def run(args):
# create parser
logger = multi_out()
logger.register('stderr', sys.stderr)
logger2 = multi_out()
logger2.register('stdout', sys.stdout)
parser = CCTBXParser(program_class=cablam.Program, logger=logger)
namespace = parser.parse_args(sys.argv[1:])
# start program
print('Starting job', file=logger)
print('=' * 79, file=logger)
task = cablam.Program(parser.data_manager,
parser.working_phil.extract(),
logger=logger2)
# validate inputs
task.validate()
# run program
task.run()
# stop timer
print('', file=logger)
print('=' * 79, file=logger)
print('Job complete', file=logger)
show_total_time(out=logger)
def run(args):
# create parser
#logger = multi_out() #logging.getLogger('main')
#logger.register('stdout', sys.stdout)
#logger = null_out()
logger = multi_out()
logger.register('stderr', sys.stderr)
logger2 = multi_out()
logger2.register('stdout', sys.stdout)
#only omegalyze output is sent to stdout for backward compatibility with
# MolProbity website
parser = CCTBXParser(program_class=omegalyze.Program, logger=logger)
namespace = parser.parse_args(sys.argv[1:])
# start program
print('Starting job', file=logger)
print('=' * 79, file=logger)
task = omegalyze.Program(parser.data_manager,
parser.working_phil.extract(),
logger=logger2)
# validate inputs
task.validate()
# run program
task.run()
# stop timer
print('', file=logger)
print('=' * 79, file=logger)
print('Job complete', file=logger)
show_total_time(out=logger)
def run(args):
# create parser
logger = multi_out() #logging.getLogger('main')
logger.register('stdout', sys.stdout)
parser = CCTBXParser(program_class=atom_selection.Program,
custom_process_arguments=custom_args_proc,
logger=logger)
#
# Stick in additional keyword args
# They going to end up in namespace.cryst1_replacement_buffer_layer etc
# file_name is obsolet, parser takes care of it putting it in data manager
# inselections is going to be handled by custom_args_proc function
# because it is intended to be positional argument
#
# !!! This is done here for legacy support and illustrative purposes.
# Don't do it anywhere else, since we strive to have the same
# command-line flags across all programs, like --overwrite etc.
parser.add_argument(
"--cryst1-replacement-buffer-layer",
action="store",
type=float,
help="replace CRYST1 with pseudo unit cell covering the selected"
" atoms plus a surrounding buffer layer",
default=None)
parser.add_argument("--write-pdb-file",
"--write_pdb_file",
"--write_pdb-file",
"--write-pdb_file",
action="store",
help="write selected atoms to new PDB file",
default=None)
namespace = parser.parse_args(sys.argv[1:])
# start program
print('Starting job', file=logger)
print('=' * 79, file=logger)
task = atom_selection.Program(parser.data_manager,
parser.working_phil.extract(),
master_phil=parser.master_phil,
logger=logger)
# validate inputs
task.validate()
# run program
task.run()
# stop timer
print('', file=logger)
print('=' * 79, file=logger)
print('Job complete', file=logger)
show_total_time(out=logger)
def parseArgs1(Program, logger):
# create the cc tbx aspect of the parser
parser = CCTBXParser(
program_class = Program,
# custom_process_arguments = custom_args_proc,
logger=logger)
# add the old suitename aspect of the parser
buildParser(parser)
# do it
namespace = parser.parse_args(sys.argv[1:])
return parser.working_phil
def parseArgs(programClass, logger):
for i, arg in enumerate(sys.argv): # make case insensitive
if arg[0]=="-":
sys.argv[i] = arg.lower()
parser = argparse.ArgumentParser()
buildParser(parser) # set up the arguments for suite name
args, others = parser.parse_known_args()
args2 = argsToPhilForm(args, others)
args2.extend(others)
# create the cctbx aspect of the parser
parser2 = CCTBXParser(
program_class = programClass,
# custom_process_arguments = custom_args_proc,
logger=logger
)
# do it
namespace = parser2.parse_args(args2)
extracted = parser2.working_phil.extract()
# for name, value in extracted.suitename.__dict__.items():
# print(name, ":", value)
return parser2