- f -

• FA_STANDARD() : core::chemical
• FA_STANDARD_DEFAULT() : core::scoring
• FA_STANDARD_MULTIPOLE() : core::scoring
• FA_STANDARD_SOFT() : core::scoring
• facet_containing_position() : protocols::forge::methods
• factorsLTE19() : core::scoring::electron_density , core::scoring::fiber_diffraction
• factorsLTE5() : core::scoring::electron_density , core::scoring::fiber_diffraction
• fade_energy() : core::scoring::hbonds
• fake_hit() : protocols::match
• fall_back() : protocols::noesy_assign
• fast_ccd_close_loops() : protocols::loops::loop_mover::perturb
• fast_clash_check() : protocols::forge::remodel , protocols::pose_metric_calculators
• fast_forward_to_next_residue_pair() : protocols::stepwise::screener
• fast_rmsd() : protocols::cluster::calibur
• fastexp() : core::scoring
• fastlog2() : core::scoring
• fastpow() : core::scoring
• fastpow2() : core::scoring
• favor_nonnative_residue_tracer() : protocols::protein_interface_design::movers
• FBnl_R() : core::scoring::fiber_diffraction
• FE() : protocols::sic_dock::scores
• figure_out_base_pair_orientation() : core::pose::rna
• figure_out_base_pair_partner() : protocols::rna::denovo
• figure_out_chain_numbers_from_full_model_info() : core::pose::full_model_info
• figure_out_chain_numbers_from_full_model_info_const() : core::pose::full_model_info
• figure_out_conventional_chains_from_full_model_info() : core::pose::full_model_info
• figure_out_conventional_segids_from_full_model_info() : core::pose::full_model_info
• figure_out_dock_domain_map() : core::import_pose
• figure_out_dock_domain_map_from_full_model_info_const() : core::pose::full_model_info
• figure_out_fixed_domain_map() : core::import_pose
• figure_out_motif_mode() : core::import_pose
• figure_out_moving_chain_break_res() : protocols::stepwise::modeler
• figure_out_moving_chain_breaks() : protocols::stepwise::modeler
• figure_out_moving_cutpoints_closed() : protocols::stepwise::modeler
• figure_out_moving_cutpoints_closed_from_moving_res() : protocols::stepwise::modeler
• figure_out_moving_partition_res() : protocols::stepwise::modeler , protocols::toolbox::rigid_body
• figure_out_moving_partition_res_for_jump() : protocols::stepwise::modeler
• figure_out_moving_partition_res_for_suite() : protocols::stepwise::modeler
• figure_out_moving_rna_chain_breaks() : protocols::stepwise::modeler::rna
• figure_out_number_base_contacts() : core::pose::rna
• figure_out_pose_domain_map() : core::pose::full_model_info
• figure_out_pose_domain_map_const() : core::pose::full_model_info
• figure_out_protein_modeling_info() : protocols::stepwise::modeler::protein
• figure_out_reasonable_rna_fold_tree() : core::pose::rna
• figure_out_rebuild_bulge_mode() : protocols::stepwise::modeler::working_parameters
• figure_out_reference_res_for_jump() : protocols::toolbox::rigid_body
• figure_out_reference_res_for_suite() : protocols::stepwise::modeler
• figure_out_repackable_residues() : core::pack
• figure_out_residue_numbers_from_line() : core::io::silent
• figure_out_rna_chains() : core::pose::rna
• figure_out_root_and_moving_partition_res() : protocols::stepwise::modeler
• figure_out_root_partition_res() : protocols::stepwise::modeler
• figure_out_sample_both_sugar_base_rotamer() : protocols::stepwise::modeler::working_parameters
• figure_out_sample_res() : core::import_pose
• figure_out_secstruct() : core::fragment::rna , core::pose::rna
• figure_out_stepwise_movemap() : protocols::stepwise::modeler::movemap
• figure_out_working_interface_res() : protocols::stepwise::modeler::packer
• figure_out_working_res() : core::import_pose
• file_full_path() : protocols::toolbox
• file_is_atom_tree_diff() : core::import_pose::atom_tree_diffs
• filename() : protocols::abinitio
• filenames_from_list_file() : core::import_pose::pose_stream
