Rosetta Utilities  2014.35
Namespaces | Functions
OptionKeys.cc.gen3.hh File Reference

Namespaces

 pb_potential
 
 PCS
 
 PCSTS1
 
 PCSTS2
 
 PCSTS3
 
 PCSTS4
 
 pepspec
 
 pH
 
 pH::calc_pka
 
 pocket_grid
 
 ProQ
 
 qsar
 
 rbe
 
 RBSegmentRelax
 
 rdc
 
 relax
 
 relax::centroid
 
 remodel
 
 remodel::staged_sampling
 
 remodel::domainFusion
 
 remodel::design
 
 remodel::RemodelLoopMover
 
 resample
 
 rescore
 
 rna
 
 rotamerdump
 
 sicdock
 
 sewing
 
 SSrbrelax
 
 stepwise
 
 stepwise::monte_carlo
 
 stepwise::rna
 
 stepwise::protein
 
 full_model
 
 full_model::rna
 
 strand_assembly
 
 TailSegment
 
 templates
 
 templates::cst
 
 templates::fragsteal
 
 unfolded_state
 
 wum
 
 blivens
 
 blivens::disulfide_scorer
 
 cmiles
 
 cmiles::kcluster
 
 cmiles::jumping
 
 crossmatch
 
 dwkulp
 
 evolution
 
 james
 
 krassk
 
 murphp
 
 phil
 
 robert
 
 rot_anl
 
 smhybrid
 
 threadsc
 
 ufv
 
 ufv::insert
 
 willmatch
 

Functions

BooleanOptionKey const pb_potential::calcenergy ("pb_potential:calcenergy")
 
BooleanOptionKey const PCS::PCS ("PCS")
 
FileOptionKey const PCS::write_extra ("PCS:write_extra")
 
IntegerOptionKey const PCS::normalization_id ("PCS:normalization_id")
 
BooleanOptionKey const PCSTS1::PCSTS1 ("PCSTS1")
 
FileOptionKey const PCSTS1::write_extra ("PCSTS1:write_extra")
 
IntegerOptionKey const PCSTS1::normalization_id ("PCSTS1:normalization_id")
 
BooleanOptionKey const PCSTS2::PCSTS2 ("PCSTS2")
 
FileOptionKey const PCSTS2::write_extra ("PCSTS2:write_extra")
 
IntegerOptionKey const PCSTS2::normalization_id ("PCSTS2:normalization_id")
 
BooleanOptionKey const PCSTS3::PCSTS3 ("PCSTS3")
 
FileOptionKey const PCSTS3::write_extra ("PCSTS3:write_extra")
 
IntegerOptionKey const PCSTS3::normalization_id ("PCSTS3:normalization_id")
 
BooleanOptionKey const PCSTS4::PCSTS4 ("PCSTS4")
 
FileOptionKey const PCSTS4::write_extra ("PCSTS4:write_extra")
 
IntegerOptionKey const PCSTS4::normalization_id ("PCSTS4:normalization_id")
 
BooleanOptionKey const pepspec::pepspec ("pepspec")
 
StringOptionKey const pepspec::soft_wts ("pepspec:soft_wts")
 
StringOptionKey const pepspec::cen_wts ("pepspec:cen_wts")
 
BooleanOptionKey const pepspec::binding_score ("pepspec:binding_score")
 
BooleanOptionKey const pepspec::no_cen ("pepspec:no_cen")
 
BooleanOptionKey const pepspec::no_cen_rottrials ("pepspec:no_cen_rottrials")
 
BooleanOptionKey const pepspec::run_sequential ("pepspec:run_sequential")
 
IntegerOptionKey const pepspec::pep_anchor ("pepspec:pep_anchor")
 
StringOptionKey const pepspec::pep_chain ("pepspec:pep_chain")
 
IntegerOptionKey const pepspec::n_peptides ("pepspec:n_peptides")
 
IntegerOptionKey const pepspec::n_build_loop ("pepspec:n_build_loop")
 
IntegerOptionKey const pepspec::n_cgrelax_loop ("pepspec:n_cgrelax_loop")
 
IntegerOptionKey const pepspec::n_dock_loop ("pepspec:n_dock_loop")
 
RealOptionKey const pepspec::interface_cutoff ("pepspec:interface_cutoff")
 
BooleanOptionKey const pepspec::use_input_bb ("pepspec:use_input_bb")
 
BooleanOptionKey const pepspec::remove_input_bb ("pepspec:remove_input_bb")
 
StringOptionKey const pepspec::homol_csts ("pepspec:homol_csts")
 
RealOptionKey const pepspec::p_homol_csts ("pepspec:p_homol_csts")
 
BooleanOptionKey const pepspec::gen_pep_bb_sequential ("pepspec:gen_pep_bb_sequential")
 
StringOptionKey const pepspec::input_seq ("pepspec:input_seq")
 
StringOptionKey const pepspec::ss_type ("pepspec:ss_type")
 
BooleanOptionKey const pepspec::upweight_interface ("pepspec:upweight_interface")
 
BooleanOptionKey const pepspec::calc_sasa ("pepspec:calc_sasa")
 
BooleanOptionKey const pepspec::diversify_pep_seqs ("pepspec:diversify_pep_seqs")
 
IntegerOptionKey const pepspec::diversify_lvl ("pepspec:diversify_lvl")
 
BooleanOptionKey const pepspec::dump_cg_bb ("pepspec:dump_cg_bb")
 
BooleanOptionKey const pepspec::save_low_pdbs ("pepspec:save_low_pdbs")
 
BooleanOptionKey const pepspec::save_all_pdbs ("pepspec:save_all_pdbs")
 
BooleanOptionKey const pepspec::no_design ("pepspec:no_design")
 
StringOptionKey const pepspec::pdb_list ("pepspec:pdb_list")
 
StringOptionKey const pepspec::ref_pdb_list ("pepspec:ref_pdb_list")
 
