- f -

• f0() : core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::KromerMann
• f00() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• F1() : core::optimization::DOF_Node
• f1() : core::scoring::DerivVectorPair
• f11() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• f1_force() : core::scoring::epr_deer::DEERDataCache
• f1ij() : core::scoring::CSA , core::scoring::DC
• F2() : core::optimization::DOF_Node
• f2() : core::scoring::DerivVectorPair
• f22() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• f2_force() : core::scoring::epr_deer::DEERDataCache
• f2c() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• f2ij() : core::scoring::CSA , core::scoring::DC
• f3ij() : core::scoring::CSA
• f_cavity() : core::conformation::membrane::ImplicitLipidInfo
• f_cavity_gradient() : core::conformation::membrane::ImplicitLipidInfo
• f_depth() : core::conformation::membrane::ImplicitLipidInfo
• f_depth_gradient() : core::conformation::membrane::ImplicitLipidInfo
• f_hydration() : core::conformation::membrane::ImplicitLipidInfo
• f_hydration_gradient() : core::conformation::membrane::ImplicitLipidInfo
• fa_and_cen_sizes_for_archives() : protocols::multistage_rosetta_scripts::MRSJobQueenChecker
• fa_atr() : core::scoring::motif::ResPairMotif
• fa_atr_bb() : core::scoring::motif::ResPairMotif
• fa_atr_sc_bb() : core::scoring::motif::ResPairMotif
• fa_center() : core::scoring::Membrane_FAEmbed
• fa_depth() : core::scoring::Membrane_FAEmbed
• fa_dun_cutoff() : protocols::match::upstream::BuildSet
• fa_dun_dev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_rot() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_semi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• fa_dun_tot() : core::pack::dunbrack::RotamerLibraryScratchSpace
• FA_ElecEnergy() : core::scoring::elec::FA_ElecEnergy
• FA_ElecEnergyAroAll() : core::scoring::elec::FA_ElecEnergyAroAll
• FA_ElecEnergyAroAro() : core::scoring::elec::FA_ElecEnergyAroAro
• FA_GrpElecEnergy() : core::scoring::elec::FA_GrpElecEnergy
• fa_hatr() : core::scoring::etable::Etable
• fa_is_independent() : core::conformation::symmetry::SymmetryInfo
• Fa_MbenvEnergy() : core::scoring::methods::Fa_MbenvEnergy
• Fa_MbsolvEnergy() : core::scoring::methods::Fa_MbsolvEnergy
• Fa_Membed_update() : core::scoring::Membrane_FAEmbed
• fa_penalty() : core::scoring::Membrane_FAEmbed
• fa_proj() : core::scoring::Membrane_FAEmbed
• fa_proj_coord() : core::scoring::Membrane_FAEmbed
• fa_proj_deriv() : core::scoring::Membrane_FAEmbed
• fa_projection() : core::scoring::Membrane_FAPotential
• fa_relax_stage() : protocols::forge::remodel::RemodelLoopMover
• fa_score() : protocols::abinitio::IterativeBase
• fa_score_patch() : protocols::abinitio::IterativeBase
• fa_scorefxn() : protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover
• fa_ssdist_scores() : core::scoring::disulfides::SG_Dist_Func
• fa_ssdist_scores_deriv() : core::scoring::disulfides::SG_Dist_Func
• fa_stack_base_all() : core::scoring::methods::EnergyMethodOptions
• FabConstraint() : core::scoring::constraints::FabConstraint
• FabConstraintCreator() : core::scoring::constraints::FabConstraintCreator
• factor() : core::scoring::BondOrderParser , core::scoring::dna::TorsionFourierComponent
• factorA() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorB() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorC() : protocols::simple_moves::BBConRotMover
• factory_begin() : protocols::task_operations::StoreCompoundTaskMover
• factory_clear() : protocols::task_operations::StoreCompoundTaskMover
• factory_end() : protocols::task_operations::StoreCompoundTaskMover
• factory_name() : protocols::genetic_algorithm::EntityElementFactory
• factory_register() : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::io::silent::SilentStructFactory , core::pack::palette::PackerPaletteFactory , 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::jump_selector::JumpSelectorFactory , core::select::residue_selector::ResidueSelectorFactory , core::sequence::SequenceFactory , core::simple_metrics::SimpleMetricFactory , protocols::constraint_generator::ConstraintGeneratorFactory , protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::jd2::JobInputterFactory , protocols::jd2::JobOutputterFactory , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory , protocols::jd3::full_model_inputters::FullModelInputterFactory , protocols::jd3::pose_inputters::PoseInputterFactory , protocols::jd3::pose_outputters::PoseOutputterFactory , protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::moves::MoverFactory , protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory , protocols::parser::DataLoaderFactory , protocols::qsar::scoring_grid::GridFactory , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::rotamer_recovery::RotamerRecoveryFactory , protocols::sewing::requirements::AssemblyRequirementFactory , protocols::sewing::scoring::AssemblyScorerFactory
• FACTSEnergy() : core::scoring::methods::FACTSEnergy
• FACTSPoseInfo() : core::scoring::FACTSPoseInfo
• FACTSPotential() : core::scoring::FACTSPotential
• FACTSResidueInfo() : core::scoring::FACTSResidueInfo
• FACTSRotamerSetInfo() : core::scoring::FACTSRotamerSetInfo
• FACTSRsdTypeMap() : core::scoring::FACTSRsdTypeMap
• fade() : core::scoring::CenHBPotential
• fade_energy() : core::scoring::hbonds::HBondOptions
• fade_hbonding_group_score() : core::scoring::elec::GroupElec
• fade_type() : core::scoring::elec::GroupElec
• fade_zone() : core::scoring::func::FadeFunc
• FadeFunc() : core::scoring::func::FadeFunc
• FadeInterval() : core::scoring::hbonds::FadeInterval
• FaDockingSlideIntoContact() : protocols::docking::FaDockingSlideIntoContact
• FAElecContextData() : core::scoring::elec::FAElecContextData
• fafilter() : protocols::loop_grower::LoopGrower , protocols::loophash::LoopHashMoverWrapper
• fail_verification() : protocols::environment::ProtectedConformation
• failed_jobs() : protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobTracker
• fallback() : protocols::antibody::design::CDRSeqDesignOptions
• fallback_strategy() : protocols::antibody::design::CDRSeqDesignOptions
• false_behavior() : protocols::task_operations::StoreCompoundTaskMover
• false_movemap() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• FalseFilter() : protocols::filters::FalseFilter
• FalseResidueSelector() : core::select::residue_selector::FalseResidueSelector
• 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
• farray_to_array() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• FAScatter() : core::scoring::fiber_diffraction::FAScatter
• fascore() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• FASelectSlidingWindowLoopClosure() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• fasol_cubic_poly_far_xhi() : core::scoring::etable::Etable
• fasol_cubic_poly_far_xlo() : core::scoring::etable::Etable
• fasol_max_dis2() : core::scoring::lkball::LK_BallEnergy
• fast() : protocols::idealize::IdealizeMover
• fast_ccd_close_loops() : protocols::LoopRebuild
• fast_eval_etable_split_fasol() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• 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::sugar::VirtualSugarSampler
• fast_get_lk_fractional_contribution() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• fast_get_lkbr_fractional_contribution() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• fast_loopclose() : protocols::seeded_abinitio::CloseFold
• fast_sample_torsions_from_info() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• fast_scan() : protocols::rna::movers::RNA_LoopCloser
• fasta_file() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• fasta_file_contents() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• FastDensEnergy() : core::scoring::electron_density::FastDensEnergy
• FastDesign() : protocols::denovo_design::movers::FastDesign
• fastdistancemap() : core::scoring::atomic_depth::AtomicDepth
• 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
• FASTERNode() : core::pack::interaction_graph::FASTERNode
• FastForwardToNextResidueAlternative() : protocols::stepwise::screener::FastForwardToNextResidueAlternative
• FastForwardToNextRigidBody() : protocols::stepwise::screener::FastForwardToNextRigidBody
• FastGapMover() : protocols::loophash::FastGapMover
• FastLinearFunc() : protocols::moves::FastLinearFunc
• fastoneshell() : core::scoring::atomic_depth::AtomicDepth
• FastRelax() : protocols::relax::FastRelax
• FastSAXSEnergy() : core::scoring::saxs::FastSAXSEnergy
• FastSAXSEnergyCreator() : core::scoring::saxs::FastSAXSEnergyCreator
• FaSymDockingSlideTogether() : protocols::symmetry::FaSymDockingSlideTogether
• 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
• FaWaterToBilayerEnergy() : protocols::membrane::scoring::FaWaterToBilayerEnergy
• fcen10() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen12() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• fcen6() : core::scoring::CenListInfo , core::scoring::SigmoidWeightedCenList< T >
• 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::SimpleMetricFeatures , 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_xml_schema_group_name() : protocols::features::FeaturesReporterFactory
• FeaturesReporter() : protocols::features::FeaturesReporter
• FeaturesReporterCreator() : protocols::features::FeaturesReporterCreator
• FeaturesReporterFactory() : protocols::features::FeaturesReporterFactory
• FeaturesReporterRegistrator() : protocols::features::FeaturesReporterRegistrator< T >
• 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_and_organize_data() : core::scoring::epr_deer::DEERDataCache
• fetch_stored_derivatives() : core::optimization::LineMinimizationAlgorithm
• ff() : core::scoring::saxs::FormFactor
• FiberDiffraction() : core::scoring::fiber_diffraction::FiberDiffraction
• FiberDiffractionEnergy() : core::scoring::fiber_diffraction::FiberDiffractionEnergy
• FiberDiffractionEnergyCreator() : core::scoring::fiber_diffraction::FiberDiffractionEnergyCreator
• FiberDiffractionEnergyDens() : core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• FiberDiffractionEnergyDensCreator() : core::scoring::fiber_diffraction::FiberDiffractionEnergyDensCreator
