- f -

• f0() : core::scoring::electron_density::KromerMann
• f00() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• F1() : core::optimization::DOF_Node
• f1() : core::scoring::DerivVectorPair
• f11() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• f1ij() : core::scoring::CSA , core::scoring::DC
• F2() : core::optimization::DOF_Node
• f2() : core::scoring::DerivVectorPair
• f22() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• f2ij() : core::scoring::CSA , core::scoring::DC
• f3ij() : core::scoring::CSA
• fa_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_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_score() : protocols::abinitio::IterativeBase
• fa_score_patch() : protocols::abinitio::IterativeBase
• fa_scorefxn() : protocols::comparative_modeling::LoopRelaxMover
• fa_ssdist_scores() : core::scoring::disulfides::SG_Dist_Func
• fa_ssdist_scores_deriv() : core::scoring::disulfides::SG_Dist_Func
• FabConstraint() : core::scoring::constraints::FabConstraint
• FabConstraintCreator() : core::scoring::constraints::FabConstraintCreator
• factor() : core::scoring::dna::TorsionFourierComponent
• factorA() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBG8T3AMover
• factorB() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBG8T3AMover
• factorC() : protocols::simple_moves::BBConRotMover
• factory_name() : protocols::genetic_algorithm::EntityElementFactory
• factory_register() : core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , core::scoring::constraints::ConstraintFactory , core::scoring::ScoringManager , core::sequence::SequenceFactory , protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::jd2::JobInputterFactory , protocols::jd2::JobOutputterFactory , protocols::jd2::parser::DataLoaderFactory , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::moves::MoverFactory , protocols::qsar::scoring_grid::GridFactory , protocols::rotamer_recovery::RotamerRecoveryFactory , core::io::silent::SilentStructFactory
• FACTSEnergy() : core::scoring::methods::FACTSEnergy
• FACTSPoseInfo() : core::scoring::FACTSPoseInfo
• FACTSPotential() : core::scoring::FACTSPotential
• FACTSResidueInfo() : core::scoring::FACTSResidueInfo
• FACTSRotamerSetInfo() : core::scoring::FACTSRotamerSetInfo
• fade_zone() : core::scoring::constraints::FadeFunc
• FadeFunc() : core::scoring::constraints::FadeFunc
• FadeInterval() : core::scoring::hbonds::FadeInterval
• FaDockingSlideIntoContact() : protocols::docking::FaDockingSlideIntoContact
• fafilter() : protocols::loophash::LoopHashMoverWrapper
• fallback_specified() : protocols::loops::LoopsFileFallbackConfiguration
• false_movemap() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• FalseFilter() : protocols::filters::FalseFilter
• FARFAR_setup_using_user_input_VDW_pose() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• farray_to_array() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• 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
• FaSlideAwayFromSurface() : protocols::surface_docking::FaSlideAwayFromSurface
• FaSlideIntoSurface() : protocols::surface_docking::FaSlideIntoSurface
• fast() : protocols::idealize::IdealizeMover
• fast_ccd_close_loops() : protocols::LoopRebuild
• fast_loopclose() : protocols::seeded_abinitio::CloseFold
• fast_memb_env_energy() : core::scoring::etable::BaseEtableEnergy< Derived >
• fast_scan() : protocols::rna::RNA_LoopCloser
• FastaInputter() : protocols::inputter::FastaInputter
• FastDensEnergy() : core::scoring::electron_density::FastDensEnergy
• FASTER_IG_Repacker() : protocols::pack_daemon::FASTER_IG_Repacker
• FASTERAnnealer() : core::pack::annealer::FASTERAnnealer
• FASTEREdge() : core::pack::interaction_graph::FASTEREdge
• FASTERInteractionGraph() : core::pack::interaction_graph::FASTERInteractionGraph
• FASTERNode() : core::pack::interaction_graph::FASTERNode
• FastGapMover() : protocols::loophash::FastGapMover
• FastLinearFunc() : protocols::moves::FastLinearFunc
• FastRelax() : protocols::relax::FastRelax
• FastSAXSEnergy() : core::scoring::saxs::FastSAXSEnergy
• FastSAXSEnergyCreator() : core::scoring::saxs::FastSAXSEnergyCreator
• 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
• FB_Pose_Data() : protocols::swa::rna::FB_Pose_Data
• 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::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomTypesFeatures , protocols::features::BatchFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ChargeChargeFeatures , protocols::features::FeaturesReporter , protocols::features::GeometricSolvationFeatures , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::HelixBundleFeatures , 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::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::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::UnrecognizedAtomFeatures
• FeaturesReporterCreator() : protocols::features::FeaturesReporterCreator
• FeaturesReporterFactory() : protocols::features::FeaturesReporterFactory
• FeaturesReporterRegistrator() : protocols::features::FeaturesReporterRegistrator< T >
• featurizer_state() : core::scoring::dssp::StrandPairingSet
• fetch() : protocols::match::output::UpstreamHitCacher
• fetch_stored_derivatives() : core::optimization::LineMinimizationAlgorithm
• ff() : core::scoring::saxs::FormFactor
• FibrilModelingClaimer() : protocols::topology_broker::FibrilModelingClaimer
• Field() : core::io::pdb::Field
• field_message() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• figure_out_actual_five_prime_chain_break_res() : protocols::swa::rna::StepWiseRNA_Minimizer
• figure_out_appended_and_prepended_res_list() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• figure_out_best_working_alignment() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• figure_out_chain_boundaries() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• figure_out_chunk_coverage() : protocols::rna::RNA_ChunkLibrary
