- i -

• i : protocols::cluster::DataPoint
• i2c : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• i2c_ : core::scoring::PoissonBoltzmannPotential
• i_ : protocols::frag_picker::Contact
• i_param : core::scoring::APBSConfig
• IAM_ : protocols::anchored_design::AnchoredDesignMover , protocols::pmut_scan::AlterSpecDisruptionDriver
• ibx : core::scoring::APBSResult
• iby : core::scoring::APBSResult
• ibz : core::scoring::APBSResult
• iCode : core::io::pdb::AtomInformation , core::io::pdb::ResidueInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• icode_ : protocols::pmut_scan::MutationData
• icoor_ : core::chemical::Atom , core::chemical::Orbital , core::chemical::ResidueConnection
• ID : Entry , protocols::swa::rna::Cluster_Member
• id : core::optimization::AtomNode , core::optimization::DOF_Node , core::scoring::packstat::Sphere , protocols::swa::rna::Torsion_Info
• id2proftag_ : protocols::abinitio::FragmentSampler
• id2string_ : protocols::abinitio::FragmentSampler
• id_ : protocols::forge::remodel::RemodelConstraintGenerator , protocols::frag_picker::scores::FragmentScoringMethod , protocols::frag_picker::VallResidue , protocols::optimize_weights::OptEVariableExpression , protocols::wum::WorkUnitBase::WU_Header , protocols::wum2::WorkUnit , core::fragment::picking_old::vall::VallResidue , core::id::EXCN_AtomNotFound , core::scoring::packstat::CavityBall , core::scoring::saxs::FormFactor , core::sequence::Sequence
• id_for_current_rotamer_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• id_to_index_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• idCode_ : core::io::pdb::HeaderInformation
• ideal_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• ideal_bond_length_sets_ : core::chemical::ChemicalManager
• ideal_coord_ : protocols::rna::RNA_HelixAssembler
• ideal_delta_north_ : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_delta_south_ : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_geometry_ : protocols::simple_moves::MinimalRotamer
• ideal_jump : protocols::rna::RNA_HelixAssembler
• ideal_nu1_north_ : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_nu1_south_ : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_nu2_north_ : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_nu2_south_ : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_val_ : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• ideal_xyz_ : core::chemical::Atom , core::chemical::Orbital
• idealize_ : protocols::seeded_abinitio::CloseFold
• idealize_conformers_ : protocols::match::downstream::LigandConformerBuilder
• idealize_loop_first_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• ident_string_ : protocols::loophash::MPI_LoopHashRefine
• identical_tag_found_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• identity_obs_hub_ : core::conformation::Conformation
• idl_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::swa::protein::StepWiseProteinLoopBridger
• idl_C_N_CA_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::swa::protein::StepWiseProteinLoopBridger
• idl_CA_C_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• idl_CA_C_N_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::swa::protein::StepWiseProteinLoopBridger
• 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::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::BasicSimAnnealerRepacker , 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_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::swa::rna::StepWiseRNA_Clusterer
• ignore_FARFAR_no_auto_bulge_tag_ : protocols::swa::rna::StepWiseRNA_Clusterer
• ignore_h_collisions_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• ignore_list_ : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_loops_ : protocols::fldsgn::NcontactsCalculator
• ignore_negative_intensity_ : protocols::noesy_assign::PeakFileFormat_Base
• ignore_o2star_hbonds_in_filter_ : protocols::swa::RigidBodySampler
• 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::rna::RNA_DeNovoProtocol
• ignore_template_indices_ : protocols::hybridization::ChunkTrialMover
• ignore_unmatched_virtual_res_ : protocols::swa::rna::StepWiseRNA_Clusterer
• ignore_unrecognized_res_ : protocols::rotamer_recovery::RotamerRecovery , core::io::pdb::FileDataOptions
• ignore_waters_ : core::io::pdb::FileDataOptions
• ignore_zero_byte_ : protocols::simple_filters::FileExistFilter
• ignore_zero_occupancy_ : core::io::pdb::FileDataOptions
• ignorefinished_ : protocols::jobdist::BaseJobDistributor
• illegal_variable_names_ : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• image_start_ : protocols::simple_moves::SymmetricFragmentMover , protocols::simple_moves::SmoothSymmetricFragmentMover
