Rosetta Utilities  2014.35
Namespaces | Functions
score Namespace Reference

Namespaces

 saxs
 

Functions

BooleanOptionKey const score_pose_cutpoint_variants ("score:score_pose_cutpoint_variants")
 
BooleanOptionKey const score ("score")
 
StringOptionKey const weights ("score:weights")
 
StringVectorOptionKey const set_weights ("score:set_weights")
 
StringOptionKey const pack_weights ("score:pack_weights")
 
StringOptionKey const soft_wts ("score:soft_wts")
 
BooleanOptionKey const docking_interface_score ("score:docking_interface_score")
 
RealOptionKey const min_score_score ("score:min_score_score")
 
StringOptionKey const custom_atom_pair ("score:custom_atom_pair")
 
FileVectorOptionKey const patch ("score:patch")
 
BooleanOptionKey const empty ("score:empty")
 
RealOptionKey const fa_max_dis ("score:fa_max_dis")
 
BooleanOptionKey const fa_Hatr ("score:fa_Hatr")
 
BooleanOptionKey const no_smooth_etables ("score:no_smooth_etables")
 
BooleanOptionKey const no_lk_polar_desolvation ("score:no_lk_polar_desolvation")
 
StringOptionKey const input_etables ("score:input_etables")
 
StringOptionKey const output_etables ("score:output_etables")
 
BooleanOptionKey const analytic_etable_evaluation ("score:analytic_etable_evaluation")
 
RealOptionKey const rms_target ("score:rms_target")
 
BooleanOptionKey const ramaneighbors ("score:ramaneighbors")
 
StringOptionKey const optH_weights ("score:optH_weights")
 
StringOptionKey const optH_patch ("score:optH_patch")
 
StringOptionKey const hbond_params ("score:hbond_params")
 
BooleanOptionKey const hbond_bb_per_residue_energy ("score:hbond_bb_per_residue_energy")
 
BooleanOptionKey const hbond_disable_bbsc_exclusion_rule ("score:hbond_disable_bbsc_exclusion_rule")
 
IntegerOptionKey const symE_units ("score:symE_units")
 
RealOptionKey const symE_bonus ("score:symE_bonus")
 
RealOptionKey const NV_lbound ("score:NV_lbound")
 
RealOptionKey const NV_ubound ("score:NV_ubound")
 
StringOptionKey const NV_table ("score:NV_table")
 
BooleanOptionKey const disable_orientation_dependent_rna_ch_o_bonds ("score:disable_orientation_dependent_rna_ch_o_bonds")
 
StringOptionKey const rna_torsion_potential ("score:rna_torsion_potential")
 
StringOptionKey const rna_suite_potential ("score:rna_suite_potential")
 
BooleanOptionKey const rna_torsion_skip_chainbreak ("score:rna_torsion_skip_chainbreak")
 
StringOptionKey const rna_chemical_shift_exp_data ("score:rna_chemical_shift_exp_data")
 
StringOptionKey const rna_chemical_shift_H5_prime_mode ("score:rna_chemical_shift_H5_prime_mode")
 
IntegerVectorOptionKey const rna_chemical_shift_include_res ("score:rna_chemical_shift_include_res")
 
BooleanOptionKey const DMS_separate_features ("score:DMS_separate_features")
 
BooleanOptionKey const DMS_careful_base_pair_classifier ("score:DMS_careful_base_pair_classifier")
 
RealOptionKey const rna_chem_map_lores_weight ("score:rna_chem_map_lores_weight")
 
BooleanOptionKey const use_2prime_OH_potential ("score:use_2prime_OH_potential")
 
BooleanOptionKey const include_neighbor_base_stacks ("score:include_neighbor_base_stacks")
 
BooleanOptionKey const find_neighbors_3dgrid ("score:find_neighbors_3dgrid")
 
BooleanOptionKey const find_neighbors_stripehash ("score:find_neighbors_stripehash")
 
StringOptionKey const seqdep_refene_fname ("score:seqdep_refene_fname")
 
StringOptionKey const secondary_seqdep_refene_fname ("score:secondary_seqdep_refene_fname")
 
BooleanOptionKey const exact_occ_pairwise ("score:exact_occ_pairwise")
 
BooleanOptionKey const exact_occ_skip_Hbonders ("score:exact_occ_skip_Hbonders")
 
BooleanOptionKey const exact_occ_include_Hbond_contribution ("score:exact_occ_include_Hbond_contribution")
 
BooleanOptionKey const exact_occ_pairwise_by_res ("score:exact_occ_pairwise_by_res")
 
