- g -

• gamma() : protocols::dna::DNABase , protocols::stepwise::sampler::rigid_body::EulerAngles
• gap_distance() : protocols::hybridization::FoldTreeHybridize
• gap_size() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• gap_size_to_anchor() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• garbage_collection() : protocols::jd2::MpiFileBuffer
• GatherPosesMover() : protocols::cluster::GatherPosesMover
• gaussian_translate_ligand() : protocols::ligand_docking::Translate
• GaussianRBSegmentMover() : protocols::rbsegment_relax::GaussianRBSegmentMover
• GDB() : protocols::sparta::GDB
• gdt_by_TM() : protocols::comparative_modeling::Align_RmsdEvaluator
• gen_cen2fullatom() : protocols::abinitio::IterativeBase
• gen_cen2fullatom_non_pool_decoys() : protocols::abinitio::IterativeBase
• gen_coord_constraint() : protocols::normalmode::CartesianNormalModeMover , protocols::normalmode::NormalModeRelaxMover , protocols::normalmode::TorsionNormalModeMover
• gen_diversity_pool() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid
• gen_dynamic_patches() : protocols::abinitio::IterativeBase
• gen_enumerate_pairings() : protocols::abinitio::IterativeBase
• gen_evaluation_output() : protocols::abinitio::IterativeBase
• gen_noe_assignments() : protocols::abinitio::IterativeBase
• gen_resample_core() : protocols::abinitio::IterativeFullatom
• gen_resample_fragments() : protocols::abinitio::IterativeBase
• gen_resample_stage2() : protocols::abinitio::IterativeBase
• gen_resample_topologies() : protocols::abinitio::IterativeBase
• gen_start_structures() : protocols::abinitio::IterativeBase
• generalEvent() : protocols::moves::PyMolObserver
• GeneralizedKIC() : protocols::generalized_kinematic_closure::GeneralizedKIC
• GeneralizedKICfilter() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• GeneralizedKICperturber() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• GeneralizedKICselector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• generate_active_pose_constraints() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• generate_alc_ensemble_for_region() : protocols::enzdes::EnzdesFlexBBProtocol
• generate_and_dump_pose_found_residues_combinations() : protocols::enzdes::SecondaryMatchProtocol
• generate_atomlist() : protocols::generalized_kinematic_closure::GeneralizedKIC
• generate_backrub_ensemble_for_region() : protocols::enzdes::EnzdesFlexBBProtocol
• generate_batch() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::VarianceStatisticsArchive
• generate_bridgeobjects_data_from_atomlist() : protocols::generalized_kinematic_closure::GeneralizedKIC
• generate_claims() : protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• generate_combinations_of_motif_fragments_by_delta_variation() : protocols::motif_grafting::movers::MotifGraftMover
• generate_constraint_files() : protocols::noesy_assign::NoesyModule
• generate_constraints() : protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase , protocols::topology_broker::CoordConstraintClaimer
• generate_csts() : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• generate_dock_high_res() : protocols::antibody::design::AntibodyDesignMoverGenerator
• generate_dock_low_res() : protocols::antibody::design::AntibodyDesignMoverGenerator
• generate_edges() : protocols::toolbox::CovalentResidueNetwork , protocols::toolbox::DistanceResidueNetwork , protocols::toolbox::ResidueNetwork
• generate_ensemble_for_region() : protocols::enzdes::EnzdesFlexBBProtocol
• generate_explicit_ligand_rotamer_poses() : protocols::enzdes::EnzdesBaseProtocol
• generate_extended_pose() : protocols::abinitio::AbrelaxApplication
• generate_fa_and_cen_constraints() : protocols::noesy_assign::CrossPeakList
• generate_factory() : protocols::metal_interface::ZincHeterodimerMover
• generate_final_claims() : protocols::topology_broker::TopologyBroker
• generate_frame() : protocols::jumping::ResiduePairJump
• generate_from_frag_file() : protocols::noesy_assign::FragsToAtomDist
• generate_from_fragments() : protocols::noesy_assign::FragsToAtomDist
• generate_hits() : protocols::match::Matcher
• generate_hits_for_constraint() : protocols::match::Matcher
• generate_init_frags() : protocols::topology_broker::StartStructClaimer
• generate_inverse_rotamer_constraints() : protocols::toolbox::match_enzdes_util::InvrotTree
• generate_jump_frags() : protocols::abinitio::TemplateJumpSetup , protocols::jumping::BaseJumpSetup , protocols::jumping::BasePairingLibrary , protocols::jumping::DisulfPairingLibrary , protocols::jumping::JumpSample , protocols::jumping::PairingLibrary , protocols::jumping::ResiduePairJumpSetup , protocols::topology_broker::DisulfJumpClaimer
• generate_jump_frames() : protocols::jumping::JumpSample
• generate_match_pose() : protocols::motif_grafting::movers::MotifGraftMover
• generate_minimizer() : protocols::antibody::design::AntibodyDesignMoverGenerator
• generate_mover_for_protocol() : protocols::rosetta_scripts::RosettaScriptsParser
• generate_mover_from_job() : protocols::jd2::Parser
• generate_mover_from_pose() : protocols::jd2::Parser , protocols::rosetta_scripts::RosettaScriptsParser
• generate_ncs_csts() : protocols::forge::remodel::RemodelLoopMover
• generate_new_channel() : protocols::jd2::DebugOut_MpiFileBuffer , protocols::jd2::MpiFileBuffer , protocols::jd2::WriteOut_MpiFileBuffer
• generate_pose() : protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover
• generate_pose_specific_data() : protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• generate_pose_specific_data_for_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• generate_protocol_mover() : protocols::antibody::design::AntibodyDesignMoverGenerator
• generate_random() : protocols::simple_moves::GenericMonteCarloMover
• generate_random_tree_from_jumps() : protocols::jumping::JumpSample
• generate_relax() : protocols::antibody::design::AntibodyDesignMoverGenerator
• generate_remodel_constraints() : protocols::fldsgn::SheetConstraintsRCG , protocols::forge::constraints::ConstraintFileRCG , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoC_RCG , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::ResidueVicinityRCG
• generate_remodel_constraints_for_respair() : protocols::forge::remodel::ResidueVicinityRCG
• generate_repack_antigen_ab_interface() : protocols::antibody::design::AntibodyDesignMoverGenerator
• generate_repack_cdrs() : protocols::antibody::design::AntibodyDesignMoverGenerator
• generate_representative_target_res_for_geom_cst() : protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget
• generate_residues_to_sample() : protocols::forge::remodel::RemodelLoopMover
• generate_rigidity_jumps() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• generate_round1() : protocols::topology_broker::TopologyBroker
• generate_scaffold_matches() : protocols::motif_grafting::movers::MotifGraftMover
• generate_scorefunctions() : protocols::metal_interface::ZincHeterodimerMover
• generate_scorefxn() : protocols::abinitio::AbrelaxApplication , protocols::features::strand_assembly::SandwichFeatures
• generate_search_points() : protocols::hotspot_hashing::CartesianSearchPattern , protocols::hotspot_hashing::RotationSearchPattern , protocols::hotspot_hashing::SphericalRotationSearchPattern
• generate_sequence_claims() : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• generate_ss_strings_from_blueprint() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• generate_symmetry_claims() : protocols::topology_broker::SymmetryClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• generate_targets_and_inverse_rotamers() : protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::TheozymeInvrotTree
• generate_task_op_all_cdr_design() : protocols::antibody::design::AntibodySeqDesignTFCreator
• generate_task_op_cdr_conservative() : protocols::antibody::design::AntibodySeqDesignTFCreator
• generate_task_op_cdr_design() : protocols::antibody::design::AntibodySeqDesignTFCreator
• generate_task_op_cdr_profile() : protocols::antibody::design::AntibodySeqDesignTFCreator
• generate_temp_range() : protocols::canonical_sampling::TemperingBase
• generate_tf_seq_design() : protocols::antibody::design::AntibodySeqDesignTFCreator
• generate_tf_seq_design_graft_design() : protocols::antibody::design::AntibodySeqDesignTFCreator
• generate_tree_from_jumps_and_cuts() : protocols::jumping::JumpSample
• generate_unbound_pose_() : protocols::hotspot_hashing::HotspotStubSet
• generate_window_list() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• GenerateMap() : protocols::protein_interface_design::movers::MapHotspot
• GenerateProbTable() : protocols::docking::ConformerSwitchMover
• generateRankedAlignments() : protocols::comparative_modeling::AlignmentClustering
• generates_primary_hits() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::output::WriteUpstreamCoordinateKinemage
• GenerateStoredRBConfs() : protocols::enzdes::GenerateStoredRBConfs
• generations() : protocols::genetic_algorithm::GeneticAlgorithmBase
• generations_checkpoint_filename() : protocols::genetic_algorithm::GeneticAlgorithmBase
• generic_taskfactory() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• GenericJobInputter() : protocols::comparative_modeling::GenericJobInputter
• GenericMonteCarloMover() : protocols::simple_moves::GenericMonteCarloMover
• GeneticAlgorithm() : protocols::genetic_algorithm::GeneticAlgorithm
• GeneticAlgorithmBase() : protocols::genetic_algorithm::GeneticAlgorithmBase
• geom_cst_id() : protocols::match::downstream::DownstreamAlgorithm
• geom_csts_downstream_output() : protocols::match::MatcherTask
• geom_id() : protocols::match::output::WriteUpstreamHitKinemage
• GeometricFunc() : protocols::moves::GeometricFunc
• GeometricSolvationFeatures() : protocols::features::GeometricSolvationFeatures
• GeometricSolvationFeaturesCreator() : protocols::features::GeometricSolvationFeaturesCreator
• geometry_is_initialized() : protocols::fldsgn::topology::HSSTriplet
• GeometryFilter() : protocols::simple_filters::GeometryFilter
• GeometrySecMatchRPE() : protocols::match::downstream::GeometrySecMatchRPE
• GeomSampleInfo() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• get() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::hybridization::TemplateHistory , protocols::jobdist::BasicJob , protocols::neighbor::Neighborhood , protocols::toolbox::AllowInsert , protocols::toolbox::pose_metric_calculators::MetricValueGetter
• get_10A_neighbors() : protocols::enzdes::EnzdesFlexibleRegion
• get_a() : protocols::pockets::UnionEdge
• get_A() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• get_A_all() : protocols::scoring::methods::pcs2::PcsDataCenter
• get_a_axis() : protocols::docking::EllipsoidalRandomizationMover
• get_A_index() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• get_ABGEO_string() : protocols::canonical_sampling::CanonicalSamplingMover
• get_abort_on_failed_loop() : protocols::LoopRebuild
• get_accept_aborted_loops() : protocols::loops::loop_mover::IndependentLoopMover
• get_accessible_states() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_act_alignment_res() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• get_act_calc_rms_res() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• get_act_full_to_sub() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• get_act_is_prepend_map() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• get_add_or_delete_element() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_additional_output() : protocols::loophash::LoopHashMoverWrapper , protocols::motif_grafting::movers::MotifGraftMover , protocols::moves::IfMover , protocols::moves::Mover , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol
• get_additional_output_false_mover() : protocols::moves::IfMover
• get_additional_output_true_mover() : protocols::moves::IfMover
• get_additional_task_operarations() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• get_addresses_at_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• get_adjacent_flexbb_node() : protocols::flexpack::interaction_graph::FlexbbNode
• get_adjacent_minimalistflexbb_node() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_adjacent_otfflexbb_node() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• get_ads_secondary_struct() : protocols::surface_docking::FullatomRelaxMover
• get_akash_dyepos() : protocols::anchored_design::AnchorMoversData
• get_align_depth() : protocols::farna::FragmentLibrary
• get_alignment() : protocols::evaluation::AlignEvaluator
• get_alignment_from_chunk_mapping() : protocols::hybridization::ChunkTrialMover
• get_alignment_from_template() : protocols::hybridization::ChunkTrialMover
• get_all() : protocols::loophash::LoopHashLibrary
• get_all_data() : protocols::analysis::InterfaceAnalyzerMover
• get_all_exemplars() : protocols::cluster::APCluster
• get_all_features_names() : protocols::features::FeaturesReporterFactory
• get_all_function_names() : protocols::ligand_docking::rdf::RDFFunctionFactory
• get_all_loops_closed() : protocols::loops::loop_mover::IndependentLoopMover
• get_all_loops_definer_names() : protocols::loops::loops_definers::LoopsDefinerFactory
• get_all_per_residue_data() : protocols::analysis::InterfaceAnalyzerMover
• get_all_pose_chains() : protocols::features::InterfaceFeatures
• get_all_res_list() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• get_all_solutions() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• get_all_states() : protocols::flexpack::interaction_graph::FlexbbNode
• get_all_string_combos() : protocols::features::InterfaceFeatures
• get_AllCDRs_in_loopsop() : protocols::antibody::AntibodyInfo
• get_allow_anchor_repack() : protocols::anchored_design::AnchorMoversData
• get_allow_independent_alignment_per_fragment_mode() : protocols::motif_grafting::movers::MotifMatch
• get_allow_insert() : protocols::simple_moves::ConstrainToIdealMover
• get_allow_slide_jump_map() : protocols::simple_moves::symmetry::SymmetrySlider
• get_allowed_failure_before_extend() : protocols::LoopRebuild
• get_allowed_failure_before_stop() : protocols::LoopRebuild
• get_aln() : protocols::comparative_modeling::AlignmentCluster
• get_alt_stateE() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• get_altE_for_bb_move() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_anchor_noise_constraints_mode() : protocols::anchored_design::AnchorMoversData