• figure_out_constraint_separation_cutoff() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• figure_out_cuts() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• figure_out_dof_ids_and_offsets() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• figure_out_fold_tree() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• figure_out_forward_backward_res_by_backtracking() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_gap_size_and_first_chain_break_res() : protocols::swa::StepWisePoseSetup
• figure_out_gap_size_and_five_prime_chain_break_res() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• figure_out_Is_prepend_map() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• figure_out_Is_residue_prepend() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• figure_out_jump_partners() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• figure_out_last_appended_and_last_prepended_res() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• figure_out_loop() : protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::protein::StepWiseProteinCCD_Closer
• Figure_out_moving_residues() : protocols::swa::rna::StepWiseRNA_Minimizer
• figure_out_neighbors() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• figure_out_nested_positions() : protocols::swa::protein::StepWiseProteinPoseSetup
• figure_out_NUM_pose_list() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• figure_out_offset() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• figure_out_partition_definition() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• figure_out_pivot_res_and_scratch_res() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_pivots() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_possible_res_maps() : protocols::rna::RNA_ChunkLibrary
• figure_out_Prepend_Internal() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• figure_out_reference_energy() : protocols::swa::RigidBodySampler
• figure_out_rna_base_pairs_to_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• figure_out_rna_base_stacks_to_score() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• figure_out_which_cutpoints_were_affected() : protocols::coarse_rna::CoarseRNA_LoopCloser
• figure_out_working_moving_suite() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• figure_out_working_sequence_and_mapping() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• 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_data() : core::import_pose::PDBSilentStruct
• 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
• FileData() : core::io::pdb::FileData
• FileDataOptions() : core::io::pdb::FileDataOptions
• FileExistFilter() : protocols::simple_filters::FileExistFilter
• FileJobOutputter() : protocols::jd2::FileJobOutputter
• filename() : core::io::raw_data::DisulfideFile , core::io::silent::SilentFileData , core::pack::task::operation::ReadResfile , 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_moves::LoadPDBMover
• filenames() : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• FileRemoveFilter() : protocols::simple_filters::FileRemoveFilter
• FileSystemJobDistributor() : protocols::jd2::FileSystemJobDistributor
• fill() : core::id::AtomID_Map< T > , core::pose::PDBPoseMap , protocols::hotspot_hashing::HotspotStubSet , protocols::pockets::PocketGrid
• fill_atom_arrays_() : protocols::pockets::DarcParticleSwarmMinimizer
• fill_atom_numbers_for_backbone_oxygens() : core::scoring::rna::RNA_LowResolutionPotential
• fill_bins() : core::scoring::dna::DirectReadoutPotential
• fill_by_crossover() : protocols::genetic_algorithm::GeneticAlgorithm
• fill_by_mutation() : protocols::genetic_algorithm::GeneticAlgorithm
• fill_CA_coords() : protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• fill_cenlist() : core::scoring::EnvPairPotential
• fill_chainTORS() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• fill_chainTORS_info() : protocols::swa::protein::StepWiseProteinLoopBridger
• fill_compound_records() : core::io::pdb::HeaderInformation
• fill_contacts() : protocols::contact_map::ContactMap
• fill_coordinates() : protocols::evaluation::PCA
• fill_coords() : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• fill_covalent_gammas() : protocols::noesy_assign::PeakAssignmentResidueMap
• fill_designable_set() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• fill_energy_map() : core::scoring::EnergyEdge
• fill_energy_vector() : protocols::simple_moves::ddG
• fill_experimental_technique_records() : core::io::pdb::HeaderInformation
• fill_f1_f2() : core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::pockets::PocketConstraint
• fill_from_mol_data() : protocols::qsar::qsarMap
• 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_h2o_hbond_set() : core::scoring::WaterAdductHBondPotential
• fill_header_record() : core::io::pdb::HeaderInformation
• fill_header_records() : core::io::pdb::FileData
• fill_in_chain_terminii() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• fill_in_default_jump_atoms() : protocols::rna::RNA_StructureParameters
• 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::SilentFileJobInputter
• fill_jobs_from_stream() : protocols::jd2::JD2ResourceManagerJobInputter
• fill_keyword_records() : core::io::pdb::HeaderInformation
• fill_missing_atoms() : core::conformation::Conformation , core::conformation::Residue , core::pack::dunbrack::SingleLigandRotamerLibrary
• fill_mutations_list() : protocols::pmut_scan::PointMutScanDriver
• fill_num_neighbors() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• fill_outbound_queue() : protocols::wum::MPI_Relax
• fill_pairing_dists() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• fill_per_residue_energy_vector() : protocols::simple_moves::ddG
• fill_point_graph() : core::scoring::Energies , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricEnergies
• fill_pool() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• fill_pose() : core::import_pose::PDBSilentStruct , core::import_pose::pose_stream::ExtendedPoseInputStream , core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::MetaPoseInputStream , core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::PoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::raw_data::DecoyStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::SilentStruct , protocols::swa::rna::RNA_LoopCloseSampler
