def get_inputs(args, log, master_params):
"""
Eventually, this will be centralized.
"""
cmdline = process_command_line_with_files(args=args,
master_phil=master_params,
pdb_file_def='model_file_name')
params = cmdline.work.extract()
# Model
file_names = params.model_file_name
pdb_combined = combine_unique_pdb_files(file_names=file_names)
pdb_inp = iotbx.pdb.input(source_info=None,
lines=flex.std_string(pdb_combined.raw_records),
raise_sorry_if_format_error=True)
# Crystal symmetry
fake_crystal_symmetry = False
crystal_symmetry = pdb_inp.crystal_symmetry()
if (crystal_symmetry is None or crystal_symmetry.is_empty()
or crystal_symmetry.is_nonsence()):
fake_crystal_symmetry = True
from cctbx import uctbx
crystal_symmetry = \
uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=pdb_inp.atoms().extract_xyz(),
buffer_layer=5).crystal_symmetry()
#
model = mmtbx.model.manager(model_input=pdb_inp,
crystal_symmetry=crystal_symmetry)
#
return group_args(params=params,
pdb_file_names=file_names,
model=model,
fake_crystal_symmetry=fake_crystal_symmetry)
def run(args, log = sys.stdout):
if(len(args)==0):
print >> log, legend
defaults(log=log)
return
#
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(args = args,
log = sys.stdout, master_params = parsed)
params = processed_args.params.extract()
unit_cell = processed_args.crystal_symmetry.unit_cell()
reflection_files = processed_args.reflection_files
#
atoms_with_labels = None
if(len(processed_args.pdb_file_names)==1):
pdb_combined = combine_unique_pdb_files(
file_names=processed_args.pdb_file_names)
pdb_combined.report_non_unique()
pdb_inp = iotbx.pdb.input(source_info = None,
lines = flex.std_string(pdb_combined.raw_records))
atoms_with_labels = pdb_inp.atoms_with_labels()
if(len(params.point)==0 and atoms_with_labels is None):
raise Sorry("No points given to compute map value at.")
if(len(reflection_files) == 0 and processed_args.ccp4_map is None):
raise Sorry("No reflection or map files found.")
if(len(reflection_files) > 1):
raise Sorry("More than one reflection file found.")
crystal_symmetry = processed_args.crystal_symmetry
if(crystal_symmetry is None):
raise Sorry("No crystal symmetry found.")
if(len(reflection_files) != 0):
map_3d = map_from_reflection_file(reflection_files=reflection_files, params=params)
else:
map_3d = processed_args.ccp4_map.data.as_double()
print "Map values at specified points:"
for point in params.point:
point_frac = unit_cell.fractionalize(point)
point_formatted = ",".join([str("%10.3f"%p).strip() for p in point])
point_frac_formatted = \
",".join([str("%10.3f"%p).strip() for p in point_frac])
map_value = str(
"%10.3f"%map_3d.eight_point_interpolation(point_frac)).strip()
print " Input point: (%s) Fractionalized: (%s) Map value: %s"%(
point_formatted, point_frac_formatted, map_value)
#
if(atoms_with_labels is not None):
for point in atoms_with_labels:
point_frac = processed_args.crystal_symmetry.unit_cell().fractionalize(point.xyz)
point_formatted = ",".join([str("%8.3f"%p) for p in point.xyz])
map_value = str(
"%10.3f"%map_3d.eight_point_interpolation(point_frac)).strip()
print point.quote(), "Point: %s Map value: %s"%(point_formatted,map_value)
#
print
print "All done."
def run(args, log = sys.stdout):
if(len(args)==0):
print(legend, file=log)
defaults(log=log)
return
#
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(args = args,
log = sys.stdout, master_params = parsed)
params = processed_args.params.extract()
unit_cell = processed_args.crystal_symmetry.unit_cell()
reflection_files = processed_args.reflection_files
#
atoms_with_labels = None
if(len(processed_args.pdb_file_names)==1):
pdb_combined = combine_unique_pdb_files(
file_names=processed_args.pdb_file_names)
pdb_combined.report_non_unique()
pdb_inp = iotbx.pdb.input(source_info = None,
lines = flex.std_string(pdb_combined.raw_records))
atoms_with_labels = pdb_inp.atoms_with_labels()
if(len(params.point)==0 and atoms_with_labels is None):
raise Sorry("No points given to compute map value at.")
if(len(reflection_files) == 0 and processed_args.ccp4_map is None):
raise Sorry("No reflection or map files found.")
if(len(reflection_files) > 1):
raise Sorry("More than one reflection file found.")
crystal_symmetry = processed_args.crystal_symmetry
if(crystal_symmetry is None):
raise Sorry("No crystal symmetry found.")
