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	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")

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")

StringOptionKey const	gen_bonded_params_file ("score:gen_bonded_params_file")

StringOptionKey const	extra_improper_file ("score:extra_improper_file")

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")

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	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	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")

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_energy_threshold ( "score:approximate_buried_unsat_penalty_hbond_energy_threshold" )

RealOptionKey const score::approximate_buried_unsat_penalty_oversat_penalty ( "score:approximate_buried_unsat_penalty_oversat_penalty" )

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::compute_mg_sol_for_hydrogens ( "score:compute_mg_sol_for_hydrogens" )

RealOptionKey const score::conc ( "score:conc" )

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" )

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" )

RealOptionKey const score::free_side_chain_bonus ( "score:free_side_chain_bonus" )

StringOptionKey const score::gen_bonded_params_file ( "score:gen_bonded_params_file" )

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" )

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" )

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 main(), and rna_score_test().

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" )

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" )

Referenced by build_full_model_test(), calc_rmsf_and_avrg(), erraser2_test(), get_stepwise_score_function(), main(), MC_run(), mg_modeler_test(), nucleobase_probe_score_test(), quick_score_test(), rebuild_test(), resample_full_model_test(), RunPepSpec(), and thermal_sampler().

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Functions

Function Documentation