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Namespaces | Functions
score Namespace Reference

Namespaces

 fiber_diffraction
 
 loop_close
 
 occ_sol_fitted
 
 rna
 
 saxs
 

Functions

BooleanOptionKey const score_pose_cutpoint_variants ("score:score_pose_cutpoint_variants")
 
BooleanOptionKey const score ("score")
 
StringOptionKey const weights ("score:weights")
 
StringVectorOptionKey const set_weights ("score:set_weights")
 
StringOptionKey const pack_weights ("score:pack_weights")
 
StringOptionKey const soft_wts ("score:soft_wts")
 
BooleanOptionKey const docking_interface_score ("score:docking_interface_score")
 
RealOptionKey const min_score_score ("score:min_score_score")
 
StringOptionKey const custom_atom_pair ("score:custom_atom_pair")
 
FileVectorOptionKey const patch ("score:patch")
 
BooleanOptionKey const empty ("score:empty")
 
RealOptionKey const fa_max_dis ("score:fa_max_dis")
 
BooleanOptionKey const fa_Hatr ("score:fa_Hatr")
 
BooleanOptionKey const no_smooth_etables ("score:no_smooth_etables")
 
BooleanOptionKey const count_pair_hybrid ("score:count_pair_hybrid")
 
BooleanOptionKey const count_pair_full ("score:count_pair_full")
 
BooleanOptionKey const no_lk_polar_desolvation ("score:no_lk_polar_desolvation")
 
BooleanOptionKey const lk_polar_without_proline_N ("score:lk_polar_without_proline_N")
 
StringOptionKey const input_etables ("score:input_etables")
 
StringOptionKey const output_etables ("score:output_etables")
 
BooleanOptionKey const analytic_etable_evaluation ("score:analytic_etable_evaluation")
 
BooleanOptionKey const put_intra_into_total ("score:put_intra_into_total")
 
BooleanOptionKey const include_intra_res_protein ("score:include_intra_res_protein")
 
BooleanOptionKey const fa_stack_base_base_only ("score:fa_stack_base_base_only")
 
BooleanOptionKey const fa_stack_include_rna_protein ("score:fa_stack_include_rna_protein")
 
RealOptionKey const fa_stack_sol_prefactor ("score:fa_stack_sol_prefactor")
 
RealOptionKey const fa_stack_sol_stack_cutoff ("score:fa_stack_sol_stack_cutoff")
 
RealOptionKey const fa_stack_sol_dist_cutoff ("score:fa_stack_sol_dist_cutoff")
 
RealOptionKey const fa_stack_lr_prefactor ("score:fa_stack_lr_prefactor")
 
RealOptionKey const fa_stack_lr_stack_cutoff ("score:fa_stack_lr_stack_cutoff")
 
RealOptionKey const fa_stack_lr_dist_cutoff ("score:fa_stack_lr_dist_cutoff")
 
IntegerOptionKey const geom_sol_interres_path_distance_cutoff ("score:geom_sol_interres_path_distance_cutoff")
 
IntegerOptionKey const geom_sol_intrares_path_distance_cutoff ("score:geom_sol_intrares_path_distance_cutoff")
 
RealOptionKey const rms_target ("score:rms_target")
 
BooleanOptionKey const ramaneighbors ("score:ramaneighbors")
 
StringOptionKey const optH_weights ("score:optH_weights")
 
StringOptionKey const optH_patch ("score:optH_patch")
 
StringVectorOptionKey const hb_don_strength ("score:hb_don_strength")
 
StringVectorOptionKey const hb_acc_strength ("score:hb_acc_strength")
 
StringOptionKey const hbe_for_dH2O_aGEN_SP3SC_ssother ("score:hbe_for_dH2O_aGEN_SP3SC_ssother")
 
RealOptionKey const hb_max_energy ("score:hb_max_energy")
 
StringOptionKey const hbond_params ("score:hbond_params")
 
BooleanOptionKey const hbond_bb_per_residue_energy ("score:hbond_bb_per_residue_energy")
 
BooleanOptionKey const hbond_disable_bbsc_exclusion_rule ("score:hbond_disable_bbsc_exclusion_rule")
 
BooleanOptionKey const use_hb_env_dep ("score:use_hb_env_dep")
 
BooleanOptionKey const water_hybrid_sf ("score:water_hybrid_sf")
 
BooleanOptionKey const show_etable_contributions ("score:show_etable_contributions")
 
IntegerOptionKey const symE_units ("score:symE_units")
 
RealOptionKey const symE_bonus ("score:symE_bonus")
 
BooleanOptionKey const symmetric_gly_tables ("score:symmetric_gly_tables")
 
RealOptionKey const NV_lbound ("score:NV_lbound")
 
RealOptionKey const NV_ubound ("score:NV_ubound")
 
StringOptionKey const NV_table ("score:NV_table")
 
BooleanOptionKey const find_neighbors_3dgrid ("score:find_neighbors_3dgrid")
 
BooleanOptionKey const find_neighbors_stripehash ("score:find_neighbors_stripehash")
 
StringOptionKey const seqdep_refene_fname ("score:seqdep_refene_fname")
 
StringOptionKey const secondary_seqdep_refene_fname ("score:secondary_seqdep_refene_fname")
 
BooleanOptionKey const exact_occ_pairwise ("score:exact_occ_pairwise")
 
