basic::options::OptionKeys::score Namespace Reference

Namespaces
	fiber_diffraction
	loop_close
	occ_sol_fitted
	rna
	saxs

Variables
BooleanOptionKey const	score_pose_cutpoint_variants
BooleanOptionKey const	score
StringOptionKey const	lowres_weights
StringOptionKey const	weights
StringVectorOptionKey const	set_weights
StringOptionKey const	pack_weights
StringOptionKey const	soft_wts
BooleanOptionKey const	docking_interface_score
RealOptionKey const	min_score_score
StringOptionKey const	custom_atom_pair
FileVectorOptionKey const	patch
BooleanOptionKey const	empty
RealOptionKey const	fa_max_dis
BooleanOptionKey const	fa_Hatr
BooleanOptionKey const	no_smooth_etables
BooleanOptionKey const	count_pair_hybrid
BooleanOptionKey const	count_pair_full
BooleanOptionKey const	no_lk_polar_desolvation
BooleanOptionKey const	lk_polar_without_proline_N
StringOptionKey const	input_etables
StringOptionKey const	output_etables
BooleanOptionKey const	analytic_etable_evaluation
BooleanOptionKey const	put_intra_into_total
BooleanOptionKey const	include_intra_res_protein
BooleanOptionKey const	fa_stack_base_base_only
BooleanOptionKey const	fa_stack_include_rna_protein
RealOptionKey const	fa_stack_sol_prefactor
RealOptionKey const	fa_stack_sol_stack_cutoff
RealOptionKey const	fa_stack_sol_dist_cutoff
RealOptionKey const	fa_stack_lr_prefactor
RealOptionKey const	fa_stack_lr_stack_cutoff
RealOptionKey const	fa_stack_lr_dist_cutoff
IntegerOptionKey const	geom_sol_interres_path_distance_cutoff
IntegerOptionKey const	geom_sol_intrares_path_distance_cutoff
RealOptionKey const	rms_target
BooleanOptionKey const	ramaneighbors
StringOptionKey const	optH_weights
StringOptionKey const	optH_patch
StringVectorOptionKey const	hb_don_strength
StringVectorOptionKey const	hb_acc_strength
StringOptionKey const	hbe_for_dH2O_aGEN_SP3SC_ssother
RealOptionKey const	hb_max_energy
StringOptionKey const	hbond_params
BooleanOptionKey const	hbond_bb_per_residue_energy
BooleanOptionKey const	hbond_disable_bbsc_exclusion_rule
BooleanOptionKey const	use_hb_env_dep
BooleanOptionKey const	water_hybrid_sf
BooleanOptionKey const	show_etable_contributions
IntegerOptionKey const	symE_units
RealOptionKey const	symE_bonus
BooleanOptionKey const	symmetric_gly_tables
RealOptionKey const	NV_lbound
RealOptionKey const	NV_ubound
StringOptionKey const	NV_table
BooleanOptionKey const	find_neighbors_3dgrid
BooleanOptionKey const	find_neighbors_stripehash
StringOptionKey const	seqdep_refene_fname
StringOptionKey const	secondary_seqdep_refene_fname
BooleanOptionKey const	exact_occ_pairwise
BooleanOptionKey const	exact_occ_skip_Hbonders
BooleanOptionKey const	exact_occ_pairwise_by_res
BooleanOptionKey const	exact_occ_split_between_res
BooleanOptionKey const	exact_occ_self_res_no_occ
RealOptionKey const	exact_occ_radius_scaling
StringVectorOptionKey const	ref_offsets
RealOptionKey const	ref_offset
BooleanOptionKey const	output_residue_energies
StringOptionKey const	fa_custom_pair_distance_file
RealOptionKey const	disulf_matching_probe
RealVectorOptionKey const	bonded_params
StringOptionKey const	bonded_params_dir
StringVectorOptionKey const	extra_mm_params_dir
StringOptionKey const	gen_bonded_params_file
StringOptionKey const	torsion_distr_params_file
StringOptionKey const	gen_bonded_exclude_def_file
BooleanOptionKey const	genbonded_score_full
BooleanOptionKey const	genbonded_score_hybrid
StringOptionKey const	extra_improper_file
BooleanOptionKey const	cart_bonded_skip_cutpoints
RealOptionKey const	pro_close_planar_constraint
BooleanOptionKey const	no_pro_close_ring_closure
RealOptionKey const	ring_close_shadow_constraint
BooleanOptionKey const	linear_bonded_potential
RealOptionKey const	free_side_chain_bonus
BooleanOptionKey const	compute_mg_sol_for_hydrogens
IntegerVectorOptionKey const	rg_local_span
BooleanOptionKey const	unmodifypot
RealOptionKey const	conc
IntegerVectorOptionKey const	sidechain_buried
IntegerVectorOptionKey const	sidechain_exposed
StringVectorOptionKey const	aa_composition_setup_file
StringOptionKey const	aa_repeat_energy_penalty_file
RealOptionKey const	approximate_buried_unsat_penalty_hbond_energy_threshold
RealOptionKey const	approximate_buried_unsat_penalty_burial_atomic_depth
RealOptionKey const	approximate_buried_unsat_penalty_burial_probe_radius
RealOptionKey const	approximate_buried_unsat_penalty_burial_resolution
RealOptionKey const	approximate_buried_unsat_penalty_oversat_penalty
BooleanOptionKey const	approximate_buried_unsat_penalty_assume_const_backbone
BooleanOptionKey const	approximate_buried_unsat_penalty_natural_corrections1
RealOptionKey const	approximate_buried_unsat_penalty_hbond_bonus_cross_chain
RealOptionKey const	approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb
BooleanOptionKey const	approximate_buried_unsat_penalty_lys_ok_with_1
StringOptionKey const	target_clash_pdb
RealOptionKey const	aspartimide_penalty_value
RealOptionKey const	buried_unsatisfied_penalty_cone_angle_exponent
RealOptionKey const	buried_unsatisfied_penalty_cone_angle_shift_factor
