Here is a list of all namespace members with links to the namespace documentation for each member:

- f -

• fa_closure_protocol : basic::options::OptionKeys::loops , loops
• fa_custom_pair_distance_file : basic::options::OptionKeys::score , score
• fa_dun_thresh : basic::options::OptionKeys::willmatch , willmatch
• fa_elec_co_only : basic::options::OptionKeys::corrections::score , corrections::score
• fa_Hatr : basic::options::OptionKeys::score , score
• fa_input : basic::options::OptionKeys::loops , loops
• fa_max_dis : basic::options::OptionKeys::score , score
• Fa_Membed_update : basic::options::OptionKeys::membrane , membrane
• fa_refine : basic::options::OptionKeys::smhybrid , smhybrid
• fa_relax_moves : basic::options::OptionKeys::remodel::staged_sampling , 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 : basic::options::OptionKeys::score , score
• facts_adjbb_solv_scale : basic::options::OptionKeys::score , score
• facts_adjbs_elec_scale : basic::options::OptionKeys::score , score
• facts_adjbs_solv_scale : basic::options::OptionKeys::score , score
• facts_asp_patch : basic::options::OptionKeys::score , score
• facts_binding_affinity : basic::options::OptionKeys::score , score
• facts_charge_dir : basic::options::OptionKeys::score , score
• facts_default : basic::options::OptionKeys::corrections , corrections
• facts_die : basic::options::OptionKeys::score , score
• facts_dshift : basic::options::OptionKeys::score , score
• facts_eff_charge_dir : basic::options::OptionKeys::score , score
• facts_eq_type : basic::options::OptionKeys::score , score
• facts_GBpair_cut : basic::options::OptionKeys::score , score
• FACTS_GET_ALL_BORN_RADII : basic
• facts_intbb_elec_scale : basic::options::OptionKeys::score , score
• facts_intbb_solv_scale : basic::options::OptionKeys::score , score
• facts_intbs_elec_scale : basic::options::OptionKeys::score , score
• facts_intbs_solv_scale : basic::options::OptionKeys::score , score
• facts_intrascale_by_level : basic::options::OptionKeys::score , score
• facts_intsc_elec_scale : basic::options::OptionKeys::score , score
• facts_intsc_solv_scale : basic::options::OptionKeys::score , score
• facts_kappa : basic::options::OptionKeys::score , score
• facts_plane_aa : basic::options::OptionKeys::score , score
• facts_plane_to_self : basic::options::OptionKeys::score , score
• FACTS_ROTAMER_BACKGROUND_ENERGIES : basic
• FACTS_ROTAMER_PAIR_ENERGIES : basic
• facts_saltbridge_correction : basic::options::OptionKeys::score , score
• FACTS_SETUP_FOR_PACKING : basic
• fail_on_bad_hbond : basic::options::OptionKeys::in::file , in::file
• fail_unclosed() : abrelax , basic::options::OptionKeys::abrelax
• FallbackConfigurationCOP : basic::resource_manager
• FallbackConfigurationCreatorCOP : basic::resource_manager
• FallbackConfigurationCreatorOP : basic::resource_manager
• FallbackConfigurationOP : basic::resource_manager
• false_negative : numeric
• false_positive : numeric
• FARRAY_MANIPULATION : basic
• 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 , basic::options::OptionKeys::relax , 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 , basic::options::OptionKeys::out::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_list_tracer : basic::resource_manager::locator
• file_prefix : basic::options::OptionKeys::motifs , motifs
• file_size() : utility::file
• FileContentsMapCOP : utility::io
• FileContentsMapOP : utility::io
• FileListResourceLocatorCOP : basic::resource_manager::locator
• FileListResourceLocatorOP : basic::resource_manager::locator
• filename() : utility
• FileOption : basic::options
• FileOptionKey : basic::options
• FileStreamCOP : basic::resource_manager::locator
• FileStreamOP : basic::resource_manager::locator
• FileSystemResourceLocatorCOP : basic::resource_manager::locator
• FileSystemResourceLocatorOP : basic::resource_manager::locator
• FileVectorOption : basic::options
• FileVectorOptionKey : basic::options
• filter : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::smhybrid , 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 : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• filter_output_filename : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• filter_stage2_beginning : basic::options::OptionKeys::relax , relax
• filter_stage2_end : basic::options::OptionKeys::relax , relax
• filter_stage2_half : basic::options::OptionKeys::relax , relax
• filter_stage2_quarter : basic::options::OptionKeys::relax , 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 : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• filters() : abrelax , AnchoredDesign::filters , basic::options::OptionKeys::abrelax , basic::options::OptionKeys::AnchoredDesign::filters , basic::options::OptionKeys::filters , filters
• final_channel : basic
• 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
• FINALIZE : basic
• find_closest() : utility
• find_disulf : basic::options::OptionKeys::run , run
• find_first_non_zero() : utility::json_spirit
• find_nearest_value() : numeric
• find_neighbors : basic::options::OptionKeys::remodel::design , remodel::design
• find_neighbors_3dgrid : basic::options::OptionKeys::score , score
• find_neighbors_stripehash : basic::options::OptionKeys::score , score
• FIND_SUGAR_AND_SUITE_FRAGS_I : basic
• FIND_SUGAR_AND_SUITE_FRAGS_II : basic
• find_value() : utility::json_spirit
• findUU() : numeric::model_quality
• finer_sampling_at_chain_closure : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• fingerprint : basic::options::OptionKeys::fingerprint , fingerprint
