run_strategies.py

import os
import time
import datetime
from libtbx import easy_run
import iotbx.pdb

def run():
    """This runner script is used to carry out a large set of refinements using different strategies."""
# print "Executing qRefine scripts: " datetime.now()
    total_start_time = time.time()

    # These are the 4 strategies
    #               Quantum REFINE  Classical Refine   Quantum Optimization             Classical Optimization
    strategies = {"refine_cctbx":"restraints=cctbx ","refine_qm":"restraints=qm ","opt_qm":"restraints=qm data_weight=0","opt_cctbx":"restraints=cctbx data_weight=0 "}
    print "Strategies selected are: "

    # This gives us the ability to direct the output PDBs of the script
    results_prefix = "./results_b_rmsd_0.03_terachem_selectrmsd_max32/"
    perturbed_prefix="./perturbed/"
    mtz_prefix="./"
   
    folder_name=results_prefix
    make_folder(folder_name)

    #Loop over refinement or optimization strategies
    strategy_start_time = 0

    for strategy_name,strategy in strategies.iteritems():
      if(strategy_name=="refine_cctbx"  ):  
        print strategy
        strategy_start_time = time.time()
	folder_name=results_prefix+strategy_name
        make_folder(folder_name)
	file_out_prefix = [results_prefix]
	file_out_prefix.append(strategy_name)
        #Loop over data files
        data_files = os.listdir(mtz_prefix)
        for data_file in data_files:
            data_file_start_time = time.time()
            if(data_file.endswith(".mtz")):
                data_file_name = "." # drop the .mtz extension  
		folder_name=results_prefix+strategy_name+"/"+data_file_name
		make_folder(folder_name)	      
                file_out_prefix.append(data_file_name)
		pertubations = os.listdir(perturbed_prefix+data_file_name+"/")
		for pertubation in pertubations:
		  if(os.path.isdir(perturbed_prefix+"/"+data_file_name+"/"+pertubation)):
		    file_out_prefix.append(pertubation)
                    make_folder(results_prefix+strategy_name+"/"+data_file_name+"/"+pertubation)
                #Loop over Snapshots
                    snapshotdir_name=perturbed_prefix+data_file_name+"/"+pertubation+"/"
                    snapshots = os.listdir(snapshotdir_name)
                    for snapshot in snapshots:
                        if(snapshot.endswith("pdb")):
                           snapshot_file_name = snapshot[:-4]
                           file_out_prefix.append(snapshot_file_name)
	                   output=results_prefix+strategy_name+"/"+data_file_name+"/"+pertubation+"/"+snapshot_file_name
			   result_pdb=output+".pdb"
			   result_pdb_exists=os.path.exists(result_pdb) 
                           if( result_pdb_exists != True):
			   #Execute job
                             cmd =  " ".join(["phenix.python ./qr-core/qrefine.py ",snapshotdir_name+snapshot, mtz_prefix+data_file, strategy, "update_all_scales=False"," file_out_prefix="+output, "  >  ", output+ ".log" ])
			     print cmd
                             easy_run.call(cmd)                           
                # for logging timings, if needed.
                if(0):
                    data_file_time = time.time() - data_file_start_time
                    print "Time taken for " ,data_file_name, "was " , data_file_time
        strategy_time = time.time() - strategy_start_time
        print "Time taken for " ,strategy ,"was ", strategy_time


    total_time = time.time() - total_start_time
    print "Time taken for entire batch was:", total_time

def  make_folder(folder_name):
   if(os.path.exists(folder_name)!=True):
       os.mkdir(folder_name)	

if (__name__ == "__main__"):
  run()