BooleanOptionKey const exact_occ_skip_Hbonders ("score:exact_occ_skip_Hbonders")
 
BooleanOptionKey const exact_occ_pairwise_by_res ("score:exact_occ_pairwise_by_res")
 
BooleanOptionKey const exact_occ_split_between_res ("score:exact_occ_split_between_res")
 
BooleanOptionKey const exact_occ_self_res_no_occ ("score:exact_occ_self_res_no_occ")
 
RealOptionKey const exact_occ_radius_scaling ("score:exact_occ_radius_scaling")
 
StringVectorOptionKey const ref_offsets ("score:ref_offsets")
 
RealOptionKey const ref_offset ("score:ref_offset")
 
BooleanOptionKey const output_residue_energies ("score:output_residue_energies")
 
StringOptionKey const fa_custom_pair_distance_file ("score:fa_custom_pair_distance_file")
 
RealOptionKey const disulf_matching_probe ("score:disulf_matching_probe")
 
RealVectorOptionKey const bonded_params ("score:bonded_params")
 
StringOptionKey const bonded_params_dir ("score:bonded_params_dir")
 
StringVectorOptionKey const extra_mm_params_dir ("score:extra_mm_params_dir")
 
StringOptionKey const gen_bonded_params_file ("score:gen_bonded_params_file")
 
StringOptionKey const gen_bonded_exclude_def_file ("score:gen_bonded_exclude_def_file")
 
BooleanOptionKey const genbonded_score_full ("score:genbonded_score_full")
 
BooleanOptionKey const genbonded_score_hybrid ("score:genbonded_score_hybrid")
 
StringOptionKey const extra_improper_file ("score:extra_improper_file")
 
BooleanOptionKey const cart_bonded_skip_cutpoints ("score:cart_bonded_skip_cutpoints")
 
RealOptionKey const pro_close_planar_constraint ("score:pro_close_planar_constraint")
 
BooleanOptionKey const no_pro_close_ring_closure ("score:no_pro_close_ring_closure")
 
RealOptionKey const ring_close_shadow_constraint ("score:ring_close_shadow_constraint")
 
BooleanOptionKey const linear_bonded_potential ("score:linear_bonded_potential")
 
RealOptionKey const free_side_chain_bonus ("score:free_side_chain_bonus")
 
BooleanOptionKey const compute_mg_sol_for_hydrogens ("score:compute_mg_sol_for_hydrogens")
 
IntegerVectorOptionKey const rg_local_span ("score:rg_local_span")
 
BooleanOptionKey const unmodifypot ("score:unmodifypot")
 
RealOptionKey const conc ("score:conc")
 
IntegerVectorOptionKey const sidechain_buried ("score:sidechain_buried")
 
IntegerVectorOptionKey const sidechain_exposed ("score:sidechain_exposed")
 
StringVectorOptionKey const aa_composition_setup_file ("score:aa_composition_setup_file")
 
StringOptionKey const aa_repeat_energy_penalty_file ("score:aa_repeat_energy_penalty_file")
 
RealOptionKey const approximate_buried_unsat_penalty_hbond_energy_threshold ("score:approximate_buried_unsat_penalty_hbond_energy_threshold")
 
RealOptionKey const approximate_buried_unsat_penalty_burial_atomic_depth ("score:approximate_buried_unsat_penalty_burial_atomic_depth")
 
RealOptionKey const approximate_buried_unsat_penalty_burial_probe_radius ("score:approximate_buried_unsat_penalty_burial_probe_radius")
 
RealOptionKey const approximate_buried_unsat_penalty_burial_resolution ("score:approximate_buried_unsat_penalty_burial_resolution")
 
RealOptionKey const approximate_buried_unsat_penalty_oversat_penalty ("score:approximate_buried_unsat_penalty_oversat_penalty")
 
BooleanOptionKey const approximate_buried_unsat_penalty_assume_const_backbone ("score:approximate_buried_unsat_penalty_assume_const_backbone")
 
BooleanOptionKey const approximate_buried_unsat_penalty_natural_corrections1 ("score:approximate_buried_unsat_penalty_natural_corrections1")
 
RealOptionKey const approximate_buried_unsat_penalty_hbond_bonus_cross_chain ("score:approximate_buried_unsat_penalty_hbond_bonus_cross_chain")
 
RealOptionKey const approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb ("score:approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb")
 
StringOptionKey const target_clash_pdb ("score:target_clash_pdb")
 
RealOptionKey const aspartimide_penalty_value ("score:aspartimide_penalty_value")
 
RealOptionKey const buried_unsatisfied_penalty_cone_angle_exponent ("score:buried_unsatisfied_penalty_cone_angle_exponent")
 
RealOptionKey const buried_unsatisfied_penalty_cone_angle_shift_factor ("score:buried_unsatisfied_penalty_cone_angle_shift_factor")
 
RealOptionKey const buried_unsatisfied_penalty_cone_dist_exponent ("score:buried_unsatisfied_penalty_cone_dist_exponent")
 
RealOptionKey const buried_unsatisfied_penalty_cone_dist_midpoint ("score:buried_unsatisfied_penalty_cone_dist_midpoint")
 
RealOptionKey const buried_unsatisfied_penalty_burial_threshold ("score:buried_unsatisfied_penalty_burial_threshold")
 
