Index

A

abort_job() (in module pipeliner.job_manager) (pipeliner.api.manage_project.PipelinerProject method) acquire() (pipeliner.utils.DirectoryBasedLock method) add_all_settings() (pipeliner.user_settings.Settings method) add_bool_setting() (pipeliner.user_settings.Settings method) add_compatibility_joboptions() (pipeliner.pipeliner_job.PipelinerJob method) add_emdb_deposition_data() (pipeliner.pipeliner_job.PipelinerJob method) add_int_setting() (pipeliner.user_settings.Settings method) add_job() (pipeliner.project_graph.ProjectGraph method) add_main_emdb_processing_data() (pipeliner.pipeliner_job.PipelinerJob method) add_md_to_summary_data() (in module pipeliner.metadata_tools) add_missing_nodes_from_all_jobs() (pipeliner.api.manage_project.PipelinerProject method) add_new_input_edge() (pipeliner.project_graph.ProjectGraph method) add_new_output_edge() (pipeliner.project_graph.ProjectGraph method) add_node() (pipeliner.project_graph.ProjectGraph method) add_onedep_metadata_import() (pipeliner.pipeliner_job.PipelinerJob method) add_optional_int_setting() (pipeliner.user_settings.Settings method) add_optional_string_setting() (pipeliner.user_settings.Settings method) add_output_node() (pipeliner.pipeliner_job.PipelinerJob method) add_path_list_setting() (pipeliner.user_settings.Settings method) add_process() (pipeliner.project_graph.ProjectGraph method) add_qsub_extra_settings() (pipeliner.user_settings.Settings method) add_string_setting() (pipeliner.user_settings.Settings method) add_to_node_display_file() (in module pipeliner.nodes) add_to_node_summary_list() (in module pipeliner.nodes) additional_joboption_validation() (pipeliner.pipeliner_job.PipelinerJob method)

alias (pipeliner.pipeliner_job.PipelinerJob attribute) (pipeliner.process.Process attribute) alias_checks() (pipeliner.project_graph.ProjectGraph method) all_options_as_dict() (pipeliner.starfile_handler.JobStar method) allow_failure (pipeliner.pipeliner_job.PipelinerCommand attribute) allowed_ext (pipeliner.nodes.GenNodeFormatConverter attribute) alt_dict (pipeliner.deposition_tools.deposition_tools.DepositionObject attribute) alternative_unavailable_reason (pipeliner.pipeliner_job.JobInfo attribute) apix (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute) associated_data (pipeliner.results_display_objects.ResultsDisplayGallery attribute) (pipeliner.results_display_objects.ResultsDisplayGraph attribute) (pipeliner.results_display_objects.ResultsDisplayImage attribute) (pipeliner.results_display_objects.ResultsDisplayImageCarousel attribute) (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) (pipeliner.results_display_objects.ResultsDisplayMontage attribute) (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute) (pipeliner.results_display_objects.ResultsDisplayTable attribute) (pipeliner.results_display_objects.ResultsDisplayText attribute) associated_nodes (pipeliner.results_display_objects.ResultsDisplayGallery attribute) AtomCoordsGroupMetadataNode (class in pipeliner.nodes) AtomCoordsNode (class in pipeliner.nodes) atomic_write_json() (in module pipeliner.utils) authors (pipeliner.pipeliner_job.Ref attribute)

B

bild_files (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) bodycount (pipeliner.starfile_handler.BodyFile attribute)

BodyFile (class in pipeliner.starfile_handler) BooleanJobOption (class in pipeliner.job_options) BoolSettingDefinition (class in pipeliner.user_settings)

C

can_continue (pipeliner.pipeliner_job.JobInfo attribute) category (pipeliner.deposition_tools.deposition_tools.DepositionObject attribute) CATEGORY_LABEL (pipeliner.job_factory.UnavailableJob attribute) (pipeliner.pipeliner_job.PipelinerJob attribute) check_condition_is_met() (pipeliner.job_options.JobOptionCondition method) check_dir() (pipeliner.job_options.DirPathJobOption method) (pipeliner.job_options.JobOption method) check_file() (pipeliner.job_options.ExternalFileJobOption method) (pipeliner.job_options.InputNodeJobOption method) (pipeliner.job_options.JobOption method) (pipeliner.job_options.MultiExternalFileJobOption method) (pipeliner.job_options.MultiInputNodeJobOption method) (pipeliner.job_options.SearchStringJobOption method) check_file_is_cif() (in module pipeliner.nodes) check_file_is_json() (in module pipeliner.nodes) check_file_is_text() (in module pipeliner.nodes) check_for_extra_keys() (pipeliner.user_settings.Settings method) check_for_illegal_symbols() (in module pipeliner.utils) check_funct (pipeliner.nodes.GenNodeFormatConverter attribute) check_joboption_is_now_deactivated() (pipeliner.pipeliner_job.PipelinerJob method) check_joboption_is_now_required() (pipeliner.pipeliner_job.PipelinerJob method) check_multiseries_arguments() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method) check_plottype_list() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method) check_process_completion() (pipeliner.project_graph.ProjectGraph method) check_process_status() (pipeliner.project_graph.ProjectGraph static method) check_qsub_extras() (pipeliner.user_settings.Settings method) check_singleplot_arguments() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method) check_subplot_arguments() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method) clean_dobj_cross_references() (in module pipeliner.deposition_tools.emdb_deposition) clean_job_dirname() (in module pipeliner.utils)

