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

- g -

• g1_ : core::chemical::CopyEdge< Graph1, Graph2 > , core::chemical::CopyVertex< Graph1, Graph2 >
• g2_ : core::chemical::CopyEdge< Graph1, Graph2 > , core::chemical::CopyVertex< Graph1, Graph2 >
• g_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , protocols::denovo_design::components::FoldGraph , 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
• G_bins : core::scoring::dna::DirectReadoutPotential
• g_radius() : core::conformation::membrane::ImplicitLipidInfo
• g_radius_gradient() : core::conformation::membrane::ImplicitLipidInfo
• GA_Minimizer() : core::optimization::GA_Minimizer
• ga_mutation_probability() : core::optimization::MinimizerOptions
• ga_mutation_probability_ : core::optimization::MinimizerOptions
• GADockStageParams() : protocols::ligand_docking::ga_ligand_dock::GADockStageParams
• GALigandDock() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• gamma() : core::io::CrystInfo , core::pose::Pose , core::scoring::APBSConfig::R_PARAM , core::scoring::CSA , protocols::cryst::Spacegroup , protocols::dna::DNABase
• Gamma() : protocols::md::MDBase
• gamma : protocols::protein_interface_design::Transformation , protocols::stepwise::sampler::rigid_body::EulerAngles , Transformation
• gamma_ : core::io::CrystInfo , core::scoring::CSA , core::scoring::nmr::NMRTensor , protocols::antibody::H3RefineCCD , protocols::canonical_sampling::BiasEnergy , protocols::cryst::Spacegroup , protocols::dna::DNABase
• Gamma_ : protocols::md::MDBase
• gamma_ : protocols::simple_filters::ResidueDepthFilter , protocols::stepwise::sampler::rigid_body::EulerAngles
• gamma_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• gamma_atom_names_ : core::scoring::dna::DNATorsionPotential
• gamma_components() : core::scoring::dna::DNATorsionPotential
• gamma_components_ : core::scoring::dna::DNATorsionPotential
• gamma_cutoff1 : core::pose::rna::RNA_SuiteName
• gamma_cutoff2 : core::pose::rna::RNA_SuiteName
• gamma_potential_ : core::scoring::rna::RNA_TorsionPotential
• gammammax : core::pose::rna::RNA_SuiteName
• gammammin : core::pose::rna::RNA_SuiteName
• gammapmax : core::pose::rna::RNA_SuiteName
• gammapmin : core::pose::rna::RNA_SuiteName
• gammatmax : core::pose::rna::RNA_SuiteName
• gammatmin : core::pose::rna::RNA_SuiteName
• GAOptimizer() : protocols::ligand_docking::ga_ligand_dock::GAOptimizer
• gap_char() : core::sequence::Sequence
• gap_char_ : core::sequence::Sequence
• gap_closer_ : protocols::backbone_moves::local_backbone_mover::LocalBackboneMover
• gap_distance_cutoff_ : protocols::rna::movers::RNA_LoopCloser
• gap_extend() : core::sequence::ScoringScheme
• gap_extend_ : core::sequence::ScoringScheme
• gap_open() : core::sequence::ScoringScheme
• gap_open_ : core::sequence::ScoringScheme
• gap_size() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• gap_size_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• gap_size_to_anchor() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• gap_solved() : protocols::backbone_moves::local_backbone_mover::GapCloser
• gap_solved_ : protocols::backbone_moves::local_backbone_mover::GapCloser
• GapCloser() : protocols::backbone_moves::local_backbone_mover::GapCloser
• gapped_positions() : core::sequence::SequenceAlignment
• gapspan_ : protocols::dna::DesignProteinBackboneAroundDNA
• garbage_collection() : protocols::jd2::MpiFileBuffer , protocols::jd3::JobGenealogist
• garbage_collector_ : protocols::jd2::MpiFileBuffer
• GarbageList : protocols::jd2::MpiFileBuffer
• gasteiger_atom_type() : core::chemical::Atom , core::chemical::ResidueType
• gasteiger_atom_type_ : core::chemical::Atom
• gasteiger_atom_type_index_ : core::chemical::ResidueType
• gasteiger_atom_type_set() : core::chemical::ChemicalManager , core::chemical::gasteiger::PossibleAtomTypesForAtom
• gasteiger_atom_type_set_ : core::chemical::gasteiger::PossibleAtomTypesForAtom
• gasteiger_atom_type_sets_ : core::chemical::ChemicalManager
• gasteiger_atom_types_ : core::chemical::ResidueTypeBase
• gasteiger_atom_typeset() : core::chemical::ResidueTypeBase
• GasteigerAtomTypeData() : core::chemical::gasteiger::GasteigerAtomTypeData
• GasteigerAtomTypeSet() : core::chemical::gasteiger::GasteigerAtomTypeSet
• GasteigerAtomTypeSets : core::chemical::ChemicalManager
• gate_pssm_scores() : core::scoring::methods::NMerPSSMEnergy
• gate_pssm_scores_ : core::scoring::methods::NMerPSSMEnergy
• gate_svm_scores() : core::scoring::methods::NMerSVMEnergy
• gate_svm_scores_ : core::scoring::methods::NMerSVMEnergy
• GatherPosesMover() : protocols::cluster::GatherPosesMover
• gauss() : core::scoring::epr_deer::EPRSpinLabel
• gaussian() : core::scoring::SmoothScoreTermCoeffs
• gaussian_ : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• gaussian_1d() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• gaussian_coeffs_ : core::scoring::SmoothScoreTermCoeffs
• gaussian_max_d : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• gaussian_move() : core::kinematics::Jump
• gaussian_move_single_rb() : core::kinematics::Jump
• gaussian_param_ : core::scoring::func::MixtureFunc
• gaussian_parameter_costheta_exocyclic_oxygen_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_exocyclic_oxygen_indirect_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_imine_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_imine_indirect_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_nonpolar_H_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_o2prime_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_o2prime_indirect_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_phosphate_oxygen_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_phosphate_oxygen_indirect_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_polar_H_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_costheta_water_oxygen_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_exocyclic_oxygen_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_exocyclic_oxygen_indirect_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_imine_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_imine_indirect_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_nonpolar_H_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_o2prime_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_o2prime_indirect_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_phosphate_oxygen_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_phosphate_oxygen_indirect_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_phosphate_p_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_polar_H_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_parameter_set_alpha() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_alpha_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_beta() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_beta_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_chi_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_chi_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_chi_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_chi_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_delta_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_delta_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_delta_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_delta_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_epsilon_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_epsilon_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_epsilon_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_epsilon_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_gamma() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_gamma_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu1_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu1_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu1_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu1_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu2_north() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu2_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu2_south() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_nu2_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_ap() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_ap_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_sc_minus() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_sc_minus_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_sc_plus() : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_set_zeta_alpha_sc_plus_ : core::chemical::rna::RNA_FittedTorsionInfo
• gaussian_parameter_water_oxygen_ : core::scoring::magnesium::MgKnowledgeBasedPotential
• gaussian_stdev_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::recces::sampler::rna::MC_RNA_Suite
• gaussian_translate_ligand() : protocols::ligand_docking::Translate
• gaussian_variance_ : core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainGeneralFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc
• GaussianChainDoubleFunc() : core::scoring::func::GaussianChainDoubleFunc
• GaussianChainFunc() : core::scoring::func::GaussianChainFunc
• GaussianChainFuncPotentialEvaluator() : core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator
• GaussianChainGeneralFunc() : core::scoring::func::GaussianChainGeneralFunc
• GaussianChainQuadrupleFunc() : core::scoring::func::GaussianChainQuadrupleFunc
• GaussianChainSingleFunc() : core::scoring::func::GaussianChainSingleFunc
• GaussianChainTripleFunc() : core::scoring::func::GaussianChainTripleFunc
• GaussianFunc() : core::scoring::func::GaussianFunc
• GaussianOverlapEnergy() : core::scoring::methods::GaussianOverlapEnergy
• GaussianParameter() : core::chemical::rna::GaussianParameter
• GaussianParameterSet : core::chemical::rna::RNA_FittedTorsionInfo
• GaussianRBSegmentMover() : protocols::rbsegment_relax::GaussianRBSegmentMover
• gb_shell_intxn() : core::scoring::GenBornPotential
• gb_shell_intxn_deriv() : core::scoring::GenBornPotential
• GBPair_cut() : core::scoring::FACTSPotential
• GBpair_cut_ : core::scoring::FACTSPotential
• GDB() : protocols::sparta::GDB
• GDB_Entry : protocols::sparta::GDB
• GDBfileName : protocols::sparta::GDB
• GDT() : protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter
• gdt_ : protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter
• GDT_ : protocols::loop_grower::LoopPartialSolution
• gdt_by_TM() : protocols::comparative_modeling::Align_RmsdEvaluator
• gdt_by_TM_ : protocols::comparative_modeling::Align_RmsdEvaluator
• GDTHA : core::scoring::TMscoreStore
• GDThatonative() : protocols::loop_grower::LoopGrower
• GDTTS : core::scoring::TMscoreStore
• gen_alg_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• GEN_BONDED_EXCL_INFO : core::pose::datacache::CacheableDataType
• GEN_BORN_POSE_INFO : core::pose::datacache::CacheableDataType
• gen_born_potential_ : core::scoring::ScoringManager
• gen_cen2fullatom() : protocols::abinitio::IterativeBase
• gen_cen2fullatom_non_pool_decoys() : protocols::abinitio::IterativeBase
• gen_coord_constraint() : protocols::normalmode::NormalModeRelaxMover
• 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_fixed_ : protocols::simple_moves::ExplicitWaterMover
• gen_fixed_byres_ : protocols::simple_moves::ExplicitWaterMover
• 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
• genbonded_score_full() : core::scoring::methods::EnergyMethodOptions
• genbonded_score_full_ : core::scoring::methods::EnergyMethodOptions
• genbonded_score_hybrid() : core::scoring::methods::EnergyMethodOptions
• genbonded_score_hybrid_ : core::scoring::methods::EnergyMethodOptions
• GenBondedExclInfo() : core::scoring::GenBondedExclInfo
• GenBornEnergy() : core::scoring::methods::GenBornEnergy
• GenBornPoseInfo() : core::scoring::GenBornPoseInfo
• GenBornPotential() : core::scoring::GenBornPotential
• GenBornResidueInfo() : core::scoring::GenBornResidueInfo
• GenBornRotamerSetInfo() : core::scoring::GenBornRotamerSetInfo
• general : protocols::network::UIObserver
• general_base_pair_step_library() : core::import_pose::libraries::RNA_LibraryManager
• general_base_pair_step_library_ : core::import_pose::libraries::RNA_LibraryManager
• general_event_link_ : protocols::moves::PyMOLObserver , protocols::network::UIObserver
• general_name : core::chemical::rings::RingConformer
• general_obs_hub_ : core::conformation::Conformation , core::pose::Pose
• general_observer : protocols::moves::PyMOLObserver
• general_permit_overlap_ : protocols::match::BumpGrid
• general_phi_sd_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• general_property_status_ : core::chemical::ResidueProperties
• general_psi_sd_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• GeneralAntibodyModeler() : protocols::antibody::design::GeneralAntibodyModeler
• GeneralEvent : core::conformation::Conformation , core::conformation::signals::GeneralEvent , core::pose::Pose , core::pose::signals::GeneralEvent
• generalEvent() : protocols::moves::PyMOLObserver , protocols::network::UIObserver
• 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() : protocols::denovo_design::components::IdealAbegoGenerator
• generate_active_pose_constraints() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• generate_alc_ensemble_for_region() : protocols::enzdes::EnzdesFlexBBProtocol
• generate_all_residue_types() : core::chemical::GlobalResidueTypeSet
• generate_allowed_partners() : protocols::cyclic_peptide::PeptideInternalHbondsMetric
• generate_and_dump_pose_found_residues_combinations() : protocols::enzdes::SecondaryMatchProtocol
• generate_assembly() : protocols::legacy_sewing::LegacyAssemblyMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyGivenPathAssemblyMover , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::legacy_sewing::LegacyRepeatAssemblyMover , protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMover
• generate_atom_pair_constraints() : protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• 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_best_final_pose() : protocols::pose_length_moves::ConnectChainsMover
• generate_binary_score_file() : protocols::legacy_sewing::SewGraph
• 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_connected_chains() : protocols::pose_length_moves::ConnectChainsMover
• generate_constraint_files() : protocols::noesy_assign::NoesyModule
• generate_constraints() : protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::relax::AtomCoordinateCstMover , protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase , protocols::topology_broker::CoordConstraintClaimer
• generate_coordinate_constraints() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• generate_counts() : protocols::simple_moves::StructProfileMover
• generate_csts() : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• generate_cubic_polynomial_func() : protocols::membrane::AqueousPoreFinder
• generate_custom_rama_cdf() : core::scoring::Ramachandran
• generate_data() : core::scoring::epr_deer::DEERIO
• generate_data_for_input_pose_id() : protocols::multistage_rosetta_scripts::TagManager
• generate_default_remarks() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• generate_default_title_section() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• generate_derived_types() : protocols::residue_optimization::MetapatchEnumeration
• generate_disulf_permutations() : protocols::cyclic_peptide::TryDisulfPermutations
• generate_disulfides() : protocols::cyclic_peptide::TryDisulfPermutations
• generate_edge_file() : protocols::sewing::hashing::EdgeMapGenerator
• 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_from_sequence() : core::sequence::SequenceProfile
• generate_full_tracer_report() : protocols::helical_bundle::BundleReporterFilter
• generate_gaussian_1d() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• generate_HELIXInformation() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• generate_hits() : protocols::match::Matcher
• generate_hits_for_constraint() : protocols::match::Matcher
• generate_id() : core::environment::EnvCore
• generate_impropers_map_res() : core::scoring::methods::IdealParametersDatabase
• generate_init_frags() : protocols::topology_broker::StartStructClaimer
• generate_insert_map() : core::fragment::FragSet
• generate_inverse_rotamer_constraints() : protocols::toolbox::match_enzdes_util::InvrotTree
• generate_invrot_csts_ : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• 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::loop_grower::SheetSampler , protocols::topology_broker::DisulfJumpClaimer
• generate_jump_frames() : protocols::jumping::JumpSample
• generate_key() : protocols::legacy_sewing::Hasher , protocols::sewing::hashing::Hasher
• generate_ligand_key() : protocols::sewing::hashing::LigandBindingResPlacer
• generate_lookback_rmsd() : protocols::pose_length_moves::AnalyzeLoopModeling
• generate_mainchain_potential() : protocols::mainchain_potential::GenerateMainchainPotential
• generate_match_pose() : protocols::motif_grafting::movers::MotifGraftMover
• generate_metapatched_variants() : protocols::residue_optimization::MetapatchEnumeration
• generate_monte_carlo_move() : protocols::helical_bundle_predict::HBP_FinalFullatomRefinementMoveGenerator , protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator , protocols::helical_bundle_predict::HBP_MoveGenerator
• generate_mover() : protocols::rosetta_scripts::RosettaScriptsParser
• generate_mover_for_protocol() : protocols::rosetta_scripts::RosettaScriptsParser
• generate_mover_xml_string() : protocols::rosetta_scripts::RosettaScriptsParser
• generate_N2C_cyclic_peptide_protein_complex() : protocols::peptide_deriver::PeptideDeriverFilter
• generate_native_rotamers_map() : protocols::legacy_sewing::Assembly
• generate_ncs_csts() : protocols::forge::remodel::RemodelLoopMover
• generate_new_channel() : protocols::jd2::DebugOut_MpiFileBuffer , protocols::jd2::MpiFileBuffer , protocols::jd2::WriteOut_MpiFileBuffer
• generate_output_pose() : protocols::pose_length_moves::PossibleLoop
• generate_overlap() : protocols::simple_moves::RepeatPropagationMover
• generate_overlaps() : protocols::pose_creation::MergePDBMover
• generate_perturbed_structures() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• generate_perturbed_value() : core::conformation::parametric::RealValuedParameter
• generate_piecewise_cubic_poly_func() : protocols::membrane::AqueousPoreFinder
• generate_pose() : protocols::mainchain_potential::GenerateMainchainPotential , 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_profile_from_seq() : protocols::splice::SpliceManager
• generate_profile_score() : protocols::simple_moves::StructProfileMover
• generate_profile_score_wo_background() : protocols::simple_moves::StructProfileMover
• generate_random() : protocols::monte_carlo::GenericMonteCarloMover
• generate_random_tree_from_jumps() : protocols::jumping::JumpSample
• generate_remodel_constraints() : protocols::fldsgn::SheetRemodelConstraintGenerator , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::remodel::GenericRemodelConstraintGenerator , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::ResidueVicinityRCG
• generate_remodel_constraints_for_respair() : protocols::forge::remodel::ResidueVicinityRCG
• generate_representative_target_res_for_geom_cst() : protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::SingleResidueInvrotTarget
• generate_residue_subset_fragment_store() : protocols::indexed_structure_store::FragmentStore
• generate_residue_type() : core::chemical::ResidueTypeSet
• generate_residue_type_constraints() : protocols::constraint_generator::ResidueTypeConstraintGenerator
• generate_residue_type_write_locked() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• generate_residues_to_sample() : protocols::forge::remodel::RemodelLoopMover
• generate_result_pose() : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• generate_reversed() : core::scoring::dssp::Pairing
• 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_secondary_structure_informations() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• generate_seqmap() : protocols::constraint_generator::CoordinateConstraintGenerator , protocols::relax::AtomCoordinateCstMover
• generate_sequence_claims() : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• generate_sequence_profile() : protocols::splice::Splice , protocols::splice::SpliceManager
• generate_sfxn() : protocols::mainchain_potential::GenerateMainchainPotential
• generate_SHEETInformation() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• generate_ss_strings_from_blueprint() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• generate_start_pose() : protocols::pose_creation::MakeJunctionsMover
• generate_stub_rmsd() : protocols::pose_length_moves::PossibleLoop
• generate_sub_fragment() : core::fragment::AnnotatedFragData , core::fragment::FragData
• generate_sub_frame() : core::fragment::Frame
• generate_subset_residues_to_compare() : protocols::indexed_structure_store::SSHashedFragmentStore
• 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_design() : protocols::antibody::design::AntibodySeqDesignTFCreator
• generate_task_op_cdr_profiles() : 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_torsion_values_for_helices() : protocols::helical_bundle_predict::HBPHelixAssignments
• generate_tree_from_jumps_and_cuts() : protocols::jumping::JumpSample
• generate_unbound_pose_() : protocols::hotspot_hashing::HotspotStubSet
• generate_uncached_stub_rmsd() : protocols::pose_length_moves::PossibleLoop
• generate_window_list() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• GenerateConcaveSurface() : core::scoring::sc::MolecularSurfaceCalculator
• GenerateConvexSurface() : core::scoring::sc::MolecularSurfaceCalculator
• GenerateMainchainPotential() : protocols::mainchain_potential::GenerateMainchainPotential
• GenerateMainchainPotentialOptions() : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• GenerateMap() : protocols::protein_interface_design::movers::MapHotspot
• GenerateMolecularSurfaces() : core::scoring::sc::MolecularSurfaceCalculator
• GenerateProbTable() : protocols::docking::ConformerSwitchMover
• generateRankedAlignments() : protocols::comparative_modeling::AlignmentClustering
• generates_aa() : core::chemical::Patch
• generates_base_residue() : core::chemical::PatchOperation
• generates_interchangeability_group() : core::chemical::Patch , core::chemical::PatchCase , core::chemical::PatchOperation , core::chemical::SetInterchangeabilityGroup_String
• generates_name3() : core::chemical::PatchOperation , core::chemical::SetIO_String
• generates_new_name3() : core::chemical::Patch , core::chemical::PatchCase
• generates_patched_residue_type_with_interchangeability_group() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• generates_patched_residue_type_with_name3() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• 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
• GenerateToroidalSurface() : core::scoring::sc::MolecularSurfaceCalculator
• generation_tag() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• generation_tag_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• generations() : protocols::genetic_algorithm::GeneticAlgorithmBase
• generations_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• generations_checkpoint_filename() : protocols::genetic_algorithm::GeneticAlgorithmBase
• generator_ : protocols::forge::constraints::RemoveRemodelCsts
• generator_id_ : protocols::forge::constraints::RemoveRemodelCsts
• generators() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• generators_ : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex , protocols::constraint_generator::AddConstraints , protocols::constraint_generator::RemoveConstraints
• generic_bonded_potential_ : core::scoring::ScoringManager
• generic_enzdes_header() : protocols::denovo_design::components::StructureData
• generic_output_number_ : protocols::match::output::MatchScoreWriter
• generic_pose_build_resids_ : protocols::match::MatcherTask
• generic_taskfactory() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• GenericBondedEnergy() : core::scoring::methods::GenericBondedEnergy
• GenericBondedPotential() : core::scoring::GenericBondedPotential
• GenericJobInputter() : protocols::comparative_modeling::GenericJobInputter
• GenericMonteCarloMover() : protocols::monte_carlo::GenericMonteCarloMover
• genericRB_sigR : protocols::rbsegment_relax::RBSegmentRelax
• genericRB_sigT : protocols::rbsegment_relax::RBSegmentRelax
• GenericRBMoveSet_ : protocols::rbsegment_relax::RBSegmentRelax
• GenericRemodelConstraintGenerator() : protocols::forge::remodel::GenericRemodelConstraintGenerator
• GenericResidueConnectionData() : core::scoring::etable::etrie::GenericResidueConnectionData
• GenericSimulatedAnnealer() : protocols::monte_carlo::GenericSimulatedAnnealer
• generous_hbonds_ : protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• GeneticAlgorithm() : protocols::genetic_algorithm::GeneticAlgorithm
• GeneticAlgorithmBase() : protocols::genetic_algorithm::GeneticAlgorithmBase
• GeneticAlgorithmOP : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• genkic_close() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• genkic_closure_attempts_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• genkic_min_solution_count_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• GenMeanFieldMover() : protocols::mean_field::GenMeanFieldMover
• GenTorsionParams() : core::scoring::GenTorsionParams
• geo_dim_type2name_ : core::scoring::hbonds::HBondTypeManager
• geo_dim_type_from_name() : core::scoring::hbonds::HBondTypeManager
• geo_sol_energy_ : protocols::features::GeometricSolvationFeatures
• geom_cst_ : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• geom_cst_has_primary_modification_ : protocols::match::Matcher
• geom_cst_id() : protocols::match::downstream::DownstreamAlgorithm
• geom_cst_id_ : protocols::match::downstream::DownstreamAlgorithm
• geom_csts_downstream_output() : protocols::match::MatcherTask
• geom_csts_downstream_output_ : protocols::match::MatcherTask
• geom_csts_with_primary_hitlist_modificiations_ : protocols::match::Matcher
• geom_id() : protocols::match::output::WriteUpstreamHitKinemage
• geom_id_ : protocols::match::output::WriteUpstreamHitKinemage
• geom_sol_interres_path_distance_cutoff() : core::scoring::methods::EnergyMethodOptions
• geom_sol_interres_path_distance_cutoff_ : core::scoring::methods::EnergyMethodOptions
• geom_sol_intrares_path_distance_cutoff() : core::scoring::methods::EnergyMethodOptions
• geom_sol_intrares_path_distance_cutoff_ : core::scoring::methods::EnergyMethodOptions
• geomcst_is_upstream_only_ : protocols::match::Matcher
• geomcst_seqpos_ : protocols::forge::constraints::InvrotTreeRCG
• geomcsts_for_superposition_ : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• geometric_dimension() : core::scoring::hbonds::Polynomial_1d
• geometric_dimension_ : core::scoring::hbonds::Polynomial_1d
• geometric_sol_one_way_bb_bb() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• geometric_sol_one_way_sc() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• geometric_sol_scale_ : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• GeometricFunc() : protocols::moves::GeometricFunc
• GeometricRenameIsomorphismCallback() : core::io::pose_from_sfr::GeometricRenameIsomorphismCallback
• GeometricRenameVerticiesEquivalent() : core::io::pose_from_sfr::GeometricRenameVerticiesEquivalent
• GeometricSolEnergyEvaluator() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• GeometricSolvationFeatures() : protocols::features::GeometricSolvationFeatures
• geometry() : protocols::hybridization::FragmentBiasAssigner
• geometry_is_initialized() : protocols::fldsgn::topology::HSSTriplet
• geometry_is_initialized_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• geometry_score_threshold : protocols::sewing::data_storage::LigandDescription
• geometry_score_weight_ : protocols::sewing::hashing::LigandBindingResPlacer
• GeometryFilter() : protocols::score_filters::GeometryFilter
• GeometrySecMatchRPE() : protocols::match::downstream::GeometrySecMatchRPE
• GeomSampleInfo() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• get() : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::id::AtomID_Map< T > , core::id::NamedAtomID_Map< T > , core::kinematics::MoveMap , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::rotamers::SingleResidueRotamerLibraryFactory , core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::PoseMetricContainer , core::pose::metrics::StructureDependentCalculator , core::pose::toolbox::AtomLevelDomainMap , core::scoring::electron_density::ElectronDensity , core::scoring::EMapVector , core::scoring::mm::MMBondAngleResidueTypeParamSet , core::scoring::saxs::DistanceHistogram , core::scoring::saxs::FormFactor , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::hybridization::TemplateHistory , protocols::jobdist::BasicJob , protocols::neighbor::Neighborhood , protocols::pose_metric_calculators::MetricValueGetter
• get_10A_neighbors() : protocols::enzdes::EnzdesFlexibleRegion
• get_1b_energy() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_2b_energy() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_2D_histogram() : core::scoring::orbitals::OrbitalsStatistics
• get_2d_torsion() : protocols::simple_moves::bb_sampler::BBDihedralSampler2D
• get_2way_orientation() : core::scoring::sasa::LeGrandSasa
• get_3d_torsion() : protocols::simple_moves::bb_sampler::BBDihedralSampler3D
• 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_aa() : core::chemical::rotamers::CenrotRotamerLibrarySpecification , core::chemical::rotamers::DunbrackRotamerLibrarySpecification
• get_aa_for_state() : protocols::hbnet::HBNet
• get_aa_submatrix_energies() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_aa_submatrix_energies_for_edge() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph
• get_aa_to_use() : core::scoring::P_AA
• get_aa_type() : core::pack::interaction_graph::SparseMatrixIndex
• get_abego() : protocols::fldsgn::SheetConstraintGenerator
• get_abego_string() : core::sequence::ABEGOManager
• get_ABGEO_string() : protocols::canonical_sampling::CanonicalSamplingMover
• get_abort_on_failed_loop() : protocols::LoopRebuild
• get_absolute_threshold() : protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerElecDensDiff
• get_accept_aborted_loops() : protocols::loops::loop_mover::IndependentLoopMover
• get_accept_rate() : protocols::docking::DockingLowRes
• get_acceptor_base_atm_xyz() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get_accessible_states() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_accuracy_weight() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• 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_actual_moving_res() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_add_constraints() : protocols::simple_moves::SetupMetalsMover
• get_add_or_delete_element() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_add_probability() : protocols::sewing::movers::AssemblyMover
• get_add_res() : protocols::stepwise::monte_carlo::mover::AddMover
• get_additional_output() : protocols::antibody::design::AntibodyDesignMover , protocols::hbnet::HBNet , protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::loophash::LoopHashMoverWrapper , protocols::motif_grafting::movers::MotifGraftMover , protocols::moves::IfMover , protocols::moves::Mover , protocols::normalmode::NormalModeRelaxMover , protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MergePDBMover , protocols::pose_creation::SliceToMiniProteinMover , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser , protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol , protocols::switches::GraftSwitchMover
• get_additional_output_false_mover() : protocols::moves::IfMover
• get_additional_output_true_mover() : protocols::moves::IfMover
• get_additional_output_with_rmsd() : protocols::pose_length_moves::NearNativeLoopCloser
• get_additional_task_operarations() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• get_address() : protocols::moves::UDPSocketClient
• get_addresses_at_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• get_adjacent_background_node() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_adjacent_dlazy_node() : core::pack::interaction_graph::DoubleLazyNode
• get_adjacent_dpd_node() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode
• get_adjacent_faster_node() : core::pack::interaction_graph::FASTERNode
• get_adjacent_first_class_node() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• get_adjacent_flexbb_node() : protocols::flexpack::interaction_graph::FlexbbNode
• get_adjacent_heavy_atoms() : core::conformation::Residue
• get_adjacent_lazy_node() : core::pack::interaction_graph::LazyNode
• get_adjacent_linmem_node() : core::pack::interaction_graph::LinearMemNode
• get_adjacent_minimalistflexbb_node() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_adjacent_node() : core::pack::interaction_graph::NodeBase
• get_adjacent_npd_hbond_bg_node() : core::pack::interaction_graph::NPDHBondNode< V, E, G >
• get_adjacent_npd_hbond_node() : core::pack::interaction_graph::NPDHBondNode< V, E, G >
• get_adjacent_otf_node() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• get_adjacent_otfflexbb_node() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• get_adjacent_symmin_node() : core::pack::interaction_graph::SymmMinimalistNode
• get_adjacent_symmlinmem_node() : core::pack::interaction_graph::SymmLinearMemNode
• get_ads_secondary_struct() : protocols::surface_docking::FullatomRelaxMover
• get_AHDangle() : core::scoring::hbonds::HBond
• get_akash_dyepos() : protocols::anchored_design::AnchorMoversData
• get_al_tensor_max_z() : core::scoring::ResidualDipolarCoupling
• get_al_tensor_trace() : core::scoring::ResidualDipolarCoupling
• get_ala_pose() : protocols::hbnet::HBNet
• get_ali_params() : core::scoring::TMscore
• get_align_depth() : core::fragment::rna::FragmentLibrary
• get_aligner() : core::sequence::AlignerFactory
• get_alignment() : protocols::calc_taskop_filters::RelativePoseFilter , protocols::evaluation::AlignEvaluator
• get_alignment_atoms() : protocols::sewing::data_storage::LigandResidue
• get_alignment_domain() : core::import_pose::libraries::RNA_ChunkLibrary
• get_alignment_from_template() : protocols::hybridization::ChunkTrialMover
• get_alignment_medium_label() : core::scoring::nmr::rdc::RDCMultiSet
• get_alignments() : protocols::sewing::hashing::BasisMapGenerator
• get_all() : protocols::cyclic_peptide::PeptideCyclizeMover , protocols::loophash::LoopHashLibrary
• get_all_alignments() : protocols::sewing::hashing::AlignmentGenerator
• get_all_atom_types_in_database() : core::chemical::AtomTypeDatabaseIO
• get_all_born_radii() : core::scoring::GenBornPotential
• get_all_cdrs() : protocols::antibody::AntibodyInfo
• get_all_cdrs_present() : protocols::antibody::AntibodyInfo
• get_all_comments() : core::io::silent::SilentStruct
• get_all_constraints() : core::scoring::constraints::ConstraintSet
• get_all_data() : protocols::analysis::InterfaceAnalyzerMover
• get_all_disulfides() : core::scoring::disulfides::DisulfideMatchingDatabase
• get_all_exemplars() : protocols::cluster::APCluster
• get_all_features_names() : protocols::features::FeaturesReporterFactory
• get_all_function_names() : protocols::ligand_docking::rdf::RDFFunctionFactory
• get_all_jacobians() : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• get_all_loops_closed() : protocols::loops::loop_mover::IndependentLoopMover
• get_all_loops_definer_names() : protocols::loops::loops_definers::LoopsDefinerFactory
• get_all_nondegenerate_conformers() : core::chemical::rings::RingConformerSet
• get_all_per_residue_data() : protocols::analysis::InterfaceAnalyzerMover
• get_all_pose_chains() : protocols::features::InterfaceFeatures
• get_all_poses() : core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::PoseInputStream
• get_all_possible_residue_types() : core::chemical::ResidueTypeFinder
• get_all_properties() : core::chemical::AtomType
• get_all_register_and_bulges() : core::scoring::dssp::StrandPairing
• get_all_residues_in_database() : core::chemical::ResidueDatabaseIO
• get_all_rotamer_samples() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_all_rotamer_samples_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• get_all_sasas() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_all_scores() : protocols::features::InterfaceDdGMover , protocols::legacy_sewing::scoring::LegacyAssemblyScoreFunction
• get_all_sm_data() : core::simple_metrics::SimpleMetricData
• get_all_solutions() : protocols::rna::denovo::coarse::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_all_trees() : core::conformation::carbohydrates::GlycanTreeSet
