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OptionKeys.cc.gen3.hh File Reference

Namespaces

 carbohydrates
 
 carbohydrates::clash_check
 
 rings
 
 chemical
 
 constraints
 
 corrections
 
 corrections::score
 
 corrections::chemical
 
 corrections::genpotential
 
 corrections::shapovalov_lib
 
 corrections::water
 
 enzymes
 
 evaluation
 
 filters
 
 gpu
 
 jumps
 
 loops
 

Functions

StringVectorOptionKey const carbohydrates::clash_check::glycan_branches ("carbohydrates:clash_check:glycan_branches")
 
StringVectorOptionKey const carbohydrates::clash_check::check_chains ("carbohydrates:clash_check:check_chains")
 
RealOptionKey const carbohydrates::clash_check::soft_clash ("carbohydrates:clash_check:soft_clash")
 
RealOptionKey const carbohydrates::clash_check::cb_clash_distance ("carbohydrates:clash_check:cb_clash_distance")
 
BooleanOptionKey const carbohydrates::clash_check::ignore_hydrogens ("carbohydrates:clash_check:ignore_hydrogens")
 
BooleanOptionKey const carbohydrates::clash_check::ignore_full_res_output ("carbohydrates:clash_check:ignore_full_res_output")
 
BooleanOptionKey const carbohydrates::clash_check::output_per_glycan_data ("carbohydrates:clash_check:output_per_glycan_data")
 
BooleanOptionKey const rings::rings ("rings")
 
FileOptionKey const rings::ring_conformer_dbpath ("rings:ring_conformer_dbpath")
 
BooleanOptionKey const rings::lock_rings ("rings:lock_rings")
 
BooleanOptionKey const rings::idealize_rings ("rings:idealize_rings")
 
BooleanOptionKey const rings::sample_high_energy_conformers ("rings:sample_high_energy_conformers")
 
BooleanOptionKey const chemical::chemical ("chemical")
 
StringVectorOptionKey const chemical::exclude_patches ("chemical:exclude_patches")
 
StringVectorOptionKey const chemical::include_patches ("chemical:include_patches")
 
StringVectorOptionKey const chemical::add_atom_type_set_parameters ("chemical:add_atom_type_set_parameters")
 
StringVectorOptionKey const chemical::add_atom_types ("chemical:add_atom_types")
 
StringVectorOptionKey const chemical::add_mm_atom_type_set_parameters ("chemical:add_mm_atom_type_set_parameters")
 
StringVectorOptionKey const chemical::set_atom_properties ("chemical:set_atom_properties")
 
StringVectorOptionKey const chemical::patch_selectors ("chemical:patch_selectors")
 
BooleanOptionKey const chemical::override_rsd_type_limit ("chemical:override_rsd_type_limit")
 
StringVectorOptionKey const chemical::clone_atom_types ("chemical:clone_atom_types")
 
StringVectorOptionKey const chemical::reassign_atom_types ("chemical:reassign_atom_types")
 
StringVectorOptionKey const chemical::reassign_icoor ("chemical:reassign_icoor")
 
StringVectorOptionKey const chemical::set_atomic_charge ("chemical:set_atomic_charge")
 
StringVectorOptionKey const chemical::set_patch_atomic_charge ("chemical:set_patch_atomic_charge")
 
BooleanOptionKey const chemical::enlarge_H_lj ("chemical:enlarge_H_lj")
 
BooleanOptionKey const chemical::no_hbonds_to_ether_oxygens ("chemical:no_hbonds_to_ether_oxygens")
 
BooleanOptionKey const chemical::unset_acceptor_ether_oxygens ("chemical:unset_acceptor_ether_oxygens")
 
BooleanOptionKey const constraints::constraints ("constraints")
 
BooleanOptionKey const constraints::exit_on_bad_read ("constraints:exit_on_bad_read")
 
StringVectorOptionKey const constraints::cst_file ("constraints:cst_file")
 
RealOptionKey const constraints::cst_weight ("constraints:cst_weight")
 
RealOptionKey const constraints::max_cst_dist ("constraints:max_cst_dist")
 
StringVectorOptionKey const constraints::cst_fa_file ("constraints:cst_fa_file")
 
RealOptionKey const constraints::cst_fa_weight ("constraints:cst_fa_weight")
 
BooleanOptionKey const constraints::normalize_mixture_func ("constraints:normalize_mixture_func")
 
