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

- f -

• F : core::chemical::element
• fa_atr : core::scoring
• fa_atr_dummy : core::scoring
• fa_atr_ref : core::scoring
• fa_cust_pair_dist : core::scoring
• fa_custom_pair_dist_data : core::scoring
• fa_disulfide_energy : core::scoring::methods
• fa_dslf_respair_data : core::scoring
• fa_dun : core::scoring
• fa_dun_dev : core::scoring
• fa_dun_dev_ref : core::scoring
• fa_dun_ref : core::scoring
• fa_dun_rot : core::scoring
• fa_dun_rot_ref : core::scoring
• fa_dun_semi : core::scoring
• fa_dun_semi_ref : core::scoring
• fa_elec : core::scoring
• fa_elec_aro_all : core::scoring
• fa_elec_aro_aro : core::scoring
• fa_elec_bb_bb : core::scoring
• fa_elec_bb_sc : core::scoring
• fa_elec_ref : core::scoring
• fa_elec_rna_base_base : core::scoring
• fa_elec_rna_base_base_fast : core::scoring
• fa_elec_rna_phos_base : core::scoring
• fa_elec_rna_phos_base_fast : core::scoring
• fa_elec_rna_phos_phos : core::scoring
• fa_elec_rna_phos_phos_fast : core::scoring
• fa_elec_rna_phos_sugr : core::scoring
• fa_elec_rna_phos_sugr_fast : core::scoring
• fa_elec_rna_sugr_base : core::scoring
• fa_elec_rna_sugr_base_fast : core::scoring
• fa_elec_rna_sugr_sugr : core::scoring
• fa_elec_rna_sugr_sugr_fast : core::scoring
• fa_elec_sc_sc : core::scoring
• FA_ElecEnergyAroAllCreator_registrator : core::init
• FA_ElecEnergyAroAroCreator_registrator : core::init
• FA_ElecEnergyCOP : core::scoring::elec
• FA_ElecEnergyCreator_registrator : core::init
• FA_ElecEnergyOP : core::scoring::elec
• fa_grpelec : core::scoring
• FA_GrpElecEnergyCOP : core::scoring::elec
• FA_GrpElecEnergyCreator_registrator : core::init
• FA_GrpElecEnergyOP : core::scoring::elec
• fa_intra_atr : core::scoring
• fa_intra_atr_nonprotein : core::scoring
• fa_intra_atr_ref : core::scoring
• fa_intra_atr_xover4 : core::scoring
• fa_intra_elec : core::scoring
• fa_intra_rep : core::scoring
• fa_intra_rep_nonprotein : core::scoring
• fa_intra_rep_ref : core::scoring
• fa_intra_rep_xover4 : core::scoring
• fa_intra_RNA_base_phos_atr : core::scoring
• fa_intra_RNA_base_phos_rep : core::scoring
• fa_intra_RNA_base_phos_sol : core::scoring
• fa_intra_sol : core::scoring
• fa_intra_sol_nonprotein : core::scoring
• fa_intra_sol_ref : core::scoring
• fa_intra_sol_xover4 : core::scoring
• fa_mbenv : core::scoring
• Fa_MbenvEnergyCreator_registrator : core::init
• Fa_MbenvEnergyOP : core::scoring::methods
• fa_mbsolv : core::scoring
• Fa_MbsolvEnergyCreator_registrator : core::init
• fa_pair : core::scoring
• fa_pair_aro_aro : core::scoring
• fa_pair_aro_pol : core::scoring
• fa_pair_pol_pol : core::scoring
• fa_rep : core::scoring
• fa_rep_dummy : core::scoring
• fa_rep_ref : core::scoring
• FA_REP_SCORE : core::conformation::symmetry
• fa_sasa : core::scoring
• fa_sol : core::scoring
• fa_sol_dummy : core::scoring
• fa_sol_ref : core::scoring
• fa_stack : core::scoring
• fa_stack_aro : core::scoring
• fa_stack_ext : core::scoring
• fa_stack_lower : core::scoring
• fa_stack_lr : core::scoring
• FA_STACK_NBLIST : core::scoring::EnergiesCacheableDataType
• fa_stack_pair_nblist : core::scoring
• fa_stack_rna_protein : core::scoring
• fa_stack_rna_protein_aro : core::scoring
• fa_stack_sol : core::scoring
• fa_stack_upper : core::scoring
• FA_STANDARD : core::chemical
• FA_STANDARD_DEFAULT : core::scoring
• FA_STANDARD_MULTIPOLE : core::scoring
• FA_STANDARD_SOFT : core::scoring
• fa_vdw_tinker : core::scoring
• fa_water_to_bilayer : core::scoring
• FabConstraintCOP : core::scoring::constraints
• FabConstraintCreator_registrator : core::init
• FabConstraintOP : core::scoring::constraints
