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_no_merge_original_index(file_name):
scalepack_file = no_merge_original_index.reader(file_name,
header_only=True)
return crystal.symmetry(unit_cell=None,
space_group_info=scalepack_file.space_group_info())
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():
from iotbx.scalepack import no_merge_original_index
from cctbx import crystal
# input from xia2 with one slight modification to the (44,0,-25) observation,
# as pointless/aimless seem to have a slightly different convention for ASU
# mapping. (Scalepack itself is even more deviant.)
sca_raw = """\
2 P 1 21 1
1 0 0 0 1 0 0 0 1
0 0 0
-1 0 0 0 1 0 0 0 -1
0 6 0
44 0 -25 -44 0 25 316 0 0 2 91.7 108.2
-44 1 11 -44 1 11 35 1 0 1 110.2 112.9
-44 -1 11 -44 1 11 34 2 0 2 28.7 115.0
-44 1 12 -44 1 12 34 1 0 1 129.1 116.3
-44 -1 12 -44 1 12 33 2 0 2 133.1 118.2
-44 1 14 -44 1 14 31 1 0 1 159.7 116.1
-44 -1 14 -44 1 14 30 2 0 2 136.8 90.9
-44 1 15 -44 1 15 30 1 0 1 106.4 85.8
-44 -1 15 -44 1 15 29 2 0 2 39.1 87.4
-44 1 17 -44 1 17 27 1 0 1 115.9 87.0
-44 -1 17 -44 1 17 26 2 0 2 138.1 89.8
-44 -1 18 -44 1 18 25 2 0 2 10.3 84.4
-38 2 53 -38 2 53 212 1 0 1 246.7 141.4
38 -2 -53 -38 2 53 272 2 0 1 6.1 157.7
38 2 -53 -38 2 53 272 1 0 2 322.5 159.5
38 -2 -54 -38 2 54 271 2 0 1 -68.4 152.1
38 2 -54 -38 2 54 271 1 0 2 211.0 153.3
38 -2 -55 -38 2 55 270 2 0 1 78.6 153.6
38 2 -55 -38 2 55 270 1 0 2 220.4 157.0
38 -2 -56 -38 2 56 269 2 0 1 -25.5 148.6
38 2 -56 -38 2 56 269 1 0 2 -55.1 143.6
38 2 -57 -38 2 57 268 1 0 2 -32.3 89.2
38 -2 -57 -38 2 57 268 2 0 1 -265.7 138.8
38 2 -58 -38 2 58 267 1 0 2 69.6 92.7
38 -2 -58 -38 2 58 267 2 0 1 -153.1 132.2
"""
hkl_in = "tst_scalepack_unmerged_writer.sca"
hkl_out = "tst_scalepack_unmerged_writer_out.sca"
open(hkl_in, "w").write(sca_raw)
reader = no_merge_original_index.reader(hkl_in)
symm = crystal.symmetry(space_group_symbol="P21", unit_cell=(80.882, 51.511, 141.371, 90.0, 106.588, 90.0))
i_obs = reader.as_miller_array(crystal_symmetry=symm, merge_equivalents=False)
i_obs.export_as_scalepack_unmerged(
file_name=hkl_out, batch_numbers=reader.batch_numbers, spindle_flags=reader.spindle_flags
)
sca_recycled = open(hkl_out).read()
assert not show_diff(sca_recycled, sca_raw)
batches = reader.batch_as_miller_array(crystal_symmetry=symm)
assert batches.indices().all_eq(i_obs.indices())
assert batches.data()[0] == 316
mas = reader.as_miller_arrays()
assert len(mas) == 2
assert mas[0].info().labels == ["I(+)", "SIGI(+)", "I(-)", "SIGI(-)"]
assert mas[1].info().labels == ["BATCH"]
