Rosetta 3.3
Variables
loops_kic Namespace Reference

Variables

int MAX_KIC_BUILD_ATTEMPTS = 100
list args
tuple p = Pose()
tuple starting_p = Pose()
tuple scorefxn_low = create_score_function( 'cen_std' )
tuple scorefxn_high = create_score_function_ws_patch( 'standard', 'score12' )
tuple pymol = rosetta.PyMOL_Mover()
int loop_begin = 145
int loop_end = 155
int loop_cut = 150
tuple my_loop = Loop( loop_begin, loop_end, loop_cut )
tuple my_loops = Loops()
tuple movemap = MoveMap()
tuple kic_mover = KinematicMover()
tuple to_centroid = SwitchResidueTypeSetMover( 'centroid' )
tuple to_fullatom = SwitchResidueTypeSetMover( 'fa_standard' )
tuple recover_sidechains = ReturnSidechainMover( starting_p )
tuple task_pack = TaskFactory.create_packer_task( starting_p )
tuple pack = PackRotamersMover( scorefxn_high, task_pack )
tuple mm = MoveMap()
float tol = 0.001
string min_type = "linmin"
tuple linmin_mover = MinMover( mm, scorefxn_low, min_type, tol, True )
tuple starting_p_centroid = Pose()
 success = False
int outer_cycles = 10
int inner_cycles = 30
float init_temp = 2.0
float final_temp = 1.0
tuple gamma = math.pow( ( final_temp/init_temp ),( 1.0/( outer_cycles*inner_cycles ) ) )
 kT = init_temp
tuple mc = MonteCarlo( p, scorefxn_low, kT )
tuple kic_start = randrange( loop_begin, loop_end - 1 )
tuple kic_end = randrange( kic_start+2, loop_end+1 )
tuple middle_offset = ( kic_end - kic_start )
 kic_middle = kic_start+middle_offset
tuple rms = loop_rmsd( p, starting_p, my_loops )
tuple loop_refine = LoopMover_Refine_KIC( my_loops )

Variable Documentation

Initial value:
00001 [ "app", 
00002          "-database minirosetta_database", \
00003          "-loops:fast" ]
float loops_kic::final_temp = 1.0
tuple loops_kic::gamma = math.pow( ( final_temp/init_temp ),( 1.0/( outer_cycles*inner_cycles ) ) )
float loops_kic::init_temp = 2.0
tuple loops_kic::kic_end = randrange( kic_start+2, loop_end+1 )
tuple loops_kic::kic_mover = KinematicMover()
tuple loops_kic::kic_start = randrange( loop_begin, loop_end - 1 )
tuple loops_kic::linmin_mover = MinMover( mm, scorefxn_low, min_type, tol, True )
tuple loops_kic::loop_refine = LoopMover_Refine_KIC( my_loops )
tuple loops_kic::mc = MonteCarlo( p, scorefxn_low, kT )
string loops_kic::min_type = "linmin"
tuple loops_kic::mm = MoveMap()
tuple loops_kic::movemap = MoveMap()
tuple loops_kic::my_loops = Loops()
tuple loops_kic::p = Pose()
tuple loops_kic::pack = PackRotamersMover( scorefxn_high, task_pack )
tuple loops_kic::pymol = rosetta.PyMOL_Mover()
tuple loops_kic::recover_sidechains = ReturnSidechainMover( starting_p )
tuple loops_kic::rms = loop_rmsd( p, starting_p, my_loops )
tuple loops_kic::scorefxn_high = create_score_function_ws_patch( 'standard', 'score12' )
tuple loops_kic::scorefxn_low = create_score_function( 'cen_std' )
tuple loops_kic::starting_p = Pose()
tuple loops_kic::task_pack = TaskFactory.create_packer_task( starting_p )
tuple loops_kic::to_centroid = SwitchResidueTypeSetMover( 'centroid' )
tuple loops_kic::to_fullatom = SwitchResidueTypeSetMover( 'fa_standard' )
float loops_kic::tol = 0.001
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