- f -

• f0() : core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::KromerMann
• f00() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• F1() : core::optimization::DOF_Node
• f1() : core::scoring::DerivVectorPair
• f11() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• f1ij() : core::scoring::CSA , core::scoring::DC
• F2() : core::optimization::DOF_Node
• f2() : core::scoring::DerivVectorPair
• f22() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• f2ij() : core::scoring::CSA , core::scoring::DC
• f3ij() : core::scoring::CSA
• fa_atr() : core::scoring::motif::ResPairMotif
• fa_atr_bb() : core::scoring::motif::ResPairMotif
• fa_atr_sc_bb() : core::scoring::motif::ResPairMotif
• fa_center() : core::scoring::Membrane_FAEmbed
• fa_depth() : core::scoring::Membrane_FAEmbed
• fa_dun_dev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_rot() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_semi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_tot() : core::pack::dunbrack::RotamerLibraryScratchSpace
• FA_ElecEnergy() : core::scoring::elec::FA_ElecEnergy
• FA_ElecEnergyAroAll() : core::scoring::elec::FA_ElecEnergyAroAll
• FA_ElecEnergyAroAro() : core::scoring::elec::FA_ElecEnergyAroAro
• FA_GrpElecEnergy() : core::scoring::elec::FA_GrpElecEnergy
• fa_is_independent() : core::conformation::symmetry::SymmetryInfo
• Fa_MbenvEnergy() : core::scoring::methods::Fa_MbenvEnergy
• Fa_MbsolvEnergy() : core::scoring::methods::Fa_MbsolvEnergy
• Fa_Membed_update() : core::scoring::Membrane_FAEmbed
• fa_penalty() : core::scoring::Membrane_FAEmbed
• fa_proj() : core::scoring::Membrane_FAEmbed
• fa_proj_coord() : core::scoring::Membrane_FAEmbed
• fa_proj_deriv() : core::scoring::Membrane_FAEmbed
• fa_projection() : core::scoring::Membrane_FAPotential
• fa_ssdist_scores() : core::scoring::disulfides::SG_Dist_Func
• fa_ssdist_scores_deriv() : core::scoring::disulfides::SG_Dist_Func
• FabConstraint() : core::scoring::constraints::FabConstraint
• FabConstraintCreator() : core::scoring::constraints::FabConstraintCreator
• factor() : core::scoring::dna::TorsionFourierComponent
• factory_register() : core::io::silent::SilentStructFactory , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , core::pack::task::residue_selector::ResidueSelectorFactory , core::scoring::constraints::ConstraintFactory , core::scoring::ScoringManager , core::sequence::SequenceFactory
• FACTSEnergy() : core::scoring::methods::FACTSEnergy
• FACTSPoseInfo() : core::scoring::FACTSPoseInfo
• FACTSPotential() : core::scoring::FACTSPotential
• FACTSResidueInfo() : core::scoring::FACTSResidueInfo
• FACTSRotamerSetInfo() : core::scoring::FACTSRotamerSetInfo
• fade_energy() : core::scoring::hbonds::HBondOptions
• fade_hbonding_group_score() : core::scoring::elec::GroupElec
• fade_type() : core::scoring::elec::GroupElec
• fade_zone() : core::scoring::func::FadeFunc
• FadeFunc() : core::scoring::func::FadeFunc
• FadeInterval() : core::scoring::hbonds::FadeInterval
• FAElecContextData() : core::scoring::elec::FAElecContextData
• FaMPEnvEnergy() : core::scoring::membrane::FaMPEnvEnergy
• FaMPEnvSmoothEnergy() : core::scoring::membrane::FaMPEnvSmoothEnergy
• FaMPSolvEnergy() : core::scoring::membrane::FaMPSolvEnergy
• FAScatter() : core::scoring::fiber_diffraction::FAScatter
• fasol_cubic_poly_far_xhi() : core::scoring::etable::Etable
• fasol_cubic_poly_far_xlo() : core::scoring::etable::Etable
• FastDensEnergy() : core::scoring::electron_density::FastDensEnergy
• FASTERAnnealer() : core::pack::annealer::FASTERAnnealer
• FASTEREdge() : core::pack::interaction_graph::FASTEREdge
• FASTERInteractionGraph() : core::pack::interaction_graph::FASTERInteractionGraph
• FASTERNode() : core::pack::interaction_graph::FASTERNode
• FastSAXSEnergy() : core::scoring::saxs::FastSAXSEnergy
• FastSAXSEnergyCreator() : core::scoring::saxs::FastSAXSEnergyCreator
• fcen10() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen12() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen6() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• featurizer_state() : core::scoring::dssp::StrandPairingSet
• fetch_stored_derivatives() : core::optimization::LineMinimizationAlgorithm
• ff() : core::scoring::saxs::FormFactor
• FiberDiffraction() : core::scoring::fiber_diffraction::FiberDiffraction
• FiberDiffractionEnergy() : core::scoring::fiber_diffraction::FiberDiffractionEnergy
• FiberDiffractionEnergyCreator() : core::scoring::fiber_diffraction::FiberDiffractionEnergyCreator
