Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Variables
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 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
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_2().

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
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_2().

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_2().

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
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().

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_2().

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_2().

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_2().

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

Referenced by add_rosetta_options_1().

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