|
| int | loops_kic.MAX_KIC_BUILD_ATTEMPTS = 10000 |
| |
| list | loops_kic.args |
| |
| | loops_kic.p = Pose() |
| |
| | loops_kic.starting_p = Pose() |
| |
| | loops_kic.scorefxn_low = create_score_function( 'cen_std' ) |
| |
| | loops_kic.scorefxn_high = create_score_function( 'standard', 'score12' ) |
| |
| | loops_kic.pymol = rosetta.PyMOLMover() |
| |
| int | loops_kic.loop_begin = 145 |
| |
| int | loops_kic.loop_end = 155 |
| |
| int | loops_kic.loop_cut = 150 |
| |
| | loops_kic.my_loop = Loop( loop_begin, loop_end, loop_cut ) |
| |
| | loops_kic.my_loops = Loops() |
| |
| | loops_kic.movemap = MoveMap() |
| |
| | loops_kic.kic_mover = KinematicMover() |
| |
| | loops_kic.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover( 'centroid' ) |
| |
| | loops_kic.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover( 'fa_standard' ) |
| |
| | loops_kic.recover_sidechains = protocols.simple_moves.ReturnSidechainMover( starting_p ) |
| |
| | loops_kic.task_pack = TaskFactory.create_packer_task( starting_p ) |
| |
| | loops_kic.pack = protocols.minimization_packing.PackRotamersMover( scorefxn_high, task_pack ) |
| |
| | loops_kic.mm = MoveMap() |
| |
| float | loops_kic.tol = 0.001 |
| |
| string | loops_kic.min_type = "linmin" |
| |
| | loops_kic.linmin_mover = protocols.minimization_packing.MinMover( mm, scorefxn_low, min_type, tol, True ) |
| |
| | loops_kic.starting_p_centroid = Pose() |
| |
| bool | loops_kic.success = False |
| |
| int | loops_kic.outer_cycles = 10 |
| |
| int | loops_kic.inner_cycles = 30 |
| |
| float | loops_kic.init_temp = 2.0 |
| |
| float | loops_kic.final_temp = 1.0 |
| |
| | loops_kic.gamma = math.pow( ( final_temp/init_temp ),( 1.0/( outer_cycles*inner_cycles ) ) ) |
| |
| float | loops_kic.kT = init_temp |
| |
| | loops_kic.mc = MonteCarlo( p, scorefxn_low, kT ) |
| |
| | loops_kic.kic_start = randrange( loop_begin, loop_end - 1 ) |
| |
| | loops_kic.kic_end = randrange( kic_start+2, loop_end+1 ) |
| |
| tuple | loops_kic.middle_offset = ( kic_end - kic_start ) / 2 |
| |
| tuple | loops_kic.kic_middle = kic_start + middle_offset |
| |
| | loops_kic.rms = loop_rmsd( p, starting_p, my_loops ) |
| |
| | loops_kic.loop_refine = LoopMover_Refine_KIC( my_loops ) |
| |