• get_all_types_with_variants_aa() : core::chemical::GlobalResidueTypeSet , core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• get_all_types_with_variants_by_basetype() : core::chemical::ResidueTypeSet
• get_all_types_with_variants_name1() : core::chemical::ResidueTypeSet
• get_all_types_with_variants_name3() : core::chemical::ResidueTypeSet
• 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_slide_jump_map() : protocols::symmetry::SymmetrySlider
• get_allowed_failure_before_extend() : protocols::LoopRebuild
• get_allowed_failure_before_stop() : protocols::LoopRebuild
• get_allowed_norm_lin() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• get_allowed_norm_rot() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• get_aln() : protocols::comparative_modeling::AlignmentCluster
• get_alpha() : core::scoring::nmr::NMRTensor , core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_alpha_beta_pattern() : protocols::ncbb::SecStructMinimizeMover
• get_alphabet() : core::scoring::constraints::ResidueCouplingConstraint
• get_alt_hASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_alt_pd_energy_total() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• get_alt_score_() : core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl
• get_alt_state_atom_atom_overlaps() : core::pack::interaction_graph::HPatchEdge< V, E, G >
• get_alt_state_hASA_for_node_and_nbs() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_alt_state_num_atoms() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_alt_state_rotamer_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• get_alt_stateE() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• get_altE_for_bb_move() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_alternate() : core::pack::interaction_graph::SimpleNode
• get_alternate_3_letter_code_map() : core::io::NomenclatureManager
• get_alternate_for_node() : core::pack::interaction_graph::SimpleInteractionGraph
• get_alternate_ref() : core::pack::interaction_graph::SimpleNode
• get_alternate_sasa() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_alternate_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• get_alternate_state_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge
• get_alternate_state_energy_first_node() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_alternate_state_energy_second_node() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_alternate_state_sasa() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_amide_mm() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_amino_acid_type() : protocols::sewing::data_storage::SmartSewingResidue
• get_anchor_noise_constraints_mode() : protocols::anchored_design::AnchorMoversData
• get_anchor_residue() : core::conformation::symmetry::SymmData
• get_anchor_rsd() : protocols::cyclic_peptide::PeptideStubMover
• get_anchor_via_constraints() : protocols::anchored_design::AnchorMoversData
• get_anchors() : protocols::hybridization::HybridizeFoldtreeDynamic , protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• get_and_cache_pdb() : protocols::pose_creation::MakeJunctionsMover
• get_ands() : protocols::antibody::AntibodyDatabaseManager
• get_angle() : protocols::membrane::FlipMover , protocols::membrane::TiltMover
• get_angle_cutoff() : protocols::membrane::MPLipidAccessibility
• get_angle_diffs() : protocols::matdes::SymDofMoverSampler
• get_angle_max() : protocols::simple_moves::BackboneMover , protocols::simple_moves::bb_sampler::SmallBBSampler
• get_angle_multiplier() : protocols::sewing::scoring::LigandScorer
• get_angle_range() : protocols::simple_moves::TorsionDOFMover
• get_angle_score() : core::scoring::methods::GoapEnergy
• get_angles() : core::scoring::sasa::LeGrandSasa , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• get_angular_momentum_quantum_number() : core::chemical::ElectronConfiguration
• get_ANN_data() : protocols::sparta::Sparta::SpartaLib
• get_annealer_pick_table() : protocols::RotamerDump::RotamerDumpMover
• get_annotation() : core::io::rna::RDAT
• 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_numbering_info() : protocols::antibody::AntibodyInfo
• 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_antiparallel_weight() : core::scoring::SecondaryStructureWeights
• get_apply_offset() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• get_arbitrary_score_data_from_pose() : core::io::raw_data::ScoreMap
• get_arbitrary_string_data_from_pose() : core::io::raw_data::ScoreMap
• get_aro_axis_score_ANGLE() : core::scoring::hackaro::HackAroEnergy
• get_aro_axis_score_DIST() : core::scoring::hackaro::HackAroEnergy
• get_array_indices() : core::scoring::dna::DNA_BasePotential
• get_assembly_scorer() : protocols::sewing::scoring::AssemblyScorerFactory
• get_assembly_scorers() : protocols::sewing::movers::AssemblyMover
• get_asu_rotamer() : core::pack::interaction_graph::SymmOnTheFlyNode
• get_asymmetric_seqpos() : core::conformation::symmetry::SymmetryInfo
• get_atom() : core::io::nmr::AtomSelection , core::optimization::CartesianMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , protocols::sewing::data_storage::SmartSewingResidue
• get_atom_atom_carbon_hbond_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• get_atom_atom_coverage() : core::pack::interaction_graph::RotamerDots
• get_atom_atom_geometric_solvation_for_acceptor() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get_atom_atom_geometric_solvation_for_donor() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get_atom_atom_occ_solvation() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• get_atom_atom_overlaps_for_state() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• get_atom_atom_self_overlaps() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_atom_atom_self_overlaps_for_state() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_atom_bin_size() : core::pose::rna::VDW_Grid
• get_atom_collision_radius() : protocols::vardist_solaccess::VarSolDRotamerDots
• get_atom_coordinates() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• get_atom_coords_xyz() : core::pack::interaction_graph::RotamerDots , protocols::vardist_solaccess::VarSolDRotamerDots
• get_atom_counts() : core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache
• get_atom_derivatives() : core::scoring::nmr::pcs::PCSSingle , core::scoring::nmr::pre::PRESingle , core::scoring::nmr::rdc::RDCSingle
• get_atom_dist_from_connolly_surface() : protocols::pockets::ElectrostaticpotentialGrid
• get_atom_h2o_hbond_derivative() : core::scoring::methods::WaterAdductHBondEnergy
• get_atom_id_domain_map_for_rosetta_library_chunk() : core::import_pose::libraries::ChunkSet
• get_atom_id_map() : core::import_pose::libraries::ChunkSet
• get_atom_IDs() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_atom_ids_by_torsion() : core::scoring::dna::DNATorsionPotential
• get_atom_index() : core::optimization::CartesianMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::scoring::saxs::FormFactorManager
• get_atom_interaction_radius() : protocols::vardist_solaccess::VarSolDRotamerDots
• get_atom_level_domain_map() : protocols::simple_moves::ConstrainToIdealMover
• get_atom_lk_energy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• get_atom_name() : protocols::scoring::methods::pcs2::PcsInputLine
• get_atom_name_from_database_atom_index() : core::chemical::ResidueDatabaseIO
• get_atom_name_to_vd_map() : core::chemical::MutableResidueType
• get_atom_overlap_masks() : protocols::vardist_solaccess::VarSolDRotamerDots
• get_atom_pair_func_list() : core::scoring::custom_pair_distance::PairFuncMap
• get_atom_pos() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• get_atom_positions() : core::pack::rotamers::SingleLigandRotamerLibrary
• get_atom_radius() : core::pack::interaction_graph::RotamerDots
• get_atom_sasa() : core::pack::interaction_graph::RotamerDots , core::scoring::sasa::SasaCalc
• get_atom_table() : core::scoring::nmr::NMRDummySpinlabelConformer
• get_atom_type() : protocols::frag_picker::scores::AtomBasedConstraintsScore , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::InterbondAngleScore
• get_atom_type_property() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_atom_type_set_name() : core::scoring::AtomVDW
• get_atom_vector() : protocols::sewing::data_storage::SmartSewingResidue
• get_atom_weight() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• get_atomic_number() : core::chemical::Element
• get_atomID() : protocols::normalmode::NormalMode
• get_atomname() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• get_atomnames_size() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• get_atoms() : core::kinematics::MoveMap
• get_atoms_exocyclic_to_ring_atom() : core::conformation::Residue
• get_atoms_within_radius() : core::scoring::sc::ElectrostaticComplementarityCalculator
• get_AtomVDW() : core::scoring::ScoringManager
• get_attachment_point_string() : protocols::analysis::GlycanInfoMover
• get_attachments() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_atype_index() : protocols::membrane::scoring::FaWaterToBilayerEnergy
• get_autoinitialize() : protocols::anchored_design::AnchoredDesignMover
• get_average_cation_pi_ip_to_neutral_ip_ratio() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_cation_sigma_ip_to_neutral_ip_ratio() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_energy() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• get_average_ip_change_cation_to_neutral() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_ip_change_neutral_to_anion() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_neutral_pi_ip_to_anion_ip_ratio() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_neutral_sigma_ip_to_anion_ip_ratio() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_average_structure() : protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Serial_Refine
• get_averaging_type() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::pre::PREMultiSet , core::scoring::nmr::rdc::RDCMultiSet
• get_avg_dis_CA_CA() : protocols::features::strand_assembly::StrandBundleFeatures
• get_ax() : core::scoring::nmr::NMRTensor
• get_axis() : protocols::membrane::FlipMover
• get_b() : protocols::pockets::UnionEdge
• get_b_axis() : protocols::docking::EllipsoidalRandomizationMover
• get_backbone() : protocols::loop_grower::LoopPartialSolution
• get_backbone_centroid() : protocols::rna::denovo::movers::RNA_HelixMover
• 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_mover() : protocols::coupled_moves::CoupledMovesProtocol , protocols::simple_moves::CoupledMover
• get_backbone_segment() : protocols::loophash::BackboneDB
• get_backbone_segments() : protocols::loop_modeler::perturbers::LoopHashPerturber
• get_background_node() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• get_background_node_index() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• get_backrubmover() : protocols::simple_moves::ShortBackrubMover
• get_BAHangle() : core::scoring::hbonds::HBond
• get_base_atom_name() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_base_atr_rep_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• get_base_backbone() : core::scoring::rna::RNA_LowResolutionPotential
• get_base_base_atom_name() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_base_centroid() : core::scoring::rna::RNA_CentroidInfo
• get_base_coordinate_system() : core::scoring::hackaro::HackAroEnergy , core::scoring::rna::RNA_CentroidInfo
• get_base_names_by_properties() : core::pack::palette::PackerPalette
• get_base_pair_steps() : core::import_pose::RNA_BasePairHandler
• get_base_residue_types() : core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::DefaultPackerPalette , core::pack::palette::NCAADefaultPackerPalette , core::pack::palette::NoDesignPackerPalette , core::pack::palette::PackerPalette
• get_base_residue_types_cached() : core::pack::palette::PackerPalette
• get_base_type_cop() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::chemical::ResidueTypeBase
• get_base_type_raw_ptr() : core::pack::palette::PackerPalette
• get_base_types_aa() : core::chemical::ResidueTypeSet
• get_base_types_name1() : core::chemical::ResidueTypeSet
• get_base_types_name3() : core::chemical::ResidueTypeSet
• get_base_vector() : core::scoring::methods::LK_PolarNonPolarEnergy
• get_basis_map_generator() : protocols::sewing::movers::AssemblyMover
• get_basis_pair() : protocols::sewing::data_storage::SmartSegment
• get_basis_pair_for_local_segments() : protocols::sewing::hashing::BasisMapGenerator
• get_basis_pair_for_segment() : protocols::sewing::hashing::BasisMapGenerator
• get_basis_pair_for_segment_pair() : protocols::sewing::hashing::BasisMapGenerator
• get_basis_res_bounds() : protocols::sewing::hashing::BasisMapGenerator
• get_batch_description() : protocols::features::ReportToDB
• get_batch_id() : protocols::features::ProteinSilentReport
• get_batch_name() : protocols::features::ReportToDB
• get_BAtorsion() : core::scoring::hbonds::HBond
• get_bb() : core::kinematics::MoveMap , 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_bbE() : core::pack::rotamer_set::RotamerSets
• get_bb_bins() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• get_bb_distance() : protocols::motif_grafting::movers::MotifGraftMover
• get_bb_E() : core::pack::interaction_graph::SimpleEdge
• 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_index() : core::pack::interaction_graph::SimpleEdge
• get_bb_interface_builder() : protocols::ligand_docking::MoveMapBuilder
• get_bb_pos() : protocols::rna::denovo::movers::RNA_HelixMover
• get_bb_range() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_bbdep_nrchi_bin() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• get_bbs() : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData
• get_below_distance_threshold() : protocols::pose_length_moves::PossibleLoop
• get_best_energy_stub() : protocols::hotspot_hashing::HotspotStubSet
• get_best_exp_to_calc_chem_shift_mapping() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_best_geometry_score() : protocols::sewing::hashing::LigandBindingResPlacer
• get_best_grid_point() : core::scoring::nmr::NMRGridSearch
• get_best_hxyz() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• get_best_match_residue_type_for_atom_names() : core::chemical::ResidueTypeFinder
• get_best_neighboring_shift_RMSD_and_output_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• get_best_z() : protocols::membrane::OptimizeMembranePositionMover
• get_bestpose() : protocols::flxbb::FilterStructs
• get_beta() : core::scoring::nmr::NMRTensor
• get_beta_pairs() : core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet
• get_bg_bg_atom_atom_overlaps() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_bg_edge_list_begin() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• get_bg_edge_list_end() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• get_bg_edge_vector_up_to_date_() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_bias_sampling() : protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_big_bin() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_bin() : core::pose::rna::VDW_Grid
• get_bin_and_pos() : protocols::match::VoxelSetIterator
• get_bin_max() : core::pose::rna::VDW_Grid
• get_bin_offset() : core::pose::rna::VDW_Grid
• get_bin_size() : core::scoring::func::SplineFunc
• get_binary_name() : core::pack::dunbrack::RotamerLibrary
• get_binary_name_02() : core::pack::dunbrack::RotamerLibrary
• get_binary_name_10() : core::pack::dunbrack::RotamerLibrary
• get_binding_cycles() : protocols::sewing::movers::LigandBindingAssemblyMover
• get_binding_energy() : core::scoring::rna::data::RNA_DMS_Potential
• get_bins_per_A2() : core::scoring::etable::Etable
• get_bins_per_A2_ : core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack , core::scoring::rna::RNA_LJ_BaseEnergy
• get_bins_vect() : core::scoring::func::SplineFunc
• get_bins_vect_size() : core::scoring::func::SplineFunc
• get_boinc_wu_cpu_time() : protocols::boinc::Boinc
• get_boltzman_factor() : core::scoring::nmr::NMRSpinlabel
• get_boltzmann_rotamer_mover() : protocols::simple_moves::CoupledMover
• get_boltzmann_temp() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• get_bond_length() : core::chemical::IdealBondLengthSet
• get_bonus_map() : core::scoring::constraints::ResidueTypeLinkingConstraint
• get_bonus_score() : protocols::loop_grower::LoopPartialSolution
• get_bound_mut_pose() : protocols::features::InterfaceDdGMover
• get_bound_wt_pose() : protocols::features::InterfaceDdGMover
• get_boundary_neighs() : core::scoring::elec::FAElecContextData
• get_boundary_residues() : protocols::hbnet::HBNet
• get_boundary_selector() : protocols::hbnet::HBNet
• get_bp_center() : protocols::rna::denovo::movers::RNA_HelixMover
• get_branches() : core::kinematics::MoveMap
• 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_build_site_only() : protocols::sewing::movers::LigandBindingAssemblyMover
• get_builder() : protocols::nonlocal::TreeBuilderFactory
• get_bump_check() : protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_bump_overlap_factor() : core::pack::task::residue_selector::ClashBasedShellSelector , 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_c2f() : core::scoring::electron_density::ElectronDensity
• get_C4_C3_distance_range() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• get_c_axis() : protocols::docking::EllipsoidalRandomizationMover
• get_c_cyd_seqpos() : protocols::simple_moves::DisulfideInsertionMover
• get_c_most_segment() : protocols::sewing::data_storage::SmartSegment
• get_c_terminal_helix() : protocols::switches::GraftSwitchMover
• get_c_terminal_neighbor() : protocols::sewing::data_storage::SmartSegment
• get_c_terminal_parent() : protocols::sewing::data_storage::SmartSegment
• get_c_terminal_segment() : protocols::sewing::data_storage::SmartAssembly
• get_ca_bfactors() : protocols::match::BfactorMPM
• get_CA_xyz() : core::import_pose::PDBSilentStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• get_cacheable_cluster_data() : protocols::antibody::clusters::CDRClusterSet
• get_cachetag() : core::pack::rotamers::SingleResidueRotamerLibraryFactory
• get_CAcrd() : protocols::simple_filters::ResidueDepthFrag
• get_calc_chem_shift_value() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_calc_chem_shift_value_larmord() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_calc_chem_shift_value_nuchemics() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_calc_rms_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_calc_rot_freq() : core::pack::annealer::SimAnnealerBase
• get_calculator() : core::pose::metrics::PoseMetricContainer , protocols::task_operations::RestrictToNeighborhoodOperation
• get_calculator_for_helix() : protocols::helical_bundle::PerturbBundle
• get_calculator_name() : protocols::task_operations::RestrictToNeighborhoodOperation
• get_calphas() : protocols::loop_grower::LoopPartialSolution
• 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_canonical_base_pair_steps() : core::import_pose::RNA_BasePairHandler
• get_CarbonHBondPotential() : core::scoring::ScoringManager
• get_cartesian() : protocols::mpi_refinement::WorkUnit_CombinePose , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin
• get_cartesian_bonded_linear() : core::scoring::methods::EnergyMethodOptions
• get_cartesian_bonded_parameters() : core::scoring::methods::EnergyMethodOptions
• get_cartesian_bonded_skip_cutpoints() : core::scoring::methods::EnergyMethodOptions
• 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_h3_loop() : protocols::antibody::AntibodyModelerProtocol
• 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::GeneralAntibodyModeler
• get_CDR_loops() : protocols::antibody::AntibodyInfo
• get_cdr_loops() : protocols::antibody::design::GeneralAntibodyModeler
• get_cdr_loops_with_overhang() : protocols::antibody::design::GeneralAntibodyModeler
• get_CDR_name() : protocols::antibody::AntibodyInfo
• get_CDR_name_enum() : protocols::antibody::AntibodyInfo
• get_cdr_sequence() : protocols::antibody::design::NativeAntibodySeq
• get_CDR_sequence_with_stem() : protocols::antibody::AntibodyInfo
• get_cdr_set_index_list() : protocols::antibody::design::AntibodyDesignMover
• get_CDR_start() : protocols::antibody::AntibodyInfo
• get_CDR_start_PDB_num() : protocols::antibody::AntibodyInfo
• get_CDRNameEnum_of_residue() : protocols::antibody::AntibodyInfo
• get_cdrs_movemap_with_overhang() : protocols::antibody::design::GeneralAntibodyModeler
• get_cellDimensions() : core::scoring::electron_density::ElectronDensity
• get_cen_deviation() : protocols::simple_moves::StructProfileMover
• get_cen_dist() : protocols::make_rot_lib::RotData
• get_CENcrd() : protocols::simple_filters::ResidueDepthFrag
• get_CenHBPotential() : core::scoring::ScoringManager
• get_cenlist_from_pose() : core::scoring::membrane::MembraneData
• get_cenrot_library_by_aa() : core::pack::dunbrack::cenrot::CenrotLibrary
• get_CenRotEnvPairPotential() : core::scoring::ScoringManager
• get_center() : protocols::cyclic_peptide::FlipChiralityMover , protocols::pockets::SmallMol , protocols::qsar::scoring_grid::SingleGrid
• get_center_ndx() : protocols::toolbox::KClusterElement
• get_center_of_mass() : protocols::pose_length_moves::PossibleLoop , protocols::simple_moves::RepeatPropagationMover
• get_center_resnumber() : protocols::relax::membrane::MPRangeRelaxMover
• get_central_residues() : protocols::task_operations::RestrictToNeighborhoodOperation
• get_centroid() : core::scoring::hackaro::HackAroEnergy , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::rna::denovo::coarse::MultipleDomainMover
• get_centroid_data() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_centroid_dG() : protocols::analysis::InterfaceAnalyzerMover
• get_centroid_information() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• get_centroid_pose() : protocols::legacy_sewing::LegacyAssemblyMover
• get_centroid_scorefunction() : protocols::anchored_design::AnchorMoversData
• get_centroid_scorefunction_min() : protocols::anchored_design::AnchorMoversData
• get_CentroidDisulfidePotential() : core::scoring::ScoringManager
• get_chain() : core::io::nmr::AtomSelection , protocols::nmr::pcs::PCSLigandTransformMover , 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::peptide_deriver::PeptideDeriverFilter
• get_chainbreak_scores() : protocols::analysis::LoopAnalyzerMover
• get_chainbreak_weight() : protocols::anchored_design::AnchorMoversData
• get_chainbreak_xyz() : protocols::rna::movers::RNA_LoopCloser
• get_charge() : core::io::nmr::ParaIon
• get_charged_residues_map() : core::scoring::methods::PBLifetimeCache
• 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_chem_comp_type() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• get_chemical_edges() : core::kinematics::FoldTree
• get_chemical_name() : core::chemical::Element
• get_chemical_shift_energy() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_chemical_symbol() : core::chemical::Element
• get_chi() : core::kinematics::MoveMap
• get_chi_data() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_chi_weight() : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• 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_CHIEnergyFunction() : core::scoring::ScoringManager
• get_children() : core::conformation::carbohydrates::GlycanNode , protocols::loop_modeling::LoopMover
• get_children_names() : protocols::kinematic_closure::KicMover , protocols::loop_modeling::LoopMover , protocols::loop_modeling::utilities::LoopMoverGroup
• get_chimera_segments() : protocols::legacy_sewing::Assembly
• get_chis() : protocols::sewing::data_storage::SmartSewingResidue
• get_chunk() : protocols::frag_picker::FragmentCandidate
• get_cid() : protocols::constel::ChainTerm
• get_circular_permutation_first_in_alphabetical_order() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• get_clash_checking() : protocols::match::downstream::TargetRotamerCoords
• get_clash_radius() : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::LigandClashRequirement
• get_clash_score() : core::scoring::nmr::NMRDummySpinlabelConformer , protocols::motif_grafting::movers::MotifMatch
• get_clash_score_from_pose() : protocols::motif_grafting::movers::MotifGraftMover
• get_classifier() : core::pose::rna::RNA_SuiteName
• get_cloned_aa_comp_setup_helpers() : core::scoring::ScoringManager
• get_cloned_mhc_epitope_setup_helpers() : core::scoring::ScoringManager
• get_cloned_netcharge_setup_helpers() : core::scoring::ScoringManager
• get_cloned_saved_pose() : protocols::rosetta_scripts::SavePoseMover
• get_closest_cluster() : protocols::antibody::clusters::CDRClusterMatcher
• get_closest_heavy_atom() : protocols::simple_moves::AddCavitiesMover
• get_closest_rotamer() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• get_closest_sequence_at_res() : protocols::simple_moves::StructProfileMover
• get_closest_sequences() : protocols::simple_moves::StructProfileMover
• 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_metric() : protocols::multistage_rosetta_scripts::MRSJob
• get_cluster_name() : protocols::antibody::AntibodyInfo
• get_cluster_name_by_PDB() : protocols::splice::SpliceSegment
• get_cluster_num() : protocols::make_rot_lib::RotData
• get_cluster_radius() : protocols::cluster::ClusterBase
• get_cluster_string_vec() : protocols::antibody::AntibodyDatabaseManager
• get_cluster_totals() : protocols::antibody::AntibodyDatabaseManager
• get_clusterCenter() : protocols::comparative_modeling::AlignmentCluster
• get_co_substrate() : protocols::enzymatic_movers::EnzymaticMover
• get_coarse_crd() : protocols::simple_filters::ResidueDepthCalculator
• get_code() : core::scoring::nmr::NMRSpinlabel
• get_coeff() : protocols::simple_filters::SecretionPredictionFilter
• get_combine_if_fail_exist() : protocols::LoopRebuild
• get_comment() : core::io::silent::SilentStruct
• get_complex_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_complexed_sasa() : protocols::analysis::InterfaceAnalyzerMover
• get_component() : core::conformation::symmetry::SymmetryInfo , protocols::frag_picker::scores::FragmentScoreManager
• get_component_bounds() : core::conformation::symmetry::SymmetryInfo
• get_component_by_name() : protocols::frag_picker::scores::FragmentScoreManager
• get_component_file() : protocols::simple_moves::ConcatenatePosesMover
• get_component_lower_bound() : core::conformation::symmetry::SymmetryInfo
• get_component_of_residue() : core::conformation::symmetry::SymmetryInfo
• get_component_upper_bound() : core::conformation::symmetry::SymmetryInfo
• get_components() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_composite_real_metric_data() : core::simple_metrics::SimpleMetricData
• get_composite_string_metric_data() : core::simple_metrics::SimpleMetricData
• get_comprehensive_assembly_string() : protocols::sewing::data_storage::SmartAssembly
• get_comprehensive_forward_assembly() : protocols::sewing::data_storage::SmartAssembly
• get_comprehensive_reverse_assembly() : protocols::sewing::data_storage::SmartAssembly
• get_computation_type() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet
• get_computed() : core::scoring::PolymerBondedEnergyContainer
• get_conformation_to_turn_type_map() : protocols::features::BetaTurnDetection
• get_conformer() : protocols::docking::DockingEnsemble
• get_conformer_cen() : protocols::docking::DockingEnsemble
• get_conformer_switch_probability() : protocols::sewing::movers::AssemblyMover
• get_conformer_table() : core::scoring::nmr::NMRDummySpinlabelEnsemble
• get_conformers_for_ring_size_and_type() : core::chemical::rings::RingConformerManager
• get_connecting_id_for_append_by_bond() : protocols::cyclic_peptide::PeptideStubMover
• get_connection() : protocols::generalized_kinematic_closure::GeneralizedKIC
• get_connectivity_annotation_info() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• 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_consensus_residues() : core::enzymes::EnzymeManager
• get_consensus_sequence() : core::enzymes::EnzymeManager
• get_consensus_sequence_type() : core::enzymes::EnzymeManager
• get_const_atom_vector() : protocols::sewing::data_storage::SmartSewingResidue
• get_const_deer_data() : core::energy_methods::DEEREnergy
• get_const_EnzConstraintIO_for_cstfile() : protocols::enzdes::AddOrRemoveMatchCsts
• get_const_job_node() : protocols::jd3::JobGenealogist
• get_const_owned_ligand_residues() : protocols::sewing::data_storage::LigandSegment
• get_const_reference_segment() : protocols::sewing::data_storage::SmartSegment
• get_const_residue_vector() : protocols::sewing::data_storage::SmartSegment
• get_const_result_node() : protocols::jd3::JobGenealogist
• get_constrain() : protocols::ncbb::SecStructMinimizeMover
• get_constrain_to_closest() : protocols::constraint_generator::MetalContactsConstraintGenerator
• 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_constraint_target_pose() : protocols::relax::AtomCoordinateCstMover
• get_constraint_weight() : protocols::simple_moves::DisulfideInsertionMover
• get_constraints_from_file() : protocols::constraint_movers::CstInfoMover
• get_constraints_from_pose() : protocols::constraint_movers::CstInfoMover
• get_constraints_only() : protocols::simple_moves::SetupMetalsMover
• get_contact() : protocols::contact_map::ContactMap
• get_contact_distance_cutoff() : protocols::sewing::requirements::KeepLigandContactsRequirement
• get_contact_resnum_string() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_contact_resnums() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_contact_resnums_string() : protocols::simple_moves::SetupMetalsMover
• get_contact_selector() : protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::simple_moves::SetupMetalsMover
• get_contacting_reslist() : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• get_contacts() : protocols::frag_picker::nonlocal::NonlocalPair
• get_containing_helix_index() : protocols::helical_bundle_predict::HBPHelixAssignments
• get_coordinate_system() : core::scoring::disulfides::RT_helper
• get_coordinates() : core::scoring::nmr::VoxelGridPoint , protocols::nmr::pcs::AtomGridPoint , protocols::pockets::SmallMol
• get_coordinates_from_pose() : protocols::pose_length_moves::PossibleLoop
• get_coords() : core::scoring::epr_deer::EPRSpinLabel
• get_coords_for_clash_check() : protocols::match::downstream::TargetRotamerCoords
• get_core_chunk_index_from_position() : protocols::hybridization::HybridizeFoldtreeDynamic
• get_core_residues() : protocols::hbnet::HBNet
• get_core_selector() : protocols::hbnet::HBNet
• get_corresponding_residue_in_current() : core::id::SequenceMapping
• get_cos_angle() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• get_count_pair_data_for_residue() : core::scoring::trie::RotamerTrieBase
• get_count_pair_function() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy
• get_count_pair_function_trie() : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDW_Energy
• get_countpair_representative_atom() : core::scoring::elec::FA_ElecEnergy
• get_cp_rep_map_byname() : core::scoring::ScoringManager
• get_cps() : protocols::constel::ChainTerm
• get_creator() : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::io::silent::SilentStructFactory , core::scoring::constraints::ConstraintFactory , core::sequence::SequenceFactory
• get_crick_parameters() : protocols::helical_bundle::FitSimpleHelix
• get_crosslinker_enum() : protocols::cyclic_peptide::CrosslinkerMover
• get_crosslinker_name() : protocols::cyclic_peptide::CrosslinkerMover
• get_crossterm_interface_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_crossterm_interface_energy_ratio() : protocols::analysis::InterfaceAnalyzerMover
• get_CSA_data() : core::scoring::ChemicalShiftAnisotropy
• get_cst_factory() : core::scoring::constraints::ConstraintIO
• get_cst_file_name() : protocols::simple_moves::SequenceProfileMover
• get_cst_list() : protocols::abinitio::Templates
• get_cst_names() : core::scoring::constraints::ConstraintFactory
• get_cst_weight() : core::scoring::mhc_epitope_energy::MHCEpitopeConstraint
• 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_insert_flexibility() : protocols::grafting::AnchoredGraftMover
• get_cterm_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• get_cube() : core::scoring::packstat::Octree2D
• get_cur_ncluster() : protocols::toolbox::KClusterElement
• get_curr_pd_energy_total() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• get_curr_state_energy_following_partial_state_assignment() : core::pack::interaction_graph::FASTEREdge
• get_curr_state_recent_state_id() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• get_curr_state_surface_energy() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_curr_upper_hbond_energies() : core::pack::interaction_graph::NPDHBSimpleNode
• get_current() : core::pack::interaction_graph::SimpleNode
• 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_conformer_ensemble1() : protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble
• get_current_conformer_ensemble2() : protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble
• get_current_contacts() : protocols::sewing::data_storage::LigandResidue
• get_current_cycle() : protocols::features::TrajectoryMapFeatures
• get_current_energy() : core::pack::interaction_graph::SimpleEdge
• get_current_ensemble_size() : core::scoring::nmr::NMRSpinlabel
• get_current_eqxyz() : protocols::md::CartesianMD
• get_current_for_node() : core::pack::interaction_graph::SimpleInteractionGraph
• get_current_hASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_current_job() : protocols::moves::Mover
• get_current_jump() : protocols::symmetry::SymmetrySlider
• get_current_network_state() : core::pack::interaction_graph::FASTERInteractionGraph
• get_current_output_tag() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• get_current_ref() : core::pack::interaction_graph::SimpleNode
• get_current_res_symmetric() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• get_current_rotamer() : core::pack::interaction_graph::LinearMemNode
• get_current_sasa() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_current_seg() : protocols::splice::Splice
• get_current_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• get_current_state_atom_atom_overlaps() : core::pack::interaction_graph::HPatchEdge< V, E, G >
• get_current_state_for_node() : core::pack::interaction_graph::FASTERInteractionGraph
• get_current_state_num_atoms() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_current_state_rotamer_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• get_current_state_sasa() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_current_tag() : protocols::moves::Mover
• get_current_two_body_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• get_custom_rama_table_filename() : core::scoring::Ramachandran
• get_custom_type() : core::simple_metrics::SimpleMetric
• get_cutoff() : protocols::frag_picker::SidechainContactDistCutoff
• get_cutoff_angle() : protocols::sewing::scoring::LigandScorer
• get_cutoff_distance() : protocols::sewing::scoring::LigandScorer
• get_cutoff_squared() : protocols::frag_picker::SidechainContactDistCutoff
• get_cutpoint() : core::import_pose::RNA_HelixAssembler , protocols::loop_grower::LoopPartialSolutionStore
• get_cutpoint_open_from_pdb_info() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• get_cutpoints() : protocols::seeded_abinitio::SeedFoldTree
• get_cutpoints_closed() : protocols::rna::movers::RNA_LoopCloser
• get_cycle_counts() : protocols::features::TrajectoryReportToDB
• get_cyclization_name_from_type() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• get_cyclization_type_from_name() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• get_d2_low() : core::scoring::lkball::LK_BallEnergy
• get_d_equivalent() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• get_Da() : core::scoring::nmr::rdc::RDCTensor
• get_data() : core::scoring::electron_density::ElectronDensity , core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData , protocols::antibody::design::MutateFrameworkForCluster , protocols::frag_picker::JCouplingIO
• get_data_int() : protocols::denovo_design::components::StructureData
• get_data_ndx() : protocols::toolbox::KClusterElement
• get_data_real() : protocols::denovo_design::components::StructureData
• get_data_ref() : core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData
• get_data_score() : core::pose::rna::RNA_FilteredBaseBaseInfo
• get_data_str() : protocols::denovo_design::components::StructureData
• get_database() : core::scoring::hbonds::HBondDatabase , core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal
• get_database_name() : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• get_database_pq_schema() : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• get_DatabaseOccSolEne() : core::scoring::ScoringManager
• get_dataset_name() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::pre::PRESingleSet , core::scoring::nmr::rdc::RDCSingleSet
