- e -

• e : test.T009_Exceptions
• e2_catalytic_resnum : basic::options::OptionKeys
• e2_chain : basic::options::OptionKeys
• E2_residue : basic::options::OptionKeys::chemically_conjugated_docking
• E2pdb : basic::options::OptionKeys::chemically_conjugated_docking
• e3_catalytic_resnum : basic::options::OptionKeys
• e3_hinge_chain : basic::options::OptionKeys
• e3_hinge_start_resnum : basic::options::OptionKeys
• e3_hinge_stop_resnum : basic::options::OptionKeys
• E_string : make_symmdef_file_denovo
• easy_vip_acceptance : basic::options::OptionKeys::cp
• edensity : basic::options::OptionKeys::edensity
• edensity_weight_for_sampling : basic::options::OptionKeys::lh
• edge_file_name : basic::options::OptionKeys::sewing
• efficiency : basic::options::OptionKeys::enzymes
• eggshell_dist : basic::options::OptionKeys::pocket_grid
• eig_vals : spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• eig_vecs : spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• elaborate_rotamer_clash_check : basic::options::OptionKeys::nmr::spinlabel
• elec_context_maxburial : basic::options::OptionKeys::score
• elec_context_minburial : basic::options::OptionKeys::score
• elec_context_minstrength : basic::options::OptionKeys::score
• elec_die : basic::options::OptionKeys::score
• elec_group_extrafile : basic::options::OptionKeys::score
• elec_group_file : basic::options::OptionKeys::score
• elec_max_dis : basic::options::OptionKeys::score
• elec_max_threshold : basic::options::OptionKeys::motifs
• elec_min_dis : basic::options::OptionKeys::score
• elec_min_threshold : basic::options::OptionKeys::motifs
• elec_r_option : basic::options::OptionKeys::score
• elec_representative_cp : basic::options::OptionKeys::score
• elec_representative_cp_flip : basic::options::OptionKeys::score
• elec_sigmoidal_die : basic::options::OptionKeys::score
• elec_sigmoidal_die_D : basic::options::OptionKeys::score
• elec_sigmoidal_die_D0 : basic::options::OptionKeys::score
• elec_sigmoidal_die_S : basic::options::OptionKeys::score
• elem : build_restypes
• elimer : test.T500_Packing
• elimerTO : test.T500_Packing
• eliminate_weak_motifs : basic::options::OptionKeys::motifs
• emap : test.T200_Scoring , test.T220_AtomAtomPairEnergies , test.Workshop3test
• embedding : basic::options::OptionKeys::mp::visualize
• empty : basic::options::OptionKeys::score
• enable_adapt_graft_cartesian : basic::options::OptionKeys::antibody::design
• enable_backbone_moves_pp : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• enable_pymol_viewer : basic::options::OptionKeys::docking
• end : basic::options::OptionKeys::cutoutdomain , test.T200_Scoring , test.T650_LoopsKIC
• end_bias : basic::options::OptionKeys::abinitio
• end_cys : ss_loop_builder
• END_NODE_ANGLE_CUTOFF : auto-DRRAFTER_setup
• end_res : indel
• end_weight : rpb
• energy : oop_conformations
• energy_based_clustering : basic::options::OptionKeys::cluster::energy_based_clustering
• energycut : basic::options::OptionKeys::relax
• enlarge_H_lj : basic::options::OptionKeys::chemical
• ens_variation : basic::options::OptionKeys::ddg
• ensemble1 : basic::options::OptionKeys::docking
• ensemble2 : basic::options::OptionKeys::docking
• enumerate : basic::options::OptionKeys::stepwise
• enumerate_ligand_rotamers : basic::options::OptionKeys::match
• envhb : basic::options::OptionKeys::hotspot
• envsmooth_zero_negatives : basic::options::OptionKeys::score
• enz_debug : basic::options::OptionKeys::enzdes
• enz_loops_file : basic::options::OptionKeys::enzdes
• enz_repack : basic::options::OptionKeys::enzdes
• enz_score : basic::options::OptionKeys::enzdes
• enzdes : basic::options::OptionKeys::enzdes
• enzdes_out : basic::options::OptionKeys::jd2
• enzyme : basic::options::OptionKeys::enzymes
• enzymes : basic::options::OptionKeys::enzymes
• epitope : basic::options::OptionKeys::antibody::design
• epr_deer : basic::options::OptionKeys::epr_deer
• epr_distance : basic::options::OptionKeys::constraints
• erraser : basic::options::OptionKeys::rna::erraser , basic::options::OptionKeys::stepwise::rna
• ERRASER_rna_validate_data : erraser_analysis
• error : closure_error , explosion_error
• escaped_chars : make_static_database
• esp_buffer_dist : basic::options::OptionKeys::pocket_grid
