- i -

• I : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• i : protocols::cluster::DataPoint
• i2_ : core::scoring::methods::GoapRsdType
• i2c : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• i2c_ : core::scoring::PoissonBoltzmannPotential
• i3_ : core::scoring::methods::GoapRsdType
• i_ : protocols::frag_picker::Contact
• i_param : core::scoring::APBSConfig
• i_str : protocols::environment::claims::DOFElement
• i_str_ : protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• i_to_a_ : protocols::normalmode::NormalMode
• iA_ : core::scoring::TMscore
• IAM_ : protocols::anchored_design::AnchoredDesignMover , protocols::pmut_scan::AlterSpecDisruptionDriver
• iB_ : core::scoring::TMscore
• ibx : core::scoring::APBSResult
• iby : core::scoring::APBSResult
• ibz : core::scoring::APBSResult
• iCode : core::io::AtomInformation , core::io::ModifiedResidueInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• icode : core::scoring::packstat::SimplePDB_Atom , protocols::antibody::design::PDBNumbering
• icode1 : core::io::CisPeptideInformation
• iCode1 : core::io::LinkInformation , core::io::SSBondInformation
• icode2 : core::io::CisPeptideInformation
• iCode2 : core::io::LinkInformation , core::io::SSBondInformation
• iCode_ : core::io::ResidueInformation
• icode_ : protocols::pmut_scan::MutationData
• icoor_ : core::chemical::Orbital , core::chemical::ResidueConnection , core::chemical::ResidueType
• id : core::optimization::DOF_Node , core::scoring::packstat::Sphere , protocols::environment::claims::DOFElement , protocols::features::Segment , protocols::features::TaskOperationFeatures::Taskop_id_name_factory_
• ID : protocols::stepwise::legacy::modeler::rna::Cluster_Member
• id : protocols::stepwise::modeler::rna::Torsion_Info , protocols::toolbox::Node
• id2proftag_ : protocols::abinitio::FragmentSampler
• id2string_ : protocols::abinitio::FragmentSampler
• id_ : core::environment::EnvCore , core::fragment::picking_old::vall::VallResidue , core::id::EXCN_AtomNotFound , core::scoring::packstat::CavityBall , core::scoring::saxs::FormFactor , core::sequence::Sequence , protocols::denovo_design::components::NamedMover , protocols::denovo_design::components::StructureData , protocols::environment::EXCN_Env_Security_Exception , protocols::features::strand_assembly::StrandFragment , protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::VallResidue , protocols::moves::ConstraintGenerator , protocols::optimize_weights::OptEVariableExpression , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::wum::WorkUnitBase::WU_Header
• id_for_current_rotamer_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• id_list_ : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• id_list_cached_ : protocols::stepwise::sampler::StepWiseSamplerOneValueComb
• id_map_ : protocols::abinitio::abscript::AbscriptMover
• id_to_index_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• idCode_ : core::io::HeaderInformation
• ideal_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser
• ideal_bond_length_sets_ : core::chemical::ChemicalManager
• ideal_delta_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_delta_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_distance_ : protocols::sewing::NodeConstraint
• ideal_geometry_ : protocols::simple_moves::MinimalRotamer
• ideal_hoist_ : protocols::sewing::NodeConstraint
• ideal_meridian_ : protocols::sewing::NodeConstraint
• ideal_nu1_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_nu1_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_nu2_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_nu2_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_packing_ : protocols::sewing::NodeConstraint
• ideal_val_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• ideal_xyz_ : core::chemical::Atom , core::chemical::Orbital
• idealExtension_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• idealize_ : protocols::relax::RangeRelaxMover , protocols::seeded_abinitio::CloseFold
• idealize_conformers_ : protocols::match::downstream::LigandConformerBuilder
• idealize_coord_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• idealize_glycosylation_ : protocols::carbohydrates::SimpleGlycosylateMover
• idealize_graft_cdrs_ : protocols::antibody::design::AntibodyDesignMover
• idealize_h3_stems_ : protocols::antibody::ModelCDRH3
• idealize_h3_stems_before_modeling_ : protocols::antibody::AntibodyModelerProtocol
• idealize_insert_ : protocols::grafting::AnchoredGraftMover
• idealize_loop_first_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idealize_torsions_ : protocols::carbohydrates::LinkageConformerMover
• idealized_abego_ : protocols::denovo_design::connection::Connection
• ident_string_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• identical_tag_found_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• identities_ : protocols::toolbox::task_operations::RestrictIdentitiesOperation
• identity_obs_hub_ : core::conformation::Conformation
• idl_beta_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_C_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_CA_CM_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_CA_CM_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_CM_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_CM_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_beta_N_CA_CM_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• idl_C_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• idl_CA_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_CA_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• idl_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_N_CA_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• ids_ : core::scoring::SecondaryStructurePotential
• idsn_ : core::scoring::SecondaryStructurePotential
