- i -

• i : protocols::cluster::DataPoint
• i_ : protocols::frag_picker::Contact
• 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
• IAM_ : protocols::anchored_design::AnchoredDesignMover , protocols::pmut_scan::AlterSpecDisruptionDriver
• icode : protocols::antibody::design::PDBNumbering
• icode_ : protocols::pmut_scan::MutationData
• id : protocols::environment::claims::DOFElement , 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_ : protocols::features::strand_assembly::StrandFragment , protocols::forge::remodel::RemodelConstraintGenerator , protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::VallResidue , protocols::optimize_weights::OptEVariableExpression , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::wum2::WorkUnit , protocols::wum::WorkUnitBase::WU_Header
• id_list_ : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• id_list_cached_ : protocols::stepwise::sampler::StepWiseSamplerOneValueComb
• id_map_ : protocols::abinitio::abscript::AbscriptMover
• ideal_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• ideal_geometry_ : protocols::simple_moves::MinimalRotamer
• ideal_val_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• idealize_ : 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_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
• 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
• 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
• if_dock_pert_ : protocols::docking::DockingInitialPerturbation
• if_ensemble_ : protocols::docking::DockingProtocol
• if_fit_area_ : protocols::scoring::methods::saxs::PDDFEnergy
• if_hydrogens_ : 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_ : 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_p_ : protocols::multistate_design::PackingState
• ignore_assignments_ : protocols::noesy_assign::PeakFileFormat_Base
• 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_profile_length_mismatch_ : protocols::simple_moves::ConsensusDesignMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• 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::RNA_DeNovoProtocol
• ignore_template_indices_ : protocols::hybridization::ChunkTrialMover
• ignore_unmatched_virtual_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ignore_unrecognized_res_ : protocols::rotamer_recovery::RotamerRecovery
• ignore_virtual_ : protocols::simple_moves::CopyDofMover
• ignore_zero_byte_ : protocols::simple_filters::FileExistFilter
• 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
• 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
• in_charge_ : protocols::loops::GuardedLoopsFromFile
• 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
• incl_nonopt_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• 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_count_ : protocols::optimize_weights::IterativeOptEDriver
• include_cstE_ : protocols::enzdes::LigInterfaceEnergyFilter
• include_current_ : protocols::protein_interface_design::movers::TryRotamers , protocols::symmetric_docking::SymRestrictTaskForDocking
• include_default_linear_chainbreak_ : protocols::farna::RNA_Minimizer
• include_dna_potentials_in_specificity_calculations_ : protocols::dna::DnaInterfacePacker
• include_lips_ : protocols::membrane::AddMembraneMover
• include_metals_ : protocols::enzdes::GenerateStoredRBConfs
• include_native_aa_ : protocols::antibody::design::ConservativeDesignOperation
• include_native_restype_ : protocols::antibody::design::ResidueProbDesignOperation
• include_neighbor_sc_ : protocols::antibody::design::AntibodyDesignMoverGenerator
• 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_residue_ : protocols::analysis::InterfaceAnalyzerMover
• include_terms_ : protocols::optimize_weights::IterativeOptEDriver
• include_trp_ : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• include_water_ : protocols::analysis::PackStatMover
• included_nres_ : protocols::analysis::InterfaceAnalyzerMover
• incoming_allocated : protocols::wum2::StatusResponse
• 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 : 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_ : protocols::enzdes::EnzdesFlexibleRegion , protocols::genetic_algorithm::EntityElement , protocols::kinematic_closure::ClosureSolution , protocols::match::upstream::ScaffoldBuildPoint , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• index_for_rotamer_ : protocols::match::output::UpstreamHitCacher
• 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
• 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_ : 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_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_denovo_scorefxn_ : protocols::farna::RNA_DeNovoProtocol
• initial_perturb_ : protocols::antibody::design::AntibodyGraftDesignMover , 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 , protocols::hybridization::HybridizeSetup
• initial_values_ : protocols::qsar::qsarOptFunc
• initialization_state_ : protocols::dna::DnaInterfacePacker
• initialize_ : protocols::qsar::qsarMover
• initialize_map_helix_pairings_ : protocols::fldsgn::topology::HelixPairingSet
• initialize_pose_by_templates_ : protocols::hybridization::FoldTreeHybridize
• initialized : protocols::features::ReportToDB , protocols::moves::StructureRestrictor
• initialized_ : protocols::branch_angle::BranchAngleOptimizer , protocols::dna::DnaInterfaceFinder , protocols::farna::BasePairStepLibrary , protocols::farna::RNA_SecStructInfo , 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::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_pattern_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• InitialJumps_ : protocols::simple_moves::symmetry::SymmetrySlider
• inittime_ : protocols::md::CartesianMD
• inName : protocols::sparta::Sparta::SpartaLib
• inNames : protocols::sparta::Sparta::SpartaLib
• inner_cycle_list_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• inner_cycle_steps_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• inner_cycles_ : protocols::antibody::H3RefineCCD , protocols::docking::DockingLowRes , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::moves::RampingMover , protocols::symmetric_docking::SymDockingLowRes
• inner_job_ : protocols::jd2::Job , protocols::jd2::MultiThreadingJob
• 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
• 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_id_ : protocols::jobdist::BasicJob
• input_is_positive_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• 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::RNA_DeNovoProtocol , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• input_res_vectors_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• input_rigid_core_ : protocols::topology_broker::FibrilModelingClaimer
• input_sequence_ : protocols::topology_broker::SequenceClaimer
• input_sheet_sizes_ : protocols::jumping::RandomSheetBuilder
• input_source_ : protocols::comparative_modeling::ThreadingJobInputter
• input_ss_ : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::flxbb::InterlockAroma
• input_stream_ : protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler
• input_streams_ : 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