BooleanOptionKey const pepspec::add_buffer_res ("pepspec:add_buffer_res")
 
StringOptionKey const pepspec::cg_res_type ("pepspec:cg_res_type")
 
IntegerOptionKey const pepspec::native_pep_anchor ("pepspec:native_pep_anchor")
 
StringOptionKey const pepspec::native_pep_chain ("pepspec:native_pep_chain")
 
BooleanOptionKey const pepspec::native_align ("pepspec:native_align")
 
BooleanOptionKey const pepspec::rmsd_analysis ("pepspec:rmsd_analysis")
 
StringOptionKey const pepspec::anchor_type ("pepspec:anchor_type")
 
BooleanOptionKey const pepspec::no_prepack_prot ("pepspec:no_prepack_prot")
 
BooleanOptionKey const pepspec::prep_use_ref_rotamers ("pepspec:prep_use_ref_rotamers")
 
IntegerOptionKey const pepspec::n_prepend ("pepspec:n_prepend")
 
IntegerOptionKey const pepspec::n_append ("pepspec:n_append")
 
RealOptionKey const pepspec::clash_cutoff ("pepspec:clash_cutoff")
 
RealOptionKey const pepspec::n_anchor_dock_std_devs ("pepspec:n_anchor_dock_std_devs")
 
RealOptionKey const pepspec::prep_trans_std_dev ("pepspec:prep_trans_std_dev")
 
RealOptionKey const pepspec::prep_rot_std_dev ("pepspec:prep_rot_std_dev")
 
BooleanOptionKey const pepspec::seq_align ("pepspec:seq_align")
 
StringOptionKey const pepspec::prep_align_prot_to ("pepspec:prep_align_prot_to")
 
BooleanOptionKey const pH::pH ("pH")
 
BooleanOptionKey const pH::pH_mode ("pH:pH_mode")
 
BooleanOptionKey const pH::keep_input_protonation_state ("pH:keep_input_protonation_state")
 
RealOptionKey const pH::value_pH ("pH:value_pH")
 
BooleanOptionKey const pH::calc_pka::calc_pka ("pH:calc_pka")
 
BooleanOptionKey const pH::calc_pka::pka_all ("pH:calc_pka:pka_all")
 
RealVectorOptionKey const pH::calc_pka::pka_for_resnos ("pH:calc_pka:pka_for_resnos")
 
StringOptionKey const pH::calc_pka::pka_for_chainno ("pH:calc_pka:pka_for_chainno")
 
BooleanOptionKey const pH::calc_pka::pH_neighbor_pack ("pH:calc_pka:pH_neighbor_pack")
 
RealOptionKey const pH::calc_pka::pka_rad ("pH:calc_pka:pka_rad")
 
BooleanOptionKey const pH::calc_pka::pH_prepack ("pH:calc_pka:pH_prepack")
 
BooleanOptionKey const pH::calc_pka::pH_relax ("pH:calc_pka:pH_relax")
 
BooleanOptionKey const pH::calc_pka::rotamer_prot_stats ("pH:calc_pka:rotamer_prot_stats")
 
FileVectorOptionKey const pH::pH_unbound ("pH:pH_unbound")
 
BooleanOptionKey const pH::output_raw_scores ("pH:output_raw_scores")
 
BooleanOptionKey const pH::pre_process ("pH:pre_process")
 
StringOptionKey const pH::cognate_partners ("pH:cognate_partners")
 
FileOptionKey const pH::cognate_pdb ("pH:cognate_pdb")
 
BooleanOptionKey const pocket_grid::pocket_grid ("pocket_grid")
 
RealOptionKey const pocket_grid::pocket_grid_size ("pocket_grid:pocket_grid_size")
 
RealOptionKey const pocket_grid::pocket_grid_size_x ("pocket_grid:pocket_grid_size_x")
 
RealOptionKey const pocket_grid::pocket_grid_size_y ("pocket_grid:pocket_grid_size_y")
 
RealOptionKey const pocket_grid::pocket_grid_size_z ("pocket_grid:pocket_grid_size_z")
 
RealOptionKey const pocket_grid::pocket_grid_spacing ("pocket_grid:pocket_grid_spacing")
 
RealOptionKey const pocket_grid::pocket_max_spacing ("pocket_grid:pocket_max_spacing")
 
RealOptionKey const pocket_grid::pocket_min_size ("pocket_grid:pocket_min_size")
 
RealOptionKey const pocket_grid::pocket_max_size ("pocket_grid:pocket_max_size")
 
RealOptionKey const pocket_grid::pocket_probe_radius ("pocket_grid:pocket_probe_radius")
 
StringOptionKey const pocket_grid::central_relax_pdb_num ("pocket_grid:central_relax_pdb_num")
 
IntegerOptionKey const pocket_grid::pocket_ntrials ("pocket_grid:pocket_ntrials")
 
IntegerOptionKey const pocket_grid::pocket_num_angles ("pocket_grid:pocket_num_angles")
 
BooleanOptionKey const pocket_grid::pocket_side ("pocket_grid:pocket_side")
 
BooleanOptionKey const pocket_grid::pocket_dump_pdbs ("pocket_grid:pocket_dump_pdbs")
 
BooleanOptionKey const pocket_grid::pocket_dump_exemplars ("pocket_grid:pocket_dump_exemplars")
 
BooleanOptionKey const pocket_grid::pocket_filter_by_exemplar ("pocket_grid:pocket_filter_by_exemplar")
 
BooleanOptionKey const pocket_grid::pocket_restrict_size ("pocket_grid:pocket_restrict_size")
 
BooleanOptionKey const pocket_grid::pocket_ignore_buried ("pocket_grid:pocket_ignore_buried")
 
BooleanOptionKey const pocket_grid::pocket_only_buried ("pocket_grid:pocket_only_buried")
 
BooleanOptionKey const pocket_grid::pocket_psp ("pocket_grid:pocket_psp")
 