• facet_containing_position() : protocols::forge::methods
• factorsLTE19() : core::scoring::electron_density , core::scoring::fiber_diffraction
• factorsLTE5() : core::scoring::electron_density , core::scoring::fiber_diffraction
• facts_elec : core::scoring
• FACTS_ROTAMER_SET_INFO : core::conformation::RotamerSetCacheableDataType
• facts_sasa : core::scoring
• facts_solv : core::scoring
• FACTSEnergyCreator_registrator : core::init
• FACTSPoseInfoOP : core::scoring
• FACTSPotentialOP : core::scoring
• FACTSResidueInfoOP : core::scoring
• FACTSRotamerSetInfoOP : core::scoring
• FACTSRsdTypeInfoCOP : core::scoring
• FACTSRsdTypeInfoOP : core::scoring
• fade_energy() : core::scoring::hbonds
• FadeFuncCOP : core::scoring::func
• FadeFuncOP : core::scoring::func
• FadeIntervalCOP : core::scoring::hbonds
• FadeIntervalOP : core::scoring::hbonds
• FaDockingSlideIntoContactCOP : protocols::docking
• FaDockingSlideIntoContactOP : protocols::docking
• FAElecContextDataCOP : core::scoring::elec
• FAElecContextDataOP : core::scoring::elec
• FAIL : protocols::moves
• FAIL_BAD_INPUT : protocols::moves
• FAIL_DO_NOT_RETRY : protocols::moves
• FAIL_RETRY : protocols::moves
• FAILED : protocols::monte_carlo
• Failure : protocols::loops::loop_mover
• fake_hit() : protocols::match
• fall_back() : protocols::noesy_assign
• FalseFilterCOP : protocols::filters
• FalseFilterOP : protocols::filters
• FalseResidueSelectorCOP : core::select::residue_selector
• FalseResidueSelectorOP : core::select::residue_selector
• FaMPEnv : core::scoring
• FaMPEnvEnergyCOP : core::scoring::membrane
• FaMPEnvEnergyCreator_registrator : core::init
• FaMPEnvEnergyOP : core::scoring::membrane
• FaMPEnvSmooth : core::scoring
• FaMPEnvSmoothEnergyCOP : core::scoring::membrane
• FaMPEnvSMoothEnergyCreator_registrator : core::init
• FaMPEnvSmoothEnergyOP : core::scoring::membrane
• FaMPSolv : core::scoring
• FaMPSolvEnergyCOP : core::scoring::membrane
• FaMPSolvEnergyCreator_registrator : core::init
• FaMPSolvEnergyOP : core::scoring::membrane
• FArray1D_Energy : core::scoring
• FArray1D_Length : core::scoring
• FArray1D_Probability : core::scoring
• FArray1D_Real : core::scoring::dna
• FArray1D_TableEnergy : core::scoring
• FArray1D_TableProbability : core::scoring
• FArray1D_Weight : core::scoring
• FArray2D_double : protocols::canonical_sampling::mc_convergence_checks
• FArray2D_Energy : core::scoring
• FArray2D_Length : core::scoring
• FArray2D_Probability : core::scoring
• FArray2D_TableEnergy : core::scoring
• FArray2D_TableProbability : core::scoring
• FArray2D_Weight : core::scoring
• FArray3D_Energy : core::scoring
• FArray3D_Length : core::scoring
• FArray3D_Probability : core::scoring
• FArray3D_TableEnergy : core::scoring
• FArray3D_TableProbability : core::scoring
• FArray3D_Weight : core::scoring
• FArray4D_Energy : core::scoring
• FArray4D_Length : core::scoring
• FArray4D_Probability : core::scoring
• FArray4D_TableEnergy : core::scoring
• FArray4D_TableProbability : core::scoring
• FArray4D_Weight : core::scoring
• FArray5D_Energy : core::scoring
• FArray5D_Length : core::scoring
• FArray5D_Probability : core::scoring
• FArray5D_TableEnergy : core::scoring
• FArray5D_TableProbability : core::scoring
• FArray5D_Weight : core::scoring
• FAScatterOP : core::scoring::fiber_diffraction
• FASelectSlidingWindowLoopClosureCOP : protocols::loops::loop_closure::ccd
• FASelectSlidingWindowLoopClosureOP : protocols::loops::loop_closure::ccd
• fast_ccd_close_loops() : protocols::loops::loop_mover::perturb
• fast_clash_check() : protocols::forge::remodel , protocols::pose_metric_calculators
• FAST_FORWARD_TO_NEXT_RESIDUE_ALTERNATIVE : protocols::stepwise::screener
