- f -

• fa_dun_cutoff() : protocols::match::upstream::BuildSet
• 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
• 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::toolbox::task_operations::StoreCompoundTaskMover
• factory_clear() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_end() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_name() : protocols::genetic_algorithm::EntityElementFactory
• factory_register() : protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::jd2::JobInputterFactory , protocols::jd2::JobOutputterFactory , protocols::jd2::parser::DataLoaderFactory , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::moves::MoverFactory , protocols::qsar::scoring_grid::GridFactory , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::rotamer_recovery::RotamerRecoveryFactory
• FaDockingSlideIntoContact() : protocols::docking::FaDockingSlideIntoContact
• fafilter() : protocols::loophash::LoopHashMoverWrapper
• fail_verification() : protocols::environment::ProtectedConformation
• fallback_specified() : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• false_behavior() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• false_movemap() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• FalseFilter() : protocols::filters::FalseFilter
• 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 , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• farray_to_string() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• fascore() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• FASelectSlidingWindowLoopClosure() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• fast() : protocols::idealize::IdealizeMover
• fast_ccd_close_loops() : protocols::LoopRebuild
• fast_forward() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::IntegrationTestBreaker , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::StepWiseResiduePairScreener , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::VDW_BinScreener
• fast_forward_to_end() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• fast_forward_to_next_euler_gamma() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_forward_to_next_residue() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• fast_forward_to_next_residue_pair() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• fast_forward_to_next_rigid_body() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_forward_to_next_translation() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_full_atom_VDW_repulsion_screen() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• fast_loopclose() : protocols::seeded_abinitio::CloseFold
• fast_sample_torsions_from_info() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• fast_scan() : protocols::farna::RNA_LoopCloser
• FastaInputter() : protocols::inputter::FastaInputter
• FASTER_IG_Repacker() : protocols::pack_daemon::FASTER_IG_Repacker
• FastForwardToNextResidueAlternative() : protocols::stepwise::screener::FastForwardToNextResidueAlternative
• FastForwardToNextRigidBody() : protocols::stepwise::screener::FastForwardToNextRigidBody
• FastGapMover() : protocols::loophash::FastGapMover
• FastLinearFunc() : protocols::moves::FastLinearFunc
• FastRelax() : protocols::relax::FastRelax
• FaSymDockingSlideTogether() : protocols::simple_moves::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
• 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::OrbitalsFeatures , protocols::features::PairFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ProtocolFeatures , protocols::features::RadiusOfGyrationFeatures , protocols::features::ResidueBurialFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTypesFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::RuntimeFeatures , protocols::features::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures
• FeaturesReporter() : protocols::features::FeaturesReporter
• FeaturesReporterCreator() : protocols::features::FeaturesReporterCreator
• FeaturesReporterFactory() : protocols::features::FeaturesReporterFactory
• FeaturesReporterRegistrator() : protocols::features::FeaturesReporterRegistrator< T >
• 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
• FibrilModelingClaimer() : protocols::topology_broker::FibrilModelingClaimer
• field_message() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• figure_out_actual_sample_res() : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• figure_out_and_remove_dangling_ends() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• figure_out_appended_and_prepended_res_list() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• figure_out_best_working_alignment() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_chain_boundaries() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_chunk_coverage() : protocols::farna::RNA_ChunkLibrary
• figure_out_constraint_separation_cutoff() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• figure_out_cuts() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_dof_ids_and_offsets() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• figure_out_fold_tree() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• figure_out_forward_backward_res_by_backtracking() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_from_scratch_delete_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• figure_out_gap_size_and_first_chain_break_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• figure_out_gap_size_and_five_prime_chain_break_res() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_is_prepend_map() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_is_residue_prepend() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_jump_partners() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_last_appended_and_last_prepended_res() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• figure_out_loop() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• 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() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• figure_out_partition_definition() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_pivot_res_and_scratch_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_pivots() : protocols::coarse_rna::CoarseRNA_LoopCloser
