OptionKeys.cc.gen8.hh File Reference

Namespaces
	edensity
	enzdes
	fast_loops
	flexpack
	flexpack::annealer
	flexPepDocking
	FloppyTail
	FloppyTail::short_tail
	flxbb
	flxbb::layer
	fold_and_dock
	fold_cst
	fold_from_loops
	frags

Functions
BooleanOptionKey const	edensity::score_symm_complex ("edensity:score_symm_complex")
RealOptionKey const	edensity::sc_scaling ("edensity:sc_scaling")
IntegerOptionKey const	edensity::n_kbins ("edensity:n_kbins")
BooleanOptionKey const	edensity::unmask_bb ("edensity:unmask_bb")
BooleanOptionKey const	enzdes::enzdes ("enzdes")
StringOptionKey const	enzdes::checkpoint ("enzdes:checkpoint")
BooleanOptionKey const	enzdes::enz_score ("enzdes:enz_score")
BooleanOptionKey const	enzdes::enz_repack ("enzdes:enz_repack")
BooleanOptionKey const	enzdes::cst_opt ("enzdes:cst_opt")
BooleanOptionKey const	enzdes::cst_predock ("enzdes:cst_predock")
RealOptionKey const	enzdes::trans_magnitude ("enzdes:trans_magnitude")
RealOptionKey const	enzdes::rot_magnitude ("enzdes:rot_magnitude")
RealOptionKey const	enzdes::dock_trials ("enzdes:dock_trials")
BooleanOptionKey const	enzdes::cst_min ("enzdes:cst_min")
BooleanOptionKey const	enzdes::cst_design ("enzdes:cst_design")
IntegerOptionKey const	enzdes::design_min_cycles ("enzdes:design_min_cycles")
BooleanOptionKey const	enzdes::make_consensus_mutations ("enzdes:make_consensus_mutations")
BooleanOptionKey const	enzdes::bb_min ("enzdes:bb_min")
RealOptionKey const	enzdes::bb_min_allowed_dev ("enzdes:bb_min_allowed_dev")
RealOptionKey const	enzdes::loop_bb_min_allowed_dev ("enzdes:loop_bb_min_allowed_dev")
RealOptionKey const	enzdes::minimize_ligand_torsions ("enzdes:minimize_ligand_torsions")
RealOptionKey const	enzdes::minimize_all_ligand_torsions ("enzdes:minimize_all_ligand_torsions")
BooleanOptionKey const	enzdes::chi_min ("enzdes:chi_min")
BooleanOptionKey const	enzdes::min_all_jumps ("enzdes:min_all_jumps")
BooleanOptionKey const	enzdes::cst_dock ("enzdes:cst_dock")
BooleanOptionKey const	enzdes::run_ligand_motifs ("enzdes:run_ligand_motifs")
BooleanOptionKey const	enzdes::enz_debug ("enzdes:enz_debug")
FileOptionKey const	enzdes::cstfile ("enzdes:cstfile")
FileOptionKey const	enzdes::enz_loops_file ("enzdes:enz_loops_file")
BooleanOptionKey const	enzdes::flexbb_protocol ("enzdes:flexbb_protocol")
BooleanOptionKey const	enzdes::remodel_protocol ("enzdes:remodel_protocol")
BooleanOptionKey const	enzdes::kic_loop_sampling ("enzdes:kic_loop_sampling")
StringOptionKey const	enzdes::dump_loop_samples ("enzdes:dump_loop_samples")
BooleanOptionKey const	enzdes::fix_catalytic_aa ("enzdes:fix_catalytic_aa")
IntegerOptionKey const	enzdes::additional_packing_ligand_rb_confs ("enzdes:additional_packing_ligand_rb_confs")
IntegerOptionKey const	enzdes::ex_catalytic_rot ("enzdes:ex_catalytic_rot")
IntegerOptionKey const	enzdes::single_loop_ensemble_size ("enzdes:single_loop_ensemble_size")
IntegerOptionKey const	enzdes::loop_generator_trials ("enzdes:loop_generator_trials")
BooleanOptionKey const	enzdes::no_catres_min_in_loopgen ("enzdes:no_catres_min_in_loopgen")
RealOptionKey const	enzdes::mc_kt_low ("enzdes:mc_kt_low")
