Here is a list of all class members with links to the classes they belong to:

- f -

• f : core::scoring::fiber_diffraction::Hankel
• f0() : core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::Hankel , core::scoring::fiber_diffraction::KromerMann
• f00() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• 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
• f11_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• F1_ : core::optimization::DOF_Node
• f1_ : core::scoring::DerivVectorPair
• f1ij() : core::scoring::CSA , core::scoring::DC
• f1ij_ : core::scoring::CSA , core::scoring::DC
• F2() : core::optimization::DOF_Node
• f2() : core::scoring::DerivVectorPair
• F2 : core::scoring::electron_density::ElectronDensity
• f22() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• f22_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• F2_ : core::optimization::DOF_Node
• f2_ : core::scoring::DerivVectorPair
• f2c : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• f2ij() : core::scoring::CSA , core::scoring::DC
• f2ij_ : core::scoring::CSA , core::scoring::DC
• f3ij() : core::scoring::CSA
• f3ij_ : core::scoring::CSA
• F_aa1 : core::scoring::motif::RPM_FilterStats
• F_aa2 : core::scoring::motif::RPM_FilterStats
• F_coorderr : core::scoring::motif::RPM_FilterStats
• F_dssp1 : core::scoring::motif::RPM_FilterStats
• F_dssp2 : core::scoring::motif::RPM_FilterStats
• F_faatr : core::scoring::motif::RPM_FilterStats
• F_faatr_or_hb : core::scoring::motif::RPM_FilterStats
• F_faatr_or_hbbb : core::scoring::motif::RPM_FilterStats
• F_hb_bb : core::scoring::motif::RPM_FilterStats
• F_hb_bb_sc : core::scoring::motif::RPM_FilterStats
• F_hb_sc : core::scoring::motif::RPM_FilterStats
• F_lig : core::scoring::motif::RPM_FilterStats
• F_max_seqsep : core::scoring::motif::RPM_FilterStats
• F_maxdist2 : core::scoring::motif::RPM_FilterStats
• F_mindist2 : core::scoring::motif::RPM_FilterStats
• F_no_hb_bb : core::scoring::motif::RPM_FilterStats
• F_nodisulf : core::scoring::motif::RPM_FilterStats
• F_noloops : core::scoring::motif::RPM_FilterStats
• F_not_restype : core::scoring::motif::RPM_FilterStats
• F_not_restype_one : core::scoring::motif::RPM_FilterStats
• F_occupancy : core::scoring::motif::RPM_FilterStats
• F_oneloop : core::scoring::motif::RPM_FilterStats
• F_pdb : core::scoring::motif::RPM_FilterStats
• F_restype : core::scoring::motif::RPM_FilterStats
• F_restype1 : core::scoring::motif::RPM_FilterStats
• F_restype2 : core::scoring::motif::RPM_FilterStats
• F_restype_one : core::scoring::motif::RPM_FilterStats
• F_s2 : core::scoring::electron_density::ElectronDensity
• F_score : core::scoring::motif::RPM_FilterStats
• F_seqsep : core::scoring::motif::RPM_FilterStats
• F_ss1 : core::scoring::motif::RPM_FilterStats
• F_ss2 : core::scoring::motif::RPM_FilterStats
• F_type_BB_BB : core::scoring::motif::RPM_FilterStats
• F_type_BB_PH : core::scoring::motif::RPM_FilterStats
• F_type_BB_PO : core::scoring::motif::RPM_FilterStats
• F_type_PH_PO : core::scoring::motif::RPM_FilterStats
• F_type_SC_BB : core::scoring::motif::RPM_FilterStats
• F_type_SC_PH : core::scoring::motif::RPM_FilterStats
• F_type_SC_PO : core::scoring::motif::RPM_FilterStats
• F_type_SC_SC : core::scoring::motif::RPM_FilterStats
• F_uniformfrag : core::scoring::motif::RPM_FilterStats
• FA_ : core::scoring::ResidualDipolarCoupling
• fa_atr() : core::scoring::motif::ResPairMotif
• fa_atr_ : core::scoring::motif::ResPairMotif
• fa_atr_bb() : core::scoring::motif::ResPairMotif
• fa_atr_bb_ : core::scoring::motif::ResPairMotif
• fa_atr_sc_bb() : core::scoring::motif::ResPairMotif
• fa_atr_sc_bb_ : core::scoring::motif::ResPairMotif
• fa_center() : core::scoring::Membrane_FAEmbed
• fa_center_ : core::scoring::Membrane_FAEmbed
• fa_cfg_file_ : core::scoring::saxs::SAXSEnergy
• fa_depth() : core::scoring::Membrane_FAEmbed