• FiberDiffractionEnergyDens() : core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• FiberDiffractionEnergyDensCreator() : core::scoring::fiber_diffraction::FiberDiffractionEnergyDensCreator
• FiberDiffractionEnergyGpuCreator() : core::scoring::fiber_diffraction::FiberDiffractionEnergyGpuCreator
• FiberDiffractionLoader() : core::scoring::fiber_diffraction::FiberDiffractionLoader
• FiberDiffractionLoaderCreator() : core::scoring::fiber_diffraction::FiberDiffractionLoaderCreator
• FiberDiffractionOptions() : core::scoring::fiber_diffraction::FiberDiffractionOptions
• FiberDiffractionOptionsCreator() : core::scoring::fiber_diffraction::FiberDiffractionOptionsCreator
• Field() : core::io::pdb::Field
• figure_out_chi_order() : core::chemical::rna::RNA_ResidueType
• figure_out_dofs() : core::pose::copydofs::CopyDofs
• figure_out_loop_cycles() : core::scoring::loop_graph::LoopGraph
• figure_out_low_resolution_potential() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• figure_out_offset() : core::scoring::rna::RNA_SuitePotential
• figure_out_potential() : core::scoring::rna::data::RNA_DMS_Potential
• figure_out_residue_numbers_from_line() : core::io::silent::SilentStruct
• figure_out_rna_base_pairs_to_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• figure_out_rna_base_stacks_to_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• fij() : core::scoring::RDC
• file_data() : core::import_pose::PDBSilentStruct
• FileData() : core::io::pdb::FileData
• FileDataOptions() : core::io::pdb::FileDataOptions
• filename() : core::io::raw_data::DisulfideFile , core::io::silent::SilentFileData , core::pack::task::operation::ReadResfile
• filenames() : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• fill() : core::id::AtomID_Map< T > , core::id::NamedAtomID_Map< T > , core::pose::PDBPoseMap
• fill_atom_numbers_for_backbone_oxygens() : core::scoring::rna::RNA_LowResolutionPotential
• fill_backbone_array() : core::io::rna::RNA_DataReader
• fill_bins() : core::scoring::dna::DirectReadoutPotential
• fill_cenlist() : core::scoring::EnvPairPotential
• fill_compound_records() : core::io::pdb::HeaderInformation
• fill_data() : core::scoring::sasa::SasaCalc
• fill_data_annotations_if_empty() : core::io::rna::RDAT
• fill_data_from_features() : core::io::rna::RDAT
• fill_energy_map() : core::scoring::EnergyEdge
• fill_experimental_technique_records() : core::io::pdb::HeaderInformation
• fill_f1_f2() : core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint
• fill_from_spanfile() : core::conformation::membrane::SpanningTopology
• fill_from_string() : core::fragment::picking_old::vall::VallResidue
• fill_from_structure() : core::conformation::membrane::SpanningTopology
• fill_h2o_hbond_set() : core::scoring::WaterAdductHBondPotential
• fill_header_information() : core::io::rna::RDAT
• fill_header_record() : core::io::pdb::HeaderInformation
• fill_header_records() : core::io::pdb::FileData
• fill_ideal_xyz_from_icoor() : core::chemical::ResidueType
• fill_if_empty() : core::io::rna::RDAT
• fill_in_chain_terminii() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• fill_keyword_records() : core::io::pdb::HeaderInformation
• fill_missing_atoms() : core::conformation::Conformation , core::conformation::Residue , core::pack::dunbrack::SingleLigandRotamerLibrary
• fill_other_struct_list() : core::io::silent::SilentStruct
• fill_parameter_values() : core::pose::full_model_info::FullModelParameters
• fill_point_graph() : core::scoring::Energies , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricEnergies
• fill_pose() : core::import_pose::PDBSilentStruct , core::import_pose::pose_stream::ExtendedPoseInputStream , core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::MetaPoseInputStream , core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::PoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::raw_data::DecoyStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::raw_data::ScoreStructText , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• fill_pose_with_motif() : core::scoring::motif::ResPairMotif
• fill_records() : core::io::pdb::HeaderInformation
• fill_rna_data_info() : core::io::rna::RNA_DataReader
• fill_rotamer_vector() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary
• fill_rotamer_vector_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• fill_rotamer_vector_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• fill_seqpos() : core::io::rna::RDAT
• fill_sequences_and_structures() : core::io::rna::RDAT