• get_db() : core::scoring::methods::CartesianBondedEnergy
• get_DC_data() : core::scoring::DipolarCoupling
• get_DC_data_type() : core::scoring::DC
• get_ddg_bisect_score() : protocols::simple_ddg::SSElementBisectddGFilter
• get_DDPLookupTable() : core::scoring::ScoringManager
• get_debug() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_debug_rmsd() : core::import_pose::PDBSilentStruct , core::io::raw_data::DecoyStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::raw_data::ScoreStructText , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• get_deep_apo_atoms() : protocols::simple_filters::BuriedUnsatHbondFilter
• get_deer_data() : core::energy_methods::DEEREnergy
• get_default() : protocols::pose_selectors::AndSelector , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::OrSelector
• get_default_bonus() : core::scoring::constraints::ResidueTypeLinkingConstraint
• get_default_bridge_type() : protocols::dna_dock::PropagateClashCheckFilter
• get_default_parameter() : core::chemical::AtomTypeSet
• get_default_task_factory() : protocols::loop_modeler::LoopModeler
• get_degrees() : protocols::nonlocal::HelixRotate
• get_delete_interface_native_sidechains() : protocols::anchored_design::AnchoredDesignMover
• get_delete_probability() : protocols::sewing::movers::AssemblyMover
• 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_deltaE_for_neighbor_following_perturbation() : core::pack::interaction_graph::FASTEREdge
• get_deltaE_for_perturbation() : core::pack::interaction_graph::FASTEREdge
• get_deltaE_for_relaxed_state_following_perturbation() : core::pack::interaction_graph::FASTERNode
• get_den_fit_metric() : core::select::residue_selector::DensityFitResidueSelector
• get_density() : protocols::loop_grower::DensSkeleton
• get_density_sc_scale_byres() : core::scoring::methods::EnergyMethodOptions
• get_deriv() : core::scoring::rna::TNA_SuitePotential
• get_deriv_count() : core::optimization::func_1d
• get_deriv_for_chemical_shift() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_deriv_for_chemical_shift_data_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_derivative() : core::scoring::loop_graph::evaluator::SixDTransRotPotential
• get_description() : protocols::pose_length_moves::PossibleLoop
• get_descriptor() : core::chemical::ElectronConfiguration
• 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_design_cdrs() : protocols::antibody::task_operations::AddCDRProfilesOperation
• get_design_positions() : protocols::coupled_moves::CoupledMovesProtocol
• get_designable_residues() : protocols::task_operations::DesignAroundOperation , protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• get_desired_loops_exist() : protocols::LoopRebuild
• get_desriptor_data() : protocols::features::ScreeningFeatures
• get_detect_interface() : protocols::enzdes::DetectProteinLigandInterface
• get_determinant() : protocols::simple_moves::BBConRotMover
• get_dihedral_pattern() : protocols::ncbb::SecStructMinimizeMover
• get_dihedrals() : protocols::ncbb::SecStructMinimizeMover
• get_dimensions() : protocols::qsar::scoring_grid::SingleGrid
• get_DirectReadoutPotential() : core::scoring::ScoringManager
• get_disabled() : protocols::checkpoint::CheckPointer
• get_dist() : protocols::nmr::pre::PREDistanceRecord , protocols::pockets::UnionEdge
• get_dist_bins() : protocols::scoring::methods::saxs::PDDFEnergy
• get_dist_cutoff() : protocols::membrane::MPLipidAccessibility
• get_dist_cutoff_multiplier() : protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::residue_selectors::LigandMetalContactSelector
• get_dist_err() : protocols::rna::movers::RNA_LoopCloser
• get_distance() : protocols::kinematic_closure::ClosureSolution , protocols::mpi_refinement::Clusterer , protocols::nonlocal::SheetTranslate , protocols::toolbox::KClusterElement
• get_distance_center_to_atom1() : core::scoring::nmr::NMRGridSearch
• get_distance_cutoff() : protocols::sewing::movers::LigandBindingAssemblyMover , protocols::task_operations::RestrictToNeighborhoodOperation
• get_distance_measure() : protocols::cluster::ClusterPhilStyle_Loop , protocols::cluster::ClusterPhilStyle_PoseReporter , protocols::cluster::GatherPosesMover
• get_distance_potential_histogram_file() : core::scoring::nmr::NMRSpinlabel
• get_distance_score() : core::scoring::methods::GoapEnergy
• get_distance_to_start() : core::conformation::carbohydrates::GlycanNode , core::conformation::carbohydrates::GlycanTreeSet
• get_disulf_jump() : protocols::splice::RBOutMover
• get_disulfide_atom_name() : core::chemical::ResidueTypeBase
• get_disulfide_derivatives() : core::scoring::disulfides::FullatomDisulfidePotential
• get_disulfide_derivatives_old() : core::scoring::disulfides::FullatomDisulfidePotential
• get_disulfide_params() : core::scoring::disulfides::FullatomDisulfidePotential
• get_DisulfideMatchingPotential() : core::scoring::ScoringManager
• get_dlazy_edge() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• get_dlazy_ig_owner() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyNode
• get_dlazy_node() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph
• get_Dmax() : core::scoring::nmr::rdc::RDCTensor
• get_dna_a_path() : protocols::dna_dock::DNAClashCheckFilter
• get_dna_b_path() : protocols::dna_dock::DNAClashCheckFilter
• get_DNA_BasePotential() : core::scoring::ScoringManager
• get_DNA_DihedralPotential() : core::scoring::ScoringManager
• get_DNA_EnvPairPotential() : core::scoring::ScoringManager
• get_DNABFormPotential() : core::scoring::ScoringManager
• get_DNATorsionPotential() : core::scoring::ScoringManager
• get_dock_chains() : protocols::antibody::design::GeneralAntibodyModeler
• get_dock_domains() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_Dock_ScoreFxn() : protocols::antibody::AntibodyInfo
• get_docking_add_and_delete_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_docking_add_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_docking_delete_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_docking_split_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_DOF() : protocols::simple_moves::TorsionDOFMover
• get_dof_axis_and_end_pos() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• get_dof_derivative_weight() : core::conformation::symmetry::SymmetryInfo
• get_dof_id() : core::optimization::CartesianMinimizerMap
• get_dofs() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_dofs_for_pose0() : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• get_dofs_from_energy_map() : protocols::optimize_weights::OptEMultifunc
• get_dofs_map() : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• get_dofs_pdb_name() : protocols::splice::Splice
• get_domain() : core::pose::toolbox::AtomLevelDomainMap
• get_donor_acceptor_group_from_heavyatom_index() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• get_dot_covered() : core::pack::interaction_graph::DotSphere , protocols::vardist_solaccess::VarSolDRotamerDots
• get_downstream_connections() : core::conformation::carbohydrates::GlycanNode
• get_dpd_edge() : core::pack::interaction_graph::DensePDInteractionGraph
• get_dpd_node() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph
• get_dpdig_owner() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDNode
• get_dq_max_allowed() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• 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_dssp_code() : protocols::sewing::data_storage::SmartSegment , protocols::sewing::requirements::DsspSpecificLengthRequirement
• get_dssp_plus_abego_L_def() : core::scoring::dssp::Dssp
• get_dssp_reduced_IG_as_L_secstruct() : core::scoring::dssp::Dssp
• get_dssp_secstruct() : core::scoring::dssp::Dssp
• get_dssp_unreduced_secstruct() : core::scoring::dssp::Dssp
• get_dummy_ensemble() : core::scoring::nmr::NMRSpinlabel
• get_dummy_rotation_matrix() : protocols::membrane::AqueousPoreFinder
• get_dun02_aa_parameters() : core::pack::dunbrack::DunbrackAAParameterSet
• get_dun10_aa_parameters() : core::pack::dunbrack::DunbrackAAParameterSet
• get_dw_dr() : core::scoring::elec::FAElecContextData
• get_dwell_times() : core::pack::annealer::FixbbPwatSimAnnealer
• get_dynamic_scale() : protocols::normalmode::NormalModeRelaxMover
• get_E_haro_one_way() : core::scoring::orbitals::OrbitalsScore
• get_E_hpol_one_way() : core::scoring::orbitals::OrbitalsScore
• get_edge() : core::pack::interaction_graph::InteractionGraphBase
• get_edge_exists() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , core::pack::interaction_graph::InteractionGraphBase
• get_edge_file_name() : protocols::sewing::movers::AssemblyMover
• get_edge_list_begin() : core::pack::interaction_graph::InteractionGraphBase
• get_edge_list_end() : core::pack::interaction_graph::InteractionGraphBase
• get_edge_map_generator() : protocols::sewing::movers::AssemblyMover
• get_edge_memory_usage() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_edge_reweight() : core::pack::task::IGEdgeReweighter , protocols::toolbox::IGInterfaceEdgeUpweighter , protocols::toolbox::IGLigandDesignEdgeUpweighter , protocols::toolbox::ResidueGroupIGEdgeUpweighter
• get_edge_table_ptr() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_edge_to_bg_node() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_edge_to_hpatch_bg_node() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_edge_to_npd_hbond_bg_node() : core::pack::interaction_graph::NPDHBondNode< V, E, G >
• get_edge_to_surface_bg_node() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_edge_vector_up_to_date() : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• get_edge_weight() : core::pack::interaction_graph::InteractionGraphBase
• get_edges() : protocols::sewing::hashing::EdgeMapGenerator
• get_edges_position_in_nodes_edge_vector() : core::pack::interaction_graph::EdgeBase
• get_effective_radii() : core::scoring::MultipoleElecPotential
• get_efficiency() : core::enzymes::EnzymeManager , protocols::enzymatic_movers::EnzymaticMover
• get_eggshell_distance() : protocols::pockets::EggshellGrid
• get_Eig_xx() : core::scoring::nmr::NMRTensor
• get_Eig_yy() : core::scoring::nmr::NMRTensor
• get_Eig_zz() : core::scoring::nmr::NMRTensor
• get_eigval() : protocols::normalmode::NormalMode
• get_eigvec_cart() : protocols::normalmode::NormalMode
• get_eigvec_tor() : protocols::normalmode::NormalMode
• get_elec_scale() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_electron_affinity() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_electron_configuration() : core::chemical::Element
• get_electronegativity() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_electrostatics_energy() : protocols::pockets::NonPlaidFingerprint
• get_element_type() : core::chemical::gasteiger::GasteigerAtomTypeData
• 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_end_temperature() : protocols::sewing::movers::AssemblyMover
• get_energies() : protocols::moves::PyMOLMover
• get_energies_cache() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• get_energies_map_from_scored_pose() : core::io::raw_data::ScoreMap
• get_energy() : core::io::silent::SilentStruct , core::scoring::PolymerBondedEnergyContainer , protocols::make_rot_lib::RotData , protocols::mpi_refinement::WorkUnit_Sampler
• get_energy_current_state_assignment() : core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_energy_following_partial_state_assignment() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• get_energy_following_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• get_energy_for_alt_state() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• get_energy_for_perturbed_state() : core::pack::interaction_graph::FASTEREdge
• get_energy_for_state_pair() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge
• get_energy_map() : protocols::relax::EnergyMapContainer
• get_energy_map_from_dofs() : protocols::optimize_weights::OptEMultifunc
• get_energy_node() : core::scoring::EnergyGraph
• get_energy_owner() : core::scoring::EnergyEdge
• get_energy_PD_current_state_assignment() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• get_energy_state() : core::scoring::methods::PBLifetimeCache
• get_energy_sum_for_vertex_group() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_enforce_bb_contiguity() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_ensemble() : protocols::docking::ConformerSwitchMover
• get_ensemble_ca_rmsd() : protocols::simple_moves::ShakeStructureMover
• get_ensemble_diversity() : protocols::simple_moves::ShakeStructureMover
• get_ensemble_size() : core::scoring::nmr::NMRDummySpinlabelEnsemble
• get_ensured_sites() : protocols::enzymatic_movers::EnzymaticMover
• get_entries() : protocols::frag_picker::CSTalosIO
• get_entries_per_torsion_bin() : core::scoring::Ramachandran , protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber
• get_entries_per_torsion_bin_left() : core::scoring::Ramachandran2B
• get_entries_per_torsion_bin_right() : core::scoring::Ramachandran2B
• get_entry() : protocols::frag_picker::PhiPsiTalosIO
• get_env_nbr_bin() : core::scoring::dna::DNA_EnvPairPotential
• get_EnvPairPotential() : core::scoring::ScoringManager
• get_EnzConstraintIO_for_cstfile() : protocols::enzdes::AddOrRemoveMatchCsts
• get_enzyme() : protocols::enzymatic_movers::EnzymaticMover
• get_enzyme_family() : protocols::enzymatic_movers::EnzymaticMover
• 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() : core::pack::rotamer_set::RotamerLinks , protocols::symmetry::NCSResMapping
• get_equivalent_landmark() : protocols::antibody::AntibodyNumberingParser
• get_euler_convention() : core::scoring::nmr::NMRTensor
• get_eval_count() : core::optimization::func_1d
• get_ex_flags() : core::pack::task::ResidueLevelTask_
• get_exact() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_excluded_sites() : protocols::enzymatic_movers::EnzymaticMover
• get_exclusion_index() : protocols::simple_filters::ResidueDepthCalculator
• get_execution_summary_id() : protocols::network::NetworkQueue
• get_exemplar_for() : protocols::cluster::APCluster
• get_exp_val() : core::scoring::func::SplineFunc
• get_extend_existing_networks() : protocols::hbnet::HBNet
• get_extend_mode() : protocols::sewing::movers::AppendAssemblyMover
• get_extended() : protocols::pose_creation::PoseFromSequenceMover
• get_extension() : protocols::jd2::wwPDBJobOutputter
• get_extra() : protocols::loophash::LoopHashLibrary
• get_extra_bodies() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_extra_bodies_chains() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_extra_data() : protocols::loophash::BackboneDB
• get_f1_f2() : core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator , core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator , core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionPotential , core::scoring::rna::TNA_SuiteEnergy
• get_f2c() : core::scoring::electron_density::ElectronDensity
• get_fa_rep_thresh() : protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter
• get_fa_score() : protocols::rpc::JSON_RPC
• get_fa_stack_deriv() : core::scoring::rna::RNA_FullAtomStackingEnergy
• get_fa_stack_score() : core::scoring::rna::RNA_FullAtomStackingEnergy
• get_FACTSPotential() : core::scoring::ScoringManager
• get_far_c_terminal_parent() : protocols::sewing::data_storage::SmartSegment
• get_far_n_terminal_parent() : protocols::sewing::data_storage::SmartSegment
• get_faster_edge() : core::pack::interaction_graph::FASTERInteractionGraph
• get_faster_node() : core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph
• get_fasterig_owner() : core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERNode
• get_favor_native_bonus() : core::scoring::constraints::ResidueTypeConstraint , protocols::constraint_generator::ResidueTypeConstraintGenerator
• get_features() : core::scoring::rna::data::RNA_DMS_Potential
• get_features_reporter() : protocols::features::FeaturesReporterFactory
• get_ff() : core::scoring::saxs::FormFactorManager
• get_field_strength() : core::scoring::nmr::pre::PRESingleSet
• get_file_contents() : protocols::pack_daemon::DynamicAggregateFunction
• get_file_lines() : protocols::relax::RelaxScriptFileContents
• get_file_name() : protocols::hbnet::HBNet
• get_filename() : core::scoring::func::SplineFunc , 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_filenames() : core::import_pose::pose_stream::PDBPoseInputStream
• get_filter() : protocols::cluster::GatherPosesMover , protocols::filters::FilterCollection , protocols::moves::FilterReportAsPoseExtraScoresMover , protocols::moves::FilterReporterMover , protocols::rosetta_scripts::XmlObjects
• 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_filtered_secstruct() : protocols::fldsgn::filters::SecondaryStructureFilter
• get_filtered_sheet_topology() : protocols::fldsgn::filters::SheetTopologyFilter
• get_filteronly_solutions() : protocols::loop_grower::LoopPartialSolutionStore
• get_final_energy() : protocols::vip::VIP_Mover
• get_final_fragments() : protocols::frag_picker::FragmentPicker
• get_final_min_mover() : protocols::ligand_docking::FinalMinimizer
• get_final_pose() : protocols::vip::VIP_Mover
• get_final_RMSD() : protocols::pose_length_moves::PossibleLoop
• get_final_sm_type() : core::simple_metrics::SimpleMetric
• get_finalPoseOP() : protocols::pose_length_moves::PossibleLoop
• get_first() : core::scoring::packstat::trace
• get_first_atom() : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• get_first_class_node() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• get_first_class_node_index() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• get_first_index_in_query() : protocols::frag_picker::FragmentCandidate
• get_first_index_in_vall() : protocols::frag_picker::FragmentCandidate
• get_first_node_ind() : core::pack::interaction_graph::EdgeBase
• 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_fixedbb_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• get_fixedbb_node() : core::pack::interaction_graph::FixedBBInteractionGraph
• 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_fmax() : core::scoring::hbonds::FadeInterval
• get_fmin() : core::scoring::hbonds::FadeInterval
• get_fobj() : protocols::mpi_refinement::MultiObjective
• get_focus() : core::select::residue_selector::NeighborhoodResidueSelector
• 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_vertices() : 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_foldtree_seqsep() : core::scoring::SecondaryStructurePotential
• get_formal_charge() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_forward_assembly() : protocols::sewing::data_storage::SmartAssembly
• 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_atoms() : core::kinematics::AtomTree
• get_frag_data() : protocols::frag_picker::FragmentCandidate
• get_frag_descendant_local_xyz() : core::kinematics::AtomTree
• 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_factory() : core::fragment::FragmentIO
• get_frag_local_stub() : core::kinematics::AtomTree
• get_frag_local_xyz() : core::kinematics::AtomTree
• get_frag_mover_ptr() : protocols::topology_broker::FragmentClaimer
• get_frag_parent_local_xyz() : core::kinematics::AtomTree
• get_frag_pseudo_stub_id() : core::kinematics::AtomTree
• get_frag_sizes() : protocols::frag_picker::FragmentPicker
• get_frag_weight_file() : protocols::struct_fragment::StructFragmentMover
• get_fragment_centers_of_mass() : protocols::indexed_structure_store::search::StructureData
• get_fragment_centers_of_mass_copy() : protocols::indexed_structure_store::search::StructureData
• get_fragment_coordinates() : protocols::indexed_structure_store::FragmentStore , protocols::indexed_structure_store::SSHashedFragmentStore
• get_fragment_indicies() : protocols::indexed_structure_store::search::StructureData
• get_fragment_indicies_copy() : protocols::indexed_structure_store::search::StructureData
• get_fragment_length() : protocols::indexed_structure_store::SSHashedFragmentStore
• get_fragment_library_pointer() : core::fragment::rna::FullAtomRNA_Fragments , core::fragment::rna::RNA_Fragments
• get_fragment_lines() : core::fragment::rna::RNA_FragmentHomologyExclusion
• get_fragment_residue_spans() : protocols::indexed_structure_store::FragmentLookup
• get_fragment_store() : protocols::indexed_structure_store::BinaryFragmentStoreBackend , protocols::indexed_structure_store::FragmentStoreProvider , protocols::indexed_structure_store::SSHashedFragmentStore
• get_fragment_torsion() : core::fragment::rna::FragmentLibrary
• get_fragment_torsion_set() : core::fragment::rna::FragmentLibrary
• get_fragmentLookup() : protocols::indexed_structure_store::FragmentStore
• get_fragments() : protocols::struct_fragment::StructFragmentMover
• 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_fragset() : protocols::struct_fragment::StructFragmentMover
• get_framelist() : protocols::denovo_design::components::Picker
• get_framework_conservative_op() : protocols::antibody::design::AntibodySeqDesignTFCreator
• get_frequency() : core::scoring::nmr::NMRDummySpinlabelConformer
• get_from_const_pose() : protocols::denovo_design::components::StructureDataFactory
• get_from_pose() : protocols::denovo_design::components::StructureDataFactory
• get_from_scratch_add_and_delete_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_from_scratch_add_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_from_scratch_delete_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• 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_ft_node_bounds() : core::kinematics::TreeVizBuilder
• get_ft_node_lower_bound() : core::kinematics::TreeVizBuilder
• get_ft_node_subroot() : core::kinematics::TreeVizBuilder
• get_full_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_full_motif_bb_alignment_mode() : protocols::motif_grafting::movers::MotifMatch
• get_full_sequence() : protocols::antibody::design::NativeAntibodySeq
• get_full_strands() : protocols::features::strand_assembly::StrandBundleFeatures
• get_full_type_name() : protocols::sewing::data_storage::SmartSewingResidue
• get_fullatom_pose() : protocols::legacy_sewing::LegacyAssemblyMover
• get_fullatom_scorefunction() : protocols::anchored_design::AnchorMoversData , protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_FullatomDisulfidePotential() : core::scoring::ScoringManager
• get_func() : core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::RTConstraint , protocols::sewing::scoring::LigandScorer
• get_func_factory() : core::scoring::constraints::ConstraintIO
• 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_gamma() : core::scoring::nmr::NMRTensor
• get_gap_distance() : protocols::rna::movers::RNA_LoopCloser
• get_gdt() : protocols::loop_grower::LoopPartialSolution
• get_GDTHA() : core::scoring::TMscore
• get_GDTTS() : core::scoring::TMscore
• get_GenBornPotential() : core::scoring::ScoringManager
• get_general_loop_task_op() : protocols::antibody::design::AntibodySeqDesignTFCreator
• get_GenericBondedPotential() : core::scoring::ScoringManager
• get_geometry_score_weight() : protocols::sewing::hashing::LigandBindingResPlacer
• get_gJ() : core::io::nmr::ParaIon
• get_global() : protocols::mpi_refinement::WorkUnit_LoopHash
• get_global_coords_as_FArray2D() : protocols::toolbox::match_enzdes_util::LigandConformer
• get_global_i() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• get_global_requirement() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• get_gly_interface_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_glycan_sampler_rounds() : protocols::carbohydrates::GlycanSampler
• get_glycan_tree_set() : core::conformation::carbohydrates::GlycanTreeSetObserver
• get_glycine_correction() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_glycine_correction_for_node() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• 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::GridSet , protocols::qsar::scoring_grid::SingleGrid
• get_grid_all_atomtypes() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_grid_atom1() : core::scoring::nmr::NMRGridSearch
• get_grid_atom2() : core::scoring::nmr::NMRGridSearch
• 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_atomtypes() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• 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_max_radius() : core::scoring::nmr::NMRGridSearch
• get_grid_min_radius() : core::scoring::nmr::NMRGridSearch
• get_grid_names() : protocols::qsar::scoring_grid::GridSet
• 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_center() : core::scoring::nmr::NMRGridSearch
• 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_grids() : protocols::qsar::scoring_grid::GridManager
• get_gridsearch_iterator() : core::scoring::nmr::pcs::PCSMultiSet , core::scoring::nmr::pre::PREMultiSet
• get_gridsearch_range() : protocols::nmr::pcs::PCSLigandTransformMover
• get_group() : core::scoring::elec::GroupElec
• get_grow_attempts() : protocols::loops::loop_mover::IndependentLoopMover
• get_grp_countpair() : core::scoring::elec::GroupElec
• get_grpdis2() : core::scoring::elec::GroupElec
• get_GTPase_lys() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_H3_kink_type() : protocols::antibody::AntibodyInfo
• get_H3_kink_type_name() : protocols::antibody::AntibodyInfo
• get_HAdist() : core::scoring::hbonds::HBond
• get_half_width() : core::scoring::func::LinearPenaltyFunction
• get_handedness_score_flag() : core::scoring::SecondaryStructureWeights
• get_hardsphere_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_harmonic_ca_cst_std_dev() : protocols::simple_moves::ShakeStructureMover
• get_harmonic_cluster_constraint_db_directory() : protocols::antibody::constraints::CDRDihedralConstraintMover
• get_harmonic_cluster_constraint_filename() : protocols::antibody::constraints::CDRDihedralConstraintMover
• get_hASA_for_node_and_nbs() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_hash_map_size() : protocols::sewing::hashing::Hasher
• get_hashed() : protocols::sewing::movers::AssemblyMover
• get_hashed_fragment_store() : protocols::indexed_structure_store::SSHashedFragmentStore
• get_hb_e_cutoff() : protocols::simple_filters::SimpleHbondsToAtomFilter
• get_hbond_energy() : core::scoring::methods::FreeDOF_Energy
• get_hbond_energy_cutoff() : protocols::residue_selectors::HBondSelector
• get_helical_axis_and_center() : protocols::rna::denovo::movers::RNA_HelixMover
• get_helical_params() : protocols::forge::remodel::RemodelGlobalFrame
• get_helices() : protocols::features::helixAssembly::HelixBundleFeatures
• get_helix() : protocols::nonlocal::HelixRotate
• get_helix_ends() : protocols::rna::denovo::movers::RNA_HelixMover
• get_helix_id() : protocols::hbnet::HBNetStapleInterface
• get_helix_pairings() : protocols::denovo_design::architects::BlueprintArchitect , protocols::denovo_design::components::SegmentPairing , protocols::fldsgn::potentials::SetSecStructEnergies
• get_helix_start_stop() : protocols::simple_filters::HelixHelixAngleFilter
• get_helpers_from_pose() : core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::mhc_epitope_energy::MHCEpitopeEnergy , core::scoring::netcharge_energy::NetChargeEnergy
• get_heuristic_water_hydrogen_score() : protocols::magnesium::MgWaterHydrogenPacker
• get_highres_conformer_filter_type() : core::scoring::nmr::NMRSpinlabel
• get_highres_scorefxn() : protocols::docking::DockingProtocol , protocols::symmetric_docking::SymDockBaseProtocol
• get_hightemp() : core::pack::annealer::SimAnnealerBase
• get_hist() : protocols::recces::Histogram
• get_histogram_vector() : core::scoring::orbitals::OrbitalsStatistics
• get_history() : protocols::loop_grower::LoopPartialSolution
• get_hits_below_rms() : protocols::indexed_structure_store::SSHashedFragmentStore
• get_homogeneous_transform_com_from_orig() : protocols::motif_grafting::movers::MotifMatch
• get_homologs() : protocols::indexed_structure_store::FragmentStore
• get_hpatch_bg_edge() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_hpatch_bg_node() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_hpatch_node() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_hpatch_owner() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• get_hpatch_score() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• get_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• get_hss3s() : protocols::fldsgn::filters::HSSTripletFilter
• get_hss_triplets() : protocols::denovo_design::components::SegmentPairing
• get_hssop() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• get_hybrid_orbital_type() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_hydrogens_bonded_to_ring_atom() : core::conformation::Residue
• get_HydroxylTorsionPotential() : core::scoring::ScoringManager
• get_i() : core::scoring::packstat::Octree2D , protocols::features::strand_assembly::StrandFragment
• get_IAM() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_id() : core::scoring::nmr::NMRDummySpinlabelConformer , protocols::features::strand_assembly::StrandFragment , protocols::frag_picker::scores::FragmentScoringMethod , protocols::loop_grower::LoopPartialSolution
• get_ideal_angle_about_contact() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_ideal_angle_about_metal() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_ideal_conformer_by_CP_parameters() : core::chemical::rings::RingConformerSet
• get_ideal_conformer_by_name() : core::chemical::rings::RingConformerSet
• get_ideal_conformer_from_nus() : core::chemical::rings::RingConformerSet
• get_ideal_contacts() : protocols::sewing::data_storage::LigandResidue
• get_ideal_dihedral_3() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_ideal_dihedral_about_contact() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_ideal_dihedral_about_metal() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_ideal_distance() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_ideal_hxyz_positions() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• get_ideal_hydrogenBond_atoms() : protocols::pockets::GenPharmacophore
• get_idealize_loop_first() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_idx_for_other_pose() : core::pose::full_model_info::FullModelInfo
• get_idx_for_other_pose_with_residue() : core::pose::full_model_info::FullModelInfo
• get_idx_for_other_pose_with_residues() : core::pose::full_model_info::FullModelInfo
• get_ignore_unrecognized_res() : protocols::rotamer_recovery::RotamerRecovery
• get_importance() : protocols::normalmode::NormalMode
• get_incident_dlazy_edge() : core::pack::interaction_graph::DoubleLazyNode
• get_incident_dpd_edge() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode
• get_incident_edge() : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• get_incident_faster_edge() : core::pack::interaction_graph::FASTERNode
• get_incident_flexbb_edge() : protocols::flexpack::interaction_graph::FlexbbNode
• get_incident_hpatch_edge() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_incident_lazy_edge() : core::pack::interaction_graph::LazyNode
• get_incident_linmem_edge() : core::pack::interaction_graph::LinearMemNode
• get_incident_minimalistflexbb_edge() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• get_incident_npd_hbond_edge() : core::pack::interaction_graph::NPDHBondNode< V, E, G >
• get_incident_otf_edge() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• get_incident_otfflexbb_edge() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• get_incident_pd_edge() : core::pack::interaction_graph::PDNode
• get_incident_surface_edge() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_incident_symmin_edge() : core::pack::interaction_graph::SymmMinimalistNode
• get_incident_symmlinmem_edge() : core::pack::interaction_graph::SymmLinearMemNode
• get_include_backbone_atoms() : protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• get_include_bb_bb() : protocols::residue_selectors::HBondSelector
• get_include_focus() : core::pack::task::residue_selector::ClashBasedShellSelector
• get_include_only_end() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• get_include_only_start() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• get_include_subunit() : core::conformation::symmetry::SymmData
• get_ind_res() : core::pack::hbonds::HBondGraphInitializerIG , protocols::hbnet::HBNet
• get_index() : core::chemical::Element , core::grid::CartGrid< T > , protocols::kinematic_closure::ClosureSolution
• get_index_in_vall() : core::fragment::rna::TorsionSet
• get_index_of_adjacent_background_node() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_index_of_adjacent_first_class_node() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• get_index_of_adjacent_node() : core::pack::interaction_graph::NodeBase
• get_indices_of_moving_chunks() : core::import_pose::libraries::RNA_ChunkLibrary
• get_indices_of_voxel_from_coordinates() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• get_individual_scale() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsEnergyParameter
• get_init_value() : protocols::matdes::GetRBDOFValues
• get_init_value_ : protocols::matdes::GetRBDOFValues
• get_initial() : protocols::hybridization::TMalign
• get_initial_fgt() : protocols::hybridization::TMalign
• get_initial_job_dag_and_queue() : protocols::jd3::job_distributors::JobExtractor
• get_initial_local() : protocols::hybridization::TMalign
• get_initial_ss() : protocols::hybridization::TMalign
• get_initial_ssplus() : protocols::hybridization::TMalign
• get_inner_cycles() : protocols::docking::DockingLowRes
• get_inneriterations() : core::pack::annealer::SimAnnealerBase
• 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_input_poses_to_deallocate() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• get_input_set() : core::select::residue_selector::BondedResidueSelector
• get_input_set_defined() : protocols::residue_selectors::HBondSelector
• get_input_set_selector() : protocols::residue_selectors::HBondSelector , protocols::residue_selectors::LigandMetalContactSelector
• get_input_set_str() : protocols::residue_selectors::HBondSelector
• get_input_streams() : core::import_pose::pose_stream::MetaPoseInputStream
• get_input_stub() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• get_instance() : protocols::jd2::JobDistributor , protocols::noesy_assign::PeakAssignmentParameters , 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_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_interfaces() : core::conformation::symmetry::SymmData
• get_InterfaceSasaDefinition() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_internal_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_interpolated_esp_energy() : protocols::pockets::NonPlaidFingerprint
• get_interpolated_esp_energy_with_type() : protocols::pockets::NonPlaidFingerprint
• get_intersections_for_atom() : core::scoring::power_diagram::PowerDiagram
• get_intra_atr() : protocols::make_rot_lib::RotData
• get_intra_rep() : protocols::make_rot_lib::RotData
• get_intra_segment_requirement() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• get_intramolecular_add_and_delete_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_intramolecular_add_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_intramolecular_delete_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_intramolecular_split_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_intrares_countpair() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy
• get_inversion() : core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• get_invert_downstream() : core::kinematics::Jump
• get_invert_upstream() : core::kinematics::Jump
• get_ion_data() : core::io::nmr::ParamagneticDatabaseHandler
• get_ion_data_table() : core::io::nmr::ParamagneticDatabaseHandler
• get_ion_label() : core::io::nmr::ParaIon
• get_ion_type() : core::scoring::nmr::pre::PREMultiSet
• get_ionization_potential() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_irms() : protocols::rpc::JSON_RPC
• get_is_do_minimize() : protocols::peptide_deriver::PeptideDeriverFilter
• get_is_dump_cyclic_poses() : protocols::peptide_deriver::PeptideDeriverFilter
• get_is_dump_peptide_pose() : protocols::peptide_deriver::PeptideDeriverFilter
• get_is_dump_prepared_pose() : protocols::peptide_deriver::PeptideDeriverFilter
• get_is_dump_report_file() : protocols::peptide_deriver::PeptideDeriverFilter
• get_is_report_gzip() : protocols::peptide_deriver::PeptideDeriverFilter
• get_is_skip_zero_isc() : protocols::peptide_deriver::PeptideDeriverFilter
• get_iterations() : protocols::rna::movers::RNAIdealizeMover , protocols::trajectory::DbTrajectoryReader
• get_iterator_for_tag() : core::io::silent::SilentFileData
• get_IV_from_rsd() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• get_IVs_from_rsd() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• get_J() : core::io::nmr::ParaIon
• get_j() : core::scoring::packstat::Octree2D , protocols::features::strand_assembly::StrandFragment
• get_jacobian() : protocols::kinematic_closure::ClosureSolution , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• get_job_graph() : protocols::jd3::JobQueen
