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

- f -

• FA1Dd : protocols::toolbox::KClusterData
• FA2d : protocols::toolbox::KCluster , protocols::toolbox::KClusterData
• FA2Dd : protocols::toolbox::KCluster , protocols::toolbox::KClusterData
• FA2Pd : protocols::toolbox::KCluster , protocols::toolbox::KClusterData
• FA3Pd : protocols::toolbox::KClusterData
• fa_atr_weight_ : protocols::stepwise::screener::PartitionContactScreener
• fa_attr : protocols::features::helixAssembly::FragmentPair
• fa_constraints_ : protocols::constraints_additional::ConstraintEvaluator , protocols::topology_broker::ConstraintClaimer
• fa_cst_fn_ : protocols::hybridization::HybridizeProtocol
• fa_dock_slide_into_contact_ : protocols::docking::DockingPrepackProtocol
• fa_dun_cutoff() : protocols::match::upstream::BuildSet
• fa_dun_cutoff_ : protocols::match::upstream::BuildSet
• fa_dun_danger_ : protocols::fldsgn::filters::CoreDunbrackFilter
• fa_filename_ : protocols::topology_broker::ConstraintClaimer
• fa_fraction : protocols::features::helixAssembly::FragmentPair
• fa_pose_ : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• fa_relax_stage() : protocols::forge::remodel::RemodelLoopMover
• fa_rep_cut_ : protocols::matdes::BuildingBlockInterfaceOperation
• fa_rep_weight_ : protocols::stepwise::screener::PartitionContactScreener
• fa_score() : protocols::abinitio::IterativeBase
• fa_score_ : protocols::abinitio::IterativeBase
• fa_score_patch() : protocols::abinitio::IterativeBase
• fa_score_patch_ : protocols::abinitio::IterativeBase
• fa_scorefxn() : protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover
• fa_scorefxn_ : protocols::antibody_legacy::CDRH3Modeler , protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover , protocols::hybridization::CartesianSampler , protocols::hybridization::HybridizeProtocol , protocols::hybridization::MRMover , protocols::rbsegment_relax::AutoRBMover , protocols::relax::CentroidRelax , protocols::seeded_abinitio::CloseFold , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• facet_alpha_ : protocols::match::Bool3DGridKinemageWriter
• facet_color_ : protocols::match::Bool3DGridKinemageWriter
• facet_master_ : protocols::match::Bool3DGridKinemageWriter
• factorA() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorA_ : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorB() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorB_ : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• factorC() : protocols::simple_moves::BBConRotMover
• factorC_ : protocols::simple_moves::BBConRotMover
• factors_ : protocols::scoring::methods::saxs::PDDFEnergy
• factory_ : protocols::flexpack::FlexPacker , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::InterbondAngleScore , protocols::metal_interface::ZincHeterodimerMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::TaskAwareMinMover
• factory_begin() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_clear() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_end() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_iterator : protocols::toolbox::task_operations::StoreCompoundTaskMover
• factory_name() : protocols::genetic_algorithm::EntityElementFactory
• factory_register() : 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
• fade_width_ : protocols::electron_density::ScaleMapIntensities
• FaDockingSlideIntoContact() : protocols::docking::FaDockingSlideIntoContact
• fafilter() : protocols::loophash::LoopHashMoverWrapper
• fafilter_ : protocols::loophash::LoopHashMoverWrapper
• fail_on_constraints_missing_ : protocols::enzdes::AddOrRemoveMatchCsts
• fail_verification() : protocols::environment::ProtectedConformation
• fake_working_moving_suite : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• fallback_resource_descriptions_created_ : protocols::jd2::JD2ResourceManager
• fallback_specified() : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• false_behavior() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• false_behavior_ : protocols::toolbox::task_operations::StoreCompoundTaskMover
• false_movemap() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• false_movemap_ : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• false_mover_ : protocols::moves::IfMover
• FalseFilter() : protocols::filters::FalseFilter
• FARFAR_setup_using_user_input_VDW_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• FArray1D_int : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• FArray1D_real : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• FArray2D_PackerEnergy : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• FArray4D_real : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• farray_coord_ptr_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• farray_to_array() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• farray_to_string() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• fascore() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• FASelectSlidingWindowLoopClosure() : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• fast() : protocols::idealize::IdealizeMover
• fast_ : protocols::idealize::IdealizeMover , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• fast_build_ : protocols::forge::remodel::RemodelMover::instruction_flags
• fast_calc_ : protocols::simple_filters::RotamerBoltzmannWeight
• fast_ccd_close_loops() : protocols::LoopRebuild
• fast_forward() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::IntegrationTestBreaker , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::StepWiseResiduePairScreener , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::VDW_BinScreener
• fast_forward_to_end() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• fast_forward_to_next_euler_gamma() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_forward_to_next_residue() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• fast_forward_to_next_residue_pair() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• fast_forward_to_next_rigid_body() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_forward_to_next_translation() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• fast_full_atom_VDW_repulsion_screen : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct , protocols::stepwise::modeler::rna::sugar::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
• fast_scan_ : protocols::farna::RNA_LoopCloser
• fasta2template_ : protocols::comparative_modeling::ThreadingJob
• FastaInputter() : protocols::inputter::FastaInputter
• FASTER_IG_Repacker() : protocols::pack_daemon::FASTER_IG_Repacker
• FASTERInteractionGraphOP : 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
• fastrelax_ : protocols::loophash::LoopHashMoverWrapper
• FaSymDockingSlideTogether() : protocols::simple_moves::symmetry::FaSymDockingSlideTogether
• favor_bonus_ : protocols::simple_moves::ResidueTypeConstraintMover
• favor_native_constraints_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• favorable_energies : protocols::vip::VIP_Mover
• favorable_mutations : protocols::vip::VIP_Mover
• favorable_positions : protocols::vip::VIP_Mover
• favorable_residues : protocols::vip::VIP_Mover
• 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
• feature_types_ : protocols::comparative_modeling::features::ResidueFeatureFactory
• features_reporter_dependencies() : protocols::antibody::clusters::CDRClusterFeatures , protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomTypesFeatures , protocols::features::BatchFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ChargeChargeFeatures , protocols::features::DdGFeatures , protocols::features::FeaturesReporter , protocols::features::GeometricSolvationFeatures , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceFeatures , protocols::features::JobDataFeatures , protocols::features::LoopAnchorFeatures , protocols::features::OrbitalsFeatures , protocols::features::PairFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ProtocolFeatures , protocols::features::RadiusOfGyrationFeatures , protocols::features::ResidueBurialFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTypesFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::RuntimeFeatures , protocols::features::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures
• features_reporter_factory_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• features_reporters_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• FeaturesReporter() : protocols::features::FeaturesReporter
• FeaturesReporterCreator() : protocols::features::FeaturesReporterCreator
• FeaturesReporterCreatorMap : protocols::features::FeaturesReporterFactory
• FeaturesReporterFactory() : protocols::features::FeaturesReporterFactory
• FeaturesReporterRegistrator() : protocols::features::FeaturesReporterRegistrator< T >
• FeaturesReporters : protocols::features::Report
• feedback_structure_to_emperor() : protocols::mpi_refinement::MPI_Refine_Master
• feedback_structures_to_emperor() : protocols::mpi_refinement::MPI_Refine_Master
• fetch() : protocols::match::output::UpstreamHitCacher
• fetch_foldtree : protocols::seeded_abinitio::GrowPeptides
• ff_manager_ : protocols::scoring::methods::saxs::PDDFEnergy
• fi_ : protocols::frag_picker::DiversifyCrmsdSelector
• FibrilModelingClaimer() : protocols::topology_broker::FibrilModelingClaimer
• field_ : protocols::wum::find_SilentStructOPs , protocols::wum::sort_SilentStructOPs
• field_message() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• figure_out_actual_sample_res() : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• figure_out_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_prepack_res_ : protocols::stepwise::modeler::StepWiseModeler
• figure_out_Prepend_Internal() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• figure_out_prepend_internal() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• figure_out_reference_res() : protocols::stepwise::modeler::StepWiseConnectionSampler
• figure_out_reference_res_with_rigid_body_rotamer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• figure_out_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_ : protocols::canonical_sampling::PatchOperation , protocols::canonical_sampling::TrialCounterObserver
• file_2_data_map_ : protocols::scoring::methods::pcs::PCS_data_input_manager , protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4
• file_buf_rank() : protocols::jd2::MPIFileBufJobDistributor
• file_buf_rank_ : protocols::jd2::archive::ArchiveManager , protocols::jd2::MPIFileBufJobDistributor
• file_buffer : protocols::checkpoint::CheckPointer
• file_buffer_size() : protocols::checkpoint::CheckPointer
• file_contents_ : protocols::pack_daemon::DynamicAggregateFunction
• file_inputs_for_job() : protocols::pack_daemon::DynamicAggregateFunction
• file_name() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• file_name_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder , protocols::constraints_additional::ConstraintEvaluator
• file_name_prefix_ : protocols::protein_interface_design::movers::MapHotspot
• file_names() : protocols::simple_filters::FileRemoveFilter
• file_names_ : protocols::inputter::FastaInputter , protocols::inputter::PDBInputter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::MultipleSigmoids
• file_out_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• file_read() : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• file_read_ : protocols::toolbox::match_enzdes_util::EnzdesLoopsFile
• file_reading_token() : protocols::loops::Loops
• file_reading_token_ : protocols::loops::Loops
• file_to_read_ : protocols::ddG::ddGData
• FileBuffer() : protocols::checkpoint::FileBuffer
• FileExistFilter() : protocols::simple_filters::FileExistFilter
• FileJobOutputter() : protocols::jd2::FileJobOutputter
• FileList : protocols::comparative_modeling::ThreadingJobInputter
• filename() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::jd2::JobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::SingleFileBuffer , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakFileFormat_Base , protocols::simple_filters::FileExistFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_moves::LoadPDBMover
• filename_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::checkpoint::FileBuffer , protocols::forge::constraints::ConstraintFileRCG , protocols::jd2::parser::FragmentReader , protocols::jd2::SingleFileBuffer , protocols::loophash::EXCN_DB_IO_Failed , protocols::loophash::EXCN_Wrong_DB_Format , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakFileFormat_Base , protocols::qsar::RenderGridsToKinemage , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4 , protocols::simple_filters::FileExistFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_moves::LoadPDBMover , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• filename_root_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• filenameparts_ : protocols::outputter::FormatStringOutputter
• Filenames : protocols::jd2::MpiFileBuffer
• FileNames : protocols::motifs::MotifLibrary
• filenames() : protocols::simple_filters::StemFinder
• filenames_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::simple_filters::StemFinder , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• FileRemoveFilter() : protocols::simple_filters::FileRemoveFilter
• files_for_state_ : protocols::pack_daemon::DynamicAggregateFunction
• FileSystemJobDistributor() : protocols::jd2::FileSystemJobDistributor
• fill() : 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::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::filters::Filter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter
• filter() : protocols::hotspot_hashing::HotspotStubSet
• Filter : protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter
• filter() : protocols::moves::IteratedConvergenceMover
• Filter() : protocols::pose_selectors::Filter
• filter() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• Filter : protocols::simple_filters::ConservedPosMutationFilter
• filter() : protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter
• Filter : protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter
• filter() : protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ReportFilter
• Filter : protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter
• filter() : protocols::simple_filters::Sigmoid
• Filter : protocols::simple_filters::TaskAwareSASAFilter
• filter() : protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ddG , protocols::simple_moves::ResetBaselineMover , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_ : protocols::cluster::GatherPosesMover , protocols::docking::DockMCMProtocol , protocols::enzdes::RemoveLigandFilter , protocols::flxbb::FlxbbDesignPack , protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::loop_modeling::utilities::LoopFilter , protocols::moves::FilterReporterMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::pose_reporters::FilterReporter , protocols::pose_selectors::Filter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::Sigmoid , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ddG , protocols::simple_moves::ResetBaselineMover
• filter_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_beta : protocols::loophash::FilterBucket
• filter_big_bin() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_by_lj() : protocols::match::output::MatchCollisionFilter
• filter_by_lj_ : protocols::match::output::MatchCollisionFilter
• filter_by_phipsi_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• filter_by_sample_res() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• filter_chain_closure_ : protocols::farna::RNA_DeNovoProtocol
• filter_chain_closure_distance_ : protocols::farna::RNA_DeNovoProtocol
• filter_chain_closure_halfway_ : protocols::farna::RNA_DeNovoProtocol
• filter_creator_map_ : protocols::filters::FilterFactory
• filter_cst_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• filter_cst_weight_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• filter_deltas() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_deltas_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_during_design_ : protocols::flxbb::FlxbbDesign
