|
| int | test.T650_LoopsKIC.MAX_KIC_BUILD_ATTEMPTS = 10000 |
| |
| | test.T650_LoopsKIC.extra_options |
| |
| | test.T650_LoopsKIC.p = core.import_pose.pose_from_file( "../test/data/2cpl_min.pdb" ) |
| |
| | test.T650_LoopsKIC.starting_p = Pose() |
| |
| | test.T650_LoopsKIC.scorefxn_low = protocols.loops.get_cen_scorefxn() |
| |
| | test.T650_LoopsKIC.scorefxn_high = protocols.loops.get_fa_scorefxn() |
| |
| | test.T650_LoopsKIC.pymol = PyMOLMover() |
| |
| int | test.T650_LoopsKIC.loop_begin = 145 |
| |
| int | test.T650_LoopsKIC.loop_end = 155 |
| |
| int | test.T650_LoopsKIC.loop_cut = 150 |
| |
| | test.T650_LoopsKIC.my_loop = protocols.loops.Loop( loop_begin, loop_end, loop_cut ) |
| |
| | test.T650_LoopsKIC.my_loops = protocols.loops.Loops() |
| |
| | test.T650_LoopsKIC.movemap = MoveMap() |
| |
| | test.T650_LoopsKIC.kic_mover = KinematicMover() |
| |
| | test.T650_LoopsKIC.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover( 'centroid' ) |
| |
| | test.T650_LoopsKIC.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover( 'fa_standard' ) |
| |
| | test.T650_LoopsKIC.recover_sidechains = protocols.simple_moves.ReturnSidechainMover( starting_p ) |
| |
| | test.T650_LoopsKIC.task_pack = core.pack.task.TaskFactory.create_packer_task( starting_p ) |
| |
| | test.T650_LoopsKIC.pack = protocols.minimization_packing.PackRotamersMover( scorefxn_high, task_pack ) |
| |
| | test.T650_LoopsKIC.mm = MoveMap() |
| |
| float | test.T650_LoopsKIC.tol = 0.001 |
| |
| string | test.T650_LoopsKIC.min_type = "linmin" |
| |
| | test.T650_LoopsKIC.linmin_mover = protocols.minimization_packing.MinMover( mm, scorefxn_low, min_type, tol, True ) |
| |
| | test.T650_LoopsKIC.starting_p_centroid = Pose() |
| |
| | test.T650_LoopsKIC.end |
| |
| bool | test.T650_LoopsKIC.success = False |
| |
| | test.T650_LoopsKIC.i |
| |
| int | test.T650_LoopsKIC.outer_cycles = 1 |
| |
| int | test.T650_LoopsKIC.inner_cycles = 1 |
| |
| float | test.T650_LoopsKIC.init_temp = 2.0 |
| |
| float | test.T650_LoopsKIC.final_temp = 1.0 |
| |
| | test.T650_LoopsKIC.gamma = math.pow( ( final_temp/init_temp ),( 1.0/( outer_cycles*inner_cycles ) ) ) |
| |
| float | test.T650_LoopsKIC.kT = init_temp |
| |
| | test.T650_LoopsKIC.mc = MonteCarlo( p, scorefxn_low, kT ) |
| |
| | test.T650_LoopsKIC.kic_start = randrange( loop_begin, loop_end - 1 ) |
| |
| | test.T650_LoopsKIC.kic_end = randrange( kic_start+2, loop_end+1 ) |
| |
| tuple | test.T650_LoopsKIC.middle_offset = ( kic_end - kic_start ) // 2 |
| |
| tuple | test.T650_LoopsKIC.kic_middle = kic_start + middle_offset |
| |
| | test.T650_LoopsKIC.rms = protocols.loops.loop_rmsd( p, starting_p, my_loops ) |
| |
| | test.T650_LoopsKIC.loop_refine = rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC( my_loops ) |
| |