• get_anchor_via_constraints() : protocols::anchored_design::AnchorMoversData
• get_anchors() : protocols::hybridization::HybridizeFoldtreeDynamic , protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• get_angle_diffs() : protocols::matdes::SymDofMoverSampler
• get_angle_max() : protocols::simple_moves::BackboneMover
• get_angle_range() : protocols::simple_moves::TorsionDOFMover
• get_angles() : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• get_ANN_data() : protocols::sparta::Sparta::SpartaLib
• get_annealer_pick_table() : protocols::RotamerDump::RotamerDumpMover
• get_antibody_chain_ids() : protocols::antibody::AntibodyInfo
• get_antibody_chain_string() : protocols::antibody::AntibodyInfo
• get_antibody_chains() : protocols::antibody::AntibodyInfo
• get_antibody_enum_manager() : protocols::antibody::AntibodyInfo
• get_antibody_numbering() : protocols::antibody::AntibodyNumberingParser
• get_antibody_sequence() : protocols::antibody::AntibodyInfo
• get_AntibodyFrameworkInfo() : protocols::antibody::AntibodyInfo
• get_antigen_chain_ids() : protocols::antibody::AntibodyInfo
• get_antigen_chain_string() : protocols::antibody::AntibodyInfo
• get_antigen_chains() : protocols::antibody::AntibodyInfo
• get_antiparallel_beta_jumps() : protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler
• get_atom_bin() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• get_atom_coordinates() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• get_atom_dist_from_connolly_surface() : protocols::pockets::ElectrostaticpotentialGrid
• get_atom_id_map() : protocols::farna::ChunkSet
• get_atom_name() : protocols::scoring::methods::pcs2::PcsInputLine
• get_atom_pos() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• get_atom_type() : protocols::frag_picker::scores::AtomBasedConstraintsScore , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::InterbondAngleScore
• get_atomID() : protocols::normalmode::NormalMode
• get_attachments() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_autoinitialize() : protocols::anchored_design::AnchoredDesignMover
• get_average_structure() : protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Serial_Refine
• get_avg_dis_CA_CA() : protocols::features::strand_assembly::StrandBundleFeatures
• get_b() : protocols::pockets::UnionEdge
• get_b_axis() : protocols::docking::EllipsoidalRandomizationMover
• get_backbone_currently_assigned() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_backbone_for_current_state() : protocols::flexpack::interaction_graph::FlexbbNode
• get_backbone_list() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_backbone_segment() : protocols::loophash::BackboneDB
• get_backrubmover() : protocols::simple_moves::ShortBackrubMover
• get_base_atr_rep_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• get_base_pair_steps() : protocols::farna::RNA_StructureParameters
• get_batch_description() : protocols::features::ReportToDB
• get_batch_id() : protocols::features::ProteinSilentReport
• get_batch_name() : protocols::features::ReportToDB
• get_bb() : protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex , protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData
• get_bb_alignment_and_transformation() : protocols::motif_grafting::movers::MotifGraftMover
• get_bb_alignment_and_transformation_wTipsExtraInfo() : protocols::motif_grafting::movers::MotifGraftMover
• get_bb_atoms_for_residue() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_bb_distance() : protocols::motif_grafting::movers::MotifGraftMover
• get_bb_for_state() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode
• get_bb_id() : protocols::make_rot_lib::RotData
• get_bb_ids() : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibOptionsData
• get_bb_interface_builder() : protocols::ligand_docking::MoveMapBuilder
• get_bb_range() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_bbs() : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData
• get_best_energy_stub() : protocols::hotspot_hashing::HotspotStubSet
• get_best_neighboring_shift_RMSD_and_output_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• get_bestpose() : protocols::flxbb::FilterStructs
• get_bias_sampling() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_big_bin() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_bin_and_pos() : protocols::match::VoxelSetIterator
• get_boinc_wu_cpu_time() : protocols::boinc::Boinc
• get_boltzmann_rotamer_mover() : protocols::simple_moves::CoupledMover
• get_boltzmann_temp() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• get_build_all_loops() : protocols::loops::loop_mover::IndependentLoopMover
• get_build_attempts() : protocols::loops::loop_mover::IndependentLoopMover
• get_build_ideal_geometry() : protocols::generalized_kinematic_closure::GeneralizedKIC
• get_builder() : protocols::nonlocal::TreeBuilderFactory
• get_bump_check() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_bump_overlap_factor() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_bumpcheck_atom_count_for_residue() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_bumpcheck_atoms_for_residue() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_C4_C3_distance_range() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• get_c_alpha_centroid() : protocols::docking::EllipsoidalRandomizationMover
• get_c_alpha_non_ellipsoid_centroid() : protocols::docking::EllipsoidalRandomizationMover
• get_c_axis() : protocols::docking::EllipsoidalRandomizationMover
• get_ca_bfactors() : protocols::match::BfactorMPM
• get_cacheable_cluster_data() : protocols::antibody::clusters::CDRClusterSet
• get_cached_scores() : protocols::qsar::scoring_grid::GridManager
• get_calc_rms_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_calculator() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• get_calculator_name() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• get_candidate_i() : protocols::frag_picker::nonlocal::NonlocalPair
• get_candidate_i_rank() : protocols::frag_picker::nonlocal::NonlocalPair
• get_candidate_j() : protocols::frag_picker::nonlocal::NonlocalPair
• get_candidate_j_rank() : protocols::frag_picker::nonlocal::NonlocalPair
• get_candidates() : 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
• get_candidates_collector() : protocols::frag_picker::FragmentPicker
• get_cartesian() : protocols::mpi_refinement::WorkUnit_CombinePose , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin
• get_cav_approx() : protocols::vip::VIP_Mover
• get_cavities() : protocols::simple_moves::AddCavitiesMover
• get_cavity_positions() : protocols::vip::VIP_Mover
• get_ccd_closure_exist() : protocols::LoopRebuild
• get_CDR_chain() : protocols::antibody::AntibodyInfo
• get_CDR_cluster() : protocols::antibody::AntibodyInfo
• get_cdr_cluster() : protocols::antibody::clusters::CDRClusterMatcher
• get_cdr_cluster_enum_manager() : protocols::antibody::AntibodyInfo
• get_CDR_cluster_set() : protocols::antibody::AntibodyInfo
• get_cdr_definition_transform() : protocols::antibody::AntibodyInfo
• get_cdr_design_options() : protocols::antibody::design::AntibodySeqDesignTFCreator
• get_CDR_end() : protocols::antibody::AntibodyInfo
• get_CDR_end_PDB_num() : protocols::antibody::AntibodyInfo
• get_cdr_enum_for_cluster() : protocols::antibody::AntibodyInfo
• get_CDR_in_loopsop() : protocols::antibody::AntibodyInfo
• get_CDR_length() : protocols::antibody::AntibodyInfo
• get_CDR_loop() : protocols::antibody::AntibodyInfo
• get_cdr_loop_with_overhang() : protocols::antibody::design::AntibodyDesignModeler
• get_CDR_loops() : protocols::antibody::AntibodyInfo
• get_cdr_loops() : protocols::antibody::design::AntibodyDesignModeler
• get_cdr_loops_with_overhang() : protocols::antibody::design::AntibodyDesignModeler
• get_CDR_name() : protocols::antibody::AntibodyInfo
• get_CDR_name_enum() : protocols::antibody::AntibodyInfo
• get_CDR_sequence_with_stem() : protocols::antibody::AntibodyInfo
• get_cdr_set_index_list() : protocols::antibody::design::AntibodyGraftDesignMover
• get_CDR_start() : protocols::antibody::AntibodyInfo
• get_CDR_start_PDB_num() : protocols::antibody::AntibodyInfo
• get_cdrs_movemap_with_overhang() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• get_cen_dist() : protocols::make_rot_lib::RotData
• get_center() : protocols::pockets::SmallMol , protocols::qsar::scoring_grid::SingleGrid
• get_center_ndx() : protocols::toolbox::KClusterElement
• get_central_residues() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• get_centroid() : protocols::farna::MultipleDomainMover , protocols::mpi_refinement::WorkUnit_bbGauss
• get_centroid_data() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_centroid_dG() : protocols::analysis::InterfaceAnalyzerMover
• get_centroid_scorefunction() : protocols::anchored_design::AnchorMoversData
• get_centroid_scorefunction_min() : protocols::anchored_design::AnchorMoversData
• get_chain() : protocols::qsar::scoring_grid::SingleGrid
• get_chain_break_tolerance() : protocols::LoopRebuild
• get_chain_groups() : protocols::analysis::InterfaceAnalyzerMover
• get_chain_id() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::VallChunk , protocols::ligand_docking::Translate
• get_chain_indices() : protocols::analysis::PeptideDeriverFilter
• get_chainbreak_scores() : protocols::analysis::LoopAnalyzerMover
• get_chainbreak_weight() : protocols::anchored_design::AnchorMoversData
• get_chainbreak_xyz() : protocols::farna::RNA_LoopCloser
• get_cheating_frags() : protocols::frags::VallData
• get_checkpoint_recoveries() : protocols::checkpoint::CheckPointer
• get_checkpoints() : protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicTaskControl , protocols::abinitio::Protocol , protocols::canonical_sampling::MetropolisHastingsMover , protocols::loops::loop_mover::LoopMover , protocols::relax::ClassicRelax
• get_chi_data() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_chi_xx() : protocols::scoring::methods::pcs2::PcsTensor
• get_chi_xy() : protocols::scoring::methods::pcs2::PcsTensor
• get_chi_xz() : protocols::scoring::methods::pcs2::PcsTensor
• get_chi_yy() : protocols::scoring::methods::pcs2::PcsTensor
• get_chi_yz() : protocols::scoring::methods::pcs2::PcsTensor
• get_chi_zz() : protocols::scoring::methods::pcs2::PcsTensor
• get_children() : protocols::loop_modeling::LoopMover
• get_children_names() : protocols::kinematic_closure::KicMover , protocols::loop_modeling::LoopMover , protocols::loop_modeling::utilities::LoopMoverGroup
• get_chunk() : protocols::frag_picker::FragmentCandidate
• get_clash_checking() : protocols::match::downstream::TargetRotamerCoords
• get_clash_score() : protocols::motif_grafting::movers::MotifMatch
• get_clash_score_from_pose() : protocols::motif_grafting::movers::MotifGraftMover
• get_closest_cluster() : protocols::antibody::clusters::CDRClusterMatcher
• get_closest_heavy_atom() : protocols::simple_moves::AddCavitiesMover
• get_closure_attempts() : protocols::generalized_kinematic_closure::GeneralizedKIC
• get_closure_solution() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• get_cluster() : protocols::antibody::clusters::BasicCDRClusterSet , protocols::antibody::clusters::CDRClusterSet
• get_cluster_center() : protocols::cluster::Cluster
• get_cluster_data() : protocols::antibody::clusters::CDRClusterSet
• get_cluster_enum() : protocols::antibody::AntibodyInfo
• get_cluster_for() : protocols::cluster::APCluster
• get_cluster_length() : protocols::antibody::AntibodyInfo
• get_cluster_list() : protocols::cluster::ClusterBase
• get_cluster_name() : protocols::antibody::AntibodyInfo
• get_cluster_num() : protocols::make_rot_lib::RotData
• get_cluster_radius() : protocols::cluster::ClusterBase
• get_cluster_string_vec() : protocols::antibody::AntibodyDatabaseManager
• get_clusterCenter() : protocols::comparative_modeling::AlignmentCluster
• get_combine_if_fail_exist() : protocols::LoopRebuild
• get_complex_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_complexed_sasa() : protocols::analysis::InterfaceAnalyzerMover
• get_component() : protocols::frag_picker::scores::FragmentScoreManager
• get_conformation_to_turn_type_map() : protocols::features::BetaTurnDetection
• get_conformer() : protocols::docking::DockingEnsemble
• get_conformer_cen() : protocols::docking::DockingEnsemble
• get_connection() : protocols::generalized_kinematic_closure::GeneralizedKIC
• get_connolly_eggshell() : protocols::pockets::EggshellGrid
• get_connolly_eggshell_on_grid() : protocols::pockets::EggshellGrid
• get_connolly_surfacePoints() : protocols::pockets::PocketGrid
• get_connolly_surfacePoints_within_grid() : protocols::pockets::PocketGrid
• get_conservative_design_residues() : protocols::antibody::design::AntibodySeqDesignTFCreator
• get_const_EnzConstraintIO_for_cstfile() : protocols::enzdes::AddOrRemoveMatchCsts
• get_constrainable_atoms_map() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• get_constrained_atom_id() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• get_constrained_atom_name() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• get_constrained_lig_atoms() : protocols::enzdes::PredesignPerturbMover
• get_constraint_for_target_state() : protocols::toolbox::match_enzdes_util::InvrotTree
• get_contact() : protocols::contact_map::ContactMap
• get_contacts() : protocols::frag_picker::nonlocal::NonlocalPair
• get_coordinates() : protocols::pockets::SmallMol
• get_coords_for_clash_check() : protocols::match::downstream::TargetRotamerCoords
• get_core_chunk_index_from_position() : protocols::hybridization::HybridizeFoldtreeDynamic
• get_crick_parameters() : protocols::helical_bundle::FitSimpleHelix
• get_crossterm_interface_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_crossterm_interface_energy_ratio() : protocols::analysis::InterfaceAnalyzerMover
• get_cst_file_name() : protocols::simple_moves::SequenceProfileMover
• get_cst_list() : protocols::abinitio::Templates
• get_Cstem_foldtree() : protocols::antibody::GraftedStemOptimizer
• get_cstweight() : protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_Relax