• filter_failcounts_ : protocols::match::output::MatchProcessor
• filter_for_chain_closable_geometry_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_for_moving_res_contact : protocols::stepwise::modeler::rna::Filterer_Count
• filter_for_moving_res_contact_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_for_previous_clash : protocols::stepwise::modeler::rna::Filterer_Count
• filter_for_previous_clash_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_for_previous_contact : protocols::stepwise::modeler::rna::Filterer_Count
• filter_for_previous_contact_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filter_gly : protocols::loophash::FilterBucket
• filter_helix_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• filter_helix_sheet_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• filter_intrabb_ : protocols::matdes::BuildingBlockInterfaceOperation
• filter_is_over() : protocols::flxbb::FilterStructs
• filter_loop_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• filter_lores_base_pairs_ : protocols::farna::RNA_DeNovoProtocol
• filter_lores_base_pairs_early_ : protocols::farna::RNA_DeNovoProtocol
• filter_main_chain_torsion_sets() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_max_angle() : protocols::fldsgn::filters::HSSTripletFilter
• filter_max_angle_ : protocols::fldsgn::filters::HSSTripletFilter
• filter_max_dist() : protocols::fldsgn::filters::HSSTripletFilter
• filter_max_dist_ : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_angle() : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_angle_ : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_dist() : protocols::fldsgn::filters::HSSTripletFilter
• filter_min_dist_ : protocols::fldsgn::filters::HSSTripletFilter
• filter_mode_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• filter_mover_ : protocols::moves::FilterReporterMover
• filter_name() : protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator , protocols::match::output::MatchFilter , protocols::simple_filters::RelativePoseFilter , protocols::topology_broker::ConstraintClaimer
• filter_name_ : protocols::match::output::MatchFilter , protocols::simple_filters::RelativePoseFilter , protocols::topology_broker::ConstraintClaimer
• filter_names() : protocols::match::MatcherTask
• filter_names_ : protocols::match::MatcherTask
• filter_native_big_bins() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• filter_native_BIG_BINS() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• filter_native_big_bins() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• filter_native_big_bins_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• filter_on() : protocols::flxbb::FilterStructs
• filter_on_ : protocols::flxbb::FilterStructs
• filter_params_bool_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• filter_params_real_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• filter_params_size_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• filter_params_string_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• filter_pareto_opt_poses() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_path() : protocols::coarse_rna::CoarseRNA_LoopCloser
• filter_pro : protocols::loophash::FilterBucket
• filter_SASA_ : protocols::anchored_design::AnchoredDesignMover
• filter_score() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• filter_score_ : protocols::anchored_design::AnchoredDesignMover
• filter_seqpos_pareto_opt_ptmuts() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• filter_sheet_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• filter_similar() : protocols::mpi_refinement::MultiObjective
• filter_solutions() : protocols::generalized_kinematic_closure::GeneralizedKIC
• filter_stage2_beginning : protocols::relax::ClassicRelax
• filter_stage2_end : protocols::relax::ClassicRelax
• filter_stage2_half : protocols::relax::ClassicRelax
• filter_stage2_quarter : protocols::relax::ClassicRelax
• filter_structs() : protocols::flxbb::DesignTask
• filter_structs_ : protocols::flxbb::DesignTask
• filter_templates() : protocols::hybridization::FoldTreeHybridize
• filter_templates_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• filter_thresholds() : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• filter_thresholds_ : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• filter_type() : protocols::fldsgn::filters::CoreDunbrackFilter
• filter_upstream_and_downstream_collisions_by_score_ : protocols::match::MatcherTask
• filter_upstream_and_downstream_residue_collisions_ : protocols::match::MatcherTask
• filter_upstream_collisions_by_score() : protocols::match::MatcherTask
• filter_upstream_collisions_by_score_ : protocols::match::MatcherTask
• filter_upstream_downstream_collisions() : protocols::match::MatcherTask
• filter_upstream_downstream_collisions_by_score() : protocols::match::MatcherTask
• filter_upstream_residue_collisions() : protocols::match::MatcherTask
• filter_upstream_residue_collisions_ : protocols::match::MatcherTask
• filter_user_alignment_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• filter_val() : protocols::simple_filters::ReportFilter
• filter_val_ : protocols::simple_filters::ReportFilter
• filter_value() : protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• filter_value_ : protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• filter_virtual_atoms() : protocols::stepwise::modeler::align::StepWisePoseAligner
• filter_virtual_res_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• filter_weight() : protocols::topology_broker::ConstraintClaimer
• filter_weight_ : protocols::topology_broker::ConstraintClaimer
• FilterBucket() : protocols::loophash::FilterBucket
• FilterCreator() : protocols::filters::FilterCreator
• filtered_abego() : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_abego_ : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_area() : protocols::simple_filters::ShapeComplementarityFilter
• filtered_area_ : protocols::simple_filters::ShapeComplementarityFilter
• filtered_sc() : protocols::simple_filters::ShapeComplementarityFilter
• filtered_sc_ : protocols::simple_filters::ShapeComplementarityFilter
• filtered_score() : protocols::simple_filters::PackStatFilter
• filtered_score_ : protocols::simple_filters::PackStatFilter
• filtered_sheet_topology() : protocols::fldsgn::filters::SheetTopologyFilter
• filtered_sheet_topology_ : protocols::fldsgn::filters::SheetTopologyFilter
• filtered_ss() : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_ss_ : protocols::fldsgn::filters::SecondaryStructureFilter
• filtered_type() : protocols::fldsgn::filters::FragQualFilter
• filtered_type_ : protocols::fldsgn::filters::FragQualFilter
• filtered_value() : protocols::fldsgn::filters::FragQualFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter
• 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
• filterer_count_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• filterered_combine_tag_info_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• FilterFactory() : protocols::filters::FilterFactory
• FilterList : protocols::filters::CombinedFilter
• filterlist_ : protocols::filters::CombinedFilter , protocols::generalized_kinematic_closure::GeneralizedKIC
• FilterMap : protocols::filters::FilterFactory
• FilterMover() : protocols::moves::FilterMover
• FilterOP : protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::moves::FilterMover , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::GenericMonteCarloMover
• FilterRegistrator() : protocols::filters::FilterRegistrator< T >
• FilterReporter() : protocols::pose_reporters::FilterReporter
• FilterReporterMover() : protocols::moves::FilterReporterMover
• filters() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::simple_filters::Operator , protocols::simple_moves::GenericMonteCarloMover
