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
• 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 , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• f2c_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• 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_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
• FA1Dd : protocols::toolbox::KClusterData
• FA2d : protocols::toolbox::KCluster , protocols::toolbox::KClusterData
• FA2Dd : protocols::toolbox::KCluster , protocols::toolbox::KClusterData
• FA2Pd : protocols::toolbox::KCluster , protocols::toolbox::KClusterData
• FA3Pd : protocols::toolbox::KClusterData
• 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_atr_weight_ : protocols::stepwise::screener::PartitionContactScreener
• fa_attr : protocols::features::helixAssembly::FragmentPair
• fa_center() : core::scoring::Membrane_FAEmbed
• fa_center_ : core::scoring::Membrane_FAEmbed
• fa_cfg_file_ : core::scoring::saxs::SAXSEnergy
• fa_constraints_ : protocols::constraints_additional::ConstraintEvaluator , protocols::topology_broker::ConstraintClaimer
• fa_cst_fn_ : protocols::hybridization::HybridizeProtocol
• fa_depth() : core::scoring::Membrane_FAEmbed
• fa_depth_ : core::scoring::Membrane_FAEmbed
• fa_disulfide_potential_ : core::scoring::ScoringManager
• fa_dock_slide_into_contact_ : protocols::docking::DockingPrepackProtocol
• fa_dun_cutoff() : protocols::match::upstream::BuildSet
• fa_dun_cutoff_ : protocols::match::upstream::BuildSet
• fa_dun_danger_ : protocols::fldsgn::filters::CoreDunbrackFilter
• 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_filename_ : protocols::topology_broker::ConstraintClaimer
• fa_fraction : protocols::features::helixAssembly::FragmentPair
• 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_pose_ : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• 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_relax_stage() : protocols::forge::remodel::RemodelLoopMover
• fa_rep_cut_ : protocols::matdes::BuildingBlockInterfaceOperation
• fa_rep_weight_ : protocols::stepwise::screener::PartitionContactScreener
• fa_score() : protocols::abinitio::IterativeBase
• fa_score_ : protocols::abinitio::IterativeBase
• fa_score_patch() : protocols::abinitio::IterativeBase
• fa_score_patch_ : protocols::abinitio::IterativeBase
• fa_scorefxn() : protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover
• fa_scorefxn_ : protocols::antibody_legacy::CDRH3Modeler , protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover , protocols::hybridization::CartesianSampler , protocols::hybridization::HybridizeProtocol , protocols::hybridization::MRMover , protocols::rbsegment_relax::AutoRBMover , protocols::relax::CentroidRelax , protocols::seeded_abinitio::CloseFold , protocols::sewing::AssemblyMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• 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
• facet_alpha_ : protocols::match::Bool3DGridKinemageWriter
• facet_color_ : protocols::match::Bool3DGridKinemageWriter
• facet_master_ : protocols::match::Bool3DGridKinemageWriter
• factor() : core::scoring::dna::TorsionFourierComponent
• factor_ : core::scoring::dna::TorsionFourierComponent , core::scoring::saxs::DistanceHistogram
• factorA() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorA_ : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorB() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorB_ : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorC() : protocols::simple_moves::BBConRotMover
• factorC_ : protocols::simple_moves::BBConRotMover
• factors_ : protocols::scoring::methods::saxs::PDDFEnergy
• factory_ : protocols::flexpack::FlexPacker , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::InterbondAngleScore , protocols::metal_interface::ZincHeterodimerMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TaskAwareMinMover
• factory_begin() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_clear() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_end() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_iterator : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_name() : protocols::genetic_algorithm::EntityElementFactory
• factory_register() : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::io::silent::SilentStructFactory , core::pack::rotamers::SingleResidueRotamerLibraryFactory , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , core::scoring::constraints::ConstraintFactory , core::scoring::ScoringManager , core::select::residue_selector::ResidueSelectorFactory , core::sequence::SequenceFactory , protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::jd2::JobInputterFactory , protocols::jd2::JobOutputterFactory , protocols::jd2::parser::DataLoaderFactory , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::moves::MoverFactory , protocols::qsar::scoring_grid::GridFactory , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::rotamer_recovery::RotamerRecoveryFactory , protocols::sewing::sampling::requirements::RequirementFactory
• 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_width_ : protocols::electron_density::ScaleMapIntensities
• fade_zone() : core::scoring::func::FadeFunc
• fade_zone_ : core::scoring::func::FadeFunc
• FadeFunc() : core::scoring::func::FadeFunc
• FadeInterval() : core::scoring::hbonds::FadeInterval
• FaDockingSlideIntoContact() : protocols::docking::FaDockingSlideIntoContact
• FAELEC_CONTEXT_DATA : core::pose::datacache::CacheableDataType
• FAElecContextData() : core::scoring::elec::FAElecContextData
• fafilter() : protocols::loophash::LoopHashMoverWrapper
• fafilter_ : protocols::loophash::LoopHashMoverWrapper
• fail_on_constraints_missing_ : protocols::enzdes::AddOrRemoveMatchCsts
• fail_verification() : protocols::environment::ProtectedConformation
• fake_working_moving_suite : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• fallback() : protocols::antibody::design::CDRSeqDesignOptions
• fallback_resource_descriptions_created_ : protocols::jd2::JD2ResourceManager
• fallback_specified() : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• fallback_strategy() : protocols::antibody::design::CDRSeqDesignOptions
• fallback_strategy_ : protocols::antibody::design::CDRSeqDesignOptions
• false_behavior() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• false_behavior_ : protocols::toolbox::task_operations::StoreCompoundTaskMover
• false_movemap() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• false_movemap_ : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• false_mover_ : protocols::moves::IfMover
• FalseFilter() : protocols::filters::FalseFilter
• FaMPEnvEnergy() : core::scoring::membrane::FaMPEnvEnergy
• FaMPEnvSmoothEnergy() : core::scoring::membrane::FaMPEnvSmoothEnergy
• FaMPSolvEnergy() : core::scoring::membrane::FaMPSolvEnergy
• FARFAR_setup_using_user_input_VDW_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• FARNA_Optimizer() : protocols::farna::FARNA_Optimizer
• FArray1_real : core::scoring::SecondaryStructurePotential
• FArray1A_real : core::scoring::SecondaryStructurePotential
• FArray1D_int : core::scoring::Helices , core::scoring::SecondaryStructurePotential , core::scoring::Strands , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• FArray1D_real : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• FArray2D_int : core::scoring::Helices , core::scoring::Strands
• FArray2D_PackerEnergy : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• FArray2D_real : core::scoring::SecondaryStructurePotential
• FArray3D_Real : core::scoring::dna::DNA_BasePotential
• FArray4D_Real : core::scoring::dna::DNA_BasePotential
• FArray4D_real : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• farray_coord_ptr_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• farray_to_array() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• farray_to_string() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• FAScatter() : core::scoring::fiber_diffraction::FAScatter
• fascore() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• FASelectSlidingWindowLoopClosure() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• 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
• fast() : protocols::idealize::IdealizeMover
• fast_ : protocols::idealize::IdealizeMover , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• fast_build_ : protocols::forge::remodel::RemodelMover::instruction_flags
• fast_calc_ : protocols::simple_filters::RotamerBoltzmannWeight
• fast_ccd_close_loops() : protocols::LoopRebuild
• fast_forward() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::IntegrationTestBreaker , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::StepWiseResiduePairScreener , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::VDW_BinScreener
• fast_forward_to_end() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• fast_forward_to_next_euler_gamma() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_forward_to_next_residue() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• fast_forward_to_next_residue_pair() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• fast_forward_to_next_rigid_body() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_forward_to_next_translation() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_full_atom_VDW_repulsion_screen : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• fast_loopclose() : protocols::seeded_abinitio::CloseFold
• fast_relax_rounds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• fast_sample_torsions_from_info() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• fast_scan() : protocols::farna::movers::RNA_LoopCloser
• fast_scan_ : protocols::farna::movers::RNA_LoopCloser
• fasta2template_ : protocols::comparative_modeling::ThreadingJob
• fastdens_perres_weights_ : core::scoring::methods::EnergyMethodOptions
• fastdens_score : core::scoring::electron_density::ElectronDensity
• FastDensEnergy() : core::scoring::electron_density::FastDensEnergy
• FASTER_IG_Repacker() : protocols::pack_daemon::FASTER_IG_Repacker
• FASTERAnnealer() : core::pack::annealer::FASTERAnnealer
• FASTEREdge() : core::pack::interaction_graph::FASTEREdge
• FASTERInteractionGraph() : core::pack::interaction_graph::FASTERInteractionGraph
• FASTERInteractionGraphOP : protocols::pack_daemon::FASTER_IG_Repacker
• FASTERNode() : core::pack::interaction_graph::FASTERNode
• FastForwardToNextResidueAlternative() : protocols::stepwise::screener::FastForwardToNextResidueAlternative
• FastForwardToNextRigidBody() : protocols::stepwise::screener::FastForwardToNextRigidBody
• FastGapMover() : protocols::loophash::FastGapMover
• fastgrid : core::scoring::electron_density::ElectronDensity
• FastLinearFunc() : protocols::moves::FastLinearFunc
• fastorigin : core::scoring::electron_density::ElectronDensity
• FastRelax() : protocols::relax::FastRelax
• fastrelax_ : protocols::loophash::LoopHashMoverWrapper
• FastSAXSEnergy() : core::scoring::saxs::FastSAXSEnergy
• FastSAXSEnergyCreator() : core::scoring::saxs::FastSAXSEnergyCreator
• FaSymDockingSlideTogether() : protocols::simple_moves::symmetry::FaSymDockingSlideTogether
• favor_bonus_ : protocols::simple_moves::ResidueTypeConstraintMover
• favor_native_bonus_ : core::scoring::constraints::ResidueTypeConstraint
• favor_native_constraints_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• favor_non_native_bonus_ : core::scoring::constraints::NonResidueTypeConstraint
• favorable_energies : protocols::vip::VIP_Mover
• favorable_mutations : protocols::vip::VIP_Mover
• favorable_positions : protocols::vip::VIP_Mover
• favorable_residues : protocols::vip::VIP_Mover
• favored_rotamer_numbers_ : core::pack::dunbrack::RotamerConstraint
• favored_rotamers_ : core::pack::dunbrack::RotamerConstraint
• FavorNativeResidue() : protocols::protein_interface_design::FavorNativeResidue
• FavorNativeResiduePreCycle() : protocols::protein_interface_design::movers::FavorNativeResiduePreCycle
• FavorNonNativeResidue() : protocols::protein_interface_design::FavorNonNativeResidue
• FavorNonNativeResiduePreCycle() : protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle
• FavorSequenceProfile() : protocols::simple_moves::FavorSequenceProfile
• FavorSymmetricSequence() : protocols::simple_moves::FavorSymmetricSequence
• 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
• Fdensity : core::scoring::electron_density::ElectronDensity
• feature_types_ : protocols::comparative_modeling::features::ResidueFeatureFactory
• features_reporter_dependencies() : protocols::antibody::clusters::CDRClusterFeatures , protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomTypesFeatures , protocols::features::BatchFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ChargeChargeFeatures , protocols::features::DdGFeatures , protocols::features::FeaturesReporter , protocols::features::GeometricSolvationFeatures , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceFeatures , protocols::features::JobDataFeatures , protocols::features::LoopAnchorFeatures , protocols::features::ModelFeatures , protocols::features::OrbitalsFeatures , protocols::features::PairFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ProtocolFeatures , protocols::features::RadiusOfGyrationFeatures , protocols::features::ResidueBurialFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTypesFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::RuntimeFeatures , protocols::features::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures
• features_reporter_factory_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• features_reporters_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• FeaturesReporter() : protocols::features::FeaturesReporter
• FeaturesReporterCreator() : protocols::features::FeaturesReporterCreator
• FeaturesReporterCreatorMap : protocols::features::FeaturesReporterFactory
• FeaturesReporterFactory() : protocols::features::FeaturesReporterFactory
• FeaturesReporterRegistrator() : protocols::features::FeaturesReporterRegistrator< T >
• FeaturesReporters : protocols::features::Report
• featurizer_state() : core::scoring::dssp::StrandPairingSet
• feedback_structure_to_emperor() : protocols::mpi_refinement::MPI_Refine_Master
• feedback_structures_to_emperor() : protocols::mpi_refinement::MPI_Refine_Master
• fetch() : protocols::match::output::UpstreamHitCacher
• fetch_foldtree : protocols::seeded_abinitio::GrowPeptides
• fetch_stored_derivatives() : core::optimization::LineMinimizationAlgorithm
• ff() : core::scoring::saxs::FormFactor
• ff_manager_ : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• 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
