add_option(utility::options::OptionKey const &key) | protocols::jd3::standard::StandardJobQueen | protected |
add_options(utility::options::OptionKeyList const &opts) | protocols::jd3::standard::StandardJobQueen | protected |
all_settings_to_defualt() | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
allow_pose_inputter(pose_inputters::PoseInputterCreatorOP creator) | protocols::jd3::standard::StandardJobQueen | protected |
allow_pose_outputter(pose_outputters::PoseOutputterCreatorOP creator) | protocols::jd3::standard::StandardJobQueen | protected |
append_common_tag_subelements(utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaComplexTypeGenerator &ct_gen) const override | protocols::multistage_rosetta_scripts::MRSJobQueen | protectedvirtual |
append_job_tag_subelements(utility::tag::XMLSchemaDefinition &job_definition_xsd, utility::tag::XMLSchemaComplexTypeGenerator &job_ct_gen) const override | protocols::multistage_rosetta_scripts::MRSJobQueen | protectedvirtual |
assign_output_index(jd3::LarvalJobCOP larval_job, jd3::ResultIndex result_index_for_job, core::Size n_results_for_job, jd3::JobOutputIndex &output_index) override | protocols::multistage_rosetta_scripts::MRSJobQueen | protectedvirtual |
assign_output_index(jd3::GlobalJobID global_job_id, jd3::ResultIndex result_id, jd3::JobOutputIndex &output_index) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
build_output_index(protocols::jd3::LarvalJobCOP larval_job, ResultIndex result_index_for_job, Size n_results_for_job) | protocols::jd3::standard::StandardJobQueen | protected |
checkpoints_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
cluster(jd3::JobDAGNodeID stage_about_to_start) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
cluster_data_for_results_of_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
cluster_metric_tag_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
common_block_tags() const | protocols::jd3::standard::StandardJobQueen | protected |
complete_larval_job_maturation(jd3::LarvalJobCOP larval_job, utility::options::OptionCollectionCOP job_options, utility::vector1< jd3::JobResultCOP > const &input_job_results) override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
completed_job_summary(jd3::GlobalJobID job_id, jd3::ResultIndex result_index, jd3::JobSummaryOP summary) | protocols::multistage_rosetta_scripts::MRSJobQueen | |
completed_job_summary(jd3::LarvalJobCOP job, jd3::ResultIndex result_index, jd3::JobSummaryOP summary) override | protocols::multistage_rosetta_scripts::MRSJobQueen | inlinevirtual |
create_and_init_inner_larval_job_from_preliminary(core::Size nstruct, PrelimJobNodeID prelim_job_node, JobDAGNodeID job_node) const | protocols::jd3::standard::StandardJobQueen | protected |
create_and_set_initial_job_dag() | protocols::jd3::JobQueen | |
create_and_store_output_specification_for_job_result(LarvalJobCOP job, ResultIndex result_index, core::Size nresults) | protocols::jd3::standard::StandardJobQueen | protected |
create_and_store_output_specification_for_job_result(LarvalJobCOP job, utility::options::OptionCollection const &job_options, ResultIndex result_index, core::Size nresults) | protocols::jd3::standard::StandardJobQueen | protected |
create_initial_job_dag() override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
create_inner_larval_job(core::Size nstruct, JobDAGNodeID job_node, PrelimJobNodeID preliminary_job_node) const | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
create_larval_job(InnerLarvalJobOP job, NStructIndex nstruct_index, core::Size larval_job_index) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
create_output_specification_for_job_result(LarvalJobCOP job, utility::options::OptionCollection const &job_options, ResultIndex result_index, core::Size nresults) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
current_inner_larval_job_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
current_job_index() const | protocols::jd3::standard::StandardJobQueen | protected |
deallocation_messages() override | protocols::jd3::standard::StandardJobQueen | virtual |
derived_process_deallocation_message(deallocation::DeallocationMessageOP message) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
determine_job_list(jd3::JobDAGNodeID job_dag_node_index, Size max_njobs) override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
determine_job_list_and_track(JobDAGNodeID job_dag_node_index, Size max_njobs) | protocols::jd3::JobQueen | |
determine_preliminary_job_list() | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