BooleanOptionKey const constraints::penalize_mixture_func ("constraints:penalize_mixture_func")
 
FileOptionKey const constraints::forest_file ("constraints:forest_file")
 
BooleanOptionKey const constraints::compute_total_dist_cst ("constraints:compute_total_dist_cst")
 
IntegerOptionKey const constraints::cull_with_native ("constraints:cull_with_native")
 
FileOptionKey const constraints::dump_cst_set ("constraints:dump_cst_set")
 
IntegerVectorOptionKey const constraints::evaluate_max_seq_sep ("constraints:evaluate_max_seq_sep")
 
BooleanOptionKey const constraints::named ("constraints:named")
 
BooleanOptionKey const constraints::no_cst_in_relax ("constraints:no_cst_in_relax")
 
BooleanOptionKey const constraints::no_linearize_bounded ("constraints:no_linearize_bounded")
 
RealOptionKey const constraints::pocket_constraint_weight ("constraints:pocket_constraint_weight")
 
BooleanOptionKey const constraints::pocket_zero_derivatives ("constraints:pocket_zero_derivatives")
 
BooleanOptionKey const constraints::viol ("constraints:viol")
 
IntegerOptionKey const constraints::viol_level ("constraints:viol_level")
 
StringOptionKey const constraints::viol_type ("constraints:viol_type")
 
RealOptionKey const constraints::sog_cst_param ("constraints:sog_cst_param")
 
RealOptionKey const constraints::sog_upper_bound ("constraints:sog_upper_bound")
 
BooleanOptionKey const constraints::epr_distance ("constraints:epr_distance")
 
IntegerOptionKey const constraints::combine ("constraints:combine")
 
FileOptionKey const constraints::combine_exclude_region ("constraints:combine_exclude_region")
 
BooleanOptionKey const constraints::skip_redundant ("constraints:skip_redundant")
 
IntegerOptionKey const constraints::skip_redundant_width ("constraints:skip_redundant_width")
 
BooleanVectorOptionKey const constraints::force_pdb_info_mapping ("constraints:force_pdb_info_mapping")
 
BooleanOptionKey const corrections::corrections ("corrections")
 
BooleanOptionKey const corrections::beta ("corrections:beta")
 
BooleanOptionKey const corrections::beta_cart ("corrections:beta_cart")
 
BooleanOptionKey const corrections::beta_nov16 ("corrections:beta_nov16")
 
BooleanOptionKey const corrections::beta_nov16_cart ("corrections:beta_nov16_cart")
 
BooleanOptionKey const corrections::beta_july15 ("corrections:beta_july15")
 
BooleanOptionKey const corrections::beta_july15_cart ("corrections:beta_july15_cart")
 
BooleanOptionKey const corrections::gen_potential ("corrections:gen_potential")
 
BooleanOptionKey const corrections::newdna ("corrections:newdna")
 
BooleanOptionKey const corrections::restore_talaris_behavior ("corrections:restore_talaris_behavior")
 
BooleanOptionKey const corrections::correct ("corrections:correct")
 
BooleanOptionKey const corrections::hbond_sp2_correction ("corrections:hbond_sp2_correction")
 
BooleanOptionKey const corrections::facts_default ("corrections:facts_default")
 
BooleanOptionKey const corrections::score::score ("corrections:score")
 
BooleanOptionKey const corrections::score::bbdep_omega ("corrections:score:bbdep_omega")
 
BooleanOptionKey const corrections::score::bbdep_bond_params ("corrections:score:bbdep_bond_params")
 
BooleanOptionKey const corrections::score::bbdep_bond_devs ("corrections:score:bbdep_bond_devs")
 
BooleanOptionKey const corrections::score::fa_dun_canonicals_use_voronoi ("corrections:score:fa_dun_canonicals_use_voronoi")
 
BooleanOptionKey const corrections::score::fa_dun_noncanonicals_use_voronoi ("corrections:score:fa_dun_noncanonicals_use_voronoi")
 
BooleanOptionKey const corrections::score::fa_dun_correct_rotamer_well_order ("corrections:score:fa_dun_correct_rotamer_well_order")
 
BooleanOptionKey const corrections::score::fa_dun_correct_achiral_peptoid_libraries ("corrections:score:fa_dun_correct_achiral_peptoid_libraries")
 
