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 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 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...
dataset_id = dataset_ids[0]
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 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()