- f -

• f : demo::D060_Folding
• fa_closure_protocol : basic::options::OptionKeys::loops
• fa_custom : pyrosetta::toolbox::load_ligand , toolbox::load_ligand
• fa_custom_pair_distance_file : basic::options::OptionKeys::score
• fa_dun_thresh : basic::options::OptionKeys::willmatch
• fa_Hatr : basic::options::OptionKeys::score
• fa_max_dis : basic::options::OptionKeys::score
• Fa_Membed_update : basic::options::OptionKeys::membrane
• fa_refine : basic::options::OptionKeys::smhybrid
• fa_relax : app::surface_docking::surface_docking
• fa_relax_moves : basic::options::OptionKeys::remodel::staged_sampling
• fa_stack_base_base_only : basic::options::OptionKeys::score
• fa_stack_lr_dist_cutoff : basic::options::OptionKeys::score
• fa_stack_lr_prefactor : basic::options::OptionKeys::score
• fa_stack_lr_stack_cutoff : basic::options::OptionKeys::score
• fa_stack_sol_dist_cutoff : basic::options::OptionKeys::score
• fa_stack_sol_prefactor : basic::options::OptionKeys::score
• fa_stack_sol_stack_cutoff : basic::options::OptionKeys::score
• fa_standard : pyrosetta::toolbox::load_ligand , toolbox::load_ligand
• faatr : basic::options::OptionKeys::mh::filter
• faatr_or_hb : basic::options::OptionKeys::mh::filter
• faatr_or_hbbb : basic::options::OptionKeys::mh::filter
• factorA : basic::options::OptionKeys::bbg
• factorB : basic::options::OptionKeys::bbg
• facts_adjbb_elec_scale : basic::options::OptionKeys::score
• facts_adjbb_solv_scale : basic::options::OptionKeys::score
• facts_adjbs_elec_scale : basic::options::OptionKeys::score
• facts_adjbs_solv_scale : basic::options::OptionKeys::score
• facts_asp_patch : basic::options::OptionKeys::score
• facts_binding_affinity : basic::options::OptionKeys::score
• facts_charge_dir : basic::options::OptionKeys::score
• facts_default : basic::options::OptionKeys::corrections
• facts_die : basic::options::OptionKeys::score
• facts_dshift : basic::options::OptionKeys::score
• facts_eff_charge_dir : basic::options::OptionKeys::score
• facts_eq_type : basic::options::OptionKeys::score
• facts_GBpair_cut : basic::options::OptionKeys::score
• facts_intbb_elec_scale : basic::options::OptionKeys::score
• facts_intbb_solv_scale : basic::options::OptionKeys::score
• facts_intbs_elec_scale : basic::options::OptionKeys::score
• facts_intbs_solv_scale : basic::options::OptionKeys::score
• facts_intrascale_by_level : basic::options::OptionKeys::score
• facts_intsc_elec_scale : basic::options::OptionKeys::score
• facts_intsc_solv_scale : basic::options::OptionKeys::score
• facts_kappa : basic::options::OptionKeys::score
• facts_plane_aa : basic::options::OptionKeys::score
• facts_plane_to_self : basic::options::OptionKeys::score
• facts_saltbridge_correction : basic::options::OptionKeys::score
• fail_on_bad_hbond : basic::options::OptionKeys::in::file
• fail_unclosed : basic::options::OptionKeys::abrelax
• failed_job_exception : basic::options::OptionKeys::jd2
• farna : basic::options::OptionKeys::rna::farna
• fast : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::loops , basic::options::OptionKeys::relax
• fast_loops : basic::options::OptionKeys::fast_loops
• fast_relax_rounds : basic::options::OptionKeys::cyclic_peptide
• fast_relax_sequence_file : basic::options::OptionKeys::fast_loops
• fast_sc_moves : basic::options::OptionKeys::canonical_sampling::probabilities
• fast_sc_moves_ntrials : basic::options::OptionKeys::canonical_sampling::probabilities
• fasta : basic::options::OptionKeys::in::file
• fasta_filename : demo::D060_Folding
• fastaid : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• fastaseq : clean_pdb_keep_ligand
• fastdens_params : basic::options::OptionKeys::edensity
• fastdens_wt : basic::options::OptionKeys::edensity
• fastrelax : basic::options::OptionKeys::abinitio