BooleanOptionKey const corrections::score::no_his_his_pairE ("corrections:score:no_his_his_pairE")
 
BooleanOptionKey const corrections::score::no_his_DE_pairE ("corrections:score:no_his_DE_pairE")
 
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")
 
FileOptionKey const corrections::score::rama_pp_map ("corrections:score:rama_pp_map")
 
FileOptionKey const corrections::score::rama_map_average_L_flat ("corrections:score:rama_map_average_L_flat")
 
FileOptionKey const corrections::score::rama_map_sym_average_L_flat ("corrections:score:rama_map_sym_average_L_flat")
 
FileOptionKey const corrections::score::rama_map_sym_gly_flat ("corrections:score:rama_map_sym_gly_flat")
 
FileOptionKey const corrections::score::rama_map_sym_pro_flat ("corrections:score:rama_map_sym_pro_flat")
 
FileOptionKey const corrections::score::rama_map_average_L_flat_stringent ("corrections:score:rama_map_average_L_flat_stringent")
 
FileOptionKey const corrections::score::rama_map_sym_average_L_flat_stringent ("corrections:score:rama_map_sym_average_L_flat_stringent")
 
FileOptionKey const corrections::score::rama_map_sym_gly_flat_stringent ("corrections:score:rama_map_sym_gly_flat_stringent")
 
FileOptionKey const corrections::score::rama_map_sym_pro_flat_stringent ("corrections:score:rama_map_sym_pro_flat_stringent")
 
BooleanOptionKey const corrections::score::rama_prepro_steep ("corrections:score:rama_prepro_steep")
 
BooleanOptionKey const corrections::score::rama_prepro_nobidentate ("corrections:score:rama_prepro_nobidentate")
 
BooleanOptionKey const corrections::score::cenrot ("corrections:score:cenrot")
 
BooleanOptionKey const corrections::score::dun10 ("corrections:score:dun10")
 
StringOptionKey const corrections::score::dun10_dir ("corrections:score:dun10_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")
 
RealOptionKey const corrections::score::lj_hbond_hdis ("corrections:score:lj_hbond_hdis")
 
RealOptionKey const corrections::score::lj_hbond_OH_donor_dis ("corrections:score:lj_hbond_OH_donor_dis")
 
BooleanOptionKey const corrections::score::score12prime ("corrections:score:score12prime")
 
RealOptionKey const corrections::score::hbond_energy_shift ("corrections:score:hbond_energy_shift")
 
RealOptionKey const corrections::score::hb_sp2_BAH180_rise ("corrections:score:hb_sp2_BAH180_rise")
 
RealOptionKey const corrections::score::hb_sp2_outer_width ("corrections:score:hb_sp2_outer_width")
 
BooleanOptionKey const corrections::score::hb_sp2_chipen ("corrections:score:hb_sp2_chipen")
 
BooleanOptionKey const corrections::score::hbond_measure_sp3acc_BAH_from_hvy ("corrections:score:hbond_measure_sp3acc_BAH_from_hvy")
 
BooleanOptionKey const corrections::score::hb_fade_energy ("corrections:score:hb_fade_energy")
 
BooleanOptionKey const corrections::score::hb_exclude_ether_oxygens ("corrections:score:hb_exclude_ether_oxygens")
 
BooleanOptionKey const corrections::score::hb_cen_soft ("corrections:score:hb_cen_soft")
 
BooleanOptionKey const corrections::score::use_bicubic_interpolation ("corrections:score:use_bicubic_interpolation")
 
BooleanOptionKey const corrections::score::dun_normsd ("corrections:score:dun_normsd")
 
BooleanOptionKey const corrections::score::dun_entropy_correction ("corrections:score:dun_entropy_correction")
 
BooleanOptionKey const corrections::score::no_autogen_cart_improper ("corrections:score:no_autogen_cart_improper")
 
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 corrections::chemical::expand_st_chi2sampling ("corrections:chemical:expand_st_chi2sampling")
 
StringOptionKey const corrections::chemical::alternate_fullatom_ats ("corrections:chemical:alternate_fullatom_ats")
 
BooleanOptionKey const corrections::genpotential::genpotential ("corrections:genpotential")
 
StringVectorOptionKey const corrections::genpotential::set_torsion_params ("corrections:genpotential:set_torsion_params")
 