BooleanOptionKey const exact_occ_split_between_res ("score:exact_occ_split_between_res")
 
BooleanOptionKey const exact_occ_self_res_no_occ ("score:exact_occ_self_res_no_occ")
 
RealOptionKey const exact_occ_radius_scaling ("score:exact_occ_radius_scaling")
 
StringVectorOptionKey const ref_offsets ("score:ref_offsets")
 
RealOptionKey const ref_offset ("score:ref_offset")
 
BooleanOptionKey const output_residue_energies ("score:output_residue_energies")
 
StringOptionKey const fa_custom_pair_distance_file ("score:fa_custom_pair_distance_file")
 
RealOptionKey const disulf_matching_probe ("score:disulf_matching_probe")
 
RealVectorOptionKey const bonded_params ("score:bonded_params")
 
StringOptionKey const bonded_params_dir ("score:bonded_params_dir")
 
StringOptionKey const extra_improper_file ("score:extra_improper_file")
 
RealOptionKey const pro_close_planar_constraint ("score:pro_close_planar_constraint")
 
BooleanOptionKey const linear_bonded_potential ("score:linear_bonded_potential")
 
RealOptionKey const free_suite_bonus ("score:free_suite_bonus")
 
RealOptionKey const free_sugar_bonus ("score:free_sugar_bonus")
 
RealOptionKey const free_2HOprime_bonus ("score:free_2HOprime_bonus")
 
RealOptionKey const syn_G_potential_bonus ("score:syn_G_potential_bonus")
 
RealOptionKey const pack_phosphate_penalty ("score:pack_phosphate_penalty")
 
RealOptionKey const free_side_chain_bonus ("score:free_side_chain_bonus")
 
IntegerVectorOptionKey const rg_local_span ("score:rg_local_span")
 
BooleanOptionKey const unmodifypot ("score:unmodifypot")
 
RealOptionKey const conc ("score:conc")
 
RealOptionKey const loop_fixed_cost ("score:loop_fixed_cost")
 
IntegerVectorOptionKey const sidechain_buried ("score:sidechain_buried")
 
IntegerVectorOptionKey const sidechain_exposed ("score:sidechain_exposed")
 
RealOptionKey const elec_min_dis ("score:elec_min_dis")
 
RealOptionKey const elec_max_dis ("score:elec_max_dis")
 
RealOptionKey const elec_die ("score:elec_die")
 
BooleanOptionKey const elec_r_option ("score:elec_r_option")
 
RealOptionKey const intrares_elec_correction_scale ("score:intrares_elec_correction_scale")
 
BooleanOptionKey const smooth_fa_elec ("score:smooth_fa_elec")
 
RealOptionKey const facts_GBpair_cut ("score:facts_GBpair_cut")
 
RealOptionKey const facts_kappa ("score:facts_kappa")
 
IntegerOptionKey const facts_asp_patch ("score:facts_asp_patch")
 
BooleanOptionKey const facts_plane_to_self ("score:facts_plane_to_self")
 
RealOptionKey const facts_saltbridge_correction ("score:facts_saltbridge_correction")
 
RealVectorOptionKey const facts_dshift ("score:facts_dshift")
 
RealOptionKey const facts_die ("score:facts_die")
 
BooleanOptionKey const facts_binding_affinity ("score:facts_binding_affinity")
 
BooleanOptionKey const facts_intrascale_by_level ("score:facts_intrascale_by_level")
 
RealVectorOptionKey const facts_intbb_elec_scale ("score:facts_intbb_elec_scale")
 
RealVectorOptionKey const facts_intbb_solv_scale ("score:facts_intbb_solv_scale")
 
RealVectorOptionKey const facts_adjbb_elec_scale ("score:facts_adjbb_elec_scale")
 
RealVectorOptionKey const facts_adjbb_solv_scale ("score:facts_adjbb_solv_scale")
 
RealVectorOptionKey const facts_intbs_elec_scale ("score:facts_intbs_elec_scale")
 
RealVectorOptionKey const facts_intbs_solv_scale ("score:facts_intbs_solv_scale")
 
RealVectorOptionKey const facts_adjbs_elec_scale ("score:facts_adjbs_elec_scale")
 
RealVectorOptionKey const facts_adjbs_solv_scale ("score:facts_adjbs_solv_scale")
 
RealVectorOptionKey const facts_intsc_elec_scale ("score:facts_intsc_elec_scale")
 
RealVectorOptionKey const facts_intsc_solv_scale ("score:facts_intsc_solv_scale")
 
StringOptionKey const facts_charge_dir ("score:facts_charge_dir")
 