• fill_records() : core::io::pdb::HeaderInformation
• fill_res_map() : protocols::rna::RNA_ChunkLibrary
• fill_rotamer_vector() : core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueRotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleLigandRotamerLibrary
• fill_rotamer_vector_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• fill_rotamer_vector_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• fill_sin_x_over_x_table() : core::scoring::saxs::SinXOverX
• fill_smooth_cenlist() : core::scoring::SmoothEnvPairPotential
• fill_smooth_dcenlist() : core::scoring::SmoothEnvPairPotential
• fill_solution() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• fill_struct() : core::import_pose::PDBSilentStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::SilentStruct
• fill_title_records() : core::io::pdb::HeaderInformation
• fill_top_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• fill_water_grid() : core::scoring::geometric_solvation::WaterWeightGridSet
• fill_with() : core::id::AtomID_Map< T >
• fill_with_random_entities() : protocols::genetic_algorithm::GeneticAlgorithm
• fill_with_value() : protocols::qsar::qsarMap , protocols::qsar::scoring_grid::SingleGrid
• fill_wrapped_records() : core::io::pdb::HeaderInformation
• fillarray() : protocols::sic_dock::XfoxmScore
• fillTargetPockets() : protocols::pockets::PocketGrid
• Filter() : protocols::filters::Filter
• filter() : core::pack::task::operation::OperateOnCertainResidues , protocols::anchored_design::AnchoredDesignMover , protocols::hotspot_hashing::HotspotStubSet , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::Sigmoid , protocols::swa::protein::StepWiseProteinFilterer , protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::StepWiseFilterer
• filter_and_output() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• filter_atom_id_map_with_mask() : protocols::rna::ChunkSet
• filter_based_on_desired_secstruct() : protocols::swa::protein::StepWiseProteinScreener
• filter_big_bin() : protocols::swa::protein::StepWiseProteinScreener
• filter_by_lj() : protocols::match::output::MatchCollisionFilter
• filter_deltas() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• filter_is_over() : protocols::flxbb::FilterStructs
• filter_main_chain_torsion_sets() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• 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::match::output::MatchFilter , protocols::simple_filters::RelativePoseFilter , protocols::topology_broker::ConstraintClaimer
• filter_names() : protocols::match::MatcherTask
• filter_native_BIG_BINS() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• filter_on() : protocols::flxbb::FilterStructs
• filter_path() : protocols::coarse_rna::CoarseRNA_LoopCloser
• filter_score() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• filter_seqpos_pareto_opt_ptmuts() : protocols::design_opt::GreedyOptMutationMover
• filter_structs() : protocols::flxbb::DesignTask
• filter_templates() : protocols::hybridization::FoldTreeHybridize
• 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_value() : protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• 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_base_axis_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_pair_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stack_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stack_axis_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• filtered_base_stagger_array() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• 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
• Filterer_Count() : protocols::swa::rna::Filterer_Count
• FilterFactory() : protocols::filters::FilterFactory
• FilterMover() : protocols::moves::FilterMover
• FilterRegistrator() : protocols::filters::FilterRegistrator< T >
• filters() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::simple_filters::Operator
• FilterScanFilter() : protocols::protein_interface_design::filters::FilterScanFilter
• FilterStructs() : protocols::flxbb::FilterStructs
• FilterStructs_Packstat() : protocols::flxbb::FilterStructs_Packstat
• FilterStructs_TotalCharge() : protocols::flxbb::FilterStructs_TotalCharge
• 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_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_score() : protocols::rosetta_scripts::ParsedProtocol
• final_scorefxn() : protocols::rosetta_scripts::ParsedProtocol
• final_test() : protocols::motifs::MotifHit
• final_visit_to_edge() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• finalize() : core::chemical::ResidueType , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::scoring::EnvPairPotential , core::scoring::Membrane_FAPotential , core::scoring::MembranePotential , core::scoring::rna::RNA_LowResolutionPotential , core::scoring::SmoothEnvPairPotential , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::StrandPairingSet , protocols::scoring::InterchainPotential
• finalize_after_derivatives() : core::scoring::dna::DNATorsionEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::methods::EnergyMethod , core::scoring::orbitals::OrbitalsScore , core::scoring::ScoreFunction
• finalize_batch() : protocols::jd2::archive::ArchiveManager
• finalize_born_radii() : core::scoring::GenBornPotential
• finalize_claims() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• finalize_compound_records() : core::io::pdb::HeaderInformation
• finalize_experimental_technique_records() : core::io::pdb::HeaderInformation
• finalize_header_information() : core::io::pdb::FileData
• finalize_keyword_records() : core::io::pdb::HeaderInformation
• finalize_output() : core::pack::annealer::FASTERAnnealer
• finalize_parse() : core::io::pdb::HeaderInformation
• finalize_scoring() : protocols::noesy_assign::DistanceScoreMover
• finalize_setup() : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::GraftOneCDRLoop , protocols::antibody2::H3PerturbCCD , protocols::antibody2::H3RefineCCD , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::RefineBetaBarrel , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::RefineOneCDRLoopCentroid , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• finalize_simulation() : protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicMover , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrialCounterObserver
• finalize_total_energy() : core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::BurialEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneLipo , core::scoring::methods::MetalloPlacementEnergy , core::scoring::methods::PackStatEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::RG_Energy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy
• finalized() : protocols::fldsgn::topology::StrandPairingSet
• finalized_energies() : core::scoring::Energies
• FinalizeMovers() : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• FinalMinimizer() : protocols::ligand_docking::FinalMinimizer
• find() : core::kinematics::MoveMap , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• find_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• find_all_allowed_positions() : protocols::enzdes::SecondaryMatchProtocol
• find_another_representative_for_unlikely_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• 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_backbone_oxygen_atom() : core::scoring::rna::RNA_LowResolutionPotential
• find_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• 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_dbase_entry() : protocols::protein_interface_design::movers::Splice
• find_dependency() : protocols::forge::build::BuildManager
• find_design_interface() : protocols::enzdes::DetectProteinLigandInterface
• find_design_interface_arg_sweep() : protocols::enzdes::DetectProteinLigandInterface
• find_disulfides() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• find_disulfides_in_the_neighborhood() : protocols::forge::remodel::RemodelDesignMover
• find_edge() : core::graph::Node , core::graph::Graph , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::InteractionGraphBase
• find_effective_plane() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• find_energy_edge() : core::scoring::EnergyGraph
• find_exchange_partner() : protocols::canonical_sampling::HamiltonianExchange
• 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::RNA_Relaxer
• find_geometric_center_for_constrained_lig_atoms() : protocols::enzdes::PredesignPerturbMover
• 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::ligand_docking::InterfaceBuilder
• find_interface_rsds() : protocols::ligand_docking::LigandBaseProtocol
• 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_minimization_edge() : core::scoring::MinimizationGraph
• 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_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_res_maps() : protocols::rna::RNA_ChunkLibrary
• find_root_from_atom_pointer() : core::kinematics::AtomTree
• 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
• findCartomAtom() : protocols::cartesian::MolecularDynamics
• findClusters() : protocols::pockets::PocketGrid , protocols::pockets::PClusterSet
• findEdgeId() : core::sequence::SequenceCoupling
• FindExtraParameter() : core::chemical::sdf::ctabV3000Parser , core::chemical::sdf::V3Parser
• FindNbrAtom() : core::chemical::sdf::MolFileParser
• 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
• findPSP() : protocols::pockets::PocketGrid
• findSPS() : protocols::pockets::PocketGrid
• FingerprintBase() : protocols::pockets::FingerprintBase
• FingerprintMultifunc() : protocols::pockets::FingerprintMultifunc
• finish_arc() : core::scoring::packstat::trace
• finish_hit_generation_for_constraint() : protocols::match::Matcher
• finish_pose() : core::io::silent::SilentStruct
• finish_protocol() : protocols::rosetta_scripts::ParsedProtocol
• finished() : protocols::jd2::archive::DebugArchive , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeAbrelax , protocols::canonical_sampling::MetropolisHastingsMover , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::simple_moves::symmetry::SymmetrySlider
• fire_all_triggers() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• first() : protocols::match::Hit
• first_atom_in_branch() : core::scoring::trie::TrieNode< AT, CPDATA >
• first_chain_break_res() : protocols::swa::StepWiseJobParameters
• first_pass_ala_scan() : protocols::simple_filters::RotamerBoltzmannWeight
• 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
• fitness() : protocols::multistate_design::SingleStateEntityData , 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
• five_prime_chain_break_res() : protocols::swa::rna::StepWiseRNA_JobParameters
• fix_anchor() : protocols::anchored_design::AnchorMoversData
• fix_atom_types() : core::chemical::sdf::CtabBase
• fix_coarsetype_geometry() : core::coarse::Translator
• fix_disulfides() : core::conformation::Conformation
• fix_his_tautomer() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• fix_phi_psi_offsets() : protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::StepWisePoseSetup
• fix_reference_energies() : protocols::optimize_weights::OptEMultifunc
• FixbbCoupledRotamerSimAnnealer() : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• FixbbLinkingRotamerSimAnnealer() : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• FixbbRotamerSets() : core::pack::rotamer_set::FixbbRotamerSets
• FixbbSimAnnealer() : core::pack::annealer::FixbbSimAnnealer
• fixed() : core::scoring::OneToAllEnergyContainer
• fixed_data() : protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• fixed_dist() : core::scoring::RDC , core::scoring::RDC_Rohl
• fixed_energies() : core::scoring::MinimizationGraph
• fixed_energy_terms() : protocols::optimize_weights::OptEData
• FixedBBEdge() : core::pack::interaction_graph::FixedBBEdge
• FixedBBInteractionGraph() : core::pack::interaction_graph::FixedBBInteractionGraph
• FixedBBNode() : core::pack::interaction_graph::FixedBBNode
• FixedTemperatureController() : protocols::canonical_sampling::FixedTemperatureController
• 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::constraints::FlatHarmonicFunc