• FibrilModelingClaimer() : protocols::topology_broker::FibrilModelingClaimer
• Field() : core::io::pdb::Field
• 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() : core::import_pose::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_Info
• figure_out_chunk_coverage() : core::import_pose::libraries::RNA_ChunkLibrary
• figure_out_constraint_separation_cutoff() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• figure_out_cuts() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_dof_ids_and_offsets() : protocols::rna::denovo::coarse::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::rna::denovo::coarse::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_if_loop_involves_current_pose() : core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator
• 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 , core::scoring::rna::TNA_SuitePotential , protocols::rna::denovo::coarse::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() : core::import_pose::RNA_BasePairHandler
• figure_out_pivot_res_and_scratch_res() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• figure_out_pivots() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• figure_out_potential() : core::scoring::rna::data::RNA_DMS_Potential
• 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::pose::rna::RNA_FilteredBaseBaseInfo
• figure_out_rna_base_stacks_to_score() : core::pose::rna::RNA_FilteredBaseBaseInfo
• figure_out_scan_res() : protocols::magnesium::SampleGrid
• figure_out_segment_ids_from_line() : core::io::silent::SilentStruct
• figure_out_stems() : core::pose::rna::RNA_SecStruct
• figure_out_which_cutpoints_were_affected() : protocols::rna::denovo::coarse::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
• file() : protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter
• file_buf_rank() : protocols::jd2::MPIFileBufJobDistributor
• file_buffer_size() : protocols::checkpoint::CheckPointer
• file_inputs_for_job() : protocols::pack_daemon::DynamicAggregateFunction
• file_name() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• file_names() : protocols::simple_filters::FileRemoveFilter
• file_read() : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• file_reading_token() : protocols::loops::Loops
• FileBuffer() : protocols::checkpoint::FileBuffer
• FileConstraintGenerator() : protocols::denovo_design::constraints::FileConstraintGenerator
• FileExistFilter() : protocols::simple_filters::FileExistFilter
• FileJobOutputter() : protocols::jd2::FileJobOutputter
• filename() : core::io::raw_data::DisulfideFile , core::io::silent::SilentFileData , core::io::StructFileRep , core::pack::task::operation::ReadResfile , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::jd2::JobOutputter , protocols::jd2::RNA_DeNovoJobOutputter , 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_for_job() : protocols::jd3::pose_outputters::ScoreFileOutputter
• filename_for_output_job() : protocols::jd3::pose_outputters::SilentFilePoseOutputter
• filenames() : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::simple_filters::StemFinder
• FileRemoveFilter() : protocols::simple_filters::FileRemoveFilter
• 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_author_records() : core::io::HeaderInformation
• 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() : core::import_pose::RNA_HelixAssembler
• fill_chainTORS() : protocols::rna::denovo::coarse::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_contacts_all_atom2() : 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::pose_metric_calculators::SequenceComparison
• fill_energy_map() : core::scoring::EnergyEdge
• fill_energy_vector() : protocols::simple_ddg::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::BasePairConstraint , 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::MembraneSpanConstraint , core::scoring::constraints::MembraneSpanTermZConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueCouplingConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::RTConstraint , 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_full_model_info() : core::import_pose::FullModelPoseBuilder
• fill_GUIP() : protocols::simple_filters::ResidueDepthFilter
• 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::MutableResidueType
• 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::EmptyPoseJobInputter , protocols::jd2::EnsembleJobInputter , protocols::jd2::JobInputter , protocols::jd2::LargeNstructJobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::ScreeningJobInputter , protocols::jd2::SerializedPoseJobInputter , protocols::jd2::SilentFileJobInputter , protocols::make_rot_lib::MakeRotLibJobInputter
• fill_keyword_records() : core::io::HeaderInformation
• fill_matrix_A_row() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet
• 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_neighs() : protocols::simple_filters::ResidueDepthFilter
• fill_num_neighbors() : protocols::pose_metric_calculators::SequenceComparison
• fill_other_struct_list() : core::io::silent::SilentStruct
• fill_pair_list() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• fill_parameter_values() : core::pose::full_model_info::FullModelParameters
• fill_per_residue_energy_vector() : protocols::simple_ddg::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 , protocols::loop_grower::LoopComparator
• fill_pose_with_motif() : core::scoring::motif::ResPairMotif
• fill_records() : core::io::HeaderInformation
• fill_rna_data_info() : core::io::rna::RNA_DataReader
• fill_rotamer_matrix_from_db_file() : protocols::splice::RotLibdb , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• fill_rotamer_vector() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< 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::rna::denovo::coarse::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_up_slices() : protocols::membrane::MPLipidAccessibility
• fill_vary_loop_length_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• fill_vp() : core::scoring::atomic_depth::AtomicDepth
• 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
• fillatom() : core::scoring::atomic_depth::AtomicDepth
• FillAUTOTaskOperation() : core::pack::task::operation::FillAUTOTaskOperation
• fillTargetPockets() : protocols::pockets::PocketGrid
• fillvoxels() : core::scoring::atomic_depth::AtomicDepth
• filter() : core::pack::task::operation::OperateOnCertainResidues , core::scoring::motif::ResPairMotif , protocols::anchored_design::AnchoredDesignMover , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::Sigmoid
• Filter() : protocols::filters::Filter
• filter() : protocols::fold_from_loops::NubInitioMover , protocols::hotspot_hashing::HotspotStubSet , protocols::loop_grower::LoopPartialSolutionStore , protocols::monte_carlo::ResetBaselineMover , protocols::moves::IteratedConvergenceMover
• Filter() : protocols::pose_selectors::Filter
• filter() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::ReportFilter , protocols::simple_moves::ContingentAcceptMover , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• 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() : core::import_pose::libraries::ChunkSet
• filter_based_on_desired_secstruct() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_behaviour() : protocols::helical_bundle::BundleReporterFilter
• filter_big_bin() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_by_aa() : core::chemical::ResidueTypeFinder
• filter_by_base_property() : core::chemical::ResidueTypeFinder
• filter_by_constraints_energy() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::CrosslinkerMover
• filter_by_constraints_energy_asymmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper , protocols::cyclic_peptide::CrosslinkerMover
• filter_by_constraints_energy_symmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper , protocols::cyclic_peptide::CrosslinkerMover
• filter_by_interchangeability_group() : core::chemical::ResidueTypeFinder
• filter_by_lj() : protocols::match::output::MatchCollisionFilter
• filter_by_name1() : core::chemical::ResidueTypeFinder
• filter_by_name3() : core::chemical::ResidueTypeFinder
• filter_by_residue_type_base_name() : core::chemical::ResidueTypeFinder
• filter_by_sidechain_distance() : protocols::cyclic_peptide::CrosslinkerMover
• filter_by_sidechain_distance_asymmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper , protocols::cyclic_peptide::CrosslinkerMover
• filter_by_sidechain_distance_symmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper , protocols::cyclic_peptide::CrosslinkerMover
• filter_by_total_score() : protocols::cyclic_peptide::CrosslinkerMover
• filter_by_total_score_cutoff_energy() : protocols::cyclic_peptide::CrosslinkerMover
• filter_chain_closure() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• filter_chain_closure_distance() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• filter_chain_closure_halfway() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• filter_chunks() : protocols::pose_creation::SliceToMiniProteinMover
• filter_complex_cycles() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• filter_connections() : core::chemical::ResidueTypeFinder
• filter_creator_map() : protocols::filters::FilterFactory
• filter_deltas() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_disallow_properties() : core::chemical::ResidueTypeFinder
• filter_disallow_variants() : core::chemical::ResidueTypeFinder
• filter_exists() : protocols::filters::FilterFactory
• filter_is_over() : protocols::flxbb::FilterStructs
• filter_is_unpublished() : protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::denovo_design::filters::CavityVolumeFilter , protocols::filters::Filter
• filter_lores_base_pairs() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• filter_lores_base_pairs_early() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• filter_main_chain_torsion_sets() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_max_angle() : protocols::fldsgn::filters::HSSTripletFilter
• filter_max_bend() : protocols::fldsgn::filters::StrandCurvatureByLevels
• filter_max_dist() : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::StrandHelixGeometryFilter