if(len(reflection_files) != 0):
map_3d = map_from_reflection_file(reflection_files=reflection_files, params=params)
else:
map_3d = processed_args.ccp4_map.map_data()
print("Map values at specified points:")
for point in params.point:
point_frac = unit_cell.fractionalize(point)
point_formatted = ",".join([str("%10.3f"%p).strip() for p in point])
point_frac_formatted = \
",".join([str("%10.3f"%p).strip() for p in point_frac])
map_value = str(
"%10.3f"%map_3d.eight_point_interpolation(point_frac)).strip()
print(" Input point: (%s) Fractionalized: (%s) Map value: %s"%(
point_formatted, point_frac_formatted, map_value))
#
if(atoms_with_labels is not None):
for point in atoms_with_labels:
point_frac = processed_args.crystal_symmetry.unit_cell().fractionalize(point.xyz)
point_formatted = ",".join([str("%8.3f"%p) for p in point.xyz])
map_value = str(
"%10.3f"%map_3d.eight_point_interpolation(point_frac)).strip()
print(point.quote(), "Point: %s Map value: %s"%(point_formatted,map_value))
#
print()
print("All done.")
def process_inputs(self, prefix):
broadcast(m=prefix, log=self.log)
self.pdb_file_names = list(self.inputs.pdb_file_names)
if (self.params.file_name is not None):
self.pdb_file_names.append(self.params.file_name)
#=================================================
cs = self.inputs.crystal_symmetry
is_non_crystallographic_unit_cell = False
import iotbx.pdb
pdb_combined = combine_unique_pdb_files(file_names=self.pdb_file_names)
pdb_inp = iotbx.pdb.input(lines=pdb_combined.raw_records,
source_info=None)
if (cs is None):
cs = pdb_inp.crystal_symmetry()
if (cs is None):
is_non_crystallographic_unit_cell = True
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=pdb_inp.atoms().extract_xyz(), buffer_layer=10)
cs = box.crystal_symmetry()
cif_objects = list(self.inputs.cif_objects)
if (len(self.params.restraints) > 0):
import iotbx.cif
for file_name in self.params.restraints:
cif_object = iotbx.cif.reader(file_path=file_name,
strict=False).model()
cif_objects.append((file_name, cif_object))
if (self.params.restraints_directory is not None):
restraint_files = os.listdir(self.params.restraints_directory)
for file_name in restraint_files:
if (file_name.endswith(".cif")):
full_path = os.path.join(self.params.restraints_directory,
file_name)
cif_object = iotbx.cif.reader(file_path=full_path,
strict=False).model()
cif_objects.append((full_path, cif_object))
self.model = mmtbx.model.manager(
model_input=pdb_inp,
crystal_symmetry=cs,
restraint_objects=cif_objects,
stop_for_unknowns=self.params.stop_for_unknowns,
log=self.log)
self.model.process(pdb_interpretation_params=self.params,
make_restraints=True)
self.ncs_obj = self.model.get_ncs_obj()
self.output_crystal_symmetry = not is_non_crystallographic_unit_cell
self.sites_cart_start = self.model.get_xray_structure().sites_cart(
).deep_copy()
if (self.params.show_states):
self.states_collector = mmtbx.utils.states(
xray_structure=self.model.get_xray_structure(),
pdb_hierarchy=self.model.get_hierarchy())
self.setup_output_file_names()
def process_input_files(inputs, params, log, mon_lib_srv=None):
pdb_file_names = []
pdb_file_names = list(inputs.pdb_file_names)
if (params.file_name is not None) :
pdb_file_names.append(params.file_name)
cs = inputs.crystal_symmetry
is_non_crystallographic_unit_cell = False
if(cs is None):
is_non_crystallographic_unit_cell = True
import iotbx.pdb
pdb_combined = combine_unique_pdb_files(file_names = pdb_file_names)
cs = iotbx.pdb.input(source_info = None, lines = flex.std_string(
pdb_combined.raw_records)).xray_structure_simple().\
cubic_unit_cell_around_centered_scatterers(
buffer_size = 10).crystal_symmetry()
cif_objects = list(inputs.cif_objects)
if (len(params.restraints) > 0) :
import iotbx.cif
for file_name in params.restraints :
cif_object = iotbx.cif.reader(file_path=file_name, strict=False).model()
cif_objects.append((file_name, cif_object))
if (params.restraints_directory is not None) :
restraint_files = os.listdir(params.restraints_directory)
for file_name in restraint_files :
if (file_name.endswith(".cif")) :
full_path = os.path.join(params.restraints_directory, file_name)
cif_object = iotbx.cif.reader(file_path=full_path,
strict=False).model()
cif_objects.append((full_path, cif_object))
processed_pdb_files_srv = mmtbx.utils.process_pdb_file_srv(
crystal_symmetry = cs,
pdb_interpretation_params = params.pdb_interpretation,
stop_for_unknowns = params.stop_for_unknowns,
log = log,
cif_objects = cif_objects,
