- f -

• fa_closure_protocol() : basic::options::OptionKeys::loops , loops
• fa_custom_pair_distance_file() : score
• fa_dun_thresh() : willmatch
• fa_elec_co_only() : basic::options::OptionKeys::corrections::score , corrections::score
• fa_Hatr() : score
• fa_input() : basic::options::OptionKeys::loops , loops
• fa_max_dis() : score
• Fa_Membed_update() : basic::options::OptionKeys::membrane , membrane
• fa_refine() : smhybrid
• fa_relax_moves() : remodel::staged_sampling
• faatr() : basic::options::OptionKeys::mh::filter , mh::filter
• faatr_or_hb() : basic::options::OptionKeys::mh::filter , mh::filter
• faatr_or_hbbb() : basic::options::OptionKeys::mh::filter , mh::filter
• factorA() : basic::options::OptionKeys::bbg , bbg
• factorB() : basic::options::OptionKeys::bbg , bbg
• facts_adjbb_elec_scale() : score
• facts_adjbb_solv_scale() : score
• facts_adjbs_elec_scale() : score
• facts_adjbs_solv_scale() : score
• facts_asp_patch() : score
• facts_binding_affinity() : score
• facts_charge_dir() : score
• facts_default() : basic::options::OptionKeys::corrections , corrections
• facts_die() : score
• facts_dshift() : score
• facts_eff_charge_dir() : score
• facts_eq_type() : score
• facts_GBpair_cut() : score
• facts_intbb_elec_scale() : score
• facts_intbb_solv_scale() : score
• facts_intbs_elec_scale() : score
• facts_intbs_solv_scale() : score
• facts_intrascale_by_level() : score
• facts_intsc_elec_scale() : score
• facts_intsc_solv_scale() : score
• facts_kappa() : score
• facts_plane_aa() : score
• facts_plane_to_self() : score
• facts_saltbridge_correction() : score
• fail_on_bad_hbond() : basic::options::OptionKeys::in::file , in::file
• fail_unclosed() : abrelax , basic::options::OptionKeys::abrelax
• FArray_to_vector_of_xyzvectors() : numeric
• FArray_to_xyzmatrix() : numeric
• fast() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::loops , dna::specificity , loops , relax
• fast_loops() : basic::options::OptionKeys::fast_loops , fast_loops
• fast_relax_sequence_file() : basic::options::OptionKeys::fast_loops , fast_loops
• fast_remainder() : numeric
• fast_sc_moves() : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• fast_sc_moves_ntrials() : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• fasta() : basic::options::OptionKeys::in::file , in::file
• fastdens_params() : basic::options::OptionKeys::edensity , edensity
• fastdens_wt() : basic::options::OptionKeys::edensity , edensity
• fastrelax() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::loops , loops
• fav_nat_bonus() : basic::options::OptionKeys::matdes::design , matdes::design
• favor_native_res() : basic::options::OptionKeys::enzdes , enzdes
• fft() : numeric::fourier
• fft2() : numeric::fourier
• fft3() : numeric::fourier
• fft3_dynamic() : numeric::fourier
• file() : basic::options::OptionKeys::in::file , in::file , out::file
• file_basename() : utility::file , utility
• file_contents() : utility
• file_delete() : utility::file
• file_exists() : utility::file
• file_extension() : utility::file
• file_prefix() : basic::options::OptionKeys::motifs , motifs
• file_size() : utility::file
• filename() : utility
• filter() : basic::options::OptionKeys::mh::filter , mh::filter , smhybrid
• filter_by_phipsi() : basic::options::OptionKeys::lh , lh
• filter_colliding_upstream_residues() : basic::options::OptionKeys::match , match
• filter_cst_file() : basic::options::OptionKeys::fast_loops , fast_loops
• filter_cst_weight() : basic::options::OptionKeys::fast_loops , fast_loops
• filter_harvest() : basic::options::OptionKeys::mh::filter , mh::filter
• filter_io() : basic::options::OptionKeys::mh::filter , mh::filter
• filter_JC() : basic::options::OptionKeys::frags , frags
• filter_native_big_bins() : stepwise::protein
• filter_output_filename() : stepwise::rna
• filter_stage2_beginning() : relax
• filter_stage2_end() : relax
• filter_stage2_half() : relax
• filter_stage2_quarter() : relax
• filter_templates() : basic::options::OptionKeys::jumps , jumps
