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Namespaces | Functions
OptionKeys.cc.gen12.hh File Reference

Namespaces

 qsar
 
 rbe
 
 RBSegmentRelax
 
 hydrate
 
 rdc
 
 relax
 
 relax::range
 
 relax::centroid
 
 remodel
 
 remodel::staged_sampling
 
 remodel::domainFusion
 
 remodel::design
 
 remodel::RemodelLoopMover
 
 resample
 
 rescore
 
 rna
 
 rna::denovo
 

Functions

StringOptionKey const qsar::weights ("qsar:weights")
 
StringOptionKey const qsar::grid_dir ("qsar:grid_dir")
 
IntegerOptionKey const qsar::max_grid_cache_size ("qsar:max_grid_cache_size")
 
BooleanOptionKey const rbe::rbe ("rbe")
 
StringOptionKey const rbe::server_url ("rbe:server_url")
 
StringOptionKey const rbe::server_port ("rbe:server_port")
 
RealOptionKey const rbe::poll_frequency ("rbe:poll_frequency")
 
BooleanOptionKey const RBSegmentRelax::RBSegmentRelax ("RBSegmentRelax")
 
FileOptionKey const RBSegmentRelax::input_pdb ("RBSegmentRelax:input_pdb")
 
FileOptionKey const RBSegmentRelax::rb_file ("RBSegmentRelax:rb_file")
 
IntegerOptionKey const RBSegmentRelax::nrbmoves ("RBSegmentRelax:nrbmoves")
 
IntegerOptionKey const RBSegmentRelax::nrboutercycles ("RBSegmentRelax:nrboutercycles")
 
StringOptionKey const RBSegmentRelax::rb_scorefxn ("RBSegmentRelax:rb_scorefxn")
 
BooleanOptionKey const RBSegmentRelax::skip_fragment_moves ("RBSegmentRelax:skip_fragment_moves")
 
BooleanOptionKey const RBSegmentRelax::skip_seqshift_moves ("RBSegmentRelax:skip_seqshift_moves")
 
BooleanOptionKey const RBSegmentRelax::skip_rb_moves ("RBSegmentRelax:skip_rb_moves")
 
RealVectorOptionKey const RBSegmentRelax::helical_movement_params ("RBSegmentRelax:helical_movement_params")
 
RealVectorOptionKey const RBSegmentRelax::strand_movement_params ("RBSegmentRelax:strand_movement_params")
 
RealVectorOptionKey const RBSegmentRelax::default_movement_params ("RBSegmentRelax:default_movement_params")
 
IntegerOptionKey const RBSegmentRelax::cst_seqwidth ("RBSegmentRelax:cst_seqwidth")
 
BooleanOptionKey const hydrate::hydrate ("hydrate")
 
FileOptionKey const hydrate::hyfile ("hydrate:hyfile")
 
BooleanOptionKey const hydrate::hydrate_all ("hydrate:hydrate_all")
 
IntegerVectorOptionKey const hydrate::ignore_fa_sol_at_positions ("hydrate:ignore_fa_sol_at_positions")
 
BooleanOptionKey const hydrate::attempt_all_polar ("hydrate:attempt_all_polar")
 
RealOptionKey const hydrate::partial_hydrate_dew ("hydrate:partial_hydrate_dew")
 
RealOptionKey const hydrate::water_energy_threshold ("hydrate:water_energy_threshold")
 
IntegerOptionKey const hydrate::water_rotamers_cap ("hydrate:water_rotamers_cap")
 
RealOptionKey const hydrate::water_packing_radius ("hydrate:water_packing_radius")
 
RealOptionKey const hydrate::water_angular_resolution ("hydrate:water_angular_resolution")
 
RealOptionKey const hydrate::water_space_resolution ("hydrate:water_space_resolution")
 
RealOptionKey const hydrate::hbond_threshold ("hydrate:hbond_threshold")
 
RealOptionKey const hydrate::hbond_entropy_threshold ("hydrate:hbond_entropy_threshold")
 
RealOptionKey const hydrate::water_desolvation ("hydrate:water_desolvation")
 