# space group symbol and symops conflict (Scalepack bug?)
sca_bad = """\
24 f4132
1 0 0 0 1 0 0 0 1
0 0 0
0 0 1 1 0 0 0 1 0
0 0 0
0 1 0 0 0 1 1 0 0
0 0 0
-1 0 0 0 0 -1 0 -1 0
9 9 9
0 -1 0 -1 0 0 0 0 -1
9 9 9
0 0 -1 0 -1 0 -1 0 0
9 9 9
1 0 0 0 -1 0 0 0 -1
6 6 0
0 0 1 -1 0 0 0 -1 0
6 6 0
0 1 0 0 0 -1 -1 0 0
6 6 0
-1 0 0 0 0 1 0 1 0
3 9 3
0 -1 0 1 0 0 0 0 1
3 9 3
0 0 -1 0 1 0 1 0 0
3 9 3
-1 0 0 0 1 0 0 0 -1
0 6 6
0 0 -1 1 0 0 0 -1 0
0 6 6
0 -1 0 0 0 1 -1 0 0
0 6 6
1 0 0 0 0 -1 0 1 0
3 3 9
0 1 0 -1 0 0 0 0 1
3 3 9
0 0 1 0 -1 0 1 0 0
3 3 9
-1 0 0 0 -1 0 0 0 1
6 0 6
0 0 -1 -1 0 0 0 1 0
6 0 6
0 -1 0 0 0 -1 1 0 0
6 0 6
1 0 0 0 0 1 0 -1 0
9 3 3
0 1 0 1 0 0 0 0 -1
9 3 3
0 0 1 0 1 0 -1 0 0
9 3 3
-2 -2 -2 2 2 2 658 0 0 4 3624.3 344.2
-2 -2 2 2 2 2 582 0 0 8 3220.1 344.8
2 2 -2 2 2 2 579 0 1 12 3376.5 344.3
1 3 1 3 1 1 320 0 0 3 544.3 55.1
1 3 1 3 1 1 677 0 1 3 476.8 53.8
-3 -1 -1 3 1 1 217 0 1 4 588.2 53.9
-3 -1 -1 3 1 1 579 0 0 4 552.4 53.9
"""
hkl_in = "tst_scalepack_unmerged_writer2.sca"
hkl_out = "tst_scalepack_unmerged_writer2_out.sca"
open(hkl_in, "w").write(sca_bad)
reader = no_merge_original_index.reader(hkl_in)
with warnings.catch_warnings(record=True) as w:
space_group_info = reader.space_group_info()
assert len(w) == 1
assert str(space_group_info) == "F 41 3 2"
def exercise():
from iotbx.scalepack import no_merge_original_index
from cctbx import crystal
# input from xia2 with one slight modification to the (44,0,-25) observation,
# as pointless/aimless seem to have a slightly different convention for ASU
# mapping. (Scalepack itself is even more deviant.)
sca_raw = """\
2 P 1 21 1
1 0 0 0 1 0 0 0 1
0 0 0
-1 0 0 0 1 0 0 0 -1
0 6 0
44 0 -25 -44 0 25 316 0 0 2 91.7 108.2
-44 1 11 -44 1 11 35 1 0 1 110.2 112.9
-44 -1 11 -44 1 11 34 2 0 2 28.7 115.0
-44 1 12 -44 1 12 34 1 0 1 129.1 116.3
-44 -1 12 -44 1 12 33 2 0 2 133.1 118.2
-44 1 14 -44 1 14 31 1 0 1 159.7 116.1
-44 -1 14 -44 1 14 30 2 0 2 136.8 90.9
-44 1 15 -44 1 15 30 1 0 1 106.4 85.8
-44 -1 15 -44 1 15 29 2 0 2 39.1 87.4
-44 1 17 -44 1 17 27 1 0 1 115.9 87.0
-44 -1 17 -44 1 17 26 2 0 2 138.1 89.8
-44 -1 18 -44 1 18 25 2 0 2 10.3 84.4
-38 2 53 -38 2 53 212 1 0 1 246.7 141.4
38 -2 -53 -38 2 53 272 2 0 1 6.1 157.7
38 2 -53 -38 2 53 272 1 0 2 322.5 159.5
38 -2 -54 -38 2 54 271 2 0 1 -68.4 152.1
38 2 -54 -38 2 54 271 1 0 2 211.0 153.3
38 -2 -55 -38 2 55 270 2 0 1 78.6 153.6
38 2 -55 -38 2 55 270 1 0 2 220.4 157.0
38 -2 -56 -38 2 56 269 2 0 1 -25.5 148.6
38 2 -56 -38 2 56 269 1 0 2 -55.1 143.6
38 2 -57 -38 2 57 268 1 0 2 -32.3 89.2
38 -2 -57 -38 2 57 268 2 0 1 -265.7 138.8
38 2 -58 -38 2 58 267 1 0 2 69.6 92.7
38 -2 -58 -38 2 58 267 2 0 1 -153.1 132.2
"""
hkl_in = "tst_scalepack_unmerged_writer.sca"
hkl_out = "tst_scalepack_unmerged_writer_out.sca"
open(hkl_in, "w").write(sca_raw)
reader = no_merge_original_index.reader(hkl_in)
symm = crystal.symmetry(space_group_symbol="P21",
unit_cell=(80.882, 51.511, 141.371, 90., 106.588,
90.))