• import_ID : protocols::swa::rna::VDW_RepScreeninfo
• impose_constraints_ : protocols::idealize::IdealizeMover
• 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_range_CCD_torsion : protocols::swa::rna::SillyCountStruct
• in_root_partition : protocols::swa::rna::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
• 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::PackDaemon , protocols::pack_daemon::DaemonSet
• include_count_ : protocols::optimize_weights::IterativeOptEDriver
• include_cstE_ : protocols::enzdes::LigInterfaceEnergyFilter
• include_current_ : core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask_ , protocols::symmetric_docking::SymRestrictTaskForDocking
• include_default_linear_chainbreak_ : protocols::rna::RNA_Minimizer
• include_dna_potentials_in_specificity_calculations_ : protocols::dna::DnaInterfacePacker
• include_intra_res_RNA_ : core::scoring::hbonds::HBondOptions
• include_magnetic_anisotropy_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_metals_ : protocols::enzdes::GenerateStoredRBConfs
• include_neighbor_base_stacks_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• include_neighbors_ : protocols::antibody2::H3RefineCCD , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• 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_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_ring_current_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_subunit_ : core::conformation::symmetry::SymmData
• include_syn_chi_ : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• include_terms_ : protocols::optimize_weights::IterativeOptEDriver
• include_torsion_value_in_tag_ : protocols::swa::rna::StepWiseRNA_ResidueSampler
• include_trp_ : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• include_water_ : protocols::analysis::PackStatMover
• incoming_allocated : protocols::wum2::StatusResponse
• incoming_structures_ : protocols::abinitio::HedgeArchive
• incorporate_matches_into_pose_ : protocols::match::MatcherMover
• increase_cycles_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• independent_cycles_ : protocols::forge::remodel::RemodelLoopMover
• index : core::graph::DS_Node , protocols::cartesian::CartesianAtom , protocols::dna::Reversion , protocols::forge::remodel::LineObject , protocols::loophash::LeapIndex
• index1 : protocols::cartesian::MD_Bond , protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral
• index2 : protocols::cartesian::MD_Bond , protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral
• index3 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral
• index4 : protocols::cartesian::MD_HarmonicDihedral
• index_ : core::chemical::AtomICoor , core::chemical::ResidueConnection , core::fragment::picking_old::vall::VallSection , core::graph::UEVertex< V, E > , core::pack::dunbrack::ProbSortClass , protocols::enzdes::EnzdesFlexibleRegion , protocols::genetic_algorithm::EntityElement , protocols::match::upstream::ScaffoldBuildPoint , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• index_for_rotamer_ : protocols::match::output::UpstreamHitCacher
• index_to_id_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• index_to_names_map_ : core::chemical::sdf::CtabBase , core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::ctabV3000Parser
• indices_ : core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResiduePDBIndexIs
• indirect_numerator_ : protocols::qsar::scoring_grid::ChargeGrid
• individual_distance_cutoff_ : protocols::noesy_assign::DistanceScoreMover
• 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_weights_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• 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
• init_all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• init_d77_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• 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::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::JumpClaimer
• init_pose_ : protocols::abinitio::ResolutionSwitcher , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• init_pose_obj_ : protocols::abinitio::AbrelaxApplication
• init_task_factory_ : protocols::antibody::AntibodyModeler , protocols::antibody::CDRH3Modeler , protocols::antibody::LoopRlxMover , protocols::ub_e2c::ubi_e2c_modeler , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol
• init_temp : protocols::rbsegment_relax::RBSegmentRelax
• init_temp_ : protocols::antibody2::H3RefineCCD
• initial_asymm_foldtree_ : protocols::hybridization::HybridizeFoldtreeDynamic