• fi_ : protocols::frag_picker::DiversifyCrmsdSelector
• FIBER_DIFFRACTION : core::io::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
• FibrilModelingClaimer() : protocols::topology_broker::FibrilModelingClaimer
• Field() : core::io::pdb::Field
• field_ : protocols::wum::find_SilentStructOPs , protocols::wum::sort_SilentStructOPs
• field_message() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• figure_out_actual_sample_res() : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• figure_out_all_possible_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• figure_out_already_docked() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• figure_out_and_remove_dangling_ends() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• figure_out_appended_and_prepended_res_list() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• figure_out_attachment() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• figure_out_best_working_alignment() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_box_bounds() : protocols::magnesium::SampleGrid
• figure_out_chain_boundaries() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_chi_order() : core::chemical::rna::RNA_ResidueType
• figure_out_chunk_coverage() : protocols::farna::libraries::RNA_ChunkLibrary
• figure_out_constraint_separation_cutoff() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_FragmentMonteCarlo
• figure_out_cuts() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_dof_ids_and_offsets() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• figure_out_dofs() : core::pose::copydofs::CopyDofs
• figure_out_first_res_in_pose() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• figure_out_fold_tree() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• figure_out_forward_backward_res_by_backtracking() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_from_scratch_delete_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• figure_out_gap_size_and_first_chain_break_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• figure_out_gap_size_and_five_prime_chain_break_res() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_is_prepend_map() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_is_residue_prepend() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_jump_partners() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_last_appended_and_last_prepended_res() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• figure_out_last_patch_from_name() : core::chemical::ResidueTypeSet
• figure_out_loop() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• figure_out_loop_cycles() : core::scoring::loop_graph::LoopGraph
• figure_out_loop_cycles_legacy() : core::scoring::loop_graph::LoopGraph
• figure_out_loop_cycles_tiernan() : core::scoring::loop_graph::LoopGraph
• figure_out_low_resolution_potential() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• figure_out_movemap() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• figure_out_moving_res_list() : protocols::stepwise::modeler::StepWiseModeler
• figure_out_moving_res_list_from_most_distal_res() : protocols::stepwise::modeler::StepWiseModeler
• figure_out_neighbors() : protocols::stepwise::modeler::packer::StepWisePacker
• figure_out_NUM_pose_list() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• figure_out_offset() : core::scoring::rna::RNA_SuitePotential , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• figure_out_partition_definition() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_partner() : protocols::farna::base_pairs::RNA_BasePairHandler
• figure_out_pivot_res_and_scratch_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_pivots() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_potential() : core::scoring::rna::data::RNA_DMS_Potential
• figure_out_prepack_res_ : protocols::stepwise::modeler::StepWiseModeler
• figure_out_Prepend_Internal() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• figure_out_prepend_internal() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_reference_res() : protocols::stepwise::modeler::StepWiseConnectionSampler
• figure_out_reference_res_with_rigid_body_rotamer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• 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
• figure_out_scan_res() : protocols::magnesium::SampleGrid
• figure_out_segment_ids_from_line() : core::io::silent::SilentStruct
• figure_out_which_cutpoints_were_affected() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_working_alignment() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_working_minimize_res() : protocols::stepwise::modeler::StepWiseMinimizer
• figure_out_working_moving_suite() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_working_sequence_and_mapping() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• fij() : core::scoring::RDC
• fij_ : core::scoring::RDC
• file() : protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter
• file_ : protocols::canonical_sampling::PatchOperation , protocols::canonical_sampling::TrialCounterObserver
• file_2_data_map_ : protocols::scoring::methods::pcs::PCS_data_input_manager , protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4
• file_buf_rank() : protocols::jd2::MPIFileBufJobDistributor
• file_buf_rank_ : protocols::jd2::archive::ArchiveManager , protocols::jd2::MPIFileBufJobDistributor
• file_buffer : protocols::checkpoint::CheckPointer
• file_buffer_size() : protocols::checkpoint::CheckPointer
• file_contents_ : protocols::pack_daemon::DynamicAggregateFunction
• file_inputs_for_job() : protocols::pack_daemon::DynamicAggregateFunction
• file_name() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• file_name_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder , protocols::constraints_additional::ConstraintEvaluator
• file_name_prefix_ : protocols::protein_interface_design::movers::MapHotspot
• file_names() : protocols::simple_filters::FileRemoveFilter
• file_names_ : protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::MultipleSigmoids
• file_node_2_instance_node_ : core::pack::interaction_graph::PDInteractionGraph
• file_out_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• file_read() : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• file_read_ : core::import_pose::atom_tree_diffs::AtomTreeDiff , protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• file_reading_token() : protocols::loops::Loops
• file_reading_token_ : protocols::loops::Loops
• file_to_read_ : protocols::ddG::ddGData
• file_was_read_ : core::pack::task::operation::ReadResfile
• FileBuffer() : protocols::checkpoint::FileBuffer
• FileConstraintGenerator() : protocols::denovo_design::constraints::FileConstraintGenerator
• FileExistFilter() : protocols::simple_filters::FileExistFilter
• FileJobOutputter() : protocols::jd2::FileJobOutputter
• FileList : protocols::comparative_modeling::ThreadingJobInputter
• FileName : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• filename() : core::io::raw_data::DisulfideFile , core::io::silent::SilentFileData , core::io::StructFileRep , core::pack::task::operation::ReadResfile
• FileName : core::sequence::ChemicalShiftSequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• filename() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::jd2::JobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::SingleFileBuffer , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakFileFormat_Base , protocols::simple_filters::FileExistFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_moves::LoadPDBMover
• filename_ : core::io::raw_data::DecoyFileData , core::io::raw_data::DisulfideFile , core::io::raw_data::ScoreFileData , core::io::silent::SilentFileData , core::io::StructFileRep , core::scoring::func::SplineFunc , protocols::abinitio::abscript::ConstraintPreparer , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::checkpoint::FileBuffer , protocols::denovo_design::constraints::FileConstraintGenerator , protocols::farna::setup::RNA_DeNovoParameters , protocols::jd2::parser::FragmentReader , protocols::jd2::SingleFileBuffer , protocols::loophash::EXCN_DB_IO_Failed , protocols::loophash::EXCN_Wrong_DB_Format , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakFileFormat_Base , protocols::qsar::RenderGridsToKinemage , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4 , protocols::simple_filters::FileExistFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_moves::LoadPDBMover , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• filename_root_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• filenames() : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• Filenames : protocols::jd2::MpiFileBuffer
• FileNames : protocols::motifs::MotifLibrary
• filenames() : protocols::simple_filters::StemFinder
• filenames_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::simple_filters::StemFinder , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• FileRemoveFilter() : protocols::simple_filters::FileRemoveFilter
• files_for_state_ : protocols::pack_daemon::DynamicAggregateFunction
• FileSystemJobDistributor() : protocols::jd2::FileSystemJobDistributor
• fill() : core::id::AtomID_Map< T > , core::id::NamedAtomID_Map< T > , core::pose::PDBPoseMap , protocols::hotspot_hashing::HotspotStubSet , protocols::pockets::PocketGrid
• fill_atom_arrays_() : protocols::pockets::DarcParticleSwarmMinimizer
• fill_atom_arrays_for_electrostatics_() : protocols::pockets::DarcParticleSwarmMinimizer
• fill_atom_numbers_for_backbone_oxygens() : core::scoring::rna::RNA_LowResolutionPotential
• fill_backbone_array() : core::io::rna::RNA_DataReader
• fill_bb_coords() : protocols::frag_picker::scores::FragmentChunkCrms
• fill_bins() : core::scoring::dna::DirectReadoutPotential
• fill_by_crossover() : protocols::genetic_algorithm::GeneticAlgorithmBase
• fill_by_mutation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• fill_CA_coords() : protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• fill_cenlist() : core::scoring::EnvPairPotential
• fill_chain_info() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• fill_chainTORS() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• fill_chainTORS_info() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• fill_compound_records() : core::io::HeaderInformation
• fill_contacts() : protocols::contact_map::ContactMap
• fill_coordinates() : protocols::evaluation::PCA
• fill_coords() : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• fill_covalent_gammas() : protocols::noesy_assign::PeakAssignmentResidueMap
• fill_data() : core::scoring::sasa::SasaCalc
• fill_data_annotations_if_empty() : core::io::rna::RDAT
• fill_data_from_features() : core::io::rna::RDAT
• fill_denovo_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• fill_designable_set() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• fill_energy_map() : core::scoring::EnergyEdge
• fill_energy_vector() : protocols::simple_moves::ddG
• fill_espGrid_values() : protocols::pockets::ElectrostaticpotentialGrid
• fill_espGrid_values_with_type() : protocols::pockets::ElectrostaticpotentialGrid
• fill_experimental_technique_records() : core::io::HeaderInformation
• fill_f1_f2() : core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::aa_composition_energy::SequenceConstraint , 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 , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::pockets::PocketConstraint
• fill_from_spanfile() : core::conformation::membrane::SpanningTopology
• fill_from_string() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• fill_from_string_cs() : protocols::frag_picker::VallResidue
• fill_from_string_residue_depth_version1() : protocols::frag_picker::VallResidue
• fill_from_string_version1() : protocols::frag_picker::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::HeaderInformation
• 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_input_cache() : protocols::rosetta_scripts::MultiplePoseMover
• fill_jobs() : protocols::comparative_modeling::GenericJobInputter , protocols::comparative_modeling::ThreadingJobInputter , protocols::features::DatabaseJobInputter , protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::BatchJobInputter , protocols::jd2::EnsembleJobInputter , protocols::jd2::JD2ResourceManagerJobInputter , protocols::jd2::JobInputter , protocols::jd2::LargeNstructJobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::ScreeningJobInputter , protocols::jd2::SilentFileJobInputter , protocols::make_rot_lib::MakeRotLibJobInputter
• fill_jobs_from_stream() : protocols::jd2::JD2ResourceManagerJobInputter
• fill_keyword_records() : core::io::HeaderInformation
• fill_missing_atoms() : core::conformation::Conformation , core::conformation::Residue , core::pack::rotamers::SingleLigandRotamerLibrary , protocols::environment::ProtectedConformation
• fill_moves_for_other_poses() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• fill_moves_for_pose() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• fill_mutations_list() : protocols::pmut_scan::PointMutScanDriver
• fill_name_map() : core::io::pose_from_sfr::PoseFromSFRBuilder
• fill_num_neighbors() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• fill_other_struct_list() : core::io::silent::SilentStruct
• fill_pairing_dists() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• fill_parameter_values() : core::pose::full_model_info::FullModelParameters
• fill_per_residue_energy_vector() : protocols::simple_moves::ddG
• fill_point_graph() : core::scoring::Energies , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricEnergies
• fill_pool() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• 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::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::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::rotamers::SingleBasicRotamerLibrary , core::pack::rotamers::SingleLigandRotamerLibrary , core::pack::rotamers::SingleResidueRotamerLibrary
• fill_rotamer_vector_bbdep() : 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_solution() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• 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_struct_with_submotif_info_list() : 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::HeaderInformation
• fill_top_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• fill_vary_loop_length_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• fill_water_grid() : core::scoring::geometric_solvation::WaterWeightGridSet
• fill_with() : core::id::AtomID_Map< T >
