- a -

• a_to_i() : protocols::normalmode::NormalMode
• aa() : protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::frag_picker::VallResidue , protocols::noesy_assign::MethylNames , protocols::noesy_assign::Resonance , protocols::optimize_weights::PNatRotOptEPositionData , protocols::simple_moves::MinimalRotamer
• aa_exists() : protocols::antibody::design::ResidueProbDesignOperation
• aa_from_resid() : protocols::noesy_assign::ResonanceList
• aa_name() : protocols::noesy_assign::MethylNames
• AACompositionEnergy() : protocols::fldsgn::potentials::AACompositionEnergy
• ab_dock_chains() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• ab_fold_tree() : protocols::protein_interface_design::movers::SetAtomTree
• Ab_TemplateInfo() : protocols::antibody::Ab_TemplateInfo
• abego() : protocols::jd2::parser::BluePrint
• abego_char() : protocols::frag_picker::quota::ABEGO_SS_Map
• ABEGO_SS_Config() : protocols::frag_picker::quota::ABEGO_SS_Config
• ABEGO_SS_Map() : protocols::frag_picker::quota::ABEGO_SS_Map
• ABEGO_SS_Pool() : protocols::frag_picker::quota::ABEGO_SS_Pool
• ABEGO_SS_Score() : protocols::frag_picker::scores::ABEGO_SS_Score
• abinitio_stage() : protocols::forge::remodel::RemodelLoopMover
• AbinitioBaseFilter() : protocols::simple_filters::AbinitioBaseFilter
• abort_min() : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• AbrelaxApplication() : protocols::abinitio::AbrelaxApplication
• AbrelaxMover() : protocols::abinitio::AbrelaxMover
• AbscriptLoopCloserCM() : protocols::abinitio::abscript::AbscriptLoopCloserCM
• AbscriptMover() : protocols::abinitio::abscript::AbscriptMover
• AbscriptStageMover() : protocols::abinitio::abscript::AbscriptStageMover
• AbstractArchiveBase() : protocols::jd2::archive::AbstractArchiveBase
• acc_dist_cutoff() : protocols::features::WaterFeatures
• accept() : protocols::simple_moves::GenericMonteCarloMover
• accept_claims() : protocols::topology_broker::TopologyBroker
• accept_counter() : protocols::simple_moves::GenericMonteCarloMover
• accept_declined_claim() : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• accept_new_conformation() : protocols::loops::loop_closure::ccd::RamaCheckBase
• acceptable_rmsd_change() : protocols::LoopRebuild
• acceptance_rate() : protocols::moves::MoverStatistics , protocols::moves::TrialMover
• AcceptanceCheck() : protocols::loop_modeling::utilities::AcceptanceCheck
• accepted() : protocols::moves::MoverStatistics , protocols::moves::TrialCounter
• accepts() : protocols::frag_picker::quota::ABEGO_SS_Pool
• accepts_since_last_batch() : protocols::jd2::archive::ArchiveBase
• acid_base_coefficient() : protocols::simple_moves::IonizableResidue
• acknowledge_neighbors_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• acknowledge_partial_state_assignment() : protocols::flexpack::interaction_graph::FlexbbEdge
• acknowledge_state_zeroed() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• acknowledge_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• act_on_status_response() : protocols::wum2::EndPoint
• activate_daemon_mode() : protocols::pack_daemon::DaemonSet
• active_angle() : protocols::stepwise::sampler::MC_OneTorsion
• active_environment() : protocols::environment::ClientMover
• active_pose_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• active_site_grid() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder
• active_site_grid_set() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder
• active_variables() : protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VMax , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMin , protocols::pack_daemon::VMinBy
• active_variables_vector() : protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VectorExpression
• ActiveSiteGrid() : protocols::match::downstream::ActiveSiteGrid
• actual_bb() : protocols::match::Bool3DGrid
• actual_cycles() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• actually_moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• adaptation_period() : protocols::simple_moves::GenericMonteCarloMover
• adaptive_movers() : protocols::simple_moves::GenericMonteCarloMover
• AdaptiveScoreHistogram() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• add() : protocols::abinitio::StructureStore , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::forge::build::BuildManager , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool , protocols::kinematic_closure::perturbers::PerturberSet , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::topology_broker::TopologyBroker , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue , protocols::wum::WorkUnitQueue_Swapped
• add_aa_virt_rsd_as_root() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• add_acceptance_check() : protocols::loop_modeling::LoopProtocol
• add_additional_low_resolution_step() : protocols::docking::DockingProtocol
• add_additional_task_operaration() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• add_all_atoms() : protocols::noesy_assign::PeakAssignmentResidueMap
• add_all_evaluators() : protocols::evaluation::EvaluatorFactory
• add_aln() : protocols::comparative_modeling::AlignmentCluster
• add_apply_mover() : protocols::environment::EnvMover
• add_assignment() : protocols::noesy_assign::CrossPeak::Spin
• add_at_ind() : protocols::match::downstream::AtomGeometrySecMatchRPE
• add_atom() : protocols::pockets::SmallMol
• add_atom_set() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• add_atomgeom_evaluator() : protocols::match::downstream::GeometrySecMatchRPE
• add_atomset_to_perturber_atomset_list() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_backrub_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_batch() : protocols::jd2::JobDistributor
• add_bb_csts_to_loop() : protocols::protein_interface_design::movers::PlaceOnLoop
• add_big_fragments() : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• add_blacklist() : protocols::wum::WorkUnitBase
• add_bond_angle_constraint() : protocols::simple_moves::ConstrainToIdealMover
• add_bond_dihedral_constraint() : protocols::simple_moves::ConstrainToIdealMover
• add_bond_length_constraint() : protocols::simple_moves::ConstrainToIdealMover
• add_build_set() : protocols::match::upstream::ProteinUpstreamBuilder
• add_capping_base_pairs_to_full_sequence() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• add_CDR_to_MoveMap() : protocols::antibody::AntibodyInfo
• add_chainbreak_variants() : protocols::abinitio::KinematicControl , protocols::environment::EnvClaimBroker , protocols::topology_broker::TopologyBroker
• add_chainbreaks() : protocols::jumping::JumpSample
• add_chainbreaks_as_distance_constraint() : protocols::jumping::JumpSample
• add_chainbreakweights() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• add_chem_shift_info() : protocols::farna::RNA_DeNovoProtocol
• add_child() : protocols::loop_modeling::LoopMover
• add_choice() : protocols::genetic_algorithm::DiscreteRandomizer
• add_chunk() : protocols::abinitio::abscript::ResidueChunkSelection
• add_chunk_filter() : protocols::frag_picker::FragmentPicker
• add_chunk_set() : protocols::farna::RNA_ChunkLibrary
• add_claim() : protocols::environment::ScriptCM
• add_cluster_comments_to_pose() : protocols::antibody::design::AntibodyDesignMover
• add_complementary_sequence() : protocols::dna::DnaInterfacePacker
• add_components_to_pose_if_necessary() : protocols::matdes::SymDofMover
• add_compositeSegmentMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_condition() : protocols::filters::IfThenFilter
• add_connected_resonance() : protocols::noesy_assign::Resonance
• add_constant() : protocols::filters::CalculatorFilter
• add_constrained_atoms_from_atom_pair_constraint() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_atoms_from_multiconstraint() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_lig_atom() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_nonligand_atom() : protocols::enzdes::EnzdesConstraintReporter
• add_constraint() : protocols::forge::remodel::RemodelConstraintGenerator
• add_constraints() : protocols::abinitio::AbrelaxApplication , protocols::forge::remodel::RemodelConstraintGenerator , protocols::metal_interface::AddZincSiteConstraints , protocols::simple_moves::ConstraintSetMover , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• add_constraints_to_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_constraints_to_pose_for_block_without_clearing_and_header_processing() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_constraints_to_scorefunction() : protocols::docking::DockingProtocol
• add_coord_cst() : protocols::abinitio::LoopJumpFoldCst
• add_coordinate_constraints_from_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• add_coordinatecst_for_hotspot_packing() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• add_core_evaluator() : protocols::abinitio::IterativeBase
• add_cst_files() : protocols::relax::RelaxProtocolBase
• add_cut_points() : protocols::ligand_docking::MinimizeBackbone
• add_decoy() : protocols::optimize_weights::PNatStructureOptEData
• add_delete_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• add_delta_omega1_value() : protocols::helical_bundle::parameters::BundleParameters
• add_delta_z1_value() : protocols::helical_bundle::parameters::BundleParameters
• add_dependency_to() : protocols::forge::build::BuildInstruction
• add_design_task() : protocols::flxbb::FlxbbDesign
• add_deviations() : protocols::mpi_refinement::StructAvrgMover
• add_dist_viol_to_assignments() : protocols::noesy_assign::NoesyModule
• add_distance() : protocols::contact_map::Contact
• add_dna_states() : protocols::dna::DnaInterfaceMultiStateDesign
• add_DoF() : protocols::helical_bundle::BundleGridSamplerHelper
• add_elem_to_cache() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• add_entity() : protocols::genetic_algorithm::GeneticAlgorithmBase
• add_entry() : protocols::abinitio::PairingStatistics
• add_enz_cst_interaction_to_pose() : protocols::enzdes::SecondaryMatchProtocol
