def run(params):
log_out = multi_out()
log_out.register("log", open(params.logfile, "w"), atexit_send_to=None)
log_out.register("stdout", sys.stdout)
libtbx.phil.parse(master_params_str).format(params).show(out=log_out, prefix=" ")
xac_files = read_path_list(params.lstin, only_exists=True, err_out=log_out)
if len(xac_files) == 0:
print >>log_out, "No (existing) files in the list: %s" % params.lstin
return
if params.method == "brehm_diederichs":
rb = BrehmDiederichs(xac_files, max_delta=params.max_delta,
d_min=params.d_min, min_ios=params.min_ios,
nproc=params.nproc, log_out=log_out)
elif params.method == "selective_breeding":
rb = KabschSelectiveBreeding(xac_files, max_delta=params.max_delta,
d_min=params.d_min, min_ios=params.min_ios,
nproc=params.nproc, log_out=log_out)
elif params.method == "reference":
rb = ReferenceBased(xac_files, params.reference_file, max_delta=params.max_delta,
d_min=params.d_min, min_ios=params.min_ios,
nproc=params.nproc, log_out=log_out)
else:
raise "Unknown method: %s" % params.method
rb.assign_operators()
new_files = rb.modify_xds_ascii_files()
lstout = os.path.splitext(os.path.basename(params.lstin))[0]+"_reindexed.lst"
ofs = open(lstout, "w")
ofs.write("\n".join(new_files)+"\n")
ofs.close()
print >>log_out, "Reindexing done. For merging, use %s instead!" % lstout
if params.method == "brehm_diederichs":
print >>log_out, """
CCTBX-implementation (by Richard Gildea) of the "algorithm 2" of the following paper was used.
For publication, please cite:
Brehm, W. and Diederichs, K. Breaking the indexing ambiguity in serial crystallography.
Acta Cryst. (2014). D70, 101-109
http://dx.doi.org/10.1107/S1399004713025431"""
elif params.method == "selective_breeding":
print >>log_out, """
def run(params):
log_out = multi_out()
log_out.register("log", open(params.logfile, "w"), atexit_send_to=None)
log_out.register("stdout", sys.stdout)
libtbx.phil.parse(master_params_str).format(params).show(out=log_out,
prefix=" ")
xac_files = read_path_list(params.lstin, only_exists=True, err_out=log_out)
if len(xac_files) == 0:
print >> log_out, "No (existing) files in the list: %s" % params.lstin
return
if params.method == "brehm_diederichs":
rb = BrehmDiederichs(xac_files,
max_delta=params.max_delta,
d_min=params.d_min,
min_ios=params.min_ios,
nproc=params.nproc,
log_out=log_out)
elif params.method == "selective_breeding":
rb = KabschSelectiveBreeding(xac_files,
max_delta=params.max_delta,
d_min=params.d_min,
min_ios=params.min_ios,
nproc=params.nproc,
log_out=log_out)
elif params.method == "reference":
import iotbx.file_reader
ref_file = iotbx.file_reader.any_file(params.reference_file)
if ref_file.file_type == "hkl":
ref_arrays = ref_file.file_server.miller_arrays
if not ref_arrays:
raise "No arrays in reference file"
if params.reference_label is not None:
ref_arrays = filter(
lambda x: params.reference_label in x.info().labels,
ref_arrays)
if not ref_arrays:
raise "No arrays matched to specified label (%s)" % params.reference_label
ref_array = ref_arrays[0].as_intensity_array()
else:
ref_array = None
for array in ref_arrays:
if array.is_xray_intensity_array():
ref_array = array
print >> log_out, "Using %s as reference data" % array.info(
).label_string()
break
elif array.is_xray_amplitude_array():
ref_array = array.f_as_f_sq()
print >> log_out, "Using %s as reference data" % array.info(
).label_string()
break
elif ref_file.file_type == "pdb":
import mmtbx.utils
xrs = ref_file.file_content.xray_structure_simple()
fmodel_params = mmtbx.command_line.fmodel.fmodel_from_xray_structure_master_params.extract(
)
fmodel_params.fmodel.k_sol = 0.35
fmodel_params.fmodel.b_sol = 50
fmodel_params.high_resolution = params.d_min
ref_array = mmtbx.utils.fmodel_from_xray_structure(
xray_structure=xrs,
params=fmodel_params).f_model.as_intensity_array()
else:
raise "input file type invalid"
if ref_array is None:
raise "suitable reference data not found"
rb = ReferenceBased(xac_files,
ref_array,
max_delta=params.max_delta,
d_min=params.d_min,
min_ios=params.min_ios,
nproc=params.nproc,
log_out=log_out)
else:
raise "Unknown method: %s" % params.method
if rb.bad_files:
print "%s: %d bad files are included:" % (
"WARNING" if params.skip_bad_files else "ERROR", len(rb.bad_files))
for f in rb.bad_files:
print " %s" % f
if not params.skip_bad_files:
print
print "You may want to change d_min= or min_ios= parameters to include these files."
print "Alternatively, specify skip_bad_files=true to ignore these files (they are not included in output files)"
return
if params.method == "selective_breeding":
rb.assign_operators(max_cycle=params.max_cycles)
else:
rb.assign_operators()
rb.show_assign_summary()
if params.dry_run:
print >> log_out, "This is dry-run. Exiting here."
else:
out_prefix = os.path.splitext(os.path.basename(params.lstin))[0]
ofs_cell = open(out_prefix + "_reindexed_cells.dat", "w")
new_files = rb.modify_xds_ascii_files(cells_dat_out=ofs_cell)
lstout = out_prefix + "_reindexed.lst"
ofs = open(lstout, "w")
ofs.write("\n".join(new_files) + "\n")
ofs.close()
print >> log_out, "Reindexing done. For merging, use %s instead!" % lstout
if params.method == "brehm_diederichs":
print >> log_out, """
CCTBX-implementation (by Richard Gildea) of the "algorithm 2" of the following paper was used.