clean_jobname() (in module pipeliner.utils) clean_up_job() (pipeliner.project_graph.ProjectGraph method) cleanup_all() (pipeliner.api.manage_project.PipelinerProject method) cleanup_all_jobs() (pipeliner.project_graph.ProjectGraph method) close() (pipeliner.project_graph.ProjectGraph method) cmd (pipeliner.pipeliner_job.PipelinerCommand attribute) column_as_list() (pipeliner.starfile_handler.StarFile method) column_headers() (pipeliner.starfile_handler.StarFile method) command (pipeliner.pipeliner_job.ExternalProgram attribute) command_history (pipeliner.data_structure.JobInfoData attribute) comments (pipeliner.data_structure.JobInfoData attribute) compare_dicts() (in module pipeliner.utils) compare_job_parameters() (pipeliner.api.manage_project.PipelinerProject method) compare_nested_lists() (in module pipeliner.utils) continuation_joboption_updates() (pipeliner.pipeliner_job.PipelinerJob method) continue_job() (pipeliner.api.manage_project.PipelinerProject method) convert_old_relion_pipeline() (in module pipeliner.starfile_handler) convert_pipeline() (in module pipeliner.api.manage_project) convert_relative_filename() (in module pipeliner.utils) count_block() (pipeliner.starfile_handler.StarFile method) count_file_lines() (in module pipeliner.utils) create_archive() (pipeliner.api.manage_project.PipelinerProject method) create_input_nodes() (pipeliner.pipeliner_job.PipelinerJob method) create_job_from_proc() (in module pipeliner.job_factory) create_output_nodes() (pipeliner.pipeliner_job.PipelinerJob method) create_post_run_output_nodes() (pipeliner.pipeliner_job.PipelinerJob method) create_reference_report() (pipeliner.api.manage_project.PipelinerProject method) create_results_display() (pipeliner.pipeliner_job.PipelinerJob method) create_results_display_object() (in module pipeliner.display_tools) created (pipeliner.data_structure.JobInfoData attribute)

D

data (pipeliner.deposition_tools.deposition_tools.DepositionObject attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute) data_series_labels (pipeliner.results_display_objects.ResultsDisplayGraph attribute) date_time_tag() (in module pipeliner.utils) decompose_pipeline_filename() (in module pipeliner.utils) default (pipeliner.user_settings.BoolSettingDefinition attribute) (pipeliner.user_settings.IntSettingDefinition attribute) (pipeliner.user_settings.OptionalIntSettingDefinition attribute) (pipeliner.user_settings.OptionalStringSettingDefinition attribute) (pipeliner.user_settings.PathListSettingDefinition attribute) (pipeliner.user_settings.SettingDefinition attribute) (pipeliner.user_settings.StringSettingDefinition attribute) default_results_display() (pipeliner.nodes.AtomCoordsNode method) (pipeliner.nodes.DensityMapNode method) (pipeliner.nodes.Image2DGroupMetadataNode method) (pipeliner.nodes.Image2DNode method) (pipeliner.nodes.Image2DStackNode method) (pipeliner.nodes.Image3DNode method) (pipeliner.nodes.LogFileNode method) (pipeliner.nodes.Mask2DNode method) (pipeliner.nodes.Mask3DNode method) (pipeliner.nodes.MicrographCoordsGroupNode method) (pipeliner.nodes.MicrographGroupMetadataNode method) (pipeliner.nodes.MicrographMovieGroupMetadataNode method) (pipeliner.nodes.MicrographMovieNode method) (pipeliner.nodes.MicrographNode method) (pipeliner.nodes.MlModelNode method) (pipeliner.nodes.Node method) (pipeliner.nodes.ParticleGroupMetadataNode method) (pipeliner.nodes.TiltSeriesMovieMetadataNode method) (pipeliner.nodes.TomogramGroupMetadataNode method) (pipeliner.nodes.VisualisationScriptNode method)

default_value_string (pipeliner.job_options.JobOption property) delete_all_cleaned_job_files() (in module pipeliner.api.manage_project) delete_all_trashed_job_files() (in module pipeliner.api.manage_project) delete_cleaned_job_files() (in module pipeliner.api.manage_project) delete_job() (pipeliner.api.manage_project.PipelinerProject method) (pipeliner.project_graph.ProjectGraph method) delete_summary_data_archive() (in module pipeliner.api.manage_project) delete_summary_data_metadata_report() (in module pipeliner.api.manage_project) delete_summary_data_reference_report() (in module pipeliner.api.manage_project) delete_temp_node_file() (pipeliner.project_graph.ProjectGraph method) delete_temp_node_files() (pipeliner.project_graph.ProjectGraph method) delete_trashed_job_files() (in module pipeliner.api.manage_project) DensityMapGroupMetadataNode (class in pipeliner.nodes) DensityMapMetadataNode (class in pipeliner.nodes) DensityMapNode (class in pipeliner.nodes) DepositionObject (class in pipeliner.deposition_tools.deposition_tools) dimx (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute) dimy (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute) DirectoryBasedLock (class in pipeliner.utils) DirPathJobOption (class in pipeliner.job_options) display_data (pipeliner.results_display_objects.ResultsDisplayText attribute) display_name (pipeliner.pipeliner_job.JobInfo attribute) dobj_type (pipeliner.results_display_objects.ResultsDisplayObject attribute) documentation (pipeliner.pipeliner_job.JobInfo attribute) doi (pipeliner.pipeliner_job.Ref attribute) dtype (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)

E

edit_comment() (pipeliner.api.manage_project.PipelinerProject method) edit_jobstar() (in module pipeliner.api.api_utils) emdb_categories (pipeliner.pipeliner_job.ExternalProgram attribute) empty_trash() (pipeliner.api.manage_project.PipelinerProject static method) env_vars (pipeliner.user_settings.SettingDefinition attribute) EulerAnglesNode (class in pipeliner.nodes)

evaluate_qsub_template() (pipeliner.pipeliner_job.PipelinerJob method) EvaluationMetricNode (class in pipeliner.nodes) exe_path (pipeliner.pipeliner_job.ExternalProgram attribute) ext (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute) ExternalFileJobOption (class in pipeliner.job_options) ExternalProgram (class in pipeliner.pipeliner_job)

F

file (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute) file_in_project() (in module pipeliner.utils) file_name (pipeliner.starfile_handler.StarFile attribute) file_path (pipeliner.results_display_objects.ResultsDisplayJson attribute) (pipeliner.results_display_objects.ResultsDisplayPdfFile attribute) (pipeliner.results_display_objects.ResultsDisplayTextFile attribute) FileDescription (class in pipeliner.job_options) find_common_string() (in module pipeliner.utils) find_immediate_child_processes() (pipeliner.project_graph.ProjectGraph method) find_job_by_comment() (pipeliner.api.manage_project.PipelinerProject method)

find_node() (pipeliner.project_graph.ProjectGraph method) find_process() (pipeliner.project_graph.ProjectGraph method) find_summary_file() (pipeliner.nodes.Node method) fix_reserved_words() (in module pipeliner.starfile_handler) flag (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) (pipeliner.results_display_objects.ResultsDisplayObject attribute) FloatJobOption (class in pipeliner.job_options) format (pipeliner.nodes.Node attribute) format_converter (pipeliner.nodes.Node attribute) format_for_metadata() (in module pipeliner.metadata_tools) format_string_to_type_objs() (in module pipeliner.utils)