RealOptionKey const	enzdes::mc_kt_high ("enzdes:mc_kt_high")
RealOptionKey const	enzdes::min_cacb_deviation ("enzdes:min_cacb_deviation")
RealOptionKey const	enzdes::max_bb_deviation ("enzdes:max_bb_deviation")
RealOptionKey const	enzdes::max_bb_deviation_from_startstruct ("enzdes:max_bb_deviation_from_startstruct")
IntegerOptionKey const	enzdes::remodel_trials ("enzdes:remodel_trials")
BooleanOptionKey const	enzdes::remodel_secmatch ("enzdes:remodel_secmatch")
BooleanOptionKey const	enzdes::dump_inverse_rotamers ("enzdes:dump_inverse_rotamers")
RealOptionKey const	enzdes::remodel_aggressiveness ("enzdes:remodel_aggressiveness")
RealOptionKey const	enzdes::favor_native_res ("enzdes:favor_native_res")
BooleanOptionKey const	enzdes::detect_design_interface ("enzdes:detect_design_interface")
BooleanOptionKey const	enzdes::include_catres_in_interface_detection ("enzdes:include_catres_in_interface_detection")
BooleanOptionKey const	enzdes::arg_sweep_interface ("enzdes:arg_sweep_interface")
RealOptionKey const	enzdes::arg_sweep_cutoff ("enzdes:arg_sweep_cutoff")
RealOptionKey const	enzdes::cut1 ("enzdes:cut1")
RealOptionKey const	enzdes::cut2 ("enzdes:cut2")
RealOptionKey const	enzdes::cut3 ("enzdes:cut3")
RealOptionKey const	enzdes::cut4 ("enzdes:cut4")
RealOptionKey const	enzdes::lig_packer_weight ("enzdes:lig_packer_weight")
BooleanOptionKey const	enzdes::no_unconstrained_repack ("enzdes:no_unconstrained_repack")
RealOptionKey const	enzdes::secmatch_Ecutoff ("enzdes:secmatch_Ecutoff")
FileOptionKey const	enzdes::change_lig ("enzdes:change_lig")
StringOptionKey const	enzdes::process_ligrot_separately ("enzdes:process_ligrot_separately")
BooleanOptionKey const	enzdes::start_from_random_rb_conf ("enzdes:start_from_random_rb_conf")
RealOptionKey const	enzdes::bb_bump_cutoff ("enzdes:bb_bump_cutoff")
RealOptionKey const	enzdes::sc_sc_bump_cutoff ("enzdes:sc_sc_bump_cutoff")
BooleanOptionKey const	enzdes::no_packstat_calculation ("enzdes:no_packstat_calculation")
StringOptionKey const	enzdes::compare_native ("enzdes:compare_native")
BooleanOptionKey const	enzdes::final_repack_without_ligand ("enzdes:final_repack_without_ligand")
BooleanOptionKey const	enzdes::dump_final_repack_without_ligand_pdb ("enzdes:dump_final_repack_without_ligand_pdb")
BooleanOptionKey const	enzdes::parser_read_cloud_pdb ("enzdes:parser_read_cloud_pdb")
BooleanOptionKey const	fast_loops::fast_loops ("fast_loops")
RealOptionKey const	fast_loops::window_accept_ratio ("fast_loops:window_accept_ratio")
IntegerOptionKey const	fast_loops::nr_scored_sampling_passes ("fast_loops:nr_scored_sampling_passes")
IntegerOptionKey const	fast_loops::nr_scored_fragments ("fast_loops:nr_scored_fragments")
IntegerOptionKey const	fast_loops::min_breakout_good_loops ("fast_loops:min_breakout_good_loops")
IntegerOptionKey const	fast_loops::min_breakout_fast_loops ("fast_loops:min_breakout_fast_loops")
IntegerOptionKey const	fast_loops::min_good_loops ("fast_loops:min_good_loops")
IntegerOptionKey const	fast_loops::min_fast_loops ("fast_loops:min_fast_loops")
RealOptionKey const	fast_loops::vdw_delta ("fast_loops:vdw_delta")
IntegerOptionKey const	fast_loops::give_up ("fast_loops:give_up")