• fa_depth_ : core::scoring::Membrane_FAEmbed
• fa_disulfide_potential_ : core::scoring::ScoringManager
• fa_dun_dev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_dev_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_rot() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_rot_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_semi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_semi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_tot() : 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_mbenv_weight_ : core::scoring::membrane::FaMPEnvEnergy , core::scoring::methods::Fa_MbenvEnergy
• Fa_MbenvEnergy() : core::scoring::methods::Fa_MbenvEnergy
• fa_mbsolv_weight_ : core::scoring::methods::Fa_MbsolvEnergy
• Fa_MbsolvEnergy() : core::scoring::methods::Fa_MbsolvEnergy
• Fa_Membed_update() : core::scoring::Membrane_FAEmbed
• Fa_Membed_update_ : core::scoring::Membrane_FAEmbed
• fa_penalty() : core::scoring::Membrane_FAEmbed
• fa_penalty_ : core::scoring::Membrane_FAEmbed
• fa_proj() : core::scoring::Membrane_FAEmbed
• fa_proj_ : core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::Membrane_FAEmbed
• fa_proj_coord() : core::scoring::Membrane_FAEmbed
• fa_proj_coord_ : core::scoring::membrane::FaMPEnvEnergy , core::scoring::Membrane_FAEmbed
• fa_proj_deriv() : core::scoring::Membrane_FAEmbed
• fa_proj_deriv_ : core::scoring::membrane::FaMPEnvEnergy , 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
• fa_weight_ : core::scoring::membrane::FaMPSolvEnergy
• fa_z_position_ : core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy
• FabConstraint() : core::scoring::constraints::FabConstraint
• FabConstraintCreator() : core::scoring::constraints::FabConstraintCreator
• factor() : core::scoring::dna::TorsionFourierComponent
• factor_ : core::scoring::dna::TorsionFourierComponent , core::scoring::saxs::DistanceHistogram
• 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
• FACTS_POSE_INFO : core::pose::datacache::CacheableDataType
• facts_potential_ : core::scoring::ScoringManager
• FACTSEnergy() : core::scoring::methods::FACTSEnergy
• FACTSPoseInfo() : core::scoring::FACTSPoseInfo
• FACTSPotential() : core::scoring::FACTSPotential
• FACTSResidueInfo() : core::scoring::FACTSResidueInfo
• FACTSRotamerSetInfo() : core::scoring::FACTSRotamerSetInfo
• FACTSrsdtypemap_ : core::scoring::FACTSPotential
• fadd : core::scoring::APBSConfig
• fade_ : core::scoring::rna::RNA_LowResolutionPotential
• fade_alpha_ap_ : core::scoring::rna::RNA_TorsionPotential
• fade_alpha_sc_minus_ : core::scoring::rna::RNA_TorsionPotential
• fade_alpha_sc_plus_ : core::scoring::rna::RNA_TorsionPotential
• fade_delta_north_ : core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_TorsionPotential
• fade_delta_south_ : core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_TorsionPotential
• fade_energy() : core::scoring::hbonds::HBondOptions
• fade_energy_ : core::scoring::hbonds::HBondOptions
• fade_hbond_ : core::scoring::elec::GroupElec
• fade_hbonding_group_score() : core::scoring::elec::GroupElec
• fade_param1_ : core::scoring::elec::GroupElec
• fade_param2_ : core::scoring::elec::GroupElec
• fade_type() : core::scoring::elec::GroupElec
• fade_type_ : core::scoring::elec::GroupElec
• fade_zone() : core::scoring::func::FadeFunc
• fade_zone_ : core::scoring::func::FadeFunc
• FadeFunc() : core::scoring::func::FadeFunc
• FadeInterval() : core::scoring::hbonds::FadeInterval
• FAELEC_CONTEXT_DATA : core::pose::datacache::CacheableDataType
• FAElecContextData() : core::scoring::elec::FAElecContextData
• FaMPEnvEnergy() : core::scoring::membrane::FaMPEnvEnergy
• FaMPEnvSmoothEnergy() : core::scoring::membrane::FaMPEnvSmoothEnergy
• FaMPSolvEnergy() : core::scoring::membrane::FaMPSolvEnergy
• FArray1_real : core::scoring::SecondaryStructurePotential