RealOptionKey const buried_unsatisfied_penalty_hbond_energy_threshold ("score:buried_unsatisfied_penalty_hbond_energy_threshold")
 
FileOptionKey const covalent_labeling_input ("score:covalent_labeling_input")
 
FileOptionKey const hrf_dynamics_input ("score:hrf_dynamics_input")
 
FileOptionKey const covalent_labeling_fa_input ("score:covalent_labeling_fa_input")
 
RealOptionKey const elec_min_dis ("score:elec_min_dis")
 
RealOptionKey const elec_max_dis ("score:elec_max_dis")
 
RealOptionKey const elec_die ("score:elec_die")
 
BooleanOptionKey const elec_r_option ("score:elec_r_option")
 
BooleanOptionKey const elec_sigmoidal_die ("score:elec_sigmoidal_die")
 
RealOptionKey const elec_sigmoidal_die_D ("score:elec_sigmoidal_die_D")
 
RealOptionKey const elec_sigmoidal_die_D0 ("score:elec_sigmoidal_die_D0")
 
RealOptionKey const elec_sigmoidal_die_S ("score:elec_sigmoidal_die_S")
 
BooleanOptionKey const stack_elec_sigmoidal_die ("score:stack_elec_sigmoidal_die")
 
BooleanOptionKey const elec_representative_cp ("score:elec_representative_cp")
 
BooleanOptionKey const elec_representative_cp_flip ("score:elec_representative_cp_flip")
 
BooleanOptionKey const eval_intrares_elec_ST_only ("score:eval_intrares_elec_ST_only")
 
BooleanOptionKey const smooth_fa_elec ("score:smooth_fa_elec")
 
StringOptionKey const grpelec_fade_type ("score:grpelec_fade_type")
 
RealOptionKey const grpelec_fade_param1 ("score:grpelec_fade_param1")
 
RealOptionKey const grpelec_fade_param2 ("score:grpelec_fade_param2")
 
StringOptionKey const elec_group_file ("score:elec_group_file")
 
StringOptionKey const elec_group_extrafile ("score:elec_group_extrafile")
 
BooleanOptionKey const grpelec_fade_hbond ("score:grpelec_fade_hbond")
 
RealVectorOptionKey const grpelec_max_qeps ("score:grpelec_max_qeps")
 
BooleanOptionKey const grpelec_context_dependent ("score:grpelec_context_dependent")
 
BooleanOptionKey const grp_cpfxn ("score:grp_cpfxn")
 
RealVectorOptionKey const grpelec_cpfxn_weight ("score:grpelec_cpfxn_weight")
 
StringOptionKey const hbnet_bonus_function_ramping ("score:hbnet_bonus_function_ramping")
 
IntegerOptionKey const hbnet_max_network_size ("score:hbnet_max_network_size")
 
RealOptionKey const elec_context_minstrength ("score:elec_context_minstrength")
 
RealOptionKey const elec_context_minburial ("score:elec_context_minburial")
 
RealOptionKey const elec_context_maxburial ("score:elec_context_maxburial")
 
BooleanOptionKey const use_polarization ("score:use_polarization")
 
BooleanOptionKey const use_gen_kirkwood ("score:use_gen_kirkwood")
 
RealOptionKey const protein_dielectric ("score:protein_dielectric")
 
RealOptionKey const water_dielectric ("score:water_dielectric")
 
RealOptionKey const facts_GBpair_cut ("score:facts_GBpair_cut")
 
RealOptionKey const facts_kappa ("score:facts_kappa")
 
IntegerOptionKey const facts_asp_patch ("score:facts_asp_patch")
 
BooleanOptionKey const facts_plane_to_self ("score:facts_plane_to_self")
 
RealOptionKey const facts_saltbridge_correction ("score:facts_saltbridge_correction")
 
RealVectorOptionKey const facts_dshift ("score:facts_dshift")
 
RealOptionKey const facts_die ("score:facts_die")
 
BooleanOptionKey const facts_binding_affinity ("score:facts_binding_affinity")
 
BooleanOptionKey const facts_intrascale_by_level ("score:facts_intrascale_by_level")
 
RealVectorOptionKey const facts_intbb_elec_scale ("score:facts_intbb_elec_scale")
 
RealVectorOptionKey const facts_intbb_solv_scale ("score:facts_intbb_solv_scale")
 
RealVectorOptionKey const facts_adjbb_elec_scale ("score:facts_adjbb_elec_scale")
 
RealVectorOptionKey const facts_adjbb_solv_scale ("score:facts_adjbb_solv_scale")
 
RealVectorOptionKey const facts_intbs_elec_scale ("score:facts_intbs_elec_scale")
 
RealVectorOptionKey const facts_intbs_solv_scale ("score:facts_intbs_solv_scale")
 
RealVectorOptionKey const facts_adjbs_elec_scale ("score:facts_adjbs_elec_scale")
 
RealVectorOptionKey const facts_adjbs_solv_scale ("score:facts_adjbs_solv_scale")
 
RealVectorOptionKey const facts_intsc_elec_scale ("score:facts_intsc_elec_scale")
 
RealVectorOptionKey const facts_intsc_solv_scale ("score:facts_intsc_solv_scale")
 
StringOptionKey const facts_charge_dir ("score:facts_charge_dir")
 
StringOptionKey const facts_eff_charge_dir ("score:facts_eff_charge_dir")
 