• filters_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingLowResFilter , protocols::filters::CalculatorFilter , protocols::filters::FilterCollection , protocols::frag_picker::FragmentPicker , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::output::MatchProcessor , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::simple_filters::Operator , protocols::simple_moves::GenericMonteCarloMover
• Filters_map : protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::moves::DsspMover , protocols::moves::Mover , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• filters_with_state_ : protocols::match::output::MatchProcessor
• FilterScanFilter() : protocols::protein_interface_design::filters::FilterScanFilter
• FilterStructs() : protocols::flxbb::FilterStructs
• FilterStructs_Packstat() : protocols::flxbb::FilterStructs_Packstat
• FilterStructs_TotalCharge() : protocols::flxbb::FilterStructs_TotalCharge
• FilterStructsOP : protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Layer , protocols::flxbb::DesignTask_Normal , protocols::flxbb::FlxbbDesignPack
• filtertype_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• FilterWeightPair : protocols::filters::CombinedFilter
• final : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• final_check_sw_by_dis() : protocols::features::strand_assembly::StrandBundleFeatures
• final_cleanup() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• final_correct_oop_post_ : protocols::ncbb::oop::OopCreatorMover
• final_design_min_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• final_dist_power_ : protocols::noesy_assign::DistanceScoreMover
• final_energy : protocols::vip::VIP_Mover
• final_filter_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::TryRotamers
• final_fold_tree() : protocols::abinitio::KinematicControl , protocols::topology_broker::TopologyBroker
• final_fold_tree_ : protocols::abinitio::KinematicControl , protocols::topology_broker::TopologyBroker
• final_ft_ : protocols::abinitio::abscript::AbscriptLoopCloserCM
• final_iter() : protocols::mpi_refinement::Scheduler
• final_mc_ : protocols::ncbb::oop::OopCreatorMover
• final_minimize_ : protocols::ncbb::oop::OopCreatorMover
• final_pose() : protocols::dna::PDBOutput , protocols::enzdes::EnzdesJobOutputter , protocols::features::DatabaseJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::vip::VIP_Mover
• final_repack() : protocols::grafting::AnchoredGraftMover
• final_repack_ : protocols::grafting::AnchoredGraftMover , protocols::ncbb::oop::OopCreatorMover
• final_rotamers_ : protocols::make_rot_lib::MakeRotLibMover
• final_score() : protocols::farna::RNA_DeNovoProtocol , protocols::rosetta_scripts::ParsedProtocol
• final_scorefxn() : protocols::rosetta_scripts::ParsedProtocol
• final_scorefxn_ : protocols::farna::RNA_DeNovoProtocol , protocols::rosetta_scripts::ParsedProtocol , protocols::stepwise::modeler::StepWiseMinimizer
• final_screener_ : protocols::stepwise::screener::IntegrationTestBreaker
• final_temp : protocols::rbsegment_relax::RBSegmentRelax
• final_temp_ : protocols::loop_modeling::LoopProtocol
• final_test() : protocols::motifs::MotifHit
• final_test_ : protocols::motifs::MotifHit
• final_unrelaxed_pose : protocols::vip::VIP_Mover
• final_weight_ : protocols::abinitio::CoordinateConstraintKC
• final_weight_linear_chainbreak_ : protocols::loops::loop_closure::ccd::LoopClosure
• final_weight_overlap_chainbreak_ : protocols::loops::loop_closure::ccd::LoopClosure
• finalize() : 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_MPI_ : protocols::jd2::MPIWorkPoolJobDistributor
• 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
• 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_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
• fine_rmsd_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• finer_sampling_at_chain_closure() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• finer_sampling_at_chain_closure_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener
• FingerprintBase() : protocols::pockets::FingerprintBase
• FingerprintMultifunc : protocols::pockets::FingerprintBase , protocols::pockets::FingerprintMultifunc , protocols::pockets::PlaidFingerprint
• finish_hit_generation_for_constraint() : protocols::match::Matcher
• finish_protocol() : protocols::loop_modeling::LoopProtocol , protocols::rosetta_scripts::ParsedProtocol
• finish_scorefxn_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• finish_stage_ : protocols::abinitio::IterativeBase
• finished() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase
• FINISHED : protocols::abinitio::IterativeBase
• finished() : protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::simple_moves::symmetry::SymmetrySlider
• finished_ : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• finished_recv_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• finished_send_buffer_ : protocols::canonical_sampling::AsyncMPITemperingBase
• finished_simulation() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::TemperatureController
• fire_all_triggers() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• first() : protocols::match::Hit , protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• first_ : protocols::match::Hit , protocols::match::upstream_hit
• first_apply_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• first_apply_with_current_setup_ : protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• first_atom_ : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• first_batch_this_stage_ : protocols::abinitio::IterativeBase
• first_connected_resonance() : protocols::noesy_assign::Resonance
• first_fullatom_batch_ : protocols::abinitio::IterativeBase
• first_minimize_with_fixed_base_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• first_mover_ : protocols::moves::JumpOutMover
• first_noesy_cst_file_ : protocols::abinitio::IterativeBase
• first_noesy_fa_cst_file_ : protocols::abinitio::IterativeBase
• first_pass_ala_scan() : protocols::simple_filters::RotamerBoltzmannWeight
• first_pose_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• first_res_ : protocols::simple_moves::RepeatPropagationMover
• first_residue() : protocols::kinematic_closure::ClosureProblem
• first_residue_index_ : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• first_sampler_ : protocols::stepwise::screener::TagDefinition
• first_time_writing_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• first_zero_pos() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• firstRes : protocols::sparta::Sparta::SpartaLib
• firstResID : protocols::sparta::GDB
• FIT_Tab : protocols::sparta::Sparta::SpartaLib
• FitBfactorsMover() : protocols::cryst::FitBfactorsMover
• fitFileName : protocols::sparta::Sparta::SpartaLib
• fitness() : protocols::genetic_algorithm::Entity , protocols::multistate_design::SingleStateEntityData
• fitness_ : protocols::genetic_algorithm::Entity , protocols::multistate_design::SingleStateEntityData
• fitness_exp_ : protocols::pack_daemon::DynamicAggregateFunction
• fitness_function() : protocols::multistate_design::SingleState
• fitness_function_ : protocols::genetic_algorithm::GeneticAlgorithm , protocols::multistate_design::SingleState
• fitness_threshold() : protocols::protein_interface_design::filters::BoltzmannFilter
• fitness_threshold_ : protocols::protein_interface_design::filters::BoltzmannFilter
• fitness_valid() : protocols::genetic_algorithm::Entity
• fitness_valid_ : protocols::genetic_algorithm::Entity
• FitnessFunctionOP : protocols::genetic_algorithm::GeneticAlgorithm
• FitSimpleHelix() : protocols::helical_bundle::FitSimpleHelix
• FitSimpleHelixMultiFunc() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• five_prime_atom : protocols::stepwise::modeler::rna::Jump_point
• five_prime_chain_break : protocols::stepwise::modeler::rna::sugar::SugarModeling
