#!/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. # # Script for runnning a dummy run of mrbump and outputting XML # Ronan Keegan 14/3/07 import os, sys, string import shutil import pickle import shutil import smartie import WriteXML import Sort_dict class DummyJob: """ A class to run a dummy run of MrBUMP with data read from pickle files. """ def __init__(self): self.p_dir="" self.file_list=[] self.STOP_JOB=False self.log_list=[] def run(self, init): self.p_dir=os.path.join(os.getcwd(), "pickle_data") # Check the pickle data folder exists if os.path.isdir(self.p_dir) == False: sys.stdout.write("Error: Running in Dummy Run mode. This requires pickled data and sample log files\n" \ "to be stored in folder:\n %s" % self.p_dir) sys.stdout.write("\n") self.STOP_JOB=True if init.ONLYMODELS: self.file_list=["mstat.dat", "target.dat"] else: self.file_list=["mstat.dat", "target.dat", "refmac.log"] if "MOLREP" in init.keywords.MR_PROGRAM_LIST: self.file_list.append("molrep.log") if "PHASER" in init.keywords.MR_PROGRAM_LIST: self.file_list.append("phaser.log") # Check for each of the required files for file in self.file_list: if os.path.exists(os.path.join(self.p_dir, file)) == False: sys.stdout.write("Error: Running in Dummy Run mode. Input file not found\n") sys.stdout.write(" File name: %s\n" % file) sys.stdout.write("\n") self.STOP_JOB=True if self.STOP_JOB: sys.stdout.write("Job will exit now. Set keyword DUMMY to False if you want to run a real job.\n") sys.stdout.write("\n") sys.exit() # Read the Match structure data from its pickle file mstat_file=open(os.path.join(self.p_dir, "mstat.dat"), "r") mstat=pickle.load(mstat_file) mstat_file.close() # Use smartie to parse the various log files if init.ONLYMODELS == False: for model in mstat.sorted_model_list: if "MOLREP" in init.keywords.MR_PROGRAM_LIST: mstat.model_list[model].molrep_smartie_log=smartie.parselog(os.path.join(self.p_dir, "molrep.log")) if "PHASER" in init.keywords.MR_PROGRAM_LIST: mstat.model_list[model].phaser_smartie_log=smartie.parselog(os.path.join(self.p_dir, "phaser.log")) mstat.model_list[model].refmac_molrep_smartie_log=smartie.parselog(os.path.join(self.p_dir, "refmac.log")) mstat.model_list[model].refmac_phaser_smartie_log=smartie.parselog(os.path.join(self.p_dir, "refmac.log")) # Reset the table names if "PHASER" in init.keywords.MR_PROGRAM_LIST: table1=mstat.model_list[model].phaser_smartie_log.findtable("Translation Function Summary",-1) table1.settitle("Final Translation Function Summary for model %s" % model) table2=mstat.model_list[model].refmac_phaser_smartie_log.findtable("Rfactor analysis, stats vs cycle") table2.settitle("Rfactor analysis, stats vs cycle for model %s" % model) if "MOLREP" in init.keywords.MR_PROGRAM_LIST: table3=mstat.model_list[model].refmac_molrep_smartie_log.findtable("Rfactor analysis, stats vs cycle") table3.settitle("Rfactor analysis, stats vs cycle for model %s" % model) target_file=open(os.path.join(self.p_dir, "target.dat"), "r") target_info=pickle.load(target_file) target_file.close() # Put the results into a dictionary holding model name/final rfree pairs sorted_results=dict([]) for model in mstat.sorted_model_list: sorted_results[model]=mstat.model_list[model].refmac_finlRfree # Sort the dictionary of results s=Sort_dict.Sort_dict() sorted_list=s.sort(sorted_results) #for i in sorted_list: # sys.stdout.write("Model Name: %s\t -- Solution type: '%s'\t -- Final Rfree: %.3f\n" % (i[0], mstat.model_list[i[0]].solution_type, i[1])) #sys.stdout.write(" -- %s\n" % mstat.model_list[i[0]].model_info_string) #sys.stdout.write("\n") # Ouput the job details to an XML file if init.keywords.XMLOUT: xml=WriteXML.writeXML() xml.write_details(init, mstat, target_info, init.keywords.SUMMARYFILE) def pickle(self, init, mstat, target_info): """ Pickle the three main objects at the end of a Job. This should be the very last function to be called """ self.p_dir=os.path.join(mstat.results_dir, "pickle_data") if os.path.exists(self.p_dir) == False: os.mkdir(self.p_dir) # Temporaily set the each of the smartie logs to be "None" to avoid pickle problem with smartie for model in mstat.sorted_model_list: log=[] log.append(mstat.model_list[model].molrep_smartie_log) log.append(mstat.model_list[model].phaser_smartie_log) log.append(mstat.model_list[model].refmac_molrep_smartie_log) log.append(mstat.model_list[model].refmac_phaser_smartie_log) self.log_list.append(log) mstat.model_list[model].molrep_smartie_log=None mstat.model_list[model].phaser_smartie_log=None mstat.model_list[model].refmac_molrep_smartie_log=None mstat.model_list[model].refmac_phaser_smartie_log=None # Dump the Match structure data to its pickle file mstat_file=open(os.path.join(self.p_dir, "mstat.dat"), "w") pickle.dump(mstat, mstat_file) mstat_file.close() # Dump the Target info structure to from its pickle file target_file=open(os.path.join(self.p_dir, "target.dat"), "w") pickle.dump(target_info, target_file) target_file.close() # Dump the Init structure to from its pickle file init_file=open(os.path.join(self.p_dir, "init.dat"), "w") pickle.dump(init, init_file) init_file.close() # Restore the smartie logs for model in mstat.sorted_model_list: for log in self.log_list: mstat.model_list[model].molrep_smartie_log=log[0] mstat.model_list[model].phaser_smartie_log=log[1] mstat.model_list[model].refmac_molrep_smartie_log=log[2] mstat.model_list[model].refmac_phaser_smartie_log=log[3] # Free the log list self.log_list=[] # if init.ONLYMODELS == False: # # Copy samples of refmac/molrep/phaser log files to the pickle_dir # if mstat.model_list[mstat.sorted_model_list[0]].name[:14] != "ensemble_model" or len(mstat.sorted_model_list) == 1: # shutil.copyfile(mstat.model_list[mstat.sorted_model_list[0]].refmac_logfile, os.path.join(self.p_dir, "refmac.log")) # else: # shutil.copyfile(mstat.model_list[mstat.sorted_model_list[1]].refmac_logfile, os.path.join(self.p_dir, "refmac.log")) # if "MOLREP" in init.keywords.MR_PROGRAM_LIST: # if mstat.model_list[mstat.sorted_model_list[0]].name[:14] != "ensemble_model" or len(mstat.sorted_model_list) == 1: # shutil.copyfile(mstat.model_list[mstat.sorted_model_list[0]].molrep_logfile, os.path.join(self.p_dir, "molrep.log")) # else: # shutil.copyfile(mstat.model_list[mstat.sorted_model_list[1]].molrep_logfile, os.path.join(self.p_dir, "molrep.log")) # if "PHASER" in init.keywords.MR_PROGRAM_LIST: # shutil.copyfile(mstat.model_list[mstat.sorted_model_list[0]].phaser_logfile, os.path.join(self.p_dir, "phaser.log"))