RealOptionKey const	buried_unsatisfied_penalty_cone_dist_exponent
RealOptionKey const	buried_unsatisfied_penalty_cone_dist_midpoint
RealOptionKey const	buried_unsatisfied_penalty_burial_threshold
RealOptionKey const	buried_unsatisfied_penalty_hbond_energy_threshold
FileOptionKey const	covalent_labeling_input
FileOptionKey const	hrf_dynamics_input
FileOptionKey const	covalent_labeling_fa_input
FileOptionKey const	depc_ms_input
RealOptionKey const	elec_min_dis
RealOptionKey const	elec_max_dis
RealOptionKey const	elec_die
BooleanOptionKey const	elec_r_option
BooleanOptionKey const	elec_sigmoidal_die
RealOptionKey const	elec_sigmoidal_die_D
RealOptionKey const	elec_sigmoidal_die_D0
RealOptionKey const	elec_sigmoidal_die_S
BooleanOptionKey const	stack_elec_sigmoidal_die
BooleanOptionKey const	elec_representative_cp
BooleanOptionKey const	elec_representative_cp_flip
BooleanOptionKey const	eval_intrares_elec_ST_only
BooleanOptionKey const	smooth_fa_elec
StringOptionKey const	grpelec_fade_type
RealOptionKey const	grpelec_fade_param1
RealOptionKey const	grpelec_fade_param2
StringOptionKey const	elec_group_file
StringOptionKey const	elec_group_extrafile
BooleanOptionKey const	grpelec_fade_hbond
RealVectorOptionKey const	grpelec_max_qeps
BooleanOptionKey const	grpelec_context_dependent
BooleanOptionKey const	grp_cpfxn
RealVectorOptionKey const	grpelec_cpfxn_weight
StringOptionKey const	hbnet_bonus_function_ramping
IntegerOptionKey const	hbnet_max_network_size
RealOptionKey const	elec_context_minstrength
RealOptionKey const	elec_context_minburial
RealOptionKey const	elec_context_maxburial
BooleanOptionKey const	use_polarization
BooleanOptionKey const	use_gen_kirkwood
RealOptionKey const	protein_dielectric
RealOptionKey const	water_dielectric
RealOptionKey const	facts_GBpair_cut
RealOptionKey const	facts_kappa
IntegerOptionKey const	facts_asp_patch
BooleanOptionKey const	facts_plane_to_self
RealOptionKey const	facts_saltbridge_correction
RealVectorOptionKey const	facts_dshift
RealOptionKey const	facts_die
BooleanOptionKey const	facts_binding_affinity
BooleanOptionKey const	facts_intrascale_by_level
RealVectorOptionKey const	facts_intbb_elec_scale
RealVectorOptionKey const	facts_intbb_solv_scale
RealVectorOptionKey const	facts_adjbb_elec_scale
RealVectorOptionKey const	facts_adjbb_solv_scale
RealVectorOptionKey const	facts_intbs_elec_scale
RealVectorOptionKey const	facts_intbs_solv_scale
RealVectorOptionKey const	facts_adjbs_elec_scale
RealVectorOptionKey const	facts_adjbs_solv_scale
RealVectorOptionKey const	facts_intsc_elec_scale
RealVectorOptionKey const	facts_intsc_solv_scale
StringOptionKey const	facts_charge_dir
StringOptionKey const	facts_eff_charge_dir
StringVectorOptionKey const	facts_plane_aa
StringOptionKey const	facts_eq_type
IntegerOptionKey const	ignore_terminal_ss_elements
BooleanOptionKey const	length_dep_srbb
RealOptionKey const	ldsrbb_low_scale
RealOptionKey const	ldsrbb_high_scale
IntegerOptionKey const	ldsrbb_minlength
IntegerOptionKey const	ldsrbb_maxlength
RealOptionKey const	max_motif_per_res
IntegerOptionKey const	max_contacting_ss
BooleanOptionKey const	motif_ignore_symmmetry
IntegerVectorOptionKey const	motif_residues
StringVectorOptionKey const	netcharge_setup_file
StringVectorOptionKey const	mhc_epitope_setup_file
RealOptionKey const	ms_dist_midpoint
RealOptionKey const	ms_dist_exponent
RealOptionKey const	ms_fit_slope
RealOptionKey const	ms_fit_intercept
RealOptionKey const	ms_fade_outer
RealOptionKey const	ms_fade_dist
RealOptionKey const	ccs_exp
RealOptionKey const	ccs_prad
IntegerOptionKey const	ccs_nrots
StringOptionKey const	nmer_ref_energies
StringOptionKey const	nmer_ref_energies_list
StringOptionKey const	nmer_pssm
StringOptionKey const	nmer_pssm_list
RealOptionKey const	nmer_pssm_scorecut
StringOptionKey const	nmer_svm
StringOptionKey const	nmer_svm_list
StringOptionKey const	nmer_svm_rank
StringOptionKey const	nmer_svm_rank_list
RealOptionKey const	nmer_svm_scorecut
StringOptionKey const	nmer_svm_aa_matrix
IntegerOptionKey const	nmer_svm_term_length
BooleanOptionKey const	nmer_svm_pssm_feat
BooleanOptionKey const	nmer_svm_avg_rank_as_energy
IntegerOptionKey const	nmer_ref_seq_length
BooleanOptionKey const	just_calc_rmsd
BooleanOptionKey const	envsmooth_zero_negatives
RealOptionKey const	rama_power
BooleanOptionKey const	ideal_sugars
RealOptionKey const	hbond_fade
BooleanOptionKey const	hbond_new_sp3_acc
RealOptionKey const	alignment_sharpness
StringOptionKey const	rna_torsion_potential
BooleanOptionKey const	arg_cation_pi_his_can_be_pi
BooleanOptionKey const	mc_optimize_dG
RealOptionKey const	mc_interface_weight
RealOptionKey const	mc_total_weight
BooleanOptionKey const	force_sugar_bb_zero
IntegerOptionKey const	voids_penalty_energy_containing_cones_cutoff
RealOptionKey const	voids_penalty_energy_cone_dotproduct_cutoff
RealOptionKey const	voids_penalty_energy_cone_distance_cutoff
BooleanOptionKey const	voids_penalty_energy_disabled_except_during_packing
RealOptionKey const	voids_penalty_energy_voxel_size
RealOptionKey const	voids_penalty_energy_voxel_grid_padding

