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	lowres_weights ("score:lowres_weights")
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	torsion_distr_params_file ("score:torsion_distr_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")
BooleanOptionKey const	approximate_buried_unsat_penalty_lys_ok_with_1 ("score:approximate_buried_unsat_penalty_lys_ok_with_1")
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")
FileOptionKey const	depc_ms_input ("score:depc_ms_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")
RealOptionKey const	ccs_exp ("score:ccs_exp")
RealOptionKey const	ccs_prad ("score:ccs_prad")
IntegerOptionKey const	ccs_nrots ("score:ccs_nrots")
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

aa_composition_setup_file()

StringVectorOptionKey const score::aa_composition_setup_file

(

"score:aa_composition_setup_file"

)

aa_repeat_energy_penalty_file()

StringOptionKey const score::aa_repeat_energy_penalty_file

(

"score:aa_repeat_energy_penalty_file"

)

alignment_sharpness()

RealOptionKey const score::alignment_sharpness

(

"score:alignment_sharpness"

)

analytic_etable_evaluation()

BooleanOptionKey const score::analytic_etable_evaluation

(

"score:analytic_etable_evaluation"

)

approximate_buried_unsat_penalty_assume_const_backbone()

BooleanOptionKey const score::approximate_buried_unsat_penalty_assume_const_backbone

(

"score:approximate_buried_unsat_penalty_assume_const_backbone"

)

approximate_buried_unsat_penalty_burial_atomic_depth()

RealOptionKey const score::approximate_buried_unsat_penalty_burial_atomic_depth

(

"score:approximate_buried_unsat_penalty_burial_atomic_depth"

)

approximate_buried_unsat_penalty_burial_probe_radius()

RealOptionKey const score::approximate_buried_unsat_penalty_burial_probe_radius

(

"score:approximate_buried_unsat_penalty_burial_probe_radius"

)

approximate_buried_unsat_penalty_burial_resolution()

RealOptionKey const score::approximate_buried_unsat_penalty_burial_resolution

(

"score:approximate_buried_unsat_penalty_burial_resolution"

)

approximate_buried_unsat_penalty_hbond_bonus_cross_chain()

RealOptionKey const score::approximate_buried_unsat_penalty_hbond_bonus_cross_chain

(

"score:approximate_buried_unsat_penalty_hbond_bonus_cross_chain"

)

approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb()

RealOptionKey const score::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb

(

"score:approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb"

)

approximate_buried_unsat_penalty_hbond_energy_threshold()

RealOptionKey const score::approximate_buried_unsat_penalty_hbond_energy_threshold

(

"score:approximate_buried_unsat_penalty_hbond_energy_threshold"

)

approximate_buried_unsat_penalty_lys_ok_with_1()

BooleanOptionKey const score::approximate_buried_unsat_penalty_lys_ok_with_1

(

"score:approximate_buried_unsat_penalty_lys_ok_with_1"

)

approximate_buried_unsat_penalty_natural_corrections1()

BooleanOptionKey const score::approximate_buried_unsat_penalty_natural_corrections1

(

"score:approximate_buried_unsat_penalty_natural_corrections1"

)

approximate_buried_unsat_penalty_oversat_penalty()

RealOptionKey const score::approximate_buried_unsat_penalty_oversat_penalty

(

"score:approximate_buried_unsat_penalty_oversat_penalty"

)

arg_cation_pi_his_can_be_pi()

BooleanOptionKey const score::arg_cation_pi_his_can_be_pi

(

"score:arg_cation_pi_his_can_be_pi"

)

aspartimide_penalty_value()

RealOptionKey const score::aspartimide_penalty_value

(

"score:aspartimide_penalty_value"

)

bonded_params()

RealVectorOptionKey const score::bonded_params

(

"score:bonded_params"

)

bonded_params_dir()

StringOptionKey const score::bonded_params_dir

(

"score:bonded_params_dir"

)

buried_unsatisfied_penalty_burial_threshold()

RealOptionKey const score::buried_unsatisfied_penalty_burial_threshold

(

"score:buried_unsatisfied_penalty_burial_threshold"