• fill_with_perturbations_of_existing_entities() : protocols::genetic_algorithm::GeneticAlgorithmBase
• fill_with_random_entities() : protocols::genetic_algorithm::GeneticAlgorithmBase
• fill_with_value() : protocols::qsar::qsarMap , protocols::qsar::scoring_grid::SingleGrid
• fill_wrapped_records() : core::io::HeaderInformation
• fillarray() : protocols::sic_dock::XfoxmScore
• filled_substitution_history_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• fillTargetPockets() : protocols::pockets::PocketGrid
• filter() : core::pack::task::operation::OperateOnCertainResidues , core::scoring::motif::ResPairMotif , protocols::anchored_design::AnchoredDesignMover
• Filter : protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::filters::Filter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter
• filter() : protocols::hotspot_hashing::HotspotStubSet
• Filter : protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter
• filter() : protocols::moves::IteratedConvergenceMover
• Filter() : protocols::pose_selectors::Filter
• filter() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• Filter : protocols::simple_filters::ConservedPosMutationFilter
• filter() : protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter
• Filter : protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter
• filter() : protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ReportFilter
• Filter : protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter
• filter() : protocols::simple_filters::Sigmoid
• Filter : protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter
• filter() : protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ddG , protocols::simple_moves::ResetBaselineMover , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_ : core::pack::task::operation::OperateOnCertainResidues , protocols::cluster::GatherPosesMover , protocols::docking::DockMCMProtocol , protocols::enzdes::RemoveLigandFilter , protocols::flxbb::FlxbbDesignPack , protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::loop_modeling::utilities::LoopFilter , protocols::moves::FilterReporterMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::pose_reporters::FilterReporter , protocols::pose_selectors::Filter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::Sigmoid , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ddG , protocols::simple_moves::ResetBaselineMover
• filter_add_submotif_moves_to_not_redock_domain() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• filter_all_patch_names() : core::chemical::ResidueTypeFinder
• filter_all_properties() : core::chemical::ResidueTypeFinder
• filter_all_variants_matched() : core::chemical::ResidueTypeFinder
• filter_and_save() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_atom_id_map_with_mask() : protocols::farna::libraries::ChunkSet
• filter_based_on_desired_secstruct() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_behaviour() : protocols::helical_bundle::BundleReporterFilter
• filter_beta : protocols::loophash::FilterBucket
• filter_big_bin() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_by_aa() : core::chemical::ResidueTypeFinder
• filter_by_base_property() : core::chemical::ResidueTypeFinder
• filter_by_interchangeability_group() : core::chemical::ResidueTypeFinder
• filter_by_lj() : protocols::match::output::MatchCollisionFilter
• filter_by_lj_ : protocols::match::output::MatchCollisionFilter
• filter_by_name1() : core::chemical::ResidueTypeFinder
• filter_by_name3() : core::chemical::ResidueTypeFinder
• filter_by_phipsi_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• filter_by_residue_type_base_name() : core::chemical::ResidueTypeFinder
• filter_chain_closure() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_chain_closure_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_chain_closure_distance() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_chain_closure_distance_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_chain_closure_halfway() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_chain_closure_halfway_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_complex_cycles() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• filter_complex_cycles_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• filter_creator_map_ : core::pack::task::operation::ResFilterFactory , protocols::filters::FilterFactory
• filter_cst_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• filter_cst_weight_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• filter_deltas() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_deltas_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_disallow_properties() : core::chemical::ResidueTypeFinder
• filter_disallow_variants() : core::chemical::ResidueTypeFinder
• filter_during_design_ : protocols::flxbb::FlxbbDesign
• filter_failcounts_ : protocols::match::output::MatchProcessor
• filter_for_chain_closable_geometry_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_for_moving_res_contact : protocols::stepwise::modeler::rna::Filterer_Count
• filter_for_moving_res_contact_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_for_previous_clash : protocols::stepwise::modeler::rna::Filterer_Count
• filter_for_previous_clash_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_for_previous_contact : protocols::stepwise::modeler::rna::Filterer_Count
• filter_for_previous_contact_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_gly : protocols::loophash::FilterBucket
• filter_helix_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• filter_helix_sheet_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• filter_intrabb_ : protocols::matdes::BuildingBlockInterfaceOperation
• filter_is_over() : protocols::flxbb::FilterStructs
• filter_loop_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• filter_lores_base_pairs() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_lores_base_pairs_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_lores_base_pairs_early() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_lores_base_pairs_early_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• filter_main_chain_torsion_sets() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_max_angle() : protocols::fldsgn::filters::HSSTripletFilter
• filter_max_angle_ : protocols::fldsgn::filters::HSSTripletFilter
• filter_max_dist() : protocols::fldsgn::filters::HSSTripletFilter
• filter_max_dist_ : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_angle() : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_angle_ : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_dist() : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_dist_ : protocols::fldsgn::filters::HSSTripletFilter
• filter_mode_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• filter_mover_ : protocols::moves::FilterReporterMover
• filter_name() : protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator , protocols::denovo_design::filters::PreProlineFilterCreator , protocols::match::output::MatchFilter , protocols::simple_filters::RelativePoseFilter , protocols::topology_broker::ConstraintClaimer
• filter_name_ : protocols::match::output::MatchFilter , protocols::simple_filters::RelativePoseFilter , protocols::topology_broker::ConstraintClaimer
• filter_names() : protocols::match::MatcherTask
• filter_names_ : protocols::match::MatcherTask
• filter_native_big_bins() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• filter_native_BIG_BINS() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_native_big_bins() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• filter_native_big_bins_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• filter_on() : protocols::flxbb::FilterStructs
• filter_on_ : protocols::flxbb::FilterStructs
• filter_params_bool_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• filter_params_real_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• filter_params_size_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• filter_params_string_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• filter_pareto_opt_poses() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_path() : protocols::coarse_rna::CoarseRNA_LoopCloser
• filter_pose_order() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• filter_poses_have_same_sequence_and_variants() : protocols::farna::libraries::ChunkSet
• filter_pro : protocols::loophash::FilterBucket
• filter_redundant() : core::scoring::motif::MotifHits
• filter_SASA_ : protocols::anchored_design::AnchoredDesignMover
• filter_score() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• filter_score_ : protocols::anchored_design::AnchoredDesignMover
• filter_seqpos_pareto_opt_ptmuts() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_sheet_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• filter_similar() : protocols::mpi_refinement::MultiObjective
• filter_solutions() : protocols::generalized_kinematic_closure::GeneralizedKIC
• filter_special_cases() : core::chemical::ResidueTypeFinder
• FILTER_STAGE2_BEGINNING : core::pose::datacache::CacheableDataType
• filter_stage2_beginning : protocols::relax::ClassicRelax
• FILTER_STAGE2_END : core::pose::datacache::CacheableDataType
• filter_stage2_end : protocols::relax::ClassicRelax
• FILTER_STAGE2_HALF : core::pose::datacache::CacheableDataType
• filter_stage2_half : protocols::relax::ClassicRelax
• FILTER_STAGE2_QUARTER : core::pose::datacache::CacheableDataType
• filter_stage2_quarter : protocols::relax::ClassicRelax
• filter_structs() : protocols::flxbb::DesignTask
• filter_structs_ : protocols::flxbb::DesignTask
• filter_structurally_identical_motifs() : core::scoring::motif::ResPairMotifs
• filter_structurally_similar_motifs() : core::scoring::motif::ResPairMotifs
• filter_templates() : protocols::hybridization::FoldTreeHybridize
• filter_templates_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• filter_thresholds() : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• filter_thresholds_ : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• filter_type() : protocols::fldsgn::filters::CoreDunbrackFilter
• filter_upstream_and_downstream_collisions_by_score_ : protocols::match::MatcherTask
• filter_upstream_and_downstream_residue_collisions_ : protocols::match::MatcherTask
• filter_upstream_collisions_by_score() : protocols::match::MatcherTask
• filter_upstream_collisions_by_score_ : protocols::match::MatcherTask
• filter_upstream_downstream_collisions() : protocols::match::MatcherTask
• filter_upstream_downstream_collisions_by_score() : protocols::match::MatcherTask
• filter_upstream_residue_collisions() : protocols::match::MatcherTask
• filter_upstream_residue_collisions_ : protocols::match::MatcherTask
• filter_user_alignment_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• filter_val() : protocols::simple_filters::ReportFilter
• filter_val_ : protocols::simple_filters::ReportFilter
• filter_value() : protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• filter_value_ : protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• filter_virtual_atoms() : protocols::stepwise::modeler::align::StepWisePoseAligner
• filter_virtual_res_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• filter_weight() : protocols::topology_broker::ConstraintClaimer
• filter_weight_ : protocols::topology_broker::ConstraintClaimer
• FilterBucket() : protocols::loophash::FilterBucket
• FilterCreator() : protocols::filters::FilterCreator
• filtered_abego() : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_abego_ : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_area() : protocols::simple_filters::ShapeComplementarityFilter
• filtered_area_ : protocols::simple_filters::ShapeComplementarityFilter
• 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
• filtered_sc() : protocols::simple_filters::ShapeComplementarityFilter
• filtered_sc_ : protocols::simple_filters::ShapeComplementarityFilter
• filtered_score() : protocols::simple_filters::PackStatFilter
• filtered_score_ : protocols::simple_filters::PackStatFilter
• filtered_sheet_topology() : protocols::fldsgn::filters::SheetTopologyFilter
• filtered_sheet_topology_ : protocols::fldsgn::filters::SheetTopologyFilter
• filtered_ss() : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_ss_ : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_type() : protocols::fldsgn::filters::FragQualFilter
• filtered_type_ : protocols::fldsgn::filters::FragQualFilter
• filtered_value() : protocols::fldsgn::filters::FragQualFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::SSElementMotifContactFilter
• filtered_value_ : protocols::fldsgn::filters::FragQualFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::SSElementMotifContactFilter
• FilteredSolutions() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• Filterer_Count() : protocols::stepwise::modeler::rna::Filterer_Count
• filterer_count_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filterered_combine_tag_info_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• FilterFactory() : protocols::filters::FilterFactory
• FilterList : protocols::filters::CombinedFilter
• filterlist_ : protocols::filters::CombinedFilter , protocols::generalized_kinematic_closure::GeneralizedKIC
• FilterMap : protocols::filters::FilterFactory
• FilterMover() : protocols::moves::FilterMover
• FilterOP : protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::moves::FilterMover , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::GenericMonteCarloMover
• FilterRegistrator() : protocols::filters::FilterRegistrator< T >
• FilterReporter() : protocols::pose_reporters::FilterReporter
• FilterReporterMover() : protocols::moves::FilterReporterMover
• filters() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::simple_filters::Operator , protocols::simple_moves::GenericMonteCarloMover
• filters_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingLowResFilter , protocols::filters::CalculatorFilter , protocols::filters::FilterCollection , protocols::frag_picker::FragmentPicker , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::output::MatchProcessor , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::simple_filters::Operator , protocols::simple_moves::GenericMonteCarloMover
• Filters_map : protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::moves::DsspMover , protocols::moves::Mover , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• filters_with_state_ : protocols::match::output::MatchProcessor
• FilterScanFilter() : protocols::protein_interface_design::filters::FilterScanFilter