Variable Documentation

aa_composition_setup_file

StringVectorOptionKey const basic::options::OptionKeys::score::aa_composition_setup_file

extern

aa_repeat_energy_penalty_file

StringOptionKey const basic::options::OptionKeys::score::aa_repeat_energy_penalty_file

extern

alignment_sharpness

RealOptionKey const basic::options::OptionKeys::score::alignment_sharpness

extern

analytic_etable_evaluation

BooleanOptionKey const basic::options::OptionKeys::score::analytic_etable_evaluation

extern

Referenced by HDmakerMover::bb_score().

approximate_buried_unsat_penalty_assume_const_backbone

BooleanOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_assume_const_backbone

extern

approximate_buried_unsat_penalty_burial_atomic_depth

RealOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_burial_atomic_depth

extern

approximate_buried_unsat_penalty_burial_probe_radius

RealOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_burial_probe_radius

extern

approximate_buried_unsat_penalty_burial_resolution

RealOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_burial_resolution

extern

approximate_buried_unsat_penalty_hbond_bonus_cross_chain

RealOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_hbond_bonus_cross_chain

extern

approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb

RealOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb

extern

approximate_buried_unsat_penalty_hbond_energy_threshold

RealOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_hbond_energy_threshold

extern

approximate_buried_unsat_penalty_lys_ok_with_1

BooleanOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_lys_ok_with_1

extern

approximate_buried_unsat_penalty_natural_corrections1

BooleanOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_natural_corrections1

extern

approximate_buried_unsat_penalty_oversat_penalty

RealOptionKey const basic::options::OptionKeys::score::approximate_buried_unsat_penalty_oversat_penalty

extern

arg_cation_pi_his_can_be_pi

BooleanOptionKey const basic::options::OptionKeys::score::arg_cation_pi_his_can_be_pi

extern

aspartimide_penalty_value

RealOptionKey const basic::options::OptionKeys::score::aspartimide_penalty_value

extern

bonded_params

RealVectorOptionKey const basic::options::OptionKeys::score::bonded_params

extern

bonded_params_dir

StringOptionKey const basic::options::OptionKeys::score::bonded_params_dir

extern

buried_unsatisfied_penalty_burial_threshold

RealOptionKey const basic::options::OptionKeys::score::buried_unsatisfied_penalty_burial_threshold

extern

buried_unsatisfied_penalty_cone_angle_exponent

RealOptionKey const basic::options::OptionKeys::score::buried_unsatisfied_penalty_cone_angle_exponent

extern

buried_unsatisfied_penalty_cone_angle_shift_factor

RealOptionKey const basic::options::OptionKeys::score::buried_unsatisfied_penalty_cone_angle_shift_factor