StringVectorOptionKey const corrections::genpotential::set_special_torsion_params ("corrections:genpotential:set_special_torsion_params")
 
BooleanOptionKey const corrections::shapovalov_lib_fixes_enable ("corrections:shapovalov_lib_fixes_enable")
 
BooleanOptionKey const corrections::shapovalov_lib::shapovalov_lib ("corrections:shapovalov_lib")
 
BooleanOptionKey const corrections::shapovalov_lib::shap_dun10_enable ("corrections:shapovalov_lib:shap_dun10_enable")
 
StringOptionKey const corrections::shapovalov_lib::shap_dun10_smooth_level ("corrections:shapovalov_lib:shap_dun10_smooth_level")
 
StringOptionKey const corrections::shapovalov_lib::shap_dun10_dir ("corrections:shapovalov_lib:shap_dun10_dir")
 
BooleanOptionKey const corrections::shapovalov_lib::shap_dun10_use_minus_log_P_ignore_P ("corrections:shapovalov_lib:shap_dun10_use_minus_log_P_ignore_P")
 
BooleanOptionKey const corrections::shapovalov_lib::shap_rama_enable ("corrections:shapovalov_lib:shap_rama_enable")
 
StringOptionKey const corrections::shapovalov_lib::shap_rama_smooth_level ("corrections:shapovalov_lib:shap_rama_smooth_level")
 
FileOptionKey const corrections::shapovalov_lib::shap_rama_map ("corrections:shapovalov_lib:shap_rama_map")
 
BooleanOptionKey const corrections::shapovalov_lib::shap_rama_nogridshift ("corrections:shapovalov_lib:shap_rama_nogridshift")
 
BooleanOptionKey const corrections::shapovalov_lib::shap_p_aa_pp_enable ("corrections:shapovalov_lib:shap_p_aa_pp_enable")
 
StringOptionKey const corrections::shapovalov_lib::shap_p_aa_pp_smooth_level ("corrections:shapovalov_lib:shap_p_aa_pp_smooth_level")
 
StringOptionKey const corrections::shapovalov_lib::shap_p_aa_pp ("corrections:shapovalov_lib:shap_p_aa_pp")
 
BooleanOptionKey const corrections::water::water ("corrections:water")
 
BooleanOptionKey const corrections::water::water_bump_check ("corrections:water:water_bump_check")
 
RealOptionKey const corrections::water::lkb_overlap_distance ("corrections:water:lkb_overlap_distance")
 
RealOptionKey const corrections::water::lkb_cluster_radius ("corrections:water:lkb_cluster_radius")
 
RealOptionKey const corrections::water::lkb_rotset_radius ("corrections:water:lkb_rotset_radius")
 
StringOptionKey const corrections::water::wat_rot_params ("corrections:water:wat_rot_params")
 
RealOptionKey const corrections::water::dwell_cutoff ("corrections:water:dwell_cutoff")
 
RealOptionKey const corrections::water::cluster_radius ("corrections:water:cluster_radius")
 
RealOptionKey const corrections::water::cluster_cutoff ("corrections:water:cluster_cutoff")
 
RealOptionKey const corrections::water::watlim_scale ("corrections:water:watlim_scale")
 
StringOptionKey const corrections::water::pointwater_params ("corrections:water:pointwater_params")
 
RealOptionKey const corrections::water::ordered_pt_wat_penalty ("corrections:water:ordered_pt_wat_penalty")
 
RealOptionKey const corrections::water::pointwat_wat_bonus ("corrections:water:pointwat_wat_bonus")
 
RealOptionKey const corrections::water::pointwat_wat_bonus_width ("corrections:water:pointwat_wat_bonus_width")
 
RealOptionKey const corrections::water::ordered_wat_penalty ("corrections:water:ordered_wat_penalty")
 
RealOptionKey const corrections::water::wat_rot_sampling ("corrections:water:wat_rot_sampling")
 
BooleanOptionKey const corrections::water::wat_axis_sampling ("corrections:water:wat_axis_sampling")
 
RealOptionKey const corrections::water::axis_rot_sampling ("corrections:water:axis_rot_sampling")
 
BooleanOptionKey const corrections::water::include_vrt ("corrections:water:include_vrt")
 
BooleanOptionKey const enzymes::enzymes ("enzymes")
 
StringOptionKey const enzymes::species ("enzymes:species")
 