StringVectorOptionKey const facts_plane_aa ("score:facts_plane_aa")
 
StringOptionKey const facts_eq_type ("score:facts_eq_type")
 
IntegerOptionKey const ignore_terminal_ss_elements ("score:ignore_terminal_ss_elements")
 
BooleanOptionKey const length_dep_srbb ("score:length_dep_srbb")
 
RealOptionKey const ldsrbb_low_scale ("score:ldsrbb_low_scale")
 
RealOptionKey const ldsrbb_high_scale ("score:ldsrbb_high_scale")
 
IntegerOptionKey const ldsrbb_minlength ("score:ldsrbb_minlength")
 
IntegerOptionKey const ldsrbb_maxlength ("score:ldsrbb_maxlength")
 
RealOptionKey const max_motif_per_res ("score:max_motif_per_res")
 
IntegerOptionKey const max_contacting_ss ("score:max_contacting_ss")
 
BooleanOptionKey const motif_ignore_symmmetry ("score:motif_ignore_symmmetry")
 
IntegerVectorOptionKey const motif_residues ("score:motif_residues")
 
StringVectorOptionKey const netcharge_setup_file ("score:netcharge_setup_file")
 
StringVectorOptionKey const mhc_epitope_setup_file ("score:mhc_epitope_setup_file")
 
RealOptionKey const ms_dist_midpoint ("score:ms_dist_midpoint")
 
RealOptionKey const ms_dist_exponent ("score:ms_dist_exponent")
 
RealOptionKey const ms_fit_slope ("score:ms_fit_slope")
 
RealOptionKey const ms_fit_intercept ("score:ms_fit_intercept")
 
RealOptionKey const ms_fade_outer ("score:ms_fade_outer")
 
RealOptionKey const ms_fade_dist ("score:ms_fade_dist")
 
StringOptionKey const nmer_ref_energies ("score:nmer_ref_energies")
 
StringOptionKey const nmer_ref_energies_list ("score:nmer_ref_energies_list")
 
StringOptionKey const nmer_pssm ("score:nmer_pssm")
 
StringOptionKey const nmer_pssm_list ("score:nmer_pssm_list")
 
RealOptionKey const nmer_pssm_scorecut ("score:nmer_pssm_scorecut")
 
StringOptionKey const nmer_svm ("score:nmer_svm")
 
StringOptionKey const nmer_svm_list ("score:nmer_svm_list")
 
StringOptionKey const nmer_svm_rank ("score:nmer_svm_rank")
 
StringOptionKey const nmer_svm_rank_list ("score:nmer_svm_rank_list")
 
RealOptionKey const nmer_svm_scorecut ("score:nmer_svm_scorecut")
 
StringOptionKey const nmer_svm_aa_matrix ("score:nmer_svm_aa_matrix")
 
IntegerOptionKey const nmer_svm_term_length ("score:nmer_svm_term_length")
 
BooleanOptionKey const nmer_svm_pssm_feat ("score:nmer_svm_pssm_feat")
 
BooleanOptionKey const nmer_svm_avg_rank_as_energy ("score:nmer_svm_avg_rank_as_energy")
 
IntegerOptionKey const nmer_ref_seq_length ("score:nmer_ref_seq_length")
 
BooleanOptionKey const just_calc_rmsd ("score:just_calc_rmsd")
 
BooleanOptionKey const envsmooth_zero_negatives ("score:envsmooth_zero_negatives")
 
RealOptionKey const rama_power ("score:rama_power")
 
BooleanOptionKey const ideal_sugars ("score:ideal_sugars")
 
RealOptionKey const hbond_fade ("score:hbond_fade")
 
BooleanOptionKey const hbond_new_sp3_acc ("score:hbond_new_sp3_acc")
 
RealOptionKey const alignment_sharpness ("score:alignment_sharpness")
 
StringOptionKey const rna_torsion_potential ("score:rna_torsion_potential")
 
BooleanOptionKey const arg_cation_pi_his_can_be_pi ("score:arg_cation_pi_his_can_be_pi")
 
BooleanOptionKey const mc_optimize_dG ("score:mc_optimize_dG")
 
RealOptionKey const mc_interface_weight ("score:mc_interface_weight")
 
RealOptionKey const mc_total_weight ("score:mc_total_weight")
 
BooleanOptionKey const force_sugar_bb_zero ("score:force_sugar_bb_zero")
 
IntegerOptionKey const voids_penalty_energy_containing_cones_cutoff ("score:voids_penalty_energy_containing_cones_cutoff")
 
RealOptionKey const voids_penalty_energy_cone_dotproduct_cutoff ("score:voids_penalty_energy_cone_dotproduct_cutoff")
 
RealOptionKey const voids_penalty_energy_cone_distance_cutoff ("score:voids_penalty_energy_cone_distance_cutoff")
 
BooleanOptionKey const voids_penalty_energy_disabled_except_during_packing ("score:voids_penalty_energy_disabled_except_during_packing")
 
RealOptionKey const voids_penalty_energy_voxel_size ("score:voids_penalty_energy_voxel_size")
 
RealOptionKey const voids_penalty_energy_voxel_grid_padding ("score:voids_penalty_energy_voxel_grid_padding")
 