• add_equiv_atoms() : protocols::comparative_modeling::ThreadingMover
• add_evaluated_structure() : protocols::abinitio::HedgeArchive , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• add_evaluation() : protocols::abinitio::AbrelaxApplication , protocols::abinitio::Protocol , protocols::evaluation::MetaPoseEvaluator , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::JobOutputter
• add_evaluator() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• add_evaluator_for_target_restype() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• add_evaluators() : protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::evaluation::EvaluatorCreator , protocols::evaluation::EvaluatorFactory , protocols::simple_filters::CamShiftEvaluatorCreator , protocols::simple_filters::ChiWellRmsdEvaluatorCreator , protocols::simple_filters::ContactMapEvaluatorCreator , protocols::simple_filters::ExtraScoreEvaluatorCreator , protocols::simple_filters::JScoreEvaluatorCreator , protocols::simple_filters::JumpNrEvaluatorCreator , protocols::simple_filters::NativeEvaluatorCreator , protocols::simple_filters::PalesEvaluatorCreator , protocols::simple_filters::PoolEvaluatorCreator , protocols::simple_filters::PredictedBurialFnEvaluatorCreator , protocols::simple_filters::RdcEvaluatorCreator , protocols::simple_filters::RdcSelectEvaluatorCreator , protocols::simple_filters::RdcTargetEvaluatorCreator , protocols::simple_filters::RmsdEvaluatorCreator , protocols::simple_filters::RmsdTargetEvaluatorCreator , protocols::simple_filters::StructureSimilarityEvaluatorCreator , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::topology_broker::ConstraintEvaluatorWrapperCreator
• add_excluded_chains() : protocols::ligand_docking::Translate
• add_external_geom_sampler() : protocols::match::downstream::ClassicMatchAlgorithm
• add_external_geometry_samples_for_constraint() : protocols::match::Matcher
• add_external_loop_rotamer() : protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::rna::RNA_MC_MultiSuite , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneValueComb , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• add_extra_data() : protocols::loophash::BackboneDB
• add_features_reporter() : protocols::features::ReportToDB
• add_file_contents() : protocols::pack_daemon::DynamicAggregateFunction
• add_filename() : protocols::simple_filters::StemFinder
• add_filter() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::filters::CalculatorFilter , protocols::filters::FilterCollection , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::MatcherTask , protocols::match::output::MatchProcessor , protocols::matdes::MatDesGreedyOptMutationMover , protocols::moves::FilterMover , protocols::simple_filters::Operator , protocols::simple_moves::GenericMonteCarloMover
• add_filter_param() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• add_filter_parameter() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_flexible_region() : protocols::enzdes::EnzdesFlexBBProtocol
• add_fragments() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• add_fragments_big() : protocols::hybridization::HybridizeSetup
• add_fragments_small() : protocols::hybridization::HybridizeSetup
• add_frags() : protocols::abinitio::abscript::AbscriptMover
• add_fresh_param() : protocols::mpi_refinement::Scheduler
• add_from_file() : protocols::motifs::MotifLibrary
• add_full_assignment() : protocols::noesy_assign::CrossPeak
• add_fullatom_flags() : protocols::abinitio::IterativeBase
• add_function_name() : protocols::ligand_docking::rdf::RDFBase
• add_gap_constraints_to_pose() : protocols::hybridization::FoldTreeHybridize
• add_genericRBMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_group() : protocols::simple_moves::symmetry::SetupNCSMover , protocols::toolbox::task_operations::LinkResidues
• add_groupD() : protocols::simple_moves::symmetry::SetupNCSMover
• add_groupE() : protocols::simple_moves::symmetry::SetupNCSMover
• add_helix() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• add_helixMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_hetatm() : protocols::hybridization::HybridizeSetup
• add_hits() : protocols::match::HitNeighborFinder , protocols::match::MatchCounter
• add_hotspot_constraints_to_pose() : protocols::hotspot_hashing::HotspotStubSet
• add_hotspot_constraints_to_wholepose() : protocols::hotspot_hashing::HotspotStubSet
• add_hsstriplets() : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::topology::HSSTripletSet
• add_info() : protocols::dna::PDBOutput
• add_inner_cycle_step() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• add_inputter() : protocols::inputter::InputterStream
• add_inputvalue() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• add_instruction() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
• add_internal_loop_rotamer() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• add_ionized_restype() : protocols::simple_moves::IonizableResidue
• add_jump() : protocols::docking::DockingProtocol , protocols::docking::RigidBodyInfo , protocols::docking::TemperedDocking , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::scoring::InterfaceInfo , protocols::simple_filters::InterfaceSasaFilter , protocols::toolbox::task_operations::RestrictToInterface
• add_kic_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_leap() : protocols::loophash::LoopHashMap
• add_legacyleap() : protocols::loophash::LoopHashMap
• add_ligand_from_file() : protocols::motifs::MotifLibrary
• add_line() : protocols::frags::RMSVallData , protocols::frags::VallData
• add_loop() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::Loops
• add_loop_residue() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_loop_size() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• add_mainchain_segments() : protocols::backrub::BackrubMover
• add_mainchain_segments_from_options() : protocols::backrub::BackrubMover
• add_match() : protocols::match::output::BestMatchesCollection , protocols::match::output::MatchScoreWriter
• add_match_dspos1() : protocols::match::output::BestMatchesCollection
• add_member() : protocols::cluster::Cluster
• add_member_front() : protocols::cluster::Cluster
• add_methyl() : protocols::noesy_assign::MethylNames
• add_metric_value_getter() : protocols::multistate_design::MultiStateFitnessFunction
• add_motif() : protocols::simple_filters::SymmetricMotifFilter
• add_movable_jump() : protocols::toolbox::task_operations::InterfaceTaskOperation
• add_mover() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::moves::CompositionMover , protocols::moves::MoverContainer , protocols::stepwise::screener::AnchorSugarScreener , protocols::stepwise::screener::BulgeApplier , protocols::stepwise::screener::O2PrimeScreener , protocols::stepwise::screener::PackScreener , protocols::stepwise::screener::PhosphateScreener , protocols::stepwise::screener::ProteinCCD_ClosureScreener , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::SugarInstantiator , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• add_mover_group() : protocols::loop_modeling::utilities::LoopMoverGroup
• add_mutant() : protocols::optimize_weights::DDGMutationOptEData
• add_mutant_complex() : protocols::optimize_weights::DDGBindOptEData
• add_mutant_unbounds() : protocols::optimize_weights::DDGBindOptEData
• add_mutation() : protocols::optimize_weights::DDGBindOptEData , protocols::pmut_scan::Mutant
• add_native() : protocols::optimize_weights::PNatStructureOptEData
• add_native_fasta() : protocols::toolbox::task_operations::JointSequenceOperation
• add_native_pdb() : protocols::toolbox::task_operations::JointSequenceOperation
• add_native_pose() : protocols::toolbox::task_operations::JointSequenceOperation
• add_negative_filter() : protocols::protein_interface_design::filters::BoltzmannFilter
• add_neutral_restype() : protocols::simple_moves::IonizableResidue
• add_new() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• add_new_chain() : protocols::simple_moves::AddChainMover
• add_new_cluster() : protocols::toolbox::KClusterElement
• add_new_data() : protocols::toolbox::KClusterElement
• add_new_RNA_jump() : protocols::farna::RNA_StructureParameters
• add_npd_property_calculator_for_state() : protocols::pack_daemon::DaemonSet
• add_npdpro_calculator_creator() : protocols::pack_daemon::DaemonSet
• add_number_base_pairs() : protocols::farna::RNA_DeNovoProtocol
• add_number_native_base_pairs() : protocols::farna::RNA_DeNovoProtocol
• add_objective_function_info() : protocols::mpi_refinement::MultiObjective
• add_observer() : protocols::canonical_sampling::MetropolisHastingsMover
• add_observer_cache_segments_to_set() : protocols::enzdes::DetectProteinLigandInterface
• add_or_delete_mover() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• add_output_observer() : protocols::jd2::Job
• add_overlap_loop() : protocols::loops::Loops
• add_overlapping_pair_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• add_pack_daemon() : protocols::pack_daemon::DaemonSet
• add_packer_screeners() : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• add_pair() : protocols::fldsgn::topology::StrandPairing
• add_pairing() : protocols::abinitio::AlternativePairings , protocols::abinitio::PairingStatEntry , protocols::abinitio::StrandConstraints
• add_parameter_info_to_pose() : protocols::helical_bundle::MakeBundleHelix
• add_parent_entity() : protocols::genetic_algorithm::GeneticAlgorithmBase
• add_parents_from_current_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• add_pdb() : protocols::toolbox::task_operations::JointSequenceOperation
• add_pdb_id() : protocols::frag_picker::PdbIdChunkFilter
• add_pdb_ids() : protocols::frag_picker::PdbIdChunkFilter
• add_peak() : protocols::noesy_assign::PeakCalibrator
• add_perturber() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover
• add_point() : protocols::qsar::qsarMap
• add_pool() : protocols::frag_picker::quota::QuotaCollector
