test.Workshop4test Namespace Reference

Functions
def	random_move (pose)

Variables
	extra_options
int	PHI = 0
int	PSI = 1
float	kT = 1.0
	last_pose = Pose()
	low_pose = Pose()
	p = pose_from_sequence("AAAAAAAAAA", "fa_standard")
	pmm = PyMOLMover()
	score = ScoreFunction()
	low_score = score(p)
	last_score = score(p)
	new_score = score(p)
	deltaE = new_score - last_score
	P = math.exp(-deltaE/kT)
	roll = random.uniform(0.0, 1.0)
	ras = pose_from_file("../test/data/workshops/6Q21.clean.pdb")
	score2 = get_score_function()
	switch = SwitchResidueTypeSetMover("centroid")
	score3 = create_score_function("score3")
	switch2 = SwitchResidueTypeSetMover("fa_standard")
	fragset = core.fragment.ConstantLengthFragSet(3)
	movemap = MoveMap()
	mover_3mer = protocols.simple_moves.ClassicFragmentMover(fragset, movemap)
	pose = pose_from_sequence("RFPMMSTFKVLLCGAVLSRIDAG", "centroid")

Function Documentation

random_move()

def test.Workshop4test.random_move

(

pose

)

Referenced by Bola.random_nonclashing_move().

Variable Documentation

deltaE

test.Workshop4test.deltaE = new_score - last_score

extra_options

test.Workshop4test.extra_options

fragset

test.Workshop4test.fragset = core.fragment.ConstantLengthFragSet(3)

Referenced by apply_all_frags(), gen_pep_bb_sequential(), main(), make_1mer_frags(), make_frags(), HECTMover.make_frags(), rebuild_centroid_test(), and run().

kT

float test.Workshop4test.kT = 1.0

last_pose

test.Workshop4test.last_pose = Pose()

Referenced by myMC.myMC(), and myMC.roll().

last_score

test.Workshop4test.last_score = score(p)

Referenced by main(), myMC.myMC(), myMC.roll(), and run_trace().

low_pose

test.Workshop4test.low_pose = Pose()

Referenced by main().

low_score

test.Workshop4test.low_score = score(p)

movemap

test.Workshop4test.movemap = MoveMap()

mover_3mer

test.Workshop4test.mover_3mer = protocols.simple_moves.ClassicFragmentMover(fragset, movemap)

new_score

test.Workshop4test.new_score = score(p)

Referenced by add_scores(), opt_bicelle_params(), opt_double_vesicle_params(), opt_vesicle_params(), and perturb_and_rescore().

p

test.Workshop4test.p = pose_from_sequence("AAAAAAAAAA", "fa_standard")

P

test.Workshop4test.P = math.exp(-deltaE/kT)

PHI

int test.Workshop4test.PHI = 0

pmm

test.Workshop4test.pmm = PyMOLMover()

Referenced by DougsDockDesignMinimizeMagicMover.apply(), PeptiodMovieMover.apply(), and main().

pose

test.Workshop4test.pose = pose_from_sequence("RFPMMSTFKVLLCGAVLSRIDAG", "centroid")

PSI

int test.Workshop4test.PSI = 1

ras

test.Workshop4test.ras = pose_from_file("../test/data/workshops/6Q21.clean.pdb")

roll

test.Workshop4test.roll = random.uniform(0.0, 1.0)

score

test.Workshop4test.score = ScoreFunction()

score2

test.Workshop4test.score2 = get_score_function()

Referenced by get_ddG(), main(), and motif_scan().

score3

test.Workshop4test.score3 = create_score_function("score3")

Referenced by main(), and motif_scan().

switch

test.Workshop4test.switch = SwitchResidueTypeSetMover("centroid")

switch2

test.Workshop4test.switch2 = SwitchResidueTypeSetMover("fa_standard")