• fav_nat_bonus : basic::options::OptionKeys::matdes::design
• favor_native_res : basic::options::OptionKeys::enzdes
• fiber_diffraction : basic::options::OptionKeys::score::fiber_diffraction
• file : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
• file_ : tools::CppParser
• file_list_tracer : basic::resource_manager::locator
• file_prefix : basic::options::OptionKeys::motifs
• filename : test::G202_Module_PythonPDB
• filter : basic::options::OptionKeys::mh::filter
• filter_by_phipsi : basic::options::OptionKeys::lh
• filter_chain_closure : basic::options::OptionKeys::rna::farna
• filter_chain_closure_distance : basic::options::OptionKeys::rna::farna
• filter_chain_closure_halfway : basic::options::OptionKeys::rna::farna
• filter_colliding_upstream_residues : basic::options::OptionKeys::match
• filter_cst_file : basic::options::OptionKeys::fast_loops
• filter_cst_weight : basic::options::OptionKeys::fast_loops
• filter_harvest : basic::options::OptionKeys::mh::filter
• filter_io : basic::options::OptionKeys::mh::filter
• filter_JC : basic::options::OptionKeys::frags
• filter_lores_base_pairs : basic::options::OptionKeys::rna::farna
• filter_lores_base_pairs_early : basic::options::OptionKeys::rna::farna
• filter_native_big_bins : basic::options::OptionKeys::stepwise::protein
• filter_omega : basic::options::OptionKeys::remodel
• filter_output_filename : basic::options::OptionKeys::stepwise::rna
• filter_oversaturated_hbond_acceptors : basic::options::OptionKeys::cyclic_peptide
• filter_radius : basic::options::OptionKeys::remodel
• filter_rise : basic::options::OptionKeys::remodel
• filter_stage2_beginning : basic::options::OptionKeys::relax
• filter_stage2_end : basic::options::OptionKeys::relax
• filter_stage2_half : basic::options::OptionKeys::relax
• filter_stage2_quarter : basic::options::OptionKeys::relax
• filter_templates : basic::options::OptionKeys::jumps
• filter_trial : basic::options::OptionKeys::flxbb
• filter_type : basic::options::OptionKeys::flxbb
• filter_up_to_maxlib : basic::options::OptionKeys::lh
• filter_upstream_downstream_collisions : basic::options::OptionKeys::match
• filter_user_alignment_res : basic::options::OptionKeys::stepwise::rna
• filters : basic::options::OptionKeys::AnchoredDesign::filters , basic::options::OptionKeys::filters
• final_clean_fastrelax : basic::options::OptionKeys::loops
• final_clean_relax : basic::options::OptionKeys::abinitio
• final_min_glycans : basic::options::OptionKeys::carbohydrates::glycan_relax
• final_repack_without_ligand : basic::options::OptionKeys::enzdes
• final_score_filter : basic::options::OptionKeys::loops
• final_temp : loops , loops_kic , test::T650_LoopsKIC
• final_temp_high : demo::D080_Loop_modeling
• final_temp_low : demo::D080_Loop_modeling
• find_neighbors : basic::options::OptionKeys::remodel::design
• find_neighbors_3dgrid : basic::options::OptionKeys::score
• find_neighbors_stripehash : basic::options::OptionKeys::score
• finer_sampling_at_chain_closure : basic::options::OptionKeys::stepwise::rna
• fingerprint : basic::options::OptionKeys::fingerprint
• first : assign_charges
• fit_method : basic::options::OptionKeys::rdc
• fit_pddf_area : basic::options::OptionKeys::score::saxs
• fit_reference_energies_to_aa_profile_recovery : basic::options::OptionKeys::optE
• fix : basic::options::OptionKeys::optE
• fix_aligned_residues : basic::options::OptionKeys::templates
• fix_ca_bond_angles : basic::options::OptionKeys::loops
• fix_catalytic_aa : basic::options::OptionKeys::enzdes
• fix_chainbreak : basic::options::OptionKeys::jumps
• fix_disulf : basic::options::OptionKeys::in
• fix_frag_file : basic::options::OptionKeys::templates
• fix_his_tautomer : basic::options::OptionKeys::packing
• fix_jumps : basic::options::OptionKeys::jumps
• fix_margin : basic::options::OptionKeys::templates
