def exercise(space_group_info, anomalous_flag=False, d_min=2., verbose=0):
sg_fcalc = random_structure.xray_structure(
space_group_info,
elements=("N", "C", "C", "O"),
random_f_double_prime=anomalous_flag,
random_u_iso=True,
random_occupancy=True
).structure_factors(
anomalous_flag=anomalous_flag, d_min=d_min, algorithm="direct").f_calc()
sg_hl = generate_random_hl(sg_fcalc)
write_cns_input(sg_fcalc, sg_hl.data())
try: os.unlink("tmp_sg.hkl")
except OSError: pass
try: os.unlink("tmp_p1.hkl")
except OSError: pass
easy_run.fully_buffered(command="cns < tmp.cns > tmp.out") \
.raise_if_errors_or_output()
sg_cns = read_reflection_arrays("tmp_sg.hkl", anomalous_flag, verbose)
p1_cns = read_reflection_arrays("tmp_p1.hkl", anomalous_flag, verbose)
verify(sg_fcalc, sg_hl.data(), sg_cns, p1_cns)
if (anomalous_flag):
hl_merged = sg_hl.average_bijvoet_mates()
fc_merged = sg_fcalc.average_bijvoet_mates()
write_cns_input(sg_fcalc, sg_hl.data(), test_merge=True)
try: os.unlink("tmp_merged.hkl")
except OSError: pass
easy_run.fully_buffered(command="cns < tmp.cns > tmp.out") \
.raise_if_errors_or_output()
reflection_file = reflection_reader.cns_reflection_file(
open("tmp_merged.hkl"))
if (not sg_fcalc.space_group().is_centric()):
fc_merged_cns = reflection_file.reciprocal_space_objects["FCALC"]
fc_merged_cns = fc_merged.customized_copy(
indices=fc_merged_cns.indices,
data=fc_merged_cns.data).map_to_asu().common_set(fc_merged)
assert fc_merged_cns.indices().all_eq(fc_merged.indices())
fc_merged_a = fc_merged.select_acentric()
fc_merged_cns_a = fc_merged_cns.select_acentric()
for part in [flex.real, flex.imag]:
cc = flex.linear_correlation(
part(fc_merged_a.data()),
part(fc_merged_cns_a.data())).coefficient()
if (cc < 1-1.e-6):
print "FAILURE acentrics", sg_fcalc.space_group_info()
if (0): return
raise AssertionError
names, miller_indices, hl = reflection_file.join_hl_group()
assert names == ["PA", "PB", "PC", "PD"]
hl_merged_cns = hl_merged.customized_copy(indices=miller_indices, data=hl)\
.map_to_asu().common_set(hl_merged)
assert hl_merged_cns.indices().all_eq(hl_merged.indices())
for h,a,b in zip(hl_merged.indices(),
hl_merged.data(),
hl_merged_cns.data()):
if (not approx_equal(a, b, eps=5.e-3)):
print h
print "cctbx:", a
print " cns:", b
if (0): return
raise AssertionError
def __init__(self, file_name, anomalous_flag, verbose):
reflection_file = reflection_reader.cns_reflection_file(open(file_name))
if (0 or verbose):
print reflection_file.show_summary()
assert reflection_file.anomalous == anomalous_flag
names, self.miller_indices, self.hl = reflection_file.join_hl_group()
self.fcalc = reflection_file.reciprocal_space_objects["FCALC"]
self.pi = reflection_file.reciprocal_space_objects["PI"]
assert not miller.match_indices(
self.miller_indices, self.fcalc.indices).have_singles()
assert not miller.match_indices(
self.miller_indices, self.pi.indices).have_singles()
def __init__(self, file_name, anomalous_flag, verbose):
reflection_file = reflection_reader.cns_reflection_file(
open(file_name))
if (0 or verbose):
print(reflection_file.show_summary())
assert reflection_file.anomalous == anomalous_flag
names, self.miller_indices, self.hl = reflection_file.join_hl_group()
self.fcalc = reflection_file.reciprocal_space_objects["FCALC"]
self.pi = reflection_file.reciprocal_space_objects["PI"]
assert not miller.match_indices(self.miller_indices,
self.fcalc.indices).have_singles()
assert not miller.match_indices(self.miller_indices,
self.pi.indices).have_singles()
def exercise(space_group_info, anomalous_flag=False, d_min=2., verbose=0):
crystal_symmetry = crystal.symmetry(
space_group_info.any_compatible_unit_cell(1000),
space_group_info=space_group_info)