• if_dock_pert_ : protocols::docking::DockingInitialPerturbation
• if_ensemble_ : protocols::docking::DockingProtocol
• if_fit_area_ : protocols::scoring::methods::saxs::PDDFEnergy
• if_hydrogens_ : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• if_metrics_ : protocols::flexpep_docking::FlexPepDockingProtocol
• if_uniform_trans_ : protocols::docking::DockingInitialPerturbation
• iface_cutoff_ : protocols::protein_interface_design::movers::LoopFinder
• ifc_ : protocols::kinmatch::FunGroupTK
• iffilters_ : protocols::filters::IfThenFilter
• ifit_ : protocols::evaluation::PCA
• ig_ : core::pack::annealer::DebuggingAnnealer , core::pack::annealer::FASTERAnnealer , core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::annealer::FixbbSimAnnealer , core::pack::annealer::MultiCoolAnnealer , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• ig_edge_list_ : core::pack::interaction_graph::InteractionGraphBase
• IG_edge_reweights_ : core::pack::task::PackerTask_
• ig_nodes_ : core::pack::interaction_graph::InteractionGraphBase
• ig_p_ : protocols::multistate_design::PackingState
• ignore_assignments_ : protocols::noesy_assign::PeakFileFormat_Base
• ignore_atom_named_H_ : core::chemical::ResidueTypeFinder
• ignore_bs_ : protocols::electron_density::ScaleMapIntensities
• ignore_chain_ : protocols::fldsgn::CircularPermutation
• ignore_cmdline_enzdes_cstfile_ : protocols::forge::components::VarLengthBuild
• ignore_cmdline_for_build_points_ : protocols::match::MatcherTask
• ignore_default_docking_task_ : protocols::docking::DockingProtocol
• ignore_default_task_ : protocols::docking::DockingHighRes
• ignore_FARFAR_no_auto_bulge_parent_tag_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ignore_FARFAR_no_auto_bulge_tag_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ignore_h_collisions_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• ignore_helix_direction_ : protocols::fldsgn::filters::HSSTripletFilter
• ignore_list_ : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_loops_ : protocols::fldsgn::NcontactsCalculator
• ignore_negative_intensity_ : protocols::noesy_assign::PeakFileFormat_Base
• ignore_pikaa_natro_ : protocols::flxbb::LayerDesignOperation
• ignore_pose_datacache_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• ignore_pose_profile_length_mismatch_ : protocols::simple_moves::ConsensusDesignMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• ignore_register_shift_ : protocols::fldsgn::filters::SheetTopologyFilter
• ignore_residues_in_csts_ : protocols::idealize::IdealizeMover
• ignore_resonancefile_intensities_ : protocols::noesy_assign::PeakAssignmentParameters
• ignore_resonancefile_tolerances_ : protocols::noesy_assign::PeakAssignmentParameters
• ignore_same_sheet_ : protocols::fldsgn::NcontactsCalculator
• ignore_same_sselement_ : protocols::fldsgn::NcontactsCalculator
• ignore_secstruct_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• ignore_sugars_ : core::io::StructFileRepOptions
• ignore_template_indices_ : protocols::hybridization::ChunkTrialMover
• ignore_terminal_res_ : protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_moves::StructProfileMover
• ignore_terminal_SS_ : protocols::simple_filters::SSElementMotifContactFilter
• ignore_unconnected_upper_ : core::select::residue_selector::PhiSelector
• ignore_unmatched_virtual_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ignore_unrecognized_res_ : core::io::StructFileRepOptions , protocols::rotamer_recovery::RotamerRecovery
• ignore_virtual_ : protocols::simple_moves::CopyDofMover
• ignore_waters_ : core::io::StructFileRepOptions
• ignore_zero_byte_ : protocols::simple_filters::FileExistFilter
• ignore_zero_occupancy_ : core::io::StructFileRepOptions
• ignoreBuriedPockets_ : protocols::pockets::PocketGrid
• ignored_chains_ : protocols::analysis::InterfaceAnalyzerMover
• ignoreExposedPockets_ : protocols::pockets::PocketGrid
• ignorefinished_ : protocols::jobdist::BaseJobDistributor
• illegal_variable_names_ : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• image_start_ : protocols::simple_moves::SymmetricFragmentMover
• implicit_radii_set_ : core::scoring::sasa::SasaCalc
• implies : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• import_ID : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• import_pose_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• importance_ : protocols::normalmode::NormalMode
• impose_constraints_ : protocols::idealize::IdealizeMover
• improper_dihedral_atom_sets_ : core::chemical::ResidueType
• improper_dihedrals_for_atom_ : core::chemical::ResidueType
• improper_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• in_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• in_charge_ : protocols::loops::GuardedLoopsFromFile
• in_FASTER_mode_ : core::pack::interaction_graph::FASTERNode
• in_list : protocols::toolbox::Node
• in_range_CCD_torsion : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• in_root_partition : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• inbound_wus_ : protocols::wum::WorkUnitManager
• incident_edge_list_ : core::graph::Node , core::pack::interaction_graph::NodeBase
• incident_edge_vector_ : core::pack::interaction_graph::NodeBase
• incl_nonopt_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• include_adjacent_residues_ : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• include_all_design_targets_in_design_interface_ : protocols::enzdes::EnzdesBaseProtocol
• include_backbone_ : protocols::simple_filters::SidechainRmsdFilter
• include_backbone_atoms_ : protocols::rotamer_recovery::RRComparerAutomorphicRMSD
• include_background_energies_ : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• include_c_s_only_in_hsasa_ : core::scoring::sasa::SasaCalc