• 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_HNQ() : core::pack::task::ResidueLevelTask_ , core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask
• flip_upstream_downstream_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• floating_base_sampling() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• FloatingBaseChainClosureJobParameter() : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• FloatingResonance() : protocols::noesy_assign::FloatingResonance
• FloppyTailMover() : protocols::floppy_tail::FloppyTailMover
• fluff() : core::grid::CartGrid< T >
• flush() : protocols::jd2::SilentFileJobOutputter , protocols::features::DatabaseJobOutputter , protocols::jd2::JobOutputter , 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
• focused_edge() : core::graph::Graph
• fold() : protocols::abinitio::AbrelaxApplication
• 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() : protocols::protein_interface_design::movers::Splice , protocols::swa::rna::StepWiseRNA_JobParameters , core::pose::MiniPose , core::conformation::symmetry::SymmetricConformation , core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pose::Pose , protocols::jumping::JumpSample , protocols::rigid::RigidBodyMotionMover , protocols::seeded_abinitio::SeedFoldTree
• fold_tree_io() : core::import_pose::ImportPoseOptions
• FoldandDockClaimer() : protocols::topology_broker::FoldandDockClaimer
• FoldConstraints() : protocols::abinitio::FoldConstraints
• folder() : protocols::noesy_assign::CrossPeak
• FoldResonance() : protocols::noesy_assign::FoldResonance
• foldTree() : protocols::simple_moves::CutChainMover
• FoldTree() : core::kinematics::FoldTree
• FoldTreeFromLoops() : protocols::loops::FoldTreeFromLoops
• FoldTreeHybridize() : protocols::hybridization::FoldTreeHybridize
• foldtype_from_name() : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype_from_spairs() : protocols::fldsgn::topology::SheetFoldTypeManager
• footprint() : core::graph::ArrayPool< T >
• force_aa_neighbors() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FixedBBEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::LazyEdge
• force_aa_neighbors_for_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• force_all_aa_neighbors() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::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 , core::pack::interaction_graph::DoubleLazyEdge
• force_all_aa_neighbors_for_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• force_antiparallel() : protocols::swa::RigidBodySampler
• force_const() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• force_coplanar() : protocols::swa::RigidBodySampler
• force_nbr_atom_orient() : core::chemical::ResidueType
• force_north_ribose_list() : protocols::swa::rna::StepWiseRNA_JobParameters
• force_parallel() : protocols::swa::RigidBodySampler
• force_south_ribose_list() : protocols::swa::rna::StepWiseRNA_JobParameters
• force_syn_chi_res_list() : protocols::swa::rna::StepWiseRNA_JobParameters
• 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
• FORMAT_str_parser() : protocols::sparta::GDB
• format_string() : protocols::frag_picker::VallResidue , protocols::outputter::FormatStringOutputter , 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
• FormatStringOutputter() : protocols::outputter::FormatStringOutputter
• FormFactor() : core::scoring::saxs::FormFactor
• FormFactorManager() : core::scoring::saxs::FormFactorManager
• forward_check() : protocols::motifs::Motif
• forward_deviation() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• forward_jump() : protocols::motifs::Motif
• FourAtomsConstraintData() : protocols::frag_picker::scores::FourAtomsConstraintData
• FourPointsFunc() : core::scoring::constraints::FourPointsFunc
• fp_compare() : protocols::pockets::PlaidFingerprint
• fp_compare_deriv() : protocols::pockets::PlaidFingerprint
• frac2cart() : core::scoring::electron_density::ElectronDensity
• frac2index() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• 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 , protocols::comparative_modeling::MultiThreadingMover
• frag_type() : core::fragment::FragFactory
• FragCache() : core::fragment::FragCache< T >
• FragData() : core::fragment::FragData
• FragFactory() : core::fragment::FragFactory
• FragID() : core::fragment::FragID
• fragID() : core::fragment::FrameList
• FragID_Iterator() : core::fragment::FragID_Iterator
• FragInsertAndAlignMover() : protocols::rbsegment_relax::FragInsertAndAlignMover
• fragment() : core::fragment::Frame , core::fragment::FragID , core::fragment::Frame , core::fragment::FragID , core::fragment::FragmentRmsd
• fragment_as_pose() : core::fragment::Frame
• fragment_contacts() : protocols::frag_picker::FragmentPicker
• fragment_num() : protocols::nonlocal::SmoothPolicy::Candidate
• fragment_ptr() : core::fragment::Frame , core::fragment::FragID , core::fragment::Frame
• FragmentAllAtomCrmsd() : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• FragmentCandidate() : protocols::frag_picker::FragmentCandidate
• FragmentClaimer() : protocols::topology_broker::FragmentClaimer
• FragmentCost() : protocols::simple_moves::FragmentCost
• FragmentCrmsd() : protocols::frag_picker::scores::FragmentCrmsd
• FragmentCrmsdResDepth() : protocols::frag_picker::scores::FragmentCrmsdResDepth
• FragmentDME() : protocols::frag_picker::scores::FragmentDME
• FragmentIO() : core::fragment::FragmentIO
• FragmentLibraryManager() : core::fragment::picking_old::FragmentLibraryManager
• FragmentMover() : protocols::simple_moves::FragmentMover
• FragmentPair() : protocols::features::helixAssembly::FragmentPair
• FragmentPicker() : protocols::frag_picker::FragmentPicker
• FragmentReader() : protocols::jd2::parser::FragmentReader
• FragmentRmsd() : core::fragment::FragmentRmsd
• fragments() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::simple_moves::FragmentMover , core::fragment::picking_old::vall::VallLibrarian , protocols::nonlocal::Policy
• fragments_to_string() : protocols::ligand_docking::LigandDesign , protocols::ligand_docking::GrowLigand
• 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_per_pos() : protocols::frag_picker::FragmentSelectingRule