• filetype() : protocols::cluster::calibur
• fill_A_line() : protocols::scoring::methods::pcs , protocols::scoring::methods::pcsTs1 , protocols::scoring::methods::pcsTs2 , protocols::scoring::methods::pcsTs3 , protocols::scoring::methods::pcsTs4
• fill_A_line_fast() : protocols::scoring::methods::pcs2
• fill_A_line_slow() : protocols::scoring::methods::pcs2
• fill_atom_derivs_for_acceptor() : core::scoring::geometric_solvation
• fill_atom_derivs_for_donor() : core::scoring::geometric_solvation
• fill_bb_pos() : core::scoring
• fill_CA_coords() : protocols::toolbox
• fill_chi_rotamers_with_center_and_stddev() : core::pack::rotamer_set
• fill_data() : protocols::recces
• fill_downstream_children_res_and_tips() : core::conformation::carbohydrates , core::pose::carbohydrates
• fill_gaps_and_remove_isolated_res() : protocols::rna::movers
• fill_grid_with_backbone_heavyatom_spheres() : protocols::match
• fill_grid_with_residue_heavyatom_spheres() : protocols::match
• fill_grid_with_residue_spheres() : protocols::match
• fill_hbond_bb_pair_score_dssp() : core::scoring::dssp
• fill_hbond_set() : core::scoring::hbonds
• fill_hbond_set_by_AHdist_threshold() : core::scoring::hbonds
• fill_ideal_xyz_from_icoor() : core::chemical
• fill_in_chain_terminii() : core::select::util
• fill_in_default_jump_atoms() : core::pose::rna
• fill_in_filelines() : protocols::relax
• fill_in_gaps() : protocols::frags
• fill_intra_res_hbond_set() : core::scoring::hbonds
• fill_neighbor_residues() : core::select
• fill_non_loop_cst_set() : protocols::forge::methods
• fill_orientation_info() : protocols::denovo_design::architects
• fill_plane_hash() : protocols::sic_dock
• fill_rmsd_coordinates() : core::scoring
• fill_score_range() : core::scoring
• fill_tags_() : protocols::jumping
• fill_template_frames_from_pdb() : core::fragment
• fill_tenA_neighbor_residues() : core::select
• fill_vdw_cached_rep_screen_info_from_command_line() : protocols::scoring
• fill_vdw_cached_rep_screen_info_from_options() : protocols::scoring
• fill_xform_score_from_file() : core::scoring::motif
• filter_acceptor_ligands() : protocols::magnesium
• filter_chem_shift_data_list() : core::scoring::rna::chemical_shift
• filter_for_proximity() : protocols::stepwise::monte_carlo::mover
• filter_loop_neighbors_by_distance() : protocols::loops
• filter_motifs() : core::scoring::motif
• filter_neighbors_by_distance() : core::select
• filter_spinlabel_ensemble_by_packerenergy() : protocols::nmr
• filter_torsions_by_iname() : core::scoring::dna
• filter_water_ligands() : protocols::magnesium
• filtered_num_vertices() : core::chemical
• final_design_min() : protocols::ncbb
• finalize_stub_set() : protocols::protein_interface_design::movers
• finalize_stub_sets() : protocols::protein_interface_design::movers
• find_attach_pt() : protocols::ligand_docking
• find_basepairs() : core::scoring::dna , protocols::dna
• find_best_match() : core::chemical
• find_bond_torsion_with_nearest_orientation() : core::conformation
• find_bonds_in_rings() : core::chemical
• find_bound_waters_that_are_daughters_in_fold_tree() : protocols::magnesium
• find_carbohydrate_order() : core::io
• find_carbohydrate_subbranch_order() : core::io
• find_chi_bonds() : core::chemical
• find_clashing_shell() : core::pack::task::residue_selector
• find_clashing_shells() : core::pack::task::residue_selector
• find_closest() : core::membrane
• find_closest_atom() : protocols::metal_interface
• Find_Closest_Intersect_SQ() : protocols::pockets
• find_common_intersection_atoms() : core::scoring::power_diagram
• find_connecting_jump() : protocols::forge::methods
• find_cutpoint() : protocols::forge::methods
• find_cutpoint_from_secondary_structure() : protocols::fold_from_loops::utils
• find_cutpoint_variants() : core::scoring::methods