• add_pose() : protocols::loophash::BackboneDB , protocols::toolbox::task_operations::JointSequenceOperation
• add_pose_to_pool() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• add_position() : protocols::environment::claims::EnvLabelSelector
• add_position_data() : protocols::optimize_weights::OptEData
• add_position_in_pose() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• add_positive_filter() : protocols::protein_interface_design::filters::BoltzmannFilter
• add_precomputed_energies() : protocols::simple_moves::GreenPacker
• add_pregenerated_constraints_to_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_pregenerated_enzdes_constraints() : protocols::enzdes::EnzdesBaseProtocol
• add_preparer() : protocols::abinitio::abscript::AbscriptStageMover
• add_protein() : protocols::loophash::BackboneDB
• add_proton() : protocols::noesy_assign::MethylNames
• add_protonated_H1_adenosine_variants() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• add_query_ss() : protocols::frag_picker::FragmentPicker
• add_r1_value() : protocols::helical_bundle::parameters::BundleParameters
• add_rcg() : protocols::forge::components::VarLengthBuild
• add_refiner() : protocols::loop_modeling::LoopProtocol
• add_registered_mover() : protocols::environment::EnvMover
• add_relax_batch() : protocols::loophash::MPI_LoopHashRefine_Master
• add_relax_simple() : protocols::mpi_refinement::MPI_Refine_Master
• add_remodel_constraints_to_pose() : protocols::forge::remodel::RemodelConstraintGenerator
• add_required_connection_for_residue() : protocols::simple_filters::PackerNeighborGraphFilter
• add_required_connections_between_regions() : protocols::simple_filters::PackerNeighborGraphFilter
• add_rerelaxed() : protocols::mpi_refinement::Scheduler
• add_res() : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• add_resid_to_entity_list() : protocols::pack_daemon::EntityCorrespondence
• add_residue() : protocols::cyclic_peptide::PeptideStubMover , protocols::enzdes::PoseFoundResiduesCombination , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• add_residue_alternative_rotamer() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• add_residue_alternative_set() : protocols::stepwise::modeler::StepWiseConnectionSampler
• add_residue_constraints() : protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue
• add_residue_pair() : protocols::jumping::ResiduePairJump
• add_residue_pair_jump() : protocols::jumping::ResiduePairJumpSetup
• add_residue_single() : protocols::jumping::ResiduePairJump
• add_residue_to_perturber_residue_list() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_residue_type_by_name() : protocols::simple_filters::ResidueCountFilter
• add_rigidity_jumps() : protocols::abinitio::LoopJumpFoldCst
• add_rotamer_line_data() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData
• add_rv_info() : protocols::forge::remodel::ResidueVicinityRCG
• add_score() : protocols::moves::MoverStatistics , protocols::sic_dock::JointScore
• add_score_type() : protocols::simple_filters::ScoreCutoffFilter
• add_score_weights() : protocols::abinitio::CoordinateConstraintKC , protocols::abinitio::KinematicControl
• add_scores_to_job() : protocols::ligand_docking::GrowLigand , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDesign
• add_scoring_method() : protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::FragmentScoreManager
• add_secondary_downstream_match_geometry_for_constraint() : protocols::match::Matcher
• add_secondary_upstream_match_geometry_for_constraint() : protocols::match::Matcher
• add_segment() : protocols::backrub::BackrubMover
• add_selector() : protocols::frag_picker::CompositeFragmentSelector
• add_setup_mover() : protocols::forge::components::VarLengthBuild
• add_shear_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_sidechain_mc_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_sidechain_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_silent_struct() : protocols::jd2::SilentFileJobOutputter
• add_similarity() : protocols::cluster::DataPoint
• add_small_fragments() : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• add_small_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_spanning_region() : protocols::abinitio::MembraneAbinitio
• add_start_from() : protocols::ligand_docking::LigandDockProtocol
• add_starting_templates() : protocols::hybridization::HybridizeSetup
• add_state() : protocols::multistate_design::MultiStateFitnessFunction
• add_states() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• add_strand_pairing() : protocols::hybridization::FoldTreeHybridize
• add_strand_pairings() : protocols::hybridization::FoldTreeHybridize
• add_strandMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_string() : protocols::jd2::Job
• add_string_real_pair() : protocols::jd2::Job
• add_string_string_pair() : protocols::jd2::Job
• add_strings() : protocols::jd2::Job
• add_structure() : protocols::abinitio::IterativeBase , protocols::cluster::ClusterBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive
• add_structure_at_position() : protocols::abinitio::IterativeCentroid , protocols::jd2::archive::ArchiveBase
• add_structure_based_on_rms() : protocols::optimize_weights::IterativeOptEDriver
• add_structure_to_library() : protocols::loophash::MPI_LoopHashRefine , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::MPI_Refinement
• add_structure_to_library_add_n_replace() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• add_structure_to_library_direct() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• add_structure_to_library_single_replace() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• add_structures_to_library() : protocols::loophash::MPI_LoopHashRefine , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refinement
• add_stub_() : protocols::hotspot_hashing::HotspotStubSet
• add_stub_set() : protocols::hotspot_hashing::HotspotStubSet
• add_submover() : protocols::abinitio::abscript::AbscriptStageMover
• add_suckers() : protocols::simple_moves::AddCavitiesMover
• add_sym_dof_name() : protocols::simple_filters::InterfaceSasaFilter
• add_tail_residue() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_target_constraints() : protocols::abinitio::Templates
• add_target_restype() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• add_task_operation() : protocols::flxbb::DesignTask
• add_task_operations() : protocols::flxbb::DesignTask
• add_template() : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• add_terminal_res_repulsion() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• add_to_allowed_aas() : protocols::antibody::design::ConservativeDesignOperation
• add_to_atom_id_map_after_checks() : protocols::stepwise::modeler::align::StepWisePoseAligner
• add_to_library() : protocols::motifs::MotifLibrary
• add_to_one_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• add_to_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• add_to_swap() : protocols::wum::WorkUnitQueue_Swapped
• add_to_targets() : protocols::toolbox::match_enzdes_util::InvrotTree
• add_to_top_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• add_topology() : protocols::abinitio::PairingStatistics
• add_torerelax() : protocols::mpi_refinement::Scheduler
• add_torsion() : protocols::canonical_sampling::MetricRecorder , protocols::farna::FragmentLibrary
• add_trigger() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• add_type() : protocols::comparative_modeling::features::ResidueFeatureFactory , protocols::protein_interface_design::DockDesignFilterFactory , protocols::topology_broker::TopologyClaimerFactory
• add_unfolded_energy_data() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• add_upstream_restype_for_constraint() : protocols::match::Matcher
• add_user_provided_mover() : protocols::forge::components::VarLengthBuild
• add_value_to_perturber_value_list() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_values_to_job() : protocols::canonical_sampling::BiasEnergy , protocols::jd2::JobOutputterObserver , protocols::rosetta_scripts::ParsedProtocol
• add_vec() : protocols::evaluation::PCA
• add_virt_res_as_root() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• add_virtual_residues() : protocols::environment::EnvClaimBroker
• add_wholeStructureMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_wt() : protocols::optimize_weights::DDGMutationOptEData
• add_wt_complex() : protocols::optimize_weights::DDGBindOptEData
• add_wt_unbounds() : protocols::optimize_weights::DDGBindOptEData
• AddAllPositionsMPM() : protocols::match::AddAllPositionsMPM
• AddAssemblyConstraints() : protocols::domain_assembly::AddAssemblyConstraints
• AddCavitiesMover() : protocols::simple_moves::AddCavitiesMover
• AddChainBreak() : protocols::protein_interface_design::movers::AddChainBreak
• AddChainMover() : protocols::simple_moves::AddChainMover
• AddConstraintsToCurrentConformationMover() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• addEntry() : protocols::sparta::GDB
• AddGood2BPairEnergyRotamers() : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• AddHydrogen() : protocols::ligand_docking::AddHydrogen
• AddHydrogens() : protocols::ligand_docking::AddHydrogens
• additional_setup_for_floating_base() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• AdditionalOutputWrapper() : protocols::rosetta_scripts::AdditionalOutputWrapper
• AddJobPairData() : protocols::simple_moves::AddJobPairData
• AddLigandMotifRotamers() : protocols::enzdes::AddLigandMotifRotamers
• addloopgeometry() : protocols::generalized_kinematic_closure::GeneralizedKIC
• addloweranchor() : protocols::generalized_kinematic_closure::GeneralizedKIC
• addLowResStatistics() : protocols::flexpep_docking::FlexPepDockingProtocol
• AddMembraneMover() : protocols::membrane::AddMembraneMover
• AddMover() : protocols::stepwise::monte_carlo::mover::AddMover
• AddOrDeleteMover() : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• AddOrRemoveMatchCsts() : protocols::enzdes::AddOrRemoveMatchCsts
• addRemark() : protocols::sparta::GDB
