Index

_

__assemble_particle() (assemblers.t4ss_assembler.T4SSAssembler method) __convert_coordinates() (simulation.tem_simulation.Simulation method) __get_random_angle() (assemblers.t4ss_assembler.T4SSAssembler method) __get_random_position() (assemblers.t4ss_assembler.T4SSAssembler method) __get_random_tbl_orientation() (assemblers.t4ss_assembler.T4SSAssembler method) __open_membrane() (assemblers.t4ss_assembler.T4SSAssembler method)

__replace() (simulation.tem_simulation.Simulation method) __replace_nonoise() (simulation.tem_simulation.Simulation method) __send_commands_to_chimera() (assemblers.t4ss_assembler.T4SSAssembler method) __write_coord_file() (simulation.tem_simulation.Simulation method) __write_fiducials_particle_set_section() (simulation.tem_simulation.Simulation method) __write_particle_section() (simulation.tem_simulation.Simulation method) __write_particle_set_section() (simulation.tem_simulation.Simulation method)

A

ack_event (assemblers.basic_assembler.BasicAssembler attribute) (assemblers.t4ss_assembler.T4SSAssembler attribute) (simulation.chimera_server.ChimeraCommandSet attribute) add_defocus_to_adoc() (in module processors.imod_processor)

add_orientation() (simulation.tem_simulation.Simulation method) angle (assemblers.t4ss_assembler.Barrel attribute) (assemblers.t4ss_assembler.Rod attribute) apix (simulation.tem_simulation.Simulation attribute)

B

Barrel (class in assemblers.t4ss_assembler)

base_coord_file (simulation.tem_simulation.Simulation attribute) BasicAssembler (class in assemblers.basic_assembler)

C

center (assemblers.t4ss_assembler.Rod attribute) center_coordinates() (in module processors.i3_processor) check_and_fix_names_starting_with_numbers() (in module processors.i3_processor) chimera_exec_path (simulation.chimera_server.ChimeraServer attribute) chimera_queue (assemblers.basic_assembler.BasicAssembler attribute) (assemblers.t4ss_assembler.T4SSAssembler attribute) ChimeraCommandSet (class in simulation.chimera_server) ChimeraServer (class in simulation.chimera_server) chosen_angles (assemblers.t4ss_assembler.T4SSAssembler attribute) chosen_orientations (assemblers.t4ss_assembler.T4SSAssembler attribute) chosen_positions (assemblers.t4ss_assembler.T4SSAssembler attribute) close() (assemblers.basic_assembler.BasicAssembler method) (assemblers.t4ss_assembler.T4SSAssembler method)

commands (assemblers.basic_assembler.BasicAssembler attribute) (assemblers.t4ss_assembler.T4SSAssembler attribute) (simulation.chimera_server.ChimeraCommandSet attribute) config_file (simulation.tem_simulation.Simulation attribute) configure_listener() (in module simulation.logger) configure_root_logger() (in module ets_generate_data) convert_slicer_to_motl() (in module processors.artiatomi_processor) convert_tlt_eman2() (in module processors.i3_processor) convert_tlt_imod() (in module processors.i3_processor) create_fiducials() (simulation.tem_simulation.Simulation method) create_particle_lists() (simulation.tem_simulation.Simulation method) custom_data (simulation.tem_simulation.Simulation attribute)

D

degrees (assemblers.t4ss_assembler.Rod attribute)

dynamo_main() (in module processors.dynamo_processor)

E

edit_output_files() (simulation.tem_simulation.Simulation method) eman2_main() (in module processors.eman2_processor) eman2_process module eman2_processor_to_dynamo() (in module processors.dynamo_processor) eman2_processor_to_i3() (in module processors.i3_processor) eman2_real_to_dynamo() (in module processors.dynamo_processor) eman2_real_to_i3() (in module processors.i3_processor) estimate_ctf() (in module eman2_process)

ets_generate_data module ets_process_data module extend_orientations() (simulation.tem_simulation.Simulation method) extend_positions() (simulation.tem_simulation.Simulation method) extract_e2_particles() (in module processors.dynamo_processor) (in module processors.i3_processor) extract_particles() (in module eman2_process) extract_tilt_range() (in module processors.dynamo_processor)

G

generate_extract_script() (in module processors.artiatomi_processor) generate_reconstructions_script() (in module processors.artiatomi_processor) generate_refinement_script() (in module processors.artiatomi_processor) generate_sta_script() (in module processors.artiatomi_processor) get_commands() (assemblers.t4ss_assembler.Barrel method) (assemblers.t4ss_assembler.Rod method) get_defocus_values() (in module processors.imod_processor) get_eman2_info() (in module processors.dynamo_processor) get_eman2_tilts() (in module processors.i3_processor) get_imod_filename() (in module processors.imod_processor) get_latest_motl() (in module processors.artiatomi_processor)

get_latest_ref() (in module processors.artiatomi_processor) get_metadata() (simulation.tem_simulation.Simulation method) get_mrc_size() (in module processors.dynamo_processor) (in module processors.i3_processor) get_new_orientation() (assemblers.basic_assembler.BasicAssembler method) get_num_particles() (simulation.tem_simulation.Simulation method) get_port() (simulation.chimera_server.ChimeraServer method) get_slicer_info() (in module processors.artiatomi_processor) (in module processors.dynamo_processor) (in module processors.i3_processor) get_trf_lines_imod() (in module processors.i3_processor) global_stack_no (simulation.tem_simulation.Simulation attribute)

