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Rosetta Utilities
2014.35
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Rosetta Utilities
2014.35
|
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") |
| 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" | ) |
1.8.7