IntegerOptionKey const hydrate::pack_nloop ("hydrate:pack_nloop")
 
BooleanOptionKey const hydrate::pre_bump_check ("hydrate:pre_bump_check")
 
BooleanOptionKey const hydrate::bias_design_search_to_native ("hydrate:bias_design_search_to_native")
 
BooleanOptionKey const hydrate::show_derivatives_check ("hydrate:show_derivatives_check")
 
BooleanOptionKey const hydrate::keep_non_buried_waters ("hydrate:keep_non_buried_waters")
 
BooleanOptionKey const hydrate::display_water_hb_network ("hydrate:display_water_hb_network")
 
BooleanOptionKey const hydrate::show_pre_post_filter_water_rotamers ("hydrate:show_pre_post_filter_water_rotamers")
 
BooleanOptionKey const hydrate::show_pre_filtered_water_rotamers_count ("hydrate:show_pre_filtered_water_rotamers_count")
 
BooleanOptionKey const hydrate::show_residues_near_water ("hydrate:show_residues_near_water")
 
BooleanOptionKey const hydrate::only_remove_non_buried_waters ("hydrate:only_remove_non_buried_waters")
 
BooleanOptionKey const hydrate::just_score ("hydrate:just_score")
 
BooleanOptionKey const hydrate::show_rotamer_count ("hydrate:show_rotamer_count")
 
StringOptionKey const hydrate::protein_flexibility ("hydrate:protein_flexibility")
 
RealOptionKey const hydrate::near_water_threshold ("hydrate:near_water_threshold")
 
BooleanOptionKey const hydrate::minimize_bb_where_packing ("hydrate:minimize_bb_where_packing")
 
BooleanOptionKey const hydrate::dont_hydrate_hb_engaged_bb_O ("hydrate:dont_hydrate_hb_engaged_bb_O")
 
BooleanOptionKey const hydrate::short_residence_time_mode ("hydrate:short_residence_time_mode")
 
FileOptionKey const hydrate::min_backbone_file ("hydrate:min_backbone_file")
 
BooleanOptionKey const hydrate::single_away_rotamer ("hydrate:single_away_rotamer")
 
BooleanOptionKey const hydrate::force_enforce_all_waters ("hydrate:force_enforce_all_waters")
 
BooleanOptionKey const rdc::rdc ("rdc")
 
BooleanOptionKey const rdc::correct_NH_length ("rdc:correct_NH_length")
 
BooleanOptionKey const rdc::reduced_couplings ("rdc:reduced_couplings")
 
FileOptionKey const rdc::weights ("rdc:weights")
 
RealOptionKey const rdc::iterate_weights ("rdc:iterate_weights")
 
FileOptionKey const rdc::segment_file ("rdc:segment_file")
 
StringOptionKey const rdc::segment_scoring_mode ("rdc:segment_scoring_mode")
 
RealOptionKey const rdc::total_weight ("rdc:total_weight")
 
RealOptionKey const rdc::tensor_weight ("rdc:tensor_weight")
 
FileOptionKey const rdc::print_rdc_values ("rdc:print_rdc_values")
 
RealOptionKey const rdc::iterate_tol ("rdc:iterate_tol")
 
BooleanOptionKey const rdc::iterate_reset ("rdc:iterate_reset")
 
FileOptionKey const rdc::dump_weight_trajectory ("rdc:dump_weight_trajectory")
 
RealVectorOptionKey const rdc::fix_normAzz ("rdc:fix_normAzz")
 
StringOptionKey const rdc::fit_method ("rdc:fit_method")
 
RealVectorOptionKey const rdc::fixDa ("rdc:fixDa")
 
RealVectorOptionKey const rdc::fixR ("rdc:fixR")
 
IntegerOptionKey const rdc::nlsrepeat ("rdc:nlsrepeat")
 
BooleanOptionKey const relax::relax ("relax")
 
BooleanOptionKey const relax::fast ("relax:fast")
 
BooleanOptionKey const relax::thorough ("relax:thorough")
 
BooleanOptionKey const relax::centroid_mode ("relax:centroid_mode")
 
IntegerOptionKey const relax::default_repeats ("relax:default_repeats")
 
