def exercise_xds_input():
xds_file = libtbx.env.find_in_repositories(
relative_path=
"phenix_regression/reflection_files/xds_correct_unmerged.hkl",
test=os.path.isfile)
if (xds_file is None):
print "phenix_regression not available, skipping exercise_xds_input"
return False
xds_in = file_reader.any_file(xds_file)
wl = xds_in.file_server.miller_arrays[0].info().wavelength
p = reflection_file_editor.run(args=[
xds_file,
"output_file=xds.mtz",
],
out=null_out())
mtz_in = file_reader.any_file("xds.mtz")
wl2 = mtz_in.file_server.miller_arrays[0].info().wavelength
assert approx_equal(wl, wl2)
p = reflection_file_editor.run(args=[
xds_file,
"output_file=xds.mtz",
"wavelength=0.9792",
],
out=null_out())
mtz_in = file_reader.any_file("xds.mtz")
wl2 = mtz_in.file_server.miller_arrays[0].info().wavelength
assert approx_equal(wl2, 0.9792)
def exercise_xds_input () :
xds_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/xds_correct_unmerged.hkl",
test=os.path.isfile)
if (xds_file is None) :
print "phenix_regression not available, skipping exercise_xds_input"
return False
xds_in = file_reader.any_file(xds_file)
wl = xds_in.file_server.miller_arrays[0].info().wavelength
p = reflection_file_editor.run(
args=[xds_file, "output_file=xds.mtz",],
out=null_out())
mtz_in = file_reader.any_file("xds.mtz")
wl2 = mtz_in.file_server.miller_arrays[0].info().wavelength
assert approx_equal(wl, wl2)
p = reflection_file_editor.run(
args=[xds_file, "output_file=xds.mtz", "wavelength=0.9792",],
out=null_out())
mtz_in = file_reader.any_file("xds.mtz")
wl2 = mtz_in.file_server.miller_arrays[0].info().wavelength
assert approx_equal(wl2, 0.9792)
def exercise_command_line():
if (not libtbx.env.has_module("phenix_regression")):
print "phenix_regression not available, skipping"
return
file1 = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/enk.mtz",
test=os.path.isfile)
file2 = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/enk_r1A.mtz",
test=os.path.isfile)
log = null_out()
test_file = "tst_hkl_editor_cmdline-1.mtz"
test_file2 = "tst_hkl_editor_cmdline-2.mtz"
if os.path.exists(test_file2):
os.remove(test_file2)
try:
p = reflection_file_editor.run(args=[file1, file2, "dry_run=True"],
out=log)
except Sorry, e:
assert str(e).startswith("Duplicate column label 'R-free-flags'.")
def exercise_command_line () :
if (not libtbx.env.has_module("phenix_regression")) :
print "phenix_regression not available, skipping"
return
file1 = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/enk.mtz",
test=os.path.isfile)
file2 = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/enk_r1A.mtz",
test=os.path.isfile)
log = null_out()
test_file = "tst_hkl_editor_cmdline-1.mtz"
test_file2 = "tst_hkl_editor_cmdline-2.mtz"
if os.path.exists(test_file2) :
os.remove(test_file2)
try :
p = reflection_file_editor.run(
args=[file1, file2, "dry_run=True"],
out=log)
except Sorry, e :
assert str(e).startswith("Duplicate column label 'R-free-flags'.")
test=os.path.isfile)
log = null_out()
test_file = "tst_hkl_editor_cmdline-1.mtz"
test_file2 = "tst_hkl_editor_cmdline-2.mtz"
if os.path.exists(test_file2):
os.remove(test_file2)
try:
p = reflection_file_editor.run(args=[file1, file2, "dry_run=True"],
out=log)
except Sorry, e:
assert str(e).startswith("Duplicate column label 'R-free-flags'.")
else:
raise Exception_expected
p = reflection_file_editor.run(args=[
file1, file2, "dry_run=True", "resolve_label_conflicts=True",
"output_file=%s" % test_file
],
out=log)
assert ([c.label() for c in p.mtz_object.columns()] == [
'H', 'K', 'L', 'I-obs', 'SIGI-obs', 'F-obs', 'R-free-flags',
'R-free-flags_2'
])
p.finish()
mtz_in = file_reader.any_file(test_file)
miller_arrays = mtz_in.file_object.as_miller_arrays()
flags1 = miller_arrays[-2]
assert flags1.info().label_string() == "R-free-flags"
(d_max, d_min) = flags1.d_max_min()
assert (approx_equal(d_max, 11.14, eps=0.01)
and approx_equal(d_min, 1.503, eps=0.01))
flags2 = miller_arrays[-1]
def exercise_command_line():
if (not libtbx.env.has_module("phenix_regression")):
print("phenix_regression not available, skipping")
return
file1 = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/enk.mtz",
test=os.path.isfile)
file2 = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/enk_r1A.mtz",
test=os.path.isfile)
log = null_out()
test_file = "tst_hkl_editor_cmdline-1.mtz"
test_file2 = "tst_hkl_editor_cmdline-2.mtz"
if os.path.exists(test_file2):
os.remove(test_file2)
try:
p = reflection_file_editor.run(args=[file1, file2, "dry_run=True"],
out=log)
except Sorry as e:
assert str(e).startswith("Duplicate column label 'R-free-flags'.")