• filter_trial() : basic::options::OptionKeys::flxbb , flxbb
• filter_type() : basic::options::OptionKeys::flxbb , flxbb
• filter_upstream_downstream_collisions() : basic::options::OptionKeys::match , match
• filter_user_alignment_res() : stepwise::rna
• filters() : abrelax , AnchoredDesign::filters , basic::options::OptionKeys::abrelax , basic::options::OptionKeys::AnchoredDesign::filters , basic::options::OptionKeys::filters , filters
• final_clean_fastrelax() : basic::options::OptionKeys::loops , loops
• final_clean_relax() : abinitio , basic::options::OptionKeys::abinitio
• final_repack_without_ligand() : basic::options::OptionKeys::enzdes , enzdes
• final_score_filter() : basic::options::OptionKeys::loops , loops
• find_closest() : utility
• find_disulf() : run
• find_first_non_zero() : utility::json_spirit
• find_nearest_value() : numeric
• find_neighbors() : remodel::design
• find_neighbors_3dgrid() : score
• find_neighbors_stripehash() : score
• find_value() : utility::json_spirit
• findUU() : numeric::model_quality
• finer_sampling_at_chain_closure() : stepwise::rna
• fingerprint() : basic::options::OptionKeys::fingerprint , fingerprint
• first_principal_component() : numeric
• fit_method() : rdc
• fit_pddf_area() : score::saxs
• fit_reference_energies_to_aa_profile_recovery() : basic::options::OptionKeys::optE , optE
• fix() : basic::options::OptionKeys::optE , optE
• fix_aligned_residues() : templates
• fix_ca_bond_angles() : basic::options::OptionKeys::loops , loops
• fix_catalytic_aa() : basic::options::OptionKeys::enzdes , enzdes
• fix_chainbreak() : basic::options::OptionKeys::jumps , jumps
• fix_disulf() : basic::options::OptionKeys::in , in
• fix_frag_file() : templates
• fix_his_tautomer() : packing
• fix_jumps() : basic::options::OptionKeys::jumps , jumps
• fix_margin() : templates
• fix_natsc() : basic::options::OptionKeys::loops , loops
• fix_normAzz() : rdc
• fix_omega() : relax
• fix_residues_to_native() : abinitio , basic::options::OptionKeys::abinitio
• fix_short_segment() : basic::options::OptionKeys::bbg , bbg
• fixbb_substitutions_scale() : basic::options::OptionKeys::flexpack::annealer , flexpack::annealer
• fixDa() : rdc
• fixed() : basic::options::OptionKeys::optE , optE
• fixed_membrane() : basic::options::OptionKeys::membrane , membrane
• fixed_res() : stepwise , willmatch
• fixed_res_files() : smhybrid
• fixEigenvector() : numeric::model_quality
• fixR() : rdc
• flank_residue_min() : antibody , basic::options::OptionKeys::antibody
• fldsgn() : basic::options::OptionKeys::fldsgn , fldsgn
• flex_sugar() : basic::options::OptionKeys::motifs , motifs
• flexbb_outstructs() : basic::options::OptionKeys::enzdes , enzdes
• flexbb_protocol() : basic::options::OptionKeys::enzdes , enzdes
• flexible_bb_docking() : basic::options::OptionKeys::docking , docking
• flexible_bb_docking_interface_dist() : basic::options::OptionKeys::docking , docking
• flexible_chain() : basic::options::OptionKeys::FloppyTail , FloppyTail
• flexible_start_resnum() : basic::options::OptionKeys::FloppyTail , FloppyTail
• flexible_stop_resnum() : basic::options::OptionKeys::FloppyTail , FloppyTail
• flexpack() : basic::options::OptionKeys::flexpack , flexpack
• flexpep_noprepack1() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• flexpep_noprepack2() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• flexpep_prepack() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• flexpep_score_only() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• flexPepDocking() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• flexPepDockingMinimizeOnly() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• flip_HNQ() : packing
• floating_base() : stepwise::rna
• floating_base_anchor_res() : stepwise::rna
• floating_scs_rep() : smhybrid
• FloppyTail() : basic::options::OptionKeys::FloppyTail , FloppyTail
• flush() : basic::options::OptionKeys::dna::design , dna::design
