def _prepare_pointless_hklin(working_directory,
hklin,
phi_width):
'''Prepare some data for pointless - this will take only 180 degrees
of data if there is more than this (through a "rebatch" command) else
will simply return hklin.'''
# also remove blank images?
if not Flags.get_microcrystal() and not Flags.get_small_molecule():
Debug.write('Excluding blank images')
hklout = os.path.join(
working_directory,
'%s_noblank.mtz' % (os.path.split(hklin)[-1][:-4]))
FileHandler.record_temporary_file(hklout)
hklin = remove_blank(hklin, hklout)
# find the number of batches
md = Mtzdump()
md.set_working_directory(working_directory)
auto_logfiler(md)
md.set_hklin(hklin)
md.dump()
batches = max(md.get_batches()) - min(md.get_batches())
phi_limit = 180
if batches * phi_width < phi_limit or Flags.get_small_molecule():
return hklin
hklout = os.path.join(
working_directory,
'%s_prepointless.mtz' % (os.path.split(hklin)[-1][:-4]))
rb = Rebatch()
rb.set_working_directory(working_directory)
auto_logfiler(rb)
rb.set_hklin(hklin)
rb.set_hklout(hklout)
first = min(md.get_batches())
last = first + int(phi_limit / phi_width)
Debug.write('Preparing data for pointless - %d batches (%d degrees)' % \
((last - first), phi_limit))
rb.limit_batches(first, last)
# we will want to delete this one exit
FileHandler.record_temporary_file(hklout)
return hklout
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()
def merge(self):
'''Merge multiple reflection files into one file.'''
if not self._hklin_files:
raise RuntimeError('no hklin files defined')
self.check_hklout()
hklin_counter = 0
# for each reflection file, need to gather the column names
# and so on, to put in the cad input here - also check to see
# if the column names clash... check also that the spacegroups
# match up...
spacegroup = None
column_names = []
column_names_by_file = {}
for hklin in self._hklin_files:
md = Mtzdump()
md.set_working_directory(self.get_working_directory())
md.set_hklin(hklin)
md.dump()
columns = md.get_columns()
spag = md.get_spacegroup()
if spacegroup is None:
spacegroup = spag
if spag != spacegroup:
raise RuntimeError('spacegroups do not match')
column_names_by_file[hklin] = []
for c in columns:
name = c[0]
if name in ['H', 'K', 'L']:
continue
if name in column_names:
raise RuntimeError('duplicate column names')
column_names.append(name)
column_names_by_file[hklin].append(name)
# if we get to here then this is a good set up...
# create the command line
hklin_counter = 0
for hklin in self._hklin_files:
hklin_counter += 1
self.add_command_line('hklin%d' % hklin_counter)
self.add_command_line(hklin)
self.start()
hklin_counter = 0
for hklin in self._hklin_files:
column_counter = 0
hklin_counter += 1
labin_command = 'labin file_number %d' % hklin_counter
for column in column_names_by_file[hklin]:
column_counter += 1
labin_command += ' E%d=%s' % (column_counter, column)
self.input(labin_command)
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()
