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OptionKeys.cc.gen2.hh File Reference

Namespaces

 score
 
 score::rna
 
 score::saxs
 
 score::fiber_diffraction
 
 score::occ_sol_fitted
 
 score::loop_close
 
 multithreading
 
 recon
 
 packing
 
 packing::ex1
 
 packing::ex2
 
 packing::ex3
 
 packing::ex4
 
 packing::ex1aro
 
 packing::ex2aro
 
 packing::ex1aro_exposed
 
 packing::ex2aro_exposed
 
 packing::exdna
 
 packing::packer_palette
 
 archive
 
 carbohydrates
 
 carbohydrates::glycopeptide_docking
 
 carbohydrates::glycan_sampler
 
 carbohydrates::clash_check
 

Functions

RealOptionKey const score::facts_kappa ("score:facts_kappa")
 
IntegerOptionKey const score::facts_asp_patch ("score:facts_asp_patch")
 
BooleanOptionKey const score::facts_plane_to_self ("score:facts_plane_to_self")
 
RealOptionKey const score::facts_saltbridge_correction ("score:facts_saltbridge_correction")
 
RealVectorOptionKey const score::facts_dshift ("score:facts_dshift")
 
RealOptionKey const score::facts_die ("score:facts_die")
 
BooleanOptionKey const score::facts_binding_affinity ("score:facts_binding_affinity")
 
BooleanOptionKey const score::facts_intrascale_by_level ("score:facts_intrascale_by_level")
 
RealVectorOptionKey const score::facts_intbb_elec_scale ("score:facts_intbb_elec_scale")
 
RealVectorOptionKey const score::facts_intbb_solv_scale ("score:facts_intbb_solv_scale")
 
RealVectorOptionKey const score::facts_adjbb_elec_scale ("score:facts_adjbb_elec_scale")
 
RealVectorOptionKey const score::facts_adjbb_solv_scale ("score:facts_adjbb_solv_scale")
 
RealVectorOptionKey const score::facts_intbs_elec_scale ("score:facts_intbs_elec_scale")
 
RealVectorOptionKey const score::facts_intbs_solv_scale ("score:facts_intbs_solv_scale")
 
RealVectorOptionKey const score::facts_adjbs_elec_scale ("score:facts_adjbs_elec_scale")
 
RealVectorOptionKey const score::facts_adjbs_solv_scale ("score:facts_adjbs_solv_scale")
 
RealVectorOptionKey const score::facts_intsc_elec_scale ("score:facts_intsc_elec_scale")
 
RealVectorOptionKey const score::facts_intsc_solv_scale ("score:facts_intsc_solv_scale")
 
StringOptionKey const score::facts_charge_dir ("score:facts_charge_dir")
 
StringOptionKey const score::facts_eff_charge_dir ("score:facts_eff_charge_dir")
 
StringVectorOptionKey const score::facts_plane_aa ("score:facts_plane_aa")
 
StringOptionKey const score::facts_eq_type ("score:facts_eq_type")
 
IntegerOptionKey const score::ignore_terminal_ss_elements ("score:ignore_terminal_ss_elements")
 
BooleanOptionKey const score::length_dep_srbb ("score:length_dep_srbb")
 
RealOptionKey const score::ldsrbb_low_scale ("score:ldsrbb_low_scale")
 
RealOptionKey const score::ldsrbb_high_scale ("score:ldsrbb_high_scale")
 
IntegerOptionKey const score::ldsrbb_minlength ("score:ldsrbb_minlength")
 
IntegerOptionKey const score::ldsrbb_maxlength ("score:ldsrbb_maxlength")
 
RealOptionKey const score::max_motif_per_res ("score:max_motif_per_res")
 
IntegerOptionKey const score::max_contacting_ss ("score:max_contacting_ss")
 
BooleanOptionKey const score::motif_ignore_symmmetry ("score:motif_ignore_symmmetry")
 
IntegerVectorOptionKey const score::motif_residues ("score:motif_residues")
 