• filter_max_orthoangle() : protocols::fldsgn::filters::StrandHelixGeometryFilter
• filter_max_planeangle() : protocols::fldsgn::filters::StrandHelixGeometryFilter
• filter_max_twist() : protocols::fldsgn::filters::StrandCurvatureByLevels
• filter_min_angle() : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_bend() : protocols::fldsgn::filters::StrandCurvatureByLevels
• filter_min_dist() : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::StrandHelixGeometryFilter
• filter_min_orthoangle() : protocols::fldsgn::filters::StrandHelixGeometryFilter
• filter_min_planeangle() : protocols::fldsgn::filters::StrandHelixGeometryFilter
• filter_min_twist() : protocols::fldsgn::filters::StrandCurvatureByLevels
• filter_name() : protocols::calc_taskop_filters::RelativePoseFilter , protocols::denovo_design::movers::EXCN_FilterFailed , protocols::match::output::MatchFilter , protocols::topology_broker::ConstraintClaimer
• 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_num() : protocols::denovo_design::movers::EXCN_FilterFailed
• filter_on() : protocols::flxbb::FilterStructs
• filter_out_high() : protocols::simple_filters::LongestContinuousPolarSegmentFilter
• filter_out_low() : protocols::simple_filters::BuriedSurfaceAreaFilter
• filter_pareto_opt_poses() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_path() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• filter_permutations() : protocols::denovo_design::architects::BetaSheetArchitect
• filter_pose_order() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• filter_poses_have_same_sequence_and_variants() : core::import_pose::libraries::ChunkSet
• filter_provides_citation_info() : protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::filters::Filter , protocols::indexed_structure_store::filters::FragmentLookupFilter
• filter_redundant() : core::scoring::motif::MotifHits
• filter_score() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• filter_scorefxn() : protocols::fold_from_loops::NubInitioMover
• filter_seqpos_pareto_opt_ptmuts() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_similar() : protocols::mpi_refinement::MultiObjective
• filter_solutions() : protocols::generalized_kinematic_closure::GeneralizedKIC
• filter_special_cases() : core::chemical::ResidueTypeFinder
• filter_spinlabel_ensemble_by_distance_check() : core::scoring::nmr::NMRSpinlabel
• filter_spinlabel_ensemble_by_mask() : core::scoring::nmr::NMRSpinlabel
• 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_thresholds() : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• filter_type() : protocols::fldsgn::filters::CoreDunbrackFilter
• 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_val() : protocols::simple_filters::ReportFilter
• filter_value() : protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• filter_vdw() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• filter_virtual_atoms() : protocols::stepwise::modeler::align::StepWisePoseAligner
• filter_water_rotamers() : core::pack::rotamer_set::RotamerSet_
• filter_weight() : protocols::topology_broker::ConstraintClaimer
• filter_xml_schema_group_name() : protocols::filters::FilterFactory
• FilterBucket() : protocols::loophash::FilterBucket
• FilterCreator() : protocols::filters::FilterCreator
• filtered_abego() : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_area() : protocols::simple_filters::ShapeComplementarityFilter
• filtered_base_axis_array() : core::pose::rna::RNA_FilteredBaseBaseInfo
• filtered_base_pair_array() : core::pose::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stack_array() : core::pose::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stack_axis_array() : core::pose::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stagger_array() : core::pose::rna::RNA_FilteredBaseBaseInfo
• filtered_median_distance() : protocols::simple_filters::ShapeComplementarityFilter
• filtered_sc() : protocols::simple_filters::ShapeComplementarityFilter
• filtered_score() : protocols::simple_filters::PackStatFilter
• filtered_sheet_topology() : protocols::fldsgn::filters::SheetTopologyFilter
• filtered_ss() : protocols::fldsgn::filters::SecondaryStructureFilter
• 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
• FilteredSolutions() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• Filterer_Count() : protocols::stepwise::modeler::rna::Filterer_Count
• FilterFactory() : protocols::filters::FilterFactory
• FilterMover() : protocols::moves::FilterMover
• filterprevious() : protocols::loop_grower::LoopPartialSolutionStore
• FilterRegistrator() : protocols::filters::FilterRegistrator< T >
• FilterReportAsPoseExtraScoresMover() : protocols::moves::FilterReportAsPoseExtraScoresMover
• FilterReporter() : protocols::pose_reporters::FilterReporter
• FilterReporterMover() : protocols::moves::FilterReporterMover
• filters() : protocols::calc_taskop_filters::Operator , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::monte_carlo::GenericMonteCarloMover
• filters_ct_naming_func() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• FilterScanFilter() : protocols::protein_interface_design::filters::FilterScanFilter
• FilterStructs() : protocols::flxbb::FilterStructs
• FilterStructs_Packstat() : protocols::flxbb::FilterStructs_Packstat
• FilterStructs_TotalCharge() : protocols::flxbb::FilterStructs_TotalCharge
• FilterValueMetric() : protocols::filters::FilterValueMetric
• final_cartligmin() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• 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_dump_stuff() : protocols::recces::RECCES_Mover
• final_exact_cartmin() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• final_exact_scmin() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• final_fold_tree() : protocols::abinitio::KinematicControl , protocols::topology_broker::TopologyBroker
• final_frlx_rounds() : protocols::cyclic_peptide::CrosslinkerMover
• final_iter() : protocols::mpi_refinement::Scheduler
• 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::RNA_DeNovoJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::wwPDBJobOutputter
• final_repack() : protocols::grafting::AnchoredGraftMover
• final_sampling() : protocols::residue_optimization::MetapatchEnumeration
• final_score() : protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::rosetta_scripts::ParsedProtocol
• final_scorefxn() : protocols::rosetta_scripts::ParsedProtocol
• final_scores() : protocols::residue_optimization::MetapatchEnumeration
• final_solvate() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• final_test() : protocols::motifs::MotifHit
• final_visit_to_edge() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• Finalize() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• finalize() : 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::Pool_RMSD , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::StrandPairingSet , protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies , protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter , 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_after_minimizing() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::methods::EnergyMethod , core::scoring::mhc_epitope_energy::MHCEpitopeEnergy , core::scoring::ScoreFunction , core::scoring::util_methods::DumpTrajectoryEnergy
• finalize_author_records() : core::io::HeaderInformation
• 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_de_novo_scoretable_from_energies() : core::chemical::mainchain_potential::MainchainScoreTable
• finalize_experimental_technique_records() : core::io::HeaderInformation
• finalize_hbond_graph() : core::pack::hbonds::HBondGraphInitializerIG
• finalize_job_result() : protocols::jd3::chunk_library::MoverAndChunkLibraryJob
• finalize_job_summary() : protocols::jd3::chunk_library::MoverAndChunkLibraryJob
• finalize_keyword_records() : core::io::HeaderInformation
• finalize_output() : core::pack::annealer::FASTERAnnealer
• finalize_parse() : core::io::HeaderInformation
• finalize_pose() : protocols::antibody::design::AntibodyDesignMover
• 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::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::MPLipidAccessibility , 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::energy_methods::DEEREnergy , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , 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::elec::RNA_FA_ElecEnergy , 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::hbonds::NPDHBondEnergy , 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::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPSpanAngleEnergy , core::scoring::membrane::MPSpanInsertionEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::methods::Abego , core::scoring::methods::BranchEnergy , core::scoring::methods::Burial_v2Energy , 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::CovalentLabelingEnergy , core::scoring::methods::CovalentLabelingFAEnergy , 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::HRF_MSLabelingEnergy , core::scoring::methods::HRFDynamicsEnergy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearBranchEnergy , 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::mhc_epitope_energy::MHCEpitopeEnergy , core::scoring::netcharge_energy::NetChargeEnergy , 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::RNA_PartitionEnergy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::util_methods::DumpTrajectoryEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::membrane::scoring::FaWaterToBilayerEnergy , protocols::nmr::pcs::PCSEnergy , protocols::nmr::pre::PREEnergy , protocols::nmr::rdc::RDCEnergy , protocols::rna::AlignmentEnergy , 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 , protocols::scoring::methods::TargetClashEnergy , protocols::scoring::VDW_GridEnergy
• FinalizeAromatic() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• finalized() : protocols::fldsgn::topology::StrandPairingSet
• 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