• address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• address_exists_in_cache() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• address_to_buf() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• address_to_string() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• AddRigidBodyLigandConfs() : protocols::enzdes::AddRigidBodyLigandConfs
• AddSearchPatternRotSetOp() : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• AddSidechainConstraintsToHotspots() : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• addtailgeometry() : protocols::generalized_kinematic_closure::GeneralizedKIC
• addupperanchor() : protocols::generalized_kinematic_closure::GeneralizedKIC
• addVAR() : protocols::sparta::GDB
• addVirtualResAsRootMembrane() : protocols::topology_broker::MembraneTopologyClaimer
• AddZincSiteConstraints() : protocols::metal_interface::AddZincSiteConstraints
• adjust_relax_movemap() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• adjust_residue_to_minimize_deviation() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• advance_to_next_pose_segment() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• affixed_numbered_name() : protocols::jd2::JobOutputter
• aggregate_function() : protocols::multistate_design::MultiStateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• ala_pose_loop() : protocols::protein_interface_design::movers::PlaceOnLoop
• AlaScan() : protocols::simple_filters::AlaScan
• algorithm() : protocols::match::upstream::BuildSet
• algorithm_inputs() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• align() : protocols::fibril::SetupForFibrilMover
• align_all_pose() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• align_and_output_to_silent_file() : protocols::farna::RNA_DeNovoProtocol
• align_angle() : protocols::fldsgn::topology::HelixPairing
• align_by_domain() : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• align_c() : protocols::sic_dock::Rose
• align_n() : protocols::sic_dock::Rose
• align_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• align_poses() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• Align_RmsdEvaluator() : protocols::comparative_modeling::Align_RmsdEvaluator
• Align_RotamerEvaluator() : protocols::comparative_modeling::Align_RotamerEvaluator
• align_segment() : protocols::forge::remodel::RemodelGlobalFrame
• align_to_chunk() : protocols::farna::RNA_ChunkLibrary
• align_to_frame() : protocols::simple_filters::RepeatParameterFilter
• align_to_native() : protocols::antibody_legacy::Antibody
• align_to_quick_alignment_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• align_VDW_rep_screen_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• AlignChainMover() : protocols::simple_moves::AlignChainMover
• aligned() : protocols::star::Extender
• AlignedThreadOperation() : protocols::toolbox::task_operations::AlignedThreadOperation
• AlignEvaluator() : protocols::evaluation::AlignEvaluator
• alignment() : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingJob , protocols::comparative_modeling::ThreadingMover
• alignment2AtomMap() : protocols::hybridization::TMalign
• alignment2strings() : protocols::hybridization::TMalign
• alignment_file() : protocols::toolbox::task_operations::AlignedThreadOperation
• alignment_id() : protocols::comparative_modeling::ThreadingJob
• AlignmentCluster() : protocols::comparative_modeling::AlignmentCluster
• AlignmentClustering() : protocols::comparative_modeling::AlignmentClustering
• alignments() : protocols::comparative_modeling::AlignmentSet , protocols::jd2::InnerMultiThreadingJob
• AlignmentSet() : protocols::comparative_modeling::AlignmentSet
• AlignPoseToInvrotTreeMover() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• AlignRmsdTargetEvaluatorCreator() : protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator
• all_add_energy() : protocols::wum::SilentStructStore
• all_broker_files() : protocols::jd2::archive::Batch
• all_cdr_fold_tree() : protocols::antibody_legacy::Antibody
• all_cdr_VL_VH_fold_tree() : protocols::antibody_legacy::AntibodyModeler
• all_energies() : protocols::toolbox::DecoySetEvaluation
• all_ref_poses() : protocols::jd2::AtomTreeDiffJobInputter
• all_sort_silent_scores() : protocols::wum::SilentStructStore
• all_target_res() : protocols::toolbox::match_enzdes_util::InvrotTarget
• all_target_residues() : protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• all_turn_residues_are_on_the_same_chain() : protocols::features::BetaTurnDetection
• AllAtomNormalization() : protocols::qsar::scoring_grid::AllAtomNormalization
• allocate_buffers() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::ParallelTempering
• allow_all_aas() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• allow_base_pair_only_centroid_screen() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_base_pair_only_screen() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• allow_bondangles() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• allow_bondlengths() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• allow_bulge_at_chainbreak() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_claim() : protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• allow_delete() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_design() : protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• allow_design_around() : protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::ThreadSequenceOperation
• allow_dihedrals() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• allow_insert() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::farna::RNA_ChunkLibrary , protocols::farna::RNA_StructureParameters
• allow_internal_hinge() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_internal_hinge_moves() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_internal_local() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_internal_local_moves() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_pure_movers() : protocols::environment::Environment
• allow_reading_cancelled_decoys() : protocols::jd2::archive::Batch
• allow_repacking() : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• allow_skip_bulge() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::SWA_MoveSelector
• allow_split_off() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_syn_pyrimidine() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_virtual_o2prime_hydrogens() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_virtual_side_chains() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allowed_closure_attempts() : protocols::forge::remodel::RemodelLoopMover
• allowed_current_slide() : protocols::simple_moves::symmetry::SymmetrySlider
• allowed_res_name3_at_position() : protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• allowed_res_name3s() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_res_types() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_res_types_pointers() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_seqpos() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_surface_aa() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• allowed_types() : protocols::dna::DnaInterfacePacker , protocols::motifs::BuildPosition
• AllowedSeqposForGeomCst() : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• AllowInsert() : protocols::toolbox::AllowInsert
• AllResiduesChanged() : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• allsc() : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• alpha() : protocols::dna::DNABase , protocols::stepwise::sampler::rigid_body::EulerAngles
• already_connected() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• already_in_queue() : protocols::match::output::UpstreamHitCacher
• already_instantiated_in_pose() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• also_check_fix_disulf() : protocols::frag_picker::CS2ndShift
• alt_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• alt_e_up_to_date() : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_energy() : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_rot() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• alter_espGrid() : protocols::pockets::PocketGrid
• alter_espGrid_with_bound_ligand() : protocols::pockets::PocketGrid
• alter_rotamer_set() : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• alternate_state() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_info() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_is_being_considered() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_two_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• alternative_decoys_out() : protocols::jd2::archive::Batch
• AlterSpecDisruptionDriver() : protocols::pmut_scan::AlterSpecDisruptionDriver
• AmbigCSScore() : protocols::frag_picker::scores::AmbigCSScore
• ambiguity() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• ambiguous() : protocols::noesy_assign::CrossPeak
• ambiguous_hnq() : protocols::relax::AtomCoordinateCstMover
• AmbiguousMultiConstraint() : protocols::constraints_additional::AmbiguousMultiConstraint
• amplitude() : protocols::dna::DNABase
• Anchor() : protocols::anchored_design::Anchor
• anchor_end() : protocols::anchored_design::AnchorMoversData
• anchor_noise_constraints_setup() : protocols::anchored_design::AnchorMoversData
• anchor_offset() : protocols::multistate_design::PartitionAggregateFunction< T >
• anchor_resnum() : protocols::protein_interface_design::movers::TaskAwareCsts
• anchor_specified() : protocols::seeded_abinitio::SeedFoldTree
• anchor_start() : protocols::anchored_design::AnchorMoversData
• anchor_sugar_modeling() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• anchor_sugar_solution_number() : protocols::stepwise::screener::AnchorSugarScreener
• anchored_loop() : protocols::anchored_design::AnchorMoversData
• AnchoredDesignMover() : protocols::anchored_design::AnchoredDesignMover
• AnchoredGraftMover() : protocols::grafting::AnchoredGraftMover
• AnchoredPerturbMover() : protocols::anchored_design::AnchoredPerturbMover