• FragSet() : core::fragment::FragSet
• FragSetCollection() : core::fragment::FragSetCollection
• FragSetLoader() : protocols::jd2::parser::FragSetLoader
• FragsToAtomDist() : protocols::noesy_assign::FragsToAtomDist
• FragStore() : core::fragment::FragStore< T >
• Frame() : core::fragment::Frame
• frame() : core::fragment::FragID , core::fragment::FragFactory , core::fragment::FragmentRmsd
• Frame() : core::fragment::Frame
• frame() : core::fragment::FragID
• Frame() : core::fragment::Frame
• frame() : protocols::match::upstream::FullChiSampleSet
• Frame() : core::fragment::Frame
• frame_from_global_orientation() : protocols::toolbox::match_enzdes_util::LigandConformer
• frame_ptr() : core::fragment::ConstantLengthFragSetIterator_ , core::fragment::FrameIteratorWorker_ , core::fragment::FrameListIterator_ , core::fragment::OrderedFragSetIterator_ , core::fragment::FrameIterator , core::fragment::ConstantLengthFragSetIterator_ , core::fragment::FragID , core::fragment::FrameListIterator_ , core::fragment::OrderedFragSetIterator_ , core::fragment::FrameIterator
• FrameIterator() : core::fragment::FrameIterator
• FrameListIterator_() : core::fragment::FrameListIterator_
• frames() : core::fragment::OrderedFragSet , core::fragment::FragSet
• free() : boost::unordered_object_pool< T, UserAllocator >
• free_data() : protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• 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::swa::rna::StepWiseRNA_Minimizer
• freq() : protocols::noesy_assign::Resonance , protocols::noesy_assign::CrossPeak::Spin
• frequency() : protocols::abinitio::PairingStatEntry
• frequency_in_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• fresh_instance() : protocols::loops::FoldTreeFromLoops , protocols::simple_moves::MakePolyXMover , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::flxbb::FilterStructs_TotalCharge , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_moves::ExtendedPoseMover , protocols::enzdes::BackboneSampler , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::canonical_sampling::MetricRecorder , protocols::medal::MedalExchangeMover , protocols::abinitio::DomainAssembly , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::simple_filters::AtomicDistanceFilter , protocols::dna::SeparateDnaFromNonDna , protocols::simple_filters::DdgFilter , protocols::docking::DockingHighResFilter , protocols::design_opt::GreedyOptMutationMover , protocols::enzdes::AddOrRemoveMatchCsts , protocols::dna::DnaInterfaceMultiStateDesign , protocols::ligand_docking::HBondDonorFilter , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::FileExistFilter , protocols::enzdes::LigDSasaFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::AbinitioBaseFilter , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::seeded_abinitio::PlaceFragments , protocols::features::ReportToDB , protocols::simple_filters::InterfaceSasaFilter , protocols::filters::FalseFilter , protocols::filters::CombinedFilter , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::star::StarAbinitio , protocols::filters::ContingentFilter , protocols::simple_moves::RepackSidechainsMover , protocols::abinitio::AbrelaxMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::simple_filters::HolesFilter , protocols::docking::DockingLowResFilter , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::PDBReloadMover , protocols::rosetta_scripts::ParsedProtocol , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::simple_filters::PoseInfoFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::movers::TryRotamers , protocols::simple_moves::symmetry::SymMinMover , protocols::fldsgn::BluePrintBDR , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::movers::VLB , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::PDDFScoreFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::simple_filters::PackStatFilter , protocols::qsar::scoring_grid::GridInitMover , protocols::protein_interface_design::filters::Torsion , protocols::simple_moves::SequenceProfileMover , protocols::protein_interface_design::movers::Splice , protocols::flxbb::FilterStructs_Packstat , protocols::nonlocal::SheetTranslate , protocols::simple_moves::SetTorsion , protocols::moves::DsspMover , protocols::simple_filters::AtomicContactFilter , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::forge::constraints::InvrotTreeRCG , protocols::flxbb::FlxbbDesign , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::RepackMinimize , protocols::forge::remodel::ResidueVicinityRCG , protocols::simple_filters::SheetFilter , protocols::forge::remodel::RemodelMover , protocols::idealize::IdealizeMover , protocols::protein_interface_design::filters::StubScoreFilter , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::movers::PlaceStubMover , protocols::ligand_docking::ChainExistsFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_filters::ScoreTypeFilter , protocols::protein_interface_design::movers::PrepackMover , protocols::simple_moves::SuperimposeMover , protocols::motifs::MotifDnaPacker , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::ligand_docking::HighResDocker , protocols::moves::CyclicMover , protocols::enzdes::LigInterfaceEnergyFilter , protocols::ligand_docking::MolarMassFilter , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::ligand_docking::Rotates , protocols::ligand_docking::Rotate , protocols::forge::components::VarLengthBuild , protocols::ligand_docking::RandomConformers , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::fldsgn::filters::SheetTopologyFilter , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::ligand_docking::StartFrom , protocols::filters::TimeFilter , protocols::loophash::LoopHashLibrary , protocols::simple_moves::FavorSequenceProfile , protocols::loophash::LoopHashRelaxProtocol , protocols::enzdes::EnzdesScorefileFilter , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::dna::DnaInterfaceMinMover , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_moves::LoadUnboundRotMover , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::simple_moves::DumpPdb , protocols::forge::remodel::RemodelMover , protocols::ligand_docking::Transform , protocols::simple_moves::ConsensusDesignMover , protocols::ligand_docking::AddHydrogens , protocols::floppy_tail::FloppyTailMover , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::forge::constraints::RemoveCsts , protocols::simple_moves::CutChainMover , protocols::loophash::FastGapMover , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::filters::Filter , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::NullDesignMover , protocols::loophash::Mover_LoopHashRefine , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::loophash::LoopHashDiversifier , protocols::filters::TrueFilter , protocols::simple_moves::ForceDisulfidesMover , protocols::ligand_docking::SlideTogether , protocols::forge::remodel::RemodelDesignMover , protocols::simple_filters::Operator , protocols::fldsgn::filters::FragQualFilter , protocols::ligand_docking::HBondAcceptorFilter , protocols::filters::HeavyAtomFilter , protocols::simple_moves::ClearConstraintsMover , protocols::ligand_docking::LigandDockMain , protocols::forge::constraints::NtoC_RCG , protocols::ligand_docking::CompleteConnectionsFilter , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::ligand_docking::LigandDesign , protocols::protein_interface_design::movers::LoopOver , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::ligand_docking::HeavyAtomFilter , protocols::simple_moves::ConstrainToIdealMover , protocols::genetic_algorithm::EntityElement , protocols::ligand_docking::FinalMinimizer , protocols::loophash::LoopHashMoverWrapper , protocols::forge::remodel::RemodelLoopMover , protocols::simple_moves::MutateResidue , protocols::ligand_docking::AtomCountFilter , protocols::moves::Mover , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_filters::RotamerBoltzmannWeight , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::hybridization::CartesianSampler , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::ligand_docking::CompoundTranslate , protocols::simple_moves::MembraneTopology , protocols::simple_moves::ddG , protocols::ligand_docking::MolecularMassFilter , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_moves::ConstraintSetMover , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::InterfaceScoreCalculator , protocols::forge::constraints::ConstraintFileRCG , protocols::simple_filters::SymmetricMotifFilter , protocols::filters::ReplicateFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::nonlocal::SingleFragmentMover , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::hybridization::HybridizeProtocol , protocols::forge::remodel::RemodelAccumulator , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::fldsgn::SheetConstraintsRCG , protocols::simple_filters::SAXSScoreFilter , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::forge::components::BDR , protocols::simple_filters::ResidueIEFilter , protocols::forge::constraints::InverseRotamersRCG , protocols::simple_filters::RGFilter , protocols::rigid::RollMover , protocols::simple_filters::ResidueBurialFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::simple_moves::MonteCarloRecover , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::MatchResiduesMover , protocols::relax::RelaxProtocolBase , protocols::flxbb::InterlockAroma , protocols::protein_interface_design::movers::SubroutineMover , protocols::simple_filters::ReportFilter , protocols::flxbb::FilterStructs , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::loops::loop_mover::refine::RepackTrial , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::ligand_docking::Translate , protocols::fldsgn::filters::HelixKinkFilter , protocols::backrub::BackrubSidechainMover , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_moves::MinPackMover , protocols::simple_filters::DeltaFilter , protocols::dna::DnaInterfacePacker , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::contact_map::ContactMap , protocols::backrub::BackrubMover , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::enzdes::PredesignPerturbMover , protocols::simple_filters::NeighborTypeFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::seeded_abinitio::CAcstGenerator , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::filters::CalculatorFilter , protocols::filters::IfThenFilter , protocols::moves::IteratedConvergenceMover , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::simple_filters::RangeFilter , protocols::fldsgn::CircularPermutation , protocols::simple_filters::Sigmoid , protocols::simple_moves::ModifyVariantTypeMover , protocols::medal::MedalMover , protocols::seeded_abinitio::DefineMovableLoops , protocols::fldsgn::filters::HelixPairingFilter , protocols::seeded_abinitio::CoordinateCst , protocols::noesy_assign::PeakCalibrator , protocols::protein_interface_design::movers::SetAtomTree , protocols::seeded_abinitio::CloseFold , protocols::dna::DesignProteinBackboneAroundDNA , protocols::rosetta_scripts::SavePoseMover , protocols::filters::MoveBeforeFilter , protocols::enzdes::EnzRepackMinimize , protocols::simple_filters::COFilter , protocols::simple_filters::AlaScan , protocols::filters::StochasticFilter , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::enzdes::DiffAtomSasaFilter , protocols::simple_filters::ExpiryFilter , protocols::comparative_modeling::LoopRelaxMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::docking::DockingProtocol , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::design_opt::ParetoOptMutationMover , protocols::antibody2::SnugDockProtocol , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::enzdes::RepackWithoutLigandFilter , protocols::analysis::InterfaceAnalyzerMover , protocols::antibody2::SnugDock , protocols::anchored_design::AnchoredDesignMover , protocols::filters::CompoundFilter , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::fldsgn::filters::NcontactsFilter , protocols::protein_interface_design::movers::LoopLengthChange , protocols::simple_moves::ScoreMover , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_moves::GenericMonteCarloMover , protocols::moves::IfMover , protocols::moves::NullMover , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::multistate_design::PosType , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::seeded_abinitio::GrowPeptides , protocols::moves::StructureRestrictor , protocols::simple_moves::MinMover , protocols::simple_filters::PackerNeighborGraphFilter , protocols::match::MatcherMover , protocols::nonlocal::HelixRotate , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::movers::AddChainBreak , protocols::noesy_assign::StructureIndependentPeakCalibrator , protocols::ligand_docking::GrowLigand , protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::TaskAwareMinMover , protocols::protein_interface_design::movers::LoopRemodel , protocols::simple_moves::MonteCarloTest , protocols::simple_filters::ScoreCutoffFilter , protocols::fldsgn::filters::InterlockingAromaFilter
