def main( 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 model in range( args.nstruct ):
pose = Pose() # empty pose
pose.initialization( scorefxn._density_score_dict, args.initialization ) # default initialize by random
pose.show_state( "initialization" )
temp = args.starting_temperature
steps = args.steps_per_temp
mc = MonteCarlo( scorefxn, temp )
trajectory_tracker_dict = {}
while temp>=0 or anneal_temp==0: # it would never reach this criteria
run_tag = "model_" + str( model ) + "_temp_" + str( temp )
mc.apply( pose, steps )
pose.show_state( run_tag )
#pose.dump_pickle( run_tag + ".pickle" )
trajectory_tracker_dict[ run_tag ] = pose
anneal_temp = round( temp*args.cooling_rate, 1 )
temp -= anneal_temp
if temp == mc.temperature(): break
mc.set_temperature( temp )
pickle.dump( trajectory_tracker_dict, open( "model_" + str( model ) + ".pickle", "w" ) )
pose.show_state( "model_" + str( model ) + "_end", True ) # True for verbose
def run( self, runid ):
''' run id is a identification for a model to dump '''
self.__fragidx_pose.clear()
self.__fragidx_pose.initialization( self._scorefxn.get_density_score_dict(), self._initialization ) # default initialize by random
#print self.__fragidx_pose.show_state( "initialization" )
mc = MonteCarlo( self._scorefxn, self._temperature )
mc.apply( self.__fragidx_pose, self._steps ) # to prevent a silly bug that at the very first state SCORE==0, such that you wouldn't lower than that during high temperatures sampling
self._lowest_score_pose = self.__fragidx_pose.clone()
tracker = TrajectoryTracker( runid )
tag = "model_" + str( runid )
while self._temperature >=0 : # it would never reach this criteria
if self._quench:
self.recover_low() # retrieve the lowest-score pose from previous runs
mc.apply( self.__fragidx_pose, self._steps )
residual_pose = self._scorefxn.residualize_pose() # residual_pose will be filled with
#print residual_pose.show_state( tag + "_" + str( self._temperature ) )
self.set_annealing_temperature() # update self._temperature
if self._temperature == mc.get_temperature(): break
mc.set_temperature( self._temperature )
if self._record_trajectory: tracker.save( self._temperature, self.__fragidx_pose )
tracker.save( self._temperature, self._scorefxn.residualize_pose() )
tracker.dump_pickle( tag )
residual_pose.show_state( tag + "_final", True ) # True for verbose showing all residues states
def main( 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 )
pose = Pose() # empty pose
pose.initialization( scorefxn._density_score_dict ) # default initialize by random
temp = args.temperature
mc = MonteCarlo( scorefxn, temp )
for each_round in range( 1, args.round+1 ):
mc.apply( pose, args.steps )
pose.show_state( temp )
temp -= round( temp*0.1, 2 )
if temp <= 0: break
mc.set_temperature( temp )
pose.dump_pickle()