determine_preliminary_job_list_from_xml_file(std::string const &job_def_string) | protocols::jd3::standard::StandardJobQueen | |
determine_validity_of_stage_tags() | protocols::multistage_rosetta_scripts::MRSJobQueen | |
do_not_accept_all_pose_inputters_from_factory() | protocols::jd3::standard::StandardJobQueen | protected |
do_not_accept_all_pose_outputters_from_factory() | protocols::jd3::standard::StandardJobQueen | protected |
expand_job_list(InnerLarvalJobOP inner_job, core::Size max_larval_jobs_to_create) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
flush() override | protocols::jd3::standard::StandardJobQueen | virtual |
get_job_graph() const | protocols::jd3::JobQueen | protected |
get_job_tracker() | protocols::jd3::JobQueen | protected |
get_job_tracker() const | protocols::jd3::JobQueen | protected |
get_nth_job_for_initial_stage(jd3::LocalJobID local_job_id) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
get_nth_job_for_noninitial_stage(jd3::JobDAGNodeID stage, jd3::LocalJobID local_job_id) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
get_prelim_larval_job_tracker() | protocols::jd3::standard::StandardJobQueen | protected |
get_prelim_larval_job_tracker() const | protocols::jd3::standard::StandardJobQueen | protected |
get_preliminary_larval_jobs() const | protocols::jd3::standard::StandardJobQueen | protected |
get_preliminary_larval_jobs_determined() const | protocols::jd3::standard::StandardJobQueen | protected |
has_been_initialized_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
has_job_previously_been_output(protocols::jd3::LarvalJobCOP job) override | protocols::jd3::standard::StandardJobQueen | virtual |
input_job_tags_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
input_pose_id_for_jobid(jd3::GlobalJobID global_jobid) const | protocols::multistage_rosetta_scripts::MRSJobQueen | inlineprotected |
job_def_complex_type_name(std::string const &type) | protocols::jd3::standard::StandardJobQueen | static |
job_definition_xsd() const override | protocols::jd3::standard::StandardJobQueen | virtual |
job_genealogist_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
job_results_have_been_discarded_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
job_results_that_should_be_discarded() override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
job_subelement_mangler(std::string const &name) | protocols::multistage_rosetta_scripts::MRSJobQueen | inlineprotectedstatic |
JobQueen() | protocols::jd3::JobQueen | |
jobs_that_should_be_output() override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
mature_larval_job(protocols::jd3::LarvalJobCOP job, utility::vector1< JobResultCOP > const &input_job_results) override | protocols::jd3::standard::StandardJobQueen | virtual |
max_num_results_to_keep_per_input_struct_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
max_num_results_to_keep_per_instance_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
most_recent_cluster_results_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
most_recent_pose_id_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
MRSJobQueen() | protocols::multistage_rosetta_scripts::MRSJobQueen | |
next_batch_of_larval_jobs_for_job_node(JobDAGNodeID job_dag_node_index, Size max_njobs) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
node_managers_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
note_job_completed(jd3::GlobalJobID job_id, jd3::JobStatus status, core::Size nresults, bool are_you_a_unit_test) | protocols::multistage_rosetta_scripts::MRSJobQueen | |
note_job_completed(core::Size, jd3::JobStatus, core::Size) | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
note_job_completed(jd3::LarvalJobCOP job, jd3::JobStatus status, core::Size nresults) override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
note_job_completed_and_track(LarvalJobCOP job, JobStatus status, Size nresults) | protocols::jd3::JobQueen | |
note_preliminary_job_node_is_complete(PrelimJobNodeID pjn_index) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
num_input_structs() const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
num_input_structs_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
num_jobs_per_input_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
num_results_to_keep_after_clustering_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
num_results_to_keep_for_stage(core::Size stage) const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
num_results_to_keep_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
