def as_table(self, cluster_info):
from libtbx.str_utils import wordwrap
headers = [
"Cluster",
"No. datasets",
"Datasets",
"Height",
"Multiplicity",
"Completeness",
]
rows = []
for info in cluster_info:
rows.append(
[
"%i" % info.cluster_id,
"%i" % len(info.labels),
wordwrap(" ".join("%s" % l for l in info.labels)),
"%.2g" % info.height,
"%.1f" % info.multiplicity,
"%.2f" % info.completeness,
]
)
rows.insert(0, headers)
return rows
def print_resids(resids):
assert (len(resids) > 0)
w = 0
line = " ".join([ resid.strip() for resid in resids ])
lines = str_utils.wordwrap(line, 60).split("\n")
print(" residue IDs: %s" % lines[0], file=out)
for line in lines[1:] :
print(" %s" % line, file=out)
def print_resids (resids) :
assert (len(resids) > 0)
w = 0
line = " ".join([ resid.strip() for resid in resids ])
lines = str_utils.wordwrap(line, 60).split("\n")
print >> out, " residue IDs: %s" % lines[0]
for line in lines[1:] :
print >> out, " %s" % line
def get_reflection_file_server(data_manager, params, datatype='x_ray'):
'''
Convenience function for getting a reflection file server based on a selection
of Miller arrays from the iotbx.data_manager.miller_array.miller_array_phil_str
PHIL scope
:params data_manager: DataManager with processed files
:type data_manager: iotbx.data_manager.DataManager object
:params params: PHIL extract with set parameters
:type params: libtbx.phil.scope_extract object
:params datatype: matches type property in miller_array_phil_str
:type datatype: str
:rtype: iotbx.reflection_file_utils.reflection_file_server object or None
The function returns None if there are no files that match datatype.
'''
filenames = list()
labels = list()
# find files
if (hasattr(params, 'data')):
try:
for scope in params.data:
if (scope.type == datatype):
filenames.append(scope.file_name)
labels.append(scope.labels)
except (TypeError, AttributeError):
raise Sorry(
wordwrap(
'The "data" scope is not in the expected format. See iotbx.data_manager.miller_array.miller_array_phil_str for the expected format.'
))
# get file server
rfs = None
if (len(filenames) > 0):
rfs = data_manager.get_reflection_file_server(filenames=filenames,
labels=labels)
return rfs
def as_table(self, cluster_info):
from libtbx.str_utils import wordwrap
rows = []
headers = [
'Cluster', 'Datasets', 'Height', 'Multiplicity', 'Completeness'
]
for info in cluster_info:
rows.append([
'%i' % info.cluster_id,
wordwrap(' '.join('%s' % l for l in info.labels)),
'%.2g' % info.height,
'%.1f' % info.multiplicity,
'%.2f' % info.completeness,
])
# sort table by completeness
perm = flex.sort_permutation(
flex.double(c.completeness for c in cluster_info))
rows = [rows[i] for i in perm]
import tabulate
return tabulate.tabulate(rows, headers, tablefmt='rst')
def process_phil(self, phil_list):
''''
Process PHIL arguments
Currently only handles command-line changes
Will add inclusion of PHIL files from data_manager first, then
command-line options
'''
print('Processing PHIL parameters:', file=self.logger)
print('-' * self.text_width, file=self.logger)
print('', file=self.logger)
printed_something = False
data_sources = list()
sources = list()
unused_phil = list()
# PHIL files are processed in order from command-line
if (self.data_manager.has_phils()):
phil_names = self.data_manager.get_phil_names()
phil = list()
print(' Adding PHIL files:', file=self.logger)
print(' ------------------', file=self.logger)
for name in phil_names:
# remove DataManager scope since input files are already loaded
phil_scope = self.data_manager.get_phil(name)
for phil_object in phil_scope.objects:
if (phil_object.name == 'data_manager'):
phil_scope.objects.remove(phil_object)
phil.append(phil_scope)
print(' %s' % name, file=self.logger)
data_sources.extend(phil)
print('', file=self.logger)
printed_something = True
# command-line PHIL arguments override any previous settings and are
# processed in given order
def custom_processor(arg):
unused_phil.append(arg)
return True
if (len(phil_list) > 0):
interpreter = self.master_phil.command_line_argument_interpreter(
home_scope='')
print(' Adding command-line PHIL:', file=self.logger)
print(' -------------------------', file=self.logger)
for phil in phil_list:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
printed_something = True
working = interpreter.process_args(
phil_list, custom_processor=custom_processor)
if (len(working) > 0):
sources.extend(working)
if (self.namespace.overwrite): # override overwrite if True
sources.append(iotbx.phil.parse('output.overwrite=True'))
if ((len(data_sources) + len(sources)) > 0):