• fill_sequences_if_empty() : core::io::rna::RDAT
• fill_sin_x_over_x_table() : core::scoring::saxs::SinXOverX
• fill_smooth_cenlist() : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• fill_smooth_dcenlist() : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• fill_struct() : core::import_pose::PDBSilentStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• fill_struct_with_residue_numbers() : core::io::silent::SilentStruct
• fill_structures_if_empty() : core::io::rna::RDAT
• fill_suiteness_derivative_7d() : core::pose::rna::RNA_SuiteName
• fill_title_records() : core::io::pdb::HeaderInformation
• fill_water_grid() : core::scoring::geometric_solvation::WaterWeightGridSet
• fill_with() : core::id::AtomID_Map< T >
• fill_wrapped_records() : core::io::pdb::HeaderInformation
• filter() : core::pack::task::operation::OperateOnCertainResidues , core::scoring::motif::ResPairMotif
• filter_redundant() : core::scoring::motif::MotifHits
• filter_structurally_identical_motifs() : core::scoring::motif::ResPairMotifs
• filter_structurally_similar_motifs() : core::scoring::motif::ResPairMotifs
• filtered_base_axis_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_pair_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stack_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stack_axis_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stagger_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• final_visit_to_edge() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• Finalize() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• finalize() : core::chemical::ResidueType , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::scoring::bin_transitions::BinTransitionData , core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::Membrane_FAPotential , core::scoring::MembranePotential , core::scoring::rna::RNA_LowResolutionPotential , core::scoring::SmoothEnvPairPotential
• finalize_after_derivatives() : core::scoring::dna::DNATorsionEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::methods::EnergyMethod , core::scoring::orbitals::OrbitalsScore , core::scoring::ScoreFunction
• finalize_born_radii() : core::scoring::GenBornPotential
• finalize_compound_records() : core::io::pdb::HeaderInformation
• finalize_experimental_technique_records() : core::io::pdb::HeaderInformation
• finalize_header_information() : core::io::pdb::FileData
• finalize_keyword_records() : core::io::pdb::HeaderInformation
• finalize_output() : core::pack::annealer::FASTERAnnealer
• finalize_parse() : core::io::pdb::HeaderInformation
• finalize_total_energy() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::cryst::XtalMLEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPLipoEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::methods::BurialEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::D2H_SA_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FreeDOF_Energy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneLipo , core::scoring::methods::MissingEnergy , core::scoring::methods::OtherPoseEnergy , core::scoring::methods::PackStatEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential , core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy
• FinalizeAromatic() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• finalized_energies() : core::scoring::Energies
• FinalizeNitrogenSingleDouble() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• FinalizeNitrogenThreeSingle() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• FinalizeNitrogenTwoSingle() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• FinalizeOxygenSingleDouble() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• FinalizeOxygenThreeSingle() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• FinalizeOxygenTwoSingle() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• FinalizeUnhybridized() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• find() : core::kinematics::MoveMap , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• find_another_representative_for_unlikely_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• find_backbone_oxygen_atom() : core::scoring::rna::RNA_LowResolutionPotential
• find_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• find_disulfides() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• find_edge() : core::graph::Graph , core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase
• find_energy_edge() : core::scoring::EnergyGraph
• find_first_slice() : core::scoring::packstat::LeeRichards