use_neutron_distances = params.pdb_interpretation.use_neutron_distances,
mon_lib_srv = mon_lib_srv)
processed_pdb_file, junk = processed_pdb_files_srv.\
process_pdb_files(pdb_file_names = pdb_file_names) # XXX remove junk
processed_pdb_file.is_non_crystallographic_unit_cell = \
is_non_crystallographic_unit_cell # XXX bad hack
return processed_pdb_file
def process_input_files(inputs, params, log, mon_lib_srv=None):
pdb_file_names = []
pdb_file_names = list(inputs.pdb_file_names)
if (params.file_name is not None) :
pdb_file_names.append(params.file_name)
cs = inputs.crystal_symmetry
is_non_crystallographic_unit_cell = False
if(cs is None):
is_non_crystallographic_unit_cell = True
import iotbx.pdb
pdb_combined = combine_unique_pdb_files(file_names = pdb_file_names)
cs = iotbx.pdb.input(source_info = None, lines = flex.std_string(
pdb_combined.raw_records)).xray_structure_simple().\
cubic_unit_cell_around_centered_scatterers(
buffer_size = 10).crystal_symmetry()
cif_objects = list(inputs.cif_objects)
if (len(params.restraints) > 0) :
import iotbx.cif
for file_name in params.restraints :
cif_object = iotbx.cif.reader(file_path=file_name, strict=False).model()
cif_objects.append((file_name, cif_object))
if (params.restraints_directory is not None) :
restraint_files = os.listdir(params.restraints_directory)
for file_name in restraint_files :
if (file_name.endswith(".cif")) :
full_path = os.path.join(params.restraints_directory, file_name)
cif_object = iotbx.cif.reader(file_path=full_path,
strict=False).model()
cif_objects.append((full_path, cif_object))
processed_pdb_files_srv = mmtbx.utils.process_pdb_file_srv(
crystal_symmetry = cs,
pdb_interpretation_params = params.pdb_interpretation,
stop_for_unknowns = params.stop_for_unknowns,
log = log,
cif_objects = cif_objects,
use_neutron_distances = params.pdb_interpretation.use_neutron_distances,
mon_lib_srv = mon_lib_srv)
processed_pdb_file, junk = processed_pdb_files_srv.\
process_pdb_files(pdb_file_names = pdb_file_names) # XXX remove junk
processed_pdb_file.is_non_crystallographic_unit_cell = \
is_non_crystallographic_unit_cell # XXX bad hack
return processed_pdb_file
def exercise_combine_unique_pdb_files():
for file_name,s in [("tmp1", "1"),
("tmp2", " 2"),
("tmp3", "1\t"),
("tmp4", " \t2"),
("tmp5", "1 ")]:
open(file_name, "w").write(s)
for file_names in [[], ["tmp1"], ["tmp1", "tmp2"]]:
c = pdb.combine_unique_pdb_files(file_names=file_names)
assert len(c.file_name_registry) == len(file_names)
assert len(c.md5_registry) == len(file_names)
assert len(c.unique_file_names) == len(file_names)
assert len(c.raw_records) == len(file_names)
s = StringIO()
c.report_non_unique(out=s)
assert len(s.getvalue()) == 0
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp1"])
assert len(c.file_name_registry) == 1
assert len(c.md5_registry) == 1
assert len(c.unique_file_names) == 1
assert len(c.raw_records) == 1
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(s.getvalue(), """\
INFO: PDB file name appears 2 times: "tmp1"
1 repeated file name ignored.
""")
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp1", "tmp2", "tmp1"])
assert len(c.file_name_registry) == 2
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s, prefix="^")
assert not show_diff(s.getvalue(), """\
^INFO: PDB file name appears 3 times: "tmp1"
^ 2 repeated file names ignored.
^
""")
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp2", "tmp3"])
assert len(c.file_name_registry) == 3
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(s.getvalue(), """\
INFO: PDB files with identical content:
"tmp1"
"tmp3"
1 file with repeated content ignored.
""")
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp2", "tmp3", "tmp5"])
assert len(c.file_name_registry) == 4
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s, prefix=": ")
assert not show_diff(s.getvalue(), """\
: INFO: PDB files with identical content:
: "tmp1"
: "tmp3"
: "tmp5"
: 2 files with repeated content ignored.
:
""")
c = pdb.combine_unique_pdb_files(file_names=[
"tmp1", "tmp2", "tmp3", "tmp4", "tmp5", "tmp4", "tmp5"])
assert len(c.file_name_registry) == 5
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(s.getvalue(), """\
INFO: PDB file name appears 2 times: "tmp4"
INFO: PDB file name appears 2 times: "tmp5"
2 repeated file names ignored.
INFO: PDB files with identical content:
"tmp2"
"tmp4"
INFO: PDB files with identical content:
"tmp1"
"tmp3"
"tmp5"
3 files with repeated content ignored.
