def getInitRejoinCmds(self, exe="python", script="decoy_file.py"):
"""
return the first time rejoin cmds, prepared for multiprocessing on one node,
taking advantage of multiple cores
"""
complex_ids = self.tasks
argv_zip = zip(complex_ids)
# form the cmds
cmds = multi_process.formCmds(argv_zip, exe=exe, script=script)
return cmds
def getSecondRejoinCmds(self, exe='python', script='RepPt.py'):
"""
return the second time rejoin cmds, prepared for multiprocessing on one node,
taking advantage of multiple cores
"""
complex_ids = self.tasks
argv_zip = zip(complex_ids)
# form the cmds
cmds = multi_process.formCmds(argv_zip, exe=exe, script=script)
return cmds
def getMccCmds(self, exe="bash", script="mcc.sh"):
"""join the argvs to series of individual argument,
return a list of these argvs for mcc matrix generating"""
# zip the parameters
ligs = self.tasks
prts = [lig_id[0:-1] for lig_id in ligs]
ffs = [lig_id + self.ff for lig_id in ligs]
argv_zip = zip(prts, ligs, ffs)
# form the cmds
cmds = multi_process.formCmds(argv_zip, exe=exe, script=script)
return cmds
def getDecoysCmds(self, exe="bash", script="dc.sh"):
"""
join the argvs to series of individual argument,
return a list of these argvs for decoy generating
"""
# zip the parameters
ligs = self.tasks
prts = [lig_id[0:-1] for lig_id in ligs]
ffs = [lig_id + self.ff for lig_id in ligs]
mc_stp, replica_cycles = [], []
for i in range(len(ligs)):
mc_stp.append(str(self.mc_stp))
replica_cycles.append(str(self.replica_cycles))
argv_zip = zip(prts, ligs, ffs, mc_stp, replica_cycles)
# form the cmds
cmds = multi_process.formCmds(argv_zip, exe=exe, script=script)
return cmds