• find() : core::kinematics::MoveMap , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::constraint_generator::ConstraintsMap , protocols::recces::sampler::MC_Comb , protocols::recces::sampler::MC_OneTorsion , protocols::recces::sampler::MC_Sampler , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::recces::sampler::rna::MC_RNA_OneJump , protocols::recces::sampler::rna::MC_RNA_Sugar , protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler
• find_aa_composition() : protocols::simple_filters::TMsAACompFilter
• find_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• find_adjacent_helix() : protocols::helical_bundle_predict::HBPHelixAssignments
• find_aligned_atoms() : protocols::sewing::hashing::Hasher
• 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 >
• 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_available_job() : protocols::jobdist::BaseJobDistributor
• find_backbone_oxygen_atom() : core::scoring::rna::RNA_LowResolutionPotential
• find_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• find_best_anchor() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• find_best_ligand_pose_with_grid_search() : protocols::nmr::pcs::PCSLigandTransformMover
• find_by_atmpairno() : core::scoring::ResidueExclParams
• find_by_bondno() : core::scoring::ResidueExclParams
• find_char_location_in_string() : protocols::evolution::AlignmentGapInserter
• find_chunk() : protocols::frag_picker::VallProvider
• find_closest() : protocols::simple_moves::ExplicitWaterMover
• find_closest_backbone() : protocols::motifs::IRCollection
• find_closest_occupied_point() : protocols::loop_grower::DensSkeleton
• find_closest_pnts() : protocols::simple_filters::HelixHelixAngleFilter
• find_closest_res() : protocols::simple_filters::HelixHelixAngleFilter
• find_closest_to_average() : protocols::toolbox::DecoySetEvaluation
• find_constraints_to_ligand() : protocols::enzdes::EnzdesConstraintReporter , protocols::enzdes::PredesignPerturbMover
• find_contact_resnums() : protocols::simple_moves::SetupMetalsMover
• find_curr_hbonds_to_upper_neighbors() : core::pack::interaction_graph::NPDHBSimpleNode
• find_current_disulfides() : protocols::denovo_design::DisulfidizeMover
• find_cutpoint_in_range() : protocols::denovo_design::components::FoldGraph
• find_cutpoints() : protocols::denovo_design::components::FoldGraph
• find_data() : core::scoring::bin_transitions::BinTransitionCalculator
• find_data_and_bin() : core::scoring::bin_transitions::BinTransitionCalculator
• find_dbase_entry() : protocols::splice::Splice , protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInTail
• find_dependency() : protocols::forge::build::BuildManager
• find_design_interface() : protocols::enzdes::DetectProteinLigandInterface
• find_design_interface_arg_sweep() : protocols::enzdes::DetectProteinLigandInterface
• find_disulfide_postions() : protocols::splice::RBInMover , protocols::splice::RBOutMover , protocols::splice::SpliceInAntibody , protocols::splice::SpliceOutAntibody
• 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::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , 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_and_last_isopeptide_residues() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• find_first_disulf_res() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• 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::rna::denovo::movers::RNA_Relaxer
• find_geometric_center_for_constrained_lig_atoms() : protocols::enzdes::PredesignPerturbMover
• find_global_pose_number() : protocols::topology_broker::SequenceNumberResolver
• find_grid_set() : protocols::qsar::scoring_grid::GridManager
• find_hash_edge() : protocols::legacy_sewing::SewGraph
• find_hb_paths() : core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric
• find_hbs_for_nbrs_alt_state_step1() : core::pack::interaction_graph::NPDHBSimpleNode
• find_hbs_for_nbrs_alt_state_step2() : core::pack::interaction_graph::NPDHBSimpleNode
• find_helices() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• find_helix_vector() : core::scoring::membrane::MPSpanAngleEnergy , protocols::simple_filters::HelixHelixAngleFilter
• 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::ligand_docking::InterfaceBuilder , protocols::peptide_deriver::PeptideDeriverFilter
• find_interface_rsds() : protocols::ligand_docking::LigandBaseProtocol
• find_job_edge() : protocols::jd3::JobDigraph
• find_jobs_for_next_node() : protocols::jd3::job_distributors::JobExtractor
• find_label() : protocols::topology_broker::SequenceNumberResolver
• find_labels() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• find_labels2() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• find_last_disulf_res() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• find_length() : protocols::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_matching_res() : protocols::splice::RotLibOut
• find_max_frag() : protocols::hybridization::TMalign
• find_max_over() : core::chemical::VDDistanceMatrix
• find_max_z() : protocols::membrane::AqueousPoreFinder
• find_metal_resnums() : protocols::simple_moves::SetupMetalsMover
• find_min_z() : protocols::membrane::AqueousPoreFinder
• find_minimalist_flexbb_edge() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• find_minimization_edge() : core::scoring::MinimizationGraph
• find_missing_helices() : protocols::fldsgn::filters::HelixPairingFilter
• find_motifs() : core::scoring::motif::MotifHash
• find_motifs_with_radius() : core::scoring::motif::MotifHash
• find_native() : protocols::hbnet::HBNet
• find_nbrs() : protocols::ddg::ddGMover
• find_nearest_res() : protocols::cutoutdomain::CutOutDomain
• find_neighboring_stubs() : protocols::hotspot_hashing::HotspotStubSet
• find_neighbors() : protocols::evolution::NucleotideMutation
• 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_non_active_site_cut_site() : protocols::splice::Splice , protocols::splice::SpliceOut
• find_non_polymer_bond() : protocols::denovo_design::components::StructureData
• find_optimal_rotation() : protocols::pockets::PlaidFingerprint
• find_otfflexbb_edge() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• find_para_ion_position_and_compute_pre_score() : core::scoring::nmr::pre::PREMultiSet
• 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::legacy_sewing::Assembly
• find_protein_residues() : protocols::ligand_docking::InterfaceBuilder
• find_reference_and_current_rotamer_correspondence() : protocols::minimization_packing::GreenPacker
• find_resnum() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• find_root_from_atom_pointer() : core::kinematics::AtomTree
• find_roots() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• 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_segment_name() : protocols::denovo_design::components::StructureData
• find_segments() : protocols::features::ModelFeatures
• find_SilentStructOPs() : protocols::wum::find_SilentStructOPs
• find_source_positions() : protocols::rna::denovo::coarse::CoarseRNA_Fragments
• find_start_of_next_interface_region() : protocols::ligand_docking::ligand_options::Interface
• find_starting_segment() : protocols::sewing::movers::AppendAssemblyMover
• find_stop_of_this_interface_region() : protocols::ligand_docking::ligand_options::Interface
• find_symmetric_hbonds() : core::pack::hbonds::HBondGraphInitializerIG
• find_tag() : protocols::features::FeaturesReporter
• find_template_segments() : protocols::denovo_design::components::ExtendedPoseBuilder
• find_tilt_center() : protocols::rigid::RigidBodyTiltMover
• find_tm_regions() : protocols::simple_filters::SecretionPredictionFilter
• find_type_matches() : protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• find_uninstantiated_phosphates() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• find_unsats() : protocols::hbnet::HBNet
• find_upper_terminus() : protocols::denovo_design::components::StructureData
• find_vl_vh_cut() : protocols::splice::RBInMover , protocols::splice::RBOutMover , protocols::splice::SpliceInAntibody , protocols::splice::SpliceOutAntibody
• find_water_neighbor_vecs() : protocols::magnesium::MgWaterHydrogenPacker
• find_zinc_site() : protocols::metal_interface::ZincSiteFinder
• findCartomAtom() : protocols::cartesian::MolecularDynamics
• findchar() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• findClusters() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::pockets::TargetPocketGrid
• findClustersByExemplars() : protocols::pockets::PocketGrid
• FindConsensusSequence() : protocols::recon_design::FindConsensusSequence
• findDecoyWithMostNeighbors() : protocols::cluster::calibur::Clustering
• findEdgeId() : core::sequence::SequenceCoupling
• FindEndpointsOperation() : protocols::splice::FindEndpointsOperation
• findExemplars() : protocols::pockets::PocketGrid
• findLargestClusters() : protocols::cluster::calibur::Clustering
• 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
• finer_sampling_at_chain_closure() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• FingerprintBase() : protocols::pockets::FingerprintBase
• FingerprintMultifunc() : protocols::pockets::FingerprintMultifunc
• finish_arc() : core::scoring::packstat::trace
• finish_creating_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• finish_hit_generation_for_constraint() : protocols::match::Matcher
• finish_parse_string_to_residue_selector() : core::select::residue_selector::SelectorLogicParser
• finish_pose() : core::io::silent::SilentStruct
• finish_protocol() : protocols::loop_modeling::LoopProtocol , protocols::rosetta_scripts::ParsedProtocol
• finished() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::denovo_design::components::StructureDataPerturber , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::symmetry::SymmetrySlider
• finished_simulation() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::TemperatureController
• finite() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• fire_all_triggers() : protocols::monte_carlo::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• first() : protocols::match::Hit
• first_adjacent_heavy_atom() : core::conformation::Residue
• first_atom_in_branch() : core::scoring::trie::TrieNode< AT, CPDATA >
• first_connected_resonance() : protocols::noesy_assign::Resonance
• first_node_is_donor() : core::scoring::hbonds::graph::HBondInfo
