Rosetta 3.3
Namespaces | Functions
src/basic/options/keys/OptionKeys.cc.gen1.hh File Reference

Namespaces

namespace  abinitio
namespace  fold_cst
namespace  resample
namespace  loopfcst
namespace  jumps
namespace  templates
namespace  templates::cst
namespace  templates::fragsteal
namespace  abrelax
namespace  chemical
namespace  score
namespace  score::saxs
namespace  corrections
namespace  corrections::score
namespace  corrections::chemical
namespace  holes
namespace  packstat
namespace  crossmatch
namespace  smhybrid
namespace  evolution
namespace  cluster
namespace  rescore
namespace  mc
namespace  batch_relax
namespace  relax
namespace  enzdes
namespace  packing
namespace  packing::ex1
namespace  packing::ex2
namespace  packing::ex3
namespace  packing::ex4
namespace  packing::ex1aro
namespace  packing::ex2aro
namespace  packing::ex1aro_exposed
namespace  packing::ex2aro_exposed
namespace  packing::exdna
namespace  phil
namespace  wum
namespace  lh

Functions

FileOptionKey const abinitio::log_frags ("abinitio:log_frags")
BooleanOptionKey const abinitio::only_stage1 ("abinitio:only_stage1")
RealOptionKey const abinitio::end_bias ("abinitio:end_bias")
IntegerOptionKey const abinitio::symmetry_residue ("abinitio:symmetry_residue")
RealOptionKey const abinitio::vdw_weight_stage1 ("abinitio:vdw_weight_stage1")
BooleanOptionKey const abinitio::override_vdw_all_stages ("abinitio:override_vdw_all_stages")
IntegerVectorOptionKey const abinitio::recover_low_in_stages ("abinitio:recover_low_in_stages")
IntegerVectorOptionKey const abinitio::skip_stages ("abinitio:skip_stages")
BooleanOptionKey const abinitio::close_chbrk ("abinitio:close_chbrk")
BooleanOptionKey const abinitio::include_stage5 ("abinitio:include_stage5")
BooleanOptionKey const abinitio::close_loops_by_idealizing ("abinitio:close_loops_by_idealizing")
BooleanOptionKey const abinitio::optimize_cutpoints_using_kic ("abinitio:optimize_cutpoints_using_kic")
IntegerOptionKey const abinitio::optimize_cutpoints_margin ("abinitio:optimize_cutpoints_margin")
FileOptionKey const abinitio::HD_EX_Info ("abinitio:HD_EX_Info")
RealOptionKey const abinitio::HD_penalty ("abinitio:HD_penalty")
RealOptionKey const abinitio::HD_fa_penalty ("abinitio:HD_fa_penalty")
FileOptionKey const abinitio::sheet_edge_pred ("abinitio:sheet_edge_pred")
RealOptionKey const abinitio::SEP_score_scalling ("abinitio:SEP_score_scalling")
BooleanOptionKey const fold_cst::fold_cst ("fold_cst")
RealOptionKey const fold_cst::constraint_skip_rate ("fold_cst:constraint_skip_rate")
IntegerOptionKey const fold_cst::violation_skip_basis ("fold_cst:violation_skip_basis")
IntegerOptionKey const fold_cst::violation_skip_ignore ("fold_cst:violation_skip_ignore")
BooleanOptionKey const fold_cst::keep_skipped_csts ("fold_cst:keep_skipped_csts")
BooleanOptionKey const fold_cst::no_minimize ("fold_cst:no_minimize")
BooleanOptionKey const fold_cst::force_minimize ("fold_cst:force_minimize")
RealVectorOptionKey const fold_cst::seq_sep_stages ("fold_cst:seq_sep_stages")
IntegerOptionKey const fold_cst::reramp_cst_cycles ("fold_cst:reramp_cst_cycles")
RealOptionKey const fold_cst::reramp_start_cstweight ("fold_cst:reramp_start_cstweight")
IntegerOptionKey const fold_cst::reramp_iterations ("fold_cst:reramp_iterations")
BooleanOptionKey const fold_cst::skip_on_noviolation_in_stage1 ("fold_cst:skip_on_noviolation_in_stage1")
RealOptionKey const fold_cst::stage1_ramp_cst_cycle_factor ("fold_cst:stage1_ramp_cst_cycle_factor")
RealOptionKey const fold_cst::stage2_constraint_threshold ("fold_cst:stage2_constraint_threshold")
BooleanOptionKey const fold_cst::ignore_sequence_seperation ("fold_cst:ignore_sequence_seperation")
BooleanOptionKey const fold_cst::no_recover_low_at_constraint_switch ("fold_cst:no_recover_low_at_constraint_switch")
BooleanOptionKey const fold_cst::ramp_coord_cst ("fold_cst:ramp_coord_cst")
BooleanOptionKey const resample::resample ("resample")
FileOptionKey const resample::silent ("resample:silent")
StringOptionKey const resample::tag ("resample:tag")
BooleanOptionKey const resample::stage1 ("resample:stage1")
BooleanOptionKey const resample::stage2 ("resample:stage2")
BooleanOptionKey const resample::jumps ("resample:jumps")
RealVectorOptionKey const resample::min_max_start_seq_sep ("resample:min_max_start_seq_sep")
BooleanOptionKey const loopfcst::loopfcst ("loopfcst")
RealOptionKey const loopfcst::coord_cst_weight ("loopfcst:coord_cst_weight")
BooleanOptionKey const loopfcst::coord_cst_all_atom ("loopfcst:coord_cst_all_atom")
BooleanOptionKey const loopfcst::use_general_protocol ("loopfcst:use_general_protocol")
FileOptionKey const loopfcst::coord_cst_weight_array ("loopfcst:coord_cst_weight_array")
FileOptionKey const loopfcst::dump_coord_cst_weight_array ("loopfcst:dump_coord_cst_weight_array")
BooleanOptionKey const jumps::jumps ("jumps")
BooleanOptionKey const jumps::evaluate ("jumps:evaluate")
FileOptionKey const jumps::extra_frags_for_ss ("jumps:extra_frags_for_ss")
BooleanOptionKey const jumps::fix_chainbreak ("jumps:fix_chainbreak")
FileOptionKey const jumps::fix_jumps ("jumps:fix_jumps")
FileOptionKey const jumps::jump_lib ("jumps:jump_lib")