• FilterStructs() : protocols::flxbb::FilterStructs
• FilterStructs_Packstat() : protocols::flxbb::FilterStructs_Packstat
• FilterStructs_TotalCharge() : protocols::flxbb::FilterStructs_TotalCharge
• FilterStructsOP : protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Layer , protocols::flxbb::DesignTask_Normal , protocols::flxbb::FlxbbDesignPack
• filtertype_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• FilterWeightPair : protocols::filters::CombinedFilter
• final : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• final_check_sw_by_dis() : protocols::features::strand_assembly::StrandBundleFeatures
• final_cleanup() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• final_correct_oop_post_ : protocols::ncbb::oop::OopCreatorMover
• final_design_min_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• final_dist_power_ : protocols::noesy_assign::DistanceScoreMover
• final_energy : protocols::vip::VIP_Mover
• final_filter_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::TryRotamers
• final_fold_tree() : protocols::abinitio::KinematicControl , protocols::topology_broker::TopologyBroker
• final_fold_tree_ : protocols::abinitio::KinematicControl , protocols::topology_broker::TopologyBroker
• final_ft_ : protocols::abinitio::abscript::AbscriptLoopCloserCM
• final_iter() : protocols::mpi_refinement::Scheduler
• final_mc_ : protocols::ncbb::oop::OopCreatorMover
• final_min_ : protocols::carbohydrates::GlycanRelaxMover
• final_minimize_ : protocols::ncbb::oop::OopCreatorMover
• final_pose() : protocols::dna::PDBOutput , protocols::enzdes::EnzdesJobOutputter , protocols::features::DatabaseJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::vip::VIP_Mover
• final_repack() : protocols::grafting::AnchoredGraftMover
• final_repack_ : protocols::grafting::AnchoredGraftMover , protocols::ncbb::oop::OopCreatorMover
• final_rmsd_ : protocols::pose_length_moves::PossibleLoop
• final_rotamers_ : protocols::make_rot_lib::MakeRotLibMover
• final_sampling() : protocols::residue_optimization::MetapatchEnumeration
• final_score() : protocols::farna::RNA_FragmentMonteCarlo , protocols::rosetta_scripts::ParsedProtocol
• final_scorefxn() : protocols::rosetta_scripts::ParsedProtocol
• final_scorefxn_ : protocols::farna::RNA_FragmentMonteCarlo , protocols::rosetta_scripts::ParsedProtocol , protocols::stepwise::modeler::StepWiseMinimizer
• final_scores() : protocols::residue_optimization::MetapatchEnumeration
• final_scores_ : protocols::residue_optimization::MetapatchEnumeration
• final_screener_ : protocols::stepwise::screener::IntegrationTestBreaker
• final_temp : protocols::rbsegment_relax::RBSegmentRelax
• final_temp_ : protocols::loop_modeling::LoopProtocol
• final_test() : protocols::motifs::MotifHit
• final_test_ : protocols::motifs::MotifHit
• final_unrelaxed_pose : protocols::vip::VIP_Mover
• final_visit_to_edge() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• final_weight_ : protocols::abinitio::CoordinateConstraintKC
• final_weight_linear_chainbreak_ : protocols::loops::loop_closure::ccd::LoopClosure
• final_weight_overlap_chainbreak_ : protocols::loops::loop_closure::ccd::LoopClosure
• 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 , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::StrandPairingSet , protocols::scoring::InterchainPotential , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::trajectory::DbTrajectoryWriter
• finalize_after_derivatives() : core::scoring::dna::DNATorsionEnergy , core::scoring::methods::EnergyMethod , core::scoring::orbitals::OrbitalsScore , core::scoring::ScoreFunction
• finalize_batch() : protocols::jd2::archive::BaseArchiveManager
• finalize_born_radii() : core::scoring::GenBornPotential
• finalize_claims() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• finalize_compound_records() : core::io::HeaderInformation
• finalize_experimental_technique_records() : core::io::HeaderInformation
• finalize_keyword_records() : core::io::HeaderInformation
• finalize_MPI_ : protocols::jd2::MPIWorkPoolJobDistributor
• finalize_output() : core::pack::annealer::FASTERAnnealer
• finalize_parse() : core::io::HeaderInformation
• finalize_results() : protocols::jd3::MoverAndPoseJob
• finalize_scoring() : protocols::noesy_assign::DistanceScoreMover
• finalize_setup() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop , protocols::antibody::RefineOneCDRLoopCentroid , protocols::backrub::BackrubProtocol , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::TemperedDocking , protocols::membrane::MPMutateRelaxMover , protocols::relax::RangeRelaxMover
• finalize_simulation() : protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicMover , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrialCounterObserver
• finalize_total_energy() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::aa_repeat_energy::AARepeatEnergy , 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_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::lkball::LK_BallEnergy , 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::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy , 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::DNA_EnvPairEnergy , 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::methods::SSElementMotifContactEnergy , 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 , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy
• FinalizeAromatic() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• finalized() : core::chemical::ResidueType , protocols::fldsgn::topology::StrandPairingSet
• finalized_ : core::chemical::ResidueType , protocols::fldsgn::topology::StrandPairingSet
• 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
• FinalMinimizer() : protocols::ligand_docking::FinalMinimizer
• finalPoseOP_ : protocols::pose_length_moves::PossibleLoop
• find() : core::kinematics::MoveMap , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• find_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• find_all_allowed_positions() : protocols::enzdes::SecondaryMatchProtocol
• find_alternate_codes_file() : core::io::NomenclatureManager
• find_another_representative_for_unlikely_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• find_antiparallel() : protocols::features::strand_assembly::StrandBundleFeatures
• find_assignments() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList
• find_atom_tree_root_for_metal_ion() : core::io::pose_from_sfr::PoseFromSFRBuilder
• find_attach_pts() : protocols::ligand_docking::MinimizeBackbone
• find_automatically() : protocols::protein_interface_design::movers::AddChainBreak
• find_automatically_ : protocols::protein_interface_design::movers::AddChainBreak
• find_available_job() : protocols::jobdist::BaseJobDistributor
• find_available_lower_termini() : protocols::denovo_design::connection::Connection
• find_available_upper_termini() : protocols::denovo_design::connection::Connection
• find_backbone_oxygen_atom() : core::scoring::rna::RNA_LowResolutionPotential
• find_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• find_best_anchor() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• find_chunk() : protocols::frag_picker::VallProvider
• find_closest_backbone() : protocols::motifs::IRCollection
• find_closest_to_average() : protocols::toolbox::DecoySetEvaluation
• find_constraints_to_ligand() : protocols::enzdes::EnzdesConstraintReporter , protocols::enzdes::PredesignPerturbMover
• find_current_disulfides() : protocols::denovo_design::DisulfidizeMover
• find_data() : core::scoring::bin_transitions::BinTransitionCalculator
• find_data_and_bin() : core::scoring::bin_transitions::BinTransitionCalculator
• find_dependency() : protocols::forge::build::BuildManager
• find_design_interface() : protocols::enzdes::DetectProteinLigandInterface
• find_design_interface_arg_sweep() : protocols::enzdes::DetectProteinLigandInterface
• find_disulfides() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• find_disulfides_in_the_neighborhood() : protocols::forge::remodel::RemodelDesignMover
• 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_effective_plane() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• find_energy_edge() : core::scoring::EnergyGraph
• find_exchange_partner() : protocols::canonical_sampling::AsyncMPITemperingBase
• find_first_interface_residue() : protocols::ligand_docking::ligand_options::Interface
• find_first_slice() : core::scoring::packstat::LeeRichards
• find_flexbb_edge() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• find_fragment_by_simple_rmsd_cutoff() : protocols::farna::movers::RNA_Relaxer
• find_geometric_center_for_constrained_lig_atoms() : protocols::enzdes::PredesignPerturbMover
• find_global_pose_number() : protocols::topology_broker::SequenceNumberResolver
• find_hash_edge() : protocols::sewing::SewGraph
• find_hits() : protocols::match::Matcher
• find_in_pose_if_missing_from_header() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• 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_instruction() : protocols::forge::build::BuildManager
• find_interface_backbone() : protocols::ligand_docking::LigandBaseProtocol
• find_interface_residues() : protocols::analysis::PeptideDeriverFilter , protocols::ligand_docking::InterfaceBuilder
• find_interface_rsds() : protocols::ligand_docking::LigandBaseProtocol
• find_jump() : protocols::denovo_design::components::StructureData
• find_label() : protocols::topology_broker::SequenceNumberResolver
• find_length() : protocols::toolbox::task_operations::DatabaseThread
• find_linkage_conformer_data_file() : core::chemical::carbohydrates::CarbohydrateInfoManager
• find_local_pose_number() : protocols::topology_broker::SequenceNumberResolver
• find_loops() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• find_lower_terminus() : protocols::denovo_design::components::StructureData
• find_max_frag() : protocols::hybridization::TMalign
• find_minimalist_flexbb_edge() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• find_minimization_edge() : core::scoring::MinimizationGraph
• find_motifs() : core::scoring::motif::MotifHash
• find_motifs_with_radius() : core::scoring::motif::MotifHash
• find_nbrs() : protocols::ddg::ddGMover
• find_neighboring_stubs() : protocols::hotspot_hashing::HotspotStubSet
• find_new_jump_residue() : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
• find_next_bin() : protocols::match::HitNeighborFinder
• find_next_gap() : protocols::loophash::FastGapMover
• find_optimal_rotation() : protocols::pockets::PlaidFingerprint
• find_otfflexbb_edge() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• find_parallel() : protocols::features::strand_assembly::StrandBundleFeatures
• find_params_and_neighbors() : core::scoring::MultipoleElecPotential
• find_partner() : protocols::dna::DNAParameters
• find_phosphate_contacts_other_partition() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• find_points_for_atom() : protocols::qsar::qsarMap
• find_points_of_type() : protocols::qsar::qsarMap
• find_positions() : protocols::analysis::LoopAnalyzerMover
• find_possible_disulfides() : protocols::denovo_design::DisulfidizeMover
• find_possible_orders() : protocols::sewing::Assembly
• find_protein_residues() : protocols::ligand_docking::InterfaceBuilder
• find_reference_and_current_rotamer_correspondence() : protocols::simple_moves::GreenPacker
• find_resnum() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• find_root_from_atom_pointer() : core::kinematics::AtomTree
• find_rosettascript_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• find_rotation_center() : protocols::enzdes::PredesignPerturbMover
• find_segid_from_RDC_line() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• find_segment() : protocols::denovo_design::components::StructureData
• find_segments() : protocols::features::ModelFeatures
• find_SilentStructOPs() : protocols::wum::find_SilentStructOPs
• find_source_positions() : protocols::coarse_rna::CoarseRNA_Fragments
• find_start_of_next_interface_region() : protocols::ligand_docking::ligand_options::Interface
• find_stop_of_this_interface_region() : protocols::ligand_docking::ligand_options::Interface
• find_tag() : protocols::features::FeaturesReporter
• find_tilt_center() : protocols::rigid::RigidBodyTiltMover
• find_uninstantiated_phosphates() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• find_upper_terminus() : protocols::denovo_design::components::StructureData
• find_water_neighbor_vecs() : protocols::magnesium::MgWaterHydrogenPacker
• find_zinc_site() : protocols::metal_interface::ZincSiteFinder
• findCartomAtom() : protocols::cartesian::MolecularDynamics
• findClusters() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::pockets::TargetPocketGrid
• findClustersByExemplars() : protocols::pockets::PocketGrid
• FindConsensusSequence() : protocols::simple_moves::FindConsensusSequence
• findEdgeId() : core::sequence::SequenceCoupling
• findExemplars() : protocols::pockets::PocketGrid
• FindNeighbordsAndBuriedAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• FindNeighborsForAtom() : core::scoring::sc::MolecularSurfaceCalculator
• findNeighors() : protocols::sparta::PDB
• findPockets() : protocols::pockets::PocketGrid
• findpos() : protocols::hybridization::DDomainParse
• findpos2() : protocols::hybridization::DDomainParse
• FindPossibleAtomTypesForAtom() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• findPSP() : protocols::pockets::PocketGrid
• findRoot() : protocols::pockets::SmallMol
• findSPS() : protocols::pockets::PocketGrid
• fine_centering_mode : core::scoring::APBSConfig::I_PARAM
• fine_rmsd_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• finer_sampling_at_chain_closure() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• finer_sampling_at_chain_closure_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener
• FingerprintBase() : protocols::pockets::FingerprintBase
• FingerprintMultifunc : protocols::pockets::FingerprintBase , protocols::pockets::FingerprintMultifunc , protocols::pockets::PlaidFingerprint
• finish_arc() : core::scoring::packstat::trace
• finish_hit_generation_for_constraint() : protocols::match::Matcher
• finish_pose() : core::io::silent::SilentStruct
• finish_protocol() : protocols::loop_modeling::LoopProtocol , protocols::rosetta_scripts::ParsedProtocol
• finish_scorefxn_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• finish_stage_ : protocols::abinitio::IterativeBase
• finished() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase
• FINISHED : protocols::abinitio::IterativeBase
