- e -

• E2_residue : basic::options::OptionKeys::chemically_conjugated_docking
• E2pdb : basic::options::OptionKeys::chemically_conjugated_docking
• 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
• eggshell_dist : basic::options::OptionKeys::pocket_grid
• elec : app::surface_docking::surface_docking
• 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
• 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
• end : basic::options::OptionKeys::cutoutdomain
• end_bias : basic::options::OptionKeys::abinitio
• 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
• epitope : basic::options::OptionKeys::antibody::design
• epr_distance : basic::options::OptionKeys::constraints
• epsilon : basic::options::OptionKeys::pb_potential
• epsilon_start_val : mrlo
• erraser : basic::options::OptionKeys::rna::farna::erraser , basic::options::OptionKeys::stepwise::rna
• 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
• 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_max_seq_sep : basic::options::OptionKeys::constraints
• 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_include_Hbond_contribution : basic::options::OptionKeys::score
• 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_header_list : exclude
• exclude_homo : 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_patches : basic::options::OptionKeys::chemical
• 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
• excluded_residues_from_rmsd : basic::options::OptionKeys::mc
• exdna : basic::options::OptionKeys::packing::exdna
• 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
• 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_only_low : basic::options::OptionKeys::cluster
• 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
• 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::farna::minimize
• extra_minimize_res : basic::options::OptionKeys::rna::farna::minimize
• 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_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_native_only : basic::options::OptionKeys::strand_assembly
• extractor : tools::doxygen