FileOptionKey const jumps::loop_definition_from_file ("jumps:loop_definition_from_file")
BooleanOptionKey const jumps::no_chainbreak_in_relax ("jumps:no_chainbreak_in_relax")
FileOptionKey const jumps::pairing_file ("jumps:pairing_file")
IntegerVectorOptionKey const jumps::random_sheets ("jumps:random_sheets")
FileOptionKey const jumps::residue_pair_jump_file ("jumps:residue_pair_jump_file")
IntegerVectorOptionKey const jumps::sheets ("jumps:sheets")
FileOptionKey const jumps::topology_file ("jumps:topology_file")
BooleanOptionKey const jumps::bb_moves ("jumps:bb_moves")
BooleanOptionKey const jumps::no_wobble ("jumps:no_wobble")
BooleanOptionKey const jumps::no_shear ("jumps:no_shear")
BooleanOptionKey const jumps::no_sample_ss_jumps ("jumps:no_sample_ss_jumps")
IntegerOptionKey const jumps::invrate_jump_move ("jumps:invrate_jump_move")
RealOptionKey const jumps::chainbreak_weight_stage1 ("jumps:chainbreak_weight_stage1")
RealOptionKey const jumps::chainbreak_weight_stage2 ("jumps:chainbreak_weight_stage2")
RealOptionKey const jumps::chainbreak_weight_stage3 ("jumps:chainbreak_weight_stage3")
RealOptionKey const jumps::chainbreak_weight_stage4 ("jumps:chainbreak_weight_stage4")
BooleanOptionKey const jumps::ramp_chainbreaks ("jumps:ramp_chainbreaks")
RealOptionKey const jumps::increase_chainbreak ("jumps:increase_chainbreak")
BooleanOptionKey const jumps::overlap_chainbreak ("jumps:overlap_chainbreak")
RealOptionKey const jumps::sep_switch_accelerate ("jumps:sep_switch_accelerate")
BooleanOptionKey const jumps::dump_frags ("jumps:dump_frags")
IntegerOptionKey const jumps::njumps ("jumps:njumps")
IntegerOptionKey const jumps::max_strand_gap_allowed ("jumps:max_strand_gap_allowed")
RealOptionKey const jumps::contact_score ("jumps:contact_score")
BooleanOptionKey const templates::templates ("templates")
FileOptionKey const templates::config ("templates:config")
BooleanOptionKey const templates::fix_aligned_residues ("templates:fix_aligned_residues")
FileOptionKey const templates::fix_frag_file ("templates:fix_frag_file")
IntegerOptionKey const templates::fix_margin ("templates:fix_margin")
IntegerOptionKey const templates::min_nr_large_frags ("templates:min_nr_large_frags")
IntegerOptionKey const templates::min_nr_small_frags ("templates:min_nr_small_frags")
BooleanOptionKey const templates::no_pick_fragments ("templates:no_pick_fragments")
IntegerOptionKey const templates::nr_large_copies ("templates:nr_large_copies")
IntegerOptionKey const templates::nr_small_copies ("templates:nr_small_copies")
BooleanOptionKey const templates::pairings ("templates:pairings")
BooleanOptionKey const templates::pick_multiple_sizes ("templates:pick_multiple_sizes")
BooleanOptionKey const templates::strand_constraint ("templates:strand_constraint")
BooleanOptionKey const templates::vary_frag_size ("templates:vary_frag_size")
BooleanOptionKey const templates::no_culling ("templates:no_culling")
FileOptionKey const templates::helix_pairings ("templates:helix_pairings")
FileOptionKey const templates::prefix ("templates:prefix")
IntegerOptionKey const templates::change_movemap ("templates:change_movemap")
BooleanOptionKey const templates::force_native_topology ("templates:force_native_topology")
RealOptionKey const templates::topology_rank_cutoff ("templates:topology_rank_cutoff")
IntegerOptionKey const templates::min_frag_size ("templates:min_frag_size")
IntegerOptionKey const templates::max_shrink ("templates:max_shrink")
IntegerOptionKey const templates::shrink_step ("templates:shrink_step")
IntegerOptionKey const templates::shrink_pos_step ("templates:shrink_pos_step")
IntegerOptionKey const templates::min_padding ("templates:min_padding")
IntegerOptionKey const templates::min_align_pos ("templates:min_align_pos")
IntegerOptionKey const templates::max_align_pos ("templates:max_align_pos")
BooleanOptionKey const templates::cst::cst ("templates:cst")
IntegerOptionKey const templates::cst::topN ("templates:cst:topN")
RealOptionKey const templates::cst::wTopol ("templates:cst:wTopol")
RealOptionKey const templates::cst::wExtern ("templates:cst:wExtern")
BooleanOptionKey const templates::fragsteal::fragsteal ("templates:fragsteal")
IntegerOptionKey const templates::fragsteal::topN ("templates:fragsteal:topN")
RealOptionKey const templates::fragsteal::wTopol ("templates:fragsteal:wTopol")
RealOptionKey const templates::fragsteal::wExtern ("templates:fragsteal:wExtern")
BooleanOptionKey const abrelax::abrelax ("abrelax")
BooleanOptionKey const abrelax::filters ("abrelax:filters")
BooleanOptionKey const abrelax::fail_unclosed ("abrelax:fail_unclosed")
BooleanOptionKey const chemical::chemical ("chemical")
StringVectorOptionKey const chemical::exclude_patches ("chemical:exclude_patches")
BooleanOptionKey const score::score ("score")
StringOptionKey const score::weights ("score:weights")
StringOptionKey const score::custom_atom_pair ("score:custom_atom_pair")
StringOptionKey const score::patch ("score:patch")
BooleanOptionKey const score::empty ("score:empty")
RealOptionKey const score::fa_max_dis ("score:fa_max_dis")
BooleanOptionKey const score::fa_Hatr ("score:fa_Hatr")
BooleanOptionKey const score::no_smooth_etables ("score:no_smooth_etables")