• include_cdr4_ : protocols::antibody::AntibodyCDRGrafter
• include_count_ : protocols::optimize_weights::IterativeOptEDriver
• include_cstE_ : protocols::enzdes::LigInterfaceEnergyFilter
• include_current_ : core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask_ , protocols::protein_interface_design::movers::TryRotamers , protocols::symmetric_docking::SymRestrictTaskForDocking
• include_current_ds_ : protocols::denovo_design::DisulfidizeMover
• include_default_linear_chainbreak_ : protocols::farna::movers::RNA_Minimizer
• include_dna_potentials_in_specificity_calculations_ : protocols::dna::DnaInterfacePacker
• include_hydrogens_ : core::scoring::sasa::SasaCalc
• include_lips_ : core::scoring::membrane::MPLipoEnergy , protocols::membrane::AddMembraneMover
• include_magnetic_anisotropy_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_metals_ : protocols::enzdes::GenerateStoredRBConfs
• include_native_aa_ : protocols::toolbox::task_operations::ConservativeDesignOperation , protocols::toolbox::task_operations::MutationSetDesignOperation
• include_native_restype_ : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::toolbox::task_operations::ResidueProbDesignOperation
• include_neighbor_base_stacks_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• include_neighbors_ : protocols::antibody::H3RefineCCD , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• include_only_clusters_ : protocols::antibody::CDRSetOptions
• include_only_end_ : protocols::scoring::methods::pcs2::PcsEnergyParameter
• include_only_end_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_end_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_end_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_end_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_germlines_ : protocols::antibody::CDRSetOptions
• include_only_pdb_ids_ : protocols::antibody::CDRSetOptions
• include_only_species_ : protocols::antibody::CDRSetOptions
• include_only_start_ : protocols::scoring::methods::pcs2::PcsEnergyParameter
• include_only_start_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_start_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_start_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_only_start_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• include_probe_radius_ : core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• include_proto_cdr4_ : protocols::antibody::AntibodyFeatures
• include_residue_ : protocols::analysis::InterfaceAnalyzerMover
• include_residues_ : protocols::hybridization::CartesianSampler
• include_ring_current_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_submotifs_from_jump_library_ : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• include_subunit_ : core::conformation::symmetry::SymmData
• include_terminal_loops_ : core::select::residue_selector::SecondaryStructureSelector
• include_terms_ : protocols::optimize_weights::IterativeOptEDriver
• include_trp_ : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• include_virtual_side_chain_ : core::pack::task::ResidueLevelTask_
• include_water_ : protocols::analysis::PackStatMover
• included_nres_ : protocols::analysis::InterfaceAnalyzerMover
• included_properties_ : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• included_types_ : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• incoming_structures_ : protocols::abinitio::HedgeArchive
• incorporate_matches_into_pose_ : protocols::match::MatcherMover
• increase_cycles_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• independent_cycles_ : protocols::forge::remodel::RemodelLoopMover
• index : core::graph::DS_Node , core::scoring::motif::MotifHit , protocols::cartesian::CartesianAtom , protocols::dna::Reversion , protocols::forge::remodel::LineObject , protocols::loophash::LeapIndex , protocols::mpi_refinement::MethodParams
• index1 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• index2 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• index3 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral
• index4 : protocols::cartesian::MD_HarmonicDihedral
• index_ : core::chemical::ResidueConnection , core::chemical::sdf::MolFileIOAtom , core::chemical::sdf::MolFileIOBond , core::fragment::picking_old::vall::VallSection , core::graph::UEVertex< V, E > , core::pack::dunbrack::ProbSortClass , protocols::enzdes::EnzdesFlexibleRegion , protocols::genetic_algorithm::EntityElement , protocols::kinematic_closure::ClosureSolution , protocols::match::upstream::ScaffoldBuildPoint , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• index_atom_map_ : core::chemical::sdf::MolFileIOMolecule
• index_for_rotamer_ : protocols::match::output::UpstreamHitCacher
• index_str_ : core::select::residue_selector::ResidueIndexSelector
• index_to_id_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• indices_ : core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResiduePDBIndexIs
• indirect_numerator_ : protocols::qsar::scoring_grid::ChargeGrid
• individual_hbonds_ : protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• individual_scale_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsEnergyParameter
• individual_scale_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• individual_scale_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• individual_scale_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• individual_scale_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• individual_tasks_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• individual_weights_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• induced_dipole_ : core::scoring::MultipoleElecResidueInfo
• induced_rf_dipole_ : core::scoring::MultipoleElecResidueInfo
• INFINITE_SEPARATION : core::scoring::trie::TrieCountPairBase