G

gather_metadata() (pipeliner.pipeliner_job.PipelinerJob method) gen_nodetype() (pipeliner.nodes.GenNodeFormatConverter method) generalise_format() (pipeliner.nodes.Node method) generate_multiseries_plots() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method) generate_subplots() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method) GenNodeFormatConverter (class in pipeliner.nodes) get_additional_program_paths() (in module pipeliner.user_settings) get_additional_reference_info() (pipeliner.pipeliner_job.PipelinerJob method) get_archives_list_from_summary_file() (in module pipeliner.api.manage_project) get_aretomo_executable() (in module pipeliner.user_settings) get_batchtomo_executable() (in module pipeliner.user_settings) get_block() (pipeliner.starfile_handler.StarFile method) get_block_names() (pipeliner.starfile_handler.StarFile method) get_bool() (pipeliner.user_settings.Settings method) get_boolean() (pipeliner.job_options.BooleanJobOption method) (pipeliner.job_options.JobOption method) get_category_label() (pipeliner.pipeliner_job.PipelinerJob method) get_ccpem_share_dir() (in module pipeliner.user_settings) get_citation_data() (in module pipeliner.deposition_tools.empiar_deposition) get_cleaned_up_jobs_and_sizes() (in module pipeliner.api.manage_project) get_commands() (pipeliner.pipeliner_job.PipelinerJob method) get_commands_and_nodes() (in module pipeliner.api.manage_project) get_continuation_job() (pipeliner.api.manage_project.PipelinerProject method) get_cryocare_executables_dir() (in module pipeliner.user_settings) get_ctffind_executable() (in module pipeliner.user_settings) get_current_output_nodes() (pipeliner.pipeliner_job.PipelinerJob method) get_default_nrmpi() (in module pipeliner.user_settings) get_default_nrthreads() (in module pipeliner.user_settings) get_default_params_dict() (pipeliner.pipeliner_job.PipelinerJob method) get_deleted_jobs_and_sizes() (in module pipeliner.api.manage_project) get_deposition_objects_empiar() (in module pipeliner.deposition_tools.empiar_deposition) get_deposition_objs_emdb() (in module pipeliner.deposition_tools.emdb_deposition) get_directory_info() (in module pipeliner.utils) get_directory_size() (in module pipeliner.utils) get_downstream_network() (pipeliner.project_graph.ProjectGraph method) get_dynamight_executable() (in module pipeliner.user_settings) get_extra_options() (pipeliner.pipeliner_job.PipelinerJob method) get_file_size_mb() (in module pipeliner.utils) get_final_command() (pipeliner.pipeliner_job.PipelinerCommand method) get_gctf_executable() (in module pipeliner.user_settings) get_image_metadata() (pipeliner.nodes.DensityMapGroupMetadataNode method) (pipeliner.nodes.DensityMapMetadataNode method) (pipeliner.nodes.DensityMapNode method) (pipeliner.nodes.MicrographCoordsGroupNode method) (pipeliner.nodes.MicrographGroupMetadataNode method) (pipeliner.nodes.MicrographMovieGroupMetadataNode method) (pipeliner.nodes.Node method) (pipeliner.nodes.TiltSeriesGroupMetadataNode method) (pipeliner.nodes.TiltSeriesMovieNode method) get_image_metadata_from_node() (in module pipeliner.api.manage_project) get_imgfile_info() (in module pipeliner.deposition_tools.empiar_deposition_objects) get_input_nodes() (pipeliner.job_options.InputNodeJobOption method) (pipeliner.job_options.JobOption method) (pipeliner.job_options.MultiInputNodeJobOption method) get_int() (pipeliner.user_settings.Settings method) get_job() (pipeliner.api.manage_project.PipelinerProject method) get_job_from_entrypoint() (in module pipeliner.job_factory) get_job_info() (in module pipeliner.api.api_utils) get_job_metadata() (in module pipeliner.metadata_tools) get_job_number() (in module pipeliner.utils) get_job_runner_command() (in module pipeliner.utils) get_job_script() (in module pipeliner.utils) get_job_subdirs() (pipeliner.pipeliner_job.PipelinerJob method) get_job_types() (in module pipeliner.job_factory) get_joboption_groups() (pipeliner.pipeliner_job.PipelinerJob method) get_list() (pipeliner.job_options.JobOption method) (pipeliner.job_options.MultiStringJobOption method) (pipeliner.job_options.SearchStringJobOption method) (pipeliner.user_settings.Settings method) get_metadata_chain() (in module pipeliner.metadata_tools) get_metadata_reports_from_summary_file() (in module pipeliner.api.manage_project) get_minimum_dedicated() (in module pipeliner.user_settings)