RealOptionKey const score::etable_lr ("score:etable_lr")
BooleanOptionKey const score::no_lk_polar_desolvation ("score:no_lk_polar_desolvation")
StringOptionKey const score::input_etables ("score:input_etables")
StringOptionKey const score::output_etables ("score:output_etables")
RealOptionKey const score::rms_target ("score:rms_target")
BooleanOptionKey const score::ramaneighbors ("score:ramaneighbors")
StringOptionKey const score::optH_weights ("score:optH_weights")
StringOptionKey const score::optH_patch ("score:optH_patch")
StringOptionKey const score::hbond_params ("score:hbond_params")
IntegerOptionKey const score::symE_units ("score:symE_units")
RealOptionKey const score::symE_bonus ("score:symE_bonus")
RealOptionKey const score::NV_lbound ("score:NV_lbound")
RealOptionKey const score::NV_ubound ("score:NV_ubound")
StringOptionKey const score::NV_table ("score:NV_table")
BooleanOptionKey const score::disable_orientation_dependent_rna_ch_o_bonds ("score:disable_orientation_dependent_rna_ch_o_bonds")
BooleanOptionKey const score::find_neighbors_3dgrid ("score:find_neighbors_3dgrid")
StringOptionKey const score::seqdep_refene_fname ("score:seqdep_refene_fname")
StringOptionKey const score::secondary_seqdep_refene_fname ("score:secondary_seqdep_refene_fname")
BooleanOptionKey const score::exact_occ_pairwise ("score:exact_occ_pairwise")
BooleanOptionKey const score::exact_occ_skip_Hbonders ("score:exact_occ_skip_Hbonders")
BooleanOptionKey const score::exact_occ_include_Hbond_contribution ("score:exact_occ_include_Hbond_contribution")
BooleanOptionKey const score::exact_occ_pairwise_by_res ("score:exact_occ_pairwise_by_res")
BooleanOptionKey const score::exact_occ_split_between_res ("score:exact_occ_split_between_res")
BooleanOptionKey const score::exact_occ_self_res_no_occ ("score:exact_occ_self_res_no_occ")
RealOptionKey const score::exact_occ_radius_scaling ("score:exact_occ_radius_scaling")
StringVectorOptionKey const score::ref_offsets ("score:ref_offsets")
BooleanOptionKey const score::output_residue_energies ("score:output_residue_energies")
StringOptionKey const score::fa_custom_pair_distance_file ("score:fa_custom_pair_distance_file")
RealOptionKey const score::disulf_matching_probe ("score:disulf_matching_probe")
RealVectorOptionKey const score::bonded_params ("score:bonded_params")
BooleanOptionKey const score::hb_sp2_chipen ("score:hb_sp2_chipen")
RealOptionKey const score::hb_sp2_amp ("score:hb_sp2_amp")
RealOptionKey const score::hb_sp2_peak_heigh_above_trough ("score:hb_sp2_peak_heigh_above_trough")
BooleanOptionKey const score::saxs::saxs ("score:saxs")
RealOptionKey const score::saxs::min_score ("score:saxs:min_score")
StringOptionKey const score::saxs::custom_ff ("score:saxs:custom_ff")
StringOptionKey const score::saxs::print_i_calc ("score:saxs:print_i_calc")
FileOptionKey const score::saxs::ref_fa_spectrum ("score:saxs:ref_fa_spectrum")
FileOptionKey const score::saxs::ref_cen_spectrum ("score:saxs:ref_cen_spectrum")
FileOptionKey const score::saxs::ref_spectrum ("score:saxs:ref_spectrum")
FileOptionKey const score::saxs::ref_pddf ("score:saxs:ref_pddf")
BooleanOptionKey const score::saxs::skip_hydrogens ("score:saxs:skip_hydrogens")
RealOptionKey const score::saxs::d_min ("score:saxs:d_min")
RealOptionKey const score::saxs::d_max ("score:saxs:d_max")
RealOptionKey const score::saxs::d_step ("score:saxs:d_step")
RealOptionKey const score::saxs::q_min ("score:saxs:q_min")
RealOptionKey const score::saxs::q_max ("score:saxs:q_max")
RealOptionKey const score::saxs::q_step ("score:saxs:q_step")
BooleanOptionKey const score::saxs::fit_pddf_area ("score:saxs:fit_pddf_area")
IntegerVectorOptionKey const score::sidechain_buried ("score:sidechain_buried")
IntegerVectorOptionKey const score::sidechain_exposed ("score:sidechain_exposed")
RealOptionKey const score::hackelec_max_dis ("score:hackelec_max_dis")
RealOptionKey const score::hackelec_die ("score:hackelec_die")
BooleanOptionKey const score::hackelec_r_option ("score:hackelec_r_option")
BooleanOptionKey const corrections::corrections ("corrections")
BooleanOptionKey const corrections::correct ("corrections:correct")
BooleanOptionKey const corrections::score::score ("corrections:score")
BooleanOptionKey const corrections::score::no_his_his_pairE ("corrections:score:no_his_his_pairE")
BooleanOptionKey const corrections::score::hbond_His_Phil_fix ("corrections:score:hbond_His_Phil_fix")
BooleanOptionKey const corrections::score::helix_hb_06_2009 ("corrections:score:helix_hb_06_2009")
BooleanOptionKey const corrections::score::use_incorrect_hbond_deriv ("corrections:score:use_incorrect_hbond_deriv")
StringOptionKey const corrections::score::p_aa_pp ("corrections:score:p_aa_pp")
BooleanOptionKey const corrections::score::p_aa_pp_nogridshift ("corrections:score:p_aa_pp_nogridshift")
BooleanOptionKey const corrections::score::rama_not_squared ("corrections:score:rama_not_squared")
FileOptionKey const corrections::score::rama_map ("corrections:score:rama_map")
BooleanOptionKey const corrections::score::dun10 ("corrections:score:dun10")
StringOptionKey const corrections::score::dun10_dir ("corrections:score:dun10_dir")