• find_disulfide_partner() : protocols::abinitio::abscript
• find_disulfs_in_range() : protocols::splice
• find_downstream_connection_res() : protocols::stepwise::modeler
• find_existing_residues() : protocols::evaluation
• find_farthest() : core::membrane
• find_filter_or_die() : protocols::moves
• find_first_root_residue() : protocols::stepwise::modeler
• find_glycan_sequence_file() : core::chemical::carbohydrates
• find_hb_paths() : core::scoring::hbonds
• find_HBondResStruct() : protocols::hbnet
• find_hbonds_in_residue_pair() : core::pack::hbonds
• find_helices_over_length() : protocols::aa_composition
• find_implied_cut() : protocols::environment
• find_interface_pointing_residues_from_neighbs() : core::select::util
• find_intersections() : core::scoring::power_diagram
• find_jump_number_at_suite() : protocols::stepwise::modeler
• find_jump_partners_within_CB_cutoff() : core::select::util
• find_jump_rec() : protocols::denovo_design
• find_ligands() : protocols::flxbb
• find_likely_first_chain_ending() : protocols::recces::scratch
• find_lowest_constraint_energy_residue() : protocols::protein_interface_design
• find_max_r() : core::scoring::fiber_diffraction
• find_metalbinding_atoms() : core::util
• find_metalbinding_atoms_for_complex() : core::util
• find_metalbinding_atoms_helper() : core::util
• find_min_xyz() : core::scoring::fiber_diffraction
• find_mover() : protocols::environment
• find_mover_or_die() : protocols::moves
• find_nbr_dist() : core::chemical
• find_nearby_res() : protocols::rna::movers
• find_nearest_disulfide() : protocols::rosetta_scripts
• find_nearest_res() : protocols::rosetta_scripts
• find_nearest_residue() : protocols::protein_interface_design , protocols::seeded_abinitio
• find_nearest_residue_to_coord() : protocols::protein_interface_design::movers
• find_neighbor() : core::pose::carbohydrates
• find_neighbors() : core::conformation
• find_neighbors_3dgrid() : core::conformation
• find_neighbors_3dgrid_restricted() : core::conformation
• find_neighbors_naive() : core::conformation
• find_neighbors_naive_restricted() : core::conformation
• find_neighbors_naive_surface() : core::conformation
• find_neighbors_octree() : core::conformation
• find_neighbors_octree_restricted() : core::conformation
• find_neighbors_restricted() : core::conformation
• find_neighbors_stripe() : core::conformation
• find_neighbors_within_CB_cutoff() : core::select::util
• find_new_symmetric_jump_residues() : core::pose::symmetry
• find_next_vertex_with_smallest_dist() : core::scoring::power_diagram
• find_non_protein_chunks() : protocols::loops
• find_num_scattering_atoms() : core::scoring::fiber_diffraction
• find_orientations_and_lengths() : protocols::denovo_design::components
• find_pairing() : protocols::fldsgn::filters
• find_pairing_idx() : protocols::fldsgn::filters
• find_peptide_attach_pt() : protocols::ligand_docking
• find_pitch() : core::scoring::fiber_diffraction
• find_pose_in_vector() : protocols::recon_design
• find_regions_with_minimum_size() : protocols::nonlocal
• find_relevant_connections() : core::scoring::methods
• find_relevant_connections_onersd() : core::scoring::methods
• find_res_unsat_polars() : protocols::pose_metric_calculators
• find_residue_max_radii() : core::pack
• find_residues_on_chain1_inside_interface() : protocols::splice
• find_root_without_virtual_ribose() : protocols::stepwise::modeler
• find_sampling_cuts() : protocols::abinitio
• find_satisfying_interactions_with_background() : core::pack::hbonds
• find_seqpos_of_saccharides_child_residue_at() : core::conformation::carbohydrates
• find_seqpos_of_saccharides_mainchain_child() : core::conformation::carbohydrates
• find_seqpos_of_saccharides_parent_residue() : core::conformation::carbohydrates