• 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
• InputPose_has_antigen_ : protocols::antibody::AntibodyInfo
• inputstream : protocols::ddG::ddGData
• inputters_ : protocols::inputter::InputterStream
• inputvalues_real_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• inq_ : protocols::wum2::EndPoint
• insert_connection_scheme_ : protocols::forge::build::SegmentInsert
• insert_map_ : protocols::farna::RNA_FragmentMover , protocols::simple_moves::FragmentMover
• insert_map_frag_size_ : protocols::farna::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_size_ : protocols::simple_moves::FragmentMover
• inserter_ : protocols::loophash::LoopHashSampler
• inserting_pdb_ : protocols::forge::remodel::RemodelMover::instruction_flags
• insertion_ : protocols::jd2::parser::BluePrint
• insertion_code_ : protocols::antibody::PDBLandmark , protocols::loops::ResidueIndexDescription
• 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_ : protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::jd2::JobDistributor , protocols::jd2::parser::DataLoaderFactory , protocols::ligand_docking::DistributionMap , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::moves::MoverFactory , protocols::noesy_assign::PeakAssignmentParameters , protocols::qsar::scoring_grid::GridManager , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton , protocols::scoring::methods::pcs2::PcsInputCenterManager , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1 , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4 , protocols::topology_broker::TopologyClaimerFactory
• instance_initialized_ : protocols::canonical_sampling::TemperingBase
• 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_path_ : protocols::antibody::design::AntibodySeqDesignMover
• instructions_ : protocols::forge::build::BuildManager
• instructions_path_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• int_buf1_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• inTab : protocols::sparta::Sparta::SpartaLib
• integration_test_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_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_rep_ : protocols::make_rot_lib::RotData
• inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• interchain_env_log_ : protocols::scoring::InterchainPotential
• interchain_pair_log_ : protocols::scoring::InterchainPotential
• interchain_potential_ : protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy
• 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_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::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• interface_dist_ : protocols::docking::InterfaceSidechainMinMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover
• interface_distance_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover
• 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_jump_ : protocols::analysis::InterfaceAnalyzerMover
• interface_list_ : protocols::scoring::InterfaceInfo
• interface_nres : protocols::analysis::InterfaceData
• 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_set_ : protocols::analysis::InterfaceAnalyzerMover , protocols::pmut_scan::AlterSpecDisruptionDriver
• interface_tf_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::flexpep_docking::FlexPepDockingProtocol
• interface_to_surface_fraction : protocols::analysis::InterfaceData
• InterfaceDeltaEnergetics_ : protocols::analysis::InterfaceAnalyzerMover
• InterfaceNeighborDefinition_ : protocols::analysis::InterfaceAnalyzerMover
• interfaces_ : protocols::features::InterfaceFeatures
• InterfaceSasaDefinition_ : protocols::analysis::InterfaceAnalyzerMover
• InterGroupNeighborsCalculator_ : 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::protein_interface_design::movers::LoopMoverFromCommandLine
• internal_cycles_ : protocols::stepwise::monte_carlo::mover::AddMover
• internal_geometry_ : protocols::simple_moves::MinimalRotamer
• 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
• intra_atr_ : protocols::make_rot_lib::RotData
• intra_rep_ : protocols::make_rot_lib::RotData
• intrabb_only_ : protocols::matdes::BuildingBlockInterfaceOperation
• inv_one_minus_xval_at_0p5_ : protocols::moves::InvGeometricFunc
• 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::SelectByDensityFitOperation , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover
• invert_helix_ : protocols::helical_bundle::parameters::BundleParameters
• invert_task_ : protocols::simple_moves::ConsensusDesignMover
• 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
• io_stride_ : protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrialCounterObserver
• ionizables_ : protocols::simple_moves::ReportEffectivePKA
• ionized_restype_ : protocols::simple_moves::IonizableResidue
• ipca_ : protocols::evaluation::PCA
• irun : protocols::mpi_refinement::MethodParams
• is_a_neighbor_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• is_backbone_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• is_backward_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• is_barrel_ : protocols::fldsgn::topology::Sheet
• is_build_stage_enabled_ : protocols::loop_modeling::LoopModeler
• 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_covalent_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• is_cstE_ : protocols::enzdes::EnzScoreFilter
• is_cutpoint_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• is_default_ : protocols::kinematic_closure::perturbers::PerturberSet , protocols::loop_modeling::utilities::LoopMoverGroup
• is_do_minimize_ : protocols::analysis::PeptideDeriverFilter
• 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_frozen_ : protocols::cluster::APCluster
• is_fullatom_stage_enabled_ : protocols::loop_modeling::LoopModeler
• is_geometry_initialized_ : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Base
• is_glob_ : protocols::scoring::methods::saxs::PDDFEnergy
• 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_moving_res_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_ngb : protocols::neighbor::Neighborhood
• is_on_ : protocols::checkpoint::Timer
• is_pivot_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• 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_proton_ : protocols::noesy_assign::Resonance
• is_random_ : protocols::mpi_refinement::Scheduler
• is_reference_xyz_setup_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• is_representative_resonance_ : protocols::noesy_assign::FloatingResonance
• is_scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• 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_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_VDW_screen_bin_setup_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• 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
• isch_ : protocols::mpi_refinement::Scheduler
• isDesignable : protocols::forge::remodel::LineObject
• isep_residue_ : protocols::fldsgn::NcontactsCalculator
• istart : protocols::mpi_refinement::MethodParams
• it_ : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• iter64_ : protocols::match::VoxelSetIterator
• iter_ : 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