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OptionKeys.cc.gen0.hh File Reference

Namespaces

 in
 
 in::dbms
 
 in::path
 
 in::file
 
 in::rdf
 
 inout
 
 inout::dbms
 
 out
 
 out::file
 
 out::path
 

Functions

BooleanOptionKey const in::in ("in")
 
FileVectorOptionKey const in::fconfig ("in:fconfig")
 
BooleanOptionKey const in::no_fconfig ("in:no_fconfig")
 
BooleanOptionKey const in::skip_classic_cart_setup ("in:skip_classic_cart_setup")
 
BooleanOptionKey const in::skip_new_cart_setup ("in:skip_new_cart_setup")
 
StringOptionKey const in::Ntermini ("in:Ntermini")
 
StringOptionKey const in::Ctermini ("in:Ctermini")
 
BooleanOptionKey const in::use_truncated_termini ("in:use_truncated_termini")
 
BooleanOptionKey const in::ignore_unrecognized_res ("in:ignore_unrecognized_res")
 
BooleanOptionKey const in::ignore_waters ("in:ignore_waters")
 
StringOptionKey const in::water_type_if_unspecified ("in:water_type_if_unspecified")
 
BooleanOptionKey const in::guarantee_no_DNA ("in:guarantee_no_DNA")
 
BooleanOptionKey const in::add_orbitals ("in:add_orbitals")
 
BooleanOptionKey const in::show_all_fixes ("in:show_all_fixes")
 
BooleanOptionKey const in::include_sugars ("in:include_sugars")
 
BooleanOptionKey const in::include_lipids ("in:include_lipids")
 
BooleanOptionKey const in::include_surfaces ("in:include_surfaces")
 
BooleanOptionKey const in::read_only_ATOM_entries ("in:read_only_ATOM_entries")
 
BooleanOptionKey const in::auto_detect_glycan_connections ("in:auto_detect_glycan_connections")
 
RealOptionKey const in::max_bond_length ("in:max_bond_length")
 
RealOptionKey const in::min_bond_length ("in:min_bond_length")
 
RealOptionKey const in::glycan_virtual_offset ("in:glycan_virtual_offset")
 
BooleanOptionKey const in::membrane ("in:membrane")
 
BooleanOptionKey const in::remember_unrecognized_res ("in:remember_unrecognized_res")
 
BooleanOptionKey const in::remember_unrecognized_water ("in:remember_unrecognized_water")
 
BooleanOptionKey const in::preserve_crystinfo ("in:preserve_crystinfo")
 
BooleanOptionKey const in::detect_oops ("in:detect_oops")
 
BooleanOptionKey const in::detect_disulf ("in:detect_disulf")
 
RealOptionKey const in::detect_disulf_tolerance ("in:detect_disulf_tolerance")
 
BooleanOptionKey const in::constraints_from_link_records ("in:constraints_from_link_records")
 
BooleanOptionKey const in::auto_setup_metals ("in:auto_setup_metals")
 
BooleanOptionKey const in::prevent_auto_setup_metal_bb_variants ("in:prevent_auto_setup_metal_bb_variants")
 
RealOptionKey const in::metals_detection_LJ_multiplier ("in:metals_detection_LJ_multiplier")
 
RealOptionKey const in::metals_distance_constraint_multiplier ("in:metals_distance_constraint_multiplier")
 
RealOptionKey const in::metals_angle_constraint_multiplier ("in:metals_angle_constraint_multiplier")
 
StringVectorOptionKey const in::name3_property_codes ("in:name3_property_codes")
 
StringVectorOptionKey const in::alternate_3_letter_codes ("in:alternate_3_letter_codes")
 
BooleanOptionKey const in::maintain_links ("in:maintain_links")
 
FileOptionKey const in::fix_disulf ("in:fix_disulf")
 
BooleanOptionKey const in::missing_density_to_jump ("in:missing_density_to_jump")
 
IntegerVectorOptionKey const in::target_residues ("in:target_residues")
 
IntegerVectorOptionKey const in::replonly_residues ("in:replonly_residues")
 
BooleanOptionKey const in::replonly_loops ("in:replonly_loops")
 
BooleanOptionKey const in::use_database ("in:use_database")
 
StringVectorOptionKey const in::select_structures_from_database ("in:select_structures_from_database")
 