StringVectorOptionKey const score::netcharge_setup_file ("score:netcharge_setup_file")
 
StringVectorOptionKey const score::mhc_epitope_setup_file ("score:mhc_epitope_setup_file")
 
RealOptionKey const score::ms_dist_midpoint ("score:ms_dist_midpoint")
 
RealOptionKey const score::ms_dist_exponent ("score:ms_dist_exponent")
 
RealOptionKey const score::ms_fit_slope ("score:ms_fit_slope")
 
RealOptionKey const score::ms_fit_intercept ("score:ms_fit_intercept")
 
RealOptionKey const score::ms_fade_outer ("score:ms_fade_outer")
 
RealOptionKey const score::ms_fade_dist ("score:ms_fade_dist")
 
StringOptionKey const score::nmer_ref_energies ("score:nmer_ref_energies")
 
StringOptionKey const score::nmer_ref_energies_list ("score:nmer_ref_energies_list")
 
StringOptionKey const score::nmer_pssm ("score:nmer_pssm")
 
StringOptionKey const score::nmer_pssm_list ("score:nmer_pssm_list")
 
RealOptionKey const score::nmer_pssm_scorecut ("score:nmer_pssm_scorecut")
 
StringOptionKey const score::nmer_svm ("score:nmer_svm")
 
StringOptionKey const score::nmer_svm_list ("score:nmer_svm_list")
 
StringOptionKey const score::nmer_svm_rank ("score:nmer_svm_rank")
 
StringOptionKey const score::nmer_svm_rank_list ("score:nmer_svm_rank_list")
 
RealOptionKey const score::nmer_svm_scorecut ("score:nmer_svm_scorecut")
 
StringOptionKey const score::nmer_svm_aa_matrix ("score:nmer_svm_aa_matrix")
 
IntegerOptionKey const score::nmer_svm_term_length ("score:nmer_svm_term_length")
 
BooleanOptionKey const score::nmer_svm_pssm_feat ("score:nmer_svm_pssm_feat")
 
BooleanOptionKey const score::nmer_svm_avg_rank_as_energy ("score:nmer_svm_avg_rank_as_energy")
 
IntegerOptionKey const score::nmer_ref_seq_length ("score:nmer_ref_seq_length")
 
BooleanOptionKey const score::just_calc_rmsd ("score:just_calc_rmsd")
 
BooleanOptionKey const score::envsmooth_zero_negatives ("score:envsmooth_zero_negatives")
 
RealOptionKey const score::rama_power ("score:rama_power")
 
BooleanOptionKey const score::ideal_sugars ("score:ideal_sugars")
 
RealOptionKey const score::hbond_fade ("score:hbond_fade")
 
BooleanOptionKey const score::hbond_new_sp3_acc ("score:hbond_new_sp3_acc")
 
RealOptionKey const score::alignment_sharpness ("score:alignment_sharpness")
 
StringOptionKey const score::rna_torsion_potential ("score:rna_torsion_potential")
 
BooleanOptionKey const score::arg_cation_pi_his_can_be_pi ("score:arg_cation_pi_his_can_be_pi")
 
BooleanOptionKey const score::mc_optimize_dG ("score:mc_optimize_dG")
 
RealOptionKey const score::mc_interface_weight ("score:mc_interface_weight")
 
RealOptionKey const score::mc_total_weight ("score:mc_total_weight")
 
BooleanOptionKey const score::force_sugar_bb_zero ("score:force_sugar_bb_zero")
 
IntegerOptionKey const score::voids_penalty_energy_containing_cones_cutoff ("score:voids_penalty_energy_containing_cones_cutoff")
 
RealOptionKey const score::voids_penalty_energy_cone_dotproduct_cutoff ("score:voids_penalty_energy_cone_dotproduct_cutoff")
 
RealOptionKey const score::voids_penalty_energy_cone_distance_cutoff ("score:voids_penalty_energy_cone_distance_cutoff")
 