StringOptionKey const enzymes::enzyme ("enzymes:enzyme")
 
RealOptionKey const enzymes::efficiency ("enzymes:efficiency")
 
BooleanOptionKey const evaluation::evaluation ("evaluation")
 
FileVectorOptionKey const evaluation::rmsd_target ("evaluation:rmsd_target")
 
StringVectorOptionKey const evaluation::rmsd_column ("evaluation:rmsd_column")
 
FileVectorOptionKey const evaluation::rmsd_select ("evaluation:rmsd_select")
 
FileVectorOptionKey const evaluation::align_rmsd_target ("evaluation:align_rmsd_target")
 
FileVectorOptionKey const evaluation::structural_similarity ("evaluation:structural_similarity")
 
BooleanOptionKey const evaluation::contact_map ("evaluation:contact_map")
 
StringVectorOptionKey const evaluation::jscore_evaluator ("evaluation:jscore_evaluator")
 
StringVectorOptionKey const evaluation::align_rmsd_column ("evaluation:align_rmsd_column")
 
FileVectorOptionKey const evaluation::align_rmsd_fns ("evaluation:align_rmsd_fns")
 
StringOptionKey const evaluation::align_rmsd_format ("evaluation:align_rmsd_format")
 
StringOptionKey const evaluation::rms_type ("evaluation:rms_type")
 
StringOptionKey const evaluation::predicted_burial_fn ("evaluation:predicted_burial_fn")
 
FileOptionKey const evaluation::pool ("evaluation:pool")
 
FileVectorOptionKey const evaluation::rmsd ("evaluation:rmsd")
 
FileVectorOptionKey const evaluation::chirmsd ("evaluation:chirmsd")
 
BooleanOptionKey const evaluation::gdtmm ("evaluation:gdtmm")
 
BooleanOptionKey const evaluation::gdttm ("evaluation:gdttm")
 
BooleanOptionKey const evaluation::score_with_rmsd ("evaluation:score_with_rmsd")
 
FileVectorOptionKey const evaluation::constraints ("evaluation:constraints")
 
FileVectorOptionKey const evaluation::constraints_column ("evaluation:constraints_column")
 
FileVectorOptionKey const evaluation::combined_constraints ("evaluation:combined_constraints")
 
FileVectorOptionKey const evaluation::combined_constraints_column ("evaluation:combined_constraints_column")
 
IntegerOptionKey const evaluation::combine_statistics ("evaluation:combine_statistics")
 
StringVectorOptionKey const evaluation::chemical_shifts ("evaluation:chemical_shifts")
 
StringOptionKey const evaluation::sparta_dir ("evaluation:sparta_dir")
 
StringVectorOptionKey const evaluation::cam_shifts ("evaluation:cam_shifts")
 
StringVectorOptionKey const evaluation::pales ("evaluation:pales")
 
FileVectorOptionKey const evaluation::extra_score ("evaluation:extra_score")
 
FileVectorOptionKey const evaluation::extra_score_patch ("evaluation:extra_score_patch")
 
StringVectorOptionKey const evaluation::extra_score_column ("evaluation:extra_score_column")
 
FileVectorOptionKey const evaluation::extra_score_select ("evaluation:extra_score_select")
 
FileVectorOptionKey const evaluation::rdc_target ("evaluation:rdc_target")
 
BooleanOptionKey const evaluation::symmetric_rmsd ("evaluation:symmetric_rmsd")
 
StringVectorOptionKey const evaluation::rdc_column ("evaluation:rdc_column")
 
StringVectorOptionKey const evaluation::rdc ("evaluation:rdc")
 
StringOptionKey const evaluation::built_in_rdc ("evaluation:built_in_rdc")
 
BooleanOptionKey const evaluation::jump_nr ("evaluation:jump_nr")
 
IntegerVectorOptionKey const evaluation::score_exclude_res ("evaluation:score_exclude_res")
 
IntegerOptionKey const evaluation::score_sscore_short_helix ("evaluation:score_sscore_short_helix")
 
IntegerOptionKey const evaluation::score_sscore_maxloop ("evaluation:score_sscore_maxloop")
 
IntegerOptionKey const evaluation::window_size ("evaluation:window_size")
 
StringOptionKey const evaluation::I_sc ("evaluation:I_sc")
 
BooleanOptionKey const evaluation::Irms ("evaluation:Irms")
 