• FArray1A_real : core::scoring::SecondaryStructurePotential
• FArray1D_int : core::scoring::Helices , core::scoring::SecondaryStructurePotential , core::scoring::Strands
• FArray1D_real : core::scoring::SecondaryStructurePotential
• FArray2D_int : core::scoring::Helices , core::scoring::Strands
• FArray2D_real : core::scoring::SecondaryStructurePotential
• FArray3D_Real : core::scoring::dna::DNA_BasePotential
• FArray4D_Real : core::scoring::dna::DNA_BasePotential
• FArray4D_real : core::scoring::SecondaryStructurePotential
• FAScatter() : core::scoring::fiber_diffraction::FAScatter
• fasol_cubic_poly1_close : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly1_close_flat : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly1_far : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly2_close : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly2_close_flat : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly2_far : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly_close : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly_close_end : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly_close_flat : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly_close_start : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly_far : core::scoring::etable::EtableParamsOnePair
• fasol_cubic_poly_far_xhi() : core::scoring::etable::Etable
• fasol_cubic_poly_far_xhi_ : core::scoring::etable::Etable
• fasol_cubic_poly_far_xlo() : core::scoring::etable::Etable
• fasol_cubic_poly_far_xlo_ : core::scoring::etable::Etable
• fasol_final_weight : core::scoring::etable::EtableParamsOnePair
• fastdens_perres_weights_ : core::scoring::methods::EnergyMethodOptions
• fastdens_score : core::scoring::electron_density::ElectronDensity
• 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
• fastgrid : core::scoring::electron_density::ElectronDensity
• fastorigin : core::scoring::electron_density::ElectronDensity
• FastSAXSEnergy() : core::scoring::saxs::FastSAXSEnergy
• FastSAXSEnergyCreator() : core::scoring::saxs::FastSAXSEnergyCreator
• favor_native_bonus_ : core::scoring::constraints::ResidueTypeConstraint
• favor_non_native_bonus_ : core::scoring::constraints::NonResidueTypeConstraint
• favored_rotamer_numbers_ : core::pack::dunbrack::RotamerConstraint
• favored_rotamers_ : core::pack::dunbrack::RotamerConstraint
• fc_bg_ : core::pack::interaction_graph::exposed_hydrophobic_data
• fc_exp_hphobe_djs_offsets_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• fc_n_exp_hphobes_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• fc_neighbor_map : core::pack::interaction_graph::SurfaceNode< V, E, G >
• fc_node_alt_state_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• fc_node_curr_state_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• fc_nodes_near_rotsub_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• fc_nodes_near_rotsub_bool_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• fcen10() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen10_ : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen12() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen12_ : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen6() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen6_ : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcenter : core::scoring::APBSConfig
• fd_ : core::import_pose::PDBSilentStruct
• Fdensity : core::scoring::electron_density::ElectronDensity
• Fdrhoc_dx : core::scoring::electron_density::ElectronDensity
• Fdrhoc_dy : core::scoring::electron_density::ElectronDensity
• Fdrhoc_dz : core::scoring::electron_density::ElectronDensity
• featurizer_state() : core::scoring::dssp::StrandPairingSet
• fetch_stored_derivatives() : core::optimization::LineMinimizationAlgorithm
• ff() : core::scoring::saxs::FormFactor