• get_cstyle_A() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• get_cstyle_b() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• get_cstyle_b_individual_scale() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• get_Cter_loop_end() : protocols::grafting::AnchoredGraftMover
• get_cterm_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• get_cur_ncluster() : protocols::toolbox::KClusterElement
• get_current_AntibodyNumberingScheme() : protocols::antibody::AntibodyInfo
• get_current_batch() : protocols::jd2::JobDistributor
• get_current_CDRDefinition() : protocols::antibody::AntibodyInfo
• get_current_confnum() : protocols::docking::DockingEnsemble
• get_current_conformer() : protocols::enzdes::ResidueConformerFilter
• get_current_cycle() : protocols::features::TrajectoryMapFeatures
• get_current_eqxyz() : protocols::md::CartesianMD
• get_current_job() : protocols::moves::Mover
• get_current_jump() : protocols::simple_moves::symmetry::SymmetrySlider
• get_current_output_tag() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• get_current_state() : protocols::flexpack::interaction_graph::FlexbbNode
• get_current_tag() : protocols::moves::Mover
• get_cutoff() : protocols::frag_picker::SidechainContactDistCutoff
• get_cutoff_squared() : protocols::frag_picker::SidechainContactDistCutoff
• get_cutpoint() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• get_cutpoints() : protocols::seeded_abinitio::SeedFoldTree
• get_cycle_counts() : protocols::features::TrajectoryReportToDB
• get_data() : protocols::frag_picker::JCouplingIO
• get_data_ndx() : protocols::toolbox::KClusterElement
• get_database_name() : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• get_database_pq_schema() : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• get_debug() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover
• get_default() : protocols::pose_selectors::AndSelector , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::OrSelector
• get_default_movemap() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• get_degrees() : protocols::nonlocal::HelixRotate
• get_delete_interface_native_sidechains() : protocols::anchored_design::AnchoredDesignMover
• get_DELPHI_espGrid_values() : protocols::pockets::ElectrostaticpotentialGrid
• get_delta_energy_components() : protocols::ddg::ddGMover
• get_delta_X_xx() : protocols::scoring::methods::pcs2::PcsTensor
• get_delta_X_yy() : protocols::scoring::methods::pcs2::PcsTensor
• get_delta_X_zz() : protocols::scoring::methods::pcs2::PcsTensor
• get_design() : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::EnzRepackMinimize
• get_design_cdr_loops() : protocols::antibody::design::AntibodySeqDesignTFCreator
• get_design_cdr_loops_with_stem() : protocols::antibody::design::AntibodySeqDesignTFCreator
• get_designable_residues() : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache , protocols::toolbox::task_operations::DesignAroundOperation
• get_desired_loops_exist() : protocols::LoopRebuild
• get_desriptor_data() : protocols::features::ScreeningFeatures
• get_determinant() : protocols::simple_moves::BBConRotMover
• get_dimensions() : protocols::qsar::scoring_grid::SingleGrid
• get_disabled() : protocols::checkpoint::CheckPointer
• get_discovered_out() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• get_dist() : protocols::pockets::UnionEdge
• get_dist_bins() : protocols::scoring::methods::saxs::PDDFEnergy
• get_dist_err() : protocols::farna::RNA_LoopCloser
• get_distance() : protocols::kinematic_closure::ClosureSolution , protocols::mpi_refinement::Clusterer , protocols::nonlocal::SheetTranslate , protocols::toolbox::KClusterElement
• get_distance_cutoff() : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• get_distance_measure() : protocols::cluster::ClusterPhilStyle_Loop , protocols::cluster::ClusterPhilStyle_PoseReporter , protocols::cluster::GatherPosesMover
• get_Dock_ScoreFxn() : protocols::antibody::AntibodyInfo
• get_dock_tf() : protocols::antibody::design::AntibodyDesignMoverGenerator
• get_docking_add_and_delete_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_docking_add_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_docking_delete_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_docking_split_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_DOF() : protocols::simple_moves::TorsionDOFMover
• get_dofs_for_pose0() : protocols::normalmode::NormalModeMultifunc
• get_dofs_from_energy_map() : protocols::optimize_weights::OptEMultifunc
• get_dofs_map() : protocols::normalmode::NormalModeMultifunc
• get_domain() : protocols::toolbox::AllowInsert
• get_dRdPhi() : protocols::simple_moves::BBGaussianMover
• get_dRdTheta() : protocols::simple_moves::BBGaussianMover
• get_ds_atom_ids_needed() : protocols::match::downstream::TargetRotamerCoords
• get_dsbuilder() : protocols::match::downstream::DownstreamAlgorithm
• get_dynamic_scale() : protocols::normalmode::NormalModeRelaxMover
• get_edge_memory_usage() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_edge_reweight() : protocols::toolbox::IGLigandDesignEdgeUpweighter , protocols::toolbox::ResidueGroupIGEdgeUpweighter
• get_eggshell_distance() : protocols::pockets::EggshellGrid
• get_eigval() : protocols::normalmode::NormalMode
• get_eigvec_cart() : protocols::normalmode::NormalMode
• get_eigvec_tor() : protocols::normalmode::NormalMode
• get_electrostatics_energy() : protocols::pockets::NonPlaidFingerprint
• get_end() : protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment , protocols::loophash::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_LoopHash
• get_end_res() : protocols::simple_moves::ReturnSidechainMover
• get_energy() : protocols::make_rot_lib::RotData , protocols::mpi_refinement::WorkUnit_Sampler
• get_energy_current_state_assignment() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_energy_map_from_dofs() : protocols::optimize_weights::OptEMultifunc
• get_energy_sum_for_vertex_group() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_enforce_bb_contiguity() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_ensemble_ca_rmsd() : protocols::simple_moves::ShakeStructureMover
• get_ensemble_diversity() : protocols::simple_moves::ShakeStructureMover
• get_entries() : protocols::frag_picker::CSTalosIO
• get_entries_per_torsion_bin() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber
• get_entry() : protocols::frag_picker::PhiPsiTalosIO
• get_EnzConstraintIO_for_cstfile() : protocols::enzdes::AddOrRemoveMatchCsts
• get_epitope_residues() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• get_eps() : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData
• get_eps_range() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_equiv() : protocols::simple_moves::symmetry::NCSResMapping
• get_equivalent_landmark() : protocols::antibody::AntibodyNumberingParser
• get_exemplar_for() : protocols::cluster::APCluster
• get_extra() : protocols::loophash::LoopHashLibrary
• get_extra_cutpoints() : protocols::farna::RNA_LoopCloser
• get_extra_data() : protocols::loophash::BackboneDB
• get_fa_score() : protocols::rpc::JSON_RPC
• get_features_reporter() : protocols::features::FeaturesReporterFactory
• get_file_contents() : protocols::pack_daemon::DynamicAggregateFunction
• get_filename() : protocols::anchored_design::Anchor , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• get_filter() : protocols::filters::FilterCollection , protocols::moves::FilterReporterMover
• get_filter_by_phipsi() : protocols::loophash::LoopHashSampler
• get_filter_omega() : protocols::anchored_design::AnchoredDesignMover
• get_filter_param() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• get_filter_SASA() : protocols::anchored_design::AnchoredDesignMover
• get_filter_score() : protocols::anchored_design::AnchoredDesignMover
• get_filter_type_by_name() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• get_filter_type_name() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• get_final_energy() : protocols::vip::VIP_Mover
• get_final_min_mover() : protocols::ligand_docking::FinalMinimizer
• get_final_pose() : protocols::vip::VIP_Mover
• get_first_atom() : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• get_first_index_in_query() : protocols::frag_picker::FragmentCandidate
• get_first_index_in_vall() : protocols::frag_picker::FragmentCandidate
• get_first_residue_id() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• get_fix_backbone() : protocols::simple_moves::CoupledMover
• get_fixed_chains() : protocols::analysis::InterfaceAnalyzerMover
• get_fixed_pt() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• get_flags() : protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::Filter , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::TopNByProperty , protocols::rosetta_scripts::PoseSelector
• get_flexbb_node() : protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_flexbbig_owner() : protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbNode
• get_flexseg_bb_offset() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_flexseg_for_bb() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_fobj() : protocols::mpi_refinement::MultiObjective
• get_fold_tree() : protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• get_fold_tree_root() : protocols::simple_moves::SetTorsion
• get_folding_verteces() : protocols::seeded_abinitio::SeedFoldTree
• get_FoldTree_AllCDRs() : protocols::antibody::AntibodyInfo
• get_FoldTree_AllCDRs_LHDock() : protocols::antibody::AntibodyInfo
• get_FoldTree_L_HA() : protocols::antibody::AntibodyInfo
• get_FoldTree_LA_H() : protocols::antibody::AntibodyInfo
• get_FoldTree_LH_A() : protocols::antibody::AntibodyInfo
• get_fourth_atom() : protocols::frag_picker::scores::FourAtomsConstraintData
• get_fourth_offset() : protocols::frag_picker::scores::FourAtomsConstraintData
• get_fraction() : protocols::frag_picker::quota::QuotaConfig , protocols::frag_picker::quota::QuotaPool
• get_frag3() : protocols::anchored_design::AnchorMoversData
• get_frag_data() : protocols::frag_picker::FragmentCandidate
• get_frag_energy_for_alt_bb_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_frag_mover_ptr() : protocols::topology_broker::FragmentClaimer
• get_fragment_torsion() : protocols::farna::FragmentLibrary
• get_fragment_torsion_set() : protocols::farna::FragmentLibrary
• get_fragments_by_CA_distances_and_NCpoints_restrains() : protocols::motif_grafting::movers::MotifGraftMover
• get_frags() : protocols::anchored_design::AnchorMoversData , protocols::frags::RMSVallData , protocols::frags::VallData
• get_from_scratch_add_and_delete_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_from_scratch_add_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_from_scratch_delete_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_fstyle_b() : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• get_full_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_full_motif_bb_alignment_mode() : protocols::motif_grafting::movers::MotifMatch
• get_full_strands() : protocols::features::strand_assembly::StrandBundleFeatures
• get_fullatom_scorefunction() : protocols::anchored_design::AnchorMoversData
• get_function() : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• get_function_names() : protocols::ligand_docking::rdf::RDFBase
• get_G() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• get_gap_distance() : protocols::farna::RNA_LoopCloser
• get_general_loop_task_op() : protocols::antibody::design::AntibodySeqDesignTFCreator
• get_global() : protocols::mpi_refinement::WorkUnit_LoopHash
• get_global_coords_as_FArray2D() : protocols::toolbox::match_enzdes_util::LigandConformer
• get_gly_interface_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_GOE_packstat_report() : protocols::vip::VIP_Report
• get_GOE_relaxed_report() : protocols::vip::VIP_Report
• get_GOE_repack_report() : protocols::vip::VIP_Report
• get_grid() : protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::SingleGrid
• get_grid_atom_name_1() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_atom_name_2() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_cone_angle_cutoff() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_edge() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_k_vector() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_large_cutoff() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_names() : protocols::qsar::scoring_grid::GridManager
• get_grid_residue_num_1() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_residue_num_2() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_search_parameters() : protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• get_grid_small_cutoff() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grid_step() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_grow_attempts() : protocols::loops::loop_mover::IndependentLoopMover
• get_gs() : protocols::viewer::ConformationViewer
• get_H3_kink_type() : protocols::antibody::AntibodyInfo
• get_H3_kink_type_name() : protocols::antibody::AntibodyInfo
• get_hardsphere_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_harmonic_ca_cst_std_dev() : protocols::simple_moves::ShakeStructureMover
• get_helical_params() : protocols::forge::remodel::RemodelGlobalFrame
• get_helix() : protocols::nonlocal::HelixRotate
• get_helix_fragments() : protocols::features::helixAssembly::HelixBundleFeatures
• get_helix_pairs() : protocols::features::helixAssembly::HelixBundleFeatures
• get_highres_scorefxn() : protocols::symmetric_docking::SymDockBaseProtocol
• get_i() : protocols::features::strand_assembly::StrandFragment
• get_id() : protocols::features::strand_assembly::StrandFragment , protocols::frag_picker::scores::FragmentScoringMethod
• get_ideal_hydrogenBond_atoms() : protocols::pockets::GenPharmacophore
• get_idealize_loop_first() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_ignore_unrecognized_res() : protocols::rotamer_recovery::RotamerRecovery
• get_importance() : protocols::normalmode::NormalMode
• get_incident_flexbb_edge() : protocols::flexpack::interaction_graph::FlexbbNode
• get_incident_minimalistflexbb_edge() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_incident_otfflexbb_edge() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• get_include_backbone_atoms() : protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• get_include_only_end() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• get_include_only_start() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• get_index() : protocols::kinematic_closure::ClosureSolution