• 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_which_cutpoints_were_affected() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_working_alignment() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• 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
• 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
• FileExistFilter() : protocols::simple_filters::FileExistFilter
• FileJobOutputter() : protocols::jd2::FileJobOutputter
• filename() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::jd2::JobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::SingleFileBuffer , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakFileFormat_Base , protocols::simple_filters::FileExistFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_moves::LoadPDBMover
• filenames() : protocols::simple_filters::StemFinder
• FileRemoveFilter() : protocols::simple_filters::FileRemoveFilter
• FileSystemJobDistributor() : protocols::jd2::FileSystemJobDistributor
• fill() : protocols::hotspot_hashing::HotspotStubSet , protocols::pockets::PocketGrid
• fill_atom_arrays_() : protocols::pockets::DarcParticleSwarmMinimizer
• fill_atom_arrays_for_electrostatics_() : protocols::pockets::DarcParticleSwarmMinimizer
• fill_bb_coords() : protocols::frag_picker::scores::FragmentChunkCrms
• 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_chain_info() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• fill_chainTORS() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• fill_chainTORS_info() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• fill_contacts() : protocols::contact_map::ContactMap
• fill_coordinates() : protocols::evaluation::PCA
• fill_coords() : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• fill_covalent_gammas() : protocols::noesy_assign::PeakAssignmentResidueMap
• fill_designable_set() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• fill_energy_vector() : protocols::simple_moves::ddG
• fill_espGrid_values() : protocols::pockets::ElectrostaticpotentialGrid
• fill_espGrid_values_with_type() : protocols::pockets::ElectrostaticpotentialGrid
• fill_f1_f2() : 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_string() : 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_in_default_jump_atoms() : protocols::farna::RNA_StructureParameters
• 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::JD2ResourceManagerJobInputter , protocols::jd2::JobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::ScreeningJobInputter , protocols::jd2::SilentFileJobInputter , protocols::make_rot_lib::MakeRotLibJobInputter
• fill_jobs_from_stream() : protocols::jd2::JD2ResourceManagerJobInputter
• fill_missing_atoms() : protocols::environment::ProtectedConformation
• fill_mutations_list() : protocols::pmut_scan::PointMutScanDriver
• fill_num_neighbors() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• fill_pairing_dists() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• fill_per_residue_energy_vector() : protocols::simple_moves::ddG
• fill_pool() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• fill_solution() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• fill_top_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• 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
• fillarray() : protocols::sic_dock::XfoxmScore
• fillTargetPockets() : protocols::pockets::PocketGrid
• filter() : protocols::anchored_design::AnchoredDesignMover
• Filter() : protocols::filters::Filter
• filter() : protocols::hotspot_hashing::HotspotStubSet , protocols::moves::IteratedConvergenceMover
• Filter() : protocols::pose_selectors::Filter
• filter() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::Sigmoid , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ddG , protocols::simple_moves::ResetBaselineMover , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_and_save() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_atom_id_map_with_mask() : protocols::farna::ChunkSet
• filter_based_on_desired_secstruct() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_big_bin() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_by_lj() : protocols::match::output::MatchCollisionFilter
• filter_by_sample_res() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• filter_deltas() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_is_over() : protocols::flxbb::FilterStructs
• filter_main_chain_torsion_sets() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_max_angle() : protocols::fldsgn::filters::HSSTripletFilter
• filter_max_dist() : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_angle() : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_dist() : protocols::fldsgn::filters::HSSTripletFilter
• filter_name() : protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator , protocols::match::output::MatchFilter , protocols::simple_filters::RelativePoseFilter , 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_on() : protocols::flxbb::FilterStructs
• filter_pareto_opt_poses() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_path() : protocols::coarse_rna::CoarseRNA_LoopCloser
• filter_score() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• 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_structs() : protocols::flxbb::DesignTask