RealOptionKey const	fast_loops::chainbreak_max ("fast_loops:chainbreak_max")
FileOptionKey const	fast_loops::fragsample_score ("fast_loops:fragsample_score")
FileOptionKey const	fast_loops::fragsample_patch ("fast_loops:fragsample_patch")
FileOptionKey const	fast_loops::overwrite_filter_scorefxn ("fast_loops:overwrite_filter_scorefxn")
FileOptionKey const	fast_loops::patch_filter_scorefxn ("fast_loops:patch_filter_scorefxn")
FileOptionKey const	fast_loops::filter_cst_file ("fast_loops:filter_cst_file")
RealOptionKey const	fast_loops::filter_cst_weight ("fast_loops:filter_cst_weight")
FileOptionKey const	fast_loops::fast_relax_sequence_file ("fast_loops:fast_relax_sequence_file")
BooleanOptionKey const	flexpack::flexpack ("flexpack")
BooleanOptionKey const	flexpack::annealer::annealer ("flexpack:annealer")
RealOptionKey const	flexpack::annealer::inner_iteration_scale ("flexpack:annealer:inner_iteration_scale")
RealOptionKey const	flexpack::annealer::outer_iteration_scale ("flexpack:annealer:outer_iteration_scale")
RealOptionKey const	flexpack::annealer::fixbb_substitutions_scale ("flexpack:annealer:fixbb_substitutions_scale")
RealOptionKey const	flexpack::annealer::pure_movebb_substitutions_scale ("flexpack:annealer:pure_movebb_substitutions_scale")
RealOptionKey const	flexpack::annealer::rotsub_movebb_substitutions_scale ("flexpack:annealer:rotsub_movebb_substitutions_scale")
BooleanOptionKey const	flexPepDocking::flexPepDocking ("flexPepDocking")
StringOptionKey const	flexPepDocking::params_file ("flexPepDocking:params_file")
IntegerOptionKey const	flexPepDocking::peptide_anchor ("flexPepDocking:peptide_anchor")
StringOptionKey const	flexPepDocking::receptor_chain ("flexPepDocking:receptor_chain")
StringOptionKey const	flexPepDocking::peptide_chain ("flexPepDocking:peptide_chain")
BooleanOptionKey const	flexPepDocking::pep_fold_only ("flexPepDocking:pep_fold_only")
BooleanOptionKey const	flexPepDocking::lowres_abinitio ("flexPepDocking:lowres_abinitio")
BooleanOptionKey const	flexPepDocking::lowres_preoptimize ("flexPepDocking:lowres_preoptimize")
BooleanOptionKey const	flexPepDocking::flexPepDockingMinimizeOnly ("flexPepDocking:flexPepDockingMinimizeOnly")
BooleanOptionKey const	flexPepDocking::extend_peptide ("flexPepDocking:extend_peptide")
BooleanOptionKey const	flexPepDocking::place_peptide_on_binding_site ("flexPepDocking:place_peptide_on_binding_site")
IntegerOptionKey const	flexPepDocking::sample_pcs ("flexPepDocking:sample_pcs")
BooleanOptionKey const	flexPepDocking::SlideIntoContact ("flexPepDocking:SlideIntoContact")
BooleanOptionKey const	flexPepDocking::recalculate_foldtree ("flexPepDocking:recalculate_foldtree")
BooleanOptionKey const	flexPepDocking::pep_refine ("flexPepDocking:pep_refine")
BooleanOptionKey const	flexPepDocking::rbMCM ("flexPepDocking:rbMCM")
BooleanOptionKey const	flexPepDocking::torsionsMCM ("flexPepDocking:torsionsMCM")
BooleanOptionKey const	flexPepDocking::peptide_loop_model ("flexPepDocking:peptide_loop_model")
BooleanOptionKey const	flexPepDocking::backrub_peptide ("flexPepDocking:backrub_peptide")
