#! /usr/bin/env ccp4-python # # 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. # # A MrBUMP wrapper for running Acorn jobs # Ronan Keegan - 29/10/06 # import os, sys, string import CCP4_Submit class Acorn: """ A class to submit Eclac jobs to the local machine or a batch system on a cluster. """ def __init__(self): self.logfile="" self.acorn_logfile="" self.jobname="" self.hklin="" self.hklout="" self.xyzin="" self.cc_value=0.0 self.no_cycles=0 if os.name=="nt": self.acornEXE = os.path.join(os.environ["CCP4_BIN"], "acorn.exe") else: self.acornEXE = os.path.join(os.environ["CCP4_BIN"], "acorn") self.CLUSTER = False self.QTYPE = "SGE" self.jobid_array = [] self.jobid_dict = dict([]) try: self.debug=eval(os.environ['MRBUMP_DEBUG']) except: self.debug=False def setLogfile(self, filename): self.logfile=filename def setHKLIN(self, filename): self.hklin=filename def setHKLOUT(self, filename): self.hklout=filename def setXYZIN(self, filename): self.xyzin=filename def setAcornLogfile(self, filename): self.acorn_logfile=filename def submit_job_standalone(self, F_flag, SIGF_flag, E_flag, hklin, hklout, xyzin, dir=os.getcwd()): """ Function to launch an acorn job for a given model as a standalone job. """ # Create a job and first set up the Acorn details # Make the model build folder if os.path.isdir(os.path.join(dir, "building")) == False: os.mkdir(os.path.join(dir, "building")) # Check to see if the logfile has been specified, otherwise give it a default name if self.logfile=="": self.setLogfile(os.path.join(dir, "building", "acorn_job.log")) # Set the input and output MTZ file names self.setHKLIN(hklin) self.setXYZIN(xyzin) self.setHKLOUT(os.path.join(dir, "building", hklout)) self.setAcornLogfile(self.logfile) # Setup the job MR_job=CCP4_Submit.CCP4_sub() MR_job.setProgram(self.acornEXE) MR_job.setProgramLogfile(self.logfile) MR_job.setCommandLine("HKLIN %s HKLOUT %s XYZIN %s" % (self.hklin, self.hklout, self.xyzin)) # Setup the keywords for the job MR_job.setKEYWORD("LABIn FP=" + F_flag + " SIGFP=" + SIGF_flag + " E=" + E_flag) MR_job.setKEYWORD("POSI 1") # Fire off the job # Run the job locally MR_job.submit_job(self.jobname,\ self.logfile,\ os.path.join(dir, "building"), queue_type="LOCAL") def submit_job(self, init, mstat, model, target_info): """ Function to launch an acorn job for a given model. """ # Create a job and first set up the Acorn details # Create the build directory if it does not already exist build_DIR = os.path.join(model.model_directory, "building") if os.path.isdir(build_DIR) == False: os.mkdir(build_DIR) # Check to see if the logfile has been specified, otherwise give it a default name if self.logfile=="": self.logfile=os.path.join(build_DIR, "acorn_job.log") # Set the various Acorn parameters and filenames model.setAcornLogfile(os.path.join(build_DIR, "acorn_" + model.name + ".log")) model.setAcornMTZOUTfile(os.path.join(build_DIR, "acorn_" + model.name +".mtz")) model.setAcornJobname(os.path.join(build_DIR, "acorn_" + model.name)) # Set up local links to the input/output files self.setHKLIN(model.ecalc_MTZOUTfile) self.setHKLOUT(model.acorn_MTZOUTfile) self.setXYZIN(model.refmac_PDBfile) self.setAcornLogfile(model.acorn_logfile) # Setup the job MR_job=CCP4_Submit.CCP4_sub() MR_job.setProgram(self.acornEXE) MR_job.setProgramLogfile(model.acorn_logfile) MR_job.setCommandLine("HKLIN %s HKLOUT %s XYZIN %s" \ % (model.ecalc_MTZOUTfile, model.acorn_MTZOUTfile, model.refmac_PDBfile)) # Setup the keywords for the job MR_job.setKEYWORD("LABIn FP=" + target_info.mtz_coldata['F'] \ + " SIGFP=" + target_info.mtz_coldata['SIGF'] \ + " E=" + target_info.mtz_coldata['E']) MR_job.setKEYWORD("POSI 1") # Fire off the job if init.keywords.CLUSTER: # Submit the job to a batch queue MR_job.submit_job(model.acorn_jobname,\ self.logfile,\ build_DIR,\ queue_type=init.keywords.QTYPE, qsub_command=init.keywords.QSUBCOM) # Note the job number and the job name model.setMR_JobID(MR_job.job_number) mstat.jobid_array.add(model.MR_jobID) mstat.jobid_dict[model.MR_jobID]=model.acorn_jobname mstat.jobname_dict[model.acorn_jobname]=model.name else: # Run the job locally MR_job.submit_job(model.acorn_jobname,\ self.logfile,\ build_DIR, queue_type="LOCAL") def read_logfile(self, logfile): """ Read any relavent details from the Acorn log file. """ # Setup a variable to hold the data cc_data="" # Open the logfile for reading f=open(logfile, "r") line=f.readline() while line: if "$TABLE:Correlation Coefficient vs number of cycles" in line: cc_data = cc_data + line cc_line=f.readline() while cc_line: cc_data = cc_data + cc_line cc_line=f.readline() if "************************" in cc_line: self.cc_value=float(string.split(cc_data)[-2]) self.no_cycles=int(string.split(cc_data)[-4]) break line=f.readline() f.close() # Output the results sys.stdout.write("################################################################\n") sys.stdout.write("####### Correlation Coefficient from Acorn #######\n") sys.stdout.write("################################################################\n") sys.stdout.write("\n") sys.stdout.write(string.strip(cc_data) + "\n") sys.stdout.write("\n") sys.stdout.write("Final CC value after %i cycles: %.5f\n" % (self.no_cycles, self.cc_value)) sys.stdout.write("\n") sys.stdout.write("Acorn Logfile:\n") sys.stdout.write(" %s\n" % self.acorn_logfile) sys.stdout.write("\n") sys.stdout.write("Output MTZ file from Acorn: \n") sys.stdout.write(" %s\n" % self.hklout) sys.stdout.write("\n") sys.stdout.write("################################################################\n") sys.stdout.write("\n") if __name__ == "__main__": # An example for running the job as a standalone function # Check and read the command line if len(sys.argv) != 7: print "Usage: python MRBUMP_Acorn.py " sys.exit() hklin=sys.argv[1] hklout=sys.argv[2] xyzin=sys.argv[3] F=sys.argv[4] SIGF=sys.argv[5] E=sys.argv[6] # Call the job a=Acorn() a.submit_job_standalone(F, SIGF, E, hklin, hklout, xyzin) a.read_logfile(a.logfile)