get_modelangelo_executable() (in module pipeliner.user_settings) get_modelcraft_executable() (in module pipeliner.user_settings) get_most_recent_processing_depobjs() (in module pipeliner.deposition_tools.emdb_deposition) get_motioncor2_executable() (in module pipeliner.user_settings) get_mpi_command() (pipeliner.pipeliner_job.PipelinerJob method) get_mpi_max() (in module pipeliner.user_settings) get_mpirun_command() (in module pipeliner.user_settings) get_mrc_map_header_string() (in module pipeliner.utils) get_mrc_map_summary() (in module pipeliner.utils) get_next_resultsfile_name() (in module pipeliner.results_display_objects) get_node_name() (pipeliner.project_graph.ProjectGraph static method) get_node_results_display_file_name() (in module pipeliner.nodes) get_node_summary_file_from_list() (in module pipeliner.nodes) get_nr_mpi() (pipeliner.pipeliner_job.PipelinerJob method) get_nr_threads() (pipeliner.pipeliner_job.PipelinerJob method) get_number() (pipeliner.job_options.FloatJobOption method) (pipeliner.job_options.IntJobOption method) (pipeliner.job_options.JobOption method) get_optional_int() (pipeliner.user_settings.Settings method) get_optional_string() (pipeliner.user_settings.Settings method) get_ordered_classes_arrays() (in module pipeliner.display_tools) get_particle_box_size_from_starfile() (in module pipeliner.starfile_handler) get_path_to_source_files() (in module pipeliner.user_settings) get_percentile_from_emdb_json() (in module pipeliner.utils) get_pipeline_edges() (pipeliner.project_graph.ProjectGraph method) get_pipeliner_root() (in module pipeliner.utils) get_pixel_size_from_starfile() (in module pipeliner.starfile_handler) get_project_procs_list() (pipeliner.project_graph.ProjectGraph method) get_python_command() (in module pipeliner.utils) get_qsub_command() (in module pipeliner.user_settings) get_qsub_extra_count() (in module pipeliner.user_settings) get_qsub_extras() (in module pipeliner.user_settings) (pipeliner.user_settings.Settings method) get_qsub_template() (in module pipeliner.user_settings) get_queue_name() (in module pipeliner.user_settings) get_queue_use() (in module pipeliner.user_settings) get_ref_reports_from_summary_file() (in module pipeliner.api.manage_project) get_regenerate_results_command() (in module pipeliner.utils) get_resmap_executable() (in module pipeliner.user_settings) get_result_display_object() (pipeliner.nodes.Node method) get_runtab_options() (pipeliner.pipeliner_job.PipelinerJob method) get_scratch_dir() (in module pipeliner.user_settings) get_setting_value() (pipeliner.user_settings.Settings method) get_starfile_loop_headers() (in module pipeliner.starfile_handler) get_string() (pipeliner.job_options.JobOption method) (pipeliner.user_settings.Settings method) get_summary_file_name() (pipeliner.nodes.Node method) get_summary_string() (pipeliner.nodes.AtomCoordsNode method) (pipeliner.nodes.DensityMapNode method) (pipeliner.nodes.Image2DNode method) (pipeliner.nodes.Image2DStackNode method) (pipeliner.nodes.Image3DNode method) (pipeliner.nodes.Mask2DNode method) (pipeliner.nodes.Mask3DNode method) (pipeliner.nodes.MicrographMovieNode method) (pipeliner.nodes.MicrographNode method) (pipeliner.nodes.Node method) (pipeliner.nodes.VisualisationScriptNode method) get_thread_max() (in module pipeliner.user_settings) get_topaz_executable() (in module pipeliner.user_settings) get_unique_basenames() (in module pipeliner.utils) get_upstream_network() (pipeliner.project_graph.ProjectGraph method) get_value_from_string() (pipeliner.user_settings.BoolSettingDefinition static method) (pipeliner.user_settings.IntSettingDefinition static method) (pipeliner.user_settings.OptionalIntSettingDefinition static method) (pipeliner.user_settings.OptionalStringSettingDefinition static method) (pipeliner.user_settings.PathListSettingDefinition static method) (pipeliner.user_settings.SettingDefinition static method) (pipeliner.user_settings.StringSettingDefinition static method) get_version() (pipeliner.pipeliner_job.ExternalProgram method) get_warning_local_mpi() (in module pipeliner.user_settings) get_whole_project_network() (pipeliner.project_graph.ProjectGraph method) graph_from_starfile_cols() (in module pipeliner.display_tools)

H

handle_doppio_uploads() (pipeliner.pipeliner_job.PipelinerJob method) header_tooltips (pipeliner.results_display_objects.ResultsDisplayTable attribute) headers (pipeliner.results_display_objects.ResultsDisplayTable attribute) headtype (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute)

histogram_from_starfile_col() (in module pipeliner.display_tools) history (pipeliner.data_structure.JobInfoData attribute) html_dir (pipeliner.results_display_objects.ResultsDisplayHtml attribute) html_file (pipeliner.results_display_objects.ResultsDisplayHtml attribute) html_str (pipeliner.results_display_objects.ResultsDisplayHtml attribute)

I

Image2DGroupMetadataNode (class in pipeliner.nodes) Image2DMetadataNode (class in pipeliner.nodes) Image2DNode (class in pipeliner.nodes) Image2DStackNode (class in pipeliner.nodes) Image3DGroupMetadataNode (class in pipeliner.nodes) Image3DMetadataNode (class in pipeliner.nodes) Image3DNode (class in pipeliner.nodes) image_desc (pipeliner.results_display_objects.ResultsDisplayImage attribute) image_index_file (pipeliner.results_display_objects.ResultsDisplayImageCarousel attribute) image_names (pipeliner.results_display_objects.ResultsDisplayImageCarousel attribute) image_path (pipeliner.results_display_objects.ResultsDisplayImage attribute) images (pipeliner.results_display_objects.ResultsDisplayGallery attribute) img (pipeliner.results_display_objects.ResultsDisplayMontage attribute) input_for_processes_list (pipeliner.nodes.Node attribute)

input_nodes (pipeliner.pipeliner_job.PipelinerJob attribute) (pipeliner.process.Process attribute) InputNodeJobOption (class in pipeliner.job_options) interconvert_box_star_coords() (in module pipeliner.starfile_handler) IntJobOption (class in pipeliner.job_options) IntSettingDefinition (class in pipeliner.user_settings) is_available (pipeliner.pipeliner_job.JobInfo property) is_blank (pipeliner.job_options.JobOption property) is_continue (pipeliner.pipeliner_job.PipelinerJob attribute) (pipeliner.starfile_handler.JobStar attribute) is_submit_to_queue() (pipeliner.pipeliner_job.PipelinerJob method) is_tomo (pipeliner.pipeliner_job.PipelinerJob attribute) (pipeliner.starfile_handler.JobStar attribute) is_uuid4() (in module pipeliner.utils) issue (pipeliner.pipeliner_job.Ref attribute)