BooleanOptionKey const pocket_grid::pocket_sps ("pocket_grid:pocket_sps")
 
BooleanOptionKey const pocket_grid::pocket_search13 ("pocket_grid:pocket_search13")
 
RealOptionKey const pocket_grid::pocket_surface_score ("pocket_grid:pocket_surface_score")
 
RealOptionKey const pocket_grid::pocket_surface_dist ("pocket_grid:pocket_surface_dist")
 
RealOptionKey const pocket_grid::pocket_buried_score ("pocket_grid:pocket_buried_score")
 
RealOptionKey const pocket_grid::pocket_buried_dist ("pocket_grid:pocket_buried_dist")
 
RealOptionKey const pocket_grid::pocket_exemplar_vdw_pen ("pocket_grid:pocket_exemplar_vdw_pen")
 
BooleanOptionKey const pocket_grid::print_grid ("pocket_grid:print_grid")
 
RealOptionKey const pocket_grid::extra_eggshell_dist ("pocket_grid:extra_eggshell_dist")
 
RealOptionKey const pocket_grid::eggshell_dist ("pocket_grid:eggshell_dist")
 
BooleanOptionKey const pocket_grid::pocket_static_grid ("pocket_grid:pocket_static_grid")
 
BooleanOptionKey const ProQ::ProQ ("ProQ")
 
IntegerOptionKey const ProQ::svmmodel ("ProQ:svmmodel")
 
StringOptionKey const ProQ::basename ("ProQ:basename")
 
BooleanOptionKey const ProQ::membrane ("ProQ:membrane")
 
BooleanOptionKey const ProQ::prof_bug ("ProQ:prof_bug")
 
BooleanOptionKey const ProQ::output_feature_vector ("ProQ:output_feature_vector")
 
BooleanOptionKey const ProQ::output_local_prediction ("ProQ:output_local_prediction")
 
StringOptionKey const ProQ::prefix ("ProQ:prefix")
 
BooleanOptionKey const ProQ::use_gzip ("ProQ:use_gzip")
 
RealOptionKey const ProQ::normalize ("ProQ:normalize")
 
BooleanOptionKey const qsar::qsar ("qsar")
 
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 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::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::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")
 
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")
 
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")
 
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")
 
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::staged_sampling::staged_sampling ("remodel:staged_sampling")
 
FileOptionKey const remodel::staged_sampling::residues_to_sample ("remodel:staged_sampling:residues_to_sample")
 
StringOptionKey const remodel::staged_sampling::starting_sequence ("remodel:staged_sampling:starting_sequence")
 
FileOptionKey const remodel::staged_sampling::starting_pdb ("remodel:staged_sampling:starting_pdb")
 
BooleanOptionKey const remodel::staged_sampling::require_frags_match_blueprint ("remodel:staged_sampling:require_frags_match_blueprint")
 
BooleanOptionKey const remodel::staged_sampling::start_w_ideal_helices ("remodel:staged_sampling:start_w_ideal_helices")
 
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")
 
BooleanOptionKey const remodel::staged_sampling::fa_relax_moves ("remodel:staged_sampling:fa_relax_moves")
 
BooleanOptionKey const remodel::domainFusion::domainFusion ("remodel:domainFusion")
 
FileOptionKey const remodel::domainFusion::insert_segment_from_pdb ("remodel:domainFusion:insert_segment_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::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")
 
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")
 
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")
 
IntegerOptionKey const rna::minimize_rounds ("rna:minimize_rounds")
 
BooleanOptionKey const rna::corrected_geo ("rna:corrected_geo")
 
BooleanOptionKey const rna::vary_geometry ("rna:vary_geometry")
 
BooleanOptionKey const rna::skip_coord_constraints ("rna:skip_coord_constraints")
 
BooleanOptionKey const rna::skip_o2prime_trials ("rna:skip_o2prime_trials")
 
StringOptionKey const rna::vall_torsions ("rna:vall_torsions")
 
BooleanOptionKey const rna::jump_database ("rna:jump_database")
 
BooleanOptionKey const rna::bps_database ("rna:bps_database")
 
BooleanOptionKey const rna::rna_prot_erraser ("rna:rna_prot_erraser")
 
BooleanOptionKey const rna::deriv_check ("rna:deriv_check")
 
StringOptionKey const rna::data_file ("rna:data_file")
 
BooleanOptionKey const rotamerdump::rotamerdump ("rotamerdump")
 
BooleanOptionKey const rotamerdump::xyz ("rotamerdump:xyz")
 
BooleanOptionKey const rotamerdump::one_body ("rotamerdump:one_body")
 
BooleanOptionKey const rotamerdump::two_body ("rotamerdump:two_body")
 
BooleanOptionKey const rotamerdump::annealer ("rotamerdump:annealer")
 
BooleanOptionKey const sicdock::sicdock ("sicdock")
 
RealOptionKey const sicdock::clash_dis ("sicdock:clash_dis")
 
RealOptionKey const sicdock::contact_dis ("sicdock:contact_dis")
 
RealOptionKey const sicdock::hash_2D_vs_3D ("sicdock:hash_2D_vs_3D")
 
BooleanOptionKey const sewing::sewing ("sewing")
 
FileOptionKey const sewing::query_structure_path ("sewing:query_structure_path")
 
IntegerOptionKey const sewing::frag1_start ("sewing:frag1_start")
 
IntegerOptionKey const sewing::frag1_end ("sewing:frag1_end")
 
IntegerOptionKey const sewing::frag2_start ("sewing:frag2_start")
 
IntegerOptionKey const sewing::frag2_end ("sewing:frag2_end")
 
IntegerOptionKey const sewing::minimum_helix_contacts ("sewing:minimum_helix_contacts")
 
IntegerOptionKey const sewing::helices_to_add ("sewing:helices_to_add")
 
RealOptionKey const sewing::single_helix_rmsd_cutoff ("sewing:single_helix_rmsd_cutoff")
 