• initial_decoy_stddev_ : protocols::optimize_weights::PNatStructureOptEData
• initial_denovo_scorefxn_ : protocols::rna::RNA_DeNovoProtocol
• 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_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::datacache::CacheableDataType , core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondTypeManager , core::scoring::MembraneTopology , core::scoring::ScoreTypeManager , protocols::abinitio::AllResiduesChanged , protocols::branch_angle::BranchAngleOptimizer , protocols::dna::DnaInterfaceFinder , protocols::features::ProteinSilentReport , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::topology::SheetFoldTypeManager , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::loops::JSONFormattedLoopsFileReader , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash , protocols::qsar::scoring_grid::GridManager , protocols::rna::RNA_SecStructInfo , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::simple_filters::SheetFilter
• initialized_atom_id_map_for_rmsd_ : protocols::swa::StepWiseClusterer
• 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
• inName : protocols::sparta::Sparta::SpartaLib
• inNames : protocols::sparta::Sparta::SpartaLib
• inner_ : core::fragment::OrderedFragSetIterator_
• inner_cycle_list_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• inner_cycle_steps_ : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• inner_cycles_ : protocols::antibody2::H3RefineCCD , protocols::docking::DockingLowRes , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::moves::RampingMover , protocols::symmetric_docking::SymDockingLowRes
• inner_end_ : core::fragment::OrderedFragSetIterator_
• inner_job_ : protocols::jd2::Job , protocols::jd2::MultiThreadingJob
• inner_loop_counter_ : protocols::optimize_weights::IterativeOptEDriver
• 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::MakeRotLib::RotData
• inPDB : protocols::sparta::Sparta::SpartaLib
• inprogress_ : protocols::jobdist::BaseJobDistributor
• input_ : protocols::jd2::PoseInputStreamJobInputter , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer , protocols::wum::MPI_Relax
• 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::antibody2::H3PerturbCCD
• input_pose_ : protocols::moves::_BoolMover , protocols::moves::Mover , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::JumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::RigidChunkClaimer
• input_pose_ONE_appended_res_list_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_ONE_last_appended_res_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_TWO_last_prepended_res_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• input_pose_TWO_prepended_res_list_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• input_poses_ : protocols::pmut_scan::PointMutScanDriver
• input_protocol_id_ : protocols::features::DatabaseJobInputter
• input_res_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol , protocols::swa::InputStreamWithResidueInfo
• input_res_vectors_ : protocols::swa::rna::StepWiseRNA_JobParameters
• input_residue_array_ : protocols::swa::protein::StepWiseProteinPoseSetup
• 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_sheet_sizes_ : protocols::jumping::RandomSheetBuilder
• input_silent_file_data_ : protocols::swa::protein::StepWiseProteinPoseMinimizer
• input_source_ : protocols::comparative_modeling::ThreadingJobInputter
• input_ss_ : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::flxbb::InterlockAroma
• input_stream_ : protocols::swa::StepWiseIdentitySampleGenerator
• input_streams_ : core::import_pose::pose_stream::MetaPoseInputStream , protocols::swa::StepWisePoseCombineSampleGenerator
• input_streams_with_residue_info_ : protocols::swa::StepWisePoseSetup
• input_string : protocols::swa::rna::VDW_RepScreeninfo
• input_stubs_ : protocols::seeded_abinitio::PlaceFragments
• input_tag_ : protocols::jd2::InnerJob
• input_tags_ : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::rna::StepWiseRNA_PoseSetup
• input_vector_expressions_ : protocols::pack_daemon::IterativeVectorExpression
• InputPose_has_antigen_ : protocols::antibody2::AntibodyInfo
• inputstream : protocols::ddG::ddGData
• inputted_bin_size_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• inputters_ : protocols::inputter::InputterStream
• inq_ : protocols::wum2::EndPoint
• insert_connection_scheme_ : protocols::forge::build::SegmentInsert
• insert_map_ : protocols::rna::RNA_FragmentMover , protocols::simple_moves::FragmentMover
• insert_map_frag_size_ : protocols::rna::RNA_FragmentMover
• insert_movemap_ : protocols::grafting::GraftMoverBase