• AnchoredRefineMover() : protocols::anchored_design::AnchoredRefineMover
• AnchorMoversData() : protocols::anchored_design::AnchorMoversData
• anchors() : protocols::protein_interface_design::filters::BoltzmannFilter
• AnchorSugarScreener() : protocols::stepwise::screener::AnchorSugarScreener
• and_allow_insert() : protocols::toolbox::AllowInsert
• and_with() : protocols::match::Bool3DGrid , protocols::match::BumpGrid
• AndSelector() : protocols::pose_selectors::AndSelector
• ang_U1D2() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• ang_U1D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U2D1() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• ang_U2D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• angle() : protocols::loophash::BackboneDB , protocols::matdes::GetRBDOFValues , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::SetChiMover
• angle_conv() : protocols::stepwise::sampler::screener::RNA_TorsionScreener
• angle_diff() : protocols::make_rot_lib::MakeRotLibMover
• angle_disp() : protocols::backrub::BackrubSegment
• angle_magnitude() : protocols::rigid::RigidBodyDeterministicSpinMover
• angle_max() : protocols::simple_moves::BackboneMover
• angle_with_x_axis_proj_y() : protocols::simple_moves::symmetry::DetectSymmetry
• angle_with_y_axis_proj_x() : protocols::simple_moves::symmetry::DetectSymmetry
• angle_with_y_axis_proj_z() : protocols::simple_moves::symmetry::DetectSymmetry
• angle_with_z_axis_proj_y() : protocols::simple_moves::symmetry::DetectSymmetry
• AngleToVector() : protocols::simple_filters::AngleToVector
• animate() : protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• ANN() : protocols::sparta::ANN
• anneal_missing() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• annotate() : protocols::environment::claims::EnvClaim
• annotate_fold_tree() : protocols::environment::EnvClaimBroker
• annotated_sequence() : protocols::topology_broker::claims::SequenceClaim
• annotations() : protocols::environment::Environment , protocols::environment::ProtectedConformation
• Antibody() : protocols::antibody_legacy::Antibody
• antibody_modeling_insert_ter() : protocols::antibody_legacy::CDRH3Modeler
• AntibodyDatabaseManager() : protocols::antibody::AntibodyDatabaseManager
• AntibodyDesignModeler() : protocols::antibody::design::AntibodyDesignModeler
• AntibodyDesignMover() : protocols::antibody::design::AntibodyDesignMover
• AntibodyDesignMoverGenerator() : protocols::antibody::design::AntibodyDesignMoverGenerator
• AntibodyEnumManager() : protocols::antibody::AntibodyEnumManager
• AntibodyFeatures() : protocols::antibody::AntibodyFeatures
• AntibodyFeaturesCreator() : protocols::antibody::AntibodyFeaturesCreator
• AntibodyGraftDesignMover() : protocols::antibody::design::AntibodyGraftDesignMover
• AntibodyInfo() : protocols::antibody::AntibodyInfo
• AntibodyModeler() : protocols::antibody_legacy::AntibodyModeler
• AntibodyModelerProtocol() : protocols::antibody::AntibodyModelerProtocol
• AntibodyNumberingParser() : protocols::antibody::AntibodyNumberingParser
• AntibodySeqDesignMover() : protocols::antibody::design::AntibodySeqDesignMover
• AntibodySeqDesignTFCreator() : protocols::antibody::design::AntibodySeqDesignTFCreator
• antigen_present() : protocols::antibody::AntibodyInfo
• antiparallel() : protocols::abinitio::AlternativePairings
• any_node_finished() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• APCluster() : protocols::cluster::APCluster
• append() : protocols::simple_moves::LoadPDBMover
• append_Aform_residue() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• append_cached_scores() : protocols::qsar::scoring_grid::GridManager
• append_choices() : protocols::genetic_algorithm::PositionSpecificRandomizer
• append_combine_history() : protocols::simple_moves::CombinePoseMover
• append_downstream_atom_to_active_site_required_list() : protocols::match::MatcherTask
• append_fragment() : protocols::frags::SingleResidueTorsionFragmentLibrary
• append_ligand_docking_scores() : protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDockProtocol
• append_other_pose() : protocols::stepwise::monte_carlo::mover::AddMover
• append_polymer_residue_after_seqpos() : protocols::environment::ProtectedConformation
• append_residue() : protocols::stepwise::monte_carlo::mover::AddMover , protocols::toolbox::AllowInsert
• append_residue_by_jump() : protocols::environment::ProtectedConformation
• append_residues_cterminally() : protocols::seeded_abinitio::GrowPeptides
• append_residues_nterminally() : protocols::seeded_abinitio::GrowPeptides
• append_to_tag() : protocols::stepwise::screener::TagDefinition
• append_upstream_resiue_as_defining_active_site() : protocols::match::MatcherTask
• append_virtual_anchor() : protocols::farna::RNA_StructureParameters
• applicable() : protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::simple_filters::CamShiftEvaluator , protocols::simple_filters::ExternalEvaluator , protocols::simple_filters::PalesEvaluator , protocols::simple_filters::ScoreEvaluator , protocols::sparta::ChemicalShiftEvaluator
• apply() : protocols::abinitio::AbrelaxMover , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::DomainAssembly , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::MembraneAbinitio , protocols::abinitio::PcaEvaluator , protocols::abinitio::Protocol , protocols::abinitio::ResolutionSwitcher , protocols::abinitio::ShowViolation , protocols::abinitio::Stage1Sampler , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::analysis::PackStatMover , protocols::analysis::PeptideDeriverFilter , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::CloseOneCDRLoop , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover , protocols::antibody::design::ConservativeDesignOperation , protocols::antibody::design::ResidueProbDesignOperation , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop , protocols::antibody::RefineOneCDRLoopCentroid , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::CloseOneMover , protocols::antibody_legacy::GraftMover , protocols::antibody_legacy::GraftOneMover , protocols::antibody_legacy::LoopRlxMover , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PatchOperation , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrajectoryRecorder , protocols::cluster::AssignToClustersMover , protocols::cluster::GatherPosesMover , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::comparative_modeling::Align_RmsdEvaluator , protocols::comparative_modeling::Align_RotamerEvaluator , protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::PartialThreadingMover , protocols::comparative_modeling::RecoverSideChainsMover , protocols::comparative_modeling::StealLigandMover , protocols::comparative_modeling::StealSideChainsMover , protocols::comparative_modeling::ThreadingMover , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::contact_map::ContactMap , protocols::cryst::FitBfactorsMover , protocols::cryst::LoadDensityMapMover , protocols::cryst::RecomputeDensityMapMover , protocols::cryst::SetCrystWeightMover , protocols::cryst::SetRefinementOptionsMover , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::cryst::UpdateSolventMover , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideStubMover , protocols::ddg::ddGMover , 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::RestrictDesignToProteinDNAInterface , protocols::dna::SeparateDnaFromNonDna , protocols::dna::WatsonCrickRotamerCouplings , protocols::docking::ConformerSwitchMover , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingHighRes , protocols::docking::DockingHighResFilter , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingLowResFilter , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::DockingSlideIntoContact , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockMinMover , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::FaDockingSlideIntoContact , protocols::docking::InterfaceSidechainMinMover , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::SidechainMinMover , protocols::docking::stateless::SaneDockingProtocol , protocols::docking::TemperedDocking , protocols::domain_assembly::AddAssemblyConstraints , protocols::domain_assembly::AssembleLinkerMover , protocols::domain_assembly::CombineChainsMover , protocols::domain_assembly::PostDockAssemblyScorer , protocols::electron_density::BfactorFittingMover , protocols::electron_density::DensityMorphingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::SetupForDensityScoringMover , protocols::environment::claims::EnvLabelSelector , protocols::environment::CoMTrackerCM , protocols::environment::EnvMover , protocols::environment::ScriptCM , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::ApplyRandomStoredRBConf , protocols::enzdes::BackboneSampler , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::DiversifyStoredRBConfs , protocols::enzdes::EnzdesFixBBProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::EnzScoreFilter , protocols::enzdes::GenerateStoredRBConfs , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::ModifyStoredRBConfs , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::enzdes::SecondaryMatchProtocol , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::UpdateEnzdesHeaderMover , protocols::evaluation::AlignEvaluator , protocols::evaluation::MetaPoseEvaluator , protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::evaluation::TimeEvaluator , protocols::farna::MultipleDomainMover , protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_FragmentMover , protocols::farna::RNA_LoopCloser , protocols::farna::RNA_Minimizer , protocols::farna::RNA_Relaxer , protocols::features::ProteinSilentReport , protocols::features::Report , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , protocols::fibril::SetupForFibrilMover , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::FalseFilter , protocols::filters::Filter , protocols::filters::FilterCollection , 