Rosetta 3.3
Namespaces | Functions
src/basic/options/keys/OptionKeys.cc.gen2.hh File Reference

Namespaces

namespace  lh
namespace  blivens
namespace  blivens::disulfide_scorer
namespace  krassk
namespace  robert
namespace  james
namespace  membrane
namespace  casp
namespace  pose_metrics
namespace  ddg
namespace  murphp
namespace  motifs
namespace  constraints
namespace  dna
namespace  dna::specificity
namespace  dna::design
namespace  dna::design::specificity
namespace  dna::design::reversion
namespace  flxbb
namespace  flxbb::layer
namespace  fldsgn
namespace  rna
namespace  cm
namespace  ms
namespace  ms::checkpoint
namespace  loops
namespace  assembly
namespace  fast_loops
namespace  SSrbrelax
namespace  boinc
namespace  LoopModel
namespace  AnchoredDesign
namespace  AnchoredDesign::filters
namespace  AnchoredDesign::akash
namespace  AnchoredDesign::testing
namespace  DenovoProteinDesign

Functions

StringOptionKey const lh::homo_file ("lh:homo_file")
RealVectorOptionKey const lh::createdb_rms_cutoff ("lh:createdb_rms_cutoff")
RealOptionKey const lh::min_bbrms ("lh:min_bbrms")
RealOptionKey const lh::max_bbrms ("lh:max_bbrms")
RealOptionKey const lh::min_rms ("lh:min_rms")
RealOptionKey const lh::max_rms ("lh:max_rms")
RealOptionKey const lh::grid_space_multiplier ("lh:grid_space_multiplier")
RealOptionKey const lh::grid_angle_multiplier ("lh:grid_angle_multiplier")
IntegerOptionKey const lh::skim_size ("lh:skim_size")
IntegerOptionKey const lh::rounds ("lh:rounds")
StringOptionKey const lh::jobname ("lh:jobname")
IntegerOptionKey const lh::max_lib_size ("lh:max_lib_size")
IntegerOptionKey const lh::max_emperor_lib_size ("lh:max_emperor_lib_size")
IntegerOptionKey const lh::max_emperor_lib_round ("lh:max_emperor_lib_round")
IntegerOptionKey const lh::library_expiry_time ("lh:library_expiry_time")
StringOptionKey const lh::objective_function ("lh:objective_function")
IntegerOptionKey const lh::expire_after_rounds ("lh:expire_after_rounds")
StringOptionKey const lh::mpi_resume ("lh:mpi_resume")
StringOptionKey const lh::mpi_feedback ("lh:mpi_feedback")
IntegerOptionKey const lh::mpi_batch_relax_chunks ("lh:mpi_batch_relax_chunks")
IntegerOptionKey const lh::mpi_batch_relax_absolute_max ("lh:mpi_batch_relax_absolute_max")
IntegerOptionKey const lh::mpi_outbound_wu_buffer_size ("lh:mpi_outbound_wu_buffer_size")
IntegerOptionKey const lh::mpi_loophash_split_size ("lh:mpi_loophash_split_size ")
RealOptionKey const lh::mpi_metropolis_temp ("lh:mpi_metropolis_temp")
IntegerOptionKey const lh::mpi_save_state_interval ("lh:mpi_save_state_interval")
BooleanOptionKey const lh::mpi_master_save_score_only ("lh:mpi_master_save_score_only")
IntegerOptionKey const lh::max_loophash_per_structure ("lh:max_loophash_per_structure")
RealOptionKey const lh::rms_limit ("lh:rms_limit")
BooleanOptionKey const lh::centroid_only ("lh:centroid_only")
BooleanOptionKey const lh::write_centroid_structs ("lh:write_centroid_structs")
BooleanOptionKey const lh::sandbox ("lh:sandbox")
BooleanOptionKey const lh::create_db ("lh:create_db")
BooleanOptionKey const blivens::blivens ("blivens")
BooleanOptionKey const blivens::disulfide_scorer::disulfide_scorer ("blivens:disulfide_scorer")
RealOptionKey const blivens::disulfide_scorer::nds_prob ("blivens:disulfide_scorer:nds_prob")
RealOptionKey const blivens::disulfide_scorer::cys_prob ("blivens:disulfide_scorer:cys_prob")
StringOptionKey const blivens::score_type ("blivens:score_type")
BooleanOptionKey const krassk::krassk ("krassk")
IntegerOptionKey const krassk::left_tail ("krassk:left_tail")
IntegerOptionKey const krassk::right_tail ("krassk:right_tail")
BooleanOptionKey const krassk::tail_mode ("krassk:tail_mode")
IntegerOptionKey const krassk::tail_mode_name ("krassk:tail_mode_name")
StringOptionKey const krassk::tail_output_file_name ("krassk:tail_output_file_name")
BooleanOptionKey const robert::robert ("robert")
StringOptionKey const robert::pairdata_input_pdb_list ("robert:pairdata_input_pdb_list")
RealOptionKey const robert::pcs_maxsub_filter ("robert:pcs_maxsub_filter")
RealOptionKey const robert::pcs_maxsub_rmsd ("robert:pcs_maxsub_rmsd")
BooleanOptionKey const robert::pcs_dump_cluster ("robert:pcs_dump_cluster")
RealOptionKey const robert::pcs_cluster_coverage ("robert:pcs_cluster_coverage")
BooleanOptionKey const robert::pcs_cluster_lowscoring ("robert:pcs_cluster_lowscoring")
BooleanOptionKey const james::james ("james")
IntegerOptionKey const james::min_seqsep ("james:min_seqsep")
StringVectorOptionKey const james::atom_names ("james:atom_names")
RealVectorOptionKey const james::dist_thresholds ("james:dist_thresholds")
RealVectorOptionKey const james::torsion_thresholds ("james:torsion_thresholds")
RealOptionKey const james::sog_cutoff ("james:sog_cutoff")
BooleanOptionKey const james::shift_sog_func ("james:shift_sog_func")
StringOptionKey const james::min_type ("james:min_type")
RealOptionKey const james::min_tol ("james:min_tol")
BooleanOptionKey const james::debug ("james:debug")