• get_indices_of_moving_chunks() : protocols::farna::RNA_ChunkLibrary
• get_individual_scale() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsEnergyParameter
• get_init_value() : protocols::matdes::GetRBDOFValues
• get_initial() : protocols::hybridization::TMalign
• get_initial_fgt() : protocols::hybridization::TMalign
• get_initial_local() : protocols::hybridization::TMalign
• get_initial_ss() : protocols::hybridization::TMalign
• get_initial_ssplus() : protocols::hybridization::TMalign
• get_inp_chi() : protocols::make_rot_lib::RotData
• get_input_data() : protocols::scoring::methods::pcs::PCS_data_input_manager , protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4
• get_input_pose() : protocols::moves::Mover
• get_instance() : protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::jd2::JobDistributor , protocols::jd2::parser::DataLoaderFactory , protocols::ligand_docking::DistributionMap , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::moves::MoverFactory , protocols::noesy_assign::PeakAssignmentParameters , protocols::qsar::scoring_grid::GridManager , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton , protocols::scoring::methods::pcs2::PcsInputCenterManager , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1 , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4 , protocols::topology_broker::TopologyClaimerFactory
• get_inter_atr() : protocols::make_rot_lib::RotData
• get_inter_rep() : protocols::make_rot_lib::RotData
• get_interface_delta_hbond_unsat() : protocols::analysis::InterfaceAnalyzerMover
• get_interface_delta_sasa() : protocols::analysis::InterfaceAnalyzerMover
• get_interface_dG() : protocols::analysis::InterfaceAnalyzerMover
• get_interface_packstat() : protocols::analysis::InterfaceAnalyzerMover
• get_interface_residues() : protocols::docking::EllipsoidalRandomizationMover , protocols::ligand_docking::ligand_options::Interface
• get_interface_set() : protocols::analysis::InterfaceAnalyzerMover
• get_internal_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_interpolated_esp_energy() : protocols::pockets::NonPlaidFingerprint
• get_interpolated_esp_energy_with_type() : protocols::pockets::NonPlaidFingerprint
• get_intra_atr() : protocols::make_rot_lib::RotData
• get_intra_rep() : protocols::make_rot_lib::RotData
• get_intramolecular_add_and_delete_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_intramolecular_add_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_intramolecular_delete_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_intramolecular_split_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_irms() : protocols::rpc::JSON_RPC
• get_is_do_minimize() : protocols::analysis::PeptideDeriverFilter
• get_is_dump_cyclic_poses() : protocols::analysis::PeptideDeriverFilter
• get_is_dump_peptide_pose() : protocols::analysis::PeptideDeriverFilter
• get_is_dump_prepared_pose() : protocols::analysis::PeptideDeriverFilter
• get_is_dump_report_file() : protocols::analysis::PeptideDeriverFilter
• get_is_skip_zero_isc() : protocols::analysis::PeptideDeriverFilter
• get_iterations() : protocols::canonical_sampling::DbTrajectoryReader , protocols::trajectory::DbTrajectoryReader
• get_j() : protocols::features::strand_assembly::StrandFragment
• get_jacobian() : protocols::kinematic_closure::ClosureSolution
• get_jd2_resource_manager_instance() : protocols::jd2::JD2ResourceManager
• get_JobInputter_from_string() : protocols::jd2::JobInputterFactory
• get_JobOutputter_from_string() : protocols::jd2::JobOutputterFactory
• get_jobs() : protocols::jd2::JobDistributor
• get_jump() : protocols::toolbox::AllowInsert
• get_jump_anchors() : protocols::hybridization::FoldTreeHybridize
• get_jump_num() : protocols::docking::DockingSlideIntoContact , protocols::docking::FaDockingSlideIntoContact
• get_k() : protocols::normalmode::NormalMode
• get_kT() : protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_RamaPerturber
• get_L_move() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• get_L_prime() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• get_label() : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• get_landmark_resnum() : protocols::antibody::AntibodyInfo
• get_largest_chunk_size() : protocols::frag_picker::VallProvider
• get_last_checkpoint() : protocols::canonical_sampling::MetropolisHastingsMover
• get_last_move_status() : protocols::moves::Mover
• get_last_residue_id() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• get_last_struct_id() : protocols::features::ReportToDB
• get_late_factory() : protocols::anchored_design::AnchorMoversData
• get_length() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::JCouplingIO , protocols::viewer::ConformationViewer
• get_length_combos() : protocols::features::InterfaceFeatures
• get_lib_chi_val() : protocols::make_rot_lib::RotData
• get_lig_conformers() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• get_lig_restype() : protocols::toolbox::match_enzdes_util::LigandConformer
• get_ligand_areas() : protocols::ligand_docking::InterfaceBuilder
• get_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• get_ligand_atom_name() : protocols::metal_interface::MetalSiteResidue
• get_ligand_atom_xyz() : protocols::metal_interface::MetalSiteResidue
• get_ligand_id() : protocols::ligand_docking::LigandBaseProtocol
• get_ligand_jump_id() : protocols::ligand_docking::LigandBaseProtocol , protocols::simple_moves::CoupledMover
• get_ligand_resnum() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_ligand_tether() : protocols::ligand_docking::TetherLigand
• get_ligand_weight() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_light_chain_type() : protocols::antibody::AntibodyInfo
• get_light_chain_type_enum() : protocols::antibody::AntibodyInfo
• get_local_sequence_mapping() : protocols::hybridization::InsertChunkMover
• get_locator_id() : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• get_loop() : protocols::loop_modeling::LoopMover
• get_loop_combine_rate() : protocols::LoopRebuild , protocols::loops::loop_mover::IndependentLoopMover
• get_loop_file() : protocols::anchored_design::AnchorMoversData
• get_loop_file_reader() : protocols::loops::Loops
• get_loop_index() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• get_loop_sequence() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_loop_size() : protocols::loophash::LoopHashMap
• get_LoopCentral_ScoreFxn() : protocols::antibody::AntibodyInfo
• get_LoopHighRes_ScoreFxn() : protocols::antibody::AntibodyInfo
• get_looprlx_cycle_ratio() : protocols::LoopRebuild
• get_loops() : protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover , protocols::loop_modeling::LoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• get_loops_filename_from_options() : protocols::loops::LoopsFileFallbackConfiguration
• get_lowres_scorefxn() : protocols::symmetric_docking::SymDockBaseProtocol
• get_machine_letter() : protocols::wum::MPI_WorkUnitManager
• get_main_chain_torsion_set_list() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_main_chain_torsion_set_list_c_terminus() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_main_chain_torsion_set_list_coarse() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_main_chain_torsion_set_list_full() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_main_chain_torsion_set_list_n_terminus() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_main_chain_torsion_set_list_sample_phi_only() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_main_chain_torsion_set_list_sample_psi_only() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_matching_fragments() : protocols::motif_grafting::movers::MotifGraftMover
• get_matching_res_in_VDW_rep_screen_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• get_max_attempts() : protocols::loop_modeling::LoopBuilder
• get_max_bbrms() : protocols::loophash::LoopHashSampler
• get_max_chainbreak() : protocols::analysis::LoopAnalyzerMover
• get_max_dist_ndx() : protocols::toolbox::KClusterElement
• get_max_distance() : protocols::toolbox::KClusterElement
• get_max_kic_build_attempts() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• get_max_nstruct() : protocols::loophash::LoopHashSampler
• get_max_ntries() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_max_omega() : protocols::analysis::LoopAnalyzerMover
• get_max_pbond() : protocols::analysis::LoopAnalyzerMover
• get_max_rama() : protocols::analysis::LoopAnalyzerMover
• get_max_rms() : protocols::loophash::LoopHashSampler
• get_max_value() : protocols::qsar::scoring_grid::SingleGrid
• get_maximum_torsion_deltas_for_residue() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• get_maxscale() : protocols::mpi_refinement::WorkUnit_NormalMode
• get_mc() : protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::LoopRebuild , protocols::relax::ClassicRelax
• get_MC() : protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest
• get_mc() : protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes
• get_mc_temperature() : protocols::simple_moves::ShakeStructureMover
• get_median_rms() : protocols::cluster::ClusterBase
• get_mem_foot_print() : protocols::loophash::BackboneDB , protocols::loophash::BackboneSegment
• get_membrane_embed() : protocols::topology_broker::TMHTopologySamplerClaimer
• get_membrane_topology() : protocols::topology_broker::TMHTopologySamplerClaimer
• get_middle_residue() : protocols::frag_picker::FragmentCandidate
• get_middle_ss() : protocols::frag_picker::FragmentCandidate
• get_min_allowed_score() : protocols::frag_picker::scores::FragmentScoringMethod
• get_min_bb() : protocols::enzdes::EnzRepackMinimize
• get_min_bbrms() : protocols::loophash::LoopHashSampler
• get_min_cent_dist() : protocols::make_rot_lib::RotData
• get_min_chi() : protocols::make_rot_lib::RotData
• get_min_cst() : protocols::ddg::ddGMover , protocols::simple_moves::ShakeStructureMover
• get_min_eps() : protocols::make_rot_lib::RotData
• get_min_lig() : protocols::enzdes::EnzRepackMinimize
• get_min_omg() : protocols::make_rot_lib::RotData
• get_min_options() : protocols::loop_modeling::refiners::MinimizationRefiner
• get_min_rb() : protocols::enzdes::EnzRepackMinimize
• get_min_rms() : protocols::loophash::LoopHashSampler
• get_min_sc() : protocols::enzdes::EnzRepackMinimize
• get_min_scorefunction() : protocols::simple_moves::ShakeStructureMover
• get_min_sep_d2_from_upstream_atoms() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• get_min_type() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover
• get_min_value() : protocols::qsar::scoring_grid::SingleGrid
• get_minimalistflexbb_node() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_minimalistflexbbig_owner() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_minimize_best_tensor() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_minimize_with_cst() : protocols::simple_moves::ShakeStructureMover
• get_missing_template_other_res() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• get_missing_template_res() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• get_modescale() : protocols::normalmode::NormalModeMultifunc
• get_mono_aa_pose_copy() : protocols::motif_grafting::movers::MotifGraftMover
• get_most_recent_total_score() : protocols::frag_picker::scores::FragmentScoreMap
• get_motif_fragments_RMSD() : protocols::motif_grafting::movers::MotifMatch
• get_motif_ranges() : protocols::motif_grafting::movers::MotifMatch
• get_motif_scaffold_superposition_and_RMSD() : protocols::motif_grafting::movers::MotifGraftMover
• get_move_map_and_allow_insert() : protocols::stepwise::modeler::StepWiseMinimizer
• get_movemap() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::mpi_refinement::WorkUnit_Sampler , protocols::relax::RelaxProtocolBase , protocols::simple_moves::DisulfideInsertionMover
• get_MoveMap_for_AllCDRsSideChains_and_H3backbone() : protocols::antibody::AntibodyInfo
• get_MoveMap_for_Loops() : protocols::antibody::AntibodyInfo
• get_MoveMap_for_LoopsandDock() : protocols::antibody::AntibodyInfo
• get_movemap_from_blueprint() : protocols::flxbb::FlxbbDesign
• get_movemap_from_task() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• get_movement() : protocols::rbsegment_relax::RBSegment
• get_mover() : protocols::moves::FilterReporterMover , protocols::moves::MoverContainer , protocols::moves::RepeatMover , protocols::rosetta_scripts::ParsedProtocol , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::LoopFragmentClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TopologyClaimer , protocols::wum::MoverList
• get_mover_cycles() : protocols::loop_modeling::LoopProtocol
• get_mover_filter_pair() : protocols::rosetta_scripts::ParsedProtocol
• get_movers() : protocols::moves::CompositionMover
• get_moving_res() : protocols::farna::RNA_DeNovoProtocol
• get_moving_rsd_list() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_multichain_constructor() : protocols::analysis::InterfaceAnalyzerMover
• get_mutant_averaged_score_components() : protocols::ddg::ddGMover
• get_mutant_averaged_totals() : protocols::ddg::ddGMover
• get_mutant_min_score_components() : protocols::ddg::ddGMover
• get_mutant_min_totals() : protocols::ddg::ddGMover
• get_my_master() : protocols::wum::MPI_WorkUnitManager_Slave
• get_n_bb() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_N_C_stems_foldtree() : protocols::antibody::GraftedStemOptimizer
