Rosetta 3.3
Variables
test::T650_LoopsKIC Namespace Reference

Variables

int MAX_KIC_BUILD_ATTEMPTS = 100
tuple p = pose_from_pdb( "test/data/2cpl_min.pdb" )
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

tuple test::T650_LoopsKIC::kic_end = randrange( kic_start+2, loop_end+1 )
tuple test::T650_LoopsKIC::kic_mover = KinematicMover()
tuple test::T650_LoopsKIC::loop_refine = LoopMover_Refine_KIC( my_loops )
tuple test::T650_LoopsKIC::mc = MonteCarlo( p, scorefxn_low, kT )
string test::T650_LoopsKIC::min_type = "linmin"
tuple test::T650_LoopsKIC::mm = MoveMap()
tuple test::T650_LoopsKIC::movemap = MoveMap()

Referenced by add_rosetta_options_2().

tuple test::T650_LoopsKIC::p = pose_from_pdb( "test/data/2cpl_min.pdb" )
tuple test::T650_LoopsKIC::pack = PackRotamersMover( scorefxn_high, task_pack )
tuple test::T650_LoopsKIC::pymol = rosetta.PyMOL_Mover()
tuple test::T650_LoopsKIC::recover_sidechains = ReturnSidechainMover( starting_p )
tuple test::T650_LoopsKIC::scorefxn_high = create_score_function_ws_patch( 'standard', 'score12' )
tuple test::T650_LoopsKIC::scorefxn_low = create_score_function( 'cen_std' )
tuple test::T650_LoopsKIC::task_pack = TaskFactory.create_packer_task( starting_p )
tuple test::T650_LoopsKIC::to_centroid = SwitchResidueTypeSetMover( 'centroid' )
tuple test::T650_LoopsKIC::to_fullatom = SwitchResidueTypeSetMover( 'fa_standard' )
float test::T650_LoopsKIC::tol = 0.001
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