"""main routine for Ample testing"""
import logging
import os
import sys
from ample.util import exit_util, logging_util
from ample.testing import run_tests
logger = logging_util.setup_console_logging(level=logging.INFO, formatstr='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
#############################################################################
## Multiprocessing crashes on Windows when running multiple jobs.
# Issue recorded
# 1) https://docs.python.org/2/library/multiprocessing.html#windows
if sys.platform.startswith("win"):
msg = """
*****************************************************************************
A bug prevents you from invoking our testing framework via the module loader.
Please invoke using the following command:
% ccp4-python {0}{1}run_tests.py <command> [<args>]
*****************************************************************************
"""
msg.format(os.path.dirname(__file__), os.sep)
logger.critical(msg)
sys.exit(1)
#############################################################################
## On Unix systems we can run as normal
try:
run_tests.main()
from ample.util import exit_util
from ample.util import logging_util
from ample.util import mrbump_util
from ample.util import options_processor
from ample.util import pdb_edit
from ample.util import pyrvapi_results
from ample.util import reference_manager
from ample.util import workers_util
from ample.util import version
__author__ = "Jens Thomas, Felix Simkovic, Adam Simpkin, Ronan Keegan, and Jaclyn Bibby"
__credits__ = "Daniel Rigden, Martyn Winn, and Olga Mayans"
__email__ = "*****@*****.**"
__version__ = version.__version__
logger = logging_util.setup_console_logging()
monitor = None
class Ample(object):
"""Class to generate ensembles from ab inito models (all models must have same sequence)
"""
def __init__(self):
self.amopt = None
self.ample_output = None
return
def main(self, args=None):
"""Main AMPLE routine.
msg = 'Cannot find ensemble pkl file: {0}'.format(optd['restart_pkl'])
exit_util.exit_error(msg)
try:
optd = ample_util.read_amoptd(optd['restart_pkl'])
except Exception as e:
msg = "Error unpickling ensemble pkl: {0}".format(e.message)
exit_util.exit_error(msg, sys.exc_info()[2])
restart = True
else:
# We're running purely from command-line arguments
amopt = config_util.AMPLEConfigOptions()
amopt.populate(optd)
optd = amopt.d
# Start logging to the console
logger = logging_util.setup_console_logging()
# Make sure we have models if in standalone mode
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])