• get_n_centroids() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_n_chi() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_n_lanthanides() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• get_n_multi_data() : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton , protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• get_n_pcs() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• get_n_trial_min() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• get_name() : 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::FragmentJumpCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::DomainAssembly , protocols::abinitio::DoubleLayerKinematicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::LoopJumpFoldCst , protocols::abinitio::MembraneAbinitio , protocols::abinitio::Protocol , protocols::abinitio::ResolutionSwitcher , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::analysis::PackStatMover , 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::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::CanonicalSamplingMover , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::FixedTemperatureController , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::ProgressBarObserver , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver , protocols::canonical_sampling::WTEBiasEnergy , protocols::cluster::AssignToClustersMover , protocols::cluster::ClusterBase , protocols::cluster::ClusterPhilStyle , protocols::cluster::ClusterPhilStyle_Loop , protocols::cluster::ClusterPhilStyle_PoseReporter , protocols::cluster::EnsembleConstraints , protocols::cluster::EnsembleConstraints_Simple , protocols::cluster::GatherPosesMover , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_LoopCloser , 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::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::SeparateDnaFromNonDna , protocols::docking::ConformerSwitchMover , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , 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::AddOrRemoveMatchCsts , protocols::enzdes::ApplyRandomStoredRBConf , protocols::enzdes::BackboneSampler , protocols::enzdes::DiversifyStoredRBConfs , protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFixBBProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::GenerateStoredRBConfs , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::ModifyStoredRBConfs , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::enzdes::SecondaryMatchProtocol , protocols::enzdes::UpdateEnzdesHeaderMover , 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::ReportToDB , protocols::features::TrajectoryReportToDB , protocols::fibril::SetupForFibrilMover , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintsRCG , protocols::flexpack::FlexPacker , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::FlxbbDesign , protocols::flxbb::FlxbbDesignPack , protocols::flxbb::InterlockAroma , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::ConstraintFileRCG , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoC_RCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::ResidueVicinityRCG , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::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::CCDEndsGraftMover , protocols::grafting::GraftMoverBase , 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::hotspot_hashing::movers::PlaceSurfaceProbe , 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::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover , protocols::idealize::IdealizeMover , protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover , protocols::kinematic_closure::perturbers::BondAnglePerturber , protocols::kinematic_closure::perturbers::FragmentPerturber , protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi , protocols::kinematic_closure::perturbers::LogFilePerturber , protocols::kinematic_closure::perturbers::OmegaPerturber , protocols::kinematic_closure::perturbers::Perturber , protocols::kinematic_closure::perturbers::PerturberSet , protocols::kinematic_closure::perturbers::Rama2bPerturber , protocols::kinematic_closure::perturbers::RamaPerturber , protocols::kinematic_closure::perturbers::UniformPerturber , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber , protocols::kinematic_closure::pivot_pickers::EndToEndPivots , protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::kinematic_closure::pivot_pickers::LoopPivots , protocols::kinematic_closure::pivot_pickers::PivotPicker , protocols::kinematic_closure::pivot_pickers::StandardPivots , protocols::ligand_docking::AddHydrogen , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::GrowLigand , 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::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_build::LoopMover_SlidingWindow , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopModeler , protocols::loop_modeling::LoopMover , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loop_modeling::utilities::AcceptanceCheck , protocols::loop_modeling::utilities::LoopFilter , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loop_modeling::utilities::PrepareForCentroid , protocols::loop_modeling::utilities::PrepareForFullatom , 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::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure , 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::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves , 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::make_rot_lib::MakeRotLibMover , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::match::MatcherMover , protocols::matdes::ExtractSubposeMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , 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::symmetry::SymmetricAddMembraneMover , 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::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::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::pb_potential::SetupPoissonBoltzmannPotential , protocols::pockets::SmallMol , protocols::pose_reporters::EnergyReporter , protocols::pose_reporters::FilterReporter , protocols::pose_reporters::RMSDReporter , protocols::pose_selectors::AndSelector , protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::Filter , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::OrSelector , protocols::pose_selectors::TopNByProperty , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::qsar::qsarMover , protocols::qsar::qsarPoint , protocols::qsar::RenderGridsToKinemage , protocols::qsar::scoring_grid::AllAtomNormalization , protocols::qsar::scoring_grid::ChiAngleNormalization , protocols::qsar::scoring_grid::GridInitMover , protocols::qsar::scoring_grid::HeavyAtomNormalization , protocols::qsar::scoring_grid::MolecularWeightNormalization , protocols::qsar::scoring_grid::ScoreNormalization , 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::PosePropertyReporter , protocols::rosetta_scripts::PoseSelector , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::rotamer_recovery::RRComparer , protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerElecDensDiff , protocols::rotamer_recovery::RRComparerRotBins , protocols::rotamer_recovery::RRProtocol , protocols::rotamer_recovery::RRProtocolMinPack , protocols::rotamer_recovery::RRProtocolMover , protocols::rotamer_recovery::RRProtocolPackRotamers , protocols::rotamer_recovery::RRProtocolReferenceStructure , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRotamerTrials , protocols::rotamer_recovery::RRProtocolRTMin , 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::EvaluatedTrialMover , 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::BBG8T3AMover , 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::LoggedFragmentMover , 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::OopDPuckMinusMover , protocols::simple_moves::oop::OopDPuckPlusMover , protocols::simple_moves::oop::OopMover , protocols::simple_moves::oop::OopPatcher , protocols::simple_moves::oop::OopPuckMinusMover , protocols::simple_moves::oop::OopPuckPlusMover , 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::ShearMover , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , 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::SmallMover , protocols::simple_moves::SmoothFragmentMover , protocols::simple_moves::SmoothSymmetricFragmentMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::SymmetricFragmentMover , 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::SymMinMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::simple_moves::symmetry::SymShakeStructureMover , 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::simple_moves::WobbleMover , 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::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::ResidueAlternativeStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , 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::MC_StepWiseSampler , protocols::stepwise::sampler::NoOpStepWiseSampler , protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler , protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::sampler::rna::RNA_MC_MultiSuite , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerOneValueComb , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , 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::SymSidechainMinMover , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover , protocols::topology_broker::RigidBodyRandomTMHMover , protocols::ub_e2c::ubi_e2c_modeler , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• get_name_individual_mover() : protocols::moves::RandomMover
• get_nat_aa_opte_data() : protocols::optimize_weights::IterativeOptEDriver
• get_nat_rot_opte_data() : protocols::optimize_weights::IterativeOptEDriver
• get_native_info() : protocols::md::CartesianMD
• get_native_pdb_names() : protocols::optimize_weights::IterativeOptEDriver
• get_native_pose() : protocols::moves::Mover
• get_native_topology() : protocols::abinitio::PairingStatistics
• get_natom() : protocols::toolbox::KClusterData
• get_Ncap_scores() : protocols::helix_capper::HelixNCapperMover
• get_ndata() : protocols::toolbox::KClusterData , protocols::toolbox::KClusterElement
• get_ndx_list() : protocols::toolbox::KClusterElement
• get_near_interface_residues() : protocols::ligand_docking::ligand_options::Interface
• get_nearest_dist_to_O2prime() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• get_nearest_neighbour_esp_energy() : protocols::pockets::NonPlaidFingerprint
• get_nearest_res_from_strand() : protocols::features::strand_assembly::StrandBundleFeatures
• get_nearest_residue() : protocols::hotspot_hashing::HotspotStub
• get_nearest_stub() : protocols::hotspot_hashing::HotspotStubSet
• get_negative_filters() : protocols::protein_interface_design::filters::BoltzmannFilter
• get_neighbors() : protocols::vip::VIP_Mover
• get_net_sim() : protocols::cluster::APCluster
• get_new_job_id() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::MSDJobDistributor , protocols::jd2::ShuffleFileSystemJobDistributor
• get_new_JobInputter() : protocols::jd2::JobInputterFactory
• get_new_JobOutputter() : protocols::jd2::JobOutputterFactory
• get_new_ramping_scorefxn() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• get_next_candidate() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• get_next_filenames() : protocols::ddG::ddGData
• get_next_random_range() : protocols::jobdist::BaseJobDistributor
• get_next_valid_bb() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• get_NMmover() : protocols::mpi_refinement::WorkUnit_NormalMode
• get_nmodes() : protocols::mpi_refinement::WorkUnit_NormalMode
• get_nmoves() : protocols::moves::RepeatMover
• get_nmtype() : protocols::mpi_refinement::WorkUnit_NormalMode
• get_no_design_cys() : protocols::enzdes::DetectProteinLigandInterface
• get_no_frags() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchorMoversData
• get_nodes_from_same_flexseg() : protocols::flexpack::interaction_graph::FlexbbEdge
• get_non_bb_clashing_rotamers() : protocols::ligand_docking::LigandBaseProtocol
• get_nonconst_instance() : protocols::noesy_assign::PeakAssignmentParameters
• get_nonideal() : protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin
• get_nonpivot_torsion_sampling() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover
• get_norepack1() : protocols::docking::DockTaskFactory
• get_norepack2() : protocols::docking::DockTaskFactory
• get_normal_to_plane() : protocols::docking::EllipsoidalRandomizationMover
• get_normalization_factor() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• get_normalization_factor_inversed() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• get_nr_frags() : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• get_nrepeat() : protocols::mpi_refinement::WorkUnit_Relax
• get_nresidues() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• get_nrounds() : protocols::simple_moves::ShakeStructureMover
• get_Nstem_foldtree() : protocols::antibody::GraftedStemOptimizer
• get_nsteps() : protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber
• get_nstruct() : protocols::jd2::JobInputter , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_MD
• get_nterm_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• get_nth_pose() : protocols::inputter::FastaInputter , protocols::inputter::Inputter , protocols::inputter::PDBInputter , protocols::inputter::SilentFileInputter
• get_ntries_before_giving_up() : protocols::generalized_kinematic_closure::GeneralizedKIC
• get_nucleoside_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• get_num_aa_types() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_num_bbs() : protocols::make_rot_lib::RotData
• get_num_chi() : protocols::make_rot_lib::RotData
• get_num_clusters() : protocols::make_rot_lib::RotData
• get_num_decoys_used_in_calculations() : protocols::ddg::ddGMover
• get_num_distinct_backbones() : protocols::flexpack::interaction_graph::FlexbbNode
• get_num_exemplars() : protocols::cluster::APCluster
• get_num_interface_residues() : protocols::analysis::InterfaceAnalyzerMover
• get_num_iterations() : protocols::canonical_sampling::DbTrajectoryReader , protocols::trajectory::DbTrajectoryReader
• get_num_nodes_changing_state() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_num_pose_kept() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_num_sampled() : protocols::stepwise::modeler::StepWiseModeler
• get_num_states_for_aa_type_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• get_num_states_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• get_num_states_per_backbone_for_node() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_numbering_scheme_landmarks() : protocols::antibody::AntibodyInfo
• get_numbering_scheme_used_for_cdr_definition() : protocols::antibody::AntibodyNumberingParser
• get_obligate_pairing_sets() : protocols::farna::RNA_StructureParameters
• get_oegrid_dimensions() : protocols::pockets::ElectrostaticpotentialGrid
• get_offset() : protocols::frag_picker::scores::AtomPairConstraintsData
