def __init__(self,in_queue,out_queue,auriga_output_directory_root):

Thread.__init__(self)

self.in_queue = in_queue

self.out_queue = out_queue

self.auriga_output_directory_root = auriga_output_directory_root

def create_coot_start_script(self,dir_for_scr,output_file_root):

script_location = os.path.join(dir_for_scr ,"coot_start.sh")

cootscr = open(script_location,"w")

coot_str = """#!/bin/bash\n

coot --auto {output_file_root}.2.mtz --pdb {output_file_root}.2.pdb""".format(output_file_root = output_file_root)

print coot_str

safe_write_script(coot_str,cootscr)

def run(self):

while True:

my_mtz = self.in_queue.get()

if my_mtz == None:

self.out_queue.put(None)

self.in_queue.task_done()

break

refmac5_run_object = Refmac5RunScriptCreator(my_mtz,self.auriga_output_directory_root)

runscript = refmac5_run_object.write_runscript_and_return_name()

try:

subprocess.check_call([runscript],close_fds=True,bufsize=0)

except subprocess.CalledProcessError:

self.in_queue.put(my_mtz)

continue

# self.in_queue.task_done()

except OSError:

self.in_queue.put(my_mtz)

continue

# self.in_queue.task_done()

self.out_queue.put(my_mtz)

self.create_coot_start_script(refmac5_run_object.proj_name,refmac5_run_object.phaseroutput_root)