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::flexpack::FlexPacker , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::CombinedTaskOperation , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::FlxbbDesignPack , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelEnzdesCstModule , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelRotamerLinks , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::frags::TorsionFragmentMover , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::generalized_kinematic_closure::selector::GeneralizedKICselector , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , 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::helix_capper::HelixNCapperMover , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::ChunkTrialMover , protocols::hybridization::DomainAssembly , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetupMover , protocols::hybridization::InsertChunkMover , protocols::hybridization::MRMover , protocols::hybridization::TMalign , protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::jd2::parser::FragmentReader , protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::ClosureSolution , protocols::ligand_docking::AddHydrogen , 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::LigandBaseProtocol , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::LigandDockMain , protocols::ligand_docking::LigandDockProtocol , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MinimizeLigand , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::RandomConformerMover , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::RigidSearchMover , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::TetherLigand , protocols::ligand_docking::Transform , protocols::ligand_docking::Translate , protocols::ligand_docking::UnconstrainedTorsionsMover , protocols::ligand_docking::WriteLigandMolFile , protocols::loop_build::LoopBuildMover , protocols::loop_build::LoopmodelWrapper , protocols::loop_modeling::LoopMover , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::Mover_LoopHashRefine , protocols::LoopRebuild , protocols::LoopRefine , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::ShortLoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::KinematicWrapper , protocols::loops::loop_mover::IndependentLoopMover , protocols::loops::loop_mover::LoopCM , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , 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::loops::loops_definers::LoopsDatabaseDefiner , protocols::loops::loops_definers::LoopsDefiner , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsFileDefiner , protocols::make_rot_lib::MakeRotLibMover , protocols::match::MatcherMover , protocols::matdes::BuildingBlockInterfaceOperation , 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::md::MDBase , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , protocols::membrane::AddMembraneMover , protocols::membrane::FlipMover , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::RandomPositionRotationMover , protocols::membrane::RandomPositionTranslationMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::metal_interface::ZincHeterodimerMover , protocols::motif_grafting::movers::MotifGraftMover , protocols::motifs::MotifDnaPacker , protocols::moves::ChangeFoldTreeMover , protocols::moves::CompositionMover , protocols::moves::CycleMover , protocols::moves::CyclicMover , protocols::moves::DsspMover , protocols::moves::FilterMover , protocols::moves::FilterReporterMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::JumpOutMover , protocols::moves::MCShowMover , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::MoverContainer , protocols::moves::MoverForPoseList , protocols::moves::NullMover , protocols::moves::PDBDumpMover , protocols::moves::ProfilerMover , protocols::moves::PyMolMover , protocols::moves::RampingMover , protocols::moves::RandomMover , protocols::moves::RepeatMover , protocols::moves::SequenceMover , protocols::moves::StructureRestrictor , protocols::moves::TrialMover , protocols::moves::VectorPoseMover , protocols::moves::WhileMover , protocols::mpi_refinement::Clusterer , protocols::mpi_refinement::Serial_Refine , protocols::mpi_refinement::StructAvrgMover , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::noesy_assign::DistanceScoreMover , protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::CartesianNormalModeMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::TorsionNormalModeMover , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , 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::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::protein_interface_design::Revert , protocols::qsar::qsarMover , protocols::qsar::RenderGridsToKinemage , protocols::qsar::scoring_grid::GridInitMover , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::CCDMoveWrapper , protocols::rbsegment_relax::FragInsertAndAlignMover , protocols::rbsegment_relax::GaussianRBSegmentMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::rbsegment_relax::RBSegmentMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::rbsegment_relax::SequenceShiftMover , protocols::rbsegment_relax::StrandTwistingMover , protocols::RBSegmentRelaxImpl , protocols::relax::AtomCoordinateCstMover , protocols::relax::CentroidRelax , protocols::relax::ClassicRelax , protocols::relax::FastRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::MiniRelax , protocols::rigid::MembraneCenterPerturbationMover , protocols::rigid::MembraneNormalPerturbationMover , protocols::rigid::MovePoseToMembraneCenterMover , protocols::rigid::RigidBodyDeterministicSpinMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyDofSeqRandomizeMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyMotionMover , protocols::rigid::RigidBodyMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyPerturbRandomJumpMover , protocols::rigid::RigidBodyRandomizeMover , protocols::rigid::RigidBodySpinMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::RotateJumpAxisMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rigid::UniformSphereTransMover , protocols::rigid::WholeBodyRotationMover , protocols::rigid::WholeBodyTranslationMover , 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::RotamerDump::RotamerDumpMover , 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::BatchEvaluator , protocols::simple_filters::BatchNrEvaluator , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::COFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::ContactMapEvaluator , 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::EvaluatedTrialMover , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::ExternalEvaluator , 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::JScoreEvaluator , protocols::simple_filters::JumpEvaluator , protocols::simple_filters::JumpNrEvaluator , protocols::simple_filters::LoopRmsdEvaluator , 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::PoseMetricEvaluator< T > , protocols::simple_filters::PredictedBurialEvaluator , protocols::simple_filters::RangeFilter , protocols::simple_filters::RDC_Evaluator , 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::RmsdEvaluator , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreEvaluator , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::SelectRDC_Evaluator , protocols::simple_filters::SelectRmsdEvaluator , 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::StructuralSimilarityEvaluator , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::SymmetricRmsdEvaluator , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_filters::TruncatedScoreEvaluator , protocols::simple_moves::AddCavitiesMover , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AlignChainMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover , 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::chiral::ChiralMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::ClearConstraintsMover , protocols::simple_moves::CombinePoseMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::CopyDofMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::CyclizationMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DME_FilterMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::EnergyCutRotamerTrialsMinMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FavorSymmetricSequence , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::hbs::HbsPatcher , 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::O2M_MutateMover , protocols::simple_moves::oop::OopMover , protocols::simple_moves::oop::OopPatcher , protocols::simple_moves::oop::OopRandomPuckMover , protocols::simple_moves::oop::OopRandomSmallMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeptideStapleMover , protocols::simple_moves::ProlineFixMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RepeatPropagationMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RepulsiveOnlyMover , protocols::simple_moves::ResetBaselineMover , protocols::simple_moves::ResidueTypeConstraintMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::SaneMinMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetReturningPackRotamersMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::symmetry::DetectSymmetry , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , protocols::simple_moves::symmetry::SymDockingSlideIntoContact , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymmetricRMSMover , protocols::simple_moves::symmetry::SymmetrySlider , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TailsScoreMover , protocols::simple_moves::TaskAwareMinMover , protocols::simple_moves::TorsionDOFMover , protocols::simple_moves::TorsionSetMover , protocols::simple_moves::Tumble , protocols::simple_moves::UniformRotationMover , protocols::simple_moves::UniformTranslationMover , protocols::simple_moves::VirtualRootMover , protocols::sparta::ChemicalShiftEvaluator , protocols::star::StarAbinitio , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWisePoseAligner , protocols::stepwise::modeler::packer::SideChainCopier , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker , protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::modeler::rna::bulge::BulgeApplyMover , protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList , protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover , protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover , protocols::stepwise::monte_carlo::rna::RNA_TorsionMover , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::JumpStepWiseSampler , protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::NoOpStepWiseSampler , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler , protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::stepwise::setup::StepWiseCSA_JobDistributor , protocols::stepwise::setup::StepWiseJobDistributor , protocols::stepwise::setup::StepWiseMonteCarloJobDistributor , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::surface_docking::SurfaceOrientMover , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::symmetric_docking::SymDockBaseProtocol , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::symmetric_docking::SymSidechainMinMover , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::CrystalContactsOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::DsspDesignOperation , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InteractingRotamerExplosion , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::ModifyAnnealer , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::toolbox::task_operations::RestrictByCalculatorsOperation , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictToCDRH3Loop , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToLoops , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::toolbox::task_operations::RestrictToTerminiOperation , protocols::toolbox::task_operations::RetrieveStoredTaskOperation , protocols::toolbox::task_operations::SelectByDeltaScoreOperation , protocols::toolbox::task_operations::SelectByDensityFitOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::toolbox::task_operations::SetIGTypeOperation , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover , protocols::toolbox::task_operations::ThreadSequenceOperation , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::topology_broker::RigidBodyRandomTMHMover , protocols::topology_broker::TopologyBroker , protocols::ub_e2c::ubi_e2c_modeler , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover , protocols::vip::VIP_Mover
• apply_Aform_torsions_to_five_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• apply_Aform_torsions_to_three_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• apply_after_jump_change() : protocols::coarse_rna::CoarseRNA_LoopCloser
• apply_and_return_jump() : protocols::farna::MultipleDomainMover
• apply_at_all_positions() : protocols::simple_moves::FragmentMover
• apply_at_domain() : protocols::farna::MultipleDomainMover
• apply_atom_pair_distance() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• apply_body() : protocols::docking::DockingInitialPerturbation
• apply_bulge_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• apply_by_jump() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• apply_check() : protocols::motifs::Motif
• apply_chem_shift_data() : protocols::farna::RNA_DeNovoProtocol
• apply_const() : protocols::analysis::InterfaceAnalyzerMover
• apply_constraints() : protocols::hybridization::CartesianSampler
• apply_current_pose_segment() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• apply_cutpoint_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• apply_disulfides() : protocols::relax::RelaxProtocolBase
• apply_dof_conformer() : protocols::jumping::ResiduePairJump
• apply_dof_tasks_to_movemap() : protocols::simple_moves::MinMover
• apply_filter() : protocols::rosetta_scripts::ParsedProtocol , protocols::topology_broker::TopologyBroker
• apply_frag() : protocols::hybridization::CartesianHybridize
• apply_fragcsts() : protocols::hybridization::CartesianSampler
• apply_fragment() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::LoggedFragmentMover , protocols::simple_moves::SymmetricFragmentMover , protocols::simple_moves::WobbleMover
• apply_frame() : protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::seeded_abinitio::SegmentHybridizer
• apply_frames() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::ResTypeFragmentMover
• apply_full_to_sub_mapping() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• apply_helper() : protocols::toolbox::task_operations::RestrictToLoops
• apply_holes() : protocols::vip::VIP_Mover
• apply_if_reasonable() : protocols::kinematic_closure::ClosureSolution
• apply_internal_coordinates() : protocols::kinematic_closure::ClosureProblem
• apply_LH_A_foldtree() : protocols::antibody::design::AntibodyDesignModeler
• apply_linked_constraints() : protocols::simple_moves::MSDMover
• apply_loop_bump_check() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• apply_lowest_delta_torsion_selector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• apply_lowest_energy_selector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• apply_lowest_rmsd_selector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• apply_mover() : protocols::rosetta_scripts::ParsedProtocol , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::StepWiseScreener
• apply_mover_if_defined() : protocols::moves::CompositionMover
• apply_nucleoside_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_nucleoside_torsion_Aform() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_parsed_protocol() : protocols::jd2::MSDJobDistributor
• apply_peptide_plane_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• apply_peptide_plane_variants_OLD() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• apply_perturb_backbone_by_bins() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_perturb_dihedral_bbg() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_perturbations() : protocols::generalized_kinematic_closure::GeneralizedKIC
• apply_probability() : protocols::rosetta_scripts::ParsedProtocol
• apply_random() : protocols::loophash::LoopHashLibrary
• apply_random_fragment() : protocols::coarse_rna::CoarseRNA_Fragments , protocols::farna::FullAtomRNA_Fragments , protocols::farna::RNA_Fragments
• apply_random_nucleoside_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_random_selector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• apply_random_suite_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_randomize_alpha_backbone_by_rama() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_randomize_backbone_by_bins() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_ranked_fragment() : protocols::enzdes::EnzdesFlexibleRegion
• apply_residue() : protocols::ligand_docking::RandomConformers
• apply_rigid_body_moves() : protocols::ligand_docking::HighResDocker
• apply_rigid_body_only() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• apply_rotation_offset_to_pose_() : protocols::pockets::PlaidFingerprint
• apply_sample_cis_peptide_bond() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_set_bondangle() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_set_bondlength() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_set_dihedral() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_solutions() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• apply_suite_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_suite_torsion_Aform() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_terminus_variants_at_protein_rna_boundaries() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• apply_to() : protocols::jumping::JumpSample
• apply_to_cdr() : protocols::antibody::design::AntibodyGraftDesignMover
• apply_to_pose() : protocols::loophash::BackboneSegment
• apply_to_rotpack() : protocols::simple_moves::PackRotamersMoverLazy
• apply_transform() : protocols::hybridization::CartesianSampler
• apply_transformation() : protocols::simple_filters::RepeatParameterFilter
• apply_virtual_phosphate_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• apply_virtual_res_variant() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• applyANNTransformation() : protocols::sparta::ANN
• applyForces_BeeMan() : protocols::cartesian::MolecularDynamics
• applyForces_ConjugateGradient() : protocols::cartesian::MolecularDynamics
• applyForces_LangevinIntegration() : protocols::cartesian::MolecularDynamics
• ApplyRandomStoredRBConf() : protocols::enzdes::ApplyRandomStoredRBConf
• applyRotation() : protocols::rbsegment_relax::RBSegmentMover
• applySpin() : protocols::rbsegment_relax::RBSegmentMover
• applyTransformation() : protocols::rbsegment_relax::RBSegmentMover
• applyTranslation() : protocols::rbsegment_relax::RBSegmentMover
• applyVecAverage() : protocols::sparta::ANN
• applyVecNormalization() : protocols::sparta::ANN
• approved() : protocols::topology_broker::claims::DofClaim
• aquireNextQueue() : protocols::viewer::triangleIterator
• arccos_() : protocols::sparta::PDB
• archive_rank() : protocols::jd2::archive::MPIArchiveJobDistributor
• ArchiveBase() : protocols::jd2::archive::ArchiveBase
• ArchiveManager() : protocols::jd2::archive::ArchiveManager
• are_colliding() : protocols::match::downstream::DownstreamAlgorithm
• aromatic_motifs() : protocols::motifs::MotifDnaPacker
• array_to_farray() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• assemble_enzdes_fragdata() : protocols::enzdes::EnzdesFlexibleRegion
• assemble_next_best_loop_combination() : protocols::enzdes::EnzdesFlexBBProtocol
• assemble_outtag() : protocols::match::output::PDBWriter
• assemble_remark_lines() : protocols::match::output::PDBWriter
• AssembleLinkerMover() : protocols::domain_assembly::AssembleLinkerMover
• assert_calculators() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• assign() : protocols::analysis::PeptideDeriverFilter , protocols::moves::FilterReporterMover , protocols::noesy_assign::NoesyModule , protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster , protocols::toolbox::KMedoid