BooleanOptionKey const relax::dualspace ("relax:dualspace")
 
BooleanOptionKey const relax::cyclic_peptide ("relax:cyclic_peptide")
 
BooleanOptionKey const relax::range::range ("relax:range")
 
BooleanOptionKey const relax::range::set_tm_helical ("relax:range:set_tm_helical")
 
RealOptionKey const relax::range::kT ("relax:range:kT")
 
RealOptionKey const relax::range::angle_max ("relax:range:angle_max")
 
StringOptionKey const relax::range::nmoves ("relax:range:nmoves")
 
BooleanOptionKey const relax::range::spherical_wave ("relax:range:spherical_wave")
 
BooleanOptionKey const relax::range::repack_again ("relax:range:repack_again")
 
IntegerOptionKey const relax::range::cycles ("relax:range:cycles")
 
IntegerOptionKey const relax::range::min_cycles ("relax:range:min_cycles")
 
BooleanOptionKey const relax::range::idealize ("relax:range:idealize")
 
BooleanOptionKey const relax::range::skip_relax ("relax:range:skip_relax")
 
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")
 
BooleanOptionKey const relax::coord_constrain_sidechains ("relax:coord_constrain_sidechains")
 
RealOptionKey const relax::sc_cst_maxdist ("relax:sc_cst_maxdist")
 
BooleanOptionKey const relax::limit_aroma_chi2 ("relax:limit_aroma_chi2")
 
BooleanOptionKey const relax::respect_resfile ("relax:respect_resfile")
 
BooleanOptionKey const relax::use_explicit_water ("relax:use_explicit_water")
 
BooleanOptionKey const relax::movemap_disables_packing_of_fixed_chi_positions ("relax:movemap_disables_packing_of_fixed_chi_positions")
 
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::dna_move ("relax:dna_move")
 
BooleanOptionKey const relax::fix_omega ("relax:fix_omega")
 
BooleanOptionKey const relax::minimize_bond_lengths ("relax:minimize_bond_lengths")
 
BooleanOptionKey const relax::minimize_bond_angles ("relax:minimize_bond_angles")
 
IntegerOptionKey const relax::minimize_bondlength_subset ("relax:minimize_bondlength_subset")
 
IntegerOptionKey const relax::minimize_bondangle_subset ("relax:minimize_bondangle_subset")
 
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 relax::centroid::centroid ("relax:centroid")
 
StringOptionKey const relax::centroid::weights ("relax:centroid:weights")
 
BooleanOptionKey const relax::centroid::ramp_vdw ("relax:centroid:ramp_vdw")
 
BooleanOptionKey const relax::centroid::ramp_rama ("relax:centroid:ramp_rama")
 
StringOptionKey const relax::centroid::parameters ("relax:centroid:parameters")
 
BooleanOptionKey const relax::centroid::do_final_repack ("relax:centroid:do_final_repack")
 
BooleanOptionKey const relax::centroid::increase_vdw_radii ("relax:centroid:increase_vdw_radii")
 
BooleanOptionKey const remodel::remodel ("remodel")
 
FileOptionKey const remodel::blueprint ("remodel:blueprint")
 
FileOptionKey const remodel::cstfile ("remodel:cstfile")
 
BooleanOptionKey const remodel::cst_fa_only ("remodel:cst_fa_only")
 
IntegerOptionKey const remodel::cstfilter ("remodel:cstfilter")
 
StringOptionKey const remodel::cen_sfxn ("remodel:cen_sfxn")
 
BooleanOptionKey const remodel::check_scored_centroid ("remodel:check_scored_centroid")
 
IntegerOptionKey const remodel::num_trajectory ("remodel:num_trajectory")
 
IntegerOptionKey const remodel::save_top ("remodel:save_top")
 
BooleanOptionKey const remodel::swap_refine_confirm_protocols ("remodel:swap_refine_confirm_protocols")
 
BooleanOptionKey const remodel::bypass_fragments ("remodel:bypass_fragments")
 
BooleanOptionKey const remodel::use_same_length_fragments ("remodel:use_same_length_fragments")
 
