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	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
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
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
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

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1(), and HDmakerMover::bb_score().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by pyrosetta.distributed.cluster.io.IO::_parse_results(), numeric::expression_parser::LiteralExpression::active_variables(), add_rosetta_options_1(), basic::resource_manager::ResourceManager::deallocate_resource(), ObjexxFCL::ObserverMulti::do_has_observer(), erraser2_test(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), UBQ_E2Mover::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(), utility::split_by_newlines(), utility::vectorL< L, bool, A >::u(), utility::vectorL< 1, std::string, A >::u(), and binder::vector_binder< T, Allocator >::vector_binder().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1(), UBQ_GTPase_disulfide_Mover::analyze_and_filter(), UBQ_E2Mover::analyze_and_filter(), calculate_average_residue_scores(), CAtrace::CAtrace(), do_color_by_score(), fit_helix_in_map(), helix_from_sequence(), main(), myMC::myMC(), numeric::interpolation::polycubic_interpolation(), basic::options::process(), read_silent_input_as_library(), myMC::roll(), SolutionRescoreMover::run(), basic::svd::SVD_Solver::run_score_svd_on_matrix(), basic::svd::SVD_Solver::run_score_svd_without_solving(), save_per_residue_scores(), and numeric::VoxelGrid< typename >::SetupGrid().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_2().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1().

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

Referenced by add_rosetta_options_1(), create_scorefxn(), main(), my_main(), read_silent_input_as_library(), rna_build_helix_test(), and setup_score_function().