• find_sheet() : protocols::features::strand_assembly
• find_stub_transform() : core::kinematics
• find_symmetric_basejump_anchor() : core::pose::symmetry
• find_template() : protocols::tcr
• find_template_from_multiple_input_db() : protocols::tcr
• find_unconnected_residues() : protocols::ligand_docking
• find_uncovered_residues() : protocols::hybridization
• find_weights_file() : core::scoring
• FindBoundaries() : core::fragment
• findLoopFromDensity() : protocols::electron_density
• findSampling() : core::scoring::electron_density , core::scoring::fiber_diffraction
• findSampling5() : core::scoring::electron_density , core::scoring::fiber_diffraction
• first_base_atom() : core::chemical::rna
• first_base_atom_index() : core::chemical::rna
• first_protein_residue() : protocols::constraint_generator
• fit_centered_coords() : protocols::toolbox
• fit_layer_lines_with_splines() : core::scoring::fiber_diffraction
• fix_bfactorsH() : core::scoring::cryst
• fix_bfactorsMissing() : core::scoring::cryst
• fix_chain_break_residue() : protocols::splice
• fix_chainbreak_patch() : protocols::abinitio
• fix_glycan_order() : core::io
• fix_internal_coords_of_siblings() : protocols::abinitio::abscript , protocols::topology_broker
• fix_mainchain_connect() : protocols::abinitio::abscript , protocols::topology_broker
• fix_pdbinfo_damaged_by_insertion() : core::pose
• fix_protein_jump_atom() : protocols::stepwise::modeler
• fix_sugar_coords() : core::pose::rna
• fix_tag_suffix() : protocols::toolbox
• fix_up_jump_atoms() : protocols::stepwise::modeler
• fix_up_jump_atoms_and_residue_type_variants() : protocols::stepwise::modeler
• fix_up_residue_type_variants() : core::pose
• fix_up_residue_type_variants_at_floating_base() : core::pose
• fix_up_residue_type_variants_at_strand_beginning() : core::pose
• fix_up_residue_type_variants_at_strand_end() : core::pose
• fix_water_jump() : protocols::magnesium
• fix_with_coord_cst() : protocols::loops
• fix_worst_bad_ramas() : protocols::relax
• FIXED_DOMAIN() : core::pose::copydofs
• fixH() : protocols::relax
• fixup_magnesiums() : protocols::magnesium
• fixup_patches() : core::chemical
• flatten_center() : ndarray
• flatten_list() : core::fragment
• flip_atom_xyz() : core::io::pose_from_sfr
• flood_fill3D() : protocols::sic_dock
• FlxbbDesign_main() : protocols::flxbb
• fold_tree_entry_point() : core::conformation::symmetry
• fold_tree_from_loops() : protocols::forge::methods , protocols::loops
• fold_tree_from_pose() : protocols::forge::methods
• foreach_movemap_tag() : protocols::rosetta_scripts
• form_disulfide() : core::conformation
• form_disulfide_helper() : core::conformation
• formatted_icoord_tree() : core::chemical
• frac_atoms_within() : protocols::ligand_docking
• fragbias_tr() : protocols::hybridization
• fragext_subelement_ct_name() : protocols::loop_grower
• fragment_set_slice() : core::fragment
• frdc() : core::scoring
• frdcDa() : core::scoring
• frdcDaR() : core::scoring
• frdcR() : core::scoring
• freeze_repack_positions() : core::pack::task::residue_selector
• freeze_sugar_torsions() : protocols::stepwise::modeler::rna
• freeze_waters() : protocols::stepwise::modeler
• from_json() : protocols::indexed_structure_store , protocols::indexed_structure_store::search , protocols::pdbinfo_manipulations
• ft_nfft() : core::scoring::fiber_diffraction
• ftoa() : protocols::sparta
• full_hit() : protocols::match
• full_length_rmsd_over_residue_list() : protocols::stepwise::legacy::modeler::rna
• full_model_info_defined() : core::pose::full_model_info
• full_model_inputter_xsd_type_definition_w_attributes() : protocols::jd3::full_model_inputters
• full_model_parameter_type_from_string() : core::pose::full_model_info
• full_model_size() : core::pose::full_model_info
• full_to_sub() : core::pose::full_model_info