• five_prime_chain_break_res() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• five_prime_chain_break_res_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• five_prime_phosphate_res_input_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• five_prime_res() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• five_prime_res_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• five_prime_seq_num : protocols::stepwise::modeler::rna::Jump_point
• five_prime_xyz_ : protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener
• fix_anchor() : protocols::anchored_design::AnchorMoversData
• fix_backbone_ : protocols::simple_moves::CoupledMover
• fix_catalytic_ : protocols::enzdes::EnzRepackMinimize
• fix_catalytic_aa_ : protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::SetCatalyticResPackBehavior
• fix_disulfides() : protocols::environment::ProtectedConformation
• fix_jump_atoms_at_loop_boundaries() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• fix_ligands_ : protocols::rbsegment_relax::RBSegmentRelax
• fix_natsc_ : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• fix_omega() : protocols::relax::RelaxProtocolBase
• fix_omega_ : protocols::relax::RelaxProtocolBase
• fix_phi_psi_offsets() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• fix_reference_energies() : protocols::optimize_weights::OptEMultifunc
• fix_reference_energies_ : protocols::optimize_weights::OptEMultifunc
• fix_short_segment_ : protocols::simple_moves::BBGaussianMover
• FIXED : protocols::flxbb::LayerDesignOperation
• fixed_chains_ : protocols::analysis::InterfaceAnalyzerMover
• fixed_count_ : protocols::optimize_weights::IterativeOptEDriver
• fixed_data() : protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• fixed_data_ : protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• fixed_energy_terms() : protocols::optimize_weights::OptEData
• fixed_energy_terms_ : protocols::optimize_weights::OptEData
• fixed_parameters_ : protocols::optimize_weights::IterativeOptEDriver
• fixed_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• fixed_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• fixed_residues_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• fixed_score_list_ : protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc
• fixed_score_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• fixed_scores_ : protocols::optimize_weights::WrapperOptEMultifunc
• fixed_terms_ : protocols::optimize_weights::OptEMultifunc
• fixed_to_metal_ : protocols::metal_interface::ZincHeterodimerMover
• FixedBBInteractionGraphCOP : protocols::pack_daemon::PackDaemon
• FixedBBInteractionGraphOP : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• FixedOffsetPivots() : protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots
• FixedPivots() : protocols::kinematic_closure::pivot_pickers::FixedPivots
• FixedTemperatureController() : protocols::canonical_sampling::FixedTemperatureController
• fixResidue() : protocols::jumping::ResiduePairJumpSingle
• fixResidue_ : protocols::jumping::ResiduePairJumpSingle
• FixTemplateJumpSetup() : protocols::abinitio::FixTemplateJumpSetup
• fj_ : protocols::frag_picker::DiversifyCrmsdSelector
• flag_file() : protocols::jd2::archive::Batch
• flags_ : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingPoseMetrics , protocols::flexpep_docking::FlexPepDockingProtocol
• flags_and_objects_are_in_sync_ : protocols::antibody::AntibodyModelerProtocol , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• flank_cdrh3_map_ : protocols::antibody::H3RefineCCD
• flank_relax_ : protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop , protocols::antibody_legacy::CDRH3Modeler
• flank_residue_min() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• flank_residue_min_ : protocols::antibody::AntibodyModelerProtocol , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• flank_residue_size_ : protocols::antibody::AntibodyModelerProtocol
• flank_size_ : protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop
• flanking_left_aa() : protocols::forge::build::SegmentInsert
• flanking_left_nres() : protocols::forge::build::SegmentInsert
• flanking_left_ss() : protocols::forge::build::SegmentInsert
• flanking_residues_ : protocols::antibody::CloseOneCDRLoop , protocols::antibody_legacy::CloseOneMover
• flanking_right_aa() : protocols::forge::build::SegmentInsert
• flanking_right_nres() : protocols::forge::build::SegmentInsert
• flanking_right_ss() : protocols::forge::build::SegmentInsert
• flex_cter_ : protocols::ub_e2c::ubi_e2c_modeler
• flex_cter_map_ : protocols::ub_e2c::ubi_e2c_modeler
• flex_dna_sugar_ : protocols::motifs::MotifDnaPacker
• flex_regions_ : protocols::enzdes::EnzdesFlexBBProtocol
• FlexbbEdge() : protocols::flexpack::interaction_graph::FlexbbEdge
• FlexbbInteractionGraph() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• FlexbbNode() : protocols::flexpack::interaction_graph::FlexbbNode
• FlexbbRotamerSet() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• FlexbbRotamerSets() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• FlexbbSimAnnealer() : protocols::flexpack::annealer::FlexbbSimAnnealer
• FlexbbSparseMatrixIndex() : protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex
• flexpack_neighbor_graph() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• FlexPacker() : protocols::flexpack::FlexPacker
• FlexPepDockingAbInitio() : protocols::flexpep_docking::FlexPepDockingAbInitio
• FlexPepDockingFlags() : protocols::flexpep_docking::FlexPepDockingFlags
• FlexPepDockingLowRes() : protocols::flexpep_docking::FlexPepDockingLowRes
• FlexPepDockingPoseMetrics() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• FlexPepDockingProtocol() : protocols::flexpep_docking::FlexPepDockingProtocol
• flexseg_bb_offset_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_considering_alt_bb() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_considering_alt_bb_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_for_bb_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_for_moltenres() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_for_moltenres_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_members() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexseg_members_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• flexsegid_for_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegid_for_res() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_size() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_span_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_start_moltenresid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_start_resid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_stop_moltenresid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flexsegment_stop_resid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• flip_in_pcs() : protocols::flexpep_docking::FlexPepDockingProtocol
• flip_input_about_axes_ : protocols::matdes::SymDofMover
• flip_rate_ : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• flip_sign_ : protocols::simple_moves::GenericMonteCarloMover
• flip_upstream_downstream_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• FlipMover() : protocols::membrane::FlipMover
• float_ambiguity() : protocols::noesy_assign::PeakAssignment
• float_label() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• floating_acceptance_ratio_ : protocols::jd2::archive::ArchiveBase
• floating_base() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_base_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_base_anchor_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_base_anchor_res_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• floating_pairs_ : protocols::hybridization::FoldTreeHybridize
• FloatingResonance() : protocols::noesy_assign::FloatingResonance
• FloatList : protocols::noesy_assign::FloatingResonance
• floor_ : protocols::filters::IfThenFilter
• 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
• fname_ : protocols::loops::ResidueIndexDescriptionFromFile , protocols::simple_moves::AddChainMover , protocols::simple_moves::DumpPdb
• fname_prefix_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• FNatFilter() : protocols::protein_interface_design::filters::FNatFilter