BooleanOptionKey const corrections::score::dun08 ("corrections:score:dun08")
StringOptionKey const corrections::score::dun08_dir ("corrections:score:dun08_dir")
StringOptionKey const corrections::score::dun02_file ("corrections:score:dun02_file")
StringOptionKey const corrections::score::ch_o_bond_potential ("corrections:score:ch_o_bond_potential")
BooleanOptionKey const corrections::score::hack_elec_co_only ("corrections:score:hack_elec_co_only")
RealOptionKey const corrections::score::lj_hbond_hdis ("corrections:score:lj_hbond_hdis")
FileOptionKey const corrections::score::PB_potential_file ("corrections:score:PB_potential_file")
IntegerVectorOptionKey const corrections::score::PB_score_residue_range ("corrections:score:PB_score_residue_range")
RealOptionKey const corrections::score::lj_hbond_OH_donor_dis ("corrections:score:lj_hbond_OH_donor_dis")
BooleanOptionKey const corrections::score::score12prime ("corrections:score:score12prime")
BooleanOptionKey const corrections::chemical::chemical ("corrections:chemical")
BooleanOptionKey const corrections::chemical::icoor_05_2009 ("corrections:chemical:icoor_05_2009")
BooleanOptionKey const corrections::chemical::parse_charge ("corrections:chemical:parse_charge")
BooleanOptionKey const holes::holes ("holes")
FileOptionKey const holes::dalphaball ("holes:dalphaball")
FileOptionKey const holes::params ("holes:params")
IntegerOptionKey const holes::h_mode ("holes:h_mode")
BooleanOptionKey const holes::water ("holes:water")
BooleanOptionKey const holes::make_pdb ("holes:make_pdb")
BooleanOptionKey const holes::make_voids ("holes:make_voids")
BooleanOptionKey const holes::atom_scores ("holes:atom_scores")
BooleanOptionKey const holes::residue_scores ("holes:residue_scores")
RealOptionKey const holes::cav_shrink ("holes:cav_shrink")
StringOptionKey const holes::minimize ("holes:minimize")
BooleanOptionKey const packstat::packstat ("packstat")
BooleanOptionKey const packstat::include_water ("packstat:include_water")
IntegerOptionKey const packstat::oversample ("packstat:oversample")
BooleanOptionKey const packstat::packstat_pdb ("packstat:packstat_pdb")
BooleanOptionKey const packstat::surface_accessibility ("packstat:surface_accessibility")
BooleanOptionKey const packstat::residue_scores ("packstat:residue_scores")
RealOptionKey const packstat::cavity_burial_probe_radius ("packstat:cavity_burial_probe_radius")
BooleanOptionKey const packstat::raw_stats ("packstat:raw_stats")
IntegerOptionKey const packstat::threads ("packstat:threads")
RealOptionKey const packstat::cluster_min_volume ("packstat:cluster_min_volume")
RealOptionKey const packstat::min_surface_accessibility ("packstat:min_surface_accessibility")
RealOptionKey const packstat::min_cluster_overlap ("packstat:min_cluster_overlap")
RealOptionKey const packstat::min_cav_ball_radius ("packstat:min_cav_ball_radius")
RealOptionKey const packstat::max_cav_ball_radius ("packstat:max_cav_ball_radius")
BooleanOptionKey const crossmatch::crossmatch ("crossmatch")
StringVectorOptionKey const crossmatch::write_reduced_matchset ("crossmatch:write_reduced_matchset")
IntegerOptionKey const crossmatch::interface_size ("crossmatch:interface_size")
RealOptionKey const crossmatch::max_dis_any ("crossmatch:max_dis_any")
RealOptionKey const crossmatch::max_dis_all ("crossmatch:max_dis_all")
RealOptionKey const crossmatch::max_dis_metal ("crossmatch:max_dis_metal")
RealOptionKey const crossmatch::clash_dis ("crossmatch:clash_dis")
RealOptionKey const crossmatch::identical_match_dis ("crossmatch:identical_match_dis")
BooleanOptionKey const smhybrid::smhybrid ("smhybrid")
BooleanOptionKey const smhybrid::add_cavities ("smhybrid:add_cavities")
BooleanOptionKey const smhybrid::abinitio_design ("smhybrid:abinitio_design")
BooleanOptionKey const smhybrid::fa_refine ("smhybrid:fa_refine")
BooleanOptionKey const smhybrid::virtual_nterm ("smhybrid:virtual_nterm")
BooleanOptionKey const smhybrid::debug ("smhybrid:debug")
BooleanOptionKey const smhybrid::refine ("smhybrid:refine")
BooleanOptionKey const smhybrid::filter ("smhybrid:filter")
BooleanOptionKey const smhybrid::floating_scs_rep ("smhybrid:floating_scs_rep")
BooleanOptionKey const smhybrid::flxbb ("smhybrid:flxbb")
BooleanOptionKey const smhybrid::centroid_all_val ("smhybrid:centroid_all_val")
BooleanOptionKey const smhybrid::subsubs_attract ("smhybrid:subsubs_attract")
BooleanOptionKey const smhybrid::linker_cst ("smhybrid:linker_cst")
BooleanOptionKey const smhybrid::pseudosym ("smhybrid:pseudosym")
BooleanOptionKey const smhybrid::design_linker ("smhybrid:design_linker")
BooleanOptionKey const smhybrid::design ("smhybrid:design")
BooleanOptionKey const smhybrid::restrict_design_to_interface ("smhybrid:restrict_design_to_interface")
BooleanOptionKey const smhybrid::restrict_design_to_subsub_interface ("smhybrid:restrict_design_to_subsub_interface")
BooleanOptionKey const smhybrid::design_hydrophobic ("smhybrid:design_hydrophobic")
BooleanOptionKey const smhybrid::add_metal_at_0 ("smhybrid:add_metal_at_0")
IntegerOptionKey const smhybrid::nres_mono ("smhybrid:nres_mono")
IntegerOptionKey const smhybrid::abinitio_cycles ("smhybrid:abinitio_cycles")
