loops Namespace Reference

Variables
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')
int	loop_begin = 77
int	loop_end = 85
int	cutpoint = 81
tuple	my_loop = Loop( loop_begin, loop_end, cutpoint)
tuple	movemap = MoveMap()
tuple	fragset3mer = ConstantLengthFragSet(3, "test_in3_fragments")
tuple	mover_3mer = ClassicFragmentMover(fragset3mer,movemap)
tuple	ccd_closure = CCDLoopClosureMover(my_loop, movemap)
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	starting_p_centroid = Pose()
tuple	jd = Job_dist("loop_output", 100, scorefxn_high)
int	outer_cycles = 10
int	inner_cycles = 30
float	init_temp = 2.0
float	final_temp = 0.8
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	my_loops = Loops()
tuple	loop_refine = LoopMover_Refine_CCD(my_loops)
tuple	Lrms = loop_rmsd(p, starting_p, my_loops, True)

Variable Documentation

tuple loops.ccd_closure = CCDLoopClosureMover(my_loop, movemap)

Definition at line 39 of file loops.py.

int loops.cutpoint = 81

Definition at line 22 of file loops.py.

float loops.final_temp = 0.8

Definition at line 77 of file loops.py.

tuple loops.fragset3mer = ConstantLengthFragSet(3, "test_in3_fragments")

Definition at line 37 of file loops.py.

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

Definition at line 78 of file loops.py.

float loops.init_temp = 2.0

Definition at line 76 of file loops.py.

int loops.inner_cycles = 30

Definition at line 75 of file loops.py.

tuple loops.jd = Job_dist("loop_output", 100, scorefxn_high)

Definition at line 59 of file loops.py.

loops.kT = init_temp

Definition at line 79 of file loops.py.

int loops.loop_begin = 77

Definition at line 20 of file loops.py.

int loops.loop_end = 85

Definition at line 21 of file loops.py.

tuple loops.loop_refine = LoopMover_Refine_CCD(my_loops)

Definition at line 102 of file loops.py.

tuple loops.Lrms = loop_rmsd(p, starting_p, my_loops, True)

Definition at line 106 of file loops.py.

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

Definition at line 81 of file loops.py.

tuple loops.movemap = MoveMap()

Definition at line 29 of file loops.py.

Referenced by LigandRepackMinimizeProtocol.apply(), main(), SmallMoverBenchmark.setUp(), ShearMoverBenchmark.setUp(), SmallMoverBenchmark.tearDown(), and ShearMoverBenchmark.tearDown().

tuple loops.mover_3mer = ClassicFragmentMover(fragset3mer,movemap)

Definition at line 38 of file loops.py.

tuple loops.my_loop = Loop( loop_begin, loop_end, cutpoint)

Definition at line 23 of file loops.py.

tuple loops.my_loops = Loops()

Definition at line 100 of file loops.py.

int loops.outer_cycles = 10

Definition at line 74 of file loops.py.

tuple loops.p = Pose()

Definition at line 11 of file loops.py.

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

Definition at line 50 of file loops.py.

Referenced by CoupledMovesProtocol.apply(), main(), packmin_unbound_pep(), InteractionGraphPerformanceBenchmark.prepare_rotamer_sets(), rebuild_test(), repack_test(), InteractionGraphPerformanceBenchmark.run(), ConsensusFragmentMover.run(), and SolutionRescoreMover.run().

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

Definition at line 44 of file loops.py.

tuple loops.scorefxn_high = create_score_function_ws_patch('standard', 'score12')

Definition at line 18 of file loops.py.

tuple loops.scorefxn_low = create_score_function('cen_std')

Definition at line 17 of file loops.py.

tuple loops.starting_p = Pose()

Definition at line 14 of file loops.py.

tuple loops.starting_p_centroid = Pose()

Definition at line 55 of file loops.py.

tuple loops.task_pack = TaskFactory.create_packer_task(starting_p)

Definition at line 47 of file loops.py.

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

Definition at line 42 of file loops.py.

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

Definition at line 43 of file loops.py.