RealOptionKey const james::real ("james:real")
IntegerOptionKey const james::n_designs ("james:n_designs")
BooleanOptionKey const james::awesome_mode ("james:awesome_mode")
IntegerOptionKey const james::n_clusters ("james:n_clusters")
BooleanOptionKey const james::thread_unaligned ("james:thread_unaligned")
BooleanOptionKey const membrane::membrane ("membrane")
IntegerOptionKey const membrane::normal_cycles ("membrane:normal_cycles")
RealOptionKey const membrane::normal_mag ("membrane:normal_mag")
RealOptionKey const membrane::center_mag ("membrane:center_mag")
RealOptionKey const membrane::smooth_move_frac ("membrane:smooth_move_frac")
BooleanOptionKey const membrane::no_interpolate_Mpair ("membrane:no_interpolate_Mpair")
BooleanOptionKey const membrane::Menv_penalties ("membrane:Menv_penalties")
BooleanOptionKey const membrane::Membed_init ("membrane:Membed_init")
BooleanOptionKey const membrane::Fa_Membed_update ("membrane:Fa_Membed_update")
BooleanOptionKey const membrane::center_search ("membrane:center_search")
BooleanOptionKey const membrane::normal_search ("membrane:normal_search")
IntegerOptionKey const membrane::center_max_delta ("membrane:center_max_delta")
IntegerOptionKey const membrane::normal_start_angle ("membrane:normal_start_angle")
IntegerOptionKey const membrane::normal_delta_angle ("membrane:normal_delta_angle")
IntegerOptionKey const membrane::normal_max_angle ("membrane:normal_max_angle")
BooleanOptionKey const membrane::debug ("membrane:debug")
BooleanOptionKey const membrane::fixed_membrane ("membrane:fixed_membrane")
RealVectorOptionKey const membrane::membrane_center ("membrane:membrane_center")
RealVectorOptionKey const membrane::membrane_normal ("membrane:membrane_normal")
BooleanOptionKey const membrane::view ("membrane:view")
BooleanOptionKey const membrane::Mhbond_depth ("membrane:Mhbond_depth")
BooleanOptionKey const casp::casp ("casp")
StringOptionKey const casp::decoy ("casp:decoy")
StringOptionKey const casp::wt ("casp:wt")
StringOptionKey const casp::rots ("casp:rots")
RealOptionKey const casp::opt_radius ("casp:opt_radius")
BooleanOptionKey const casp::repack ("casp:repack")
BooleanOptionKey const casp::sc_min ("casp:sc_min")
BooleanOptionKey const casp::sequential ("casp:sequential")
RealOptionKey const casp::num_iterations ("casp:num_iterations")
StringOptionKey const casp::weight_file ("casp:weight_file")
StringOptionKey const casp::refine_res ("casp:refine_res")
BooleanOptionKey const pose_metrics::pose_metrics ("pose_metrics")
RealOptionKey const pose_metrics::atomic_burial_cutoff ("pose_metrics:atomic_burial_cutoff")
RealOptionKey const pose_metrics::sasa_calculator_probe_radius ("pose_metrics:sasa_calculator_probe_radius")
RealOptionKey const pose_metrics::interface_cutoff ("pose_metrics:interface_cutoff")
IntegerOptionKey const pose_metrics::min_sequence_separation ("pose_metrics:min_sequence_separation")
RealOptionKey const pose_metrics::contact_cutoffE ("pose_metrics:contact_cutoffE")
RealOptionKey const pose_metrics::neighbor_by_distance_cutoff ("pose_metrics:neighbor_by_distance_cutoff")
RealOptionKey const pose_metrics::inter_group_neighbors_cutoff ("pose_metrics:inter_group_neighbors_cutoff")
BooleanOptionKey const ddg::ddg ("ddg")
BooleanOptionKey const ddg::avg_rot_cst_enrg ("ddg:avg_rot_cst_enrg")
BooleanOptionKey const ddg::use_bound_cst ("ddg:use_bound_cst")
RealOptionKey const ddg::cap_rot_cst_enrg ("ddg:cap_rot_cst_enrg")
BooleanOptionKey const ddg::opt_input_structure ("ddg:opt_input_structure")
BooleanOptionKey const ddg::pack_until_converge ("ddg:pack_until_converge")
BooleanOptionKey const ddg::no_constraints ("ddg:no_constraints")
RealOptionKey const ddg::apply_rot_cst_to_mutation_region_only ("ddg:apply_rot_cst_to_mutation_region_only")
RealOptionKey const ddg::rot_cst_enrg_cutoff ("ddg:rot_cst_enrg_cutoff")
BooleanOptionKey const ddg::use_rotamer_constraints_to_native ("ddg:use_rotamer_constraints_to_native")
BooleanOptionKey const ddg::single_res_scoring ("ddg:single_res_scoring")
BooleanOptionKey const ddg::downweight_by_sasa ("ddg:downweight_by_sasa")
BooleanOptionKey const ddg::global ("ddg:global")
BooleanOptionKey const ddg::exclude_solvent_exposed_res ("ddg:exclude_solvent_exposed_res")
RealOptionKey const ddg::radius ("ddg:radius")
StringOptionKey const ddg::wt ("ddg:wt")
StringOptionKey const ddg::mut ("ddg:mut")
BooleanOptionKey const ddg::suppress_checkpointing ("ddg:suppress_checkpointing")
BooleanOptionKey const ddg::wt_only ("ddg:wt_only")
BooleanOptionKey const ddg::mut_only ("ddg:mut_only")
BooleanOptionKey const ddg::output_silent ("ddg:output_silent")
StringOptionKey const ddg::minimization_scorefunction ("ddg:minimization_scorefunction")
StringOptionKey const ddg::minimization_patch ("ddg:minimization_patch")
BooleanOptionKey const ddg::min_cst ("ddg:min_cst")
IntegerOptionKey const ddg::lowest_x_decoys ("ddg:lowest_x_decoys")
BooleanOptionKey const ddg::local_opt_only ("ddg:local_opt_only")
BooleanOptionKey const ddg::print_per_res_diff ("ddg:print_per_res_diff")