Function Documentation

StringVectorOptionKey const score::aa_composition_setup_file ( "score:aa_composition_setup_file"  )
StringOptionKey const score::aa_repeat_energy_penalty_file ( "score:aa_repeat_energy_penalty_file"  )
RealOptionKey const score::alignment_sharpness ( "score:alignment_sharpness"  )
BooleanOptionKey const score::analytic_etable_evaluation ( "score:analytic_etable_evaluation"  )
BooleanOptionKey const score::approximate_buried_unsat_penalty_assume_const_backbone ( "score:approximate_buried_unsat_penalty_assume_const_backbone"  )
RealOptionKey const score::approximate_buried_unsat_penalty_burial_atomic_depth ( "score:approximate_buried_unsat_penalty_burial_atomic_depth"  )
RealOptionKey const score::approximate_buried_unsat_penalty_burial_probe_radius ( "score:approximate_buried_unsat_penalty_burial_probe_radius"  )
RealOptionKey const score::approximate_buried_unsat_penalty_burial_resolution ( "score:approximate_buried_unsat_penalty_burial_resolution"  )
RealOptionKey const score::approximate_buried_unsat_penalty_hbond_bonus_cross_chain ( "score:approximate_buried_unsat_penalty_hbond_bonus_cross_chain"  )
RealOptionKey const score::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb ( "score:approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb"  )
RealOptionKey const score::approximate_buried_unsat_penalty_hbond_energy_threshold ( "score:approximate_buried_unsat_penalty_hbond_energy_threshold"  )
BooleanOptionKey const score::approximate_buried_unsat_penalty_natural_corrections1 ( "score:approximate_buried_unsat_penalty_natural_corrections1"  )
RealOptionKey const score::approximate_buried_unsat_penalty_oversat_penalty ( "score:approximate_buried_unsat_penalty_oversat_penalty"  )
BooleanOptionKey const score::arg_cation_pi_his_can_be_pi ( "score:arg_cation_pi_his_can_be_pi"  )
RealOptionKey const score::aspartimide_penalty_value ( "score:aspartimide_penalty_value"  )
RealVectorOptionKey const score::bonded_params ( "score:bonded_params"  )
StringOptionKey const score::bonded_params_dir ( "score:bonded_params_dir"  )
RealOptionKey const score::buried_unsatisfied_penalty_burial_threshold ( "score:buried_unsatisfied_penalty_burial_threshold"  )
RealOptionKey const score::buried_unsatisfied_penalty_cone_angle_exponent ( "score:buried_unsatisfied_penalty_cone_angle_exponent"  )
RealOptionKey const score::buried_unsatisfied_penalty_cone_angle_shift_factor ( "score:buried_unsatisfied_penalty_cone_angle_shift_factor"  )
RealOptionKey const score::buried_unsatisfied_penalty_cone_dist_exponent ( "score:buried_unsatisfied_penalty_cone_dist_exponent"  )
RealOptionKey const score::buried_unsatisfied_penalty_cone_dist_midpoint ( "score:buried_unsatisfied_penalty_cone_dist_midpoint"  )
RealOptionKey const score::buried_unsatisfied_penalty_hbond_energy_threshold ( "score:buried_unsatisfied_penalty_hbond_energy_threshold"  )
BooleanOptionKey const score::cart_bonded_skip_cutpoints ( "score:cart_bonded_skip_cutpoints"  )
BooleanOptionKey const score::compute_mg_sol_for_hydrogens ( "score:compute_mg_sol_for_hydrogens"  )
RealOptionKey const score::conc ( "score:conc"  )
BooleanOptionKey const score::count_pair_full ( "score:count_pair_full"  )
BooleanOptionKey const score::count_pair_hybrid ( "score:count_pair_hybrid"  )
FileOptionKey const score::covalent_labeling_fa_input ( "score:covalent_labeling_fa_input"  )
FileOptionKey const score::covalent_labeling_input ( "score:covalent_labeling_input"  )
StringOptionKey const score::custom_atom_pair ( "score:custom_atom_pair"  )
RealOptionKey const score::disulf_matching_probe ( "score:disulf_matching_probe"  )
BooleanOptionKey const score::docking_interface_score ( "score:docking_interface_score"  )
RealOptionKey const score::elec_context_maxburial ( "score:elec_context_maxburial"  )
RealOptionKey const score::elec_context_minburial ( "score:elec_context_minburial"  )
RealOptionKey const score::elec_context_minstrength ( "score:elec_context_minstrength"  )
RealOptionKey const score::elec_die ( "score:elec_die"  )
StringOptionKey const score::elec_group_extrafile ( "score:elec_group_extrafile"  )
StringOptionKey const score::elec_group_file ( "score:elec_group_file"  )
RealOptionKey const score::elec_max_dis ( "score:elec_max_dis"  )
RealOptionKey const score::elec_min_dis ( "score:elec_min_dis"  )
BooleanOptionKey const score::elec_r_option ( "score:elec_r_option"  )
BooleanOptionKey const score::elec_representative_cp ( "score:elec_representative_cp"  )
BooleanOptionKey const score::elec_representative_cp_flip ( "score:elec_representative_cp_flip"  )
BooleanOptionKey const score::elec_sigmoidal_die ( "score:elec_sigmoidal_die"  )
RealOptionKey const score::elec_sigmoidal_die_D ( "score:elec_sigmoidal_die_D"  )
RealOptionKey const score::elec_sigmoidal_die_D0 ( "score:elec_sigmoidal_die_D0"  )
RealOptionKey const score::elec_sigmoidal_die_S ( "score:elec_sigmoidal_die_S"  )
BooleanOptionKey const score::empty ( "score:empty"  )
BooleanOptionKey const score::envsmooth_zero_negatives ( "score:envsmooth_zero_negatives"  )
BooleanOptionKey const score::eval_intrares_elec_ST_only ( "score:eval_intrares_elec_ST_only"  )
BooleanOptionKey const score::exact_occ_pairwise ( "score:exact_occ_pairwise"  )
BooleanOptionKey const score::exact_occ_pairwise_by_res ( "score:exact_occ_pairwise_by_res"  )
RealOptionKey const score::exact_occ_radius_scaling ( "score:exact_occ_radius_scaling"  )
BooleanOptionKey const score::exact_occ_self_res_no_occ ( "score:exact_occ_self_res_no_occ"  )
BooleanOptionKey const score::exact_occ_skip_Hbonders ( "score:exact_occ_skip_Hbonders"  )
BooleanOptionKey const score::exact_occ_split_between_res ( "score:exact_occ_split_between_res"  )
StringOptionKey const score::extra_improper_file ( "score:extra_improper_file"  )
StringVectorOptionKey const score::extra_mm_params_dir ( "score:extra_mm_params_dir"  )
StringOptionKey const score::fa_custom_pair_distance_file ( "score:fa_custom_pair_distance_file"  )
BooleanOptionKey const score::fa_Hatr ( "score:fa_Hatr"  )
RealOptionKey const score::fa_max_dis ( "score:fa_max_dis"  )