RealOptionKey const sewing::helix_pair_rmsd_cutoff ("sewing:helix_pair_rmsd_cutoff")
 
FileOptionKey const sewing::nat_ro_file ("sewing:nat_ro_file")
 
RealOptionKey const sewing::helix_cap_dist_cutoff ("sewing:helix_cap_dist_cutoff")
 
RealOptionKey const sewing::helix_contact_dist_cutoff ("sewing:helix_contact_dist_cutoff")
 
IntegerOptionKey const sewing::min_helix_size ("sewing:min_helix_size")
 
BooleanOptionKey const SSrbrelax::SSrbrelax ("SSrbrelax")
 
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 stepwise::stepwise ("stepwise")
 
StringVectorOptionKey const stepwise::s1 ("stepwise:s1")
 
StringVectorOptionKey const stepwise::s2 ("stepwise:s2")
 
StringVectorOptionKey const stepwise::silent1 ("stepwise:silent1")
 
StringVectorOptionKey const stepwise::silent2 ("stepwise:silent2")
 
StringVectorOptionKey const stepwise::tags1 ("stepwise:tags1")
 
StringVectorOptionKey const stepwise::tags2 ("stepwise:tags2")
 
IntegerVectorOptionKey const stepwise::slice_res1 ("stepwise:slice_res1")
 
IntegerVectorOptionKey const stepwise::slice_res2 ("stepwise:slice_res2")
 
IntegerVectorOptionKey const stepwise::input_res1 ("stepwise:input_res1")
 
IntegerVectorOptionKey const stepwise::input_res2 ("stepwise:input_res2")
 
BooleanOptionKey const stepwise::backbone_only1 ("stepwise:backbone_only1")
 
BooleanOptionKey const stepwise::backbone_only2 ("stepwise:backbone_only2")
 
IntegerVectorOptionKey const stepwise::fixed_res ("stepwise:fixed_res")
 
BooleanOptionKey const stepwise::test_encapsulation ("stepwise:test_encapsulation")
 
BooleanOptionKey const stepwise::choose_random ("stepwise:choose_random")
 
IntegerOptionKey const stepwise::num_random_samples ("stepwise:num_random_samples")
 
IntegerOptionKey const stepwise::num_pose_minimize ("stepwise:num_pose_minimize")
 
BooleanOptionKey const stepwise::atr_rep_screen ("stepwise:atr_rep_screen")
 
StringOptionKey const stepwise::align_pdb ("stepwise:align_pdb")
 
BooleanOptionKey const stepwise::enumerate ("stepwise:enumerate")
 
BooleanOptionKey const stepwise::preminimize ("stepwise:preminimize")
 
BooleanOptionKey const stepwise::dump ("stepwise:dump")
 
BooleanOptionKey const stepwise::VERBOSE ("stepwise:VERBOSE")
 
BooleanOptionKey const stepwise::use_green_packer ("stepwise:use_green_packer")
 
RealOptionKey const stepwise::rmsd_screen ("stepwise:rmsd_screen")
 
BooleanOptionKey const stepwise::skip_minimize ("stepwise:skip_minimize")
 
StringOptionKey const stepwise::sampler_silent_file ("stepwise:sampler_silent_file")
 
StringVectorOptionKey const stepwise::move ("stepwise:move")
 
BooleanOptionKey const stepwise::monte_carlo::monte_carlo ("stepwise:monte_carlo")
 
BooleanOptionKey const stepwise::monte_carlo::verbose_scores ("stepwise:monte_carlo:verbose_scores")
 
BooleanOptionKey const stepwise::monte_carlo::skip_deletions ("stepwise:monte_carlo:skip_deletions")
 
BooleanOptionKey const stepwise::monte_carlo::allow_internal_hinge_moves ("stepwise:monte_carlo:allow_internal_hinge_moves")
 
BooleanOptionKey const stepwise::monte_carlo::allow_internal_local_moves ("stepwise:monte_carlo:allow_internal_local_moves")
 
BooleanOptionKey const stepwise::monte_carlo::allow_skip_bulge ("stepwise:monte_carlo:allow_skip_bulge")
 
RealOptionKey const stepwise::monte_carlo::from_scratch_frequency ("stepwise:monte_carlo:from_scratch_frequency")
 
BooleanOptionKey const stepwise::monte_carlo::allow_split_off ("stepwise:monte_carlo:allow_split_off")
 
IntegerOptionKey const stepwise::monte_carlo::cycles ("stepwise:monte_carlo:cycles")
 
RealOptionKey const stepwise::monte_carlo::temperature ("stepwise:monte_carlo:temperature")
 
RealOptionKey const stepwise::monte_carlo::add_delete_frequency ("stepwise:monte_carlo:add_delete_frequency")
 
RealOptionKey const stepwise::monte_carlo::intermolecular_frequency ("stepwise:monte_carlo:intermolecular_frequency")
 
RealOptionKey const stepwise::monte_carlo::minimize_single_res_frequency ("stepwise:monte_carlo:minimize_single_res_frequency")
 
BooleanOptionKey const stepwise::monte_carlo::allow_variable_bond_geometry ("stepwise:monte_carlo:allow_variable_bond_geometry")
 
RealOptionKey const stepwise::monte_carlo::switch_focus_frequency ("stepwise:monte_carlo:switch_focus_frequency")
 
RealOptionKey const stepwise::monte_carlo::just_min_after_mutation_frequency ("stepwise:monte_carlo:just_min_after_mutation_frequency")
 
BooleanOptionKey const stepwise::monte_carlo::local_redock_only ("stepwise:monte_carlo:local_redock_only")
 
BooleanOptionKey const stepwise::monte_carlo::make_movie ("stepwise:monte_carlo:make_movie")
 
BooleanOptionKey const stepwise::rna::rna ("stepwise:rna")
 
IntegerOptionKey const stepwise::rna::sampler_num_pose_kept ("stepwise:rna:sampler_num_pose_kept")
 