BooleanOptionKey const remodel::no_jumps ("remodel:no_jumps")
 
IntegerOptionKey const remodel::reroot_tree ("remodel:reroot_tree")
 
BooleanOptionKey const remodel::use_blueprint_sequence ("remodel:use_blueprint_sequence ")
 
BooleanOptionKey const remodel::quick_and_dirty ("remodel:quick_and_dirty ")
 
BooleanOptionKey const remodel::checkpoint ("remodel:checkpoint ")
 
BooleanOptionKey const remodel::use_pose_relax ("remodel:use_pose_relax ")
 
BooleanOptionKey const remodel::use_cart_relax ("remodel:use_cart_relax ")
 
BooleanOptionKey const remodel::free_relax ("remodel:free_relax ")
 
StringOptionKey const remodel::generic_aa ("remodel:generic_aa")
 
RealOptionKey const remodel::cluster_radius ("remodel:cluster_radius")
 
BooleanOptionKey const remodel::use_clusters ("remodel:use_clusters")
 
BooleanOptionKey const remodel::run_confirmation ("remodel:run_confirmation")
 
BooleanOptionKey const remodel::cluster_on_entire_pose ("remodel:cluster_on_entire_pose")
 
IntegerOptionKey const remodel::dr_cycles ("remodel:dr_cycles")
 
IntegerOptionKey const remodel::two_chain_tree ("remodel:two_chain_tree")
 
IntegerOptionKey const remodel::repeat_structure ("remodel:repeat_structure")
 
IntegerOptionKey const remodel::lh_ex_limit ("remodel:lh_ex_limit")
 
StringVectorOptionKey const remodel::lh_filter_string ("remodel:lh_filter_string")
 
IntegerOptionKey const remodel::lh_cbreak_selection ("remodel:lh_cbreak_selection")
 
BooleanOptionKey const remodel::lh_closure_filter ("remodel:lh_closure_filter")
 
BooleanOptionKey const remodel::cen_minimize ("remodel:cen_minimize")
 
IntegerOptionKey const remodel::core_cutoff ("remodel:core_cutoff")
 
IntegerOptionKey const remodel::boundary_cutoff ("remodel:boundary_cutoff")
 
StringOptionKey const remodel::coreAA ("remodel:coreAA")
 
StringOptionKey const remodel::boundaryAA ("remodel:boundaryAA")
 
StringOptionKey const remodel::surfaceAA ("remodel:surfaceAA")
 
BooleanOptionKey const remodel::design_around_ligand ("remodel:design_around_ligand")
 
BooleanOptionKey const remodel::move_ligand ("remodel:move_ligand")
 
BooleanOptionKey const remodel::resclass_by_sasa ("remodel:resclass_by_sasa")
 
RealOptionKey const remodel::helical_rise ("remodel:helical_rise")
 
RealOptionKey const remodel::helical_radius ("remodel:helical_radius")
 
RealOptionKey const remodel::helical_omega ("remodel:helical_omega")
 
RealVectorOptionKey const remodel::filter_rise ("remodel:filter_rise")
 
RealVectorOptionKey const remodel::filter_radius ("remodel:filter_radius")
 
RealVectorOptionKey const remodel::filter_omega ("remodel:filter_omega")
 
RealOptionKey const remodel::COM_sd ("remodel:COM_sd")
 
RealOptionKey const remodel::COM_tolerance ("remodel:COM_tolerance")
 
RealOptionKey const remodel::vdw ("remodel:vdw")
 
RealOptionKey const remodel::rama ("remodel:rama")
 
RealOptionKey const remodel::cbeta ("remodel:cbeta")
 
RealOptionKey const remodel::cenpack ("remodel:cenpack")
 
RealOptionKey const remodel::rg_local ("remodel:rg_local")
 
RealOptionKey const remodel::hb_lrbb ("remodel:hb_lrbb")
 
RealOptionKey const remodel::hb_srbb ("remodel:hb_srbb")
 
RealOptionKey const remodel::rg ("remodel:rg")
 
RealOptionKey const remodel::rsigma ("remodel:rsigma")
 
