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Variables
test.T650_LoopsKIC Namespace Reference

Variables

int MAX_KIC_BUILD_ATTEMPTS = 10000
 
tuple p = core.import_pose.pose_from_file( "../test/data/2cpl_min.pdb" )
 
tuple starting_p = Pose()
 
tuple scorefxn_low = protocols.loops.get_cen_scorefxn()
 
tuple scorefxn_high = protocols.loops.get_fa_scorefxn()
 
tuple pymol = PyMOLMover()
 
int loop_begin = 145
 
int loop_end = 155
 
int loop_cut = 150
 
tuple my_loop = protocols.loops.Loop( loop_begin, loop_end, loop_cut )
 
tuple my_loops = protocols.loops.Loops()
 
tuple movemap = MoveMap()
 
tuple kic_mover = KinematicMover()
 
tuple to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover( 'centroid' )
 
tuple to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover( 'fa_standard' )
 
tuple recover_sidechains = protocols.simple_moves.ReturnSidechainMover( starting_p )
 
tuple task_pack = core.pack.task.TaskFactory.create_packer_task( starting_p )
 
tuple pack = protocols.minimization_packing.PackRotamersMover( scorefxn_high, task_pack )
 
tuple mm = MoveMap()
 
float tol = 0.001
 
string min_type = "linmin"
 
tuple linmin_mover = protocols.minimization_packing.MinMover( mm, scorefxn_low, min_type, tol, True )
 
tuple starting_p_centroid = Pose()
 
 success = False
 
int outer_cycles = 1
 
int inner_cycles = 1
 
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 = protocols.loops.loop_rmsd( p, starting_p, my_loops )
 
tuple loop_refine = rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC( my_loops )
 

Variable Documentation

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