• info1_ : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakFileFormat_Base
• info2_ : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakFileFormat_Base
• info_ : protocols::moves::Mover
• info_map_ : protocols::dna::PDBOutput
• inherit_scorefxn_temperature_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• init_ : core::scoring::MembraneTopology , protocols::electron_density::BfactorFittingMover
• init_all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_angle_ : protocols::matdes::GetRBDOFValues
• init_d77_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_disp_ : protocols::matdes::GetRBDOFValues
• init_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_fa_ : protocols::abinitio::ResolutionSwitcher
• init_flex_cter_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_for_input_yet_ : protocols::anchored_design::AnchoredDesignMover , protocols::antibody_legacy::AntibodyModeler , protocols::floppy_tail::FloppyTailMover
• init_from_command_line_ : core::pack::task::operation::OptH
• init_k48r_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_monoub_all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_monoub_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_monoub_flex_cter_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_mover_ : protocols::topology_broker::FragmentJumpClaimer
• init_pose_ : protocols::abinitio::ResolutionSwitcher , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• init_pose_obj_ : protocols::abinitio::AbrelaxApplication
• init_pucker_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• init_tag_is_done_ : protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• init_task_factory_ : protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::LoopRlxMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• init_temp : protocols::rbsegment_relax::RBSegmentRelax
• init_temp_ : protocols::antibody::H3RefineCCD
• init_torsions_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• initial_asymm_foldtree_ : protocols::hybridization::HybridizeFoldtreeDynamic
• initial_cluster_set_size_ : protocols::pose_selectors::ClusterPoseSelector
• initial_decoy_stddev_ : protocols::optimize_weights::PNatStructureOptEData
• initial_density_ : protocols::simple_moves::PeriodicBoxMover
• initial_pack_ : protocols::backrub::BackrubProtocol
• initial_perturb_ : protocols::ligand_docking::Transform
• initial_phis : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• initial_pose : protocols::vip::VIP_Mover
• initial_psis : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• initial_rms : protocols::relax::SRelaxPose
• initial_score : protocols::relax::SRelaxPose
• initial_temp_ : protocols::loop_modeling::LoopProtocol
• initial_template_index_ : protocols::hybridization::FoldTreeHybridize
• initial_values_ : protocols::qsar::qsarOptFunc
• initialization_state_ : protocols::dna::DnaInterfacePacker
• initialize_ : protocols::qsar::qsarMover
• initialize_map_helix_pairings_ : protocols::fldsgn::topology::HelixPairingSet
• initialized : protocols::features::ReportToDB , protocols::moves::StructureRestrictor
• initialized_ : core::pose::xyzStripeHashPose , core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondTypeManager , core::scoring::lkball::LKB_ResPairMinData , core::scoring::MembraneTopology , core::scoring::methods::MultipoleElecResPairMinData , core::scoring::methods::VdWTinkerResPairMinData , core::scoring::ScoreTypeManager , protocols::branch_angle::BranchAngleOptimizer , protocols::dna::DnaInterfaceFinder , protocols::features::ProteinSilentReport , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::topology::SheetFoldTypeManager , protocols::loops::JSONFormattedLoopsFileReader , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash , protocols::qsar::scoring_grid::GridManager , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::sewing::AppendAssemblyMover , protocols::simple_filters::SheetFilter , protocols::stepwise::modeler::align::StepWiseClusterer
• initialized_atom_id_map_for_rmsd_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialized_databases_ : core::scoring::hbonds::HBondDatabase
• initialized_pattern_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• initialized_SASA_radii : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• InitialJumps_ : protocols::simple_moves::symmetry::SymmetrySlider
• inittime_ : protocols::md::CartesianMD
• inName : protocols::sparta::Sparta::SpartaLib
• inNames : protocols::sparta::Sparta::SpartaLib
• inner_ : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• inner_cycle_list_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• inner_cycle_steps_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• inner_cycles_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::H3RefineCCD , protocols::docking::DockingLowRes , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::moves::RampingMover , protocols::symmetric_docking::SymDockingLowRes
• inner_end_ : core::fragment::MinimalFragSetIterator_ , core::fragment::OrderedFragSetIterator_
• inner_job_ : protocols::jd2::Job , protocols::jd2::MultiThreadingJob , protocols::jd3::LarvalJob
• inner_kt_ : protocols::antibody::design::AntibodyDesignMover
• inner_loop_counter_ : protocols::optimize_weights::IterativeOptEDriver
• inner_loop_cycles_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• inner_loop_rotamer_recovery_rate_ : protocols::optimize_weights::IterativeOptEDriver
• inner_loop_sequence_recovery_rate_ : protocols::optimize_weights::IterativeOptEDriver
• inner_radius_ : protocols::qsar::scoring_grid::AtrGrid
• inneriterations_ : core::pack::annealer::SimAnnealerBase
• inneriterations_scaling_ : core::pack::annealer::SimAnnealerBase
• inp_chi_ : protocols::make_rot_lib::RotData
• inPDB : protocols::sparta::Sparta::SpartaLib
