test.Workshop4test Namespace Reference

Functions
def	random_move

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

Function Documentation

def test.Workshop4test.random_move

(

pose

)

Variable Documentation

test.Workshop4test.deltaE = new_score-last_score

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

Referenced by gen_pep_bb_sequential(), make_1mer_frags(), make_frags(), and run().

float test.Workshop4test.kT = 1.0

tuple test.Workshop4test.last_pose = Pose()

tuple test.Workshop4test.last_score = score(p)

tuple test.Workshop4test.low_pose = Pose()

test.Workshop4test.low_score = score(p)

tuple test.Workshop4test.movemap = MoveMap()

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

tuple test.Workshop4test.new_score = score(p)

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

Referenced by binder.add_relevant_include_for_decl(), add_rosetta_options_2(), binder.bind_function(), utility.down_cast(), ObjexxFCL::format.F(), basic::resource_manager::locator::FileStream.FileStream(), ObjexxFCL.fixed_Fstring_of(), ObjexxFCL.fixed_string_of(), fmt::BasicFormatter< CharType, ArgFormatter >.format(), binder.function_arguments_for_py_overload(), ObjexxFCL.general_Fstring_of(), ObjexxFCL.general_string_of(), fmt::BasicWriter< Char >.get(), numeric::interpolation::spline::SplineGenerator.get_interpolator(), get_max_and_intervals(), harvest_scores(), numeric.hsv_to_rgb(), numeric::geometry::hashing::SixDOffsetTree.init(), numeric::interpolation::InterpolatedPotential< N >.InterpolatedPotential(), binder.is_bindable(), numeric::fourier.kf_bfly_generic(), numeric::fourier.kf_factor(), numeric::fourier.kf_work(), numeric::statistics.kl_divergence(), numeric::geometry::hashing::SixDOffsetTree.lookup(), main(), rosetta_binders::utility_vector_binder< Vector, L, T, Allocator >.maybe_has_equal_operator(), merge_motifs(), minimize_with_constraints(), fmt::BufferedFile.operator Proxy(), fmt::File.operator Proxy(), numeric::interpolation::TempStruct< T, N >.operator()(), numeric::interpolation::TempStruct< T, 1 >.operator()(), numeric.operator<<(), numeric::sphericalVector< typename >.operator=(), numeric::xyzTriple< typename >.operator=(), numeric::xyzVector< core::Real >.operator=(), fmt::BasicWriter< Char >.prepare_int_buffer(), ObjexxFCL::CArrayP< typename >.Proxy(), basic::sampling::orientations::QuaternionGrid.QuaternionGrid(), numeric.read_probabilities_or_die(), numeric::MathNTensor< double, 2 >.replace_layer(), numeric::geometry::BoundingBox< Vector >.reset(), myMC.roll(), ObjexxFCL.scientific_Fstring_of(), ObjexxFCL.scientific_string_of(), numeric::geometry::BoundingBox< Vector >.set_lower(), numeric::geometry::BoundingBox< Vector >.set_upper(), numeric::fourier::SHT.setup_Pmls(), sigmoid_train(), binder.simplify_std_class_name(), binder::Context.sort_binders(), numeric::interpolation::spline.spline_second_derivative(), binder.standard_name(), utility.strip(), svm_load_model(), svm_predict_values(), svm_save_model(), svm_train(), utility::json_spirit.to_str(), numeric::interpolation::spline::PolycubicSpline< N >.train(), numeric::kinematic_closure.triaxialCoefficients(), numeric::kinematic_closure::radians.triaxialCoefficients(), fmt::BasicWriter< Char >.write_double(), and fmt::BasicWriter< Char >.write_int().

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

Referenced by numeric::deriv.angle_p1_deriv(), numeric::deriv.angle_p1_p2_p3_deriv(), numeric::deriv.angle_p2_deriv(), numeric::deriv.dihedral_deriv_second(), numeric::deriv.dihedral_p1_cosine_deriv(), numeric::deriv.dihedral_p1_cosine_deriv_first(), numeric::deriv.dihedral_p2_cosine_deriv(), numeric::deriv.dihedral_p2_cosine_deriv_first(), numeric::deriv.distance_f1_f2_deriv(), numeric::geometry::hashing::bin_index_hasher.operator()(), numeric::deriv.p1_theta_deriv(), and numeric::deriv.x_and_dtheta_dx().

int test.Workshop4test.PHI = 0

tuple test.Workshop4test.pmm = PyMOLMover()

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

int test.Workshop4test.PSI = 1

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

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

tuple test.Workshop4test.score = ScoreFunction()

tuple test.Workshop4test.score2 = get_score_function()

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

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

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