BooleanOptionKey const	flexPepDocking::boost_fa_atr ("flexPepDocking:boost_fa_atr")
BooleanOptionKey const	flexPepDocking::ramp_fa_rep ("flexPepDocking:ramp_fa_rep")
BooleanOptionKey const	flexPepDocking::ramp_rama ("flexPepDocking:ramp_rama")
BooleanOptionKey const	flexPepDocking::flexpep_score_only ("flexPepDocking:flexpep_score_only")
FileOptionKey const	flexPepDocking::ref_startstruct ("flexPepDocking:ref_startstruct")
BooleanOptionKey const	flexPepDocking::use_cen_score ("flexPepDocking:use_cen_score")
BooleanOptionKey const	flexPepDocking::design_peptide ("flexPepDocking:design_peptide")
IntegerOptionKey const	flexPepDocking::rep_ramp_cycles ("flexPepDocking:rep_ramp_cycles")
IntegerOptionKey const	flexPepDocking::mcm_cycles ("flexPepDocking:mcm_cycles")
RealOptionKey const	flexPepDocking::random_phi_psi_preturbation ("flexPepDocking:random_phi_psi_preturbation")
RealOptionKey const	flexPepDocking::smove_angle_range ("flexPepDocking:smove_angle_range")
BooleanOptionKey const	flexPepDocking::min_receptor_bb ("flexPepDocking:min_receptor_bb")
RealOptionKey const	flexPepDocking::random_trans_start ("flexPepDocking:random_trans_start")
RealOptionKey const	flexPepDocking::random_rot_start ("flexPepDocking:random_rot_start")
BooleanOptionKey const	flexPepDocking::flexpep_prepack ("flexPepDocking:flexpep_prepack")
BooleanOptionKey const	flexPepDocking::flexpep_noprepack1 ("flexPepDocking:flexpep_noprepack1")
BooleanOptionKey const	flexPepDocking::flexpep_noprepack2 ("flexPepDocking:flexpep_noprepack2")
RealOptionKey const	flexPepDocking::score_filter ("flexPepDocking:score_filter")
IntegerOptionKey const	flexPepDocking::hb_filter ("flexPepDocking:hb_filter")
IntegerOptionKey const	flexPepDocking::hotspot_filter ("flexPepDocking:hotspot_filter")
StringOptionKey const	flexPepDocking::frag5 ("flexPepDocking:frag5")
RealOptionKey const	flexPepDocking::frag9_weight ("flexPepDocking:frag9_weight")
RealOptionKey const	flexPepDocking::frag5_weight ("flexPepDocking:frag5_weight")
RealOptionKey const	flexPepDocking::frag3_weight ("flexPepDocking:frag3_weight")
BooleanOptionKey const	flexPepDocking::pSer2Asp_centroid ("flexPepDocking:pSer2Asp_centroid")
BooleanOptionKey const	flexPepDocking::pSer2Glu_centroid ("flexPepDocking:pSer2Glu_centroid")
BooleanOptionKey const	flexPepDocking::dumpPDB_abinitio ("flexPepDocking:dumpPDB_abinitio")
BooleanOptionKey const	flexPepDocking::dumpPDB_lowres ("flexPepDocking:dumpPDB_lowres")
BooleanOptionKey const	flexPepDocking::dumpPDB_hires ("flexPepDocking:dumpPDB_hires")
BooleanOptionKey const	FloppyTail::FloppyTail ("FloppyTail")
IntegerOptionKey const	FloppyTail::flexible_start_resnum ("FloppyTail:flexible_start_resnum")
IntegerOptionKey const	FloppyTail::flexible_stop_resnum ("FloppyTail:flexible_stop_resnum")
StringOptionKey const	FloppyTail::flexible_chain ("FloppyTail:flexible_chain")
RealOptionKey const	FloppyTail::shear_on ("FloppyTail:shear_on")
BooleanOptionKey const	FloppyTail::pair_off ("FloppyTail:pair_off")
BooleanOptionKey const	FloppyTail::publication ("FloppyTail:publication")
BooleanOptionKey const	FloppyTail::C_root ("FloppyTail:C_root")