RealOptionKey const remodel::ss_pair ("remodel:ss_pair")
 
BooleanOptionKey const remodel::build_disulf ("remodel:build_disulf")
 
RealOptionKey const remodel::match_rt_limit ("remodel:match_rt_limit")
 
IntegerVectorOptionKey const remodel::disulf_landing_range ("remodel:disulf_landing_range")
 
BooleanOptionKey const remodel::rank_by_bsasa ("remodel:rank_by_bsasa")
 
BooleanOptionKey const remodel::staged_sampling::staged_sampling ("remodel:staged_sampling")
 
StringOptionKey const remodel::staged_sampling::loop_9mer_score_file ("remodel:staged_sampling:loop_9mer_score_file")
 
StringOptionKey const remodel::staged_sampling::loop_3mer_score_file ("remodel:staged_sampling:loop_3mer_score_file")
 
StringOptionKey const remodel::staged_sampling::all_9mer_score_file ("remodel:staged_sampling:all_9mer_score_file")
 
StringOptionKey const remodel::staged_sampling::all_3mer_score_file ("remodel:staged_sampling:all_3mer_score_file")
 
IntegerOptionKey const remodel::staged_sampling::loop_9mer_cycles ("remodel:staged_sampling:loop_9mer_cycles")
 
IntegerOptionKey const remodel::staged_sampling::loop_3mer_cycles ("remodel:staged_sampling:loop_3mer_cycles")
 
IntegerOptionKey const remodel::staged_sampling::all_9mer_cycles ("remodel:staged_sampling:all_9mer_cycles")
 
IntegerOptionKey const remodel::staged_sampling::all_3mer_cycles ("remodel:staged_sampling:all_3mer_cycles")
 
BooleanOptionKey const remodel::staged_sampling::fa_mode ("remodel:staged_sampling:fa_mode")
 
BooleanOptionKey const remodel::staged_sampling::fa_relax_moves ("remodel:staged_sampling:fa_relax_moves")
 
BooleanOptionKey const remodel::staged_sampling::loop_btw_parametric_components ("remodel:staged_sampling:loop_btw_parametric_components")
 
BooleanOptionKey const remodel::staged_sampling::pre_centroid ("remodel:staged_sampling:pre_centroid")
 
BooleanOptionKey const remodel::staged_sampling::sample_over_loops ("remodel:staged_sampling:sample_over_loops")
 
BooleanOptionKey const remodel::staged_sampling::small_moves ("remodel:staged_sampling:small_moves")
 
StringOptionKey const remodel::staged_sampling::starting_sequence ("remodel:staged_sampling:starting_sequence")
 
FileOptionKey const remodel::staged_sampling::starting_pdb ("remodel:staged_sampling:starting_pdb")
 
StringOptionKey const remodel::staged_sampling::starting_non_canonical ("remodel:staged_sampling:starting_non_canonical")
 
BooleanOptionKey const remodel::staged_sampling::start_w_ideal_helices ("remodel:staged_sampling:start_w_ideal_helices")
 
BooleanOptionKey const remodel::staged_sampling::sym_move ("remodel:staged_sampling:sym_move")
 
FileOptionKey const remodel::staged_sampling::residues_to_sample ("remodel:staged_sampling:residues_to_sample")
 
BooleanOptionKey const remodel::staged_sampling::require_frags_match_blueprint ("remodel:staged_sampling:require_frags_match_blueprint")
 
BooleanOptionKey const remodel::domainFusion::domainFusion ("remodel:domainFusion")
 
FileOptionKey const remodel::domainFusion::insert_segment_from_pdb ("remodel:domainFusion:insert_segment_from_pdb")
 
FileOptionKey const remodel::domainFusion::insert_segment2_from_pdb ("remodel:domainFusion:insert_segment2_from_pdb")
 
BooleanOptionKey const remodel::design::design ("remodel:design")
 
BooleanOptionKey const remodel::design::no_design ("remodel:design:no_design ")
 
BooleanOptionKey const remodel::design::design_all ("remodel:design:design_all")
 
BooleanOptionKey const remodel::design::allow_rare_aro_chi ("remodel:design:allow_rare_aro_chi")
 