IntegerOptionKey const smhybrid::primary_subsubunit ("smhybrid:primary_subsubunit")
IntegerOptionKey const smhybrid::minbb ("smhybrid:minbb")
IntegerOptionKey const smhybrid::switch_concert_sub ("smhybrid:switch_concert_sub")
RealOptionKey const smhybrid::temperature ("smhybrid:temperature")
BooleanOptionKey const smhybrid::inter_subsub_cst ("smhybrid:inter_subsub_cst")
RealOptionKey const smhybrid::rb_mag ("smhybrid:rb_mag")
StringOptionKey const smhybrid::ss ("smhybrid:ss")
FileOptionKey const smhybrid::symm_def_template ("smhybrid:symm_def_template")
FileOptionKey const smhybrid::symm_def_template_reduced ("smhybrid:symm_def_template_reduced")
IntegerVectorOptionKey const smhybrid::attach_as_sc ("smhybrid:attach_as_sc")
IntegerVectorOptionKey const smhybrid::attach_as_sc_sub ("smhybrid:attach_as_sc_sub")
IntegerVectorOptionKey const smhybrid::inversion_subs ("smhybrid:inversion_subs")
BooleanVectorOptionKey const smhybrid::chainbreaks ("smhybrid:chainbreaks")
StringVectorOptionKey const smhybrid::design_res_files ("smhybrid:design_res_files")
StringVectorOptionKey const smhybrid::fixed_res_files ("smhybrid:fixed_res_files")
StringVectorOptionKey const smhybrid::frag_res_files ("smhybrid:frag_res_files")
StringVectorOptionKey const smhybrid::scattach_res_files ("smhybrid:scattach_res_files")
StringVectorOptionKey const smhybrid::rep_edge_files ("smhybrid:rep_edge_files")
StringVectorOptionKey const smhybrid::virtual_res_files ("smhybrid:virtual_res_files")
StringVectorOptionKey const smhybrid::jumpcut_files ("smhybrid:jumpcut_files")
StringVectorOptionKey const smhybrid::cst_sub_files ("smhybrid:cst_sub_files")
StringVectorOptionKey const smhybrid::symm_file_tag ("smhybrid:symm_file_tag")
StringVectorOptionKey const smhybrid::attach_atom ("smhybrid:attach_atom")
StringVectorOptionKey const smhybrid::add_res_before ("smhybrid:add_res_before")
StringVectorOptionKey const smhybrid::add_res_after ("smhybrid:add_res_after")
StringVectorOptionKey const smhybrid::add_ss_before ("smhybrid:add_ss_before")
StringVectorOptionKey const smhybrid::add_ss_after ("smhybrid:add_ss_after")
StringVectorOptionKey const smhybrid::add_atom_at_cen ("smhybrid:add_atom_at_cen")
StringVectorOptionKey const smhybrid::attach_rsd ("smhybrid:attach_rsd")
BooleanOptionKey const evolution::evolution ("evolution")
FileVectorOptionKey const evolution::parentlist ("evolution:parentlist")
FileVectorOptionKey const evolution::childlist ("evolution:childlist")
StringOptionKey const evolution::action ("evolution:action")
RealOptionKey const evolution::rms_threshold ("evolution:rms_threshold")
RealOptionKey const evolution::rms_topmargin ("evolution:rms_topmargin")
StringOptionKey const evolution::targetdir ("evolution:targetdir")
RealOptionKey const evolution::padding_score_filter ("evolution:padding_score_filter")
RealOptionKey const evolution::padding_stage2_filter ("evolution:padding_stage2_filter")
BooleanOptionKey const cluster::cluster ("cluster")
BooleanOptionKey const cluster::lite ("cluster:lite")
RealOptionKey const cluster::input_score_filter ("cluster:input_score_filter")
RealOptionKey const cluster::output_score_filter ("cluster:output_score_filter")
IntegerVectorOptionKey const cluster::exclude_res ("cluster:exclude_res")
RealOptionKey const cluster::thinout_factor ("cluster:thinout_factor")
IntegerOptionKey const cluster::max_cluster_seeds ("cluster:max_cluster_seeds")
RealOptionKey const cluster::radius ("cluster:radius")
IntegerOptionKey const cluster::limit_cluster_size ("cluster:limit_cluster_size")
IntegerOptionKey const cluster::limit_clusters ("cluster:limit_clusters")
IntegerOptionKey const cluster::limit_total_structures ("cluster:limit_total_structures")
IntegerOptionKey const cluster::max_total_cluster ("cluster:max_total_cluster")
BooleanOptionKey const cluster::gdtmm ("cluster:gdtmm")
BooleanOptionKey const cluster::sort_groups_by_energy ("cluster:sort_groups_by_energy")
BooleanOptionKey const cluster::remove_singletons ("cluster:remove_singletons")
BooleanOptionKey const cluster::export_only_low ("cluster:export_only_low")
BooleanOptionKey const cluster::remove_highest_energy_member ("cluster:remove_highest_energy_member")
BooleanOptionKey const cluster::idealize_final_structures ("cluster:idealize_final_structures")
IntegerOptionKey const cluster::limit_dist_matrix ("cluster:limit_dist_matrix")
BooleanOptionKey const cluster::make_ensemble_cst ("cluster:make_ensemble_cst")
BooleanOptionKey const cluster::hotspot_hash ("cluster:hotspot_hash")
BooleanOptionKey const cluster::loops ("cluster:loops")
RealOptionKey const cluster::population_weight ("cluster:population_weight")
StringOptionKey const cluster::template_scores ("cluster:template_scores")
IntegerOptionKey const cluster::K_level ("cluster:K_level")
RealVectorOptionKey const cluster::K_radius ("cluster:K_radius")
IntegerVectorOptionKey const cluster::K_n_cluster ("cluster:K_n_cluster")
StringVectorOptionKey const cluster::K_style ("cluster:K_style")
RealOptionKey const cluster::K_threshold ("cluster:K_threshold")
IntegerOptionKey const cluster::K_n_sub ("cluster:K_n_sub")