• fast_forward_to_next_residue_pair() : protocols::stepwise::screener
• FAST_FORWARD_TO_NEXT_RIGID_BODY : protocols::stepwise::screener
• fast_one_shell_cut : core::scoring::atomic_depth
• fast_one_shell_highb : core::scoring::atomic_depth
• fast_one_shell_lowb : core::scoring::atomic_depth
• fast_rmsd() : protocols::cluster::calibur
• FastDensEnergyCreator_registrator : core::init
• FastDesignAP : protocols::denovo_design::movers
• FastDesignCAP : protocols::denovo_design::movers
• FastDesignCOP : protocols::denovo_design::movers
• FastDesignOP : protocols::denovo_design::movers
• FASTERAnnealerCOP : core::pack::annealer
• FASTERAnnealerOP : core::pack::annealer
• FASTERInteractionGraphCOP : core::pack::interaction_graph
• FASTERInteractionGraphOP : core::pack::interaction_graph
• fastexp() : core::scoring
• FastForwardToNextResidueAlternativeCOP : protocols::stepwise::screener
• FastForwardToNextResidueAlternativeOP : protocols::stepwise::screener
• FastForwardToNextRigidBodyCOP : protocols::stepwise::screener
• FastForwardToNextRigidBodyOP : protocols::stepwise::screener
• FastGapMoverCOP : protocols::loophash
• FastGapMoverOP : protocols::loophash
• fastlog2() : core::scoring
• fastpow() : core::scoring
• fastpow2() : core::scoring
• FastRelaxAP : protocols::relax
• FastRelaxCAP : protocols::relax
• FastRelaxCOP : protocols::relax
• FastRelaxOP : protocols::relax
• fastsaxs : core::scoring
• FastSAXSEnergyCreator_registrator : core::init
• FaSymDockingSlideTogetherCOP : protocols::symmetry
• FaSymDockingSlideTogetherOP : protocols::symmetry
• favor_nonnative_residue_tracer() : protocols::protein_interface_design::movers
• FavorSymmetricSequenceCOP : protocols::simple_moves
• FavorSymmetricSequenceOP : protocols::simple_moves
• FaWaterToBilayerEnergyCOP : protocols::membrane::scoring
• FaWaterToBilayerEnergyOP : protocols::membrane::scoring
• FBnl_R() : core::scoring::fiber_diffraction
• Fd_like : protocols::fldsgn::topology
• Fe : core::chemical::element
• FE() : protocols::sic_dock::scores
• FE2_COORDINATION : core::chemical
• FE3_COORDINATION : core::chemical
• FeaturesReporterCOP : protocols::features
• FeaturesReporterCreatorCOP : protocols::features
• FeaturesReporterCreatorOP : protocols::features
• FeaturesReporterOP : protocols::features
• FIBER_DIFFRACTION : core::io::rcsb
• fiberdiffraction : core::scoring
• FiberDiffractionCOP : core::scoring::fiber_diffraction
• fiberdiffractiondens : core::scoring
• FiberDiffractionEnergyCreator_registrator : core::init
• FiberDiffractionEnergyDensCreator_registrator : core::init
• FiberDiffractionOP : core::scoring::fiber_diffraction
• FibrilModelingClaimerAP : protocols::topology_broker
• FibrilModelingClaimerCAP : protocols::topology_broker
• FibrilModelingClaimerCOP : protocols::topology_broker
• FibrilModelingClaimerOP : protocols::topology_broker
• 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
• FileConstraintGeneratorCAP : protocols::denovo_design::constraints
• FileConstraintGeneratorOP : protocols::denovo_design::constraints
• FileContentsMapCOP : protocols::pack_daemon
• FileContentsMapOP : protocols::pack_daemon
• FileJobOutputterOP : protocols::jd2
• FileName : core::import_pose::pose_stream
• filename() : protocols::abinitio
• filenames_from_list_file() : core::import_pose::pose_stream
• FileType : core::import_pose
• 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
• FillAUTOTaskOperationCOP : core::pack::task::operation
• FillAUTOTaskOperationOP : core::pack::task::operation
• 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_type : protocols::generalized_kinematic_closure::filter
