def exercise_scalepack():
sca_in = """\
4 i41
1 0 0 0 1 0 0 0 1
0 0 0
-1 0 0 0 -1 0 0 0 1
0 0 0
0 -1 0 1 0 0 0 0 1
0 6 3
0 1 0 -1 0 0 0 0 1
0 6 3
0 0 4 0 0 4 188 1 1 1 80331.8 8648.0
0 0 -4 0 0 4 8 2 1 1104526.7 11623.3
0 0 8 0 0 8 19 1 0 1 44883.6 4527.6
0 0 8 0 0 8 184 1 1 1 41134.1 4431.9
0 0 -8 0 0 8 4 2 1 1 53386.0 5564.1
0 0 -8 0 0 8 198 2 0 1 50401.8 5464.6
0 0 12 0 0 12 22 1 0 1119801.4 12231.2
0 0 12 0 0 12 180 1 1 1105312.9 12602.2
0 0 16 0 0 16 26 1 0 1 14877.6 2161.5
1 0 3 1 0 3 10 1 0 1 19407.0 2301.4
1 0 3 1 0 3 184 1 1 1 19337.0 2204.0
-1 0 3 1 0 3 19 1 0 2 19513.6 2220.3
-1 0 3 1 0 3 193 1 1 2 20702.3 2227.8
0 -1 3 1 0 3 11 1 0 3 20041.6 2360.2
0 -1 3 1 0 3 185 1 1 3 20043.9 2296.8
0 1 3 1 0 3 18 1 0 4 19677.4 2125.2
-1 0 -3 1 0 3 4 2 1 1 17056.4 1829.7
-1 0 -3 1 0 3 189 2 0 1 16545.2 2065.9
1 0 -3 1 0 3 13 2 1 2 17169.5 1768.9
1 0 -3 1 0 3 198 2 0 2 16195.8 1927.5
"""
sca_file = prefix + "_in.sca"
with open(sca_file, "w") as f:
f.write(sca_in)
ofn = export_scalepack_unmerged.run(args=[sca_file], out=null_out())[0]
assert (ofn == "tst_export_scalepack_unmerged_in_unmerged.sca")
hkl_in = any_reflection_file(ofn).file_content()
i_obs = hkl_in.as_miller_arrays(merge_equivalents=False)[0]
assert (not i_obs.is_unique_set_under_symmetry())
assert (list(hkl_in.batch_numbers) == [
188, 8, 19, 184, 4, 198, 22, 180, 26, 10, 184, 19, 193, 11, 185, 18, 4,
189, 13, 198
])
def exercise_scalepack () :
sca_in = """\
4 i41
1 0 0 0 1 0 0 0 1
0 0 0
-1 0 0 0 -1 0 0 0 1
0 0 0
0 -1 0 1 0 0 0 0 1
0 6 3
0 1 0 -1 0 0 0 0 1
0 6 3
0 0 4 0 0 4 188 1 1 1 80331.8 8648.0
0 0 -4 0 0 4 8 2 1 1104526.7 11623.3
0 0 8 0 0 8 19 1 0 1 44883.6 4527.6
0 0 8 0 0 8 184 1 1 1 41134.1 4431.9
0 0 -8 0 0 8 4 2 1 1 53386.0 5564.1
0 0 -8 0 0 8 198 2 0 1 50401.8 5464.6
0 0 12 0 0 12 22 1 0 1119801.4 12231.2
0 0 12 0 0 12 180 1 1 1105312.9 12602.2
0 0 16 0 0 16 26 1 0 1 14877.6 2161.5
1 0 3 1 0 3 10 1 0 1 19407.0 2301.4
1 0 3 1 0 3 184 1 1 1 19337.0 2204.0
-1 0 3 1 0 3 19 1 0 2 19513.6 2220.3
-1 0 3 1 0 3 193 1 1 2 20702.3 2227.8
0 -1 3 1 0 3 11 1 0 3 20041.6 2360.2
0 -1 3 1 0 3 185 1 1 3 20043.9 2296.8
0 1 3 1 0 3 18 1 0 4 19677.4 2125.2
-1 0 -3 1 0 3 4 2 1 1 17056.4 1829.7
-1 0 -3 1 0 3 189 2 0 1 16545.2 2065.9
1 0 -3 1 0 3 13 2 1 2 17169.5 1768.9
1 0 -3 1 0 3 198 2 0 2 16195.8 1927.5
"""
sca_file = prefix + "_in.sca"
open(sca_file, "w").write(sca_in)
ofn = export_scalepack_unmerged.run(args=[sca_file], out=null_out())[0]
assert (ofn == "tst_export_scalepack_unmerged_in_unmerged.sca")
hkl_in = any_reflection_file(ofn).file_content()
i_obs = hkl_in.as_miller_arrays(merge_equivalents=False)[0]
assert (not i_obs.is_unique_set_under_symmetry())
assert (list(hkl_in.batch_numbers) == [188, 8, 19, 184, 4, 198, 22, 180, 26,
10, 184, 19, 193, 11, 185, 18, 4, 189, 13, 198])
def exercise_cif():
# .cif input
cif_in = """\
data_r2etdsf
#
_cell.entry_id 2etd
_cell.length_a 80.4540
_cell.length_b 85.2590
_cell.length_c 53.3970
_cell.angle_alpha 90.0000
_cell.angle_beta 90.0000
_cell.angle_gamma 90.0000
#
_symmetry.entry_id 2etd