""")
def run(args, command_name="phenix.fobs_minus_fobs_map", log=None):
if (len(args) == 0): args = ["--help"]
examples = """Examples:
phenix.fobs_minus_fobs_map f_obs_1_file=data1.mtz f_obs_2_file=data2.sca \
f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 model.pdb
phenix.fobs_minus_fobs_map f_obs_1_file=data.mtz f_obs_2_file=data.mtz \
f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 phase_source=model.pdb \
high_res=2.0 sigma_cutoff=2 scattering_table=neutron"""
command_line = (iotbx_option_parser(
usage="%s [options]" % command_name,
description=examples).option("--silent",
action="store_true",
help="Suppress output to the screen.").
enable_symmetry_comprehensive()).process(args=args)
#
if (log is None):
log = sys.stdout
if (not command_line.options.silent):
utils.print_header("phenix.fobs_minus_fobs_map", out=log)
print("Command line arguments: ", file=log)
print(args, file=log)
print(file=log)
#
processed_args = utils.process_command_line_args(
args=command_line.args,
cmd_cs=command_line.symmetry,
master_params=fo_minus_fo_master_params(),
absolute_angle_tolerance=5,
absolute_length_tolerance=1,
log=log,
suppress_symmetry_related_errors=True)
working_phil = processed_args.params
if (not command_line.options.silent):
print("*** Parameters:", file=log)
working_phil.show(out=log)
print(file=log)
params = working_phil.extract()
consensus_symmetry = None
if (params.ignore_non_isomorphous_unit_cells):
if (None in [
params.f_obs_1_file_name, params.f_obs_2_file_name,
params.phase_source
]):
raise Sorry(
"The file parameters (f_obs_1_file_name, f_obs_2_file_name, " +
"phase_source) must be specified explicitly when " +
"ignore_non_isomorphous_unit_cells=True.")
symm_manager = iotbx.symmetry.manager()
pdb_in = iotbx.file_reader.any_file(params.phase_source,
force_type="pdb")
symm_manager.process_pdb_file(pdb_in)
hkl_in_1 = iotbx.file_reader.any_file(params.f_obs_1_file_name,
force_type="hkl")
sg_err_1, uc_err_1 = symm_manager.process_reflections_file(hkl_in_1)
hkl_in_2 = iotbx.file_reader.any_file(params.f_obs_2_file_name,
force_type="hkl")
sg_err_2, uc_err_2 = symm_manager.process_reflections_file(hkl_in_2)
out = StringIO()
symm_manager.show(out=out)
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). "
+
"Please note that any symmetry information in the PDB file will be "
+ "used first.") % out.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 (or if not available, the "
+
"first reflection file), but the maps should be treated with "
+ "extreme suspicion.") % out.getvalue())
crystal_symmetry = symm_manager.as_symmetry_object()
else:
processed_args = utils.process_command_line_args(
args=command_line.args,
cmd_cs=command_line.symmetry,
master_params=fo_minus_fo_master_params(),
suppress_symmetry_related_errors=False,
absolute_angle_tolerance=5,
absolute_length_tolerance=1,
log=StringIO())
crystal_symmetry = processed_args.crystal_symmetry
#
pdb_file_names = processed_args.pdb_file_names
if (len(processed_args.pdb_file_names) == 0):
if (params.phase_source is not None):
pdb_file_names = [params.phase_source]
else:
raise Sorry("No PDB file found.")
# Extaract Fobs1, Fobs2
f_obss = []
if (len(processed_args.reflection_files) == 2):
for reflection_file in processed_args.reflection_files:
reflection_file_server = reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=[reflection_file],
err=null_out())
# XXX UGLY !!!
try:
parameters = utils.data_and_flags_master_params().extract()
if (params.f_obs_1_label is not None):
parameters.labels = [params.f_obs_1_label]
determine_data_and_flags_result = utils.determine_data_and_flags(
reflection_file_server=reflection_file_server,
keep_going=True,
parameters=parameters,
log=null_out())
except: # intentional
parameters = utils.data_and_flags_master_params().extract()
if (params.f_obs_2_label is not None):
parameters.labels = [params.f_obs_2_label]
determine_data_and_flags_result = utils.determine_data_and_flags(
reflection_file_server=reflection_file_server,
keep_going=True,
parameters=parameters,
log=null_out())
f_obss.append(determine_data_and_flags_result.f_obs)
else:
if ([params.f_obs_1_file_name,
params.f_obs_2_file_name].count(None) == 2):
raise Sorry("No reflection data file found.")
for file_name, label in zip(
[params.f_obs_1_file_name, params.f_obs_2_file_name],
[params.f_obs_1_label, params.f_obs_2_label]):
reflection_file = reflection_file_reader.any_reflection_file(
file_name=file_name, ensure_read_access=False)
reflection_file_server = reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=[reflection_file],
err=null_out())
parameters = utils.data_and_flags_master_params().extract()
if (label is not None):
parameters.labels = [label]
determine_data_and_flags_result = utils.determine_data_and_flags(
reflection_file_server=reflection_file_server,
parameters=parameters,
keep_going=True,
log=null_out())
f_obss.append(determine_data_and_flags_result.f_obs)
if (len(f_obss) != 2):
raise Sorry(" ".join(errors))
if (not command_line.options.silent):
for ifobs, fobs in enumerate(f_obss):
print("*** Summary for data set %d:" % ifobs, file=log)
fobs.show_comprehensive_summary(f=log)
print(file=log)
pdb_combined = combine_unique_pdb_files(file_names=pdb_file_names)
pdb_combined.report_non_unique(out=log)
if (len(pdb_combined.unique_file_names) == 0):
raise Sorry("No coordinate file given.")
