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" ]

Definition at line 20 of file loops_kic.py.

float loops_kic.final_temp = 1.0

Definition at line 109 of file loops_kic.py.

tuple loops_kic.gamma = math.pow( ( final_temp/init_temp ),( 1.0/( outer_cycles*inner_cycles ) ) )

Definition at line 110 of file loops_kic.py.

float loops_kic.init_temp = 2.0

Definition at line 108 of file loops_kic.py.

int loops_kic.inner_cycles = 30

Definition at line 107 of file loops_kic.py.

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

Definition at line 121 of file loops_kic.py.

loops_kic.kic_middle = kic_start+middle_offset

Definition at line 123 of file loops_kic.py.

tuple loops_kic.kic_mover = KinematicMover()

Definition at line 54 of file loops_kic.py.

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

Definition at line 120 of file loops_kic.py.

loops_kic.kT = init_temp

Definition at line 111 of file loops_kic.py.

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

Definition at line 77 of file loops_kic.py.

int loops_kic.loop_begin = 145

Definition at line 36 of file loops_kic.py.

int loops_kic.loop_cut = 150

Definition at line 38 of file loops_kic.py.

int loops_kic.loop_end = 155

Definition at line 37 of file loops_kic.py.

tuple loops_kic.loop_refine = LoopMover_Refine_KIC( my_loops )

Definition at line 139 of file loops_kic.py.

int loops_kic.MAX_KIC_BUILD_ATTEMPTS = 10000

Definition at line 18 of file loops_kic.py.

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

Definition at line 112 of file loops_kic.py.

tuple loops_kic.middle_offset = ( kic_end - kic_start )

Definition at line 122 of file loops_kic.py.

string loops_kic.min_type = "linmin"

Definition at line 76 of file loops_kic.py.

Referenced by 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 loops_kic.mm = MoveMap()

Definition at line 71 of file loops_kic.py.

tuple loops_kic.movemap = MoveMap()

Definition at line 46 of file loops_kic.py.

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

Definition at line 39 of file loops_kic.py.

tuple loops_kic.my_loops = Loops()

Definition at line 40 of file loops_kic.py.

int loops_kic.outer_cycles = 10

Definition at line 106 of file loops_kic.py.

tuple loops_kic.p = Pose()

Definition at line 25 of file loops_kic.py.

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

Definition at line 65 of file loops_kic.py.

tuple loops_kic.pymol = rosetta.PyMOL_Mover()

Definition at line 34 of file loops_kic.py.

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

Definition at line 59 of file loops_kic.py.

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

Definition at line 130 of file loops_kic.py.

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' )

Definition at line 32 of file loops_kic.py.

tuple loops_kic.scorefxn_low = create_score_function( 'cen_std' )

Definition at line 31 of file loops_kic.py.

tuple loops_kic.starting_p = Pose()

Definition at line 28 of file loops_kic.py.

tuple loops_kic.starting_p_centroid = Pose()

Definition at line 80 of file loops_kic.py.

loops_kic.success = False

Definition at line 85 of file loops_kic.py.

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

tuple loops_kic.task_pack = TaskFactory.create_packer_task( starting_p )

Definition at line 62 of file loops_kic.py.

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

Definition at line 57 of file loops_kic.py.

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

Definition at line 58 of file loops_kic.py.

float loops_kic.tol = 0.001

Definition at line 75 of file loops_kic.py.

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().

Variables

Variable Documentation