score Namespace Reference

Namespaces
	fiber_diffraction
	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	no_lk_polar_desolvation ("score:no_lk_polar_desolvation")
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")
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	hb_env_dep_new ("score:hb_env_dep_new")
RealOptionKey const	hb_env_dep_new_low_scale ("score:hb_env_dep_new_low_scale")
RealOptionKey const	hb_env_dep_new_low_nneigh ("score:hb_env_dep_new_low_nneigh")
RealOptionKey const	hb_env_dep_new_high_nneigh ("score:hb_env_dep_new_high_nneigh")
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	disable_orientation_dependent_rna_ch_o_bonds ("score:disable_orientation_dependent_rna_ch_o_bonds")
StringOptionKey const	rna_torsion_potential ("score:rna_torsion_potential")
StringOptionKey const	rna_suite_potential ("score:rna_suite_potential")
StringOptionKey const	suiteness_bonus ("score:suiteness_bonus")
BooleanOptionKey const	rna_torsion_skip_chainbreak ("score:rna_torsion_skip_chainbreak")
BooleanOptionKey const	rna_chemical_shift_verbose ("score:rna_chemical_shift_verbose")
BooleanOptionKey const	rna_chemical_shift_larmord ("score:rna_chemical_shift_larmord")
StringOptionKey const	rna_chemical_shift_exp_data ("score:rna_chemical_shift_exp_data")
StringOptionKey const	rna_chemical_shift_larmord_par ("score:rna_chemical_shift_larmord_par")
StringOptionKey const	rna_chemical_shift_larmord_wt ("score:rna_chemical_shift_larmord_wt")
StringOptionKey const	rna_chemical_shift_larmord_ref ("score:rna_chemical_shift_larmord_ref")
StringOptionKey const	rna_chemical_shift_larmord_nei ("score:rna_chemical_shift_larmord_nei")
RealOptionKey const	rna_chemical_shift_larmord_cut ("score:rna_chemical_shift_larmord_cut")
RealOptionKey const	rna_chemical_shift_larmord_beta ("score:rna_chemical_shift_larmord_beta")
StringOptionKey const	rna_chemical_shift_H5_prime_mode ("score:rna_chemical_shift_H5_prime_mode")
IntegerVectorOptionKey const	rna_chemical_shift_include_res ("score:rna_chemical_shift_include_res")
BooleanOptionKey const	DMS_separate_features ("score:DMS_separate_features")
BooleanOptionKey const	DMS_careful_base_pair_classifier ("score:DMS_careful_base_pair_classifier")
RealOptionKey const	rna_chem_map_lores_weight ("score:rna_chem_map_lores_weight")
BooleanOptionKey const	use_2prime_OH_potential ("score:use_2prime_OH_potential")
BooleanOptionKey const	include_neighbor_base_stacks ("score:include_neighbor_base_stacks")
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_include_Hbond_contribution ("score:exact_occ_include_Hbond_contribution")
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	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_suite_bonus ("score:free_suite_bonus")
RealOptionKey const	free_sugar_bonus ("score:free_sugar_bonus")
RealOptionKey const	free_2HOprime_bonus ("score:free_2HOprime_bonus")
RealOptionKey const	syn_G_potential_bonus ("score:syn_G_potential_bonus")
RealOptionKey const	pack_phosphate_penalty ("score:pack_phosphate_penalty")
RealOptionKey const	free_side_chain_bonus ("score:free_side_chain_bonus")
RealOptionKey const	bond_angle_sd_polar_hydrogen ("score:bond_angle_sd_polar_hydrogen")
RealOptionKey const	bond_torsion_sd_polar_hydrogen ("score:bond_torsion_sd_polar_hydrogen")
BooleanOptionKey const	rna_bulge_bonus_once_per_loop ("score:rna_bulge_bonus_once_per_loop")
BooleanOptionKey const	allow_complex_loop_graph ("score:allow_complex_loop_graph")
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")
RealOptionKey const	loop_fixed_cost ("score:loop_fixed_cost")
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	aspartimide_penalty_value ("score:aspartimide_penalty_value")
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	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")
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")
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")
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")
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")

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"

)

BooleanOptionKey const score::allow_complex_loop_graph

(

"score:allow_complex_loop_graph"

)

BooleanOptionKey const score::analytic_etable_evaluation

(

"score:analytic_etable_evaluation"

)

RealOptionKey const score::aspartimide_penalty_value

(

"score:aspartimide_penalty_value"

)

RealOptionKey const score::bond_angle_sd_polar_hydrogen

(

"score:bond_angle_sd_polar_hydrogen"

)

RealOptionKey const score::bond_torsion_sd_polar_hydrogen

(

"score:bond_torsion_sd_polar_hydrogen"

)

RealVectorOptionKey const score::bonded_params

(

"score:bonded_params"

)

StringOptionKey const score::bonded_params_dir

(

"score:bonded_params_dir"

)

BooleanOptionKey const score::compute_mg_sol_for_hydrogens

(

"score:compute_mg_sol_for_hydrogens"

)

RealOptionKey const score::conc

(

"score:conc"

)

StringOptionKey const score::custom_atom_pair

(

"score:custom_atom_pair"

)

BooleanOptionKey const score::disable_orientation_dependent_rna_ch_o_bonds

(

"score:disable_orientation_dependent_rna_ch_o_bonds"

)