#
raw_recs = flex.std_string()
for rec in pdb_combined.raw_records:
if (rec.upper().count("CRYST1") == 0):
raw_recs.append(rec)
raw_recs.append(
iotbx.pdb.format_cryst1_record(crystal_symmetry=crystal_symmetry))
#
pdb_in = iotbx.pdb.input(source_info=None, lines=raw_recs)
model = mmtbx.model.manager(model_input=pdb_in)
d_min = min(f_obss[0].d_min(), f_obss[1].d_min())
model.setup_scattering_dictionaries(
scattering_table=params.scattering_table, d_min=d_min)
xray_structure = model.get_xray_structure()
hierarchy = model.get_hierarchy()
#
omit_sel = flex.bool(hierarchy.atoms_size(), False)
if (params.advanced.omit_selection is not None):
print("Will omit selection from phasing model:", file=log)
print(" " + params.advanced.omit_selection, file=log)
omit_sel = hierarchy.atom_selection_cache().selection(
params.advanced.omit_selection)
print("%d atoms selected for removal" % omit_sel.count(True), file=log)
del hierarchy
xray_structure = xray_structure.select(~omit_sel)
if (not command_line.options.silent):
print("*** Model summary:", file=log)
xray_structure.show_summary(f=log)
print(file=log)
info0 = f_obss[0].info()
info1 = f_obss[1].info()
f_obss[0] = f_obss[0].resolution_filter(
d_min=params.high_resolution,
d_max=params.low_resolution).set_info(info0)
f_obss[1] = f_obss[1].resolution_filter(
d_min=params.high_resolution,
d_max=params.low_resolution).set_info(info1)
if (params.sigma_cutoff is not None):
for i in [0, 1]:
if (f_obss[i].sigmas() is not None):
sel = f_obss[i].data(
) > f_obss[i].sigmas() * params.sigma_cutoff
f_obss[i] = f_obss[i].select(sel).set_info(info0)
for k, f_obs in enumerate(f_obss):
if (f_obs.indices().size() == 0):
raise Sorry(
"No data left in array %d (labels=%s) after filtering!" %
(k + 1, f_obs.info().label_string()))
output_file_name = params.output_file
if (output_file_name is None) and (params.file_name_prefix is not None):
output_file_name = "%s_%s.mtz" % (params.file_name_prefix,
params.job_id)
output_files = compute_fo_minus_fo_map(
data_arrays=f_obss,
xray_structure=xray_structure,
log=log,
silent=command_line.options.silent,
output_file=output_file_name,
peak_search=params.find_peaks_holes,
map_cutoff=params.map_cutoff,
peak_search_params=params.peak_search,
multiscale=params.advanced.multiscale,
anomalous=params.advanced.anomalous).file_names
return output_files
def run(args, command_name = "phenix.fobs_minus_fobs_map", log=None):
if(len(args) == 0): args = ["--help"]
examples = """Examples:
phenix.fobs_minus_fobs_map f_obs_1_file=data1.mtz f_obs_2_file=data2.sca \
f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 model.pdb
phenix.fobs_minus_fobs_map f_obs_1_file=data.mtz f_obs_2_file=data.mtz \
f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 phase_source=model.pdb \
high_res=2.0 sigma_cutoff=2 scattering_table=neutron"""
command_line = (iotbx_option_parser(
usage="%s [options]" % command_name,
description=examples)
.option("--silent",
action="store_true",
help="Suppress output to the screen.")
.enable_symmetry_comprehensive()
).process(args=args)
#
if (log is None) :
log = sys.stdout
if(not command_line.options.silent):
utils.print_header("phenix.fobs_minus_fobs_map", out = log)
print >> log, "Command line arguments: "
print >> log, args
print >> log
#
processed_args = utils.process_command_line_args(
args=command_line.args,
cmd_cs=command_line.symmetry,
master_params=fo_minus_fo_master_params(),
absolute_angle_tolerance=5,
absolute_length_tolerance=1,
log=log,
suppress_symmetry_related_errors=True)
working_phil = processed_args.params
if(not command_line.options.silent):
print >> log, "*** Parameters:"
working_phil.show(out = log)
print >> log
params = working_phil.extract()
consensus_symmetry = None
if (params.ignore_non_isomorphous_unit_cells) :
if (None in [params.f_obs_1_file_name, params.f_obs_2_file_name,
params.phase_source]):
raise Sorry("The file parameters (f_obs_1_file_name, f_obs_2_file_name, "+
"phase_source) must be specified explicitly when "+
"ignore_non_isomorphous_unit_cells=True.")