BooleanOptionKey const in::dbms::dbms ("in:dbms")
 
StringVectorOptionKey const in::dbms::struct_ids ("in:dbms:struct_ids")
 
PathVectorOptionKey const in::path::path ("in:path")
 
PathVectorOptionKey const in::path::fragments ("in:path:fragments")
 
PathVectorOptionKey const in::path::pdb ("in:path:pdb")
 
PathVectorOptionKey const in::path::database ("in:path:database")
 
PathOptionKey const in::path::database_cache_dir ("in:path:database_cache_dir")
 
BooleanOptionKey const in::file::file ("in:file")
 
FileVectorOptionKey const in::file::s ("in:file:s")
 
FileVectorOptionKey const in::file::t ("in:file:t")
 
FileVectorOptionKey const in::file::l ("in:file:l")
 
FileOptionKey const in::file::job_definition_file ("in:file:job_definition_file")
 
FileVectorOptionKey const in::file::list ("in:file:list")
 
BooleanOptionKey const in::file::srlz ("in:file:srlz")
 
BooleanOptionKey const in::file::srlz_override ("in:file:srlz_override")
 
FileVectorOptionKey const in::file::screening_list ("in:file:screening_list")
 
FileOptionKey const in::file::screening_job_file ("in:file:screening_job_file")
 
BooleanOptionKey const in::file::shuffle_screening_jobs ("in:file:shuffle_screening_jobs")
 
FileOptionKey const in::file::native ("in:file:native")
 
FileOptionKey const in::file::torsion_bin_probs ("in:file:torsion_bin_probs")
 
FileOptionKey const in::file::PCS_frag_cst ("in:file:PCS_frag_cst")
 
FileOptionKey const in::file::talos_phi_psi ("in:file:talos_phi_psi")
 
FileOptionKey const in::file::talos_cs ("in:file:talos_cs")
 
FileOptionKey const in::file::ambig_talos_cs_A ("in:file:ambig_talos_cs_A")
 
FileOptionKey const in::file::ambig_talos_cs_B ("in:file:ambig_talos_cs_B")
 
IntegerVectorOptionKey const in::file::native_exclude_res ("in:file:native_exclude_res")
 
BooleanOptionKey const in::file::no_detect_pseudobonds ("in:file:no_detect_pseudobonds")
 
StringVectorOptionKey const in::file::tags ("in:file:tags")
 
StringVectorOptionKey const in::file::user_tags ("in:file:user_tags")
 
FileOptionKey const in::file::tagfile ("in:file:tagfile")
 
FileVectorOptionKey const in::file::frag_files ("in:file:frag_files")
 
StringVectorOptionKey const in::file::remap_pdb_atom_names_for ("in:file:remap_pdb_atom_names_for")
 
FileVectorOptionKey const in::file::extra_res ("in:file:extra_res")
 
FileVectorOptionKey const in::file::extra_res_fa ("in:file:extra_res_fa")
 
FileVectorOptionKey const in::file::extra_res_mol ("in:file:extra_res_mol")
 
FileVectorOptionKey const in::file::extra_res_mmCIF ("in:file:extra_res_mmCIF")
 
BooleanOptionKey const in::file::load_PDB_components ("in:file:load_PDB_components")
 
StringOptionKey const in::file::PDB_components_directory ("in:file:PDB_components_directory")
 
StringVectorOptionKey const in::file::PDB_components_overrides ("in:file:PDB_components_overrides")
 
BooleanOptionKey const in::file::check_all_PDB_components ("in:file:check_all_PDB_components")
 
StringOptionKey const in::file::extra_res_database ("in:file:extra_res_database")
 
StringOptionKey const in::file::extra_res_pq_schema ("in:file:extra_res_pq_schema")
 
StringOptionKey const in::file::extra_res_database_mode ("in:file:extra_res_database_mode")
 
FileOptionKey const in::file::extra_res_database_resname_list ("in:file:extra_res_database_resname_list")
 
FileVectorOptionKey const in::file::extra_res_cen ("in:file:extra_res_cen")
 
PathVectorOptionKey const in::file::extra_res_path ("in:file:extra_res_path")
 
PathVectorOptionKey const in::file::extra_rot_lib_path ("in:file:extra_rot_lib_path")
 
PathVectorOptionKey const in::file::override_rot_lib_path ("in:file:override_rot_lib_path")
 
