loops.py File Reference

Namespaces
	loops

Variables
tuple	loops.p = Pose()
tuple	loops.starting_p = Pose()
tuple	loops.scorefxn_low = create_score_function('cen_std')
tuple	loops.scorefxn_high = create_score_function('standard', 'score12')
int	loops.loop_begin = 77
int	loops.loop_end = 85
int	loops.cutpoint = 81
tuple	loops.my_loop = Loop( loop_begin, loop_end, cutpoint)
tuple	loops.movemap = MoveMap()
tuple	loops.fragset3mer = ConstantLengthFragSet(3, "test_in3_fragments")
tuple	loops.mover_3mer = ClassicFragmentMover(fragset3mer,movemap)
tuple	loops.ccd_closure = CCDLoopClosureMover(my_loop, movemap)
tuple	loops.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover('centroid')
tuple	loops.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover('fa_standard')
tuple	loops.recover_sidechains = protocols.simple_moves.ReturnSidechainMover(starting_p)
tuple	loops.task_pack = TaskFactory.create_packer_task(starting_p)
tuple	loops.pack = protocols.minimization_packing.PackRotamersMover( scorefxn_high, task_pack )
tuple	loops.starting_p_centroid = Pose()
tuple	loops.jd = Job_dist("loop_output", 100, scorefxn_high)
int	loops.outer_cycles = 10
int	loops.inner_cycles = 30
float	loops.init_temp = 2.0
float	loops.final_temp = 0.8
tuple	loops.gamma = math.pow((final_temp/init_temp),(1.0/(outer_cycles*inner_cycles)))
	loops.kT = init_temp
tuple	loops.mc = MonteCarlo(p, scorefxn_low, kT)
tuple	loops.my_loops = Loops()
tuple	loops.loop_refine = LoopMover_Refine_CCD(my_loops)
tuple	loops.Lrms = loop_rmsd(p, starting_p, my_loops, True)