• esp_protein_wt : basic::options::OptionKeys::fingerprint
• esp_surface_wt : basic::options::OptionKeys::fingerprint
• esp_weight : basic::options::OptionKeys::fingerprint
• estimator : score_vs_rmsd
• euclid_bin_size : basic::options::OptionKeys::match
• euler_bin_size : basic::options::OptionKeys::match
• euler_tolerance : basic::options::OptionKeys::loodo
• ev_map : basic::options::OptionKeys::cm
• eval_intrares_elec_ST_only : basic::options::OptionKeys::score
• evaluate : basic::options::OptionKeys::jumps
• evaluate_base_pairs : basic::options::OptionKeys::rna
• evaluate_coordinating_res_energies : local
• evaluate_coordinating_res_types : local
• evaluate_ligand_sasa : local
• evaluate_max_seq_sep : basic::options::OptionKeys::constraints
• evaluate_mutations_native : local
• evaluate_mutations_native_pdb : local
• evaluate_zinc_geometry : local
• evaluate_zinc_neighbors : local
• evaluate_zinc_second_shell : local
• evaluation : basic::options::OptionKeys::evaluation
• evolution : basic::options::OptionKeys::evolution
• ex1 : basic::options::OptionKeys::packing::ex1
• ex1aro : basic::options::OptionKeys::packing::ex1aro
• ex1aro_exposed : basic::options::OptionKeys::packing::ex1aro_exposed
• ex2 : basic::options::OptionKeys::packing::ex2
• ex2aro : basic::options::OptionKeys::packing::ex2aro
• ex2aro_exposed : basic::options::OptionKeys::packing::ex2aro_exposed
• ex3 : basic::options::OptionKeys::packing::ex3
• ex4 : basic::options::OptionKeys::packing::ex4
• ex_catalytic_rot : basic::options::OptionKeys::enzdes
• exact_occ_pairwise : basic::options::OptionKeys::score
• exact_occ_pairwise_by_res : basic::options::OptionKeys::score
• exact_occ_radius_scaling : basic::options::OptionKeys::score
• exact_occ_self_res_no_occ : basic::options::OptionKeys::score
• exact_occ_skip_Hbonders : basic::options::OptionKeys::score
• exact_occ_split_between_res : basic::options::OptionKeys::score
• exclude_ala : basic::options::OptionKeys::willmatch
• exclude_badrep_ddGs : basic::options::OptionKeys::optE
• exclude_dna_dna : basic::options::OptionKeys::dna::specificity
• exclude_file : basic::options::OptionKeys::cp
• exclude_fragment_files : basic::options::OptionKeys::rna::denovo
• exclude_fragments : basic::options::OptionKeys::rna::denovo
• exclude_homo : basic::options::OptionKeys::indexed_structure_store , basic::options::OptionKeys::lh
• exclude_homologs : basic::options::OptionKeys::antibody
• exclude_homologs_cdr_cutoff : basic::options::OptionKeys::antibody
• exclude_homologs_fr_cutoff : basic::options::OptionKeys::antibody
• exclude_native_fragments : basic::options::OptionKeys::rna::denovo
• exclude_nonclashing_positions : basic::options::OptionKeys::coupled_moves
• exclude_patches : basic::options::OptionKeys::chemical
• exclude_patterns : conf
• exclude_pdbs : basic::options::OptionKeys::antibody
• exclude_polar_atoms_by_charge_in_hsasa : basic::options::OptionKeys::sasa
• exclude_res : basic::options::OptionKeys::cluster
• exclude_res1 : basic::options::OptionKeys::willmatch
• exclude_res2 : basic::options::OptionKeys::willmatch
• exclude_residues_from_rms : basic::options::OptionKeys::cyclic_peptide
• exclude_submotifs : basic::options::OptionKeys::stepwise::monte_carlo
• excluded_residues_from_rmsd : basic::options::OptionKeys::mc
• exclusion_match_type : basic::options::OptionKeys::rna::denovo
• exdna : basic::options::OptionKeys::packing::exdna
• execute_flags : app_runner
• exhaustive_fragment_insertion : basic::options::OptionKeys::rna::denovo
• existing_ft : test.T700_FoldTree
• exit : utility::options::OptionKeys::options
• exit_if_missing_heavy_atoms : basic::options::OptionKeys::run
• exit_on_bad_read : basic::options::OptionKeys::constraints
• expa2n2 : numeric::statistics
• expa2n2_length : numeric::statistics
• expand_loop_takeoff : basic::options::OptionKeys::stepwise::protein
• expand_motifs : basic::options::OptionKeys::motifs
• expand_st_chi2sampling : basic::options::OptionKeys::corrections::chemical
• expected : make_comparison
• expire_after_rounds : basic::options::OptionKeys::lh
• explicit_hydrogen_radii_set : basic::options::OptionKeys::sasa
• explicit_motif_score : basic::options::OptionKeys::mh