• assign_conformer_group_to_residue() : protocols::match::downstream::LigandConformerBuilder
• assign_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• assign_downstream_position_group_for_match() : protocols::match::output::SameSequenceAndDSPositionGrouper
• assign_entity_sequence_to_variables() : protocols::pack_daemon::EntityFunc
• assign_esp_for_atom_grid_points() : protocols::pockets::ElectrostaticpotentialGrid
• assign_esp_for_protein_grid_points() : protocols::pockets::ElectrostaticpotentialGrid
• assign_esp_for_surface_grid_points() : protocols::pockets::ElectrostaticpotentialGrid
• assign_esp_for_surface_grid_points_by_nn() : protocols::pockets::ElectrostaticpotentialGrid
• assign_exemplars() : protocols::cluster::APCluster
• assign_group_for_match() : protocols::match::output::MatchGrouper , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::SameSequenceGrouper
• assign_jobs_to_local_daemon_set() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• assign_jobs_to_remote_daemon_sets() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• assign_labelled_spin() : protocols::noesy_assign::CrossPeak3D
• assign_last_rotamers_to_pose() : protocols::pack_daemon::PackDaemon
• assign_loop_info() : protocols::mpi_refinement::MPI_Refine_Master
• assign_non_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• assign_passport() : protocols::environment::Environment
• assign_passports() : protocols::environment::EnvClaimBroker
• assign_spin() : protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak
• assign_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• assign_state_energies_to_variables_and_subexpressions() : protocols::pack_daemon::DynamicAggregateFunction
• assign_tag() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• assign_type_data() : protocols::toolbox::KClusterElement
• assign_zero_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• assigned() : protocols::noesy_assign::CrossPeak
• assignment() : protocols::noesy_assign::CrossPeak::Spin
• assignment_index() : protocols::noesy_assign::CrossPeak::Spin
• assignments() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakAssignmentResidueMap
• AssignToClustersMover() : protocols::cluster::AssignToClustersMover
• AsymFoldandDockClaimer() : protocols::topology_broker::AsymFoldandDockClaimer
• AsymFoldandDockMoveRbJumpMover() : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
• AsymFoldandDockRbTrialMover() : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover
• AsyncMPITemperingBase() : protocols::canonical_sampling::AsyncMPITemperingBase
• at() : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::scores::FragmentScoreMap , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider
• at_end() : protocols::match::VoxelSetIterator
• at_inds() : protocols::match::downstream::AtomGeometrySecMatchRPE
• atm1() : protocols::simple_filters::AngleToVector
• atm2() : protocols::simple_filters::AngleToVector
• atom() : protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::noesy_assign::EXCN_UnknownResonance , protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::Resonance , protocols::pockets::PocketConstraint
• atom1_atom2_atom3_angle() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atom1_atom2_distance() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atom1_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom1_radius() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom2_atom3_distance() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atom2_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom2_radius() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom3_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom3_radius() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom_controlled_by_any_chi() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_coordinate_unacceptable() : protocols::match::upstream::ProteinUpstreamBuilder
• atom_geom_rpes() : protocols::match::downstream::GeometrySecMatchRPE
• atom_has_nonchi_coordinate() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_inds_for_restype() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_inds_for_restype_begin() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_inds_for_restype_end() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_is_chitip() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_is_ideal() : protocols::simple_moves::MinimalRotamer
• atom_name() : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• atom_name1() : protocols::farna::RNA_PairingTemplate
• atom_name2() : protocols::farna::RNA_PairingTemplate
• atom_pair_constraint_weight() : protocols::idealize::IdealizeMover
• atom_radius() : protocols::match::upstream::BuildSet
• atom_score() : protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid
• atom_type() : protocols::noesy_assign::PeakCalibrator
• AtomAngleSecMatchRPE() : protocols::match::downstream::AtomAngleSecMatchRPE
• AtomAtomPairFeatures() : protocols::features::AtomAtomPairFeatures
• AtomAtomPairFeaturesCreator() : protocols::features::AtomAtomPairFeaturesCreator
• AtomBasedConstraintsScore() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• AtomCoordinateCstMover() : protocols::relax::AtomCoordinateCstMover
• AtomCountFilter() : protocols::ligand_docking::AtomCountFilter
• AtomDihedralSecMatchRPE() : protocols::match::downstream::AtomDihedralSecMatchRPE
• AtomDistanceSecMatchRPE() : protocols::match::downstream::AtomDistanceSecMatchRPE
• AtomGeometrySecMatchRPE() : protocols::match::downstream::AtomGeometrySecMatchRPE
• atomic_interaction_cutoff() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::InterchainPairEnergy
• AtomicContactCountFilter() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• AtomicContactFilter() : protocols::simple_filters::AtomicContactFilter
• AtomicDistanceFilter() : protocols::simple_filters::AtomicDistanceFilter
• AtomInResidueAtomInResiduePairFeatures() : protocols::features::AtomInResidueAtomInResiduePairFeatures
• AtomInResidueAtomInResiduePairFeaturesCreator() : protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator
• atomname() : protocols::contact_map::ContactPartner
• AtomPack() : protocols::abinitio::abscript::AtomPack
• AtomPairConstraintsData() : protocols::frag_picker::scores::AtomPairConstraintsData
• AtomPairConstraintsScore() : protocols::frag_picker::scores::AtomPairConstraintsScore
• AtomPairData() : protocols::ligand_docking::rdf::AtomPairData
• atoms() : protocols::environment::claims::JumpClaim
• atoms_are_equiv() : protocols::comparative_modeling::ThreadingMover
• AtomTreeDiffJobDistributor() : protocols::jobdist::AtomTreeDiffJobDistributor
• AtomTreeDiffJobInputter() : protocols::jd2::AtomTreeDiffJobInputter
• AtomTreeDiffJobOutputter() : protocols::jd2::AtomTreeDiffJobOutputter
• AtomTypesFeatures() : protocols::features::AtomTypesFeatures
• AtomTypesFeaturesCreator() : protocols::features::AtomTypesFeaturesCreator
• atr_rep_screen() : protocols::stepwise::options::StepWiseBasicOptions
• AtrGrid() : protocols::qsar::scoring_grid::AtrGrid
• attach() : protocols::moves::PyMolObserver
• attach_annotation() : protocols::environment::ProtectedConformation
• attach_impl() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• attach_observer_to_last_accepted_conformation() : protocols::moves::MonteCarlo
• attach_observer_to_last_accepted_pose() : protocols::moves::MonteCarlo
• attach_observer_to_lowest_score_conformation() : protocols::moves::MonteCarlo
• attach_observer_to_lowest_score_pose() : protocols::moves::MonteCarlo
• attach_secondary_structure_pools() : protocols::frag_picker::quota::QuotaCollector
• attach_to() : protocols::boinc::BoincCurrentPoseObserver , protocols::forge::build::BuildInstruction , protocols::viewer::ConformationViewer , protocols::viewer::SilentObserver
• attached_res() : protocols::stepwise::monte_carlo::Attachment , protocols::stepwise::monte_carlo::SWA_Move
• Attachment() : protocols::stepwise::monte_carlo::Attachment
• attachment_type() : protocols::stepwise::monte_carlo::Attachment , protocols::stepwise::monte_carlo::SWA_Move
• attachments() : protocols::stepwise::monte_carlo::SWA_Move
• attempt_ccd() : protocols::abinitio::abscript::AbscriptLoopCloserCM
• attempt_idealize() : protocols::abinitio::abscript::AbscriptLoopCloserCM
• attempt_loop_move() : protocols::loop_modeling::LoopProtocol
• auction_results() : protocols::protein_interface_design::movers::PlacementAuctionMover
• auto_choose_cutpoint() : protocols::loops::Loop
• auto_choose_cutpoints() : protocols::loops::Loops
• auto_cut() : protocols::environment::Environment
• auto_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• AutoCutData() : protocols::environment::AutoCutData
• autoexpanding_pocket_eval() : protocols::pockets::PocketGrid
• autofill() : protocols::hotspot_hashing::HotspotStubSet
• autogenerate_constseq_frags() : protocols::anchored_design::AnchorMoversData
• autogenerate_design_frags() : protocols::anchored_design::AnchorMoversData
• autogenerate_frags() : protocols::anchored_design::AnchorMoversData
• automatic_distance_cutoff() : protocols::protein_interface_design::movers::AddChainBreak
• AutoRBMover() : protocols::rbsegment_relax::AutoRBMover
• autotemp_accept() : protocols::moves::MonteCarlo
• autotemp_reject() : protocols::moves::MonteCarlo
• average() : protocols::ddg::ddGMover
• average_change_in_rama_score_over_range() : protocols::loops::loop_closure::ccd::RamaCheckBase
• average_dist() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• average_dist6() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• average_score_components() : protocols::ddg::ddGMover
• average_shortest_path_length() : protocols::toolbox::ResidueNetwork
• AverageDegreeFilter() : protocols::protein_interface_design::filters::AverageDegreeFilter
• AveragePathLengthFilter() : protocols::simple_filters::AveragePathLengthFilter
• axis() : protocols::matdes::GetRBDOFValues