extern

buried_unsatisfied_penalty_cone_dist_exponent

RealOptionKey const basic::options::OptionKeys::score::buried_unsatisfied_penalty_cone_dist_exponent

extern

buried_unsatisfied_penalty_cone_dist_midpoint

RealOptionKey const basic::options::OptionKeys::score::buried_unsatisfied_penalty_cone_dist_midpoint

extern

buried_unsatisfied_penalty_hbond_energy_threshold

RealOptionKey const basic::options::OptionKeys::score::buried_unsatisfied_penalty_hbond_energy_threshold

extern

cart_bonded_skip_cutpoints

BooleanOptionKey const basic::options::OptionKeys::score::cart_bonded_skip_cutpoints

extern

ccs_exp

RealOptionKey const basic::options::OptionKeys::score::ccs_exp

extern

ccs_nrots

IntegerOptionKey const basic::options::OptionKeys::score::ccs_nrots

extern

ccs_prad

RealOptionKey const basic::options::OptionKeys::score::ccs_prad

extern

compute_mg_sol_for_hydrogens

BooleanOptionKey const basic::options::OptionKeys::score::compute_mg_sol_for_hydrogens

extern

conc

RealOptionKey const basic::options::OptionKeys::score::conc

extern

count_pair_full

BooleanOptionKey const basic::options::OptionKeys::score::count_pair_full

extern

count_pair_hybrid

BooleanOptionKey const basic::options::OptionKeys::score::count_pair_hybrid

extern

covalent_labeling_fa_input

FileOptionKey const basic::options::OptionKeys::score::covalent_labeling_fa_input

extern

covalent_labeling_input

FileOptionKey const basic::options::OptionKeys::score::covalent_labeling_input

extern

custom_atom_pair

StringOptionKey const basic::options::OptionKeys::score::custom_atom_pair

extern

depc_ms_input

FileOptionKey const basic::options::OptionKeys::score::depc_ms_input

extern

disulf_matching_probe

RealOptionKey const basic::options::OptionKeys::score::disulf_matching_probe

extern

docking_interface_score

BooleanOptionKey const basic::options::OptionKeys::score::docking_interface_score

extern

elec_context_maxburial

RealOptionKey const basic::options::OptionKeys::score::elec_context_maxburial

extern

elec_context_minburial

RealOptionKey const basic::options::OptionKeys::score::elec_context_minburial

extern

elec_context_minstrength

RealOptionKey const basic::options::OptionKeys::score::elec_context_minstrength

extern

elec_die

RealOptionKey const basic::options::OptionKeys::score::elec_die

extern

elec_group_extrafile

StringOptionKey const basic::options::OptionKeys::score::elec_group_extrafile

extern

elec_group_file

StringOptionKey const basic::options::OptionKeys::score::elec_group_file

extern

elec_max_dis

RealOptionKey const basic::options::OptionKeys::score::elec_max_dis

extern

elec_min_dis

RealOptionKey const basic::options::OptionKeys::score::elec_min_dis

extern

elec_r_option

BooleanOptionKey const basic::options::OptionKeys::score::elec_r_option

extern

elec_representative_cp

BooleanOptionKey const basic::options::OptionKeys::score::elec_representative_cp

extern

elec_representative_cp_flip

BooleanOptionKey const basic::options::OptionKeys::score::elec_representative_cp_flip

extern

elec_sigmoidal_die

BooleanOptionKey const basic::options::OptionKeys::score::elec_sigmoidal_die

extern

elec_sigmoidal_die_D

RealOptionKey const basic::options::OptionKeys::score::elec_sigmoidal_die_D

extern

elec_sigmoidal_die_D0

RealOptionKey const basic::options::OptionKeys::score::elec_sigmoidal_die_D0

extern

elec_sigmoidal_die_S

RealOptionKey const basic::options::OptionKeys::score::elec_sigmoidal_die_S

extern

empty

BooleanOptionKey const basic::options::OptionKeys::score::empty

extern

Referenced by pyrosetta.distributed.cluster.io.IO::_parse_results(), numeric::expression_parser::LiteralExpression::active_variables(), binder::bind_function(), bind_std_array(), bind_std_forward_list(), bind_std_stl_vector(), bind_std_stl_vector_1(), bind_T20_template_variadic(), basic::resource_manager::ResourceManager::deallocate_resource(), ObjexxFCL::ObserverMulti::do_has_observer(), erraser2_test(), binder::Context::generate(), get_symm_residue_name(), UBQ_E2Mover::init_on_new_input(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), FloppyTailMover::init_on_new_input(), main(), utility::SimulateMPIData::pop_next_message_for_node_of_type(), utility::SimulateMPIData::pop_next_message_of_type(), utility::SimulateMPIData::retrieve_next_message(), run(), utility::split_by_newlines(), utility::vectorL< L, T, A >::u(), utility::vectorL< L, bool, A >::u(), and binder::vector_binder< T, Allocator >::vector_binder().