• ff_manager_ : core::scoring::saxs::SAXSEnergy
• ff_map_ : core::scoring::saxs::FormFactorManager , core::scoring::saxs::SAXSEnergy
• ff_ops_ : core::scoring::saxs::SAXSEnergy
• ff_values_ : core::scoring::saxs::FormFactor
• ff_vector_ : core::scoring::saxs::FormFactorManager
• fglen : core::scoring::APBSConfig
• FIBER_DIFFRACTION : core::io::pdb::HeaderInformation
• FIBER_DIFFRACTION_CEN_SCATTERING : core::pose::datacache::CacheableDataType
• FIBER_DIFFRACTION_FA_SCATTERING : core::pose::datacache::CacheableDataType
• 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
• fij_ : core::scoring::RDC
• file_data() : core::import_pose::PDBSilentStruct
• file_node_2_instance_node_ : core::pack::interaction_graph::PDInteractionGraph
• file_read_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• FileData() : core::io::pdb::FileData
• FileDataOptions() : core::io::pdb::FileDataOptions
• FileName : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• filename : core::io::pdb::FileData , core::io::raw_data::DisulfideFile , core::io::silent::SilentFileData , core::pack::task::operation::ReadResfile
• FileName : core::sequence::ChemicalShiftSequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• filename_ : core::io::raw_data::DecoyFileData , core::io::raw_data::DisulfideFile , core::io::raw_data::ScoreFileData , core::io::silent::SilentFileData , core::scoring::func::SplineFunc
• filenames() : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• filenames_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::PDBPoseInputStream , 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
• filled_substitution_history_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• filter() : core::pack::task::operation::OperateOnCertainResidues , core::scoring::motif::ResPairMotif
• filter_ : core::pack::task::operation::OperateOnCertainResidues
• filter_creator_map_ : core::pack::task::operation::ResFilterFactory
• filter_redundant() : core::scoring::motif::MotifHits
• FILTER_STAGE2_BEGINNING : core::pose::datacache::CacheableDataType
• FILTER_STAGE2_END : core::pose::datacache::CacheableDataType
• FILTER_STAGE2_HALF : core::pose::datacache::CacheableDataType
• FILTER_STAGE2_QUARTER : core::pose::datacache::CacheableDataType
• 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_axis_array_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_pair_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_array_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stack_axis_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
• 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_ : core::chemical::ResidueType
• finalized_energies() : core::scoring::Energies
• 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
• fine_centering_mode : core::scoring::APBSConfig::I_PARAM
• finish_arc() : core::scoring::packstat::trace
• finish_pose() : core::io::silent::SilentStruct
• first : core::fragment::FragID
• first_atom_in_branch() : core::scoring::trie::TrieNode< AT, CPDATA >
• first_atom_in_branch_ : core::scoring::trie::TrieNode< AT, CPDATA >
• first_class_node_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• first_class_node_index_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• first_nbr_ : core::optimization::ParticleSwarmMinimizer
• first_node_num_states_per_aatype_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• first_residue() : core::conformation::parametric::Parameters
• first_sidechain_atom() : core::chemical::ResidueType , core::conformation::Residue
• first_sidechain_hydrogen() : core::chemical::ResidueType , core::conformation::Residue
• first_sidechain_hydrogen_ : core::chemical::ResidueType
• first_time_prepping_for_simA_ : core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• first_upper_edge_ : core::graph::Node
• FirstClassEdge() : core::pack::interaction_graph::FirstClassEdge< V, E, G >
