def exercise () :
from mmtbx.regression.make_fake_anomalous_data import generate_cd_cl_inputs
from mmtbx.command_line import mtz2map
import mmtbx.utils
from iotbx import file_reader
from scitbx.array_family import flex
mtz_file, pdb_file = generate_cd_cl_inputs(file_base = "tst_mmtbx_mtz2map")
pdb_in = file_reader.any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
xrs = pdb_in.file_object.xray_structure_simple()
mtz_in = file_reader.any_file(mtz_file)
f_obs = mtz_in.file_server.miller_arrays[0]
f_obs_mean = f_obs.average_bijvoet_mates()
flags = mtz_in.file_server.miller_arrays[1]
flags = flags.customized_copy(data=flags.data()==1)
fmodel = mmtbx.utils.fmodel_simple(
f_obs=f_obs,
r_free_flags=flags,
xray_structures=[xrs],
scattering_table="n_gaussian",
skip_twin_detection=True)
assert f_obs.anomalous_flag()
mtz_data = f_obs.as_mtz_dataset(column_root_label="F")
#mtz_data.add_miller_array(
# miller_array=f_obs.average_bijvoet_mates(),
# column_root_label="F_mean")
mtz_data.add_miller_array(
miller_array=fmodel.f_model(),
column_root_label="FMODEL")
mtz_data.add_miller_array(
miller_array=fmodel.f_model().average_bijvoet_mates().phases(deg=True),
column_root_label="PHI",
column_types="P")
mtz_data.add_miller_array(
miller_array=f_obs_mean.customized_copy(
data=flex.double(f_obs_mean.data().size(), 0.95),
sigmas=None).set_observation_type(None),
column_root_label="FOM",
column_types="W")
two_fofc_map = fmodel.map_coefficients(map_type="2mFo-DFc")
fofc_map = fmodel.map_coefficients(map_type="mFo-Dfc")
anom_map = fmodel.map_coefficients(map_type="anom")
mtz_data.add_miller_array(
miller_array=two_fofc_map.average_bijvoet_mates(),
column_root_label="2FOFCWT")
mtz_data.add_miller_array(
miller_array=fmodel.map_coefficients(map_type="mFo-DFc"),
column_root_label="FOFCWT")
mtz_data.add_miller_array(
miller_array=fmodel.map_coefficients(map_type="anom"),
column_root_label="ANOM")
mtz_data.add_miller_array(flags,
column_root_label="FreeR_flag")
map_file = "tst_mmtbx_mtz2map_map_coeffs.mtz"
mtz_data.mtz_object().write(map_file)
# exercise defaults with PDB file
file_info = mtz2map.run([pdb_file, map_file], log=null_out())
file_info = [ (os.path.basename(fn), desc) for fn, desc in file_info ]
assert (file_info == [
('tst_mmtbx_mtz2map_map_coeffs_2mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_anom.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_4.ccp4', 'CCP4 map')
])
# without PDB file
file_info_2 = mtz2map.run([map_file], log=null_out())
file_info_2 = [ (os.path.basename(fn), desc) for fn, desc in file_info_2 ]
assert file_info_2 == file_info, file_info_2
# with FMODEL
file_info_3 = mtz2map.run([pdb_file, map_file, "include_fmodel=True"],
log=null_out())
file_info_3 = [ (os.path.basename(fn), desc) for fn, desc in file_info_3 ]
assert (file_info_3 == [
('tst_mmtbx_mtz2map_map_coeffs_fmodel.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_2mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_anom.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_5.ccp4', 'CCP4 map')
])
# exercise bad parameter
try :
file_info = mtz2map.run([pdb_file, "1yjp_mtz2map_map_coeffs.mtz",
"output.directory=1yjp_mtz2map_map_coeffs.mtz"],
log=null_out())
except Sorry :
pass
else :
raise Exception_expected
# bad atom selection
try :
file_info = mtz2map.run([pdb_file, map_file, "selection=\"resname ZN\""],
log=null_out())
except Sorry, s :
assert (str(s) == "No atoms found matching the specified selection.")