• filter_water_ligands() : protocols::magnesium
• FilterCollectionCOP : protocols::filters
• FilterCollectionOP : protocols::filters
• FilterCOP : protocols::filters
• FilterCOPs : protocols::filters
• FilterCreatorCOP : protocols::filters
• FilterCreatorOP : protocols::filters
• filtered_num_vertices() : core::chemical
• FilteredSolutionsCOP : protocols::kinematic_closure::solution_pickers
• FilteredSolutionsOP : protocols::kinematic_closure::solution_pickers
• FilterFactoryCOP : protocols::filters
• FilterFactoryOP : protocols::filters
• FilterMoverOP : protocols::moves
• FilterOP : protocols::filters
• FilterOPs : protocols::filters
• FilterReportAsPoseExtraScoresMoverCOP : protocols::moves
• FilterReportAsPoseExtraScoresMoverOP : protocols::moves
• FilterReporterMoverCOP : protocols::moves
• FilterReporterMoverOP : protocols::moves
• FilterScanFilterCOP : protocols::protein_interface_design::filters
• FilterScanFilterOP : protocols::protein_interface_design::filters
• FilterStructs_PackstatOP : protocols::flxbb
• FilterStructs_TotalChargeOP : protocols::flxbb
• FilterStructsOP : protocols::flxbb
• FilterValueMetricCOP : protocols::filters
• FilterValueMetricOP : protocols::filters
• final_design_min() : protocols::ncbb
• finalize_stub_set() : protocols::protein_interface_design::movers
• finalize_stub_sets() : protocols::protein_interface_design::movers
• FinalMinimizerCOP : protocols::ligand_docking
• FinalMinimizerCOPs : protocols::ligand_docking
• FinalMinimizerOP : protocols::ligand_docking
• FinalMinimizerOPs : protocols::ligand_docking
• 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
• FindConsensusSequenceCOP : protocols::recon_design
• FindConsensusSequenceOP : protocols::recon_design
• FindEndpointsOperationCOP : protocols::splice
• FindEndpointsOperationOP : protocols::splice
• findLoopFromDensity() : protocols::electron_density
• findSampling() : core::scoring::electron_density , core::scoring::fiber_diffraction
• findSampling5() : core::scoring::electron_density , core::scoring::fiber_diffraction
• FingerprintManagerCOP : protocols::pockets
• FingerprintManagerOP : protocols::pockets
• FINISHED : protocols::monte_carlo
• First : protocols::indexed_structure_store::filters
• FIRST_ATOM_PROPERTY : core::chemical
• first_base_atom() : core::chemical::rna
• first_base_atom_index() : core::chemical::rna
• first_beta3_aa : core::chemical
• first_D_aa : core::chemical
• first_DNA_aa : core::chemical
• first_l_aa : core::chemical
• FIRST_LINK_TYPE : core::scoring::carbohydrates
• first_oligourea : core::chemical
• FIRST_PROPERTY : core::chemical
• first_protein_residue() : protocols::constraint_generator
• FIRST_VARIANT : core::chemical
• FirstResidAdded : protocols::cyclic_peptide
• fit_centered_coords() : protocols::toolbox
• fit_layer_lines_with_splines() : core::scoring::fiber_diffraction
• FitnessFilterCOP : protocols::recon_design
• FitnessFilterOP : protocols::recon_design
• FitSimpleHelixCOP : protocols::helical_bundle
• FitSimpleHelixCOPs : protocols::helical_bundle
• FitSimpleHelixOP : protocols::helical_bundle
• FitSimpleHelixOPs : protocols::helical_bundle
• FIVE : core::pack::dunbrack
• FIVE_PRIME : core::pose::rna
• FIVE_PRIME_END_OH : core::chemical
• FIVE_PRIME_END_PHOSPHATE : core::chemical
• FIVE_PRIME_PACKABLE_PHOSPHATE : core::chemical
• FIVE_PRIME_PACKABLE_TRIPHOSPHATE : core::chemical
• FIVE_PRIME_PHOSPHATE : core::chemical , protocols::stepwise::modeler::rna::phosphate
• FIVE_PRIME_RME_PHOSPHATE : core::chemical
• FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE : core::chemical
• FIVEPRIME_CAP : core::chemical , core::pose::full_model_info
• FiveReal4 : core::pack::dunbrack