J

job_author (pipeliner.pipeliner_job.JobInfo attribute) job_can_run() (in module pipeliner.job_factory) job_counter (pipeliner.project_graph.ProjectGraph attribute) job_default_parameters_dict() (in module pipeliner.api.api_utils) job_directory (pipeliner.data_structure.JobInfoData attribute) job_from_dict() (in module pipeliner.job_factory) JobInfo (class in pipeliner.pipeliner_job) jobinfo (pipeliner.pipeliner_job.PipelinerJob attribute) JobInfoData (class in pipeliner.data_structure) JobOption (class in pipeliner.job_options) joboption_type (pipeliner.job_options.BooleanJobOption attribute) (pipeliner.job_options.DirPathJobOption attribute) (pipeliner.job_options.ExternalFileJobOption attribute) (pipeliner.job_options.FloatJobOption attribute) (pipeliner.job_options.InputNodeJobOption attribute) (pipeliner.job_options.IntJobOption attribute) (pipeliner.job_options.JobOption attribute) (pipeliner.job_options.MultiExternalFileJobOption attribute) (pipeliner.job_options.MultiInputNodeJobOption attribute) (pipeliner.job_options.MultipleChoiceJobOption attribute) (pipeliner.job_options.MultiStringJobOption attribute) (pipeliner.job_options.SearchStringJobOption attribute) (pipeliner.job_options.StringJobOption attribute)

JobOptionCondition (class in pipeliner.job_options) joboptions (pipeliner.pipeliner_job.PipelinerJob attribute) (pipeliner.starfile_handler.JobStar attribute) JobOptionValidationResult (class in pipeliner.job_options) JobStar (class in pipeliner.starfile_handler) jobtype (pipeliner.starfile_handler.JobStar attribute) journal (pipeliner.pipeliner_job.Ref attribute)

K

kwds (pipeliner.nodes.Node attribute)

L

labels (pipeliner.results_display_objects.ResultsDisplayGallery attribute) (pipeliner.results_display_objects.ResultsDisplayMontage attribute) launch_detached_process() (in module pipeliner.utils) LigandDescriptionNode (class in pipeliner.nodes) load_results_display_file() (pipeliner.nodes.Node method)

load_results_display_files() (pipeliner.pipeliner_job.PipelinerJob method) LogFileNode (class in pipeliner.nodes) long_desc (pipeliner.pipeliner_job.JobInfo attribute) look_for_project() (in module pipeliner.api.manage_project) loop_as_list() (pipeliner.starfile_handler.StarFile method)

M

make_additional_args() (pipeliner.pipeliner_job.PipelinerJob method) make_atomic_model_summary() (in module pipeliner.utils) make_em_software_depobj() (in module pipeliner.deposition_tools.emdb_deposition_objects) make_final_emdb_deposition_objects() (pipeliner.pipeliner_job.PipelinerJob method) make_image_carousel() (in module pipeliner.display_tools) make_job_parameters_schema() (in module pipeliner.metadata_tools) make_job_results_schema() (in module pipeliner.metadata_tools) make_map_model_thumb_and_display() (in module pipeliner.display_tools) make_maps_slice_montage_and_3d_display() (in module pipeliner.display_tools) make_mollweide_angular_distribution() (in module pipeliner.display_tools) make_moorhen_display() (in module pipeliner.display_tools) make_mrcs_central_slices_montage() (in module pipeliner.display_tools) make_particle_coords_thumb() (in module pipeliner.display_tools) make_pretty_header() (in module pipeliner.utils) make_pretty_size() (in module pipeliner.utils) make_queue_options() (pipeliner.pipeliner_job.PipelinerJob method) make_substitutions() (pipeliner.starfile_handler.JobStar method) maps (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) maps_colours (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) maps_data (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) maps_opacity (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) Mask2DNode (class in pipeliner.nodes) Mask3DNode (class in pipeliner.nodes) merge_empiar_dep_objs() (in module pipeliner.deposition_tools.empiar_deposition) message (pipeliner.job_options.JobOptionValidationResult attribute) Micrograph (class in pipeliner.deposition_tools.empiar_deposition_objects) MicrographCoordsGroupNode (class in pipeliner.nodes) MicrographCoordsNode (class in pipeliner.nodes) MicrographGroupMetadataNode (class in pipeliner.nodes) MicrographMetadataNode (class in pipeliner.nodes) MicrographMovieGroupMetadataNode (class in pipeliner.nodes) MicrographMovieMetadataNode (class in pipeliner.nodes) MicrographMovieNode (class in pipeliner.nodes) MicrographNode (class in pipeliner.nodes) MicroscopeDataNode (class in pipeliner.nodes) mini_montage_from_many_files() (in module pipeliner.display_tools)

mini_montage_from_stack() (in module pipeliner.display_tools) mini_montage_from_starfile() (in module pipeliner.display_tools) MlModelNode (class in pipeliner.nodes) models (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) models_colours (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) models_data (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) modes (pipeliner.results_display_objects.ResultsDisplayGraph attribute) modify() (pipeliner.starfile_handler.JobStar method) module pipeliner.api.api_utils pipeliner.api.manage_project pipeliner.data_structure pipeliner.deposition_tools.deposition_tools pipeliner.deposition_tools.emdb_deposition pipeliner.deposition_tools.emdb_deposition_objects pipeliner.deposition_tools.empiar_deposition pipeliner.deposition_tools.empiar_deposition_objects pipeliner.display_tools pipeliner.job_factory pipeliner.job_manager pipeliner.job_options pipeliner.metadata_tools pipeliner.nodes pipeliner.pipeliner_job pipeliner.process pipeliner.project_graph pipeliner.results_display_objects pipeliner.scripts.job_runner pipeliner.star_writer pipeliner.starfile_handler pipeliner.user_settings pipeliner.utils MultiExternalFileJobOption (class in pipeliner.job_options) MultiInputNodeJobOption (class in pipeliner.job_options) MultipleChoiceJobOption (class in pipeliner.job_options) MultiStringJobOption (class in pipeliner.job_options)

