- f -

facet_containing_position() : protocols::forge::methods
fake_hit() : protocols::match
fall_back() : protocols::noesy_assign
fast2DRotAlignPose() : protocols::electron_density
fast_ccd_close_loops() : protocols::loops::loop_mover::perturb
fast_clash_check() : protocols::forge::remodel , protocols::toolbox::pose_metric_calculators
fast_forward_to_next_residue_pair() : protocols::stepwise::screener
fastTransAlignPose() : protocols::electron_density
favor_nonnative_residue_tracer() : protocols::protein_interface_design::movers
figure_out_base_pair_partner() : protocols::farna
figure_out_dock_domain_map() : protocols::stepwise::setup
figure_out_fixed_domain_map() : protocols::stepwise::setup
figure_out_motif_mode() : protocols::stepwise::setup
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_protein_modeling_info() : protocols::stepwise::modeler::protein
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_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() : protocols::stepwise::setup
figure_out_secstruct() : protocols::farna
figure_out_stepwise_movemap() : protocols::stepwise::modeler::movemap
figure_out_working_interface_res() : protocols::stepwise::modeler::packer
figure_out_working_res() : protocols::stepwise::setup
file_exists() : protocols::stepwise::modeler::rna
file_full_path() : protocols::toolbox
filename() : protocols::abinitio
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_CA_coords() : protocols::toolbox
fill_full_model_info_from_command_line() : protocols::stepwise::setup
fill_grid_with_backbone_heavyatom_spheres() : protocols::match
fill_grid_with_residue_heavyatom_spheres() : protocols::match
fill_grid_with_residue_spheres() : protocols::match
fill_in_gaps() : protocols::frags
fill_non_loop_cst_set() : protocols::forge::methods
fill_plane_hash() : protocols::sic_dock
fill_tags_() : protocols::jumping
filter_for_proximity() : protocols::stepwise::monte_carlo::mover
filter_loop_neighbors_by_distance() : protocols::loops
filter_out_bulge_res() : protocols::stepwise::monte_carlo
FinalMinimizer_tracer() : protocols::ligand_docking
find_attach_pt() : protocols::ligand_docking
find_basepairs() : protocols::dna
find_best_anchor() : protocols::electron_density
find_closest_atom() : protocols::metal_interface
Find_Closest_Intersect_SQ() : protocols::pockets
find_connecting_jump() : protocols::forge::methods
find_cutpoint() : protocols::forge::methods
find_disulfide_partner() : protocols::abinitio::abscript
find_downstream_connection_res() : protocols::stepwise::modeler
find_existing_residues() : protocols::evaluation
find_filter_or_die() : protocols::moves
find_first_root_residue() : protocols::stepwise::modeler
find_implied_cut() : protocols::environment
find_jump_number_at_suite() : protocols::stepwise::modeler
find_ligands() : protocols::flxbb
find_lowest_constraint_energy_residue() : protocols::protein_interface_design
find_mover() : protocols::environment
find_mover_or_die() : protocols::moves
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_non_protein_chunks() : protocols::loops
find_peptide_attach_pt() : protocols::ligand_docking
find_regions_with_minimum_size() : protocols::nonlocal
find_root_without_virtual_ribose() : protocols::stepwise::modeler
find_sampling_cuts() : protocols::abinitio
find_sheet() : protocols::features::strand_assembly
find_unconnected_residues() : protocols::ligand_docking
find_uncovered_residues() : protocols::hybridization
findLoopFromDensity() : protocols::electron_density
findLoopFromPatterson() : protocols::electron_density
fit_centered_coords() : protocols::toolbox
fix_chainbreak_patch() : protocols::abinitio
fix_internal_coords_of_siblings() : protocols::abinitio::abscript , protocols::topology_broker
fix_mainchain_connect() : protocols::abinitio::abscript , protocols::topology_broker
fix_protein_jump_atom() : protocols::stepwise::modeler
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() : protocols::stepwise::modeler
fix_up_residue_type_variants_at_floating_base() : protocols::stepwise::modeler
fix_up_residue_type_variants_at_strand_beginning() : protocols::stepwise::modeler
fix_up_residue_type_variants_at_strand_end() : protocols::stepwise::modeler
fix_with_coord_cst() : protocols::loops
fix_worst_bad_ramas() : protocols::relax
FIXED_DOMAIN() : protocols::toolbox
fixH() : protocols::forge::methods
flood_fill3D() : protocols::sic_dock
FlxbbDesign_main() : protocols::flxbb
fold_tree_from_loops() : protocols::forge::methods , protocols::loops
fold_tree_from_pose() : protocols::forge::methods
foreach_movemap_tag() : protocols::rosetta_scripts
frac_atoms_within() : protocols::ligand_docking
freeze_sugar_torsions() : protocols::stepwise::modeler::rna
ftoa() : protocols::sparta
full_hit() : protocols::match
full_length_rmsd_over_residue_list() : protocols::stepwise::legacy::modeler::rna