parse_args(args)
# start program
print('Starting job', file=logger)
print('=' * 79, file=logger)
task = program_class(parser.data_manager,
parser.working_phil.extract(),
master_phil=parser.master_phil,
logger=logger)
# validate inputs
task.validate()
# run program
task.run()
# clean up (optional)
task.clean_up()
# stop timer
print('', file=logger)
print('=' * 79, file=logger)
print('Job complete', file=logger)
t()
return task.get_results()
def run_molprobity_program(program_class=None,
custom_process_arguments=None,
args=None,
logger=None):
'''
Function for running programs using CCTBXParser and the program template
:param program_class: ProgramTemplate type (required)
:param custom_process_arguments:
Custom function to parse unknown arguments (optional)
:param args: list of command-line arguments (optional)
:param logger: logger (e.g. multi_out) for output (optional)
:rtype: whatever is returned from program_class.get_results()
'''
assert (program_class is not None)
if (args is None):
args = sys.argv[1:]
# create logger
if (logger is None):
logger = multi_out()
logger.register('stdout', sys.stdout)
# start timer
t = show_times(out=logger)
# create parser
parser = MolProbityParser(
program_class=program_class,
custom_process_arguments=custom_process_arguments,
logger=logger)
namespace = parser.parse_args(args)
# start program
print('Starting job', file=logger)
print('=' * 79, file=logger)
task = program_class(parser.data_manager,
parser.working_phil.extract(),
master_phil=parser.master_phil,
logger=logger)
# custom constructor (optional)
task.custom_init()
# validate inputs
task.validate()
# run program
task.run()
# clean up (optional)
task.clean_up()
# output JSON file for PDB
if (namespace.write_pdb_json):
filename, ext = os.path.splitext(
os.path.basename(parser.data_manager.get_default_model_name()))
filename += '_pdb.json'
json_text = task.get_results_as_PDB_JSON()
print('\nJSON output')
print('-' * 79, file=logger)
print(' Writing results in JSON format to %s.' % filename,
file=logger)
parser.data_manager._write_text(None,
filename,
json_text,
overwrite=namespace.overwrite)
# stop timer
print('', file=logger)
print('=' * 79, file=logger)
print('Job complete', file=logger)
t()
return task.get_results()
def run_program(program_class=None,
parser_class=CCTBXParser,
custom_process_arguments=None,
unused_phil_raises_sorry=True,
args=None,
json=False,
logger=None):
'''
Function for running programs using CCTBXParser and the program template
Parameters
----------
program_class: ProgramTemplate
The class defining the program. It must be a subclass of ProgramTemplate
parser_class: CCTBXParser
The parser class to use for parsing. It must be the CCTBXParser or a subclass
custom_process_arguments: function(parser)
Custom function to parse unknown arguments (optional)
unused_phil_raises_sorry: bool
If False, any unused PHIL parameters are kept for parsing later
args: list
List of command-line arguments (optional)
json: bool
If True, get_results_as_JSON is called for the return value instead of get_results
logger: multi_out
For logging output (optional)
Returns
-------
Whatever is returned from program_class.get_results() or program_class.get_results_as_JSON()
'''
assert program_class is not None
if args is None:
args = sys.argv[1:]
# start profiling
pr = None
if '--profile' in args:
import cProfile
pr = cProfile.Profile()
pr.enable()
# keep output in quiet mode
if '--quiet' in args:
logger = multi_out()
logger.register('parser_log', StringIO())
# create logger
if logger is None:
logger = multi_out()
logger.register('stdout', sys.stdout)
logger.register('parser_log', StringIO())
# start timer
t = show_times(out=logger)
# create parser
parser = parser_class(program_class=program_class,
custom_process_arguments=custom_process_arguments,
unused_phil_raises_sorry=unused_phil_raises_sorry,
logger=logger)
namespace = parser.parse_args(args)
# start program
if namespace.dry_run:
print('Starting dry run', file=logger)
else:
print('Starting job', file=logger)
print('=' * 79, file=logger)
task = program_class(parser.data_manager,
parser.working_phil.extract(),
master_phil=parser.master_phil,
logger=logger)
# validate inputs
task.validate()
# stop if dry_run is set
if namespace.dry_run:
print('\nArguments have been validated by the program.\n', file=logger)
print('=' * 79, file=logger)
return
# run program
task.run()
# clean up (optional)
task.clean_up()
# dump profiling stats
if pr is not None:
pr.disable()
pr.dump_stats('profile.out')
# output JSON
if namespace.json:
result = task.get_results_as_JSON()
if result is not None:
with open(parser.json_filename, 'w') as f:
f.write(result)
else:
print('', file=logger)
print('!' * 79, file=logger)
print(
'WARNING: The get_results_as_JSON function has not been defined for this program'
)
print('!' * 79, file=logger)
# stop timer
print('', file=logger)
print('=' * 79, file=logger)
print('Job complete', file=logger)
t()
# clean up file for quiet mode
if namespace.quiet:
logger.close()
if json:
result = task.get_results_as_JSON()
else:
result = task.get_results()
return result