)

buried_unsatisfied_penalty_cone_angle_exponent()

RealOptionKey const score::buried_unsatisfied_penalty_cone_angle_exponent

(

"score:buried_unsatisfied_penalty_cone_angle_exponent"

)

buried_unsatisfied_penalty_cone_angle_shift_factor()

RealOptionKey const score::buried_unsatisfied_penalty_cone_angle_shift_factor

(

"score:buried_unsatisfied_penalty_cone_angle_shift_factor"

)

buried_unsatisfied_penalty_cone_dist_exponent()

RealOptionKey const score::buried_unsatisfied_penalty_cone_dist_exponent

(

"score:buried_unsatisfied_penalty_cone_dist_exponent"

)

buried_unsatisfied_penalty_cone_dist_midpoint()

RealOptionKey const score::buried_unsatisfied_penalty_cone_dist_midpoint

(

"score:buried_unsatisfied_penalty_cone_dist_midpoint"

)

buried_unsatisfied_penalty_hbond_energy_threshold()

RealOptionKey const score::buried_unsatisfied_penalty_hbond_energy_threshold

(

"score:buried_unsatisfied_penalty_hbond_energy_threshold"

)

cart_bonded_skip_cutpoints()

BooleanOptionKey const score::cart_bonded_skip_cutpoints

(

"score:cart_bonded_skip_cutpoints"

)

ccs_exp()

RealOptionKey const score::ccs_exp

(

"score:ccs_exp"

)

ccs_nrots()

IntegerOptionKey const score::ccs_nrots

(

"score:ccs_nrots"

)

ccs_prad()

RealOptionKey const score::ccs_prad

(

"score:ccs_prad"

)

compute_mg_sol_for_hydrogens()

BooleanOptionKey const score::compute_mg_sol_for_hydrogens

(

"score:compute_mg_sol_for_hydrogens"

)

conc()

RealOptionKey const score::conc

(

"score:conc"

)

count_pair_full()

BooleanOptionKey const score::count_pair_full

(

"score:count_pair_full"

)

count_pair_hybrid()

BooleanOptionKey const score::count_pair_hybrid

(

"score:count_pair_hybrid"

)

covalent_labeling_fa_input()

FileOptionKey const score::covalent_labeling_fa_input

(

"score:covalent_labeling_fa_input"

)

covalent_labeling_input()

FileOptionKey const score::covalent_labeling_input

(

"score:covalent_labeling_input"

)

custom_atom_pair()

StringOptionKey const score::custom_atom_pair

(

"score:custom_atom_pair"

)

depc_ms_input()

FileOptionKey const score::depc_ms_input

(

"score:depc_ms_input"

)

disulf_matching_probe()

RealOptionKey const score::disulf_matching_probe

(

"score:disulf_matching_probe"

)

docking_interface_score()

BooleanOptionKey const score::docking_interface_score

(

"score:docking_interface_score"

)

elec_context_maxburial()

RealOptionKey const score::elec_context_maxburial

(

"score:elec_context_maxburial"

)

elec_context_minburial()

RealOptionKey const score::elec_context_minburial

(

"score:elec_context_minburial"

)

elec_context_minstrength()

RealOptionKey const score::elec_context_minstrength

(

"score:elec_context_minstrength"

)

elec_die()

RealOptionKey const score::elec_die

(

"score:elec_die"

)

elec_group_extrafile()

StringOptionKey const score::elec_group_extrafile

(

"score:elec_group_extrafile"

)

elec_group_file()

StringOptionKey const score::elec_group_file

(

"score:elec_group_file"

)

elec_max_dis()

RealOptionKey const score::elec_max_dis

(

"score:elec_max_dis"

)

elec_min_dis()

RealOptionKey const score::elec_min_dis

(

"score:elec_min_dis"

)

elec_r_option()

BooleanOptionKey const score::elec_r_option

(

"score:elec_r_option"

)

elec_representative_cp()

BooleanOptionKey const score::elec_representative_cp

(

"score:elec_representative_cp"

)

elec_representative_cp_flip()

