#
#     Copyright (C) 2005 Ronan Keegan 
#
#     This code is distributed under the terms and conditions of the
#     CCP4 Program Suite Licence Agreement as a CCP4 Application.
#     A copy of the CCP4 licence can be obtained by writing to the
#     CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
#

# Master executable for running MrBUMP. To be placed in the CCP4 bin directory or else in the users
# local CCP4 folder.
# Ronan Keegan 05/05/05

# setup the environment

import os, sys, string, time
import shutil
import urllib

# Test for environment variables

if not "CCP4" in sorted(os.environ.keys()):
    raise RuntimeError('CCP4 not found')
if not "http_proxy" in sorted(os.environ.keys()):
    sys.stdout.write("http_proxy not specified in environemnt\n")

# Output OS and Python version info for debugging
#sys.stdout.write("\n")
#sys.stdout.write("Operating System: %s\n" % sys.platform)
#sys.stdout.write("Python Version:\n%s\n" % sys.version)
#sys.stdout.write("\n")

# Update the python path with the mrbump folders
if os.path.isdir(os.path.join(os.environ["CCP4"], "share", "mrbump")):
   mrbump = os.path.join(os.environ["CCP4"], "share", "mrbump") 
elif os.path.isdir(os.path.join(os.environ["MRBUMP"], "share", "mrbump")):
   mrbump = os.path.join(os.environ["MRBUMP"], "share", "mrbump") 
else:
    sys.stdout.write("Error: MrBUMP installation not found\n")
    sys.stdout.write("\n")

mrbump_incl = os.path.join(mrbump, "include")
mrbump_data = os.path.join(mrbump, "data")

if os.path.isdir(os.path.join(os.environ["CCP4"], "share", "ample")):
   ample = os.path.join(os.environ["CCP4"], "share", "ample") 
else:
    sys.stdout.write("Error: AMPLE installation not found\n")
    sys.stdout.write("\n")

# Set the envionment deubg flag and any python specific variables
os.environ['MRBUMP_DEBUG'] = "False"
os.environ['MRBUMP_CLUSTER'] = "False"
os.environ['PYTHONUNBUFFERED'] = "True"
os.environ["GFORTRAN_UNBUFFERED_ALL"] = "Y"
os.environ["MRBUMP_CLUSTBIN"] = os.path.join(mrbump_incl, "cluster")

if 'CCP4_BIN' not in os.environ:
   os.environ['CCP4_BIN'] = os.path.join(os.environ['CCP4'], "bin")
if os.path.isdir(os.path.join(os.environ['CCP4'], 'libexec')) and os.name=="nt":
    os.environ['PATH'] = os.environ['PATH'] + os.pathsep + os.path.join(os.environ["CCP4"], "libexec")

#os.environ['DBCCP4I_TOP'] = os.path.join(mrbump_incl, "dbccp4i")

# Import the MRBUMP classes
sys.path.append(os.path.join(mrbump_incl, 'dev'))
sys.path.append(os.path.join(mrbump_incl, 'file_info'))
sys.path.append(os.path.join(mrbump_incl, 'modelling'))
sys.path.append(os.path.join(mrbump_incl, 'mr'))
sys.path.append(os.path.join(mrbump_incl, 'output'))
sys.path.append(os.path.join(mrbump_incl, 'seq_align'))
sys.path.append(os.path.join(mrbump_incl, 'ccp4'))
sys.path.append(os.path.join(mrbump_incl, 'structures'))
sys.path.append(os.path.join(mrbump_incl, 'tools'))
sys.path.append(os.path.join(mrbump_incl, 'initialisation'))
sys.path.append(os.path.join(mrbump_incl, 'building'))
sys.path.append(os.path.join(mrbump_incl, 'cluster'))
sys.path.append(os.path.join(mrbump_incl, 'dispatchers'))
sys.path.append(os.path.join(mrbump_incl, 'parsers'))
sys.path.append(os.path.join(mrbump_incl, 'phasing'))
sys.path.append(os.path.join(ample, 'python'))

# Import the MRBUMP classes
import MRBUMP_initialise
import MRBUMP_master
import Matches, MRBUMP_target_info

# Call the inialisation class
init=MRBUMP_initialise.Initialise()

# Initialise the mstat and target_info structures
mstat=Matches.Match_struct()
target_info=MRBUMP_target_info.TargetInfo()

# Set the environment variables
init.setMRBUMP(mrbump)
init.setMRBUMP_INCL(mrbump_incl)
init.setMRBUMP_DATA(mrbump_data)

mstat,target_info = init.mrbump_initialisation(sys.argv, mstat, target_info)

# Call the master script for doing a full search and Molecular Replacement
master=MRBUMP_master.Master()


if init.ONLYMODELS:
   # Call the search and prepare function (split these at a later date)
   master.fast_search_MR(init, target_info, mstat)
elif init.MRONLY:
   # Call the MR function with the models from the prep step
   master.runMR(init, target_info, mstat)
else:
   # Call the search and prepare function (split these at a later date)
   queue = master.fast_search_MR(init, target_info, mstat)
   # Call the MR function with the models from the prep step
   master.runMR(init, target_info, mstat, queue)