symm_manager = iotbx.symmetry.manager()
pdb_in = iotbx.file_reader.any_file(params.phase_source, force_type="pdb")
symm_manager.process_pdb_file(pdb_in)
hkl_in_1 = iotbx.file_reader.any_file(params.f_obs_1_file_name,
force_type="hkl")
sg_err_1, uc_err_1 = symm_manager.process_reflections_file(hkl_in_1)
hkl_in_2 = iotbx.file_reader.any_file(params.f_obs_2_file_name,
force_type="hkl")
sg_err_2, uc_err_2 = symm_manager.process_reflections_file(hkl_in_2)
out = StringIO()
symm_manager.show(out=out)
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). "+
"Please note that any symmetry information in the PDB file will be "+
"used first.") % out.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 (or if not available, the "+
"first reflection file), but the maps should be treated with "+
"extreme suspicion.") % out.getvalue())
crystal_symmetry = symm_manager.as_symmetry_object()
else :
processed_args = utils.process_command_line_args(
args=command_line.args,
cmd_cs=command_line.symmetry,
master_params=fo_minus_fo_master_params(),
absolute_angle_tolerance=5,
absolute_length_tolerance=1,
log=StringIO())
crystal_symmetry = processed_args.crystal_symmetry
#
pdb_file_names = processed_args.pdb_file_names
if(len(processed_args.pdb_file_names) == 0):
if(params.phase_source is not None):
pdb_file_names = [params.phase_source]
else:
raise Sorry("No PDB file found.")
# Extaract Fobs1, Fobs2
f_obss = []
if(len(processed_args.reflection_files)==2):
for reflection_file in processed_args.reflection_files:
reflection_file_server = reflection_file_utils.reflection_file_server(
crystal_symmetry = crystal_symmetry,
force_symmetry = True,
reflection_files = [reflection_file],
err = null_out())
# XXX UGLY !!!
try:
parameters = utils.data_and_flags_master_params().extract()
if(params.f_obs_1_label is not None):
parameters.labels = [params.f_obs_1_label]
determine_data_and_flags_result = utils.determine_data_and_flags(
reflection_file_server = reflection_file_server,
keep_going = True,
parameters = parameters,
log = null_out())
except: # intentional
parameters = utils.data_and_flags_master_params().extract()
if(params.f_obs_2_label is not None):
parameters.labels = [params.f_obs_2_label]
determine_data_and_flags_result = utils.determine_data_and_flags(
reflection_file_server = reflection_file_server,
keep_going = True,
parameters = parameters,
log = null_out())
f_obss.append(determine_data_and_flags_result.f_obs)
else:
if([params.f_obs_1_file_name,params.f_obs_2_file_name].count(None)==2):
raise Sorry("No reflection data file found.")
for file_name, label in zip([params.f_obs_1_file_name,params.f_obs_2_file_name],
[params.f_obs_1_label,params.f_obs_2_label]):
reflection_file = reflection_file_reader.any_reflection_file(
file_name = file_name, ensure_read_access = False)
reflection_file_server = reflection_file_utils.reflection_file_server(
crystal_symmetry = crystal_symmetry,
force_symmetry = True,
reflection_files = [reflection_file],
err = null_out())
parameters = utils.data_and_flags_master_params().extract()
if(label is not None):
parameters.labels = [label]
determine_data_and_flags_result = utils.determine_data_and_flags(
reflection_file_server = reflection_file_server,
parameters = parameters,
keep_going = True,
log = null_out())
f_obss.append(determine_data_and_flags_result.f_obs)
if(len(f_obss)!=2):
raise Sorry(" ".join(errors))
if(not command_line.options.silent):
for ifobs, fobs in enumerate(f_obss):
print >> log, "*** Summary for data set %d:"%ifobs
fobs.show_comprehensive_summary(f = log)
print >> log
pdb_combined = combine_unique_pdb_files(file_names = pdb_file_names)
pdb_combined.report_non_unique(out = log)
if(len(pdb_combined.unique_file_names) == 0):
raise Sorry("No coordinate file given.")
#
raw_recs = flex.std_string()
for rec in pdb_combined.raw_records:
if(rec.upper().count("CRYST1")==0):
raw_recs.append(rec)
raw_recs.append(iotbx.pdb.format_cryst1_record(
crystal_symmetry = crystal_symmetry))
#
pdb_in = iotbx.pdb.input(source_info = None, lines = raw_recs)
hierarchy = pdb_in.construct_hierarchy()
omit_sel = flex.bool(hierarchy.atoms_size(), False)
if (params.advanced.omit_selection is not None) :
print >> log, "Will omit selection from phasing model:"
print >> log, " " + params.advanced.omit_selection
omit_sel = hierarchy.atom_selection_cache().selection(
params.advanced.omit_selection)
print >> log, "%d atoms selected for removal" % omit_sel.count(True)
xray_structure = pdb_in.xray_structure_simple()
xray_structure = xray_structure.select(~omit_sel)
if(not command_line.options.silent):
print >> log, "*** Model summary:"
xray_structure.show_summary(f = log)
print >> log
info0 = f_obss[0].info()
info1 = f_obss[1].info()
f_obss[0] = f_obss[0].resolution_filter(d_min = params.high_resolution,
d_max = params.low_resolution).set_info(info0)
f_obss[1] = f_obss[1].resolution_filter(d_min = params.high_resolution,