I

imod_main() (in module processors.imod_processor) imod_processor_to_dynamo() (in module processors.dynamo_processor) imod_processor_to_i3() (in module processors.i3_processor) imod_real_to_dynamo() (in module processors.dynamo_processor)

imod_real_to_i3() (in module processors.i3_processor) imod_setup_sta() (in module processors.artiatomi_processor) import_tiltseries() (in module eman2_process) invert_z_coordinates() (in module eman2_process)

K

kill() (simulation.chimera_server.ChimeraServer method)

L

loaded_orientations (assemblers.t4ss_assembler.T4SSAssembler attribute)

log_listener_process() (in module simulation.logger)

M

main() (in module ets_generate_data) (in module ets_process_data) make_initial_model() (in module eman2_process) make_particle_set() (in module eman2_process) metadata_log_listener_process() (in module simulation.logger) model (assemblers.basic_assembler.BasicAssembler attribute) (assemblers.t4ss_assembler.T4SSAssembler attribute) module eman2_process ets_generate_data ets_process_data processors.artiatomi_processor processors.dynamo_processor processors.eman2_processor processors.i3_processor processors.imod_processor simulation.tem_simulation

N

nonoise_tilts_file (simulation.tem_simulation.Simulation attribute)

O

orientations (simulation.tem_simulation.Simulation attribute)

orig_coord_sys (assemblers.t4ss_assembler.Rod attribute)

P

parse_coordinates() (simulation.tem_simulation.Simulation method) parse_inputs() (in module ets_generate_data) (in module ets_process_data) parse_lst_file() (in module processors.dynamo_processor) (in module processors.i3_processor) pid (assemblers.basic_assembler.BasicAssembler attribute) (assemblers.t4ss_assembler.T4SSAssembler attribute) (simulation.chimera_server.ChimeraCommandSet attribute) port (simulation.chimera_server.ChimeraServer attribute) positions (simulation.tem_simulation.Simulation attribute)

process (simulation.chimera_server.ChimeraServer attribute) processors.artiatomi_processor module processors.dynamo_processor module processors.eman2_processor module processors.i3_processor module processors.imod_processor module

Q

quit() (simulation.chimera_server.ChimeraServer method)

R

read_particle_params() (in module processors.dynamo_processor) (in module processors.i3_processor) reconstruct_tomograms() (in module eman2_process) record_eman2_particle() (in module eman2_process) replace_adoc_values() (in module processors.imod_processor) replace_batchtomo_start_and_end_steps() (in module processors.imod_processor) reset_temp_dir() (assemblers.basic_assembler.BasicAssembler method) (assemblers.t4ss_assembler.T4SSAssembler method) restart_chimera_server() (simulation.chimera_server.ChimeraServer method) retrieve_orientations() (in module processors.imod_processor) Rod (class in assemblers.t4ss_assembler) rotate_positions_around_z() (in module eman2_process) (in module processors.artiatomi_processor) (in module processors.dynamo_processor) (in module processors.i3_processor)

run_binvol() (in module processors.imod_processor) run_chimera_server() (in module ets_generate_data) run_flip() (in module processors.imod_processor) run_process() (in module ets_generate_data) run_process_with_params() (in module eman2_process) run_refinement() (in module eman2_process) run_rotx() (in module processors.imod_processor) run_submfg() (in module processors.imod_processor) run_tem_simulator() (simulation.tem_simulation.Simulation method) run_tomo3d() (in module processors.imod_processor)

S

save_processor_info() (in module ets_process_data) scale_mrc() (in module ets_generate_data) send_and_wait() (simulation.chimera_server.ChimeraCommandSet method) set_custom_data() (simulation.tem_simulation.Simulation method) set_up_batchtomo() (in module processors.imod_processor) set_up_tiltseries() (assemblers.basic_assembler.BasicAssembler method) (assemblers.t4ss_assembler.T4SSAssembler method) setup_reconstructions_script() (in module processors.artiatomi_processor) shift_coordinates_bottom_left() (in module processors.artiatomi_processor) (in module processors.dynamo_processor) (in module processors.i3_processor) sim_log_file (simulation.tem_simulation.Simulation attribute)

simulation (assemblers.basic_assembler.BasicAssembler attribute) (assemblers.t4ss_assembler.T4SSAssembler attribute) Simulation (class in simulation.tem_simulation) simulation.tem_simulation module slicer_angles_to_dynamo_angles() (in module processors.dynamo_processor) slicer_angles_to_i3_matrix() (in module processors.i3_processor) source (assemblers.t4ss_assembler.Barrel attribute) (assemblers.t4ss_assembler.Rod attribute) split_coords() (in module processors.i3_processor) start_chimera_server() (simulation.chimera_server.ChimeraServer method) start_logger() (in module ets_generate_data)

T

T4SSAssembler (class in assemblers.t4ss_assembler) temp_dir (assemblers.basic_assembler.BasicAssembler attribute) (assemblers.t4ss_assembler.T4SSAssembler attribute) (simulation.tem_simulation.Simulation attribute)

tiltseries_file (simulation.tem_simulation.Simulation attribute) transformation_matrix_to_euler() (in module processors.dynamo_processor) truncate_utf8_chars() (in module simulation.logger)

V

validate_steps_to_run() (in module processors.eman2_processor)

volume_id (assemblers.t4ss_assembler.Barrel attribute) (assemblers.t4ss_assembler.Rod attribute)

W

write_out_motl_files_real() (in module processors.artiatomi_processor)

write_out_motl_files_simulated() (in module processors.artiatomi_processor) write_trf_eman2_extracted() (in module processors.i3_processor)