• fobj_ : protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• fobjnames() : protocols::mpi_refinement::MultiObjective
• fobjnames_ : protocols::mpi_refinement::MultiObjective
• focused_geomcst_id_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• focused_iterative_vector_expression_ : protocols::pack_daemon::DynamicAggregateFunction
• fold() : protocols::abinitio::AbrelaxApplication
• fold_label_resonance() : protocols::noesy_assign::CrossPeakInfo
• fold_label_resonance_ : protocols::noesy_assign::CrossPeakInfo
• fold_proton_resonance() : protocols::noesy_assign::CrossPeakInfo
• fold_proton_resonance_ : protocols::noesy_assign::CrossPeakInfo
• fold_resonance() : protocols::noesy_assign::CrossPeak
• fold_tree() : protocols::environment::ProtectedConformation , protocols::jumping::JumpSample , protocols::protein_interface_design::movers::SetAtomTree , protocols::rigid::RigidBodyMotionMover , protocols::seeded_abinitio::SeedFoldTree , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• fold_tree_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::jumping::JumpSample , protocols::moves::ChangeFoldTreeMover , protocols::protein_interface_design::movers::SetAtomTree , protocols::seeded_abinitio::SeedFoldTree , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters , protocols::topology_broker::TopologyBroker
• fold_tree_root_ : protocols::simple_moves::SetTorsion
• fold_tree_save_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• FoldandDockClaimer() : protocols::topology_broker::FoldandDockClaimer
• FoldConstraints() : protocols::abinitio::FoldConstraints
• folder() : protocols::noesy_assign::CrossPeak
• folding_verteces_ : protocols::seeded_abinitio::SeedFoldTree
• FoldResonance() : protocols::noesy_assign::FoldResonance
• FoldTree : protocols::nonlocal::SingleFragmentMover
• foldTree() : protocols::simple_moves::CutChainMover
• foldtree_ : protocols::floppy_tail::FloppyTailMover
• foldtree_mover_ : protocols::hybridization::FoldTreeHybridize
• FoldTreeFromLoops() : protocols::loops::FoldTreeFromLoops
• FoldTreeHybridize() : protocols::hybridization::FoldTreeHybridize
• FoldTreeOP : protocols::nonlocal::SingleFragmentMover
• FoldTreeSketch : protocols::environment::claims::CutBiasClaim , protocols::environment::claims::EnvClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::environment::EnvClaimBroker
• foldtype2name_ : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype2spairs_ : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype_from_name() : protocols::fldsgn::topology::SheetFoldTypeManager
• foldtype_from_spairs() : protocols::fldsgn::topology::SheetFoldTypeManager
• footer_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• forbidden_names_ : protocols::moves::MoverFactory
• force : protocols::cartesian::CartesianAtom , protocols::ligand_docking::Translate_info
• force_align_ : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• force_centroid_interaction() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_centroid_interaction_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::screener::BaseCentroidScreener
• force_const() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• force_const_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• force_fold_tree() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• force_fold_tree_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• force_ideal_chainbreak_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::toolbox::AllowInsert
• force_internal_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• force_natro() : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• force_natro_ : protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• force_natro_for_stored_task_names() : protocols::matdes::MatDesGreedyOptMutationMover
• force_natro_for_stored_task_names_ : protocols::matdes::MatDesGreedyOptMutationMover
• force_nonideal_ : protocols::relax::FastRelax
• force_north_paper_db_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• force_north_sugar_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_north_sugar_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_phosphate_instantiation() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_phosphate_instantiation_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• force_repack_ : protocols::loop_modeling::utilities::PrepareForFullatom
• force_south_sugar_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_south_sugar_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_ss_ : protocols::hybridization::CartesianSampler
• force_stub_intra_residue : protocols::environment::claims::JumpElement
• force_syn_chi_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_syn_chi_res_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• force_user_defined_jumps_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• forced_pos_ : protocols::simple_filters::SymmetricMotifFilter
• forced_silent_struct_type_ : protocols::jd2::SilentFileJobOutputter
• ForceDisulfidesMover() : protocols::simple_moves::ForceDisulfidesMover
• forget_chains_and_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• forget_chains_and_interface_ : protocols::dna::RestrictDesignToProteinDNAInterface
• forget_initial_loops() : protocols::anchored_design::AnchoredDesignMover
• form_disulfide() : protocols::protein_interface_design::movers::DisulfideMover
• FORMAT : protocols::sparta::GDB
• format_silent_struct() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• FORMAT_str : protocols::sparta::GDB
• FORMAT_str_parser() : protocols::sparta::GDB
• format_string() : protocols::frag_picker::VallResidue , protocols::outputter::FormatStringOutputter
• format_string_ : 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
• FormatList : protocols::sparta::GDB
• 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
• forward_jump_ : protocols::motifs::Motif
• forward_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• forward_threshold_ : protocols::simple_moves::WobbleMover
• found_centroid_interaction() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• found_centroid_interaction_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• found_res_compatibility_ : protocols::enzdes::SecondaryMatchProtocol
• found_res_compatibility_determined_ : protocols::enzdes::SecondaryMatchProtocol
• found_resis_ : protocols::enzdes::SecondaryMatchProtocol
• FourAtomsConstraintData() : protocols::frag_picker::scores::FourAtomsConstraintData
• fourth_atom_ : protocols::frag_picker::scores::FourAtomsConstraintData
• fourth_offset_ : protocols::frag_picker::scores::FourAtomsConstraintData
• fp_compare() : protocols::pockets::PlaidFingerprint
• fp_compare_deriv() : protocols::pockets::PlaidFingerprint
• fpdock_metrics_ : protocols::flexpep_docking::FlexPepDockingProtocol
• fraction_by_recombination() : protocols::genetic_algorithm::GeneticAlgorithmBase
• fraction_by_recombination_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• fraction_done : protocols::boinc::BoincSharedMemory
• fraction_done_ : protocols::boinc::Boinc
• frag1_ : protocols::forge::components::VarLengthBuild , protocols::protein_interface_design::movers::LoopRemodel
• frag3_ : protocols::anchored_design::AnchorMoversData , protocols::forge::components::VarLengthBuild , protocols::protein_interface_design::movers::LoopRemodel
• frag3_weight : protocols::flexpep_docking::FlexPepDockingFlags
• frag5_weight : protocols::flexpep_docking::FlexPepDockingFlags
• frag9_ : protocols::forge::components::VarLengthBuild , protocols::protein_interface_design::movers::LoopRemodel
• frag9_weight : protocols::flexpep_docking::FlexPepDockingFlags
• frag_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• frag_1mer_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• frag_bias_ : protocols::hybridization::CartesianSampler
• frag_cache_ : protocols::simple_moves::GunnCost
• frag_designabilities_ : protocols::enzdes::EnzdesFlexibleRegion