N

n_frames (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute) name (pipeliner.nodes.Node attribute) (pipeliner.pipeliner_job.ExternalProgram attribute) (pipeliner.process.Process attribute) (pipeliner.project_graph.ProjectGraph property) (pipeliner.user_settings.SettingDefinition attribute)

new_job_of_type() (in module pipeliner.job_factory) Node (class in pipeliner.nodes) node_list (pipeliner.project_graph.ProjectGraph attribute) not_compatible_with_default_output() (pipeliner.nodes.Node method)

O

OPERATORS (pipeliner.job_options.JobOptionCondition attribute) OptimiserDataNode (class in pipeliner.nodes) OptionalIntSettingDefinition (class in pipeliner.user_settings) OptionalStringSettingDefinition (class in pipeliner.user_settings) other_metadata (pipeliner.pipeliner_job.Ref attribute)

OUT_DIR (pipeliner.pipeliner_job.PipelinerJob attribute) outdir (pipeliner.process.Process attribute) output_dir (pipeliner.pipeliner_job.PipelinerJob attribute) output_from_process (pipeliner.nodes.Node attribute) output_nodes (pipeliner.pipeliner_job.PipelinerJob attribute) (pipeliner.process.Process attribute)

P

pages (pipeliner.pipeliner_job.Ref attribute) pairs_as_dict() (pipeliner.starfile_handler.StarFile method) ParamsDataNode (class in pipeliner.nodes) parent_job (pipeliner.deposition_tools.deposition_tools.DepositionObject attribute) parse_additional_args() (pipeliner.pipeliner_job.PipelinerJob method) parse_empiar_jobstar() (in module pipeliner.deposition_tools.empiar_deposition) parse_onedep_cif() (in module pipeliner.deposition_tools.deposition_tools) parse_proclist() (pipeliner.api.manage_project.PipelinerProject method) parse_procname() (pipeliner.api.manage_project.PipelinerProject method) ParticleGroupMetadataNode (class in pipeliner.nodes) PathListSettingDefinition (class in pipeliner.user_settings) pipeline_dir (pipeliner.project_graph.ProjectGraph property) pipeline_name (pipeliner.api.manage_project.PipelinerProject attribute) pipeliner.api.api_utils module pipeliner.api.manage_project module pipeliner.data_structure module pipeliner.deposition_tools.deposition_tools module pipeliner.deposition_tools.emdb_deposition module pipeliner.deposition_tools.emdb_deposition_objects module pipeliner.deposition_tools.empiar_deposition module pipeliner.deposition_tools.empiar_deposition_objects module pipeliner.display_tools module pipeliner.job_factory module pipeliner.job_manager module pipeliner.job_options module pipeliner.metadata_tools module pipeliner.nodes module pipeliner.pipeliner_job module pipeliner.process module

pipeliner.project_graph module pipeliner.results_display_objects module pipeliner.scripts.job_runner module pipeliner.star_writer module pipeliner.starfile_handler module pipeliner.user_settings module pipeliner.utils module PipelinerCommand (class in pipeliner.pipeliner_job) PipelinerJob (class in pipeliner.pipeliner_job) PipelinerProject (class in pipeliner.api.manage_project) plot_type (pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute) plotlyfig (pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute) prepare_clean_up_lists() (pipeliner.pipeliner_job.PipelinerJob method) prepare_deposition() (pipeliner.api.manage_project.PipelinerProject static method) prepare_emdb_deposition() (in module pipeliner.deposition_tools.emdb_deposition) prepare_emdb_deposition_data() (pipeliner.pipeliner_job.PipelinerJob method) prepare_empiar_corrparts() (in module pipeliner.deposition_tools.empiar_deposition_objects) prepare_empiar_deposition() (in module pipeliner.deposition_tools.empiar_deposition) prepare_empiar_deposition_data() (pipeliner.pipeliner_job.PipelinerJob method) prepare_empiar_mics() (in module pipeliner.deposition_tools.empiar_deposition_objects) prepare_empiar_mics_parts_data() (in module pipeliner.deposition_tools.empiar_deposition_objects) prepare_empiar_parts() (in module pipeliner.deposition_tools.empiar_deposition_objects) prepare_empiar_raw_mics() (in module pipeliner.deposition_tools.empiar_deposition_objects) prepare_for_continuation() (pipeliner.pipeliner_job.PipelinerJob method) prepare_metadata_report() (pipeliner.api.manage_project.PipelinerProject method) prepare_to_run() (pipeliner.pipeliner_job.PipelinerJob method) print_nice_columns() (in module pipeliner.utils) Process (class in pipeliner.process) process_list (pipeliner.project_graph.ProjectGraph attribute) PROCESS_NAME (pipeliner.pipeliner_job.PipelinerJob attribute) ProcessDataNode (class in pipeliner.nodes) programs (pipeliner.pipeliner_job.JobInfo attribute) ProjectGraph (class in pipeliner.project_graph) ProjectMetadataNode (class in pipeliner.nodes)

Q

quotate_starfile_line() (in module pipeliner.starfile_handler)

R

raised_by (pipeliner.job_options.JobOptionValidationResult attribute) raw_options (pipeliner.pipeliner_job.PipelinerJob attribute) read() (pipeliner.pipeliner_job.PipelinerJob method) read_job() (in module pipeliner.job_factory) read_only (pipeliner.project_graph.ProjectGraph property) read_relion_optimiser_starfile() (in module pipeliner.starfile_handler) Ref (class in pipeliner.pipeliner_job) references (pipeliner.pipeliner_job.JobInfo attribute) release() (pipeliner.utils.DirectoryBasedLock method) relion_control (pipeliner.pipeliner_job.PipelinerCommand attribute) relion_joboption_conversion() (pipeliner.pipeliner_job.PipelinerJob method) remake_node_directory() (pipeliner.project_graph.ProjectGraph method) remove_from_node_display_file() (in module pipeliner.nodes) remove_from_node_summary_list() (in module pipeliner.nodes) remove_md_from_summary_data() (in module pipeliner.metadata_tools) remove_nonexistent_nodes() (pipeliner.process.Process method) restore_all_cleaned_up_files() (pipeliner.api.manage_project.PipelinerProject method) restore_cleaned_up_files() (pipeliner.project_graph.ProjectGraph method) restore_from_cleanup() (pipeliner.api.manage_project.PipelinerProject method) RestraintsNode (class in pipeliner.nodes) ResultsDisplayGallery (class in pipeliner.results_display_objects) ResultsDisplayGraph (class in pipeliner.results_display_objects) ResultsDisplayHistogram (class in pipeliner.results_display_objects) ResultsDisplayHtml (class in pipeliner.results_display_objects) ResultsDisplayImage (class in pipeliner.results_display_objects) ResultsDisplayImageCarousel (class in pipeliner.results_display_objects)