StringOptionKey const facts_eff_charge_dir ("score:facts_eff_charge_dir")
 
StringVectorOptionKey const facts_plane_aa ("score:facts_plane_aa")
 
StringOptionKey const facts_eq_type ("score:facts_eq_type")
 
BooleanOptionKey const length_dep_srbb ("score:length_dep_srbb")
 
RealOptionKey const ldsrbb_low_scale ("score:ldsrbb_low_scale")
 
RealOptionKey const ldsrbb_high_scale ("score:ldsrbb_high_scale")
 
IntegerOptionKey const ldsrbb_minlength ("score:ldsrbb_minlength")
 
IntegerOptionKey const ldsrbb_maxlength ("score:ldsrbb_maxlength")
 
StringOptionKey const nmer_ref_energies ("score:nmer_ref_energies")
 
StringOptionKey const nmer_ref_energies_list ("score:nmer_ref_energies_list")
 
StringOptionKey const nmer_pssm ("score:nmer_pssm")
 
StringOptionKey const nmer_pssm_list ("score:nmer_pssm_list")
 
RealOptionKey const nmer_pssm_scorecut ("score:nmer_pssm_scorecut")
 
StringOptionKey const nmer_svm ("score:nmer_svm")
 
StringOptionKey const nmer_svm_list ("score:nmer_svm_list")
 
RealOptionKey const nmer_svm_scorecut ("score:nmer_svm_scorecut")
 
StringOptionKey const nmer_svm_aa_matrix ("score:nmer_svm_aa_matrix")
 
IntegerOptionKey const nmer_svm_term_length ("score:nmer_svm_term_length")
 
BooleanOptionKey const nmer_svm_pssm_feat ("score:nmer_svm_pssm_feat")
 
IntegerOptionKey const nmer_ref_seq_length ("score:nmer_ref_seq_length")
 
BooleanOptionKey const just_calc_rmsd ("score:just_calc_rmsd")
 