RealOptionKey const stepwise::rna::native_edensity_score_cutoff ("stepwise:rna:native_edensity_score_cutoff")
 
BooleanOptionKey const stepwise::rna::o2prime_legacy_mode ("stepwise:rna:o2prime_legacy_mode")
 
BooleanOptionKey const stepwise::rna::sampler_perform_phosphate_pack ("stepwise:rna:sampler_perform_phosphate_pack")
 
BooleanOptionKey const stepwise::rna::distinguish_pucker ("stepwise:rna:distinguish_pucker")
 
BooleanOptionKey const stepwise::rna::finer_sampling_at_chain_closure ("stepwise:rna:finer_sampling_at_chain_closure")
 
BooleanOptionKey const stepwise::rna::PBP_clustering_at_chain_closure ("stepwise:rna:PBP_clustering_at_chain_closure")
 
BooleanOptionKey const stepwise::rna::sampler_allow_syn_pyrimidine ("stepwise:rna:sampler_allow_syn_pyrimidine")
 
BooleanOptionKey const stepwise::rna::sampler_extra_chi_rotamer ("stepwise:rna:sampler_extra_chi_rotamer")
 
BooleanOptionKey const stepwise::rna::sampler_extra_beta_rotamer ("stepwise:rna:sampler_extra_beta_rotamer")
 
BooleanOptionKey const stepwise::rna::sampler_extra_epsilon_rotamer ("stepwise:rna:sampler_extra_epsilon_rotamer")
 
BooleanOptionKey const stepwise::rna::force_centroid_interaction ("stepwise:rna:force_centroid_interaction")
 
BooleanOptionKey const stepwise::rna::virtual_sugar_legacy_mode ("stepwise:rna:virtual_sugar_legacy_mode")
 
BooleanOptionKey const stepwise::rna::erraser ("stepwise:rna:erraser")
 
BooleanOptionKey const stepwise::rna::centroid_screen ("stepwise:rna:centroid_screen")
 
BooleanOptionKey const stepwise::rna::VDW_atr_rep_screen ("stepwise:rna:VDW_atr_rep_screen")
 
BooleanOptionKey const stepwise::rna::minimize_and_score_native_pose ("stepwise:rna:minimize_and_score_native_pose")
 
BooleanOptionKey const stepwise::rna::rm_virt_phosphate ("stepwise:rna:rm_virt_phosphate")
 
StringVectorOptionKey const stepwise::rna::VDW_rep_screen_info ("stepwise:rna:VDW_rep_screen_info")
 
RealOptionKey const stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF ("stepwise:rna:VDW_rep_alignment_RMSD_CUTOFF")
 
StringVectorOptionKey const stepwise::rna::VDW_rep_delete_matching_res ("stepwise:rna:VDW_rep_delete_matching_res")
 
RealOptionKey const stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff ("stepwise:rna:VDW_rep_screen_physical_pose_clash_dist_cutoff")
 
BooleanOptionKey const stepwise::rna::integration_test ("stepwise:rna:integration_test")
 
BooleanOptionKey const stepwise::rna::allow_bulge_at_chainbreak ("stepwise:rna:allow_bulge_at_chainbreak")
 
BooleanOptionKey const stepwise::rna::parin_favorite_output ("stepwise:rna:parin_favorite_output")
 
BooleanOptionKey const stepwise::rna::reinitialize_CCD_torsions ("stepwise:rna:reinitialize_CCD_torsions")
 
BooleanOptionKey const stepwise::rna::sample_both_sugar_base_rotamer ("stepwise:rna:sample_both_sugar_base_rotamer")
 
BooleanOptionKey const stepwise::rna::sampler_include_torsion_value_in_tag ("stepwise:rna:sampler_include_torsion_value_in_tag")
 
BooleanOptionKey const stepwise::rna::sampler_assert_no_virt_sugar_sampling ("stepwise:rna:sampler_assert_no_virt_sugar_sampling")
 
BooleanOptionKey const stepwise::rna::sampler_try_sugar_instantiation ("stepwise:rna:sampler_try_sugar_instantiation")
 
BooleanOptionKey const stepwise::rna::do_not_sample_multiple_virtual_sugar ("stepwise:rna:do_not_sample_multiple_virtual_sugar")
 
BooleanOptionKey const stepwise::rna::sample_ONLY_multiple_virtual_sugar ("stepwise:rna:sample_ONLY_multiple_virtual_sugar")
 
BooleanOptionKey const stepwise::rna::allow_base_pair_only_centroid_screen ("stepwise:rna:allow_base_pair_only_centroid_screen")
 
BooleanOptionKey const stepwise::rna::minimizer_rename_tag ("stepwise:rna:minimizer_rename_tag")
 
IntegerVectorOptionKey const stepwise::rna::minimize_res ("stepwise:rna:minimize_res")
 
StringVectorOptionKey const stepwise::rna::alignment_res ("stepwise:rna:alignment_res")
 
IntegerVectorOptionKey const stepwise::rna::native_alignment_res ("stepwise:rna:native_alignment_res")
 
IntegerVectorOptionKey const stepwise::rna::rmsd_res ("stepwise:rna:rmsd_res")
 
IntegerVectorOptionKey const stepwise::rna::missing_res ("stepwise:rna:missing_res")
 
IntegerVectorOptionKey const stepwise::rna::missing_res2 ("stepwise:rna:missing_res2")
 
IntegerOptionKey const stepwise::rna::job_queue_ID ("stepwise:rna:job_queue_ID")
 
BooleanOptionKey const stepwise::rna::minimize_and_score_sugar ("stepwise:rna:minimize_and_score_sugar")
 
IntegerVectorOptionKey const stepwise::rna::global_sample_res_list ("stepwise:rna:global_sample_res_list")
 
FileOptionKey const stepwise::rna::filter_output_filename ("stepwise:rna:filter_output_filename")
 
BooleanOptionKey const stepwise::rna::combine_long_loop_mode ("stepwise:rna:combine_long_loop_mode")
 