• inprogress_ : protocols::jobdist::BaseJobDistributor
• input_ : protocols::jd2::PoseInputStreamJobInputter , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• input_as_ref_ : protocols::hybridization::CartesianSampler
• input_code : protocols::sparta::ANN
• input_conformation_ : protocols::match::upstream::OriginalBackboneBuildPoint
• input_file : update_ResidueType_enum_files.EnumInfo
• input_id_ : protocols::jobdist::BasicJob
• input_is_positive_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• input_kind_ : protocols::jd3::PoseInputSource
• input_loop_ : protocols::antibody::H3PerturbCCD
• input_pose : protocols::pockets::PocketExemplarMultifunc
• input_pose_ : protocols::environment::Environment , protocols::moves::Mover , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::RigidChunkClaimer
• input_pose_counter_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• input_pose_list_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer
• input_pose_ONE_appended_res_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_ONE_last_appended_res_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_TWO_last_prepended_res_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_TWO_prepended_res_list_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• input_poses_ : protocols::pmut_scan::PointMutScanDriver
• input_res_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• input_res_vectors_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• input_rigid_core_ : protocols::topology_broker::FibrilModelingClaimer
• input_rotamer_coords_ : core::pack::rotamer_set::ContinuousRotamerSet
• input_rotamer_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• input_rotamer_samplingrot_index_ : core::pack::rotamer_set::ContinuousRotamerSet
• input_scan_res_ : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• input_sequence_ : protocols::topology_broker::SequenceClaimer
• input_sheet_sizes_ : protocols::jumping::RandomSheetBuilder
• input_source_ : protocols::comparative_modeling::ThreadingJobInputter
• input_sources_ : protocols::jd3::InnerLarvalJob
• input_ss_ : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::flxbb::InterlockAroma
• input_stream_ : protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler
• input_streams_ : core::import_pose::pose_stream::MetaPoseInputStream , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler
• input_streams_with_residue_info_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• input_string : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• input_tag_ : protocols::jd2::InnerJob , protocols::jd3::InnerLarvalJob , protocols::jd3::PoseInputSource
• input_tags_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• input_vector_expressions_ : protocols::pack_daemon::IterativeVectorExpression
• inputpose_ : protocols::rpc::JSON_RPC
• inputstream : protocols::ddG::ddGData
• inputvalues_real_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• insert_connection_scheme_ : protocols::forge::build::SegmentInsert
• insert_map_ : protocols::farna::movers::RNA_FragmentMover , protocols::simple_moves::FragmentMover
• insert_map_frag_size_ : protocols::farna::movers::RNA_FragmentMover
• insert_movemap_ : protocols::grafting::AnchoredGraftMover
• insert_pdb_ : protocols::forge::remodel::RemodelMover::instruction_flags
• insert_pos_ : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler
• insert_pose_ : protocols::forge::build::SegmentInsert
• insert_pose_torsion_override_movemap_ : protocols::forge::build::SegmentInsert
• insert_position_ : core::fragment::picking_old::vall::eval::EnergyEval
• insert_size_ : protocols::simple_moves::FragmentMover
• insertedAfterLoopRes_ : protocols::pose_length_moves::PossibleLoop
• insertedBeforeLoopRes_ : protocols::pose_length_moves::PossibleLoop
• inserter_ : protocols::loophash::LoopHashSampler
• inserting_pdb_ : protocols::forge::remodel::RemodelMover::instruction_flags
• insertion_ : protocols::jd2::parser::BluePrint
• insertion_code_ : core::pose::ResidueIndexDescription , protocols::antibody::PDBLandmark
• insertion_length_ : protocols::grafting::GraftMoverBase
• insertion_prob_ : protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• insertionEndIndex : protocols::forge::remodel::RemodelWorkingSet
• insertionSize : protocols::forge::remodel::RemodelData
• insertionSS : protocols::forge::remodel::RemodelData
• insertionStartIndex : protocols::forge::remodel::RemodelWorkingSet
• insertPose : protocols::forge::remodel::RemodelData
• instance_ : core::chemical::orbitals::OrbitalTypeMapper , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::TaskOperationFactory , core::scoring::motif::MotifHashManager , core::select::residue_selector::ResidueSelectorFactory , core::SVNVersion , protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::jd2::JobDistributor , protocols::jd2::parser::DataLoaderFactory , protocols::ligand_docking::DistributionMap , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::moves::MoverFactory , protocols::noesy_assign::PeakAssignmentParameters , protocols::qsar::scoring_grid::GridManager , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton , protocols::scoring::methods::pcs2::PcsInputCenterManager , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1 , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4 , protocols::sewing::sampling::requirements::RequirementFactory , protocols::topology_broker::TopologyClaimerFactory
• instance_initialized_ : protocols::canonical_sampling::TemperingBase
• instance_node_2_file_node_ : core::pack::interaction_graph::PDInteractionGraph
• instantiate_sugar_ : protocols::stepwise::screener::SugarInstantiator
• instantiated_phosphate_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• instantiated_some_phosphate_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• instruction_dependencies_ : protocols::forge::build::BuildManager