PathVectorOptionKey const in::file::extra_res_batch_path ("in:file:extra_res_batch_path")
 
FileVectorOptionKey const in::file::extra_patch_fa ("in:file:extra_patch_fa")
 
FileVectorOptionKey const in::file::extra_patch_cen ("in:file:extra_patch_cen")
 
StringOptionKey const in::file::frag3 ("in:file:frag3")
 
StringOptionKey const in::file::frag9 ("in:file:frag9")
 
StringOptionKey const in::file::fragA ("in:file:fragA")
 
StringOptionKey const in::file::fragB ("in:file:fragB")
 
StringOptionKey const in::file::surface_vectors ("in:file:surface_vectors")
 
StringOptionKey const in::file::xyz ("in:file:xyz")
 
BooleanOptionKey const in::file::keep_input_scores ("in:file:keep_input_scores")
 
BooleanOptionKey const in::file::lazy_silent ("in:file:lazy_silent")
 
FileVectorOptionKey const in::file::silent ("in:file:silent")
 
BooleanOptionKey const in::file::force_silent_bitflip_on_read ("in:file:force_silent_bitflip_on_read")
 
FileVectorOptionKey const in::file::atom_tree_diff ("in:file:atom_tree_diff")
 
StringOptionKey const in::file::zip ("in:file:zip")
 
FileVectorOptionKey const in::file::boinc_wu_zip ("in:file:boinc_wu_zip")
 
BooleanOptionKey const in::file::fullatom ("in:file:fullatom")
 
BooleanOptionKey const in::file::centroid_input ("in:file:centroid_input")
 
BooleanOptionKey const in::file::centroid ("in:file:centroid")
 
BooleanOptionKey const in::file::assign_gasteiger_atom_types ("in:file:assign_gasteiger_atom_types")
 
StringOptionKey const in::file::treat_residues_in_these_chains_as_separate_chemical_entities ("in:file:treat_residues_in_these_chains_as_separate_chemical_entities")
 
StringOptionKey const in::file::residue_type_set ("in:file:residue_type_set")
 
FileOptionKey const in::file::pca ("in:file:pca")
 
RealOptionKey const in::file::silent_energy_cut ("in:file:silent_energy_cut")
 
FileVectorOptionKey const in::file::silent_list ("in:file:silent_list")
 
BooleanOptionKey const in::file::silent_renumber ("in:file:silent_renumber")
 
StringOptionKey const in::file::silent_struct_type ("in:file:silent_struct_type")
 
BooleanOptionKey const in::file::silent_read_through_errors ("in:file:silent_read_through_errors")
 
StringOptionKey const in::file::silent_score_prefix ("in:file:silent_score_prefix")
 
IntegerOptionKey const in::file::silent_select_random ("in:file:silent_select_random")
 
IntegerOptionKey const in::file::silent_select_range_start ("in:file:silent_select_range_start")
 
IntegerOptionKey const in::file::silent_select_range_mul ("in:file:silent_select_range_mul")
 
IntegerOptionKey const in::file::silent_select_range_len ("in:file:silent_select_range_len")
 
BooleanOptionKey const in::file::skip_failed_simulations ("in:file:skip_failed_simulations")
 
StringVectorOptionKey const in::file::silent_scores_wanted ("in:file:silent_scores_wanted")
 
FileVectorOptionKey const in::file::fasta ("in:file:fasta")
 
FileVectorOptionKey const in::file::pssm ("in:file:pssm")
 
StringVectorOptionKey const in::file::seq ("in:file:seq")
 
FileOptionKey const in::file::checkpoint ("in:file:checkpoint")
 
FileOptionKey const in::file::binary_chk ("in:file:binary_chk")
 
FileVectorOptionKey const in::file::alignment ("in:file:alignment")
 
FileVectorOptionKey const in::file::alignment2 ("in:file:alignment2")
 
FileOptionKey const in::file::rama2b_map ("in:file:rama2b_map")
 
FileOptionKey const in::file::psipred_ss2 ("in:file:psipred_ss2")
 
FileOptionKey const in::file::dssp ("in:file:dssp")
 
BooleanOptionKey const in::file::fail_on_bad_hbond ("in:file:fail_on_bad_hbond")
 
FileOptionKey const in::file::movemap ("in:file:movemap")
 
