Variables
int	MAX_KIC_BUILD_ATTEMPTS = 10000

	extra_options

	p = core.import_pose.pose_from_file( "../test/data/2cpl_min.pdb" )

	starting_p = Pose()

	scorefxn_low = protocols.loops.get_cen_scorefxn()

	scorefxn_high = protocols.loops.get_fa_scorefxn()

	pymol = PyMOLMover()

int	loop_begin = 145

int	loop_end = 155

int	loop_cut = 150

	my_loop = protocols.loops.Loop( loop_begin, loop_end, loop_cut )

	my_loops = protocols.loops.Loops()

	movemap = MoveMap()

	kic_mover = KinematicMover()

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

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

	recover_sidechains = protocols.simple_moves.ReturnSidechainMover( starting_p )

	task_pack = core.pack.task.TaskFactory.create_packer_task( starting_p )

	pack = protocols.minimization_packing.PackRotamersMover( scorefxn_high, task_pack )

	mm = MoveMap()

float	tol = 0.001

string	min_type = "linmin"

	linmin_mover = protocols.minimization_packing.MinMover( mm, scorefxn_low, min_type, tol, True )

	starting_p_centroid = Pose()

	end

bool	success = False

	i

int	outer_cycles = 1

int	inner_cycles = 1

float	init_temp = 2.0

float	final_temp = 1.0

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

float	kT = init_temp

	mc = MonteCarlo( p, scorefxn_low, kT )

	kic_start = randrange( loop_begin, loop_end - 1 )

	kic_end = randrange( kic_start+2, loop_end+1 )

tuple	middle_offset = ( kic_end - kic_start ) // 2

tuple	kic_middle = kic_start + middle_offset

	rms = protocols.loops.loop_rmsd( p, starting_p, my_loops )

	loop_refine = rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC( my_loops )

Variable Documentation

◆ end

test.T650_LoopsKIC.end

◆ extra_options

test.T650_LoopsKIC.extra_options

◆ final_temp

float test.T650_LoopsKIC.final_temp = 1.0

◆ gamma

test.T650_LoopsKIC.gamma = math.pow( ( final_temp/init_temp ),( 1.0/( outer_cycles*inner_cycles ) ) )

◆ i

test.T650_LoopsKIC.i

◆ init_temp

float test.T650_LoopsKIC.init_temp = 2.0

◆ inner_cycles

int test.T650_LoopsKIC.inner_cycles = 1

◆ kic_end

test.T650_LoopsKIC.kic_end = randrange( kic_start+2, loop_end+1 )

◆ kic_middle

tuple test.T650_LoopsKIC.kic_middle = kic_start + middle_offset

◆ kic_mover

test.T650_LoopsKIC.kic_mover = KinematicMover()

◆ kic_start

test.T650_LoopsKIC.kic_start = randrange( loop_begin, loop_end - 1 )

◆ kT

float test.T650_LoopsKIC.kT = init_temp

◆ linmin_mover

test.T650_LoopsKIC.linmin_mover = protocols.minimization_packing.MinMover( mm, scorefxn_low, min_type, tol, True )

◆ loop_begin

int test.T650_LoopsKIC.loop_begin = 145

◆ loop_cut

int test.T650_LoopsKIC.loop_cut = 150

◆ loop_end

int test.T650_LoopsKIC.loop_end = 155

◆ loop_refine

test.T650_LoopsKIC.loop_refine = rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC( my_loops )

◆ MAX_KIC_BUILD_ATTEMPTS

int test.T650_LoopsKIC.MAX_KIC_BUILD_ATTEMPTS = 10000

◆ mc

test.T650_LoopsKIC.mc = MonteCarlo( p, scorefxn_low, kT )

◆ middle_offset

tuple test.T650_LoopsKIC.middle_offset = ( kic_end - kic_start ) // 2

◆ min_type

string test.T650_LoopsKIC.min_type = "linmin"

◆ mm

test.T650_LoopsKIC.mm = MoveMap()

◆ movemap

test.T650_LoopsKIC.movemap = MoveMap()

◆ my_loop

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

◆ my_loops

test.T650_LoopsKIC.my_loops = protocols.loops.Loops()

◆ outer_cycles

int test.T650_LoopsKIC.outer_cycles = 1

◆ p

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

◆ pack

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

◆ pymol

test.T650_LoopsKIC.pymol = PyMOLMover()

◆ recover_sidechains

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

◆ rms

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

◆ scorefxn_high

test.T650_LoopsKIC.scorefxn_high = protocols.loops.get_fa_scorefxn()

◆ scorefxn_low

test.T650_LoopsKIC.scorefxn_low = protocols.loops.get_cen_scorefxn()

◆ starting_p

test.T650_LoopsKIC.starting_p = Pose()

◆ starting_p_centroid

test.T650_LoopsKIC.starting_p_centroid = Pose()

◆ success

bool test.T650_LoopsKIC.success = False

◆ task_pack

test.T650_LoopsKIC.task_pack = core.pack.task.TaskFactory.create_packer_task( starting_p )

◆ to_centroid

test.T650_LoopsKIC.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover( 'centroid' )

◆ to_fullatom

test.T650_LoopsKIC.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover( 'fa_standard' )

◆ tol

float test.T650_LoopsKIC.tol = 0.001

Variables