• 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
• FixAllLoopsMoverCOP : protocols::pose_length_moves
• FixAllLoopsMoverOP : protocols::pose_length_moves
• FixbbPwatSimAnnealerOP : core::pack::annealer
• FixbbRotamerSetsCOP : core::pack::rotamer_set
• FixbbRotamerSetsOP : core::pack::rotamer_set
• FixbbSimAnnealerOP : core::pack::annealer
• FIXED_DOMAIN : core::pose::copydofs , core::pose::full_model_info
• FixedBBInteractionGraphCOP : core::pack::interaction_graph
• FixedBBInteractionGraphOP : core::pack::interaction_graph
• FixedOffsetPivotsCOP : protocols::kinematic_closure::pivot_pickers
• FixedOffsetPivotsOP : protocols::kinematic_closure::pivot_pickers
• FixedOffsetsPivotsCOP : protocols::kinematic_closure::pivot_pickers
• FixedOffsetsPivotsOP : protocols::kinematic_closure::pivot_pickers
• FixedPivotsCOP : protocols::kinematic_closure::pivot_pickers
• FixedPivotsOP : protocols::kinematic_closure::pivot_pickers
• fixH() : protocols::relax
• fixup_magnesiums() : protocols::magnesium
• fixup_patches() : core::chemical
• Fl : core::chemical::element
• flat_d_aa_ramatable : core::scoring
• flat_d_aa_ramatable_stringent : core::scoring
• flat_l_aa_ramatable : core::scoring
• flat_l_aa_ramatable_stringent : core::scoring
• flat_symm_dl_aa_ramatable : core::scoring
• flat_symm_dl_aa_ramatable_stringent : core::scoring
• flat_symm_gly_ramatable : core::scoring
• flat_symm_gly_ramatable_stringent : core::scoring
• flat_symm_pro_ramatable : core::scoring
• flat_symm_pro_ramatable_stringent : core::scoring
• FlatHarmonicFuncCOP : core::scoring::func
• FlatHarmonicFuncOP : core::scoring::func
• flatten_center() : ndarray
• flatten_list() : core::fragment
• Flavodoxin : protocols::fldsgn::topology
• FlexBBDesignMeanFieldCOP : protocols::mean_field
• FlexBBDesignMeanFieldOP : protocols::mean_field
• FlexbbInteractionGraphCOP : protocols::flexpack::interaction_graph
• FlexbbInteractionGraphOP : protocols::flexpack::interaction_graph
• FlexBBMeanFieldCOP : protocols::mean_field
• FlexBBMeanFieldOP : protocols::mean_field
• FlexbbRotamerSetCOP : protocols::flexpack::rotamer_set
• FlexbbRotamerSetOP : protocols::flexpack::rotamer_set
• FlexbbRotamerSetsAP : protocols::flexpack::rotamer_set
• FlexbbRotamerSetsCAP : protocols::flexpack::rotamer_set
• FlexbbRotamerSetsCOP : protocols::flexpack::rotamer_set
• FlexbbRotamerSetsOP : protocols::flexpack::rotamer_set
• FlexbbSimAnnealerOP : protocols::flexpack::annealer
• FlexPackerCOP : protocols::flexpack
• FlexPackerOP : protocols::flexpack
• FlexPepDockingAbInitioCOP : protocols::flexpep_docking
• FlexPepDockingAbInitioOP : protocols::flexpep_docking
• FlexPepDockingFlagsAP : protocols::flexpep_docking
• FlexPepDockingFlagsCAP : protocols::flexpep_docking
• FlexPepDockingFlagsCOP : protocols::flexpep_docking
• FlexPepDockingFlagsOP : protocols::flexpep_docking
• FlexPepDockingLowResCOP : protocols::flexpep_docking
• FlexPepDockingLowResOP : protocols::flexpep_docking
• FlexPepDockingPoseMetricsCOP : protocols::flexpep_docking
• FlexPepDockingPoseMetricsOP : protocols::flexpep_docking
• FlexPepDockingProtocolCOP : protocols::flexpep_docking
• FlexPepDockingProtocolOP : protocols::flexpep_docking
• flip_atom_xyz() : core::io::pose_from_sfr
• FLIP_CHIRALITY : protocols::simple_moves::chiral
• FlipChiralityMoverCOP : protocols::cyclic_peptide
• FlipChiralityMoverCOPs : protocols::cyclic_peptide
• FlipChiralityMoverOP : protocols::cyclic_peptide
• FlipChiralityMoverOPs : protocols::cyclic_peptide
• FlipMoverCOP : protocols::membrane
• FlipMoverOP : protocols::membrane
• float20 : core::scoring::motif
• float9 : core::scoring::motif