BooleanOptionKey const ddg::mean ("ddg:mean")
BooleanOptionKey const ddg::min ("ddg:min")
BooleanOptionKey const ddg::rb_restrict_to_mutsite_nbrs ("ddg:rb_restrict_to_mutsite_nbrs")
BooleanOptionKey const ddg::no_bb_movement ("ddg:no_bb_movement")
BooleanOptionKey const ddg::initial_repack ("ddg:initial_repack")
StringOptionKey const ddg::rb_file ("ddg:rb_file")
IntegerOptionKey const ddg::interface_ddg ("ddg:interface_ddg")
RealOptionKey const ddg::ens_variation ("ddg:ens_variation")
BooleanOptionKey const ddg::sc_min_only ("ddg:sc_min_only")
StringOptionKey const ddg::min_cst_weights ("ddg:min_cst_weights")
RealOptionKey const ddg::opt_radius ("ddg:opt_radius")
StringOptionKey const ddg::output_dir ("ddg:output_dir")
StringOptionKey const ddg::last_accepted_pose_dir ("ddg:last_accepted_pose_dir")
BooleanOptionKey const ddg::min_with_cst ("ddg:min_with_cst")
RealOptionKey const ddg::temperature ("ddg:temperature")
BooleanOptionKey const ddg::ramp_repulsive ("ddg:ramp_repulsive")
StringOptionKey const ddg::mut_file ("ddg:mut_file")
StringOptionKey const ddg::out_pdb_prefix ("ddg:out_pdb_prefix")
RealOptionKey const ddg::constraint_weight ("ddg:constraint_weight")
RealOptionKey const ddg::harmonic_ca_tether ("ddg:harmonic_ca_tether")
IntegerOptionKey const ddg::iterations ("ddg:iterations")
StringOptionKey const ddg::out ("ddg:out")
BooleanOptionKey const ddg::debug_output ("ddg:debug_output")
BooleanOptionKey const ddg::dump_pdbs ("ddg:dump_pdbs")
StringOptionKey const ddg::weight_file ("ddg:weight_file")
BooleanOptionKey const murphp::murphp ("murphp")
StringOptionKey const murphp::inv_kin_lig_loop_design_filename ("murphp:inv_kin_lig_loop_design_filename")
BooleanOptionKey const motifs::motifs ("motifs")
RealOptionKey const motifs::close_enough ("motifs:close_enough")
IntegerOptionKey const motifs::max_depth ("motifs:max_depth")
FileVectorOptionKey const motifs::list_motifs ("motifs:list_motifs")
StringOptionKey const motifs::motif_filename ("motifs:motif_filename")
StringOptionKey const motifs::BPData ("motifs:BPData")
FileVectorOptionKey const motifs::list_dnaconformers ("motifs:list_dnaconformers")
StringVectorOptionKey const motifs::target_dna_defs ("motifs:target_dna_defs")
StringVectorOptionKey const motifs::motif_build_defs ("motifs:motif_build_defs")
StringOptionKey const motifs::motif_build_position_chain ("motifs:motif_build_position_chain")
IntegerVectorOptionKey const motifs::motif_build_positions ("motifs:motif_build_positions")
RealOptionKey const motifs::r1 ("motifs:r1")
RealOptionKey const motifs::r2 ("motifs:r2")
RealOptionKey const motifs::z1 ("motifs:z1")
RealOptionKey const motifs::z2 ("motifs:z2")
RealOptionKey const motifs::dtest ("motifs:dtest")
IntegerOptionKey const motifs::rotlevel ("motifs:rotlevel")
IntegerOptionKey const motifs::num_repacks ("motifs:num_repacks")
BooleanOptionKey const motifs::minimize ("motifs:minimize")
BooleanOptionKey const motifs::minimize_dna ("motifs:minimize_dna")
BooleanOptionKey const motifs::run_motifs ("motifs:run_motifs")
BooleanOptionKey const motifs::expand_motifs ("motifs:expand_motifs")
BooleanOptionKey const motifs::dump_motifs ("motifs:dump_motifs")
BooleanOptionKey const motifs::quick_and_dirty ("motifs:quick_and_dirty")
RealOptionKey const motifs::special_rotweight ("motifs:special_rotweight")
StringOptionKey const motifs::output_file ("motifs:output_file")
StringOptionKey const motifs::data_file ("motifs:data_file")
RealOptionKey const motifs::constraint_max ("motifs:constraint_max")
BooleanOptionKey const motifs::flex_sugar ("motifs:flex_sugar")
BooleanOptionKey const motifs::clear_bprots ("motifs:clear_bprots")
IntegerOptionKey const motifs::rots2add ("motifs:rots2add")
RealOptionKey const motifs::ligand_motif_sphere ("motifs:ligand_motif_sphere")
BooleanOptionKey const constraints::constraints ("constraints")
RealOptionKey const constraints::CA_tether ("constraints:CA_tether")
BooleanOptionKey const constraints::exit_on_bad_read ("constraints:exit_on_bad_read")
StringVectorOptionKey const constraints::cst_file ("constraints:cst_file")
RealOptionKey const constraints::cst_weight ("constraints:cst_weight")
RealOptionKey const constraints::max_cst_dist ("constraints:max_cst_dist")
StringVectorOptionKey const constraints::cst_fa_file ("constraints:cst_fa_file")
RealOptionKey const constraints::cst_fa_weight ("constraints:cst_fa_weight")
BooleanOptionKey const constraints::normalize_mixture_func ("constraints:normalize_mixture_func")
BooleanOptionKey const constraints::penalize_mixture_func ("constraints:penalize_mixture_func")
FileOptionKey const constraints::forest_file ("constraints:forest_file")
BooleanOptionKey const constraints::compute_total_dist_cst ("constraints:compute_total_dist_cst")
IntegerOptionKey const constraints::cull_with_native ("constraints:cull_with_native")
FileOptionKey const constraints::dump_cst_set ("constraints:dump_cst_set")
IntegerVectorOptionKey const constraints::evaluate_max_seq_sep ("constraints:evaluate_max_seq_sep")