BooleanOptionKey const	FloppyTail::force_linear_fold_tree ("FloppyTail:force_linear_fold_tree")
BooleanOptionKey const	FloppyTail::debug ("FloppyTail:debug")
StringOptionKey const	FloppyTail::cen_weights ("FloppyTail:cen_weights")
BooleanOptionKey const	FloppyTail::perturb_show ("FloppyTail:perturb_show")
IntegerOptionKey const	FloppyTail::perturb_cycles ("FloppyTail:perturb_cycles")
RealOptionKey const	FloppyTail::perturb_temp ("FloppyTail:perturb_temp")
IntegerOptionKey const	FloppyTail::refine_cycles ("FloppyTail:refine_cycles")
RealOptionKey const	FloppyTail::refine_temp ("FloppyTail:refine_temp")
IntegerOptionKey const	FloppyTail::refine_repack_cycles ("FloppyTail:refine_repack_cycles")
BooleanOptionKey const	FloppyTail::short_tail::short_tail ("FloppyTail:short_tail")
RealOptionKey const	FloppyTail::short_tail::short_tail_fraction ("FloppyTail:short_tail:short_tail_fraction")
RealOptionKey const	FloppyTail::short_tail::short_tail_off ("FloppyTail:short_tail:short_tail_off")
BooleanOptionKey const	flxbb::flxbb ("flxbb")
BooleanOptionKey const	flxbb::view ("flxbb:view")
IntegerOptionKey const	flxbb::ncycle ("flxbb:ncycle")
RealOptionKey const	flxbb::constraints_sheet ("flxbb:constraints_sheet")
BooleanOptionKey const	flxbb::constraints_sheet_include_cacb_pseudotorsion ("flxbb:constraints_sheet_include_cacb_pseudotorsion")
RealOptionKey const	flxbb::constraints_NtoC ("flxbb:constraints_NtoC")
IntegerOptionKey const	flxbb::filter_trial ("flxbb:filter_trial")
StringOptionKey const	flxbb::filter_type ("flxbb:filter_type")
FileOptionKey const	flxbb::blueprint ("flxbb:blueprint")
BooleanOptionKey const	flxbb::movemap_from_blueprint ("flxbb:movemap_from_blueprint")
StringOptionKey const	flxbb::layer::layer ("flxbb:layer")
BooleanOptionKey const	fold_and_dock::fold_and_dock ("fold_and_dock")
BooleanOptionKey const	fold_and_dock::move_anchor_points ("fold_and_dock:move_anchor_points")
BooleanOptionKey const	fold_and_dock::set_anchor_at_closest_point ("fold_and_dock:set_anchor_at_closest_point")
BooleanOptionKey const	fold_and_dock::rotate_anchor_to_x ("fold_and_dock:rotate_anchor_to_x")
RealOptionKey const	fold_and_dock::trans_mag_smooth ("fold_and_dock:trans_mag_smooth")
RealOptionKey const	fold_and_dock::rot_mag_smooth ("fold_and_dock:rot_mag_smooth")
RealOptionKey const	fold_and_dock::rb_rot_magnitude ("fold_and_dock:rb_rot_magnitude")
RealOptionKey const	fold_and_dock::rb_trans_magnitude ("fold_and_dock:rb_trans_magnitude")
IntegerOptionKey const	fold_and_dock::rigid_body_cycles ("fold_and_dock:rigid_body_cycles")
RealOptionKey const	fold_and_dock::move_anchor_frequency ("fold_and_dock:move_anchor_frequency")
RealOptionKey const	fold_and_dock::rigid_body_frequency ("fold_and_dock:rigid_body_frequency")
BooleanOptionKey const	fold_and_dock::rigid_body_disable_mc ("fold_and_dock:rigid_body_disable_mc")
RealOptionKey const	fold_and_dock::slide_contact_frequency ("fold_and_dock:slide_contact_frequency")
BooleanOptionKey const	fold_cst::fold_cst ("fold_cst")
RealOptionKey const	fold_cst::constraint_skip_rate ("fold_cst:constraint_skip_rate")
IntegerOptionKey const	fold_cst::violation_skip_basis ("fold_cst:violation_skip_basis")
