- i -

• I : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• i2_ : core::scoring::methods::GoapRsdType
• i2c : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• i2c_ : core::scoring::PoissonBoltzmannPotential
• i3_ : core::scoring::methods::GoapRsdType
• i_param : core::scoring::APBSConfig
• iA_ : core::scoring::TMscore
• iB_ : core::scoring::TMscore
• 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 : core::scoring::packstat::SimplePDB_Atom
• iCode1 : core::io::pdb::LinkInformation
• iCode2 : core::io::pdb::LinkInformation
• icoor_ : core::chemical::Orbital , core::chemical::ResidueConnection , core::chemical::ResidueType
• id : core::optimization::DOF_Node , core::scoring::packstat::Sphere
• 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
• 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_bond_length_sets_ : core::chemical::ChemicalManager
• ideal_delta_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_delta_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• 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_xyz_ : core::chemical::Atom , core::chemical::Orbital
• identity_obs_hub_ : core::conformation::Conformation
• ids_ : core::scoring::SecondaryStructurePotential
• idsn_ : core::scoring::SecondaryStructurePotential
• if_hydrogens_ : core::scoring::saxs::SAXSEnergy
• 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
• ig_edge_list_ : core::pack::interaction_graph::InteractionGraphBase
• IG_edge_reweights_ : core::pack::task::PackerTask_
• ig_nodes_ : core::pack::interaction_graph::InteractionGraphBase
• ignore_unrecognized_res_ : core::io::pdb::FileDataOptions
• ignore_waters_ : core::io::pdb::FileDataOptions
• ignore_zero_occupancy_ : core::io::pdb::FileDataOptions
• implicit_radii_set_ : core::scoring::sasa::SasaCalc
• 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_FASTER_mode_ : core::pack::interaction_graph::FASTERNode
• incident_edge_list_ : core::graph::Node , core::pack::interaction_graph::NodeBase
• incident_edge_vector_ : core::pack::interaction_graph::NodeBase
• include_c_s_only_in_hsasa_ : core::scoring::sasa::SasaCalc
• include_current_ : core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask_
• include_hydrogens_ : core::scoring::sasa::SasaCalc
• include_lips_ : core::scoring::membrane::MPLipoEnergy
• include_magnetic_anisotropy_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_neighbor_base_stacks_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• include_probe_radius_ : core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• include_ring_current_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_subunit_ : core::conformation::symmetry::SymmData
• include_virtual_side_chain_ : core::pack::task::ResidueLevelTask_
• index : core::graph::DS_Node , core::scoring::motif::MotifHit
• 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
• index_atom_map_ : core::chemical::sdf::MolFileIOMolecule
• index_str_ : core::pack::task::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
• INFINITE_SEPARATION : core::scoring::trie::TrieCountPairBase
• init_ : core::scoring::MembraneTopology
• init_from_command_line_ : core::pack::task::operation::OptH
• initialized_ : core::pose::xyzStripeHashPose , core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondTypeManager , core::scoring::MembraneTopology , core::scoring::methods::LKB_ResPairMinData , core::scoring::ScoreTypeManager
• initialized_databases_ : core::scoring::hbonds::HBondDatabase
• initialized_SASA_radii : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• inner_ : core::fragment::OrderedFragSetIterator_
• inner_end_ : core::fragment::OrderedFragSetIterator_
• inneriterations_ : core::pack::annealer::SimAnnealerBase
• inneriterations_scaling_ : core::pack::annealer::SimAnnealerBase
• input_file : update_ResidueType_enum_files.EnumInfo
• 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_streams_ : core::import_pose::pose_stream::MetaPoseInputStream
• insert_position_ : core::fragment::picking_old::vall::eval::EnergyEval
• instance_ : core::chemical::orbitals::OrbitalTypeMapper , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::TaskOperationFactory , core::pack::task::residue_selector::ResidueSelectorFactory , core::scoring::motif::MotifHashManager , core::SVNVersion
• instance_node_2_file_node_ : core::pack::interaction_graph::PDInteractionGraph
• 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
• 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::util::Line
• intercept_ : core::scoring::packing::HolesParams
• intercepts_ : core::scoring::packing::HolesParams
• interchangeability_group_ : core::chemical::ResidueType
• interchangeability_group_map_ : core::chemical::ResidueTypeSet
• interface_atoms_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• interface_only_ : core::scoring::motif::ResPairMotifQuery
• interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• interfaces_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• internal_allowed_ : core::scoring::packstat::Slice
• internal_coords_need_updating_ : core::kinematics::AtomTree
• 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
• intgrp_ : core::chemical::SetInterchangeabilityGroup_String
• intgrp_addendum_ : core::chemical::AppendInterchangeabilityGroup_String
• intra_elec_scale_ : core::scoring::FACTSRsdTypeInfo
• intra_residue_constraints_ : core::scoring::constraints::ConstraintSet
• intra_solv_scale_ : core::scoring::FACTSRsdTypeInfo
• 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_rho_mask : core::scoring::electron_density::ElectronDensity
• INWARDS : core::scoring::dssp::Pairing
• ionc : core::scoring::APBSConfig
• ionq : core::scoring::APBSConfig
• ionr : core::scoring::APBSConfig
• iparam19 : core::scoring::APBSConfig::I_PARAM
• ipos_ : core::fragment::FragID_Iterator
• iptsn_ : core::scoring::SecondaryStructurePotential
• is_acceptor_ : core::chemical::Atom , core::chemical::AtomType
• is_aromatic_ : core::chemical::AtomType
• is_backbone_ : core::scoring::hbonds::hbtrie::HBAtom
• 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_bulged_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_chargedH_ : core::scoring::FACTSRsdTypeInfo
• is_cutpoint_ : core::kinematics::FoldTree
• is_dna_ : core::scoring::hbonds::hbtrie::HBAtom
• is_donor_ : core::chemical::AtomType
• is_freedof_ : core::scoring::FACTSRsdTypeInfo
• is_gasteiger_type_ : core::chemical::gasteiger::GasteigerAtomTypeData
• is_glycoside_ : core::chemical::carbohydrates::CarbohydrateInfo
• is_h2o_ : core::chemical::AtomType
• is_haro_ : core::chemical::Atom
• 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_jump_point_ : core::kinematics::FoldTree
• is_magnesium_ : core::scoring::rna::RNA_ScoringInfo
• is_map_loaded : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• is_orbital_acceptor_ : core::chemical::orbitals::OrbitalType
• is_orbital_donor_ : core::chemical::orbitals::OrbitalType
• is_phosphate_ : core::chemical::rna::RNA_ResidueType
• is_polar_hydrogen_ : core::chemical::Atom , core::chemical::AtomType
• is_protected_values_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_protein_ : core::scoring::hbonds::hbtrie::HBAtom
• is_proton_chi_ : core::chemical::ResidueType
• 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_surface_ : core::scoring::solid_surface::SurfaceEnergies
• is_term_ : core::scoring::trie::TrieNode< AT, CPDATA >
• is_using_ : core::scoring::methods::GoapRsdType
• is_virtual_ : core::chemical::Atom , core::chemical::rna::RNA_ResidueType
• isbb_ : core::scoring::elec::ElecAtom
• isHet : core::io::pdb::AtomInformation , core::pose::PDBInfo::AtomRecord
• isLoaded : core::scoring::electron_density::ElectronDensity , core::scoring::fiber_diffraction::FiberDiffraction
• isometry_ : core::chemical::Bond
• isRepacking : core::scoring::electron_density::PattersonCorrEnergy
• 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