BooleanOptionKey const constraints::named ("constraints:named")
BooleanOptionKey const constraints::no_cst_in_relax ("constraints:no_cst_in_relax")
BooleanOptionKey const constraints::no_linearize_bounded ("constraints:no_linearize_bounded")
RealOptionKey const constraints::pocket_constraint_weight ("constraints:pocket_constraint_weight")
BooleanOptionKey const constraints::pocket_zero_derivatives ("constraints:pocket_zero_derivatives")
BooleanOptionKey const constraints::viol ("constraints:viol")
IntegerOptionKey const constraints::viol_level ("constraints:viol_level")
StringOptionKey const constraints::viol_type ("constraints:viol_type")
RealOptionKey const constraints::sog_cst_param ("constraints:sog_cst_param")
BooleanOptionKey const constraints::epr_distance ("constraints:epr_distance")
IntegerOptionKey const constraints::combine ("constraints:combine")
FileOptionKey const constraints::combine_exclude_region ("constraints:combine_exclude_region")
BooleanOptionKey const constraints::skip_redundant ("constraints:skip_redundant")
IntegerOptionKey const constraints::skip_redundant_width ("constraints:skip_redundant_width")
RealOptionKey const constraints::increase_constraints ("constraints:increase_constraints")
BooleanOptionKey const dna::dna ("dna")
BooleanOptionKey const dna::specificity::specificity ("dna:specificity")
RealVectorOptionKey const dna::specificity::params ("dna:specificity:params")
FileVectorOptionKey const dna::specificity::frag_files ("dna:specificity:frag_files")
BooleanOptionKey const dna::specificity::exclude_bb_sc_hbonds ("dna:specificity:exclude_bb_sc_hbonds")
BooleanOptionKey const dna::specificity::only_repack ("dna:specificity:only_repack")
BooleanOptionKey const dna::specificity::design_DNA ("dna:specificity:design_DNA")
BooleanOptionKey const dna::specificity::run_test ("dna:specificity:run_test")
BooleanOptionKey const dna::specificity::soft_rep ("dna:specificity:soft_rep")
BooleanOptionKey const dna::specificity::dump_pdbs ("dna:specificity:dump_pdbs")
BooleanOptionKey const dna::specificity::fast ("dna:specificity:fast")
BooleanOptionKey const dna::specificity::randomize_motif ("dna:specificity:randomize_motif")
RealOptionKey const dna::specificity::Whack_elec ("dna:specificity:Whack_elec")
RealOptionKey const dna::specificity::Wdna_bs ("dna:specificity:Wdna_bs")
RealOptionKey const dna::specificity::Wdna_bp ("dna:specificity:Wdna_bp")
RealOptionKey const dna::specificity::minimize_tolerance ("dna:specificity:minimize_tolerance")
StringOptionKey const dna::specificity::weights_tag ("dna:specificity:weights_tag")
StringOptionKey const dna::specificity::weights_tag_list ("dna:specificity:weights_tag_list")
StringOptionKey const dna::specificity::min_type ("dna:specificity:min_type")
StringOptionKey const dna::specificity::tf ("dna:specificity:tf")
StringOptionKey const dna::specificity::mode ("dna:specificity:mode")
StringOptionKey const dna::specificity::score_function ("dna:specificity:score_function")
BooleanOptionKey const dna::specificity::pre_minimize ("dna:specificity:pre_minimize")
BooleanOptionKey const dna::specificity::post_minimize ("dna:specificity:post_minimize")
BooleanOptionKey const dna::specificity::pre_pack ("dna:specificity:pre_pack")
IntegerOptionKey const dna::specificity::nloop ("dna:specificity:nloop")
IntegerOptionKey const dna::specificity::n_inner ("dna:specificity:n_inner")
IntegerOptionKey const dna::specificity::n_outer ("dna:specificity:n_outer")
IntegerOptionKey const dna::specificity::nstep_water ("dna:specificity:nstep_water")
IntegerOptionKey const dna::specificity::moving_jump ("dna:specificity:moving_jump")
IntegerOptionKey const dna::specificity::motif_begin ("dna:specificity:motif_begin")
IntegerOptionKey const dna::specificity::motif_size ("dna:specificity:motif_size")
StringVectorOptionKey const dna::specificity::pdb_pos ("dna:specificity:pdb_pos")
StringVectorOptionKey const dna::specificity::methylate ("dna:specificity:methylate")
BooleanOptionKey const dna::design::design ("dna:design")
BooleanOptionKey const dna::design::output_initial_pdb ("dna:design:output_initial_pdb")
BooleanOptionKey const dna::design::output_unbound_pdb ("dna:design:output_unbound_pdb")
RealOptionKey const dna::design::z_cutoff ("dna:design:z_cutoff")
StringOptionKey const dna::design::protein_scan ("dna:design:protein_scan")
StringOptionKey const dna::design::checkpoint ("dna:design:checkpoint")
BooleanOptionKey const dna::design::minimize ("dna:design:minimize")
IntegerOptionKey const dna::design::iterations ("dna:design:iterations")
StringOptionKey const dna::design::bb_moves ("dna:design:bb_moves")
StringVectorOptionKey const dna::design::dna_defs ("dna:design:dna_defs")
StringOptionKey const dna::design::dna_defs_file ("dna:design:dna_defs_file")
BooleanOptionKey const dna::design::preminimize_interface ("dna:design:preminimize_interface")
BooleanOptionKey const dna::design::prepack_interface ("dna:design:prepack_interface")