• instruction_file_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignProtocol
• instructions_ : protocols::forge::build::BuildManager
• instructions_path_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• int64_groups : core::indexed_structure_store::FragmentStore
• int_buf1_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• inTab : protocols::sparta::Sparta::SpartaLib
• integration_test_ : protocols::magnesium::MgScanner
• integration_test_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• intensity_ : protocols::noesy_assign::Resonance
• inter_atr_ : protocols::make_rot_lib::RotData
• inter_chain_ : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• inter_clash1_ : core::scoring::motif::ResPairMotifQuery
• inter_clash1_xform_ : core::scoring::motif::ResPairMotifQuery
• inter_clash2_ : core::scoring::motif::ResPairMotifQuery
• inter_clash2_xform_ : core::scoring::motif::ResPairMotifQuery
• inter_rep_ : protocols::make_rot_lib::RotData
• inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• interacting_atompair_list_ : core::scoring::custom_pair_distance::AtomPairFuncList
• INTERACTION_RADIUS : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• intercept : core::sequence::Line
• intercept_ : core::scoring::packing::HolesParams
• intercepts_ : core::scoring::packing::HolesParams
• interchain_env_log_ : protocols::scoring::InterchainPotential
• interchain_pair_log_ : protocols::scoring::InterchainPotential
• interchain_potential_ : protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy
• interchangeability_group_ : core::chemical::ResidueType , core::chemical::ResidueTypeFinder
• interchangeability_group_generated_by_base_residue_name_ : core::chemical::ResidueTypeSet
• interE : protocols::simple_moves::ThermodynamicData
• interface_ : protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::dna::DnaInterfaceMinMover , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::docking::InterfaceSidechainMinMover , protocols::protein_interface_design::movers::LoopFinder , protocols::rigid::RigidBodyPerturbMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover
• interface_analyzer_ : protocols::features::InterfaceFeatures
• interface_atoms_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• interface_builder_ : protocols::ligand_docking::MinimizeBackbone
• interface_calc_ : protocols::anchored_design::AnchorMoversData
• interface_chi1_ : protocols::seeded_abinitio::SeedSetupMover
• interface_chi2_ : protocols::seeded_abinitio::SeedSetupMover
• interface_data_ : protocols::antibody::AntibodyFeatures
• interface_data_res_ : protocols::antibody::AntibodyFeatures
• interface_ddg_ : protocols::ddg::ddGMover
• interface_dis_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::GeneralAntibodyModeler
• interface_dist_ : protocols::docking::InterfaceSidechainMinMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover
• interface_distance_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• interface_distance_cutoff_ : protocols::enzdes::LigInterfaceEnergyFilter , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• interface_hbonds : protocols::analysis::InterfaceData
• interface_jump_ : protocols::analysis::InterfaceAnalyzerMover
• interface_list_ : protocols::scoring::InterfaceInfo
• interface_nres : protocols::analysis::InterfaceData
• interface_only_ : core::scoring::motif::ResPairMotifQuery
• interface_packer_ : protocols::flexpep_docking::FlexPepDockingProtocol
• interface_radius_ : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• interface_res_ : protocols::stepwise::monte_carlo::mover::DeleteMover
• interface_residues : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• interface_set_ : protocols::analysis::InterfaceAnalyzerMover , protocols::pmut_scan::AlterSpecDisruptionDriver
• interface_tf_ : protocols::antibody::design::GeneralAntibodyModeler , protocols::flexpep_docking::FlexPepDockingProtocol
• interface_to_surface_fraction : protocols::analysis::InterfaceData
• InterfaceDeltaEnergetics_ : protocols::analysis::InterfaceAnalyzerMover
• InterfaceNeighborDefinition_ : protocols::analysis::InterfaceAnalyzerMover
• interfaces_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo , protocols::features::InterfaceFeatures
• InterfaceSasaDefinition_ : protocols::analysis::InterfaceAnalyzerMover
• intermediate_interfaces_ : protocols::antibody::AntibodyFeatures
• intermediate_structs_ : protocols::jd2::archive::Batch
• intermediate_weights_ : protocols::moves::RampingMover
• intermedrelax_ : protocols::comparative_modeling::LoopRelaxMover , protocols::indel::IndelOptimizationMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• internal_allowed_ : core::scoring::packstat::Slice
• internal_coords_need_updating_ : core::kinematics::AtomTree
• internal_cycles_ : protocols::stepwise::monte_carlo::mover::AddMover
• internal_geometry_ : protocols::simple_moves::MinimalRotamer
• interp_ : core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::SuckerEnergy
• interpolate_ : core::scoring::rna::RNA_LowResolutionPotential
• interpolator_ : core::scoring::func::SplineFunc
• interres_evaluator_ : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• interres_path_distance_cutoff_ : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• interval_ : protocols::checkpoint::Timer , protocols::constraints_additional::COMCoordinateConstraint , protocols::forge::build::Bridge , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• interval_posedump_ : protocols::canonical_sampling::CanonicalSamplingMover
• interval_transitiondump_ : protocols::canonical_sampling::CanonicalSamplingMover
• intervals_ : protocols::forge::constraints::InverseRotamersRCG