• insert_pdb_ : protocols::forge::remodel::RemodelMover::instruction_flags
• insert_pos_ : protocols::swa::protein::StepWiseProteinFragmentSampleGenerator , protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• 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
• inserter_ : protocols::loophash::LoopHashSampler
• inserting_pdb_ : protocols::forge::remodel::RemodelMover::instruction_flags
• insertion_ : protocols::jd2::parser::BluePrint
• insertion_code_ : protocols::loops::ResidueIndexDescription
• insertion_length_ : protocols::grafting::GraftMoverBase
• insertion_prob_ : protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• insertionEndIndex : protocols::forge::remodel::WorkingRemodelSet
• insertionSize : protocols::forge::remodel::RemodelData
• insertionSS : protocols::forge::remodel::RemodelData
• insertionStartIndex : protocols::forge::remodel::WorkingRemodelSet
• insertPose : protocols::forge::remodel::RemodelData
• instance_ : protocols::genetic_algorithm::EntityElementFactory , protocols::scoring::methods::pcs2::PcsInputCenterManager , protocols::qsar::scoring_grid::GridManager , protocols::noesy_assign::CovalentCompliance , protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory , core::sequence::SequenceFactory , core::scoring::geometric_solvation::GridInfo , core::io::silent::SilentStructFactory , core::chemical::ChemicalManager , core::chemical::orbitals::OrbitalTypeMapper , core::fragment::picking_old::FragmentLibraryManager , core::pack::interaction_graph::RotamerDotsRadiusData , core::pack::interaction_graph::SurfacePotential , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , core::scoring::constraints::ConstraintFactory , core::scoring::constraints::ConstraintIO , core::scoring::geometric_solvation::WaterWeightGridSet , core::scoring::saxs::SinXOverX , core::scoring::ScoringManager , protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::jd2::JobDistributor , protocols::jd2::JobInputterFactory , protocols::jd2::JobOutputterFactory , protocols::jd2::parser::DataLoaderFactory , protocols::jumping::StandardDisulfPairingLibrary , protocols::jumping::StandardPairingLibrary , protocols::ligand_docking::DistributionMap , protocols::loops::LoopMoverFactory , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::moves::MoverFactory , protocols::noesy_assign::MethylNameLibrary , protocols::noesy_assign::PeakAssignmentParameters , protocols::qsar::scoring_grid::GridFactory , protocols::rotamer_recovery::RotamerRecoveryFactory , protocols::scoring::InterchainPotential , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcs::PCS_data_input_manager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton , protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameterManager , protocols::topology_broker::TopologyClaimerFactory
• instance_initialized_ : protocols::canonical_sampling::TemperingBase
• instance_node_2_file_node_ : core::pack::interaction_graph::PDInteractionGraph
• instruction_dependencies_ : protocols::forge::build::BuildManager
• instructions_ : protocols::forge::build::BuildManager
• int_buf1_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• inTab : protocols::sparta::Sparta::SpartaLib
• integration_test_mode_ : protocols::swa::rna::StepWiseRNA_ResidueSampler
• intensity_ : protocols::noesy_assign::Resonance
• inter_atr_ : protocols::MakeRotLib::RotData
• inter_rep_ : protocols::MakeRotLib::RotData
• interacting_atompair_list_ : core::scoring::custom_pair_distance::AtomPairFuncList
• INTERACTION_RADIUS : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• intercept : core::util::Line
• intercept_ : core::scoring::packing::HolesParams
• intercepts_ : core::scoring::packing::HolesParams
• interchain_env_log_ : protocols::scoring::InterchainPotential
• interchain_pair_log_ : protocols::scoring::InterchainPotential
• interface_ : protocols::rigid::RigidBodyPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover , protocols::anchored_design::AnchoredDesignMover , protocols::protein_interface_design::movers::LoopFinder , protocols::dna::DnaInterfaceMinMover , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::docking::InterfaceSidechainMinMover , protocols::anchored_design::AnchoredPerturbMover
• 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_ddg_ : protocols::ddg::ddGMover
• interface_delta_sasa_ : protocols::analysis::InterfaceAnalyzerMover
• interface_dist_ : protocols::symmetric_docking::SymInterfaceSidechainMinMover , protocols::docking::InterfaceSidechainMinMover
