def exercise_intensity_output () :
if (os.path.isfile("tst_fmodel_anomalous.mtz")) :
os.remove("tst_fmodel_anomalous.mtz")
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base="tst_fmodel_anomalous")
# phenix.fmodel (with wavelength)
args = [
pdb_file,
"high_resolution=1.0",
"wavelength=1.116",
"obs_type=intensities",
"type=real",
"output.file_name=tst_fmodel_intensity.mtz",
"r_free_flags_fraction=0.1",
]
args2 = args + ["label=Imodel"]
fmodel.run(args=args2, log=null_out())
assert os.path.isfile("tst_fmodel_intensity.mtz")
mtz_in = file_reader.any_file("tst_fmodel_intensity.mtz")
assert mtz_in.file_server.miller_arrays[0].is_xray_intensity_array()
try :
fmodel.run(args=args, log=null_out())
except Sorry :
pass
else :
raise Exception_expected
try :
fmodel.run(args=args+["format=cns"], log=null_out())
except Sorry :
pass
else :
raise Exception_expected
def exercise () :
if (os.path.isfile("tst_fmodel_anomalous.mtz")) :
os.remove("tst_fmodel_anomalous.mtz")
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base="tst_fmodel_anomalous")
# phenix.fmodel (with wavelength)
args = [
pdb_file,
"high_resolution=1.0",
"wavelength=1.116",
"label=F",
"type=real",
"output.file_name=tst_fmodel_anomalous.mtz",
"r_free_flags_fraction=0.1",
]
fmodel.run(args=args, log=null_out())
assert os.path.isfile("tst_fmodel_anomalous.mtz")
mtz_in = file_reader.any_file("tst_fmodel_anomalous.mtz")
array = mtz_in.file_server.miller_arrays[0]
assert (array.anomalous_flag())
anom_diffs = array.anomalous_differences()
assert approx_equal(flex.max(anom_diffs.data()), 5.72, eps=0.01)
# mmtbx.fmodel_simple
result = easy_run.call(
"mmtbx.fmodel_simple \"%s\" tst_fmodel_anomalous.mtz high_resolution=2.0"
% pdb_file)
print "OK"
def exercise_heavy () :
from mmtbx.regression import make_fake_anomalous_data
from mmtbx.command_line import validate_waters
import mmtbx.ions.utils
from iotbx.file_reader import any_file
file_base = "tst_validate_waters_1"
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(file_base=file_base)
mtz_file = make_fake_anomalous_data.generate_mtz_file(
file_base="tst_validate_waters_1",
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CD", fp=-0.29, fdp=2.676),
group_args(selection="element CL", fp=0.256, fdp=0.5),
])
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
hierarchy.write_pdb_file("%s_start.pdb" % file_base,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
args = ["tst_validate_waters_1_start.pdb", "tst_validate_waters_1.mtz",
"skip_twin_detection=True"]
results = validate_waters.run(args=args, out=null_out())
out = StringIO()
results.show(out=out)
s = easy_pickle.dumps(results)
r2 = easy_pickle.loads(s)
out2 = StringIO()
r2.show(out=out2)
assert not show_diff(out.getvalue(), out2.getvalue())
assert (results.n_bad >= 1) and (results.n_heavy == 2)
def exercise_heavy():
from mmtbx.regression import make_fake_anomalous_data
from mmtbx.command_line import validate_waters
import mmtbx.ions.utils
from iotbx.file_reader import any_file
file_base = "tst_validate_waters_1"
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base=file_base)
mtz_file = make_fake_anomalous_data.generate_mtz_file(
file_base="tst_validate_waters_1",
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CD", fp=-0.29, fdp=2.676),
group_args(selection="element CL", fp=0.256, fdp=0.5),
])
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
hierarchy.write_pdb_file(
"%s_start.pdb" % file_base,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
args = [
"tst_validate_waters_1_start.pdb", "tst_validate_waters_1.mtz",
"skip_twin_detection=True"
]
results = validate_waters.run(args=args, out=null_out())
out = StringIO()
results.show(out=out)
s = easy_pickle.dumps(results)
r2 = easy_pickle.loads(s)
out2 = StringIO()
r2.show(out=out2)
assert not show_diff(out.getvalue(), out2.getvalue())
assert (results.n_bad >= 1) and (results.n_heavy == 2)
def exercise () :
from mmtbx.command_line import b_factor_statistics
from mmtbx.regression import make_fake_anomalous_data
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base="tst_b_factor_stats")
out = StringIO()
stats = b_factor_statistics.run(args=[pdb_file], out=out)
assert ("""\
| all : 79 0 7.73 42.64 13.18 None None None |""" in
out.getvalue())
out = StringIO()
stats = b_factor_statistics.run(args=[pdb_file, "selection=element CD"],
out=out)
assert ("""\
| all(noH): 1 0 15.00 15.00 15.00 None None None |""" in
out.getvalue())
print "OK"
def exercise():
from mmtbx.command_line import b_factor_statistics
from mmtbx.regression import make_fake_anomalous_data
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base="tst_b_factor_stats")
out = StringIO()
stats = b_factor_statistics.run(args=[pdb_file], out=out)
assert ("""\
| all : 79 0 7.73 42.64 13.18 None None None |"""
in out.getvalue())
out = StringIO()
stats = b_factor_statistics.run(args=[pdb_file, "selection=element CD"],
out=out)
assert ("""\
| all(noH): 1 0 15.00 15.00 15.00 None None None |"""
in out.getvalue())
print "OK"