BooleanOptionKey const score::voids_penalty_energy_disabled_except_during_packing ("score:voids_penalty_energy_disabled_except_during_packing")
 
RealOptionKey const score::voids_penalty_energy_voxel_size ("score:voids_penalty_energy_voxel_size")
 
RealOptionKey const score::voids_penalty_energy_voxel_grid_padding ("score:voids_penalty_energy_voxel_grid_padding")
 
BooleanOptionKey const score::rna::rna ("score:rna")
 
StringOptionKey const score::rna::rna_base_pair_xy_filename ("score:rna:rna_base_pair_xy_filename")
 
BooleanOptionKey const score::rna::disable_orientation_dependent_rna_ch_o_bonds ("score:rna:disable_orientation_dependent_rna_ch_o_bonds")
 
StringOptionKey const score::rna::rna_suite_potential ("score:rna:rna_suite_potential")
 
StringOptionKey const score::rna::suiteness_bonus ("score:rna:suiteness_bonus")
 
BooleanOptionKey const score::rna::rna_torsion_skip_chainbreak ("score:rna:rna_torsion_skip_chainbreak")
 
BooleanOptionKey const score::rna::rna_chemical_shift_verbose ("score:rna:rna_chemical_shift_verbose")
 
BooleanOptionKey const score::rna::rna_chemical_shift_larmord ("score:rna:rna_chemical_shift_larmord")
 
StringOptionKey const score::rna::rna_chemical_shift_exp_data ("score:rna:rna_chemical_shift_exp_data")
 
StringOptionKey const score::rna::rna_chemical_shift_larmord_par ("score:rna:rna_chemical_shift_larmord_par")
 
StringOptionKey const score::rna::rna_chemical_shift_larmord_wt ("score:rna:rna_chemical_shift_larmord_wt")
 
StringOptionKey const score::rna::rna_chemical_shift_larmord_ref ("score:rna:rna_chemical_shift_larmord_ref")
 
StringOptionKey const score::rna::rna_chemical_shift_larmord_nei ("score:rna:rna_chemical_shift_larmord_nei")
 
RealOptionKey const score::rna::rna_chemical_shift_larmord_cut ("score:rna:rna_chemical_shift_larmord_cut")
 
RealOptionKey const score::rna::rna_chemical_shift_larmord_beta ("score:rna:rna_chemical_shift_larmord_beta")
 
StringOptionKey const score::rna::rna_chemical_shift_H5_prime_mode ("score:rna:rna_chemical_shift_H5_prime_mode")
 
IntegerVectorOptionKey const score::rna::rna_chemical_shift_include_res ("score:rna:rna_chemical_shift_include_res")
 
BooleanOptionKey const score::rna::DMS_separate_features ("score:rna:DMS_separate_features")
 
BooleanOptionKey const score::rna::DMS_careful_base_pair_classifier ("score:rna:DMS_careful_base_pair_classifier")
 
RealOptionKey const score::rna::rna_chem_map_lores_weight ("score:rna:rna_chem_map_lores_weight")
 
BooleanOptionKey const score::rna::use_2prime_OH_potential ("score:rna:use_2prime_OH_potential")
 
BooleanOptionKey const score::rna::use_rna_chi_potential ("score:rna:use_rna_chi_potential")
 
BooleanOptionKey const score::rna::include_neighbor_base_stacks ("score:rna:include_neighbor_base_stacks")
 
BooleanOptionKey const score::rna::FA_low_res_rnp_scoring ("score:rna:FA_low_res_rnp_scoring")
 
RealOptionKey const score::rna::free_suite_bonus ("score:rna:free_suite_bonus")
 
RealOptionKey const score::rna::free_sugar_bonus ("score:rna:free_sugar_bonus")
 
RealOptionKey const score::rna::free_2HOprime_bonus ("score:rna:free_2HOprime_bonus")
 
RealOptionKey const score::rna::syn_G_potential_bonus ("score:rna:syn_G_potential_bonus")
 