• 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_virtual_atoms() : protocols::stepwise::modeler::align::StepWisePoseAligner
• filter_weight() : protocols::topology_broker::ConstraintClaimer
• FilterBucket() : protocols::loophash::FilterBucket
• FilterCreator() : protocols::filters::FilterCreator
• filtered_abego() : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_area() : 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
• FilteredSolutions() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• Filterer_Count() : protocols::stepwise::modeler::rna::Filterer_Count
• FilterFactory() : protocols::filters::FilterFactory
• FilterMover() : protocols::moves::FilterMover
• FilterRegistrator() : protocols::filters::FilterRegistrator< T >
• FilterReporter() : protocols::pose_reporters::FilterReporter
• FilterReporterMover() : protocols::moves::FilterReporterMover
• filters() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::simple_filters::Operator , protocols::simple_moves::GenericMonteCarloMover
• FilterScanFilter() : protocols::protein_interface_design::filters::FilterScanFilter
• FilterStructs() : protocols::flxbb::FilterStructs
• FilterStructs_Packstat() : protocols::flxbb::FilterStructs_Packstat
• FilterStructs_TotalCharge() : protocols::flxbb::FilterStructs_TotalCharge
• 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_fold_tree() : protocols::abinitio::KinematicControl , protocols::topology_broker::TopologyBroker
• 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::PDBJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter
• final_repack() : protocols::grafting::AnchoredGraftMover
• final_score() : protocols::farna::RNA_DeNovoProtocol , protocols::rosetta_scripts::ParsedProtocol
• final_scorefxn() : protocols::rosetta_scripts::ParsedProtocol
• final_test() : protocols::motifs::MotifHit
• finalize() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::StrandPairingSet , protocols::scoring::InterchainPotential , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::trajectory::DbTrajectoryWriter
• finalize_batch() : protocols::jd2::archive::BaseArchiveManager
• finalize_claims() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• finalize_scoring() : protocols::noesy_assign::DistanceScoreMover
• finalize_setup() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop , protocols::antibody::RefineOneCDRLoopCentroid , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::membrane::MPDockingMover , protocols::docking::TemperedDocking
• 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() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy
• finalized() : protocols::fldsgn::topology::StrandPairingSet
• FinalMinimizer() : protocols::ligand_docking::FinalMinimizer
• find() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• find_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• find_all_allowed_positions() : protocols::enzdes::SecondaryMatchProtocol
• find_antiparallel() : protocols::features::strand_assembly::StrandBundleFeatures
• find_assignments() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList
• find_attach_pts() : protocols::ligand_docking::MinimizeBackbone
• find_automatically() : protocols::protein_interface_design::movers::AddChainBreak
• find_available_job() : protocols::jobdist::BaseJobDistributor
• find_chunk() : protocols::frag_picker::VallProvider
• find_closest_backbone() : protocols::motifs::IRCollection
• find_closest_to_average() : protocols::toolbox::DecoySetEvaluation
• find_constraints_to_ligand() : protocols::enzdes::EnzdesConstraintReporter , protocols::enzdes::PredesignPerturbMover
• find_dependency() : protocols::forge::build::BuildManager
• find_design_interface() : protocols::enzdes::DetectProteinLigandInterface
• find_design_interface_arg_sweep() : protocols::enzdes::DetectProteinLigandInterface
• find_disulfides_in_the_neighborhood() : protocols::forge::remodel::RemodelDesignMover
• find_effective_plane() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• find_exchange_partner() : protocols::canonical_sampling::AsyncMPITemperingBase
• find_first_interface_residue() : protocols::ligand_docking::ligand_options::Interface
• find_flexbb_edge() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• find_fragment_by_simple_rmsd_cutoff() : protocols::farna::RNA_Relaxer
• find_geometric_center_for_constrained_lig_atoms() : protocols::enzdes::PredesignPerturbMover
• find_global_pose_number() : protocols::topology_broker::SequenceNumberResolver
• find_hits() : protocols::match::Matcher
• find_in_pose_if_missing_from_header() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• find_instruction() : protocols::forge::build::BuildManager
• find_interface_backbone() : protocols::ligand_docking::LigandBaseProtocol
• find_interface_residues() : protocols::analysis::PeptideDeriverFilter , protocols::ligand_docking::InterfaceBuilder
• find_interface_rsds() : protocols::ligand_docking::LigandBaseProtocol
• find_label() : protocols::topology_broker::SequenceNumberResolver
• find_length() : protocols::toolbox::task_operations::DatabaseThread
• find_local_pose_number() : protocols::topology_broker::SequenceNumberResolver
• find_loops() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• find_max_frag() : protocols::hybridization::TMalign
• find_minimalist_flexbb_edge() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• find_nbrs() : protocols::ddg::ddGMover
• find_neighboring_stubs() : protocols::hotspot_hashing::HotspotStubSet
• find_new_jump_residue() : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
• find_next_bin() : protocols::match::HitNeighborFinder
• find_next_gap() : protocols::loophash::FastGapMover
• find_optimal_rotation() : protocols::pockets::PlaidFingerprint