• fix_natsc : basic::options::OptionKeys::loops
• fix_normAzz : basic::options::OptionKeys::rdc
• fix_omega : basic::options::OptionKeys::relax
• fix_residues_to_native : basic::options::OptionKeys::abinitio
• fix_short_segment : basic::options::OptionKeys::bbg
• fixbb_substitutions_scale : basic::options::OptionKeys::flexpack::annealer
• fixDa : basic::options::OptionKeys::rdc
• fixed : basic::options::OptionKeys::optE
• fixed_membrane : basic::options::OptionKeys::membrane
• fixed_res : basic::options::OptionKeys::rna::farna::erraser , basic::options::OptionKeys::stepwise , basic::options::OptionKeys::willmatch
• fixed_res_files : basic::options::OptionKeys::smhybrid
• fixed_stems : basic::options::OptionKeys::rna::farna
• fixR : basic::options::OptionKeys::rdc
• fixup : basic::options::OptionKeys::magnesium
• flag_altpos : clean_pdb_keep_ligand
• flag_file_builder_import : app::pyrosetta_toolkit::window_main::menu
• flag_insres : clean_pdb_keep_ligand
• flag_misdns : clean_pdb_keep_ligand
• flag_modres : clean_pdb_keep_ligand
• flag_successful : clean_pdb_keep_ligand
• flank_residue_min : basic::options::OptionKeys::antibody
• flex_sugar : basic::options::OptionKeys::motifs
• flexbb_protocol : basic::options::OptionKeys::enzdes
• flexible_bb : basic::options::OptionKeys::mp::dock
• flexible_bb_docking : basic::options::OptionKeys::docking
• flexible_bb_docking_interface_dist : basic::options::OptionKeys::docking
• flexible_chain : basic::options::OptionKeys::FloppyTail
• flexible_sc : basic::options::OptionKeys::mp::dock
• flexible_start_resnum : basic::options::OptionKeys::FloppyTail
• flexible_stop_resnum : basic::options::OptionKeys::FloppyTail
• flexpack : basic::options::OptionKeys::flexpack
• flexpep_noprepack1 : basic::options::OptionKeys::flexPepDocking
• flexpep_noprepack2 : basic::options::OptionKeys::flexPepDocking
• flexpep_prepack : basic::options::OptionKeys::flexPepDocking
• flexpep_score_only : basic::options::OptionKeys::flexPepDocking
• flexPepDocking : basic::options::OptionKeys::flexPepDocking
• flexPepDockingMinimizeOnly : basic::options::OptionKeys::flexPepDocking
• flip_HNQ : basic::options::OptionKeys::packing
• floating_base : basic::options::OptionKeys::stepwise::rna
• floating_base_anchor_res : basic::options::OptionKeys::stepwise::rna
• FloppyTail : basic::options::OptionKeys::FloppyTail
• flxbb : basic::options::OptionKeys::flxbb
• Fnat : basic::options::OptionKeys::evaluation
• Fnonnat : basic::options::OptionKeys::evaluation
• fold_and_dock : basic::options::OptionKeys::fold_and_dock
• fold_cst : basic::options::OptionKeys::fold_cst
• fold_from_loops : basic::options::OptionKeys::fold_from_loops
• fold_tree : basic::options::OptionKeys::in::file
• fold_tree_io : basic::options::OptionKeys::inout
• folding : demo::D060_Folding
• folding_mover : demo::D060_Folding
• Footer : make_templates
• forbid_residues : basic::options::OptionKeys::willmatch
• force_anti_chi_res_list : basic::options::OptionKeys::full_model::rna
• force_apix : basic::options::OptionKeys::edensity
• force_centroid_interaction : basic::options::OptionKeys::stepwise::rna
• force_cutting_index : basic::options::OptionKeys::remodel::RemodelLoopMover
• force_cutting_N : basic::options::OptionKeys::remodel::RemodelLoopMover
• force_linear_fold_tree : basic::options::OptionKeys::FloppyTail
• force_minimize : basic::options::OptionKeys::fold_cst
• force_mutate_framework_for_cluster : basic::options::OptionKeys::antibody::design
• force_native_topology : basic::options::OptionKeys::templates
• force_nonideal_structure : basic::options::OptionKeys::out::file
• force_north_sugar_list : basic::options::OptionKeys::full_model::rna
• force_pdb_info_mapping : basic::options::OptionKeys::constraints
• force_phosphate_instantiation : basic::options::OptionKeys::stepwise::rna