envsmooth_zero_negatives

BooleanOptionKey const basic::options::OptionKeys::score::envsmooth_zero_negatives

extern

eval_intrares_elec_ST_only

BooleanOptionKey const basic::options::OptionKeys::score::eval_intrares_elec_ST_only

extern

exact_occ_pairwise

BooleanOptionKey const basic::options::OptionKeys::score::exact_occ_pairwise

extern

exact_occ_pairwise_by_res

BooleanOptionKey const basic::options::OptionKeys::score::exact_occ_pairwise_by_res

extern

exact_occ_radius_scaling

RealOptionKey const basic::options::OptionKeys::score::exact_occ_radius_scaling

extern

exact_occ_self_res_no_occ

BooleanOptionKey const basic::options::OptionKeys::score::exact_occ_self_res_no_occ

extern

exact_occ_skip_Hbonders

BooleanOptionKey const basic::options::OptionKeys::score::exact_occ_skip_Hbonders

extern

exact_occ_split_between_res

BooleanOptionKey const basic::options::OptionKeys::score::exact_occ_split_between_res

extern

extra_improper_file

StringOptionKey const basic::options::OptionKeys::score::extra_improper_file

extern

extra_mm_params_dir

StringVectorOptionKey const basic::options::OptionKeys::score::extra_mm_params_dir

extern

fa_custom_pair_distance_file

StringOptionKey const basic::options::OptionKeys::score::fa_custom_pair_distance_file

extern

fa_Hatr

BooleanOptionKey const basic::options::OptionKeys::score::fa_Hatr

extern

fa_max_dis

RealOptionKey const basic::options::OptionKeys::score::fa_max_dis

extern

fa_stack_base_base_only

BooleanOptionKey const basic::options::OptionKeys::score::fa_stack_base_base_only

extern

fa_stack_include_rna_protein

BooleanOptionKey const basic::options::OptionKeys::score::fa_stack_include_rna_protein

extern

fa_stack_lr_dist_cutoff

RealOptionKey const basic::options::OptionKeys::score::fa_stack_lr_dist_cutoff

extern

fa_stack_lr_prefactor

RealOptionKey const basic::options::OptionKeys::score::fa_stack_lr_prefactor

extern

fa_stack_lr_stack_cutoff

RealOptionKey const basic::options::OptionKeys::score::fa_stack_lr_stack_cutoff

extern

fa_stack_sol_dist_cutoff

RealOptionKey const basic::options::OptionKeys::score::fa_stack_sol_dist_cutoff

extern

fa_stack_sol_prefactor

RealOptionKey const basic::options::OptionKeys::score::fa_stack_sol_prefactor

extern

fa_stack_sol_stack_cutoff

RealOptionKey const basic::options::OptionKeys::score::fa_stack_sol_stack_cutoff

extern

facts_adjbb_elec_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_adjbb_elec_scale

extern

facts_adjbb_solv_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_adjbb_solv_scale

extern

facts_adjbs_elec_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_adjbs_elec_scale

extern

facts_adjbs_solv_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_adjbs_solv_scale

extern

facts_asp_patch

IntegerOptionKey const basic::options::OptionKeys::score::facts_asp_patch

extern

facts_binding_affinity

BooleanOptionKey const basic::options::OptionKeys::score::facts_binding_affinity

extern

facts_charge_dir

StringOptionKey const basic::options::OptionKeys::score::facts_charge_dir

extern

facts_die

RealOptionKey const basic::options::OptionKeys::score::facts_die

extern

facts_dshift

RealVectorOptionKey const basic::options::OptionKeys::score::facts_dshift

extern

facts_eff_charge_dir

StringOptionKey const basic::options::OptionKeys::score::facts_eff_charge_dir

extern

facts_eq_type

StringOptionKey const basic::options::OptionKeys::score::facts_eq_type

extern

facts_GBpair_cut

RealOptionKey const basic::options::OptionKeys::score::facts_GBpair_cut

extern

facts_intbb_elec_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_intbb_elec_scale

extern

facts_intbb_solv_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_intbb_solv_scale

extern

facts_intbs_elec_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_intbs_elec_scale

extern

facts_intbs_solv_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_intbs_solv_scale

extern

facts_intrascale_by_level

BooleanOptionKey const basic::options::OptionKeys::score::facts_intrascale_by_level

extern

facts_intsc_elec_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_intsc_elec_scale

extern

facts_intsc_solv_scale

RealVectorOptionKey const basic::options::OptionKeys::score::facts_intsc_solv_scale

extern

facts_kappa

RealOptionKey const basic::options::OptionKeys::score::facts_kappa

extern

facts_plane_aa

StringVectorOptionKey const basic::options::OptionKeys::score::facts_plane_aa

extern

facts_plane_to_self

BooleanOptionKey const basic::options::OptionKeys::score::facts_plane_to_self

extern

facts_saltbridge_correction

RealOptionKey const basic::options::OptionKeys::score::facts_saltbridge_correction

extern

find_neighbors_3dgrid

BooleanOptionKey const basic::options::OptionKeys::score::find_neighbors_3dgrid

extern

Referenced by test_find_neighbors().