IntegerOptionKey const cluster::K_deque_size ("cluster:K_deque_size")
IntegerOptionKey const cluster::K_deque_level ("cluster:K_deque_level")
BooleanOptionKey const cluster::K_redundant ("cluster:K_redundant")
BooleanOptionKey const cluster::K_not_fit_xyz ("cluster:K_not_fit_xyz")
BooleanOptionKey const cluster::K_save_headers ("cluster:K_save_headers")
BooleanOptionKey const rescore::rescore ("rescore")
BooleanOptionKey const rescore::pose_metrics ("rescore:pose_metrics")
BooleanOptionKey const rescore::skip ("rescore:skip")
BooleanOptionKey const rescore::verbose ("rescore:verbose")
StringOptionKey const rescore::msms_analysis ("rescore:msms_analysis")
BooleanOptionKey const mc::mc ("mc")
StringOptionKey const mc::hierarchical_pool ("mc:hierarchical_pool")
FileOptionKey const mc::read_structures_into_pool ("mc:read_structures_into_pool")
IntegerOptionKey const mc::convergence_check_frequency ("mc:convergence_check_frequency")
FileOptionKey const mc::known_structures ("mc:known_structures")
RealOptionKey const mc::max_rmsd_against_known_structures ("mc:max_rmsd_against_known_structures")
IntegerOptionKey const mc::heat_convergence_check ("mc:heat_convergence_check")
BooleanOptionKey const batch_relax::batch_relax ("batch_relax")
IntegerOptionKey const batch_relax::batch_size ("batch_relax:batch_size")
BooleanOptionKey const relax::relax ("relax")
BooleanOptionKey const relax::fast ("relax:fast")
BooleanOptionKey const relax::thorough ("relax:thorough")
BooleanOptionKey const relax::membrane ("relax:membrane")
IntegerOptionKey const relax::default_repeats ("relax:default_repeats")
BooleanOptionKey const relax::ramady ("relax:ramady")
RealOptionKey const relax::ramady_rms_limit ("relax:ramady_rms_limit")
RealOptionKey const relax::ramady_cutoff ("relax:ramady_cutoff")
IntegerOptionKey const relax::ramady_max_rebuild ("relax:ramady_max_rebuild")
BooleanOptionKey const relax::ramady_force ("relax:ramady_force")
FileOptionKey const relax::script ("relax:script")
IntegerOptionKey const relax::script_max_accept ("relax:script_max_accept")
BooleanOptionKey const relax::superimpose_to_native ("relax:superimpose_to_native")
FileOptionKey const relax::superimpose_to_file ("relax:superimpose_to_file")
BooleanOptionKey const relax::constrain_relax_to_native_coords ("relax:constrain_relax_to_native_coords")
BooleanOptionKey const relax::constrain_relax_to_start_coords ("relax:constrain_relax_to_start_coords")
RealOptionKey const relax::sc_cst_maxdist ("relax:sc_cst_maxdist")
BooleanOptionKey const relax::limit_aroma_chi2 ("relax:limit_aroma_chi2")
BooleanOptionKey const relax::bb_move ("relax:bb_move")
BooleanOptionKey const relax::chi_move ("relax:chi_move")
BooleanOptionKey const relax::jump_move ("relax:jump_move")
BooleanOptionKey const relax::minimize_bond_lengths ("relax:minimize_bond_lengths")
BooleanOptionKey const relax::minimize_bond_angles ("relax:minimize_bond_angles")
BooleanOptionKey const relax::minimize_mainchain_bond_lengths ("relax:minimize_mainchain_bond_lengths")
BooleanOptionKey const relax::minimize_mainchain_bond_angles ("relax:minimize_mainchain_bond_angles")
StringOptionKey const relax::min_type ("relax:min_type")
BooleanOptionKey const relax::cartesian ("relax:cartesian")
RealOptionKey const relax::chainbreak_weight ("relax:chainbreak_weight")
RealOptionKey const relax::linear_chainbreak_weight ("relax:linear_chainbreak_weight")
RealOptionKey const relax::overlap_chainbreak_weight ("relax:overlap_chainbreak_weight")
BooleanOptionKey const relax::classic ("relax:classic")
FileOptionKey const relax::sequence_file ("relax:sequence_file")
BooleanOptionKey const relax::quick ("relax:quick")
BooleanOptionKey const relax::sequence ("relax:sequence")
IntegerOptionKey const relax::minirelax_repeats ("relax:minirelax_repeats")
RealOptionKey const relax::minirelax_sdev ("relax:minirelax_sdev")
BooleanOptionKey const relax::wobblemoves ("relax:wobblemoves")
FileOptionKey const relax::constrain_relax_segments ("relax:constrain_relax_segments")
RealOptionKey const relax::coord_cst_width ("relax:coord_cst_width")
RealOptionKey const relax::coord_cst_stdev ("relax:coord_cst_stdev")
BooleanOptionKey const relax::ramp_constraints ("relax:ramp_constraints")
RealOptionKey const relax::energycut ("relax:energycut")
BooleanOptionKey const relax::mini ("relax:mini")
IntegerOptionKey const relax::stage1_ramp_cycles ("relax:stage1_ramp_cycles")
IntegerOptionKey const relax::stage1_ramp_inner_cycles ("relax:stage1_ramp_inner_cycles")
IntegerOptionKey const relax::stage2_repack_period ("relax:stage2_repack_period")
IntegerOptionKey const relax::stage2_cycles ("relax:stage2_cycles")
RealOptionKey const relax::min_tolerance ("relax:min_tolerance")
IntegerOptionKey const relax::stage3_cycles ("relax:stage3_cycles")
RealOptionKey const relax::cycle_ratio ("relax:cycle_ratio")
RealOptionKey const relax::filter_stage2_beginning ("relax:filter_stage2_beginning")
RealOptionKey const relax::filter_stage2_quarter ("relax:filter_stage2_quarter")
RealOptionKey const relax::filter_stage2_half ("relax:filter_stage2_half")
RealOptionKey const relax::filter_stage2_end ("relax:filter_stage2_end")
BooleanOptionKey const enzdes::enzdes ("enzdes")