• frag_files() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• frag_files_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• frag_length_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• frag_libs() : protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::loops::loop_mover::LoopMover
• frag_libs_ : protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::domain_assembly::AssembleLinkerMover , protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover , protocols::kinematic_closure::perturbers::FragmentPerturber , protocols::loop_build::LoopMover_SlidingWindow , protocols::LoopRebuild , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::RBSegmentRelax
• frag_libs_1mer_ : protocols::hybridization::FoldTreeHybridize
• frag_libs_big_ : protocols::hybridization::FoldTreeHybridize
• frag_libs_small_ : protocols::hybridization::FoldTreeHybridize
• frag_map_ : protocols::frags::FragLib
• frag_mover_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::loops::loop_closure::ccd::LoopClosure
• frag_num : protocols::simple_moves::LoggedFragmentMover::Item
• frag_pos_coordinates_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• frag_size() : protocols::frags::TorsionFragmentMover
• frag_size_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::electron_density::DensityMorphingMover , protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_FragmentMover , protocols::frag_picker::quota::QuotaCollector , protocols::frags::TorsionFragmentMover , protocols::jd2::parser::FragmentReader , protocols::topology_broker::TemplateFragmentClaimer
• frag_sizes() : protocols::frags::FragLib
• frag_sizes_ : protocols::frag_picker::FragmentPicker , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::frag_picker::scores::GunnCostScore , protocols::hybridization::CartesianSampler
• frag_source_file_ : protocols::coarse_rna::CoarseRNA_Fragments
• frag_source_pose_ : protocols::coarse_rna::CoarseRNA_Fragments
• frag_source_secstruct_ : protocols::coarse_rna::CoarseRNA_Fragments
• frag_weight_aligned_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• fragfull_ : protocols::forge::components::VarLengthBuild
• FragInsertAndAlignMover() : protocols::rbsegment_relax::FragInsertAndAlignMover
• FragLib() : protocols::frags::FragLib
• fraglib_ : protocols::frags::TorsionFragmentMover
• FragMap : protocols::frags::FragLib
• fragment_1 : protocols::features::helixAssembly::FragmentPair
• fragment_2 : protocols::features::helixAssembly::FragmentPair
• fragment_bias_strategy_ : protocols::hybridization::CartesianSampler
• fragment_check() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• fragment_contacts() : protocols::frag_picker::FragmentPicker
• fragment_coordinates_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• fragment_counters_ : protocols::enzdes::EnzdesFlexBBProtocol
• fragment_library_pointer_map : protocols::farna::FullAtomRNA_Fragments
• fragment_num() : protocols::nonlocal::SmoothPolicy::Candidate
• fragment_num_ : protocols::nonlocal::SmoothPolicy::Candidate
• fragment_pose_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms
• fragment_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
• fragmentLength_ : protocols::frag_picker::FragmentCandidate
• FragmentLookupFilter() : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentLookupFilterCreator : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentLookupOP : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentLookupResult : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentMover() : protocols::simple_moves::FragmentMover
• FragmentMoverOP : protocols::forge::remodel::RemodelLoopMover
• FragmentMoverOPs : protocols::forge::remodel::RemodelLoopMover
• FragmentPair() : protocols::features::helixAssembly::FragmentPair
• FragmentPerturber() : protocols::kinematic_closure::perturbers::FragmentPerturber
• FragmentPicker() : protocols::frag_picker::FragmentPicker
• FragmentReader() : protocols::jd2::parser::FragmentReader
• fragments() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::nonlocal::Policy , protocols::simple_moves::FragmentMover , protocols::topology_broker::FragmentClaimer
• fragments9_ : protocols::hybridization::CartesianHybridize
• fragments_ : protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragmentLibrary , protocols::hybridization::CartesianSampler , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign , protocols::medal::MedalExchangeMover , protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::Policy , protocols::nonlocal::SingleFragmentMover , protocols::seeded_abinitio::CloseFold
• fragments_big() : protocols::hybridization::HybridizeSetup
• fragments_big_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup , protocols::hybridization::MRMover , protocols::seeded_abinitio::SegmentHybridizer
• fragments_big_trim_ : protocols::hybridization::MRMover
• fragments_lg_ : protocols::medal::MedalMover , protocols::star::StarAbinitio
• fragments_permutation_test_by_CA_distances() : protocols::motif_grafting::movers::MotifGraftMover
• fragments_picked_ : protocols::forge::components::VarLengthBuild
• fragments_set_ : protocols::abinitio::DomainAssembly
• fragments_sm_ : protocols::medal::MedalMover , protocols::star::StarAbinitio
• fragments_small() : protocols::hybridization::HybridizeSetup
• fragments_small_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup , protocols::hybridization::MRMover , protocols::seeded_abinitio::SegmentHybridizer
• fragments_small_trim_ : protocols::hybridization::MRMover
• fragments_to_string() : protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign
• FragmentSampler() : protocols::abinitio::FragmentSampler
• FragmentScoreManager() : protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::FragmentScoreMap
• FragmentScoreMap() : protocols::frag_picker::scores::FragmentScoreMap
• FragmentScoringMethod() : protocols::frag_picker::scores::FragmentScoringMethod
• FragmentSelectingRule() : protocols::frag_picker::FragmentSelectingRule
• FragmentSpecification : protocols::indexed_structure_store::filters::FragmentLookupFilter
• fragpick_list_ : protocols::abinitio::Templates
• FragQualCalculator() : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• FragQualFilter() : protocols::fldsgn::filters::FragQualFilter
• frags_ : protocols::noesy_assign::FragsToAtomDist
• frags_for_pos_ : protocols::frag_picker::quota::QuotaCollector
• frags_large() : protocols::topology_broker::FragmentContainer
• frags_large_ : protocols::topology_broker::FragmentContainer
• frags_per_pos() : protocols::frag_picker::FragmentSelectingRule
• frags_per_pos_ : protocols::frag_picker::FragmentSelectingRule
• frags_small() : protocols::topology_broker::FragmentContainer
• frags_small_ : protocols::topology_broker::FragmentContainer
• FragSet : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• fragset3mer_ : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::floppy_tail::FloppyTailMover
• fragset5mer_ : protocols::flexpep_docking::FlexPepDockingAbInitio
• fragset9mer_ : protocols::flexpep_docking::FlexPepDockingAbInitio
• fragset_ : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::anchored_design::AnchorMoversData , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::simple_moves::FragmentMover
• fragset_large_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::DomainAssembly
• fragset_small_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::DomainAssembly
• fragset_small_top25_ : protocols::abinitio::AbrelaxApplication
• fragset_templates_ : protocols::abinitio::AbrelaxApplication
• FragSetCOP : protocols::abinitio::DomainAssembly , protocols::forge::remodel::RemodelLoopMover , protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::Policy , protocols::nonlocal::SmoothPolicy , protocols::nonlocal::UniformPolicy
• FragSetLoader() : protocols::jd2::parser::FragSetLoader
• FragSetOP : protocols::abinitio::DomainAssembly , protocols::forge::remodel::RemodelLoopMover , protocols::jd2::parser::FragmentReader , protocols::nonlocal::SingleFragmentMover , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• FragSetOPs : protocols::forge::remodel::RemodelLoopMover