• get_omg() : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData
• get_omg_range() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• get_one_body_energy_for_node_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_one_random_loop() : protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• get_one_template_pose() : protocols::antibody::Ab_TemplateInfo
• get_onebody_energy_table() : protocols::RotamerDump::RotamerDumpMover
• get_optimize_cyclic_threshold() : protocols::analysis::PeptideDeriverFilter
• get_option() : protocols::jd2::JD2ResourceManager
• get_options() : protocols::wum::WorkUnitBase
• get_options_data() : protocols::make_rot_lib::MakeRotLibJob
• get_oriented_pose() : protocols::pockets::PlaidFingerprint
• get_otfflexbb_node() : protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• get_otfflexbbig_owner() : protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbNode
• get_out() : protocols::moves::FilterReporterMover
• get_out_tag() : protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• get_output_filename() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• get_output_level() : protocols::rotamer_recovery::RRReporterSQLite
• get_output_tag() : protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• get_pack_input() : protocols::analysis::InterfaceAnalyzerMover
• get_Pack_ScoreFxn() : protocols::antibody::AntibodyInfo
• get_packer_task() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::CoupledMover
• get_PackingAngleResidues() : protocols::antibody::AntibodyInfo
• get_pair_core_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• get_pair_dist() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• get_pairing() : protocols::jumping::JumpSample
• get_pairings_from_line() : protocols::farna::RNA_StructureParameters
• get_pairings_jump_mover() : protocols::hybridization::FoldTreeHybridize
• get_pairings_residues() : protocols::hybridization::FoldTreeHybridize
• get_parameters() : protocols::frag_picker::JCouplingIO , protocols::rotamer_recovery::RRComparer , protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerElecDensDiff , protocols::rotamer_recovery::RRComparerRotBins , protocols::rotamer_recovery::RRProtocol , protocols::rotamer_recovery::RRProtocolMinPack , protocols::rotamer_recovery::RRProtocolMover , protocols::rotamer_recovery::RRProtocolPackRotamers , protocols::rotamer_recovery::RRProtocolReferenceStructure , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRotamerTrials , protocols::rotamer_recovery::RRProtocolRTMin
• get_params() : protocols::mpi_refinement::Scheduler
• get_parent() : protocols::pockets::SmallMol
• get_parent_tag() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• get_partition_res() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_partner_residue_start_stop() : protocols::docking::EllipsoidalRandomizationMover
• get_path() : protocols::generalized_kinematic_closure::GeneralizedKIC
• get_PCS_data_all() : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• get_PCS_data_input_reference() : protocols::scoring::methods::pcs::PCS_data_input , protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4
• get_PCS_data_line_all_reference() : protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• get_PCS_data_line_all_spin() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• get_pcs_data_per_lanthanides_all() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• get_PCS_experimental() : protocols::scoring::methods::pcs2::PcsInputLine
• get_PCS_tolerance() : protocols::scoring::methods::pcs2::PcsInputLine
• get_pcs_weight() : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_PcsEnergyParameter_for() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• get_PcsInputCenter_for() : protocols::scoring::methods::pcs2::PcsInputCenterManager
• get_PcsInputFile_all() : protocols::scoring::methods::pcs2::PcsInputCenter
• get_PcsInputLine_all() : protocols::scoring::methods::pcs2::PcsInputFile
• get_pdb_coords() : protocols::qsar::scoring_grid::SingleGrid
• get_pdb_id() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::VallChunk
• get_pdb_source() : protocols::features::strand_assembly::StrandFragment
• get_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• get_pep_lengths() : protocols::analysis::PeptideDeriverFilter
• get_peptide() : protocols::loophash::LoopHashMap
• get_peptide_chain() : protocols::simple_moves::DisulfideInsertionMover
• get_per_residue_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_perturb_CCD_off() : protocols::anchored_design::AnchoredPerturbMover
• get_perturb_cycles() : protocols::anchored_design::AnchoredPerturbMover
• get_perturb_KIC_off() : protocols::anchored_design::AnchoredPerturbMover
• get_perturb_show() : protocols::anchored_design::AnchoredPerturbMover
• get_perturb_temp() : protocols::anchored_design::AnchoredPerturbMover
• get_perturbedloop_rsd() : protocols::generalized_kinematic_closure::GeneralizedKIC
• get_perturber_effect() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• get_perturber_effect_from_name() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• get_perturber_effect_name() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• get_perturber_names() : protocols::kinematic_closure::perturbers::PerturberSet
• get_phi() : protocols::make_rot_lib::RotData , protocols::rigid::RigidBodyRandomizeMover
• get_pivot_picker() : protocols::kinematic_closure::KicMover
• get_pocket_distance() : protocols::pockets::PocketGrid
• get_point() : protocols::qsar::qsarMap , protocols::qsar::scoring_grid::SingleGrid
• get_point_score() : protocols::qsar::scoring_grid::ShapeGrid
• get_point_value_list_within_range() : protocols::qsar::scoring_grid::SingleGrid
• get_policy() : protocols::nonlocal::PolicyFactory
• get_polymer_type() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_pool() : protocols::frag_picker::quota::QuotaCollector
• get_pool_bins() : protocols::frag_picker::quota::ABEGO_SS_Config
• get_pool_diff() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• get_pool_name() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::quota::QuotaConfig , protocols::frag_picker::quota::QuotaPool
• get_pose() : protocols::canonical_sampling::DbTrajectoryReader , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::frag_picker::VallChunk , protocols::inputter::InputterStream , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::trajectory::DbTrajectoryReader , protocols::wum::SilentStructStore
• get_pose_angles() : protocols::antibody::clusters::CDRClusterMatcher
• get_pose_build_resids() : protocols::match::Matcher
• get_pose_data() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• get_pose_from_claimer() : protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• get_pose_list() : protocols::cluster::GatherPosesMover , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::StepWiseConnectionSampler
• get_pose_resnum() : protocols::pockets::NonPlaidFingerprint
• get_poseOP() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• get_poses() : protocols::canonical_sampling::DbTrajectoryReader , protocols::trajectory::DbTrajectoryReader
• get_position() : protocols::topology_broker::claims::CutClaim , protocols::topology_broker::claims::LegacyRootClaim
• get_positive_filters() : protocols::protein_interface_design::filters::BoltzmannFilter
• get_possible_hbond_acceptors() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• get_pre_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• get_pre_pre_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• get_prediction_name() : protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• get_previously_closed_cutpoint_from_imported_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• get_priority() : protocols::frag_picker::scores::FragmentScoringMethod
• get_probability() : protocols::make_rot_lib::RotData
• get_profile() : protocols::frag_picker::VallChunk
• get_profile_wgt() : protocols::simple_moves::SequenceProfileMover
• get_project_pref_max_cpu_run_time() : protocols::boinc::Boinc
• get_project_pref_max_gfx_cpu() : protocols::boinc::Boinc
• get_project_pref_max_gfx_fps() : protocols::boinc::Boinc
• get_protein() : protocols::loophash::BackboneDB
• get_protein_sstype() : protocols::simple_filters::AbinitioBaseFilter
• get_protocol_id() : protocols::features::ProteinSilentReport
• get_psi() : protocols::make_rot_lib::RotData , protocols::rigid::RigidBodyRandomizeMover
• get_ptask() : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• get_PyMol_model_name() : protocols::moves::PyMolMover
• get_pymol_sel_hbond_unsat() : protocols::analysis::InterfaceAnalyzerMover
• get_pymol_sel_interface() : protocols::analysis::InterfaceAnalyzerMover
• get_pymol_sel_packing() : protocols::analysis::InterfaceAnalyzerMover
• get_python_string() : protocols::ligand_docking::ligand_options::Interface
• get_qt_mapping() : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• get_query_middle_res_id() : protocols::frag_picker::FragmentCandidate
• get_query_phi_prediction() : protocols::frag_picker::FragmentPicker
• get_query_phi_prediction_conf() : protocols::frag_picker::FragmentPicker
• get_query_pos_i() : protocols::frag_picker::nonlocal::NonlocalPair
• get_query_pos_j() : protocols::frag_picker::nonlocal::NonlocalPair
• get_query_psi_prediction() : protocols::frag_picker::FragmentPicker
• get_query_psi_prediction_conf() : protocols::frag_picker::FragmentPicker
• get_query_residue_depth() : protocols::frag_picker::FragmentPicker
• get_query_sa_prediction() : protocols::frag_picker::FragmentPicker
• get_query_seq() : protocols::frag_picker::FragmentPicker
• get_query_seq_string() : protocols::frag_picker::FragmentPicker
• get_query_size() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• get_query_ss() : protocols::frag_picker::FragmentPicker
• get_query_ss_string() : protocols::frag_picker::FragmentPicker
• get_quota_score() : protocols::frag_picker::scores::FragmentScoreMap
• get_radial_disp_diffs() : protocols::matdes::SymDofMoverSampler
• get_radial_disps() : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• get_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_ramp_fa_rep() : protocols::simple_moves::ShakeStructureMover
• get_random_base_pair_jump() : protocols::farna::RNA_JumpLibrary
• get_random_beta_sheet_jump() : protocols::jumping::PairingLibrary
• get_random_loop_flag() : protocols::LoopRebuild
• get_random_o2prime_residue() : protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• get_random_o2prime_residue_near_moving_residue() : protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover
• get_random_order() : protocols::loops::loop_mover::IndependentLoopMover
• get_random_phi_psi_for_residue() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber
• get_random_point_on_ellipsoid() : protocols::docking::EllipsoidalRandomizationMover
• get_random_tmh_jump() : protocols::jumping::PairingLibrary
• get_randomize_input_sequence() : protocols::anchored_design::AnchoredDesignMover
• get_randomize_resnum() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• get_rdf_function() : protocols::ligand_docking::rdf::RDFFunctionFactory
• get_reconstruct() : protocols::mpi_refinement::WorkUnit_PartialAbinitio
• get_recovery_threshold() : protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerElecDensDiff
• get_redesign_loop() : protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• get_reference_energies_from_dofs() : protocols::optimize_weights::OptEMultifunc
• get_reference_pose() : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• get_reference_xyz() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• get_refine_CCD_off() : protocols::anchored_design::AnchoredRefineMover
• get_refine_cycles() : protocols::anchored_design::AnchoredRefineMover
• get_refine_KIC_off() : protocols::anchored_design::AnchoredRefineMover
• get_refine_only() : protocols::anchored_design::AnchoredDesignMover
• get_refine_repack_cycles() : protocols::anchored_design::AnchoredRefineMover
• get_refine_temp() : protocols::anchored_design::AnchoredRefineMover
• get_region_mm_bend_score() : protocols::enzdes::EnzdesFlexibleRegion
• get_region_of_residue() : protocols::antibody::AntibodyInfo
• get_region_total_score() : protocols::enzdes::EnzdesFlexibleRegion
• get_relaxtype() : protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_Relax
• get_relevant_residues() : protocols::features::ReportToDB
• get_relevant_residues_mode() : protocols::features::FeaturesReporter , protocols::features::ReportToDB
• get_relevant_residues_task_factory() : protocols::features::ReportToDB
• get_remaining_cpu_time() : protocols::boinc::Boinc
• get_remodel_res() : protocols::stepwise::monte_carlo::mover::ResampleMover
• get_repack_period() : protocols::loop_modeling::refiners::RepackingRefiner
• get_repacked_poses() : protocols::simple_moves::SetReturningPackRotamersMover
• get_report_format() : protocols::analysis::PeptideDeriverFilter
• get_res1() : protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber
• get_res2() : protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber
• get_res_energy() : protocols::protein_interface_design::ReportSequenceDifferences
• get_res_list_in_reference() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_res_res_score() : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• get_resample_internal_local_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_resample_internal_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_resample_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_resample_terminal_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_resfile_1() : protocols::anchored_design::AnchorMoversData
• get_resfile_2() : protocols::anchored_design::AnchorMoversData
• get_resid() : protocols::moves::ResId
• get_residue() : protocols::frag_picker::FragmentCandidate , protocols::qsar::qsarMap , protocols::qsar::qsarPoint , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• get_residue_at_origin() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• get_residue_at_origin_with_matching_type() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• get_residue_feature() : protocols::comparative_modeling::features::ResidueFeatureFactory
• get_residue_indices_to_output() : protocols::dna::PDBOutput