BooleanOptionKey const dna::design::flush ("dna:design:flush")
BooleanOptionKey const dna::design::nopdb ("dna:design:nopdb")
BooleanOptionKey const dna::design::nopack ("dna:design:nopack")
BooleanOptionKey const dna::design::more_stats ("dna:design:more_stats")
BooleanOptionKey const dna::design::pdb_each_iteration ("dna:design:pdb_each_iteration")
BooleanOptionKey const dna::design::designable_second_shell ("dna:design:designable_second_shell")
BooleanOptionKey const dna::design::base_contacts_only ("dna:design:base_contacts_only")
IntegerOptionKey const dna::design::probe_specificity ("dna:design:probe_specificity")
BooleanOptionKey const dna::design::specificity::specificity ("dna:design:specificity")
BooleanOptionKey const dna::design::specificity::output_structures ("dna:design:specificity:output_structures")
BooleanOptionKey const dna::design::specificity::include_dna_potentials ("dna:design:specificity:include_dna_potentials")
BooleanOptionKey const dna::design::reversion_scan ("dna:design:reversion_scan")
BooleanOptionKey const dna::design::reversion::reversion ("dna:design:reversion")
RealOptionKey const dna::design::reversion::dscore_cutoff ("dna:design:reversion:dscore_cutoff")
RealOptionKey const dna::design::reversion::dspec_cutoff ("dna:design:reversion:dspec_cutoff")
BooleanOptionKey const dna::design::binding ("dna:design:binding")
RealOptionKey const dna::design::Boltz_temp ("dna:design:Boltz_temp")
BooleanOptionKey const dna::design::repack_only ("dna:design:repack_only")
BooleanOptionKey const dna::design::sparse_pdb_output ("dna:design:sparse_pdb_output")
BooleanOptionKey const flxbb::flxbb ("flxbb")
BooleanOptionKey const flxbb::view ("flxbb:view")
IntegerOptionKey const flxbb::ncycle ("flxbb:ncycle")
RealOptionKey const flxbb::constraints_sheet ("flxbb:constraints_sheet")
RealOptionKey const flxbb::constraints_NtoC ("flxbb:constraints_NtoC")
IntegerOptionKey const flxbb::filter_trial ("flxbb:filter_trial")
StringOptionKey const flxbb::filter_type ("flxbb:filter_type")
BooleanOptionKey const flxbb::exclude_Met ("flxbb:exclude_Met")
BooleanOptionKey const flxbb::exclude_Ala ("flxbb:exclude_Ala")
FileOptionKey const flxbb::blueprint ("flxbb:blueprint")
BooleanOptionKey const flxbb::movemap_from_blueprint ("flxbb:movemap_from_blueprint")
StringOptionKey const flxbb::layer::layer ("flxbb:layer")
RealOptionKey const flxbb::layer::pore_radius ("flxbb:layer:pore_radius")
RealOptionKey const flxbb::layer::burial ("flxbb:layer:burial")
RealOptionKey const flxbb::layer::surface ("flxbb:layer:surface")
BooleanOptionKey const fldsgn::fldsgn ("fldsgn")
BooleanOptionKey const fldsgn::view ("fldsgn:view")
FileVectorOptionKey const fldsgn::blueprint ("fldsgn:blueprint")
IntegerOptionKey const fldsgn::dr_cycles ("fldsgn:dr_cycles")
StringOptionKey const fldsgn::centroid_sfx ("fldsgn:centroid_sfx")
StringOptionKey const fldsgn::centroid_sfx_patch ("fldsgn:centroid_sfx_patch")
StringOptionKey const fldsgn::fullatom_sfx ("fldsgn:fullatom_sfx")
StringOptionKey const fldsgn::fullatom_sfx_patch ("fldsgn:fullatom_sfx_patch")
IntegerOptionKey const fldsgn::run_flxbb ("fldsgn:run_flxbb")
BooleanOptionKey const rna::rna ("rna")
IntegerOptionKey const rna::minimize_rounds ("rna:minimize_rounds")
BooleanOptionKey const cm::cm ("cm")
BooleanOptionKey const cm::start_models_only ("cm:start_models_only")
StringOptionKey const cm::aln_format ("cm:aln_format")
BooleanOptionKey const cm::recover_side_chains ("cm:recover_side_chains")
StringOptionKey const cm::loop_mover ("cm:loop_mover")
IntegerOptionKey const cm::loop_close_level ("cm:loop_close_level")
IntegerOptionKey const cm::min_loop_size ("cm:min_loop_size")
IntegerOptionKey const cm::max_loop_rebuild ("cm:max_loop_rebuild")
RealOptionKey const cm::loop_rebuild_filter ("cm:loop_rebuild_filter")
RealOptionKey const cm::aln_length_filter_quantile ("cm:aln_length_filter_quantile")
IntegerOptionKey const cm::aln_length_filter ("cm:aln_length_filter")
StringVectorOptionKey const cm::template_ids ("cm:template_ids")
FileOptionKey const cm::ligand_pdb ("cm:ligand_pdb")
StringVectorOptionKey const cm::seq_score ("cm:seq_score")
StringOptionKey const cm::aligner ("cm:aligner")
RealOptionKey const cm::min_gap_open ("cm:min_gap_open")
RealOptionKey const cm::max_gap_open ("cm:max_gap_open")
RealOptionKey const cm::min_gap_extend ("cm:min_gap_extend")
RealOptionKey const cm::max_gap_extend ("cm:max_gap_extend")
IntegerOptionKey const cm::nn ("cm:nn")
RealOptionKey const cm::fr_temperature ("cm:fr_temperature")
FileVectorOptionKey const cm::ev_map ("cm:ev_map")
FileVectorOptionKey const cm::hh_map ("cm:hh_map")
BooleanOptionKey const ms::ms ("ms")
BooleanOptionKey const ms::share_data ("ms:share_data")
BooleanOptionKey const ms::verbose ("ms:verbose")
BooleanOptionKey const ms::restrict_to_canonical ("ms:restrict_to_canonical")
IntegerOptionKey const ms::pop_from_ss ("ms:pop_from_ss")
IntegerOptionKey const ms::pop_size ("ms:pop_size")
IntegerOptionKey const ms::generations ("ms:generations")