• first_node_is_the_acceptor() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• first_pass_ala_scan() : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• first_res_types() : core::scoring::methods::AspartimidePenaltyEnergy
• first_residue() : core::conformation::parametric::Parameters , protocols::kinematic_closure::ClosureProblem
• first_residue_index() : core::conformation::parametric::Parameters
• first_sidechain_atom() : core::chemical::ResidueType , core::conformation::Residue
• first_sidechain_hydrogen() : core::chemical::ResidueType , core::conformation::Residue
• 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 >
• fit_intensities() : core::scoring::saxs::SAXSEnergy
• fit_k() : core::scoring::epr_deer::Simulated4PDEERTrace
• fit_stdev() : core::scoring::epr_deer::DEERDecayData
• fit_trace() : core::scoring::epr_deer::Simulated4PDEERTrace
• fitBfactors() : core::scoring::cryst::PhenixInterface
• FitBfactorsMover() : protocols::cryst::FitBfactorsMover
• fitness() : protocols::genetic_algorithm::Entity , protocols::multistate_design::SingleStateEntityData
• fitness_function() : protocols::multistate_design::SingleState
• fitness_pbest() : core::optimization::Particle
• fitness_threshold() : protocols::protein_interface_design::filters::BoltzmannFilter
• fitness_valid() : protocols::genetic_algorithm::Entity
• fitnessCostPerATP() : protocols::evolution::AASynthesisFitnessCost
• FitnessFilter() : protocols::recon_design::FitnessFilter
• FitSimpleHelix() : protocols::helical_bundle::FitSimpleHelix
• FitSimpleHelixMultiFunc() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• five_prime_chain_break_res() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• five_prime_res() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• fiveprime_cap() : core::import_pose::RNA_DeNovoParameters , core::pose::full_model_info::FullModelInfo
• fix_anchor() : protocols::anchored_design::AnchorMoversData
• fix_disulfides() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• fix_fold_tree_in_excised_pose_for_mg_bound_waters() : protocols::magnesium::MgHydrater
• fix_fragment() : protocols::fold_from_loops::utils::Nub
• fix_fragments() : protocols::fold_from_loops::utils::Nub
• fix_his_tautomer() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• fix_jump_atoms_at_loop_boundaries() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• fix_ligand_residues() : protocols::simple_moves::RepeatPropagationMover
• fix_omega() : protocols::relax::RelaxProtocolBase
• fix_phi_psi_offsets() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• fix_ranges() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• fix_reference_energies() : protocols::optimize_weights::OptEMultifunc
• fix_secstruct_definition() : core::select::residue_selector::SecondaryStructureSelector
• fix_tensor() : core::scoring::nmr::rdc::RDCMultiSet
• fix_tensors() : core::scoring::nmr::pcs::PCSMultiSet
• FixAllLoopsMover() : protocols::pose_length_moves::FixAllLoopsMover
• FixbbCoupledRotamerSimAnnealer() : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• FixbbLinkingRotamerSimAnnealer() : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• FixbbPwatSimAnnealer() : core::pack::annealer::FixbbPwatSimAnnealer
• FixbbRotamerSets() : core::pack::rotamer_set::FixbbRotamerSets
• FixbbSimAnnealer() : core::pack::annealer::FixbbSimAnnealer
• fixed() : core::scoring::OneToAllEnergyContainer
• 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_energy_terms() : protocols::optimize_weights::OptEData
• fixed_nodes() : protocols::denovo_design::components::SolutionSorter
• fixed_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• fixed_stems() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• FixedBBEdge() : core::pack::interaction_graph::FixedBBEdge
• FixedBBInteractionGraph() : core::pack::interaction_graph::FixedBBInteractionGraph
• FixedBBNode() : core::pack::interaction_graph::FixedBBNode
• FixedOffsetPivots() : protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots
• FixedOffsetsPivots() : protocols::kinematic_closure::pivot_pickers::FixedOffsetsPivots
• FixedPivots() : protocols::kinematic_closure::pivot_pickers::FixedPivots
• FixedTemperatureController() : protocols::canonical_sampling::FixedTemperatureController
• fixes_connects() : core::chemical::ResidueTypeFinder
• fixes_interchangeability_group() : core::chemical::ResidueTypeFinder
• fixes_name3() : core::chemical::ResidueTypeFinder
• fixResidue() : protocols::jumping::ResiduePairJumpSingle
• FixTemplateJumpSetup() : protocols::abinitio::FixTemplateJumpSetup
• flag_file() : protocols::jd2::archive::Batch
• flag_for_calculation() : core::scoring::FACTSResidueInfo
• flank_residue_min() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• flanking_left_aa() : protocols::forge::build::SegmentInsert
• flanking_left_nres() : protocols::forge::build::SegmentInsert
• flanking_left_ss() : protocols::forge::build::SegmentInsert
• flanking_right_aa() : protocols::forge::build::SegmentInsert
• flanking_right_nres() : protocols::forge::build::SegmentInsert
• flanking_right_ss() : protocols::forge::build::SegmentInsert
• flat_size() : core::fragment::FrameList
• FlatHarmonicFunc() : core::scoring::func::FlatHarmonicFunc
• flexbb() : protocols::evolution::NucleotideMutation
• FlexBBDesignMeanField() : protocols::mean_field::FlexBBDesignMeanField
• FlexbbEdge() : protocols::flexpack::interaction_graph::FlexbbEdge
• FlexbbInteractionGraph() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• FlexBBMeanField() : protocols::mean_field::FlexBBMeanField
• 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_label() : protocols::fold_from_loops::utils::Nub
• 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_considering_alt_bb() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_for_moltenres() : 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_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_HNQ() : core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• flip_in_pcs() : protocols::flexpep_docking::FlexPepDockingProtocol
• flip_subset() : core::pack::task::operation::OperateOnResidueSubset
• flip_upstream_downstream_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• FlipChiralityMover() : protocols::cyclic_peptide::FlipChiralityMover
• FlipMover() : protocols::membrane::FlipMover
• flipped() : core::pose::rna::BasePair , core::pose::rna::BaseStack
• float_ambiguity() : protocols::noesy_assign::PeakAssignment
• float_label() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• floating_base() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_base_anchor_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• FloatingResonance() : protocols::noesy_assign::FloatingResonance
• FloppyTailMover() : protocols::floppy_tail::FloppyTailMover
• flush() : protocols::features::DatabaseJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::RNA_DeNovoJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::SingleFileBuffer , protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::output::MultipleOutputter , protocols::jd3::output::ResultOutputter , protocols::jd3::output::StandardResultOutputter , protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::pose_outputters::ScoreFileOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputter , protocols::jd3::standard::StandardJobQueen
• flush_channel() : protocols::jd2::MpiFileBuffer
• flush_checkpoints() : protocols::checkpoint::CheckPointer
• FlxbbDesign() : protocols::flxbb::FlxbbDesign
• FlxbbDesignPack() : protocols::flxbb::FlxbbDesignPack
• fname() : core::pose::RID_FileSource , protocols::simple_moves::AddChainMover
• fname_initialized_from() : core::pack::task::ResfileContents
• FNatFilter() : protocols::protein_interface_design::filters::FNatFilter
• fobjnames() : protocols::mpi_refinement::MultiObjective
• fold() : protocols::abinitio::AbrelaxApplication , protocols::denovo_design::movers::BuildDeNovoBackboneMover
• fold_attempt() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• fold_in_rb_deltas() : core::kinematics::Jump , core::kinematics::RT
• fold_label_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::splice::Splice , protocols::splice::SpliceManager , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• fold_tree_from_silent_file() : core::import_pose::RNA_DeNovoParameters
• fold_tree_io() : core::import_pose::ImportPoseOptions , core::io::StructFileRepOptions
• fold_tree_rec() : protocols::denovo_design::components::FoldGraph
• FoldandDockClaimer() : protocols::topology_broker::FoldandDockClaimer
• FoldConstraints() : protocols::abinitio::FoldConstraints
• folder() : protocols::noesy_assign::CrossPeak
• folder_ct_namer() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• folder_group_name() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• FoldGraph() : protocols::denovo_design::components::FoldGraph
• foldInChanges() : protocols::electron_density::VoxelSpacingMultifunc
• folding_score() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• FoldResonance() : protocols::noesy_assign::FoldResonance
• FoldTree() : core::kinematics::FoldTree
• foldTree() : protocols::simple_moves::CutChainMover
• foldtree_string() : core::io::StructFileRep
• FoldTreeFromFoldGraphMover() : protocols::denovo_design::movers::FoldTreeFromFoldGraphMover
• FoldTreeFromLoops() : protocols::loops::FoldTreeFromLoops
• FoldTreeFromMotif() : protocols::simple_moves::FoldTreeFromMotif
• FoldTreeHybridize() : protocols::hybridization::FoldTreeHybridize
• FoldTreeSketch() : core::environment::FoldTreeSketch
• foldtype_from_name() : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype_from_spairs() : protocols::fldsgn::topology::SheetFoldTypeManager
• follow_edge() : protocols::legacy_sewing::Assembly
• follow_random_edge_from_node() : protocols::legacy_sewing::LegacyAssemblyMover
• forbidden_aas() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• 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_add_base_residue_type_already_write_locked() : core::chemical::ResidueTypeSet
• 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_bitflip() : core::io::silent::SilentStruct