RealOptionKey const score::disulf_matching_probe

(

"score:disulf_matching_probe"

)

BooleanOptionKey const score::DMS_careful_base_pair_classifier

(

"score:DMS_careful_base_pair_classifier"

)

BooleanOptionKey const score::DMS_separate_features

(

"score:DMS_separate_features"

)

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_include_Hbond_contribution

(

"score:exact_occ_include_Hbond_contribution"

)

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"

)

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_2HOprime_bonus

(

"score:free_2HOprime_bonus"

)

RealOptionKey const score::free_side_chain_bonus

(

"score:free_side_chain_bonus"

)

RealOptionKey const score::free_sugar_bonus

(

"score:free_sugar_bonus"

)

RealOptionKey const score::free_suite_bonus

(

"score:free_suite_bonus"

)

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"

)

BooleanOptionKey const score::hb_env_dep_new

(

"score:hb_env_dep_new"

)

RealOptionKey const score::hb_env_dep_new_high_nneigh

(

"score:hb_env_dep_new_high_nneigh"

)

RealOptionKey const score::hb_env_dep_new_low_nneigh

(

"score:hb_env_dep_new_low_nneigh"

)

RealOptionKey const score::hb_env_dep_new_low_scale

(

"score:hb_env_dep_new_low_scale"

)

StringOptionKey const score::hbe_for_dH2O_aGEN_SP3SC_ssother

(

"score:hbe_for_dH2O_aGEN_SP3SC_ssother"

)

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"

)

StringOptionKey const score::hbond_params

(

"score:hbond_params"

)

IntegerOptionKey const score::ignore_terminal_ss_elements

(

"score:ignore_terminal_ss_elements"

)

BooleanOptionKey const score::include_intra_res_protein

(

"score:include_intra_res_protein"

)

BooleanOptionKey const score::include_neighbor_base_stacks

(

"score:include_neighbor_base_stacks"

)

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"

)

RealOptionKey const score::loop_fixed_cost

(

"score:loop_fixed_cost"

)

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::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"

)

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"

)

StringOptionKey const score::nmer_svm_list

(

"score:nmer_svm_list"

)

BooleanOptionKey const score::nmer_svm_pssm_feat

(

"score:nmer_svm_pssm_feat"

)

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"

)

Referenced by basic::options::process().

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"

)

RealOptionKey const score::pack_phosphate_penalty

(

"score:pack_phosphate_penalty"

)

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"

)

BooleanOptionKey const score::rna_bulge_bonus_once_per_loop

(

"score:rna_bulge_bonus_once_per_loop"

)

RealOptionKey const score::rna_chem_map_lores_weight

(

"score:rna_chem_map_lores_weight"

)

StringOptionKey const score::rna_chemical_shift_exp_data

(

"score:rna_chemical_shift_exp_data"

)

Referenced by compute_chem_shift_RMSD(), and cs_rosetta_rna_pdb().

StringOptionKey const score::rna_chemical_shift_H5_prime_mode

(

"score:rna_chemical_shift_H5_prime_mode"

)

IntegerVectorOptionKey const score::rna_chemical_shift_include_res

(

"score:rna_chemical_shift_include_res"

)

BooleanOptionKey const score::rna_chemical_shift_larmord

(

"score:rna_chemical_shift_larmord"

)

RealOptionKey const score::rna_chemical_shift_larmord_beta

(

"score:rna_chemical_shift_larmord_beta"

)

RealOptionKey const score::rna_chemical_shift_larmord_cut

(

"score:rna_chemical_shift_larmord_cut"

)

StringOptionKey const score::rna_chemical_shift_larmord_nei

(

"score:rna_chemical_shift_larmord_nei"

)

StringOptionKey const score::rna_chemical_shift_larmord_par

(

"score:rna_chemical_shift_larmord_par"

)

StringOptionKey const score::rna_chemical_shift_larmord_ref

(

"score:rna_chemical_shift_larmord_ref"

)

StringOptionKey const score::rna_chemical_shift_larmord_wt

(

"score:rna_chemical_shift_larmord_wt"

)

BooleanOptionKey const score::rna_chemical_shift_verbose

(

"score:rna_chemical_shift_verbose"

)

StringOptionKey const score::rna_suite_potential

(

"score:rna_suite_potential"

)

StringOptionKey const score::rna_torsion_potential

(

"score:rna_torsion_potential"

)

BooleanOptionKey const score::rna_torsion_skip_chainbreak

(

"score:rna_torsion_skip_chainbreak"

)

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"

)

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"

)

StringOptionKey const score::suiteness_bonus

(

"score:suiteness_bonus"

)

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"

)

RealOptionKey const score::syn_G_potential_bonus

(

"score:syn_G_potential_bonus"

)

BooleanOptionKey const score::unmodifypot

(

"score:unmodifypot"

)

BooleanOptionKey const score::use_2prime_OH_potential

(

"score:use_2prime_OH_potential"

)

BooleanOptionKey const score::use_gen_kirkwood

(

"score:use_gen_kirkwood"

)

BooleanOptionKey const score::use_polarization

(

"score:use_polarization"

)

RealOptionKey const score::water_dielectric

(

"score:water_dielectric"

)

StringOptionKey const score::weights

(

"score:weights"

)

Referenced by main(), MC_run(), mg_modeler_test(), nucleobase_probe_score_test(), quick_score_test(), rebuild_test(), RunPepSpec(), and stepwise_monte_carlo().