Referenced by main().

BooleanOptionKey const score::fa_stack_base_base_only ( "score:fa_stack_base_base_only"  )
BooleanOptionKey const score::fa_stack_include_rna_protein ( "score:fa_stack_include_rna_protein"  )
RealOptionKey const score::fa_stack_lr_dist_cutoff ( "score:fa_stack_lr_dist_cutoff"  )
RealOptionKey const score::fa_stack_lr_prefactor ( "score:fa_stack_lr_prefactor"  )
RealOptionKey const score::fa_stack_lr_stack_cutoff ( "score:fa_stack_lr_stack_cutoff"  )
RealOptionKey const score::fa_stack_sol_dist_cutoff ( "score:fa_stack_sol_dist_cutoff"  )
RealOptionKey const score::fa_stack_sol_prefactor ( "score:fa_stack_sol_prefactor"  )
RealOptionKey const score::fa_stack_sol_stack_cutoff ( "score:fa_stack_sol_stack_cutoff"  )
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_adjbs_elec_scale ( "score:facts_adjbs_elec_scale"  )
RealVectorOptionKey const score::facts_adjbs_solv_scale ( "score:facts_adjbs_solv_scale"  )
IntegerOptionKey const score::facts_asp_patch ( "score:facts_asp_patch"  )
BooleanOptionKey const score::facts_binding_affinity ( "score:facts_binding_affinity"  )
StringOptionKey const score::facts_charge_dir ( "score:facts_charge_dir"  )
RealOptionKey const score::facts_die ( "score:facts_die"  )
RealVectorOptionKey const score::facts_dshift ( "score:facts_dshift"  )
StringOptionKey const score::facts_eff_charge_dir ( "score:facts_eff_charge_dir"  )
StringOptionKey const score::facts_eq_type ( "score:facts_eq_type"  )
RealOptionKey const score::facts_GBpair_cut ( "score:facts_GBpair_cut"  )
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_intbs_elec_scale ( "score:facts_intbs_elec_scale"  )
RealVectorOptionKey const score::facts_intbs_solv_scale ( "score:facts_intbs_solv_scale"  )
BooleanOptionKey const score::facts_intrascale_by_level ( "score:facts_intrascale_by_level"  )
RealVectorOptionKey const score::facts_intsc_elec_scale ( "score:facts_intsc_elec_scale"  )
RealVectorOptionKey const score::facts_intsc_solv_scale ( "score:facts_intsc_solv_scale"  )
RealOptionKey const score::facts_kappa ( "score:facts_kappa"  )
StringVectorOptionKey const score::facts_plane_aa ( "score:facts_plane_aa"  )
BooleanOptionKey const score::facts_plane_to_self ( "score:facts_plane_to_self"  )
RealOptionKey const score::facts_saltbridge_correction ( "score:facts_saltbridge_correction"  )
BooleanOptionKey const score::find_neighbors_3dgrid ( "score:find_neighbors_3dgrid"  )
BooleanOptionKey const score::find_neighbors_stripehash ( "score:find_neighbors_stripehash"  )
BooleanOptionKey const score::force_sugar_bb_zero ( "score:force_sugar_bb_zero"  )
RealOptionKey const score::free_side_chain_bonus ( "score:free_side_chain_bonus"  )
StringOptionKey const score::gen_bonded_exclude_def_file ( "score:gen_bonded_exclude_def_file"  )
StringOptionKey const score::gen_bonded_params_file ( "score:gen_bonded_params_file"  )
BooleanOptionKey const score::genbonded_score_full ( "score:genbonded_score_full"  )
BooleanOptionKey const score::genbonded_score_hybrid ( "score:genbonded_score_hybrid"  )
IntegerOptionKey const score::geom_sol_interres_path_distance_cutoff ( "score:geom_sol_interres_path_distance_cutoff"  )
IntegerOptionKey const score::geom_sol_intrares_path_distance_cutoff ( "score:geom_sol_intrares_path_distance_cutoff"  )
BooleanOptionKey const score::grp_cpfxn ( "score:grp_cpfxn"  )
BooleanOptionKey const score::grpelec_context_dependent ( "score:grpelec_context_dependent"  )
RealVectorOptionKey const score::grpelec_cpfxn_weight ( "score:grpelec_cpfxn_weight"  )
BooleanOptionKey const score::grpelec_fade_hbond ( "score:grpelec_fade_hbond"  )
RealOptionKey const score::grpelec_fade_param1 ( "score:grpelec_fade_param1"  )
RealOptionKey const score::grpelec_fade_param2 ( "score:grpelec_fade_param2"  )
StringOptionKey const score::grpelec_fade_type ( "score:grpelec_fade_type"  )
RealVectorOptionKey const score::grpelec_max_qeps ( "score:grpelec_max_qeps"  )
StringVectorOptionKey const score::hb_acc_strength ( "score:hb_acc_strength"  )
StringVectorOptionKey const score::hb_don_strength ( "score:hb_don_strength"  )
RealOptionKey const score::hb_max_energy ( "score:hb_max_energy"  )
StringOptionKey const score::hbe_for_dH2O_aGEN_SP3SC_ssother ( "score:hbe_for_dH2O_aGEN_SP3SC_ssother"  )
StringOptionKey const score::hbnet_bonus_function_ramping ( "score:hbnet_bonus_function_ramping"  )
IntegerOptionKey const score::hbnet_max_network_size ( "score:hbnet_max_network_size"  )
BooleanOptionKey const score::hbond_bb_per_residue_energy ( "score:hbond_bb_per_residue_energy"  )
BooleanOptionKey const score::hbond_disable_bbsc_exclusion_rule ( "score:hbond_disable_bbsc_exclusion_rule"  )
RealOptionKey const score::hbond_fade ( "score:hbond_fade"  )
BooleanOptionKey const score::hbond_new_sp3_acc ( "score:hbond_new_sp3_acc"  )
StringOptionKey const score::hbond_params ( "score:hbond_params"  )
FileOptionKey const score::hrf_dynamics_input ( "score:hrf_dynamics_input"  )
BooleanOptionKey const score::ideal_sugars ( "score:ideal_sugars"  )
IntegerOptionKey const score::ignore_terminal_ss_elements ( "score:ignore_terminal_ss_elements"  )
BooleanOptionKey const score::include_intra_res_protein ( "score:include_intra_res_protein"  )
StringOptionKey const score::input_etables ( "score:input_etables"  )
BooleanOptionKey const score::just_calc_rmsd ( "score:just_calc_rmsd"  )