find_neighbors_stripehash

BooleanOptionKey const basic::options::OptionKeys::score::find_neighbors_stripehash

extern

force_sugar_bb_zero

BooleanOptionKey const basic::options::OptionKeys::score::force_sugar_bb_zero

extern

free_side_chain_bonus

RealOptionKey const basic::options::OptionKeys::score::free_side_chain_bonus

extern

gen_bonded_exclude_def_file

StringOptionKey const basic::options::OptionKeys::score::gen_bonded_exclude_def_file

extern

gen_bonded_params_file

StringOptionKey const basic::options::OptionKeys::score::gen_bonded_params_file

extern

genbonded_score_full

BooleanOptionKey const basic::options::OptionKeys::score::genbonded_score_full

extern

genbonded_score_hybrid

BooleanOptionKey const basic::options::OptionKeys::score::genbonded_score_hybrid

extern

geom_sol_interres_path_distance_cutoff

IntegerOptionKey const basic::options::OptionKeys::score::geom_sol_interres_path_distance_cutoff

extern

geom_sol_intrares_path_distance_cutoff

IntegerOptionKey const basic::options::OptionKeys::score::geom_sol_intrares_path_distance_cutoff

extern

grp_cpfxn

BooleanOptionKey const basic::options::OptionKeys::score::grp_cpfxn

extern

grpelec_context_dependent

BooleanOptionKey const basic::options::OptionKeys::score::grpelec_context_dependent

extern

grpelec_cpfxn_weight

RealVectorOptionKey const basic::options::OptionKeys::score::grpelec_cpfxn_weight

extern

grpelec_fade_hbond

BooleanOptionKey const basic::options::OptionKeys::score::grpelec_fade_hbond

extern

grpelec_fade_param1

RealOptionKey const basic::options::OptionKeys::score::grpelec_fade_param1

extern

grpelec_fade_param2

RealOptionKey const basic::options::OptionKeys::score::grpelec_fade_param2

extern

grpelec_fade_type

StringOptionKey const basic::options::OptionKeys::score::grpelec_fade_type

extern

grpelec_max_qeps

RealVectorOptionKey const basic::options::OptionKeys::score::grpelec_max_qeps

extern

hb_acc_strength

StringVectorOptionKey const basic::options::OptionKeys::score::hb_acc_strength

extern

hb_don_strength

StringVectorOptionKey const basic::options::OptionKeys::score::hb_don_strength

extern

hb_max_energy

RealOptionKey const basic::options::OptionKeys::score::hb_max_energy

extern

hbe_for_dH2O_aGEN_SP3SC_ssother

StringOptionKey const basic::options::OptionKeys::score::hbe_for_dH2O_aGEN_SP3SC_ssother

extern

hbnet_bonus_function_ramping

StringOptionKey const basic::options::OptionKeys::score::hbnet_bonus_function_ramping

extern

hbnet_max_network_size

IntegerOptionKey const basic::options::OptionKeys::score::hbnet_max_network_size

extern

hbond_bb_per_residue_energy

BooleanOptionKey const basic::options::OptionKeys::score::hbond_bb_per_residue_energy

extern

hbond_disable_bbsc_exclusion_rule

BooleanOptionKey const basic::options::OptionKeys::score::hbond_disable_bbsc_exclusion_rule

extern

hbond_fade

RealOptionKey const basic::options::OptionKeys::score::hbond_fade

extern

hbond_new_sp3_acc

BooleanOptionKey const basic::options::OptionKeys::score::hbond_new_sp3_acc

extern

hbond_params

StringOptionKey const basic::options::OptionKeys::score::hbond_params

extern

hrf_dynamics_input

FileOptionKey const basic::options::OptionKeys::score::hrf_dynamics_input

extern

ideal_sugars

BooleanOptionKey const basic::options::OptionKeys::score::ideal_sugars

extern

ignore_terminal_ss_elements

IntegerOptionKey const basic::options::OptionKeys::score::ignore_terminal_ss_elements

extern

include_intra_res_protein

BooleanOptionKey const basic::options::OptionKeys::score::include_intra_res_protein

extern

input_etables

StringOptionKey const basic::options::OptionKeys::score::input_etables

extern

just_calc_rmsd

BooleanOptionKey const basic::options::OptionKeys::score::just_calc_rmsd

extern

ldsrbb_high_scale

RealOptionKey const basic::options::OptionKeys::score::ldsrbb_high_scale

extern

ldsrbb_low_scale

RealOptionKey const basic::options::OptionKeys::score::ldsrbb_low_scale

extern

ldsrbb_maxlength

IntegerOptionKey const basic::options::OptionKeys::score::ldsrbb_maxlength

extern

ldsrbb_minlength

IntegerOptionKey const basic::options::OptionKeys::score::ldsrbb_minlength

extern

length_dep_srbb

BooleanOptionKey const basic::options::OptionKeys::score::length_dep_srbb

extern

linear_bonded_potential

BooleanOptionKey const basic::options::OptionKeys::score::linear_bonded_potential

extern

lk_polar_without_proline_N

BooleanOptionKey const basic::options::OptionKeys::score::lk_polar_without_proline_N

extern

lowres_weights

StringOptionKey const basic::options::OptionKeys::score::lowres_weights

extern

Referenced by main().

