Index

A

align_map_principal_axes() (em_map_utils.map_covariance.MapCovariance class method)

args (em_map_utils.farm_function.FarmFunction attribute) asphericity_coefficient() (in module em_map_utils.structure_size_and_shape)

B

bg_frac (em_map_utils.map_threshold.MapHistogram attribute) bg_hist_sum (em_map_utils.map_threshold.MapHistogram attribute) bg_mean (em_map_utils.map_threshold.MapHistogram attribute) bg_mean_idx (em_map_utils.map_threshold.MapHistogram attribute)

bg_sigma (em_map_utils.map_threshold.MapHistogram attribute) bg_threshold (em_map_utils.map_threshold.MapHistogram attribute) bg_var (em_map_utils.map_threshold.MapHistogram attribute) bg_var_idx (em_map_utils.map_threshold.MapHistogram attribute) bin_width (em_map_utils.map_threshold.MapHistogram attribute)

C

cent_coords (em_map_utils.map_line_projections.MapLineProjections attribute) centre_coos (em_map_utils.map_covariance.MapCovariance attribute) coords (em_map_utils.map_line_projections.MapLineProjections attribute) count_voxels_matching_criteria() (in module em_map_utils.map_threshold)

cov_matrix (em_map_utils.map_covariance.MapCovariance attribute) cum_dist_func (em_map_utils.map_threshold.MapHistogram attribute) cum_prof_width (em_map_utils.map_line_projections.MapLineProjections attribute) cumulative_profile_width() (em_map_utils.map_line_projections.MapLineProjections method)

D

db_name (em_map_utils.farm_function.FarmFunction attribute) dict_factory() (em_map_utils.farm_function.FarmFunction static method)

download_emdb_map() (in module em_map_utils.download_emdb) dummy() (in module em_map_utils.demos.demo_farm_function)

E

eigenvalues (em_map_utils.map_covariance.MapCovariance attribute) eigenvectors (em_map_utils.map_covariance.MapCovariance attribute) em_map_utils module, [1] em_map_utils.demos module, [1] em_map_utils.demos.demo_farm_function module em_map_utils.demos.demo_filled_cuboid module em_map_utils.demos.demo_filled_cylinder module em_map_utils.demos.demo_filled_sphere module em_map_utils.demos.demo_map_covariance module em_map_utils.demos.demo_map_line_projections module em_map_utils.demos.demo_map_resample module em_map_utils.demos.demo_map_rotate module em_map_utils.demos.ortho_surface_views module em_map_utils.download_emdb module

em_map_utils.farm_function module em_map_utils.filled_cuboid module em_map_utils.filled_cylinder module em_map_utils.filled_sphere module em_map_utils.map_covariance module em_map_utils.map_line_projections module em_map_utils.map_resample module em_map_utils.map_rotate module em_map_utils.map_threshold module em_map_utils.structure_size_and_shape module em_map_utils.util module emdb_root (in module em_map_utils.download_emdb) emdbid_pattern (in module em_map_utils.download_emdb)

F

f (em_map_utils.farm_function.FarmFunction attribute) fail_queue (em_map_utils.farm_function.FarmFunction attribute) FarmFunction (class in em_map_utils.farm_function) file_root (em_map_utils.farm_function.FarmFunction attribute) filled_cuboid() (in module em_map_utils.filled_cuboid)

filled_cylinder() (in module em_map_utils.filled_cylinder) filled_sphere() (in module em_map_utils.filled_sphere) find_closest_rhas() (em_map_utils.map_covariance.MapCovariance class method) fit_exp4() (em_map_utils.map_line_projections.MapLineProjections method) fit_exp4_func() (em_map_utils.map_line_projections.MapLineProjections static method)

G

get_emdb_map_name() (in module em_map_utils.download_emdb)

get_emdb_map_url() (in module em_map_utils.download_emdb) get_map_download_path() (in module em_map_utils.download_emdb)

K

kwargs (em_map_utils.farm_function.FarmFunction attribute)

L

lengths_from_eigenvalues() (em_map_utils.map_covariance.MapCovariance method) lock (em_map_utils.farm_function.FarmFunction attribute) logger (in module em_map_utils) (in module em_map_utils.demos.demo_map_covariance) (in module em_map_utils.download_emdb) (in module em_map_utils.farm_function) (in module em_map_utils.map_covariance) (in module em_map_utils.map_line_projections) (in module em_map_utils.map_threshold) (in module em_map_utils.structure_size_and_shape)

