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