• get_job_index_ending_job_node() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• get_job_index_starting_job_node() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• get_job_list_from_job_inputter() : protocols::jd2::JobDistributor
• get_job_node() : protocols::jd3::JobDigraph , protocols::jd3::JobDirectedEdge , protocols::jd3::JobGenealogist
• get_job_node_assigned() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• get_job_node_complete() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• get_job_node_for_job_index() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• get_job_owner() : protocols::jd3::JobDirectedEdge , protocols::jd3::JobDirectedNode
• get_job_time_estimate() : protocols::jd2::JobDistributor
• get_job_tracker() : protocols::jd3::JobQueen
• get_JobInputter_from_string() : protocols::jd2::JobInputterFactory
• get_JobOutputter_from_string() : protocols::jd2::JobOutputterFactory
• get_jobs() : protocols::jd2::JobDistributor
• get_jobs_nonconst() : protocols::jd2::JobDistributor
• get_jump() : core::kinematics::MoveMap , core::kinematics::ShortestPathInFoldTree , core::pose::toolbox::AtomLevelDomainMap , protocols::membrane::SpinAroundPartnerMover
• get_jump_anchors() : protocols::hybridization::FoldTreeHybridize
• get_jump_atom_id() : core::kinematics::AtomTree
• get_jump_atom_ids() : core::conformation::Conformation
• get_jump_clones() : core::conformation::symmetry::SymmData
• get_jump_edges() : core::kinematics::FoldTree
• get_jump_index_for_crosslinker() : protocols::cyclic_peptide::CrosslinkerMover
• get_jump_indices_for_symmetric_crosslinker() : protocols::cyclic_peptide::CrosslinkerMover
• get_jump_name() : core::conformation::symmetry::SymmetryInfo
• get_jump_name_to_components() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_jump_name_to_subunits() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_jump_num() : core::conformation::symmetry::SymmetryInfo , protocols::docking::DockingSlideIntoContact , protocols::docking::FaDockingSlideIntoContact , protocols::docking::SlideIntoContact , protocols::membrane::FlipMover , protocols::membrane::TiltMover
• get_jump_num_to_contig_of_resi() : core::kinematics::TreeVizBuilder
• get_jump_string_to_jump_num() : core::conformation::symmetry::SymmData
• get_jump_that_builds_residue() : core::kinematics::FoldTree
• get_k() : protocols::normalmode::NormalMode
• get_KB_description() : core::scoring::func::SplineFunc
• get_keep_existing_networks() : protocols::hbnet::HBNet
• get_known_atoms() : core::scoring::saxs::FormFactorManager
• get_kT() : protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_RamaPerturber
• get_L() : core::io::nmr::ParaIon
• get_l_equivalent() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet , core::scoring::methods::ReferenceEnergy , core::scoring::Ramachandran
• 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_large_frag_size() : protocols::struct_fragment::StructFragmentMover
• get_large_frage_file() : protocols::struct_fragment::StructFragmentMover
• get_largest_chunk_size() : protocols::frag_picker::VallProvider
• get_largest_glycan_tree_layer() : core::conformation::carbohydrates::GlycanTreeSet
• get_largest_glycan_tree_length() : core::conformation::carbohydrates::GlycanTreeSet
• get_last_change() : protocols::sewing::data_storage::SmartAssembly
• get_last_change_was_n_terminal() : protocols::sewing::data_storage::SmartAssembly
• get_last_checkpoint() : protocols::canonical_sampling::MetropolisHastingsMover
• get_last_chimaera() : protocols::sewing::data_storage::SmartAssembly
• get_last_chimaera_deleted() : protocols::sewing::data_storage::SmartAssembly
• get_last_LoopResult() : protocols::loops::loop_mover::IndependentLoopMover
• get_last_move_status() : protocols::moves::Mover
• get_last_residue_id() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• get_last_score() : protocols::sewing::scoring::AssemblyScorer , protocols::sewing::scoring::LigandAssemblyScorer , protocols::sewing::scoring::LigandScorer , protocols::sewing::scoring::MotifScorer
• get_last_sidechain_carbon_name() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• get_last_struct_id() : protocols::features::ReportToDB
• get_late_factory() : protocols::anchored_design::AnchorMoversData
• get_lazy_edge() : core::pack::interaction_graph::LazyInteractionGraph
• get_lazy_ig_owner() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyNode
• get_lazy_node() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph
• get_least_common_ancertor_jump() : core::conformation::symmetry::SymmData
• get_least_common_ancertor_virtual() : core::conformation::symmetry::SymmData
• get_length() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::JCouplingIO , protocols::sewing::data_storage::SmartAssembly , protocols::sewing::data_storage::SmartSegment
• get_length_combos() : protocols::features::InterfaceFeatures
• get_lib_chi_val() : protocols::make_rot_lib::RotData
• get_library_by_aa() : core::pack::dunbrack::RotamerLibrary
• get_library_name_02() : core::pack::dunbrack::RotamerLibrary
• get_library_name_10() : core::pack::dunbrack::RotamerLibrary
• 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() : protocols::sewing::hashing::LigandBindingResPlacer
• get_ligand_areas() : protocols::ligand_docking::InterfaceBuilder
• get_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• get_ligand_atom_name() : protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::metal_interface::MetalSiteResidue
• get_ligand_atom_xyz() : protocols::metal_interface::MetalSiteResidue
• get_ligand_com() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_ligand_contact_indices() : protocols::sewing::data_storage::LigandSegment
• get_ligand_docking_scores() : protocols::ligand_docking::InterfaceScoreCalculator
• get_ligand_id() : protocols::ligand_docking::LigandBaseProtocol , protocols::sewing::data_storage::LigandResidue
• get_ligand_jump_id() : protocols::ligand_docking::LigandBaseProtocol , protocols::simple_moves::CoupledMover
• get_ligand_local_coords() : protocols::sewing::hashing::LigandBindingResPlacer
• get_ligand_mode() : protocols::coupled_moves::CoupledMovesProtocol
• get_ligand_prob() : protocols::coupled_moves::CoupledMovesProtocol
• get_ligand_requirements() : protocols::sewing::movers::LigandBindingAssemblyMover
• get_ligand_residues() : protocols::sewing::data_storage::LigandSegment
• get_ligand_resnum() : protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_ligand_resnum_string() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_ligand_resnums() : protocols::coupled_moves::CoupledMovesProtocol
• get_ligand_selector() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_ligand_tether() : protocols::ligand_docking::TetherLigand
• get_ligand_weight() : protocols::coupled_moves::CoupledMovesProtocol , protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_ligandchi() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• get_ligandchis() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• get_ligands() : protocols::sewing::movers::AppendAssemblyMover
• get_light_chain_type() : protocols::antibody::AntibodyInfo
• get_light_chain_type_enum() : protocols::antibody::AntibodyInfo
• get_link() : protocols::moves::PyMOLMover
• get_link_record() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• get_linkage_position() : core::conformation::carbohydrates::GlycanNode , core::conformation::carbohydrates::GlycanTreeSet
• get_linker_index_asymmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper
• get_linker_indices_symmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper
• get_linmem_ig_owner() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode
• get_linmem_node() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemoryInteractionGraph
• get_list_of_custom_variants() : core::chemical::ResidueProperties
• get_list_of_custom_variants_by_reference() : core::chemical::ResidueProperties
• get_list_of_properties() : core::chemical::AtomProperties , core::chemical::ResidueProperties
• get_list_of_variant_enums() : core::chemical::ResidueProperties
• get_list_of_variants() : core::chemical::ResidueProperties
• get_lj_hbond_dis() : core::scoring::etable::Etable
• get_lj_hbond_hdis() : core::scoring::etable::Etable
• get_lj_hbond_OH_donor_dis() : core::scoring::etable::Etable
• get_lk_fractional_contribution() : core::scoring::lkball::LK_BallEnergy
• get_lk_fractional_contribution_for_single_water() : core::scoring::lkball::LK_BallEnergy
• get_lkbr_fractional_contribution() : core::scoring::lkball::LK_BallEnergy
• get_lkbr_fractional_contribution_noangle() : core::scoring::lkball::LK_BallEnergy
• get_lkbridge_angle_widthscale() : core::scoring::lkball::LK_BallEnergy
• get_loaded_job_indices() : protocols::jd2::JobsContainer
• get_local_ligands() : protocols::sewing::data_storage::SmartAssembly
• get_local_min_conformers() : core::chemical::rings::RingConformerSet
• get_local_sequence_mapping() : protocols::hybridization::InsertChunkMover
• get_localstrandpair_penalty() : core::scoring::SecondaryStructureWeights
• get_logger() : protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopProtocol
• get_logL_values() : core::scoring::rna::data::RNA_DMS_Potential
• get_loop() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::loop_modeling::LoopMover , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• get_loop_angle_conf() : protocols::struct_fragment::StructFragmentMover
• get_loop_combine_rate() : protocols::LoopRebuild , protocols::loops::loop_mover::IndependentLoopMover
• get_loop_distance2() : core::scoring::loop_graph::LoopCloseEnergy
• get_loop_distance2_deriv() : core::scoring::loop_graph::LoopCloseEnergy
• get_loop_file() : protocols::anchored_design::AnchorMoversData
• get_loop_file_reader() : protocols::loops::Loops
• get_loop_index() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• get_loop_info() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• get_loop_rmsd() : protocols::pose_length_moves::AnalyzeLoopModeling
• get_loop_sequence() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_loop_size() : protocols::coupled_moves::CoupledMovesProtocol , protocols::loophash::LoopHashMap , protocols::simple_moves::CoupledMover
• get_LoopCentral_ScoreFxn() : protocols::antibody::AntibodyInfo
• get_LoopCloseSixDPotential() : core::scoring::ScoringManager
• get_LoopHighRes_ScoreFxn() : protocols::antibody::AntibodyInfo
• get_looprlx_cycle_ratio() : protocols::LoopRebuild
• get_loops() : protocols::analysis::LoopAnalyzerMover , protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover , protocols::loop_modeling::LoopMover , protocols::loop_modeling::utilities::TrajectoryLogger , protocols::loops::filters::LoopAnalyzerFilter , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::FixAllLoopsMover
• get_lower_bound_dy() : core::scoring::func::SplineFunc
• get_lower_bound_x() : core::scoring::func::SplineFunc
• get_lower_bound_y() : core::scoring::func::SplineFunc
• get_lower_fasta() : protocols::loop_grower::LoopPartialSolutionStore
• get_lower_pose() : protocols::loop_grower::LoopPartialSolutionStore
• get_lowest_energy_conformer() : core::chemical::rings::RingConformerSet
• get_lowest_score() : protocols::sewing::movers::AssemblyMover
• get_lowres_scorefxn() : protocols::symmetric_docking::SymDockBaseProtocol
• get_lowtemp() : core::pack::annealer::SimAnnealerBase
• get_machine_letter() : protocols::wum::MPI_WorkUnitManager
• get_magnetic_anisotropy_deriv_for_src_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_magnetic_anisotropy_deriv_for_src_base() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• 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_main_group() : core::chemical::Element
• get_mainchain_child() : core::conformation::carbohydrates::GlycanNode , core::conformation::carbohydrates::GlycanTreeSet
• get_mainchain_TorsionIDs() : protocols::simple_moves::BackboneMover
• get_mainchain_torsions_covered() : core::chemical::mainchain_potential::MainchainScoreTable , core::scoring::RamaPrePro
• get_mainchain_torsions_from_coords() : core::chemical::mainchain_potential::MainchainScoreTable
• get_manager() : core::scoring::saxs::FormFactorManager
• get_map() : core::scoring::elec::CountPairRepMap
• get_mapfile() : protocols::cryst::LoadDensityMapMover
• get_masks() : core::scoring::sasa::LeGrandSasa
• get_matches() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• get_matches_for_one_submotif_sequence_set() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• get_matching_CS_data_entry() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_matching_fragments() : protocols::motif_grafting::movers::MotifGraftMover
• get_matching_model_segments() : protocols::legacy_sewing::Assembly
• get_matching_motifs() : core::scoring::motif::MotifHash , core::scoring::motif::MotifHashManager
• get_matching_res_in_VDW_rep_screen_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• get_matrix_A() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet
• get_max0() : core::scoring::hbonds::FadeInterval
• get_max_angle_dev() : protocols::membrane::FlipMover
• get_max_attempts() : protocols::loop_modeling::LoopBuilder
• get_max_bbrms() : protocols::loophash::LoopHashSampler
• get_max_chainbreak() : protocols::analysis::LoopAnalyzerMover
• get_max_cycles() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::sewing::movers::AssemblyMover
• get_max_dist_ndx() : protocols::toolbox::KClusterElement
• get_max_distance() : protocols::toolbox::KClusterElement
• get_max_dslf_energy() : protocols::simple_moves::DisulfideInsertionMover
• get_max_dslf_pot() : protocols::simple_moves::DisulfideInsertionMover
• get_max_ensemble_size() : core::scoring::nmr::NMRSpinlabel
• get_max_kic_build_attempts() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• get_max_networks_size() : protocols::hbnet::HBNet
• get_max_nstruct() : protocols::loophash::LoopHashSampler
• get_max_ntries() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_max_num_segments() : protocols::sewing::movers::AssemblyMover
• get_max_omega() : protocols::analysis::LoopAnalyzerMover
• get_max_packet_size() : protocols::moves::UDPSocketClient
• get_max_pbond() : protocols::analysis::LoopAnalyzerMover
• get_max_rama() : protocols::analysis::LoopAnalyzerMover
• get_max_rms() : protocols::loophash::LoopHashSampler
• get_max_segment_length() : protocols::sewing::movers::AssemblyMover
• get_max_segments() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• get_max_sidechain_length() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• get_max_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• get_max_surface_deltaE_guess() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• get_max_temp_for_current_round() : protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• get_max_unsat() : protocols::hbnet::HBNet
• get_max_value() : protocols::qsar::scoring_grid::SingleGrid
• get_maxE_contribution_to_pi_system() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_maximum_clashes_allowed() : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::LigandClashRequirement
• get_maximum_length() : protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::LengthInResiduesRequirement
• get_maximum_size() : protocols::sewing::requirements::SizeInSegmentsRequirement
• get_maximum_torsion_deltas_for_residue() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• get_maximum_unpenalized_variance() : protocols::sewing::scoring::IntraDesignTerminusMotifScorer , protocols::sewing::scoring::TerminusMotifScorer
• get_maxiterminimize() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_maxRad() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_maxscale() : protocols::mpi_refinement::WorkUnit_NormalMode
• get_mc() : protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::LoopRebuild
• get_MC() : protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest
• get_mc() : protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes
• get_mc_temperature() : protocols::simple_moves::ShakeStructureMover
• get_mean_sugar_pucker_dependent_chi() : core::scoring::dna::DNA_DihedralPotential
• 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_FAPotential() : core::scoring::ScoringManager
• get_membrane_topology() : protocols::topology_broker::TMHTopologySamplerClaimer
• get_MembraneData() : core::scoring::ScoringManager
• get_MembranePotential() : core::scoring::ScoringManager
• get_menv_params_for_residue() : protocols::membrane::scoring::FaWaterToBilayerEnergy
• get_message() : core::pack::task::ResfileReaderException
• get_metal_binding_atoms() : core::chemical::ResidueType , core::chemical::ResidueTypeBase , core::conformation::Residue
• get_metal_center() : core::scoring::nmr::pcs::PCSTensor
• get_metal_coord_bounds() : core::scoring::nmr::pcs::PCSSingleSet
• get_metal_ion_label() : core::scoring::nmr::pcs::PCSSingleSet
• get_metal_resnums_string() : protocols::simple_moves::SetupMetalsMover
• get_metal_selector() : protocols::simple_moves::SetupMetalsMover
• get_metals_angle_constraint_multiplier() : protocols::simple_moves::SetupMetalsMover
• get_metals_detection_LJ_multiplier() : protocols::simple_moves::SetupMetalsMover
• get_metals_distance_constraint_multiplier() : protocols::simple_moves::SetupMetalsMover
• get_metric_names() : core::simple_metrics::composite_metrics::CompositeEnergyMetric , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric , core::simple_metrics::composite_metrics::ProtocolSettingsMetric , core::simple_metrics::CompositeRealMetric , core::simple_metrics::CompositeStringMetric , core::simple_metrics::PerResidueRealMetric , core::simple_metrics::PerResidueStringMetric , core::simple_metrics::RealMetric , core::simple_metrics::SimpleMetric , core::simple_metrics::StringMetric , core::simple_metrics::TestCompositeRealMetric , core::simple_metrics::TestCompositeStringMetric
• get_mg_hoh_minimize_move_map() : protocols::magnesium::MgMinimizer
• get_mg_positions() : protocols::magnesium::SampleGrid
• get_mg_potential_costheta_gaussian_parameter() : core::scoring::magnesium::MgKnowledgeBasedPotential
• get_mg_potential_costheta_indirect_gaussian_parameter() : core::scoring::magnesium::MgKnowledgeBasedPotential
• get_mg_potential_gaussian_parameter() : core::scoring::magnesium::MgKnowledgeBasedPotential
• get_mg_potential_indirect_gaussian_parameter() : core::scoring::magnesium::MgKnowledgeBasedPotential
• get_mhc_csv_contents() : core::scoring::ScoringManager
• get_mhc_map_from_db() : core::scoring::ScoringManager
• get_mhc_matrix_contents() : core::scoring::ScoringManager
• get_middle_residue() : protocols::frag_picker::FragmentCandidate
• get_middle_ss() : protocols::frag_picker::FragmentCandidate
• get_midpoint_longest_loop() : protocols::relax::RepeatProteinRelax
• get_min0() : core::scoring::hbonds::FadeInterval
• 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_cycles() : protocols::sewing::movers::AssemblyMover
• get_min_dist() : protocols::splice::RotLibOut
• get_min_distance() : protocols::sewing::movers::LigandBindingAssemblyMover
• get_min_eps() : protocols::make_rot_lib::RotData
• get_min_lig() : protocols::enzdes::EnzRepackMinimize
• get_min_networks_size() : protocols::hbnet::HBNet
• 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_temp_for_current_round() : protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• get_min_type() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover
• get_min_value() : protocols::qsar::scoring_grid::SingleGrid
• get_mingraph_owner() : core::scoring::MinimizationNode
• 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_minimization_node() : core::scoring::MinimizationEdge , core::scoring::MinimizationGraph
• get_minimization_owner() : core::scoring::MinimizationEdge
• 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_minimum_length() : protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::LengthInResiduesRequirement
• get_minimum_size() : protocols::sewing::requirements::SizeInSegmentsRequirement
• get_mirror_bin() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• get_mirror_bin_sequence() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• get_mirror_z() : core::conformation::symmetry::VirtualCoordinate
• get_mirrored_type() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• get_missing_template_other_res() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• get_missing_template_res() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• get_MMBondAngleLibrary() : core::scoring::ScoringManager
• get_MMBondLengthLibrary() : core::scoring::ScoringManager
• get_MMLJEnergyTable() : core::scoring::ScoringManager
• get_MMLJLibrary() : core::scoring::ScoringManager
• get_MMTorsionLibrary() : core::scoring::ScoringManager
• get_mode() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• get_mode_as_string() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• get_model_file_name() : protocols::sewing::movers::AssemblyMover
• get_model_node() : protocols::legacy_sewing::SewGraph
• get_model_segments() : protocols::legacy_sewing::Assembly
• get_modescale() : protocols::normalmode::NormalModeMultifunc
• get_modifiable_terminus() : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::movers::AppendAssemblyMover
• get_molfile_molecule() : core::chemical::mmCIF::mmCIFParser
• 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_hash_BB_BB() : core::scoring::motif::MotifHashManager
• get_motif_hash_BB_PH() : core::scoring::motif::MotifHashManager
• get_motif_hash_BB_PO() : core::scoring::motif::MotifHashManager
• get_motif_hash_by_fname() : core::scoring::motif::MotifHashManager
• get_motif_hash_SC_BB() : core::scoring::motif::MotifHashManager
• get_motif_hash_SC_SC() : core::scoring::motif::MotifHashManager
• get_motif_ranges() : protocols::motif_grafting::movers::MotifMatch
• get_motif_scaffold_superposition_and_RMSD() : protocols::motif_grafting::movers::MotifGraftMover
• get_motif_summary() : core::scoring::motif::MotifHash
• get_motifs() : core::scoring::rna::RNA_Motifs
• get_movable_jumps() : protocols::docking::DockingLowRes , protocols::features::InterfaceDdGMover , protocols::simple_ddg::ddG
• get_movable_scs() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• get_move_map_and_atom_level_domain_map() : protocols::stepwise::modeler::StepWiseMinimizer
• get_move_positions() : protocols::coupled_moves::CoupledMovesProtocol
• get_move_type() : protocols::coupled_moves::CoupledMovesProtocol
• get_moveable_dofs() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• get_movemap() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::mpi_refinement::WorkUnit_Sampler , protocols::relax::RelaxProtocolBase
• get_movemap_factory() : 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::GeneralAntibodyModeler
• get_movement() : protocols::rbsegment_relax::RBSegment
• get_mover() : protocols::moves::FilterReporterMover , protocols::moves::MoverContainer , protocols::moves::RepeatMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::XmlObjects , 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_moves_for_one_submotif() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• get_moving_rsd_list() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_multi_water_fade() : core::scoring::lkball::LK_BallEnergy
• get_multichain_constructor() : protocols::analysis::InterfaceAnalyzerMover
• get_MultipoleElecPotential() : core::scoring::ScoringManager
• 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() : core::scoring::elec::FAElecContextData
• get_N1_lonepair_donor_angle() : core::scoring::rna::data::RNA_DMS_Potential
• get_n8() : protocols::simple_filters::ResidueDepthFilter
• get_n_alignments() : core::scoring::ResidualDipolarCoupling
• get_n_baserotamers_for_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• get_n_bb() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_N_C_stems_foldtree() : protocols::antibody::GraftedStemOptimizer
• get_n_candidates() : protocols::frag_picker::FragmentPicker , protocols::struct_fragment::StructFragmentMover
• get_n_centroids() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_n_chi() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_n_co_substrates() : protocols::enzymatic_movers::EnzymaticMover
• get_n_cyd_seqpos() : protocols::simple_moves::DisulfideInsertionMover
• get_n_frags() : protocols::frag_picker::FragmentPicker , protocols::struct_fragment::StructFragmentMover
• 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_most_segment() : protocols::sewing::data_storage::SmartSegment
• 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_partners() : protocols::simple_filters::SimpleHbondsToAtomFilter
• 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_reactive_sites() : protocols::enzymatic_movers::EnzymaticMover
• get_n_residue_groups() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_n_residue_types() : core::conformation::RotamerSetBase , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_n_rotamers_for_residue_group() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_n_rotamers_for_residue_type() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_n_sampling_rotamers_for_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• get_n_tail_res() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_n_terminal_helix() : protocols::switches::GraftSwitchMover
• get_n_terminal_neighbor() : protocols::sewing::data_storage::SmartSegment
• get_n_terminal_parent() : protocols::sewing::data_storage::SmartSegment
• get_n_terminal_segment() : protocols::sewing::data_storage::SmartAssembly
• get_n_trial_min() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• get_NACCESS_SASA_radii() : core::pack::interaction_graph::RotamerDotsRadiusData
• get_NACCESS_SASA_radii_with_expanded_polars() : core::pack::interaction_graph::RotamerDotsRadiusData
• get_name() : core::chemical::gasteiger::GasteigerAtomTypeData , core::grid::CartGrid< T > , core::import_pose::RNA_HelixAssembler , core::pack::task::ALLAA , core::pack::task::ALLAAwc , core::pack::task::ALLAAxc , core::pack::task::APOLA , core::pack::task::APOLAR , core::pack::task::AROMATIC , core::pack::task::AUTO , core::pack::task::CHARGED , core::pack::task::EX , core::pack::task::EX_CUTOFF , core::pack::task::FIX_HIS_TAUTOMER , core::pack::task::NATAA , core::pack::task::NATRO , core::pack::task::NO_ADDUCTS , core::pack::task::NOTAA , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::POLAR , core::pack::task::PROPERTY , core::pack::task::ResfileCommand , core::pack::task::residue_selector::ClashBasedShellSelector , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::USE_INPUT_SC , core::pose::datacache::CacheableDataType , core::scoring::hbonds::FadeInterval , core::scoring::nmr::NMRSpinlabel , core::scoring::sasa::LeGrandSasa , core::scoring::sasa::SasaMethod , core::scoring::ScoreFunction , core::select::jump_selector::AndJumpSelector , core::select::jump_selector::InterchainJumpSelector , core::select::jump_selector::JumpIndexSelector , core::select::jump_selector::JumpSelector , core::select::jump_selector::NotJumpSelector , core::select::jump_selector::OrJumpSelector , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::AsymmetricUnitSelector , core::select::residue_selector::BinSelector , core::select::residue_selector::BondedResidueSelector , core::select::residue_selector::ChainSelector , core::select::residue_selector::CloseContactResidueSelector , core::select::residue_selector::DensityFitResidueSelector , core::select::residue_selector::FalseResidueSelector , core::select::residue_selector::GlycanLayerSelector , core::select::residue_selector::GlycanPositionSelector , core::select::residue_selector::GlycanResidueSelector , core::select::residue_selector::GlycanSequonsSelector , core::select::residue_selector::InterGroupInterfaceByVectorSelector , core::select::residue_selector::JumpDownstreamSelector , core::select::residue_selector::JumpUpstreamSelector , core::select::residue_selector::LayerSelector , core::select::residue_selector::NeighborhoodResidueSelector , core::select::residue_selector::NotResidueSelector , core::select::residue_selector::NumNeighborsSelector , core::select::residue_selector::OrResidueSelector , core::select::residue_selector::PhiSelector , core::select::residue_selector::PrimarySequenceNeighborhoodSelector , core::select::residue_selector::RandomGlycanFoliageSelector , core::select::residue_selector::RandomResidueSelector , core::select::residue_selector::ResidueIndexSelector , core::select::residue_selector::ResidueInMembraneSelector , core::select::residue_selector::ResidueInSequenceMotifSelector , core::select::residue_selector::ResidueNameSelector , core::select::residue_selector::ResiduePDBInfoHasLabelSelector , core::select::residue_selector::ResiduePropertySelector , core::select::residue_selector::ResidueSelector , core::select::residue_selector::ResidueSpanSelector , core::select::residue_selector::ReturnResidueSubsetSelector , core::select::residue_selector::ScoreTermValueBasedSelector , core::select::residue_selector::SecondaryStructureSelector , core::select::residue_selector::SliceResidueSelector , core::select::residue_selector::SSElementSelector , core::select::residue_selector::SymmetricalResidueSelector , core::select::residue_selector::TrueResidueSelector , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddHelixSequenceConstraintsMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , 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::GlycanInfoMover , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::analysis::PackStatMover , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::CDRsMinPackMin , protocols::antibody::CloseOneCDRLoop , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::design::ResnumFromStringsWithRangesSelector , 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::RefineBetaBarrel , protocols::antibody::residue_selector::AntibodyRegionSelector , protocols::antibody::residue_selector::CDRResidueSelector , protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::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::backbone_moves::local_backbone_mover::LocalBackboneMover , protocols::backbone_moves::RandomizeBBByRamaPrePro , protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::backrub::BackrubSidechainMover , protocols::calc_taskop_filters::RotamerBoltzmannWeight2 , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::calc_taskop_movers::DesignRepackMover , protocols::calc_taskop_movers::ForceDisulfidesMover , 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::carbohydrates::CreateGlycanSequonMover , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeMinMover , protocols::carbohydrates::GlycanTreeModeler , protocols::carbohydrates::IdealizeAnomericHydrogens , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , 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::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::constraint_filters::ConstraintScoreFilter , protocols::constraint_generator::AddConstraints , protocols::constraint_generator::RemoveConstraints , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::constraint_movers::ClearConstraintsMover , protocols::constraint_movers::ConstraintSetMover , protocols::constraint_movers::CstInfoMover , protocols::constraint_movers::ResidueTypeConstraintMover , protocols::contact_map::ContactMap , protocols::coupled_moves::CoupledMovesProtocol , protocols::cryst::CrystRMS , protocols::cryst::DockLatticeMover , protocols::cryst::FitBfactorsMover , protocols::cryst::LoadDensityMapMover , protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::cryst::RecomputeDensityMapMover , protocols::cryst::ReportGradientsMover , protocols::cryst::SetCrystWeightMover , protocols::cryst::SetRefinementOptionsMover , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::cryst::UpdateCrystInfo , protocols::cryst::UpdateSolventMover , protocols::cutoutdomain::CutOutDomain , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::CrosslinkerMover , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::FlipChiralityMover , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::PeptideCyclizeMover , protocols::cyclic_peptide::PeptideStubMover , protocols::cyclic_peptide::RamaMutationSelector , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::cyclic_peptide::TryDisulfPermutations , protocols::ddg::ddGMover , protocols::denovo_design::DisulfidizeMover , protocols::denovo_design::filters::CavityVolumeFilter , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSShapeComplementarityFilter , protocols::denovo_design::movers::AddSegmentDataMover , protocols::denovo_design::movers::AlignResiduesMover , protocols::denovo_design::movers::BridgeChainsMover , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover , protocols::denovo_design::movers::ExtendChainMover , protocols::denovo_design::movers::FastDesign , protocols::denovo_design::movers::FoldTreeFromFoldGraphMover , protocols::denovo_design::movers::MakeAsymmetricStructureDataMover , protocols::denovo_design::movers::RotateSegmentMover , protocols::denovo_design::movers::SealFoldTreeMover , protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover , protocols::denovo_design::movers::SetResidueAliasMover , protocols::denovo_design::residue_selectors::NamedSegmentSelector , protocols::denovo_design::residue_selectors::PairedSheetResidueSelector , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::design_opt::GreedyOptMutationMover , 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::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::SidechainMinMover , protocols::docking::SlideIntoContact , 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::DockIntoDensityMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::SetupForDensityScoringMover , protocols::electron_density::VoxelSpacingRefinementMover , 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::enzymatic_movers::DNAMethyltransferaseMover , protocols::enzymatic_movers::EnzymaticMover , protocols::enzymatic_movers::GlycosyltransferaseMover , protocols::enzymatic_movers::KinaseMover , protocols::enzymatic_movers::NTerminalAcetyltransferaseMover , protocols::evolution::EvolutionaryDynamicsMover , protocols::evolution::NucleotideMutation , protocols::farnesyl::InstallFarnesylMover , protocols::farnesyl::SampleFarnesylMover , protocols::features::InterfaceDdGMover , 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::SheetRemodelConstraintGenerator , 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::fold_from_loops::movers::AlignByResidueSelectorMover , protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover , protocols::fold_from_loops::movers::SavePDBInfoMover , protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::fold_from_loops::NubInitioMover , protocols::fold_from_loops::selectors::ConstraintResidueSelector , protocols::fold_from_loops::selectors::CutpointResidueSelector , protocols::fold_from_loops::selectors::ProteinResidueSelector , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveRemodelCsts , protocols::forge::remodel::GenericRemodelConstraintGenerator , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , 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::AnchoredGraftMover , 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::hbnet::HBNet , protocols::hbnet::HBNetStapleInterface , protocols::hbnet::UnsatSelector , protocols::helical_bundle::BackboneGridSampler , 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::InsertChunkMover , protocols::hybridization::MRMover , protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover , protocols::hydrate::Hydrate , protocols::idealize::IdealizeMover , protocols::indel::IndelOptimizationMover , protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::indexed_structure_store::movers::SegmentSequenceProfileMover , 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::FixedOffsetsPivots , 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::legacy_sewing::LegacyAddStartnodeFragments , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::legacy_sewing::LegacyAssemblyMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyGivenPathAssemblyMover , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::legacy_sewing::LegacyRepeatAssemblyMover , protocols::ligand_docking::AddHydrogen , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , 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::ProtLigEnsemble , 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::TransformEnsemble , 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_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::SheetSampler , protocols::loop_modeler::LoopModeler , protocols::loop_modeler::perturbers::LoopHashPerturber , protocols::loop_modeling::LoopBuilder , 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::filters::LoopAnalyzerFilter , 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::jacobi::JacobiLoopClosureMover , 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::magnesium::MgHydrater , protocols::magnesium::MgMinimizer , protocols::magnesium::MgMonteCarlo , protocols::magnesium::MgOrbitalFrameFinder , protocols::magnesium::MgScanner , protocols::magnesium::MgWaterHydrogenPacker , 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::mean_field::GenMeanFieldMover , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , protocols::membrane::AddMembraneMover , protocols::membrane::AddMembraneSpanConstraint , protocols::membrane::AddMembraneSpanTermZConstraint , protocols::membrane::AddMPLigandMover , protocols::membrane::AqueousPoreFinder , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::FlipMover , protocols::membrane::HelixFromSequence , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::MPLipidAccessibility , protocols::membrane::MPMutateRelaxMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::OptimizeMembranePositionMover , protocols::membrane::OptimizeProteinEmbeddingMover , protocols::membrane::RandomPositionRotationMover , protocols::membrane::RandomPositionTranslationMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TiltMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::PeptideOrientationMover , protocols::metal_interface::ZincHeterodimerMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::DisulfideOptimizationMover , protocols::minimization_packing::EnergyCutRotamerTrialsMinMover , protocols::minimization_packing::EnergyCutRotamerTrialsMover , protocols::minimization_packing::GreenPacker , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::PertMinMover , protocols::minimization_packing::RepackSidechainsMover , protocols::minimization_packing::RotamerizeMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::minimization_packing::SaneMinMover , protocols::minimization_packing::SetReturningPackRotamersMover , protocols::minimization_packing::symmetry::SymEnergyCutRotamerTrialsMover , protocols::minimization_packing::symmetry::SymMinMover , protocols::minimization_packing::symmetry::SymPackRotamersMover , protocols::minimization_packing::symmetry::SymRotamerTrialsMover , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::minimization_packing::TaskAwareMinMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::GenericSimulatedAnnealer , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::monte_carlo::ResetBaselineMover , 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::FilterReportAsPoseExtraScoresMover , 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::SwitchMover , 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::ncbb::ResidueReplacementRebuildMover , protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::network::UIMover , protocols::nmr::ParaNMRScoreMover , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREMover , protocols::noesy_assign::DistanceScoreMover , protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeRelaxMover , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pdbinfo_manipulations::AlignPDBInfoToSequences , protocols::pockets::SmallMol , protocols::pose_creation::ExtendedPoseMover , protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MakePolyXMover , protocols::pose_creation::MergePDBatOverlapMover , protocols::pose_creation::MergePDBMover , protocols::pose_creation::PoseFromSequenceMover , protocols::pose_creation::SliceToMiniProteinMover , protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::ConnectChainsMover , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser , 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::HeavyAtomNormalization , protocols::qsar::scoring_grid::MolecularWeightNormalization , protocols::qsar::scoring_grid::ScoreNormalization , protocols::quantum_annealing::ExternalPackerResultLoader , 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::recces::RECCES_Mover , protocols::recces::sampler::MC_OneTorsion , protocols::recces::sampler::MC_Sampler , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::recces::sampler::rna::MC_RNA_Sugar , protocols::recces::sampler::rna::MC_RNA_Suite , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover , protocols::recon_design::FindConsensusSequence , protocols::recon_design::MSDMover , protocols::relax::AcceptToBestMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::CentroidRelax , protocols::relax::ClassicRelax , protocols::relax::FastRelax , protocols::relax::LocalRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::MiniRelax , protocols::relax::RangeRelaxMover , protocols::relax::RepeatProteinRelax , protocols::residue_selectors::HBondSelector , protocols::residue_selectors::LigandMetalContactSelector , protocols::residue_selectors::NativeSelector , protocols::residue_selectors::StoredResidueSubsetSelector , protocols::residue_selectors::StoreResidueSubsetMover , protocols::residue_selectors::TaskSelector , 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::RigidBodyTiltMover , 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::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::rna::denovo::coarse::MultipleDomainMover , protocols::rna::denovo::movers::RNA_DeNovoMasterMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::movers::RNA_FragmentMover , protocols::rna::denovo::movers::RNA_HelixMover , protocols::rna::denovo::movers::RNA_Minimizer , protocols::rna::denovo::movers::RNA_Relaxer , protocols::rna::denovo::movers::RNP_HighResMover , protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::rna::movers::ERRASER2Protocol , protocols::rna::movers::ErraserMinimizerMover , protocols::rna::movers::RNA_DeNovoOptimizer , protocols::rna::movers::RNA_LoopCloser , protocols::rna::movers::RNAIdealizeMover , protocols::rna::movers::RNAThreadAndMinimizeMover , protocols::rna::setup::RNA_JobDistributor , protocols::rna::setup::RNA_MonteCarloJobDistributor , 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::sewing::data_storage::LigandSegment , protocols::sewing::data_storage::SmartSegment , protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::movers::AppendAssemblyMover , protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMover , protocols::sewing::requirements::AssemblyRequirement , protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::KeepLigandContactsRequirement , protocols::sewing::requirements::LengthInResiduesRequirement , protocols::sewing::requirements::LigandAssemblyRequirement , protocols::sewing::requirements::LigandClashRequirement , protocols::sewing::requirements::NonTerminalStartingSegmentRequirement , protocols::sewing::requirements::SizeInSegmentsRequirement , protocols::sewing::scoring::AssemblyScorer , protocols::sewing::scoring::InterModelMotifScorer , protocols::sewing::scoring::IntraDesignTerminusMotifScorer , protocols::sewing::scoring::LigandAssemblyScorer , protocols::sewing::scoring::LigandScorer , protocols::sewing::scoring::MotifScorer , protocols::sewing::scoring::PartnerMotifScorer , protocols::sewing::scoring::SegmentContactOrderScorer , protocols::sewing::scoring::StartingNodeMotifScorer , protocols::sewing::scoring::SubsetPartnerMotifScorer , protocols::sewing::scoring::TerminusMotifScorer , protocols::sewing::scoring::TopNMotifScorer , protocols::simple_ddg::ddG , protocols::simple_filters::EvaluatedTrialMover , protocols::simple_moves::a3b_hbs::A3BHbsPatcher , protocols::simple_moves::AddCavitiesMover , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AddPDBInfoMover , protocols::simple_moves::AddResidueCouplingConstraint , protocols::simple_moves::AddResidueLabelMover , 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::bb_sampler::BBDihedralSampler2D , protocols::simple_moves::bb_sampler::BBDihedralSampler3D , protocols::simple_moves::bb_sampler::BBDihedralSampler , protocols::simple_moves::bb_sampler::BBDihedralSamplerBase , protocols::simple_moves::bb_sampler::BBDihedralSamplerND , protocols::simple_moves::bb_sampler::SmallBBSampler , protocols::simple_moves::bb_sampler::SugarBBSampler , protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::BBG8T3AMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ChainSplitMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::chiral::ChiralMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::CombinePoseMover , protocols::simple_moves::ConcatenatePosesMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::CopyDofMover , protocols::simple_moves::CopyRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::CyclizationMover , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DME_FilterMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::DumpSingleResidueRotamers , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FavorSymmetricSequence , protocols::simple_moves::FoldTreeFromMotif , protocols::simple_moves::FragmentMover , protocols::simple_moves::hbs::HbsPatcher , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::LoggedFragmentMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MissingDensityToJumpMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MutateResidue , 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::PDBReloadMover , protocols::simple_moves::PeptideStapleMover , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::PoseFromPoseResourceMover , 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::RepeatPropagationMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ReportXYZ , protocols::simple_moves::RepulsiveOnlyMover , protocols::simple_moves::ResetFoldTree , protocols::simple_moves::ResetFullModelInfoMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SaveSequenceToCommentsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::SetupMetalsMover , 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::SimpleThreadingMover , protocols::simple_moves::SmallMover , protocols::simple_moves::SmoothFragmentMover , protocols::simple_moves::SmoothSymmetricFragmentMover , protocols::simple_moves::StorePoseSnapshot , protocols::simple_moves::StructProfileMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::SymmetricFragmentMover , protocols::simple_moves::TailsScoreMover , protocols::simple_moves::TorsionDOFMover , protocols::simple_moves::TorsionSetMover , protocols::simple_moves::triazolamer::TriazolamerMover , protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover , protocols::simple_moves::Tumble , protocols::simple_moves::UniformRotationMover , protocols::simple_moves::UniformTranslationMover , protocols::simple_moves::VirtualRootMover , protocols::simple_moves::WobbleMover , protocols::simple_moves::WriteFiltersToPose , protocols::simple_moves::WriteSSEMover , protocols::splice::AlignEndsMover , protocols::splice::RBInMover , protocols::splice::RBOutMover , protocols::splice::RotLibOut , protocols::splice::Splice , protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInTail , protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::SpliceOutTail , protocols::splice::TailSegmentMover , 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_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::o2prime::O2PrimePacker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover , protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , 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::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover , 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::jump::JumpStepWiseSampler , 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_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneDOF , protocols::stepwise::sampler::StepWiseSamplerOneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerOneValueComb , protocols::stepwise::sampler::StepWiseSamplerRingConformer , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::struct_fragment::StructFragmentMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::surface_docking::SurfaceOrientMover , protocols::switches::GraftSwitchMover , 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::symmetry::DetectSymmetry , protocols::symmetry::ExtractAsymmetricPoseMover , protocols::symmetry::ExtractAsymmetricUnitMover , protocols::symmetry::FaSymDockingSlideTogether , protocols::symmetry::SetupForSequenceSymmetryMover , protocols::symmetry::SetupForSymmetryMover , protocols::symmetry::SetupNCSMover , protocols::symmetry::SymDockingInitialPerturbation , protocols::symmetry::SymDockingSlideIntoContact , protocols::symmetry::SymmetricRMSMover , protocols::symmetry::SymShakeStructureMover , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCompoundTaskMover , protocols::task_operations::StoreTaskMover , protocols::testing::BenchmarkBuildRotamersMover , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::SamplerPlusPlus , protocols::topology_broker::RigidBodyRandomTMHMover , protocols::ub_e2c::ubi_e2c_modeler , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMover
• 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() : protocols::relax::membrane::MPRangeRelaxMover
• get_native_info() : protocols::md::CartesianMD
• get_native_networks() : protocols::hbnet::HBNet
• get_native_pdb_names() : protocols::optimize_weights::IterativeOptEDriver
• get_native_pose() : protocols::jd3::chunk_library::ChunkLibraryJobResult , protocols::loop_modeling::utilities::TrajectoryLogger , protocols::moves::Mover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• get_native_sequence_matching_current_length() : protocols::antibody::design::NativeAntibodySeq
• get_native_topology() : protocols::abinitio::PairingStatistics
• get_native_vec() : protocols::hbnet::HBNet
• get_natom() : protocols::toolbox::KClusterData
• get_natoms() : core::scoring::PQR
• get_nbr_atom_centroid() : protocols::docking::EllipsoidalRandomizationMover
• get_nbr_atom_non_ellipsoid_centroid() : protocols::docking::EllipsoidalRandomizationMover
• get_nc_name_codes() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• get_ncac() : core::scoring::disulfides::RT_helper
• get_Ncap_scores() : protocols::helix_capper::HelixNCapperMover
• get_ND_torsion() : protocols::simple_moves::bb_sampler::BBDihedralSamplerND
• 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_sfxn_if_in_database() : protocols::relax::RelaxScriptManager
• get_nearest_stub() : protocols::hotspot_hashing::HotspotStubSet
• get_negative_filters() : protocols::protein_interface_design::filters::BoltzmannFilter
• get_neighbor_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_neighbor_distance() : protocols::simple_moves::SimpleThreadingMover
• get_neighbor_graph() : protocols::relax::LocalRelax
• get_neighbor_list() : protocols::cluster::calibur::Clustering
• get_neighborcount() : protocols::simple_moves::AtomHash
• get_neighbors() : protocols::ligand_docking::ga_ligand_dock::GridHash3D< T > , protocols::vip::VIP_Mover
• get_net_sim() : protocols::cluster::APCluster
• get_net_vec() : protocols::hbnet::HBNet
• get_network_by_id() : protocols::hbnet::HBNet
• get_network_state() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• get_networks() : protocols::hbnet::HBNet
• get_new_atom_serial_num() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• get_new_chainIDs() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• 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::ShuffleFileSystemJobDistributor , protocols::jd2::VectorPoseJobDistributor
• 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_filenames() : protocols::ddG::ddGData
• get_next_local_jobid() : protocols::jd3::dag_node_managers::NodeManager
• get_next_node() : protocols::hbnet::HBNet
• get_next_nonredundant_motifmatch() : protocols::motif_grafting::movers::MotifGraftMover
• get_next_output() : protocols::motif_grafting::movers::MotifGraftMover
• get_next_random_range() : protocols::jobdist::BaseJobDistributor
• get_next_reference_node() : protocols::legacy_sewing::Assembly
• get_next_solutions() : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• get_next_valid_bb() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• get_njumps_subunit() : core::conformation::symmetry::SymmetryInfo
• get_nmer_pssm() : core::scoring::ScoringManager
• get_nmer_svm() : core::scoring::ScoringManager
• get_nmer_svm_aa_matrix() : core::scoring::ScoringManager
• get_nmer_svm_list_file_contents() : core::scoring::ScoringManager
• get_nmer_svm_rank() : core::scoring::ScoringManager
• get_nmer_svm_rank_list_file_contents() : core::scoring::ScoringManager
• get_nmodes() : protocols::mpi_refinement::WorkUnit_NormalMode
• get_nmoves() : protocols::moves::RepeatMover
• get_nmr_data() : core::scoring::nmr::NMRDataFactory
• 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_nobs() : core::scoring::nmr::NMRDummySpinlabelConformer
• get_node() : core::conformation::carbohydrates::GlycanTree , core::conformation::carbohydrates::GlycanTreeSet , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::InteractionGraphBase
• get_node_index() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::NodeBase
• get_node_indices_from_model_id() : protocols::legacy_sewing::SewGraph
• get_node_label() : protocols::jd3::JobDirectedNode
• get_node_state_offset() : core::pack::interaction_graph::InteractionGraphBase
• get_nodes_from_same_flexseg() : protocols::flexpack::interaction_graph::FlexbbEdge
• get_non_bb_clashing_rotamers() : protocols::ligand_docking::LigandBaseProtocol
• get_non_ligand_requirements() : protocols::sewing::movers::LigandBindingAssemblyMover
• get_noncanonical_base_pair_steps() : core::import_pose::RNA_BasePairHandler
• get_nonconst_current_contacts() : protocols::sewing::data_storage::LigandResidue
• get_nonconst_instance() : protocols::noesy_assign::PeakAssignmentParameters
• get_nonconst_ligand_contact_indices() : protocols::sewing::data_storage::LigandSegment
• get_nonconst_ligand_residues() : protocols::sewing::data_storage::LigandSegment
• get_nonconst_ligands() : protocols::sewing::movers::AppendAssemblyMover
• get_nonconst_owner_segment() : protocols::sewing::data_storage::LigandResidue
• get_nonideal() : protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin
• get_nonjump_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• get_nonpivot_torsion_sampling() : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover
• get_nonzero_weighted_scoretypes() : core::scoring::ScoreFunction
• get_norepack1() : protocols::docking::DockTaskFactory
• get_norepack2() : protocols::docking::DockTaskFactory
• get_normal() : protocols::cyclic_peptide::FlipChiralityMover
• 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_normalization_type() : core::scoring::nmr::rdc::RDCMultiSet
• get_npd_hbond_bg_edge() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >
• get_npd_hbond_bg_node() : core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• get_npd_hbond_node() : core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• get_npd_hbond_owner() : core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• get_npd_hbond_score() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• get_npdhb_deltaE_for_substitution() : core::pack::interaction_graph::NPDHBSimpleNode
• get_npdhb_simple_ig_owner() : core::pack::interaction_graph::NPDHBSimpleEdge
• get_npdhb_simple_node() : core::pack::interaction_graph::NPDHBSimpleInteractionGraph
• get_nps() : protocols::constel::ChainTerm
• get_nr_frags() : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• get_nrepeat() : protocols::mpi_refinement::WorkUnit_Relax
• get_nres_subunit() : core::conformation::symmetry::SymmetryInfo
• get_nrot_dofs() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• 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_nsubdivisions() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• get_nterm_insert_flexibility() : protocols::grafting::AnchoredGraftMover
• get_nterm_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• get_nth_element() : protocols::jd3::dag_node_managers::NodeManagerStorageMatrix
• get_nth_job_for_initial_stage() : protocols::multistage_rosetta_scripts::MRSJobQueen
• get_nth_job_for_noninitial_stage() : protocols::multistage_rosetta_scripts::MRSJobQueen
• get_nth_job_result_id() : protocols::jd3::dag_node_managers::NodeManager
• get_ntrials() : protocols::coupled_moves::CoupledMovesProtocol
• get_ntries_before_giving_up() : protocols::generalized_kinematic_closure::GeneralizedKIC
• get_nu() : core::kinematics::MoveMap
• get_nub_pieces() : protocols::fold_from_loops::utils::Nub
• get_nucleoside_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• get_num_aa_types() : core::pack::interaction_graph::OnTheFlyNode , protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_num_aatypes() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• get_num_atoms() : core::pack::interaction_graph::RotamerDots , protocols::vardist_solaccess::VarSolDRotamerDots
• get_num_background_nodes() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• get_num_bbs() : protocols::make_rot_lib::RotData
• get_num_bg_edges() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• get_num_chains_frozen() : core::scoring::methods::IntermolEnergy
• get_num_chi() : protocols::make_rot_lib::RotData
• get_num_clusters() : protocols::make_rot_lib::RotData
• get_num_components() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_num_covered() : core::pack::interaction_graph::DotSphere
• get_num_covered_total() : core::pack::interaction_graph::RotamerDots
• get_num_decoys_used_in_calculations() : protocols::ddg::ddGMover
• get_num_distinct_backbones() : protocols::flexpack::interaction_graph::FlexbbNode
• get_num_edges() : core::pack::interaction_graph::InteractionGraphBase
• get_num_edges_to_background_nodes() : core::pack::interaction_graph::FirstClassNode< V, E, G >
• get_num_edges_to_larger_indexed_nodes() : core::pack::interaction_graph::NodeBase
• get_num_edges_to_smaller_indexed_nodes() : core::pack::interaction_graph::NodeBase
• get_num_exemplars() : protocols::cluster::APCluster
• get_num_incident_edges() : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase
• get_num_interface_residues() : protocols::analysis::InterfaceAnalyzerMover
• get_num_iterations() : protocols::trajectory::DbTrajectoryReader
• get_num_native_rot() : protocols::hbnet::HBNet
• get_num_native_seq() : protocols::hbnet::HBNet
• get_num_nodes() : core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• get_num_nodes_changing_state() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_num_pose_kept() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_num_repeats() : protocols::dna_dock::PropagateClashCheckFilter
• get_num_res_types() : core::pack::interaction_graph::SymmOnTheFlyNode
• get_num_restype_groups() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyNode
• get_num_rpe_calculations_count() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• get_num_sampled() : protocols::stepwise::modeler::StepWiseModeler
• get_num_shells() : core::pack::task::residue_selector::ClashBasedShellSelector
• get_num_states() : core::pack::interaction_graph::NodeBase
• get_num_states_for_aa_type() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• get_num_states_for_aa_type_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• get_num_states_for_aa_types() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• get_num_states_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• get_num_states_for_node() : core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• get_num_states_for_restype_group() : core::pack::interaction_graph::SymmOnTheFlyNode
• get_num_states_per_backbone_for_node() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• get_num_total_states() : core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• get_num_uncovered() : core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDots
• get_num_unrecognized_atoms() : core::pose::PDBInfo
• get_num_unrecognized_res() : core::pose::PDBInfo
• get_num_virtual() : core::conformation::symmetry::SymmData
• get_number_alignment_media() : core::scoring::nmr::rdc::RDCData
• get_number_bonds() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_dofs_() : core::kinematics::jacobian::ModuleType1
• get_number_electrons_in_bonds() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_electrons_in_p_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_experiments() : core::scoring::nmr::pre::PREMultiSet , core::scoring::nmr::rdc::RDCMultiSet
• get_number_hybrid_bonds() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_hybrid_lone_pairs() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_hybrid_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_ligands() : protocols::coupled_moves::CoupledMovesProtocol
• get_number_metal_ions() : core::scoring::nmr::pcs::PCSMultiSet
• get_number_of_histograms() : core::scoring::orbitals::OrbitalsStatistics
• get_number_of_struct_used_for_csts() : protocols::antibody::constraints::CDRDihedralConstraintMover
• get_number_pcs() : core::scoring::nmr::pcs::PCSSingleSet
• get_number_pcs_grids() : protocols::qsar::scoring_grid::PCSMultiGrid
• get_number_pi_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_pre() : core::scoring::nmr::pre::PRESingleSet
• get_number_rdc() : core::scoring::nmr::rdc::RDCSingleSet
• get_number_sigma_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_spinlabel_sites() : core::scoring::nmr::pre::PREData
• get_number_tags() : core::scoring::nmr::pcs::PCSData
• get_number_unhybridized_lone_pairs() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_number_unhybridized_sigma_orbitals() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_numbering_scheme_landmarks() : protocols::antibody::AntibodyInfo
• get_numbering_scheme_used_for_cdr_definition() : protocols::antibody::AntibodyNumberingParser
• get_numeric_property() : core::chemical::ResidueTypeBase
• get_NVLookupTable() : core::scoring::ScoringManager
• get_occupancy_densities() : core::scoring::rna::data::RNA_DMS_Potential
• get_occupancy_density() : core::scoring::rna::data::RNA_DMS_Potential
• get_oegrid_dimensions() : protocols::pockets::ElectrostaticpotentialGrid
• get_offset() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , protocols::frag_picker::scores::AtomPairConstraintsData
• get_offset_table_size_in_bytes() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• get_offsets_for_aatypes() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_old_last_score() : protocols::sewing::scoring::AssemblyScorer , protocols::sewing::scoring::LigandAssemblyScorer , protocols::sewing::scoring::LigandScorer , protocols::sewing::scoring::MotifScorer
• get_omega() : protocols::dna_dock::PropagateClashCheckFilter
• get_OmegaPreferencesFunction() : core::scoring::ScoringManager
• get_OmegaTether() : core::scoring::ScoringManager
• get_omg() : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData
• get_omg_range() : protocols::make_rot_lib::MakeRotLibOptionsData
• get_on_the_fly_node() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• get_on_the_fly_owner() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• get_one_body_energy() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::PrecomputedPairEnergiesNode , core::pack::interaction_graph::SymmOnTheFlyNode , protocols::flexpack::interaction_graph::FlexbbNode
• get_one_body_energy_current_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• get_one_body_energy_for_node_state() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• get_one_body_energy_for_relaxed_state() : core::pack::interaction_graph::FASTERNode
• get_one_body_score() : protocols::loop_grower::LoopComparator
• get_one_patch() : core::chemical::Metapatch
• 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_oneletter_codes() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• get_only_extend_existing() : protocols::hbnet::HBNet
• get_opposite_coord() : core::chemical::mainchain_potential::MainchainScoreTable
• get_optimize1() : protocols::docking::membrane::MPDockingSetupMover
• get_optimize2() : protocols::docking::membrane::MPDockingSetupMover
• get_optimize_cyclic_threshold() : protocols::peptide_deriver::PeptideDeriverFilter
• get_optimizer() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• get_optimum_distance() : protocols::sewing::scoring::IntraDesignTerminusMotifScorer , protocols::sewing::scoring::TerminusMotifScorer
• get_options() : protocols::wum::WorkUnitBase
• get_options_data() : protocols::make_rot_lib::MakeRotLibJob
• get_optmem() : protocols::relax::membrane::MPRangeRelaxMover
• get_or_set_tag_name() : protocols::rosetta_scripts::XmlObjects
• get_orb_H_distance_and_energy() : core::scoring::orbitals::OrbitalsScore
• get_orb_orb_E() : core::scoring::orbitals::OrbitalsScore
• get_orbital_E_neg_pos() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_orbital_enum() : core::chemical::orbitals::OrbitalTypeMapper
• get_orbital_frame_score_upon_rotation() : protocols::magnesium::MgOrbitalFrameFinder
• get_orbitals() : core::chemical::ResidueTypeBase
• get_orbitals_index() : core::chemical::ResidueTypeBase
• get_OrbitalsLookupTable() : core::scoring::ScoringManager
• get_orientation() : core::scoring::sasa::LeGrandSasa
• get_oriented_pose() : protocols::pockets::PlaidFingerprint
• get_orig_pose() : protocols::hbnet::HBNet
• get_origin() : core::conformation::symmetry::VirtualCoordinate
• get_original_residue() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• get_original_residue_set() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• get_orthogonal_wrenches_from_twists() : core::kinematics::jacobian::ModuleType1
• get_otf_node() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_otf_owner() : core::pack::interaction_graph::SymmOnTheFlyEdge
• 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_other_ind() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• get_other_node() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• get_out() : protocols::moves::FilterReporterMover
• get_out_tag() : protocols::rna::setup::RNA_MonteCarloJobDistributor
• get_outer_cycles() : protocols::docking::DockingLowRes
• get_outeriterations() : core::pack::annealer::SimAnnealerBase
• get_outgoing_edges() : core::kinematics::FoldTree
• get_output_filename() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• get_output_frag_files() : protocols::struct_fragment::StructFragmentMover
• get_output_jump_RT() : protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter
• get_output_jump_stub_stub() : protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter
• get_output_level() : protocols::rotamer_recovery::RRReporterSQLite
• get_output_list() : protocols::switches::GraftSwitchMover
• get_output_partner() : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::movers::AppendAssemblyMover
• get_output_pose_count() : protocols::sewing::movers::AssemblyMover
• get_output_pose_per_move() : protocols::sewing::movers::AssemblyMover
• get_output_subunit() : core::conformation::symmetry::SymmData
• get_output_tag() : protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• get_output_vector() : protocols::hbnet::HBNet
• get_outputter_from_job_tag() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• get_overhang_length() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup , core::scoring::mhc_epitope_energy::MHCEpitopePredictor
• get_overlap() : core::scoring::sasa::LeGrandSasa
• get_overlap_cache() : core::pack::interaction_graph::RotamerDots
• get_overlap_gap2() : core::scoring::lkball::LK_BallEnergy
• get_overlap_target_len2() : core::scoring::lkball::LK_BallEnergy
• get_overlap_width_A2() : core::scoring::lkball::LK_BallEnergy
• get_owned_ligand_residues() : protocols::sewing::data_storage::LigandSegment
• get_owner() : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::NodeBase
• get_owner_segment() : protocols::sewing::data_storage::LigandResidue
• get_P_AA() : core::scoring::ScoringManager
• get_P_AA_ABEGO3() : core::scoring::ScoringManager
• get_P_AA_ss() : core::scoring::ScoringManager
• get_Paa_pp_deriv() : core::scoring::P_AA
• get_pack_input() : protocols::analysis::InterfaceAnalyzerMover
• get_pack_neighbors() : protocols::simple_moves::SimpleThreadingMover
• get_Pack_ScoreFxn() : protocols::antibody::AntibodyInfo
• get_packer_cycles() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_packer_graph() : protocols::hbnet::HBNet
• get_packer_task() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::CoupledMover
• get_PackingAngleResidues() : protocols::antibody::AntibodyInfo
• get_padding() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_pair() : core::scoring::dssp::StrandPairing
• get_pair_core_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• get_pair_disbin() : core::scoring::dna::DNA_EnvPairPotential
• get_pair_dist() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• get_PairEPotential() : core::scoring::ScoringManager
• get_pairing() : protocols::jumping::JumpSample
• get_pairing_str() : protocols::denovo_design::components::SegmentPairing
• get_pairings() : protocols::denovo_design::components::SegmentPairing
• get_pairings_from_line() : core::import_pose::RNA_DeNovoParameters
• get_pairings_jump_mover() : protocols::hybridization::FoldTreeHybridize
• get_pairings_residues() : protocols::hybridization::FoldTreeHybridize
• get_pairs() : core::scoring::dna::DirectReadoutPotential
• get_parallel_weight() : core::scoring::SecondaryStructureWeights
• get_parameter() : core::pose::full_model_info::FullModelParameters
• get_parameter_as_res_lists() : core::pose::full_model_info::FullModelParameters
• 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_parametric_info() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• get_params() : core::scoring::GenTorsionParams , protocols::mpi_refinement::Scheduler
• get_paratope_residues() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• get_parent() : core::conformation::carbohydrates::GlycanNode , core::conformation::carbohydrates::GlycanTreeSet , protocols::pockets::SmallMol
• get_parent_jump() : core::conformation::symmetry::SymmData
• get_parent_remark() : core::io::silent::SilentStruct
• get_parent_remark_from_line() : core::io::silent::SilentStruct
• get_parent_residue() : core::kinematics::FoldTree
• get_parent_tag() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• get_parent_virtual() : core::conformation::symmetry::SymmData
• get_partition_res() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_partition_score() : core::scoring::rna::RNA_PartitionEnergy
• get_partition_score_from_cache() : core::scoring::rna::RNA_PartitionEnergy
• get_partner() : protocols::legacy_sewing::Assembly , protocols::sewing::data_storage::SmartAssembly
• get_partner_ligand() : protocols::sewing::data_storage::LigandResidue
• get_partner_ligands() : protocols::sewing::data_storage::SmartAssembly
• get_partner_pdb() : protocols::sewing::movers::AppendAssemblyMover
• get_partner_residue() : protocols::sewing::scoring::TerminusMotifScorer
• get_partner_residue_start_stop() : protocols::docking::EllipsoidalRandomizationMover
• get_partners() : protocols::docking::DockingHighRes
• get_path() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::jd2::wwPDBJobOutputter
• get_path_from_root() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• get_pbp() : core::scoring::methods::PBLifetimeCache
• get_pcs_calc() : core::scoring::nmr::pcs::PCSSingle
• get_pcs_data() : protocols::nmr::pcs::PCSLigandTransformMover
• get_PCS_data_all() : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• get_pcs_data_from_pose() : protocols::nmr::pcs::PCSEnergy
• 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_err() : core::scoring::nmr::pcs::PCSSingle
• get_pcs_exp() : core::scoring::nmr::pcs::PCSSingle
• get_PCS_experimental() : protocols::scoring::methods::pcs2::PcsInputLine
• get_pcs_grids() : protocols::qsar::scoring_grid::PCSMultiGrid
• get_pcs_multiset_vec() : core::scoring::nmr::pcs::PCSData
• get_pcs_single_weights() : core::scoring::nmr::pcs::PCSSingleSet
• get_pcs_singleset_vec() : core::scoring::nmr::pcs::PCSMultiSet
• get_PCS_tolerance() : protocols::scoring::methods::pcs2::PcsInputLine
• get_pcs_values() : core::scoring::nmr::pcs::PCSSingleSet , protocols::qsar::scoring_grid::PCSSingleGrid
• 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_pd_edge() : core::pack::interaction_graph::PDInteractionGraph
• get_pd_energy_delta() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• get_pd_node() : core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph
• get_pdb_coords() : protocols::qsar::scoring_grid::SingleGrid
• get_pdb_id() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::VallChunk
• get_pdb_lines() : core::import_pose::PDBSilentStruct
• get_pdb_remark() : core::conformation::parametric::ParametersSet , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet
• get_pdb_source() : protocols::features::strand_assembly::StrandFragment
• get_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• get_pdig_owner() : core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDNode
• get_pep_lengths() : protocols::peptide_deriver::PeptideDeriverFilter