M

main() (in module em_map_utils.download_emdb) (in module em_map_utils.structure_size_and_shape) map_grid (em_map_utils.map_line_projections.MapLineProjections attribute) map_hist_peak_idx (em_map_utils.map_threshold.MapHistogram attribute) map_hist_peak_val (em_map_utils.map_threshold.MapHistogram attribute) map_mean (em_map_utils.map_threshold.MapHistogram attribute) map_name_pattern (in module em_map_utils.structure_size_and_shape) map_prof (em_map_utils.map_line_projections.MapLineProjections attribute) map_resample() (in module em_map_utils.map_resample) map_rotate() (in module em_map_utils.map_rotate) map_rotate_forward_backward() (em_map_utils.map_covariance.MapCovariance class method) map_sigma (em_map_utils.map_threshold.MapHistogram attribute) map_var (em_map_utils.map_threshold.MapHistogram attribute) MapCovariance (class in em_map_utils.map_covariance) MapHistogram (class in em_map_utils.map_threshold) MapLineProjections (class in em_map_utils.map_line_projections) max (em_map_utils.map_line_projections.MapLineProjections attribute) max_cpu (em_map_utils.farm_function.FarmFunction attribute) max_eccentricity() (in module em_map_utils.structure_size_and_shape) max_tries (em_map_utils.farm_function.FarmFunction attribute) min (em_map_utils.map_line_projections.MapLineProjections attribute) module em_map_utils, [1] em_map_utils.demos, [1] em_map_utils.demos.demo_farm_function em_map_utils.demos.demo_filled_cuboid em_map_utils.demos.demo_filled_cylinder em_map_utils.demos.demo_filled_sphere em_map_utils.demos.demo_map_covariance em_map_utils.demos.demo_map_line_projections em_map_utils.demos.demo_map_resample em_map_utils.demos.demo_map_rotate em_map_utils.demos.ortho_surface_views em_map_utils.download_emdb em_map_utils.farm_function em_map_utils.filled_cuboid em_map_utils.filled_cylinder em_map_utils.filled_sphere em_map_utils.map_covariance em_map_utils.map_line_projections em_map_utils.map_resample em_map_utils.map_rotate em_map_utils.map_threshold em_map_utils.structure_size_and_shape em_map_utils.util

monitoring_interval (em_map_utils.farm_function.FarmFunction attribute)

N

num_error (em_map_utils.farm_function.FarmFunction attribute) num_processed (em_map_utils.farm_function.FarmFunction attribute)

num_success (em_map_utils.farm_function.FarmFunction attribute) num_workers (em_map_utils.farm_function.FarmFunction attribute)

O

old_values (em_map_utils.farm_function.FarmFunction attribute)

ortho_surface_views() (in module em_map_utils.demos.ortho_surface_views) output_file (em_map_utils.farm_function.FarmFunction attribute)

P

parser (in module em_map_utils.demos.demo_farm_function) (in module em_map_utils.demos.demo_filled_cuboid) (in module em_map_utils.demos.demo_filled_cylinder) (in module em_map_utils.demos.demo_filled_sphere) (in module em_map_utils.demos.demo_map_covariance) (in module em_map_utils.demos.demo_map_line_projections) (in module em_map_utils.demos.demo_map_resample) (in module em_map_utils.demos.demo_map_rotate) (in module em_map_utils.filled_cuboid) (in module em_map_utils.filled_cylinder) (in module em_map_utils.filled_sphere) (in module em_map_utils.map_covariance) (in module em_map_utils.map_line_projections) (in module em_map_utils.map_resample) (in module em_map_utils.map_rotate) (in module em_map_utils.map_threshold)

PERM_IDX (em_map_utils.map_line_projections.MapLineProjections attribute) phys_scale_eigenvectors() (em_map_utils.map_covariance.MapCovariance method) plot() (em_map_utils.map_line_projections.MapLineProjections method) plot_back_rotated_cuboid() (in module em_map_utils.demos.demo_map_covariance) plot_bg_histogram() (em_map_utils.map_threshold.MapHistogram method) plot_filled_cuboid() (in module em_map_utils.demos.demo_filled_cuboid) plot_filled_cylinder() (in module em_map_utils.demos.demo_filled_cylinder) plot_filled_sphere() (in module em_map_utils.demos.demo_filled_sphere) plot_line_projections() (in module em_map_utils.demos.demo_map_line_projections) plot_map_cdf() (em_map_utils.map_threshold.MapHistogram method) plot_map_histogram() (em_map_utils.map_threshold.MapHistogram method) plot_resampled_map() (in module em_map_utils.demos.demo_map_resample) plot_rotated_map() (in module em_map_utils.demos.demo_map_rotate) process_queue (em_map_utils.farm_function.FarmFunction attribute) prof_fit (em_map_utils.map_line_projections.MapLineProjections attribute)

R

range (em_map_utils.map_line_projections.MapLineProjections attribute) read_emdb_ids_from() (in module em_map_utils.download_emdb) read_map_list_from() (in module em_map_utils.structure_size_and_shape) resume (em_map_utils.farm_function.FarmFunction attribute)

retry (em_map_utils.farm_function.FarmFunction attribute) RHAS_ALL (em_map_utils.map_covariance.MapCovariance attribute) RHAS_BASE (em_map_utils.map_covariance.MapCovariance attribute) RHAS_XYZ (em_map_utils.map_covariance.MapCovariance attribute) RHAS_ZYX (em_map_utils.map_covariance.MapCovariance attribute)

S

save_map() (in module em_map_utils.util) sigma (em_map_utils.map_line_projections.MapLineProjections attribute) sigma_factor (em_map_utils.map_threshold.MapHistogram attribute)

sign_align_eigenvectors() (em_map_utils.map_covariance.MapCovariance static method) structure_size_and_shape() (in module em_map_utils.structure_size_and_shape) success_queue (em_map_utils.farm_function.FarmFunction attribute) sum (em_map_utils.map_line_projections.MapLineProjections attribute)

T

threshold_map() (in module em_map_utils.map_threshold)

timeout (em_map_utils.farm_function.FarmFunction attribute) two_sigma (em_map_utils.map_line_projections.MapLineProjections attribute)

V

values (em_map_utils.farm_function.FarmFunction attribute)

variance (em_map_utils.map_line_projections.MapLineProjections attribute)

W

write_to_files() (em_map_utils.farm_function.FarmFunction method)