• finished() : protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::simple_moves::symmetry::SymmetrySlider
• finished_ : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• finished_recv_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• finished_send_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• finished_simulation() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::TemperatureController
• fire_all_triggers() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• first : core::fragment::FragID , protocols::match::Hit , protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• first_ : protocols::match::Hit , protocols::match::upstream_hit
• first_adjacent_heavy_atom() : core::conformation::Residue
• first_apply_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• first_apply_with_current_setup_ : protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• first_atom_ : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• first_atom_in_branch() : core::scoring::trie::TrieNode< AT, CPDATA >
• first_atom_in_branch_ : core::scoring::trie::TrieNode< AT, CPDATA >
• first_batch_this_stage_ : protocols::abinitio::IterativeBase
• first_class_node_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• first_class_node_index_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• first_connected_resonance() : protocols::noesy_assign::Resonance
• first_fullatom_batch_ : protocols::abinitio::IterativeBase
• first_minimize_with_fixed_base_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• first_mover_ : protocols::moves::JumpOutMover
• first_nbr_ : core::optimization::ParticleSwarmMinimizer
• first_node_num_states_per_aatype_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• first_noesy_cst_file_ : protocols::abinitio::IterativeBase
• first_noesy_fa_cst_file_ : protocols::abinitio::IterativeBase
• first_pass_ala_scan() : protocols::simple_filters::RotamerBoltzmannWeight
• first_pc : protocols::features::Segment
• first_pose_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• first_res_ : protocols::simple_moves::RepeatPropagationMover
• first_res_index_ : protocols::helical_bundle::FitSimpleHelixMultiFunc
• first_residue() : core::conformation::parametric::Parameters , protocols::kinematic_closure::ClosureProblem
• first_residue_index() : core::conformation::parametric::Parameters
• first_residue_index_ : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• first_sampler_ : protocols::stepwise::screener::TagDefinition
• 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_time_writing_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• first_upper_edge_ : core::graph::Node
• first_zero_pos() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• 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 : protocols::sparta::Sparta::SpartaLib
• firstRes_ : core::scoring::methods::RG_LocalEnergy
• firstResID : protocols::sparta::GDB
• firstResidue_ : protocols::pose_length_moves::FixAllLoopsMover
• fit_intensities() : core::scoring::saxs::SAXSEnergy
• FIT_Tab : protocols::sparta::Sparta::SpartaLib
• fitBfactors() : core::scoring::cryst::PhenixInterface
• FitBfactorsMover() : protocols::cryst::FitBfactorsMover
• fitFileName : protocols::sparta::Sparta::SpartaLib
• fitness() : protocols::genetic_algorithm::Entity , protocols::multistate_design::SingleStateEntityData
• fitness_ : core::optimization::Particle , protocols::genetic_algorithm::Entity , protocols::multistate_design::SingleStateEntityData
• fitness_exp_ : protocols::pack_daemon::DynamicAggregateFunction
• fitness_function() : protocols::multistate_design::SingleState
• fitness_function_ : protocols::genetic_algorithm::GeneticAlgorithm , protocols::multistate_design::SingleState
• fitness_pbest() : core::optimization::Particle
• fitness_pbest_ : core::optimization::Particle
• fitness_threshold() : protocols::protein_interface_design::filters::BoltzmannFilter
• fitness_threshold_ : protocols::protein_interface_design::filters::BoltzmannFilter
• fitness_valid() : protocols::genetic_algorithm::Entity
• fitness_valid_ : protocols::genetic_algorithm::Entity
• FitnessFunctionOP : protocols::genetic_algorithm::GeneticAlgorithm
• FitSimpleHelix() : protocols::helical_bundle::FitSimpleHelix
• FitSimpleHelixMultiFunc() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• five_prime_atom : protocols::stepwise::modeler::rna::Jump_point
• five_prime_chain_break : protocols::stepwise::modeler::rna::sugar::SugarModeling
• five_prime_chain_break_res() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• five_prime_chain_break_res_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• five_prime_phosphate_res_input_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• five_prime_res() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• five_prime_res_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• five_prime_seq_num : protocols::stepwise::modeler::rna::Jump_point
• five_prime_xyz_ : protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener
• fix_anchor() : protocols::anchored_design::AnchorMoversData
• fix_backbone_ : protocols::simple_moves::CoupledMover
• fix_catalytic_ : protocols::enzdes::EnzRepackMinimize
• fix_catalytic_aa_ : protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::SetCatalyticResPackBehavior
• fix_disulfides() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• fix_his_tautomer() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• fix_his_tautomer_ : core::pack::task::ResidueLevelTask_
• fix_jump_atoms_at_loop_boundaries() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• fix_ligands_ : protocols::rbsegment_relax::RBSegmentRelax
• fix_natsc_ : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• fix_omega() : protocols::relax::RelaxProtocolBase
• fix_omega_ : protocols::relax::RelaxProtocolBase
• fix_phi_psi_offsets() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• fix_reference_energies() : protocols::optimize_weights::OptEMultifunc
• fix_reference_energies_ : protocols::optimize_weights::OptEMultifunc
• fix_short_segment_ : protocols::simple_moves::BBGaussianMover
• FixAllLoopsMover() : protocols::pose_length_moves::FixAllLoopsMover
• 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 : protocols::flxbb::LayerDesignOperation
• fixed_ : core::scoring::OneToAllEnergyContainer
• fixed_atom_ : core::scoring::constraints::CoordinateConstraint
• fixed_atom_id_ : core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint
• fixed_chains_ : protocols::analysis::InterfaceAnalyzerMover
• fixed_count_ : protocols::optimize_weights::IterativeOptEDriver
• fixed_data() : protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• fixed_data_ : protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• 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_energy_terms() : protocols::optimize_weights::OptEData
• fixed_energy_terms_ : protocols::optimize_weights::OptEData
• fixed_nodes() : protocols::denovo_design::components::SolutionSorter
• fixed_parameters_ : protocols::optimize_weights::IterativeOptEDriver
• fixed_reference_point_ : core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint
• fixed_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• fixed_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• fixed_residue_ : core::scoring::methods::PoissonBoltzmannEnergy
• fixed_residues_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• fixed_score_list_ : protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc
• fixed_score_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• fixed_scores_ : protocols::optimize_weights::WrapperOptEMultifunc
• fixed_stub_ : core::scoring::constraints::LocalCoordinateConstraint
• fixed_terms_ : protocols::optimize_weights::OptEMultifunc
• fixed_to_metal_ : protocols::metal_interface::ZincHeterodimerMover
• FixedBBEdge() : core::pack::interaction_graph::FixedBBEdge
• FixedBBInteractionGraph() : core::pack::interaction_graph::FixedBBInteractionGraph
• FixedBBInteractionGraphCOP : protocols::pack_daemon::PackDaemon
• FixedBBInteractionGraphOP : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• FixedBBNode() : core::pack::interaction_graph::FixedBBNode
• FixedOffsetPivots() : protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots
• FixedPivots() : protocols::kinematic_closure::pivot_pickers::FixedPivots
• FixedTemperatureController() : protocols::canonical_sampling::FixedTemperatureController
• fixes_interchangeability_group() : core::chemical::ResidueTypeFinder
• fixes_name3() : core::chemical::ResidueTypeFinder
• fixResidue() : protocols::jumping::ResiduePairJumpSingle
• fixResidue_ : protocols::jumping::ResiduePairJumpSingle
• FixTemplateJumpSetup() : protocols::abinitio::FixTemplateJumpSetup
• fj_ : protocols::frag_picker::DiversifyCrmsdSelector
• flag_file() : protocols::jd2::archive::Batch
• flag_for_calculation() : core::scoring::FACTSResidueInfo
• flag_for_calculation_ : core::scoring::FACTSResidueInfo
• flags_ : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingPoseMetrics , protocols::flexpep_docking::FlexPepDockingProtocol
• flags_and_objects_are_in_sync_ : protocols::antibody::AntibodyModelerProtocol , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• flank_cdrh3_map_ : protocols::antibody::H3RefineCCD
• flank_relax_ : protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop , protocols::antibody_legacy::CDRH3Modeler
• flank_residue_min() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• flank_residue_min_ : protocols::antibody::AntibodyModelerProtocol , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• flank_residue_size_ : protocols::antibody::AntibodyModelerProtocol
• flank_size_ : protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop
• flanking_left_aa() : protocols::forge::build::SegmentInsert
• flanking_left_nres() : protocols::forge::build::SegmentInsert
• flanking_left_ss() : protocols::forge::build::SegmentInsert
• flanking_residues_ : protocols::antibody::CloseOneCDRLoop , protocols::antibody_legacy::CloseOneMover
• flanking_right_aa() : protocols::forge::build::SegmentInsert
• flanking_right_nres() : protocols::forge::build::SegmentInsert
• flanking_right_ss() : protocols::forge::build::SegmentInsert
• flanking_rms_cutoff_ : protocols::sewing::LoophashAssemblyMover
• flat_bottom_constraints_ : protocols::fldsgn::SheetConstraintGenerator
• flat_size() : core::fragment::FrameList
• FlatHarmonicFunc() : core::scoring::func::FlatHarmonicFunc
• flex_cter_ : protocols::ub_e2c::ubi_e2c_modeler
• flex_cter_map_ : protocols::ub_e2c::ubi_e2c_modeler
• flex_dna_sugar_ : protocols::motifs::MotifDnaPacker
• flex_regions_ : protocols::enzdes::EnzdesFlexBBProtocol
• FlexbbEdge() : protocols::flexpack::interaction_graph::FlexbbEdge
• FlexbbInteractionGraph() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• FlexbbNode() : protocols::flexpack::interaction_graph::FlexbbNode
• FlexbbRotamerSet() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• FlexbbRotamerSets() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• FlexbbSimAnnealer() : protocols::flexpack::annealer::FlexbbSimAnnealer
• FlexbbSparseMatrixIndex() : protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex
• flexible_bb_ : protocols::docking::membrane::MPFindInterfaceMover
• flexible_sc_ : protocols::docking::membrane::MPFindInterfaceMover
• flexpack_neighbor_graph() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• FlexPacker() : protocols::flexpack::FlexPacker
• FlexPepDockingAbInitio() : protocols::flexpep_docking::FlexPepDockingAbInitio
• FlexPepDockingFlags() : protocols::flexpep_docking::FlexPepDockingFlags
• FlexPepDockingLowRes() : protocols::flexpep_docking::FlexPepDockingLowRes
• FlexPepDockingPoseMetrics() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• FlexPepDockingProtocol() : protocols::flexpep_docking::FlexPepDockingProtocol
• flexseg_bb_offset_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_considering_alt_bb() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_considering_alt_bb_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_for_bb_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_for_moltenres() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_for_moltenres_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_members() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_members_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexsegid_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegid_for_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_size() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_span_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_start_moltenresid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_start_resid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_stop_moltenresid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_stop_resid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flip_chirality() : core::conformation::symmetry::MirrorSymmetricConformation
• flip_cp_rep_ : core::scoring::elec::FA_ElecEnergy
• 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_
• flip_in_pcs() : protocols::flexpep_docking::FlexPepDockingProtocol
• flip_input_about_axes_ : protocols::matdes::SymDofMover
• flip_rate_ : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• flip_sign_ : protocols::simple_moves::GenericMonteCarloMover
• flip_upstream_downstream_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• FlipMover() : protocols::membrane::FlipMover
• flipped() : core::pose::rna::BasePair
• flips_ : protocols::docking::membrane::MPFindInterfaceMover
• float_ambiguity() : protocols::noesy_assign::PeakAssignment
• float_label() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• floating_acceptance_ratio_ : protocols::jd2::archive::ArchiveBase
• floating_base() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_base_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_base_anchor_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_base_anchor_res_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_pairs_ : protocols::hybridization::FoldTreeHybridize
• FLOATING_POINT_CLOUD_INFO : core::pose::datacache::CacheableDataType
• FloatingResonance() : protocols::noesy_assign::FloatingResonance
• FloatList : protocols::noesy_assign::FloatingResonance
• floor_ : protocols::filters::IfThenFilter
• FloppyTailMover() : protocols::floppy_tail::FloppyTailMover
• FLORECENCE_TRANSFER : core::io::HeaderInformation
• fluff() : core::grid::CartGrid< T >
• flush() : protocols::features::DatabaseJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::SingleFileBuffer
• flush_channel() : protocols::jd2::MpiFileBuffer