IntegerOptionKey const	fold_cst::violation_skip_ignore ("fold_cst:violation_skip_ignore")
BooleanOptionKey const	fold_cst::keep_skipped_csts ("fold_cst:keep_skipped_csts")
BooleanOptionKey const	fold_cst::no_minimize ("fold_cst:no_minimize")
BooleanOptionKey const	fold_cst::force_minimize ("fold_cst:force_minimize")
RealVectorOptionKey const	fold_cst::seq_sep_stages ("fold_cst:seq_sep_stages")
IntegerOptionKey const	fold_cst::reramp_cst_cycles ("fold_cst:reramp_cst_cycles")
RealOptionKey const	fold_cst::reramp_start_cstweight ("fold_cst:reramp_start_cstweight")
IntegerOptionKey const	fold_cst::reramp_iterations ("fold_cst:reramp_iterations")
BooleanOptionKey const	fold_cst::skip_on_noviolation_in_stage1 ("fold_cst:skip_on_noviolation_in_stage1")
RealOptionKey const	fold_cst::stage1_ramp_cst_cycle_factor ("fold_cst:stage1_ramp_cst_cycle_factor")
RealOptionKey const	fold_cst::stage2_constraint_threshold ("fold_cst:stage2_constraint_threshold")
BooleanOptionKey const	fold_cst::ignore_sequence_seperation ("fold_cst:ignore_sequence_seperation")
BooleanOptionKey const	fold_cst::no_recover_low_at_constraint_switch ("fold_cst:no_recover_low_at_constraint_switch")
BooleanOptionKey const	fold_cst::ramp_coord_cst ("fold_cst:ramp_coord_cst")
BooleanOptionKey const	fold_from_loops::fold_from_loops ("fold_from_loops")
BooleanOptionKey const	fold_from_loops::native_ca_cst ("fold_from_loops:native_ca_cst")
FileOptionKey const	fold_from_loops::swap_loops ("fold_from_loops:swap_loops")
StringOptionKey const	fold_from_loops::checkpoint ("fold_from_loops:checkpoint")
RealOptionKey const	fold_from_loops::ca_csts_dev ("fold_from_loops:ca_csts_dev")
IntegerOptionKey const	fold_from_loops::add_relax_cycles ("fold_from_loops:add_relax_cycles")
IntegerOptionKey const	fold_from_loops::loop_mov_nterm ("fold_from_loops:loop_mov_nterm")
IntegerOptionKey const	fold_from_loops::loop_mov_cterm ("fold_from_loops:loop_mov_cterm")
RealOptionKey const	fold_from_loops::ca_rmsd_cutoff ("fold_from_loops:ca_rmsd_cutoff")
IntegerVectorOptionKey const	fold_from_loops::res_design_bs ("fold_from_loops:res_design_bs")
FileOptionKey const	fold_from_loops::clear_csts ("fold_from_loops:clear_csts")
BooleanOptionKey const	fold_from_loops::output_centroid ("fold_from_loops:output_centroid")
BooleanOptionKey const	fold_from_loops::add_cst_loop ("fold_from_loops:add_cst_loop")
BooleanOptionKey const	frags::frags ("frags")
IntegerOptionKey const	frags::j ("frags:j")
BooleanOptionKey const	frags::filter_JC ("frags:filter_JC")
BooleanOptionKey const	frags::bounded_protocol ("frags:bounded_protocol")
BooleanOptionKey const	frags::keep_all_protocol ("frags:keep_all_protocol")
BooleanOptionKey const	frags::quota_protocol ("frags:quota_protocol")
BooleanOptionKey const	frags::nonlocal_pairs ("frags:nonlocal_pairs")
BooleanOptionKey const	frags::fragment_contacts ("frags:fragment_contacts")
BooleanOptionKey const	frags::p_value_selection ("frags:p_value_selection")
IntegerOptionKey const	frags::n_frags ("frags:n_frags")
FileOptionKey const	frags::allowed_pdb ("frags:allowed_pdb")
StringVectorOptionKey const	frags::ss_pred ("frags:ss_pred")