BooleanOptionKey const score::rna::rna_bulge_bonus_once_per_loop ("score:rna:rna_bulge_bonus_once_per_loop")
 
RealOptionKey const score::rna::pack_phosphate_penalty ("score:rna:pack_phosphate_penalty")
 
BooleanOptionKey const score::saxs::saxs ("score:saxs")
 
RealOptionKey const score::saxs::min_score ("score:saxs:min_score")
 
StringOptionKey const score::saxs::custom_ff ("score:saxs:custom_ff")
 
StringOptionKey const score::saxs::print_i_calc ("score:saxs:print_i_calc")
 
FileOptionKey const score::saxs::ref_fa_spectrum ("score:saxs:ref_fa_spectrum")
 
FileOptionKey const score::saxs::ref_cen_spectrum ("score:saxs:ref_cen_spectrum")
 
FileOptionKey const score::saxs::ref_spectrum ("score:saxs:ref_spectrum")
 
FileOptionKey const score::saxs::ref_pddf ("score:saxs:ref_pddf")
 
RealOptionKey const score::saxs::d_min ("score:saxs:d_min")
 
RealOptionKey const score::saxs::d_max ("score:saxs:d_max")
 
RealOptionKey const score::saxs::d_step ("score:saxs:d_step")
 
RealOptionKey const score::saxs::q_min ("score:saxs:q_min")
 
RealOptionKey const score::saxs::q_max ("score:saxs:q_max")
 
RealOptionKey const score::saxs::q_step ("score:saxs:q_step")
 
BooleanOptionKey const score::saxs::fit_pddf_area ("score:saxs:fit_pddf_area")
 
BooleanOptionKey const score::fiber_diffraction::fiber_diffraction ("score:fiber_diffraction")
 
FileOptionKey const score::fiber_diffraction::layer_lines ("score:fiber_diffraction:layer_lines")
 
RealOptionKey const score::fiber_diffraction::a ("score:fiber_diffraction:a")
 
RealOptionKey const score::fiber_diffraction::b ("score:fiber_diffraction:b")
 
RealOptionKey const score::fiber_diffraction::p ("score:fiber_diffraction:p")
 
RealOptionKey const score::fiber_diffraction::radius ("score:fiber_diffraction:radius")
 
RealOptionKey const score::fiber_diffraction::resolution_cutoff_low ("score:fiber_diffraction:resolution_cutoff_low")
 
RealOptionKey const score::fiber_diffraction::resolution_cutoff_high ("score:fiber_diffraction:resolution_cutoff_high")
 
IntegerOptionKey const score::fiber_diffraction::max_bessel_order ("score:fiber_diffraction:max_bessel_order")
 
IntegerOptionKey const score::fiber_diffraction::cn_symmetry ("score:fiber_diffraction:cn_symmetry")
 
RealOptionKey const score::fiber_diffraction::b_factor ("score:fiber_diffraction:b_factor")
 
RealOptionKey const score::fiber_diffraction::b_factor_solv ("score:fiber_diffraction:b_factor_solv")
 
RealOptionKey const score::fiber_diffraction::b_factor_solv_K ("score:fiber_diffraction:b_factor_solv_K")
 
RealOptionKey const score::fiber_diffraction::grid_reso ("score:fiber_diffraction:grid_reso")
 
IntegerOptionKey const score::fiber_diffraction::grid_r ("score:fiber_diffraction:grid_r")
 
IntegerOptionKey const score::fiber_diffraction::grid_phi ("score:fiber_diffraction:grid_phi")
 
IntegerOptionKey const score::fiber_diffraction::grid_z ("score:fiber_diffraction:grid_z")
 
RealOptionKey const score::fiber_diffraction::qfht_K1 ("score:fiber_diffraction:qfht_K1")
 
RealOptionKey const score::fiber_diffraction::qfht_K2 ("score:fiber_diffraction:qfht_K2")
 
IntegerOptionKey const score::fiber_diffraction::chi_iterations ("score:fiber_diffraction:chi_iterations")
 