max_contacting_ss

IntegerOptionKey const basic::options::OptionKeys::score::max_contacting_ss

extern

max_motif_per_res

RealOptionKey const basic::options::OptionKeys::score::max_motif_per_res

extern

mc_interface_weight

RealOptionKey const basic::options::OptionKeys::score::mc_interface_weight

extern

mc_optimize_dG

BooleanOptionKey const basic::options::OptionKeys::score::mc_optimize_dG

extern

mc_total_weight

RealOptionKey const basic::options::OptionKeys::score::mc_total_weight

extern

mhc_epitope_setup_file

StringVectorOptionKey const basic::options::OptionKeys::score::mhc_epitope_setup_file

extern

min_score_score

RealOptionKey const basic::options::OptionKeys::score::min_score_score

extern

motif_ignore_symmmetry

BooleanOptionKey const basic::options::OptionKeys::score::motif_ignore_symmmetry

extern

motif_residues

IntegerVectorOptionKey const basic::options::OptionKeys::score::motif_residues

extern

ms_dist_exponent

RealOptionKey const basic::options::OptionKeys::score::ms_dist_exponent

extern

ms_dist_midpoint

RealOptionKey const basic::options::OptionKeys::score::ms_dist_midpoint

extern

ms_fade_dist

RealOptionKey const basic::options::OptionKeys::score::ms_fade_dist

extern

ms_fade_outer

RealOptionKey const basic::options::OptionKeys::score::ms_fade_outer

extern

ms_fit_intercept

RealOptionKey const basic::options::OptionKeys::score::ms_fit_intercept

extern

ms_fit_slope

RealOptionKey const basic::options::OptionKeys::score::ms_fit_slope

extern

netcharge_setup_file

StringVectorOptionKey const basic::options::OptionKeys::score::netcharge_setup_file

extern

nmer_pssm

StringOptionKey const basic::options::OptionKeys::score::nmer_pssm

extern

nmer_pssm_list

StringOptionKey const basic::options::OptionKeys::score::nmer_pssm_list

extern

nmer_pssm_scorecut

RealOptionKey const basic::options::OptionKeys::score::nmer_pssm_scorecut

extern

nmer_ref_energies

StringOptionKey const basic::options::OptionKeys::score::nmer_ref_energies

extern

nmer_ref_energies_list

StringOptionKey const basic::options::OptionKeys::score::nmer_ref_energies_list

extern

nmer_ref_seq_length

IntegerOptionKey const basic::options::OptionKeys::score::nmer_ref_seq_length

extern

nmer_svm

StringOptionKey const basic::options::OptionKeys::score::nmer_svm

extern

nmer_svm_aa_matrix

StringOptionKey const basic::options::OptionKeys::score::nmer_svm_aa_matrix

extern

nmer_svm_avg_rank_as_energy

BooleanOptionKey const basic::options::OptionKeys::score::nmer_svm_avg_rank_as_energy

extern

nmer_svm_list

StringOptionKey const basic::options::OptionKeys::score::nmer_svm_list

extern

nmer_svm_pssm_feat

BooleanOptionKey const basic::options::OptionKeys::score::nmer_svm_pssm_feat

extern

nmer_svm_rank

StringOptionKey const basic::options::OptionKeys::score::nmer_svm_rank

extern

nmer_svm_rank_list

StringOptionKey const basic::options::OptionKeys::score::nmer_svm_rank_list

extern

nmer_svm_scorecut

RealOptionKey const basic::options::OptionKeys::score::nmer_svm_scorecut

extern

nmer_svm_term_length

IntegerOptionKey const basic::options::OptionKeys::score::nmer_svm_term_length

extern

no_lk_polar_desolvation

BooleanOptionKey const basic::options::OptionKeys::score::no_lk_polar_desolvation

extern

no_pro_close_ring_closure

BooleanOptionKey const basic::options::OptionKeys::score::no_pro_close_ring_closure

extern

no_smooth_etables

BooleanOptionKey const basic::options::OptionKeys::score::no_smooth_etables

extern

NV_lbound

RealOptionKey const basic::options::OptionKeys::score::NV_lbound

extern

NV_table

StringOptionKey const basic::options::OptionKeys::score::NV_table

extern

NV_ubound

RealOptionKey const basic::options::OptionKeys::score::NV_ubound

extern

optH_patch

StringOptionKey const basic::options::OptionKeys::score::optH_patch

extern

optH_weights

StringOptionKey const basic::options::OptionKeys::score::optH_weights

extern

output_etables

StringOptionKey const basic::options::OptionKeys::score::output_etables

extern

output_residue_energies

BooleanOptionKey const basic::options::OptionKeys::score::output_residue_energies

extern

pack_weights

StringOptionKey const basic::options::OptionKeys::score::pack_weights

extern

Referenced by main(), repack_test(), sample_trp_test(), and stepwise_template_test().