BooleanOptionKey const stepwise::rna::combine_helical_silent_file ("stepwise:rna:combine_helical_silent_file")
 
BooleanOptionKey const stepwise::rna::output_extra_RMSDs ("stepwise:rna:output_extra_RMSDs")
 
IntegerVectorOptionKey const stepwise::rna::protonated_H1_adenosine_list ("stepwise:rna:protonated_H1_adenosine_list")
 
IntegerVectorOptionKey const stepwise::rna::native_virtual_res ("stepwise:rna:native_virtual_res")
 
BooleanOptionKey const stepwise::rna::simple_append_map ("stepwise:rna:simple_append_map")
 
BooleanOptionKey const stepwise::rna::allow_fixed_res_at_moving_res ("stepwise:rna:allow_fixed_res_at_moving_res")
 
BooleanOptionKey const stepwise::rna::force_user_defined_jumps ("stepwise:rna:force_user_defined_jumps")
 
StringVectorOptionKey const stepwise::rna::jump_point_pairs ("stepwise:rna:jump_point_pairs")
 
BooleanOptionKey const stepwise::rna::add_virt_root ("stepwise:rna:add_virt_root")
 
BooleanOptionKey const stepwise::rna::floating_base ("stepwise:rna:floating_base")
 
IntegerOptionKey const stepwise::rna::floating_base_anchor_res ("stepwise:rna:floating_base_anchor_res")
 
BooleanOptionKey const stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP ("stepwise:rna:allow_chain_boundary_jump_partner_right_at_fixed_BP")
 
IntegerVectorOptionKey const stepwise::rna::bulge_res ("stepwise:rna:bulge_res")
 
BooleanOptionKey const stepwise::rna::rebuild_bulge_mode ("stepwise:rna:rebuild_bulge_mode")
 
BooleanOptionKey const stepwise::rna::virtual_sugar_keep_base_fixed ("stepwise:rna:virtual_sugar_keep_base_fixed")
 
BooleanOptionKey const stepwise::rna::virtual_sugar_do_minimize ("stepwise:rna:virtual_sugar_do_minimize")
 
RealOptionKey const stepwise::rna::sampler_max_centroid_distance ("stepwise:rna:sampler_max_centroid_distance")
 
BooleanOptionKey const stepwise::rna::filter_user_alignment_res ("stepwise:rna:filter_user_alignment_res")
 
BooleanOptionKey const stepwise::rna::tether_jump ("stepwise:rna:tether_jump")
 
BooleanOptionKey const stepwise::rna::turn_off_rna_chem_map_during_optimize ("stepwise:rna:turn_off_rna_chem_map_during_optimize")
 
BooleanOptionKey const stepwise::protein::protein ("stepwise:protein")
 
BooleanOptionKey const stepwise::protein::global_optimize ("stepwise:protein:global_optimize")
 
BooleanOptionKey const stepwise::protein::disable_sampling_of_loop_takeoff ("stepwise:protein:disable_sampling_of_loop_takeoff")
 
BooleanOptionKey const stepwise::protein::sample_beta ("stepwise:protein:sample_beta")
 
BooleanOptionKey const stepwise::protein::ghost_loops ("stepwise:protein:ghost_loops")
 
StringOptionKey const stepwise::protein::min_type ("stepwise:protein:min_type")
 
RealOptionKey const stepwise::protein::min_tolerance ("stepwise:protein:min_tolerance")
 
BooleanOptionKey const stepwise::protein::centroid_screen ("stepwise:protein:centroid_screen")
 
RealOptionKey const stepwise::protein::centroid_score_diff_cut ("stepwise:protein:centroid_score_diff_cut")
 
StringOptionKey const stepwise::protein::centroid_weights ("stepwise:protein:centroid_weights")
 
RealOptionKey const stepwise::protein::score_diff_cut ("stepwise:protein:score_diff_cut")
 
BooleanOptionKey const stepwise::protein::filter_native_big_bins ("stepwise:protein:filter_native_big_bins")
 
BooleanOptionKey const stepwise::protein::cluster_by_all_atom_rmsd ("stepwise:protein:cluster_by_all_atom_rmsd")
 
BooleanOptionKey const stepwise::protein::centroid_output ("stepwise:protein:centroid_output")
 
IntegerOptionKey const stepwise::protein::n_sample ("stepwise:protein:n_sample")
 
IntegerOptionKey const stepwise::protein::nstruct_centroid ("stepwise:protein:nstruct_centroid")
 
BooleanOptionKey const stepwise::protein::ccd_close ("stepwise:protein:ccd_close")
 
IntegerVectorOptionKey const stepwise::protein::bridge_res ("stepwise:protein:bridge_res")
 
BooleanOptionKey const stepwise::protein::cart_min ("stepwise:protein:cart_min")
 
BooleanOptionKey const stepwise::protein::move_jumps_between_chains ("stepwise:protein:move_jumps_between_chains")
 
BooleanOptionKey const stepwise::protein::use_packer_instead_of_rotamer_trials ("stepwise:protein:use_packer_instead_of_rotamer_trials")
 
BooleanOptionKey const stepwise::protein::expand_loop_takeoff ("stepwise:protein:expand_loop_takeoff")
 
BooleanOptionKey const stepwise::protein::skip_coord_constraints ("stepwise:protein:skip_coord_constraints")
 
BooleanOptionKey const stepwise::protein::allow_virtual_side_chains ("stepwise:protein:allow_virtual_side_chains")
 
BooleanOptionKey const stepwise::protein::protein_prepack ("stepwise:protein:protein_prepack")
 
BooleanOptionKey const full_model::full_model ("full_model")
 
ResidueChainVectorOptionKey const full_model::cutpoint_open ("full_model:cutpoint_open")
 
ResidueChainVectorOptionKey const full_model::cutpoint_closed ("full_model:cutpoint_closed")
 