BooleanOptionKey const score::fiber_diffraction::rfactor_refinement ("score:fiber_diffraction:rfactor_refinement")
 
BooleanOptionKey const score::fiber_diffraction::output_fiber_spectra ("score:fiber_diffraction:output_fiber_spectra")
 
IntegerOptionKey const score::fiber_diffraction::gpu_processor ("score:fiber_diffraction:gpu_processor")
 
RealOptionKey const score::fiber_diffraction::centroid_density_mass ("score:fiber_diffraction:centroid_density_mass")
 
BooleanOptionKey const score::occ_sol_fitted::occ_sol_fitted ("score:occ_sol_fitted")
 
RealOptionKey const score::occ_sol_fitted::Ntrp_amp_scaling ("score:occ_sol_fitted:Ntrp_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::NH2O_amp_scaling ("score:occ_sol_fitted:NH2O_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::Nlys_amp_scaling ("score:occ_sol_fitted:Nlys_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::Narg_amp_scaling ("score:occ_sol_fitted:Narg_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::Nbb_amp_scaling ("score:occ_sol_fitted:Nbb_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::Nhis_amp_scaling ("score:occ_sol_fitted:Nhis_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::OH_amp_scaling ("score:occ_sol_fitted:OH_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::ONH2_amp_scaling ("score:occ_sol_fitted:ONH2_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::OOC_amp_scaling ("score:occ_sol_fitted:OOC_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::Oaro_amp_scaling ("score:occ_sol_fitted:Oaro_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::Oet2_amp_scaling ("score:occ_sol_fitted:Oet2_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::Oet3_amp_scaling ("score:occ_sol_fitted:Oet3_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::OCbb_amp_scaling ("score:occ_sol_fitted:OCbb_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::HOH_amp_scaling ("score:occ_sol_fitted:HOH_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::OPha_amp_scaling ("score:occ_sol_fitted:OPha_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::OHha_amp_scaling ("score:occ_sol_fitted:OHha_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::OC3_amp_scaling ("score:occ_sol_fitted:OC3_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::OSi_amp_scaling ("score:occ_sol_fitted:OSi_amp_scaling")
 
RealOptionKey const score::occ_sol_fitted::Oice_amp_scaling ("score:occ_sol_fitted:Oice_amp_scaling")
 
BooleanOptionKey const score::loop_close::loop_close ("score:loop_close")
 
RealOptionKey const score::loop_close::loop_fixed_cost ("score:loop_close:loop_fixed_cost")
 
BooleanOptionKey const score::loop_close::allow_complex_loop_graph ("score:loop_close:allow_complex_loop_graph")
 
BooleanOptionKey const score::loop_close::use_6D_potential ("score:loop_close:use_6D_potential")
 
StringOptionKey const score::loop_close::force_6D_potential_file ("score:loop_close:force_6D_potential_file")
 
BooleanOptionKey const score::loop_close::use_cubic_interp ("score:loop_close:use_cubic_interp")
 
BooleanOptionKey const multithreading::multithreading ("multithreading")
 
IntegerOptionKey const multithreading::total_threads ("multithreading:total_threads")
 
IntegerOptionKey const multithreading::interaction_graph_threads ("multithreading:interaction_graph_threads")
 
BooleanOptionKey const recon::recon ("recon")
 
BooleanOptionKey const recon::randomize ("recon:randomize")
 
BooleanOptionKey const packing::packing ("packing")
 
BooleanOptionKey const packing::repack_only ("packing:repack_only")
 
BooleanOptionKey const packing::prevent_repacking ("packing:prevent_repacking")
 
RealOptionKey const packing::cenrot_cutoff ("packing:cenrot_cutoff")
 
BooleanOptionKey const packing::ignore_ligand_chi ("packing:ignore_ligand_chi")
 
BooleanOptionKey const packing::quasisymmetry ("packing:quasisymmetry")
 
IntegerOptionKey const packing::ndruns ("packing:ndruns")
 