• get_residue_num() : protocols::scoring::methods::pcs2::PcsInputLine
• get_residue_score_() : protocols::hotspot_hashing::HotspotStubSet
• get_residue_type_set() : protocols::simple_moves::SwitchResidueTypeSetMover
• get_residue_weights_for_1mers() : protocols::hybridization::FoldTreeHybridize
• get_residue_weights_for_big_frags() : protocols::hybridization::FoldTreeHybridize
• get_residue_weights_for_small_frags() : protocols::hybridization::FoldTreeHybridize
• get_residues() : protocols::ligand_docking::Ligand_info , protocols::loops::Loop , protocols::loops::Loops , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation
• get_residues_to_rebuild() : protocols::rbsegment_relax::SequenceShiftMover
• get_resname() : protocols::metal_interface::MetalSiteResidue
• get_resNum() : protocols::features::strand_assembly::SandwichFragment
• get_resnum() : protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• get_resource() : protocols::jd2::JD2ResourceManager
• get_resource_loader() : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• get_resource_options() : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• get_restrict_partners_to_chains() : protocols::analysis::PeptideDeriverFilter
• get_restrict_receptors_to_chains() : protocols::analysis::PeptideDeriverFilter
• get_restrictions() : protocols::flxbb::LayerDesignOperation , protocols::toolbox::task_operations::DsspDesignOperation
• get_rid_of_capping_base_pairs() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• get_rigid_body_confs() : protocols::enzdes::ModifyStoredRBConfs , protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO
• get_rigid_body_mover() : protocols::simple_moves::CoupledMover
• get_rigid_body_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• get_rmsd() : protocols::anchored_design::AnchoredDesignMover
• get_RMSD() : protocols::motif_grafting::movers::MotifMatch , protocols::normalmode::CartesianNormalModeMover
• get_rmsd() : protocols::pockets::SmallMol
• get_rmsd_no_superimpose() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_RMSD_only_this() : protocols::anchored_design::AnchoredDesignMover
• get_rmsd_over_all_poses() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_rmsd_res_and_superimpose_res_in_pose() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_rmsd_target_tolerance() : protocols::simple_moves::ShakeStructureMover
• get_rmsd_tolerance() : protocols::LoopRebuild
• get_rna_pairing_list() : protocols::farna::RNA_StructureParameters
• get_RNAring_sasa() : protocols::pockets::GenPharmacophore
• get_root() : protocols::pockets::SmallMol
• get_root_triad_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_rot_mag() : protocols::rigid::RigidBodyPerturbMover
• get_rot_magnitude() : protocols::docking::DockingHighResLegacy
• get_rotamer_angle() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_rotamer_recovery() : protocols::rotamer_recovery::RotamerRecoveryFactory , protocols::toolbox::pose_metric_calculators::RotamerRecovery
• get_rotamer_recovery_comparer() : protocols::rotamer_recovery::RotamerRecoveryFactory
• get_rotamer_recovery_protocol() : protocols::rotamer_recovery::RotamerRecoveryFactory
• get_rotamer_recovery_reporter() : protocols::rotamer_recovery::RotamerRecoveryFactory
• get_rotamer_set() : protocols::protein_interface_design::movers::TryRotamers
• get_rotamers() : protocols::motifs::LigandMotifSearch
• get_rotated_and_translated_pose() : protocols::motif_grafting::movers::MotifGraftMover
• get_rotation_magnitude() : protocols::simple_moves::CoupledMover
• get_rotation_matrix() : protocols::docking::EllipsoidalRandomizationMover
• get_rotation_parameters() : protocols::nonlocal::HelixRotate
• get_rotation_std_dev() : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• get_rsd_alternatives_rotamer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_run_time() : protocols::wum2::WorkUnit , protocols::wum::WorkUnitBase
• get_Rvalue() : protocols::pockets::NonPlaidFingerprint
• get_sample_nonpivot_torsions() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_sampler_options() : protocols::stepwise::modeler::options::StepWiseModelerOptions
• get_sc_interface_builder() : protocols::ligand_docking::MoveMapBuilder
• get_sc_min() : protocols::simple_moves::ShakeStructureMover
• get_scaffold2motif_size_change() : protocols::motif_grafting::movers::MotifMatch
• get_scaffold_fragment_data() : protocols::motif_grafting::movers::MotifMatch
• get_scaffold_ranges() : protocols::motif_grafting::movers::MotifMatch
• get_scaffold_status() : protocols::hotspot_hashing::HotspotStub
• get_score() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatLigPoseOptEData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::ScoreCutoffFilter
• get_score_components() : protocols::frag_picker::scores::FragmentScoreMap
• get_score_fast() : protocols::hybridization::TMalign
• get_score_filter_cutoff() : protocols::LoopRebuild
• get_score_from_angles() : protocols::qsar::scoring_grid::ShapeGrid
• get_score_function() : protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::utilities::PrepareForFullatom , protocols::match::downstream::ScoringSecMatchRPE
• get_score_fxn() : protocols::simple_moves::CoupledMover
• get_score_manager() : protocols::frag_picker::FragmentPicker
• get_score_name() : protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::scores::MakeFragmentScoringMethod
• get_scorefile_name() : protocols::optimize_weights::IterativeOptEDriver
• get_scorefunction() : protocols::features::DatabaseJobInputter , protocols::simple_moves::ShakeStructureMover
• get_scorefunction_header() : protocols::ddg::ddGMover
• get_scorefunction_initialized() : protocols::simple_moves::ShakeStructureMover
• get_scorefxn() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::ligand_docking::LigandBaseProtocol , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::mpi_refinement::MultiObjective , protocols::pmut_scan::PointMutScanDriver , protocols::relax::RelaxProtocolBase , protocols::simple_moves::DisulfideInsertionMover , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• get_scorefxn_deriver() : protocols::analysis::PeptideDeriverFilter
• get_scoretype() : protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_Relax
• get_second_atom() : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• get_second_offset() : protocols::frag_picker::scores::FourAtomsConstraintData
• get_secondary_prediction() : protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• get_secstruct() : protocols::farna::RNA_SecStructInfo , protocols::frags::TorsionFragment
• get_segdef() : protocols::mpi_refinement::WorkUnit_bbGauss
• get_selected_strands() : protocols::features::strand_assembly::StrandBundleFeatures
• get_selector_type() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• get_selector_type_by_name() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• get_selector_type_name() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• get_self_ptr() : protocols::abinitio::Templates , protocols::environment::Environment , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::frag_picker::FragmentPicker , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider , protocols::helical_bundle::BundleGridSamplerHelper , protocols::helical_bundle::PerturbBundleOptions , protocols::match::MatcherTask , protocols::moves::Mover , protocols::optimize_weights::WrapperOptEMultifunc , protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• get_self_weak_ptr() : protocols::abinitio::Templates , protocols::environment::Environment , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::frag_picker::FragmentPicker , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider , protocols::helical_bundle::BundleGridSamplerHelper , protocols::helical_bundle::PerturbBundleOptions , protocols::moves::Mover , protocols::optimize_weights::WrapperOptEMultifunc , protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• get_sema_name() : protocols::boinc::Boinc
• get_semaphore() : protocols::boinc::Boinc
• get_semi_energy_dist() : protocols::make_rot_lib::RotData
• get_semi_prob_dist() : protocols::make_rot_lib::RotData
• get_semirotameric() : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::make_rot_lib::RotData
• get_separated_interface_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_separated_interface_energy_ratio() : protocols::analysis::InterfaceAnalyzerMover
• get_seq_recovery_cache() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• get_seqpos() : protocols::metal_interface::MetalSiteResidue
• get_sequence() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::VallChunk , protocols::frags::TorsionFragment , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• get_sequence_recovery() : protocols::toolbox::pose_metric_calculators::SequenceComparison
• get_sequence_region() : protocols::topology_broker::FragmentClaimer
• get_sfxn_cycles() : protocols::loop_modeling::LoopProtocol
• get_sheet() : protocols::nonlocal::SheetTranslate
• get_sheet_id() : protocols::features::strand_assembly::SandwichFragment
• get_shift() : protocols::frag_picker::CSTalosIO
• get_short_backrub_mover() : protocols::simple_moves::CoupledMover
• get_shortest_among_4() : protocols::features::strand_assembly::StrandBundleFeatures
• get_show_extended() : protocols::anchored_design::AnchoredDesignMover
• get_side1_nres() : protocols::analysis::InterfaceAnalyzerMover
• get_side1_score() : protocols::analysis::InterfaceAnalyzerMover
• get_side2_nres() : protocols::analysis::InterfaceAnalyzerMover
• get_side2_score() : protocols::analysis::InterfaceAnalyzerMover
• get_size() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::farna::TorsionSet , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment , protocols::pockets::SmallMol
• get_skip_low_temp_phase() : protocols::simple_moves::ShakeStructureMover
• get_slide_axis() : protocols::docking::EllipsoidalRandomizationMover
• get_slide_threshold() : protocols::simple_moves::symmetry::SymmetrySlider
• get_sol_secondary_struct() : protocols::surface_docking::FullatomRelaxMover
• get_solution_picker() : protocols::kinematic_closure::KicMover
• get_solvation() : protocols::make_rot_lib::RotData
• get_spanfile() : protocols::membrane::AddMembraneMover
• get_sphere_aa() : protocols::motifs::LigandMotifSearch
• get_spin_center() : protocols::docking::EllipsoidalRandomizationMover
• get_ss() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• get_ss_segments() : protocols::features::SmotifFeatures
• get_ss_type() : protocols::frag_picker::quota::SecondaryStructurePool
• get_ssid() : protocols::loophash::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_LoopHash
• get_start() : protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment , protocols::loophash::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_LoopHash
• get_start_positions() : protocols::helix_capper::HelixNCapperMover
• get_start_res() : protocols::loophash::LoopHashSampler , protocols::simple_moves::ReturnSidechainMover
• get_state_offset_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• get_states_on_curr_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• get_std_dev() : protocols::make_rot_lib::RotData
• get_stem_movemap() : protocols::antibody::GraftedStemOptimizer
• get_stem_residues() : protocols::farna::RNA_StructureParameters
• get_stem_taskfactory() : protocols::antibody::GraftedStemOptimizer
• get_stepwise_jump_atom() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• get_stop_res() : protocols::loophash::LoopHashSampler
• get_strand_from_bss_id() : protocols::features::strand_assembly::StrandBundleFeatures
• get_strand_id() : protocols::features::strand_assembly::SandwichFragment
• get_strand_pairs() : protocols::features::strand_assembly::StrandBundleFeatures , protocols::hybridization::FoldTreeHybridize
• get_strict_loops() : protocols::loops::loop_mover::IndependentLoopMover
• get_stride() : protocols::features::TrajectoryReportToDB
• get_string() : protocols::antibody::PDBLandmark
• get_string_real_pairs() : protocols::jd2::Job
• get_string_string_pairs() : protocols::jd2::Job
• get_strings() : protocols::jd2::Job
• get_struct() : protocols::wum::SilentStructStore
• get_struct_data() : protocols::qsar::qsarOptFunc
• get_struct_id() : protocols::features::StructureFeatures
• get_struct_id1() : protocols::rotamer_recovery::RRReporterSQLite
• get_struct_random() : protocols::wum::SilentStructStore
• get_structure_input_tag() : protocols::features::ReportToDB
• get_structure_tag() : protocols::features::ReportToDB
• get_stub() : protocols::hotspot_hashing::HotspotStubSet , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• get_stub_scorefxn() : protocols::protein_interface_design::movers::PlacementAuctionMover
• get_subcluster() : protocols::toolbox::KClusterElement
• get_success() : protocols::LoopRebuild
• get_suck_res() : protocols::simple_moves::AddCavitiesMover
• get_sugar_modeling_set() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• get_sugar_modeling_sets_for_chainbreak() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• get_sugar_setup_scorefxns() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• get_suite_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• get_super_secret_fixed_interface_mode() : protocols::anchored_design::AnchorMoversData
• get_surface_esp() : protocols::pockets::NonPlaidFingerprint
• get_surface_vector_filename_from_options() : protocols::surface_docking::SurfaceVectorFallbackConfiguration
• get_sw_can_by_sh_id() : protocols::features::strand_assembly::SandwichFragment
• get_sym_dof_names() : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• get_symm_data() : protocols::topology_broker::claims::SymmetryClaim
• get_tag() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::toolbox::KClusterData
• get_tag_list() : protocols::cluster::GatherPosesMover
• get_targeted_sequence() : protocols::dna::DnaInterfacePacker
• get_task() : protocols::anchored_design::AnchorMoversData , protocols::toolbox::task_operations::STMStoredTask
• get_task_factory() : protocols::anchored_design::AnchorMoversData , protocols::loop_modeling::LoopModeler , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , 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::relax::RelaxProtocolBase