ResultsDisplayJson (class in pipeliner.results_display_objects) ResultsDisplayMapModel (class in pipeliner.results_display_objects) ResultsDisplayMontage (class in pipeliner.results_display_objects) ResultsDisplayMoorhen (class in pipeliner.results_display_objects) ResultsDisplayObject (class in pipeliner.results_display_objects) ResultsDisplayPdfFile (class in pipeliner.results_display_objects) ResultsDisplayPending (class in pipeliner.results_display_objects) ResultsDisplayPlotlyFigure (class in pipeliner.results_display_objects) ResultsDisplayPlotlyHistogram (class in pipeliner.results_display_objects) ResultsDisplayPlotlyObj (class in pipeliner.results_display_objects) ResultsDisplayPlotlyScatter (class in pipeliner.results_display_objects) ResultsDisplayRvapi (class in pipeliner.results_display_objects) ResultsDisplayTable (class in pipeliner.results_display_objects) ResultsDisplayText (class in pipeliner.results_display_objects) ResultsDisplayTextFile (class in pipeliner.results_display_objects) RigidBodiesNode (class in pipeliner.nodes) run() (pipeliner.job_manager.ScheduleRunner method) run_cleanup() (pipeliner.api.manage_project.PipelinerProject method) run_job() (in module pipeliner.job_manager) (pipeliner.api.manage_project.PipelinerProject method) run_repeat() (pipeliner.job_manager.ScheduleRunner method) run_schedule() (in module pipeliner.job_manager) (pipeliner.api.manage_project.PipelinerProject method) run_scheduled_job() (in module pipeliner.job_manager) (pipeliner.api.manage_project.PipelinerProject method) run_subprocess() (in module pipeliner.utils) rvapi_dir (pipeliner.results_display_objects.ResultsDisplayRvapi attribute)

S

save_job_submission_script() (pipeliner.pipeliner_job.PipelinerJob method) save_results_display_files() (pipeliner.pipeliner_job.PipelinerJob method) schedule_continue_job() (pipeliner.api.manage_project.PipelinerProject method) schedule_fail() (pipeliner.job_manager.ScheduleRunner method) schedule_job() (in module pipeliner.job_manager) (pipeliner.api.manage_project.PipelinerProject method) ScheduleRunner (class in pipeliner.job_manager) SearchStringJobOption (class in pipeliner.job_options) SequenceAlignmentNode (class in pipeliner.nodes) SequenceGroupNode (class in pipeliner.nodes) SequenceNode (class in pipeliner.nodes) session_file (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) set_alias() (pipeliner.api.manage_project.PipelinerProject method) set_job_alias() (pipeliner.project_graph.ProjectGraph method) set_joboption_order() (pipeliner.pipeliner_job.PipelinerJob method) set_multiplot_data() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method) set_option() (pipeliner.pipeliner_job.PipelinerJob method) set_singleplot_data() (pipeliner.results_display_objects.ResultsDisplayPlotlyObj method) SettingDefinition (class in pipeliner.user_settings) Settings (class in pipeliner.user_settings) short_desc (pipeliner.pipeliner_job.JobInfo attribute) sort_depobjs_by_type() (in module pipeliner.deposition_tools.emdb_deposition) spherical_aberration (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute) star_file (pipeliner.project_graph.ProjectGraph property) star_quote() (in module pipeliner.star_writer)

StarFile (class in pipeliner.starfile_handler) start_collapsed (pipeliner.results_display_objects.ResultsDisplayGallery attribute) (pipeliner.results_display_objects.ResultsDisplayGraph attribute) (pipeliner.results_display_objects.ResultsDisplayHtml attribute) (pipeliner.results_display_objects.ResultsDisplayImage attribute) (pipeliner.results_display_objects.ResultsDisplayImageCarousel attribute) (pipeliner.results_display_objects.ResultsDisplayJson attribute) (pipeliner.results_display_objects.ResultsDisplayMontage attribute) (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) (pipeliner.results_display_objects.ResultsDisplayObject attribute) (pipeliner.results_display_objects.ResultsDisplayPdfFile attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute) (pipeliner.results_display_objects.ResultsDisplayRvapi attribute) (pipeliner.results_display_objects.ResultsDisplayTable attribute) (pipeliner.results_display_objects.ResultsDisplayText attribute) (pipeliner.results_display_objects.ResultsDisplayTextFile attribute) status (pipeliner.process.Process attribute) stop_schedule() (pipeliner.api.manage_project.PipelinerProject method) str_is_hex_colour() (in module pipeliner.utils) StringJobOption (class in pipeliner.job_options) StringSettingDefinition (class in pipeliner.user_settings) StructureFactorsNode (class in pipeliner.nodes) subprocess_popen() (in module pipeliner.utils)

T

table_data (pipeliner.results_display_objects.ResultsDisplayTable attribute) temp_EMDB_deposition_object_alterations() (in module pipeliner.deposition_tools.emdb_deposition) TiltSeriesGroupMetadataNode (class in pipeliner.nodes) TiltSeriesMetadataNode (class in pipeliner.nodes) TiltSeriesMovieGroupMetadataNode (class in pipeliner.nodes) TiltSeriesMovieMetadataNode (class in pipeliner.nodes) TiltSeriesMovieNode (class in pipeliner.nodes) TiltSeriesNode (class in pipeliner.nodes) title (pipeliner.pipeliner_job.Ref attribute) (pipeliner.results_display_objects.ResultsDisplayGallery attribute) (pipeliner.results_display_objects.ResultsDisplayGraph attribute) (pipeliner.results_display_objects.ResultsDisplayImage attribute) (pipeliner.results_display_objects.ResultsDisplayImageCarousel attribute) (pipeliner.results_display_objects.ResultsDisplayMapModel attribute) (pipeliner.results_display_objects.ResultsDisplayMontage attribute) (pipeliner.results_display_objects.ResultsDisplayMoorhen attribute) (pipeliner.results_display_objects.ResultsDisplayObject attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyHistogram attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyObj attribute) (pipeliner.results_display_objects.ResultsDisplayPlotlyScatter attribute) (pipeliner.results_display_objects.ResultsDisplayTable attribute) (pipeliner.results_display_objects.ResultsDisplayText attribute)

