test.T650_LoopsKIC Namespace Reference

Variables
int	MAX_KIC_BUILD_ATTEMPTS = 10000
tuple	p = pose_from_file( "../test/data/2cpl_min.pdb" )
tuple	starting_p = Pose()
tuple	scorefxn_low = get_cen_scorefxn()
tuple	scorefxn_high = get_fa_scorefxn()
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 = 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 = TaskFactory.create_packer_task( starting_p )
tuple	pack = protocols.simple_moves.PackRotamersMover( scorefxn_high, task_pack )
tuple	mm = MoveMap()
float	tol = 0.001
string	min_type = "linmin"
tuple	linmin_mover = protocols.simple_moves.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 = 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.simple_moves.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"

Referenced by add_rosetta_options_1(), add_rosetta_options_12(), add_rosetta_options_14(), add_rosetta_options_7(), Minimize.apply(), NCMinimize.apply(), HDdesignMover.apply(), HbsDesignMover.apply(), PeptoidDesignMover.apply(), OopDesignMover.apply(), DougsDockDesignMinimizeMagicMover.apply(), UBQ_GTPaseMover.apply(), UBQ_GTPase_disulfide_Mover.apply(), UBQ_E2Mover.apply(), main(), and HDdesignMover.sym_repack_minimize().

tuple test.T650_LoopsKIC.mm = MoveMap()

tuple test.T650_LoopsKIC.movemap = MoveMap()

tuple test.T650_LoopsKIC.my_loop = Loop( loop_begin, loop_end, loop_cut )

tuple test.T650_LoopsKIC.my_loops = Loops()

int test.T650_LoopsKIC.outer_cycles = 1

tuple test.T650_LoopsKIC.p = pose_from_file( "../test/data/2cpl_min.pdb" )

tuple test.T650_LoopsKIC.pack = protocols.simple_moves.PackRotamersMover( scorefxn_high, task_pack )

tuple test.T650_LoopsKIC.pymol = rosetta.PyMOL_Mover()

tuple test.T650_LoopsKIC.recover_sidechains = protocols.simple_moves.ReturnSidechainMover( starting_p )

tuple test.T650_LoopsKIC.rms = loop_rmsd( p, starting_p, my_loops )

tuple test.T650_LoopsKIC.scorefxn_high = get_fa_scorefxn()

tuple test.T650_LoopsKIC.scorefxn_low = 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 = 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