d_max = params.low_resolution).set_info(info1)
if(params.sigma_cutoff is not None):
for i in [0,1]:
if(f_obss[i].sigmas() is not None):
sel = f_obss[i].data() > f_obss[i].sigmas()*params.sigma_cutoff
f_obss[i] = f_obss[i].select(sel).set_info(info0)
for k, f_obs in enumerate(f_obss) :
if (f_obs.indices().size() == 0) :
raise Sorry("No data left in array %d (labels=%s) after filtering!" % (k+1,
f_obs.info().label_string()))
output_file_name = params.output_file
if (output_file_name is None) and (params.file_name_prefix is not None) :
output_file_name = "%s_%s.mtz" % (params.file_name_prefix, params.job_id)
output_files = compute_fo_minus_fo_map(
data_arrays = f_obss,
xray_structure = xray_structure,
log = log,
silent = command_line.options.silent,
output_file = output_file_name,
peak_search=params.find_peaks_holes,
map_cutoff=params.map_cutoff,
peak_search_params=params.peak_search,
multiscale=params.advanced.multiscale,
anomalous=params.advanced.anomalous).file_names
return output_files
def run(args, log=sys.stderr):
if (len(args) == 0):
print >> log, msg
defaults(log=log)
return
#
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(
args=args, log=log, master_params=parsed)
params = processed_args.params.extract()
reflection_files = processed_args.reflection_files
#
atoms_with_labels = None
if (len(processed_args.pdb_file_names) == 1):
pdb_combined = combine_unique_pdb_files(
file_names=processed_args.pdb_file_names)
pdb_combined.report_non_unique()
pdb_inp = iotbx.pdb.input(source_info=None,
lines=flex.std_string(
pdb_combined.raw_records))
atoms_with_labels = pdb_inp.atoms_with_labels()
#
if (len(reflection_files) == 0):
raise Sorry("No reflection file found.")
if (len(reflection_files) > 1):
raise Sorry("More than one reflection file found.")
crystal_symmetry = processed_args.crystal_symmetry
if (crystal_symmetry is None):
raise Sorry("No crystal symmetry found.")
reflection_file_name = reflection_files[0].file_name()
miller_arrays = reflection_file_reader.any_reflection_file(
file_name=reflection_file_name).as_miller_arrays()
#
if (len(miller_arrays) == 1 and params.label is None):
ma = miller_arrays[0]
elif (len(miller_arrays) > 1 and params.label is None):
raise Sorry(
"Multiple data columns found in input file. Use label keyword to select the one."
)
elif (len(miller_arrays) == 1 and params.label is not None):
ma = miller_arrays[0]
if (ma.info().labels[0].lower() != params.label.lower()):
raise Sorry(
"Specified label 'label=%s' does not match any label in input file."
% params.label)
elif (len(miller_arrays) > 1 and params.label is not None):
for ma in miller_arrays:
if (ma.info().labels[0].lower() == params.label.lower()):
break
if (not ma.is_complex_array()):
raise Sorry("Data must be complex type (real provided).")
print >> log, "Input reflection data (Fourier map coefficients):"
ma.show_comprehensive_summary(prefix=" ")
print >> log
#
if (len(params.point) == 0 and atoms_with_labels is None):
raise Sorry("No points given to compute map value at.")
else:
fft_map = ma.fft_map(resolution_factor=params.resolution_factor)
if (params.scale == "sigma"):
fft_map.apply_sigma_scaling()
print >> log, "Using sigma scaled map.\n"
else:
fft_map.apply_volume_scaling()
print >> log, "Using volume scale map.\n"
map_3d = fft_map.real_map_unpadded()
print >> log, "Map values at specified points:"
return ma, map_3d
for point in params.point:
point_frac = ma.unit_cell().fractionalize(point)
point_formatted = ",".join(
[str("%10.3f" % p).strip() for p in point])
point_frac_formatted = \
",".join([str("%10.3f"%p).strip() for p in point_frac])
map_value = str(
"%10.3f" %
map_3d.eight_point_interpolation(point_frac)).strip()
print >> log, " Input point: (%s) Fractionalized: (%s) Map value: %s" % (
point_formatted, point_frac_formatted, map_value)
#
if (atoms_with_labels is not None):
for point in atoms_with_labels:
point_frac = ma.unit_cell().fractionalize(point.xyz)
point_formatted = ",".join(
[str("%8.3f" % p) for p in point.xyz])
map_value = str(
"%10.3f" %
map_3d.eight_point_interpolation(point_frac)).strip()
print >> log, point.quote(), "Point: %s Map value: %s" % (
point_formatted, map_value)
#
print >> log
print >> log, "All done."
def run(args, log = sys.stderr):
if(len(args)==0):
print >> log, msg
defaults(log=log)
return
#
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(args = args,
log = log, master_params = parsed)
params = processed_args.params.extract()
reflection_files = processed_args.reflection_files
#
atoms_with_labels = None
if(len(processed_args.pdb_file_names)==1):
pdb_combined = combine_unique_pdb_files(
file_names=processed_args.pdb_file_names)
pdb_combined.report_non_unique()
pdb_inp = iotbx.pdb.input(source_info = None,
lines = flex.std_string(pdb_combined.raw_records))
atoms_with_labels = pdb_inp.atoms_with_labels()
#
if(len(reflection_files) == 0):
raise Sorry("No reflection file found.")