else:
raise Exception_expected
p = reflection_file_editor.run(args=[
file1, file2, "dry_run=True", "resolve_label_conflicts=True",
"output_file=%s" % test_file
],
out=log)
assert ([c.label() for c in p.mtz_object.columns()] == [
'H', 'K', 'L', 'I-obs', 'SIGI-obs', 'F-obs', 'R-free-flags',
'R-free-flags_2'
])
p.finish()
mtz_in = file_reader.any_file(test_file)
miller_arrays = mtz_in.file_object.as_miller_arrays()
flags1 = miller_arrays[-2]
assert flags1.info().label_string() == "R-free-flags"
(d_max, d_min) = flags1.d_max_min()
assert (approx_equal(d_max, 11.14, eps=0.01)
and approx_equal(d_min, 1.503, eps=0.01))
flags2 = miller_arrays[-1]
assert flags2.info().label_string() == "R-free-flags_2"
(d_max, d_min) = flags2.d_max_min()
assert (approx_equal(d_max, 11.14, eps=0.01)
and approx_equal(d_min, 1.00, eps=0.01))
p = reflection_file_editor.run(args=[
file1, file2, "resolve_label_conflicts=True", "extend=True",
"output_file=%s" % test_file
],
out=log)
mtz_in = file_reader.any_file(test_file)
miller_arrays = mtz_in.file_object.as_miller_arrays()
(d_max_first, d_min_first) = miller_arrays[1].d_max_min()
(d_max_last, d_min_last) = miller_arrays[-1].d_max_min()
assert (d_max_first <= d_max_last)
assert (d_min_first == d_min_last)
#os.remove(test_file)
old_r_free_1 = miller_arrays[-2]
old_r_free_2 = miller_arrays[-1]
# export to CCP4 convention
p = reflection_file_editor.run(args=[
file1, file2, "resolve_label_conflicts=True", "extend=False",
"export_for_ccp4=False",
"output_file=%s" % test_file
],
out=log)
mtz_in = file_reader.any_file(test_file)
miller_arrays = mtz_in.file_object.as_miller_arrays()
# os.remove(test_file)
assert miller_arrays[-2].info().label_string() == "R-free-flags"
assert miller_arrays[-1].info().label_string() == "R-free-flags_2"
old_r_free_1 = miller_arrays[-2]
old_r_free_2 = miller_arrays[-1]
p = reflection_file_editor.run(args=[
file1, file2, "resolve_label_conflicts=True", "extend=False",
"export_for_ccp4=True", "preserve_input_values=False",
"output_file=%s" % test_file2
],
out=log)
mtz_in = file_reader.any_file(test_file2)
miller_arrays = mtz_in.file_object.as_miller_arrays()
assert (len(set(miller_arrays[-2].data())) == 5)
assert (len(set(miller_arrays[-1].data())) == 10)
old_flags_1 = (old_r_free_1.data() == 1)
old_flags_2 = (old_r_free_2.data() == 1)
new_flags_1 = (miller_arrays[-2].data() == 0)
new_flags_2 = (miller_arrays[-1].data() == 0) #.select(old_flags_2)
assert (old_flags_1 == new_flags_1).count(False) == 0
assert (old_flags_2 == new_flags_2).count(False) == 0
cns_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/l.cv",
test=os.path.isfile)
p = reflection_file_editor.run(args=[
cns_file, "space_group=P212121", "output_file=l_new.mtz",
"unit_cell=28.17,52.857,68.93,90,90,90"
],
out=log)
mtz_in = file_reader.any_file("l_new.mtz")
assert (mtz_in.file_server.miller_arrays[0].info().labels == [
'F_INFL(+)', 'S_INFL(+)', 'F_INFL(-)', 'S_INFL(-)'
])
from __future__ import division
import sys
from iotbx import reflection_file_editor
if __name__ == "__main__":
reflection_file_editor.run(sys.argv[1:])
test=os.path.isfile)
log = null_out()
test_file = "tst_hkl_editor_cmdline-1.mtz"
test_file2 = "tst_hkl_editor_cmdline-2.mtz"
if os.path.exists(test_file2) :
os.remove(test_file2)
try :
p = reflection_file_editor.run(
args=[file1, file2, "dry_run=True"],
out=log)
except Sorry, e :
assert str(e).startswith("Duplicate column label 'R-free-flags'.")
else :
raise Exception_expected
p = reflection_file_editor.run(
args=[file1, file2, "dry_run=True", "resolve_label_conflicts=True",
"output_file=%s" % test_file],
out=log)
assert ([ c.label() for c in p.mtz_object.columns() ] ==
['H','K','L','I-obs','SIGI-obs','F-obs','R-free-flags','R-free-flags_2'])
p.finish()
mtz_in = file_reader.any_file(test_file)
miller_arrays = mtz_in.file_object.as_miller_arrays()
flags1 = miller_arrays[-2]
assert flags1.info().label_string() == "R-free-flags"
(d_max, d_min) = flags1.d_max_min()
assert (approx_equal(d_max, 11.14, eps=0.01) and
approx_equal(d_min, 1.503, eps=0.01))
flags2 = miller_arrays[-1]
assert flags2.info().label_string() == "R-free-flags_2"
(d_max, d_min) = flags2.d_max_min()
assert (approx_equal(d_max, 11.14, eps=0.01) and
from __future__ import division import sys from iotbx import reflection_file_editor if __name__ == "__main__" : reflection_file_editor.run(sys.argv[1:])