• FirstClassNode() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• FirstClassNodeVector : core::pack::interaction_graph::BackgroundNode< V, E, G >
• firstRes_ : core::scoring::methods::RG_LocalEnergy
• fit_intensities() : core::scoring::saxs::SAXSEnergy
• fitBfactors() : core::scoring::cryst::PhenixInterface
• fitness_ : core::optimization::Particle
• fitness_pbest() : core::optimization::Particle
• fitness_pbest_ : core::optimization::Particle
• fix_disulfides() : core::conformation::Conformation
• fix_his_tautomer() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• fix_his_tautomer_ : core::pack::task::ResidueLevelTask_
• FixbbCoupledRotamerSimAnnealer() : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• FixbbLinkingRotamerSimAnnealer() : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• FixbbRotamerSets() : core::pack::rotamer_set::FixbbRotamerSets
• FixbbRotamerSetsCOP : core::pack::annealer::FASTERAnnealer , core::pack::annealer::RotamerAssigningAnnealer
• FixbbSimAnnealer() : core::pack::annealer::FixbbSimAnnealer
• fixed() : core::scoring::OneToAllEnergyContainer
• fixed_ : core::scoring::OneToAllEnergyContainer
• fixed_atom_ : core::scoring::constraints::CoordinateConstraint
• fixed_atom_id_ : core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint
• fixed_dist() : core::scoring::RDC , core::scoring::RDC_Rohl
• fixed_domain_map() : core::pose::full_model_info::FullModelInfo
• fixed_energies() : core::scoring::MinimizationGraph
• fixed_energies_ : core::scoring::MinimizationGraph
• fixed_reference_point_ : core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint
• fixed_residue_ : core::scoring::methods::PoissonBoltzmannEnergy
• fixed_stub_ : core::scoring::constraints::LocalCoordinateConstraint
• FixedBBEdge() : core::pack::interaction_graph::FixedBBEdge
• FixedBBInteractionGraph() : core::pack::interaction_graph::FixedBBInteractionGraph
• FixedBBNode() : core::pack::interaction_graph::FixedBBNode
• flag_for_calculation() : core::scoring::FACTSResidueInfo
• 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_
• flip_HNQ_ : core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask_
• FLOATING_POINT_CLOUD_INFO : core::pose::datacache::CacheableDataType
• FLORECENCE_TRANSFER : core::io::pdb::HeaderInformation
• fluff() : core::grid::CartGrid< T >
• fmax_ : core::scoring::func::MixtureFunc , core::scoring::hbonds::FadeInterval
• fmin_ : core::scoring::hbonds::FadeInterval
• fn_ : core::scoring::methods::CustomAtomPairEnergy
• focus_ : core::pack::task::residue_selector::NeighborhoodResidueSelector
• focus_selector_ : core::pack::task::residue_selector::NeighborhoodResidueSelector
• focus_set_ : core::pack::task::residue_selector::NeighborhoodResidueSelector
• focus_str_ : core::pack::task::residue_selector::NeighborhoodResidueSelector
• focused_bg_edge_ : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• focused_edge() : core::graph::Graph
• focused_edge_ : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• focused_edge_iterator_ : core::pack::interaction_graph::InteractionGraphBase
• focused_edge_iterator_end_ : core::pack::interaction_graph::InteractionGraphBase
• focused_node_ : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator
• focused_residue_ : core::pack::scmin::SCMinMinimizerMap , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator
• 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_ : core::conformation::Conformation , 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
• fold_tree_io() : core::import_pose::ImportPoseOptions
• fold_tree_io_ : core::import_pose::ImportPoseOptions
• FoldTree : core::conformation::Conformation , core::kinematics::FoldTree
• FoldTreeOP : core::conformation::Conformation
• FoldTreeSketch() : core::environment::FoldTreeSketch
• follows : core::kinematics::Node