i_obs = reader.as_miller_array(crystal_symmetry=symm,
merge_equivalents=False)
i_obs.export_as_scalepack_unmerged(file_name=hkl_out,
batch_numbers=reader.batch_numbers,
spindle_flags=reader.spindle_flags)
sca_recycled = open(hkl_out).read()
assert not show_diff(sca_recycled, sca_raw)
batches = reader.batch_as_miller_array(crystal_symmetry=symm)
assert batches.indices().all_eq(i_obs.indices())
assert (batches.data()[0] == 316)
mas = reader.as_miller_arrays()
assert len(mas) == 2
assert mas[0].info().labels == ["I(+)", "SIGI(+)", "I(-)", "SIGI(-)"]
assert mas[1].info().labels == ["BATCH"]
# space group symbol and symops conflict (Scalepack bug?)
sca_bad = """\
24 f4132
1 0 0 0 1 0 0 0 1
0 0 0
0 0 1 1 0 0 0 1 0
0 0 0
0 1 0 0 0 1 1 0 0
0 0 0
-1 0 0 0 0 -1 0 -1 0
9 9 9
0 -1 0 -1 0 0 0 0 -1
9 9 9
0 0 -1 0 -1 0 -1 0 0
9 9 9
1 0 0 0 -1 0 0 0 -1
6 6 0
0 0 1 -1 0 0 0 -1 0
6 6 0
0 1 0 0 0 -1 -1 0 0
6 6 0
-1 0 0 0 0 1 0 1 0
3 9 3
0 -1 0 1 0 0 0 0 1
3 9 3
0 0 -1 0 1 0 1 0 0
3 9 3
-1 0 0 0 1 0 0 0 -1
0 6 6
0 0 -1 1 0 0 0 -1 0
0 6 6
0 -1 0 0 0 1 -1 0 0
0 6 6
1 0 0 0 0 -1 0 1 0
3 3 9
0 1 0 -1 0 0 0 0 1
3 3 9
0 0 1 0 -1 0 1 0 0
3 3 9
-1 0 0 0 -1 0 0 0 1
6 0 6
0 0 -1 -1 0 0 0 1 0
6 0 6
0 -1 0 0 0 -1 1 0 0
6 0 6
1 0 0 0 0 1 0 -1 0
9 3 3
0 1 0 1 0 0 0 0 -1
9 3 3
0 0 1 0 1 0 -1 0 0
9 3 3
-2 -2 -2 2 2 2 658 0 0 4 3624.3 344.2
-2 -2 2 2 2 2 582 0 0 8 3220.1 344.8
2 2 -2 2 2 2 579 0 1 12 3376.5 344.3
1 3 1 3 1 1 320 0 0 3 544.3 55.1
1 3 1 3 1 1 677 0 1 3 476.8 53.8
-3 -1 -1 3 1 1 217 0 1 4 588.2 53.9
-3 -1 -1 3 1 1 579 0 0 4 552.4 53.9
"""
hkl_in = "tst_scalepack_unmerged_writer2.sca"
hkl_out = "tst_scalepack_unmerged_writer2_out.sca"
open(hkl_in, "w").write(sca_bad)
reader = no_merge_original_index.reader(hkl_in)
with warnings.catch_warnings(record=True) as w:
space_group_info = reader.space_group_info()
assert (len(w) == 1)
assert (str(space_group_info) == "F 41 3 2")
def extract_from_no_merge_original_index(file_name):
scalepack_file = no_merge_original_index.reader(file_name, header_only=True)
return crystal.symmetry(
unit_cell=None,
space_group_info=scalepack_file.space_group_info())