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, e:
# something went wrong; remove the output file
try:
os.remove(self.get_hklout())
except:
pass
raise e
def find_columns(self):
'''Identify columns to use with scaleit.'''
# run mtzdump to get a list of columns out and also check that
# this is a valid merged mtz file....
self.check_hklin()
md = Mtzdump()
md.set_hklin(self.get_hklin())
md.dump()
# get information to check that this is merged
# next get the column information - check that F columns are
# present
column_info = md.get_columns()
columns = []
j = 0
groups = 0
# assert that the columns for F, SIGF, DANO, SIGDANO for a
# particular group will appear in that order if anomalous,
# F, SIGF if not anomalous
while j < len(column_info):
c = column_info[j]
name = c[0]
type = c[1]
if type == 'F' and name.split('_')[0] == 'F' and \
self._anomalous:
groups += 1
for i in range(4):
columns.append(column_info[i + j][0])
j += 4
elif type == 'F' and name.split('_')[0] == 'F' and \
not self._anomalous:
groups += 1
for i in range(2):
columns.append(column_info[i + j][0])
j += 2
else:
j += 1
# ok that should be all of the groups identified
self._columns = columns
return columns
def update(self):
'''Update the information for one reflection file.'''
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]
self.check_hklout()
column_names_by_file = { }
dataset_names_by_file = { }
md = Mtzdump()
md.set_hklin(hklin)
md.dump()
columns = md.get_columns()
column_names_by_file[hklin] = []
dataset_names_by_file[hklin] = md.get_datasets()
# get a dataset ID - see FIXME 03/NOV/06 below...
dataset_ids = [md.get_dataset_info(d)['id'] for \
d in md.get_datasets()]
for c in columns:
name = c[0]
if name in ['H', 'K', 'L']:
continue
column_names_by_file[hklin].append(name)
self.add_command_line('hklin1')
self.add_command_line(hklin)
self.start()
dataset_id = dataset_ids[0]
if self._pname and self._xname and self._dname:
self.input('drename file_number 1 %d %s %s' % \
(dataset_id, self._xname, self._dname))
self.input('dpname file_number 1 %d %s' % \
(dataset_id, self._pname))
column_counter = 0
labin_command = 'labin file_number 1'
for column in column_names_by_file[hklin]:
column_counter += 1
labin_command += ' E%d=%s' % (column_counter, column)
self.input(labin_command)
# FIXME perhaps - ASSERT that we want only the information from
# the first dataset here...
pname, xname, dname = dataset_names_by_file[hklin][0].split('/')
dataset_id = dataset_ids[0]
# FIXME 03/NOV/06 this needs to id the dataset by it's number
# not by pname/xname/dname, as the latter get's confused if the
# xname is a number...
if self._new_cell_parameters:
a, b, c, alpha, beta, gamma = self._new_cell_parameters
self.input('dcell file_number 1 %d %f %f %f %f %f %f' % \
(dataset_id, a, b, c, alpha, beta, gamma))
if self._new_column_suffix:
suffix = self._new_column_suffix
column_counter = 0
labout_command = 'labout file_number 1'
for column in column_names_by_file[hklin]:
column_counter += 1
labout_command += ' E%d=%s_%s' % \
(column_counter, column, suffix)
self.input(labout_command)
self.close_wait()
try:
self.check_for_errors()
self.check_ccp4_errors()
except RuntimeError, e:
# something went wrong; remove the output file
try:
os.remove(self.get_hklout())
except:
pass
raise e
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, e:
# something went wrong; remove the output file
try:
os.remove(self.get_hklout())
except:
pass
raise e