• 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_apix_ : core::scoring::electron_density::ElectronDensity
• force_bb_ : core::chemical::ResidueType
• force_bitflip() : core::io::silent::SilentStruct
• force_bitflip_ : core::io::silent::SilentStruct
• force_combined_gaussian_approximation() : core::scoring::func::GaussianChainFunc
• force_combined_gaussian_approximation_ : core::scoring::func::GaussianChainFunc
• force_constant_ : core::scoring::constraints::BackboneStubConstraint
• force_nbr_atom_orient() : core::chemical::ResidueType
• force_nbr_atom_orient_ : core::chemical::ResidueType , core::chemical::SetOrientAtom
• form_factors_ : core::scoring::fiber_diffraction::FAScatter
• formal_charge() : core::chemical::Atom , core::chemical::sdf::MolFileIOAtom
• formal_charge_ : core::chemical::Atom , core::chemical::sdf::MolFileIOAtom
• format_ : core::fragment::picking_old::vall::VallResidue
• format_2011_ : core::fragment::picking_old::vall::VallResidue
• 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
• found_match : core::indexed_structure_store::FragmentLookupResult
• FourPointsFunc() : core::scoring::func::FourPointsFunc
• frac2cart() : core::scoring::electron_density::ElectronDensity
• frac2index() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• frac_cav_ball_required_exposed : core::scoring::packstat::SasaOptions
• fraction_chain1_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• fraction_chain2_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• frag_cache_ : core::fragment::FragmentIO
• frag_factory_ : core::fragment::FragmentIO
• frag_id() : core::fragment::FragID_Iterator , core::fragment::Frame
• frag_list_ : core::fragment::Frame
• frag_size_ : core::fragment::picking_old::vall::gen::LengthGen
• frag_type() : core::fragment::FragFactory
• frag_types_ : core::fragment::FragFactory
• FragCache() : core::fragment::FragCache< T >
• FragData() : core::fragment::FragData , core::fragment::picking_old::vall::VallLibrarian
• FragDataOP : core::fragment::picking_old::vall::VallLibrarian
• FragDataOPs : core::fragment::picking_old::vall::VallLibrarian
• FragFactory() : core::fragment::FragFactory
• FragFileCache : core::fragment::FragmentIO
• FragID() : core::fragment::FragID
• fragID() : core::fragment::FrameList
• FragID_Iterator : core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_
• fragment() : core::fragment::FragID , core::fragment::FragmentRmsd , core::fragment::Frame
• FRAGMENT : core::io::pdb::HeaderInformation
• fragment_as_pose() : core::fragment::Frame
• fragment_atoms : core::indexed_structure_store::FragmentSpecification
• fragment_coordinates : core::indexed_structure_store::FragmentStore
• fragment_length : core::indexed_structure_store::FragmentSpecification
• fragment_ptr() : core::fragment::FragID , core::fragment::Frame
• fragment_specification() : core::indexed_structure_store::FragmentLookup , core::indexed_structure_store::FragmentStore
• fragment_threshold_distances : core::indexed_structure_store::FragmentStore
• 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
• fragments_ : core::fragment::FragmentRmsd
• FragmentSpecification() : core::indexed_structure_store::FragmentSpecification
• FragmentStore() : core::indexed_structure_store::FragmentStore
• FragRT : core::conformation::Conformation , core::kinematics::AtomTree
• FragSet() : core::fragment::FragSet
• fragset_list_ : core::fragment::FragSetCollection
• FragSetCollection() : core::fragment::FragSetCollection
• FragSetList : core::fragment::FragSetCollection
• FragStore() : core::fragment::FragStore< T >
• FragXYZ : core::conformation::Conformation , core::kinematics::AtomTree
• 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_types_ : core::fragment::FragFactory
• frame_vector() : core::fragment::FrameList
• FrameIterator() : core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_