BooleanOptionKey const score::elec_representative_cp_flip

(

"score:elec_representative_cp_flip"

)

elec_sigmoidal_die()

BooleanOptionKey const score::elec_sigmoidal_die

(

"score:elec_sigmoidal_die"

)

elec_sigmoidal_die_D()

RealOptionKey const score::elec_sigmoidal_die_D

(

"score:elec_sigmoidal_die_D"

)

elec_sigmoidal_die_D0()

RealOptionKey const score::elec_sigmoidal_die_D0

(

"score:elec_sigmoidal_die_D0"

)

elec_sigmoidal_die_S()

RealOptionKey const score::elec_sigmoidal_die_S

(

"score:elec_sigmoidal_die_S"

)

empty()

BooleanOptionKey const score::empty

(

"score:empty"

)

envsmooth_zero_negatives()

BooleanOptionKey const score::envsmooth_zero_negatives

(

"score:envsmooth_zero_negatives"

)

eval_intrares_elec_ST_only()

BooleanOptionKey const score::eval_intrares_elec_ST_only

(

"score:eval_intrares_elec_ST_only"

)

exact_occ_pairwise()

BooleanOptionKey const score::exact_occ_pairwise

(

"score:exact_occ_pairwise"

)

Referenced by main().

exact_occ_pairwise_by_res()

BooleanOptionKey const score::exact_occ_pairwise_by_res

(

"score:exact_occ_pairwise_by_res"

)

exact_occ_radius_scaling()

RealOptionKey const score::exact_occ_radius_scaling

(

"score:exact_occ_radius_scaling"

)

exact_occ_self_res_no_occ()

BooleanOptionKey const score::exact_occ_self_res_no_occ

(

"score:exact_occ_self_res_no_occ"

)

exact_occ_skip_Hbonders()

BooleanOptionKey const score::exact_occ_skip_Hbonders

(

"score:exact_occ_skip_Hbonders"

)

exact_occ_split_between_res()

BooleanOptionKey const score::exact_occ_split_between_res

(

"score:exact_occ_split_between_res"

)

Referenced by main().

extra_improper_file()

StringOptionKey const score::extra_improper_file

(

"score:extra_improper_file"

)

extra_mm_params_dir()

StringVectorOptionKey const score::extra_mm_params_dir

(

"score:extra_mm_params_dir"

)

fa_custom_pair_distance_file()

StringOptionKey const score::fa_custom_pair_distance_file

(

"score:fa_custom_pair_distance_file"

)

fa_Hatr()

BooleanOptionKey const score::fa_Hatr

(

"score:fa_Hatr"

)

fa_max_dis()

RealOptionKey const score::fa_max_dis

(

"score:fa_max_dis"

)

Referenced by main().

fa_stack_base_base_only()

BooleanOptionKey const score::fa_stack_base_base_only

(

"score:fa_stack_base_base_only"

)

fa_stack_include_rna_protein()

BooleanOptionKey const score::fa_stack_include_rna_protein

(

"score:fa_stack_include_rna_protein"

)

fa_stack_lr_dist_cutoff()

RealOptionKey const score::fa_stack_lr_dist_cutoff

(

"score:fa_stack_lr_dist_cutoff"

)

fa_stack_lr_prefactor()

RealOptionKey const score::fa_stack_lr_prefactor

(

"score:fa_stack_lr_prefactor"

)

fa_stack_lr_stack_cutoff()

RealOptionKey const score::fa_stack_lr_stack_cutoff

(

"score:fa_stack_lr_stack_cutoff"

)

fa_stack_sol_dist_cutoff()

RealOptionKey const score::fa_stack_sol_dist_cutoff

(

"score:fa_stack_sol_dist_cutoff"

)

fa_stack_sol_prefactor()

RealOptionKey const score::fa_stack_sol_prefactor

(

"score:fa_stack_sol_prefactor"

)

fa_stack_sol_stack_cutoff()

RealOptionKey const score::fa_stack_sol_stack_cutoff

(

"score:fa_stack_sol_stack_cutoff"

)

facts_adjbb_elec_scale()

RealVectorOptionKey const score::facts_adjbb_elec_scale

(

"score:facts_adjbb_elec_scale"