• flush_checkpoints() : protocols::checkpoint::CheckPointer
• FlxbbDesign() : protocols::flxbb::FlxbbDesign
• FlxbbDesignPack() : protocols::flxbb::FlxbbDesignPack
• fmax_ : core::scoring::func::MixtureFunc , core::scoring::hbonds::FadeInterval
• fmin_ : core::scoring::hbonds::FadeInterval
• fn_ : core::scoring::methods::CustomAtomPairEnergy
• fname() : core::pose::ResidueIndexDescriptionFromFile , protocols::simple_moves::AddChainMover
• fname_ : core::pose::ResidueIndexDescriptionFromFile , protocols::simple_moves::AddChainMover , protocols::simple_moves::DumpPdb
• fname_initialized_from() : core::pack::task::ResfileContents
• fname_initialized_from_ : core::pack::task::ResfileContents
• fname_prefix_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• FNatFilter() : protocols::protein_interface_design::filters::FNatFilter
• fobj_ : protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• fobjnames() : protocols::mpi_refinement::MultiObjective
• fobjnames_ : protocols::mpi_refinement::MultiObjective
• focus_ : core::select::residue_selector::NeighborhoodResidueSelector
• focus_selector_ : core::select::residue_selector::NeighborhoodResidueSelector
• focus_set_ : core::select::residue_selector::NeighborhoodResidueSelector
• focus_str_ : core::select::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_geomcst_id_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• focused_iterative_vector_expression_ : protocols::pack_daemon::DynamicAggregateFunction
• 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() : protocols::abinitio::AbrelaxApplication
• fold_in_rb_deltas() : core::kinematics::Jump , core::kinematics::RT
• fold_label_resonance() : protocols::noesy_assign::CrossPeakInfo
• fold_label_resonance_ : protocols::noesy_assign::CrossPeakInfo
• fold_proton_resonance() : protocols::noesy_assign::CrossPeakInfo
• fold_proton_resonance_ : protocols::noesy_assign::CrossPeakInfo
• fold_resonance() : protocols::noesy_assign::CrossPeak
• fold_tree() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , 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 , protocols::denovo_design::components::FoldGraph , protocols::environment::ProtectedConformation , protocols::jumping::JumpSample , protocols::protein_interface_design::movers::SetAtomTree , protocols::rigid::RigidBodyMotionMover , protocols::seeded_abinitio::SeedFoldTree , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• 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 , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::jumping::JumpSample , protocols::moves::ChangeFoldTreeMover , protocols::protein_interface_design::movers::SetAtomTree , protocols::seeded_abinitio::SeedFoldTree , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters , protocols::topology_broker::TopologyBroker
• fold_tree_io() : core::import_pose::ImportPoseOptions , core::io::StructFileRepOptions
• fold_tree_io_ : core::import_pose::ImportPoseOptions , core::io::StructFileRepOptions
• fold_tree_rec() : protocols::denovo_design::components::FoldGraph
• fold_tree_root_ : protocols::simple_moves::SetTorsion
• fold_tree_save_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• FoldandDockClaimer() : protocols::topology_broker::FoldandDockClaimer
• FoldConstraints() : protocols::abinitio::FoldConstraints
• folder() : protocols::noesy_assign::CrossPeak
• FoldGraph() : protocols::denovo_design::components::FoldGraph
• foldInChanges() : protocols::electron_density::VoxelSpacingMultifunc
• folding_verteces_ : protocols::seeded_abinitio::SeedFoldTree
• FoldResonance() : protocols::noesy_assign::FoldResonance
• FoldTree : core::conformation::Conformation , core::kinematics::FoldTree , protocols::nonlocal::SingleFragmentMover
• foldTree() : protocols::simple_moves::CutChainMover
• foldtree_ : protocols::floppy_tail::FloppyTailMover
• foldtree_mover_ : protocols::hybridization::FoldTreeHybridize
• foldtree_string() : core::io::StructFileRep
• foldtree_string_ : core::io::StructFileRep
• FoldTreeFromLoops() : protocols::loops::FoldTreeFromLoops
• FoldTreeHybridize() : protocols::hybridization::FoldTreeHybridize
• FoldTreeOP : core::conformation::Conformation , protocols::nonlocal::SingleFragmentMover
• FoldTreeSketch() : core::environment::FoldTreeSketch , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::EnvClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::environment::EnvClaimBroker
• foldtype2name_ : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype2spairs_ : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype_from_name() : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype_from_spairs() : protocols::fldsgn::topology::SheetFoldTypeManager
• follow_edge() : protocols::sewing::Assembly
• follow_random_edge_from_node() : protocols::sewing::AssemblyMover , protocols::sewing::GivenPathAssemblyMover , protocols::sewing::GreedyAssemblyMover
• follows : core::kinematics::Node
• footer_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• footprint() : core::graph::ArrayPool< T >
• forbidden_names_ : protocols::moves::MoverFactory
• force : protocols::cartesian::CartesianAtom , protocols::ligand_docking::Translate_info
• 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_align_ : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• 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_anti_chi_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_anti_chi_res_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_apix_on_map_load_ : core::scoring::electron_density::ElectronDensity
• force_bb_ : core::chemical::ResidueType
• force_bitflip() : core::io::silent::SilentStruct
• force_bitflip_ : core::io::silent::SilentStruct
• force_centroid_interaction() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_centroid_interaction_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::screener::BaseCentroidScreener
• force_cluster_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• force_combined_gaussian_approximation() : core::scoring::func::GaussianChainFunc
• force_combined_gaussian_approximation_ : core::scoring::func::GaussianChainFunc
• force_const() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• force_const_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• force_constant_ : core::scoring::constraints::BackboneStubConstraint
• force_fold_tree() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• force_fold_tree_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• force_ideal_chainbreak_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• force_internal_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• force_job_purging() : protocols::jd2::JobsContainer
• force_job_purging_ : protocols::jd2::JobsContainer
• force_natro() : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• force_natro_ : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• force_natro_for_stored_task_names() : protocols::matdes::MatDesGreedyOptMutationMover
• force_natro_for_stored_task_names_ : protocols::matdes::MatDesGreedyOptMutationMover
• force_nbr_atom_orient() : core::chemical::ResidueType
• force_nbr_atom_orient_ : core::chemical::ResidueType , core::chemical::SetOrientAtom
• force_nonideal_ : protocols::relax::FastRelax
• force_north_paper_db_ : protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• force_north_sugar_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_north_sugar_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_phosphate_instantiation() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_phosphate_instantiation_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_repack_ : protocols::loop_modeling::utilities::PrepareForFullatom
• force_south_sugar_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_south_sugar_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_ss_ : protocols::hybridization::CartesianSampler
• force_stub_intra_residue : protocols::environment::claims::JumpElement
• force_submotif_without_intervening_bulge() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• force_submotif_without_intervening_bulge_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• force_syn_chi_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_syn_chi_res_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_unique_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• force_unique_moves_ : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• force_update_residue_coordinates() : core::conformation::Conformation
• force_update_residue_torsions() : core::conformation::Conformation
• force_user_defined_jumps_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• forced_cluster_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• forced_pos_ : protocols::simple_filters::SymmetricMotifFilter
• forced_silent_struct_type_ : protocols::jd2::SilentFileJobOutputter
• ForceDisulfidesMover() : protocols::simple_moves::ForceDisulfidesMover
• forget_chains_and_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• forget_chains_and_interface_ : protocols::dna::RestrictDesignToProteinDNAInterface
• forget_initial_loops() : protocols::anchored_design::AnchoredDesignMover
• form_disulfide() : protocols::protein_interface_design::movers::DisulfideMover
• 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
• formalcharge : core::io::AtomInformation
• FORMAT : protocols::sparta::GDB
• format_ : core::fragment::picking_old::vall::VallResidue
• format_2011_ : core::fragment::picking_old::vall::VallResidue
• format_silent_struct() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• FORMAT_str : protocols::sparta::GDB
• FORMAT_str_parser() : protocols::sparta::GDB
• format_string() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• format_string_2011() : core::fragment::picking_old::vall::VallResidue
• format_string_cs() : protocols::frag_picker::VallResidue
• format_string_residue_depth_version1() : protocols::frag_picker::VallResidue
• format_string_version1() : protocols::frag_picker::VallResidue
• FormatList : protocols::sparta::GDB
• formatted_objs_names() : protocols::mpi_refinement::MultiObjective
• formatted_objs_values() : protocols::mpi_refinement::MultiObjective
• FormFactor() : core::scoring::saxs::FormFactor
• FormFactorManager() : core::scoring::saxs::FormFactorManager
• forward_check() : protocols::motifs::Motif
• forward_connections() : protocols::sewing::SegmentGraph
• forward_connections_ : protocols::sewing::SegmentGraph
• forward_jump() : protocols::motifs::Motif
• forward_jump_ : protocols::motifs::Motif
• forward_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• forward_threshold_ : protocols::simple_moves::WobbleMover
• found_centroid_interaction() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• found_centroid_interaction_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• found_match : core::indexed_structure_store::FragmentLookupResult
• found_res_compatibility_ : protocols::enzdes::SecondaryMatchProtocol
• found_res_compatibility_determined_ : protocols::enzdes::SecondaryMatchProtocol
• found_resis_ : protocols::enzdes::SecondaryMatchProtocol
• FourAtomsConstraintData() : protocols::frag_picker::scores::FourAtomsConstraintData
• FourPointsFunc() : core::scoring::func::FourPointsFunc
• fourth_atom_ : protocols::frag_picker::scores::FourAtomsConstraintData
• fourth_offset_ : protocols::frag_picker::scores::FourAtomsConstraintData
• fp_compare() : protocols::pockets::PlaidFingerprint
• fp_compare_deriv() : protocols::pockets::PlaidFingerprint
• fpdock_metrics_ : protocols::flexpep_docking::FlexPepDockingProtocol
• frac2index() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• frac_cav_ball_required_exposed : core::scoring::packstat::SasaOptions
• fraction_by_recombination() : protocols::genetic_algorithm::GeneticAlgorithmBase
• fraction_by_recombination_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• fraction_chain1_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• fraction_chain2_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• fraction_done : protocols::boinc::BoincSharedMemory
• fraction_done_ : protocols::boinc::Boinc
• fractions_small_residues() : protocols::docking::membrane::MPFindInterfaceMover
• frag1_ : protocols::forge::components::VarLengthBuild , protocols::protein_interface_design::movers::LoopRemodel
• frag3_ : protocols::anchored_design::AnchorMoversData , protocols::forge::components::VarLengthBuild , protocols::protein_interface_design::movers::LoopRemodel
• frag3_weight : protocols::flexpep_docking::FlexPepDockingFlags
• frag5_weight : protocols::flexpep_docking::FlexPepDockingFlags
• frag9_ : protocols::forge::components::VarLengthBuild , protocols::protein_interface_design::movers::LoopRemodel
• frag9_weight : protocols::flexpep_docking::FlexPepDockingFlags
• frag_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• frag_1mer_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• frag_bias_ : protocols::hybridization::CartesianSampler
• frag_cache_ : core::fragment::FragmentIO , protocols::simple_moves::GunnCost
• frag_designabilities_ : protocols::enzdes::EnzdesFlexibleRegion
• frag_factory_ : core::fragment::FragmentIO
• frag_files() : protocols::indel::IndelOptimizationMover , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• frag_files_ : protocols::indel::IndelOptimizationMover , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• frag_id() : core::fragment::FragID_Iterator , core::fragment::Frame
• frag_length_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• frag_libs() : protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::loops::loop_mover::LoopMover
• frag_libs_ : protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::domain_assembly::AssembleLinkerMover , protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover , protocols::kinematic_closure::perturbers::FragmentPerturber , protocols::loop_build::LoopMover_SlidingWindow , protocols::LoopRebuild , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::RBSegmentRelax
• frag_libs_1mer_ : protocols::hybridization::FoldTreeHybridize
• frag_libs_big_ : protocols::hybridization::FoldTreeHybridize
• frag_libs_small_ : protocols::hybridization::FoldTreeHybridize
• frag_list_ : core::fragment::Frame
• frag_map_ : protocols::frags::FragLib
• frag_mover_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::loops::loop_closure::ccd::LoopClosure
• frag_num : protocols::simple_moves::LoggedFragmentMover::Item
• frag_picker_ : protocols::denovo_design::connection::BridgeChains
• frag_pos_coordinates_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• frag_size() : protocols::frags::TorsionFragmentMover