• FrameList : core::fragment::FrameListIterator_
• FrameListIterator_() : core::fragment::FrameListIterator_
• FrameMap : core::fragment::FragmentRmsd , core::fragment::OrderedFragSet , core::fragment::OrderedFragSetIterator_
• frames() : core::fragment::FragSet , core::fragment::OrderedFragSet
• frames_ : core::fragment::ConstantLengthFragSet , core::fragment::FragmentRmsd , core::fragment::OrderedFragSet
• FrameTypes : core::fragment::FragFactory
• frdc : core::scoring::data_struct
• frdcDa : core::scoring::data_structDa
• frdcDaR : core::scoring::data_structDaR
• frdcR : core::scoring::data_structR
• free_2HOprime_bonus() : core::scoring::methods::FreeDOF_Options
• free_2HOprime_bonus_ : core::scoring::methods::FreeDOF_Options
• free_dof_options() : core::scoring::methods::EnergyMethodOptions
• free_dof_options_ : core::scoring::methods::EnergyMethodOptions
• free_res_weights_ : core::scoring::methods::FreeDOF_Energy
• free_side_chain_bonus() : core::scoring::methods::FreeDOF_Options
• free_side_chain_bonus_ : core::scoring::methods::FreeDOF_Options
• free_sugar_bonus() : core::scoring::methods::FreeDOF_Options
• free_sugar_bonus_ : core::scoring::methods::FreeDOF_Options
• free_suite_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
• Frho_calc : core::scoring::electron_density::ElectronDensity
• Frho_solv : core::scoring::electron_density::ElectronDensity
• from_bond_cst() : core::kinematics::Jump
• from_four_points() : core::kinematics::Stub
• from_stubs() : core::kinematics::Jump , core::kinematics::RT
• ft : core::kinematics::TreeVizBuilder
• FULL_MODEL_INFO : core::pose::datacache::CacheableDataType
• full_model_info_into_pose() : core::io::silent::SilentStruct
• full_model_parameters() : core::io::silent::SilentStruct , core::pose::full_model_info::FullModelInfo
• full_model_parameters_ : core::io::silent::SilentFileData , core::io::silent::SilentStruct , core::pose::full_model_info::FullModelInfo
• full_model_pose_for_constraints() : core::pose::full_model_info::FullModelParameters
• full_model_pose_for_constraints_ : core::pose::full_model_info::FullModelParameters
• full_name() : core::chemical::carbohydrates::CarbohydrateInfo
• 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_sequence_ : core::pose::full_model_info::FullModelParameters
• full_span_ : core::scoring::MembraneTopology
• full_stack_cutoff_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• 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
• 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
• fully_assigned_mm_bondangle_library_ : core::scoring::mm::MMBondAngleLibrary
• fully_assigned_mm_torsion_library_ : core::scoring::mm::MMTorsionLibrary
• fullyOccupied_ : core::grid::CartGrid< T >
• 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::optimization::GA_Minimizer , core::optimization::Minimizer , core::optimization::NelderMeadSimplex , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::ConstantConstraint , 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::custom_pair_distance::atoms_and_func_struct , core::scoring::custom_pair_distance::resatom_and_func_struct , core::scoring::func::EtableFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::MixtureFunc , core::scoring::loop_graph::LoopScoreInfo
• func_1d() : core::optimization::func_1d
• func_factory_ : core::scoring::constraints::ConstraintIO
• func_to_weight_ : core::scoring::func::CountViolFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SkipViolFunc
• func_types_ : core::scoring::func::FuncFactory
• FuncFactory : core::scoring::constraints::SequenceProfileConstraint , core::scoring::func::FuncFactory
• funcs() : core::scoring::func::SumFunc
• funcs_ : core::scoring::func::SumFunc , core::scoring::methods::CustomAtomPairEnergy
• FuncTypes : core::scoring::func::FuncFactory