StringVectorOptionKey const full_model::other_poses ("full_model:other_poses")
 
ResidueChainVectorOptionKey const full_model::extra_min_res ("full_model:extra_min_res")
 
ResidueChainVectorOptionKey const full_model::jump_res ("full_model:jump_res")
 
ResidueChainVectorOptionKey const full_model::root_res ("full_model:root_res")
 
ResidueChainVectorOptionKey const full_model::virtual_sugar_res ("full_model:virtual_sugar_res")
 
ResidueChainVectorOptionKey const full_model::virtual_res ("full_model:virtual_res")
 
ResidueChainVectorOptionKey const full_model::sample_res ("full_model:sample_res")
 
ResidueChainVectorOptionKey const full_model::calc_rms_res ("full_model:calc_rms_res")
 
ResidueChainVectorOptionKey const full_model::working_res ("full_model:working_res")
 
BooleanOptionKey const full_model::rna::rna ("full_model:rna")
 
ResidueChainVectorOptionKey const full_model::rna::terminal_res ("full_model:rna:terminal_res")
 
ResidueChainVectorOptionKey const full_model::rna::force_syn_chi_res_list ("full_model:rna:force_syn_chi_res_list")
 
ResidueChainVectorOptionKey const full_model::rna::force_north_sugar_list ("full_model:rna:force_north_sugar_list")
 
ResidueChainVectorOptionKey const full_model::rna::force_south_sugar_list ("full_model:rna:force_south_sugar_list")
 
BooleanOptionKey const strand_assembly::strand_assembly ("strand_assembly")
 
IntegerOptionKey const strand_assembly::min_num_strands_to_deal ("strand_assembly:min_num_strands_to_deal")
 
IntegerOptionKey const strand_assembly::max_num_strands_to_deal ("strand_assembly:max_num_strands_to_deal")
 
BooleanOptionKey const strand_assembly::extract_native_only ("strand_assembly:extract_native_only")
 
IntegerOptionKey const strand_assembly::min_res_in_strand ("strand_assembly:min_res_in_strand")
 
IntegerOptionKey const strand_assembly::max_res_in_strand ("strand_assembly:max_res_in_strand")
 
RealOptionKey const strand_assembly::min_O_N_dis ("strand_assembly:min_O_N_dis")
 
RealOptionKey const strand_assembly::max_O_N_dis ("strand_assembly:max_O_N_dis")
 
RealOptionKey const strand_assembly::min_sheet_dis ("strand_assembly:min_sheet_dis")
 
RealOptionKey const strand_assembly::max_sheet_dis ("strand_assembly:max_sheet_dis")
 
RealOptionKey const strand_assembly::min_sheet_torsion ("strand_assembly:min_sheet_torsion")
 
RealOptionKey const strand_assembly::max_sheet_torsion ("strand_assembly:max_sheet_torsion")
 
RealOptionKey const strand_assembly::min_sheet_angle ("strand_assembly:min_sheet_angle")
 
RealOptionKey const strand_assembly::max_sheet_angle ("strand_assembly:max_sheet_angle")
 
RealOptionKey const strand_assembly::min_shortest_dis_sidechain_inter_sheet ("strand_assembly:min_shortest_dis_sidechain_inter_sheet")
 
BooleanOptionKey const TailSegment::TailSegment ("TailSegment")
 
IntegerOptionKey const TailSegment::refine_cycles ("TailSegment:refine_cycles")
 
IntegerOptionKey const TailSegment::refine_repack_cycles ("TailSegment:refine_repack_cycles")
 
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 unfolded_state::unfolded_state ("unfolded_state")
 
FileOptionKey const unfolded_state::unfolded_energies_file ("unfolded_state:unfolded_energies_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 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 cmiles::cmiles ("cmiles")
 
BooleanOptionKey const cmiles::kcluster::kcluster ("cmiles:kcluster")
 
IntegerOptionKey const cmiles::kcluster::num_clusters ("cmiles:kcluster:num_clusters")
 
BooleanOptionKey const cmiles::jumping::jumping ("cmiles:jumping")
 
IntegerOptionKey const cmiles::jumping::resi ("cmiles:jumping:resi")
 
IntegerOptionKey const cmiles::jumping::resj ("cmiles:jumping:resj")
 
BooleanOptionKey const crossmatch::crossmatch ("crossmatch")
 
RealOptionKey const crossmatch::clash_dis ("crossmatch:clash_dis")
 
BooleanOptionKey const dwkulp::dwkulp ("dwkulp")
 
StringOptionKey const dwkulp::forcePolyAAfragments ("dwkulp:forcePolyAAfragments")
 
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 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")
 
BooleanOptionKey const james::debug ("james:debug")
 
RealOptionKey const james::real ("james:real")
 
IntegerOptionKey const james::n_designs ("james:n_designs")
 
BooleanOptionKey const james::thread_unaligned ("james:thread_unaligned")
 
BooleanOptionKey const krassk::krassk ("krassk")
 
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 murphp::murphp ("murphp")
 
StringOptionKey const murphp::inv_kin_lig_loop_design_filename ("murphp:inv_kin_lig_loop_design_filename")
 
BooleanOptionKey const phil::phil ("phil")
 
IntegerOptionKey const phil::nloop ("phil:nloop")
 
StringOptionKey const phil::vall_file ("phil:vall_file")
 
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 rot_anl::rot_anl ("rot_anl")
 
StringOptionKey const rot_anl::tag ("rot_anl:tag")
 
BooleanOptionKey const rot_anl::min ("rot_anl:min")
 
BooleanOptionKey const rot_anl::repack ("rot_anl:repack")
 
BooleanOptionKey const rot_anl::rtmin ("rot_anl:rtmin")
 
BooleanOptionKey const rot_anl::scmove ("rot_anl:scmove")
 
BooleanOptionKey const rot_anl::design ("rot_anl:design")
 
BooleanOptionKey const rot_anl::dump_pdb ("rot_anl:dump_pdb")
 