• find_otfflexbb_edge() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• find_parallel() : protocols::features::strand_assembly::StrandBundleFeatures
• find_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_protein_residues() : protocols::ligand_docking::InterfaceBuilder
• find_reference_and_current_rotamer_correspondence() : protocols::simple_moves::GreenPacker
• find_resnum() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• find_rosettascript_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• find_rotation_center() : protocols::enzdes::PredesignPerturbMover
• find_segid_from_RDC_line() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• find_SilentStructOPs() : protocols::wum::find_SilentStructOPs
• find_source_positions() : protocols::coarse_rna::CoarseRNA_Fragments
• find_start_of_next_interface_region() : protocols::ligand_docking::ligand_options::Interface
• find_stop_of_this_interface_region() : protocols::ligand_docking::ligand_options::Interface
• find_tag() : protocols::features::FeaturesReporter
• find_uninstantiated_phosphates() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• find_zinc_site() : protocols::metal_interface::ZincSiteFinder
• findCartomAtom() : protocols::cartesian::MolecularDynamics
• findClusters() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::pockets::TargetPocketGrid
• findClustersByExemplars() : protocols::pockets::PocketGrid
• FindConsensusSequence() : protocols::simple_moves::FindConsensusSequence
• findExemplars() : protocols::pockets::PocketGrid
• findNeighors() : protocols::sparta::PDB
• findPockets() : protocols::pockets::PocketGrid
• findpos() : protocols::hybridization::DDomainParse
• findpos2() : protocols::hybridization::DDomainParse
• 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_hit_generation_for_constraint() : protocols::match::Matcher
• finish_protocol() : protocols::loop_modeling::LoopProtocol , protocols::rosetta_scripts::ParsedProtocol
• finished() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::simple_moves::symmetry::SymmetrySlider
• finished_simulation() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::TemperatureController
• fire_all_triggers() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• first() : protocols::match::Hit
• first_connected_resonance() : protocols::noesy_assign::Resonance
• first_pass_ala_scan() : protocols::simple_filters::RotamerBoltzmannWeight
• first_residue() : protocols::kinematic_closure::ClosureProblem
• first_zero_pos() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• FitBfactorsMover() : protocols::cryst::FitBfactorsMover
• fitness() : protocols::genetic_algorithm::Entity , protocols::multistate_design::SingleStateEntityData
• fitness_function() : protocols::multistate_design::SingleState
• fitness_threshold() : protocols::protein_interface_design::filters::BoltzmannFilter
• fitness_valid() : protocols::genetic_algorithm::Entity
• 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
• fix_anchor() : protocols::anchored_design::AnchorMoversData
• fix_disulfides() : protocols::environment::ProtectedConformation
• fix_jump_atoms_at_loop_boundaries() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• fix_omega() : protocols::relax::RelaxProtocolBase
• fix_phi_psi_offsets() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• fix_reference_energies() : protocols::optimize_weights::OptEMultifunc
• fixed_data() : protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• fixed_energy_terms() : protocols::optimize_weights::OptEData
• fixed_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• FixedOffsetPivots() : protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots
• FixedPivots() : protocols::kinematic_closure::pivot_pickers::FixedPivots
• FixedTemperatureController() : protocols::canonical_sampling::FixedTemperatureController
• fixResidue() : protocols::jumping::ResiduePairJumpSingle
• FixTemplateJumpSetup() : protocols::abinitio::FixTemplateJumpSetup
• flag_file() : protocols::jd2::archive::Batch
• 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
• FlexbbEdge() : protocols::flexpack::interaction_graph::FlexbbEdge
• FlexbbInteractionGraph() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• FlexbbNode() : protocols::flexpack::interaction_graph::FlexbbNode
• FlexbbRotamerSet() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• FlexbbRotamerSets() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• FlexbbSimAnnealer() : protocols::flexpack::annealer::FlexbbSimAnnealer
• FlexbbSparseMatrixIndex() : protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex
• 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_in_pcs() : protocols::flexpep_docking::FlexPepDockingProtocol
• flip_upstream_downstream_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• FlipMover() : protocols::membrane::FlipMover
• 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::SilentFileJobOutputter , protocols::jd2::SingleFileBuffer
• flush_channel() : protocols::jd2::MpiFileBuffer
• flush_checkpoints() : protocols::checkpoint::CheckPointer
• FlxbbDesign() : protocols::flxbb::FlxbbDesign
• FlxbbDesignPack() : protocols::flxbb::FlxbbDesignPack
• fname() : protocols::loops::ResidueIndexDescriptionFromFile , protocols::simple_moves::AddChainMover
• FNatFilter() : protocols::protein_interface_design::filters::FNatFilter
• fobjnames() : protocols::mpi_refinement::MultiObjective
• fold() : protocols::abinitio::AbrelaxApplication
• fold_label_resonance() : protocols::noesy_assign::CrossPeakInfo
• fold_proton_resonance() : protocols::noesy_assign::CrossPeakInfo
• fold_resonance() : protocols::noesy_assign::CrossPeak