• frag_size_ : core::fragment::picking_old::vall::gen::LengthGen , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::movers::RNA_FragmentMover , protocols::farna::RNA_FragmentMonteCarlo , protocols::frag_picker::quota::QuotaCollector , protocols::frags::TorsionFragmentMover , protocols::jd2::parser::FragmentReader , protocols::topology_broker::TemplateFragmentClaimer
• frag_sizes() : protocols::frags::FragLib
• frag_sizes_ : protocols::frag_picker::FragmentPicker , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::frag_picker::scores::GunnCostScore , protocols::hybridization::CartesianSampler
• frag_source_file_ : protocols::coarse_rna::CoarseRNA_Fragments
• frag_source_pose_ : protocols::coarse_rna::CoarseRNA_Fragments
• frag_source_secstruct_ : protocols::coarse_rna::CoarseRNA_Fragments
• frag_type() : core::fragment::FragFactory
• frag_types_ : core::fragment::FragFactory
• frag_weight_aligned_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• fragbias_reporter() : protocols::hybridization::FragmentBiasAssigner
• FragCache() : core::fragment::FragCache< T >
• fragcache_ : protocols::denovo_design::components::Picker
• FragData() : core::fragment::FragData , core::fragment::picking_old::vall::VallLibrarian
• FragDataOP : core::fragment::picking_old::vall::VallLibrarian
• FragDataOPs : core::fragment::picking_old::vall::VallLibrarian
• fragDens_ : protocols::electron_density::DockIntoDensityMover
• FragFactory() : core::fragment::FragFactory
• FragFileCache : core::fragment::FragmentIO
• fragfull_ : protocols::forge::components::VarLengthBuild
• 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_
• FragInsertAndAlignMover() : protocols::rbsegment_relax::FragInsertAndAlignMover
• FragLib() : protocols::frags::FragLib
• fraglib_ : protocols::frags::TorsionFragmentMover
• FragLocation() : protocols::frag_picker::frag_movers::FragLocation
• fragLookupOP_ : core::indexed_structure_store::FragmentStore
• FragMap : protocols::frags::FragLib
• fragment() : core::fragment::FragID , core::fragment::FragmentRmsd , core::fragment::Frame
• FRAGMENT : core::io::HeaderInformation
• fragment_1 : protocols::features::helixAssembly::FragmentPair
• fragment_2 : protocols::features::helixAssembly::FragmentPair
• fragment_as_pose() : core::fragment::Frame
• fragment_atoms : core::indexed_structure_store::FragmentSpecification
• fragment_bias_strategies_ : protocols::hybridization::CartesianSampler
• fragment_check() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• fragment_contacts() : protocols::frag_picker::FragmentPicker
• fragment_coordinates : core::indexed_structure_store::FragmentStore
• fragment_coordinates_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• fragment_counters_ : protocols::enzdes::EnzdesFlexBBProtocol
• fragment_length : core::indexed_structure_store::FragmentSpecification
• fragment_library_pointer_map : protocols::farna::fragments::FullAtomRNA_Fragments
• fragment_num() : protocols::nonlocal::SmoothPolicy::Candidate
• fragment_num_ : protocols::nonlocal::SmoothPolicy::Candidate
• fragment_pose_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms
• fragment_ptr() : core::fragment::FragID , core::fragment::Frame
• fragment_specification() : core::indexed_structure_store::FragmentLookup , core::indexed_structure_store::FragmentStore , protocols::indexed_structure_store::filters::FragmentLookupFilter
• fragment_threshold_distances : core::indexed_structure_store::FragmentStore
• FragmentAllAtomCrmsd() : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• FragmentBiasAssigner() : protocols::hybridization::FragmentBiasAssigner
• FragmentCandidate() : protocols::frag_picker::FragmentCandidate
• FragmentChunkCrms() : protocols::frag_picker::scores::FragmentChunkCrms
• FragmentClaimer() : protocols::topology_broker::FragmentClaimer
• FragmentCM() : protocols::abinitio::abscript::FragmentCM
• FragmentContainer() : protocols::topology_broker::FragmentContainer
• FragmentCost() : protocols::simple_moves::FragmentCost
• FragmentCrmsd() : protocols::frag_picker::scores::FragmentCrmsd
• FragmentCrmsdResDepth() : protocols::frag_picker::scores::FragmentCrmsdResDepth
• FragmentDME() : protocols::frag_picker::scores::FragmentDME
• FragmentIO() : core::fragment::FragmentIO
• FragmentJumpClaimer() : protocols::topology_broker::FragmentJumpClaimer
• FragmentJumpCM() : protocols::abinitio::abscript::FragmentJumpCM
• fragmentLength_ : protocols::frag_picker::FragmentCandidate
• FragmentLibraryManager() : core::fragment::picking_old::FragmentLibraryManager
• FragmentLookup() : core::indexed_structure_store::FragmentLookup
• FragmentLookupFilter() : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentLookupFilterCreator : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentLookupMap : core::indexed_structure_store::StructureStoreManager
• FragmentLookupOP : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentLookupResult() : core::indexed_structure_store::FragmentLookupResult , protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentMover() : protocols::simple_moves::FragmentMover
• FragmentMoverOP : protocols::forge::remodel::RemodelLoopMover
• FragmentMoverOPs : protocols::forge::remodel::RemodelLoopMover
• FragmentPair() : protocols::features::helixAssembly::FragmentPair
• FragmentPerturber() : protocols::kinematic_closure::perturbers::FragmentPerturber
• FragmentPicker() : protocols::frag_picker::FragmentPicker
• fragmentProbs_ : protocols::hybridization::FragmentBiasAssigner
• FragmentReader() : protocols::jd2::parser::FragmentReader
• FragmentRmsd() : core::fragment::FragmentRmsd
• fragments() : core::fragment::picking_old::vall::VallLibrarian , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::nonlocal::Policy , protocols::simple_moves::FragmentMover , protocols::topology_broker::FragmentClaimer
• fragments9_ : protocols::hybridization::CartesianHybridize
• fragments_ : core::fragment::FragmentRmsd , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragmentLibrary , protocols::hybridization::CartesianSampler , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign , protocols::medal::MedalExchangeMover , protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::Policy , protocols::nonlocal::SingleFragmentMover , protocols::seeded_abinitio::CloseFold
• fragments_big_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::MRMover , protocols::seeded_abinitio::SegmentHybridizer
• fragments_big_trim_ : protocols::hybridization::MRMover
• fragments_for_permutation() : protocols::denovo_design::components::Picker
• fragments_for_permutation_take_X_from_pose() : protocols::denovo_design::components::Picker
• fragments_lg_ : protocols::medal::MedalMover , protocols::star::StarAbinitio
• fragments_permutation_test_by_CA_distances() : protocols::motif_grafting::movers::MotifGraftMover
• fragments_picked_ : protocols::forge::components::VarLengthBuild
• fragments_set_ : protocols::abinitio::DomainAssembly
• fragments_sm_ : protocols::medal::MedalMover , protocols::star::StarAbinitio
• fragments_small_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::MRMover , protocols::seeded_abinitio::SegmentHybridizer
• fragments_small_trim_ : protocols::hybridization::MRMover
• fragments_to_string() : protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign
• FragmentSampler() : protocols::abinitio::FragmentSampler
• FragmentScoreManager() : protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::FragmentScoreMap
• FragmentScoreMap() : protocols::frag_picker::scores::FragmentScoreMap
• FragmentScoringMethod() : protocols::frag_picker::scores::FragmentScoringMethod
• FragmentSelectingRule() : protocols::frag_picker::FragmentSelectingRule
• FragmentSpecification() : core::indexed_structure_store::FragmentSpecification , protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentStore() : core::indexed_structure_store::FragmentStore
• fragmentStore_groups : core::indexed_structure_store::FragmentStore
• fragpick_list_ : protocols::abinitio::Templates
• fragprob_ : protocols::hybridization::CartesianHybridize
• fragprob_stage2_ : protocols::hybridization::HybridizeProtocol
• fragProbs_assigned_ : protocols::hybridization::FragmentBiasAssigner
• FragQualCalculator() : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• FragQualFilter() : protocols::fldsgn::filters::FragQualFilter
• FragRT : core::conformation::Conformation , core::kinematics::AtomTree
• frags_ : protocols::noesy_assign::FragsToAtomDist
• frags_for_pos_ : protocols::frag_picker::quota::QuotaCollector
• frags_large() : protocols::topology_broker::FragmentContainer
• frags_large_ : protocols::topology_broker::FragmentContainer
• frags_per_pos() : protocols::frag_picker::FragmentSelectingRule
• frags_per_pos_ : protocols::frag_picker::FragmentSelectingRule
• frags_small() : protocols::topology_broker::FragmentContainer
• frags_small_ : protocols::topology_broker::FragmentContainer
• FragSet() : core::fragment::FragSet , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• fragset3mer_ : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::floppy_tail::FloppyTailMover
• fragset5mer_ : protocols::flexpep_docking::FlexPepDockingAbInitio
• fragset9mer_ : protocols::flexpep_docking::FlexPepDockingAbInitio
• fragset_ : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::anchored_design::AnchorMoversData , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::simple_moves::FragmentMover
• fragset_large_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::DomainAssembly
• fragset_list_ : core::fragment::FragSetCollection
• fragSet_needs_update() : protocols::frag_picker::frag_movers::FragSetFromH5Mover
• fragset_small_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::DomainAssembly
• fragset_small_top25_ : protocols::abinitio::AbrelaxApplication
• fragset_templates_ : protocols::abinitio::AbrelaxApplication
• FragSetCollection() : core::fragment::FragSetCollection
• FragSetCOP : protocols::abinitio::DomainAssembly , protocols::forge::remodel::RemodelLoopMover , protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::Policy , protocols::nonlocal::SmoothPolicy , protocols::nonlocal::UniformPolicy
• FragSetFromH5Mover() : protocols::frag_picker::frag_movers::FragSetFromH5Mover
• FragSetList : core::fragment::FragSetCollection
• FragSetLoader() : protocols::jd2::parser::FragSetLoader
• fragSetName_ : protocols::frag_picker::frag_movers::FragSetFromH5Mover
• FragSetOP : protocols::abinitio::DomainAssembly , protocols::forge::remodel::RemodelLoopMover , protocols::jd2::parser::FragmentReader , protocols::nonlocal::SingleFragmentMover , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• FragSetOPs : protocols::forge::remodel::RemodelLoopMover
• fragsets_ : protocols::forge::remodel::RemodelLoopMover
• fragSetUnchanged_ : protocols::frag_picker::frag_movers::FragSetFromH5Mover
• FragsToAtomDist() : protocols::noesy_assign::FragsToAtomDist
• 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() : protocols::kinematic_closure::ClosureProblem , protocols::match::upstream::FullChiSampleSet
• Frame : protocols::nonlocal::SingleFragmentMover
• frame_ : protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler
• frame_cache_ : protocols::canonical_sampling::DbTrajectoryRecorder , protocols::trajectory::DbTrajectoryWriter
• frame_called_ : protocols::kinematic_closure::ClosureProblem
• frame_count_ : protocols::viewer::SilentObserver
• frame_for_residue() : protocols::features::LoopAnchorFeatures
• frame_from_global_orientation() : protocols::toolbox::match_enzdes_util::LigandConformer
• frame_lower_pivot() : protocols::kinematic_closure::ClosureProblem
• frame_pos : protocols::simple_moves::LoggedFragmentMover::Item
• frame_ptr() : core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID , core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• frame_types_ : core::fragment::FragFactory
• frame_upper_pivot() : protocols::kinematic_closure::ClosureProblem
• frame_vector() : core::fragment::FrameList
• FrameIterator() : core::fragment::FrameIterator , core::fragment::FrameIteratorWorker_
• FrameList : core::fragment::FrameListIterator_ , protocols::forge::components::VarLengthBuild
• FrameListIterator_() : core::fragment::FrameListIterator_
• FrameMap : core::fragment::FragmentRmsd , core::fragment::MinimalFragSet , core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSet , core::fragment::OrderedFragSetIterator_ , protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• frames() : core::fragment::FragSet , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet
• frames_ : core::fragment::ConstantLengthFragSet , core::fragment::FragmentRmsd , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet , protocols::flexpack::FlexPacker , protocols::match::upstream::FullChiSampleSet , protocols::nonlocal::BiasedFragmentMover , protocols::rbsegment_relax::FragInsertAndAlignMover
• FrameTypes : core::fragment::FragFactory
• framework_dependant_clusters() : protocols::antibody::design::MutateFrameworkForCluster
• framework_dependant_mutations() : protocols::antibody::design::MutateFrameworkForCluster
• framework_dependant_positions() : protocols::antibody::design::MutateFrameworkForCluster
• framework_info_ : protocols::antibody::AntibodyInfo
• framework_mutator_ : protocols::antibody::design::AntibodyDesignMover
• free() : boost::unordered_object_pool< T, UserAllocator >
• free_2HOprime_bonus() : core::scoring::methods::FreeDOF_Options
• free_2HOprime_bonus_ : core::scoring::methods::FreeDOF_Options
• free_count_ : protocols::optimize_weights::IterativeOptEDriver
• free_data() : protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• free_data_ : protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• free_dof_options() : core::scoring::methods::EnergyMethodOptions
• free_dof_options_ : core::scoring::methods::EnergyMethodOptions
• free_lock_on_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• free_parameters_ : protocols::optimize_weights::IterativeOptEDriver
• free_res_weights_ : core::scoring::methods::FreeDOF_Energy
• free_score_list_ : protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::WrapperOptEMultifunc
• free_score_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• 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
• free_term_constraints_ : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• free_term_map_ : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• free_terms_ : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• free_terms_energy_map_from_dofs() : protocols::optimize_weights::IterativeOptEDriver