• intgrp_ : core::chemical::SetInterchangeabilityGroup_String
• intra_atr_ : protocols::make_rot_lib::RotData
• intra_elec_scale_ : core::scoring::FACTSRsdTypeInfo
• intra_rep_ : protocols::make_rot_lib::RotData
• intra_residue_constraints_ : core::scoring::constraints::ConstraintSet
• intra_segment_requirements_ : protocols::sewing::sampling::requirements::RequirementSet
• intra_segment_types_ : protocols::sewing::sampling::requirements::RequirementFactory
• intra_solv_scale_ : core::scoring::FACTSRsdTypeInfo
• intrabb_only_ : protocols::matdes::BuildingBlockInterfaceOperation
• intraE : protocols::simple_moves::ThermodynamicData
• intrares_elec_correction_scale_ : core::scoring::methods::EnergyMethodOptions
• intrares_evaluator_ : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• intrares_path_distance_cutoff_ : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• intrares_scale_ : core::scoring::elec::FA_GrpElecEnergy
• intrares_side_chain_score_ : core::scoring::rna::RNA_TorsionPotential
• intrares_upper_nblist_ : core::scoring::NeighborList
• intrascale_by_level_ : core::scoring::FACTSPotential
• inv_cov_ : core::scoring::rna::RNA_SuitePotential
• inv_die_ : core::scoring::FACTSPotential
• inv_dots_ : core::pack::interaction_graph::InvRotamerDots
• inv_neg2_tms_pi_sqrt_pi : core::scoring::magnesium::MgEnergy
• inv_one_minus_xval_at_0p5_ : protocols::moves::InvGeometricFunc
• inv_peptide_bonded_pair_indices_ : core::scoring::PolymerBondedEnergyContainer
• inv_xval_at_0p5_ : protocols::moves::GeometricFunc
• invalid_ : protocols::jd2::archive::Batch
• inverse_rotamers_ : protocols::forge::constraints::InverseRotamersRCG
• invert_ : protocols::filters::CompoundFilter , protocols::filters::IfThenFilter , protocols::toolbox::task_operations::CrystalContactsOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SelectByDensityFitOperation , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover
• invert_downstream_ : core::kinematics::Jump
• invert_helix_ : protocols::helical_bundle::parameters::BundleParameters
• invert_task_ : protocols::simple_moves::ConsensusDesignMover
• invert_upstream_ : core::kinematics::Jump
• inverted_frame_ : core::kinematics::tree::BondedAtom
• InvertJump_ : protocols::simple_moves::symmetry::SymmetrySlider
• invrot_targets_ : protocols::toolbox::match_enzdes_util::InvrotTree
• invrot_tree_ : protocols::fldsgn::BluePrintBDR , protocols::forge::constraints::InvrotTreeRCG , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• invrot_tree_constraints_ : protocols::toolbox::match_enzdes_util::InvrotTree
• invrots_ : protocols::toolbox::match_enzdes_util::InvrotCollector
• invrots_and_next_nodes_ : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• INWARDS : core::scoring::dssp::Pairing
• io_stride_ : protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrialCounterObserver
• ionc : core::scoring::APBSConfig
• ionizables_ : protocols::simple_moves::ReportEffectivePKA
• ionized_restype_ : protocols::simple_moves::IonizableResidue
• ionq : core::scoring::APBSConfig
• ionr : core::scoring::APBSConfig
• iparam19 : core::scoring::APBSConfig::I_PARAM
• ipca_ : protocols::evaluation::PCA
• ipos_ : core::fragment::FragID_Iterator
• iptsn_ : core::scoring::SecondaryStructurePotential
• irun : protocols::mpi_refinement::MethodParams
• is_a_neighbor_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• is_acceptor_ : core::chemical::AtomType
• is_aromatic_ : core::chemical::AtomType
• is_backbone_ : core::scoring::hbonds::hbtrie::HBAtom , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• is_backward_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• is_barrel_ : protocols::fldsgn::topology::Sheet
• is_below_buried_residue_no_hsasa_cutoff_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• is_bonded_values_ : core::scoring::rna::data::RNA_DMS_Potential
• is_branch_lower_terminus_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• is_build_stage_enabled_ : protocols::loop_modeling::LoopModeler
• is_bulged_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_camelid_ : protocols::antibody::AntibodyInfo , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• is_cancelled_ : protocols::jd2::archive::Batch
• is_centroid_stage_enabled_ : protocols::loop_modeling::LoopModeler
• is_chain_pair_new_ : protocols::analysis::PeptideDeriverPoseOutputter
• is_chargedH_ : core::scoring::FACTSRsdTypeInfo
• is_covalent_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• is_cstE_ : protocols::enzdes::EnzScoreFilter
• is_cutpoint_ : core::kinematics::FoldTree , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• is_cyd_res_at_termini_ : protocols::simple_moves::DisulfideInsertionMover
• is_default_ : protocols::kinematic_closure::perturbers::PerturberSet , protocols::loop_modeling::utilities::LoopMoverGroup
• is_dna_ : core::scoring::hbonds::hbtrie::HBAtom
• is_do_minimize_ : protocols::analysis::PeptideDeriverFilter
• is_donor_ : core::chemical::AtomType
• is_dump_best_peptide_pose_ : protocols::analysis::PeptideDeriverPoseOutputter
• is_dump_cyclic_poses_ : protocols::analysis::PeptideDeriverFilter , protocols::analysis::PeptideDeriverPoseOutputter
• is_dump_peptide_pose_ : protocols::analysis::PeptideDeriverFilter
• is_dump_prepared_pose_ : protocols::analysis::PeptideDeriverFilter , protocols::analysis::PeptideDeriverPoseOutputter
• is_dump_report_file_ : protocols::analysis::PeptideDeriverFilter
• is_empty_ : protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerComb
• is_fail_ : protocols::flexpep_docking::FlexPepDockingProtocol
• is_file_ : protocols::canonical_sampling::PatchOperation
• is_fixed_res_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_fixed_res_input_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• is_fold_tree_stale_ : protocols::kinematic_closure::BalancedKicMover