BooleanOptionKey const packing::soft_rep_design ("packing:soft_rep_design")
 
RealOptionKey const packing::mainchain_h_rebuild_threshold ("packing:mainchain_h_rebuild_threshold")
 
BooleanOptionKey const packing::use_electrostatic_repulsion ("packing:use_electrostatic_repulsion")
 
BooleanOptionKey const packing::dump_rotamer_sets ("packing:dump_rotamer_sets")
 
RealOptionKey const packing::dunbrack_prob_buried ("packing:dunbrack_prob_buried")
 
RealOptionKey const packing::dunbrack_prob_nonburied ("packing:dunbrack_prob_nonburied")
 
RealOptionKey const packing::dunbrack_prob_buried_semi ("packing:dunbrack_prob_buried_semi")
 
RealOptionKey const packing::dunbrack_prob_nonburied_semi ("packing:dunbrack_prob_nonburied_semi")
 
BooleanOptionKey const packing::no_optH ("packing:no_optH")
 
BooleanOptionKey const packing::optH_MCA ("packing:optH_MCA")
 
BooleanOptionKey const packing::pack_missing_sidechains ("packing:pack_missing_sidechains")
 
BooleanOptionKey const packing::preserve_c_beta ("packing:preserve_c_beta")
 
BooleanOptionKey const packing::flip_HNQ ("packing:flip_HNQ")
 
IntegerVectorOptionKey const packing::fix_his_tautomer ("packing:fix_his_tautomer")
 
BooleanOptionKey const packing::print_pymol_selection ("packing:print_pymol_selection")
 
IntegerOptionKey const packing::extrachi_cutoff ("packing:extrachi_cutoff")
 
FileVectorOptionKey const packing::resfile ("packing:resfile")
 
BooleanOptionKey const packing::sc_branch_rotamers ("packing:sc_branch_rotamers")
 
RealOptionKey const packing::outeriterations_scaling ("packing:outeriterations_scaling")
 
RealOptionKey const packing::inneriterations_scaling ("packing:inneriterations_scaling")
 
StringVectorOptionKey const packing::adducts ("packing:adducts")
 
BooleanOptionKey const packing::use_input_sc ("packing:use_input_sc")
 
FileVectorOptionKey const packing::unboundrot ("packing:unboundrot")
 
RealOptionKey const packing::max_rotbump_energy ("packing:max_rotbump_energy")
 
BooleanOptionKey const packing::lazy_ig ("packing:lazy_ig")
 
BooleanOptionKey const packing::double_lazy_ig ("packing:double_lazy_ig")
 
IntegerOptionKey const packing::linmem_ig ("packing:linmem_ig")
 
BooleanOptionKey const packing::precompute_ig ("packing:precompute_ig")
 
IntegerOptionKey const packing::multi_cool_annealer ("packing:multi_cool_annealer")
 
BooleanOptionKey const packing::sequence_symmetric_annealer ("packing:sequence_symmetric_annealer")
 
BooleanOptionKey const packing::smart_annealer ("packing:smart_annealer")
 
StringOptionKey const packing::smart_annealer_model ("packing:smart_annealer_model")
 
RealOptionKey const packing::smart_annealer_cutoff ("packing:smart_annealer_cutoff")
 
BooleanOptionKey const packing::smart_annealer_pick_again ("packing:smart_annealer_pick_again")
 
BooleanOptionKey const packing::smart_annealer_disable_during_quench ("packing:smart_annealer_disable_during_quench")
 
RealVectorOptionKey const packing::minpack_temp_schedule ("packing:minpack_temp_schedule")
 
IntegerOptionKey const packing::minpack_inner_iteration_scale ("packing:minpack_inner_iteration_scale")
 
BooleanOptionKey const packing::minpack_disable_bumpcheck ("packing:minpack_disable_bumpcheck")
 
BooleanOptionKey const packing::ex1::ex1 ("packing:ex1")
 
IntegerOptionKey const packing::ex1::level ("packing:ex1:level")
 
