def setup(self, optd):
"""We take and return an ample dictionary as an argument.
This is required because options_processor.process_restart_options Changes what
optd points at, and this means that if we just use the reference, we end up
pointing at the old, obsolete dictionary
"""
optd = options_processor.restart_amoptd(optd)
# Make a work directory - this way all output goes into this directory
if optd['work_dir'] and not optd['restart_pkl']:
logger.info('Making a named work directory: %s', optd['work_dir'])
try:
os.mkdir(optd['work_dir'])
except Exception as e:
msg = "Cannot create work_dir {0}: {1}".format(
optd['work_dir'], e)
exit_util.exit_error(msg, sys.exc_info()[2])
if not optd['work_dir']:
if not os.path.exists(optd['run_dir']):
msg = 'Cannot find run directory: {0}'.format(optd['run_dir'])
exit_util.exit_error(msg, sys.exc_info()[2])
if bool(optd['rvapi_document']):
# With JSCOFE we run in the run directory
optd['work_dir'] = optd['run_dir']
else:
logger.info('Making a run directory: '
'checking for previous runs...')
optd['work_dir'] = ample_util.make_workdir(
optd['run_dir'], ccp4i2=bool(optd['ccp4i2_xml']))
os.chdir(optd['work_dir'])
ample_log = os.path.join(optd['work_dir'], 'AMPLE.log')
debug_log = os.path.join(optd['work_dir'], 'debug.log')
optd['ample_log'] = ample_log
logging_util.setup_file_logging(ample_log, level=logging.INFO)
logging_util.setup_file_logging(debug_log, level=logging.DEBUG)
optd['ccp4_version'] = ample_util.CCP4.version.version
logger.info(reference_manager.header)
logger.info("AMPLE version: %s", str(version.__version__))
logger.info("Running with CCP4 version: %s from directory: %s",
ample_util.CCP4.version, ample_util.CCP4.root)
logger.info("Running on host: %s", platform.node())
logger.info("Running on platform: %s", platform.platform())
logger.info("Job started at: %s",
time.strftime("%a, %d %b %Y %H:%M:%S", time.gmtime()))
logger.info("Invoked with command-line:\n%s\n", " ".join(sys.argv))
logger.info("Running in directory: %s\n", optd['work_dir'])
if pyrvapi_results.pyrvapi:
self.ample_output = pyrvapi_results.AmpleOutput(optd)
self.ample_output.display_results(optd)
options_processor.check_mandatory_options(optd)
optd = options_processor.process_restart_options(optd)
if not optd['restart_pkl']:
options_processor.process_options(optd)
if optd['dry_run']:
logger.info('Dry run finished checking options - cleaning up...')
os.chdir(optd['run_dir'])
shutil.rmtree(optd['work_dir'])
sys.exit(0)
logger.info('All needed programs are found, continuing...')
return optd
def setup(self, optd):
"""We take and return an ample dictionary as an argument. This is required because options_processor.process_restart_options
Changes what optd points at, and this means that if we just use the reference, we end up pointing at the old, obselete dictionary"""
# Update the ample dictionary in case we are restarting
optd = options_processor.restart_amoptd(optd)
# Make a work directory - this way all output goes into this directory
if optd['work_dir'] and not optd['restart_pkl']:
logger.info('Making a named work directory: {0}'.format(
optd['work_dir']))
try:
os.mkdir(optd['work_dir'])
except Exception as e:
msg = "Cannot create work_dir {0}: {1}".format(
optd['work_dir'], e)
exit_util.exit_error(msg, sys.exc_info()[2])
if not optd['work_dir']:
if not os.path.exists(optd['run_dir']):
msg = 'Cannot find run directory: {0}'.format(optd['run_dir'])
exit_util.exit_error(msg, sys.exc_info()[2])
if bool(optd['rvapi_document']):
# With JSCOFE we run in the run directory
optd['work_dir'] = optd['run_dir']
else:
logger.info(
'Making a run directory: checking for previous runs...')