BooleanOptionKey const remodel::design::skip_partial ("remodel:design:skip_partial")
 
BooleanOptionKey const remodel::design::design_neighbors ("remodel:design:design_neighbors")
 
BooleanOptionKey const remodel::design::find_neighbors ("remodel:design:find_neighbors")
 
BooleanOptionKey const remodel::design::include_current ("remodel:design:include_current")
 
BooleanOptionKey const remodel::RemodelLoopMover::RemodelLoopMover ("remodel:RemodelLoopMover")
 
RealOptionKey const remodel::RemodelLoopMover::max_linear_chainbreak ("remodel:RemodelLoopMover:max_linear_chainbreak")
 
BooleanOptionKey const remodel::RemodelLoopMover::randomize_loops ("remodel:RemodelLoopMover:randomize_loops")
 
BooleanOptionKey const remodel::RemodelLoopMover::use_loop_hash ("remodel:RemodelLoopMover:use_loop_hash")
 
FileOptionKey const remodel::RemodelLoopMover::set_segment ("remodel:RemodelLoopMover:set_segment")
 
IntegerOptionKey const remodel::RemodelLoopMover::allowed_closure_attempts ("remodel:RemodelLoopMover:allowed_closure_attempts")
 
IntegerOptionKey const remodel::RemodelLoopMover::loophash_cycles ("remodel:RemodelLoopMover:loophash_cycles")
 
IntegerOptionKey const remodel::RemodelLoopMover::simultaneous_cycles ("remodel:RemodelLoopMover:simultaneous_cycles")
 
IntegerOptionKey const remodel::RemodelLoopMover::independent_cycles ("remodel:RemodelLoopMover:independent_cycles")
 
IntegerOptionKey const remodel::RemodelLoopMover::boost_closure_cycles ("remodel:RemodelLoopMover:boost_closure_cycles")
 
RealOptionKey const remodel::RemodelLoopMover::threshold_for_boost_closure ("remodel:RemodelLoopMover:threshold_for_boost_closure")
 
IntegerOptionKey const remodel::RemodelLoopMover::force_cutting_index ("remodel:RemodelLoopMover:force_cutting_index")
 
BooleanOptionKey const remodel::RemodelLoopMover::force_cutting_N ("remodel:RemodelLoopMover:force_cutting_N")
 
BooleanOptionKey const remodel::RemodelLoopMover::bypass_closure ("remodel:RemodelLoopMover:bypass_closure")
 
BooleanOptionKey const remodel::RemodelLoopMover::cyclic_peptide ("remodel:RemodelLoopMover:cyclic_peptide")
 
RealOptionKey const remodel::RemodelLoopMover::temperature ("remodel:RemodelLoopMover:temperature")
 
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 rescore::rescore ("rescore")
 
BooleanOptionKey const rescore::assign_ss ("rescore:assign_ss")
 
BooleanOptionKey const rescore::skip ("rescore:skip")
 
BooleanOptionKey const rescore::verbose ("rescore:verbose")
 
BooleanOptionKey const rna::rna ("rna")
 
BooleanOptionKey const rna::corrected_geo ("rna:corrected_geo")
 
BooleanOptionKey const rna::vary_geometry ("rna:vary_geometry")
 
StringOptionKey const rna::data_file ("rna:data_file")
 
BooleanOptionKey const rna::cut_at_rna_chainbreak ("rna:cut_at_rna_chainbreak")
 
BooleanOptionKey const rna::evaluate_base_pairs ("rna:evaluate_base_pairs")
 
BooleanOptionKey const rna::denovo::denovo ("rna:denovo")
 
IntegerOptionKey const rna::denovo::cycles ("rna:denovo:cycles")
 
RealOptionKey const rna::denovo::rna_protein_docking_freq ("rna:denovo:rna_protein_docking_freq")
 
IntegerOptionKey const rna::denovo::rounds ("rna:denovo:rounds")
 
RealOptionKey const rna::denovo::temperature ("rna:denovo:temperature")
 
BooleanOptionKey const rna::denovo::minimize_rna ("rna:denovo:minimize_rna")