IntegerOptionKey const ms::num_packs ("ms:num_packs")
IntegerOptionKey const ms::numresults ("ms:numresults")
RealOptionKey const ms::anchor_offset ("ms:anchor_offset")
RealOptionKey const ms::Boltz_temp ("ms:Boltz_temp")
RealOptionKey const ms::mutate_rate ("ms:mutate_rate")
RealOptionKey const ms::fraction_by_recombination ("ms:fraction_by_recombination")
BooleanOptionKey const ms::checkpoint::checkpoint ("ms:checkpoint")
StringOptionKey const ms::checkpoint::prefix ("ms:checkpoint:prefix")
IntegerOptionKey const ms::checkpoint::interval ("ms:checkpoint:interval")
BooleanOptionKey const ms::checkpoint::gz ("ms:checkpoint:gz")
BooleanOptionKey const ms::checkpoint::rename ("ms:checkpoint:rename")
BooleanOptionKey const loops::loops ("loops")
StringOptionKey const loops::cen_weights ("loops:cen_weights")
StringOptionKey const loops::cen_patch ("loops:cen_patch")
FileOptionKey const loops::input_pdb ("loops:input_pdb")
StringVectorOptionKey const loops::loop_file ("loops:loop_file")
FileOptionKey const loops::extended_loop_file ("loops:extended_loop_file")
FileOptionKey const loops::mm_loop_file ("loops:mm_loop_file")
BooleanOptionKey const loops::fix_natsc ("loops:fix_natsc")
BooleanOptionKey const loops::refine_only ("loops:refine_only")
BooleanOptionKey const loops::fa_input ("loops:fa_input")
BooleanOptionKey const loops::fast ("loops:fast")
FileOptionKey const loops::vall_file ("loops:vall_file")
IntegerVectorOptionKey const loops::frag_sizes ("loops:frag_sizes")
FileVectorOptionKey const loops::frag_files ("loops:frag_files")
FileOptionKey const loops::output_pdb ("loops:output_pdb")
BooleanOptionKey const loops::debug ("loops:debug")
BooleanOptionKey const loops::build_initial ("loops:build_initial")
BooleanOptionKey const loops::extended ("loops:extended")
BooleanOptionKey const loops::remove_extended_loops ("loops:remove_extended_loops")
BooleanOptionKey const loops::idealize_after_loop_close ("loops:idealize_after_loop_close")
BooleanOptionKey const loops::idealize_before_loop_close ("loops:idealize_before_loop_close")
IntegerOptionKey const loops::select_best_loop_from ("loops:select_best_loop_from")
IntegerOptionKey const loops::build_attempts ("loops:build_attempts")
IntegerOptionKey const loops::grow_attempts ("loops:grow_attempts")
RealOptionKey const loops::random_grow_loops_by ("loops:random_grow_loops_by")
BooleanOptionKey const loops::accept_aborted_loops ("loops:accept_aborted_loops")
BooleanOptionKey const loops::strict_loops ("loops:strict_loops")
BooleanOptionKey const loops::superimpose_native ("loops:superimpose_native")
IntegerVectorOptionKey const loops::build_specific_loops ("loops:build_specific_loops")
BooleanOptionKey const loops::random_order ("loops:random_order")
BooleanOptionKey const loops::build_all_loops ("loops:build_all_loops")
BooleanOptionKey const loops::fa_closure_protocol ("loops:fa_closure_protocol")
RealOptionKey const loops::combine_rate ("loops:combine_rate")
StringOptionKey const loops::remodel ("loops:remodel")
StringOptionKey const loops::intermedrelax ("loops:intermedrelax")
StringOptionKey const loops::refine ("loops:refine")
StringOptionKey const loops::relax ("loops:relax")
IntegerOptionKey const loops::n_rebuild_tries ("loops:n_rebuild_tries")
BooleanOptionKey const loops::final_clean_fastrelax ("loops:final_clean_fastrelax")
BooleanOptionKey const loops::relax_with_foldtree ("loops:relax_with_foldtree")
RealOptionKey const loops::constrain_rigid_segments ("loops:constrain_rigid_segments")
StringOptionKey const loops::loopscores ("loops:loopscores")
BooleanOptionKey const loops::timer ("loops:timer")
BooleanOptionKey const loops::vicinity_sampling ("loops:vicinity_sampling")
RealOptionKey const loops::vicinity_degree ("loops:vicinity_degree")
RealOptionKey const loops::neighbor_dist ("loops:neighbor_dist")
IntegerOptionKey const loops::kic_max_seglen ("loops:kic_max_seglen")
BooleanOptionKey const loops::kic_recover_last ("loops:kic_recover_last")
BooleanOptionKey const loops::kic_min_after_repack ("loops:kic_min_after_repack")
BooleanOptionKey const loops::optimize_only_kic_region_sidechains_after_move ("loops:optimize_only_kic_region_sidechains_after_move")
IntegerOptionKey const loops::max_kic_build_attempts ("loops:max_kic_build_attempts")
IntegerOptionKey const loops::remodel_kic_attempts ("loops:remodel_kic_attempts")
IntegerOptionKey const loops::max_kic_perturber_samples ("loops:max_kic_perturber_samples")
BooleanOptionKey const loops::nonpivot_torsion_sampling ("loops:nonpivot_torsion_sampling")
IntegerOptionKey const loops::extend_length ("loops:extend_length")
IntegerOptionKey const loops::outer_cycles ("loops:outer_cycles")
IntegerOptionKey const loops::max_inner_cycles ("loops:max_inner_cycles")
IntegerOptionKey const loops::repack_period ("loops:repack_period")
BooleanOptionKey const loops::repack_never ("loops:repack_never")
RealOptionKey const loops::remodel_init_temp ("loops:remodel_init_temp")