BooleanOptionKey const packing::ex1::operate ("packing:ex1:operate")
 
BooleanOptionKey const packing::ex2::ex2 ("packing:ex2")
 
IntegerOptionKey const packing::ex2::level ("packing:ex2:level")
 
BooleanOptionKey const packing::ex2::operate ("packing:ex2:operate")
 
BooleanOptionKey const packing::ex3::ex3 ("packing:ex3")
 
IntegerOptionKey const packing::ex3::level ("packing:ex3:level")
 
BooleanOptionKey const packing::ex3::operate ("packing:ex3:operate")
 
BooleanOptionKey const packing::ex4::ex4 ("packing:ex4")
 
IntegerOptionKey const packing::ex4::level ("packing:ex4:level")
 
BooleanOptionKey const packing::ex4::operate ("packing:ex4:operate")
 
BooleanOptionKey const packing::ex1aro::ex1aro ("packing:ex1aro")
 
IntegerOptionKey const packing::ex1aro::level ("packing:ex1aro:level")
 
BooleanOptionKey const packing::ex2aro::ex2aro ("packing:ex2aro")
 
IntegerOptionKey const packing::ex2aro::level ("packing:ex2aro:level")
 
BooleanOptionKey const packing::ex1aro_exposed::ex1aro_exposed ("packing:ex1aro_exposed")
 
IntegerOptionKey const packing::ex1aro_exposed::level ("packing:ex1aro_exposed:level")
 
BooleanOptionKey const packing::ex2aro_exposed::ex2aro_exposed ("packing:ex2aro_exposed")
 
IntegerOptionKey const packing::ex2aro_exposed::level ("packing:ex2aro_exposed:level")
 
BooleanOptionKey const packing::exdna::exdna ("packing:exdna")
 
IntegerOptionKey const packing::exdna::level ("packing:exdna:level")
 
BooleanOptionKey const packing::packer_palette::packer_palette ("packing:packer_palette")
 
FileOptionKey const packing::packer_palette::extra_base_type_file ("packing:packer_palette:extra_base_type_file")
 
BooleanOptionKey const packing::packer_palette::NCAA_expanded ("packing:packer_palette:NCAA_expanded")
 
BooleanOptionKey const archive::archive ("archive")
 
BooleanOptionKey const archive::reread_all_structures ("archive:reread_all_structures")
 
IntegerOptionKey const archive::completion_notify_frequency ("archive:completion_notify_frequency")
 
BooleanOptionKey const carbohydrates::carbohydrates ("carbohydrates")
 
BooleanOptionKey const carbohydrates::glycam_pdb_format ("carbohydrates:glycam_pdb_format")
 
StringOptionKey const carbohydrates::linkage_conformer_data_file ("carbohydrates:linkage_conformer_data_file")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::glycopeptide_docking ("carbohydrates:glycopeptide_docking")
 
StringOptionKey const carbohydrates::glycopeptide_docking::residue_to_glycosylate ("carbohydrates:glycopeptide_docking:residue_to_glycosylate")
 
StringOptionKey const carbohydrates::glycopeptide_docking::anchor_residue ("carbohydrates:glycopeptide_docking:anchor_residue")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::low_res ("carbohydrates:glycopeptide_docking:low_res")
 
IntegerOptionKey const carbohydrates::glycopeptide_docking::high_res_outer_cycles ("carbohydrates:glycopeptide_docking:high_res_outer_cycles")
 
IntegerOptionKey const carbohydrates::glycopeptide_docking::low_res_outer_cycles ("carbohydrates:glycopeptide_docking:low_res_outer_cycles")
 
IntegerOptionKey const carbohydrates::glycopeptide_docking::low_res_inner_cycles ("carbohydrates:glycopeptide_docking:low_res_inner_cycles")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::high_res ("carbohydrates:glycopeptide_docking:high_res")
 
StringOptionKey const carbohydrates::glycopeptide_docking::substrate_type ("carbohydrates:glycopeptide_docking:substrate_type")
 