Referenced by RNA_ScoreMover::apply(), and main().

RealOptionKey const score::ldsrbb_high_scale ( "score:ldsrbb_high_scale"  )
RealOptionKey const score::ldsrbb_low_scale ( "score:ldsrbb_low_scale"  )
IntegerOptionKey const score::ldsrbb_maxlength ( "score:ldsrbb_maxlength"  )
IntegerOptionKey const score::ldsrbb_minlength ( "score:ldsrbb_minlength"  )
BooleanOptionKey const score::length_dep_srbb ( "score:length_dep_srbb"  )
BooleanOptionKey const score::linear_bonded_potential ( "score:linear_bonded_potential"  )
BooleanOptionKey const score::lk_polar_without_proline_N ( "score:lk_polar_without_proline_N"  )
IntegerOptionKey const score::max_contacting_ss ( "score:max_contacting_ss"  )
RealOptionKey const score::max_motif_per_res ( "score:max_motif_per_res"  )
RealOptionKey const score::mc_interface_weight ( "score:mc_interface_weight"  )
BooleanOptionKey const score::mc_optimize_dG ( "score:mc_optimize_dG"  )
RealOptionKey const score::mc_total_weight ( "score:mc_total_weight"  )
StringVectorOptionKey const score::mhc_epitope_setup_file ( "score:mhc_epitope_setup_file"  )
RealOptionKey const score::min_score_score ( "score:min_score_score"  )
BooleanOptionKey const score::motif_ignore_symmmetry ( "score:motif_ignore_symmmetry"  )
IntegerVectorOptionKey const score::motif_residues ( "score:motif_residues"  )
RealOptionKey const score::ms_dist_exponent ( "score:ms_dist_exponent"  )
RealOptionKey const score::ms_dist_midpoint ( "score:ms_dist_midpoint"  )
RealOptionKey const score::ms_fade_dist ( "score:ms_fade_dist"  )
RealOptionKey const score::ms_fade_outer ( "score:ms_fade_outer"  )
RealOptionKey const score::ms_fit_intercept ( "score:ms_fit_intercept"  )
RealOptionKey const score::ms_fit_slope ( "score:ms_fit_slope"  )
StringVectorOptionKey const score::netcharge_setup_file ( "score:netcharge_setup_file"  )
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_ref_energies ( "score:nmer_ref_energies"  )
StringOptionKey const score::nmer_ref_energies_list ( "score:nmer_ref_energies_list"  )
IntegerOptionKey const score::nmer_ref_seq_length ( "score:nmer_ref_seq_length"  )
StringOptionKey const score::nmer_svm ( "score:nmer_svm"  )
StringOptionKey const score::nmer_svm_aa_matrix ( "score:nmer_svm_aa_matrix"  )
BooleanOptionKey const score::nmer_svm_avg_rank_as_energy ( "score:nmer_svm_avg_rank_as_energy"  )
StringOptionKey const score::nmer_svm_list ( "score:nmer_svm_list"  )
BooleanOptionKey const score::nmer_svm_pssm_feat ( "score:nmer_svm_pssm_feat"  )
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"  )
IntegerOptionKey const score::nmer_svm_term_length ( "score:nmer_svm_term_length"  )
BooleanOptionKey const score::no_lk_polar_desolvation ( "score:no_lk_polar_desolvation"  )
BooleanOptionKey const score::no_pro_close_ring_closure ( "score:no_pro_close_ring_closure"  )
BooleanOptionKey const score::no_smooth_etables ( "score:no_smooth_etables"  )
RealOptionKey const score::NV_lbound ( "score:NV_lbound"  )
StringOptionKey const score::NV_table ( "score:NV_table"  )
RealOptionKey const score::NV_ubound ( "score:NV_ubound"  )
StringOptionKey const score::optH_patch ( "score:optH_patch"  )
StringOptionKey const score::optH_weights ( "score:optH_weights"  )
StringOptionKey const score::output_etables ( "score:output_etables"  )
BooleanOptionKey const score::output_residue_energies ( "score:output_residue_energies"  )
StringOptionKey const score::pack_weights ( "score:pack_weights"  )
FileVectorOptionKey const score::patch ( "score:patch"  )