RealOptionKey const loops::remodel_final_temp ("loops:remodel_final_temp")
RealOptionKey const loops::refine_init_temp ("loops:refine_init_temp")
RealOptionKey const loops::refine_final_temp ("loops:refine_final_temp")
IntegerOptionKey const loops::gapspan ("loops:gapspan")
IntegerOptionKey const loops::spread ("loops:spread")
IntegerOptionKey const loops::kinematic_wrapper_cycles ("loops:kinematic_wrapper_cycles")
BooleanOptionKey const loops::alternative_closure_protocol ("loops:alternative_closure_protocol")
RealOptionKey const loops::chainbreak_max_accept ("loops:chainbreak_max_accept")
BooleanOptionKey const loops::debug_loop_closure ("loops:debug_loop_closure")
BooleanOptionKey const loops::non_ideal_loop_closing ("loops:non_ideal_loop_closing")
RealOptionKey const loops::scored_frag_cycles ("loops:scored_frag_cycles")
RealOptionKey const loops::short_frag_cycles ("loops:short_frag_cycles")
RealOptionKey const loops::rmsd_tol ("loops:rmsd_tol")
RealOptionKey const loops::chain_break_tol ("loops:chain_break_tol")
BooleanOptionKey const loops::random_loop ("loops:random_loop")
FileVectorOptionKey const loops::stealfrags ("loops:stealfrags")
IntegerOptionKey const loops::stealfrags_times ("loops:stealfrags_times")
RealOptionKey const loops::coord_cst ("loops:coord_cst")
RealOptionKey const loops::skip_1mers ("loops:skip_1mers")
RealOptionKey const loops::skip_3mers ("loops:skip_3mers")
RealOptionKey const loops::skip_9mers ("loops:skip_9mers")
BooleanOptionKey const loops::loop_model ("loops:loop_model")
RealOptionKey const loops::score_filter_cutoff ("loops:score_filter_cutoff")
BooleanOptionKey const loops::loop_farlx ("loops:loop_farlx")
BooleanOptionKey const loops::ccd_closure ("loops:ccd_closure")
BooleanOptionKey const loops::skip_ccd_moves ("loops:skip_ccd_moves")
BooleanOptionKey const loops::no_randomize_loop ("loops:no_randomize_loop")
BooleanOptionKey const loops::loops_subset ("loops:loops_subset")
IntegerOptionKey const loops::num_desired_loops ("loops:num_desired_loops")
RealOptionKey const loops::loop_combine_rate ("loops:loop_combine_rate")
RealOptionKey const loops::final_score_filter ("loops:final_score_filter")
BooleanOptionKey const loops::no_combine_if_fail ("loops:no_combine_if_fail")
BooleanOptionKey const loops::shorten_long_terminal_loop ("loops:shorten_long_terminal_loop")
IntegerOptionKey const loops::backrub_trials ("loops:backrub_trials")
RealOptionKey const loops::looprlx_cycle_ratio ("loops:looprlx_cycle_ratio")
RealOptionKey const loops::extended_beta ("loops:extended_beta")
BooleanOptionKey const loops::shortrelax ("loops:shortrelax")
BooleanOptionKey const loops::fastrelax ("loops:fastrelax")
BooleanOptionKey const loops::no_looprebuild ("loops:no_looprebuild")
BooleanOptionKey const loops::allow_lig_move ("loops:allow_lig_move")
FileOptionKey const loops::keep_natro ("loops:keep_natro")
IntegerOptionKey const loops::refine_design_iterations ("loops:refine_design_iterations")
BooleanOptionKey const assembly::assembly ("assembly")
FileOptionKey const assembly::pdb1 ("assembly:pdb1")
FileOptionKey const assembly::pdb2 ("assembly:pdb2")
StringOptionKey const assembly::nterm_seq ("assembly:nterm_seq")
StringOptionKey const assembly::cterm_seq ("assembly:cterm_seq")
IntegerVectorOptionKey const assembly::linkers_pdb1 ("assembly:linkers_pdb1")
IntegerVectorOptionKey const assembly::linkers_pdb2 ("assembly:linkers_pdb2")
IntegerVectorOptionKey const assembly::preserve_sidechains_pdb1 ("assembly:preserve_sidechains_pdb1")
IntegerVectorOptionKey const assembly::preserve_sidechains_pdb2 ("assembly:preserve_sidechains_pdb2")
BooleanOptionKey const fast_loops::fast_loops ("fast_loops")
RealOptionKey const fast_loops::window_accept_ratio ("fast_loops:window_accept_ratio")
IntegerOptionKey const fast_loops::nr_scored_sampling_passes ("fast_loops:nr_scored_sampling_passes")
IntegerOptionKey const fast_loops::nr_scored_fragments ("fast_loops:nr_scored_fragments")
IntegerOptionKey const fast_loops::min_breakout_good_loops ("fast_loops:min_breakout_good_loops")
IntegerOptionKey const fast_loops::min_breakout_fast_loops ("fast_loops:min_breakout_fast_loops")
IntegerOptionKey const fast_loops::min_good_loops ("fast_loops:min_good_loops")
IntegerOptionKey const fast_loops::min_fast_loops ("fast_loops:min_fast_loops")
RealOptionKey const fast_loops::vdw_delta ("fast_loops:vdw_delta")
IntegerOptionKey const fast_loops::give_up ("fast_loops:give_up")
RealOptionKey const fast_loops::chainbreak_max ("fast_loops:chainbreak_max")
FileOptionKey const fast_loops::fragsample_score ("fast_loops:fragsample_score")
FileOptionKey const fast_loops::fragsample_patch ("fast_loops:fragsample_patch")
FileOptionKey const fast_loops::overwrite_filter_scorefxn ("fast_loops:overwrite_filter_scorefxn")
FileOptionKey const fast_loops::patch_filter_scorefxn ("fast_loops:patch_filter_scorefxn")
FileOptionKey const fast_loops::filter_cst_file ("fast_loops:filter_cst_file")
RealOptionKey const fast_loops::filter_cst_weight ("fast_loops:filter_cst_weight")