num_stages() const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
num_stages_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
num_structs_output_for_input_job_tag_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
num_total_jobs_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
options_for_job(InnerLarvalJob const &inner_job) const | protocols::jd3::standard::StandardJobQueen | protected |
options_from_tag(utility::tag::TagCOP job_options_tags) const | protocols::jd3::standard::StandardJobQueen | protected |
outputters_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
parse_common_tag(utility::tag::TagCOP common_tag) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
parse_job_definition_tags(utility::tag::TagCOP common_block_tags, utility::vector1< jd3::standard::PreliminaryLarvalJob > const &) override | protocols::multistage_rosetta_scripts::MRSJobQueen | protectedvirtual |
parse_single_job_tag(jd3::standard::PreliminaryLarvalJob const &prelim_larval_job, jd3::PrelimJobNodeID input_pose_id) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
parse_single_stage_tag(utility::tag::TagCOP subprotocol_tag) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
pose_for_inner_job(InnerLarvalJobCOP inner_job) | protocols::jd3::standard::StandardJobQueen | protected |
pose_for_inner_job(InnerLarvalJobCOP inner_job, utility::options::OptionCollection const &options) | protocols::jd3::standard::StandardJobQueen | protected |
pose_for_inner_job_derived(jd3::InnerLarvalJobCOP inner_job, utility::options::OptionCollection const &options) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
pose_for_job(LarvalJobCOP job, utility::options::OptionCollection const &options) | protocols::jd3::standard::StandardJobQueen | protected |
pose_for_job_derived(jd3::LarvalJobCOP job, utility::options::OptionCollection const &options) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
pose_inputter_for_job(InnerLarvalJob const &inner_job) const | protocols::jd3::standard::StandardJobQueen | protected |
pose_output_specification_for_job_result_id_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
pose_outputter_for_job(InnerLarvalJob const &innerJob) | protocols::jd3::standard::StandardJobQueen | protected |
pose_outputter_for_job(InnerLarvalJob const &innerJob, utility::options::OptionCollection const &job_options) | protocols::jd3::standard::StandardJobQueen | protected |
pose_outputter_for_job(pose_outputters::PoseOutputSpecification const &spec) | protocols::jd3::standard::StandardJobQueen | protected |
print_job_lineage() const | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
process_deallocation_message(deallocation::DeallocationMessageOP message) override | protocols::jd3::standard::StandardJobQueen | virtual |
protocols_subelement_mangler(std::string const &name) | protocols::multistage_rosetta_scripts::MRSJobQueen | inlineprotectedstatic |
refine_preliminary_job(PreliminaryLarvalJob const &prelim_job) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
remove_default_input_element() | protocols::jd3::standard::StandardJobQueen | protected |
resource_definition_xsd() const override | protocols::jd3::standard::StandardJobQueen | virtual |
result_cutoffs_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
result_outputter(output::OutputSpecification const &spec) override | protocols::jd3::standard::StandardJobQueen | virtual |
secondary_outputters_for_job(InnerLarvalJob const &innerJob, utility::options::OptionCollection const &job_options) | protocols::jd3::standard::StandardJobQueen | protected |
set_common_block_precedes_job_blocks(bool setting) | protocols::jd3::standard::StandardJobQueen | inlineprotected |
set_default_outputter(pose_outputters::PoseOutputterCreatorOP creator) | protocols::jd3::standard::StandardJobQueen | protected |
sorter_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
stage_for_global_job_id(jd3::GlobalJobID global_job_id) const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
StandardJobQueen() | protocols::jd3::standard::StandardJobQueen | |
tag_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
tag_manager() const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
tag_manager_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
update_job_dag(JobDigraphUpdater &updater) override | protocols::jd3::standard::StandardJobQueen | virtual |
~JobQueen() override | protocols::jd3::JobQueen | |
~MRSJobQueen() override | protocols::multistage_rosetta_scripts::MRSJobQueen | |
~StandardJobQueen() override | protocols::jd3::standard::StandardJobQueen | |