• get_peptide() : protocols::loophash::LoopHashMap
• get_peptide_chain() : protocols::simple_moves::DisulfideInsertionMover
• get_peptide_length() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup , core::scoring::mhc_epitope_energy::MHCEpitopePredictor
• get_per_residue_energy() : protocols::analysis::InterfaceAnalyzerMover
• get_per_residue_real_metric_data() : core::simple_metrics::SimpleMetricData
• get_per_residue_real_metric_output() : core::simple_metrics::SimpleMetricData
• get_per_residue_string_metric_data() : core::simple_metrics::SimpleMetricData
• get_per_residue_string_metric_output() : core::simple_metrics::SimpleMetricData
• get_period() : core::chemical::Element
• 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() : protocols::coupled_moves::CoupledMovesProtocol , protocols::simple_moves::CoupledMover
• 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_phi_from_rsd() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_phipsi_bins() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• get_pi_electron_contribution_type() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_picked_positions() : protocols::frag_picker::FragmentPicker
• get_pivot_picker() : protocols::kinematic_closure::KicMover
• get_pivot_residues() : protocols::backrub::BackrubProtocol
• get_pleating() : core::scoring::dssp::StrandPairing
• 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_PointWaterPotential() : core::scoring::ScoringManager
• get_PoissonBoltzmannPotential() : core::scoring::ScoringManager
• get_polarization_from_fields() : core::scoring::MultipoleElecPotential
• get_policy() : protocols::nonlocal::PolicyFactory
• get_polymer_residue_direction() : core::kinematics::FoldTree
• 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_name() : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::quota::QuotaConfig , protocols::frag_picker::quota::QuotaPool
• get_port() : protocols::moves::UDPSocketClient
• get_pose() : core::scoring::methods::PBLifetimeCache , core::scoring::motif::ResPairMotif , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::frag_picker::VallChunk , 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_chains() : protocols::docking::DockingEnsemblePrepackProtocol
• get_pose_crd_and_index() : protocols::simple_filters::ResidueDepthCalculator
• get_pose_data() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• get_pose_from_claimer() : protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• get_pose_intensities() : core::scoring::saxs::SAXSEnergy
• get_pose_list() : protocols::cluster::GatherPosesMover , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::StepWiseConnectionSampler
• get_pose_name() : protocols::moves::PyMOLMover
• get_pose_pack_data() : core::scoring::packstat::SimplePDB
• get_pose_resnum() : protocols::pockets::NonPlaidFingerprint
• get_pose_segment_dssp() : protocols::sewing::movers::AppendAssemblyMover
• get_pose_segment_ends_string() : protocols::sewing::movers::AppendAssemblyMover
• get_pose_segment_starts_string() : protocols::sewing::movers::AppendAssemblyMover
• get_poseOP() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• get_poses() : protocols::docking::membrane::MPDockingSetupMover , protocols::trajectory::DbTrajectoryReader
• get_position() : protocols::magnesium::SampleGrid , protocols::topology_broker::claims::CutClaim
• get_positive_filters() : protocols::protein_interface_design::filters::BoltzmannFilter
• get_possible_base_residue_types() : core::chemical::ResidueTypeFinder
• get_possible_base_unpatchable_residue_types() : core::chemical::ResidueTypeFinder
• get_possible_coordinations() : protocols::sewing::hashing::LigandBindingResPlacer
• get_possible_hbond_acceptors() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• get_possible_relax_script_names() : protocols::relax::FastRelax
• get_possible_unpatchable_residue_types() : core::chemical::ResidueTypeFinder
• get_potential() : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::PoissonBoltzmannPotential
• get_potential_RNA() : core::scoring::carbon_hbonds::CarbonHBondPotential
• get_potential_vect() : core::scoring::func::SplineFunc
• get_potential_vect_size() : core::scoring::func::SplineFunc
• get_potentials() : core::scoring::interface_::DDPlookup , core::scoring::nv::NVlookup
• get_pr_idx() : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator
• get_pre_calc() : core::scoring::nmr::pre::PRESingle
• get_pre_data() : protocols::nmr::pre::PREMover
• get_pre_data_file() : protocols::nmr::pre::PREMover
• get_pre_data_from_pose() : protocols::nmr::pre::PREEnergy
• get_pre_err() : core::scoring::nmr::pre::PRESingle
• get_pre_exp() : core::scoring::nmr::pre::PRESingle
• get_pre_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• get_pre_multiset_vec() : core::scoring::nmr::pre::PREData
• get_pre_pre_ligand_atom_id() : protocols::metal_interface::MetalSiteResidue
• get_pre_rate_type() : core::scoring::nmr::pre::PRESingleSet
• get_pre_single_vec() : core::scoring::nmr::pre::PRESingleSet
• get_pre_single_weights() : core::scoring::nmr::pre::PREMultiSet
• get_pre_singleset_vec() : core::scoring::nmr::pre::PREMultiSet
• get_pre_spin_type() : core::scoring::nmr::pre::PRESingle
• get_pre_values() : core::scoring::nmr::pre::PREMultiSet
• 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_predictor() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• get_prefix() : protocols::loop_modeling::utilities::TrajectoryLogger , protocols::struct_fragment::StructFragmentMover
• get_prelim_larval_job_tracker() : protocols::jd3::standard::StandardJobQueen
• get_preliminary_job_node_indices() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• get_preliminary_larval_jobs() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• get_preliminary_larval_jobs_determined() : protocols::jd3::standard::StandardJobQueen
• get_present_atoms() : core::scoring::sc::ElectrostaticComplementarityCalculator
• get_previously_closed_cutpoint_from_imported_silent_file() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• get_primary_graft_mover() : protocols::antibody::AntibodyCDRGrafter
• get_principal_quantum_number() : core::chemical::ElectronConfiguration
• get_priority() : protocols::frag_picker::scores::FragmentScoringMethod
• get_probability() : protocols::make_rot_lib::RotData
• get_probability_for_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_probability_for_rotamer_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• get_probe_scorefxn() : core::scoring::rna::data::RNA_DMS_Potential
• get_probe_xyz() : core::scoring::rna::data::RNA_DMS_Potential
• get_profile() : protocols::frag_picker::VallChunk , protocols::splice::SpliceSegment
• get_profile_and_design_cdrs() : protocols::antibody::task_operations::AddCDRProfilesOperation
• get_profile_set_and_design_cdrs() : protocols::antibody::task_operations::AddCDRProfilesOperation
• get_profile_wgt() : protocols::simple_moves::SequenceProfileMover
• get_project_pref_bg() : protocols::boinc::Boinc
• 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_proline_correction() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_proline_correction_for_node() : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_property() : core::chemical::Element
• get_property_effect_name() : core::scoring::bin_transitions::BinTransitionData
• get_property_from_name() : core::scoring::bin_transitions::BinTransitionData
• get_property_from_string() : core::chemical::ResidueProperties
• get_property_name() : core::chemical::Element
• get_proposed_energy() : core::pack::interaction_graph::SimpleEdge
• get_ProQPotential() : core::scoring::ScoringManager
• get_protein() : protocols::loophash::BackboneDB
• get_protein_chis() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• get_protein_mass() : core::scoring::nmr::pre::PREMultiSet
• get_protein_restype() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• get_protein_spins() : core::scoring::nmr::pcs::PCSSingle , core::scoring::nmr::pre::PRESingle
• get_protein_sstype() : protocols::simple_filters::AbinitioBaseFilter
• get_protocol_id() : protocols::features::ProteinSilentReport
• get_pseudobonds_to_residue() : core::conformation::Residue
• get_psi() : protocols::make_rot_lib::RotData , protocols::rigid::RigidBodyRandomizeMover
• get_psi_from_rsd() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_ptask() : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• get_PyMOL_model_name() : protocols::moves::PyMOLMover
• get_pymol_mover() : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• 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_q() : core::scoring::saxs::SAXSEnergy
• 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_R() : core::scoring::electron_density::ElectronDensity , core::scoring::nmr::rdc::RDCTensor
• get_radial_disp_diffs() : protocols::matdes::SymDofMoverSampler
• get_radial_disps() : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• get_radical_atom() : core::scoring::nmr::NMRSpinlabel
• get_radical_atom_coordinates() : core::scoring::nmr::NMRSpinlabel
• get_radii() : core::pack::interaction_graph::RotamerDots
• get_radius() : core::scoring::packstat::AtomRadiusMap , protocols::electron_density::DockIntoDensityMover
• get_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_rama_prepro_mainchain_torsion_potential() : core::scoring::ScoringManager
• get_rama_prepro_mainchain_torsion_potential_name() : core::chemical::ResidueTypeBase
• get_rama_prepro_map_file_name() : core::chemical::ResidueTypeBase
• get_rama_table_type_from_name() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• get_Ramachandran() : core::scoring::ScoringManager
• get_Ramachandran2B() : core::scoring::ScoringManager
• get_Ramachandran2B_ptr() : core::scoring::ScoringManager
• get_Ramachandran_ptr() : core::scoring::ScoringManager
• get_RamaPrePro() : core::scoring::ScoringManager
• get_ramatable_name_by_type() : core::scoring::Ramachandran
• get_ramatable_type_by_name() : core::scoring::Ramachandran
• get_ramp_fa_rep() : protocols::simple_moves::ShakeStructureMover
• get_ramp_width_A2() : core::scoring::lkball::LK_BallEnergy
• get_rand_range() : protocols::membrane::SpinAroundPartnerMover
• get_random_angle() : protocols::membrane::FlipMover , protocols::membrane::TiltMover
• get_random_backbone_segments() : protocols::loop_modeler::perturbers::LoopHashPerturber
• get_random_base_pair_jump() : core::import_pose::libraries::RNA_JumpLibrary
• get_random_beta_sheet_jump() : protocols::jumping::PairingLibrary
• get_random_conformer() : core::chemical::rings::RingConformerSet
• get_random_local_min_conformer() : core::chemical::rings::RingConformerSet
• get_random_loop_flag() : protocols::LoopRebuild
• get_random_neighbor() : core::pack::interaction_graph::FASTERNode
• get_random_neighbor_for_node() : core::pack::interaction_graph::FASTERInteractionGraph
• get_random_node() : protocols::legacy_sewing::SewGraph
• get_random_node_with_edges() : protocols::legacy_sewing::SewGraph
• 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_seed_info() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• get_random_segment_id() : protocols::sewing::data_storage::SmartAssembly
• get_random_tmh_jump() : protocols::jumping::PairingLibrary
• get_randomize_input_sequence() : protocols::anchored_design::AnchoredDesignMover
• get_randomize_resnum() : protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• get_range() : protocols::membrane::SpinAroundPartnerMover
• get_rb_center() : core::kinematics::Jump
• get_rb_delta() : core::kinematics::Jump
• get_rb_mover() : protocols::docking::DockingLowRes
• get_rb_seq() : protocols::docking::DockingLowRes
• get_rb_trial() : protocols::docking::DockingLowRes
• get_rdc_calc() : core::scoring::nmr::rdc::RDCSingle
• get_RDC_data() : core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl
• get_rdc_data_from_pose() : protocols::nmr::rdc::RDCEnergy
• get_RDC_data_ref() : core::scoring::ResidualDipolarCoupling
• get_RDC_data_type() : core::scoring::RDC , core::scoring::ResidualDipolarCoupling_Rohl
• get_rdc_err() : core::scoring::nmr::rdc::RDCSingle
• get_rdc_exp() : core::scoring::nmr::rdc::RDCSingle
• get_rdc_multiset_vec() : core::scoring::nmr::rdc::RDCData
• get_rdc_single_weights() : core::scoring::nmr::rdc::RDCMultiSet
• get_rdc_singleset_vec() : core::scoring::nmr::rdc::RDCMultiSet
• get_rdc_type() : core::scoring::nmr::rdc::RDCSingle , core::scoring::nmr::rdc::RDCSingleSet
• get_rdc_values() : core::scoring::nmr::rdc::RDCMultiSet
• get_rdf_function() : protocols::ligand_docking::rdf::RDFFunctionFactory
• get_reactive_atom() : core::enzymes::EnzymeManager
• get_reactive_residue_consensus_sequence_position() : core::enzymes::EnzymeManager
• get_reactive_site_atom_name() : protocols::enzymatic_movers::EnzymaticMover
• get_reactive_site_sequence_position() : protocols::enzymatic_movers::EnzymaticMover
• get_reactivity_from_rdat() : core::io::rna::RNA_DataReader
• get_real_metric_data() : core::simple_metrics::SimpleMetricData
• get_realatomdata_index() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_recent_history_size() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• get_recenter() : core::conformation::symmetry::SymmData
• get_recognized_cdr_definitions() : protocols::antibody::AntibodyEnumManager
• get_recognized_cluster_definitions() : protocols::antibody::clusters::CDRClusterEnumManager
• get_recognized_design_protocols() : protocols::antibody::design::AntibodyDesignEnumManager
• get_recognized_numbering_schemes() : protocols::antibody::AntibodyEnumManager
• get_reconstruct() : protocols::mpi_refinement::WorkUnit_PartialAbinitio
• get_recover_lowest_assembly() : protocols::sewing::movers::AssemblyMover
• 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_ref_atom_ID() : core::kinematics::jacobian::ModuleType1
• get_ref_pose() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• get_ref_tags() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• get_ref_xyz() : core::pose::rna::VDW_Grid
• get_reference_energies_from_dofs() : protocols::optimize_weights::OptEMultifunc
• get_reference_energy() : core::chemical::rotamers::StoredRotamerLibrarySpecification , core::pack::rotamers::SingleLigandRotamerLibrary
• get_reference_ft() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• get_reference_intensities() : core::scoring::saxs::SAXSEnergy
• get_reference_pose() : protocols::constraint_generator::ResidueTypeConstraintGenerator , protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• get_reference_shift() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_reference_xyz() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• get_reference_xyz_average() : 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_pose_list() : core::import_pose::RNA_DeNovoSetup
• get_refine_repack_cycles() : protocols::anchored_design::AnchoredRefineMover
• get_refine_temp() : protocols::anchored_design::AnchoredRefineMover
• get_region_end() : protocols::sewing::scoring::SubsetPartnerMotifScorer
• get_region_mm_bend_score() : protocols::enzdes::EnzdesFlexibleRegion
• get_region_of_residue() : protocols::antibody::AntibodyInfo
• get_region_start() : protocols::sewing::scoring::SubsetPartnerMotifScorer
• get_region_total_score() : protocols::enzdes::EnzdesFlexibleRegion
• get_register() : core::scoring::dssp::Pairing , core::scoring::dssp::StrandPairing
• get_rel_hphobic_sasa_by_charge() : core::scoring::sasa::SasaCalc
• get_relative() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• get_relative_additive() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• get_relax_script() : protocols::relax::RelaxScriptManager
• get_relaxed_state() : core::pack::interaction_graph::FASTERNode
• 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_remove_hydrogens() : protocols::simple_moves::SetupMetalsMover
• get_repack_neighborhood() : protocols::coupled_moves::CoupledMovesProtocol , protocols::simple_moves::CoupledMover
• get_repack_period() : protocols::loop_modeling::refiners::RepackingRefiner
• get_repack_residues() : protocols::membrane::MPMutateRelaxMover
• get_repacked_poses() : protocols::minimization_packing::SetReturningPackRotamersMover
• get_report_as() : protocols::moves::FilterReportAsPoseExtraScoresMover
• get_report_format() : protocols::peptide_deriver::PeptideDeriverFilter
• get_representative_type() : core::chemical::ResidueTypeFinder
• get_representative_type_aa() : core::chemical::ResidueTypeSet
• get_representative_type_base_name() : core::chemical::ResidueTypeSet
• get_representative_type_name1() : core::chemical::ResidueTypeSet
• get_representative_type_name3() : core::chemical::ResidueTypeSet
• get_required_resnums() : protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::movers::AppendAssemblyMover
• get_required_selector() : protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::movers::AppendAssemblyMover
• get_requirement() : protocols::sewing::requirements::AssemblyRequirementFactory
• get_requirements() : protocols::sewing::movers::AssemblyMover
• 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_centers() : core::scoring::packstat::SimplePDB
• get_res_energy() : protocols::protein_interface_design::ReportSequenceDifferences
• get_res_list() : core::pose::full_model_info::FullModelParameters
• get_res_list_as_pairs() : core::pose::full_model_info::FullModelParameters
• get_res_list_in_reference() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_res_nodenames() : core::kinematics::TreeVizBuilder
• get_res_res_elecE() : core::scoring::GenBornPotential , core::scoring::MultipoleElecPotential
• get_res_res_overlap() : core::pack::interaction_graph::RotamerDots
• get_res_res_sasa() : core::scoring::SASAPotential
• get_res_res_score() : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• get_res_res_vdw() : core::scoring::VdWTinkerPotential
• get_res_type_set() : core::chemical::CacheableResidueTypeSets
• get_resample_internal_local_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_resample_internal_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_resample_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_resample_terminal_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_resfile() : core::scoring::motif::MotifHits
• get_resfile_1() : protocols::anchored_design::AnchorMoversData
• get_resfile_2() : protocols::anchored_design::AnchorMoversData
• get_resid() : protocols::moves::ResId
• get_resID_1() : protocols::sewing::data_storage::SmartAssembly
• get_resID_2() : protocols::sewing::data_storage::SmartAssembly
• get_residue() : core::fragment::FragData , core::import_pose::RNA_HelixAssembler , core::scoring::nmr::NMRDummySpinlabelConformer , protocols::frag_picker::FragmentCandidate , protocols::legacy_sewing::Model , protocols::qsar::qsarMap , protocols::qsar::qsarPoint , protocols::sewing::data_storage::SmartSegment , 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_data() : core::scoring::GenBondedExclInfo
• get_residue_depth() : protocols::simple_filters::ResidueDepthFilter
• get_residue_edge() : core::kinematics::FoldTree
• get_residue_energy_by_svm() : core::scoring::methods::NMerSVMEnergy
• get_residue_energy_by_table() : core::scoring::methods::NMerRefEnergy
• get_residue_energy_from_sequence() : core::scoring::methods::NMerSVMEnergy
• get_residue_energy_RNA_intra() : core::scoring::methods::LK_PolarNonPolarEnergy
• get_residue_feature() : protocols::comparative_modeling::features::ResidueFeatureFactory
• get_residue_group_begin() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_residue_group_index_for_rotamer() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_residue_hbonds() : protocols::simple_pose_metric_calculators::NumberHBondsCalculator
• get_residue_hsasa() : core::scoring::sasa::SasaCalc
• get_residue_hsasa_bb() : core::scoring::sasa::SasaCalc
• get_residue_hsasa_sc() : core::scoring::sasa::SasaCalc
• get_residue_indices_to_output() : protocols::dna::PDBOutput
• get_residue_information() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• get_residue_mask() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation
• get_residue_num() : protocols::scoring::methods::pcs2::PcsInputLine
• get_residue_pair_data() : core::scoring::GenBondedExclInfo
• get_residue_pair_energy() : core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• get_residue_pair_energy_one_way() : core::scoring::methods::LK_PolarNonPolarEnergy
• get_residue_residue_h2o_hbonds_1way() : core::scoring::WaterAdductHBondPotential
• get_residue_sasa() : core::scoring::sasa::SasaCalc
• get_residue_sasa_bb() : core::scoring::sasa::SasaCalc
• get_residue_sasa_sc() : core::scoring::sasa::SasaCalc
• get_residue_score_() : protocols::hotspot_hashing::HotspotStubSet
• get_residue_selector() : protocols::constraint_generator::ResidueTypeConstraintGenerator , protocols::rosetta_scripts::XmlObjects
• get_residue_similarity() : protocols::simple_filters::ResidueDepthFilter
• get_residue_type() : core::scoring::nmr::NMRSpinlabel
• get_residue_type_begin() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_residue_type_cop_with_variant_removed() : core::pack::palette::PackerPalette
• get_residue_type_index_for_rotamer() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_residue_type_set() : protocols::pose_creation::PoseFromSequenceMover , protocols::simple_moves::SwitchResidueTypeSetMover
• get_residue_type_with_custom_variant_added() : core::chemical::ResidueTypeSet
• get_residue_type_with_variant_added() : core::chemical::ResidueTypeSet
• get_residue_type_with_variant_removed() : core::chemical::ResidueTypeSet
• get_residue_vector() : protocols::sewing::data_storage::SmartSegment
• get_residue_weight() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation
• get_residue_weights() : protocols::hybridization::FoldTreeHybridize
• get_residues() : core::conformation::carbohydrates::GlycanTree , core::kinematics::jacobian::ModuleType1 , core::kinematics::jacobian::SeriesJacobians , protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::indexed_structure_store::StructureStore , protocols::ligand_docking::Ligand_info , protocols::loops::Loop , protocols::loops::Loops , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::task_operations::PreventResiduesFromRepackingOperation , protocols::task_operations::RestrictResiduesToRepackingOperation
• get_residues_to_rebuild() : protocols::rbsegment_relax::SequenceShiftMover
• get_reslabels() : core::pose::PDBInfo
• get_resname() : protocols::metal_interface::MetalSiteResidue
• get_resnum() : core::conformation::carbohydrates::GlycanNode , core::io::silent::SilentFileData
• get_resNum() : protocols::features::strand_assembly::SandwichFragment
• get_resnum() : protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• get_resnum_string() : protocols::residue_selectors::LigandMetalContactSelector
• get_resolution_damping() : protocols::nmr::pcs::PCSLigandTransformMover
• get_resrange_hbond_energy() : protocols::loop_grower::LoopGrower
• get_restag() : core::scoring::HydroxylTorsionPotential
• get_restrict_partners_to_chains() : protocols::peptide_deriver::PeptideDeriverFilter
• get_restrict_receptors_to_chains() : protocols::peptide_deriver::PeptideDeriverFilter
• get_restrictions() : protocols::flxbb::LayerDesignOperation , protocols::task_operations::DsspDesignOperation
• get_restype_emap() : core::scoring::SplitUnfoldedTwoBodyPotential
• get_result() : protocols::frag_picker::FragmentScoreFilter
• get_result_node() : protocols::jd3::JobGenealogist
• get_reverse_assembly() : protocols::sewing::data_storage::SmartAssembly
• get_rh() : core::scoring::nmr::NMRTensor
• get_rid_of_capping_base_pairs() : core::import_pose::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_move_mags() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• 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_ring() : core::scoring::methods::ArgCationPiEnergy
• get_ring_current_deriv_for_src_base() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_ring_params() : core::scoring::methods::ArgCationPiEnergy
• get_rise() : protocols::dna_dock::PropagateClashCheckFilter
• get_rms() : protocols::loop_grower::LoopPartialSolution
• get_rmsd() : protocols::anchored_design::AnchoredDesignMover
• get_RMSD() : protocols::motif_grafting::movers::MotifMatch , protocols::normalmode::NormalModeRelaxMover
• get_rmsd() : protocols::pockets::SmallMol , protocols::rna::denovo::RNA_FragmentMonteCarlo
• get_rmsd_mat() : core::scoring::nmr::NMRDummySpinlabelEnsemble
• get_rmsd_no_superimpose() : protocols::rna::denovo::RNA_FragmentMonteCarlo , 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_stems_no_superimpose() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• get_rmsd_target_tolerance() : protocols::simple_moves::ShakeStructureMover
• get_rmsd_tolerance() : protocols::LoopRebuild
• get_RNA_AtomVDW() : core::scoring::ScoringManager
• get_rna_axis_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_backbone_backbone_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_backbone_backbone_xy() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_base_backbone_xy() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_base_pairing_status() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• get_rna_basepair_xy() : core::scoring::rna::RNA_LowResolutionPotential
• get_RNA_ChemicalShiftPotential() : core::scoring::ScoringManager
• get_RNA_CS_residue_parameters() : core::scoring::rna::chemical_shift::RNA_CS_parameters
• get_RNA_DMS_LowResolutionPotential() : core::scoring::ScoringManager
• get_RNA_DMS_Potential() : core::scoring::ScoringManager
• get_RNA_LowResolutionPotential() : core::scoring::ScoringManager
• get_rna_repulsive_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_stack_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_stagger_score() : core::scoring::rna::RNA_LowResolutionPotential
• get_rna_suite_potential() : core::scoring::ScoringManager
• get_RNAring_sasa() : protocols::pockets::GenPharmacophore
• get_RNP_LowResPairDistPotential() : core::scoring::ScoringManager
• get_RNP_LowResPotential() : core::scoring::ScoringManager
• get_RNP_LowResStackData() : core::scoring::ScoringManager
• get_root() : core::conformation::carbohydrates::GlycanTree , core::conformation::symmetry::SymmData , protocols::pockets::SmallMol
• get_root_triad_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• get_ROSETTA_SASA_radii() : core::pack::interaction_graph::RotamerDotsRadiusData
• get_rot_ind() : protocols::mean_field::ResHashMap
• get_rot_mag() : protocols::rigid::RigidBodyPerturbMover
• get_rot_magnitude() : protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes
• get_rot_step() : protocols::nmr::pcs::PCSLigandTransformMover
• get_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyNode
• get_rotamer_angle() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• get_rotamer_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• get_rotamer_bounding_box() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• get_rotamer_from_chi() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• get_rotamer_from_chi_static() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• get_rotamer_from_chi_static_voronoi() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• get_rotamer_op() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• get_rotamer_recovery() : protocols::pose_metric_calculators::RotamerRecovery , protocols::rotamer_recovery::RotamerRecoveryFactory
• 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_samples() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• get_rotamer_set() : protocols::protein_interface_design::movers::TryRotamers
• get_rotamers() : protocols::motifs::LigandMotifSearch
• get_rotamers_born_radii() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• get_rotamers_effective_radii() : core::scoring::MultipoleElecPotential
• get_rotamers_multipole_info() : core::scoring::MultipoleElecPotential
• get_rotamers_vdw_info() : core::scoring::VdWTinkerPotential
• get_rotated_and_translated_pose() : protocols::motif_grafting::movers::MotifGraftMover
• get_rotation() : core::kinematics::Jump , core::kinematics::RT , protocols::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::PeptideOrientationMover
• get_rotation_angle() : protocols::membrane::AqueousPoreFinder
• get_rotation_magnitude() : protocols::simple_moves::CoupledMover
• get_rotation_matrix() : core::conformation::symmetry::SymmData , protocols::docking::EllipsoidalRandomizationMover
• get_rotation_parameters() : protocols::nonlocal::HelixRotate
• get_rotation_std_dev() : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• get_rotblock_index_for_sampling_rotamer() : core::pack::rotamer_set::ContinuousRotamerSet
• get_rsd() : core::io::nmr::AtomSelection
• get_rsd_alternatives_rotamer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• get_rsd_type() : core::io::pose_from_sfr::PoseFromSFRBuilder
• get_rsd_type_name3() : core::scoring::constraints::ResidueTypeConstraint , protocols::constraint_generator::ResidueTypeConstraintGenerator
• get_run_time() : protocols::wum::WorkUnitBase
• get_Rvalue() : protocols::pockets::NonPlaidFingerprint
• get_S() : core::io::nmr::ParaIon
• get_safe_max_dis2() : core::scoring::etable::Etable
• get_sample_index() : protocols::task_operations::MutationSetDesignOperation
• get_sample_nonpivot_torsions() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_sampler_options() : protocols::stepwise::modeler::options::StepWiseModelerOptions
• get_sampling_data() : core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::carbohydrates::OmegaPreferencesFunction
• get_sasa() : core::pack::interaction_graph::RotamerDots
• get_sasa_difference() : core::pack::interaction_graph::HPatchNode< V, E, G >
• get_SASAfilter() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_SASAPotential() : core::scoring::ScoringManager
• get_sc_and_area() : protocols::denovo_design::filters::SSShapeComplementarityFilter
• get_sc_bbE() : core::pack::rotamer_set::RotamerSets
• get_sc_interface_builder() : protocols::ligand_docking::MoveMapBuilder
• get_sc_min() : protocols::simple_moves::ShakeStructureMover
• get_sc_scale() : protocols::cryst::LoadDensityMapMover
• 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_scaling_factor() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::pre::PRESingleSet
• get_scdepth() : protocols::simple_filters::ResidueDepthCalculator
• get_scdepth_avrg() : protocols::simple_filters::ResidueDepthCalculator , protocols::simple_filters::ResidueDepthFilter
• get_scdepth_fvar() : protocols::simple_filters::ResidueDepthCalculator , protocols::simple_filters::ResidueDepthFilter
• get_scdepth_sdev() : protocols::simple_filters::ResidueDepthCalculator , protocols::simple_filters::ResidueDepthFilter
• get_score() : core::energy_methods::DEEREnergy , core::scoring::epr_deer::DEERData , core::scoring::epr_deer::DEERDecayData , core::scoring::epr_deer::DEERDistanceBounds , core::scoring::epr_deer::DEERDistanceDistribution , core::scoring::rna::TNA_SuitePotential , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::hbnet::HBNetScore , protocols::legacy_sewing::scoring::LegacyMotifScorer , protocols::loop_grower::LoopPartialSolution , protocols::magnesium::MgScanner , 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::protein_interface_design::filters::StubScoreLoopsFilter , protocols::score_filters::ScoreCutoffFilter , protocols::sewing::scoring::MotifScorer
• get_score_against_internal_contacts() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_score_best() : protocols::membrane::OptimizeMembranePositionMover
• 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_from_sequences() : core::scoring::rna::RNA_PartitionEnergy
• 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::loop_modeling::utilities::TrajectoryLogger , protocols::match::downstream::ScoringSecMatchRPE , protocols::rosetta_scripts::XmlObjects
• get_score_function_attributes() : protocols::loop_modeling::LoopBuilder
• get_score_fxn() : protocols::simple_moves::CoupledMover
• get_score_manager() : protocols::frag_picker::FragmentPicker
• get_score_multiply_subunit() : core::conformation::symmetry::SymmData
• get_score_name() : protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::scores::MakeFragmentScoringMethod
• get_score_offset() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• get_score_result() : protocols::legacy_sewing::Assembly
• get_score_subunit() : core::conformation::symmetry::SymmData
• get_scorefile_name() : protocols::optimize_weights::IterativeOptEDriver
• get_scorefile_reporting_prefix() : protocols::analysis::InterfaceAnalyzerMover
• get_scorefilter() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_scorefunction() : protocols::features::DatabaseJobInputter , protocols::ncbb::SecStructMinimizeMover , protocols::nmr::ParaNMRScoreMover , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREMover , protocols::simple_moves::ShakeStructureMover , protocols::splice::TailSegmentMover
• get_scorefunction_header() : protocols::ddg::ddGMover
• get_scorefunction_initialized() : protocols::simple_moves::ShakeStructureMover
• get_scorefxn() : core::pack::task::residue_selector::ClashBasedShellSelector , protocols::docking::DockingLowRes , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::ligand_docking::LigandBaseProtocol , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::minimization_packing::BoltzmannRotamerMover , protocols::mpi_refinement::MultiObjective , protocols::pmut_scan::PointMutScanDriver , protocols::relax::RelaxProtocolBase , protocols::residue_selectors::HBondSelector , protocols::simple_filters::SimpleHbondsToAtomFilter , protocols::simple_moves::DisulfideInsertionMover , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• get_scorefxn_deriver() : protocols::peptide_deriver::PeptideDeriverFilter
• get_scorefxn_filename() : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• get_scorefxn_info() : core::scoring::Energies
• get_scores() : protocols::ligand_docking::InterfaceScoreCalculator , protocols::recces::Histogram
• get_scores_map() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded
• get_scores_to_keep() : protocols::sewing::scoring::TopNMotifScorer
• get_scoretype() : protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_Relax
• get_scoring_scheme() : core::sequence::ScoringSchemeFactory
• get_scratch_atom_id() : core::pose::copydofs::CopyDofs
• get_scratch_index() : core::pack::dunbrack::DunbrackEnergy
• get_SDE_score() : protocols::simple_filters::ResidueDepthFilter
• get_second_atom() : protocols::frag_picker::scores::AtomPairConstraintsData , protocols::frag_picker::scores::FourAtomsConstraintData
• get_second_node_ind() : core::pack::interaction_graph::EdgeBase
• get_second_node_num_states_per_aa() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• get_second_offset() : protocols::frag_picker::scores::FourAtomsConstraintData
• get_second_substrates_or_byproducts() : core::enzymes::EnzymeManager
• get_secondary_graft_mover() : protocols::antibody::AntibodyCDRGrafter
• get_secondary_prediction() : protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• get_SecondaryStructurePotential() : core::scoring::ScoringManager
• get_secstruct() : core::pose::rna::secstruct_legacy::RNA_SecStructLegacyInfo , core::select::residue_selector::SecondaryStructureSelector , protocols::denovo_design::residue_selectors::PairedSheetResidueSelector , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintGenerator , protocols::frags::TorsionFragment , protocols::struct_fragment::StructFragmentMover
• get_seg1() : protocols::sewing::hashing::Hasher
• get_seg2() : protocols::sewing::hashing::Hasher
• get_segdef() : protocols::mpi_refinement::WorkUnit_bbGauss
• get_segID_1() : protocols::sewing::data_storage::SmartAssembly
• get_segID_2() : protocols::sewing::data_storage::SmartAssembly
• get_segment() : protocols::sewing::data_storage::SmartAssembly
• get_segment_coords() : protocols::legacy_sewing::LegacyRepeatAssemblyMover
• get_segment_distance_cutoff() : protocols::sewing::movers::LigandBindingAssemblyMover
• get_segment_fname() : protocols::splice::RotLibdb
• get_segment_id() : protocols::sewing::data_storage::SmartSegment
• get_segment_names_ordered() : protocols::splice::Splice
• get_segment_vector() : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::movers::AssemblyMover
• get_segments_from_dssp() : protocols::sewing::movers::AppendAssemblyMover
• get_selected_mover() : protocols::moves::SwitchMover
• get_selected_strands() : protocols::features::strand_assembly::StrandBundleFeatures
• get_selector() : core::simple_metrics::PerResidueRealMetric , protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_selector_name() : core::scoring::mhc_epitope_energy::MHCEpitopeConstraint
