Example #1
0
def run():
    exercise_all_twelve_neighbors()
    exercise_groel_sampling(verbose=("--Verbose" in sys.argv[1:]))
    debug_utils.parse_options_loop_space_groups(
        sys.argv[1:], run_call_back,
        ("strictly_inside", "all_twelve_neighbors", "write_pdb"))
    print("OK")
Example #2
0
def run():
    show_times = libtbx.utils.show_times()
    debug_utils.parse_options_loop_space_groups(argv=sys.argv[1:],
                                                call_back=run_call_back,
                                                show_cpu_times=False)
    xray.structure_factors.global_counters.show()
    show_times()
Example #3
0
def run():
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back_1,
    symbols_to_stdout=True, symbols_to_stderr=False)
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back,
    symbols_to_stdout=True, symbols_to_stderr=False)
  test_grid_step()
  print "OK"
def run(args):
  from scitbx.array_family import flex
  import random
  random.seed(0)
  flex.set_random_seed(0)
  from cctbx.development import debug_utils
  debug_utils.parse_options_loop_space_groups(args, run_call_back)
Example #5
0
def run(args):
  from scitbx.array_family import flex
  import random
  random.seed(0)
  flex.set_random_seed(0)
  from cctbx.development import debug_utils
  debug_utils.parse_options_loop_space_groups(args, run_call_back)
Example #6
0
def run():
    show_times = libtbx.utils.show_times()
    debug_utils.parse_options_loop_space_groups(argv=sys.argv[1:],
                                                call_back=run_call_back,
                                                show_cpu_times=False)
    exercise_negative_parameters()
    show_times()
def exercise():
  if (mtz is None):
    print \
      "Skipping iotbx/regression/tst_reflection_statistics.py:" \
      " ccp4io not available"
    return
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
Example #8
0
def run():
  exercise_1()
  exercise_2()
  exercise_3()
  exercise_4()
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back,
    symbols_to_stdout=True, symbols_to_stderr=False)
Example #9
0
def exercise():
    if (mtz is None):
        print \
          "Skipping iotbx/regression/tst_reflection_statistics.py:" \
          " ccp4io not available"
        return
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
def run():
  exercise_all_twelve_neighbors()
  exercise_groel_sampling(verbose=("--Verbose" in sys.argv[1:]))
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back, (
    "strictly_inside",
    "all_twelve_neighbors",
    "write_pdb"))
  print "OK"
def run():
  show_times = libtbx.utils.show_times()
  debug_utils.parse_options_loop_space_groups(
    argv=sys.argv[1:],
    call_back=run_call_back,
    show_cpu_times=False)
  xray.structure_factors.global_counters.show()
  show_times()
def run():
    debug_utils.parse_options_loop_space_groups(
        sys.argv[1:],
        call_back=exercise,
        keywords=('include_high_symmetry', 'fix_seed', 'repeats'),
        symbols_to_stderr=False,
        n_sampled=50,
    )
Example #13
0
def run():
    exercise_symmetry()
    exercise_correct_rhombohedral_setting_if_necessary()
    exercise_non_crystallographic_symmetry()
    exercise_special_position_settings()
    exercise_select_crystal_symmetry()
    verify_definitions_in_paper_zwart_2007()
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
def run():
  show_times = libtbx.utils.show_times()
  debug_utils.parse_options_loop_space_groups(
    argv=sys.argv[1:],
    call_back=run_call_back,
    show_cpu_times=False)
  exercise_negative_parameters()
  show_times()
Example #15
0
def run():
  exercise_symmetry()
  exercise_correct_rhombohedral_setting_if_necessary()
  exercise_non_crystallographic_symmetry()
  exercise_special_position_settings()
  exercise_select_crystal_symmetry()
  verify_definitions_in_paper_zwart_2007()
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
def run():
  debug_utils.parse_options_loop_space_groups(
    sys.argv[1:],
    call_back=exercise,
    keywords=('include_high_symmetry', 'fix_seed', 'repeats'),
    symbols_to_stderr=False,
    n_sampled=50,
  )
Example #17
0
def run():
    exercise_1()
    exercise_2()
    exercise_3()
    exercise_4()
    debug_utils.parse_options_loop_space_groups(sys.argv[1:],
                                                run_call_back,
                                                symbols_to_stdout=True,
                                                symbols_to_stderr=False)
def exercise_charge_flipping():
    # exercise_sucrose(flipping_type=charge_flipping.weak_reflection_improved_iterator,
    # anomalous_flag=False,
    # d_min=0.7)
    import sys

    debug_utils.parse_options_loop_space_groups(
        sys.argv[1:], exercise, keywords=("repeats", "on", "algo", "fix_seed", "high_symmetry"), symbols_to_stderr=False
    )
Example #19
0
def tst_run_requiring_cns(args, call_back):
  import libtbx.path
  if (libtbx.path.full_command_path(command="cns") is None):
    print("Skipping tests: cns not available.")