• get_TaskFactory_AllCDRs() : protocols::antibody::AntibodyInfo
• get_TaskFactory_OneCDR() : protocols::antibody::AntibodyInfo
• get_temp() : protocols::canonical_sampling::CanonicalSamplingMover
• get_temp_cycles() : protocols::loop_modeling::LoopProtocol
• get_temperature() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::docking::ConformerSwitchMover , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::md::Thermostat , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_template() : protocols::abinitio::Templates
• get_template_atoms_at_pos() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• get_tenA_neighbor_residues() : protocols::enzdes::EnzdesFlexBBProtocol
• get_terminal_move_elements() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_testing_phase() : protocols::simple_moves::ShakeStructureMover
• get_third_atom() : protocols::frag_picker::scores::FourAtomsConstraintData
• get_third_offset() : protocols::frag_picker::scores::FourAtomsConstraintData
• get_this_filter_type_name() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• get_threshold() : protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster , protocols::toolbox::KMedoid
• get_tmh_inserted() : protocols::abinitio::MembraneAbinitio
• get_tolerance() : protocols::docking::FaDockingSlideIntoContact
• get_tool() : protocols::loop_modeling::LoopMover
• get_top_designs() : protocols::antibody::design::AntibodyGraftDesignMover
• get_torID() : protocols::normalmode::NormalMode
• get_torsion() : protocols::frags::TorsionFragment
• get_torsion_axis() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• get_torsions() : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• get_torsions_for_all_solutions() : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• get_total_frames() : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• get_total_Hbond_E() : protocols::analysis::InterfaceAnalyzerMover
• get_total_num_CDRs() : protocols::antibody::AntibodyInfo
• get_total_score() : protocols::analysis::LoopAnalyzerMover
• get_trans_mag() : protocols::rigid::RigidBodyPerturbMover
• get_trans_magnitude() : protocols::docking::DockingHighResLegacy
• get_transform() : protocols::hybridization::CartesianSampler
• get_translation_magnitude() : protocols::simple_moves::CoupledMover
• get_tuples() : protocols::frag_picker::CSTalosIO
• get_twist() : protocols::make_rot_lib::RotData
• get_twobody_energy_table() : protocols::RotamerDump::RotamerDumpMover
• get_type() : protocols::filters::Filter , protocols::moves::Mover , protocols::qsar::qsarPoint , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::simple_filters::DomainInterfaceFilter , protocols::toolbox::KClusterElement
• get_unbound_mode() : protocols::anchored_design::AnchorMoversData
• get_uniform_backrub() : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• get_unique_chains() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• get_unrelaxed_pose() : protocols::vip::VIP_Mover
• get_update() : protocols::stepwise::screener::BaseBinMapUpdater , protocols::stepwise::screener::FastForwardToNextResidueAlternative , protocols::stepwise::screener::FastForwardToNextRigidBody , protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::StubApplier
• get_update_boinc() : protocols::moves::MonteCarlo
• get_updates() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• get_upstream_restype() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• get_use_centroid_dG() : protocols::analysis::InterfaceAnalyzerMover
• get_use_lowest() : protocols::frag_picker::scores::FragmentScoringMethod
• get_user_defined_name() : protocols::filters::Filter , protocols::simple_filters::DomainInterfaceFilter
• get_user_input_alignment_res_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• get_valid_ramachandran_hashes() : protocols::features::BetaTurnDetection
• get_vall() : protocols::frag_picker::FragmentPicker
• get_vall_middle_res_id() : protocols::frag_picker::FragmentCandidate
• get_value() : protocols::filters::ContingentFilter , protocols::qsar::qsarPoint
• get_value_list() : protocols::stepwise::sampler::StepWiseSamplerOneValueComb
• get_values() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• get_vary_bondangles() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_vary_cutpoints() : protocols::anchored_design::AnchoredDesignMover
• get_VdRdPhi() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• get_VDW_weight() : protocols::anchored_design::AnchorMoversData
• get_vector_exclude_residues() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_vector_filename() : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_vector_weight() : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• get_vicinity_degree() : protocols::anchored_design::AnchoredRefineMover
• get_vicinity_sampling() : protocols::anchored_design::AnchoredRefineMover
• get_visited() : protocols::pockets::SmallMol
• get_weight() : protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::jd2::archive::EvaluatedArchive , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• get_weights() : protocols::antibody::design::ResidueProbDesignOperation , protocols::frag_picker::scores::FragmentScoreManager
• get_width() : protocols::viewer::ConformationViewer
• get_window_aa() : protocols::ss_prediction::SS_predictor
• get_work_unit() : protocols::wum::WorkUnitList
• get_work_unit_clone() : protocols::wum::WorkUnitList
• get_working_moving_res() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• get_working_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• get_wt_averaged_score_components() : protocols::ddg::ddGMover
• get_wt_averaged_totals() : protocols::ddg::ddGMover
• get_wt_min_score_components() : protocols::ddg::ddGMover
• get_wt_min_totals() : protocols::ddg::ddGMover
• get_wu_type() : protocols::wum::WorkUnitBase
• get_X_all() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• get_xyz() : protocols::simple_moves::BBConRotMover , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• get_xyz_coord_table() : protocols::RotamerDump::RotamerDumpMover
• get_Y_all() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• get_Z_all() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• get_ZAP_espGrid_values() : protocols::pockets::ElectrostaticpotentialGrid
• get_ZAP_espGrid_values_with_type() : protocols::pockets::ElectrostaticpotentialGrid
• getANN_PredError() : protocols::sparta::Sparta::SpartaLib
• getBondAngle() : protocols::sparta::PDB
• getBounds() : protocols::pockets::PocketGrid
• getCartesianDerivatives() : protocols::cartesian::MolecularDynamics
• getChi1() : protocols::sparta::PDB
• getChi2() : protocols::sparta::PDB
• getCoM() : protocols::rbsegment_relax::RBSegmentMover
• getConfidence() : protocols::sparta::ANN
• getContent() : protocols::pockets::SmallMol
• getCoordinateTransformation() : protocols::rbsegment_relax::GaussianRBSegmentMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::RBSegmentMover , protocols::rbsegment_relax::StrandTwistingMover
• getCutoff() : protocols::match::downstream::ScoringSecMatchRPE
• getData() : protocols::sparta::GDB
• getDihedralAngle() : protocols::sparta::PDB
• getDist() : protocols::sparta::PDB
• getEntry() : protocols::sparta::GDB , protocols::sparta::PDB
• getEntryCount() : protocols::sparta::GDB
• getField() : protocols::sparta::PDB
• getFragSet() : protocols::frag_picker::FragmentPicker
• gethash() : protocols::loophash::LoopHashLibrary
• getHBondDist() : protocols::sparta::PDB
• getLargestClusterSize() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet
• getLoopsToBuildFromBlueprint() : protocols::forge::remodel::RemodelData
• getLoopsToBuildFromFile() : protocols::forge::remodel::RemodelData
• getNetClusterSize() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet
• getNextRCadj() : protocols::sparta::Sparta::SpartaLib
• getNumberMissCS() : protocols::sparta::ANN
• getNumStatesPerAAPerBB() : protocols::flexpack::interaction_graph::FlexbbNode
• getOmega() : protocols::sparta::PDB
• getOneAAName() : protocols::sparta::PDB
• getOrbitalShift() : protocols::sparta::PDB
• getPhi() : protocols::sparta::PDB
• getPrevRCadj() : protocols::sparta::Sparta::SpartaLib
• getPsi() : protocols::sparta::PDB
• GetRBDOFValues() : protocols::matdes::GetRBDOFValues
• getRC() : protocols::sparta::Sparta::SpartaLib
• getRCadj() : protocols::sparta::Sparta::SpartaLib
• getRelaxResidues() : protocols::pockets::PocketGrid
• getResidName() : protocols::sparta::GDB
• getResidueRange() : protocols::rbsegment_relax::RBSegmentMover
• getResInfo() : protocols::sparta::Sparta::SpartaLib
• getScore() : protocols::electron_density::SetupForDensityScoringMover
• getSigAxisR() : protocols::rbsegment_relax::RBSegment
• getSigAxisT() : protocols::rbsegment_relax::RBSegment
• getSigOffAxisR() : protocols::rbsegment_relax::RBSegment
• getSigOffAxisT() : protocols::rbsegment_relax::RBSegment
• getSlashChar() : protocols::sparta::ANN
• getStubByName() : protocols::hotspot_hashing::StubGenerator
• getThreeAAName() : protocols::sparta::PDB
• getWeight() : protocols::sparta::Sparta::SpartaLib
• ghost_loops() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• global_loop_rmsd() : protocols::antibody_legacy::AntibodyModeler
• global_optimize() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• global_orientation_from_frame3() : protocols::toolbox::match_enzdes_util::LigandConformer
• global_pos1() : protocols::topology_broker::claims::JumpClaim
• global_pos2() : protocols::topology_broker::claims::JumpClaim
• global_position() : protocols::topology_broker::claims::BBClaim
• global_rotid_start_for_moltenres_in_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• global_sample_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• go() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::MSDJobDistributor , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master , protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave , protocols::wum::WorkUnitManager
• go_main() : protocols::jd2::JobDistributor
• good_jump() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• grab_main_chain_torsion_set_list() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• GrabAllCollector() : protocols::frag_picker::GrabAllCollector
• graceful_exit() : protocols::pack_daemon::DaemonSet
• graft() : protocols::metal_interface::MatchGrafter
• graft_in_cdr() : protocols::antibody::design::AntibodyGraftDesignMover
• graft_loop() : protocols::loophash::LoopHashLibrary
• GraftCDRLoopsProtocol() : protocols::antibody::GraftCDRLoopsProtocol
• GraftedStemOptimizer() : protocols::antibody::GraftedStemOptimizer
• GraftMover() : protocols::antibody_legacy::GraftMover
• GraftMoverBase() : protocols::grafting::GraftMoverBase
• GraftOneCDRLoop() : protocols::antibody::GraftOneCDRLoop
• GraftOneMover() : protocols::antibody_legacy::GraftOneMover
• grant_access() : protocols::environment::EnvClaimBroker
• GraphicsState() : protocols::viewer::GraphicsState
• greedy_around() : protocols::enzdes::PackRotamersMoverPartGreedy
• GreedyKCenter() : protocols::toolbox::GreedyKCenter
• GreedyOptMutationMover() : protocols::design_opt::GreedyOptMutationMover
• GreenPacker() : protocols::simple_moves::GreenPacker
• grid() : protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid
• grid_name() : protocols::qsar::scoring_grid::AtrGridCreator , protocols::qsar::scoring_grid::ChargeGridCreator , protocols::qsar::scoring_grid::ClassicGridCreator , protocols::qsar::scoring_grid::HbaGridCreator , protocols::qsar::scoring_grid::HbdGridCreator , protocols::qsar::scoring_grid::LigandPropertyScoreCreator , protocols::qsar::scoring_grid::RepGridCreator , protocols::qsar::scoring_grid::ShapeGridCreator , protocols::qsar::scoring_grid::SolvationGridCreator , protocols::qsar::scoring_grid::SolvationMetaGridCreator , protocols::qsar::scoring_grid::VdwGridCreator
• grid_to_kin() : protocols::qsar::scoring_grid::SingleGrid
• GridBase() : protocols::qsar::scoring_grid::GridBase
• GridCreator() : protocols::qsar::scoring_grid::GridCreator
• GridFactory() : protocols::qsar::scoring_grid::GridFactory
• GridInitMover() : protocols::qsar::scoring_grid::GridInitMover
• gridlig_active_site_definition() : protocols::match::MatcherTask
• gridlig_file_name() : protocols::match::MatcherTask
• GridManager() : protocols::qsar::scoring_grid::GridManager
• GridRegistrator() : protocols::qsar::scoring_grid::GridRegistrator< T >
• GridSearchIterator() : protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator
• GridSearchIterator_Ts1() : protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1
• GridSearchIterator_Ts2() : protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2
• GridSearchIterator_Ts3() : protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3
• GridSearchIterator_Ts4() : protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• GridSearchIteratorCA() : protocols::scoring::methods::pcs2::GridSearchIteratorCA
• group() : protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• group_id() : protocols::simple_moves::ChainGroupDiscriminator , protocols::simple_moves::GroupDiscriminator , protocols::simple_moves::UserDefinedGroupDiscriminator
• group_size() : protocols::cluster::Cluster
• grouper_ds_rmsd() : protocols::match::MatcherTask
• grouper_name() : protocols::match::MatcherTask
• groups() : protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator
• grow_all_loops() : protocols::loops::Loops
• grow_flexible() : protocols::rbsegment_relax::AutoRBMover
• grow_from_seeds() : protocols::seeded_abinitio::GrowPeptides
• grow_from_verteces() : protocols::seeded_abinitio::GrowPeptides
• grow_loop() : protocols::loops::Loops
• grow_loop_away_from_sheets() : protocols::loops::Loops
• GrowLeft() : protocols::forge::build::GrowLeft
• GrowLigand() : protocols::ligand_docking::GrowLigand
• GrowPeptides() : protocols::seeded_abinitio::GrowPeptides
• GrowRight() : protocols::forge::build::GrowRight
• GuardedLoopsFromFile() : protocols::loops::GuardedLoopsFromFile
• guess_pairings_from_secondary_structure() : protocols::abinitio::IterativeBase
• GunnCost() : protocols::frag_picker::scores::GunnCost , protocols::simple_moves::GunnCost
• GunnCostScore() : protocols::frag_picker::scores::GunnCostScore
• GunnTuple() : protocols::frag_picker::scores::GunnTuple , protocols::simple_moves::GunnTuple