#!/usr/bin/env python
__author__ = "Adam Simpkin, and Felix Simkovic"
__contributing_authors__ = "Jens Thomas, and Ronan Keegan"
__credits__ = "Daniel Rigden, William Shepard, Charles Ballard, Villi Uski, and Andrey Lebedev"
__date__ = "17 May 2017"
__email__ = "hlasimpk@liv.ac.uk"
__version__ = "0.1"
import argparse
import os
import sys
from pyjob.misc import StopWatch
import simbad.command_line
import simbad.exit
import simbad.util.pyrvapi_results
logger = None
[docs]def simbad_argparse():
"""Create the argparse options"""
p = argparse.ArgumentParser(
description="SIMBAD: Sequence Independent Molecular replacement Based on Available Database",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
simbad.command_line._argparse_core_options(p)
simbad.command_line._argparse_job_submission_options(p)
simbad.command_line._argparse_contaminant_options(p)
simbad.command_line._argparse_lattice_options(p)
simbad.command_line._argparse_rot_options(p)
simbad.command_line._argparse_mr_options(p)
simbad.command_line._argparse_mtz_options(p)
p.add_argument('mtz', help="The path to the input mtz file")
return p
[docs]def main():
"""Main SIMBAD routine"""
args = simbad_argparse().parse_args()
args.work_dir = simbad.command_line.get_work_dir(
args.run_dir, work_dir=args.work_dir, ccp4_jobid=args.ccp4_jobid, ccp4i2_xml=args.ccp4i2_xml
)
log_file = os.path.join(args.work_dir, 'simbad.log')
debug_log_file = os.path.join(args.work_dir, 'debug.log')
log_class = simbad.command_line.LogController()
log_class.add_console(level=args.debug_lvl)
log_class.add_logfile(log_file, level="info", format="%(message)s")
log_class.add_logfile(debug_log_file, level="notset",
format="%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s")
global logger
logger = log_class.get_logger()
if not os.path.isfile(args.amore_exe):
raise OSError("amore executable not found")
gui = simbad.util.pyrvapi_results.SimbadOutput(
args.rvapi_document, args.webserver_uri, args.display_gui, log_file, args.work_dir, args.ccp4i2_xml, tab_prefix=args.tab_prefix
)
simbad.command_line.print_header()
logger.info("Running in directory: %s\n", args.work_dir)
stopwatch = StopWatch()
stopwatch.start()
end_of_cycle, solution_found, all_results = False, False, {}
while not (solution_found or end_of_cycle):
# =====================================================================================
# Perform the lattice search
solution_found = simbad.command_line._simbad_lattice_search(args)
logger.info("Lattice search completed in %d days, %d hours, %d minutes, and %d seconds",
*stopwatch.lap.time_pretty)
if solution_found and not args.process_all:
logger.info(
"Lucky you! SIMBAD worked its charm and found a lattice match for you.")
continue
elif solution_found and args.process_all:
logger.info(
"SIMBAD thinks it has found a solution however process_all is set, continuing to contaminant search")
else:
logger.info("No results found - lattice search was unsuccessful")
if args.output_pdb and args.output_mtz:
csv = os.path.join(args.work_dir, 'latt/lattice_mr.csv')
all_results['latt'] = simbad.util.result_by_score_from_csv(csv, 'final_r_free', ascending=True)
gui.display_results(False, args.results_to_display)
# =====================================================================================
# Perform the contaminant search
solution_found = simbad.command_line._simbad_contaminant_search(args)
logger.info("Contaminant search completed in %d days, %d hours, %d minutes, and %d seconds",
*stopwatch.lap.time_pretty)
if solution_found:
logger.info(
"Check you out, crystallizing contaminants! But don't worry, SIMBAD figured it out and found a solution.")
continue
else:
logger.info(
"No results found - contaminant search was unsuccessful")
if args.output_pdb and args.output_mtz:
csv = os.path.join(args.work_dir, 'cont/cont_mr.csv')
all_results['cont'] = simbad.util.result_by_score_from_csv(csv, 'final_r_free', ascending=True)
gui.display_results(False, args.results_to_display)
# =====================================================================================
# Make sure we only run the loop once for now
end_of_cycle = True
if len(all_results) >= 1:
sorted_results = sorted(all_results.iteritems(), key=lambda (k, v): (v[1], k))
result = sorted_results[0][1]
run_dir = os.path.join(args.work_dir, sorted_results[0][0])
simbad.util.output_files(run_dir, result, args.output_pdb, args.output_mtz)
stopwatch.stop()
logger.info("All processing completed in %d days, %d hours, %d minutes, and %d seconds",
*stopwatch.time_pretty)
gui.display_results(True, args.results_to_display)
if args.rvapi_document:
gui.save_document()
log_class.close()
if __name__ == "__main__":
import logging
logging.basicConfig(level=logging.NOTSET)
try:
main()
except Exception:
simbad.exit.exit_error(*sys.exc_info())