BooleanOptionKey const evaluation::Ca_Irms ("evaluation:Ca_Irms")
 
BooleanOptionKey const evaluation::Fnat ("evaluation:Fnat")
 
BooleanOptionKey const evaluation::Lrmsd ("evaluation:Lrmsd")
 
BooleanOptionKey const evaluation::Fnonnat ("evaluation:Fnonnat")
 
BooleanOptionKey const evaluation::DockMetrics ("evaluation:DockMetrics")
 
BooleanOptionKey const filters::filters ("filters")
 
BooleanOptionKey const filters::disable_all_filters ("filters:disable_all_filters")
 
BooleanOptionKey const filters::disable_rg_filter ("filters:disable_rg_filter")
 
BooleanOptionKey const filters::disable_co_filter ("filters:disable_co_filter")
 
BooleanOptionKey const filters::disable_sheet_filter ("filters:disable_sheet_filter")
 
RealOptionKey const filters::set_pddf_filter ("filters:set_pddf_filter")
 
RealOptionKey const filters::set_saxs_filter ("filters:set_saxs_filter")
 
BooleanOptionKey const gpu::gpu ("gpu")
 
IntegerOptionKey const gpu::device ("gpu:device")
 
IntegerOptionKey const gpu::threads ("gpu:threads")
 
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 jumps::filter_templates ("jumps:filter_templates")
 
BooleanOptionKey const loops::loops ("loops")
 
StringOptionKey const loops::cen_weights ("loops:cen_weights")
 
StringOptionKey const loops::cen_patch ("loops:cen_patch")
 
FileOptionKey const loops::input_pdb ("loops:input_pdb")
 
StringVectorOptionKey const loops::loop_file ("loops:loop_file")
 
FileOptionKey const loops::extended_loop_file ("loops:extended_loop_file")
 
FileOptionKey const loops::mm_loop_file ("loops:mm_loop_file")
 
BooleanOptionKey const loops::fix_natsc ("loops:fix_natsc")
 
BooleanOptionKey const loops::refine_only ("loops:refine_only")
 
BooleanOptionKey const loops::fast ("loops:fast")
 
FileOptionKey const loops::vall_file ("loops:vall_file")
 
IntegerVectorOptionKey const loops::frag_sizes ("loops:frag_sizes")
 
FileVectorOptionKey const loops::frag_files ("loops:frag_files")
 
FileOptionKey const loops::output_pdb ("loops:output_pdb")
 
BooleanOptionKey const loops::debug ("loops:debug")
 
BooleanOptionKey const loops::build_initial ("loops:build_initial")
 
BooleanOptionKey const loops::extended ("loops:extended")
 
BooleanOptionKey const loops::remove_extended_loops ("loops:remove_extended_loops")
 
BooleanOptionKey const loops::idealize_after_loop_close ("loops:idealize_after_loop_close")
 
BooleanOptionKey const loops::idealize_before_loop_close ("loops:idealize_before_loop_close")
 
IntegerOptionKey const loops::select_best_loop_from ("loops:select_best_loop_from")
 
IntegerOptionKey const loops::build_attempts ("loops:build_attempts")
 
IntegerOptionKey const loops::grow_attempts ("loops:grow_attempts")
 
RealOptionKey const loops::random_grow_loops_by ("loops:random_grow_loops_by")
 
BooleanOptionKey const loops::accept_aborted_loops ("loops:accept_aborted_loops")
 
BooleanOptionKey const loops::strict_loops ("loops:strict_loops")
 
BooleanOptionKey const loops::superimpose_native ("loops:superimpose_native")
 
IntegerVectorOptionKey const loops::build_specific_loops ("loops:build_specific_loops")
 
BooleanOptionKey const loops::random_order ("loops:random_order")
 
BooleanOptionKey const loops::build_all_loops ("loops:build_all_loops")
 
BooleanOptionKey const loops::fa_closure_protocol ("loops:fa_closure_protocol")
 
RealOptionKey const loops::combine_rate ("loops:combine_rate")
 
BooleanOptionKey const loops::skip_initial_loop_build ("loops:skip_initial_loop_build")
 
StringOptionKey const loops::remodel ("loops:remodel")
 
StringOptionKey const loops::intermedrelax ("loops:intermedrelax")
 
StringOptionKey const loops::refine ("loops:refine")