BooleanOptionKey const in::file::repair_sidechains ("in:file:repair_sidechains")
 
BooleanOptionKey const in::file::no_binary_dunlib ("in:file:no_binary_dunlib")
 
IntegerOptionKey const in::file::extended_pose ("in:file:extended_pose")
 
FileVectorOptionKey const in::file::template_pdb ("in:file:template_pdb")
 
FileOptionKey const in::file::template_silent ("in:file:template_silent")
 
FileVectorOptionKey const in::file::rdc ("in:file:rdc")
 
FileVectorOptionKey const in::file::csa ("in:file:csa")
 
FileVectorOptionKey const in::file::dc ("in:file:dc")
 
FileVectorOptionKey const in::file::burial ("in:file:burial")
 
FileOptionKey const in::file::hrf_ms_labeling ("in:file:hrf_ms_labeling")
 
FileVectorOptionKey const in::file::vall ("in:file:vall")
 
BooleanOptionKey const in::file::rescore ("in:file:rescore")
 
StringOptionKey const in::file::spanfile ("in:file:spanfile")
 
StringOptionKey const in::file::lipofile ("in:file:lipofile")
 
StringOptionKey const in::file::HDX ("in:file:HDX")
 
RealOptionKey const in::file::d2h_sa_reweight ("in:file:d2h_sa_reweight")
 
FileOptionKey const in::file::sucker_params ("in:file:sucker_params")
 
FileOptionKey const in::file::fold_tree ("in:file:fold_tree")
 
BooleanOptionKey const in::file::obey_ENDMDL ("in:file:obey_ENDMDL")
 
BooleanOptionKey const in::file::new_chain_order ("in:file:new_chain_order")
 
FileOptionKey const in::file::ddg_predictions_file ("in:file:ddg_predictions_file")
 
ResidueChainVectorOptionKey const in::file::input_res ("in:file:input_res")
 
IntegerVectorOptionKey const in::file::minimize_res ("in:file:minimize_res")
 
StringOptionKey const in::file::md_schfile ("in:file:md_schfile")
 
FileOptionKey const in::file::native_contacts ("in:file:native_contacts")
 
BooleanOptionKey const in::rdf::rdf ("in:rdf")
 
BooleanOptionKey const in::rdf::sep_bb_ss ("in:rdf:sep_bb_ss")
 
BooleanOptionKey const inout::inout ("inout")
 
BooleanOptionKey const inout::fold_tree_io ("inout:fold_tree_io")
 
BooleanOptionKey const inout::skip_connect_info ("inout:skip_connect_info")
 
BooleanOptionKey const inout::write_all_connect_info ("inout:write_all_connect_info")
 
RealOptionKey const inout::connect_info_cutoff ("inout:connect_info_cutoff")
 
BooleanOptionKey const inout::mmtf_extra_data_io ("inout:mmtf_extra_data_io")
 
BooleanOptionKey const inout::output_alternate_atomids ("inout:output_alternate_atomids")
 
BooleanOptionKey const inout::dbms::dbms ("inout:dbms")
 
StringOptionKey const inout::dbms::mode ("inout:dbms:mode")
 
StringOptionKey const inout::dbms::database_name ("inout:dbms:database_name")
 
StringOptionKey const inout::dbms::pq_schema ("inout:dbms:pq_schema")
 
StringOptionKey const inout::dbms::host ("inout:dbms:host")
 
StringOptionKey const inout::dbms::user ("inout:dbms:user")
 
StringOptionKey const inout::dbms::password ("inout:dbms:password")
 
IntegerOptionKey const inout::dbms::port ("inout:dbms:port")
 
BooleanOptionKey const inout::dbms::readonly ("inout:dbms:readonly")
 
BooleanOptionKey const inout::dbms::separate_db_per_mpi_process ("inout:dbms:separate_db_per_mpi_process")
 
IntegerOptionKey const inout::dbms::database_partition ("inout:dbms:database_partition")
 
BooleanOptionKey const inout::dbms::use_compact_residue_schema ("inout:dbms:use_compact_residue_schema")
 
BooleanOptionKey const inout::dbms::retry_failed_reads ("inout:dbms:retry_failed_reads")
 
PathOptionKey const inout::dbms::path ("inout:dbms:path")
 