• fragsets_ : protocols::forge::remodel::RemodelLoopMover
• FragsToAtomDist() : protocols::noesy_assign::FragsToAtomDist
• frame() : protocols::kinematic_closure::ClosureProblem , protocols::match::upstream::FullChiSampleSet
• Frame : protocols::nonlocal::SingleFragmentMover
• frame_ : protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler
• frame_cache_ : protocols::canonical_sampling::DbTrajectoryRecorder , protocols::trajectory::DbTrajectoryWriter
• frame_called_ : protocols::kinematic_closure::ClosureProblem
• frame_count_ : protocols::viewer::SilentObserver
• frame_for_residue() : protocols::features::LoopAnchorFeatures
• frame_from_global_orientation() : protocols::toolbox::match_enzdes_util::LigandConformer
• frame_lower_pivot() : protocols::kinematic_closure::ClosureProblem
• frame_pos : protocols::simple_moves::LoggedFragmentMover::Item
• frame_upper_pivot() : protocols::kinematic_closure::ClosureProblem
• FrameList : protocols::forge::components::VarLengthBuild
• FrameMap : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• frames_ : protocols::flexpack::FlexPacker , protocols::match::upstream::FullChiSampleSet , protocols::nonlocal::BiasedFragmentMover , protocols::rbsegment_relax::FragInsertAndAlignMover
• framework_info_ : protocols::antibody::AntibodyInfo
• free_count_ : protocols::optimize_weights::IterativeOptEDriver
• free_data() : protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• free_data_ : protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData
• free_lock_on_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• free_parameters_ : protocols::optimize_weights::IterativeOptEDriver
• free_score_list_ : protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::WrapperOptEMultifunc
• free_score_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• free_term_constraints_ : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• free_term_map_ : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• free_terms_ : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• free_terms_energy_map_from_dofs() : protocols::optimize_weights::IterativeOptEDriver
• free_weights_after_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• free_weights_and_refEs_from_vars() : protocols::optimize_weights::IterativeOptEDriver
• free_weights_before_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• free_weights_inner_loop_ : protocols::optimize_weights::IterativeOptEDriver
• freeze() : protocols::cluster::APCluster , protocols::rigid::RigidBodyMover
• freeze_ : protocols::rigid::RigidBodyMover
• freeze_domains_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• freeze_h3_ : protocols::antibody_legacy::CDRH3Modeler
• freeze_sugar_torsions() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• freq() : protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::Resonance
• freq_ : protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::Resonance
• frequency() : protocols::abinitio::PairingStatEntry
• frequency_ : protocols::trajectory::DbTrajectoryWriter
• frequency_in_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• fresh_instance() : protocols::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_chain_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::SwapSegment
• from_entry() : protocols::protein_interface_design::PatchdockReader
• from_entry_ : protocols::protein_interface_design::PatchdockReader
• from_res() : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder
• 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_scratch_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::SWA_MoveSelector
• from_scratch_mover_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• 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
• frs_ : protocols::kinmatch::FunGroupTK
• fshave1 : protocols::mpi_refinement::MethodParams
• fshave2 : protocols::mpi_refinement::MethodParams
• fshave3 : protocols::mpi_refinement::MethodParams
• fstyle_A_ : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• fstyle_b_ : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• ft_mover() : protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::simple_moves::ChangeAndResetFoldTreeMover
• ft_mover_ : protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::simple_moves::ChangeAndResetFoldTreeMover
• ft_restore_ : protocols::rbsegment_relax::MakeStarTopologyMover
• ftoa() : protocols::sparta::ANN
• Full : protocols::hotspot_hashing::movers::PlaceProbeMover
• full_align_res : protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo
• full_cdr_min_ : protocols::antibody::design::AntibodySeqDesignMover
• full_constraint_ : protocols::ub_e2c::ubi_e2c_modeler
• full_constraint_set_ : protocols::abinitio::KinematicAbinitio
• full_database_ : protocols::toolbox::task_operations::DatabaseThread
• full_length_loop_rmsd_clustering_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• full_optimize_ : protocols::stepwise::legacy::screener::SimplePoseSelection
• full_score_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• full_sequence() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_sequence_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_sfxn_ : protocols::simple_moves::GreenPacker
• full_to_input_res_map_ONE_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• full_to_input_res_map_TWO_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• full_to_sub() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• full_to_sub_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• fullatom_ : protocols::abinitio::IterativeAbrelax , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::hybridization::CartesianSampler , protocols::membrane::RotationMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::symmetric_docking::SymDockProtocol , protocols::viewer::SilentObserver
• fullatom_allowed_CSP_fraction_ : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_archive_ : protocols::abinitio::IterativeAbrelax
• fullatom_constraint_cutoff_ : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_CSP_weight_ : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_filter() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_non_CSP_weight_ : protocols::ub_e2c::ubi_e2c_modeler
• fullatom_pool_ptr_ : protocols::abinitio::IterativeCentroid
• fullatom_relax_ : protocols::surface_docking::SurfaceDockingProtocol
• fullatom_scorefunction() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• fullatom_scorefunction_ : protocols::anchored_design::AnchorMoversData , protocols::floppy_tail::FloppyTailMover , protocols::metal_interface::ZincHeterodimerMover
• fullatom_scorefxn() : protocols::abinitio::Protocol
• fullatom_sfx_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• fullatom_stage() : protocols::loop_modeling::LoopModeler
• 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
• func_ : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• func_sd_ : protocols::forge::constraints::InverseRotamersRCG
• FuncFactory : protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• funcnames_ : protocols::pack_daemon::EntityCorrespondence
• function_expression() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• function_name_ : protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFHbondFunction
• function_names_ : protocols::ligand_docking::rdf::RDFBase , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• function_sign_ : protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFHbondFunction
• function_tag() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• function_tag_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• FunctionSign : protocols::ligand_docking::rdf::RDFBase
• FunGroupTK() : protocols::kinmatch::FunGroupTK
• fuzzy_topology_ : protocols::abinitio::StrandConstraints
• FuzzyTopology : protocols::abinitio::StrandConstraints
• Fv : protocols::antibody_legacy::Antibody
• Fv_sequence_ : protocols::antibody_legacy::Antibody