• interface_distance_cutoff_ : protocols::seeded_abinitio::SeedSetupMover , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::simple_moves::DesignRepackMover , protocols::enzdes::LigInterfaceEnergyFilter , protocols::simple_filters::ResidueIEFilter , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::simple_filters::EnergyPerResidueFilter
• interface_hsasa_ : protocols::analysis::InterfaceAnalyzerMover
• interface_jump_ : protocols::analysis::InterfaceAnalyzerMover
• interface_list_ : protocols::scoring::InterfaceInfo
• interface_packer_ : protocols::flexpep_docking::FlexPepDockingProtocol
• interface_packstat_ : protocols::analysis::InterfaceAnalyzerMover
• interface_polar_sasa_ : protocols::analysis::InterfaceAnalyzerMover
• interface_radius_ : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• interface_residues_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator
• interface_set_ : protocols::analysis::InterfaceAnalyzerMover , protocols::pmut_scan::AlterSpecDisruptionDriver
• interface_tf_ : protocols::flexpep_docking::FlexPepDockingProtocol
• InterfaceDeltaEnergetics_ : protocols::analysis::InterfaceAnalyzerMover
• InterfaceNeighborDefinition_ : protocols::analysis::InterfaceAnalyzerMover
• interfaces_ : core::conformation::symmetry::SymmetryInfo , core::conformation::symmetry::SymmData
• InterfaceSasaDefinition_ : protocols::analysis::InterfaceAnalyzerMover
• InterGroupNeighborsCalculator_ : protocols::analysis::InterfaceAnalyzerMover
• intermediate_structs_ : protocols::jd2::archive::Batch
• intermediate_weights_ : protocols::moves::RampingMover
• intermedrelax_ : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• internal_allowed_ : core::scoring::packstat::Slice
• internal_coords_need_updating_ : core::kinematics::AtomTree
• internal_cycles_ : protocols::swa::monte_carlo::RNA_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::constraints::SplineFunc
• interres_evaluator_ : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• interval : protocols::forge::components::BDRSegmentInfo
• interval_ : protocols::forge::build::Bridge , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentSwap , protocols::checkpoint::Timer
• interval_posedump_ : protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover
• interval_transitiondump_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• intervals_ : protocols::forge::constraints::InverseRotamersRCG
• intra_atr_ : protocols::MakeRotLib::RotData
• intra_rep_ : protocols::MakeRotLib::RotData
• intra_residue_constraints_ : core::scoring::constraints::ConstraintSet
• intrares_evaluator_ : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• intrares_upper_nblist_ : core::scoring::NeighborList
• inv_dots_ : core::pack::interaction_graph::InvRotamerDots
• 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::IfThenFilter , protocols::filters::CompoundFilter
• invert_coordinate_matrix : protocols::swa::rna::Anchor_ribose_stub
• 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
• INWARDS : core::scoring::dssp::Pairing
• ionc : core::scoring::APBSConfig
• 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
• is_a_neighbor_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• is_acceptor_ : core::chemical::AtomType
• is_acetylated_nterminus_ : core::chemical::ResidueType
• is_adduct_ : core::chemical::ResidueType
• is_aromatic_ : core::chemical::ResidueType , core::chemical::AtomType
• is_backbone_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , core::scoring::hbonds::hbtrie::HBAtom
• 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::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• is_camelid_ : protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::AntibodyInfo , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::H3PerturbCCD , protocols::antibody2::H3CterInsert , protocols::antibody2::H3RefineCCD , protocols::antibody::CDRH3Modeler , protocols::antibody2::ModelCDRH3
• is_cancelled_ : protocols::jd2::archive::Batch
• is_carbohydrate_ : core::chemical::ResidueType
• Is_chain_close : protocols::swa::rna::FB_Pose_Data
• is_charged_ : core::chemical::ResidueType
• is_coarse_ : core::chemical::ResidueType
• 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::swa::StepWisePoseSetup , protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• is_dna_ : core::scoring::hbonds::hbtrie::HBAtom
• is_DNA_ : core::chemical::ResidueType
• is_donor_ : core::chemical::AtomType
• is_fail_ : protocols::flexpep_docking::FlexPepDockingProtocol
• is_file_ : protocols::canonical_sampling::PatchOperation
• is_fixed_res_ : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• is_forward_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• is_frozen_ : protocols::cluster::APCluster