• first_principal_component() : numeric
• fit_method : basic::options::OptionKeys::rdc , rdc
• fit_pddf_area : basic::options::OptionKeys::score::saxs , score::saxs
• fit_reference_energies_to_aa_profile_recovery : basic::options::OptionKeys::optE , optE
• fix : basic::options::OptionKeys::optE , optE
• fix_aligned_residues : basic::options::OptionKeys::templates , 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 : basic::options::OptionKeys::templates , templates
• fix_his_tautomer : basic::options::OptionKeys::packing , packing
• fix_jumps : basic::options::OptionKeys::jumps , jumps
• fix_margin : basic::options::OptionKeys::templates , templates
• fix_natsc : basic::options::OptionKeys::loops , loops
• fix_normAzz : basic::options::OptionKeys::rdc , rdc
• fix_omega : basic::options::OptionKeys::relax , 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 : basic::options::OptionKeys::rdc , rdc
• fixed : basic::options::OptionKeys::optE , optE
• fixed_membrane : basic::options::OptionKeys::membrane , membrane
• fixed_res : basic::options::OptionKeys::stepwise , basic::options::OptionKeys::willmatch , stepwise , willmatch
• fixed_res_files : basic::options::OptionKeys::smhybrid , smhybrid
• fixEigenvector() : numeric::model_quality
• fixR : basic::options::OptionKeys::rdc , 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 : basic::options::OptionKeys::packing , packing
• floating_base : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• floating_base_anchor_res : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• floating_scs_rep : basic::options::OptionKeys::smhybrid , smhybrid
• FloppyTail : basic::options::OptionKeys::FloppyTail , FloppyTail
• flush : basic::options::OptionKeys::dna::design , dna::design
• flxbb() : basic::options::OptionKeys::flxbb , basic::options::OptionKeys::smhybrid , 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 : basic::options::OptionKeys::willmatch , willmatch
• force_apix : basic::options::OptionKeys::edensity , edensity
• force_centroid_interaction : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• force_cutting_N : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• force_linear_fold_tree : basic::options::OptionKeys::FloppyTail , FloppyTail
• force_minimize : basic::options::OptionKeys::fold_cst , fold_cst
• force_native_topology : basic::options::OptionKeys::templates , templates
• force_nonideal_structure : basic::options::OptionKeys::out::file , out::file
• force_north_sugar_list : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• force_output_name : basic::options::OptionKeys::out , out
• force_south_sugar_list : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• force_syn_chi_res_list : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• force_user_defined_jumps : basic::options::OptionKeys::stepwise::rna , 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 : basic::options::OptionKeys::sewing , sewing
• frag1_start : basic::options::OptionKeys::sewing , sewing
• frag2_end : basic::options::OptionKeys::sewing , sewing
• frag2_start : basic::options::OptionKeys::sewing , 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 : basic::options::OptionKeys::pepspec , pepspec
• frag_files() : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::in::file , basic::options::OptionKeys::loops , basic::options::OptionKeys::SSrbrelax , dna::specificity , in::file , loops , SSrbrelax
• frag_prefix : basic::options::OptionKeys::out::file , out::file
• frag_res_files : basic::options::OptionKeys::smhybrid , smhybrid
• frag_sizes() : basic::options::OptionKeys::frags , basic::options::OptionKeys::in::file , basic::options::OptionKeys::loops , basic::options::OptionKeys::SSrbrelax , 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 : basic::options::OptionKeys::rigid , rigid
• FRAGMENT_MOVER : basic
• FRAGMENTPICKING : basic
• FRAGMENTPICKING_ATOMPAIR_SCORE : basic
• FRAGMENTPICKING_CANDIDATES_COLLECTING : basic
• FRAGMENTPICKING_CS_SCORE : basic
• FRAGMENTPICKING_DIHEDRALCONSTR_SCORE : basic
• FRAGMENTPICKING_PHIPSI_SCORE : basic
• FRAGMENTPICKING_PROFILE_CAHING : basic
• FRAGMENTPICKING_PROFILE_SCORE : basic
• FRAGMENTPICKING_READ_VALL : basic
• FRAGMENTPICKING_SECONDARY_SCORE : basic
• 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 : basic::options::OptionKeys::templates::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 : basic::options::OptionKeys::remodel , remodel
• free_side_chain_bonus : basic::options::OptionKeys::score , score
• free_sugar_bonus : basic::options::OptionKeys::score , score
• from_degrees() : numeric::conversions
• from_radians() : numeric::conversions
• from_scratch_frequency : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• from_string() : utility
• Fsol : basic::options::OptionKeys::patterson , patterson
• full_model : basic::options::OptionKeys::full_model , full_model
• full_name() : basic::database
• fullatom : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file , in::file , out::file
• fullatom_sfx() : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::ufv , fldsgn , ufv
• fullatom_sfx_patch : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::ufv , fldsgn , ufv
• fullscreen : basic::options::OptionKeys::boinc , boinc
• FUNC : basic
• FUNCTION : numeric::expression_parser
• FunctionTokenCOP : numeric::expression_parser
• FunctionTokenOP : numeric::expression_parser
• fxnal_group : basic::options::OptionKeys::hotspot , hotspot