TomogramGroupMetadataNode (class in pipeliner.nodes) TomogramMetadataNode (class in pipeliner.nodes) TomogramNode (class in pipeliner.nodes) TomoManifoldDataNode (class in pipeliner.nodes) TomoOptimisationSetNode (class in pipeliner.nodes) TomoTrajectoryDataNode (class in pipeliner.nodes) toplevel_description (pipeliner.nodes.Node attribute) toplevel_type (pipeliner.nodes.Node attribute) touch() (in module pipeliner.utils) touch_temp_node_file() (pipeliner.project_graph.ProjectGraph method) touch_temp_node_files() (pipeliner.project_graph.ProjectGraph method) truncate_number() (in module pipeliner.utils) type (pipeliner.job_options.JobOptionValidationResult attribute) (pipeliner.nodes.Node attribute) (pipeliner.process.Process attribute)

U

unavailable_message (pipeliner.pipeliner_job.JobInfo property) UnavailableJob (class in pipeliner.job_factory) undelete_all_trashed_jobs() (pipeliner.api.manage_project.PipelinerProject method) undelete_job() (pipeliner.api.manage_project.PipelinerProject method) (pipeliner.project_graph.ProjectGraph method) update_and_format_deposition_objects() (in module pipeliner.deposition_tools.emdb_deposition)

update_job_pipeline_file() (pipeliner.project_graph.ProjectGraph static method) update_job_status() (pipeliner.api.manage_project.PipelinerProject method) update_jobinfo_file() (in module pipeliner.utils) update_lock_message() (pipeliner.project_graph.ProjectGraph method) update_status() (pipeliner.project_graph.ProjectGraph method) uuid (pipeliner.deposition_tools.deposition_tools.DepositionObject attribute)

V

validate() (pipeliner.job_options.DirPathJobOption method) (pipeliner.job_options.ExternalFileJobOption method) (pipeliner.job_options.FloatJobOption method) (pipeliner.job_options.InputNodeJobOption method) (pipeliner.job_options.IntJobOption method) (pipeliner.job_options.JobOption method) (pipeliner.job_options.MultiExternalFileJobOption method) (pipeliner.job_options.MultiInputNodeJobOption method) (pipeliner.job_options.MultipleChoiceJobOption method) (pipeliner.job_options.MultiStringJobOption method) (pipeliner.job_options.SearchStringJobOption method) (pipeliner.job_options.StringJobOption method) validate_depobj_data() (pipeliner.deposition_tools.deposition_tools.DepositionObject method)

validate_dynamically_required_joboptions() (pipeliner.pipeliner_job.PipelinerJob method) validate_input_files() (pipeliner.pipeliner_job.PipelinerJob method) validate_joboptions() (pipeliner.pipeliner_job.PipelinerJob method) validate_pipeline_file() (pipeliner.project_graph.ProjectGraph method) validate_runtab_joboptions() (pipeliner.pipeliner_job.PipelinerJob method) validate_starfile() (in module pipeliner.api.api_utils) value (pipeliner.job_options.JobOption property) value_string (pipeliner.job_options.JobOption property) vers_com (pipeliner.pipeliner_job.ExternalProgram attribute) vers_lines (pipeliner.pipeliner_job.ExternalProgram attribute) version (pipeliner.pipeliner_job.JobInfo attribute) VisualisationScriptNode (class in pipeliner.nodes) voltage (pipeliner.deposition_tools.empiar_deposition_objects.Micrograph attribute) volume (pipeliner.pipeliner_job.Ref attribute)

W

wait_for_job_to_finish() (in module pipeliner.job_manager) (pipeliner.api.manage_project.PipelinerProject method) working_dir (pipeliner.pipeliner_job.PipelinerJob attribute) wrap_text() (in module pipeliner.utils) write() (in module pipeliner.star_writer) (pipeliner.starfile_handler.JobStar method) write_cleanuplog() (pipeliner.project_graph.ProjectGraph static method) write_default_jobstar() (in module pipeliner.api.api_utils) write_default_result_file() (pipeliner.nodes.Node method) write_default_runjob() (in module pipeliner.api.api_utils) write_deposition_complete_cif() (in module pipeliner.deposition_tools.emdb_deposition)

write_deposition_onedep_cif() (in module pipeliner.deposition_tools.emdb_deposition) write_displayobj_file() (pipeliner.results_display_objects.ResultsDisplayObject method) (pipeliner.results_display_objects.ResultsDisplayPlotlyFigure method) write_jobstar() (in module pipeliner.star_writer) (pipeliner.pipeliner_job.PipelinerJob method) write_runjob() (pipeliner.pipeliner_job.PipelinerJob method) write_script_json() (in module pipeliner.utils) write_summary_file() (pipeliner.nodes.Node method) write_summary_string_as_text_file() (pipeliner.nodes.Node method) write_to_sched_log() (pipeliner.job_manager.ScheduleRunner method) write_to_stream() (in module pipeliner.star_writer)

X

xaxis_label (pipeliner.results_display_objects.ResultsDisplayGraph attribute) xrange (pipeliner.results_display_objects.ResultsDisplayGraph attribute)

xvalues (pipeliner.results_display_objects.ResultsDisplayGraph attribute) (pipeliner.results_display_objects.ResultsDisplayMontage attribute)

Y

yaxis_label (pipeliner.results_display_objects.ResultsDisplayGraph attribute) year (pipeliner.pipeliner_job.Ref attribute)

yrange (pipeliner.results_display_objects.ResultsDisplayGraph attribute) yvalues (pipeliner.results_display_objects.ResultsDisplayGraph attribute) (pipeliner.results_display_objects.ResultsDisplayMontage attribute)