def run(args, out=sys.stdout):
show_development_warning(out=out)
if (len(args) == 0) or ("--help" in args):
raise Usage("""\
cctbx.patterson_map data.mtz [options]
Calculates a simple or anomalous difference Patterson map. Output is in CCP4
format.
Full options:
%s
""" % master_phil.as_str(prefix=" "))
import iotbx.phil
from cctbx.array_family import flex
from cctbx import miller
from cctbx import xray
hkl_in = None
sources = []
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
reflection_file_def="data")
params = cmdline.work.extract()
if (params.data is None):
raise Usage("mmtbx.patterson_map data [options]\n\nFull parameters:\n%s" %
master_phil.as_str(prefix=" "))
f_obs = extract_data(
file_name=params.data,
expected_labels=params.labels,
out=out)
if (f_obs is None):
raise Sorry("No suitable data found.")
f_obs = prepare_f_obs(f_obs, params=params)
final_array = f_obs # default
is_anom = False
if (f_obs.anomalous_flag()):
if (params.map_type in ["auto", "anom"]):
print >> out, "Output will be anomalous Patterson map"
is_anom = True
final_array = f_obs.anomalous_differences()
final_array = abs(final_array)
if (params.diff_limit is not None):
final_array = final_array.select(final_array.data() < params.diff_limit)
else :
final_array = f_obs.average_bijvoet_mates()
map = calculate_patterson_map(data=final_array, params=params,
normalize=is_anom)
if (params.map_file_name is None):
base = os.path.splitext(os.path.basename(params.data))[0]
params.map_file_name = base + "_patt.ccp4"
map.as_ccp4_map(
file_name=params.map_file_name)
print >> out, "Wrote %s" % params.map_file_name
def run (args, out=sys.stdout) :
show_development_warning(out=out)
if (len(args) == 0) or ("--help" in args) :
raise Usage("""\
cctbx.patterson_map data.mtz [options]
Calculates a simple or anomalous difference Patterson map. Output is in CCP4
format.
Full options:
%s
""" % master_phil.as_str(prefix=" "))
import iotbx.phil
from cctbx.array_family import flex
from cctbx import miller
from cctbx import xray
hkl_in = None
sources = []
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
reflection_file_def="data")
params = cmdline.work.extract()
if (params.data is None) :
raise Usage("mmtbx.patterson_map data [options]\n\nFull parameters:\n%s" %
master_phil.as_str(prefix=" "))
f_obs = extract_data(
file_name=params.data,
expected_labels=params.labels,
out=out)
if (f_obs is None) :
raise Sorry("No suitable data found.")
f_obs = prepare_f_obs(f_obs, params=params)
final_array = f_obs # default
is_anom = False
if (f_obs.anomalous_flag()) :
if (params.map_type in ["auto", "anom"]) :
print >> out, "Output will be anomalous Patterson map"
is_anom = True
final_array = f_obs.anomalous_differences()
final_array = abs(final_array)
if (params.diff_limit is not None) :
final_array = final_array.select(final_array.data() < params.diff_limit)
else :
final_array = f_obs.average_bijvoet_mates()
map = calculate_patterson_map(data=final_array, params=params,
normalize=is_anom)
if (params.map_file_name is None) :
base = os.path.splitext(os.path.basename(params.data))[0]
params.map_file_name = base + "_patt.ccp4"
map.as_ccp4_map(
file_name=params.map_file_name)
print >> out, "Wrote %s" % params.map_file_name
def run (args, out=sys.stdout) :
show_development_warning(out=out)
if (len(args) == 0) or ("--help" in args) :
raise Usage("""\
cctbx.isomorphous_difference_patterson xtal1.mtz xtal2.mtz [options]
Calculate an isomorphous difference Patterson map from two datasets. You may
specify both in a single MTZ file if you want, but you must manually specify
the data_file_1 and data_file_2 parameters. Output is a CCP4-format map.
Full parameters:
%s
""" % master_phil.as_str(prefix=" "))
from iotbx.command_line import patterson_map
from iotbx import file_reader
import iotbx.symmetry
sources = []
data_file_1 = data_file_2 = None
for arg in args :
if (os.path.isfile(arg)) :
f = file_reader.any_file(arg)
if (f.file_type == "phil") :
sources.append(f.file_object)
elif (f.file_type == "hkl") :
if (data_file_1 is None) :
data_file_1 = f
elif (data_file_2 is None) :
data_file_2 = f
else :
raise Sorry("No more than two reflection files are supported.")
else :
raise Sorry("The file format for '%s' is not a supported input." % arg)
else :
try :
sources.append(libtbx.phil.parse(arg))
except RuntimeError, e :
raise Sorry("Unrecognized argument '%s'.")
def run(args, out=sys.stdout):
show_development_warning(out=out)
if (len(args) == 0) or ("--help" in args):
raise Usage("""\
cctbx.isomorphous_difference_patterson xtal1.mtz xtal2.mtz [options]
Calculate an isomorphous difference Patterson map from two datasets. You may
specify both in a single MTZ file if you want, but you must manually specify
the data_file_1 and data_file_2 parameters. Output is a CCP4-format map.