• FloatCIter : core::scoring::packstat
• FloatingResonanceAP : protocols::noesy_assign
• FloatingResonanceCAP : protocols::noesy_assign
• FloatingResonanceCOP : protocols::noesy_assign
• FloatingResonanceOP : protocols::noesy_assign
• FloatIter : core::scoring::packstat
• Floats : core::scoring::motif , core::scoring::packstat
• flood_fill3D() : protocols::sic_dock
• FloppyTailMoverOP : protocols::floppy_tail
• FLORECENCE_TRANSFER : core::io::rcsb
• FLUORO_SUGAR : core::chemical
• FlxbbDesign_main() : protocols::flxbb
• FlxbbDesignOP : protocols::flxbb
• Fm : core::chemical::element
• fold_tree_entry_point() : core::conformation::symmetry
• fold_tree_from_loops() : protocols::forge::methods , protocols::loops
• fold_tree_from_pose() : protocols::forge::methods
• FoldandDockClaimerAP : protocols::topology_broker
• FoldandDockClaimerCAP : protocols::topology_broker
• FoldandDockClaimerCOP : protocols::topology_broker
• FoldandDockClaimerOP : protocols::topology_broker
• FoldConstraintsCOP : protocols::abinitio
• FoldConstraintsOP : protocols::abinitio
• FoldGraphAP : protocols::denovo_design::components
• FoldGraphCAP : protocols::denovo_design::components
• FoldGraphCOP : protocols::denovo_design::components
• FoldGraphOP : protocols::denovo_design::components
• FoldingSolutions : protocols::denovo_design::components
• FoldTreeAP : core::kinematics
• FoldTreeCAP : core::kinematics
• FoldTreeCOP : core::kinematics
• FoldTreeFromFoldGraphMoverCOP : protocols::denovo_design::movers
• FoldTreeFromFoldGraphMoverOP : protocols::denovo_design::movers
• FoldTreeFromLoopsCOP : protocols::loops
• FoldTreeFromLoopsOP : protocols::loops
• FoldTreeFromMotifCOP : protocols::loops
• FoldTreeFromMotifOP : protocols::loops
• FoldTreeHybridizeCOP : protocols::hybridization
• FoldTreeHybridizeOP : protocols::hybridization
• FoldTreeOP : core::kinematics
• FoldTreeRequest : protocols::loop_modeling
• FoldTreeSketchCOP : core::environment
• FoldTreeSketchOP : core::environment
• follow_EX_flags : protocols::match::upstream
• FORCE_EXISTING_BASE_TYPE : core::pack::palette
• ForceDisulfideMoverCOP : protocols::calc_taskop_movers
• ForceDisulfideMoverOP : protocols::calc_taskop_movers
• foreach_movemap_tag() : protocols::rosetta_scripts
• form_disulfide() : core::conformation
• form_disulfide_helper() : core::conformation
• formatted_icoord_tree() : core::chemical
• FormFactorCOP : core::scoring::saxs
• FormFactorManagerCOP : core::scoring::saxs
• FormFactorManagerOP : core::scoring::saxs
• FormFactorOP : core::scoring::saxs
• FORMUL : core::io::pdb
• forward : protocols::carbohydrates , protocols::loops::loop_closure::ccd
• FOUR : core::pack::dunbrack
• FourAtomsConstraintDataCOP : protocols::frag_picker::scores
• FourAtomsConstraintDataOP : protocols::frag_picker::scores
• FourPointsFuncCOP : core::scoring::func
• FourPointsFuncOP : core::scoring::func
• Fr : core::chemical::element
• frac_atoms_within() : protocols::ligand_docking
• fragbias_tr() : protocols::hybridization
• FragDataCOP : core::fragment
• FragDataCOPs : core::fragment
• FragDataOP : core::fragment
• FragDataOPs : core::fragment
• fragext_subelement_ct_name() : protocols::loop_grower
• FragID_List : core::fragment
• FragInsertAndAlignMoverOP : protocols::rbsegment_relax
• FragLibCOP : protocols::frags
• FragLibOP : protocols::frags
• FRAGMENT : core::chemical
• fragment_set_slice() : core::fragment
• FragmentCandidateCOP : protocols::frag_picker
• FragmentCandidateOP : protocols::frag_picker
• FragmentClaimerAP : protocols::topology_broker
• FragmentClaimerCAP : protocols::topology_broker
• FragmentClaimerCOP : protocols::topology_broker