• 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() : core::chemical::ResidueType , core::chemical::ResidueTypeSet , core::conformation::Conformation , core::conformation::parametric::Parameter , core::conformation::parametric::Parameters , core::conformation::parametric::ParametersSet , core::conformation::parametric::ParametrizationCalculator , core::conformation::Residue , core::fragment::FragData , core::io::silent::SilentStruct , core::kinematics::tree::Atom , core::pack::palette::PackerPalette , core::pack::task::PackerTask , core::pose::Pose , core::pose::reference_pose::ReferencePose , core::pose::reference_pose::ReferencePoseSet , core::scoring::hbonds::HBond , core::scoring::ScoreFunction , 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::BackboneGridSamplerHelper , protocols::helical_bundle::BundleGridSamplerHelper , protocols::indexed_structure_store::FragmentStore , protocols::jd2::JobInputter , protocols::jd2::JobsContainer , 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 , protocols::vardist_solaccess::VarSolDistSasaCalculator
• get_self_terms() : core::scoring::FACTSPotential
• get_self_weak_ptr() : core::chemical::ResidueType , core::chemical::ResidueTypeSet , core::conformation::Conformation , core::conformation::parametric::Parameter , core::conformation::parametric::Parameters , core::conformation::parametric::ParametersSet , core::conformation::parametric::ParametrizationCalculator , core::conformation::Residue , core::kinematics::tree::Atom , core::pose::Pose , core::pose::reference_pose::ReferencePose , core::pose::reference_pose::ReferencePoseSet , 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::BackboneGridSamplerHelper , protocols::helical_bundle::BundleGridSamplerHelper , protocols::jd2::JobInputter , 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 , protocols::vardist_solaccess::VarSolDistSasaCalculator
• 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_and_resnum() : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• get_seq_names() : core::sequence::SequenceFactory
• get_seq_recovery_cache() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• get_seq_sep_scale() : core::scoring::SecondaryStructureWeights
• get_seqpos() : protocols::metal_interface::MetalSiteResidue
• get_seqpos1() : core::scoring::constraints::ResidueTypeLinkingConstraint
• get_seqpos2() : core::scoring::constraints::ResidueTypeLinkingConstraint
• get_sequence() : core::import_pose::RNA_HelixAssembler , core::io::silent::SilentFileData , core::sequence::SequenceFactory , protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::VallChunk , protocols::frags::TorsionFragment , protocols::pose_creation::PoseFromSequenceMover , protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• get_sequence_alignment_cut_max() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• get_sequence_profile() : protocols::struct_fragment::StructFragmentMover
• get_sequence_recovery() : protocols::pose_metric_calculators::SequenceComparison
• get_sequence_region() : protocols::topology_broker::FragmentClaimer
• get_sequence_with_gaps_filled_with_n() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• get_set_tm_helical() : protocols::relax::membrane::MPRangeRelaxMover
• get_sfxn() : protocols::ligand_docking::ga_ligand_dock::GridScorer , protocols::membrane::OptimizeMembranePositionMover , protocols::relax::membrane::MPRangeRelaxMover
• get_sfxn_cycles() : protocols::loop_modeling::LoopProtocol
• get_sfxn_name() : protocols::docking::SlideIntoContact
• get_shared_silent_data() : core::io::silent::SilentFileData
• get_sheet() : protocols::nonlocal::SheetTranslate
• get_sheet_id() : protocols::features::strand_assembly::SandwichFragment
• get_sheet_topology() : protocols::denovo_design::residue_selectors::PairedSheetResidueSelector
• get_shell_radius() : protocols::membrane::MPLipidAccessibility
• get_shift() : protocols::frag_picker::CSTalosIO
• get_short_backrub_mover() : protocols::simple_moves::CoupledMover
• get_short_name_to_iupac_strings_map() : core::chemical::carbohydrates::CarbohydrateInfoManager
• 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_sidechain_amide_name() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• get_sidechain_connect_index() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• get_sidechain_indices() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper
• get_silent_energies() : core::io::silent::SilentStruct
• get_silent_energy() : core::io::silent::SilentStruct
• get_silent_resnum() : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• get_silent_seq() : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• get_silent_struct() : core::io::silent::SilentStructFactory
• get_silent_struct_in() : core::io::silent::SilentStructFactory
• get_silent_struct_out() : core::io::silent::SilentStructFactory
• get_simple_ig_owner() : core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleNode
• get_simple_metric() : protocols::rosetta_scripts::XmlObjects
• get_simple_node() : core::pack::interaction_graph::SimpleInteractionGraph
• get_simscore() : protocols::simple_filters::ResidueDepthFilter
• get_single_chain() : core::kinematics::jacobian::JacobianStructure
• get_single_mg_pose() : protocols::magnesium::MgScanner
• get_single_pcs_vec() : core::scoring::nmr::pcs::PCSSingleSet
• get_single_pre_weighting_scheme() : core::scoring::nmr::pre::PRESingleSet
• get_single_rdc_vec() : core::scoring::nmr::rdc::RDCSingleSet
• get_single_rdc_weighting_scheme() : core::scoring::nmr::rdc::RDCSingleSet
• get_single_rotamer_born_radii() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• get_single_rotamer_effective_radii() : core::scoring::MultipoleElecPotential
• get_size() : core::conformation::carbohydrates::GlycanTree , core::conformation::carbohydrates::GlycanTreeSet , core::fragment::rna::TorsionSet , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment , protocols::pockets::SmallMol , protocols::sewing::data_storage::SmartAssembly
• get_skip_low_temp_phase() : protocols::simple_moves::ShakeStructureMover
• get_slice_width() : protocols::membrane::MPLipidAccessibility
• get_slide_axis() : protocols::docking::EllipsoidalRandomizationMover
• get_slide_info() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_slide_order() : core::conformation::symmetry::SymSlideInfo
• get_slide_threshold() : protocols::symmetry::SymmetrySlider
• get_slide_type() : core::conformation::symmetry::SymSlideInfo
• get_SlideCriteriaType() : core::conformation::symmetry::SymSlideInfo
• get_SlideCriteriaVal() : core::conformation::symmetry::SymSlideInfo
• get_slope() : core::scoring::func::LinearPenaltyFunction
• get_small_frag_file() : protocols::struct_fragment::StructFragmentMover
• get_small_frag_size() : protocols::struct_fragment::StructFragmentMover
• get_smallest_glycan_tree_layer() : core::conformation::carbohydrates::GlycanTreeSet
• get_smooth() : core::scoring::hbonds::FadeInterval
• get_SmoothEnvPairPotential() : core::scoring::ScoringManager
• get_smoothing() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_sol_secondary_struct() : protocols::surface_docking::FullatomRelaxMover
• get_solution_picker() : protocols::kinematic_closure::KicMover
• get_solutions() : protocols::loop_grower::LoopPartialSolutionStore
• get_solvation() : protocols::make_rot_lib::RotData
• get_source() : core::pose::ResidueIndexDescription
• get_spanfile() : protocols::membrane::AddMembraneMover
• get_spanfiles() : protocols::docking::membrane::MPDockingSetupMover
• get_spans() : core::conformation::membrane::SpanningTopology
• get_sparse_aa_info() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FixedBBEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_sparse_aa_info_for_edge() : core::pack::interaction_graph::FixedBBInteractionGraph
• get_sparse_aa_neighbor_info() : core::pack::interaction_graph::LinearMemEdge
• get_sparse_mat_info_for_curr_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• get_sparse_mat_info_for_state() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode
• get_special_region() : protocols::simple_pose_metric_calculators::NumberHBondsCalculator
• get_species() : protocols::enzymatic_movers::EnzymaticMover
• get_specific_element() : protocols::jd3::dag_node_managers::NodeManagerStorageMatrix
• get_spectrum() : protocols::electron_density::DockIntoDensityMover
• get_sphere_aa() : protocols::motifs::LigandMotifSearch
• get_spheres() : core::scoring::packstat::SimplePDB
• get_spherical_repack_residues() : protocols::relax::RangeRelaxMover
• get_spin_center() : protocols::docking::EllipsoidalRandomizationMover
• get_spin_coordinates() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::pre::PREMultiSet , core::scoring::nmr::rdc::RDCMultiSet
• get_spinlabel() : core::scoring::nmr::pcs::PCSMultiSet , core::scoring::nmr::pre::PREMultiSet
• get_spinlabel_data() : core::io::nmr::SpinlabelDatabaseHandler
• get_spinlabel_data_table() : core::io::nmr::SpinlabelDatabaseHandler
• get_spinlabel_site_rsd() : core::scoring::nmr::pre::PREMultiSet
• get_spinsAB() : core::scoring::nmr::rdc::RDCSingle
• get_splitlines() : core::scoring::epr_deer::DEERIO
• get_SplitUnfoldedTwoBodyPotential() : core::scoring::ScoringManager
• get_ss() : protocols::pose_metric_calculators::RotamerRecovery
• get_ss_cutoff() : core::scoring::SecondaryStructureWeights
• get_ss_elements() : core::scoring::methods::SSElementMotifContactEnergy , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter
• get_ss_lowstrand() : core::scoring::SecondaryStructureWeights
• get_ss_names() : core::io::silent::SilentStructFactory
• get_ss_segments() : protocols::features::SmotifFeatures
• get_ss_type() : protocols::frag_picker::quota::SecondaryStructurePool
• get_ssbond_record() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• get_SSElement() : core::select::residue_selector::SSElementSelector
• get_SSelements_in_contact() : core::scoring::methods::SSElementMotifContactEnergy , protocols::simple_filters::SSElementMotifContactFilter
• get_ssElements_in_contact_w_threshold() : core::scoring::methods::SSElementMotifContactEnergy , protocols::simple_filters::SSElementMotifContactFilter
• get_ssid() : protocols::loophash::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_LoopHash
• get_stability_metric() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_stack_elec_deriv() : core::scoring::rna::StackElecEnergy
• get_stack_elec_score() : core::scoring::rna::StackElecEnergy
• get_start() : core::conformation::carbohydrates::GlycanTree , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment , protocols::loophash::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_LoopHash
• get_start_and_end_aa() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• get_start_and_end_indices() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• get_start_node_vital_segments() : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::movers::AppendAssemblyMover
• get_start_points() : core::conformation::carbohydrates::GlycanTreeSet
• get_start_positions() : protocols::helix_capper::HelixNCapperMover
• get_start_res() : protocols::loophash::LoopHashSampler , protocols::simple_moves::ReturnSidechainMover
• get_start_res_vec() : protocols::hbnet::HBNet
• get_start_temperature() : protocols::sewing::movers::AssemblyMover
• get_start_with_current() : core::pack::annealer::SimAnnealerBase
• get_starting_pose() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_starting_z() : protocols::membrane::OptimizeMembranePositionMover
• get_starts_and_ends() : protocols::sewing::scoring::SubsetPartnerMotifScorer
• get_state_ind_for_this_aa_type() : core::pack::interaction_graph::SparseMatrixIndex
• get_state_offset_for_aatype() : core::pack::interaction_graph::OnTheFlyNode
• get_state_offset_for_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• get_state_offset_for_restype_group() : core::pack::interaction_graph::SymmOnTheFlyNode
• get_states_on_curr_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• get_std_dev() : protocols::make_rot_lib::RotData
• get_steal_large_frags() : protocols::struct_fragment::StructFragmentMover
• get_steal_small_frags() : protocols::struct_fragment::StructFragmentMover
• get_stem_movemap() : protocols::antibody::GraftedStemOptimizer
• get_stem_residues() : core::import_pose::RNA_BasePairHandler
• get_stem_taskfactory() : protocols::antibody::GraftedStemOptimizer
• get_stepsize() : core::scoring::nmr::NMRGridSearch , protocols::docking::SlideIntoContact
• get_stepsize_angle() : protocols::membrane::OptimizeMembranePositionMover
• get_stepsize_z() : protocols::membrane::OptimizeMembranePositionMover
• get_stepwise_jump_atom() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• get_stop_res() : protocols::loophash::LoopHashSampler
• get_str_str_data() : core::chemical::sdf::MolFileIOMolecule
• get_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• get_strand_from_bss_id() : protocols::features::strand_assembly::StrandBundleFeatures
• get_strand_id() : protocols::features::strand_assembly::SandwichFragment
• get_strand_pairings() : protocols::denovo_design::components::SegmentPairing , protocols::fldsgn::filters::SecondaryStructureFilter
• get_strand_pairs() : protocols::features::strand_assembly::StrandBundleFeatures , protocols::hybridization::FoldTreeHybridize
• get_strand_residue_pairs() : protocols::denovo_design::components::SegmentPairing
• get_strandpairings() : protocols::fldsgn::SheetConstraintGenerator
• get_stretch_strand_dist_cutoff() : core::scoring::SecondaryStructureWeights
• get_strict_dssp_changes() : protocols::sewing::movers::AppendAssemblyMover
• get_strict_loops() : protocols::loops::loop_mover::IndependentLoopMover
• get_stride() : protocols::features::TrajectoryReportToDB
• get_string() : protocols::antibody::PDBLandmark
• get_string_from_property() : core::chemical::ResidueProperties
• get_string_from_variant() : core::chemical::ResidueProperties
• get_string_metric_data() : core::simple_metrics::SimpleMetricData
• get_string_property() : core::chemical::ResidueTypeBase
• get_string_real_pairs() : protocols::jd2::Job
• get_string_string_pairs() : protocols::jd2::Job
• get_string_value() : core::io::silent::SilentStruct
• 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() : core::io::silent::SilentFileData , protocols::indexed_structure_store::StructureStore
• get_structure_data() : protocols::indexed_structure_store::search::StructureDatabase
• get_structure_input_tag() : protocols::features::ReportToDB
• get_structure_tag() : protocols::features::ReportToDB
• get_stub() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , protocols::hotspot_hashing::HotspotStubSet , protocols::legacy_sewing::scoring::LegacyMotifScorer , protocols::sewing::scoring::MotifScorer , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• get_stub1() : core::chemical::orbitals::ICoorOrbitalData
• get_stub2() : core::chemical::orbitals::ICoorOrbitalData
• get_stub3() : core::chemical::orbitals::ICoorOrbitalData
• get_stub_scorefxn() : protocols::protein_interface_design::movers::PlacementAuctionMover
• get_stub_transform() : core::conformation::Conformation , core::kinematics::AtomTree
• get_stubRMSD() : protocols::pose_length_moves::PossibleLoop
• get_sub_score() : core::scoring::ScoreFunction
• get_sub_score_exclude_res() : core::scoring::ScoreFunction
• get_subbin_type_from_name() : core::scoring::bin_transitions::BinTransitionData
• get_subbin_type_name() : core::scoring::bin_transitions::BinTransitionData
• get_subcluster() : protocols::toolbox::KClusterElement
• get_submatrix_index() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• get_submotif_add_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_submotif_moves() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• get_submotif_sequence_set() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• get_subset() : core::scoring::MembraneTopology , core::select::residue_selector::CachedResidueSubset
• get_subset_name() : protocols::residue_selectors::StoredResidueSubsetSelector
• get_substituents_to_ring_atom() : core::conformation::Residue
• get_subunit_name_to_component() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• get_subunit_num_to_virt_id() : core::conformation::symmetry::SymmData
• get_subunits() : core::conformation::symmetry::SymmData
• get_success() : protocols::LoopRebuild
• get_suck_res() : protocols::simple_moves::AddCavitiesMover
• get_sugar_env_score() : core::scoring::rna::data::RNA_DataBackboneEnergy
• get_sugar_modeling_set() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• get_sugar_modeling_sets_for_chainbreak() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• get_sugar_setup_scorefxns() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• get_sugar_torsion_mean_and_sdev() : core::scoring::dna::DNA_DihedralPotential
• get_suite_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• get_suiteness() : core::pose::rna::RNA_SuiteName
• get_suiteness_derivative() : core::pose::rna::RNA_SuiteName
• get_sum_water_weight_grid() : core::scoring::geometric_solvation::WaterWeightGridSet
• get_super_secret_fixed_interface_mode() : protocols::anchored_design::AnchorMoversData
• get_surface_area() : core::scoring::packstat::LeeRichards
• get_surface_bg_edge() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• get_surface_bg_node() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• get_surface_deltaE_for_neighbor() : core::pack::interaction_graph::SurfaceEdge< V, E, G >
• get_surface_deltaE_for_neighbors_state_substitution() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_surface_deltaE_for_substitution() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• get_surface_esp() : protocols::pockets::NonPlaidFingerprint
• get_surface_node() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• get_surface_owner() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_surface_score() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• get_surface_score_difference() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• get_svm() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM
• get_svm_nodes() : core::scoring::methods::NMerSVMEnergy
• get_sw_can_by_sh_id() : protocols::features::strand_assembly::SandwichFragment
• get_sym_dof_names() : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• get_symbols() : core::sequence::ABEGOManager
• get_symm_data() : protocols::topology_broker::claims::SymmetryClaim
• get_symm_info() : protocols::hbnet::HBNet
• get_symmetry_name() : core::conformation::symmetry::SymmData
• get_symmetry_type() : core::conformation::symmetry::SymmData
• get_symmin_ig_owner() : core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistNode
• get_symmin_node() : core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• get_symmlinmem_ig_owner() : core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemNode
• get_symmlinmem_node() : core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• get_symmMap() : core::scoring::electron_density::ElectronDensity
• get_symmops() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• get_t() : protocols::hybridization::TMalign
• get_T_xx() : core::scoring::nmr::NMRTensor
• get_T_xy() : core::scoring::nmr::NMRTensor
• get_T_xz() : core::scoring::nmr::NMRTensor
• get_T_yy() : core::scoring::nmr::NMRTensor
• get_T_yz() : core::scoring::nmr::NMRTensor
• get_table_size() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• get_tag() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::toolbox::KClusterData
• get_tag_list() : protocols::cluster::GatherPosesMover
• get_tag_residue_number() : core::scoring::nmr::pcs::PCSMultiSet
• get_tag_score_map() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• get_tailfunction_from_name() : core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::netcharge_energy::NetChargeEnergySetup
• get_tailfunction_name() : core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::netcharge_energy::NetChargeEnergySetup
• get_target_atom_name() : protocols::simple_filters::SimpleHbondsToAtomFilter
• get_target_residue() : protocols::simple_filters::SimpleHbondsToAtomFilter
• get_target_sequences() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• get_targeted_sequence() : protocols::dna::DnaInterfacePacker
• get_task() : protocols::anchored_design::AnchorMoversData , protocols::hbnet::HBNet , protocols::minimization_packing::BoltzmannRotamerMover , protocols::task_operations::STMStoredTask
• get_task_factory() : protocols::anchored_design::AnchorMoversData , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::loop_modeler::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_task_operation() : protocols::rosetta_scripts::XmlObjects
• get_TaskFactory_AllCDRs() : protocols::antibody::AntibodyInfo
• get_TaskFactory_OneCDR() : protocols::antibody::AntibodyInfo
• get_tau_c() : core::scoring::nmr::pre::PREMultiSet
• get_tau_c_max() : core::scoring::nmr::pre::PREMultiSet
• get_tau_c_min() : core::scoring::nmr::pre::PREMultiSet
• get_tau_e() : core::io::nmr::ParaIon
• get_tau_r() : core::scoring::nmr::pre::PREMultiSet
• get_tau_t() : core::scoring::nmr::pre::PREMultiSet
• get_temp() : protocols::canonical_sampling::CanonicalSamplingMover
• get_temp_cycles() : protocols::loop_modeling::LoopProtocol
• get_temperature() : core::pack::annealer::SimAnnealerBase , core::scoring::nmr::pre::PREMultiSet , protocols::docking::ConformerSwitchMover , protocols::docking::DockingLowRes , protocols::ligand_docking::ga_ligand_dock::EntropyEstimator , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::md::Thermostat , protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• get_template() : core::pack::rotamer_set::RotamerLinks , protocols::abinitio::Templates
• get_template_atoms_at_pos() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• get_template_born_radii() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• get_template_pieces() : protocols::fold_from_loops::NubInitioMover
• get_template_segments() : protocols::denovo_design::architects::BlueprintArchitect
• get_tenA_neighbor_residues() : protocols::enzdes::EnzdesFlexBBProtocol
• get_TenANode() : core::scoring::TenANeighborEdge
• get_tensor() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet , protocols::qsar::scoring_grid::PCSSingleGrid
• get_tensor_const() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet
• get_terminal_move_elements() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_terminal_segments() : protocols::sewing::hashing::EdgeMapGenerator
• get_terminus() : protocols::sewing::scoring::TerminusMotifScorer
• 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_thresh() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix
• get_threshold() : protocols::cluster::calibur::Clustering , protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster , protocols::toolbox::KMedoid
• get_throw_on_fail() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• get_timer() : protocols::loop_modeling::utilities::TrajectoryLogger
• get_tips() : core::conformation::carbohydrates::GlycanTree
• get_tm_alpha() : protocols::membrane::MPLipidAccessibility
• get_tmh_inserted() : protocols::abinitio::MembraneAbinitio
• get_TMscore() : core::scoring::TMscore
• get_tna_suite_potential() : core::scoring::ScoringManager
• get_tol() : protocols::nmr::pre::PREDistanceRecord
• get_tolerance() : protocols::docking::FaDockingSlideIntoContact
• get_tool() : protocols::loop_modeling::LoopMover
• get_top_designs() : protocols::antibody::design::AntibodyDesignMover
• get_torID() : protocols::normalmode::NormalMode
• get_torsion() : protocols::frags::TorsionFragment , protocols::simple_moves::bb_sampler::BBDihedralSampler , protocols::simple_moves::bb_sampler::SmallBBSampler , protocols::simple_moves::bb_sampler::SugarBBSampler
• get_torsion_angle_atom_ids() : core::conformation::Conformation
• get_torsion_axis() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• get_torsion_id() : protocols::recces::sampler::MC_OneTorsion
• get_torsion_ids() : core::scoring::rna::TNA_SuitePotential , protocols::canonical_sampling::MetricRecorder
• get_torsion_mean() : core::chemical::carbohydrates::LinkageConformerData
• get_torsion_sd() : core::chemical::carbohydrates::LinkageConformerData
• get_torsion_type() : protocols::simple_moves::bb_sampler::BBDihedralSamplerBase
• get_TorsionID() : core::optimization::CartesianMinimizerMap
• get_torsions() : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• get_torsions_for_all_solutions() : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• get_torsions_for_helix() : protocols::helical_bundle_predict::HBPHelix
• get_total() : protocols::mean_field::jagged_array< T, A >
• get_total_base_axis_score() : core::pose::rna::RNA_FilteredBaseBaseInfo
• get_total_base_pair_score() : core::pose::rna::RNA_FilteredBaseBaseInfo
• get_total_base_stack_axis_score() : core::pose::rna::RNA_FilteredBaseBaseInfo
• get_total_base_stack_score() : core::pose::rna::RNA_FilteredBaseBaseInfo
• get_total_base_stagger_score() : core::pose::rna::RNA_FilteredBaseBaseInfo
• get_total_dots() : core::pack::interaction_graph::DotSphere
• get_total_energy_in_curr_state_assignment_for_all_states() : core::pack::interaction_graph::FASTERNode
• get_total_exp_chemical_shift_data_points() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• get_total_frames() : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• get_total_Hbond_E() : protocols::analysis::InterfaceAnalyzerMover
• get_total_hbonds() : protocols::simple_pose_metric_calculators::NumberHBondsCalculator
• get_total_hsasa() : core::scoring::sasa::SasaCalc
• get_total_hsasa_bb() : core::scoring::sasa::SasaCalc
• get_total_hsasa_sc() : core::scoring::sasa::SasaCalc
• get_total_mutation_sets() : protocols::task_operations::MutationSetDesignOperation
• get_total_num_CDRs() : protocols::antibody::AntibodyInfo
• get_total_number_pcs() : core::scoring::nmr::pcs::PCSData , core::scoring::nmr::pcs::PCSMultiSet
• get_total_number_pre() : core::scoring::nmr::pre::PREData , core::scoring::nmr::pre::PREMultiSet
• get_total_number_rdc() : core::scoring::nmr::rdc::RDCData , core::scoring::nmr::rdc::RDCMultiSet
• get_total_rel_hsasa() : core::scoring::sasa::SasaCalc
• get_total_sasa() : core::scoring::sasa::SasaCalc
• get_total_sasa_bb() : core::scoring::sasa::SasaCalc
• get_total_sasa_sc() : core::scoring::sasa::SasaCalc
• get_total_score() : protocols::analysis::LoopAnalyzerMover
• get_totalE() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• get_totals_columns() : protocols::mean_field::jagged_array< T, A >
• get_trans_dofs() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• get_trans_mag() : protocols::rigid::RigidBodyPerturbMover
• get_trans_magnitude() : protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes
• get_trans_step() : protocols::nmr::pcs::PCSLigandTransformMover
• get_transform() : protocols::hybridization::CartesianSampler
• get_transformation() : core::conformation::symmetry::SymmetricConformation
• get_translation() : core::kinematics::Jump , core::kinematics::RT
• get_translation_magnitude() : protocols::simple_moves::CoupledMover
• get_translation_matrix() : core::conformation::symmetry::SymmData
• get_transrot_ref() : core::scoring::TMscore
• get_tree() : core::conformation::carbohydrates::GlycanTreeSet
• get_tree_containing_residue() : core::conformation::carbohydrates::GlycanTreeSet
• get_tree_map() : core::conformation::carbohydrates::GlycanTreeSet
• get_tree_root_of_glycan_residue() : core::conformation::carbohydrates::GlycanTreeSet
• get_tree_start_of_glycan_residue() : core::conformation::carbohydrates::GlycanTreeSet
• get_trie() : core::conformation::RotamerSetBase , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• get_tuples() : protocols::frag_picker::CSTalosIO
• get_twist() : protocols::make_rot_lib::RotData
• get_two_body_energies_for_relaxed_states() : core::pack::interaction_graph::FASTEREdge
• get_two_body_energy() : core::pack::hbonds::BareMinimumPDEdge , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FixedBBEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• get_two_body_energy_for_edge() : core::pack::hbonds::HBondGraphInitializerIG , core::pack::interaction_graph::FixedBBInteractionGraph
• get_two_body_energy_smi() : core::pack::interaction_graph::DoubleLazyEdge
• get_two_body_table_size() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• get_twobody_energy_table() : protocols::RotamerDump::RotamerDumpMover
• get_type() : protocols::filters::Filter , protocols::moves::Mover , protocols::moves::PyMOLObserver , protocols::network::UIObserver , protocols::qsar::qsarPoint , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::sewing::data_storage::SmartSewingResidue , protocols::simple_filters::DomainInterfaceFilter , protocols::toolbox::KClusterElement
• get_type_difference_name() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_type_info() : core::scoring::FACTSRsdTypeMap
• get_types_on_residue() : core::pack::palette::PackerPalette
• get_u() : protocols::hybridization::TMalign
• get_UBQpdb() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• get_unaligned() : protocols::loop_grower::FragmentExtension
• get_unbound_mode() : protocols::anchored_design::AnchorMoversData
• get_unbound_mut_pose() : protocols::features::InterfaceDdGMover
• get_unbound_wt_pose() : protocols::features::InterfaceDdGMover
• get_uncached_stubRMSD() : protocols::pose_length_moves::PossibleLoop
• get_UnfoldedStatePotential() : core::scoring::ScoringManager
• get_unfoled_potential_file_weights() : core::scoring::UnfoldedStatePotential
• get_uniform_backrub() : protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• get_unique_chains() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_unique_mg_res() : protocols::magnesium::MgScanner
• get_unique_sequences() : protocols::coupled_moves::CoupledMovesProtocol
• get_unrecognized_atoms() : core::pose::PDBInfo
• get_unrecognized_res_name() : core::pose::PDBInfo
• get_unrecognized_res_size() : core::pose::PDBInfo
• get_unrelaxed_pose() : protocols::vip::VIP_Mover
• get_unsats_for_mres() : protocols::hbnet::NetworkState
• get_unseen_score() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal , core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded
• get_unweighted_score_term() : protocols::sewing::movers::AssemblyMover
• 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::rna::setup::RNA_CSA_JobDistributor
• get_upper_bound_dy() : core::scoring::func::SplineFunc
• get_upper_bound_x() : core::scoring::func::SplineFunc
• get_upper_bound_y() : core::scoring::func::SplineFunc
• get_upper_fasta() : protocols::loop_grower::LoopPartialSolutionStore
• get_upper_npd_hbond_energy_totals() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• get_upper_pose() : protocols::loop_grower::LoopPartialSolutionStore
• get_upstream_restype() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• get_upstream_vrt() : core::conformation::symmetry::SymmetricConformation
• get_use_centroid_dG() : protocols::analysis::InterfaceAnalyzerMover
• get_use_contact_selector() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_use_input_set_selector() : protocols::residue_selectors::HBondSelector
• get_use_ligand_selector() : protocols::constraint_generator::MetalContactsConstraintGenerator
• get_use_lowest() : protocols::frag_picker::scores::FragmentScoringMethod
• get_use_symmetry() : core::conformation::symmetry::SymmetryInfo
• get_use_tracer() : protocols::analysis::LoopAnalyzerMover , protocols::loops::filters::LoopAnalyzerFilter
• get_user_defined_name() : protocols::filters::Filter , protocols::simple_filters::DomainInterfaceFilter
• get_user_input_alignment_res_list() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• get_using_a_resselect() : protocols::residue_selectors::LigandMetalContactSelector
• get_valence_electrons_sp() : core::chemical::gasteiger::GasteigerAtomTypeData
• get_valid_ramachandran_hashes() : protocols::features::BetaTurnDetection
• get_valid_resid() : protocols::indexed_structure_store::SSHashedFragmentStore , protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::PossibleLoop
• get_Vall() : core::fragment::picking_old::FragmentLibraryManager
• get_vall() : protocols::frag_picker::FragmentPicker
• get_vall_by_key() : protocols::frag_picker::VallProvider
• get_vall_count() : protocols::frag_picker::VallProvider
• get_vall_end_line_by_key() : protocols::frag_picker::VallProvider
• get_vall_file() : protocols::struct_fragment::StructFragmentMover
• get_vall_filename() : protocols::frag_picker::VallChunk
• get_vall_last_residue_key_by_key() : protocols::frag_picker::VallProvider
• get_vall_middle_res_id() : protocols::frag_picker::FragmentCandidate
• get_vall_provider() : protocols::frag_picker::VallChunk
• get_vall_start_line_by_key() : protocols::frag_picker::VallProvider
• get_value() : core::simple_metrics::SimpleMetricData , protocols::filters::ContingentFilter , protocols::qsar::qsarPoint
• get_value_list() : protocols::stepwise::sampler::StepWiseSamplerOneValueComb
• get_values() : protocols::cyclic_peptide::PeptideCyclizeMover , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• get_variant_from_string() : core::chemical::ResidueProperties
• get_vary_bondangles() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• get_vary_cutpoints() : protocols::anchored_design::AnchoredDesignMover
• get_vary_loop_length_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• get_VdRdPhi() : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• get_VDW_align_res() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• get_vdw_atom_number() : core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::rna::RNA_VDW_Energy
• get_VDW_weight() : protocols::anchored_design::AnchorMoversData
• get_VdWTinkerPotential() : core::scoring::ScoringManager
• 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_version() : core::chemical::ResidueDatabaseIO , protocols::sewing::hashing::SegmentVector
• get_vertex_member_of_energy_sum_group() : core::pack::interaction_graph::InteractionGraphBase
• get_vicinity_degree() : protocols::anchored_design::AnchoredRefineMover
• get_vicinity_sampling() : protocols::anchored_design::AnchoredRefineMover
• get_view_in_pymol() : protocols::docking::DockingLowRes
• get_virt_id_to_subunit_chain() : core::conformation::symmetry::SymmData
• get_virt_id_to_subunit_num() : core::conformation::symmetry::SymmData
• get_virt_id_to_subunit_residue() : core::conformation::symmetry::SymmData
• get_virtual_connects() : core::conformation::symmetry::SymmData
• get_virtual_coordinates() : core::conformation::symmetry::SymmData
• get_virtual_id_to_num() : core::conformation::symmetry::SymmData
• get_virtual_num_to_id() : core::conformation::symmetry::SymmData
• get_visited() : protocols::pockets::SmallMol
• get_vital_residues() : protocols::sewing::data_storage::SmartSegment
• get_voxel_coordinates() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• get_voxel_grid() : core::scoring::nmr::NMRDummySpinlabelEnsemble
• get_voxel_spacing() : core::scoring::electron_density::ElectronDensity
• get_w_rep() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• get_water_builder() : core::scoring::lkball::LKB_ResidueInfo
• get_water_builder_for_restype() : core::scoring::lkball::LKBallDatabase
• get_water_cos() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• get_water_recovery() : protocols::simple_moves::ExplicitWaterMover
• get_water_weight_grid() : core::scoring::geometric_solvation::WaterWeightGridSet
• get_WaterAdductHBondPotential() : core::scoring::ScoringManager
• get_wc_near_o2prime() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• get_weight() : core::scoring::epr_deer::EPRSpinLabel , core::scoring::func::CircularSplineFunc , core::scoring::func::SplineFunc , core::scoring::nmr::pcs::PCSMultiSet , core::scoring::nmr::pcs::PCSSingle , core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::pre::PREMultiSet , core::scoring::nmr::pre::PRESingle , core::scoring::nmr::pre::PRESingleSet , core::scoring::nmr::rdc::RDCMultiSet , core::scoring::nmr::rdc::RDCSingle , core::scoring::nmr::rdc::RDCSingleSet , core::scoring::ScoreFunction , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::jd2::archive::EvaluatedArchive , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::PCSSingleGrid , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4 , protocols::sewing::scoring::AssemblyScorer , protocols::sewing::scoring::InterModelMotifScorer , protocols::sewing::scoring::IntraDesignTerminusMotifScorer , protocols::sewing::scoring::LigandAssemblyScorer , protocols::sewing::scoring::LigandScorer , protocols::sewing::scoring::MotifScorer , protocols::sewing::scoring::PartnerMotifScorer , protocols::sewing::scoring::SegmentContactOrderScorer , protocols::sewing::scoring::StartingNodeMotifScorer , protocols::sewing::scoring::SubsetPartnerMotifScorer , protocols::sewing::scoring::TerminusMotifScorer , protocols::sewing::scoring::TopNMotifScorer
• get_weighted_energy() : core::pack::interaction_graph::PDInteractionGraph