write_cns_input(crystal_symmetry, anomalous_flag, d_min)
try: os.unlink("tmp_cns_input.hkl")
except KeyboardInterrupt: raise
except Exception: pass
easy_run.fully_buffered(
command="cns < tmp_cns_input.cns > tmp_cns_input.out") \
.raise_if_errors_or_output()
f = open("tmp_cns_input.hkl", "r")
reflection_file = reflection_reader.cns_reflection_file(f)
f.close()
if (0 or verbose):
print reflection_file.show_summary()
verify(crystal_symmetry, anomalous_flag, reflection_file)
def exercise(space_group_info, anomalous_flag=False, d_min=2., verbose=0):
crystal_symmetry = crystal.symmetry(
space_group_info.any_compatible_unit_cell(1000),
space_group_info=space_group_info)
write_cns_input(crystal_symmetry, anomalous_flag, d_min)
try: os.unlink("tmp_cns_input.hkl")
except KeyboardInterrupt: raise
except Exception: pass
easy_run.fully_buffered(
command="cns < tmp_cns_input.cns > tmp_cns_input.out") \
.raise_if_errors_or_output()
f = open("tmp_cns_input.hkl", "r")
reflection_file = reflection_reader.cns_reflection_file(f)
f.close()
if (0 or verbose):
print(reflection_file.show_summary())
verify(crystal_symmetry, anomalous_flag, reflection_file)
def try_all_readers(file_name):
try: content = mtz.object(file_name=file_name)
except RuntimeError: pass
else: return ("ccp4_mtz", content)
if (detect_binary_file.from_initial_block(file_name=file_name)):
try: content = unpickle_miller_arrays(file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("cctbx.miller.array", content)
return (None, None)
try: content = cns_reflection_reader.cns_reflection_file(
open(file_name))
except cns_reflection_reader.CNS_input_Error: pass
else: return ("cns_reflection_file", content)
try: content = cns_index_fobs_sigma_reader.reader(
file_name=file_name)
except RuntimeError: pass
else: return ("cns_index_fobs_sigma", content)
try: content = scalepack_merge.reader(
open(file_name))
except scalepack_merge.FormatError: pass
else: return ("scalepack_merge", content)
try: content = scalepack_no_merge.reader(file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("scalepack_no_merge_original_index", content)
try: content = dtrek_reflnlist_reader.reflnlist(
open(file_name))
except KeyboardInterrupt: raise
except Exception: pass
else: return ("dtrek_reflnlist", content)
try: content = shelx_hklf.reader(
file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("shelx_hklf", content)
try:
content = cif_reader(file_path=file_name)
looks_like_a_reflection_file = False
for block in content.model().values():
if '_refln_index_h' in block or '_refln.index_h' in block:
looks_like_a_reflection_file = True
break
if not looks_like_a_reflection_file:
raise RuntimeError
except KeyboardInterrupt: raise
except Exception: pass
else: return ("cif", content)
try: content = xds_ascii_reader(
open(file_name))
except KeyboardInterrupt: raise
except Exception: pass
else: return ("xds_ascii", content)
try:
content = xds_integrate_hkl_reader()
content.read_file(file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("xds_integrate_hkl", content)
try: content = solve_fpfm_reader(file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("solve_fpfm", content)
return (None, None)
def try_all_readers(file_name):
try:
content = mtz.object(file_name=file_name)
except RuntimeError:
pass
else:
return ("ccp4_mtz", content)
if (detect_binary_file.from_initial_block(file_name=file_name)):
try:
content = unpickle_miller_arrays(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("cctbx.miller.array", content)
return (None, None)
try:
content = cns_reflection_reader.cns_reflection_file(open(file_name))
except cns_reflection_reader.CNS_input_Error:
pass
else:
return ("cns_reflection_file", content)
try:
content = cns_index_fobs_sigma_reader.reader(file_name=file_name)
except RuntimeError:
pass
else:
return ("cns_index_fobs_sigma", content)
try:
content = scalepack_merge.reader(open(file_name))
except scalepack_merge.FormatError:
pass
else:
return ("scalepack_merge", content)
try:
content = scalepack_no_merge.reader(file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("scalepack_no_merge_original_index", content)
try:
content = dtrek_reflnlist_reader.reflnlist(open(file_name))
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("dtrek_reflnlist", content)
try:
content = shelx_hklf.reader(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("shelx_hklf", content)
try:
content = cif_reader(file_path=file_name)
looks_like_a_reflection_file = False
for block in content.model().values():
if '_refln_index_h' in block or '_refln.index_h' in block:
looks_like_a_reflection_file = True
break
if not looks_like_a_reflection_file:
raise RuntimeError
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("cif", content)
try:
content = xds_ascii_reader(open(file_name))
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("xds_ascii", content)
try:
content = xds_integrate_hkl_reader()
content.read_file(file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("xds_integrate_hkl", content)
try:
content = solve_fpfm_reader(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("solve_fpfm", content)
return (None, None)
def exercise(space_group_info, anomalous_flag=False, d_min=2., verbose=0):
sg_fcalc = random_structure.xray_structure(
space_group_info,
elements=("N", "C", "C", "O"),
random_f_double_prime=anomalous_flag,
random_u_iso=True,
random_occupancy=True).structure_factors(anomalous_flag=anomalous_flag,
d_min=d_min,
algorithm="direct").f_calc()
sg_hl = generate_random_hl(sg_fcalc)
write_cns_input(sg_fcalc, sg_hl.data())
try:
os.unlink("tmp_sg.hkl")
except OSError:
pass
try:
os.unlink("tmp_p1.hkl")
except OSError:
pass
easy_run.fully_buffered(command="cns < tmp.cns > tmp.out") \
.raise_if_errors_or_output()
sg_cns = read_reflection_arrays("tmp_sg.hkl", anomalous_flag, verbose)
p1_cns = read_reflection_arrays("tmp_p1.hkl", anomalous_flag, verbose)
verify(sg_fcalc, sg_hl.data(), sg_cns, p1_cns)
if (anomalous_flag):
hl_merged = sg_hl.average_bijvoet_mates()
fc_merged = sg_fcalc.average_bijvoet_mates()
write_cns_input(sg_fcalc, sg_hl.data(), test_merge=True)
try:
os.unlink("tmp_merged.hkl")
except OSError:
pass
easy_run.fully_buffered(command="cns < tmp.cns > tmp.out") \
.raise_if_errors_or_output()
reflection_file = reflection_reader.cns_reflection_file(
open("tmp_merged.hkl"))
if (not sg_fcalc.space_group().is_centric()):
fc_merged_cns = reflection_file.reciprocal_space_objects["FCALC"]
fc_merged_cns = fc_merged.customized_copy(
indices=fc_merged_cns.indices,
data=fc_merged_cns.data).map_to_asu().common_set(fc_merged)
assert fc_merged_cns.indices().all_eq(fc_merged.indices())
fc_merged_a = fc_merged.select_acentric()
fc_merged_cns_a = fc_merged_cns.select_acentric()
for part in [flex.real, flex.imag]:
cc = flex.linear_correlation(
part(fc_merged_a.data()),
part(fc_merged_cns_a.data())).coefficient()
if (cc < 1 - 1.e-6):
print("FAILURE acentrics", sg_fcalc.space_group_info())
if (0): return
raise AssertionError
names, miller_indices, hl = reflection_file.join_hl_group()
assert names == ["PA", "PB", "PC", "PD"]
hl_merged_cns = hl_merged.customized_copy(indices=miller_indices, data=hl)\
.map_to_asu().common_set(hl_merged)
assert hl_merged_cns.indices().all_eq(hl_merged.indices())
for h, a, b in zip(hl_merged.indices(), hl_merged.data(),
hl_merged_cns.data()):
if (not approx_equal(a, b, eps=5.e-3)):
print(h)
print("cctbx:", a)
print(" cns:", b)
if (0): return
raise AssertionError