• fold_tree() : protocols::environment::ProtectedConformation , protocols::jumping::JumpSample , protocols::protein_interface_design::movers::SetAtomTree , protocols::rigid::RigidBodyMotionMover , protocols::seeded_abinitio::SeedFoldTree , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• FoldandDockClaimer() : protocols::topology_broker::FoldandDockClaimer
• FoldConstraints() : protocols::abinitio::FoldConstraints
• folder() : protocols::noesy_assign::CrossPeak
• FoldResonance() : protocols::noesy_assign::FoldResonance
• foldTree() : protocols::simple_moves::CutChainMover
• FoldTreeFromLoops() : protocols::loops::FoldTreeFromLoops
• FoldTreeHybridize() : protocols::hybridization::FoldTreeHybridize
• foldtype_from_name() : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype_from_spairs() : protocols::fldsgn::topology::SheetFoldTypeManager
• force_centroid_interaction() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_const() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• force_fold_tree() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• force_natro() : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• force_natro_for_stored_task_names() : protocols::matdes::MatDesGreedyOptMutationMover
• 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_south_sugar_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_syn_chi_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• ForceDisulfidesMover() : protocols::simple_moves::ForceDisulfidesMover
• forget_chains_and_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• forget_initial_loops() : protocols::anchored_design::AnchoredDesignMover
• form_disulfide() : protocols::protein_interface_design::movers::DisulfideMover
• format_silent_struct() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• FORMAT_str_parser() : protocols::sparta::GDB
• format_string() : protocols::frag_picker::VallResidue , protocols::outputter::FormatStringOutputter
• format_string_cs() : protocols::frag_picker::VallResidue
• format_string_residue_depth_version1() : protocols::frag_picker::VallResidue
• format_string_version1() : protocols::frag_picker::VallResidue
• FormatStringOutputter() : protocols::outputter::FormatStringOutputter
• formatted_objs_names() : protocols::mpi_refinement::MultiObjective
• formatted_objs_values() : protocols::mpi_refinement::MultiObjective
• forward_check() : protocols::motifs::Motif
• forward_jump() : protocols::motifs::Motif
• found_centroid_interaction() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• FourAtomsConstraintData() : protocols::frag_picker::scores::FourAtomsConstraintData
• fp_compare() : protocols::pockets::PlaidFingerprint
• fp_compare_deriv() : protocols::pockets::PlaidFingerprint
• fraction_by_recombination() : protocols::genetic_algorithm::GeneticAlgorithmBase
• frag_files() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• frag_libs() : protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::loops::loop_mover::LoopMover
• frag_size() : protocols::frags::TorsionFragmentMover
• frag_sizes() : protocols::frags::FragLib
• FragInsertAndAlignMover() : protocols::rbsegment_relax::FragInsertAndAlignMover
• FragLib() : protocols::frags::FragLib
• fragment_check() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• fragment_contacts() : protocols::frag_picker::FragmentPicker
• fragment_num() : protocols::nonlocal::SmoothPolicy::Candidate
• fragment_specification() : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentAllAtomCrmsd() : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• 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
• FragmentJumpClaimer() : protocols::topology_broker::FragmentJumpClaimer
• FragmentJumpCM() : protocols::abinitio::abscript::FragmentJumpCM
• FragmentLookupFilter() : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentMover() : protocols::simple_moves::FragmentMover
• FragmentPair() : protocols::features::helixAssembly::FragmentPair
• FragmentPerturber() : protocols::kinematic_closure::perturbers::FragmentPerturber
• FragmentPicker() : protocols::frag_picker::FragmentPicker
• FragmentReader() : protocols::jd2::parser::FragmentReader
• fragments() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::nonlocal::Policy , protocols::simple_moves::FragmentMover , protocols::topology_broker::FragmentClaimer
• fragments_big() : protocols::hybridization::HybridizeSetup
• fragments_permutation_test_by_CA_distances() : protocols::motif_grafting::movers::MotifGraftMover
• fragments_small() : protocols::hybridization::HybridizeSetup
• fragments_to_string() : protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign
• FragmentSampler() : protocols::abinitio::FragmentSampler
• FragmentScoreManager() : protocols::frag_picker::scores::FragmentScoreManager
• FragmentScoreMap() : protocols::frag_picker::scores::FragmentScoreMap
• FragmentScoringMethod() : protocols::frag_picker::scores::FragmentScoringMethod
• FragmentSelectingRule() : protocols::frag_picker::FragmentSelectingRule
• FragQualCalculator() : protocols::toolbox::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
• FragSetLoader() : protocols::jd2::parser::FragSetLoader
• FragsToAtomDist() : protocols::noesy_assign::FragsToAtomDist
• 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_upper_pivot() : protocols::kinematic_closure::ClosureProblem
• free_data() : protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• free_lock_on_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• free_terms_energy_map_from_dofs() : protocols::optimize_weights::IterativeOptEDriver
• free_weights_and_refEs_from_vars() : protocols::optimize_weights::IterativeOptEDriver
• freeze() : protocols::cluster::APCluster , protocols::rigid::RigidBodyMover
• freeze_sugar_torsions() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• freq() : protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::Resonance