  else:
    debug_utils.parse_options_loop_space_groups(
      argv=args, call_back=call_back, show_cpu_times=False)
  from libtbx.utils import format_cpu_times
  print(format_cpu_times())
Example #20
0
def tst_run_requiring_cns(args, call_back):
  import libtbx.path
  if (libtbx.path.full_command_path(command="cns") is None):
    print "Skipping tests: cns not available."
  else:
    debug_utils.parse_options_loop_space_groups(
      argv=args, call_back=call_back, show_cpu_times=False)
  from libtbx.utils import format_cpu_times
  print format_cpu_times()
Example #21
0
def run():
  exercise_reference_table()
  for space_group_number in range(1,230+1):
    asu = reference_table.get_asu(space_group_number)
    exercise_shape_vertices(asu=asu, unit_cell=None)
  debug_utils.parse_options_loop_space_groups(
    sys.argv[1:], run_call_back, show_cpu_times=False)
  exercise_is_simple_interaction()
  exercise_non_crystallographic_asu_mappings()
  print(format_cpu_times())
def run():
  exercise_reference_table()
  for space_group_number in xrange(1,230+1):
    asu = reference_table.get_asu(space_group_number)
    exercise_shape_vertices(asu=asu, unit_cell=None)
  debug_utils.parse_options_loop_space_groups(
    sys.argv[1:], run_call_back, show_cpu_times=False)
  exercise_is_simple_interaction()
  exercise_non_crystallographic_asu_mappings()
  print format_cpu_times()
Example #23
0
def run():
    debug_utils.parse_options_loop_space_groups(sys.argv[1:],
                                                run_call_back_1,
                                                symbols_to_stdout=True,
                                                symbols_to_stderr=False)
    debug_utils.parse_options_loop_space_groups(sys.argv[1:],
                                                run_call_back,
                                                symbols_to_stdout=True,
                                                symbols_to_stderr=False)
    test_grid_step()
    print "OK"
Example #24
0
def exercise_charge_flipping():
    #exercise_sucrose(flipping_type=charge_flipping.weak_reflection_improved_iterator,
    #anomalous_flag=False,
    #d_min=0.7)
    import sys
    debug_utils.parse_options_loop_space_groups(
        sys.argv[1:],
        exercise,
        keywords=("repeats", 'on', 'algo', 'fix_seed', 'high_symmetry'),
        symbols_to_stderr=False,
    )
def run(args):
  master_phil = libtbx.phil.parse("""
    general_positions_only = True
      .type = bool
    curvature_rescaling = True
      .type = bool
    minimizer = *lbfgs lbfgs_raw lbfgsb
      .type = choice
      .optional = False
    diagco = 0
      .type = int
    lbfgs_impl_switch = 1
      .type = int
    iprint = 1, 0
      .type = ints(size=2)
    curv_filter_lim_eps = 1e-3
      .type = float
    use_max_stp = True
      .type = bool
    shake_sites_rmsd = 0.5
      .type = float
    shake_adp_spread = 20
      .type = float
    pickle_root_name = None
      .type = str
    unpickle = None
      .type = path
""")
  argument_interpreter = master_phil.command_line_argument_interpreter()
  phil_objects = []
  remaining_args = []
  for arg in args:
    if (arg.find("=") >= 0):
      phil_objects.append(argument_interpreter.process(arg=arg))
    else:
      remaining_args.append(arg)
  work_phil = master_phil.fetch(sources=phil_objects)
  work_phil.show()
  print
  params = work_phil.extract()
  if (params.unpickle is None):
    debug_utils.parse_options_loop_space_groups(
      argv=remaining_args, call_back=run_call_back, params=params)
  else:
    structure_ideal, structure_shake = easy_pickle.load(
      file_name=params.unpickle)
    run_refinement(
      structure_ideal=structure_ideal,
      structure_shake=structure_shake,
      params=params,
      run_id=params.unpickle)
Example #26
0
def run(args):
    master_phil = libtbx.phil.parse("""
    general_positions_only = True
      .type = bool
    curvature_rescaling = True
      .type = bool
    minimizer = *lbfgs lbfgs_raw lbfgsb
      .type = choice
      .optional = False
    diagco = 0
      .type = int
    lbfgs_impl_switch = 1
      .type = int
    iprint = 1, 0
      .type = ints(size=2)
    curv_filter_lim_eps = 1e-3
      .type = float
    use_max_stp = True
      .type = bool
    shake_sites_rmsd = 0.5
      .type = float
    shake_adp_spread = 20
      .type = float
    pickle_root_name = None
      .type = str
    unpickle = None
      .type = path
""")
    argument_interpreter = master_phil.command_line_argument_interpreter()
    phil_objects = []
    remaining_args = []
    for arg in args:
        if (arg.find("=") >= 0):
            phil_objects.append(argument_interpreter.process(arg=arg))
        else:
            remaining_args.append(arg)
    work_phil = master_phil.fetch(sources=phil_objects)
    work_phil.show()
    print
    params = work_phil.extract()