FileOptionKey const fast_loops::fast_relax_sequence_file ("fast_loops:fast_relax_sequence_file")
BooleanOptionKey const SSrbrelax::SSrbrelax ("SSrbrelax")
FileOptionKey const SSrbrelax::input_pdb ("SSrbrelax:input_pdb")
FileOptionKey const SSrbrelax::rb_file ("SSrbrelax:rb_file")
FileOptionKey const SSrbrelax::rb_param_file ("SSrbrelax:rb_param_file")
IntegerVectorOptionKey const SSrbrelax::frag_sizes ("SSrbrelax:frag_sizes")
FileVectorOptionKey const SSrbrelax::frag_files ("SSrbrelax:frag_files")
BooleanOptionKey const boinc::boinc ("boinc")
BooleanOptionKey const boinc::graphics ("boinc:graphics")
BooleanOptionKey const boinc::fullscreen ("boinc:fullscreen")
IntegerOptionKey const boinc::max_fps ("boinc:max_fps")
IntegerOptionKey const boinc::max_cpu ("boinc:max_cpu")
BooleanOptionKey const boinc::noshmem ("boinc:noshmem")
IntegerOptionKey const boinc::cpu_run_time ("boinc:cpu_run_time")
IntegerOptionKey const boinc::max_nstruct ("boinc:max_nstruct")
RealOptionKey const boinc::cpu_frac ("boinc:cpu_frac")
RealOptionKey const boinc::frame_rate ("boinc:frame_rate")
BooleanOptionKey const boinc::watchdog ("boinc:watchdog")
IntegerOptionKey const boinc::watchdog_time ("boinc:watchdog_time")
IntegerOptionKey const boinc::cpu_run_timeout ("boinc:cpu_run_timeout")
FileOptionKey const boinc::description_file ("boinc:description_file")
BooleanOptionKey const LoopModel::LoopModel ("LoopModel")
FileOptionKey const LoopModel::input_pdb ("LoopModel:input_pdb")
FileOptionKey const LoopModel::loop_file ("LoopModel:loop_file")
BooleanOptionKey const AnchoredDesign::AnchoredDesign ("AnchoredDesign")
FileOptionKey const AnchoredDesign::anchor ("AnchoredDesign:anchor")
BooleanOptionKey const AnchoredDesign::allow_anchor_repack ("AnchoredDesign:allow_anchor_repack")
BooleanOptionKey const AnchoredDesign::vary_cutpoints ("AnchoredDesign:vary_cutpoints")
BooleanOptionKey const AnchoredDesign::no_frags ("AnchoredDesign:no_frags")
BooleanOptionKey const AnchoredDesign::debug ("AnchoredDesign:debug")
BooleanOptionKey const AnchoredDesign::show_extended ("AnchoredDesign:show_extended")
BooleanOptionKey const AnchoredDesign::refine_only ("AnchoredDesign:refine_only")
BooleanOptionKey const AnchoredDesign::perturb_show ("AnchoredDesign:perturb_show")
IntegerOptionKey const AnchoredDesign::perturb_cycles ("AnchoredDesign:perturb_cycles")
RealOptionKey const AnchoredDesign::perturb_temp ("AnchoredDesign:perturb_temp")
BooleanOptionKey const AnchoredDesign::perturb_CCD_off ("AnchoredDesign:perturb_CCD_off")
BooleanOptionKey const AnchoredDesign::perturb_KIC_off ("AnchoredDesign:perturb_KIC_off")
BooleanOptionKey const AnchoredDesign::refine_CCD_off ("AnchoredDesign:refine_CCD_off")
BooleanOptionKey const AnchoredDesign::refine_KIC_off ("AnchoredDesign:refine_KIC_off")
IntegerOptionKey const AnchoredDesign::refine_cycles ("AnchoredDesign:refine_cycles")
RealOptionKey const AnchoredDesign::refine_temp ("AnchoredDesign:refine_temp")
IntegerOptionKey const AnchoredDesign::refine_repack_cycles ("AnchoredDesign:refine_repack_cycles")
BooleanOptionKey const AnchoredDesign::rmsd ("AnchoredDesign:rmsd")
BooleanOptionKey const AnchoredDesign::unbound_mode ("AnchoredDesign:unbound_mode")
RealOptionKey const AnchoredDesign::chainbreak_weight ("AnchoredDesign:chainbreak_weight")
BooleanOptionKey const AnchoredDesign::filters::filters ("AnchoredDesign:filters")
RealOptionKey const AnchoredDesign::filters::score ("AnchoredDesign:filters:score")
RealOptionKey const AnchoredDesign::filters::sasa ("AnchoredDesign:filters:sasa")
BooleanOptionKey const AnchoredDesign::filters::omega ("AnchoredDesign:filters:omega")
BooleanOptionKey const AnchoredDesign::akash::akash ("AnchoredDesign:akash")
IntegerOptionKey const AnchoredDesign::akash::dyepos ("AnchoredDesign:akash:dyepos")
BooleanOptionKey const AnchoredDesign::testing::testing ("AnchoredDesign:testing")
RealOptionKey const AnchoredDesign::testing::VDW_weight ("AnchoredDesign:testing:VDW_weight")
BooleanOptionKey const AnchoredDesign::testing::anchor_via_constraints ("AnchoredDesign:testing:anchor_via_constraints")
BooleanOptionKey const AnchoredDesign::testing::delete_interface_native_sidechains ("AnchoredDesign:testing:delete_interface_native_sidechains")
FileOptionKey const AnchoredDesign::testing::RMSD_only_this ("AnchoredDesign:testing:RMSD_only_this")
BooleanOptionKey const AnchoredDesign::testing::anchor_noise_constraints_mode ("AnchoredDesign:testing:anchor_noise_constraints_mode")
BooleanOptionKey const DenovoProteinDesign::DenovoProteinDesign ("DenovoProteinDesign")
BooleanOptionKey const DenovoProteinDesign::redesign_core ("DenovoProteinDesign:redesign_core")
BooleanOptionKey const DenovoProteinDesign::redesign_loops ("DenovoProteinDesign:redesign_loops")
BooleanOptionKey const DenovoProteinDesign::redesign_surface ("DenovoProteinDesign:redesign_surface")
BooleanOptionKey const DenovoProteinDesign::redesign_complete ("DenovoProteinDesign:redesign_complete")
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