• frequency() : protocols::abinitio::PairingStatEntry
• frequency_in_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• fresh_instance() : protocols::abinitio::AbrelaxMover , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::DomainAssembly , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::PeptideDeriverFilter , protocols::anchored_design::AnchoredDesignMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::ThreadingMover , protocols::contact_map::ContactMap , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideStubMover , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::SeparateDnaFromNonDna , protocols::docking::DockingHighResFilter , protocols::docking::DockingLowResFilter , protocols::docking::DockingProtocol , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::electron_density::BfactorFittingMover , protocols::electron_density::DensityMorphingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , 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::farna::RNA_FragmentMover , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::FalseFilter , protocols::filters::Filter , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::filters::TrueFilter , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintsRCG , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::ConstraintFileRCG , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoC_RCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::ResidueVicinityRCG , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::genetic_algorithm::EntityElement , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::helical_bundle::BundleGridSampler , 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::HybridizeSetupMover , protocols::hybridization::MRMover , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::LigandDockMain , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::Translate , protocols::ligand_docking::WriteLigandMolFile , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::Mover_LoopHashRefine , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::md::CartesianMD , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , protocols::membrane::AddMembraneMover , protocols::membrane::FlipMover , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::motifs::MotifDnaPacker , protocols::moves::CycleMover , protocols::moves::CyclicMover , protocols::moves::DsspMover , protocols::moves::FilterReporterMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::NullMover , protocols::moves::PyMolMover , protocols::moves::RandomMover , protocols::moves::RepeatMover , protocols::moves::SequenceMover , protocols::moves::StructureRestrictor , protocols::moves::TrialMover , protocols::multistate_design::PosType , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::noesy_assign::StructureIndependentPeakCalibrator , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeRelaxMover , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::qsar::scoring_grid::GridInitMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::RelaxProtocolBase , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::AlaScan , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::COFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AlignChainMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ChainSplitMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::ClearConstraintsMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::MissingDensityToJumpMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MSDMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ResetBaselineMover , protocols::simple_moves::ResidueTypeConstraintMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::ShearMover , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::SmallMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TaskAwareMinMover , protocols::simple_moves::Tumble , protocols::simple_moves::VirtualRootMover , protocols::star::StarAbinitio , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::toolbox::task_operations::STMStoredTask , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• from_entry() : protocols::protein_interface_design::PatchdockReader
• from_res() : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder
• from_scratch_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::SWA_MoveSelector
• from_span() : protocols::membrane::geometry::EmbeddingDef
• from_span_positive_z() : protocols::membrane::geometry::EmbeddingDef
• from_spans() : protocols::membrane::geometry::Embedding
• FromScratchMover() : protocols::stepwise::monte_carlo::mover::FromScratchMover
• front() : protocols::moves::MoverContainer
• ft_mover() : protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::simple_moves::ChangeAndResetFoldTreeMover
• ftoa() : protocols::sparta::ANN
• full_sequence() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_to_sub() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• fullatom_filter() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_scorefunction() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• fullatom_scorefxn() : protocols::abinitio::Protocol
• fullatom_stage() : protocols::loop_modeling::LoopModeler
• FullatomRelaxMover() : protocols::surface_docking::FullatomRelaxMover
• FullAtomRNA_Fragments() : protocols::farna::FullAtomRNA_Fragments
• FullChiSampleSet() : protocols::match::upstream::FullChiSampleSet
• func() : core::scoring::constraints::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
• function_expression() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• function_tag() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• FunGroupTK() : protocols::kinmatch::FunGroupTK