)

facts_adjbb_solv_scale()

RealVectorOptionKey const score::facts_adjbb_solv_scale

(

"score:facts_adjbb_solv_scale"

)

facts_adjbs_elec_scale()

RealVectorOptionKey const score::facts_adjbs_elec_scale

(

"score:facts_adjbs_elec_scale"

)

facts_adjbs_solv_scale()

RealVectorOptionKey const score::facts_adjbs_solv_scale

(

"score:facts_adjbs_solv_scale"

)

facts_asp_patch()

IntegerOptionKey const score::facts_asp_patch

(

"score:facts_asp_patch"

)

facts_binding_affinity()

BooleanOptionKey const score::facts_binding_affinity

(

"score:facts_binding_affinity"

)

facts_charge_dir()

StringOptionKey const score::facts_charge_dir

(

"score:facts_charge_dir"

)

facts_die()

RealOptionKey const score::facts_die

(

"score:facts_die"

)

facts_dshift()

RealVectorOptionKey const score::facts_dshift

(

"score:facts_dshift"

)

facts_eff_charge_dir()

StringOptionKey const score::facts_eff_charge_dir

(

"score:facts_eff_charge_dir"

)

facts_eq_type()

StringOptionKey const score::facts_eq_type

(

"score:facts_eq_type"

)

facts_GBpair_cut()

RealOptionKey const score::facts_GBpair_cut

(

"score:facts_GBpair_cut"

)

facts_intbb_elec_scale()

RealVectorOptionKey const score::facts_intbb_elec_scale

(

"score:facts_intbb_elec_scale"

)

facts_intbb_solv_scale()

RealVectorOptionKey const score::facts_intbb_solv_scale

(

"score:facts_intbb_solv_scale"

)

facts_intbs_elec_scale()

RealVectorOptionKey const score::facts_intbs_elec_scale

(

"score:facts_intbs_elec_scale"

)

facts_intbs_solv_scale()

RealVectorOptionKey const score::facts_intbs_solv_scale

(

"score:facts_intbs_solv_scale"

)

facts_intrascale_by_level()

BooleanOptionKey const score::facts_intrascale_by_level

(

"score:facts_intrascale_by_level"

)

facts_intsc_elec_scale()

RealVectorOptionKey const score::facts_intsc_elec_scale

(

"score:facts_intsc_elec_scale"

)

facts_intsc_solv_scale()

RealVectorOptionKey const score::facts_intsc_solv_scale

(

"score:facts_intsc_solv_scale"

)

facts_kappa()

RealOptionKey const score::facts_kappa

(

"score:facts_kappa"

)

facts_plane_aa()

StringVectorOptionKey const score::facts_plane_aa

(

"score:facts_plane_aa"

)

facts_plane_to_self()

BooleanOptionKey const score::facts_plane_to_self

(

"score:facts_plane_to_self"

)

facts_saltbridge_correction()

RealOptionKey const score::facts_saltbridge_correction

(

"score:facts_saltbridge_correction"

)

find_neighbors_3dgrid()

BooleanOptionKey const score::find_neighbors_3dgrid

(

"score:find_neighbors_3dgrid"

)

find_neighbors_stripehash()

BooleanOptionKey const score::find_neighbors_stripehash

(

"score:find_neighbors_stripehash"

)

force_sugar_bb_zero()

BooleanOptionKey const score::force_sugar_bb_zero

(

"score:force_sugar_bb_zero"

)

free_side_chain_bonus()

RealOptionKey const score::free_side_chain_bonus

(

"score:free_side_chain_bonus"

)

gen_bonded_exclude_def_file()

StringOptionKey const score::gen_bonded_exclude_def_file

(

"score:gen_bonded_exclude_def_file"

)

gen_bonded_params_file()

StringOptionKey const score::gen_bonded_params_file

(

"score:gen_bonded_params_file"

)

genbonded_score_full()

BooleanOptionKey const score::genbonded_score_full

(

"score:genbonded_score_full"

)

genbonded_score_hybrid()