• explicit_pdb_debug : basic::options::OptionKeys::abinitio
• export : test.T900_distributed
• export_only_low : basic::options::OptionKeys::cluster
• ext : val2thr
• extend : pyrosetta
• extend_eggshell : basic::options::OptionKeys::pocket_grid
• extend_eggshell_dist : basic::options::OptionKeys::pocket_grid
• extend_h3_before_modeling : basic::options::OptionKeys::antibody
• extend_length : basic::options::OptionKeys::loops
• extend_peptide : basic::options::OptionKeys::flexPepDocking
• extended : basic::options::OptionKeys::loops
• extended_beta : basic::options::OptionKeys::loops
• extended_loop_file : basic::options::OptionKeys::loops
• extended_pose : basic::options::OptionKeys::in::file
• extension : basic::options::OptionKeys
• extensions : conf
• extent : hist2d
• external_scoring : basic::options::OptionKeys::ligand_evolution
• extra_base_type_file : basic::options::OptionKeys::packing::packer_palette
• extra_bodies : basic::options::OptionKeys::chemically_conjugated_docking
• extra_eggshell_dist : basic::options::OptionKeys::pocket_grid
• extra_frags_for_ss : basic::options::OptionKeys::jumps
• extra_improper_file : basic::options::OptionKeys::score
• extra_longer_names : amino_acids
• extra_min_jump_res : basic::options::OptionKeys::full_model
• extra_min_res : basic::options::OptionKeys::full_model
• extra_minimize_chi_res : basic::options::OptionKeys::rna::denovo::minimize
• extra_minimize_res : basic::options::OptionKeys::rna::denovo::minimize
• extra_mm_params_dir : basic::options::OptionKeys::score
• extra_options : demo.D010_Pose_structure , demo.D020_Pose_scoring , demo.D030_Fold_tree , demo.D040_Movemap , demo.D050_Packer_task , demo.D060_Folding , demo.D070_Refinement , demo.D080_Loop_modeling , demo.D090_Ala_scan , demo.D100_Docking , demo.D110_DNA_interface , demo.D120_Ligand_interface , pyrosetta.tests.bindings.core.test_pose , test.T006_Options , test.T007_TracerIO , test.T020_Pose_Bindings , test.T040_Types , test.T100_basic , test.T110_numeric , test.T121_core , test.T150_PyMOL_Integration , test.T190_Bindings_Utility , test.T200_Scoring , test.T201_Scoring_pre_talaris , test.T220_AtomAtomPairEnergies , test.T250_Constraints , test.T400_Refinement , test.T500_Packing , test.T600_Docking , test.T650_LoopsKIC , test.T660_LoopBuilding , test.T700_FoldTree , test.T800_ClassicRelax , test.T850_SubClassing , test.T860_SubClassing_EnergyMethods , test.T870_SubClassing_EnergyMethods2 , test.T880_Other , test.Workshop2test , test.Workshop3test , test.Workshop4test , test.Workshop5test , test.Workshop6test , test.Workshop7test , test.Workshop8test , test.Workshop9test
• extra_patch_cen : basic::options::OptionKeys::in::file
• extra_patch_fa : basic::options::OptionKeys::in::file
• extra_res : basic::options::OptionKeys::in::file
• extra_res_batch_path : basic::options::OptionKeys::in::file
• extra_res_cen : basic::options::OptionKeys::in::file
• extra_res_database : basic::options::OptionKeys::in::file
• extra_res_database_mode : basic::options::OptionKeys::in::file
• extra_res_database_resname_list : basic::options::OptionKeys::in::file
• extra_res_fa : basic::options::OptionKeys::in::file
• extra_res_mmCIF : basic::options::OptionKeys::in::file
• extra_res_mol : basic::options::OptionKeys::in::file
• extra_res_path : basic::options::OptionKeys::in::file
• extra_res_pq_schema : basic::options::OptionKeys::in::file
• extra_rms_atoms : basic::options::OptionKeys::cluster::energy_based_clustering
• extra_rot_lib_path : basic::options::OptionKeys::in::file
• extra_rottrial : basic::options::OptionKeys::docking
• extra_score : basic::options::OptionKeys::evaluation
• extra_score_column : basic::options::OptionKeys::evaluation
• extra_score_patch : basic::options::OptionKeys::evaluation
• extra_score_select : basic::options::OptionKeys::evaluation
• extra_scorefxn : basic::options::OptionKeys::wum
• extra_scorefxn_ref_structure : basic::options::OptionKeys::wum
• extra_scorefxn_relax : basic::options::OptionKeys::wum
• extrachi_cutoff : basic::options::OptionKeys::packing
• extract : extract_by_sidechain_sasa_score
• extract_element_nbrs : basic::options::OptionKeys::ddg
• extract_native_only : basic::options::OptionKeys::strand_assembly