gaussian-sampling Namespace Reference

Functions
def	propose_move (input)
def	proposal_prob (move)
def	initial_accept (input, trial)
def	final_accept (input, trial)
def	plot_trajectory (trajectory)
def	plot_histogram (trajectory)
def	plot_correlation (trajectory)

Variables
	parser = argparse.ArgumentParser()
	type
	int
	default
	float
	action
	arguments = parser.parse_args()
	input = arguments.mean
list	trajectory = []
def	trial = propose_move(input)

Function Documentation

final_accept()

def gaussian-sampling.final_accept	(		input,
			trial
	)

References min(), proposal_prob(), and numeric::random.uniform().

initial_accept()

def gaussian-sampling.initial_accept	(		input,
			trial
	)

References min(), proposal_prob(), and numeric::random.uniform().

plot_correlation()

def gaussian-sampling.plot_correlation

(

trajectory

)

References bin_torsions.figure, ObjexxFCL.len(), max(), and correlation_time.title.

plot_histogram()

def gaussian-sampling.plot_histogram

(

trajectory

)

References bin_torsions.figure, 3d_histogram.hist, proposal_prob(), and correlation_time.title.

plot_trajectory()

def gaussian-sampling.plot_trajectory

(

trajectory

)

References bin_torsions.figure, ObjexxFCL.len(), and correlation_time.title.

proposal_prob()

def gaussian-sampling.proposal_prob

(

move

)

Referenced by final_accept(), initial_accept(), and plot_histogram().

propose_move()

def gaussian-sampling.propose_move

(

input

)

References normal.

Variable Documentation

action

gaussian-sampling.action

arguments

gaussian-sampling.arguments = parser.parse_args()

default

gaussian-sampling.default

float

gaussian-sampling.float

input

def gaussian-sampling.input = arguments.mean

Referenced by basic::citation_manager::CitationManager.add_citation(), basic::citation_manager::CitationManager.add_citations(), analyze_base_pair_test(), utility.arg_greatest_several(), utility.arg_least_several(), utility.arg_max(), utility.arg_min(), blosum_score_alignment(), build_full_model_test(), calc_rama_scores(), calc_rms_test(), calculate_distances(), myspace.check_clash(), check_structures(), ui::task::Task.clone(), cluster_outfile_test_OLD(), color_by_lj_test(), count_contacts(), dist_matrix_test(), do_cycpep_analysis(), do_disorder_prediction(), drrafter_error_estimation(), entropy_calculate_test(), CL.errstr(), numeric.FArray_to_vector_of_xyzvectors(), numeric.FArray_to_xyzmatrix(), fill_input_poses(), frag_extract_test(), ui::network::FunctionSetupDialog.FunctionSetupDialog(), gather_ss_pct(), get_info_test(), get_poseToRelax(), get_rmsd(), numeric::VoxelGrid< T >.GetNeighbors(), numeric::VoxelGrid< T >.HasNeighbors(), ui::task::File.init_from_local_file(), input_subset_poses(), numeric::geometry::hashing::SixDOffsetTree.insert(), utility.is_string_numeric(), load_coords(), main(), make_fragments(), utility.max(), utility.max2(), measure_disorder(), utility.min(), utility.min2(), minimizer_test(), mutate_and_score_RNP(), my_main(), obtain_start_pose(), peptide_plane_test(), ui::task::PNode.PNode(), myspace.pose_from_scratch(), read_B_vals(), read_complex_type(), read_distances(), read_ERMS(), read_in_cl_data(), read_in_pdbs(), myspace.read_input(), VallReader.read_lines(), read_rigid_body_settings(), readline(), PickSSE.readSSE(), ui::task::Task.rename_input_file(), utility.replace_environment_variables(), resample_full_model_test(), rna_fullatom_minimize_test(), rna_motif_test(), rna_suitename(), self-test.run_test(), myspace.scan_Evalue(), score_rnp(), DomainAssemblerNDocker.setup_cen_domains(), numeric::geometry::hashing::SixDOffsetTree.sum_radius(), ui::task::TaskSyncer_TaskStrategy.task_files_upload(), test_k_square(), NodeTest.test_task_serialization(), FunctorTest.test_task_upload(), thermal_sampler(), ui::task::FileTableModel.update_from_task(), numeric.vector_of_xyzvectors_to_FArray(), viewer_main(), and numeric.xyzmatrix_to_FArray().

int

gaussian-sampling.int

parser

gaussian-sampling.parser = argparse.ArgumentParser()

trajectory

list gaussian-sampling.trajectory = []

Referenced by MyProtocol.apply(), main(), my_main(), and OutputManager.OutputManager().

trial

def gaussian-sampling.trial = propose_move(input)

Referenced by SwapElementsMover1.apply(), do_backrub(), do_KIC(), doit(), main(), mathntensor_from_dist(), relax_cenrot_pose(), test(), and use_backrub().

type

gaussian-sampling.type