def write_map_file(self):
# output MTZ file with map coefficients
class map_coeffs_mtz_label_manager:
def __init__(self, amplitudes, phases):
self._amplitudes = amplitudes
self._phases = phases
def amplitudes(self):
return self._amplitudes
def phases(self, root_label, anomalous_sign=None):
assert anomalous_sign is None or not anomalous_sign
return self._phases
mtz_history_buffer = flex.std_string()
lbl_mgr = map_coeffs_mtz_label_manager(amplitudes="FoFo",
phases="PHFc")
mtz_dataset = self.map_coeff.as_mtz_dataset(
column_root_label=lbl_mgr.amplitudes(), label_decorator=lbl_mgr)
mtz_history_buffer.append("> column label %s = phenix %s" %
(lbl_mgr.amplitudes(), "FoFoPHFc"))
if self.output_file is not None:
file_name = self.output_file
else:
file_name = "FoFoPHFc.mtz"
mtz_history_buffer.append("file name %s" % file_name)
mtz_object = mtz_dataset.mtz_object()
mtz_object.add_history(mtz_history_buffer)
mtz_object.write(file_name=file_name)
self.file_names = [file_name]
if (self.peak_search):
from mmtbx.command_line import find_peaks_holes
from mmtbx import find_peaks
peak_search_log = self.log
if (self.silent): peak_search_log = null_out()
fmodel = self.fmodel
peaks = find_peaks.manager(fmodel=fmodel,
map_type=None,
map_coeffs=self.map_coeff,
map_cutoff=self.map_cutoff,
params=self.peak_search_params,
log=peak_search_log).peaks_mapped()
peaks.sites = fmodel.xray_structure.unit_cell().orthogonalize(
peaks.sites)
holes = find_peaks.manager(fmodel=fmodel,
map_type=None,
map_coeffs=self.map_coeff,
map_cutoff=-self.map_cutoff,
params=self.peak_search_params,
log=peak_search_log).peaks_mapped()
holes.sites = fmodel.xray_structure.unit_cell().orthogonalize(
holes.sites)
result = find_peaks_holes.peaks_holes_container(
peaks=peaks, holes=holes, map_cutoff=self.map_cutoff)
pdb_out = os.path.splitext(file_name)[0] + "_peaks.pdb"
result.save_pdb_file(file_name=pdb_out,
include_anom=False,
include_water=False,
log=peak_search_log)
self.file_names.append(pdb_out)
return self.file_names
def write_map_file (self) :
# output MTZ file with map coefficients
class map_coeffs_mtz_label_manager:
def __init__(self, amplitudes, phases):
self._amplitudes = amplitudes
self._phases = phases
def amplitudes(self):
return self._amplitudes
def phases(self, root_label, anomalous_sign=None):
assert anomalous_sign is None or not anomalous_sign
return self._phases
mtz_history_buffer = flex.std_string()
lbl_mgr = map_coeffs_mtz_label_manager(amplitudes = "FoFo", phases = "PHFc")
mtz_dataset = self.map_coeff.as_mtz_dataset(
column_root_label=lbl_mgr.amplitudes(),
label_decorator=lbl_mgr)
mtz_history_buffer.append("> column label %s = phenix %s" % (
lbl_mgr.amplitudes(), "FoFoPHFc"))
if self.output_file is not None :
file_name = self.output_file
else :
file_name = "FoFoPHFc.mtz"
mtz_history_buffer.append("file name %s"%file_name)
mtz_object = mtz_dataset.mtz_object()
mtz_object.add_history(mtz_history_buffer)
mtz_object.write(file_name=file_name)
self.file_names = [ file_name ]
if (self.peak_search) :
from mmtbx.command_line import find_peaks_holes
from mmtbx import find_peaks
peak_search_log = self.log
if (self.silent) : peak_search_log = null_out()
fmodel = self.fmodel
peaks = find_peaks.manager(
fmodel=fmodel,
map_type=None,
map_coeffs=self.map_coeff,
map_cutoff=self.map_cutoff,
params=self.peak_search_params,
log=peak_search_log).peaks_mapped()
peaks.sites = fmodel.xray_structure.unit_cell().orthogonalize(peaks.sites)
holes = find_peaks.manager(
fmodel=fmodel,
map_type=None,
map_coeffs=self.map_coeff,
map_cutoff=-self.map_cutoff,
params=self.peak_search_params,
log=peak_search_log).peaks_mapped()
holes.sites = fmodel.xray_structure.unit_cell().orthogonalize(holes.sites)
result = find_peaks_holes.peaks_holes_container(
peaks=peaks,
holes=holes,
map_cutoff=self.map_cutoff)
pdb_out = os.path.splitext(file_name)[0] + "_peaks.pdb"
result.save_pdb_file(
file_name=pdb_out,
include_anom=False,
include_water=False,
log=peak_search_log)
self.file_names.append(pdb_out)
return self.file_names