BooleanOptionKey const score::genbonded_score_hybrid

(

"score:genbonded_score_hybrid"

)

geom_sol_interres_path_distance_cutoff()

IntegerOptionKey const score::geom_sol_interres_path_distance_cutoff

(

"score:geom_sol_interres_path_distance_cutoff"

)

geom_sol_intrares_path_distance_cutoff()

IntegerOptionKey const score::geom_sol_intrares_path_distance_cutoff

(

"score:geom_sol_intrares_path_distance_cutoff"

)

grp_cpfxn()

BooleanOptionKey const score::grp_cpfxn

(

"score:grp_cpfxn"

)

grpelec_context_dependent()

BooleanOptionKey const score::grpelec_context_dependent

(

"score:grpelec_context_dependent"

)

grpelec_cpfxn_weight()

RealVectorOptionKey const score::grpelec_cpfxn_weight

(

"score:grpelec_cpfxn_weight"

)

grpelec_fade_hbond()

BooleanOptionKey const score::grpelec_fade_hbond

(

"score:grpelec_fade_hbond"

)

grpelec_fade_param1()

RealOptionKey const score::grpelec_fade_param1

(

"score:grpelec_fade_param1"

)

grpelec_fade_param2()

RealOptionKey const score::grpelec_fade_param2

(

"score:grpelec_fade_param2"

)

grpelec_fade_type()

StringOptionKey const score::grpelec_fade_type

(

"score:grpelec_fade_type"

)

grpelec_max_qeps()

RealVectorOptionKey const score::grpelec_max_qeps

(

"score:grpelec_max_qeps"

)

hb_acc_strength()

StringVectorOptionKey const score::hb_acc_strength

(

"score:hb_acc_strength"

)

hb_don_strength()

StringVectorOptionKey const score::hb_don_strength

(

"score:hb_don_strength"

)

hb_max_energy()

RealOptionKey const score::hb_max_energy

(

"score:hb_max_energy"

)

hbe_for_dH2O_aGEN_SP3SC_ssother()

StringOptionKey const score::hbe_for_dH2O_aGEN_SP3SC_ssother

(

"score:hbe_for_dH2O_aGEN_SP3SC_ssother"

)

hbnet_bonus_function_ramping()

StringOptionKey const score::hbnet_bonus_function_ramping

(

"score:hbnet_bonus_function_ramping"

)

hbnet_max_network_size()

IntegerOptionKey const score::hbnet_max_network_size

(

"score:hbnet_max_network_size"

)

hbond_bb_per_residue_energy()

BooleanOptionKey const score::hbond_bb_per_residue_energy

(

"score:hbond_bb_per_residue_energy"

)

hbond_disable_bbsc_exclusion_rule()

BooleanOptionKey const score::hbond_disable_bbsc_exclusion_rule

(

"score:hbond_disable_bbsc_exclusion_rule"

)

hbond_fade()

RealOptionKey const score::hbond_fade

(

"score:hbond_fade"

)

hbond_new_sp3_acc()

BooleanOptionKey const score::hbond_new_sp3_acc

(

"score:hbond_new_sp3_acc"

)

hbond_params()

StringOptionKey const score::hbond_params

(

"score:hbond_params"

)

hrf_dynamics_input()

FileOptionKey const score::hrf_dynamics_input

(

"score:hrf_dynamics_input"

)

ideal_sugars()

BooleanOptionKey const score::ideal_sugars

(

"score:ideal_sugars"

)

ignore_terminal_ss_elements()

IntegerOptionKey const score::ignore_terminal_ss_elements

(

"score:ignore_terminal_ss_elements"

)

include_intra_res_protein()

BooleanOptionKey const score::include_intra_res_protein

(

"score:include_intra_res_protein"

)

input_etables()

StringOptionKey const score::input_etables

(

"score:input_etables"

)

just_calc_rmsd()

BooleanOptionKey const score::just_calc_rmsd

(

"score:just_calc_rmsd"

)

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

ldsrbb_high_scale()

RealOptionKey const score::ldsrbb_high_scale

(

"score:ldsrbb_high_scale"

)

ldsrbb_low_scale()