• find_index_for_loop_landing_at_domain() : core::scoring::loop_graph::LoopCycle
• find_index_in_other_pose_list() : core::pose::full_model_info::FullModelInfo
• find_minimization_edge() : core::scoring::MinimizationGraph
• find_motifs() : core::scoring::motif::MotifHash
• find_motifs_with_radius() : core::scoring::motif::MotifHash
• find_root_from_atom_pointer() : core::kinematics::AtomTree
• findEdgeId() : core::sequence::SequenceCoupling
• FindNeighbordsAndBuriedAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• FindNeighborsForAtom() : core::scoring::sc::MolecularSurfaceCalculator
• FindPossibleAtomTypesForAtom() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• finish_arc() : core::scoring::packstat::trace
• finish_pose() : core::io::silent::SilentStruct
• first_atom_in_branch() : core::scoring::trie::TrieNode< AT, CPDATA >
• first_residue() : core::conformation::parametric::Parameters
• first_sidechain_atom() : core::chemical::ResidueType , core::conformation::Residue
• first_sidechain_hydrogen() : core::chemical::ResidueType , core::conformation::Residue
• FirstClassEdge() : core::pack::interaction_graph::FirstClassEdge< V, E, G >
• FirstClassNode() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• fit_intensities() : core::scoring::saxs::SAXSEnergy
• fitBfactors() : core::scoring::cryst::PhenixInterface
• fitness_pbest() : core::optimization::Particle
• fix_disulfides() : core::conformation::Conformation
• fix_his_tautomer() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• FixbbCoupledRotamerSimAnnealer() : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• FixbbLinkingRotamerSimAnnealer() : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• FixbbRotamerSets() : core::pack::rotamer_set::FixbbRotamerSets
• FixbbSimAnnealer() : core::pack::annealer::FixbbSimAnnealer
• fixed() : core::scoring::OneToAllEnergyContainer
• fixed_dist() : core::scoring::RDC , core::scoring::RDC_Rohl
• fixed_domain_map() : core::pose::full_model_info::FullModelInfo
• fixed_energies() : core::scoring::MinimizationGraph
• FixedBBEdge() : core::pack::interaction_graph::FixedBBEdge
• FixedBBInteractionGraph() : core::pack::interaction_graph::FixedBBInteractionGraph
• FixedBBNode() : core::pack::interaction_graph::FixedBBNode
• flag_for_calculation() : core::scoring::FACTSResidueInfo
• flat_size() : core::fragment::FrameList
• FlatHarmonicFunc() : core::scoring::func::FlatHarmonicFunc
• flip_HNQ() : core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• fluff() : core::grid::CartGrid< T >
• focused_edge() : core::graph::Graph
• fold_in_rb_deltas() : core::kinematics::Jump , core::kinematics::RT
• fold_tree() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::pose::MiniPose , core::pose::Pose
• fold_tree_io() : core::import_pose::ImportPoseOptions
• FoldTree() : core::kinematics::FoldTree
• FoldTreeSketch() : core::environment::FoldTreeSketch
• footprint() : core::graph::ArrayPool< T >
• force_aa_neighbors() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FixedBBEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• force_aa_neighbors_for_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• force_all_aa_neighbors() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FixedBBEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• force_all_aa_neighbors_for_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• force_bitflip() : core::io::silent::SilentStruct
• force_combined_gaussian_approximation() : core::scoring::func::GaussianChainFunc
• force_nbr_atom_orient() : core::chemical::ResidueType
• formal_charge() : core::chemical::Atom , core::chemical::sdf::MolFileIOAtom
• format_string() : core::fragment::picking_old::vall::VallResidue
• format_string_2011() : core::fragment::picking_old::vall::VallResidue
• FormFactor() : core::scoring::saxs::FormFactor
• FormFactorManager() : core::scoring::saxs::FormFactorManager
• forms_disulfide_bond() : core::chemical::ResidueType
• FourPointsFunc() : core::scoring::func::FourPointsFunc
• frac2cart() : core::scoring::electron_density::ElectronDensity
• frac2index() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• frag_id() : core::fragment::FragID_Iterator , core::fragment::Frame
• frag_type() : core::fragment::FragFactory
• FragCache() : core::fragment::FragCache< T >
• FragData() : core::fragment::FragData
• FragFactory() : core::fragment::FragFactory
• FragID() : core::fragment::FragID
• fragID() : core::fragment::FrameList
• FragID_Iterator() : core::fragment::FragID_Iterator