BooleanOptionKey const out::out ("out")
 
BooleanOptionKey const out::overwrite ("out:overwrite")
 
IntegerOptionKey const out::nstruct ("out:nstruct")
 
IntegerOptionKey const out::shuffle_nstruct ("out:shuffle_nstruct")
 
StringOptionKey const out::prefix ("out:prefix")
 
StringOptionKey const out::suffix ("out:suffix")
 
BooleanOptionKey const out::mover_controlled_output_name ("out:mover_controlled_output_name")
 
BooleanOptionKey const out::no_nstruct_label ("out:no_nstruct_label")
 
BooleanOptionKey const out::pdb_gz ("out:pdb_gz")
 
BooleanOptionKey const out::pdb ("out:pdb")
 
BooleanOptionKey const out::silent_gz ("out:silent_gz")
 
BooleanOptionKey const out::membrane_pdb ("out:membrane_pdb")
 
RealOptionKey const out::membrane_pdb_thickness ("out:membrane_pdb_thickness")
 
BooleanOptionKey const out::mmCIF ("out:mmCIF")
 
BooleanOptionKey const out::mmCIF_gz ("out:mmCIF_gz")
 
BooleanOptionKey const out::mmtf ("out:mmtf")
 
BooleanOptionKey const out::mmtf_gz ("out:mmtf_gz")
 
BooleanOptionKey const out::use_database ("out:use_database")
 
IntegerOptionKey const out::database_protocol_id ("out:database_protocol_id")
 
StringVectorOptionKey const out::database_filter ("out:database_filter")
 
IntegerVectorOptionKey const out::resume_batch ("out:resume_batch")
 
BooleanOptionKey const out::nooutput ("out:nooutput")
 
BooleanOptionKey const out::output ("out:output")
 
RealOptionKey const out::scorecut ("out:scorecut")
 
BooleanOptionKey const out::show_accessed_options ("out:show_accessed_options")
 
BooleanOptionKey const out::show_unused_options ("out:show_unused_options")
 
FileOptionKey const out::sf ("out:sf")
 
StringVectorOptionKey const out::mute ("out:mute")
 
StringVectorOptionKey const out::unmute ("out:unmute")
 
IntegerOptionKey const out::level ("out:level")
 
StringVectorOptionKey const out::levels ("out:levels")
 
BooleanOptionKey const out::no_color ("out:no_color")
 
BooleanOptionKey const out::chname ("out:chname")
 
BooleanOptionKey const out::chtimestamp ("out:chtimestamp")
 
BooleanOptionKey const out::dry_run ("out:dry_run")
 
StringOptionKey const out::mpi_tracer_to_file ("out:mpi_tracer_to_file")
 
IntegerOptionKey const out::std_IO_exit_error_code ("out:std_IO_exit_error_code")
 
StringOptionKey const out::user_tag ("out:user_tag")
 
StringOptionKey const out::output_tag ("out:output_tag")
 
BooleanOptionKey const out::save_times ("out:save_times")
 
BooleanOptionKey const out::file::file ("out:file")
 
StringOptionKey const out::file::o ("out:file:o")
 
FileOptionKey const out::file::design_contrast ("out:file:design_contrast")
 
StringOptionKey const out::file::residue_type_set ("out:file:residue_type_set")
 
BooleanOptionKey const out::file::srlz ("out:file:srlz")
 
StringOptionKey const out::file::atom_tree_diff ("out:file:atom_tree_diff")
 
IntegerOptionKey const out::file::atom_tree_diff_bb ("out:file:atom_tree_diff_bb")
 
IntegerOptionKey const out::file::atom_tree_diff_sc ("out:file:atom_tree_diff_sc")
 
IntegerOptionKey const out::file::atom_tree_diff_bl ("out:file:atom_tree_diff_bl")
 
StringOptionKey const out::file::alignment ("out:file:alignment")
 
StringOptionKey const out::file::score_only ("out:file:score_only")
 
StringOptionKey const out::file::scorefile ("out:file:scorefile")
 
StringOptionKey const out::file::scorefile_format ("out:file:scorefile_format")
 
StringOptionKey const out::file::silent ("out:file:silent")
 
StringOptionKey const out::file::silent_struct_type ("out:file:silent_struct_type")
 
BooleanOptionKey const out::file::silent_print_all_score_headers ("out:file:silent_print_all_score_headers")
 