• is_geometry_initialized_ : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Base
• 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::scoring::hbonds::hbtrie::HBAtom , core::scoring::etable::etrie::EtableAtom , core::scoring::hackelec::ElecAtom , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::mm::mmtrie::MMEnergyTableAtom
• is_hydrophobic_ : protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity
• is_interface_ : protocols::scoring::Interface
• Is_internal_ : protocols::swa::StepWiseJobParameters , protocols::swa::rna::StepWiseRNA_JobParameters
• is_jump_point_ : core::kinematics::FoldTree
• is_ligand_ : core::chemical::ResidueType
• is_lower_terminus_ : core::chemical::ResidueType
• is_magnesium_ : core::scoring::rna::RNA_ScoringInfo
• is_map_loaded : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• is_methylated_cterminus_ : core::chemical::ResidueType
• is_moving_res_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener , protocols::swa::StepWiseJobParameters
• is_NA_ : core::chemical::ResidueType
• is_on_ : protocols::checkpoint::Timer
• is_orbital_acceptor_ : core::chemical::orbitals::OrbitalType
• is_orbital_donor_ : core::chemical::orbitals::OrbitalType
• Is_phosphate_atom_list_ : core::chemical::rna::RNA_ResidueType
• is_phosphonate_ : core::chemical::ResidueType
• is_phosphonate_upper_ : core::chemical::ResidueType
• is_pivot_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• is_polar_ : core::chemical::ResidueType
• is_polar_hydrogen_ : core::chemical::AtomType
• is_polymer_ : core::chemical::ResidueType
• is_positive_state_ : protocols::multistate_design::SingleState
• is_pre_proline_ : protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::swa::protein::StepWiseProteinScreener
• Is_prepend : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• Is_prepend_ : protocols::swa::StepWiseJobParameters , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper , protocols::swa::rna::StepWiseRNA_JobParameters
• Is_prepend_map_ : protocols::swa::rna::StepWiseRNA_JobParameters
• is_properly_initialized : protocols::simple_moves::ShakeStructureMover
• is_protein_ : core::scoring::hbonds::hbtrie::HBAtom , core::chemical::ResidueType
• is_proton_ : protocols::noesy_assign::Resonance
• is_proton_chi_ : core::chemical::ResidueType
• Is_reference_xyz_setup_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• is_RNA_ : core::chemical::ResidueType
• Is_RNA_base_atom_list_ : 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_setup_ : protocols::swa::rna::SlicedPoseJobParameters
• Is_simple_full_length_job_params_ : protocols::swa::rna::StepWiseRNA_JobParameters
• Is_sliced_res_ : protocols::swa::rna::SlicedPoseJobParameters
• is_started_ : protocols::jobdist::BaseJobDistributor
• is_surface_ : core::chemical::ResidueType , core::scoring::solid_surface::SurfaceEnergies
• is_term_ : core::scoring::trie::TrieNode< AT, CPDATA >
• is_terminal_res_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• is_terminus_ : core::chemical::ResidueType
• is_trimmed_loops_ : protocols::flexpep_docking::FlexPepDockingProtocol
• is_up_to_date_ : protocols::frag_picker::scores::AdaptiveScoreHistogram
• is_upper_terminus_ : core::chemical::ResidueType
• is_uronic_acid_ : core::chemical::carbohydrates::CarbohydrateInfo
• Is_VDW_screen_bin_setup_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• Is_virtual_atom_list_ : core::chemical::rna::RNA_ResidueType
• is_virtual_base_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• is_working_res_ : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• isbb_ : core::scoring::hackelec::ElecAtom
• isDesignable : protocols::forge::remodel::LineObject
• isep_residue_ : protocols::fldsgn::NcontactsCalculator
• isHet : core::io::pdb::AtomInformation , core::pose::PDBInfo::AtomRecord
• isLoaded : core::scoring::electron_density::ElectronDensity
• isRepacking : core::scoring::electron_density::PattersonCorrEnergy
• it : protocols::sparta::Sparta::SpartaLib , protocols::sparta::ANN
• it_ : core::io::silent::SilentFileData::iterator , core::fragment::FragID_Iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP > , core::fragment::FrameListIterator_ , core::io::raw_data::RawFileData::iterator , core::io::raw_data::RawFileData::const_iterator , core::io::silent::SilentFileData::const_iterator , core::fragment::ConstantLengthFragSetIterator_ , core::fragment::FrameIterator
• iter64_ : protocols::match::VoxelSetIterator
• iterations_ : protocols::moves::CyclicMover
• itN : protocols::sparta::Sparta::SpartaLib
• ivm_ : protocols::toolbox::InteratomicVarianceMatrix