• from_bond_cst() : core::kinematics::Jump
• from_four_points() : core::kinematics::Stub
• from_res() : protocols::protein_interface_design::movers::Splice
• from_stubs() : core::kinematics::Jump , core::kinematics::RT
• front() : protocols::moves::MoverContainer
• ftoa() : protocols::sparta::ANN
• Full_atom_van_der_Waals_screening() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• Full_atom_van_der_Waals_screening_REPLICATE() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• full_list() : protocols::rna::RNA_suite_list
• full_name() : core::chemical::carbohydrates::CarbohydrateInfo
• full_sample_rot_index_2_moltenres_sample_rot_index() : core::pack::rotamer_set::ContinuousRotamerSets
• full_sequence() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::monte_carlo::SubToFullInfo
• full_to_sub() : protocols::swa::InputStreamWithResidueInfo , protocols::swa::StepWiseJobParameters , protocols::swa::rna::StepWiseRNA_JobParameters
• fullatom() : core::io::silent::BinaryProteinSilentStruct , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::BinaryProteinSilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct
• fullatom_filter() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_scorefunction() : protocols::forge::remodel::RemodelMover , protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover , protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover , protocols::forge::components::BDR
• fullatom_scorefxn() : protocols::abinitio::Protocol
• FullatomCustomPairDistanceEnergy() : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• FullatomDisulfideEnergy() : core::scoring::disulfides::FullatomDisulfideEnergy
• FullatomDisulfideEnergyComponents() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• FullatomDisulfideEnergyContainer() : core::scoring::disulfides::FullatomDisulfideEnergyContainer
• FullatomDisulfidePotential() : core::scoring::disulfides::FullatomDisulfidePotential
• FullatomRelaxMover() : protocols::surface_docking::FullatomRelaxMover
• FullAtomRNA_Fragments() : protocols::rna::FullAtomRNA_Fragments
• FullChiSampleSet() : protocols::match::upstream::FullChiSampleSet
• func() : core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::SkipViolFunc , core::scoring::constraints::CircularHarmonicFunc , core::scoring::constraints::SigmoidFunc , core::scoring::constraints::SOGFunc , core::scoring::disulfides::Cen_Distance_Func , core::scoring::constraints::CircularPowerFunc , protocols::moves::LinearFunc , core::scoring::constraints::SOGFunc_Impl , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::IdentityFunc , core::scoring::constraints::TopOutFunc , core::scoring::constraints::SplineFunc , core::scoring::constraints::MixtureFunc , core::scoring::constraints::SquareWellFunc , core::scoring::constraints::LinearPenaltyFunction , protocols::scoring::methods::pcs2::TensorsOptimizer , core::scoring::constraints::CoordinateConstraint , core::scoring::methods::LK_SigmoidalFunc , core::scoring::constraints::DOF_Constraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::KarplusFunc , core::scoring::constraints::CountViolFunc , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::constraints::SquareWell2Func , core::scoring::constraints::BoundFunc , core::scoring::constraints::ScalarWeightedFunc , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::constraints::EtableFunc , core::scoring::constraints::CircularGeneral1D_Func , core::scoring::constraints::FlatHarmonicFunc , protocols::scoring::methods::pcs2::TensorsOptimizerSvd , core::scoring::constraints::CircularSigmoidalFunc , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::ConstantFunc , core::scoring::constraints::PeriodicFunc , core::scoring::CenHBPotential , core::scoring::constraints::CharmmPeriodicFunc , core::scoring::disulfides::CB_Angle_Func , core::scoring::constraints::DihedralPairConstraint , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::constraints::AngleConstraint , core::scoring::disulfides::SG_Dist_Func , core::scoring::constraints::DihedralConstraint , protocols::moves::GeometricFunc , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , protocols::moves::RampingFunc , core::scoring::constraints::ChainbreakDistFunc , core::scoring::constraints::Func , protocols::moves::InvGeometricFunc , core::scoring::constraints::FadeFunc , core::scoring::constraints::SumFunc , protocols::moves::FastLinearFunc , core::scoring::constraints::HarmonicFunc , core::scoring::constraints::SoedingFunc , core::scoring::constraints::GaussianFunc , core::scoring::constraints::MinMultiHarmonicFunc , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::SmoothScoreTermCoeffs , core::scoring::constraints::AmberPeriodicFunc , core::scoring::constraints::USOGFunc , protocols::scoring::methods::pcs2::TensorsOptimizerFix , core::scoring::disulfides::SGSG_Dihedral_Func
• func_() : core::scoring::constraints::MixtureFunc
• func_1d() : core::optimization::func_1d
• FuncFactory() : core::scoring::constraints::FuncFactory
• funcs() : core::scoring::constraints::SumFunc
• function_expression() : protocols::pack_daemon::EntityFunc , protocols::pack_daemon::DynamicAggregateFunction
• function_tag() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• FunGroupTK() : protocols::kinmatch::FunGroupTK