• force_silent_bitflip_on_read : basic::options::OptionKeys::in::file
• force_south_sugar_list : basic::options::OptionKeys::full_model::rna
• force_submotif_without_intervening_bulge : basic::options::OptionKeys::stepwise::monte_carlo
• force_syn_chi_res_list : basic::options::OptionKeys::full_model::rna
• force_use_of_cluster_csts_with_outliers : basic::options::OptionKeys::antibody
• force_user_defined_jumps : basic::options::OptionKeys::stepwise::rna
• forcePolyAAfragments : basic::options::OptionKeys::dwkulp
• forest_file : basic::options::OptionKeys::constraints
• format : BuildPackagedBindings
• fraction_by_recombination : basic::options::OptionKeys::ms
• frag3 : app::surface_docking::surface_docking , basic::options::OptionKeys::in::file
• frag3_weight : basic::options::OptionKeys::flexPepDocking
• frag5 : basic::options::OptionKeys::flexPepDocking
• frag5_weight : basic::options::OptionKeys::flexPepDocking
• frag9 : app::surface_docking::surface_docking , basic::options::OptionKeys::in::file
• frag9_weight : basic::options::OptionKeys::flexPepDocking
• frag_1mer_insertion_weight : basic::options::OptionKeys::cm::hybridize
• frag_filename : demo::D080_Loop_modeling
• frag_files : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::in::file , basic::options::OptionKeys::loops , basic::options::OptionKeys::SSrbrelax
• frag_length : demo::D080_Loop_modeling
• frag_prefix : basic::options::OptionKeys::out::file
• frag_res_files : basic::options::OptionKeys::smhybrid
• frag_size : usec
• frag_sizes : basic::options::OptionKeys::frags , basic::options::OptionKeys::loops , basic::options::OptionKeys::SSrbrelax
• frag_weight_aligned : basic::options::OptionKeys::cm::hybridize
• fragA : basic::options::OptionKeys::in::file
• fragAlength : basic::options::OptionKeys::loodo
• fragAnative : basic::options::OptionKeys::loodo
• fragB : basic::options::OptionKeys::in::file
• fragBlength : basic::options::OptionKeys::loodo
• fragBnative : basic::options::OptionKeys::loodo
• fragment_contacts : basic::options::OptionKeys::frags
• fragment_cycles : basic::options::OptionKeys::rigid
• fragment_store : basic::options::OptionKeys::indexed_structure_store
• fragment_threshold_distance : basic::options::OptionKeys::indexed_structure_store
• fragments : basic::options::OptionKeys::in::path
• fragpdb : basic::options::OptionKeys::lh::fragpdb
• frags : basic::options::OptionKeys::frags
• fragsample_patch : basic::options::OptionKeys::fast_loops
• fragsample_score : basic::options::OptionKeys::fast_loops
• fragset : test::Workshop4test
• fragset3mer : loops , test::T400_Refinement
• fragset9mer : test::T400_Refinement
• fragsteal : basic::options::OptionKeys::templates::fragsteal
• FRAME : app::pyrosetta_toolkit::modules::prettytable::prettytable
• frame_rate : basic::options::OptionKeys::boinc
• free : basic::options::OptionKeys::optE
• free_2HOprime_bonus : basic::options::OptionKeys::score
• free_relax : basic::options::OptionKeys::remodel
• free_side_chain_bonus : basic::options::OptionKeys::score
• free_sugar_bonus : basic::options::OptionKeys::score
• free_suite_bonus : basic::options::OptionKeys::score
• frequency : amino_acids
• frh_template : basic::options::OptionKeys::antibody
• frl_template : basic::options::OptionKeys::antibody
• from_scratch_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• Fsol : basic::options::OptionKeys::patterson
• ft : test::T700_FoldTree , test::Workshop8test
• full_model : basic::options::OptionKeys::full_model
• full_version : setup
• fullatom : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
• fullatom_sfx : basic::options::OptionKeys::ufv
• fullatom_sfx_patch : basic::options::OptionKeys::ufv
• fullscreen : basic::options::OptionKeys::boinc
• fxnal_group : basic::options::OptionKeys::hotspot