_symmetry.space_group_name_H-M 'C 2 2 2'
#
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.intensity_meas
_refln.intensity_sigma
1 1 1 0 2 -8 o 1544.6 130.4
1 1 1 0 2 9 o 3450.1 264.9
1 1 1 0 -2 9 o 3243.5 268.5
1 1 1 0 -2 -9 o 3475.4 265.0
1 1 1 0 2 -9 o 3420.1 260.3
1 1 1 0 2 10 o 58.8 31.8
1 1 1 0 -2 -10 o 131.7 50.7
1 1 1 0 2 -10 o 97.9 48.7
1 1 1 0 -2 11 o 9808.3 953.5
1 1 1 0 -2 -11 o 11486.1 970.3
1 1 1 0 2 -11 o 11278.1 967.8
1 1 1 0 2 12 o 1368.9 150.7
1 1 1 0 -2 12 o 1620.9 148.7
1 1 1 0 -2 -12 o 1293.5 147.6
1 1 1 0 2 -12 o 1619.5 155.7
1 1 1 0 -2 13 o 47438.3 4104.1
1 1 1 0 2 14 o 8577.5 1188.0
1 1 1 0 -2 14 o 7996.7 1179.9
1 1 1 0 -2 -14 o 9333.7 1178.1
1 1 1 0 2 -14 o 9642.3 1197.6
1 1 1 0 2 15 o 13577.7 1852.4
1 1 1 0 -2 15 o 14100.9 1852.8
1 1 1 0 -2 -15 o 14184.2 1871.6
1 1 1 0 2 16 o 135.6 76.3
1 1 1 0 -2 16 o 117.0 60.4
"""
cif_file = prefix + "_in.cif"
with open(cif_file, "w") as f:
f.write(cif_in)
hkl_orig = any_reflection_file(cif_file).file_content()
i_obs_orig = hkl_orig.as_miller_arrays(merge_equivalents=False)[0]
ofn = export_scalepack_unmerged.run(args=[cif_file], out=null_out())[0]
assert (ofn == "tst_export_scalepack_unmerged_in_w1_unmerged.sca")
hkl_new = any_reflection_file(ofn).file_content()
i_obs_new = hkl_new.as_miller_arrays(merge_equivalents=False)[0]
assert (not i_obs_new.is_unique_set_under_symmetry())
assert i_obs_new.indices().all_eq(i_obs_orig.indices())
def exercise_cif () : # .cif input cif_in = """\ data_r2etdsf # _cell.entry_id 2etd _cell.length_a 80.4540 _cell.length_b 85.2590 _cell.length_c 53.3970 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 90.0000 # _symmetry.entry_id 2etd _symmetry.space_group_name_H-M 'C 2 2 2' # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 1 1 1 0 2 -8 o 1544.6 130.4 1 1 1 0 2 9 o 3450.1 264.9 1 1 1 0 -2 9 o 3243.5 268.5 1 1 1 0 -2 -9 o 3475.4 265.0 1 1 1 0 2 -9 o 3420.1 260.3 1 1 1 0 2 10 o 58.8 31.8 1 1 1 0 -2 -10 o 131.7 50.7 1 1 1 0 2 -10 o 97.9 48.7 1 1 1 0 -2 11 o 9808.3 953.5 1 1 1 0 -2 -11 o 11486.1 970.3 1 1 1 0 2 -11 o 11278.1 967.8 1 1 1 0 2 12 o 1368.9 150.7 1 1 1 0 -2 12 o 1620.9 148.7 1 1 1 0 -2 -12 o 1293.5 147.6 1 1 1 0 2 -12 o 1619.5 155.7 1 1 1 0 -2 13 o 47438.3 4104.1 1 1 1 0 2 14 o 8577.5 1188.0 1 1 1 0 -2 14 o 7996.7 1179.9 1 1 1 0 -2 -14 o 9333.7 1178.1 1 1 1 0 2 -14 o 9642.3 1197.6 1 1 1 0 2 15 o 13577.7 1852.4 1 1 1 0 -2 15 o 14100.9 1852.8 1 1 1 0 -2 -15 o 14184.2 1871.6 1 1 1 0 2 16 o 135.6 76.3 1 1 1 0 -2 16 o 117.0 60.4 """ cif_file = prefix + "_in.cif" open(cif_file, "w").write(cif_in) hkl_orig = any_reflection_file(cif_file).file_content() i_obs_orig = hkl_orig.as_miller_arrays(merge_equivalents=False)[0] ofn = export_scalepack_unmerged.run(args=[cif_file], out=null_out())[0] assert (ofn == "tst_export_scalepack_unmerged_in_w1_unmerged.sca") hkl_new = any_reflection_file(ofn).file_content() i_obs_new = hkl_new.as_miller_arrays(merge_equivalents=False)[0] assert (not i_obs_new.is_unique_set_under_symmetry()) assert i_obs_new.indices().all_eq(i_obs_orig.indices())