• is_forward_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• is_freedof_ : core::scoring::FACTSRsdTypeInfo
• is_frozen_ : protocols::cluster::APCluster
• is_fullatom_stage_enabled_ : protocols::loop_modeling::LoopModeler
• is_gasteiger_type_ : core::chemical::gasteiger::GasteigerAtomTypeData
• is_geometry_initialized_ : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Base
• is_ghost_ : protocols::boinc::BoincCurrentPoseObserver
• is_glob_ : protocols::scoring::methods::saxs::PDDFEnergy
• is_glycoside_ : core::chemical::carbohydrates::CarbohydrateInfo
• is_h2o_ : core::chemical::AtomType
• is_heavy_ : core::scoring::packing::PoseBalls
• is_hydrogen_ : core::chemical::Atom , core::scoring::elec::ElecAtom , core::scoring::etable::etrie::EtableAtom , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::vdwaals::VDWAtom
• is_hydrophobic_ : protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity
• is_init_ : protocols::stepwise::sampler::StepWiseSamplerBase
• is_interface_ : protocols::scoring::Interface
• is_internal_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_jump_point_ : core::kinematics::FoldTree
• is_loop : protocols::denovo_design::components::Segment
• is_lower_terminus_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• is_magnesium_ : core::scoring::rna::RNA_ScoringInfo
• is_map_loaded : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• is_moving_res_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_NA_ : core::io::NomenclatureManager
• is_ngb : protocols::neighbor::Neighborhood
• is_occupied_ : protocols::stepwise::modeler::rna::checker::VDW_Grid
• is_old_DNA_ : core::io::NomenclatureManager
• is_old_RNA_ : core::io::NomenclatureManager
• is_on_ : protocols::checkpoint::Timer
• is_orbital_acceptor_ : core::chemical::orbitals::OrbitalType
• is_orbital_donor_ : core::chemical::orbitals::OrbitalType
• is_phosphate_ : core::chemical::rna::RNA_ResidueType
• is_pivot_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• is_polar_hydrogen_ : core::chemical::AtomType
• is_positive_state_ : protocols::multistate_design::SingleState
• is_pre_proline_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• is_prepend : protocols::stepwise::modeler::rna::sugar::SugarModeling
• is_prepend_ : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::screener::AnchorSugarScreener
• is_prepend_map_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_properly_initialized : protocols::simple_moves::ShakeStructureMover
• is_protected_values_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_protein_ : core::scoring::hbonds::hbtrie::HBAtom
• is_proton_ : protocols::noesy_assign::Resonance
• is_proton_chi_ : core::chemical::ResidueType
• is_random_ : protocols::mpi_refinement::Scheduler
• is_reference_xyz_setup_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• is_report_gzip_ : protocols::analysis::PeptideDeriverFilter
• is_representative_resonance_ : protocols::noesy_assign::FloatingResonance
• is_RNA_base_ : core::chemical::rna::RNA_ResidueType
• is_sc_ : core::scoring::hbonds::hbtrie::HBCPData
• is_score_precomputed : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• is_scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• is_selection_initialized_ : core::select::util::SelectResiduesByLayer
• is_setup_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• is_simple_full_length_job_params_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_skip_zero_isc_ : protocols::analysis::PeptideDeriverFilter
• is_sliced_res_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• is_started_ : protocols::jobdist::BaseJobDistributor
• is_surface_ : core::scoring::solid_surface::SurfaceEnergies
• is_symmetric_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• is_term_ : core::scoring::trie::TrieNode< AT, CPDATA >
• is_terminal_res_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_trimmed_loops_ : protocols::flexpep_docking::FlexPepDockingProtocol
• is_up_to_date_ : protocols::frag_picker::scores::AdaptiveScoreHistogram
• is_using_ : core::scoring::methods::GoapRsdType
• is_VDW_screen_bin_setup_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• is_virtual_ : core::chemical::rna::RNA_ResidueType
• is_virtual_base_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_weighted_ : protocols::stepwise::sampler::StepWiseSamplerAny
• is_working_res_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• isbb_ : core::scoring::elec::ElecAtom
• isch_ : protocols::mpi_refinement::Scheduler
• isDesignable : protocols::forge::remodel::LineObject
• isep_residue_ : protocols::fldsgn::NcontactsCalculator
• isHet : core::io::AtomInformation , core::pose::PDBInfo::AtomRecord
• isLoaded : core::scoring::electron_density::ElectronDensity , core::scoring::fiber_diffraction::FiberDiffraction
• isometry_ : core::chemical::Bond
• istart : protocols::mpi_refinement::MethodParams
• istart_ : protocols::simple_moves::PeriodicBoxMover
• it_ : core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameListIterator_ , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• iter64_ : protocols::match::VoxelSetIterator
• iter_ : protocols::membrane::MPMutateRelaxMover , protocols::mpi_refinement::Scheduler
• iteration : protocols::canonical_sampling::DbTrajectoryRecorder::Frame , protocols::trajectory::DbTrajectoryWriter::Frame
• iteration_ : protocols::kinematic_closure::perturbers::LogFilePerturber , protocols::trajectory::DbTrajectoryWriter , protocols::vip::VIP_Mover
• iteration_counter_ : protocols::loop_modeling::refiners::RepackingRefiner
• iterations_ : protocols::abinitio::abscript::AbscriptMover::StageTracker , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::moves::CyclicMover
• ivm_ : protocols::toolbox::InteratomicVarianceMatrix