IntegerOptionKey const rot_anl::nloop_scmove ("rot_anl:nloop_scmove")
 
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::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")
 
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")
 
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 threadsc::threadsc ("threadsc")
 
StringOptionKey const threadsc::src_chain ("threadsc:src_chain")
 
StringOptionKey const threadsc::trg_chain ("threadsc:trg_chain")
 
IntegerOptionKey const threadsc::src_first_resid ("threadsc:src_first_resid")
 
IntegerOptionKey const threadsc::trg_first_resid ("threadsc:trg_first_resid")
 
IntegerOptionKey const threadsc::nres ("threadsc:nres")
 
IntegerOptionKey const threadsc::trg_anchor ("threadsc:trg_anchor")
 
BooleanOptionKey const ufv::ufv ("ufv")
 
IntegerOptionKey const ufv::left ("ufv:left")
 
IntegerOptionKey const ufv::right ("ufv:right")
 
StringOptionKey const ufv::ss ("ufv:ss")
 
StringOptionKey const ufv::aa_during_build ("ufv:aa_during_build")
 
StringOptionKey const ufv::aa_during_design_refine ("ufv:aa_during_design_refine")
 
BooleanOptionKey const ufv::keep_junction_torsions ("ufv:keep_junction_torsions")
 
FileOptionKey const ufv::ufv_loops ("ufv:ufv_loops")
 
BooleanOptionKey const ufv::use_fullmer ("ufv:use_fullmer")
 
StringOptionKey const ufv::centroid_loop_mover ("ufv:centroid_loop_mover")
 
BooleanOptionKey const ufv::no_neighborhood_design ("ufv:no_neighborhood_design")
 
IntegerOptionKey const ufv::dr_cycles ("ufv:dr_cycles")
 
StringOptionKey const ufv::centroid_sfx ("ufv:centroid_sfx")
 
StringOptionKey const ufv::centroid_sfx_patch ("ufv:centroid_sfx_patch")
 
StringOptionKey const ufv::fullatom_sfx ("ufv:fullatom_sfx")
 
StringOptionKey const ufv::fullatom_sfx_patch ("ufv:fullatom_sfx_patch")
 
BooleanOptionKey const ufv::insert::insert ("ufv:insert")
 
FileOptionKey const ufv::insert::insert_pdb ("ufv:insert:insert_pdb")
 
FileOptionKey const ufv::insert::attached_pdb ("ufv:insert:attached_pdb")
 
StringOptionKey const ufv::insert::connection_scheme ("ufv:insert:connection_scheme")
 
BooleanOptionKey const willmatch::willmatch ("willmatch")
 
StringVectorOptionKey const willmatch::write_reduced_matchset ("willmatch:write_reduced_matchset")
 
RealOptionKey const willmatch::interface_size ("willmatch:interface_size")
 
RealOptionKey const willmatch::max_dis_any ("willmatch:max_dis_any")
 
RealOptionKey const willmatch::max_dis_all ("willmatch:max_dis_all")
 
RealOptionKey const willmatch::max_dis_hb ("willmatch:max_dis_hb")
 
RealOptionKey const willmatch::min_dis_hb ("willmatch:min_dis_hb")
 
RealOptionKey const willmatch::max_dis_hb_colinear ("willmatch:max_dis_hb_colinear")
 
RealOptionKey const willmatch::max_dis_metal ("willmatch:max_dis_metal")
 
RealOptionKey const willmatch::max_ang_metal ("willmatch:max_ang_metal")
 
RealOptionKey const willmatch::clash_dis ("willmatch:clash_dis")
 
RealOptionKey const willmatch::c2_linker_dist ("willmatch:c2_linker_dist")
 
RealOptionKey const willmatch::identical_match_dis ("willmatch:identical_match_dis")
 
RealOptionKey const willmatch::chi1_increment ("willmatch:chi1_increment")
 
RealOptionKey const willmatch::chi2_increment ("willmatch:chi2_increment")
 
RealOptionKey const willmatch::c2_symm_increment ("willmatch:c2_symm_increment")
 
RealOptionKey const willmatch::cb_sasa_thresh ("willmatch:cb_sasa_thresh")
 
BooleanOptionKey const willmatch::design_interface ("willmatch:design_interface")
 
FileOptionKey const willmatch::chilist ("willmatch:chilist")
 
FileOptionKey const willmatch::fixed_res ("willmatch:fixed_res")
 
FileOptionKey const willmatch::native1 ("willmatch:native1")
 
FileOptionKey const willmatch::native2 ("willmatch:native2")
 
FileOptionKey const willmatch::exclude_res1 ("willmatch:exclude_res1")
 
FileOptionKey const willmatch::exclude_res2 ("willmatch:exclude_res2")
 
FileOptionKey const willmatch::taglist ("willmatch:taglist")
 
IntegerVectorOptionKey const willmatch::residues ("willmatch:residues")
 
BooleanOptionKey const willmatch::symmetry_d2 ("willmatch:symmetry_d2")
 
BooleanOptionKey const willmatch::symmetry_c2_dock ("willmatch:symmetry_c2_dock")
 
IntegerVectorOptionKey const willmatch::splitwork ("willmatch:splitwork")
 
BooleanOptionKey const willmatch::exclude_ala ("willmatch:exclude_ala")
 
RealOptionKey const willmatch::match_overlap_dis ("willmatch:match_overlap_dis")
 
RealOptionKey const willmatch::match_overlap_ang ("willmatch:match_overlap_ang")
 
IntegerVectorOptionKey const willmatch::forbid_residues ("willmatch:forbid_residues")
 
RealVectorOptionKey const willmatch::poi ("willmatch:poi")
 
RealOptionKey const willmatch::poidis ("willmatch:poidis")
 
BooleanOptionKey const willmatch::homodimer ("willmatch:homodimer")
 
RealOptionKey const willmatch::fa_dun_thresh ("willmatch:fa_dun_thresh")