Function Documentation

BooleanOptionKey const score::analytic_etable_evaluation ( "score:analytic_etable_evaluation"  )
RealVectorOptionKey const score::bonded_params ( "score:bonded_params"  )
StringOptionKey const score::bonded_params_dir ( "score:bonded_params_dir"  )
RealOptionKey const score::conc ( "score:conc"  )
StringOptionKey const score::custom_atom_pair ( "score:custom_atom_pair"  )
BooleanOptionKey const score::disable_orientation_dependent_rna_ch_o_bonds ( "score:disable_orientation_dependent_rna_ch_o_bonds"  )
RealOptionKey const score::disulf_matching_probe ( "score:disulf_matching_probe"  )
BooleanOptionKey const score::DMS_careful_base_pair_classifier ( "score:DMS_careful_base_pair_classifier"  )
BooleanOptionKey const score::DMS_separate_features ( "score:DMS_separate_features"  )
BooleanOptionKey const score::docking_interface_score ( "score:docking_interface_score"  )
RealOptionKey const score::elec_die ( "score:elec_die"  )
RealOptionKey const score::elec_max_dis ( "score:elec_max_dis"  )
RealOptionKey const score::elec_min_dis ( "score:elec_min_dis"  )
BooleanOptionKey const score::elec_r_option ( "score:elec_r_option"  )
BooleanOptionKey const score::empty ( "score:empty"  )
BooleanOptionKey const score::exact_occ_include_Hbond_contribution ( "score:exact_occ_include_Hbond_contribution"  )
BooleanOptionKey const score::exact_occ_pairwise ( "score:exact_occ_pairwise"  )
BooleanOptionKey const score::exact_occ_pairwise_by_res ( "score:exact_occ_pairwise_by_res"  )
RealOptionKey const score::exact_occ_radius_scaling ( "score:exact_occ_radius_scaling"  )
BooleanOptionKey const score::exact_occ_self_res_no_occ ( "score:exact_occ_self_res_no_occ"  )
BooleanOptionKey const score::exact_occ_skip_Hbonders ( "score:exact_occ_skip_Hbonders"  )
BooleanOptionKey const score::exact_occ_split_between_res ( "score:exact_occ_split_between_res"  )
StringOptionKey const score::extra_improper_file ( "score:extra_improper_file"  )
StringOptionKey const score::fa_custom_pair_distance_file ( "score:fa_custom_pair_distance_file"  )
BooleanOptionKey const score::fa_Hatr ( "score:fa_Hatr"  )
RealOptionKey const score::fa_max_dis ( "score:fa_max_dis"  )
RealVectorOptionKey const score::facts_adjbb_elec_scale ( "score:facts_adjbb_elec_scale"  )
RealVectorOptionKey const score::facts_adjbb_solv_scale ( "score:facts_adjbb_solv_scale"  )
RealVectorOptionKey const score::facts_adjbs_elec_scale ( "score:facts_adjbs_elec_scale"  )
RealVectorOptionKey const score::facts_adjbs_solv_scale ( "score:facts_adjbs_solv_scale"  )
IntegerOptionKey const score::facts_asp_patch ( "score:facts_asp_patch"  )
BooleanOptionKey const score::facts_binding_affinity ( "score:facts_binding_affinity"  )
StringOptionKey const score::facts_charge_dir ( "score:facts_charge_dir"  )
RealOptionKey const score::facts_die ( "score:facts_die"  )
RealVectorOptionKey const score::facts_dshift ( "score:facts_dshift"  )
StringOptionKey const score::facts_eff_charge_dir ( "score:facts_eff_charge_dir"  )
StringOptionKey const score::facts_eq_type ( "score:facts_eq_type"  )
RealOptionKey const score::facts_GBpair_cut ( "score:facts_GBpair_cut"  )
RealVectorOptionKey const score::facts_intbb_elec_scale ( "score:facts_intbb_elec_scale"  )
RealVectorOptionKey const score::facts_intbb_solv_scale ( "score:facts_intbb_solv_scale"  )
RealVectorOptionKey const score::facts_intbs_elec_scale ( "score:facts_intbs_elec_scale"  )
RealVectorOptionKey const score::facts_intbs_solv_scale ( "score:facts_intbs_solv_scale"  )
BooleanOptionKey const score::facts_intrascale_by_level ( "score:facts_intrascale_by_level"  )
RealVectorOptionKey const score::facts_intsc_elec_scale ( "score:facts_intsc_elec_scale"  )
RealVectorOptionKey const score::facts_intsc_solv_scale ( "score:facts_intsc_solv_scale"  )
RealOptionKey const score::facts_kappa ( "score:facts_kappa"  )
StringVectorOptionKey const score::facts_plane_aa ( "score:facts_plane_aa"  )
BooleanOptionKey const score::facts_plane_to_self ( "score:facts_plane_to_self"  )
RealOptionKey const score::facts_saltbridge_correction ( "score:facts_saltbridge_correction"  )
BooleanOptionKey const score::find_neighbors_3dgrid ( "score:find_neighbors_3dgrid"  )
BooleanOptionKey const score::find_neighbors_stripehash ( "score:find_neighbors_stripehash"  )
RealOptionKey const score::free_2HOprime_bonus ( "score:free_2HOprime_bonus"  )
RealOptionKey const score::free_side_chain_bonus ( "score:free_side_chain_bonus"  )
RealOptionKey const score::free_sugar_bonus ( "score:free_sugar_bonus"  )
RealOptionKey const score::free_suite_bonus ( "score:free_suite_bonus"  )
BooleanOptionKey const score::hbond_bb_per_residue_energy ( "score:hbond_bb_per_residue_energy"  )
BooleanOptionKey const score::hbond_disable_bbsc_exclusion_rule ( "score:hbond_disable_bbsc_exclusion_rule"  )
StringOptionKey const score::hbond_params ( "score:hbond_params"  )