• FragmentClaimerOP : protocols::topology_broker
• FragmentCMCOP : protocols::abinitio::abscript
• FragmentCMOP : protocols::abinitio::abscript
• FragmentComparatorBaseCOP : protocols::frag_picker
• FragmentComparatorBaseOP : protocols::frag_picker
• FragmentCostCOP : protocols::simple_moves
• FragmentCostOP : protocols::simple_moves
• FragmentExtensionCOP : protocols::loop_grower
• FragmentExtensionOP : protocols::loop_grower
• FragmentJumpClaimerAP : protocols::topology_broker
• FragmentJumpClaimerCAP : protocols::topology_broker
• FragmentJumpClaimerCOP : protocols::topology_broker
• FragmentJumpClaimerOP : protocols::topology_broker
• FragmentJumpCMCOP : protocols::abinitio::abscript
• FragmentJumpCMOP : protocols::abinitio::abscript
• FragmentLibraryCOP : core::fragment::rna
• FragmentLibraryOP : core::fragment::rna
• FragmentLibraryPointerKey : core::fragment::rna
• FragmentLibraryPointerMap : core::fragment::rna
• FragmentLookupAP : protocols::indexed_structure_store
• FragmentLookupCAP : protocols::indexed_structure_store
• FragmentLookupCOP : protocols::indexed_structure_store
• FragmentLookupFilterAP : protocols::indexed_structure_store::filters
• FragmentLookupFilterCAP : protocols::indexed_structure_store::filters
• FragmentLookupFilterCOP : protocols::indexed_structure_store::filters
• FragmentLookupFilterOP : protocols::indexed_structure_store::filters
• FragmentLookupOP : protocols::indexed_structure_store
• FragmentMoverCOP : protocols::simple_moves
• FragmentMoverOP : protocols::simple_moves
• FragmentPerturberCOP : protocols::kinematic_closure::perturbers
• FragmentPerturberOP : protocols::kinematic_closure::perturbers
• FragmentPickerAP : protocols::frag_picker
• FragmentPickerCAP : protocols::frag_picker
• FragmentPickerCOP : protocols::frag_picker
• FragmentPickerOP : protocols::frag_picker
• FragmentReaderOP : protocols::parser
• FragmentRmsdCOP : core::fragment
• FragmentRmsdOP : core::fragment
• FragmentSamplerCOP : protocols::abinitio
• FragmentSamplerOP : protocols::abinitio
• FragmentScoreFilterCOP : protocols::frag_picker
• FragmentScoreFilterOP : protocols::frag_picker
• FragmentScoreManagerCOP : protocols::frag_picker::scores
• FragmentScoreManagerOP : protocols::frag_picker::scores
• FragmentScoreMapCOP : protocols::frag_picker::scores
• FragmentScoreMapOP : protocols::frag_picker::scores
• FragmentScoringMethodCOP : protocols::frag_picker::scores
• FragmentScoringMethodOP : protocols::frag_picker::scores
• FragmentSelectingRuleCOP : protocols::frag_picker
• FragmentSelectingRuleOP : protocols::frag_picker
• FragmentSetLoaderCOP : core::fragment
• FragmentSetLoaderOP : core::fragment
• FragmentStoreCOP : protocols::indexed_structure_store
• FragmentStoreOP : protocols::indexed_structure_store
• FragmentStoreProviderCOP : protocols::indexed_structure_store
• FragmentStoreProviderOP : protocols::indexed_structure_store
• FragQualFilterCOP : protocols::fldsgn::filters
• FragQualFilterOP : protocols::fldsgn::filters
• FragSetCollectionCOP : core::fragment
• FragSetCollectionOP : core::fragment
• FragSetCOP : core::fragment
• FragSetOP : core::fragment
• FragsToAtomDistAP : protocols::noesy_assign
• FragsToAtomDistCAP : protocols::noesy_assign
• FragsToAtomDistCOP : protocols::noesy_assign
• FragsToAtomDistOP : protocols::noesy_assign
• FrameCOP : core::fragment
• FrameIteratorWorker_OP : core::fragment
• FrameOP : core::fragment
• framework_region : protocols::antibody
• frdc() : core::scoring
• frdcDa() : core::scoring
• frdcDaR() : core::scoring
• frdcR() : core::scoring
• free_2HOprime : core::scoring
• free_base : core::scoring
• free_dof : core::scoring
• free_res : core::scoring
