#selected_frags_Dict = {} # three object are being created etable = ScoreTable( density_score_Dict, overlap_score_Dict, nonoverlap_score_Dict ) wts = Weights( args.density_score_wt, args.overlap_score_wt, args.closab_score_wt, args.clash_score_wt ) scorefxn = ScoreFunction( etable, wts, args.null_frag_score ) for each_round in range( 1, args.round+1 ): scorefxn.clean_selected_frags_dict() #mypose = Pose() if args.starts_with: assert not args.dump_results == args.starts_with print "Initialize with %s" % args.starts_with pkl = open( args.starts_with , "rb" ) scorefxn.selected_frags_dict = pickle.load( pkl ) else: scorefxn.initialize( args.initialization ) for each_step in range( args.steps ): print "round: %s cycle: %s" %( each_round, each_step ) pos = pos_list[ random.randrange( 0, len( pos_list ) ) ] # pick a residue number to start with boltzmann_prob_Dict = {} ''' After picking a position to optimize, calculate compatibility scores for all the candidate placements at that residue''' for each_candidate_frag_id in density_score_Dict[ pos ].keys(): # loop over all candidate frags at the pos if ( each_candidate_frag_id[2], each_candidate_frag_id[3] ) == ( 0, 0 ): continue # skip null fragment container = scorefxn.score_evaluator( each_candidate_frag_id ) boltzmann_prob_Dict[ each_candidate_frag_id ] = ( boltzmann_prob( container.score_, args.temperature_ ), container.score, container.rmsd )