For publication, please cite:
Brehm, W. and Diederichs, K. Breaking the indexing ambiguity in serial crystallography.
Acta Cryst. (2014). D70, 101-109
http://dx.doi.org/10.1107/S1399004713025431"""
elif params.method == "selective_breeding":
print >> log_out, """
def run(params):
log_out = multi_out()
log_out.register("log", open(params.logfile, "w"), atexit_send_to=None)
log_out.register("stdout", sys.stdout)
libtbx.phil.parse(master_params_str).format(params).show(out=log_out, prefix=" ")
xac_files = read_path_list(params.lstin, only_exists=True, err_out=log_out)
if len(xac_files) == 0:
print >>log_out, "No (existing) files in the list: %s" % params.lstin
return
if params.method == "brehm_diederichs":
rb = BrehmDiederichs(xac_files, max_delta=params.max_delta,
d_min=params.d_min, min_ios=params.min_ios,
nproc=params.nproc, log_out=log_out)
elif params.method == "selective_breeding":
rb = KabschSelectiveBreeding(xac_files, max_delta=params.max_delta,
d_min=params.d_min, min_ios=params.min_ios,
nproc=params.nproc, log_out=log_out)
elif params.method == "reference":
import iotbx.file_reader
ref_file = iotbx.file_reader.any_file(params.reference_file)
if ref_file.file_type == "hkl":
ref_arrays = ref_file.file_server.miller_arrays
if not ref_arrays:
raise "No arrays in reference file"
if params.reference_label is not None:
ref_arrays = filter(lambda x: params.reference_label in x.info().labels, ref_arrays)
if not ref_arrays: raise "No arrays matched to specified label (%s)" % params.reference_label
ref_array = ref_arrays[0].as_intensity_array()
else:
ref_array = None
for array in ref_arrays:
if array.is_xray_intensity_array():
ref_array = array
print >>log_out, "Using %s as reference data" % array.info().label_string()
break
elif array.is_xray_amplitude_array():
ref_array = array.f_as_f_sq()
print >>log_out, "Using %s as reference data" % array.info().label_string()
break
elif ref_file.file_type == "pdb":
import mmtbx.utils
xrs = ref_file.file_content.xray_structure_simple()
fmodel_params = mmtbx.command_line.fmodel.fmodel_from_xray_structure_master_params.extract()
fmodel_params.fmodel.k_sol = 0.35
fmodel_params.fmodel.b_sol = 50
fmodel_params.high_resolution = params.d_min
ref_array = mmtbx.utils.fmodel_from_xray_structure(xray_structure=xrs, params=fmodel_params).f_model.as_intensity_array()
else:
raise "input file type invalid"
if ref_array is None:
raise "suitable reference data not found"
rb = ReferenceBased(xac_files, ref_array, max_delta=params.max_delta,
d_min=params.d_min, min_ios=params.min_ios,
nproc=params.nproc, log_out=log_out)
else:
raise "Unknown method: %s" % params.method
if params.method == "selective_breeding":
rb.assign_operators(max_cycle=params.max_cycles)
else:
rb.assign_operators()
out_prefix = os.path.splitext(os.path.basename(params.lstin))[0]
ofs_cell = open(out_prefix+"_reindexed_cells.dat", "w")
new_files = rb.modify_xds_ascii_files(cells_dat_out=ofs_cell)
lstout = out_prefix + "_reindexed.lst"
ofs = open(lstout, "w")
ofs.write("\n".join(new_files)+"\n")
ofs.close()
print >>log_out, "Reindexing done. For merging, use %s instead!" % lstout
if params.method == "brehm_diederichs":
print >>log_out, """
CCTBX-implementation (by Richard Gildea) of the "algorithm 2" of the following paper was used.
For publication, please cite:
Brehm, W. and Diederichs, K. Breaking the indexing ambiguity in serial crystallography.
Acta Cryst. (2014). D70, 101-109
http://dx.doi.org/10.1107/S1399004713025431"""
elif params.method == "selective_breeding":
print >>log_out, """
"""
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
from yamtbx.dataproc.auto.multi_merging.resolve_reindex import BrehmDiederichs
if __name__ == "__main__":
import sys
lst = sys.argv[1]
xac_files = map(lambda x: x.strip(), open(lst))
rb = BrehmDiederichs(xac_files, log_out=sys.stdout)
rb.assign_operators()
rb.modify_xds_ascii_files()
"""
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
from yamtbx.dataproc.auto.multi_merging.resolve_reindex import BrehmDiederichs
if __name__ == "__main__":
import sys
lst = sys.argv[1]
xac_files = map(lambda x: x.strip(), open(lst))
rb = BrehmDiederichs(xac_files, log_out=sys.stdout)
rb.assign_operators()
rb.modify_xds_ascii_files()