• free_weights_after_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• free_weights_and_refEs_from_vars() : protocols::optimize_weights::IterativeOptEDriver
• free_weights_before_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• free_weights_inner_loop_ : protocols::optimize_weights::IterativeOptEDriver
• FreeDOF_Energy() : core::scoring::methods::FreeDOF_Energy
• FreeDOF_Options() : core::scoring::methods::FreeDOF_Options
• freeze() : protocols::cluster::APCluster , protocols::rigid::RigidBodyMover
• freeze_ : protocols::rigid::RigidBodyMover
• freeze_domains_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• freeze_endpoints_ : protocols::hybridization::CartesianSampler
• freeze_h3_ : protocols::antibody_legacy::CDRH3Modeler
• freeze_sugar_torsions() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• freq() : protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::Resonance
• freq_ : protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::Resonance
• frequency() : protocols::abinitio::PairingStatEntry
• frequency_ : protocols::trajectory::DbTrajectoryWriter
• frequency_in_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• fresh_instance() : protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::abinitio::AbrelaxMover , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::DomainAssembly , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::PeptideDeriverFilter , protocols::anchored_design::AnchoredDesignMover , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignProtocol , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::carbohydrates::GlycanRelaxMover , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::ThreadingMover , protocols::contact_map::ContactMap , protocols::cryst::DockLatticeMover , protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::cryst::UpdateCrystInfo , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideStubMover , protocols::cyclic_peptide::TryDisulfPermutations , protocols::denovo_design::components::MultiChainStructureData , protocols::denovo_design::components::SingleChainStructureData , protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::BridgeChains , protocols::denovo_design::connection::BridgeTomponents , protocols::denovo_design::connection::ConnectTerminiWithDisulfide , protocols::denovo_design::connection::ExtendChain , protocols::denovo_design::connection::GenericConnection , protocols::denovo_design::connection::StapleChains , protocols::denovo_design::constraints::FileConstraintGenerator , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSPredictionFilter , protocols::design_opt::GreedyOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::SeparateDnaFromNonDna , protocols::docking::DockingHighResFilter , protocols::docking::DockingLowResFilter , protocols::docking::DockingProtocol , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::VoxelSpacingRefinementMover , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::BackboneSampler , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::FalseFilter , protocols::filters::Filter , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::filters::TrueFilter , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintGenerator , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveConstraints , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::ResidueVicinityRCG , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::genetic_algorithm::EntityElement , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::BundleReporterFilter , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::MRMover , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::LigandDockMain , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::Translate , protocols::ligand_docking::WriteLigandMolFile , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::Mover_LoopHashRefine , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::md::CartesianMD , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , protocols::membrane::AddMembraneMover , protocols::membrane::AddMPLigandMover , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::FlipMover , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::MPMutateRelaxMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::OptimizeMembranePositionMover , protocols::membrane::OptimizeProteinEmbeddingMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TiltMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::motifs::MotifDnaPacker , protocols::moves::CycleMover , protocols::moves::CyclicMover , protocols::moves::DsspMover , protocols::moves::FilterReporterMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::NullMover , protocols::moves::PyMolMover , protocols::moves::RandomMover , protocols::moves::RepeatMover , protocols::moves::SequenceMover , protocols::moves::StructureRestrictor , protocols::moves::TrialMover , protocols::multistate_design::PosType , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::noesy_assign::StructureIndependentPeakCalibrator , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeRelaxMover , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::qsar::scoring_grid::GridInitMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RelaxProtocolBase , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::sewing::AddStartnodeFragments , protocols::sewing::AppendAssemblyMover , protocols::sewing::AssemblyConstraintsMover , protocols::sewing::EnumerateAssemblyMover , protocols::sewing::GivenPathAssemblyMover , protocols::sewing::GreedyAssemblyMover , protocols::sewing::LoophashAssemblyMover , protocols::sewing::MonteCarloAssemblyMover , protocols::sewing::NodeConstraintAssemblyMover , protocols::sewing::RehashAssemblyMover , protocols::sewing::RepeatAssemblyMover , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::AlaScan , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::COFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AlignChainMover , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ChainSplitMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::ClearConstraintsMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::ddG , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MergePDBMover , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::MissingDensityToJumpMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MSDMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ResetBaselineMover , protocols::simple_moves::ResidueTypeConstraintMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::ShearMover , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::SimpleThreadingMover , protocols::simple_moves::SmallMover , protocols::simple_moves::StorePoseSnapshot , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TaskAwareMinMover , protocols::simple_moves::Tumble , protocols::simple_moves::VirtualRootMover , protocols::star::StarAbinitio , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::toolbox::task_operations::STMStoredTask , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• from_bond_cst() : core::kinematics::Jump
• from_chain_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::SwapSegment
• from_entry() : protocols::protein_interface_design::PatchdockReader
• from_entry_ : protocols::protein_interface_design::PatchdockReader
• from_four_points() : core::kinematics::Stub
• from_other_chains() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• from_other_chains_ : protocols::protein_interface_design::filters::HbondsToResidueFilter
• from_res() : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder
• from_res_ : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder
• from_same_chain() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• from_same_chain_ : protocols::protein_interface_design::filters::HbondsToResidueFilter
• from_scratch_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• from_scratch_frequency_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• from_scratch_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• from_span() : protocols::membrane::geometry::EmbeddingDef
• from_span_positive_z() : protocols::membrane::geometry::EmbeddingDef
• from_spans() : protocols::membrane::geometry::Embedding
• from_stubs() : core::kinematics::Jump , core::kinematics::RT
• FromScratchMover() : protocols::stepwise::monte_carlo::mover::FromScratchMover
• front() : protocols::moves::MoverContainer
• frs_ : protocols::kinmatch::FunGroupTK
• fshave1 : protocols::mpi_refinement::MethodParams
• fshave2 : protocols::mpi_refinement::MethodParams
• fshave3 : protocols::mpi_refinement::MethodParams
• fstyle_A_ : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• fstyle_b_ : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• ft : core::kinematics::TreeVizBuilder , protocols::denovo_design::CutAndJump
• ft_ : protocols::membrane::OptimizeMembranePositionMover
• ft_mover() : protocols::simple_moves::ChangeAndResetFoldTreeMover
• ft_mover_ : protocols::simple_moves::ChangeAndResetFoldTreeMover
• ft_restore_ : protocols::rbsegment_relax::MakeStarTopologyMover
• ftoa() : protocols::sparta::ANN
• Full : protocols::hotspot_hashing::movers::PlaceProbeMover
• full_align_res : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• full_constraint_ : protocols::ub_e2c::ubi_e2c_modeler
• full_constraint_set_ : protocols::abinitio::KinematicAbinitio
• full_database_ : protocols::toolbox::task_operations::DatabaseThread
• full_length_loop_rmsd_clustering_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• 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_motif_score() : protocols::sewing::scoring::InterModelMotifScorer , protocols::sewing::scoring::MotifScorer
• full_movemap_ : protocols::carbohydrates::GlycanRelaxMover
• full_name() : core::chemical::carbohydrates::CarbohydrateInfo
• full_name_ : core::chemical::carbohydrates::CarbohydrateInfo
• full_optimize_ : protocols::stepwise::legacy::screener::SimplePoseSelection
• full_sample_rot_index_2_moltenres_sample_rot_index() : core::pack::rotamer_set::ContinuousRotamerSets
• full_score_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• full_sequence() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_sequence_ : core::pose::full_model_info::FullModelParameters , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_sfxn_ : protocols::simple_moves::GreenPacker
• full_span_ : core::scoring::MembraneTopology
• full_to_conventional() : core::pose::full_model_info::FullModelParameters
• full_to_conventional_resnum_and_chain() : core::pose::full_model_info::FullModelParameters
• full_to_input_res_map_ONE_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• full_to_input_res_map_TWO_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• full_to_sub() : core::pose::full_model_info::FullModelInfo , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_to_sub_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• 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 , protocols::abinitio::IterativeAbrelax , protocols::cryst::DockLatticeMover , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::hybridization::CartesianSampler , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::symmetric_docking::SymDockProtocol , protocols::viewer::SilentObserver
• fullatom_allowed_CSP_fraction_ : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_archive_ : protocols::abinitio::IterativeAbrelax
• fullatom_constraint_cutoff_ : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_CSP_weight_ : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_filter() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_non_CSP_weight_ : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_pool_ptr_ : protocols::abinitio::IterativeCentroid
• fullatom_relax_ : protocols::surface_docking::SurfaceDockingProtocol
• fullatom_scorefunction() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• fullatom_scorefunction_ : protocols::anchored_design::AnchorMoversData , protocols::floppy_tail::FloppyTailMover , protocols::metal_interface::ZincHeterodimerMover
• fullatom_scorefxn() : protocols::abinitio::Protocol
• fullatom_sfx_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelMover
• fullatom_stage() : protocols::loop_modeling::LoopModeler
• fullatom_stage_ : protocols::loop_modeling::LoopModeler
• 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
• FullatomRelaxMover() : protocols::surface_docking::FullatomRelaxMover
• FullAtomRNA_Fragments() : protocols::farna::fragments::FullAtomRNA_Fragments
• FullChiSampleSet() : protocols::match::upstream::FullChiSampleSet
• fullLengthPoseOP_ : protocols::pose_length_moves::PossibleLoop
• 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
• fully_initialized : protocols::boinc::BoincSharedMemory
• 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::CircularSplineFunc , 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 , protocols::jumping::ChainbreakDistFunc , protocols::moves::FastLinearFunc , protocols::moves::GeometricFunc , protocols::moves::InvGeometricFunc , protocols::moves::LinearFunc , protocols::moves::RampingFunc , protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• 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 , protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• func_1d() : core::optimization::func_1d
• func_factory_ : core::scoring::constraints::ConstraintIO
• func_sd_ : protocols::forge::constraints::InverseRotamersRCG
• 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 , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• funcnames_ : protocols::pack_daemon::EntityCorrespondence
• funcs() : core::scoring::func::SumFunc
• funcs_ : core::scoring::func::SumFunc , core::scoring::methods::CustomAtomPairEnergy
• function_expression() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• function_name_ : protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFHbondFunction
• function_names_ : protocols::ligand_docking::rdf::RDFBase , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• function_sign_ : protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFHbondFunction
• function_tag() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• function_tag_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• FunctionSign : protocols::ligand_docking::rdf::RDFBase
• FuncTypes : core::scoring::func::FuncFactory
• FunGroupTK() : protocols::kinmatch::FunGroupTK
• fuzzy_topology_ : protocols::abinitio::StrandConstraints
• FuzzyTopology : protocols::abinitio::StrandConstraints
• Fv : protocols::antibody_legacy::Antibody
• Fv_sequence_ : protocols::antibody_legacy::Antibody