StringOptionKey const carbohydrates::glycopeptide_docking::tree_type ("carbohydrates:glycopeptide_docking:tree_type")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::randomize_substrate_torsions ("carbohydrates:glycopeptide_docking:randomize_substrate_torsions")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::enable_backbone_moves_pp ("carbohydrates:glycopeptide_docking:enable_backbone_moves_pp")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::prevent_anchor_repacking ("carbohydrates:glycopeptide_docking:prevent_anchor_repacking")
 
StringOptionKey const carbohydrates::glycopeptide_docking::sugardonor_residue ("carbohydrates:glycopeptide_docking:sugardonor_residue")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::output_debug_pdbs ("carbohydrates:glycopeptide_docking:output_debug_pdbs")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::fix_weights ("carbohydrates:glycopeptide_docking:fix_weights")
 
StringOptionKey const carbohydrates::glycopeptide_docking::nevery_interface ("carbohydrates:glycopeptide_docking:nevery_interface")
 
StringOptionKey const carbohydrates::glycopeptide_docking::ntotal_backbone ("carbohydrates:glycopeptide_docking:ntotal_backbone")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::allow_glycan_torsion_moves ("carbohydrates:glycopeptide_docking:allow_glycan_torsion_moves")
 
RealOptionKey const carbohydrates::glycopeptide_docking::interface_distance ("carbohydrates:glycopeptide_docking:interface_distance")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::score_only ("carbohydrates:glycopeptide_docking:score_only")
 
BooleanOptionKey const carbohydrates::glycopeptide_docking::output_distance_metrics ("carbohydrates:glycopeptide_docking:output_distance_metrics")
 
StringOptionKey const carbohydrates::glycopeptide_docking::preglycosylate_residues ("carbohydrates:glycopeptide_docking:preglycosylate_residues")
 
StringOptionKey const carbohydrates::glycopeptide_docking::preglycosylate_sugar_names ("carbohydrates:glycopeptide_docking:preglycosylate_sugar_names")
 
BooleanOptionKey const carbohydrates::glycan_sampler::glycan_sampler ("carbohydrates:glycan_sampler")
 
BooleanOptionKey const carbohydrates::glycan_sampler::glycan_sampler_test ("carbohydrates:glycan_sampler:glycan_sampler_test")
 
IntegerOptionKey const carbohydrates::glycan_sampler::glycan_sampler_rounds ("carbohydrates:glycan_sampler:glycan_sampler_rounds")
 
BooleanOptionKey const carbohydrates::glycan_sampler::min_rings ("carbohydrates:glycan_sampler:min_rings")
 
BooleanOptionKey const carbohydrates::glycan_sampler::final_min_glycans ("carbohydrates:glycan_sampler:final_min_glycans")
 
BooleanOptionKey const carbohydrates::glycan_sampler::glycan_sampler_movie ("carbohydrates:glycan_sampler:glycan_sampler_movie")
 
RealOptionKey const carbohydrates::glycan_sampler::glycan_sampler_kt ("carbohydrates:glycan_sampler:glycan_sampler_kt")
 
BooleanOptionKey const carbohydrates::glycan_sampler::glycan_sampler_refine ("carbohydrates:glycan_sampler:glycan_sampler_refine")
 
BooleanOptionKey const carbohydrates::glycan_sampler::cartmin ("carbohydrates:glycan_sampler:cartmin")
 
BooleanOptionKey const carbohydrates::glycan_sampler::tree_based_min_pack ("carbohydrates:glycan_sampler:tree_based_min_pack")
 
BooleanOptionKey const carbohydrates::glycan_sampler::population_based_conformer_sampling ("carbohydrates:glycan_sampler:population_based_conformer_sampling")
 
BooleanOptionKey const carbohydrates::glycan_sampler::use_gaussian_sampling ("carbohydrates:glycan_sampler:use_gaussian_sampling")
 
BooleanOptionKey const carbohydrates::clash_check::clash_check ("carbohydrates:clash_check")