Full parameters:
%s
""" % master_phil.as_str(prefix=" "))
from iotbx.command_line import patterson_map
from iotbx import file_reader
import iotbx.symmetry
sources = []
data_file_1 = data_file_2 = None
for arg in args:
if (os.path.isfile(arg)):
f = file_reader.any_file(arg)
if (f.file_type == "phil"):
sources.append(f.file_object)
elif (f.file_type == "hkl"):
if (data_file_1 is None):
data_file_1 = f
elif (data_file_2 is None):
data_file_2 = f
else:
raise Sorry(
"No more than two reflection files are supported.")
else:
raise Sorry(
"The file format for '%s' is not a supported input." % arg)
else:
try:
sources.append(libtbx.phil.parse(arg))
except RuntimeError as e:
raise Sorry("Unrecognized argument '%s'.")
params = master_phil.fetch(sources=sources).extract()
if (params.data_file_1 is not None):
data_file_1 = file_reader.any_file(params.data_file_1)
if (params.data_file_2 is not None):
data_file_2 = file_reader.any_file(params.data_file_2)
if (None in [data_file_1, data_file_2]):
raise Sorry(
"You must provide two datasets for this program to run. If " +
"they are different arrays within a specific file, you need to specify "
+
"the parameters explicitly, i.e. 'data_file_1=NAME data_file_2=NAME'."
)
symm_manager = iotbx.symmetry.manager()
sg_err_1, uc_err_1 = symm_manager.process_reflections_file(data_file_1)
sg_err_2, uc_err_2 = symm_manager.process_reflections_file(data_file_2)
out_tmp = StringIO()
symm_manager.show(out=out_tmp)
if (sg_err_1) or (sg_err_2):
raise Sorry((
"Incompatible space groups in input files:\n%s\nAll files " +
"must have the same point group (and ideally the same space group). "
) % out_tmp.getvalue())
elif (uc_err_1) or (uc_err_2):
libtbx.call_back(
message="warn",
data=
("Crystal symmetry mismatch:\n%s\nCalculations will continue " +
"using the symmetry in the PDB file first reflection file, but the "
+ "maps should be treated with some suspicion.") %
out_tmp.getvalue())
obs_1 = patterson_map.extract_data(file_name=None,
hkl_in=data_file_1,
expected_labels=params.labels_1,
out=out)
obs_2 = patterson_map.extract_data(file_name=None,
hkl_in=data_file_2,
expected_labels=params.labels_2,
out=out)
assert (not None in [obs_1, obs_2])
print("", file=out)
print("Data array #1 (will use symmetry from here):", file=out)
obs_1.show_summary(f=out, prefix=" ")
print("", file=out)
print("Data array #2:", file=out)
obs_2.show_summary(f=out, prefix=" ")
print("", file=out)
obs_2 = obs_2.customized_copy(crystal_symmetry=obs_1)
f_obs_1 = patterson_map.prepare_f_obs(obs_1,
params).average_bijvoet_mates()
f_obs_2 = patterson_map.prepare_f_obs(obs_2,
params).average_bijvoet_mates()
f_obs_1, f_obs_2 = f_obs_1.common_sets(other=f_obs_2)
# XXX will this work as expected?
print("Scaling second dataset...", file=out)
f_obs_2 = f_obs_1.multiscale(other=f_obs_2)
from scitbx.array_family import flex
print(" max(F1) = %.2f max(F2) = %.2f" %
(flex.max(f_obs_1.data()), flex.max(f_obs_2.data())),
file=out)
delta_f = f_obs_1.customized_copy(data=f_obs_1.data() - f_obs_2.data())
if (params.relative_diff_limit is not None):
f_obs_1_non_zero = f_obs_1.select(f_obs_1.data() > 0)
delta_f_non_zero = delta_f.common_set(other=f_obs_1_non_zero)
relative_diff = delta_f_non_zero.customized_copy(
data=delta_f_non_zero.data() / f_obs_1_non_zero.data())
delta_f = delta_f_non_zero.select(
relative_diff.data() < params.relative_diff_limit)
n_discarded = len(delta_f_non_zero.data()) - len(delta_f.data())
if (n_discarded > 0):
print("Discarded %d reflections with excessive differences." % \
n_discarded, file=out)
print(" max(delta_F) = %.2f" % flex.max(delta_f.data()), file=out)
map = patterson_map.calculate_patterson_map(data=delta_f,
params=params,
normalize=False)
if (params.map_file_name is None):
params.map_file_name = "iso_diff.ccp4"
map.as_ccp4_map(file_name=params.map_file_name)
print("Wrote %s" % params.map_file_name, file=out)