RealOptionKey const score::ldsrbb_low_scale

(

"score:ldsrbb_low_scale"

)

ldsrbb_maxlength()

IntegerOptionKey const score::ldsrbb_maxlength

(

"score:ldsrbb_maxlength"

)

ldsrbb_minlength()

IntegerOptionKey const score::ldsrbb_minlength

(

"score:ldsrbb_minlength"

)

length_dep_srbb()

BooleanOptionKey const score::length_dep_srbb

(

"score:length_dep_srbb"

)

linear_bonded_potential()

BooleanOptionKey const score::linear_bonded_potential

(

"score:linear_bonded_potential"

)

lk_polar_without_proline_N()

BooleanOptionKey const score::lk_polar_without_proline_N

(

"score:lk_polar_without_proline_N"

)

lowres_weights()

StringOptionKey const score::lowres_weights

(

"score:lowres_weights"

)

max_contacting_ss()

IntegerOptionKey const score::max_contacting_ss

(

"score:max_contacting_ss"

)

max_motif_per_res()

RealOptionKey const score::max_motif_per_res

(

"score:max_motif_per_res"

)

mc_interface_weight()

RealOptionKey const score::mc_interface_weight

(

"score:mc_interface_weight"

)

mc_optimize_dG()

BooleanOptionKey const score::mc_optimize_dG

(

"score:mc_optimize_dG"

)

mc_total_weight()

RealOptionKey const score::mc_total_weight

(

"score:mc_total_weight"

)

mhc_epitope_setup_file()

StringVectorOptionKey const score::mhc_epitope_setup_file

(

"score:mhc_epitope_setup_file"

)

min_score_score()

RealOptionKey const score::min_score_score

(

"score:min_score_score"

)

motif_ignore_symmmetry()

BooleanOptionKey const score::motif_ignore_symmmetry

(

"score:motif_ignore_symmmetry"

)

motif_residues()

IntegerVectorOptionKey const score::motif_residues

(

"score:motif_residues"

)

ms_dist_exponent()

RealOptionKey const score::ms_dist_exponent

(

"score:ms_dist_exponent"

)

ms_dist_midpoint()

RealOptionKey const score::ms_dist_midpoint

(

"score:ms_dist_midpoint"

)

ms_fade_dist()

RealOptionKey const score::ms_fade_dist

(

"score:ms_fade_dist"

)

ms_fade_outer()

RealOptionKey const score::ms_fade_outer

(

"score:ms_fade_outer"

)

ms_fit_intercept()

RealOptionKey const score::ms_fit_intercept

(

"score:ms_fit_intercept"

)

ms_fit_slope()

RealOptionKey const score::ms_fit_slope

(

"score:ms_fit_slope"

)

netcharge_setup_file()

StringVectorOptionKey const score::netcharge_setup_file

(

"score:netcharge_setup_file"

)

nmer_pssm()

StringOptionKey const score::nmer_pssm

(

"score:nmer_pssm"

)

nmer_pssm_list()

StringOptionKey const score::nmer_pssm_list

(

"score:nmer_pssm_list"

)

nmer_pssm_scorecut()

RealOptionKey const score::nmer_pssm_scorecut

(

"score:nmer_pssm_scorecut"

)

nmer_ref_energies()

StringOptionKey const score::nmer_ref_energies

(

"score:nmer_ref_energies"

)

nmer_ref_energies_list()

StringOptionKey const score::nmer_ref_energies_list

(

"score:nmer_ref_energies_list"

)

nmer_ref_seq_length()

IntegerOptionKey const score::nmer_ref_seq_length

(

"score:nmer_ref_seq_length"

)

nmer_svm()

StringOptionKey const score::nmer_svm

(

"score:nmer_svm"

)

nmer_svm_aa_matrix()

StringOptionKey const score::nmer_svm_aa_matrix

(

"score:nmer_svm_aa_matrix"

)

nmer_svm_avg_rank_as_energy()

BooleanOptionKey const score::nmer_svm_avg_rank_as_energy

(

"score:nmer_svm_avg_rank_as_energy"

)

nmer_svm_list()