Referenced by main().

RealOptionKey const score::pro_close_planar_constraint ( "score:pro_close_planar_constraint"  )
RealOptionKey const score::protein_dielectric ( "score:protein_dielectric"  )
BooleanOptionKey const score::put_intra_into_total ( "score:put_intra_into_total"  )
RealOptionKey const score::rama_power ( "score:rama_power"  )
BooleanOptionKey const score::ramaneighbors ( "score:ramaneighbors"  )
RealOptionKey const score::ref_offset ( "score:ref_offset"  )
StringVectorOptionKey const score::ref_offsets ( "score:ref_offsets"  )
IntegerVectorOptionKey const score::rg_local_span ( "score:rg_local_span"  )
RealOptionKey const score::ring_close_shadow_constraint ( "score:ring_close_shadow_constraint"  )
RealOptionKey const score::rms_target ( "score:rms_target"  )
StringOptionKey const score::rna_torsion_potential ( "score:rna_torsion_potential"  )
BooleanOptionKey const score::score ( "score"  )
BooleanOptionKey const score::score_pose_cutpoint_variants ( "score:score_pose_cutpoint_variants"  )
StringOptionKey const score::secondary_seqdep_refene_fname ( "score:secondary_seqdep_refene_fname"  )
StringOptionKey const score::seqdep_refene_fname ( "score:seqdep_refene_fname"  )
StringVectorOptionKey const score::set_weights ( "score:set_weights"  )
BooleanOptionKey const score::show_etable_contributions ( "score:show_etable_contributions"  )
IntegerVectorOptionKey const score::sidechain_buried ( "score:sidechain_buried"  )
IntegerVectorOptionKey const score::sidechain_exposed ( "score:sidechain_exposed"  )
BooleanOptionKey const score::smooth_fa_elec ( "score:smooth_fa_elec"  )
StringOptionKey const score::soft_wts ( "score:soft_wts"  )
BooleanOptionKey const score::stack_elec_sigmoidal_die ( "score:stack_elec_sigmoidal_die"  )
RealOptionKey const score::symE_bonus ( "score:symE_bonus"  )
IntegerOptionKey const score::symE_units ( "score:symE_units"  )
BooleanOptionKey const score::symmetric_gly_tables ( "score:symmetric_gly_tables"  )
StringOptionKey const score::target_clash_pdb ( "score:target_clash_pdb"  )
BooleanOptionKey const score::unmodifypot ( "score:unmodifypot"  )
BooleanOptionKey const score::use_gen_kirkwood ( "score:use_gen_kirkwood"  )
BooleanOptionKey const score::use_hb_env_dep ( "score:use_hb_env_dep"  )
BooleanOptionKey const score::use_polarization ( "score:use_polarization"  )
RealOptionKey const score::voids_penalty_energy_cone_distance_cutoff ( "score:voids_penalty_energy_cone_distance_cutoff"  )
RealOptionKey const score::voids_penalty_energy_cone_dotproduct_cutoff ( "score:voids_penalty_energy_cone_dotproduct_cutoff"  )
IntegerOptionKey const score::voids_penalty_energy_containing_cones_cutoff ( "score:voids_penalty_energy_containing_cones_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_grid_padding ( "score:voids_penalty_energy_voxel_grid_padding"  )
RealOptionKey const score::voids_penalty_energy_voxel_size ( "score:voids_penalty_energy_voxel_size"  )
RealOptionKey const score::water_dielectric ( "score:water_dielectric"  )
BooleanOptionKey const score::water_hybrid_sf ( "score:water_hybrid_sf"  )
StringOptionKey const score::weights ( "score:weights"  )