• free_side_chain : core::scoring
• free_suite : core::scoring
• FreeDOF_EnergyCreator_registrator : core::init
• FreeDOF_OptionsCOP : core::scoring::methods
• FreeDOF_OptionsOP : core::scoring::methods
• FreePeptideCOP : protocols::backbone_moves::local_backbone_mover
• FreePeptideMoverCOP : protocols::backbone_moves::local_backbone_mover::free_peptide_movers
• FreePeptideMoverOP : protocols::backbone_moves::local_backbone_mover::free_peptide_movers
• FreePeptideOP : protocols::backbone_moves::local_backbone_mover
• 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
• FROM_SCRATCH : protocols::stepwise::monte_carlo::mover
• FromScratchMoverCOP : protocols::stepwise::monte_carlo::mover
• FromScratchMoverCreatorCOP : protocols::stepwise::monte_carlo::mover
• FromScratchMoverCreatorOP : protocols::stepwise::monte_carlo::mover
• FromScratchMoverOP : protocols::stepwise::monte_carlo::mover
• ft_nfft() : core::scoring::fiber_diffraction
• ftoa() : protocols::sparta
• FTR_DONT_CARE : protocols::loop_modeling
• FTR_LOOPS_WITH_CUTS : protocols::loop_modeling
• FTR_SIMPLE_TREE : protocols::loop_modeling
• FULL_ATOM_t : core::chemical
• 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_parameter_type_name : core::pose::full_model_info
• full_model_size() : core::pose::full_model_info
• full_to_sub() : core::pose::full_model_info
• FullatomCustomPairDistanceEnergyCOP : core::scoring::custom_pair_distance
• FullatomCustomPairDistanceEnergyCreator_registrator : core::init
• FullatomCustomPairDistanceEnergyOP : core::scoring::custom_pair_distance
• FullatomDisulfideEnergyContainerAP : core::scoring::disulfides
• FullatomDisulfideEnergyContainerCAP : core::scoring::disulfides
• FullatomDisulfideEnergyContainerCOP : core::scoring::disulfides
• FullatomDisulfideEnergyContainerOP : core::scoring::disulfides
• FullatomDisulfideEnergyCOP : core::scoring::disulfides
• FullatomDisulfideEnergyCreator_registrator : core::init
• FullatomDisulfideEnergyOP : core::scoring::disulfides
• FullatomDisulfidePotentialAP : core::scoring::disulfides
• FullatomDisulfidePotentialCAP : core::scoring::disulfides
• FullatomDisulfidePotentialCOP : core::scoring::disulfides
• FullatomDisulfidePotentialOP : core::scoring::disulfides
• FullatomRelaxMoverOP : protocols::surface_docking
• FullModelInfoOP : core::pose::full_model_info
• FullModelInnerLarvalJobCOP : protocols::jd3::full_model
• FullModelInnerLarvalJobOP : protocols::jd3::full_model
• FullModelInnerLarvalJobs : protocols::jd3::full_model
• FullModelInputSourceCOP : protocols::jd3::full_model_inputters
• FullModelInputSourceOP : protocols::jd3::full_model_inputters
• FullModelInputSources : protocols::jd3::full_model_inputters
• FullModelInputterCOP : protocols::jd3::full_model_inputters
• FullModelInputterCreatorCOP : protocols::jd3::full_model_inputters
• FullModelInputterCreatorOP : protocols::jd3::full_model_inputters
• FullModelInputterOP : protocols::jd3::full_model_inputters
• FullModelJobQueenCOP : protocols::jd3::full_model
• FullModelJobQueenOP : protocols::jd3::full_model
• FullModelParametersCOP : core::pose::full_model_info
• FullModelParametersOP : core::pose::full_model_info
• FullModelParameterType : core::pose::full_model_info
• FullModelPreliminaryLarvalJobs : protocols::jd3::full_model
• func_add_resid_to_entity_list : protocols::pack_daemon
• func_entity_for_residue : protocols::pack_daemon
• func_n_residues_for_entity : protocols::pack_daemon
• func_residues_for_entity_begin : protocols::pack_daemon
• func_residues_for_entity_end : protocols::pack_daemon
• FuncCOP : core::scoring::func
• FuncOP : core::scoring::func
• FURANOSE : core::chemical