- f -

fa_closure_protocol : basic::options::OptionKeys::loops
fa_custom_pair_distance_file : basic::options::OptionKeys::score
fa_dun_thresh : basic::options::OptionKeys::willmatch
fa_elec_co_only : basic::options::OptionKeys::corrections::score
fa_Hatr : basic::options::OptionKeys::score
fa_input : basic::options::OptionKeys::loops
fa_max_dis : basic::options::OptionKeys::score
Fa_Membed_update : basic::options::OptionKeys::membrane
fa_refine : basic::options::OptionKeys::smhybrid
fa_relax_moves : basic::options::OptionKeys::remodel::staged_sampling
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
fast : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::loops , basic::options::OptionKeys::relax
fast_loops : basic::options::OptionKeys::fast_loops
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
fastdens_params : basic::options::OptionKeys::edensity
fastdens_wt : basic::options::OptionKeys::edensity
fastrelax : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::loops
fav_nat_bonus : basic::options::OptionKeys::matdes::design
favor_native_res : basic::options::OptionKeys::enzdes
file : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
file_list_tracer : basic::resource_manager::locator
file_prefix : basic::options::OptionKeys::motifs
filter : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::smhybrid
filter_by_phipsi : basic::options::OptionKeys::lh
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_native_big_bins : basic::options::OptionKeys::stepwise::protein
filter_output_filename : basic::options::OptionKeys::stepwise::rna
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_upstream_downstream_collisions : basic::options::OptionKeys::match
filter_user_alignment_res : basic::options::OptionKeys::stepwise::rna
filters : basic::options::OptionKeys::abrelax , basic::options::OptionKeys::AnchoredDesign::filters , basic::options::OptionKeys::filters
final_channel : basic
final_clean_fastrelax : basic::options::OptionKeys::loops
final_clean_relax : basic::options::OptionKeys::abinitio
final_repack_without_ligand : basic::options::OptionKeys::enzdes
final_score_filter : basic::options::OptionKeys::loops
find_disulf : basic::options::OptionKeys::run
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
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::stepwise , basic::options::OptionKeys::willmatch
fixed_res_files : basic::options::OptionKeys::smhybrid
fixR : basic::options::OptionKeys::rdc
flank_residue_min : basic::options::OptionKeys::antibody
fldsgn : basic::options::OptionKeys::fldsgn
flex_sugar : basic::options::OptionKeys::motifs
flexbb_outstructs : basic::options::OptionKeys::enzdes
flexbb_protocol : basic::options::OptionKeys::enzdes
flexible_bb_docking : basic::options::OptionKeys::docking
flexible_bb_docking_interface_dist : basic::options::OptionKeys::docking
flexible_chain : basic::options::OptionKeys::FloppyTail
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
floating_scs_rep : basic::options::OptionKeys::smhybrid
FloppyTail : basic::options::OptionKeys::FloppyTail
flush : basic::options::OptionKeys::dna::design
flxbb : basic::options::OptionKeys::flxbb , basic::options::OptionKeys::smhybrid
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
forbid_residues : basic::options::OptionKeys::willmatch
force_apix : basic::options::OptionKeys::edensity
force_centroid_interaction : basic::options::OptionKeys::stepwise::rna
force_cutting_N : basic::options::OptionKeys::remodel::RemodelLoopMover
force_linear_fold_tree : basic::options::OptionKeys::FloppyTail
force_minimize : basic::options::OptionKeys::fold_cst
force_native_topology : basic::options::OptionKeys::templates
force_nonideal_structure : basic::options::OptionKeys::out::file
force_north_sugar_list : basic::options::OptionKeys::stepwise::rna
force_output_name : basic::options::OptionKeys::out
force_south_sugar_list : basic::options::OptionKeys::stepwise::rna
force_syn_chi_res_list : basic::options::OptionKeys::stepwise::rna
force_user_defined_jumps : basic::options::OptionKeys::stepwise::rna
forcePolyAAfragments : basic::options::OptionKeys::dwkulp
forest_file : basic::options::OptionKeys::constraints
fr_temperature : basic::options::OptionKeys::cm
fraction_by_recombination : basic::options::OptionKeys::ms
frag1_end : basic::options::OptionKeys::sewing
frag1_start : basic::options::OptionKeys::sewing
frag2_end : basic::options::OptionKeys::sewing
frag2_start : basic::options::OptionKeys::sewing
frag3 : basic::options::OptionKeys::in::file
frag3_weight : basic::options::OptionKeys::flexPepDocking
frag5 : basic::options::OptionKeys::flexPepDocking
frag5_weight : basic::options::OptionKeys::flexPepDocking
frag9 : basic::options::OptionKeys::in::file
frag9_weight : basic::options::OptionKeys::flexPepDocking
frag_1mer_insertion_weight : basic::options::OptionKeys::cm::hybridize
frag_file : basic::options::OptionKeys::pepspec
frag_files : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::in::file , basic::options::OptionKeys::loops , basic::options::OptionKeys::SSrbrelax
frag_prefix : basic::options::OptionKeys::out::file
frag_res_files : basic::options::OptionKeys::smhybrid
frag_sizes : basic::options::OptionKeys::frags , basic::options::OptionKeys::in::file , basic::options::OptionKeys::loops , basic::options::OptionKeys::SSrbrelax
frag_weight_aligned : basic::options::OptionKeys::cm::hybridize
fragA : basic::options::OptionKeys::in::file
fragA_size : basic::options::OptionKeys::in::file
fragB : basic::options::OptionKeys::in::file
fragment_contacts : basic::options::OptionKeys::frags
fragment_cycles : basic::options::OptionKeys::rigid
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
fragsteal : basic::options::OptionKeys::templates::fragsteal
frame_rate : basic::options::OptionKeys::boinc
free : basic::options::OptionKeys::optE
free_relax : basic::options::OptionKeys::remodel
free_side_chain_bonus : basic::options::OptionKeys::score
free_sugar_bonus : basic::options::OptionKeys::score
from_scratch_frequency : basic::options::OptionKeys::stepwise::monte_carlo
Fsol : basic::options::OptionKeys::patterson
full_model : basic::options::OptionKeys::full_model
fullatom : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
fullatom_sfx : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::ufv
fullatom_sfx_patch : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::ufv
fullscreen : basic::options::OptionKeys::boinc
fxnal_group : basic::options::OptionKeys::hotspot