def exercise():
from mmtbx.regression.make_fake_anomalous_data import generate_cd_cl_inputs
from mmtbx.command_line import mtz2map
import mmtbx.utils
from iotbx import file_reader
from scitbx.array_family import flex
mtz_file, pdb_file = generate_cd_cl_inputs(file_base="tst_mmtbx_mtz2map")
pdb_in = file_reader.any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
xrs = pdb_in.file_object.xray_structure_simple()
mtz_in = file_reader.any_file(mtz_file)
f_obs = mtz_in.file_server.miller_arrays[0]
f_obs_mean = f_obs.average_bijvoet_mates()
flags = mtz_in.file_server.miller_arrays[1]
flags = flags.customized_copy(data=flags.data() == 1)
fmodel = mmtbx.utils.fmodel_simple(f_obs=f_obs,
r_free_flags=flags,
xray_structures=[xrs],
scattering_table="n_gaussian",
skip_twin_detection=True)
assert f_obs.anomalous_flag()
mtz_data = f_obs.as_mtz_dataset(column_root_label="F")
#mtz_data.add_miller_array(
# miller_array=f_obs.average_bijvoet_mates(),
# column_root_label="F_mean")
mtz_data.add_miller_array(miller_array=fmodel.f_model(),
column_root_label="FMODEL")
mtz_data.add_miller_array(
miller_array=fmodel.f_model().average_bijvoet_mates().phases(deg=True),
column_root_label="PHI",
column_types="P")
mtz_data.add_miller_array(miller_array=f_obs_mean.customized_copy(
data=flex.double(f_obs_mean.data().size(),
0.95), sigmas=None).set_observation_type(None),
column_root_label="FOM",
column_types="W")
two_fofc_map = fmodel.map_coefficients(map_type="2mFo-DFc")
fofc_map = fmodel.map_coefficients(map_type="mFo-Dfc")
anom_map = fmodel.map_coefficients(map_type="anom")
mtz_data.add_miller_array(
miller_array=two_fofc_map.average_bijvoet_mates(),
column_root_label="2FOFCWT")
mtz_data.add_miller_array(
miller_array=fmodel.map_coefficients(map_type="mFo-DFc"),
column_root_label="FOFCWT")
mtz_data.add_miller_array(
miller_array=fmodel.map_coefficients(map_type="anom"),
column_root_label="ANOM")
mtz_data.add_miller_array(flags, column_root_label="FreeR_flag")
map_file = "tst_mmtbx_mtz2map_map_coeffs.mtz"
mtz_data.mtz_object().write(map_file)
# exercise defaults with PDB file
file_info = mtz2map.run([pdb_file, map_file], log=null_out())
file_info = [(os.path.basename(fn), desc) for fn, desc in file_info]
assert (file_info == [
('tst_mmtbx_mtz2map_map_coeffs_2mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_anom.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_4.ccp4', 'CCP4 map')
])
# without PDB file
file_info_2 = mtz2map.run([map_file], log=null_out())
file_info_2 = [(os.path.basename(fn), desc) for fn, desc in file_info_2]
assert file_info_2 == file_info, file_info_2
# with FMODEL
file_info_3 = mtz2map.run([pdb_file, map_file, "include_fmodel=True"],
log=null_out())
file_info_3 = [(os.path.basename(fn), desc) for fn, desc in file_info_3]
assert (file_info_3 == [
('tst_mmtbx_mtz2map_map_coeffs_fmodel.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_2mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_anom.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_5.ccp4', 'CCP4 map')
])
# exercise bad parameter
try:
file_info = mtz2map.run([
pdb_file, "1yjp_mtz2map_map_coeffs.mtz",
"output.directory=1yjp_mtz2map_map_coeffs.mtz"
],
log=null_out())
except Sorry:
pass
else:
raise Exception_expected
# bad atom selection
try:
file_info = mtz2map.run(
[pdb_file, map_file, "selection=\"resname ZN\""], log=null_out())
except Sorry, s:
assert (str(s) == "No atoms found matching the specified selection.")
('tst_mmtbx_mtz2map_map_coeffs_mFo-DFc.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_anom.ccp4', 'CCP4 map'),
('tst_mmtbx_mtz2map_map_coeffs_5.ccp4', 'CCP4 map')
])
# exercise bad parameter
try :
file_info = mtz2map.run([pdb_file, "1yjp_mtz2map_map_coeffs.mtz",
"output.directory=1yjp_mtz2map_map_coeffs.mtz"],
log=null_out())
except Sorry :
pass
else :
raise Exception_expected
# bad atom selection
try :
file_info = mtz2map.run([pdb_file, map_file, "selection=\"resname ZN\""],
log=null_out())
except Sorry, s :
assert (str(s) == "No atoms found matching the specified selection.")
else :
raise Exception_expected
# remove R-free flags
out = StringIO()
mtz2map.run([pdb_file, "tst_mmtbx_mtz2map_map_coeffs.mtz",
"r_free_flags.remove=True"], log=out)
assert (out.getvalue().count("R-free flagged reflections")==4)
print "OK"
if (__name__ == "__main__") :
exercise()
file_info = mtz2map.run([
pdb_file, "1yjp_mtz2map_map_coeffs.mtz",
"output.directory=1yjp_mtz2map_map_coeffs.mtz"
],
log=null_out())
except Sorry:
pass
else:
raise Exception_expected
# bad atom selection
try:
file_info = mtz2map.run(
[pdb_file, map_file, "selection=\"resname ZN\""], log=null_out())
except Sorry, s:
assert (str(s) == "No atoms found matching the specified selection.")
else:
raise Exception_expected
# remove R-free flags
out = StringIO()
mtz2map.run([
pdb_file, "tst_mmtbx_mtz2map_map_coeffs.mtz",
"r_free_flags.remove=True"
],
log=out)
assert (out.getvalue().count("R-free flagged reflections") == 4)
print "OK"
if (__name__ == "__main__"):
exercise()