StringOptionKey const score::nmer_svm_list

(

"score:nmer_svm_list"

)

nmer_svm_pssm_feat()

BooleanOptionKey const score::nmer_svm_pssm_feat

(

"score:nmer_svm_pssm_feat"

)

nmer_svm_rank()

StringOptionKey const score::nmer_svm_rank

(

"score:nmer_svm_rank"

)

nmer_svm_rank_list()

StringOptionKey const score::nmer_svm_rank_list

(

"score:nmer_svm_rank_list"

)

nmer_svm_scorecut()

RealOptionKey const score::nmer_svm_scorecut

(

"score:nmer_svm_scorecut"

)

nmer_svm_term_length()

IntegerOptionKey const score::nmer_svm_term_length

(

"score:nmer_svm_term_length"

)

no_lk_polar_desolvation()

BooleanOptionKey const score::no_lk_polar_desolvation

(

"score:no_lk_polar_desolvation"

)

no_pro_close_ring_closure()

BooleanOptionKey const score::no_pro_close_ring_closure

(

"score:no_pro_close_ring_closure"

)

no_smooth_etables()

BooleanOptionKey const score::no_smooth_etables

(

"score:no_smooth_etables"

)

NV_lbound()

RealOptionKey const score::NV_lbound

(

"score:NV_lbound"

)

NV_table()

StringOptionKey const score::NV_table

(

"score:NV_table"

)

NV_ubound()

RealOptionKey const score::NV_ubound

(

"score:NV_ubound"

)

optH_patch()

StringOptionKey const score::optH_patch

(

"score:optH_patch"

)

optH_weights()

StringOptionKey const score::optH_weights

(

"score:optH_weights"

)

output_etables()

StringOptionKey const score::output_etables

(

"score:output_etables"

)

output_residue_energies()

BooleanOptionKey const score::output_residue_energies

(

"score:output_residue_energies"

)

pack_weights()

StringOptionKey const score::pack_weights

(

"score:pack_weights"

)

patch()

FileVectorOptionKey const score::patch

(

"score:patch"

)

Referenced by main().

pro_close_planar_constraint()

RealOptionKey const score::pro_close_planar_constraint

(

"score:pro_close_planar_constraint"

)

protein_dielectric()

RealOptionKey const score::protein_dielectric

(

"score:protein_dielectric"

)

put_intra_into_total()

BooleanOptionKey const score::put_intra_into_total

(

"score:put_intra_into_total"

)

rama_power()

RealOptionKey const score::rama_power

(

"score:rama_power"

)

ramaneighbors()

BooleanOptionKey const score::ramaneighbors

(

"score:ramaneighbors"

)

ref_offset()

RealOptionKey const score::ref_offset

(

"score:ref_offset"

)

ref_offsets()

StringVectorOptionKey const score::ref_offsets

(

"score:ref_offsets"

)

rg_local_span()

IntegerVectorOptionKey const score::rg_local_span

(

"score:rg_local_span"

)

ring_close_shadow_constraint()

RealOptionKey const score::ring_close_shadow_constraint

(

"score:ring_close_shadow_constraint"

)

rms_target()

RealOptionKey const score::rms_target

(

"score:rms_target"

)

rna_torsion_potential()

StringOptionKey const score::rna_torsion_potential

(

"score:rna_torsion_potential"

)

score()

BooleanOptionKey const score::score

(

"score"

)

score_pose_cutpoint_variants()

BooleanOptionKey const score::score_pose_cutpoint_variants

(

"score:score_pose_cutpoint_variants"

)

secondary_seqdep_refene_fname()

StringOptionKey const score::secondary_seqdep_refene_fname

(

"score:secondary_seqdep_refene_fname"

)

seqdep_refene_fname()

StringOptionKey const score::seqdep_refene_fname

(

"score:seqdep_refene_fname"

)

set_weights()

StringVectorOptionKey const score::set_weights

(

"score:set_weights"

)

show_etable_contributions()

BooleanOptionKey const score::show_etable_contributions

(

"score:show_etable_contributions"

)

sidechain_buried()

