# 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()
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:
if args.initialization == "lowdens": scorefxn.lowest_density_score_placements()
elif args.initialization == "random": scorefxn.randomize_initial_placements()
for each_step in range( args.steps ):
print "round: %s cycle: %s" %( each_round, each_step )
# pick a random mer (because I would mix different mers in the future)
mer = mer_list[ random.randrange( 0, len(mer_list) ) ]
# pick a residue number to start with
if args.designated_position: pos = args.designated_position
else: pos = pos_list[ random.randrange( 0, len( pos_list ) ) ]
boltzmann_prob_Dict = {}
''' After picking a position to optimize,
calculate compatibility scores for all the candidate placements at that residue'''