• force_centroid_interaction() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_combined_gaussian_approximation() : core::scoring::func::GaussianChainFunc
• force_const() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• force_fold_tree() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• force_job_purging() : protocols::jd2::JobsContainer
• force_moving_res_for_erraser() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_natro() : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• force_natro_for_stored_task_names() : protocols::matdes::MatDesGreedyOptMutationMover
• force_nbr_atom_orient() : core::chemical::ResidueTypeBase
• force_next_move_reject() : protocols::moves::SimulatedTempering
• 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_silent_bitflip_on_read() : core::io::silent::SilentFileOptions
• force_silent_bitflip_on_read_set() : core::io::silent::SilentFileOptions
• force_south_sugar_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_submotif_without_intervening_bulge() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• force_syn_chi_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_total_rounds() : protocols::carbohydrates::GlycanSampler
• force_unique_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• force_update_residue_coordinates() : core::conformation::Conformation
• force_update_residue_torsions() : core::conformation::Conformation
• ForceDisulfidesMover() : protocols::calc_taskop_movers::ForceDisulfidesMover
• forget_chains_and_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• forget_initial_loops() : protocols::anchored_design::AnchoredDesignMover
• form_disulfide() : protocols::protein_interface_design::movers::DisulfideMover
• formal_charge() : core::chemical::Atom , core::chemical::ResidueType , core::chemical::sdf::MolFileIOAtom
• format() : pybind11::detail::unsafe_nonpod_npy_format_descriptor< T >
• format_silent_struct() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• 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
• 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::legacy_sewing::SegmentGraph
• forward_jump() : protocols::motifs::Motif
• found_centroid_interaction() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• found_move() : protocols::recces::sampler::MC_Sampler
• FourAtomsConstraintData() : protocols::frag_picker::scores::FourAtomsConstraintData
• FourPointsFunc() : core::scoring::func::FourPointsFunc
• fp_compare() : protocols::pockets::PlaidFingerprint
• fp_compare_deriv() : protocols::pockets::PlaidFingerprint
• fpath() : core::scoring::PoissonBoltzmannPotential
• fpcs() : core::scoring::nmr::pcs::PCSSingleSet
• fpcs_Xax() : core::scoring::nmr::pcs::PCSSingleSet
• fpcs_Xax_Xrh() : core::scoring::nmr::pcs::PCSSingleSet
• fpcs_Xrh() : core::scoring::nmr::pcs::PCSSingleSet
• frac() : core::scoring::elec::electrie::ElecAtom
• frac2index() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• frac_from_AA() : core::pack::annealer::Value
• frac_intra_AA() : core::pack::annealer::Value
• frac_to_AA() : core::pack::annealer::Value
• fract_out_of_bounds_func() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• fract_property_penalty() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• fraction_by_recombination() : protocols::genetic_algorithm::GeneticAlgorithmBase
• fraction_hydrophobic_sasa() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary
• fraction_polar_sasa() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary
• fractions_small_residues() : protocols::docking::membrane::MPFindInterfaceMover
• frag_files() : protocols::indel::IndelOptimizationMover , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• frag_id() : core::fragment::FragID_Iterator , core::fragment::Frame
• frag_libs() : protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::loops::loop_mover::LoopMover
• frag_set_loader_ct_namer() : protocols::parser::FragSetLoader
• frag_size() : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::frags::TorsionFragmentMover , protocols::rna::denovo::movers::RNA_DeNovoMasterMover
• frag_sizes() : protocols::frags::FragLib
• frag_type() : core::fragment::FragFactory
• fragbias_reporter() : protocols::hybridization::FragmentBiasAssigner
• FragCache() : core::fragment::FragCache< T >
• FragData() : core::fragment::FragData
• FragFactory() : core::fragment::FragFactory
• FragID() : core::fragment::FragID
• fragID() : core::fragment::FrameList
• FragID_Iterator() : core::fragment::FragID_Iterator
• FragInsertAndAlignMover() : protocols::rbsegment_relax::FragInsertAndAlignMover
• FragLib() : protocols::frags::FragLib
• fragment() : core::fragment::FragID , core::fragment::FragmentRmsd , core::fragment::Frame
• fragment_as_pose() : core::fragment::Frame
• fragment_check() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• fragment_contacts() : protocols::frag_picker::FragmentPicker
• fragment_num() : protocols::nonlocal::SmoothPolicy::Candidate
• fragment_ptr() : core::fragment::FragID , core::fragment::Frame
• fragment_specification() : protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::indexed_structure_store::FragmentLookup
• 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
• FragmentExtension() : protocols::loop_grower::FragmentExtension
• FragmentIO() : core::fragment::FragmentIO
• FragmentJumpClaimer() : protocols::topology_broker::FragmentJumpClaimer
• FragmentJumpCM() : protocols::abinitio::abscript::FragmentJumpCM
• FragmentLibraryManager() : core::fragment::picking_old::FragmentLibraryManager
• FragmentLookup() : protocols::indexed_structure_store::FragmentLookup
• FragmentLookupFilter() : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentLookupResult() : protocols::indexed_structure_store::FragmentLookupResult
• FragmentMover() : protocols::simple_moves::FragmentMover
• FragmentPair() : protocols::features::helixAssembly::FragmentPair
• FragmentPerturber() : protocols::kinematic_closure::perturbers::FragmentPerturber
• FragmentPicker() : protocols::frag_picker::FragmentPicker
• FragmentReader() : protocols::parser::FragmentReader
• FragmentRmsd() : core::fragment::FragmentRmsd
• fragments() : core::fragment::picking_old::vall::VallLibrarian , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::nonlocal::Policy , protocols::simple_moves::FragmentMover , protocols::topology_broker::FragmentClaimer
• fragments_for_permutation() : protocols::denovo_design::components::Picker
• fragments_for_permutation_take_X_from_pose() : protocols::denovo_design::components::Picker
• fragments_id() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::NubInitioMover
• fragments_permutation_test_by_CA_distances() : protocols::motif_grafting::movers::MotifGraftMover
• fragments_to_string() : protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign
• FragmentSampler() : protocols::abinitio::FragmentSampler
• FragmentScoreFilter() : protocols::frag_picker::FragmentScoreFilter
• FragmentScoreManager() : protocols::frag_picker::scores::FragmentScoreManager
• FragmentScoreMap() : protocols::frag_picker::scores::FragmentScoreMap
• FragmentScoringMethod() : protocols::frag_picker::scores::FragmentScoringMethod
• FragmentSelectingRule() : protocols::frag_picker::FragmentSelectingRule
• FragmentSetLoader() : core::fragment::FragmentSetLoader
• FragmentSpecification() : protocols::indexed_structure_store::FragmentSpecification
• FragmentStore() : protocols::indexed_structure_store::FragmentStore
• FragmentStoreManager() : protocols::indexed_structure_store::FragmentStoreManager
• FragQualCalculator() : protocols::pose_metric_calculators::FragQualCalculator
• FragQualFilter() : protocols::fldsgn::filters::FragQualFilter
• frags_large() : protocols::topology_broker::FragmentContainer
• frags_per_pos() : protocols::frag_picker::FragmentSelectingRule
• frags_small() : protocols::topology_broker::FragmentContainer
• FragSet() : core::fragment::FragSet
• FragSetCollection() : core::fragment::FragSetCollection
• FragSetLoader() : protocols::parser::FragSetLoader
• FragsToAtomDist() : protocols::noesy_assign::FragsToAtomDist
• FragStore() : core::fragment::FragStore< T >
• frame() : core::fragment::FragFactory , core::fragment::FragID , core::fragment::FragmentRmsd
• Frame() : core::fragment::Frame
• frame() : protocols::kinematic_closure::ClosureProblem , protocols::match::upstream::FullChiSampleSet
• frame_for_residue() : protocols::features::LoopAnchorFeatures
• frame_from_global_orientation() : protocols::toolbox::match_enzdes_util::LigandConformer
• frame_lower_pivot() : protocols::kinematic_closure::ClosureProblem
• 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_upper_pivot() : protocols::kinematic_closure::ClosureProblem
• frame_vector() : core::fragment::FrameList
• FrameIterator() : core::fragment::FrameIterator
• FrameListIterator_() : core::fragment::FrameListIterator_
• frames() : core::fragment::FragSet , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet
• framework_dependant_clusters() : protocols::antibody::design::MutateFrameworkForCluster
• framework_dependant_mutations() : protocols::antibody::design::MutateFrameworkForCluster
• framework_dependant_positions() : protocols::antibody::design::MutateFrameworkForCluster
• frdc() : core::scoring::nmr::rdc::RDCMultiSet
• frdc_Da() : core::scoring::nmr::rdc::RDCMultiSet
• frdc_Da_R() : core::scoring::nmr::rdc::RDCMultiSet
• frdc_R() : core::scoring::nmr::rdc::RDCMultiSet
• free_2HOprime_bonus() : core::scoring::methods::FreeDOF_Options
• free_data() : protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• free_dof_options() : core::scoring::methods::EnergyMethodOptions
• free_lock_on_silent_file() : protocols::rna::setup::RNA_CSA_JobDistributor
• free_residues() : protocols::recces::options::RECCES_Options
• free_rsd() : protocols::recces::scratch::ThermalSamplingMover
• free_side_chain_bonus() : core::scoring::methods::FreeDOF_Options
• free_sugar_bonus() : core::scoring::methods::FreeDOF_Options
• free_suite_bonus() : core::scoring::methods::FreeDOF_Options
• free_terms_energy_map_from_dofs() : protocols::optimize_weights::IterativeOptEDriver
