def copyfree(self):
'''Copy the free column from freein into hklin -> hklout.'''
if not self._hklin_files:
raise RuntimeError('no hklin files defined')
if len(self._hklin_files) > 1:
raise RuntimeError('can have only one hklin to update')
hklin = self._hklin_files[0]
# get the resolution limit to give as a limit for the FreeR
# column
md = Mtzdump()
md.set_working_directory(self.get_working_directory())
md.set_hklin(hklin)
md.dump()
resolution_range = md.get_resolution_range()
self.check_hklout()
if self._freein is None:
raise RuntimeError('freein not defined')
if self._freein_column is None:
raise RuntimeError('freein column not defined')
self.add_command_line('hklin1')
self.add_command_line(self._freein)
self.add_command_line('hklin2')
self.add_command_line(hklin)
self.start()
self.input('labin file_number 1 E1=%s' % self._freein_column)
self.input('resolution file_number 1 %f %f' % resolution_range)
self.input('labin file_number 2 all')
self.close_wait()
try:
self.check_for_errors()
self.check_ccp4_errors()
except RuntimeError as e:
# something went wrong; remove the output file
try:
os.remove(self.get_hklout())
except Exception:
pass
raise e
return self.get_ccp4_status()
assert(dose_column in columns)
continue
if 'DOSE' in columns:
dose_range = md.get_column_range('DOSE')[:2]
if dose_range[0] != dose_range[1]:
dose_column = 'DOSE'
if 'BATCH' in columns and not dose_column:
dose_column = 'BATCH'
if not dose_column:
raise RuntimeError, 'no DOSE/BATCH column found'
dmin = min(md.get_resolution_range())
if overall_dmin is None:
overall_dmin = dmin
if dmin > overall_dmin:
overall_dmin = dmin
Stdout.write('Selected column: %s' % dose_column)
for argv in sys.argv[1:]:
chef.add_hklin(argv)
chef.set_labin(dose_column)
chef.set_resolution(overall_dmin)
chef.write_log_file('chef.log')
assert(dose_column in columns)
continue
if 'DOSE' in columns:
dose_range = md.get_column_range('DOSE')[:2]
if dose_range[0] != dose_range[1]:
dose_column = 'DOSE'
if 'BATCH' in columns and not dose_column:
dose_column = 'BATCH'
if not dose_column:
raise RuntimeError('no DOSE/BATCH column found')
dmin = min(md.get_resolution_range())
if overall_dmin is None:
overall_dmin = dmin
if dmin > overall_dmin:
overall_dmin = dmin
Stdout.write('Selected column: %s' % dose_column)
for argv in sys.argv[1:]:
chef.add_hklin(argv)
chef.set_labin(dose_column)
chef.set_resolution(overall_dmin)
chef.write_log_file('chef.log')
