parser.add_argument("--verbose", default=False, action="store_true", help="")
args = parser.parse_args()
print print_args(args)
Wts = Weights(args.density_score_wt, args.overlap_score_wt, args.closab_score_wt, args.clash_score_wt)
Scorefxn = ScoreFunction(
args.density_scorefile, args.overlap_scorefile, args.nonoverlap_scorefile, Wts, args.null_frag_score
)
for each_round in range(1, args.round + 1):
Pose = Pose()
Pose.initialization(Scorefxn.density_score_dict) # default initialize by random
Scorefxn.update_pose(Pose)
working_temp = args.temperature
for each_step in range(args.steps):
print "round: %s cycle: %s" % (each_round, each_step)
pos = random.sample(Pose.dict.keys(), 1)[0] # pick a residue number to start with
null_frag_id = (args.mer, pos, 0, 0)
Boltzmann = PerRsdBoltzmann(working_temp)
""" After picking a position to optimize, calculate compatibility scores for all the candidate placements at that residue """
for candidate_frag_id in Scorefxn.density_score_dict[
pos
].keys(): # loop over all candidate frags at the pos