• fragment() : core::fragment::FragID , core::fragment::FragmentRmsd , core::fragment::Frame
• fragment_as_pose() : core::fragment::Frame
• fragment_ptr() : core::fragment::FragID , core::fragment::Frame
• fragment_specification() : core::indexed_structure_store::FragmentLookup
• FragmentIO() : core::fragment::FragmentIO
• FragmentLibraryManager() : core::fragment::picking_old::FragmentLibraryManager
• FragmentLookup() : core::indexed_structure_store::FragmentLookup
• FragmentLookupResult() : core::indexed_structure_store::FragmentLookupResult
• FragmentRmsd() : core::fragment::FragmentRmsd
• fragments() : core::fragment::picking_old::vall::VallLibrarian
• FragmentSpecification() : core::indexed_structure_store::FragmentSpecification
• FragmentStore() : core::indexed_structure_store::FragmentStore
• FragSet() : core::fragment::FragSet
• FragSetCollection() : core::fragment::FragSetCollection
• FragStore() : core::fragment::FragStore< T >
• frame() : core::fragment::FragFactory , core::fragment::FragID , core::fragment::FragmentRmsd
• Frame() : core::fragment::Frame
• frame_ptr() : core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::OrderedFragSetIterator_
• frame_vector() : core::fragment::FrameList
• FrameIterator() : core::fragment::FrameIterator
• FrameListIterator_() : core::fragment::FrameListIterator_
• frames() : core::fragment::FragSet , core::fragment::OrderedFragSet
• free_2HOprime_bonus() : core::scoring::methods::FreeDOF_Options
• free_dof_options() : core::scoring::methods::EnergyMethodOptions
• free_side_chain_bonus() : core::scoring::methods::FreeDOF_Options
• free_sugar_bonus() : core::scoring::methods::FreeDOF_Options
• free_suite_bonus() : core::scoring::methods::FreeDOF_Options
• FreeDOF_Energy() : core::scoring::methods::FreeDOF_Energy
• FreeDOF_Options() : core::scoring::methods::FreeDOF_Options
• from_bond_cst() : core::kinematics::Jump
• from_four_points() : core::kinematics::Stub
• from_stubs() : core::kinematics::Jump , core::kinematics::RT
• full_model_info_into_pose() : core::io::silent::SilentStruct
• full_model_parameters() : core::io::silent::SilentStruct , core::pose::full_model_info::FullModelInfo
• full_model_pose_for_constraints() : core::pose::full_model_info::FullModelParameters
• full_name() : core::chemical::carbohydrates::CarbohydrateInfo
• full_sample_rot_index_2_moltenres_sample_rot_index() : core::pack::rotamer_set::ContinuousRotamerSets
• full_sequence() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• full_to_conventional() : core::pose::full_model_info::FullModelParameters
• full_to_conventional_resnum_and_chain() : core::pose::full_model_info::FullModelParameters
• full_to_sub() : core::pose::full_model_info::FullModelInfo
• fullatom() : core::io::raw_data::DecoyStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct
• FullatomCustomPairDistanceEnergy() : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• FullatomDisulfideEnergy() : core::scoring::disulfides::FullatomDisulfideEnergy
• FullatomDisulfideEnergyComponents() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• FullatomDisulfideEnergyContainer() : core::scoring::disulfides::FullatomDisulfideEnergyContainer
• FullatomDisulfideParams13() : core::scoring::disulfides::FullatomDisulfideParams13
• FullatomDisulfidePotential() : core::scoring::disulfides::FullatomDisulfidePotential
• FullModelInfo() : core::pose::full_model_info::FullModelInfo
• FullModelParameters() : core::pose::full_model_info::FullModelParameters
• func() : core::scoring::CenHBPotential , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::DOF_Constraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::disulfides::Cen_Distance_Func , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::disulfides::SG_Dist_Func , core::scoring::disulfides::SGSG_Dihedral_Func , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularGeneral1D_Func , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::ConstantFunc , core::scoring::func::CountViolFunc , core::scoring::func::EtableFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::MixtureFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::SumFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc , core::scoring::loop_graph::LoopScoreInfo , core::scoring::methods::LK_SigmoidalFunc , core::scoring::SmoothScoreTermCoeffs
• func_() : core::scoring::func::MixtureFunc
• func_1d() : core::optimization::func_1d
• FuncFactory() : core::scoring::func::FuncFactory
• funcs() : core::scoring::func::SumFunc