• flxbb() : basic::options::OptionKeys::flxbb , flxbb , smhybrid
• Fnat() : basic::options::OptionKeys::evaluation , evaluation
• Fnonnat() : basic::options::OptionKeys::evaluation , evaluation
• fold_and_dock() : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• fold_cst() : basic::options::OptionKeys::fold_cst , fold_cst
• fold_from_loops() : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• fold_tree() : basic::options::OptionKeys::in::file , in::file
• fold_tree_io() : basic::options::OptionKeys::inout , inout
• forbid_residues() : willmatch
• force_apix() : basic::options::OptionKeys::edensity , edensity
• force_centroid_interaction() : stepwise::rna
• force_cutting_N() : remodel::RemodelLoopMover
• force_linear_fold_tree() : basic::options::OptionKeys::FloppyTail , FloppyTail
• force_minimize() : basic::options::OptionKeys::fold_cst , fold_cst
• force_native_topology() : templates
• force_nonideal_structure() : out::file
• force_north_sugar_list() : stepwise::rna
• force_output_name() : out
• force_south_sugar_list() : stepwise::rna
• force_syn_chi_res_list() : stepwise::rna
• force_user_defined_jumps() : stepwise::rna
• forcePolyAAfragments() : basic::options::OptionKeys::dwkulp , dwkulp
• forest_file() : basic::options::OptionKeys::constraints , constraints
• fr_temperature() : basic::options::OptionKeys::cm , cm
• fraction_by_recombination() : basic::options::OptionKeys::ms , ms
• frag1_end() : sewing
• frag1_start() : sewing
• frag2_end() : sewing
• frag2_start() : sewing
• frag3() : basic::options::OptionKeys::in::file , in::file
• frag3_weight() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• frag5() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• frag5_weight() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• frag9() : basic::options::OptionKeys::in::file , in::file
• frag9_weight() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• frag_1mer_insertion_weight() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• frag_file() : pepspec
• frag_files() : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::in::file , basic::options::OptionKeys::loops , dna::specificity , in::file , loops , SSrbrelax
• frag_prefix() : out::file
• frag_res_files() : smhybrid
• frag_sizes() : basic::options::OptionKeys::frags , basic::options::OptionKeys::in::file , basic::options::OptionKeys::loops , frags , in::file , loops , SSrbrelax
• frag_weight_aligned() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• fragA() : basic::options::OptionKeys::in::file , in::file
• fragA_size() : basic::options::OptionKeys::in::file , in::file
• fragB() : basic::options::OptionKeys::in::file , in::file
• fragment_contacts() : basic::options::OptionKeys::frags , frags
• fragment_cycles() : rigid
• fragments() : basic::options::OptionKeys::in::path , in::path
• fragpdb() : basic::options::OptionKeys::lh::fragpdb , lh::fragpdb
• frags() : basic::options::OptionKeys::frags , frags
• fragsample_patch() : basic::options::OptionKeys::fast_loops , fast_loops
• fragsample_score() : basic::options::OptionKeys::fast_loops , fast_loops
• fragsteal() : templates::fragsteal
• frame() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• frame_rate() : basic::options::OptionKeys::boinc , boinc
• free() : basic::options::OptionKeys::optE , optE
• free_relax() : remodel
• free_side_chain_bonus() : score
• free_sugar_bonus() : score
• from_degrees() : numeric::conversions
• from_radians() : numeric::conversions
• from_scratch_frequency() : stepwise::monte_carlo
• from_string() : utility
• Fsol() : patterson
• full_model() : basic::options::OptionKeys::full_model , full_model
• full_name() : basic::database
• fullatom() : basic::options::OptionKeys::in::file , in::file , out::file
• fullatom_sfx() : basic::options::OptionKeys::fldsgn , fldsgn , ufv
• fullatom_sfx_patch() : basic::options::OptionKeys::fldsgn , fldsgn , ufv
• fullscreen() : basic::options::OptionKeys::boinc , boinc
• fxnal_group() : basic::options::OptionKeys::hotspot , hotspot