patch

FileVectorOptionKey const basic::options::OptionKeys::score::patch

extern

Referenced by main().

pro_close_planar_constraint

RealOptionKey const basic::options::OptionKeys::score::pro_close_planar_constraint

extern

protein_dielectric

RealOptionKey const basic::options::OptionKeys::score::protein_dielectric

extern

put_intra_into_total

BooleanOptionKey const basic::options::OptionKeys::score::put_intra_into_total

extern

rama_power

RealOptionKey const basic::options::OptionKeys::score::rama_power

extern

ramaneighbors

BooleanOptionKey const basic::options::OptionKeys::score::ramaneighbors

extern

ref_offset

RealOptionKey const basic::options::OptionKeys::score::ref_offset

extern

ref_offsets

StringVectorOptionKey const basic::options::OptionKeys::score::ref_offsets

extern

rg_local_span

IntegerVectorOptionKey const basic::options::OptionKeys::score::rg_local_span

extern

ring_close_shadow_constraint

RealOptionKey const basic::options::OptionKeys::score::ring_close_shadow_constraint

extern

rms_target

RealOptionKey const basic::options::OptionKeys::score::rms_target

extern

rna_torsion_potential

StringOptionKey const basic::options::OptionKeys::score::rna_torsion_potential

extern

score

BooleanOptionKey const basic::options::OptionKeys::score::score

extern

score_pose_cutpoint_variants

BooleanOptionKey const basic::options::OptionKeys::score::score_pose_cutpoint_variants

extern

secondary_seqdep_refene_fname

StringOptionKey const basic::options::OptionKeys::score::secondary_seqdep_refene_fname

extern

seqdep_refene_fname

StringOptionKey const basic::options::OptionKeys::score::seqdep_refene_fname

extern

set_weights

StringVectorOptionKey const basic::options::OptionKeys::score::set_weights

extern

show_etable_contributions

BooleanOptionKey const basic::options::OptionKeys::score::show_etable_contributions

extern

sidechain_buried

IntegerVectorOptionKey const basic::options::OptionKeys::score::sidechain_buried

extern

sidechain_exposed

IntegerVectorOptionKey const basic::options::OptionKeys::score::sidechain_exposed

extern

smooth_fa_elec

BooleanOptionKey const basic::options::OptionKeys::score::smooth_fa_elec

extern

soft_wts

StringOptionKey const basic::options::OptionKeys::score::soft_wts

extern

stack_elec_sigmoidal_die

BooleanOptionKey const basic::options::OptionKeys::score::stack_elec_sigmoidal_die

extern

symE_bonus

RealOptionKey const basic::options::OptionKeys::score::symE_bonus

extern

symE_units

IntegerOptionKey const basic::options::OptionKeys::score::symE_units

extern

symmetric_gly_tables

BooleanOptionKey const basic::options::OptionKeys::score::symmetric_gly_tables

extern

target_clash_pdb

StringOptionKey const basic::options::OptionKeys::score::target_clash_pdb

extern

torsion_distr_params_file

StringOptionKey const basic::options::OptionKeys::score::torsion_distr_params_file

extern

unmodifypot

BooleanOptionKey const basic::options::OptionKeys::score::unmodifypot

extern

use_gen_kirkwood

BooleanOptionKey const basic::options::OptionKeys::score::use_gen_kirkwood

extern

use_hb_env_dep

BooleanOptionKey const basic::options::OptionKeys::score::use_hb_env_dep

extern

use_polarization

BooleanOptionKey const basic::options::OptionKeys::score::use_polarization

extern

voids_penalty_energy_cone_distance_cutoff

RealOptionKey const basic::options::OptionKeys::score::voids_penalty_energy_cone_distance_cutoff

extern

voids_penalty_energy_cone_dotproduct_cutoff

RealOptionKey const basic::options::OptionKeys::score::voids_penalty_energy_cone_dotproduct_cutoff

extern

voids_penalty_energy_containing_cones_cutoff

IntegerOptionKey const basic::options::OptionKeys::score::voids_penalty_energy_containing_cones_cutoff

extern

voids_penalty_energy_disabled_except_during_packing

BooleanOptionKey const basic::options::OptionKeys::score::voids_penalty_energy_disabled_except_during_packing

extern

voids_penalty_energy_voxel_grid_padding

RealOptionKey const basic::options::OptionKeys::score::voids_penalty_energy_voxel_grid_padding

extern

voids_penalty_energy_voxel_size

RealOptionKey const basic::options::OptionKeys::score::voids_penalty_energy_voxel_size

extern

water_dielectric

RealOptionKey const basic::options::OptionKeys::score::water_dielectric

extern

water_hybrid_sf

BooleanOptionKey const basic::options::OptionKeys::score::water_hybrid_sf

extern

weights

StringOptionKey const basic::options::OptionKeys::score::weights

extern

Referenced by check_structures(), count_contacts(), create_scorefxn(), get_rmsd(), lariat_modeling(), main(), my_main(), OPT_KEY(), read_silent_input_as_library(), rna_build_helix_test(), score_rnp(), and setup_score_function().