BooleanOptionKey const score::include_neighbor_base_stacks ( "score:include_neighbor_base_stacks"  )
StringOptionKey const score::input_etables ( "score:input_etables"  )
RealOptionKey const score::intrares_elec_correction_scale ( "score:intrares_elec_correction_scale"  )
BooleanOptionKey const score::just_calc_rmsd ( "score:just_calc_rmsd"  )
RealOptionKey const score::ldsrbb_high_scale ( "score:ldsrbb_high_scale"  )
RealOptionKey const score::ldsrbb_low_scale ( "score:ldsrbb_low_scale"  )
IntegerOptionKey const score::ldsrbb_maxlength ( "score:ldsrbb_maxlength"  )
IntegerOptionKey const score::ldsrbb_minlength ( "score:ldsrbb_minlength"  )
BooleanOptionKey const score::length_dep_srbb ( "score:length_dep_srbb"  )
BooleanOptionKey const score::linear_bonded_potential ( "score:linear_bonded_potential"  )
RealOptionKey const score::loop_fixed_cost ( "score:loop_fixed_cost"  )
RealOptionKey const score::min_score_score ( "score:min_score_score"  )
StringOptionKey const score::nmer_pssm ( "score:nmer_pssm"  )
StringOptionKey const score::nmer_pssm_list ( "score:nmer_pssm_list"  )
RealOptionKey const score::nmer_pssm_scorecut ( "score:nmer_pssm_scorecut"  )
StringOptionKey const score::nmer_ref_energies ( "score:nmer_ref_energies"  )
StringOptionKey const score::nmer_ref_energies_list ( "score:nmer_ref_energies_list"  )
IntegerOptionKey const score::nmer_ref_seq_length ( "score:nmer_ref_seq_length"  )
StringOptionKey const score::nmer_svm ( "score:nmer_svm"  )
StringOptionKey const score::nmer_svm_aa_matrix ( "score:nmer_svm_aa_matrix"  )
StringOptionKey const score::nmer_svm_list ( "score:nmer_svm_list"  )
BooleanOptionKey const score::nmer_svm_pssm_feat ( "score:nmer_svm_pssm_feat"  )
RealOptionKey const score::nmer_svm_scorecut ( "score:nmer_svm_scorecut"  )
IntegerOptionKey const score::nmer_svm_term_length ( "score:nmer_svm_term_length"  )
BooleanOptionKey const score::no_lk_polar_desolvation ( "score:no_lk_polar_desolvation"  )
BooleanOptionKey const score::no_smooth_etables ( "score:no_smooth_etables"  )
RealOptionKey const score::NV_lbound ( "score:NV_lbound"  )
StringOptionKey const score::NV_table ( "score:NV_table"  )
RealOptionKey const score::NV_ubound ( "score:NV_ubound"  )
StringOptionKey const score::optH_patch ( "score:optH_patch"  )
StringOptionKey const score::optH_weights ( "score:optH_weights"  )
StringOptionKey const score::output_etables ( "score:output_etables"  )
BooleanOptionKey const score::output_residue_energies ( "score:output_residue_energies"  )
RealOptionKey const score::pack_phosphate_penalty ( "score:pack_phosphate_penalty"  )
StringOptionKey const score::pack_weights ( "score:pack_weights"  )
FileVectorOptionKey const score::patch ( "score:patch"  )
RealOptionKey const score::pro_close_planar_constraint ( "score:pro_close_planar_constraint"  )
BooleanOptionKey const score::ramaneighbors ( "score:ramaneighbors"  )
RealOptionKey const score::ref_offset ( "score:ref_offset"  )
StringVectorOptionKey const score::ref_offsets ( "score:ref_offsets"  )
IntegerVectorOptionKey const score::rg_local_span ( "score:rg_local_span"  )
RealOptionKey const score::rms_target ( "score:rms_target"  )
RealOptionKey const score::rna_chem_map_lores_weight ( "score:rna_chem_map_lores_weight"  )
StringOptionKey const score::rna_chemical_shift_exp_data ( "score:rna_chemical_shift_exp_data"  )
StringOptionKey const score::rna_chemical_shift_H5_prime_mode ( "score:rna_chemical_shift_H5_prime_mode"  )
IntegerVectorOptionKey const score::rna_chemical_shift_include_res ( "score:rna_chemical_shift_include_res"  )
StringOptionKey const score::rna_suite_potential ( "score:rna_suite_potential"  )
StringOptionKey const score::rna_torsion_potential ( "score:rna_torsion_potential"  )
BooleanOptionKey const score::rna_torsion_skip_chainbreak ( "score:rna_torsion_skip_chainbreak"  )
BooleanOptionKey const score::score ( "score"  )
BooleanOptionKey const score::score_pose_cutpoint_variants ( "score:score_pose_cutpoint_variants"  )
StringOptionKey const score::secondary_seqdep_refene_fname ( "score:secondary_seqdep_refene_fname"  )
StringOptionKey const score::seqdep_refene_fname ( "score:seqdep_refene_fname"  )
StringVectorOptionKey const score::set_weights ( "score:set_weights"  )
IntegerVectorOptionKey const score::sidechain_buried ( "score:sidechain_buried"  )
IntegerVectorOptionKey const score::sidechain_exposed ( "score:sidechain_exposed"  )
BooleanOptionKey const score::smooth_fa_elec ( "score:smooth_fa_elec"  )
StringOptionKey const score::soft_wts ( "score:soft_wts"  )
RealOptionKey const score::symE_bonus ( "score:symE_bonus"  )
IntegerOptionKey const score::symE_units ( "score:symE_units"  )
RealOptionKey const score::syn_G_potential_bonus ( "score:syn_G_potential_bonus"  )
BooleanOptionKey const score::unmodifypot ( "score:unmodifypot"  )
BooleanOptionKey const score::use_2prime_OH_potential ( "score:use_2prime_OH_potential"  )
StringOptionKey const score::weights ( "score:weights"  )