• get_weighted_energy_with_higher_indexed_nodes() : core::pack::interaction_graph::PDNode
• get_weights() : core::scoring::SplitUnfoldedTwoBodyPotential , protocols::frag_picker::scores::FragmentScoreManager , protocols::task_operations::ResidueProbDesignOperation
• get_weights_for_one_partner_hbonder() : core::scoring::hbonds::NPDHBondSet
• get_weights_for_two_partner_hbonder() : core::scoring::hbonds::NPDHBondSet
• get_well_depth() : core::scoring::func::LinearPenaltyFunction
• get_window() : protocols::cryst::LoadDensityMapMover
• get_window_aa() : protocols::ss_prediction::SS_predictor
• get_window_at_index() : protocols::simple_filters::SecretionPredictionFilter
• get_window_repack_residues() : protocols::relax::RangeRelaxMover
• get_window_width() : protocols::sewing::data_storage::HashedSmartAssembly , protocols::sewing::data_storage::SmartAssembly , protocols::sewing::movers::AssemblyMover
• get_work_unit() : protocols::wum::WorkUnitList
• get_work_unit_clone() : protocols::wum::WorkUnitList
• 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() : core::conformation::symmetry::VirtualCoordinate , protocols::membrane::SpinAroundPartnerMover
• 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_x_middle() : core::scoring::func::LinearPenaltyFunction
• get_xform_score_BB_BB() : core::scoring::motif::MotifHashManager
• get_xform_score_BB_PH() : core::scoring::motif::MotifHashManager
• get_xform_score_BB_PO() : core::scoring::motif::MotifHashManager
• get_xform_score_frags() : core::scoring::motif::MotifHashManager
• get_xform_score_PH_PO() : core::scoring::motif::MotifHashManager
• get_xform_score_SC_BB() : core::scoring::motif::MotifHashManager
• get_xform_score_SC_SC() : core::scoring::motif::MotifHashManager
• get_xml_attributes() : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::KeepLigandContactsRequirement
• get_xml_schema_attributes() : core::pack::task::operation::ChainIs , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBInfoHasLabel
• get_xsd_complex_type() : protocols::calc_taskop_movers::DesignRepackMover
• get_xy_bin() : core::scoring::dna::DirectReadoutPotential
• get_xyz() : protocols::simple_moves::BBConRotMover , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• get_xyz_bin() : core::pose::rna::VDW_Grid
• get_xyz_coord_table() : protocols::RotamerDump::RotamerDumpMover
• get_y() : core::conformation::symmetry::VirtualCoordinate , protocols::membrane::SpinAroundPartnerMover
• 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_z_bin() : core::scoring::dna::DirectReadoutPotential
• get_ZAP_espGrid_values() : protocols::pockets::ElectrostaticpotentialGrid
• get_ZAP_espGrid_values_with_type() : protocols::pockets::ElectrostaticpotentialGrid
• get_zeta_cutoff() : core::scoring::rna::RNA_LowResolutionPotential
• getAANeighborOffsets() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• getAllFiberData() : core::scoring::fiber_diffraction::FiberDiffraction
• getANN_PredError() : protocols::sparta::Sparta::SpartaLib
• getAtomMask() : core::scoring::electron_density::ElectronDensity
• GetAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• getBase() : core::grid::CartGrid< T >
• getBondAngle() : protocols::sparta::PDB
• getBounds() : protocols::pockets::PocketGrid
• getCachedScore() : core::scoring::electron_density::ElectronDensity
• 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
• getD() : protocols::cluster::calibur::AdjacentList
• getData() : protocols::sparta::GDB
• getDihedralAngle() : protocols::sparta::PDB
• getDist() : protocols::sparta::PDB
• GetDots() : core::scoring::sc::MolecularSurfaceCalculator
• getEffectiveBfactor() : core::scoring::electron_density::ElectronDensity
• getEntry() : protocols::sparta::GDB , protocols::sparta::PDB
• getEntryCount() : protocols::sparta::GDB
• GetExemplarNumAtoms() : protocols::pockets::PocketGrid
• GetExemplarNumClusters() : protocols::pockets::PocketGrid
• GetExemplarNumPolarAtoms() : protocols::pockets::PocketGrid
• getFdrhoc() : core::scoring::electron_density::ElectronDensity
• getField() : protocols::sparta::PDB
• getFragSet() : protocols::frag_picker::FragmentPicker
• getFSC() : core::scoring::electron_density::ElectronDensity
• getGrid() : core::scoring::electron_density::ElectronDensity
• gethash() : protocols::loophash::LoopHashLibrary
• getHBondDist() : protocols::sparta::PDB
• getInfoLine() : core::scoring::cryst::PhenixInterface
• getIntensities() : core::scoring::electron_density::ElectronDensity , core::scoring::fiber_diffraction::FiberDiffraction
• getK() : core::scoring::constraints::KofNConstraint
• getLargestClusterSize() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet
• getline() : core::chemical::sdf::CtabV3000Parser
• getListNames() : core::io::sequence_comparation::DesignContrast
• getLoopsToBuildFromBlueprint() : protocols::forge::remodel::RemodelData
• getLoopsToBuildFromFile() : protocols::forge::remodel::RemodelData
• getMapSpacingAndOrigin() : protocols::electron_density::VoxelSpacingMultifunc
• getMatrixPointer() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• getMax() : core::scoring::electron_density::ElectronDensity
• GetMaximumElectrons() : core::chemical::Bond
• getMaxValue() : core::grid::CartGrid< T >
• getMean() : core::scoring::electron_density::ElectronDensity
• getMemoryUsageInBytes() : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• getMin() : core::scoring::electron_density::ElectronDensity
• GetMinimumElectrons() : core::chemical::Bond
• getMinValue() : core::grid::CartGrid< T >
• GetMostStableType() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• getNeighbors() : core::io::sequence_comparation::DesignContrast
• getNetClusterSize() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet
• getNextRCadj() : protocols::sparta::Sparta::SpartaLib
• getNumberMissCS() : protocols::sparta::ANN
• GetNumberOfElectrons() : core::chemical::Bond
• getNumberOfPoints() : core::grid::CartGrid< T >
• GetNumberPossibleTypes() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• getNumStatesPerAAPerBB() : protocols::flexpack::interaction_graph::FlexbbNode
• getNVals() : core::scoring::fiber_diffraction::FiberDiffraction
• getOmega() : protocols::sparta::PDB
• getOneAAName() : protocols::sparta::PDB
• getOrbitalShift() : protocols::sparta::PDB
• getOrigin() : core::scoring::electron_density::ElectronDensity
• getPdbCodes() : core::io::sequence_comparation::DesignContrast
• getPdbNames() : core::io::sequence_comparation::DesignContrast
• getPDBs() : protocols::cluster::calibur::Clustering
• getPhaseError() : core::scoring::electron_density::ElectronDensity
• getPhi() : protocols::sparta::PDB
• getPose() : core::pose::signals::GeneralEvent
• getPrevRCadj() : protocols::sparta::Sparta::SpartaLib
• GetPropertyName() : core::chemical::gasteiger::GasteigerAtomTypeData
• getPsi() : protocols::sparta::PDB
• getR() : core::scoring::cryst::PhenixInterface
• getRandomDecoyNames() : protocols::cluster::calibur::Clustering
• GetRBDOFValues() : protocols::matdes::GetRBDOFValues
• getRC() : protocols::sparta::Sparta::SpartaLib
• getRCadj() : protocols::sparta::Sparta::SpartaLib
• getReciprocalRs() : core::scoring::fiber_diffraction::FiberDiffraction
• getRelaxResidues() : protocols::pockets::PocketGrid
• getResidName() : protocols::sparta::GDB
• getResidueRange() : protocols::rbsegment_relax::RBSegmentMover
• getResInfo() : protocols::sparta::Sparta::SpartaLib
• getResolution() : core::scoring::electron_density::ElectronDensity
• getResolutionBins() : core::scoring::electron_density::ElectronDensity
• GetResults() : core::scoring::sc::ElectrostaticComplementarityCalculator , core::scoring::sc::MolecularSurfaceCalculator
• getRfree() : core::scoring::cryst::PhenixInterface
• getRSCC() : core::scoring::electron_density::ElectronDensity
• getRT() : protocols::cryst::MakeLatticeMover
• getScore() : core::scoring::cryst::PhenixInterface , protocols::electron_density::SetupForDensityScoringMover
• getScoreAndDerivs() : core::scoring::cryst::PhenixInterface
• getScoreWindowContext() : core::scoring::electron_density::ElectronDensity
• getSCscaling() : core::scoring::electron_density::ElectronDensity
• GetSDAltFileID() : core::chemical::Bond
• GetSDFileID() : core::chemical::Bond
• getSecStruct() : core::io::sequence_comparation::DesignContrast
• getSigAxisR() : protocols::rbsegment_relax::RBSegment
• getSigAxisT() : protocols::rbsegment_relax::RBSegment
• getSigOffAxisR() : protocols::rbsegment_relax::RBSegment
• getSigOffAxisT() : protocols::rbsegment_relax::RBSegment
• getSimPDB() : protocols::cluster::calibur::PreloadedPDB
• getSlashChar() : protocols::sparta::ANN
• getSolutionSet() : protocols::loop_grower::LoopGrower
• getStdev() : core::scoring::electron_density::ElectronDensity
• getStubByName() : protocols::hotspot_hashing::StubGenerator
• getsymmOps() : core::scoring::electron_density::ElectronDensity
• getThreeAAName() : protocols::sparta::PDB
• getThresholdAndDecoys() : protocols::cluster::calibur::Clustering
• getTop() : core::grid::CartGrid< T >
• getTotalMemoryUsage() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase
• getTransform() : core::scoring::electron_density::ElectronDensity
• GetTrimmedDots() : core::scoring::sc::MolecularSurfaceCalculator
• getValue() : core::grid::CartGrid< T >
• getValues() : core::scoring::fiber_diffraction::CentroidScatter , core::scoring::fiber_diffraction::FAScatter
• getWeight() : protocols::sparta::Sparta::SpartaLib
• getWindow() : core::scoring::electron_density::ElectronDensity
• ghost_loops() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• ghost_loops_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• ghost_map_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• ghost_native_pose_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• ghost_pose_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• give_up_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• gJ_ : core::io::nmr::ParaIon
• glen : core::scoring::APBSConfig
• glob_flag_ : core::scoring::saxs::FormFactor
• global2local() : core::kinematics::Stub
• global_auto_rescale() : core::sequence::SequenceProfile
• global_bundle_calculator_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_crick_params_file_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_delta_omega1_max_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_delta_omega1_min_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_for_parameters_set() : core::conformation::parametric::Parameter , core::conformation::parametric::ParameterizationCalculatorProperties
• global_for_parameters_set_ : core::conformation::parametric::Parameter
• global_fractional_perturbation_magnitude_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_i_ : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• global_job_id : protocols::jd3::dag_node_managers::ResultElements , protocols::jd3::JGJobNode
• global_job_id_ : protocols::jd3::JGJobNode
• global_loop_rmsd() : protocols::antibody_legacy::AntibodyModeler
• global_mapping() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• global_mapping_ : core::pose::full_model_info::FullModelParameters , core::scoring::rna::RNA_PartitionEnergy
• global_offset() : core::fragment::FragSet
• global_offset_ : core::fragment::FragSet
• global_omega0_max_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_omega0_min_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_optimize() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• global_optimize_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• global_orientation_from_frame3() : protocols::toolbox::match_enzdes_util::LigandConformer
• global_perturbation_prob_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_pos1() : protocols::topology_broker::claims::JumpClaim
• global_pos2() : protocols::topology_broker::claims::JumpClaim
• global_position() : protocols::topology_broker::claims::BBClaim
• global_r0_max_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_r0_min_ : protocols::helical_bundle_predict::HBPHelixAssignments
• global_requirements_ : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• global_rotamer_id() : core::scoring::hbonds::graph::HBondNode
• global_rotid_start_for_moltenres_in_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• global_sample_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• global_sample_res_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• global_seq_file_ : core::import_pose::FullModelPoseBuilder
• global_sequence() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• global_sequence_ : core::pose::full_model_info::FullModelParameters
• global_types_ : protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory
• GlobalResidueTypeSet() : core::chemical::GlobalResidueTypeSet
• GlobalResidueTypeSets : core::chemical::ChemicalManager
• gly_dG : protocols::analysis::InterfaceData
• gly_switch_ : core::pack::task::operation::RestrictYSDesign
• glycam_pdb_format() : core::io::StructFileReaderOptions
• glycam_pdb_format_ : core::io::StructFileReaderOptions
• glycan_position_ : core::conformation::carbohydrates::GlycanNode
• glycan_positions_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• glycan_res_to_tree_ : core::conformation::carbohydrates::GlycanTreeSet
• glycan_sampler_kt_ : protocols::carbohydrates::GlycanTreeModeler
• glycan_sampler_rounds_ : protocols::carbohydrates::GlycanTreeModeler
• glycan_tree_branch_sequence() : core::pose::Pose
• glycan_tree_roots_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• glycan_tree_sequence() : core::pose::Pose
• glycan_tree_set() : core::conformation::Conformation , core::pose::Pose
• glycan_tree_set_ : core::conformation::carbohydrates::GlycanTreeSet , core::conformation::carbohydrates::GlycanTreeSetObserver
• GlycanInfoMover() : protocols::analysis::GlycanInfoMover
• GlycanLayerSelector() : core::select::residue_selector::GlycanLayerSelector
• GlycanNode() : core::conformation::carbohydrates::GlycanNode
• GlycanPositionSelector() : core::select::residue_selector::GlycanPositionSelector
• GlycanResidueSelector() : core::select::residue_selector::GlycanResidueSelector
• GlycanSampler() : protocols::carbohydrates::GlycanSampler
• GlycanSequonsSelector() : core::select::residue_selector::GlycanSequonsSelector
• GlycanTree() : core::conformation::carbohydrates::GlycanTree
• GlycanTreeMinMover() : protocols::carbohydrates::GlycanTreeMinMover
• GlycanTreeModeler() : protocols::carbohydrates::GlycanTreeModeler
• GlycanTreeSet() : core::conformation::carbohydrates::GlycanTreeSet
• GlycanTreeSetObserver() : core::conformation::carbohydrates::GlycanTreeSetObserver
• glycine_corrections_ : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• glycorr_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• glycorr_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• glycorr_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• glycosylation_weights_ : protocols::carbohydrates::SimpleGlycosylateMover
• glycosylations_ : protocols::carbohydrates::SimpleGlycosylateMover
• GlycosyltransferaseMover() : protocols::enzymatic_movers::GlycosyltransferaseMover
• gm : protocols::tcr::TCRmodel::tcrtmplts
• gmax_cutoff_for_convergence() : core::optimization::MinimizerOptions
• gmax_cutoff_for_convergence_ : core::optimization::MinimizerOptions
• go() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol , 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::VectorPoseJobDistributor , protocols::jd3::job_distributors::VanillaJobDistributor , protocols::jd3::JobDistributor , 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
• go_mpi() : protocols::jd2::VectorPoseJobDistributor
• go_serial() : protocols::jd2::VectorPoseJobDistributor
• GoapEnergy() : core::scoring::methods::GoapEnergy
• GoapRsdType() : core::scoring::methods::GoapRsdType
• GOOD : core::scoring::Energies
• good : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• good_ : protocols::abinitio::Template , protocols::abinitio::Templates
• good_angle_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• good_atr_rotamer_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• good_bin_rep_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• good_data_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• good_distance_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• good_fix_pos_ : protocols::topology_broker::RigidChunkClaimer::CM_SuggestFixResidue
• good_jump() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• good_rep_rotamer_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• goodfrags_ : protocols::pose_metric_calculators::FragQualCalculator
• got_chain_numbers_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• got_termination_signal_ : protocols::mpi_refinement::MPI_Refine_Master
• gp_b_allow_independent_alignment_per_fragment_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_b_allow_repeat_same_graft_output_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_b_full_motif_bb_alignment_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_b_graft_only_hotspots_by_sidechain_replacement_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_b_is_first_run_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_b_only_allow_if_C_point_match_aa_identity_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_b_only_allow_if_N_point_match_aa_identity_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_b_revert_graft_to_native_sequence_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_f_output_filter_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_i_clash_score_cutoff_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_i_min_fragment_size_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_p_contextStructure_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_p_motif_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_p_target_pose_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_r_clash_atom_scale_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_r_NC_points_RMSD_tolerance_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_r_output_cluster_tolerance_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_r_RMSD_tolerance_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_s_clash_test_residue_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_vp_combinatory_fragment_size_delta_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_vp_max_fragment_replacement_size_delta_ : protocols::motif_grafting::movers::MotifGraftMover
• gp_vvr_hotspots_ : protocols::motif_grafting::movers::MotifGraftMover
• gpeptide_ : protocols::denovo_design::components::FoldGraph
• grab_additional_pose_data() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_conect_records_for_atom() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_foldtree() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_main_chain_torsion_set_list() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• grab_membrane_info() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_pdb_comments() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_pdb_parents() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_pdbinfo_labels() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_pose_cache_data() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_pose_energies_table() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_simple_metric_data() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• grab_torsion_records() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• GrabAllCollector() : protocols::frag_picker::GrabAllCollector
• graceful_exit() : protocols::pack_daemon::DaemonSet
• grad() : core::scoring::electron_density::ElectronDensity
• gradient() : core::chemical::mainchain_potential::MainchainScoreTable
• gradient_bins_ : protocols::qsar::RenderGridsToKinemage
• gradPtr : protocols::viewer::triangleIterator
• gradual_constraints() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• gradual_constraints_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• graft() : protocols::metal_interface::MatchGrafter
• graft_design_override_ : protocols::antibody::design::AntibodyDesignMover
• graft_h1_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::GraftMover
• graft_h2_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::GraftMover
• graft_h3_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::GraftMover
• graft_in_cdr() : protocols::antibody::design::AntibodyDesignMover
• graft_is_closed() : protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover
• graft_is_closed_ : protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover
• graft_l1_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::GraftMover
• graft_l2_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::GraftMover
• graft_l3_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::GraftMover
• graft_log_ : protocols::antibody::design::AntibodyDesignMover
• graft_loop() : protocols::loophash::LoopHashLibrary
• graft_loop_ : protocols::switches::GraftSwitchMover
• graft_mover_ : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::design::AntibodyDesignMover
• graft_sequence_ : protocols::antibody::GraftCDRLoopsProtocol
• GraftCDRLoopsProtocol() : protocols::antibody::GraftCDRLoopsProtocol
• GraftedStemOptimizer() : protocols::antibody::GraftedStemOptimizer
• GraftMap : protocols::antibody::GraftCDRLoopsProtocol
• GraftMover() : protocols::antibody_legacy::GraftMover
• GraftMoverBase() : protocols::grafting::GraftMoverBase
• GraftOneCDRLoop() : protocols::antibody::GraftOneCDRLoop
• GraftOneMover() : protocols::antibody_legacy::GraftOneMover
• GraftSwitchMover() : protocols::switches::GraftSwitchMover
• grandparent : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::RNA_FA_ElecEnergy , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• grant_access() : protocols::environment::EnvClaimBroker
• graph() : core::chemical::MutableResidueType , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer
• Graph : core::scoring::constraints::ConstraintGraph , core::scoring::Energies , protocols::minimization_packing::GreenPacker
• graph_ : core::chemical::AcceptorAtomFilter , core::chemical::APolarHydrogenFilter , core::chemical::AromaticAtomFilter , core::chemical::HeavyAtomFilter , core::chemical::HeavyAtomWithHydrogensFilter , core::chemical::HeavyAtomWithPolarHydrogensFilter , core::chemical::HydrogenAtomFilter , core::chemical::MutableResidueType , core::chemical::PolarHydrogenFilter , core::chemical::RealFilter , core::chemical::RerootEdgeSorter , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer , protocols::legacy_sewing::LegacyAssemblyMover
• graph_options_ : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• graph_state_ : core::scoring::Energies
• GraphCOP : protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::task_operations::LimitAromaChi2_RotamerSetOperation
• GraphicsState() : protocols::viewer::GraphicsState
• GraphOP : protocols::minimization_packing::GreenPacker
• GraphvizPropertyWriter() : core::chemical::GraphvizPropertyWriter , core::io::pose_from_sfr::GraphvizPropertyWriter
• greedy_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::rbsegment_relax::OptimizeThreadingMover
• greedy_around() : protocols::enzdes::PackRotamersMoverPartGreedy
• GreedyKCenter() : protocols::toolbox::GreedyKCenter
• GreedyOptMutationMover() : protocols::design_opt::GreedyOptMutationMover
• greek_d_ : core::chemical::Atom
• greek_distance() : core::chemical::Atom
• GreenPacker() : protocols::minimization_packing::GreenPacker
• grid : core::scoring::APBSConfig , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• Grid : core::scoring::geometric_solvation::WaterWeightGridSet , protocols::canonical_sampling::HamiltonianExchange
• grid() : protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid
• grid_ : core::scoring::electron_density::ElectronDensity , core::scoring::nmr::NMRDummySpinlabelEnsemble , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::Translate , protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid , protocols::nmr::pcs::PCSLigandTransformMover , protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid , protocols::qsar::scoring_grid::SingleGrid
• grid_atom1_ : core::scoring::nmr::NMRGridSearch
• grid_atom2_ : core::scoring::nmr::NMRGridSearch
• 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
• grid_atom_name_1_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_atom_name_1_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_atom_name_1_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_atom_name_1_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• 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
• grid_atom_name_2_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_atom_name_2_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_atom_name_2_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_atom_name_2_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_bound_penalty_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• grid_centering_mode : core::scoring::APBSConfig::I_PARAM
• 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
• grid_cone_angle_cutoff_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_cone_angle_cutoff_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_cone_angle_cutoff_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_cone_angle_cutoff_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_creator_map_ : protocols::qsar::scoring_grid::GridFactory
• grid_data : core::scoring::APBSResult
• 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
• grid_edge_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_edge_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_edge_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_edge_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_indices_ : protocols::qsar::qsarOptFunc
• 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
• grid_k_vector_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_k_vector_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_k_vector_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_k_vector_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• 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
• grid_large_cutoff_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_large_cutoff_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_large_cutoff_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_large_cutoff_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_max_ : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• grid_max_radius_ : core::scoring::nmr::NMRGridSearch
• grid_meta : core::scoring::APBSResult
• grid_min_ : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• grid_min_radius_ : core::scoring::nmr::NMRGridSearch
• grid_name() : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::PCSSingleGrid , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SiteGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid
• grid_name_ : protocols::qsar::RenderGridsToKinemage
• grid_output_file_ : protocols::canonical_sampling::BiasEnergy
• 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
• grid_residue_num_1_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_residue_num_1_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_residue_num_1_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_residue_num_1_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• 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
• grid_residue_num_2_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_residue_num_2_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_residue_num_2_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_residue_num_2_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_s_p_all_ : protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• grid_scores() : protocols::qsar::scoring_grid::GridSet
• grid_set_ : protocols::qsar::scoring_grid::SolvationMetaGrid
• grid_set_cache_ : protocols::qsar::scoring_grid::GridManager
• grid_set_poses_ : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• grid_set_prototype() : protocols::ligand_docking::InterfaceScoreCalculator
• grid_set_prototype_ : protocols::features::ResidueGridScoresFeatures , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::Rotate , protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble , protocols::ligand_docking::Translate , protocols::qsar::qsarMover , protocols::qsar::RenderGridsToKinemage
• grid_sets_ : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• 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
• grid_small_cutoff_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_small_cutoff_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_small_cutoff_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_small_cutoff_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_spacing : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• grid_spacing_ : core::scoring::PoissonBoltzmannPotential
• 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
• grid_step_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_step_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_step_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_step_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• grid_to_kin() : protocols::qsar::scoring_grid::SingleGrid
• grid_vdw_weight() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• grid_vdw_weight_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• grid_weights_ : protocols::qsar::scoring_grid::GridSet
• GridBase() : protocols::qsar::scoring_grid::GridBase
• GridCoord : protocols::canonical_sampling::TemperatureController
• GridCreator() : protocols::qsar::scoring_grid::GridCreator
• GriddedAtomTreeMultifunc() : protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc
• GridFactory() : protocols::qsar::scoring_grid::GridFactory
• GridHash3D() : protocols::ligand_docking::ga_ligand_dock::GridHash3D< T >
• GridInfo() : core::scoring::geometric_solvation::GridInfo
• gridlig_active_site_definition() : protocols::match::MatcherTask
• gridlig_active_site_definition_ : protocols::match::MatcherTask
• gridlig_file_name() : protocols::match::MatcherTask
• gridlig_fname_ : protocols::match::Matcher , protocols::match::MatcherTask
• GridManager() : protocols::qsar::scoring_grid::GridManager
• gridpt() : core::grid::CartGrid< T >
• GridPt : core::grid::CartGrid< T >
• GridRegistrator() : protocols::qsar::scoring_grid::GridRegistrator< T >
• grids_ : protocols::match::BumpGrid , protocols::qsar::scoring_grid::GridSet
• grids_to_use_ : protocols::qsar::qsarMover
• GridScorer() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• gridsearch_iterator_ : core::scoring::nmr::pcs::PCSMultiSet , core::scoring::nmr::pre::PREMultiSet
• 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
• GridSet : protocols::qsar::scoring_grid::GridFactory , protocols::qsar::scoring_grid::GridSet
• gridStep_ : protocols::electron_density::DockIntoDensityMover
• group() : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• group1_ : protocols::toolbox::ResidueGroupIGEdgeUpweighter
• group1_resstring() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group1_resstring_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group1_selector() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group1_selector_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group1_set() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group1_set_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group2_ : protocols::toolbox::ResidueGroupIGEdgeUpweighter
• group2_resstring() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group2_resstring_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group2_selector() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group2_selector_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group2_set() : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group2_set_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector
• group_ : core::conformation::ResidueKinWriter , core::scoring::methods::D2H_SA_Energy , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• group_atom_index : core::io::mmtf::sd_index
• group_discriminator_ : protocols::minimization_packing::GreenPacker
• group_file_ : core::scoring::elec::GroupElec
• group_heavyatom_index_to_group_index() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData
• group_heavyatom_index_to_group_index_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData
• group_id() : protocols::minimization_packing::ChainGroupDiscriminator , protocols::minimization_packing::GroupDiscriminator , protocols::minimization_packing::UserDefinedGroupDiscriminator
• group_ids_ : protocols::minimization_packing::GreenPacker , protocols::minimization_packing::UserDefinedGroupDiscriminator
• group_index : core::io::mmtf::sd_index
• group_members_ : core::scoring::MultipoleParameter , protocols::minimization_packing::GreenPacker
• group_pair : protocols::analysis::InterfaceAnalyzerMover , protocols::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::CalcInterNeighborGroup
• group_set : protocols::analysis::InterfaceAnalyzerMover , protocols::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::CalcInterNeighborGroup
• group_size() : protocols::cluster::Cluster
• group_size_ : protocols::cluster::Cluster
• group_vector : protocols::task_operations::RestrictInterGroupVectorOperation
• grouped_fragment_map_ : protocols::indexed_structure_store::FragmentStoreManager
• GroupedFragmentMap : protocols::indexed_structure_store::FragmentStoreManager
• groupelec() : core::scoring::elec::FA_GrpElecEnergy
• GroupElec() : core::scoring::elec::GroupElec
• groupelec_ : core::scoring::elec::FA_GrpElecEnergy
• grouper_ : protocols::match::output::CloudPDBWriter , protocols::match::output::MatchConsolidator
• grouper_ds_rmsd() : protocols::match::MatcherTask
• grouper_ds_rmsd_ : protocols::match::MatcherTask
• grouper_name() : protocols::match::MatcherTask
• grouper_name_ : protocols::match::MatcherTask
• groups() : protocols::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::CalcInterNeighborGroup
• groups_ : protocols::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::CalcInterNeighborGroup
• grow_all_loops() : protocols::loops::Loops
• grow_attempts_ : protocols::loops::loop_mover::IndependentLoopMover
• grow_flexible() : protocols::rbsegment_relax::AutoRBMover
• grow_from_seeds() : protocols::seeded_abinitio::GrowPeptides
• grow_from_vertices() : protocols::seeded_abinitio::GrowPeptides
• grow_loop() : protocols::loops::Loops
• grow_loop_away_from_sheets() : protocols::loops::Loops
• grow_toward_Nterm_ : protocols::pose_length_moves::InsertResMover
• GrowLeft() : protocols::forge::build::GrowLeft
• GrowLigand() : protocols::ligand_docking::GrowLigand
• GrowPeptides() : protocols::seeded_abinitio::GrowPeptides
• GrowPeptidesSegment() : protocols::seeded_abinitio::GrowPeptidesSegment
• GrowRight() : protocols::forge::build::GrowRight
• grp_cpfxn() : core::scoring::methods::EnergyMethodOptions
• grp_cpfxn_ : core::scoring::elec::GroupElec , core::scoring::methods::EnergyMethodOptions
• grpelec_context_dependent() : core::scoring::methods::EnergyMethodOptions
• grpelec_context_dependent_ : core::scoring::methods::EnergyMethodOptions
• grpelec_fade_hbond() : core::scoring::methods::EnergyMethodOptions
• grpelec_fade_hbond_ : core::scoring::methods::EnergyMethodOptions
• grpelec_fade_param1() : core::scoring::methods::EnergyMethodOptions
• grpelec_fade_param1_ : core::scoring::methods::EnergyMethodOptions
• grpelec_fade_param2() : core::scoring::methods::EnergyMethodOptions
• grpelec_fade_param2_ : core::scoring::methods::EnergyMethodOptions
• grpelec_fade_type() : core::scoring::methods::EnergyMethodOptions
• grpelec_fade_type_ : core::scoring::methods::EnergyMethodOptions
• grsa_sc_feature() : core::scoring::methods::ProQ_Energy
• gs_box_ : protocols::nmr::pcs::PCSLigandTransformMover
• gss_sc_feature() : core::scoring::methods::ProQ_Energy
• GTPase_lys_ : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• guarantee_no_DNA() : core::io::StructFileRepOptions
• guarantee_no_DNA_ : core::io::StructFileRepOptions
• guarded_loops_ : protocols::comparative_modeling::LoopRelaxMover , protocols::loops::loop_mover::LoopMover
• GuardedLoopsFromFile() : protocols::loops::GuardedLoopsFromFile
• guess_pairings_from_secondary_structure() : protocols::abinitio::IterativeBase
• GUIP_matrix_ : protocols::simple_filters::ResidueDepthFilter
• GUIP_matrix_file_ : protocols::simple_filters::ResidueDepthFilter
• gunn_cost_ : protocols::frag_picker::scores::GunnCostScore
• GunnCost() : protocols::frag_picker::scores::GunnCost , protocols::nonlocal::SmoothPolicy , protocols::simple_moves::GunnCost
• GunnCostScore() : protocols::frag_picker::scores::GunnCostScore
• GunnCostTest : protocols::simple_moves::GunnCost
• GunnTuple() : protocols::frag_picker::scores::GunnTuple , protocols::simple_moves::GunnTuple
• gzipped_ : protocols::checkpoint::FileBuffer