    if (params.unpickle is None):
        debug_utils.parse_options_loop_space_groups(argv=remaining_args,
                                                    call_back=run_call_back,
                                                    params=params)
    else:
        structure_ideal, structure_shake = easy_pickle.load(
            file_name=params.unpickle)
        run_refinement(structure_ideal=structure_ideal,
                       structure_shake=structure_shake,
                       params=params,
                       run_id=params.unpickle)
Example #27
0
def exercise():
    if (mtz is None):
        print "Skipping iotbx/mtz/tst.py: ccp4io not available"
        return
    from cctbx import sgtbx
    exercise_unmerged(sgtbx.space_group_info("I23"))
    exercise_wavelength()
    exercise_extract_delta_anomalous()
    exercise_repair_ccp4i_import_merged_data()
    exercise_miller_array_data_types()
    for anomalous_flag in [False, True]:
        exercise_hl_ab_only(anomalous_flag=anomalous_flag)
    exercise_util()
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
Example #28
0
def run():
  match_symmetry = emma.euclidean_match_symmetry(
    space_group_info=sgtbx.space_group_info(symbol="P1"),
    use_k2l=True,
    use_l2n=False)
  out = StringIO()
  match_symmetry.show(title="test", f=out)
  assert not show_diff(out.getvalue(), """\
euclidean_match_symmetry: test
P -1
((1, 0, 0), (0, 1, 0), (0, 0, 1))
""")
  #
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back, (
    "StaticModels",))
Example #29
0
def exercise():
    if mtz is None:
        print "Skipping iotbx/mtz/tst.py: ccp4io not available"
        return
    from cctbx import sgtbx

    exercise_unmerged(sgtbx.space_group_info("I23"))
    exercise_wavelength()
    exercise_extract_delta_anomalous()
    exercise_repair_ccp4i_import_merged_data()
    exercise_miller_array_data_types()
    for anomalous_flag in [False, True]:
        exercise_hl_ab_only(anomalous_flag=anomalous_flag)
    exercise_util()
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
Example #30
0
def run():
  match_symmetry = emma.euclidean_match_symmetry(
    space_group_info=sgtbx.space_group_info(symbol="P1"),
    use_k2l=True,
    use_l2n=False)
  out = StringIO()
  match_symmetry.show(title="test", f=out)
  assert not show_diff(out.getvalue(), """\
euclidean_match_symmetry: test
P -1
((1, 0, 0), (0, 1, 0), (0, 0, 1))
""")
  #
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back, (
    "StaticModels",))
Example #31
0
def run(args):
  master_phil = dev.get_master_phil()
  argument_interpreter = master_phil.command_line_argument_interpreter()
  phil_objects = []
  remaining_args = []
  for arg in args:
    if (arg.find("=") >= 0):
      phil_objects.append(argument_interpreter.process(arg=arg))
    else:
      remaining_args.append(arg)
  work_phil = master_phil.fetch(sources=phil_objects)
  work_phil.show()
  print()
  params = work_phil.extract()
  debug_utils.parse_options_loop_space_groups(
    argv=remaining_args, call_back=run_call_back, params=params)
Example #32
0
def run(args):
  master_phil = dev.get_master_phil()
  argument_interpreter = master_phil.command_line_argument_interpreter()
  phil_objects = []
  remaining_args = []
  for arg in args:
    if (arg.find("=") >= 0):
      phil_objects.append(argument_interpreter.process(arg=arg))
    else:
      remaining_args.append(arg)
  work_phil = master_phil.fetch(sources=phil_objects)
  work_phil.show()
  print
  params = work_phil.extract()
  debug_utils.parse_options_loop_space_groups(
    argv=remaining_args, call_back=run_call_back, params=params)
def run():
  cmd_args = ['--F', '--F_sq', '--debugging']
  extra = []
  args = []
  for arg in sys.argv[1:]:
    if arg in cmd_args:
      extra.append(arg[2:])
    else:
      args.append(arg)
  extra = tuple(extra)
  debug = ()
  if 'debugging' in extra:
    extra = ()
    if 0:
      extra += ('F_sq',)
  assert not('F' in extra and 'F_sq' in extra)
  if 'F' in extra: print 'Refinement against F'
  if 'F_sq' in extra: print 'Refinement against F^2'
  debug_utils.parse_options_loop_space_groups(
    args, run_call_back, keywords=extra+debug)
Example #34
0
def run():
  cmd_args = ['--F', '--F_sq', '--debugging']
  extra = []
  args = []
  for arg in sys.argv[1:]:
    if arg in cmd_args:
      extra.append(arg[2:])
    else:
      args.append(arg)
  extra = tuple(extra)
  debug = ()
  if 'debugging' in extra:
    extra = ()
    if 0:
      extra += ('F_sq',)
  assert not('F' in extra and 'F_sq' in extra)
  if 'F' in extra: print('Refinement against F')
  if 'F_sq' in extra: print('Refinement against F^2')
  debug_utils.parse_options_loop_space_groups(
    args, run_call_back, keywords=extra+debug)
Example #35
0
def run(args):
    if (libtbx.path.full_command_path(command="shelxl") is None):
        print "shelxl not available."