• free_weights_and_refEs_from_vars() : protocols::optimize_weights::IterativeOptEDriver
• FreeDOF_Energy() : core::scoring::methods::FreeDOF_Energy
• FreeDOF_Options() : core::scoring::methods::FreeDOF_Options
• FreePeptide() : protocols::backbone_moves::local_backbone_mover::FreePeptide
• freeze() : protocols::cluster::APCluster , protocols::rigid::RigidBodyMover
• freq() : protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::Resonance
• frequencies() : protocols::denovo_design::task_operations::ConsensusLoopDatabase
• frequency() : core::scoring::nmr::NMRDummySpinlabelConformer , protocols::abinitio::PairingStatEntry , protocols::denovo_design::task_operations::AAFrequencies , protocols::denovo_design::task_operations::AAFrequency , protocols::denovo_design::task_operations::ConsensusLoopDatabase
• frequency_in_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• fresh_instance() : core::select::residue_selector::CachedResidueSubset , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddHelixSequenceConstraintsMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::abinitio::AbrelaxMover , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::DomainAssembly , protocols::analysis::GlycanInfoMover , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::anchored_design::AnchoredDesignMover , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol , protocols::backbone_moves::local_backbone_mover::LocalBackboneMover , protocols::backbone_moves::RandomizeBBByRamaPrePro , protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::backrub::BackrubSidechainMover , protocols::calc_taskop_filters::ConservedPosMutationFilter , protocols::calc_taskop_filters::MultipleSigmoids , protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::RotamerBoltzmannWeight2 , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_filters::Sigmoid , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::calc_taskop_movers::ForceDisulfidesMover , 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::CreateGlycanSequonMover , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeMinMover , protocols::carbohydrates::GlycanTreeModeler , protocols::carbohydrates::IdealizeAnomericHydrogens , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::ThreadingMover , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::constraint_filters::ConstraintScoreFilter , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_filters::ShowConstraintsFilter , protocols::constraint_generator::AddConstraints , protocols::constraint_generator::RemoveConstraints , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::constraint_movers::ClearConstraintsMover , protocols::constraint_movers::ConstraintSetMover , protocols::constraint_movers::CstInfoMover , protocols::constraint_movers::ResidueTypeConstraintMover , protocols::contact_map::ContactMap , protocols::coupled_moves::CoupledMovesProtocol , protocols::cryst::CrystRMS , protocols::cryst::DockLatticeMover , protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::cryst::UpdateCrystInfo , protocols::cutoutdomain::CutOutDomain , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::CrosslinkerMover , protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::FlipChiralityMover , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::PeptideCyclizeMover , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideStubMover , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::cyclic_peptide::TryDisulfPermutations , protocols::denovo_design::filters::CavityVolumeFilter , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSPredictionFilter , protocols::denovo_design::filters::SSShapeComplementarityFilter , protocols::denovo_design::movers::AddSegmentDataMover , protocols::denovo_design::movers::AlignResiduesMover , protocols::denovo_design::movers::BridgeChainsMover , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover , protocols::denovo_design::movers::ExtendChainMover , protocols::denovo_design::movers::FastDesign , protocols::denovo_design::movers::FoldTreeFromFoldGraphMover , protocols::denovo_design::movers::MakeAsymmetricStructureDataMover , protocols::denovo_design::movers::RotateSegmentMover , protocols::denovo_design::movers::SealFoldTreeMover , protocols::denovo_design::movers::SetResidueAliasMover , protocols::design_opt::GreedyOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::SeparateDnaFromNonDna , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::docking::DockingHighResFilter , protocols::docking::DockingLowResFilter , protocols::docking::DockingProtocol , protocols::docking::DockingSlideIntoContact , 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::enzymatic_movers::DNAMethyltransferaseMover , protocols::enzymatic_movers::EnzymaticMover , protocols::enzymatic_movers::GlycosyltransferaseMover , protocols::enzymatic_movers::KinaseMover , protocols::enzymatic_movers::NTerminalAcetyltransferaseMover , protocols::evolution::AASynthesisFitnessCost , protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter , protocols::evolution::EvolutionaryDynamicsMover , protocols::evolution::NucleotideMutation , protocols::farnesyl::InstallFarnesylMover , protocols::farnesyl::SampleFarnesylMover , protocols::features::InterfaceDdGMover , 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::HelixBendFilter , 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::filters::StrandCurvatureByLevels , protocols::fldsgn::filters::StrandHelixGeometryFilter , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter , protocols::fold_from_loops::movers::AlignByResidueSelectorMover , protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover , protocols::fold_from_loops::movers::SavePDBInfoMover , protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::fold_from_loops::NubInitioMover , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveRemodelCsts , 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::FragmentScoreFilter , 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::hbnet::HBNet , protocols::hbnet::HBNetScore , protocols::hbnet::HBNetStapleInterface , 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::hydrate::Hydrate , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::legacy_sewing::LegacyAddStartnodeFragments , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyGivenPathAssemblyMover , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::legacy_sewing::LegacyRepeatAssemblyMover , 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::ga_ligand_dock::GALigandDock , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , 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::ProtLigEnsemble , 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::TransformEnsemble , protocols::ligand_docking::Translate , protocols::ligand_docking::WriteLigandMolFile , protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::Mover_LoopHashRefine , protocols::loops::filters::LoopAnalyzerFilter , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , 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::mean_field::GenMeanFieldMover , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , protocols::membrane::AddMembraneMover , protocols::membrane::AddMembraneSpanConstraint , protocols::membrane::AddMembraneSpanTermZConstraint , protocols::membrane::AddMPLigandMover , protocols::membrane::AqueousPoreFinder , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::FlipMover , protocols::membrane::HelixFromSequence , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::MPLipidAccessibility , 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::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::PeptideOrientationMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::DisulfideOptimizationMover , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::PertMinMover , protocols::minimization_packing::RepackSidechainsMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::minimization_packing::symmetry::SymMinMover , protocols::minimization_packing::symmetry::SymPackRotamersMover , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::minimization_packing::TaskAwareMinMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::GenericSimulatedAnnealer , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::monte_carlo::ResetBaselineMover , protocols::motifs::MotifDnaPacker , protocols::moves::CycleMover , protocols::moves::CyclicMover , protocols::moves::DsspMover , protocols::moves::FilterReportAsPoseExtraScoresMover , 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::SwitchMover , protocols::moves::TrialMover , protocols::multistate_design::PosType , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::ResidueReplacementRebuildMover , protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::nmr::ParaNMRScoreMover , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREMover , 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::pdbinfo_manipulations::AlignPDBInfoToSequences , protocols::peptide_deriver::PeptideDeriverFilter , protocols::pose_creation::ExtendedPoseMover , protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MakePolyXMover , protocols::pose_creation::MergePDBatOverlapMover , protocols::pose_creation::MergePDBMover , protocols::pose_creation::PoseFromSequenceMover , protocols::pose_creation::SliceToMiniProteinMover , 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::quantum_annealing::ExternalPackerResultLoader , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover , protocols::recon_design::FindConsensusSequence , protocols::recon_design::FitnessFilter , protocols::recon_design::MSDMover , protocols::relax::AcceptToBestMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RelaxProtocolBase , protocols::residue_selectors::StoreResidueSubsetMover , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::movers::ERRASER2Protocol , protocols::rna::movers::RNAIdealizeMover , protocols::rna::movers::RNAThreadAndMinimizeMover , 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::score_filters::GeometryFilter , protocols::score_filters::ScoreCutoffFilter , protocols::score_filters::ScoreTypeFilter , 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::hashing::AlignmentFileGeneratorMover , protocols::sewing::movers::AppendAssemblyMover , protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMover , protocols::simple_ddg::AlaScan , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter , protocols::simple_ddg::DdGScan , protocols::simple_ddg::InterfaceBindingEnergyDensityFilter , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedSurfaceAreaFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ChainBreak , protocols::simple_filters::ChainCountFilter , protocols::simple_filters::COFilter , protocols::simple_filters::ContactMolecularSurfaceFilter , 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::HelixHelixAngleFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceHbondsFilter , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::LongestContinuousApolarSegmentFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilter , protocols::simple_filters::MembAccesResidueLipophilicityFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MPSpanAngleFilter , 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::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::ReadPoseExtraScoreFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueChiralityFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDepthFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueLipophilicityFilter , protocols::simple_filters::ResidueSelectionDistanceFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::SequenceDistance , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::SimpleHbondsToAtomFilter , protocols::simple_filters::SimpleMetricFilter , protocols::simple_filters::SpanTopologyMatchPoseFilter , protocols::simple_filters::SSElementLengthFilter , 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::TMsAACompFilter , protocols::simple_filters::TMsSpanMembraneFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AddPDBInfoMover , protocols::simple_moves::AddResidueLabelMover , protocols::simple_moves::AlignChainMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ChainSplitMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::ConcatenatePosesMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::CopyRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::DumpSingleResidueRotamers , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FoldTreeFromMotif , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MissingDensityToJumpMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::PoseFromPoseResourceMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ReportXYZ , protocols::simple_moves::ResetFoldTree , protocols::simple_moves::ResetFullModelInfoMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SaveSequenceToCommentsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::SetupMetalsMover , 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::Tumble , protocols::simple_moves::VirtualRootMover , protocols::simple_moves::WriteFiltersToPose , protocols::simple_moves::WriteSSEMover , protocols::splice::AlignEndsMover , protocols::splice::RBInMover , protocols::splice::RBOutMover , protocols::splice::RotLibOut , protocols::splice::Splice , protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInTail , protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::SpliceOutTail , protocols::splice::TailSegmentMover , protocols::star::StarAbinitio , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::struct_fragment::StructFragmentMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::switches::GraftSwitchMover , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::task_operations::STMStoredTask , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCompoundTaskMover , protocols::task_operations::StoreTaskMover , protocols::testing::BenchmarkBuildRotamersMover , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• frob_distance() : protocols::mean_field::AAMatrix
• from_bond_cst() : core::kinematics::Jump
• from_chain() : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• from_entry() : protocols::protein_interface_design::PatchdockReader , protocols::splice::RBInMover
• from_four_points() : core::kinematics::Stub
• from_other_chains() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• from_pose_datacache() : core::select::residue_selector::CachedResidueSubset
• from_remark() : protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover
• from_res() : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::splice::Splice
• from_same_chain() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• from_scratch_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• 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
• from_subset() : core::select::residue_selector::ResidueRanges , core::select::residue_selector::ResidueVector
• FromScratchMover() : protocols::stepwise::monte_carlo::mover::FromScratchMover
• front() : protocols::moves::MoverContainer
• ft_close_chains() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• ft_mover() : protocols::simple_moves::ChangeAndResetFoldTreeMover
• ftoa() : protocols::sparta::ANN
• full_annotated_sequence() : core::pose::full_model_info::FullModelParameters
• full_atom_beam() : protocols::loop_grower::LoopGrower
• full_model_from_input_source() : protocols::jd3::full_model_inputters::FullModelInputter , protocols::jd3::full_model_inputters::PDBFullModelInputter , protocols::jd3::full_model_inputters::SilentFileFullModelInputter
• full_model_info_into_pose() : core::io::silent::SilentStruct
• full_model_input_sources_from_command_line() : protocols::jd3::full_model_inputters::FullModelInputter , protocols::jd3::full_model_inputters::PDBFullModelInputter , protocols::jd3::full_model_inputters::SilentFileFullModelInputter
• full_model_input_sources_from_tag() : protocols::jd3::full_model_inputters::FullModelInputter , protocols::jd3::full_model_inputters::PDBFullModelInputter , protocols::jd3::full_model_inputters::SilentFileFullModelInputter
• full_model_inputs_from_command_line() : protocols::jd3::full_model_inputters::FullModelInputterFactory
• full_model_inputter_creators() : protocols::jd3::full_model_inputters::FullModelInputterFactory
• full_model_inputter_for_job() : protocols::jd3::full_model::FullModelJobQueen
• full_model_inputter_xml_schema_group_name() : protocols::jd3::full_model_inputters::FullModelInputterFactory
• full_model_parameters() : core::io::silent::SilentStruct , core::pose::full_model_info::FullModelInfo
• full_model_pose_for_constraints() : core::pose::full_model_info::FullModelParameters
• full_motif_score() : protocols::legacy_sewing::scoring::LegacyCalciumMotifScorer , protocols::legacy_sewing::scoring::LegacyInterModelMotifScorer , protocols::legacy_sewing::scoring::LegacyMotifScorer , protocols::sewing::scoring::InterModelMotifScorer , protocols::sewing::scoring::MotifScorer , protocols::sewing::scoring::StartingNodeMotifScorer , protocols::sewing::scoring::TopNMotifScorer
• full_name() : core::chemical::carbohydrates::CarbohydrateInfo
• full_rescore() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergy
• full_sample_rot_index_2_moltenres_sample_rot_index() : core::pack::rotamer_set::ContinuousRotamerSets
• full_sequence() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_to_conventional() : core::pose::full_model_info::FullModelParameters
• full_to_conventional_resnum_and_chain_and_segid() : core::pose::full_model_info::FullModelParameters
• full_to_sub() : core::pose::full_model_info::FullModelInfo , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_twobody_energy() : protocols::hbnet::NetworkState
• fullatom() : core::io::raw_data::DecoyStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct
• fullatom_fast_relax_rounds() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• fullatom_filter() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_find_disulfides() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• fullatom_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_scorefunction() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover , protocols::splice::TailSegmentMover
• fullatom_scorefxn() : protocols::abinitio::Protocol , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::NubInitioMover
• fullatom_stage() : protocols::loop_modeler::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() : core::fragment::rna::FullAtomRNA_Fragments
• FullChiSampleSet() : protocols::match::upstream::FullChiSampleSet
• FullModelInfo() : core::pose::full_model_info::FullModelInfo
• FullModelInnerLarvalJob() : protocols::jd3::full_model::FullModelInnerLarvalJob
• FullModelInputSource() : protocols::jd3::full_model_inputters::FullModelInputSource
• FullModelInputter() : protocols::jd3::full_model_inputters::FullModelInputter
• FullModelInputterFactory() : protocols::jd3::full_model_inputters::FullModelInputterFactory
• FullModelInputterRegistrator() : protocols::jd3::full_model_inputters::FullModelInputterRegistrator< T >
• FullModelJobQueen() : protocols::jd3::full_model::FullModelJobQueen
• FullModelParameters() : core::pose::full_model_info::FullModelParameters
• FullModelPoseBuilder() : core::import_pose::FullModelPoseBuilder
• FullModelPreliminaryLarvalJob() : protocols::jd3::full_model::FullModelPreliminaryLarvalJob
• fullname() : core::io::nmr::SpinlabelDatabaseEntry
• fully_counted() : core::scoring::ResidueExclParams
• fully_excluded_1b() : core::scoring::ResidueExclParams
• 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::GaussianChainGeneralFunc , 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::SmoothStepFunc , 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::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::scoring::func::MixtureFunc
• func_1d() : core::optimization::func_1d
• func_groups() : protocols::relax::AtomCoordinateCstMover
• func_soft() : core::scoring::CenHBPotential
• FuncFactory() : core::scoring::func::FuncFactory
• funcs() : core::scoring::func::SumFunc
• function_expression() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• function_tag() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• FunGroupTK() : protocols::kinmatch::FunGroupTK
• fuzzy_find_grid_set() : protocols::qsar::scoring_grid::GridManager