def exercise_overloads():
open("overloads.sca", "w").write("""\
1
-987
50.000 50.000 80.000 90.000 90.000 120.000 p3121
19 2 3 ******* 47482.6 ******* 26861.1
19 2 2 16333.4 17143.9 38472.0 22574.8
19 2 1 49448.5 24728.9 28427.6 18873.9
19 2 0 34296.1 24479.1 25846.4 22660.4
19 2 -1 27513.6 23318.8 30341.0 19273.1""")
file_in = merge.reader(file_handle=open("overloads.sca"))
arrays = file_in.as_miller_arrays()
assert (len(arrays[0].indices()) == 8)
def exercise_overloads () :
open("overloads.sca", "w").write("""\
1
-987
50.000 50.000 80.000 90.000 90.000 120.000 p3121
19 2 3 ******* 47482.6 ******* 26861.1
19 2 2 16333.4 17143.9 38472.0 22574.8
19 2 1 49448.5 24728.9 28427.6 18873.9
19 2 0 34296.1 24479.1 25846.4 22660.4
19 2 -1 27513.6 23318.8 30341.0 19273.1""")
file_in = merge.reader(file_handle=open("overloads.sca"))
arrays = file_in.as_miller_arrays()
assert (len(arrays[0].indices()) == 8)
def recycle(miller_array):
merge.write(file_name="tmp.sca", miller_array=miller_array)
read_back_file = merge.reader(file_handle=open("tmp.sca"))
read_back_arrays = read_back_file.as_miller_arrays()
assert len(read_back_arrays) == 1
read_back_array = read_back_arrays[0]
read_back_input_indexing = read_back_array.adopt_set(miller_array)
if (miller_array.is_xray_amplitude_array()):
read_back_input_indexing = read_back_input_indexing.f_sq_as_f()
regression = flex.linear_regression(miller_array.data(),
read_back_input_indexing.data())
assert approx_equal(regression.slope(), 1, eps=1.e-3)
assert abs(regression.y_intercept()) < 1
regression = flex.linear_regression(miller_array.sigmas(),
read_back_input_indexing.sigmas())
if (miller_array.is_xray_intensity_array()):
assert approx_equal(regression.slope(), 1, eps=1.e-3)
else:
assert approx_equal(regression.slope(), 1, eps=1.e-1)
assert abs(regression.y_intercept()) < 1
def recycle(miller_array):
merge.write(file_name="tmp.sca", miller_array=miller_array)
read_back_file = merge.reader(file_handle=open("tmp.sca"))
read_back_arrays = read_back_file.as_miller_arrays()
assert len(read_back_arrays) == 1
read_back_array = read_back_arrays[0]
read_back_input_indexing = read_back_array.adopt_set(miller_array)
if (miller_array.is_xray_amplitude_array()):
read_back_input_indexing = read_back_input_indexing.f_sq_as_f()
regression = flex.linear_regression(
miller_array.data(),
read_back_input_indexing.data())
assert approx_equal(regression.slope(), 1, eps=1.e-3)
assert abs(regression.y_intercept()) < 1
regression = flex.linear_regression(
miller_array.sigmas(),
read_back_input_indexing.sigmas())
if (miller_array.is_xray_intensity_array()):
assert approx_equal(regression.slope(), 1, eps=1.e-3)
else:
assert approx_equal(regression.slope(), 1, eps=1.e-1)
assert abs(regression.y_intercept()) < 1
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 extract_from_merge(file):
return merge.reader(file, header_only=True).crystal_symmetry()
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 extract_from_merge(file): return merge.reader(file, header_only=True).crystal_symmetry()