        return
    debug_utils.parse_options_loop_space_groups(args, run_call_back)
def run():
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back,
                                                ("Frac", "Cart"))
Example #37
0
def run():
    import sys
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], exercise)
Example #38
0
def run():
  exercise_sys_absent_intensity_distribution()
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
  print("OK")
Example #39
0
def run():
  structure = exercise_with_fixed_structure()
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
def run():
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], exercise_all_wyckoff)
Example #41
0
def run():
  debug_utils.parse_options_loop_space_groups(
    argv=sys.argv[1:], call_back=run_call_back, keywords=("quick",),
    symbols_to_stdout=True, symbols_to_stderr=False)
def run():
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
  if (0):
    print "len(cond_dict):", len(cond_dict)
    for k in cond_dict.keys():
      print k
Example #43
0
def run():
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
    print "OK"
Example #44
0
def run():
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back, (
    "HighSymmetry",
    "Atom",
    "Molecule",
    "Shift"))
def run(args):
  debug_utils.parse_options_loop_space_groups(args, run_call_back, (
    "chunk",
    "isotropic",
    "anisotropic",
    "tag"))
def run():
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
Example #47
0
def run():
  exercise_constraint_matrix()
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
def run():
  exercise_sys_absent_intensity_distribution()
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
  print "OK"
Example #49
0
def run():
    debug_utils.parse_options_loop_space_groups(argv=sys.argv[1:],
                                                call_back=run_call_back,
                                                keywords=("quick", ),
                                                symbols_to_stdout=True,
                                                symbols_to_stderr=False)
Example #50
0
def run():
  debug_utils.parse_options_loop_space_groups(
    sys.argv[1:],
    run_call_back,
    keywords=("fix_random_seeds",),
  )
def run(args):
  exercise(
    space_group_info=sgtbx.space_group_info(symbol="P222"),
    redundancy_counter=1)
  debug_utils.parse_options_loop_space_groups(args, run_call_back)
def run():
  debug_utils.parse_options_loop_space_groups(
    sys.argv[1:],
    run_call_back,
    keywords=("fix_random_seeds",),
  )
Example #53
0
def run():
    debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
    exercise_overloads()
def run(args):
    debug_utils.parse_options_loop_space_groups(args, run_call_back,
                                                ("isotropic", "anisotropic"))
Example #55
0
  mo3 = mmtbx.masks.mask_from_xray_structure(
    xray_structure=xrs,
    p1=True,
    solvent_radius=1,
    shrink_truncation_radius=1,
    for_structure_factors=True,
    n_real=n_real)
  f_mask_3 = dummy_set.structure_factors_from_map(map=mo3.mask_data,
    use_scale = True, anomalous_flag = False, use_sg = False) # Note use_sg = False !
  #
  assert approx_equal(f_mask_1.data(), f_mask_2.data())
  assert approx_equal(f_mask_1.data(), f_mask_3.data())

def run_call_back(flags, space_group_info):
  exercise_mask_data_1(space_group_info)
  exercise_mask_data_2(space_group_info)
  exercise_mask_data_3(space_group_info)

if (__name__ == "__main__"):
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back,
    symbols_to_stdout=True, symbols_to_stderr=False)
  try:
    run()
  except Exception :
    log = cout.getvalue()
    if len(log) != 0:
      print "<<<<<<<< Start Log:"
      print cout.getvalue()
      print ">>>>>>>> End Log"
    raise
def run():
  exercise_incompatible_flags_replacement()
  exercise_split_unmerged()
  debug_utils.parse_options_loop_space_groups(sys.argv[1:], run_call_back)
  print "OK"