optd['work_dir'] = ample_util.make_workdir(
optd['run_dir'], ccp4i2=bool(optd['ccp4i2_xml']))
# Go to the work directory
os.chdir(optd['work_dir'])
# Set up logging
ample_log = os.path.join(optd['work_dir'], 'AMPLE.log')
debug_log = os.path.join(optd['work_dir'], 'debug.log')
optd['ample_log'] = ample_log
# Set up ample output file and debug log file.
logging_util.setup_file_logging(ample_log, level=logging.INFO)
logging_util.setup_file_logging(debug_log, level=logging.DEBUG)
# Make sure the CCP4 environment is set up properly
ccp4_home = self.setup_ccp4(optd)
ccp4_version = ".".join([str(x) for x in optd['ccp4_version']])
# Print out Version and invocation
logger.info(ample_util.header)
logger.info("AMPLE version: {0}".format(version.__version__))
logger.info(
"Running with CCP4 version: {0} from directory: {1}".format(
ccp4_version, ccp4_home))
logger.info("Running on host: {0}".format(platform.node()))
logger.info("Running on platform: {0}".format(platform.platform()))
logger.info("Job started at: {0}".format(
time.strftime("%a, %d %b %Y %H:%M:%S", time.gmtime())))
logger.info("Invoked with command-line:\n{0}\n".format(" ".join(
sys.argv)))
logger.info("Running in directory: {0}\n".format(optd['work_dir']))
# Display pyrvapi results
if pyrvapi_results.pyrvapi:
self.ample_output = pyrvapi_results.AmpleOutput(optd)
self.ample_output.display_results(optd)
# Check mandatory/exclusive options
options_processor.check_mandatory_options(optd)
# Check if we are restarting from an existing pkl file - we don't process the options from this
# run if so
optd = options_processor.process_restart_options(optd)
if not optd['restart_pkl']:
# Only process the remaining options if we aren't in restart mode
options_processor.process_options(optd)
# Bail and clean up if we were only checking the options
if optd['dry_run']:
logger.info('Dry run finished checking options - cleaning up...')
os.chdir(optd['run_dir'])
shutil.rmtree(optd['work_dir'])
sys.exit(0)
logger.info('All needed programs are found, continuing...')
return optd
if not restart and not ('models' in optd and optd['models'] and os.path.exists(optd['models'])):
msg = 'AMPLE ensembler requires a -models argument with a file/directory of pdbs'
exit_util.exit_error(msg, sys.exc_info()[2])
# Set up the working directory if one doesn't already exist
if not ('work_dir' in optd and optd['work_dir']):
optd['work_dir'] = os.path.join(os.path.abspath(os.path.curdir), ENSEMBLE_DIRNAME)
if not os.path.isdir(optd['work_dir']):
try:
os.mkdir(optd['work_dir'])
except OSError as e:
msg = 'Error making ensemble workdir {0} : {1}'.format(optd['work_dir'], e)
exit_util.exit_error(msg, sys.exc_info()[2])
assert os.path.isdir(optd['work_dir'])
# Start logging to a file
logging_util.setup_file_logging(os.path.join(optd['work_dir'], "ensemble.log"))
try:
if not restart:
results = process_models.extract_and_validate_models(optd)
process_models.handle_model_import(optd, results)
process_ensemble_options(optd)
optd['ensemble_ok'] = os.path.join(optd['work_dir'], 'ensemble.ok')
optd['results_path'] = os.path.join(optd['work_dir'], AMPLE_PKL)
ensembler.create_ensembles(optd)
ample_util.save_amoptd(optd)
except Exception as e:
msg = "Error running ensembling: {0}".format(e.message)
exit_util.exit_error(msg, sys.exc_info()[2])
# Set up the working directory if one doesn't already exist
if not ('work_dir' in optd and optd['work_dir']):
optd['work_dir'] = os.path.join(os.path.abspath(os.path.curdir),
ENSEMBLE_DIRNAME)
if not os.path.isdir(optd['work_dir']):
try:
os.mkdir(optd['work_dir'])
except OSError as e:
msg = 'Error making ensemble workdir {0} : {1}'.format(
optd['work_dir'], e)
exit_util.exit_error(msg, sys.exc_info()[2])
assert os.path.isdir(optd['work_dir'])
# Start logging to a file
logging_util.setup_file_logging(os.path.join(optd['work_dir'], "ensemble.log"))
try:
if not restart:
optd['models'] = ample_util.extract_models(optd)
if optd['subcluster_program'] == 'gesamt':
optd['gesamt_exe'] = ample_util.find_exe('gesamt')
elif optd['subcluster_program'] == 'maxcluster':
optd['maxcluster_exe'] = ample_util.find_exe('maxcluster')
else:
raise RuntimeError("Unknown subcluster_program: {0}".format(
optd['subcluster_program']))
optd['theseus_exe'] = ample_util.find_exe('theseus')
optd['ensemble_ok'] = os.path.join(optd['work_dir'], 'ensemble.ok')
optd['results_path'] = os.path.join(optd['work_dir'], AMPLE_PKL)
ensembler.create_ensembles(optd)
ample_util.save_amoptd(optd)