- i -

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::AtomNode , core::optimization::DOF_Node , core::scoring::packstat::Sphere
ID : Entry
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_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_intra_res_RNA_ : core::scoring::hbonds::HBondOptions
include_lips_ : core::membrane::MembraneProteinFactory
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
index_ : core::chemical::AtomICoor , core::chemical::ResidueConnection , core::fragment::picking_old::vall::VallSection , core::graph::UEVertex< V, E > , core::pack::dunbrack::ProbSortClass
index_str_ : core::pack::task::residue_selector::ResidueIndexSelector
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
INFINITE_SEPARATION : core::scoring::trie::TrieCountPairBase
init_ : core::scoring::MembraneTopology
init_from_command_line_ : core::pack::task::operation::OptH
initialized_ : core::pose::datacache::CacheableDataType , 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_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::ChemicalManager , core::chemical::orbitals::OrbitalTypeMapper , core::fragment::picking_old::FragmentLibraryManager , core::io::silent::SilentStructFactory , 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::pack::task::residue_selector::ResidueSelectorFactory , core::scoring::constraints::ConstraintFactory , core::scoring::constraints::ConstraintIO , core::scoring::geometric_solvation::GridInfo , core::scoring::geometric_solvation::WaterWeightGridSet , core::scoring::saxs::SinXOverX , core::scoring::ScoringManager , core::sequence::SequenceFactory , core::SVNVersion
instance_node_2_file_node_ : core::pack::interaction_graph::PDInteractionGraph
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_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
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_upper_nblist_ : core::scoring::NeighborList
intrascale_by_level_ : core::scoring::FACTSPotential
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_acetylated_nterminus_ : core::chemical::ResidueType
is_adduct_ : core::chemical::ResidueType
is_alpha_aa_ : core::chemical::ResidueType
is_aromatic_ : core::chemical::AtomType , core::chemical::ResidueType
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_beta_aa_ : core::chemical::ResidueType
is_branch_lower_terminus_ : core::chemical::ResidueType
is_carbohydrate_ : core::chemical::ResidueType
is_charged_ : core::chemical::ResidueType
is_chargedH_ : core::scoring::FACTSRsdTypeInfo
is_coarse_ : core::chemical::ResidueType
is_cutpoint_ : core::kinematics::FoldTree
is_cyclic_ : core::chemical::ResidueType
is_d_aa_ : core::chemical::ResidueType
is_DNA_ : core::chemical::ResidueType
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_l_aa_ : core::chemical::ResidueType
is_ligand_ : core::chemical::ResidueType
is_lipid_ : 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_metal_ : core::chemical::ResidueType
is_metalbinding_ : core::chemical::ResidueType
is_methylated_cterminus_ : core::chemical::ResidueType
is_NA_ : core::chemical::ResidueType
is_orbital_acceptor_ : core::chemical::orbitals::OrbitalType
is_orbital_donor_ : core::chemical::orbitals::OrbitalType
is_phosphate_ : core::chemical::rna::RNA_ResidueType
is_phosphonate_ : core::chemical::ResidueType
is_phosphonate_upper_ : core::chemical::ResidueType
is_polar_ : core::chemical::ResidueType
is_polar_hydrogen_ : core::chemical::Atom , core::chemical::AtomType
is_polymer_ : core::chemical::ResidueType
is_protein_ : core::chemical::ResidueType , core::scoring::hbonds::hbtrie::HBAtom
is_proton_chi_ : core::chemical::ResidueType
is_RNA_ : 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::chemical::ResidueType , core::scoring::solid_surface::SurfaceEnergies
is_term_ : core::scoring::trie::TrieNode< AT, CPDATA >
is_terminus_ : core::chemical::ResidueType
is_upper_terminus_ : core::chemical::ResidueType
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
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