if(len(reflection_files) > 1):
raise Sorry("More than one reflection file found.")
crystal_symmetry = processed_args.crystal_symmetry
if(crystal_symmetry is None):
raise Sorry("No crystal symmetry found.")
reflection_file_name = reflection_files[0].file_name()
miller_arrays = reflection_file_reader.any_reflection_file(file_name =
reflection_file_name).as_miller_arrays()
#
if(len(miller_arrays)==1 and params.label is None):
ma = miller_arrays[0]
elif(len(miller_arrays)>1 and params.label is None):
raise Sorry("Multiple data columns found in input file. Use label keyword to select the one.")
elif(len(miller_arrays)==1 and params.label is not None):
ma = miller_arrays[0]
if(ma.info().labels[0].lower() != params.label.lower()):
raise Sorry("Specified label 'label=%s' does not match any label in input file."%params.label)
elif(len(miller_arrays)>1 and params.label is not None):
for ma in miller_arrays:
if(ma.info().labels[0].lower() == params.label.lower()):
break
if(not ma.is_complex_array()):
raise Sorry("Data must be complex type (real provided).")
print >> log, "Input reflection data (Fourier map coefficients):"
ma.show_comprehensive_summary(prefix=" ")
print >> log
#
if(len(params.point)==0 and atoms_with_labels is None):
raise Sorry("No points given to compute map value at.")
else:
fft_map = ma.fft_map(resolution_factor=params.resolution_factor)
if(params.scale == "sigma"):
fft_map.apply_sigma_scaling()
print >> log, "Using sigma scaled map.\n"
else:
fft_map.apply_volume_scaling()
print >> log, "Using volume scale map.\n"
map_3d = fft_map.real_map_unpadded()
print >> log, "Map values at specified points:"
return ma,map_3d
for point in params.point:
point_frac = ma.unit_cell().fractionalize(point)
point_formatted = ",".join([str("%10.3f"%p).strip() for p in point])
point_frac_formatted = \
",".join([str("%10.3f"%p).strip() for p in point_frac])
map_value = str(
"%10.3f"%map_3d.eight_point_interpolation(point_frac)).strip()
print >> log, " Input point: (%s) Fractionalized: (%s) Map value: %s"%(
point_formatted, point_frac_formatted, map_value)
#
if(atoms_with_labels is not None):
for point in atoms_with_labels:
point_frac = ma.unit_cell().fractionalize(point.xyz)
point_formatted = ",".join([str("%8.3f"%p) for p in point.xyz])
map_value = str(
"%10.3f"%map_3d.eight_point_interpolation(point_frac)).strip()
print >> log, point.quote(), "Point: %s Map value: %s"%(point_formatted,map_value)
#
print >> log
print >> log, "All done."
def exercise_combine_unique_pdb_files():
for file_name, s in [("tmp1", "1"), ("tmp2", " 2"), ("tmp3", "1\t"), ("tmp4", " \t2"), ("tmp5", "1 ")]:
open(file_name, "w").write(s)
for file_names in [[], ["tmp1"], ["tmp1", "tmp2"]]:
c = pdb.combine_unique_pdb_files(file_names=file_names)
assert len(c.file_name_registry) == len(file_names)
assert len(c.md5_registry) == len(file_names)
assert len(c.unique_file_names) == len(file_names)
assert len(c.raw_records) == len(file_names)
s = StringIO()
c.report_non_unique(out=s)
assert len(s.getvalue()) == 0
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp1"])
assert len(c.file_name_registry) == 1
assert len(c.md5_registry) == 1
assert len(c.unique_file_names) == 1
assert len(c.raw_records) == 1
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(
s.getvalue(),
"""\
INFO: PDB file name appears 2 times: "tmp1"
1 repeated file name ignored.
""",
)
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp1", "tmp2", "tmp1"])
assert len(c.file_name_registry) == 2
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s, prefix="^")
assert not show_diff(
s.getvalue(),
"""\
^INFO: PDB file name appears 3 times: "tmp1"
^ 2 repeated file names ignored.
^
""",
)
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp2", "tmp3"])
assert len(c.file_name_registry) == 3
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(
s.getvalue(),
"""\
INFO: PDB files with identical content:
"tmp1"
"tmp3"
1 file with repeated content ignored.
""",
)
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp2", "tmp3", "tmp5"])
assert len(c.file_name_registry) == 4
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s, prefix=": ")
assert not show_diff(
s.getvalue(),
"""\
: INFO: PDB files with identical content:
: "tmp1"
: "tmp3"
: "tmp5"
: 2 files with repeated content ignored.
:
""",
)
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp2", "tmp3", "tmp4", "tmp5", "tmp4", "tmp5"])
assert len(c.file_name_registry) == 5
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(
s.getvalue(),
"""\
INFO: PDB file name appears 2 times: "tmp4"
INFO: PDB file name appears 2 times: "tmp5"
2 repeated file names ignored.
INFO: PDB files with identical content:
"tmp2"
"tmp4"
INFO: PDB files with identical content:
"tmp1"
"tmp3"
"tmp5"
3 files with repeated content ignored.
""",
)