self.working_phil, more_unused_phil = self.master_phil.fetch(
sources=data_sources + sources, track_unused_definitions=True)
unused_phil.extend(more_unused_phil)
else:
self.working_phil = self.master_phil
# show unrecognized parameters and abort
if (len(unused_phil) > 0):
print(' Unrecognized PHIL parameters:', file=self.logger)
print(' -----------------------------', file=self.logger)
for phil in unused_phil:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
error_message = 'Some PHIL parameters are not recognized by %s.\n' % \
self.prog
error_message += wordwrap(
'Please run this program with the --show-defaults option to see what parameters are available.',
max_chars=self.text_width) + '\n'
error_message += wordwrap(
'PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")',
max_chars=self.text_width) + '\n'
raise Sorry(error_message)
if (not printed_something):
print(' No PHIL parameters found', file=self.logger)
print('', file=self.logger)
def process_phil(self, phil_list):
''''
Process PHIL arguments
Also checks PHIL arguments (command line and files) for parameters that
specify files (.type = path)
'''
print('Processing PHIL parameters:', file=self.logger)
print('-' * self.text_width, file=self.logger)
print('', file=self.logger)
printed_something = False
data_sources = list()
sources = list()
unused_phil = list()
# PHIL files are processed in order from command-line
if (self.data_manager.has_phils()):
phil_names = self.data_manager.get_phil_names()
phil = list()
print(' Adding PHIL files:', file=self.logger)
print(' ------------------', file=self.logger)
for name in phil_names:
# remove DataManager scope since input files are already loaded
phil_scope = self.data_manager.get_phil(name)
for phil_object in phil_scope.objects:
if (phil_object.name == 'data_manager'):
phil_scope.objects.remove(phil_object)
phil.append(phil_scope)
print(' %s' % name, file=self.logger)
data_sources.extend(phil)
print('', file=self.logger)
printed_something = True
# command-line PHIL arguments override any previous settings and are
# processed in given order
def custom_processor(arg):
unused_phil.append(arg)
return True
if (len(phil_list) > 0):
interpreter = self.master_phil.command_line_argument_interpreter(
home_scope='')
print(' Adding command-line PHIL:', file=self.logger)
print(' -------------------------', file=self.logger)
for phil in phil_list:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
printed_something = True
working = interpreter.process_args(
phil_list, custom_processor=custom_processor)
if (len(working) > 0):
sources.extend(working)
if (self.namespace.overwrite): # override overwrite if True
sources.append(iotbx.phil.parse('output.overwrite=True'))
if ((len(data_sources) + len(sources)) > 0):
self.working_phil, more_unused_phil = self.master_phil.fetch(
sources=data_sources + sources, track_unused_definitions=True)
unused_phil.extend(more_unused_phil)
else:
self.working_phil = self.master_phil.fetch()
# show unrecognized parameters and abort
if (len(unused_phil) > 0):
print(' Unrecognized PHIL parameters:', file=self.logger)
print(' -----------------------------', file=self.logger)
for phil in unused_phil:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
error_message = 'Some PHIL parameters are not recognized by %s.\n' % \
self.prog
error_message += wordwrap(
'Please run this program with the --show-defaults option to see what parameters are available.',
max_chars=self.text_width) + '\n'
error_message += wordwrap(
'PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")',
max_chars=self.text_width) + '\n'
raise Sorry(error_message)
# process input phil for file/directory defintions and add to DataManager
# Note: if a PHIL file is input as a PHIL parameter, the contents of the
# file will NOT be parsed and validated. The PHIL file should be provided
# as a command-line argument. This is mostly for finding data files
# defined by PHIL parameters that should be added to the DataManager
diff_phil = self.master_phil.fetch_diff(self.working_phil)
paths = self.check_phil_for_paths(diff_phil)
if (len(paths) > 0):
files = list()
dirs = list()
for path in paths:
if (path is not None):
if (os.path.isfile(path)):
files.append(path)
elif (os.path.isdir(path)):
dirs.append(path)
if (self.parse_files):
self.process_files(files,
message='Processing files from PHIL:')
if (self.parse_dir):
self.process_dir(dirs,
message='Processing directories from PHIL:')
if (not printed_something):
print(' No PHIL parameters found', file=self.logger)
print('', file=self.logger)