BooleanOptionKey const out::file::raw ("out:file:raw")
 
BooleanOptionKey const out::file::weight_silent_scores ("out:file:weight_silent_scores")
 
BooleanOptionKey const out::file::silent_preserve_H ("out:file:silent_preserve_H")
 
BooleanOptionKey const out::file::fullatom ("out:file:fullatom")
 
BooleanOptionKey const out::file::suppress_zero_occ_pdb_output ("out:file:suppress_zero_occ_pdb_output")
 
BooleanOptionKey const out::file::output_ligands_as_separate_chains ("out:file:output_ligands_as_separate_chains")
 
BooleanOptionKey const out::file::output_virtual ("out:file:output_virtual")
 
BooleanOptionKey const out::file::output_virtual_zero_occ ("out:file:output_virtual_zero_occ")
 
BooleanOptionKey const out::file::no_chainend_ter ("out:file:no_chainend_ter")
 
BooleanOptionKey const out::file::no_output_cen ("out:file:no_output_cen")
 
BooleanOptionKey const out::file::output_orbitals ("out:file:output_orbitals")
 
BooleanOptionKey const out::file::renumber_pdb ("out:file:renumber_pdb")
 
BooleanOptionKey const out::file::pdb_parents ("out:file:pdb_parents")
 
BooleanOptionKey const out::file::per_chain_renumbering ("out:file:per_chain_renumbering")
 
BooleanOptionKey const out::file::output_secondary_structure ("out:file:output_secondary_structure")
 
BooleanOptionKey const out::file::do_not_autoassign_SS ("out:file:do_not_autoassign_SS")
 
BooleanOptionKey const out::file::output_torsions ("out:file:output_torsions")
 
BooleanOptionKey const out::file::use_occurrence_data ("out:file:use_occurrence_data")
 
BooleanOptionKey const out::file::pdb_comments ("out:file:pdb_comments")
 
BooleanOptionKey const out::file::force_nonideal_structure ("out:file:force_nonideal_structure")
 
StringOptionKey const out::file::set_pdb_author ("out:file:set_pdb_author")
 
BooleanOptionKey const out::file::write_pdb_title_section_records ("out:file:write_pdb_title_section_records")
 
BooleanOptionKey const out::file::write_pdb_link_records ("out:file:write_pdb_link_records")
 
BooleanOptionKey const out::file::use_pdb_format_HETNAM_records ("out:file:use_pdb_format_HETNAM_records")
 
BooleanOptionKey const out::file::write_pdb_parametric_info ("out:file:write_pdb_parametric_info")
 
BooleanOptionKey const out::file::write_glycan_pdb_codes ("out:file:write_glycan_pdb_codes")
 
BooleanOptionKey const out::file::write_seqres_records ("out:file:write_seqres_records")
 
BooleanOptionKey const out::file::output_pose_energies_table ("out:file:output_pose_energies_table")
 
BooleanOptionKey const out::file::output_pose_cache_data ("out:file:output_pose_cache_data")
 
BooleanOptionKey const out::file::output_pose_fold_tree ("out:file:output_pose_fold_tree")
 
BooleanOptionKey const out::file::output_only_asymmetric_unit ("out:file:output_only_asymmetric_unit")
 
BooleanOptionKey const out::file::cif_extra_data_separate_file ("out:file:cif_extra_data_separate_file")
 
BooleanOptionKey const out::file::dont_rewrite_dunbrack_database ("out:file:dont_rewrite_dunbrack_database")
 
StringOptionKey const out::file::frag_prefix ("out:file:frag_prefix")
 
BooleanOptionKey const out::file::no_extra_sdf_data ("out:file:no_extra_sdf_data")
 
BooleanOptionKey const out::file::no_scores_in_pdb ("out:file:no_scores_in_pdb")
 
PathOptionKey const out::path::all ("out:path:all")
 
PathOptionKey const out::path::path ("out:path")
 
PathOptionKey const out::path::pdb ("out:path:pdb")
 
PathOptionKey const out::path::db ("out:path:db")
 
PathOptionKey const out::path::score ("out:path:score")
 
PathOptionKey const out::path::scratch ("out:path:scratch")
 
BooleanOptionKey const out::path::mpi_rank_dir ("out:path:mpi_rank_dir")