StringOptionKey const enzdes::checkpoint ("enzdes:checkpoint")
BooleanOptionKey const enzdes::enz_score ("enzdes:enz_score")
BooleanOptionKey const enzdes::enz_repack ("enzdes:enz_repack")
BooleanOptionKey const enzdes::cst_opt ("enzdes:cst_opt")
BooleanOptionKey const enzdes::cst_predock ("enzdes:cst_predock")
RealOptionKey const enzdes::trans_magnitude ("enzdes:trans_magnitude")
RealOptionKey const enzdes::rot_magnitude ("enzdes:rot_magnitude")
RealOptionKey const enzdes::dock_trials ("enzdes:dock_trials")
BooleanOptionKey const enzdes::cst_min ("enzdes:cst_min")
BooleanOptionKey const enzdes::cst_design ("enzdes:cst_design")
IntegerOptionKey const enzdes::design_min_cycles ("enzdes:design_min_cycles")
BooleanOptionKey const enzdes::make_consensus_mutations ("enzdes:make_consensus_mutations")
BooleanOptionKey const enzdes::bb_min ("enzdes:bb_min")
RealOptionKey const enzdes::bb_min_allowed_dev ("enzdes:bb_min_allowed_dev")
RealOptionKey const enzdes::loop_bb_min_allowed_dev ("enzdes:loop_bb_min_allowed_dev")
RealOptionKey const enzdes::minimize_ligand_torsions ("enzdes:minimize_ligand_torsions")
RealOptionKey const enzdes::minimize_all_ligand_torsions ("enzdes:minimize_all_ligand_torsions")
BooleanOptionKey const enzdes::chi_min ("enzdes:chi_min")
BooleanOptionKey const enzdes::min_all_jumps ("enzdes:min_all_jumps")
BooleanOptionKey const enzdes::cst_dock ("enzdes:cst_dock")
BooleanOptionKey const enzdes::run_ligand_motifs ("enzdes:run_ligand_motifs")
BooleanOptionKey const enzdes::enz_debug ("enzdes:enz_debug")
FileOptionKey const enzdes::cstfile ("enzdes:cstfile")
FileOptionKey const enzdes::enz_loops_file ("enzdes:enz_loops_file")
BooleanOptionKey const enzdes::flexbb_protocol ("enzdes:flexbb_protocol")
BooleanOptionKey const enzdes::remodel_protocol ("enzdes:remodel_protocol")
BooleanOptionKey const enzdes::kic_loop_sampling ("enzdes:kic_loop_sampling")
StringOptionKey const enzdes::dump_loop_samples ("enzdes:dump_loop_samples")
BooleanOptionKey const enzdes::fix_catalytic_aa ("enzdes:fix_catalytic_aa")
IntegerOptionKey const enzdes::additional_packing_ligand_rb_confs ("enzdes:additional_packing_ligand_rb_confs")
IntegerOptionKey const enzdes::ex_catalytic_rot ("enzdes:ex_catalytic_rot")
IntegerOptionKey const enzdes::single_loop_ensemble_size ("enzdes:single_loop_ensemble_size")
IntegerOptionKey const enzdes::loop_generator_trials ("enzdes:loop_generator_trials")
BooleanOptionKey const enzdes::no_catres_min_in_loopgen ("enzdes:no_catres_min_in_loopgen")
RealOptionKey const enzdes::mc_kt_low ("enzdes:mc_kt_low")
RealOptionKey const enzdes::mc_kt_high ("enzdes:mc_kt_high")
RealOptionKey const enzdes::min_cacb_deviation ("enzdes:min_cacb_deviation")
RealOptionKey const enzdes::max_bb_deviation ("enzdes:max_bb_deviation")
RealOptionKey const enzdes::max_bb_deviation_from_startstruct ("enzdes:max_bb_deviation_from_startstruct")
IntegerOptionKey const enzdes::flexbb_outstructs ("enzdes:flexbb_outstructs")
IntegerOptionKey const enzdes::remodel_trials ("enzdes:remodel_trials")
BooleanOptionKey const enzdes::remodel_secmatch ("enzdes:remodel_secmatch")
BooleanOptionKey const enzdes::dump_inverse_rotamers ("enzdes:dump_inverse_rotamers")
RealOptionKey const enzdes::remodel_aggressiveness ("enzdes:remodel_aggressiveness")
RealOptionKey const enzdes::favor_native_res ("enzdes:favor_native_res")
BooleanOptionKey const enzdes::detect_design_interface ("enzdes:detect_design_interface")
BooleanOptionKey const enzdes::include_catres_in_interface_detection ("enzdes:include_catres_in_interface_detection")
BooleanOptionKey const enzdes::arg_sweep_interface ("enzdes:arg_sweep_interface")
RealOptionKey const enzdes::cut1 ("enzdes:cut1")
RealOptionKey const enzdes::cut2 ("enzdes:cut2")
RealOptionKey const enzdes::cut3 ("enzdes:cut3")
RealOptionKey const enzdes::cut4 ("enzdes:cut4")
RealOptionKey const enzdes::lig_packer_weight ("enzdes:lig_packer_weight")
BooleanOptionKey const enzdes::no_unconstrained_repack ("enzdes:no_unconstrained_repack")
RealOptionKey const enzdes::secmatch_Ecutoff ("enzdes:secmatch_Ecutoff")
FileOptionKey const enzdes::change_lig ("enzdes:change_lig")
StringOptionKey const enzdes::process_ligrot_separately ("enzdes:process_ligrot_separately")
BooleanOptionKey const enzdes::start_from_random_rb_conf ("enzdes:start_from_random_rb_conf")
RealOptionKey const enzdes::bb_bump_cutoff ("enzdes:bb_bump_cutoff")
RealOptionKey const enzdes::sc_sc_bump_cutoff ("enzdes:sc_sc_bump_cutoff")
BooleanOptionKey const enzdes::no_packstat_calculation ("enzdes:no_packstat_calculation")
StringOptionKey const enzdes::compare_native ("enzdes:compare_native")
BooleanOptionKey const enzdes::final_repack_without_ligand ("enzdes:final_repack_without_ligand")
BooleanOptionKey const enzdes::dump_final_repack_without_ligand_pdb ("enzdes:dump_final_repack_without_ligand_pdb")
BooleanOptionKey const enzdes::parser_read_cloud_pdb ("enzdes:parser_read_cloud_pdb")
BooleanOptionKey const packing::packing ("packing")
BooleanOptionKey const packing::repack_only ("packing:repack_only")
BooleanOptionKey const packing::prevent_repacking ("packing:prevent_repacking")
IntegerOptionKey const packing::ndruns ("packing:ndruns")