IntegerVectorOptionKey const score::sidechain_buried

(

"score:sidechain_buried"

)

Referenced by main().

sidechain_exposed()

IntegerVectorOptionKey const score::sidechain_exposed

(

"score:sidechain_exposed"

)

Referenced by main().

smooth_fa_elec()

BooleanOptionKey const score::smooth_fa_elec

(

"score:smooth_fa_elec"

)

soft_wts()

StringOptionKey const score::soft_wts

(

"score:soft_wts"

)

Referenced by repack_cluster(), and repack_step().

stack_elec_sigmoidal_die()

BooleanOptionKey const score::stack_elec_sigmoidal_die

(

"score:stack_elec_sigmoidal_die"

)

symE_bonus()

RealOptionKey const score::symE_bonus

(

"score:symE_bonus"

)

symE_units()

IntegerOptionKey const score::symE_units

(

"score:symE_units"

)

symmetric_gly_tables()

BooleanOptionKey const score::symmetric_gly_tables

(

"score:symmetric_gly_tables"

)

target_clash_pdb()

StringOptionKey const score::target_clash_pdb

(

"score:target_clash_pdb"

)

torsion_distr_params_file()

StringOptionKey const score::torsion_distr_params_file

(

"score:torsion_distr_params_file"

)

unmodifypot()

BooleanOptionKey const score::unmodifypot

(

"score:unmodifypot"

)

use_gen_kirkwood()

BooleanOptionKey const score::use_gen_kirkwood

(

"score:use_gen_kirkwood"

)

use_hb_env_dep()

BooleanOptionKey const score::use_hb_env_dep

(

"score:use_hb_env_dep"

)

use_polarization()

BooleanOptionKey const score::use_polarization

(

"score:use_polarization"

)

voids_penalty_energy_cone_distance_cutoff()

RealOptionKey const score::voids_penalty_energy_cone_distance_cutoff

(

"score:voids_penalty_energy_cone_distance_cutoff"

)

voids_penalty_energy_cone_dotproduct_cutoff()

RealOptionKey const score::voids_penalty_energy_cone_dotproduct_cutoff

(

"score:voids_penalty_energy_cone_dotproduct_cutoff"

)

voids_penalty_energy_containing_cones_cutoff()

IntegerOptionKey const score::voids_penalty_energy_containing_cones_cutoff

(

"score:voids_penalty_energy_containing_cones_cutoff"

)

voids_penalty_energy_disabled_except_during_packing()

BooleanOptionKey const score::voids_penalty_energy_disabled_except_during_packing

(

"score:voids_penalty_energy_disabled_except_during_packing"

)

voids_penalty_energy_voxel_grid_padding()

RealOptionKey const score::voids_penalty_energy_voxel_grid_padding

(

"score:voids_penalty_energy_voxel_grid_padding"

)

voids_penalty_energy_voxel_size()

RealOptionKey const score::voids_penalty_energy_voxel_size

(

"score:voids_penalty_energy_voxel_size"

)

water_dielectric()

RealOptionKey const score::water_dielectric

(

"score:water_dielectric"

)

water_hybrid_sf()

BooleanOptionKey const score::water_hybrid_sf

(

"score:water_hybrid_sf"

)

weights()

StringOptionKey const score::weights

(

"score:weights"

)

Referenced by CenRelaxMover::apply(), base_pair_to_base_pair_test(), build_full_model_test(), build_next_nucleotide_test(), calc_rmsf_and_avrg(), coarse_rna_denovo_test(), delta_chi_correction_test(), dinucleotide_test(), erraser2_test(), ga_main(), get_stepwise_score_function(), graphics_main(), main(), MC_run(), mg_modeler_test(), my_main(), nucleobase_probe_score_test(), pack_phosphates(), quick_score_test(), rebuild_test(), resample_full_model_test(), rotamerize_rna_test(), myspace::Scheduler::run_md(), RunPepSpec(), sample_state_to_state(), myspace::Scheduler::Scheduler(), screen_phosphates(), swa_rna_sample(), test_NMmin(), test_NMrelaxer(), thermal_sampler(), and two_base_pairs_test().