loops_kic Namespace Reference

Variables
int	MAX_KIC_BUILD_ATTEMPTS = 10000
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 = 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 = 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

list loops_kic.args

Initial value:

= [ "app",
         "-database minirosetta_database", \
         "-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

int loops_kic.inner_cycles = 30

tuple loops_kic.kic_end = randrange( kic_start+2, loop_end+1 )

loops_kic.kic_middle = kic_start+middle_offset

tuple loops_kic.kic_mover = KinematicMover()

tuple loops_kic.kic_start = randrange( loop_begin, loop_end - 1 )

loops_kic.kT = init_temp

tuple loops_kic.linmin_mover = protocols.simple_moves.MinMover( mm, scorefxn_low, min_type, tol, True )

int loops_kic.loop_begin = 145

int loops_kic.loop_cut = 150

int loops_kic.loop_end = 155

tuple loops_kic.loop_refine = LoopMover_Refine_KIC( my_loops )

int loops_kic.MAX_KIC_BUILD_ATTEMPTS = 10000

tuple loops_kic.mc = MonteCarlo( p, scorefxn_low, kT )

tuple loops_kic.middle_offset = ( kic_end - kic_start )

string loops_kic.min_type = "linmin"

tuple loops_kic.mm = MoveMap()

tuple loops_kic.movemap = MoveMap()

tuple loops_kic.my_loop = Loop( loop_begin, loop_end, loop_cut )

tuple loops_kic.my_loops = Loops()

int loops_kic.outer_cycles = 10

tuple loops_kic.p = Pose()

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

tuple loops_kic.pymol = rosetta.PyMOL_Mover()

tuple loops_kic.recover_sidechains = protocols.simple_moves.ReturnSidechainMover( starting_p )

tuple loops_kic.rms = loop_rmsd( p, starting_p, my_loops )

Referenced by HDdesignMover.apply(), ExposedStrandMover.bb_rmsd(), numeric::model_quality.calc_rms_fast(), CAtrace.CAtrace(), go_main(), numeric::model_quality.maxsub(), ScoreFragmentSetMover.run(), and SolutionRescoreMover.run().

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.starting_p_centroid = Pose()

loops_kic.success = False

Referenced by numeric::Calculator.compute(), utility::file.create_directory_recursive(), and run().

tuple loops_kic.task_pack = TaskFactory.create_packer_task( starting_p )

tuple loops_kic.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover( 'centroid' )

tuple loops_kic.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover( 'fa_standard' )

float loops_kic.tol = 0.001

Referenced by numeric::deriv.angle_p1_deriv(), numeric::deriv.angle_p1_p2_p3_deriv(), numeric::deriv.angle_p2_deriv(), numeric.in_sin_cos_range(), numeric::Quaternion< T >.is_normalized(), numeric::xyzTriple< typename >.is_normalized(), numeric::xyzVector< core::Real >.is_normalized(), numeric::xyzTriple< typename >.is_unit(), numeric::xyzVector< core::Real >.is_unit(), numeric::BodyPosition< typename >.normalize_if_needed(), numeric::Quaternion< T >.normalize_if_needed(), numeric::Quaternion< T >.not_normalized(), and numeric.sin_cos_range().