BooleanOptionKey const packing::soft_rep_design ("packing:soft_rep_design")
BooleanOptionKey const packing::use_electrostatic_repulsion ("packing:use_electrostatic_repulsion")
BooleanOptionKey const packing::dump_rotamer_sets ("packing:dump_rotamer_sets")
RealOptionKey const packing::dunbrack_prob_buried ("packing:dunbrack_prob_buried")
RealOptionKey const packing::dunbrack_prob_nonburied ("packing:dunbrack_prob_nonburied")
RealOptionKey const packing::dunbrack_prob_nonburied_semirotameric ("packing:dunbrack_prob_nonburied_semirotameric")
BooleanOptionKey const packing::no_optH ("packing:no_optH")
BooleanOptionKey const packing::optH_MCA ("packing:optH_MCA")
BooleanOptionKey const packing::pack_missing_sidechains ("packing:pack_missing_sidechains")
BooleanOptionKey const packing::preserve_c_beta ("packing:preserve_c_beta")
BooleanOptionKey const packing::flip_HNQ ("packing:flip_HNQ")
IntegerVectorOptionKey const packing::fix_his_tautomer ("packing:fix_his_tautomer")
BooleanOptionKey const packing::print_pymol_selection ("packing:print_pymol_selection")
BooleanOptionKey const packing::ex1::ex1 ("packing:ex1")
IntegerOptionKey const packing::ex1::level ("packing:ex1:level")
BooleanOptionKey const packing::ex1::operate ("packing:ex1:operate")
BooleanOptionKey const packing::ex2::ex2 ("packing:ex2")
IntegerOptionKey const packing::ex2::level ("packing:ex2:level")
BooleanOptionKey const packing::ex2::operate ("packing:ex2:operate")
BooleanOptionKey const packing::ex3::ex3 ("packing:ex3")
IntegerOptionKey const packing::ex3::level ("packing:ex3:level")
BooleanOptionKey const packing::ex3::operate ("packing:ex3:operate")
BooleanOptionKey const packing::ex4::ex4 ("packing:ex4")
IntegerOptionKey const packing::ex4::level ("packing:ex4:level")
BooleanOptionKey const packing::ex4::operate ("packing:ex4:operate")
BooleanOptionKey const packing::ex1aro::ex1aro ("packing:ex1aro")
IntegerOptionKey const packing::ex1aro::level ("packing:ex1aro:level")
BooleanOptionKey const packing::ex2aro::ex2aro ("packing:ex2aro")
IntegerOptionKey const packing::ex2aro::level ("packing:ex2aro:level")
BooleanOptionKey const packing::ex1aro_exposed::ex1aro_exposed ("packing:ex1aro_exposed")
IntegerOptionKey const packing::ex1aro_exposed::level ("packing:ex1aro_exposed:level")
BooleanOptionKey const packing::ex2aro_exposed::ex2aro_exposed ("packing:ex2aro_exposed")
IntegerOptionKey const packing::ex2aro_exposed::level ("packing:ex2aro_exposed:level")
BooleanOptionKey const packing::exdna::exdna ("packing:exdna")
IntegerOptionKey const packing::exdna::level ("packing:exdna:level")
IntegerOptionKey const packing::extrachi_cutoff ("packing:extrachi_cutoff")
FileVectorOptionKey const packing::resfile ("packing:resfile")
RealOptionKey const packing::outeriterations_scaling ("packing:outeriterations_scaling")
RealOptionKey const packing::inneriterations_scaling ("packing:inneriterations_scaling")
BooleanOptionKey const packing::explicit_h2o ("packing:explicit_h2o")
StringVectorOptionKey const packing::adducts ("packing:adducts")
BooleanOptionKey const packing::solvate ("packing:solvate")
BooleanOptionKey const packing::use_input_sc ("packing:use_input_sc")
FileVectorOptionKey const packing::unboundrot ("packing:unboundrot")
RealOptionKey const packing::max_rotbump_energy ("packing:max_rotbump_energy")
BooleanOptionKey const packing::lazy_ig ("packing:lazy_ig")
BooleanOptionKey const packing::double_lazy_ig ("packing:double_lazy_ig")
IntegerOptionKey const packing::double_lazy_ig_mem_limit ("packing:double_lazy_ig_mem_limit")
IntegerOptionKey const packing::linmem_ig ("packing:linmem_ig")
IntegerOptionKey const packing::multi_cool_annealer ("packing:multi_cool_annealer")
RealVectorOptionKey const packing::minpack_temp_schedule ("packing:minpack_temp_schedule")
IntegerOptionKey const packing::minpack_inner_iteration_scale ("packing:minpack_inner_iteration_scale")
BooleanOptionKey const packing::minpack_disable_bumpcheck ("packing:minpack_disable_bumpcheck")
BooleanOptionKey const phil::phil ("phil")
IntegerOptionKey const phil::nloop ("phil:nloop")
StringOptionKey const phil::vall_file ("phil:vall_file")
StringOptionKey const phil::align_file ("phil:align_file")
BooleanOptionKey const wum::wum ("wum")
IntegerOptionKey const wum::n_slaves_per_master ("wum:n_slaves_per_master")
IntegerOptionKey const wum::n_masters ("wum:n_masters")
IntegerOptionKey const wum::memory_limit ("wum:memory_limit")
StringOptionKey const wum::extra_scorefxn ("wum:extra_scorefxn")
FileOptionKey const wum::extra_scorefxn_ref_structure ("wum:extra_scorefxn_ref_structure")
IntegerOptionKey const wum::extra_scorefxn_relax ("wum:extra_scorefxn_relax")
RealOptionKey const wum::trim_proportion ("wum:trim_proportion")
BooleanOptionKey const lh::lh ("lh")
StringOptionKey const lh::db_prefix ("lh:db_prefix")
IntegerVectorOptionKey const lh::loopsizes ("lh:loopsizes")
IntegerOptionKey const lh::num_partitions ("lh:num_partitions")
PathOptionKey const lh::db_path ("lh:db_path")
BooleanOptionKey const lh::exclude_homo ("lh:exclude_homo")
StringOptionKey const lh::refstruct ("lh:refstruct")
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